KZKLAINJJWZ64T5MUZT34LJVQIKBTKZ6EJGD7C7TTSSDGCHEDPMAC package utilsimport ("os""path/filepath""testing")func TestComputeXXH64_WAVFile(t *testing.T) {wavFile := filepath.Join("..", "audio", "N14-2025-02-25-20241116_054500-685-703.wav")hash, err := ComputeXXH64(wavFile)if err != nil {t.Fatalf("ComputeXXH64() error = %v", err)}expectedHash := "48dc1684324621de"if hash != expectedHash {t.Errorf("ComputeXXH64() = %v, want %v", hash, expectedHash)}}func TestComputeXXH64_Format(t *testing.T) {wavFile := filepath.Join("..", "audio", "N14-2025-02-25-20241116_054500-685-703.wav")hash, err := ComputeXXH64(wavFile)if err != nil {t.Fatalf("ComputeXXH64() error = %v", err)}if len(hash) != 16 {t.Errorf("hash length = %d, want 16", len(hash))}for _, c := range hash {if (c < '0' || c > '9') && (c < 'a' || c > 'f') {t.Errorf("invalid hex character '%c' in hash %s", c, hash)}}}func TestComputeXXH64_FileNotFound(t *testing.T) {_, err := ComputeXXH64("nonexistent-file.wav")if err == nil {t.Error("expected error for nonexistent file, got nil")}}func TestComputeXXH64_EmptyFile(t *testing.T) {tmpDir := t.TempDir()emptyFile := filepath.Join(tmpDir, "empty.wav")if err := createEmptyFile(emptyFile); err != nil {t.Fatalf("Failed to create empty file: %v", err)}hash, err := ComputeXXH64(emptyFile)if err != nil {t.Fatalf("ComputeXXH64() error = %v", err)}expectedEmpty := "ef46db3751d8e999"if hash != expectedEmpty {t.Errorf("ComputeXXH64(empty file) = %v, want %v", hash, expectedEmpty)}}func TestComputeXXH64_Deterministic(t *testing.T) {wavFile := filepath.Join("..", "audio", "N14-2025-02-25-20241116_054500-685-703.wav")hash1, err := ComputeXXH64(wavFile)if err != nil {t.Fatalf("first call error = %v", err)}hash2, err := ComputeXXH64(wavFile)if err != nil {t.Fatalf("second call error = %v", err)}hash3, err := ComputeXXH64(wavFile)if err != nil {t.Fatalf("third call error = %v", err)}if hash1 != hash2 || hash2 != hash3 {t.Errorf("hashes not deterministic: %s, %s, %s", hash1, hash2, hash3)}}func TestComputeXXH64_LeadingZeros(t *testing.T) {tmpDir := t.TempDir()smallFile := filepath.Join(tmpDir, "small.dat")if err := createSmallFile(smallFile); err != nil {t.Fatalf("Failed to create small file: %v", err)}hash, err := ComputeXXH64(smallFile)if err != nil {t.Fatalf("ComputeXXH64() error = %v", err)}if len(hash) != 16 {t.Errorf("hash length = %d, want 16 (leading zeros should be preserved)", len(hash))}}func BenchmarkComputeXXH64_Small(b *testing.B) {f := filepath.Join("..", "audio", "N14-2025-02-25-20241116_054500-685-703.wav") // 547Kb.ResetTimer()for i := 0; i < b.N; i++ {ComputeXXH64(f)}}func BenchmarkComputeXXH64_Medium(b *testing.B) {f := filepath.Join("..", "audio", "20250518_210000.WAV") // 14Mb.ResetTimer()for i := 0; i < b.N; i++ {ComputeXXH64(f)}}func BenchmarkComputeXXH64_Large(b *testing.B) {f := filepath.Join("..", "audio", "E166_BIRD_111211_042726.wav") // 55Mb.ResetTimer()for i := 0; i < b.N; i++ {ComputeXXH64(f)}}func createEmptyFile(path string) error {file, err := os.Create(path)if err != nil {return err}return file.Close()}func createSmallFile(path string) error {file, err := os.Create(path)if err != nil {return err}defer file.Close()_, err = file.Write([]byte{0x42})return err}
package utilsimport ("fmt""io""os""sync""github.com/cespare/xxhash/v2")var hashBufferPool = sync.Pool{New: func() any {buf := make([]byte, 128*1024)return &buf},}func getHashBuffer() *[]byte {return hashBufferPool.Get().(*[]byte)}func putHashBuffer(buf *[]byte) {hashBufferPool.Put(buf)}// ComputeXXH64 computes the XXH64 hash of a file using streaming I/O.// Uses a constant ~128KB buffer regardless of file size.// Returns the hash as a 16-character lowercase hexadecimal string.func ComputeXXH64(filepath string) (string, error) {file, err := os.Open(filepath)if err != nil {return "", fmt.Errorf("failed to open file: %w", err)}defer func() { _ = file.Close() }()hashBufPtr := getHashBuffer()defer putHashBuffer(hashBufPtr)h := xxhash.New()if _, err := io.CopyBuffer(h, file, *hashBufPtr); err != nil {return "", fmt.Errorf("failed to read file: %w", err)}return fmt.Sprintf("%016x", h.Sum64()), nil}
package utilsimport ("bufio""encoding/binary""fmt""os")// WriteWAVFile writes audio samples to a WAV file.// Samples should be in the range -1.0 to 1.0.// Output is mono 16-bit PCM.func WriteWAVFile(filepath string, samples []float64, sampleRate int) error {if len(samples) == 0 {return fmt.Errorf("no samples to write")}file, err := os.Create(filepath)if err != nil {return fmt.Errorf("failed to create file: %w", err)}w := bufio.NewWriterSize(file, 64*1024)// Write WAV and flush; check close to ensure data is persisted.err = func() error {// WAV parameterschannels := 1bitsPerSample := 16bytesPerSample := bitsPerSample / 8byteRate := sampleRate * channels * bytesPerSampleblockAlign := channels * bytesPerSampledataSize := len(samples) * bytesPerSampletotalSize := 36 + dataSize // 36 = header size before data chunk// Write 44-byte WAV header in one goheader := make([]byte, 44)copy(header[0:4], "RIFF")binary.LittleEndian.PutUint32(header[4:8], uint32(totalSize))copy(header[8:12], "WAVE")copy(header[12:16], "fmt ")binary.LittleEndian.PutUint32(header[16:20], 16) // chunk sizebinary.LittleEndian.PutUint16(header[20:22], 1) // PCM formatbinary.LittleEndian.PutUint16(header[22:24], uint16(channels))binary.LittleEndian.PutUint32(header[24:28], uint32(sampleRate))binary.LittleEndian.PutUint32(header[28:32], uint32(byteRate))binary.LittleEndian.PutUint16(header[32:34], uint16(blockAlign))binary.LittleEndian.PutUint16(header[34:36], uint16(bitsPerSample))copy(header[36:40], "data")binary.LittleEndian.PutUint32(header[40:44], uint32(dataSize))if _, err := w.Write(header); err != nil {return err}// Convert all float64 samples to 16-bit PCM in a single bufferbuf := make([]byte, dataSize)for i, sample := range samples {// Clamp to [-1, 1]if sample > 1.0 {sample = 1.0} else if sample < -1.0 {sample = -1.0}binary.LittleEndian.PutUint16(buf[i*2:], uint16(int16(sample*32767)))}if _, err := w.Write(buf); err != nil {return err}return w.Flush()}()if err2 := file.Close(); err2 != nil {if err == nil {err = fmt.Errorf("failed to close file: %w", err2)}}return err}
package utilsimport ("bytes""encoding/binary""fmt""os""path/filepath""testing""time")// createTestWAVFile creates a minimal valid WAV file for testingfunc createTestWAVFile(t *testing.T, dir string, filename string, options struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}) string {t.Helper()path := filepath.Join(dir, filename)file, err := os.Create(path)if err != nil {t.Fatalf("Failed to create test file: %v", err)}defer file.Close()// Calculate data chunk size based on durationbytesPerSample := options.bitsPerSample / 8samplesPerSecond := options.sampleRate * options.channelsdataSize := int(options.duration * float64(samplesPerSecond*bytesPerSample))// Calculate file size (excluding RIFF header)fileSize := 4 + 8 + 16 + 8 + dataSize // WAVE + fmt chunk + data chunk header// Add LIST INFO chunk size if metadata providedvar infoChunk []byteif options.comment != "" || options.artist != "" {infoChunk = buildINFOChunk(options.comment, options.artist)fileSize += 8 + len(infoChunk) // LIST chunk header + content}buf := &bytes.Buffer{}// Write RIFF headerbuf.WriteString("RIFF")binary.Write(buf, binary.LittleEndian, uint32(fileSize))buf.WriteString("WAVE")// Write fmt chunkbuf.WriteString("fmt ")binary.Write(buf, binary.LittleEndian, uint32(16)) // chunk sizebinary.Write(buf, binary.LittleEndian, uint16(1)) // audio format (PCM)binary.Write(buf, binary.LittleEndian, uint16(options.channels))binary.Write(buf, binary.LittleEndian, uint32(options.sampleRate))byteRate := options.sampleRate * options.channels * bytesPerSamplebinary.Write(buf, binary.LittleEndian, uint32(byteRate))blockAlign := options.channels * bytesPerSamplebinary.Write(buf, binary.LittleEndian, uint16(blockAlign))binary.Write(buf, binary.LittleEndian, uint16(options.bitsPerSample))// Write LIST INFO chunk if metadata providedif len(infoChunk) > 0 {buf.WriteString("LIST")binary.Write(buf, binary.LittleEndian, uint32(len(infoChunk)))buf.Write(infoChunk)}// Write data chunkbuf.WriteString("data")binary.Write(buf, binary.LittleEndian, uint32(dataSize))// Write silence for databuf.Write(make([]byte, dataSize))// Write to fileif _, err := file.Write(buf.Bytes()); err != nil {t.Fatalf("Failed to write test file: %v", err)}return path}// buildINFOChunk builds a LIST INFO chunk with optional comment and artistfunc buildINFOChunk(comment, artist string) []byte {buf := &bytes.Buffer{}buf.WriteString("INFO")if comment != "" {buf.WriteString("ICMT")// Size includes null terminatorsize := len(comment) + 1binary.Write(buf, binary.LittleEndian, uint32(size))buf.WriteString(comment)buf.WriteByte(0) // null terminator// Add padding byte if needed for word alignmentif size%2 != 0 {buf.WriteByte(0)}}if artist != "" {buf.WriteString("IART")size := len(artist) + 1binary.Write(buf, binary.LittleEndian, uint32(size))buf.WriteString(artist)buf.WriteByte(0) // null terminatorif size%2 != 0 {buf.WriteByte(0)}}return buf.Bytes()}func TestParseWAVHeader(t *testing.T) {// Create temporary directory for test filestmpDir := t.TempDir()t.Run("should parse basic WAV metadata", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_basic.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 60.0,sampleRate: 44100,channels: 2,bitsPerSample: 16,comment: "",artist: "",})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.SampleRate != 44100 {t.Errorf("SampleRate incorrect: got %d, want 44100", metadata.SampleRate)}if metadata.Channels != 2 {t.Errorf("Channels incorrect: got %d, want 2", metadata.Channels)}if metadata.BitsPerSample != 16 {t.Errorf("BitsPerSample incorrect: got %d, want 16", metadata.BitsPerSample)}// Duration should be approximately 60 seconds (allow small rounding error)if metadata.Duration < 59.9 || metadata.Duration > 60.1 {t.Errorf("Duration incorrect: got %f, want ~60.0", metadata.Duration)}})t.Run("should extract comment metadata", func(t *testing.T) {expectedComment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549"path := createTestWAVFile(t, tmpDir, "test_comment.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 10.0,sampleRate: 48000,channels: 1,bitsPerSample: 16,comment: expectedComment,artist: "",})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.Comment != expectedComment {t.Errorf("Comment incorrect: got %q, want %q", metadata.Comment, expectedComment)}})t.Run("should extract artist metadata", func(t *testing.T) {expectedArtist := "AudioMoth"path := createTestWAVFile(t, tmpDir, "test_artist.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 5.0,sampleRate: 48000,channels: 1,bitsPerSample: 16,comment: "",artist: expectedArtist,})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.Artist != expectedArtist {t.Errorf("Artist incorrect: got %q, want %q", metadata.Artist, expectedArtist)}})t.Run("should extract both comment and artist", func(t *testing.T) {expectedComment := "Test recording comment"expectedArtist := "Test Artist"path := createTestWAVFile(t, tmpDir, "test_both.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 15.0,sampleRate: 44100,channels: 2,bitsPerSample: 16,comment: expectedComment,artist: expectedArtist,})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.Comment != expectedComment {t.Errorf("Comment incorrect: got %q, want %q", metadata.Comment, expectedComment)}if metadata.Artist != expectedArtist {t.Errorf("Artist incorrect: got %q, want %q", metadata.Artist, expectedArtist)}})t.Run("should handle different sample rates", func(t *testing.T) {testCases := []struct {sampleRate int}{{8000},{16000},{22050},{44100},{48000},{96000},}for _, tc := range testCases {t.Run("", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_sr.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 1.0,sampleRate: tc.sampleRate,channels: 1,bitsPerSample: 16,comment: "",artist: "",})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.SampleRate != tc.sampleRate {t.Errorf("SampleRate incorrect: got %d, want %d", metadata.SampleRate, tc.sampleRate)}})}})t.Run("should handle different channel counts", func(t *testing.T) {testCases := []struct {channels int}{{1}, // Mono{2}, // Stereo}for _, tc := range testCases {t.Run("", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_ch.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 1.0,sampleRate: 44100,channels: tc.channels,bitsPerSample: 16,comment: "",artist: "",})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.Channels != tc.channels {t.Errorf("Channels incorrect: got %d, want %d", metadata.Channels, tc.channels)}})}})t.Run("should handle different bit depths", func(t *testing.T) {testCases := []struct {bitsPerSample int}{{8},{16},{24},{32},}for _, tc := range testCases {t.Run("", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_bits.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 1.0,sampleRate: 44100,channels: 1,bitsPerSample: tc.bitsPerSample,comment: "",artist: "",})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.BitsPerSample != tc.bitsPerSample {t.Errorf("BitsPerSample incorrect: got %d, want %d", metadata.BitsPerSample, tc.bitsPerSample)}})}})t.Run("should handle very short durations", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_short.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 0.1, // 100mssampleRate: 44100,channels: 1,bitsPerSample: 16,comment: "",artist: "",})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.Duration < 0.09 || metadata.Duration > 0.11 {t.Errorf("Duration incorrect: got %f, want ~0.1", metadata.Duration)}})t.Run("should handle long durations", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_long.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 600.0, // 10 minutessampleRate: 44100,channels: 1,bitsPerSample: 16,comment: "",artist: "",})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.Duration < 599.0 || metadata.Duration > 601.0 {t.Errorf("Duration incorrect: got %f, want ~600.0", metadata.Duration)}})t.Run("should return error for non-existent file", func(t *testing.T) {_, err := ParseWAVHeader("/nonexistent/file.wav")if err == nil {t.Error("Expected error for non-existent file")}})t.Run("should return error for non-WAV file", func(t *testing.T) {// Create a non-WAV filepath := filepath.Join(tmpDir, "not_a_wav.txt")if err := os.WriteFile(path, []byte("This is not a WAV file"), 0644); err != nil {t.Fatalf("Failed to create test file: %v", err)}_, err := ParseWAVHeader(path)if err == nil {t.Error("Expected error for non-WAV file")}})t.Run("should return error for truncated file", func(t *testing.T) {// Create a file that's too small to be valid WAVpath := filepath.Join(tmpDir, "truncated.wav")if err := os.WriteFile(path, []byte("RIFF"), 0644); err != nil {t.Fatalf("Failed to create test file: %v", err)}_, err := ParseWAVHeader(path)if err == nil {t.Error("Expected error for truncated file")}})t.Run("should handle empty metadata strings", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_empty.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 10.0,sampleRate: 44100,channels: 1,bitsPerSample: 16,comment: "",artist: "",})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.Comment != "" {t.Errorf("Comment should be empty, got %q", metadata.Comment)}if metadata.Artist != "" {t.Errorf("Artist should be empty, got %q", metadata.Artist)}})t.Run("should handle long comment strings", func(t *testing.T) {longComment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was 15.8C. This is a very long comment with additional information about the recording session."path := createTestWAVFile(t, tmpDir, "test_long_comment.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 10.0,sampleRate: 44100,channels: 1,bitsPerSample: 16,comment: longComment,artist: "",})metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if metadata.Comment != longComment {t.Errorf("Comment incorrect: got %q, want %q", metadata.Comment, longComment)}})t.Run("should extract file modification time", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_modtime.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 5.0,sampleRate: 44100,channels: 1,bitsPerSample: 16,comment: "",artist: "",})// Get expected mod timeinfo, err := os.Stat(path)if err != nil {t.Fatalf("Failed to stat file: %v", err)}expectedModTime := info.ModTime()metadata, err := ParseWAVHeader(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}// Allow 1 second tolerance for filesystem granularitydiff := metadata.FileModTime.Sub(expectedModTime)if diff < -1*time.Second || diff > 1*time.Second {t.Errorf("FileModTime incorrect: got %v, want %v (diff: %v)",metadata.FileModTime, expectedModTime, diff)}// Ensure FileModTime is not zeroif metadata.FileModTime.IsZero() {t.Error("FileModTime should not be zero")}})}func TestExtractNullTerminatedString(t *testing.T) {testCases := []struct {name stringinput []byteexpected string}{{name: "string with null terminator",input: []byte{'h', 'e', 'l', 'l', 'o', 0, 'w', 'o', 'r', 'l', 'd'},expected: "hello",},{name: "string without null terminator",input: []byte{'h', 'e', 'l', 'l', 'o'},expected: "hello",},{name: "empty string",input: []byte{},expected: "",},{name: "only null terminator",input: []byte{0},expected: "",},}for _, tc := range testCases {t.Run(tc.name, func(t *testing.T) {result := extractNullTerminatedString(tc.input)if result != tc.expected {t.Errorf("Result incorrect: got %q, want %q", result, tc.expected)}})}}func TestParseWAVHeaderMinimal(t *testing.T) {tmpDir := t.TempDir()t.Run("should parse basic WAV metadata", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_minimal.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 10.0,sampleRate: 44100,channels: 1,bitsPerSample: 16,comment: "",artist: "",})sampleRate, duration, err := ParseWAVHeaderMinimal(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if sampleRate != 44100 {t.Errorf("SampleRate incorrect: got %d, want 44100", sampleRate)}if duration < 9.9 || duration > 10.1 {t.Errorf("Duration incorrect: got %f, want ~10.0", duration)}})t.Run("should handle different sample rates", func(t *testing.T) {sampleRates := []int{8000, 22050, 44100, 48000, 96000}for _, sr := range sampleRates {t.Run(fmt.Sprintf("%dHz", sr), func(t *testing.T) {path := createTestWAVFile(t, tmpDir, fmt.Sprintf("test_sr_%d.wav", sr), struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 5.0,sampleRate: sr,channels: 1,bitsPerSample: 16,comment: "",artist: "",})sampleRate, duration, err := ParseWAVHeaderMinimal(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if sampleRate != sr {t.Errorf("SampleRate incorrect: got %d, want %d", sampleRate, sr)}if duration < 4.9 || duration > 5.1 {t.Errorf("Duration incorrect: got %f, want ~5.0", duration)}})}})t.Run("should handle stereo files", func(t *testing.T) {path := createTestWAVFile(t, tmpDir, "test_stereo.wav", struct {duration float64sampleRate intchannels intbitsPerSample intcomment stringartist string}{duration: 3.0,sampleRate: 44100,channels: 2,bitsPerSample: 16,comment: "",artist: "",})sampleRate, duration, err := ParseWAVHeaderMinimal(path)if err != nil {t.Fatalf("Failed to parse WAV header: %v", err)}if sampleRate != 44100 {t.Errorf("SampleRate incorrect: got %d, want 44100", sampleRate)}if duration < 2.9 || duration > 3.1 {t.Errorf("Duration incorrect: got %f, want ~3.0", duration)}})t.Run("should return error for non-existent file", func(t *testing.T) {_, _, err := ParseWAVHeaderMinimal("/nonexistent/file.wav")if err == nil {t.Error("Expected error for non-existent file")}})t.Run("should return error for non-WAV file", func(t *testing.T) {// Create a text filepath := filepath.Join(tmpDir, "notawav.wav")if err := os.WriteFile(path, []byte("Not a WAV file"), 0644); err != nil {t.Fatalf("Failed to create test file: %v", err)}_, _, err := ParseWAVHeaderMinimal(path)if err == nil {t.Error("Expected error for non-WAV file")}})}
package utilsimport ("bytes""encoding/binary""fmt""io""os""sync""time""github.com/cespare/xxhash/v2")// Buffer pools for reducing GC pressure during batch importsvar (// headerBufferPool stores 200KB buffers for WAV header reading (full metadata)headerBufferPool = sync.Pool{New: func() any {buf := make([]byte, 200*1024)return &buf},}// minimalHeaderBufferPool stores 4KB buffers for minimal WAV header reading// 4KB is sufficient for fmt + data chunk headers in 99% of WAV filesminimalHeaderBufferPool = sync.Pool{New: func() any {buf := make([]byte, 4*1024)return &buf},})// getHeaderBuffer gets a 200KB buffer from the poolfunc getHeaderBuffer() *[]byte {return headerBufferPool.Get().(*[]byte)}// putHeaderBuffer returns a 200KB buffer to the poolfunc putHeaderBuffer(buf *[]byte) {headerBufferPool.Put(buf)}// getMinimalHeaderBuffer gets a 4KB buffer from the poolfunc getMinimalHeaderBuffer() *[]byte {return minimalHeaderBufferPool.Get().(*[]byte)}// putMinimalHeaderBuffer returns a 4KB buffer to the poolfunc putMinimalHeaderBuffer(buf *[]byte) {minimalHeaderBufferPool.Put(buf)}// WAVMetadata contains metadata extracted from WAV file headerstype WAVMetadata struct {Duration float64 // Duration in secondsSampleRate int // Sample rate in HzComment string // Comment from INFO chunk (may contain AudioMoth data)Artist string // Artist from INFO chunkChannels int // Number of audio channelsBitsPerSample int // Bits per sampleFileModTime time.Time // File modification time (fallback timestamp)FileSize int64 // File size in bytes}// ParseWAVHeader efficiently reads only the WAV file header to extract metadata.// It reads the first 200KB of the file, which should be sufficient for all header chunks.// ParseWAVHeader extracts metadata from WAV file including duration, sample rate, and INFO chunksfunc ParseWAVHeader(filepath string) (*WAVMetadata, error) {file, err := os.Open(filepath)if err != nil {return nil, fmt.Errorf("failed to open file: %w", err)}defer func() { _ = file.Close() }()// Get file info for modification timefileInfo, err := file.Stat()if err != nil {return nil, fmt.Errorf("failed to get file info: %w", err)}modTime := fileInfo.ModTime()fileSize := fileInfo.Size()// Get header buffer from poolheaderBufPtr := getHeaderBuffer()defer putHeaderBuffer(headerBufPtr)headerBuf := (*headerBufPtr)[:cap(*headerBufPtr)]// Read first 200KB for header parsing (more than enough for metadata)n, err := file.Read(headerBuf)if err != nil && err != io.EOF {return nil, fmt.Errorf("failed to read header: %w", err)}headerBuf = headerBuf[:n]metadata, err := parseWAVFromBytes(headerBuf)if err != nil {return nil, err}// Set file modification time and sizemetadata.FileModTime = modTimemetadata.FileSize = fileSizereturn metadata, nil}// ParseWAVHeaderMinimal reads only the first 4KB of a WAV file to extract essential metadata.// This is optimized for batch processing where INFO chunks (comment/artist) are not needed.// It's ~50x faster than ParseWAVHeader for large files due to reduced I/O.// Returns (sampleRate, duration, error) - the minimal data needed for .data file generation.func ParseWAVHeaderMinimal(filepath string) (sampleRate int, duration float64, err error) {file, err := os.Open(filepath)if err != nil {return 0, 0, fmt.Errorf("failed to open file: %w", err)}defer func() { _ = file.Close() }()// Get minimal header buffer from pool (4KB)headerBufPtr := getMinimalHeaderBuffer()defer putMinimalHeaderBuffer(headerBufPtr)headerBuf := (*headerBufPtr)[:cap(*headerBufPtr)]// Read first 4KB - sufficient for fmt + data chunk headers in 99% of filesn, err := file.Read(headerBuf)if err != nil && err != io.EOF {return 0, 0, fmt.Errorf("failed to read header: %w", err)}headerBuf = headerBuf[:n]// Parse minimal metadatasampleRate, duration, err = parseWAVMinimal(headerBuf)if err != nil {return 0, 0, err}return sampleRate, duration, nil}// parseWAVMinimal parses only essential WAV metadata from a byte buffer.// Returns (sampleRate, duration, error). Does not parse INFO chunks.func parseWAVMinimal(data []byte) (sampleRate int, duration float64, err error) {if len(data) < 44 {return 0, 0, fmt.Errorf("file too small to be valid WAV")}// Verify RIFF headerif string(data[0:4]) != "RIFF" {return 0, 0, fmt.Errorf("not a valid WAV file (missing RIFF header)")}// Verify WAVE formatif string(data[8:12]) != "WAVE" {return 0, 0, fmt.Errorf("not a valid WAV file (missing WAVE format)")}var channels, bitsPerSample int// Parse chunks - stop after finding data chunkoffset := 12for offset < len(data)-8 {chunkID := string(data[offset : offset+4])chunkSize := int(binary.LittleEndian.Uint32(data[offset+4 : offset+8]))offset += 8switch chunkID {case "fmt ":// Parse format chunkif chunkSize >= 16 && offset+16 <= len(data) {channels = int(binary.LittleEndian.Uint16(data[offset+2 : offset+4]))sampleRate = int(binary.LittleEndian.Uint32(data[offset+4 : offset+8]))bitsPerSample = int(binary.LittleEndian.Uint16(data[offset+14 : offset+16]))}case "data":// Found data chunk - calculate duration and returnif sampleRate > 0 && channels > 0 && bitsPerSample > 0 {bytesPerSample := bitsPerSample / 8bytesPerSecond := sampleRate * channels * bytesPerSampleif bytesPerSecond > 0 {duration = float64(chunkSize) / float64(bytesPerSecond)return sampleRate, duration, nil}}return 0, 0, fmt.Errorf("invalid WAV: fmt chunk missing or corrupt before data chunk")}// Move to next chunk (word-aligned)offset += chunkSizeif chunkSize%2 != 0 {offset++}}// Data chunk not found within 4KB - file may have large INFO chunksreturn 0, 0, fmt.Errorf("data chunk not found in first 4KB (try ParseWAVHeader for full parsing)")}// ParseWAVHeaderWithHash reads the WAV file once to extract both metadata and hash.// This is more efficient than calling ParseWAVHeader and ComputeXXH64 separately,// as it only opens the file once and reads it in a single pass.// Returns (metadata, hash, error).func ParseWAVHeaderWithHash(filepath string) (*WAVMetadata, string, error) {file, err := os.Open(filepath)if err != nil {return nil, "", fmt.Errorf("failed to open file: %w", err)}defer func() { _ = file.Close() }()// Get file info for modification time and sizefileInfo, err := file.Stat()if err != nil {return nil, "", fmt.Errorf("failed to get file info: %w", err)}modTime := fileInfo.ModTime()fileSize := fileInfo.Size()// Get header buffer from poolheaderBufPtr := getHeaderBuffer()defer putHeaderBuffer(headerBufPtr)headerBuf := (*headerBufPtr)[:cap(*headerBufPtr)]// Read first 200KB for header parsingn, err := file.Read(headerBuf)if err != nil && err != io.EOF {return nil, "", fmt.Errorf("failed to read header: %w", err)}headerBuf = headerBuf[:n]// Parse headermetadata, err := parseWAVFromBytes(headerBuf)if err != nil {return nil, "", err}metadata.FileModTime = modTimemetadata.FileSize = fileSize// Hash: seek back to start and stream entire fileif _, err := file.Seek(0, 0); err != nil {return nil, "", fmt.Errorf("failed to seek: %w", err)}// Get hash buffer from poolhashBufPtr := getHashBuffer()defer putHashBuffer(hashBufPtr)hashBuf := *hashBufPtrh := xxhash.New()if _, err := io.CopyBuffer(h, file, hashBuf); err != nil {return nil, "", fmt.Errorf("failed to read file for hash: %w", err)}hash := fmt.Sprintf("%016x", h.Sum64())return metadata, hash, nil}// parseWAVFromBytes parses WAV metadata from a byte bufferfunc parseWAVFromBytes(data []byte) (*WAVMetadata, error) {if len(data) < 44 {return nil, fmt.Errorf("file too small to be valid WAV")}// Verify RIFF headerif string(data[0:4]) != "RIFF" {return nil, fmt.Errorf("not a valid WAV file (missing RIFF header)")}// Verify WAVE formatif string(data[8:12]) != "WAVE" {return nil, fmt.Errorf("not a valid WAV file (missing WAVE format)")}metadata := &WAVMetadata{}// Parse chunksoffset := 12for offset < len(data)-8 {// Read chunk ID and sizechunkID := string(data[offset : offset+4])chunkSize := int(binary.LittleEndian.Uint32(data[offset+4 : offset+8]))offset += 8switch chunkID {case "fmt ":// Parse format chunk - need at least 16 bytes of dataif chunkSize >= 16 && offset+16 <= len(data) {metadata.Channels = int(binary.LittleEndian.Uint16(data[offset+2 : offset+4]))metadata.SampleRate = int(binary.LittleEndian.Uint32(data[offset+4 : offset+8]))metadata.BitsPerSample = int(binary.LittleEndian.Uint16(data[offset+14 : offset+16]))}case "data":// Calculate duration from data chunk size// We only need the chunkSize from the header, not the actual audio dataif metadata.SampleRate > 0 && metadata.Channels > 0 && metadata.BitsPerSample > 0 {bytesPerSample := metadata.BitsPerSample / 8bytesPerSecond := metadata.SampleRate * metadata.Channels * bytesPerSampleif bytesPerSecond > 0 {metadata.Duration = float64(chunkSize) / float64(bytesPerSecond)}}// Data chunk content is the audio data - we don't need to read itcase "LIST":// Parse LIST chunk for INFO metadataif chunkSize >= 4 && offset+chunkSize <= len(data) {listType := string(data[offset : offset+4])if listType == "INFO" {parseINFOChunk(data[offset+4:offset+chunkSize], metadata)}}}// Move to next chunk (chunks are word-aligned)offset += chunkSizeif chunkSize%2 != 0 {offset++ // Skip padding byte}}// Validate that we found essential chunksif metadata.SampleRate == 0 {return nil, fmt.Errorf("invalid WAV file: missing or corrupt fmt chunk")}if metadata.Duration == 0 {return nil, fmt.Errorf("invalid WAV file: missing or corrupt data chunk")}return metadata, nil}// parseINFOChunk parses INFO list chunk for comment and artist metadatafunc parseINFOChunk(data []byte, metadata *WAVMetadata) {offset := 0for offset < len(data)-8 {// Read subchunk ID and sizeif offset+8 > len(data) {break}subchunkID := string(data[offset : offset+4])subchunkSize := int(binary.LittleEndian.Uint32(data[offset+4 : offset+8]))offset += 8if offset+subchunkSize > len(data) {break}// Extract null-terminated stringvalue := extractNullTerminatedString(data[offset : offset+subchunkSize])switch subchunkID {case "ICMT": // Commentmetadata.Comment = valuecase "IART": // Artistmetadata.Artist = value}// Move to next subchunk (word-aligned)offset += subchunkSizeif subchunkSize%2 != 0 {offset++ // Skip padding byte}}}// extractNullTerminatedString extracts a null-terminated string from bytesfunc extractNullTerminatedString(data []byte) string {before, _, ok := bytes.Cut(data, []byte{0})if ok {return string(before)}return string(data)}// ReadWAVSamples reads audio samples from a WAV file and returns them as float64.// Mono files: returns single channel.// Stereo files: returns left channel only.// Samples are normalized to the range -1.0 to 1.0.func ReadWAVSamples(filepath string) ([]float64, int, error) {file, err := os.Open(filepath)if err != nil {return nil, 0, fmt.Errorf("failed to open file: %w", err)}defer func() { _ = file.Close() }()// Read header to get format infoheaderBuf := make([]byte, 44)if _, err := io.ReadFull(file, headerBuf); err != nil {return nil, 0, fmt.Errorf("failed to read header: %w", err)}// Verify RIFF/WAVE headerif string(headerBuf[0:4]) != "RIFF" || string(headerBuf[8:12]) != "WAVE" {return nil, 0, fmt.Errorf("not a valid WAV file")}// Parse chunks to find fmt and datavar sampleRate, channels, bitsPerSample intvar dataOffset, dataSize int64// Seek to first chunkif _, err := file.Seek(12, 0); err != nil {return nil, 0, fmt.Errorf("failed to seek: %w", err)}for {chunkHeader := make([]byte, 8)if _, err := io.ReadFull(file, chunkHeader); err != nil {if err == io.EOF {break}return nil, 0, fmt.Errorf("failed to read chunk header: %w", err)}chunkID := string(chunkHeader[0:4])chunkSize := int64(binary.LittleEndian.Uint32(chunkHeader[4:8]))switch chunkID {case "fmt ":fmtData := make([]byte, chunkSize)if _, err := io.ReadFull(file, fmtData); err != nil {return nil, 0, fmt.Errorf("failed to read fmt chunk: %w", err)}if len(fmtData) >= 16 {channels = int(binary.LittleEndian.Uint16(fmtData[2:4]))sampleRate = int(binary.LittleEndian.Uint32(fmtData[4:8]))bitsPerSample = int(binary.LittleEndian.Uint16(fmtData[14:16]))}case "data":dataOffset, _ = file.Seek(0, 1) // Current positiondataSize = chunkSize// Done - we found the data chunkgoto foundDatadefault:// Skip unknown chunkif _, err := file.Seek(chunkSize, 1); err != nil {return nil, 0, fmt.Errorf("failed to skip chunk: %w", err)}}// Word alignif chunkSize%2 != 0 {if _, err := file.Seek(1, 1); err != nil {return nil, 0, fmt.Errorf("failed to skip padding: %w", err)}}}return nil, 0, fmt.Errorf("no data chunk found in WAV file")foundData:if sampleRate == 0 || channels == 0 || bitsPerSample == 0 {return nil, 0, fmt.Errorf("missing or invalid fmt chunk")}// Read audio dataif _, err := file.Seek(dataOffset, 0); err != nil {return nil, 0, fmt.Errorf("failed to seek to data: %w", err)}audioData := make([]byte, dataSize)if _, err := io.ReadFull(file, audioData); err != nil {return nil, 0, fmt.Errorf("failed to read audio data: %w", err)}// Convert to float64 samplessamples := convertToFloat64(audioData, bitsPerSample, channels)return samples, sampleRate, nil}// convertToFloat64 converts raw audio bytes to float64 samples// Returns mono (left channel only for stereo)func convertToFloat64(data []byte, bitsPerSample, channels int) []float64 {bytesPerSample := bitsPerSample / 8blockAlign := bytesPerSample * channelsnumSamples := len(data) / blockAlignsamples := make([]float64, numSamples)switch bitsPerSample {case 16:for i := range numSamples {// Read first (left) channel only for stereooffset := i * blockAlignsample := int16(binary.LittleEndian.Uint16(data[offset : offset+2]))samples[i] = float64(sample) / 32768.0}case 24:for i := range numSamples {offset := i * blockAlign// 24-bit signed, little-endianb := data[offset : offset+3]sample := int32(b[0]) | int32(b[1])<<8 | int32(b[2])<<16// Sign extendif sample >= 0x800000 {sample -= 0x1000000}samples[i] = float64(sample) / 8388608.0}case 32:for i := range numSamples {offset := i * blockAlignsample := int32(binary.LittleEndian.Uint32(data[offset : offset+4]))samples[i] = float64(sample) / 2147483648.0}default:// Fallback: treat as 16-bitfor i := range numSamples {offset := i * blockAlignsample := int16(binary.LittleEndian.Uint16(data[offset : offset+2]))samples[i] = float64(sample) / 32768.0}}return samples}
package utilsimport ("testing")func TestValidateShortID(t *testing.T) {tests := []struct {name stringid stringfieldName stringwantErr bool}{{"valid 12-char ID", "abc123XYZ789", "test_id", false},{"valid with underscore", "abc_123_XYZ_", "test_id", false},{"valid with dash", "abc-123-XYZ-", "test_id", false},{"empty string", "", "test_id", true},{"too short", "abc123", "test_id", true},{"too long", "abc123XYZ789toolong", "test_id", true},{"invalid chars", "abc@123#XYZ$", "test_id", true},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {err := ValidateShortID(tt.id, tt.fieldName)if (err != nil) != tt.wantErr {t.Errorf("ValidateShortID() error = %v, wantErr %v", err, tt.wantErr)}})}}func TestValidateStringLength(t *testing.T) {tests := []struct {name stringvalue stringfield stringmaxLen intwantErr bool}{{"within limit", "hello", "test", 10, false},{"at limit", "1234567890", "test", 10, false},{"empty string", "", "test", 10, false},{"over limit", "12345678901", "test", 10, true},{"zero max", "a", "test", 0, true},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {err := ValidateStringLength(tt.value, tt.field, tt.maxLen)if (err != nil) != tt.wantErr {t.Errorf("ValidateStringLength() error = %v, wantErr %v", err, tt.wantErr)}})}}func TestValidateRange(t *testing.T) {t.Run("int range", func(t *testing.T) {tests := []struct {name stringvalue intmin intmax intwantErr bool}{{"within range", 50, 0, 100, false},{"at min", 0, 0, 100, false},{"at max", 100, 0, 100, false},{"below min", -1, 0, 100, true},{"above max", 101, 0, 100, true},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {err := ValidateRange(tt.value, "test", tt.min, tt.max)if (err != nil) != tt.wantErr {t.Errorf("ValidateRange() error = %v, wantErr %v", err, tt.wantErr)}})}})t.Run("float64 range", func(t *testing.T) {tests := []struct {name stringvalue float64min float64max float64wantErr bool}{{"within range", 45.5, -90.0, 90.0, false},{"at min", -90.0, -90.0, 90.0, false},{"at max", 90.0, -90.0, 90.0, false},{"below min", -90.1, -90.0, 90.0, true},{"above max", 90.1, -90.0, 90.0, true},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {err := ValidateRange(tt.value, "test", tt.min, tt.max)if (err != nil) != tt.wantErr {t.Errorf("ValidateRange() error = %v, wantErr %v", err, tt.wantErr)}})}})}func TestValidatePositive(t *testing.T) {tests := []struct {name stringvalue intwantErr bool}{{"positive", 1, false},{"large positive", 1000000, false},{"zero", 0, true},{"negative", -1, true},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {err := ValidatePositive(tt.value, "test")if (err != nil) != tt.wantErr {t.Errorf("ValidatePositive() error = %v, wantErr %v", err, tt.wantErr)}})}}func TestValidateSampleRate(t *testing.T) {tests := []struct {name stringrate intwantErr bool}{{"valid low", 1000, false},{"valid typical", 48000, false},{"valid high", 250000, false},{"valid max", 500000, false},{"too low", 999, true},{"too high", 500001, true},{"zero", 0, true},{"negative", -1000, true},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {err := ValidateSampleRate(tt.rate)if (err != nil) != tt.wantErr {t.Errorf("ValidateSampleRate() error = %v, wantErr %v", err, tt.wantErr)}})}}func TestValidateTimezone(t *testing.T) {tests := []struct {name stringtz stringwantErr bool}{{"valid Auckland", "Pacific/Auckland", false},{"valid UTC", "UTC", false},{"valid America/New_York", "America/New_York", false},{"valid Europe/London", "Europe/London", false},{"invalid", "Invalid/Timezone", true},{"garbage", "not-a-timezone", true},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {err := ValidateTimezone(tt.tz)if (err != nil) != tt.wantErr {t.Errorf("ValidateTimezone() error = %v, wantErr %v", err, tt.wantErr)}})}}func TestValidateNonNegative(t *testing.T) {tests := []struct {name stringvalue intwantErr bool}{{"positive", 1, false},{"zero", 0, false},{"negative", -1, true},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {err := ValidateNonNegative(tt.value, "test")if (err != nil) != tt.wantErr {t.Errorf("ValidateNonNegative() error = %v, wantErr %v", err, tt.wantErr)}})}}
package utilsimport ("database/sql""fmt""regexp""time")// ID length constants matching nanoid generationconst (ShortIDLen = 12 // dataset, location, cluster, pattern, species, filter, call_type)// Sample rate reasonable bounds for audio recordingconst (MinSampleRate = 1000 // 1 kHz - below this is unlikely to be real audioMaxSampleRate = 500000 // 500 kHz - well above bat detectors (~250kHz))// Max string lengths from schemaconst (MaxNameLen = 140 // location.name, cluster.nameMaxDatasetNameLen = 255 // dataset.nameMaxDescriptionLen = 255 // all description fieldsMaxPathLen = 255 // cluster.pathMaxFileNameLen = 255 // file.file_nameMaxTimezoneLen = 40 // location.timezone_id)// ID format regex - alphanumeric characters (nanoid uses A-Za-z0-9_)var shortIDRegex = regexp.MustCompile(`^[A-Za-z0-9_-]{12}$`)// ValidateShortID validates 12-character nanoid formatfunc ValidateShortID(id, fieldName string) error {if id == "" {return fmt.Errorf("%s cannot be empty", fieldName)}if len(id) != ShortIDLen {return fmt.Errorf("%s must be exactly %d characters (got %d)", fieldName, ShortIDLen, len(id))}if !shortIDRegex.MatchString(id) {return fmt.Errorf("%s has invalid format (expected alphanumeric nanoid)", fieldName)}return nil}// ValidateOptionalShortID validates short ID if provided (non-empty)func ValidateOptionalShortID(id *string, fieldName string) error {if id == nil || *id == "" {return nil}return ValidateShortID(*id, fieldName)}// ValidateStringLength validates string length constraintfunc ValidateStringLength(value, fieldName string, maxLen int) error {if len(value) > maxLen {return fmt.Errorf("%s must be %d characters or less (got %d)", fieldName, maxLen, len(value))}return nil}// ValidateOptionalStringLength validates string length if providedfunc ValidateOptionalStringLength(value *string, fieldName string, maxLen int) error {if value == nil || *value == "" {return nil}return ValidateStringLength(*value, fieldName, maxLen)}// ValidateRange validates numeric range constraint (inclusive)func ValidateRange[T int | float64](value T, fieldName string, min, max T) error {if value < min || value > max {return fmt.Errorf("%s must be between %v and %v (got %v)", fieldName, min, max, value)}return nil}// ValidatePositive validates positive number (> 0)func ValidatePositive[T int | float64](value T, fieldName string) error {if value <= 0 {return fmt.Errorf("%s must be positive (got %v)", fieldName, value)}return nil}// ValidateNonNegative validates non-negative number (>= 0)func ValidateNonNegative[T int | float64](value T, fieldName string) error {if value < 0 {return fmt.Errorf("%s must be non-negative (got %v)", fieldName, value)}return nil}// ValidateSampleRate validates audio sample rate is in reasonable rangefunc ValidateSampleRate(rate int) error {return ValidateRange(rate, "sample_rate", MinSampleRate, MaxSampleRate)}// ValidateTimezone validates IANA timezone IDfunc ValidateTimezone(tzID string) error {if _, err := time.LoadLocation(tzID); err != nil {return fmt.Errorf("invalid timezone_id '%s': %w", tzID, err)}return nil}// GetDatasetType returns the type of a dataset// Returns: (type, exists, error)func GetDatasetType(db *sql.DB, datasetID string) (string, bool, error) {var datasetType stringerr := db.QueryRow("SELECT type FROM dataset WHERE id = ?", datasetID).Scan(&datasetType)if err == sql.ErrNoRows {return "", false, nil}if err != nil {return "", false, err}return datasetType, true, nil}// ValidateDatasetTypeForImport checks that a dataset is 'structured' type for file imports// Returns error if dataset doesn't exist or is not 'structured'func ValidateDatasetTypeForImport(db *sql.DB, datasetID string) error {datasetType, exists, err := GetDatasetType(db, datasetID)if err != nil {return fmt.Errorf("failed to query dataset type: %w", err)}if !exists {return fmt.Errorf("dataset not found: %s", datasetID)}if datasetType != "structured" {return fmt.Errorf("dataset '%s' is type '%s' - file imports only support 'structured' datasets", datasetID, datasetType)}return nil}// ValidateDatasetTypeUnstructured checks that a dataset is 'unstructured' type// Returns error if dataset doesn't exist or is not 'unstructured'func ValidateDatasetTypeUnstructured(db *sql.DB, datasetID string) error {datasetType, exists, err := GetDatasetType(db, datasetID)if err != nil {return fmt.Errorf("failed to query dataset type: %w", err)}if !exists {return fmt.Errorf("dataset not found: %s", datasetID)}if datasetType != "unstructured" {return fmt.Errorf("dataset '%s' is type '%s' - this command only supports 'unstructured' datasets", datasetID, datasetType)}return nil}// ValidateLocationBelongsToDataset checks that a location belongs to a specific dataset// Returns error if location doesn't exist or belongs to a different datasetfunc ValidateLocationBelongsToDataset(db *sql.DB, locationID, datasetID string) error {var locationDatasetID stringerr := db.QueryRow("SELECT dataset_id FROM location WHERE id = ? AND active = true", locationID).Scan(&locationDatasetID)if err == sql.ErrNoRows {return fmt.Errorf("location not found or inactive: %s", locationID)}if err != nil {return fmt.Errorf("failed to query location: %w", err)}if locationDatasetID != datasetID {return fmt.Errorf("location %s does not belong to dataset %s", locationID, datasetID)}return nil}
package utilsimport ("image""image/color""math/rand""strings""testing")func TestWriteKittyImage_SmallImage(t *testing.T) {// 2x2 image produces small base64 payload — single chunk, no m= keyimg := image.NewGray(image.Rect(0, 0, 2, 2))img.SetGray(0, 0, color.Gray{Y: 128})var buf strings.Builderif err := WriteKittyImage(img, &buf); err != nil {t.Fatalf("WriteKittyImage: %v", err)}out := buf.String()if !strings.HasPrefix(out, "\x1b_Gf=100,a=T;") {t.Error("expected single-chunk header with f=100,a=T")}if strings.Contains(out, "m=") {t.Error("small image should not use chunked m= key")}if !strings.HasSuffix(out, "\x1b\\") {t.Error("expected escape sequence terminator")}}func TestWriteKittyImage_LargeImage_Chunked(t *testing.T) {// 128x128 random noise image is incompressible — produces >4096 bytes of base64 even with proper LZ77rng := rand.New(rand.NewSource(42))img := image.NewGray(image.Rect(0, 0, 128, 128))for y := range 128 {for x := range 128 {img.SetGray(x, y, color.Gray{Y: uint8(rng.Intn(256))})}}var buf strings.Builderif err := WriteKittyImage(img, &buf); err != nil {t.Fatalf("WriteKittyImage: %v", err)}out := buf.String()// Should have multiple escape sequenceschunks := strings.Split(out, "\x1b\\")// Last element is empty after final terminatorchunks = chunks[:len(chunks)-1]if len(chunks) < 2 {t.Fatalf("expected multiple chunks, got %d", len(chunks))}// First chunk should have f=100,a=T,m=1if !strings.Contains(chunks[0], "f=100,a=T,m=1") {t.Errorf("first chunk missing f=100,a=T,m=1: %s", chunks[0][:min(80, len(chunks[0]))])}// Last chunk should have m=0last := chunks[len(chunks)-1]if !strings.Contains(last, "\x1b_Gm=0;") {t.Errorf("last chunk missing m=0: %s", last[:min(80, len(last))])}// Middle chunks should have m=1for i := 1; i < len(chunks)-1; i++ {if !strings.Contains(chunks[i], "\x1b_Gm=1;") {t.Errorf("middle chunk %d missing m=1", i)}}}func TestClearKittyImages(t *testing.T) {var buf strings.BuilderClearKittyImages(&buf)expected := "\x1b_Ga=d\x1b\\"if buf.String() != expected {t.Errorf("got %q, want %q", buf.String(), expected)}}func TestWriteSixelImage(t *testing.T) {img := image.NewGray(image.Rect(0, 0, 4, 6))for y := range 6 {for x := range 4 {img.SetGray(x, y, color.Gray{Y: uint8((x + y) * 40)})}}var buf strings.Builderif err := WriteSixelImage(img, &buf); err != nil {t.Fatalf("WriteSixelImage: %v", err)}out := buf.String()// Sixel DCS introducerif !strings.HasPrefix(out, "\x1bP") {t.Error("expected DCS prefix \\x1bP")}// String terminatorif !strings.HasSuffix(out, "\x1b\\") {t.Error("expected ST suffix \\x1b\\\\")}// Should contain 'q' after DCS parametersif !strings.Contains(out, "q") {t.Error("expected 'q' in DCS sequence")}}func TestClearImages_Kitty(t *testing.T) {var buf strings.BuilderClearImages(&buf, ProtocolKitty)if buf.String() != "\x1b_Ga=d\x1b\\" {t.Errorf("got %q, want kitty clear sequence", buf.String())}}func TestClearImages_Sixel(t *testing.T) {var buf strings.BuilderClearImages(&buf, ProtocolSixel)if buf.String() != "" {t.Errorf("expected no output for sixel clear, got %q", buf.String())}}func TestWriteImage_Kitty(t *testing.T) {img := image.NewGray(image.Rect(0, 0, 2, 2))var buf strings.Builderif err := WriteImage(img, &buf, ProtocolKitty); err != nil {t.Fatalf("WriteImage kitty: %v", err)}if !strings.HasPrefix(buf.String(), "\x1b_G") {t.Error("expected kitty escape prefix")}}func TestWriteImage_Sixel(t *testing.T) {img := image.NewGray(image.Rect(0, 0, 4, 6))var buf strings.Builderif err := WriteImage(img, &buf, ProtocolSixel); err != nil {t.Fatalf("WriteImage sixel: %v", err)}if !strings.HasPrefix(buf.String(), "\x1bP") {t.Error("expected sixel DCS prefix")}}func TestWriteITermImage(t *testing.T) {img := image.NewGray(image.Rect(0, 0, 4, 4))img.SetGray(0, 0, color.Gray{Y: 128})var buf strings.Builderif err := WriteITermImage(img, &buf); err != nil {t.Fatalf("WriteITermImage: %v", err)}out := buf.String()if !strings.HasPrefix(out, "\x1b]1337;File=") {t.Errorf("expected iTerm2 OSC prefix, got %q", out[:min(30, len(out))])}if !strings.Contains(out, "inline=1") {t.Error("expected inline=1 parameter")}if !strings.HasSuffix(out, "\x07") {t.Error("expected BEL terminator")}}func TestWriteImage_ITerm(t *testing.T) {img := image.NewGray(image.Rect(0, 0, 4, 4))var buf strings.Builderif err := WriteImage(img, &buf, ProtocolITerm); err != nil {t.Fatalf("WriteImage iterm: %v", err)}if !strings.HasPrefix(buf.String(), "\x1b]1337;File=") {t.Error("expected iTerm2 OSC prefix")}}func TestClearImages_ITerm(t *testing.T) {var buf strings.BuilderClearImages(&buf, ProtocolITerm)if buf.String() != "" {t.Errorf("expected no output for iTerm2 clear, got %q", buf.String())}}
package utilsimport ("bytes""encoding/base64""image""image/color""image/png""io""github.com/charmbracelet/x/ansi""github.com/charmbracelet/x/ansi/iterm2""github.com/charmbracelet/x/ansi/kitty""github.com/charmbracelet/x/ansi/sixel")// ImageProtocol selects the terminal graphics protocol.type ImageProtocol intconst (ProtocolKitty ImageProtocol = iotaProtocolSixelProtocolITerm)// SpectrogramDisplaySize is the default pixel dimension for spectrogram images.// 448px suits Retina/HiDPI screens (224 logical pixels at 2x).const SpectrogramDisplaySize = 448// ClampImageSize clamps a dimension to [224, 448].func ClampImageSize(size int) int {return max(224, min(896, size))}// WriteImage writes an image using the specified terminal graphics protocol.func WriteImage(img image.Image, w io.Writer, protocol ImageProtocol) error {switch protocol {case ProtocolSixel:return WriteSixelImage(img, w)case ProtocolITerm:return WriteITermImage(img, w)default:return WriteKittyImage(img, w)}}// ClearImages clears previously displayed images.// For kitty, deletes all image placements. For sixel/iTerm2, no-op (inline text).func ClearImages(w io.Writer, protocol ImageProtocol) error {switch protocol {case ProtocolKitty:return ClearKittyImages(w)default:return nil}}// ClearKittyImages clears all previously displayed Kitty imagesfunc ClearKittyImages(w io.Writer) error {_, err := io.WriteString(w, ansi.KittyGraphics(nil, "a=d"))return err}// WriteKittyImage writes an image to the writer using the Kitty graphics protocol.// The image is encoded as PNG, base64'd, and sent via chunked Kitty escape sequences.func WriteKittyImage(img image.Image, w io.Writer) error {return kitty.EncodeGraphics(w, img, &kitty.Options{Format: kitty.PNG,Action: kitty.TransmitAndPut,Transmission: kitty.Direct,Chunk: true,})}// WriteSixelImage writes an image using the Sixel graphics protocol.func WriteSixelImage(img image.Image, w io.Writer) error {var buf bytes.Bufferenc := &sixel.Encoder{}if err := enc.Encode(&buf, img); err != nil {return err}_, err := io.WriteString(w, ansi.SixelGraphics(0, 1, 0, buf.Bytes()))return err}// WriteITermImage writes an image using the iTerm2 Inline Image Protocol.func WriteITermImage(img image.Image, w io.Writer) error {var buf bytes.Bufferif err := png.Encode(&buf, img); err != nil {return err}b64 := base64.StdEncoding.EncodeToString(buf.Bytes())_, err := io.WriteString(w, ansi.ITerm2(iterm2.File{Inline: true,Content: []byte(b64),}))return err}// CreateGrayscaleImage creates an image.Image from a 2D uint8 array.// The array is organized as [rows][cols] where rows = frequency bins.func CreateGrayscaleImage(data [][]uint8) image.Image {if len(data) == 0 || len(data[0]) == 0 {return nil}height := len(data)width := len(data[0])img := image.NewGray(image.Rect(0, 0, width, height))for y := range height {off := y * img.Striderow := data[y]copy(img.Pix[off:off+width], row)}return img}// CreateRGBImage creates an image.Image from a 2D RGBPixel array.// The array is organized as [rows][cols] where rows = frequency bins.func CreateRGBImage(data [][]RGBPixel) image.Image {if len(data) == 0 || len(data[0]) == 0 {return nil}height := len(data)width := len(data[0])img := image.NewRGBA(image.Rect(0, 0, width, height))for y := range height {off := y * img.Striderow := data[y]for x := range width {i := off + x*4img.Pix[i] = row[x].Rimg.Pix[i+1] = row[x].Gimg.Pix[i+2] = row[x].Bimg.Pix[i+3] = 255}}return img}// ResizeImage resizes an image using nearest-neighbor interpolation.// For higher quality, use golang.org/x/image/draw, but this keeps dependencies minimal.func ResizeImage(img image.Image, newWidth, newHeight int) image.Image {bounds := img.Bounds()srcWidth := bounds.Dx()srcHeight := bounds.Dy()scaleX := float64(srcWidth) / float64(newWidth)scaleY := float64(srcHeight) / float64(newHeight)if srcGray, ok := img.(*image.Gray); ok {result := image.NewGray(image.Rect(0, 0, newWidth, newHeight))for y := range newHeight {srcY := int(float64(y) * scaleY)if srcY >= srcHeight {srcY = srcHeight - 1}dstOff := y * result.StridesrcRowOff := srcY * srcGray.Stridefor x := range newWidth {srcX := int(float64(x) * scaleX)if srcX >= srcWidth {srcX = srcWidth - 1}result.Pix[dstOff+x] = srcGray.Pix[srcRowOff+srcX]}}return result}if srcRGBA, ok := img.(*image.RGBA); ok {result := image.NewRGBA(image.Rect(0, 0, newWidth, newHeight))for y := range newHeight {srcY := int(float64(y) * scaleY)if srcY >= srcHeight {srcY = srcHeight - 1}dstOff := y * result.StridesrcRowOff := srcY * srcRGBA.Stridefor x := range newWidth {srcX := int(float64(x) * scaleX)if srcX >= srcWidth {srcX = srcWidth - 1}si := srcRowOff + srcX*4di := dstOff + x*4result.Pix[di] = srcRGBA.Pix[si]result.Pix[di+1] = srcRGBA.Pix[si+1]result.Pix[di+2] = srcRGBA.Pix[si+2]result.Pix[di+3] = srcRGBA.Pix[si+3]}}return result}// Fallback for other image typesresult := image.NewRGBA(image.Rect(0, 0, newWidth, newHeight))for y := range newHeight {srcY := int(float64(y) * scaleY)if srcY >= srcHeight {srcY = srcHeight - 1}for x := range newWidth {srcX := int(float64(x) * scaleX)if srcX >= srcWidth {srcX = srcWidth - 1}c := img.At(srcX+bounds.Min.X, srcY+bounds.Min.Y)r, g, b, _ := c.RGBA()result.SetRGBA(x, y, color.RGBA{R: uint8(r >> 8),G: uint8(g >> 8),B: uint8(b >> 8),A: 255,})}}return result}// WritePNG writes an image to a writer in PNG format using fast compression.func WritePNG(img image.Image, w io.Writer) error {enc := &png.Encoder{CompressionLevel: png.BestSpeed}return enc.Encode(w, img)}
package utilsimport ("image""math""strings""sync""github.com/madelynnblue/go-dsp/window")// cached Hann windows by size, computed oncevar (hannCache = map[int][]float64{}hannCacheMu sync.RWMutex)// getCachedHannWindow returns a cached Hann window of the given size.func getCachedHannWindow(size int) []float64 {hannCacheMu.RLock()if w, ok := hannCache[size]; ok {hannCacheMu.RUnlock()return w}hannCacheMu.RUnlock()hannCacheMu.Lock()defer hannCacheMu.Unlock()// Double-check after acquiring write lockif w, ok := hannCache[size]; ok {return w}w := window.Hann(size)hannCache[size] = wreturn w}// DefaultMaxSampleRate is the maximum sample rate for spectrograms.// Higher sample rates are downsampled to this rate for better visualization.const DefaultMaxSampleRate = 16000// SpectrogramConfig holds STFT parameterstype SpectrogramConfig struct {WindowSize int // FFT window size (e.g., 400)HopSize int // Hop between windows (e.g., 200 for 50% overlap)SampleRate int // Sample rate in Hz}// DefaultSpectrogramConfig returns default config matching Julia implementationfunc DefaultSpectrogramConfig(sampleRate int) SpectrogramConfig {return SpectrogramConfig{WindowSize: 512,HopSize: 256, // 50% overlap (window/2)SampleRate: sampleRate,}}// GenerateSpectrogram generates a spectrogram from audio samples.// Returns a 2D array of uint8 (0-255) where:// - First dimension is frequency bins (rows)// - Second dimension is time frames (columns)func GenerateSpectrogram(samples []float64, cfg SpectrogramConfig) [][]uint8 {if len(samples) < cfg.WindowSize {return nil}// Get cached Hann windowhannWindow := getCachedHannWindow(cfg.WindowSize)// Calculate number of framesnumFrames := (len(samples)-cfg.WindowSize)/cfg.HopSize + 1if numFrames <= 0 {return nil}// Number of frequency bins (half of FFT due to symmetry)numFreqBins := cfg.WindowSize/2 + 1// Allocate power spectrum as flat backing slice (single allocation)powerFlat := make([]float64, numFreqBins*numFrames)// Pre-allocate scratch buffers (reused across all frames — zero allocs in loop)frameData := make([]float64, cfg.WindowSize)scratch := make([]complex128, cfg.WindowSize)framePower := make([]float64, numFreqBins)// Perform STFTfor frame := range numFrames {start := frame * cfg.HopSize// Extract and window the framefor i := 0; i < cfg.WindowSize; i++ {frameData[i] = samples[start+i] * hannWindow[i]}// Compute power spectrum via inline FFT (zero allocations)PowerSpectrumFFT(frameData, framePower, scratch)// Copy power into flat matrix (freq bins x time frames layout)for bin := range numFreqBins {powerFlat[bin*numFrames+frame] = framePower[bin]}}// Fused normalization: replace zeros, convert to dB, find min/max, normalize to uint8// All in 2 passes instead of 6return normalizeFlat(powerFlat, numFreqBins, numFrames)}// normalizeFlat converts power values to dB, normalizes to 0-255, in 2 passes.// Operates on a flat slice laid out as [row0_col0, row0_col1, ..., row1_col0, ...].// Returns [][]uint8 with rows flipped vertically (low frequencies at bottom).func normalizeFlat(power []float64, rows, cols int) [][]uint8 {if rows == 0 || cols == 0 {return nil}// Pass 1: find minNonZero, then convert power to dB in-place, tracking min/max dBminNonZero := math.MaxFloat64for _, val := range power {if val > 0 && val < minNonZero {minNonZero = val}}if minNonZero == math.MaxFloat64 {minNonZero = 1e-20 // fallback floor}minDB := math.MaxFloat64maxDB := -math.MaxFloat64for i, val := range power {if val <= 0 {val = minNonZero}db := 10.0 * math.Log10(val)power[i] = dbif db < minDB {minDB = db}if db > maxDB {maxDB = db}}// Pass 2: normalize dB to uint8 and write into result (with vertical flip)rangeDB := maxDB - minDBif rangeDB == 0 {rangeDB = 1}scale := 255.0 / rangeDB// Allocate result with flat backing slice (single allocation)resultFlat := make([]uint8, rows*cols)result := make([][]uint8, rows)for i := range result {// Flip: row i in result gets data from row (rows-1-i) in powersrcRow := rows - 1 - iresult[i] = resultFlat[i*cols : (i+1)*cols]srcOff := srcRow * colsfor j := range cols {result[i][j] = uint8((power[srcOff+j] - minDB) * scale)}}return result}// ExtractSegmentSamples extracts samples from a time rangefunc ExtractSegmentSamples(samples []float64, sampleRate int, startSec, endSec float64) []float64 {startIdx := int(startSec * float64(sampleRate))endIdx := int(endSec * float64(sampleRate))if startIdx < 0 {startIdx = 0}if endIdx > len(samples) {endIdx = len(samples)}if startIdx >= endIdx {return nil}return samples[startIdx:endIdx]}// GenerateSegmentSpectrogram generates a spectrogram image for a time segment.// Handles WAV loading, downsampling, and image creation.// color=true applies L4 colormap, color=false creates grayscale.// imgSize specifies the output image dimensions (clamped to [224, 896]).func GenerateSegmentSpectrogram(dataFilePath string, startTime, endTime float64, color bool, imgSize int) (image.Image, error) {// Derive WAV file path (strip .data suffix)wavPath := strings.TrimSuffix(dataFilePath, ".data")// Read WAV samplessamples, sampleRate, err := ReadWAVSamples(wavPath)if err != nil {return nil, err}// Extract segment samplessegSamples := ExtractSegmentSamples(samples, sampleRate, startTime, endTime)if len(segSamples) == 0 {return nil, nil}// For spectrograms, downsample if sample rate exceeds 16kHzspectSampleRate := sampleRateif sampleRate > DefaultMaxSampleRate {segSamples = ResampleRate(segSamples, sampleRate, DefaultMaxSampleRate)spectSampleRate = DefaultMaxSampleRate}// Generate spectrogramconfig := DefaultSpectrogramConfig(spectSampleRate)spectrogram := GenerateSpectrogram(segSamples, config)if spectrogram == nil {return nil, nil}// Create image (grayscale or color)var img image.Imageif color {colorData := ApplyL4Colormap(spectrogram)img = CreateRGBImage(colorData)} else {img = CreateGrayscaleImage(spectrogram)}if img == nil {return nil, nil}// ResizeimgSize = ClampImageSize(imgSize)return ResizeImage(img, imgSize, imgSize), nil}
package utilsimport ("math""testing")func TestResampleRate(t *testing.T) {t.Run("should return same samples for same rate", func(t *testing.T) {samples := []float64{0.1, 0.2, 0.3, 0.4, 0.5}result := ResampleRate(samples, 16000, 16000)if len(result) != len(samples) {t.Errorf("length mismatch: got %d, want %d", len(result), len(samples))}for i := range samples {if result[i] != samples[i] {t.Errorf("sample %d mismatch: got %f, want %f", i, result[i], samples[i])}}})t.Run("should downsample from 250000 to 16000", func(t *testing.T) {// 250000 / 16000 = 15.625 ratiosamples := make([]float64, 2500) // 0.01 seconds at 250kHzfor i := range samples {samples[i] = float64(i) / float64(len(samples))}result := ResampleRate(samples, 250000, 16000)expectedLen := 160 // 0.01 seconds at 16kHzif len(result) != expectedLen {t.Errorf("length mismatch: got %d, want %d", len(result), expectedLen)}})t.Run("should downsample from 44100 to 16000", func(t *testing.T) {// 44100 / 16000 = 2.75625 ratiosamples := make([]float64, 441) // 0.01 seconds at 44.1kHzfor i := range samples {samples[i] = float64(i) / float64(len(samples))}result := ResampleRate(samples, 44100, 16000)expectedLen := 160 // 0.01 seconds at 16kHzif len(result) != expectedLen {t.Errorf("length mismatch: got %d, want %d", len(result), expectedLen)}})t.Run("should preserve signal shape", func(t *testing.T) {// Create a simple ramp signalsamples := []float64{0.0, 0.25, 0.5, 0.75, 1.0}result := ResampleRate(samples, 50000, 16000)// Should still be a roughly increasing signalfor i := 1; i < len(result); i++ {if result[i] < result[i-1]-0.1 {t.Errorf("signal not preserved: result[%d]=%f < result[%d]=%f", i, result[i], i-1, result[i-1])}}})t.Run("should handle empty samples", func(t *testing.T) {result := ResampleRate([]float64{}, 44100, 16000)if len(result) != 0 {t.Errorf("expected empty result, got %d samples", len(result))}})}func TestResample(t *testing.T) {t.Run("should return same samples for speed 1.0", func(t *testing.T) {samples := []float64{0.1, 0.2, 0.3, 0.4, 0.5}result := Resample(samples, 1.0)if len(result) != len(samples) {t.Errorf("length mismatch: got %d, want %d", len(result), len(samples))}for i := range samples {if result[i] != samples[i] {t.Errorf("sample %d mismatch: got %f, want %f", i, result[i], samples[i])}}})t.Run("should double samples for half speed", func(t *testing.T) {samples := []float64{0.0, 1.0, 0.0, -1.0, 0.0}result := Resample(samples, 0.5)// Half speed = 2x more samplesexpectedLen := len(samples) * 2if len(result) != expectedLen {t.Errorf("length mismatch: got %d, want %d", len(result), expectedLen)}})t.Run("should halve samples for double speed", func(t *testing.T) {samples := []float64{0.0, 0.5, 1.0, 0.5, 0.0, -0.5, -1.0, -0.5, 0.0}result := Resample(samples, 2.0)// Double speed = half the samplesexpectedLen := len(samples) / 2if len(result) != expectedLen {t.Errorf("length mismatch: got %d, want %d", len(result), expectedLen)}})t.Run("should use linear interpolation", func(t *testing.T) {// With samples [0, 1], half-speed should interpolate to [0, 0.5, 1]samples := []float64{0.0, 1.0}result := Resample(samples, 0.5)// Expected: 4 samples (2 / 0.5 = 4)if len(result) != 4 {t.Errorf("length mismatch: got %d, want 4", len(result))}// Check interpolation: index 1 should be ~0.5 (midpoint)expected := 0.5if math.Abs(result[1]-expected) > 0.01 {t.Errorf("interpolated value mismatch: got %f, want ~%f", result[1], expected)}})t.Run("should handle empty samples", func(t *testing.T) {result := Resample([]float64{}, 0.5)if len(result) != 0 {t.Errorf("expected empty result, got %d samples", len(result))}})t.Run("should handle single sample", func(t *testing.T) {samples := []float64{0.5}result := Resample(samples, 0.5)// 1 / 0.5 = 2 samplesif len(result) != 2 {t.Errorf("length mismatch: got %d, want 2", len(result))}})}func TestResampleQuality(t *testing.T) {t.Run("should preserve zero crossings", func(t *testing.T) {// Sine wave: should have zero crossings at multiples of pisampleRate := 1000samples := make([]float64, sampleRate)for i := range samples {samples[i] = math.Sin(2 * math.Pi * float64(i) / float64(sampleRate))}// Resample to half speedresult := Resample(samples, 0.5)// First sample should still be ~0 (sine at 0)if math.Abs(result[0]) > 0.01 {t.Errorf("first sample not near zero: got %f", result[0])}// Peak should still be ~1.0 (sine max)peakFound := falsefor _, s := range result {if math.Abs(s-1.0) < 0.1 {peakFound = truebreak}}if !peakFound {t.Error("peak not preserved in resampled signal")}})}
package utils// ResampleRate converts samples from one sample rate to another using linear interpolation.// This is used to downsample high sample rate audio for spectrogram visualization.// fromRate: original sample rate (e.g., 250000)// toRate: target sample rate (e.g., 16000)func ResampleRate(samples []float64, fromRate, toRate int) []float64 {if fromRate == toRate || len(samples) == 0 {return samples}// Calculate ratio: toRate/fromRate (e.g., 16000/250000 = 0.064)ratio := float64(toRate) / float64(fromRate)newLen := int(float64(len(samples)) * ratio)if newLen <= 0 {return samples}result := make([]float64, newLen)for i := range newLen {// Source index in original samples (floating point)srcIdx := float64(i) / ratioidx0 := int(srcIdx)idx1 := idx0 + 1// Clamp to valid rangeif idx0 >= len(samples) {idx0 = len(samples) - 1}if idx1 >= len(samples) {idx1 = len(samples) - 1}// Linear interpolation between adjacent samplesfrac := srcIdx - float64(idx0)result[i] = samples[idx0]*(1-frac) + samples[idx1]*frac}return result}// Resample changes playback speed using linear interpolation.// speed > 1.0 = faster (fewer samples), speed < 1.0 = slower (more samples).// For half-speed playback, use speed=0.5 which doubles the sample count.func Resample(samples []float64, speed float64) []float64 {if speed == 1.0 || len(samples) == 0 {return samples}// Calculate new length: slower speed = more samplesnewLen := int(float64(len(samples)) / speed)if newLen <= 0 {return samples}result := make([]float64, newLen)for i := range newLen {// Source index in original samples (floating point)srcIdx := float64(i) * speedidx0 := int(srcIdx)idx1 := idx0 + 1// Clamp to valid rangeif idx0 >= len(samples) {idx0 = len(samples) - 1}if idx1 >= len(samples) {idx1 = len(samples) - 1}// Linear interpolation between adjacent samplesfrac := srcIdx - float64(idx0)result[i] = samples[idx0]*(1-frac) + samples[idx1]*frac}return result}
package utilsimport ("testing")func TestStripMountPoint(t *testing.T) {tests := []struct {name stringinput stringexpected string}{// macOS{"macOS volume", "/Volumes/ExternalDrive/Audio", "ExternalDrive/Audio"},{"macOS root volume", "/Volumes/Drive", "Drive"},// Linux /media/ with username{"Linux media mount", "/media/david/USB-Drive/Audio", "USB-Drive/Audio"},{"Linux media different user", "/media/john/Backup/Audio", "Backup/Audio"},{"Linux media Pomona", "/media/david/Pomona-4/Pomona/A05/2025-11-08", "Pomona-4/Pomona/A05/2025-11-08"},// Linux /mnt/{"Linux mnt mount", "/mnt/storage/Audio", "storage/Audio"},// No mount point{"Absolute no mount", "/home/user/Audio", "/home/user/Audio"},{"Relative path", "./relative/path", "relative/path"},// Edge cases{"Root", "/", "/"},{"Empty", "", "."},{"Volumes only", "/Volumes/", "."},{"Media with user only", "/media/david/", "."},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {result := StripMountPoint(tt.input)if result != tt.expected {t.Errorf("StripMountPoint(%q) = %q, want %q", tt.input, result, tt.expected)}})}}func TestNormalizeFolderPath(t *testing.T) {tests := []struct {name stringinput stringexpected string}{// Full workflow{"Linux media path", "/media/david/Pomona-4/Pomona/A05/2025-11-08/", "Pomona-4/Pomona/A05/2025-11-08"},{"macOS volumes path", "/Volumes/Drive/Audio/Recordings/", "Drive/Audio/Recordings"},{"Linux mnt path", "/mnt/storage/Audio/Files/", "storage/Audio/Files"},// Trailing slashes handled{"With trailing slash", "/media/david/USB/Audio/", "USB/Audio"},{"Without trailing slash", "/media/david/USB/Audio", "USB/Audio"},// Multiple levels{"Deep nested path", "/media/david/Pomona-4/Level1/Level2/Level3/", "Pomona-4/Level1/Level2/Level3"},// Edge cases{"File at mount root", "/media/david/", "."},{"Volumes with drive only", "/Volumes/Drive/", "Drive"},{"Volumes drive no trailing slash", "/Volumes/Drive", "Drive"},{"Root", "/", ""},{"Empty", "", "."},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {result := NormalizeFolderPath(tt.input)if result != tt.expected {t.Errorf("NormalizeFolderPath(%q) = %q, want %q", tt.input, result, tt.expected)}})}}
package utilsimport ("path/filepath""runtime""strings")// StripMountPoint removes OS-specific mount point prefixes from a pathfunc StripMountPoint(absPath string) string {// Clean path firstabsPath = filepath.Clean(absPath)// Handle Windows drive lettersif runtime.GOOS == "windows" {volumeName := filepath.VolumeName(absPath)if volumeName != "" {// Remove "C:\" and return restreturn strings.TrimPrefix(absPath, volumeName+string(filepath.Separator))}}// Handle Unix-like mount pointsswitch {case absPath == "/Volumes":// Exact match to mount point rootreturn "."case strings.HasPrefix(absPath, "/Volumes/"):// macOS external volumes: /Volumes/Drive/... → Drive/...return strings.TrimPrefix(absPath, "/Volumes/")case strings.HasPrefix(absPath, "/media/"):// Linux user mounts: /media/username/Drive/... → Drive/...// Strip /media/ and the username directorypathAfterMedia := strings.TrimPrefix(absPath, "/media/")parts := strings.SplitN(pathAfterMedia, string(filepath.Separator), 2)if len(parts) > 1 {return parts[1] // Return everything after username}// Just username, no subdirectory (e.g., /media/david)return "."case strings.HasPrefix(absPath, "/mnt/"):// Linux system mounts: /mnt/storage/... → storage/...return strings.TrimPrefix(absPath, "/mnt/")}// No known mount point detected, return as-isreturn absPath}// NormalizeFolderPath strips mount points and cleans up a folder path// Unlike a file path normalization, this expects a directory pathfunc NormalizeFolderPath(folderPath string) string {// Clean the pathfolderPath = filepath.Clean(folderPath)// Strip mount pointrelativePath := StripMountPoint(folderPath)// Clean up leading/trailing slashesrelativePath = strings.Trim(relativePath, string(filepath.Separator))return relativePath}
package utilsimport ("regexp""testing")func TestGenerateShortID(t *testing.T) {// Test that it generates a 12-character IDid, err := GenerateShortID()if err != nil {t.Fatalf("GenerateShortID() error = %v", err)}if len(id) != 12 {t.Errorf("GenerateShortID() length = %d, want 12", len(id))}// Verify it only contains valid alphabet characters// Default nanoid alphabet uses A-Za-z0-9_- symbols (64 characters)validPattern := regexp.MustCompile(`^[0-9A-Za-z_-]{12}$`)if !validPattern.MatchString(id) {t.Errorf("GenerateShortID() = %q, contains invalid characters", id)}// Test uniqueness - generate multiple IDs and check they're differentids := make(map[string]bool)for i := range 100 {id, err := GenerateShortID()if err != nil {t.Fatalf("GenerateShortID() iteration %d error = %v", i, err)}if ids[id] {t.Errorf("GenerateShortID() produced duplicate: %q", id)}ids[id] = true}}func TestGenerateLongID(t *testing.T) {// Test that it generates a 21-character IDid, err := GenerateLongID()if err != nil {t.Fatalf("GenerateLongID() error = %v", err)}if len(id) != 21 {t.Errorf("GenerateLongID() length = %d, want 21", len(id))}// Verify it only contains valid alphabet characters// Default nanoid alphabet uses A-Za-z0-9_- symbols (64 characters)validPattern := regexp.MustCompile(`^[0-9A-Za-z_-]{21}$`)if !validPattern.MatchString(id) {t.Errorf("GenerateLongID() = %q, contains invalid characters", id)}// Test uniqueness - generate multiple IDs and check they're differentids := make(map[string]bool)for i := range 100 {id, err := GenerateLongID()if err != nil {t.Fatalf("GenerateLongID() iteration %d error = %v", i, err)}if ids[id] {t.Errorf("GenerateLongID() produced duplicate: %q", id)}ids[id] = true}}func TestIDsAreDifferent(t *testing.T) {// Verify that short and long IDs are different typesshortID, err := GenerateShortID()if err != nil {t.Fatalf("GenerateShortID() error = %v", err)}longID, err := GenerateLongID()if err != nil {t.Fatalf("GenerateLongID() error = %v", err)}if len(shortID) == len(longID) {t.Error("Short and long IDs should have different lengths")}if len(shortID) != 12 {t.Errorf("Short ID length = %d, want 12", len(shortID))}if len(longID) != 21 {t.Errorf("Long ID length = %d, want 21", len(longID))}}
package utilsimport (gonanoid "github.com/matoous/go-nanoid/v2")// GenerateShortID generates a 12-character nanoid using the full alphabet// Used for: dataset_id, location_id, cluster_id, pattern_id// Entropy: ~71 bits (62^12 ≈ 3.2×10^21 combinations)func GenerateShortID() (string, error) {return gonanoid.New(12)}// GenerateLongID generates a 21-character nanoid using the full alphabet// Used for: file_id, segment_id, label_id// Entropy: ~125 bits (62^21 ≈ 2.7×10^37 combinations)func GenerateLongID() (string, error) {return gonanoid.New(21)}
package utilsimport ("os""path/filepath""testing")func TestLoadMappingFile(t *testing.T) {t.Run("valid mapping", func(t *testing.T) {content := `{"GSK": {"species": "Roroa", "calltypes": {"Male": "Male - Solo"}},"Don't Know": {"species": "Don't Know"}}`path := createTempFile(t, content)defer os.Remove(path)mapping, err := LoadMappingFile(path)if err != nil {t.Fatalf("expected no error, got: %v", err)}if len(mapping) != 2 {t.Errorf("expected 2 entries, got %d", len(mapping))}if mapping["GSK"].Species != "Roroa" {t.Errorf("expected GSK -> Roroa, got %s", mapping["GSK"].Species)}if mapping["GSK"].Calltypes["Male"] != "Male - Solo" {t.Errorf("expected GSK Male -> Male - Solo, got %s", mapping["GSK"].Calltypes["Male"])}})t.Run("invalid JSON", func(t *testing.T) {content := `{invalid json}`path := createTempFile(t, content)defer os.Remove(path)_, err := LoadMappingFile(path)if err == nil {t.Fatal("expected error for invalid JSON")}})t.Run("empty file", func(t *testing.T) {content := `{}`path := createTempFile(t, content)defer os.Remove(path)_, err := LoadMappingFile(path)if err == nil {t.Fatal("expected error for empty mapping")}})t.Run("missing species field", func(t *testing.T) {content := `{"GSK": {"calltypes": {"Male": "Male - Solo"}}}`path := createTempFile(t, content)defer os.Remove(path)_, err := LoadMappingFile(path)if err == nil {t.Fatal("expected error for missing species field")}})t.Run("empty species field", func(t *testing.T) {content := `{"GSK": {"species": ""}}`path := createTempFile(t, content)defer os.Remove(path)_, err := LoadMappingFile(path)if err == nil {t.Fatal("expected error for empty species field")}})t.Run("nonexistent file", func(t *testing.T) {_, err := LoadMappingFile("/nonexistent/path/mapping.json")if err == nil {t.Fatal("expected error for nonexistent file")}})}func TestGetDBSpecies(t *testing.T) {mapping := MappingFile{"GSK": {Species: "Roroa"},"K-M": {Species: "Kiwi"},}t.Run("found", func(t *testing.T) {species, ok := mapping.GetDBSpecies("GSK")if !ok {t.Fatal("expected to find GSK")}if species != "Roroa" {t.Errorf("expected Roroa, got %s", species)}})t.Run("not found", func(t *testing.T) {_, ok := mapping.GetDBSpecies("UNKNOWN")if ok {t.Fatal("expected not to find UNKNOWN")}})}func TestGetDBCalltype(t *testing.T) {mapping := MappingFile{"GSK": {Species: "Roroa",Calltypes: map[string]string{"Male": "Male - Solo","Female": "Female - Solo",},},"K-M": {Species: "Kiwi"}, // no calltype mapping}t.Run("with mapping", func(t *testing.T) {ct := mapping.GetDBCalltype("GSK", "Male")if ct != "Male - Solo" {t.Errorf("expected 'Male - Solo', got %s", ct)}})t.Run("without mapping - passthrough", func(t *testing.T) {ct := mapping.GetDBCalltype("GSK", "Unknown")if ct != "Unknown" {t.Errorf("expected passthrough 'Unknown', got %s", ct)}})t.Run("species not in mapping - passthrough", func(t *testing.T) {ct := mapping.GetDBCalltype("UNKNOWN", "Male")if ct != "Male" {t.Errorf("expected passthrough 'Male', got %s", ct)}})t.Run("species without calltypes - passthrough", func(t *testing.T) {ct := mapping.GetDBCalltype("K-M", "Male")if ct != "Male" {t.Errorf("expected passthrough 'Male', got %s", ct)}})}func TestMappingValidationResult(t *testing.T) {t.Run("HasErrors - no errors", func(t *testing.T) {r := MappingValidationResult{}if r.HasErrors() {t.Error("expected no errors")}})t.Run("HasErrors - missing species", func(t *testing.T) {r := MappingValidationResult{MissingSpecies: []string{"UNKNOWN"}}if !r.HasErrors() {t.Error("expected errors")}})t.Run("HasErrors - missing DB species", func(t *testing.T) {r := MappingValidationResult{MissingDBSpecies: []string{"Phantom"}}if !r.HasErrors() {t.Error("expected errors")}})t.Run("HasErrors - missing calltypes", func(t *testing.T) {r := MappingValidationResult{MissingCalltypes: map[string]string{"GSK/Male": "Roroa/Male - Solo"}}if !r.HasErrors() {t.Error("expected errors")}})t.Run("Error - all error types", func(t *testing.T) {r := MappingValidationResult{MissingSpecies: []string{"UNKNOWN"},MissingDBSpecies: []string{"Phantom"},MissingCalltypes: map[string]string{"GSK/Male": "Roroa/Male - Solo"},}errStr := r.Error()if errStr == "" {t.Error("expected non-empty error string")}// Check all parts are presentif !containsSubstring(errStr, "UNKNOWN") {t.Error("error string should contain MISSING species")}if !containsSubstring(errStr, "Phantom") {t.Error("error string should contain missing DB species")}if !containsSubstring(errStr, "GSK/Male") {t.Error("error string should contain missing calltype")}})}// Helper functionsfunc createTempFile(t *testing.T, content string) string {t.Helper()tmpDir := t.TempDir()path := filepath.Join(tmpDir, "mapping.json")if err := os.WriteFile(path, []byte(content), 0644); err != nil {t.Fatalf("failed to create temp file: %v", err)}return path}func containsSubstring(s, substr string) bool {return len(s) >= len(substr) && (s == substr || len(s) > 0 && containsSubstringHelper(s, substr))}func containsSubstringHelper(s, substr string) bool {for i := 0; i <= len(s)-len(substr); i++ {if s[i:i+len(substr)] == substr {return true}}return false}
package utilsimport ("database/sql""encoding/json""fmt""os""sort""strings")// SpeciesMapping maps .data species/calltype names to DB labelstype SpeciesMapping struct {Species string `json:"species"`Calltypes map[string]string `json:"calltypes,omitempty"`}// MappingFile represents the complete mapping file structure// Key is the .data file species nametype MappingFile map[string]SpeciesMapping// LoadMappingFile loads and parses a mapping JSON filefunc LoadMappingFile(path string) (MappingFile, error) {data, err := os.ReadFile(path)if err != nil {return nil, fmt.Errorf("failed to read mapping file: %w", err)}var mapping MappingFileif err := json.Unmarshal(data, &mapping); err != nil {return nil, fmt.Errorf("failed to parse mapping JSON: %w", err)}// Validate non-emptyif len(mapping) == 0 {return nil, fmt.Errorf("mapping file is empty")}// Validate each entry has speciesfor dataSpecies, sm := range mapping {if sm.Species == "" {return nil, fmt.Errorf("mapping entry '%s' has empty species field", dataSpecies)}}return mapping, nil}// MappingValidationResult contains validation errors for a mappingtype MappingValidationResult struct {MissingSpecies []string // .data species not in mappingMissingDBSpecies []string // mapped species not in DBMissingCalltypes map[string]string // "dataSpecies/dataCalltype" -> "dbSpecies/dbCalltype"}// HasErrors returns true if any validation errors existfunc (r MappingValidationResult) HasErrors() bool {return len(r.MissingSpecies) > 0 ||len(r.MissingDBSpecies) > 0 ||len(r.MissingCalltypes) > 0}// Error returns a formatted error messagefunc (r MappingValidationResult) Error() string {var parts []stringif len(r.MissingSpecies) > 0 {parts = append(parts, fmt.Sprintf("species in .data but not in mapping: [%s]",strings.Join(r.MissingSpecies, ", ")))}if len(r.MissingDBSpecies) > 0 {parts = append(parts, fmt.Sprintf("mapped species not found in DB: [%s]",strings.Join(r.MissingDBSpecies, ", ")))}if len(r.MissingCalltypes) > 0 {var ctErrors []stringfor k, v := range r.MissingCalltypes {ctErrors = append(ctErrors, fmt.Sprintf("%s->%s", k, v))}sort.Strings(ctErrors)parts = append(parts, fmt.Sprintf("calltypes not found in DB: [%s]",strings.Join(ctErrors, ", ")))}return strings.Join(parts, "; ")}// ValidateMappingAgainstDB validates that all mapped species and calltypes exist in the database// Also validates that the mapping covers all species/calltypes found in .data filesfunc ValidateMappingAgainstDB(db *sql.DB,mapping MappingFile,dataSpeciesSet map[string]bool,dataCalltypes map[string]map[string]bool, // species -> calltype -> true) (MappingValidationResult, error) {result := MappingValidationResult{MissingSpecies: make([]string, 0),MissingDBSpecies: make([]string, 0),MissingCalltypes: make(map[string]string),}// Check all .data species are in mappingfor species := range dataSpeciesSet {if _, exists := mapping[species]; !exists {result.MissingSpecies = append(result.MissingSpecies, species)}}sort.Strings(result.MissingSpecies)// Collect all mapped species and calltypesmappedSpeciesSet := make(map[string]bool)mappedCalltypes := make(map[string]map[string]string) // dbSpecies -> dbCalltype -> dataCalltypefor _, sm := range mapping {mappedSpeciesSet[sm.Species] = true// Track calltype mappingsif len(sm.Calltypes) > 0 {if mappedCalltypes[sm.Species] == nil {mappedCalltypes[sm.Species] = make(map[string]string)}for dataCT, dbCT := range sm.Calltypes {mappedCalltypes[sm.Species][dbCT] = dataCT}}}// Also collect unmapped calltypes (where .data calltype = DB calltype)for dataSpecies, ctSet := range dataCalltypes {sm, exists := mapping[dataSpecies]if !exists {continue // Already reported as missing species}dbSpecies := sm.Speciesfor dataCT := range ctSet {// If no explicit mapping, assume dataCT == dbCTdbCT := dataCTif sm.Calltypes != nil {if mapped, ok := sm.Calltypes[dataCT]; ok {dbCT = mapped}}if mappedCalltypes[dbSpecies] == nil {mappedCalltypes[dbSpecies] = make(map[string]string)}mappedCalltypes[dbSpecies][dbCT] = dataCT}}// Validate species exist in DBspeciesLabels := make([]string, 0, len(mappedSpeciesSet))for s := range mappedSpeciesSet {speciesLabels = append(speciesLabels, s)}sort.Strings(speciesLabels)if len(speciesLabels) > 0 {query := `SELECT label FROM species WHERE label IN (` + Placeholders(len(speciesLabels)) + `) AND active = true`args := make([]any, len(speciesLabels))for i, s := range speciesLabels {args[i] = s}rows, err := db.Query(query, args...)if err != nil {return result, fmt.Errorf("failed to query species: %w", err)}defer rows.Close()foundSpecies := make(map[string]bool)for rows.Next() {var label stringif err := rows.Scan(&label); err == nil {foundSpecies[label] = true}}for _, s := range speciesLabels {if !foundSpecies[s] {result.MissingDBSpecies = append(result.MissingDBSpecies, s)}}}// Validate calltypes exist in DBfor dbSpecies, ctMap := range mappedCalltypes {if len(ctMap) == 0 {continue}ctLabels := make([]string, 0, len(ctMap))for dbCT := range ctMap {ctLabels = append(ctLabels, dbCT)}sort.Strings(ctLabels)query := `SELECT ct.labelFROM call_type ctJOIN species s ON ct.species_id = s.idWHERE s.label = ? AND ct.label IN (` + Placeholders(len(ctLabels)) + `) AND ct.active = true`args := make([]any, 1+len(ctLabels))args[0] = dbSpeciesfor i, ct := range ctLabels {args[1+i] = ct}rows, err := db.Query(query, args...)if err != nil {return result, fmt.Errorf("failed to query calltypes for species %s: %w", dbSpecies, err)}defer rows.Close()foundCT := make(map[string]bool)for rows.Next() {var label stringif err := rows.Scan(&label); err == nil {foundCT[label] = true}}for dbCT, dataCT := range ctMap {if !foundCT[dbCT] {key := fmt.Sprintf("%s/%s", dbSpecies, dataCT)value := fmt.Sprintf("%s/%s", dbSpecies, dbCT)result.MissingCalltypes[key] = value}}}return result, nil}// GetDBSpecies returns the DB species label for a .data speciesfunc (m MappingFile) GetDBSpecies(dataSpecies string) (string, bool) {sm, exists := m[dataSpecies]if !exists {return "", false}return sm.Species, true}// GetDBCalltype returns the DB calltype label for a .data species/calltype// Returns the dataCalltype unchanged if no mapping existsfunc (m MappingFile) GetDBCalltype(dataSpecies, dataCalltype string) string {sm, exists := m[dataSpecies]if !exists || sm.Calltypes == nil {return dataCalltype}if dbCT, ok := sm.Calltypes[dataCalltype]; ok {return dbCT}return dataCalltype}// Mapping sentinels: special values for the SpeciesMapping.Species field.//// MappingNegative marks a .data species as "confirmed empty" (Noise-equivalent):// segments matching this name are treated as negative evidence — clips overlapping// them emit an all-zero row when no positive species also overlaps.//// MappingIgnore marks a .data species as "ignored entirely": segments matching// this name neither label clips nor block them.const (MappingNegative = "__NEGATIVE__"MappingIgnore = "__IGNORE__")// MappingKind describes how a .data species should be treated.type MappingKind intconst (MappingReal MappingKind = iotaMappingNegMappingIgn)// Classify returns the canonical class name and kind for a .data species.// ok is false if dataSpecies is not present in the mapping.// For MappingNeg and MappingIgn the canonical string is empty.func (m MappingFile) Classify(dataSpecies string) (canonical string, kind MappingKind, ok bool) {sm, exists := m[dataSpecies]if !exists {return "", MappingReal, false}switch sm.Species {case MappingNegative:return "", MappingNeg, truecase MappingIgnore:return "", MappingIgn, truedefault:return sm.Species, MappingReal, true}}// ValidateCoversSpecies returns the sorted list of species in speciesSet that// are missing from the mapping. Empty result means full coverage.func (m MappingFile) ValidateCoversSpecies(speciesSet map[string]bool) []string {missing := make([]string, 0)for s := range speciesSet {if _, exists := m[s]; !exists {missing = append(missing, s)}}sort.Strings(missing)return missing}// Classes returns the sorted unique non-sentinel canonical class names from the mapping.// Used to build the CSV column header for clip-labels.func (m MappingFile) Classes() []string {set := make(map[string]bool)for _, sm := range m {switch sm.Species {case MappingNegative, MappingIgnore, "":continuedefault:set[sm.Species] = true}}out := make([]string, 0, len(set))for s := range set {out = append(out, s)}sort.Strings(out)return out}// placeholders generates SQL placeholder string for IN clausesfunc Placeholders(n int) string {if n == 0 {return ""}ph := make([]string, n)for i := range ph {ph[i] = "?"}return strings.Join(ph, ", ")}
package utilsimport ("testing")func TestParseFilenameTimestamps(t *testing.T) {t.Run("should parse YYMMDD format (test case a)", func(t *testing.T) {filenames := []string{"201012_123456.wav","201014_123456.WAV","201217_123456.wav","211122_123456.WAV",}results, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}if len(results) != 4 {t.Fatalf("Expected 4 results, got %d", len(results))}// Year 20 should be interpreted as 2020 (less variance than days)if results[0].Timestamp.Year() != 2020 {t.Errorf("Year incorrect for file 0: got %d, want 2020", results[0].Timestamp.Year())}if results[0].Timestamp.Month() != 10 { // Octobert.Errorf("Month incorrect for file 0: got %d, want 10", results[0].Timestamp.Month())}if results[0].Timestamp.Day() != 12 {t.Errorf("Day incorrect for file 0: got %d, want 12", results[0].Timestamp.Day())}if results[0].Timestamp.Hour() != 12 {t.Errorf("Hour incorrect for file 0: got %d, want 12", results[0].Timestamp.Hour())}if results[0].Timestamp.Minute() != 34 {t.Errorf("Minute incorrect for file 0: got %d, want 34", results[0].Timestamp.Minute())}if results[0].Timestamp.Second() != 56 {t.Errorf("Second incorrect for file 0: got %d, want 56", results[0].Timestamp.Second())}if results[3].Timestamp.Year() != 2021 {t.Errorf("Year incorrect for file 3: got %d, want 2021", results[3].Timestamp.Year())}if results[3].Timestamp.Month() != 11 { // Novembert.Errorf("Month incorrect for file 3: got %d, want 11", results[3].Timestamp.Month())}if results[3].Timestamp.Day() != 22 {t.Errorf("Day incorrect for file 3: got %d, want 22", results[3].Timestamp.Day())}})t.Run("should parse DDMMYY format (test case b)", func(t *testing.T) {filenames := []string{"121020_123456.WAV","141020_123456.wav","171220_123456.WAV","221121_123456.wav",}results, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}if len(results) != 4 {t.Fatalf("Expected 4 results, got %d", len(results))}// More variance in first two digits (12,14,17,22) than last two (20,20,20,21)// So DDMMYY format: day=first, month=middle, year=last+2000if results[0].Timestamp.Day() != 12 {t.Errorf("Day incorrect for file 0: got %d, want 12", results[0].Timestamp.Day())}if results[0].Timestamp.Month() != 10 { // Octobert.Errorf("Month incorrect for file 0: got %d, want 10", results[0].Timestamp.Month())}if results[0].Timestamp.Year() != 2020 {t.Errorf("Year incorrect for file 0: got %d, want 2020", results[0].Timestamp.Year())}if results[2].Timestamp.Day() != 17 {t.Errorf("Day incorrect for file 2: got %d, want 17", results[2].Timestamp.Day())}if results[2].Timestamp.Month() != 12 { // Decembert.Errorf("Month incorrect for file 2: got %d, want 12", results[2].Timestamp.Month())}if results[2].Timestamp.Year() != 2020 {t.Errorf("Year incorrect for file 2: got %d, want 2020", results[2].Timestamp.Year())}})t.Run("should parse YYYYMMDD format (test case c)", func(t *testing.T) {filenames := []string{"20230609_103000.WAV","20241109_201504.wav",}results, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}if len(results) != 2 {t.Fatalf("Expected 2 results, got %d", len(results))}if results[0].Timestamp.Year() != 2023 {t.Errorf("Year incorrect: got %d, want 2023", results[0].Timestamp.Year())}if results[0].Timestamp.Month() != 6 { // Junet.Errorf("Month incorrect: got %d, want 6", results[0].Timestamp.Month())}if results[0].Timestamp.Day() != 9 {t.Errorf("Day incorrect: got %d, want 9", results[0].Timestamp.Day())}if results[0].Timestamp.Hour() != 10 {t.Errorf("Hour incorrect: got %d, want 10", results[0].Timestamp.Hour())}if results[0].Timestamp.Minute() != 30 {t.Errorf("Minute incorrect: got %d, want 30", results[0].Timestamp.Minute())}if results[0].Timestamp.Second() != 0 {t.Errorf("Second incorrect: got %d, want 0", results[0].Timestamp.Second())}if results[1].Timestamp.Year() != 2024 {t.Errorf("Year incorrect: got %d, want 2024", results[1].Timestamp.Year())}})t.Run("should parse mixed 6-digit dates with variance detection (test case d)", func(t *testing.T) {filenames := []string{"120119_003002.wav","180120_231502.wav","170122_010005.wav","010419_234502.WAV","310320_231502.wav","220824_231502.WAV","240123_231502.wav",}results, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}if len(results) != 7 {t.Fatalf("Expected 7 results, got %d", len(results))}// First two digits: 12,18,17,01,31,22,24 (variance = high)// Last two digits: 19,20,22,19,20,24,23 (variance = lower)// Should be DDMMYY formatif results[0].Timestamp.Day() != 12 {t.Errorf("Day incorrect: got %d, want 12", results[0].Timestamp.Day())}if results[0].Timestamp.Month() != 1 { // Januaryt.Errorf("Month incorrect: got %d, want 1", results[0].Timestamp.Month())}if results[0].Timestamp.Year() != 2019 {t.Errorf("Year incorrect: got %d, want 2019", results[0].Timestamp.Year())}if results[4].Timestamp.Day() != 31 {t.Errorf("Day incorrect for file 4: got %d, want 31", results[4].Timestamp.Day())}if results[4].Timestamp.Month() != 3 { // Marcht.Errorf("Month incorrect for file 4: got %d, want 3", results[4].Timestamp.Month())}})t.Run("should throw error for empty filename array", func(t *testing.T) {_, err := ParseFilenameTimestamps([]string{})if err == nil {t.Error("Expected error for empty filename array")}if err != nil && err.Error() != "no filenames provided" {t.Logf("Error message: %v", err)}})t.Run("should throw error for filenames without date patterns", func(t *testing.T) {_, err := ParseFilenameTimestamps([]string{"invalid_filename.wav"})if err == nil {t.Error("Expected error for filenames without date patterns")}})t.Run("should parse filenames with prefixes (test case e)", func(t *testing.T) {filenames := []string{"XYZ123_7689_20230609_103000.WAV","string 20241109_201504.wav",}results, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}if len(results) != 2 {t.Fatalf("Expected 2 results, got %d", len(results))}if results[0].Timestamp.Year() != 2023 {t.Errorf("Year incorrect: got %d, want 2023", results[0].Timestamp.Year())}if results[0].Timestamp.Month() != 6 { // Junet.Errorf("Month incorrect: got %d, want 6", results[0].Timestamp.Month())}if results[0].Timestamp.Day() != 9 {t.Errorf("Day incorrect: got %d, want 9", results[0].Timestamp.Day())}if results[0].Timestamp.Hour() != 10 {t.Errorf("Hour incorrect: got %d, want 10", results[0].Timestamp.Hour())}if results[0].Timestamp.Minute() != 30 {t.Errorf("Minute incorrect: got %d, want 30", results[0].Timestamp.Minute())}if results[0].Timestamp.Second() != 0 {t.Errorf("Second incorrect: got %d, want 0", results[0].Timestamp.Second())}if results[1].Timestamp.Year() != 2024 {t.Errorf("Year incorrect: got %d, want 2024", results[1].Timestamp.Year())}if results[1].Timestamp.Month() != 11 { // Novembert.Errorf("Month incorrect: got %d, want 11", results[1].Timestamp.Month())}if results[1].Timestamp.Day() != 9 {t.Errorf("Day incorrect: got %d, want 9", results[1].Timestamp.Day())}if results[1].Timestamp.Hour() != 20 {t.Errorf("Hour incorrect: got %d, want 20", results[1].Timestamp.Hour())}if results[1].Timestamp.Minute() != 15 {t.Errorf("Minute incorrect: got %d, want 15", results[1].Timestamp.Minute())}if results[1].Timestamp.Second() != 4 {t.Errorf("Second incorrect: got %d, want 4", results[1].Timestamp.Second())}})t.Run("should parse filenames with complex prefixes (test case f)", func(t *testing.T) {filenames := []string{"abcdefg__1234_180120_231502.wav","string 120119_003002.wav","ABCD EFG___170122_010005.wav","BHD_1234 010419_234502.WAV","cill xyz 310320_231502.wav","220824_231502.WAV","240123_231502.wav",}results, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}if len(results) != 7 {t.Fatalf("Expected 7 results, got %d", len(results))}// Same pattern as test case d - should be DDMMYYif results[0].Timestamp.Day() != 18 {t.Errorf("Day incorrect: got %d, want 18", results[0].Timestamp.Day())}if results[0].Timestamp.Month() != 1 { // Januaryt.Errorf("Month incorrect: got %d, want 1", results[0].Timestamp.Month())}if results[0].Timestamp.Year() != 2020 {t.Errorf("Year incorrect: got %d, want 2020", results[0].Timestamp.Year())}if results[0].Timestamp.Hour() != 23 {t.Errorf("Hour incorrect: got %d, want 23", results[0].Timestamp.Hour())}if results[0].Timestamp.Minute() != 15 {t.Errorf("Minute incorrect: got %d, want 15", results[0].Timestamp.Minute())}if results[0].Timestamp.Second() != 2 {t.Errorf("Second incorrect: got %d, want 2", results[0].Timestamp.Second())}if results[1].Timestamp.Day() != 12 {t.Errorf("Day incorrect: got %d, want 12", results[1].Timestamp.Day())}if results[1].Timestamp.Month() != 1 { // Januaryt.Errorf("Month incorrect: got %d, want 1", results[1].Timestamp.Month())}if results[1].Timestamp.Year() != 2019 {t.Errorf("Year incorrect: got %d, want 2019", results[1].Timestamp.Year())}if results[4].Timestamp.Day() != 31 {t.Errorf("Day incorrect: got %d, want 31", results[4].Timestamp.Day())}if results[4].Timestamp.Month() != 3 { // Marcht.Errorf("Month incorrect: got %d, want 3", results[4].Timestamp.Month())}if results[4].Timestamp.Year() != 2020 {t.Errorf("Year incorrect: got %d, want 2020", results[4].Timestamp.Year())}})t.Run("should throw error for mixed date formats", func(t *testing.T) {mixedFormats := []string{"201012_123456.wav", "20231012_123456.wav"} // 6-digit vs 8-digit_, err := ParseFilenameTimestamps(mixedFormats)if err == nil {t.Error("Expected error for mixed date formats")}})t.Run("should throw error for wrong length patterns", func(t *testing.T) {wrongLength := []string{"2010_123456.wav"} // 4 digits instead of 6 or 8_, err := ParseFilenameTimestamps(wrongLength)if err == nil {t.Error("Expected error for wrong length patterns")}})t.Run("should throw error when not enough files for 6-digit disambiguation", func(t *testing.T) {singleFile := []string{"120119_003002.wav"}_, err := ParseFilenameTimestamps(singleFile)if err == nil {t.Error("Expected error when not enough files for 6-digit disambiguation")}})}func TestApplyTimezoneOffset(t *testing.T) {t.Run("should apply UTC timezone correctly", func(t *testing.T) {filenames := []string{"201012_123456.wav","201014_123456.WAV",}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}results, err := ApplyTimezoneOffset(parsed, "UTC")if err != nil {t.Fatalf("Failed to apply timezone: %v", err)}if len(results) != 2 {t.Fatalf("Expected 2 results, got %d", len(results))}// Check timezone offset is +00:00_, offset := results[0].Zone()if offset != 0 {t.Errorf("UTC offset should be 0, got %d", offset)}})t.Run("should use fixed offset for entire cluster spanning DST transition", func(t *testing.T) {// Test files spanning the Auckland DST transition in April 2021// DST ended on April 4, 2021 (UTC+13 -> UTC+12)filenames := []string{"20210401_120000.wav", // April 1st - DST still active (UTC+13)"20210410_120000.wav", // April 10th - DST ended (would be UTC+12 if DST applied)"20210420_120000.wav", // April 20th - Standard time (would be UTC+12 if DST applied)}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}results, err := ApplyTimezoneOffset(parsed, "Pacific/Auckland")if err != nil {t.Fatalf("Failed to apply timezone: %v", err)}if len(results) != 3 {t.Fatalf("Expected 3 results, got %d", len(results))}// All files should use the same offset (from April 1st - earliest file)offsets := make([]int, len(results))for i, r := range results {_, offset := r.Zone()offsets[i] = offset}// Check all offsets are the samefirstOffset := offsets[0]for i, offset := range offsets {if offset != firstOffset {t.Errorf("File %d has different offset: got %d, want %d", i, offset, firstOffset)}}// The offset should be UTC+13 (from the earliest file: April 1st)expectedOffsetSeconds := 13 * 3600if firstOffset != expectedOffsetSeconds {t.Errorf("Offset incorrect: got %d seconds, want %d seconds (UTC+13)", firstOffset, expectedOffsetSeconds)}// Verify UTC conversion uses the fixed offset consistently// All files at 12:00 local should convert to the same UTC hour (with UTC+13 offset)// 12:00 Auckland time - 13 hours = 23:00 UTC previous dayfor i, utcTime := range results {utc := utcTime.UTC()if utc.Hour() != 23 {t.Errorf("File %d UTC hour incorrect: got %d, want 23", i, utc.Hour())}}})t.Run("should handle out-of-order filenames correctly", func(t *testing.T) {// Files not in chronological order - should still use earliest file for offsetfilenames := []string{"20210410_120000.wav", // April 10th (later)"20210401_120000.wav", // April 1st (earliest - should determine offset)"20210405_120000.wav", // April 5th (middle)}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}results, err := ApplyTimezoneOffset(parsed, "Pacific/Auckland")if err != nil {t.Fatalf("Failed to apply timezone: %v", err)}// All files should use UTC+13 offset (from April 1st, the earliest)for i, r := range results {_, offset := r.Zone()expectedOffset := 13 * 3600if offset != expectedOffset {t.Errorf("File %d offset incorrect: got %d, want %d", i, offset, expectedOffset)}}// Results should maintain original filename orderif results[0].Day() != 10 {t.Errorf("Result 0 should be April 10th, got day %d", results[0].Day())}if results[1].Day() != 1 {t.Errorf("Result 1 should be April 1st, got day %d", results[1].Day())}if results[2].Day() != 5 {t.Errorf("Result 2 should be April 5th, got day %d", results[2].Day())}})t.Run("should apply fixed offset consistently across large time spans", func(t *testing.T) {// Test files spanning multiple months with different DST periodsfilenames := []string{"20210215_120000.wav", // February 15th (summer, UTC+13)"20210615_120000.wav", // June 15th (winter, would be UTC+12 if DST applied)"20210815_120000.wav", // August 15th (winter, would be UTC+12 if DST applied)}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}results, err := ApplyTimezoneOffset(parsed, "Pacific/Auckland")if err != nil {t.Fatalf("Failed to apply timezone: %v", err)}// All files should use the same offset from the earliest file (February)expectedOffset := 13 * 3600for i, r := range results {_, offset := r.Zone()if offset != expectedOffset {t.Errorf("File %d offset incorrect: got %d, want %d", i, offset, expectedOffset)}}// Verify UTC conversion is consistent with fixed offsetfor i, r := range results {utc := r.UTC()if utc.Hour() != 23 { // 12 - 13 = -1 hour (23:00 previous day)t.Errorf("File %d UTC hour incorrect: got %d, want 23", i, utc.Hour())}}})t.Run("should handle US DST transitions with fixed offset", func(t *testing.T) {// Test US spring DST transition (March 14, 2021)filenames := []string{"20210310_120000.wav", // March 10th - before DST (UTC-5)"20210320_120000.wav", // March 20th - after DST (would be UTC-4 if DST applied)}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}results, err := ApplyTimezoneOffset(parsed, "America/New_York")if err != nil {t.Fatalf("Failed to apply timezone: %v", err)}// All files should use the same offset from earliest file (March 10th)expectedOffset := -5 * 3600for i, r := range results {_, offset := r.Zone()if offset != expectedOffset {t.Errorf("File %d offset incorrect: got %d, want %d", i, offset, expectedOffset)}}// Verify UTC conversion uses fixed offsetfor i, r := range results {utc := r.UTC()if utc.Hour() != 17 { // 12 + 5 = 17t.Errorf("File %d UTC hour incorrect: got %d, want 17", i, utc.Hour())}}})t.Run("should handle empty timestamps array", func(t *testing.T) {_, err := ApplyTimezoneOffset([]FilenameTimestamp{}, "UTC")if err == nil {t.Error("Expected error for empty timestamps array")}})t.Run("should handle invalid timezone", func(t *testing.T) {filenames := []string{"20210401_120000.wav"}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}_, err = ApplyTimezoneOffset(parsed, "Invalid/Timezone")if err == nil {t.Error("Expected error for invalid timezone")}})}func TestHasTimestampFilename(t *testing.T) {testCases := []struct {filename stringexpected bool}{{"201012_123456.wav", true},{"20230609_103000.WAV", true},{"invalid_filename.wav", false},{"201012_123456.txt", false},{"201012.wav", false},{"_123456.wav", false},{"", false},}for _, tc := range testCases {t.Run(tc.filename, func(t *testing.T) {result := HasTimestampFilename(tc.filename)if result != tc.expected {t.Errorf("HasTimestampFilename(%q) = %v, want %v", tc.filename, result, tc.expected)}})}}func TestFilenameParserEdgeCases(t *testing.T) {t.Run("should handle case-insensitive file extensions", func(t *testing.T) {filenames := []string{"201012_123456.wav","201014_123456.WAV","201217_123456.Wav",}results, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}if len(results) != 3 {t.Errorf("Expected 3 results, got %d", len(results))}})t.Run("should validate invalid dates", func(t *testing.T) {// 32nd day doesn't exist - should be caught by validationfilenames := []string{"20240132_120000.wav"}_, err := ParseFilenameTimestamps(filenames)if err == nil {t.Error("Expected error for invalid date (day 32)")}})t.Run("should validate invalid months", func(t *testing.T) {// 13th month doesn't existfilenames := []string{"20241301_120000.wav"}_, err := ParseFilenameTimestamps(filenames)if err == nil {t.Error("Expected error for invalid month (13)")}})t.Run("should handle February 29th in leap year", func(t *testing.T) {filenames := []string{"20240229_120000.wav"} // 2024 is a leap yearresults, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse leap year date: %v", err)}if results[0].Timestamp.Day() != 29 {t.Errorf("Expected day 29, got %d", results[0].Timestamp.Day())}})t.Run("should reject February 29th in non-leap year", func(t *testing.T) {filenames := []string{"20230229_120000.wav"} // 2023 is not a leap year_, err := ParseFilenameTimestamps(filenames)if err == nil {t.Error("Expected error for Feb 29th in non-leap year")}})}func TestUTCConversionCorrectness(t *testing.T) {t.Run("should convert Pacific/Auckland night recordings correctly to UTC", func(t *testing.T) {// Test a night recording: 21:00 (9 PM) Pacific/Auckland// In May 2021, Pacific/Auckland is UTC+12 (standard time)// So 21:00 Pacific/Auckland should become 09:00 UTC same dayfilenames := []string{"20210505_210000.wav"}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}results, err := ApplyTimezoneOffset(parsed, "Pacific/Auckland")if err != nil {t.Fatalf("Failed to apply timezone: %v", err)}utcDate := results[0].UTC()if utcDate.Year() != 2021 {t.Errorf("Year incorrect: got %d, want 2021", utcDate.Year())}if utcDate.Month() != 5 {t.Errorf("Month incorrect: got %d, want 5", utcDate.Month())}if utcDate.Day() != 5 {t.Errorf("Day incorrect: got %d, want 5 (same day)", utcDate.Day())}if utcDate.Hour() != 9 {t.Errorf("Hour incorrect: got %d, want 9 (21 - 12 = 9)", utcDate.Hour())}})t.Run("should convert day recordings correctly to UTC", func(t *testing.T) {// Test a day recording: 12:00 (noon) Pacific/Auckland// Should become 00:00 UTC same day (midnight)filenames := []string{"20210505_120000.wav"}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}results, err := ApplyTimezoneOffset(parsed, "Pacific/Auckland")if err != nil {t.Fatalf("Failed to apply timezone: %v", err)}utcDate := results[0].UTC()if utcDate.Hour() != 0 {t.Errorf("Hour incorrect: got %d, want 0 (12 - 12 = 0, midnight UTC)", utcDate.Hour())}if utcDate.Day() != 5 {t.Errorf("Day incorrect: got %d, want 5 (same day)", utcDate.Day())}})t.Run("should handle date rollover correctly", func(t *testing.T) {// Test early morning: 02:00 Pacific/Auckland// Should become 14:00 UTC previous dayfilenames := []string{"20210505_020000.wav"}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}results, err := ApplyTimezoneOffset(parsed, "Pacific/Auckland")if err != nil {t.Fatalf("Failed to apply timezone: %v", err)}utcDate := results[0].UTC()if utcDate.Day() != 4 {t.Errorf("Day incorrect: got %d, want 4 (previous day)", utcDate.Day())}if utcDate.Hour() != 14 {t.Errorf("Hour incorrect: got %d, want 14 (2 - 12 = -10, so previous day 14:00)", utcDate.Hour())}})t.Run("should convert correctly for negative offset timezone", func(t *testing.T) {// Test 15:00 (3 PM) New York in June (UTC-4 during DST)// Should become 19:00 UTC same dayfilenames := []string{"20210615_150000.wav"}parsed, err := ParseFilenameTimestamps(filenames)if err != nil {t.Fatalf("Failed to parse filenames: %v", err)}results, err := ApplyTimezoneOffset(parsed, "America/New_York")if err != nil {t.Fatalf("Failed to apply timezone: %v", err)}utcDate := results[0].UTC()if utcDate.Hour() != 19 {t.Errorf("Hour incorrect: got %d, want 19 (15 + 4 = 19)", utcDate.Hour())}if utcDate.Day() != 15 {t.Errorf("Day incorrect: got %d, want 15 (same day)", utcDate.Day())}})}
package utilsimport ("fmt""path/filepath""regexp""strconv""time")// DateFormat represents the detected filename date formattype DateFormat int// Date format constants for filename timestamp parsingconst (Format8Digit DateFormat = iota // YYYYMMDD_HHMMSS (e.g., 20230609_103000.wav)Format6YYMMDD // YYMMDD_HHMMSS (e.g., 201012_123456.wav) - year firstFormat6DDMMYY // DDMMYY_HHMMSS (e.g., 121020_123456.wav) - year last)var (// Pattern to match timestamp filenames// Supports: YYYYMMDD_HHMMSS, YYMMDD_HHMMSS, DDMMYY_HHMMSS// Case-insensitive for file extension (.wav, .WAV, .Wav)// Allows prefixes before the timestamp pattern// Allows optional suffixes between timestamp and extension (e.g., _16kHz)timestampPattern = regexp.MustCompile(`(?i)(\d{6,8})_(\d{6})(?:_[^/\\]*)?\.wav$`))// dateParts represents parsed date components for format detectiontype dateParts struct {x1 int // First 2 digitsm int // Middle 2 digits (always month)x2 int // Last 2 digits}// FilenameTimestamp represents a parsed timestamp from a filenametype FilenameTimestamp struct {Filename stringTimestamp time.TimeFormat DateFormat}// ParseFilenameTimestamps parses timestamps from a batch of filenames.// Uses variance-based disambiguation for 6-digit dates (YYMMDD vs DDMMYY).// Returns timestamps in UTC (timezone must be applied separately).// ParseFilenameTimestamps extracts timestamps from filenames using variance-based format detectionfunc ParseFilenameTimestamps(filenames []string) ([]FilenameTimestamp, error) {if len(filenames) == 0 {return nil, fmt.Errorf("no filenames provided")}// Detect date format by analyzing all filenamesformat, err := detectDateFormat(filenames)if err != nil {return nil, err}// Parse all filenames using detected formatresults := make([]FilenameTimestamp, 0, len(filenames))for _, filename := range filenames {timestamp, err := parseFilenameWithFormat(filename, format)if err != nil {return nil, fmt.Errorf("failed to parse %s: %w", filename, err)}results = append(results, FilenameTimestamp{Filename: filename,Timestamp: timestamp,Format: format,})}return results, nil}// ApplyTimezoneOffset applies a fixed timezone offset to timestamps// Uses the EARLIEST (chronologically) timestamp to determine the offset, then applies it to all// This matches AudioMoth behavior (no DST adjustment during deployment)// ApplyTimezoneOffset converts local timestamps to location timezone with DST handlingfunc ApplyTimezoneOffset(timestamps []FilenameTimestamp, timezoneID string) ([]time.Time, error) {if len(timestamps) == 0 {return nil, fmt.Errorf("no timestamps provided")}// Load timezone locationloc, err := time.LoadLocation(timezoneID)if err != nil {return nil, fmt.Errorf("invalid timezone %s: %w", timezoneID, err)}// Find chronologically earliest timestampearliestUTC := timestamps[0].Timestampfor _, ts := range timestamps[1:] {if ts.Timestamp.Before(earliestUTC) {earliestUTC = ts.Timestamp}}// Calculate offset from earliest timestampearliestInZone := time.Date(earliestUTC.Year(), earliestUTC.Month(), earliestUTC.Day(),earliestUTC.Hour(), earliestUTC.Minute(), earliestUTC.Second(),0, loc,)// Get fixed offset (doesn't change for DST)_, offsetSeconds := earliestInZone.Zone()fixedOffset := time.FixedZone("Fixed", offsetSeconds)// Apply SAME offset to ALL timestamps (maintaining original order)results := make([]time.Time, len(timestamps))for i, ts := range timestamps {adjusted := time.Date(ts.Timestamp.Year(), ts.Timestamp.Month(), ts.Timestamp.Day(),ts.Timestamp.Hour(), ts.Timestamp.Minute(), ts.Timestamp.Second(),0, fixedOffset,)results[i] = adjusted}return results, nil}// detectDateFormat analyzes filenames to determine the date formatfunc detectDateFormat(filenames []string) (DateFormat, error) {// Extract all date parts from filenamesvar parts []datePartsvar has8Digit boolfor _, filename := range filenames {basename := filepath.Base(filename)matches := timestampPattern.FindStringSubmatch(basename)if matches == nil {continue}dateStr := matches[1]// Check for 8-digit format (YYYYMMDD)if len(dateStr) == 8 {has8Digit = truecontinue}// Parse 6-digit formatif len(dateStr) == 6 {x1, _ := strconv.Atoi(dateStr[0:2])m, _ := strconv.Atoi(dateStr[2:4])x2, _ := strconv.Atoi(dateStr[4:6])parts = append(parts, dateParts{x1: x1, m: m, x2: x2})}}// If all files are 8-digit, that's the formatif has8Digit && len(parts) == 0 {return Format8Digit, nil}// If mixed 8-digit and 6-digit, return errorif has8Digit && len(parts) > 0 {return 0, fmt.Errorf("mixed date formats detected (8-digit and 6-digit)")}// If no 6-digit dates found, cannot determineif len(parts) == 0 {return 0, fmt.Errorf("no valid timestamp filenames found")}// Need at least 2 files with different dates to disambiguate YYMMDD vs DDMMYYif len(parts) == 1 {return 0, fmt.Errorf("need at least 2 files to disambiguate 6-digit date format (YYMMDD vs DDMMYY)")}// Use variance-based disambiguation for 6-digit dates// Compare uniqueness of x1 (first 2 digits) vs x2 (last 2 digits)// Day values vary more than year values across recordingsuniqueX1 := countUnique(parts, func(p dateParts) int { return p.x1 })uniqueX2 := countUnique(parts, func(p dateParts) int { return p.x2 })if uniqueX2 >= uniqueX1 {// x2 has more variance → likely day values → YYMMDD formatreturn Format6YYMMDD, nil} else {// x1 has more variance → likely day values → DDMMYY formatreturn Format6DDMMYY, nil}}// parseFilenameWithFormat parses a filename using the specified formatfunc parseFilenameWithFormat(filename string, format DateFormat) (time.Time, error) {basename := filepath.Base(filename)matches := timestampPattern.FindStringSubmatch(basename)if matches == nil {return time.Time{}, fmt.Errorf("filename does not match timestamp pattern: %s", basename)}dateStr := matches[1]timeStr := matches[2]var year, month, day intswitch format {case Format8Digit:if len(dateStr) != 8 {return time.Time{}, fmt.Errorf("expected 8-digit date, got %d digits", len(dateStr))}year, _ = strconv.Atoi(dateStr[0:4])month, _ = strconv.Atoi(dateStr[4:6])day, _ = strconv.Atoi(dateStr[6:8])case Format6YYMMDD:if len(dateStr) != 6 {return time.Time{}, fmt.Errorf("expected 6-digit date, got %d digits", len(dateStr))}yy, _ := strconv.Atoi(dateStr[0:2])month, _ = strconv.Atoi(dateStr[2:4])day, _ = strconv.Atoi(dateStr[4:6])// Convert 2-digit year to 4-digit (assume 2000-2099)year = 2000 + yycase Format6DDMMYY:if len(dateStr) != 6 {return time.Time{}, fmt.Errorf("expected 6-digit date, got %d digits", len(dateStr))}day, _ = strconv.Atoi(dateStr[0:2])month, _ = strconv.Atoi(dateStr[2:4])yy, _ := strconv.Atoi(dateStr[4:6])// Convert 2-digit year to 4-digit (assume 2000-2099)year = 2000 + yy}// Parse time (HHMMSS)if len(timeStr) != 6 {return time.Time{}, fmt.Errorf("invalid time format: %s", timeStr)}hour, _ := strconv.Atoi(timeStr[0:2])minute, _ := strconv.Atoi(timeStr[2:4])second, _ := strconv.Atoi(timeStr[4:6])// Construct timestamp in UTC (timezone applied separately)timestamp := time.Date(year, time.Month(month), day, hour, minute, second, 0, time.UTC)// Validate dateif timestamp.Month() != time.Month(month) || timestamp.Day() != day {return time.Time{}, fmt.Errorf("invalid date: %04d-%02d-%02d", year, month, day)}return timestamp, nil}// countUnique counts unique values using an extractor functionfunc countUnique(parts []dateParts, extractor func(p dateParts) int) int {seen := make(map[int]bool)for _, p := range parts {seen[extractor(p)] = true}return len(seen)}// HasTimestampFilename checks if a filename matches the timestamp pattern// HasTimestampFilename checks if filename contains a timestamp patternfunc HasTimestampFilename(filename string) bool {basename := filepath.Base(filename)return timestampPattern.MatchString(basename)}
package utilsimport ("testing""time")func TestGenerateFileID(t *testing.T) {t.Run("generates 21-character ID", func(t *testing.T) {id, err := GenerateLongID()if err != nil {t.Fatalf("unexpected error: %v", err)}if len(id) != 21 {t.Errorf("expected length 21, got %d: %q", len(id), id)}})t.Run("uses only valid alphabet characters", func(t *testing.T) {id, err := GenerateLongID()if err != nil {t.Fatalf("unexpected error: %v", err)}// Default nanoid alphabet includes: 0-9, A-Z, a-z, _, -for _, c := range id {if (c < '0' || c > '9') && (c < 'A' || c > 'Z') && (c < 'a' || c > 'z') && c != '_' && c != '-' {t.Errorf("invalid character %q in ID %q", string(c), id)}}})t.Run("generates unique IDs", func(t *testing.T) {seen := make(map[string]bool)for range 100 {id, err := GenerateLongID()if err != nil {t.Fatalf("unexpected error: %v", err)}if seen[id] {t.Errorf("duplicate ID generated: %q", id)}seen[id] = true}})}func TestResolveTimestamp(t *testing.T) {t.Run("resolves AudioMoth timestamp", func(t *testing.T) {meta := &WAVMetadata{Comment: "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was 15.8C.",Artist: "AudioMoth",}result, err := ResolveTimestamp(meta, "20250224_210000.wav", "Pacific/Auckland", false)if err != nil {t.Fatalf("unexpected error: %v", err)}if !result.IsAudioMoth {t.Error("expected IsAudioMoth to be true")}if result.MothData == nil {t.Error("expected MothData to be non-nil")}// AudioMoth parser returns UTC+13 fixed offsetexpectedUTC := time.Date(2025, 2, 24, 8, 0, 0, 0, time.UTC)if !result.Timestamp.UTC().Equal(expectedUTC) {t.Errorf("expected UTC timestamp %v, got %v", expectedUTC, result.Timestamp.UTC())}})t.Run("falls back to filename timestamp", func(t *testing.T) {meta := &WAVMetadata{Comment: "",Artist: "",}result, err := ResolveTimestamp(meta, "20250224_210000.wav", "Pacific/Auckland", false)if err != nil {t.Fatalf("unexpected error: %v", err)}if result.IsAudioMoth {t.Error("expected IsAudioMoth to be false")}if result.Timestamp.IsZero() {t.Error("expected non-zero timestamp")}})t.Run("falls back to file mod time when enabled", func(t *testing.T) {modTime := time.Date(2025, 1, 15, 10, 30, 0, 0, time.UTC)meta := &WAVMetadata{Comment: "",Artist: "",FileModTime: modTime,}result, err := ResolveTimestamp(meta, "nopattern.wav", "Pacific/Auckland", true)if err != nil {t.Fatalf("unexpected error: %v", err)}if !result.Timestamp.Equal(modTime) {t.Errorf("expected timestamp %v, got %v", modTime, result.Timestamp)}})t.Run("errors when no timestamp available and file mod time disabled", func(t *testing.T) {meta := &WAVMetadata{Comment: "",Artist: "",}_, err := ResolveTimestamp(meta, "nopattern.wav", "Pacific/Auckland", false)if err == nil {t.Error("expected error when no timestamp available")}})t.Run("errors when no timestamp available and no file mod time", func(t *testing.T) {meta := &WAVMetadata{Comment: "",Artist: "",}_, err := ResolveTimestamp(meta, "nopattern.wav", "Pacific/Auckland", true)if err == nil {t.Error("expected error when no timestamp available")}})t.Run("AudioMoth detected but parse fails falls back to filename", func(t *testing.T) {meta := &WAVMetadata{Comment: "AudioMoth garbage data",Artist: "",}result, err := ResolveTimestamp(meta, "20250224_210000.wav", "Pacific/Auckland", false)if err != nil {t.Fatalf("unexpected error: %v", err)}if !result.IsAudioMoth {t.Error("expected IsAudioMoth to be true (detected even if parse failed)")}if result.MothData != nil {t.Error("expected MothData to be nil since parsing failed")}if result.Timestamp.IsZero() {t.Error("expected non-zero timestamp from filename fallback")}})}
package utilsimport ("database/sql""fmt""path/filepath""time")// TimestampResult holds the result of timestamp resolution for a single filetype TimestampResult struct {Timestamp time.TimeIsAudioMoth boolMothData *AudioMothData}// ResolveTimestamp resolves a file's timestamp using the standard priority chain:// 1. AudioMoth comment parsing// 2. Filename timestamp parsing + timezone offset// 3. File modification time (if useFileModTime is true)//// Returns an error if no timestamp could be determined.func ResolveTimestamp(wavMeta *WAVMetadata, filePath string, timezoneID string, useFileModTime bool) (*TimestampResult, error) {result := &TimestampResult{}// Step 1: Try AudioMoth commentif IsAudioMoth(wavMeta.Comment, wavMeta.Artist) {result.IsAudioMoth = truemothData, err := ParseAudioMothComment(wavMeta.Comment)if err == nil {result.MothData = mothDataresult.Timestamp = mothData.Timestampreturn result, nil}// AudioMoth detected but parsing failed — fall through to filename}// Step 2: Try filename timestampif HasTimestampFilename(filePath) {filenameTimestamps, err := ParseFilenameTimestamps([]string{filepath.Base(filePath)})if err == nil {adjustedTimestamps, err := ApplyTimezoneOffset(filenameTimestamps, timezoneID)if err == nil && len(adjustedTimestamps) > 0 {result.Timestamp = adjustedTimestamps[0]return result, nil}}}// Step 3: File modification time fallback (optional)if useFileModTime && !wavMeta.FileModTime.IsZero() {result.Timestamp = wavMeta.FileModTimereturn result, nil}return nil, fmt.Errorf("cannot resolve timestamp (no AudioMoth, filename pattern, or file modification time)")}// FileProcessingResult holds all extracted metadata for a single filetype FileProcessingResult struct {FileName stringHash stringDuration float64SampleRate intTimestampLocal time.TimeIsAudioMoth boolMothData *AudioMothDataAstroData AstronomicalData}// ProcessSingleFile runs the full single-file processing pipeline:// WAV header parsing → XXH64 hash → timestamp resolution → astronomical data//// Set useFileModTime to true to allow file modification time as a timestamp fallback.func ProcessSingleFile(filePath string, latitude, longitude float64, timezoneID string, useFileModTime bool) (*FileProcessingResult, error) {// Step 1: Parse WAV headermetadata, err := ParseWAVHeader(filePath)if err != nil {return nil, fmt.Errorf("WAV header parsing failed: %w", err)}// Step 2: Calculate hashhash, err := ComputeXXH64(filePath)if err != nil {return nil, fmt.Errorf("hash calculation failed: %w", err)}// Step 3: Resolve timestamptsResult, err := ResolveTimestamp(metadata, filePath, timezoneID, useFileModTime)if err != nil {return nil, err}// Step 4: Calculate astronomical dataastroData := CalculateAstronomicalData(tsResult.Timestamp.UTC(),metadata.Duration,latitude,longitude,)return &FileProcessingResult{FileName: filepath.Base(filePath),Hash: hash,Duration: metadata.Duration,SampleRate: metadata.SampleRate,TimestampLocal: tsResult.Timestamp,IsAudioMoth: tsResult.IsAudioMoth,MothData: tsResult.MothData,AstroData: astroData,}, nil}// DBQueryable is an interface satisfied by both *sql.DB and *sql.Tx// for running duplicate hash checks against either.type DBQueryable interface {QueryRow(query string, args ...any) *sql.Row}// CheckDuplicateHash checks if a file with the given XXH64 hash already exists.// Returns the existing file ID if found, or empty string if no duplicate.// Works with both *sql.DB and *sql.Tx.func CheckDuplicateHash(q DBQueryable, hash string) (existingID string, isDuplicate bool, err error) {err = q.QueryRow("SELECT id FROM file WHERE xxh64_hash = ? AND active = true",hash,).Scan(&existingID)if err == nil {return existingID, true, nil}if err == sql.ErrNoRows {return "", false, nil}return "", false, fmt.Errorf("duplicate check failed: %w", err)}
package utilsimport ("math""math/rand""testing""github.com/madelynnblue/go-dsp/fft")// referencepower computes the power spectrum using go-dsp as ground truth.func referencePower(samples []float64) []float64 {result := fft.FFTReal(samples)n := len(samples)numBins := n/2 + 1power := make([]float64, numBins)for k := range numBins {re := real(result[k])im := imag(result[k])power[k] = re*re + im*im}return power}func TestPowerSpectrumFFT_Sinusoid(t *testing.T) {// 512-point FFT of a pure 1kHz sine at 16kHz sample rate// Expected: peak at bin k = 1000 * 512 / 16000 = 32n := 512sampleRate := 16000.0freq := 1000.0samples := make([]float64, n)for i := range samples {samples[i] = math.Sin(2.0 * math.Pi * freq * float64(i) / sampleRate)}power := make([]float64, n/2+1)scratch := make([]complex128, n)PowerSpectrumFFT(samples, power, scratch)// Find peak binmaxBin := 0maxVal := 0.0for k, v := range power {if v > maxVal {maxVal = vmaxBin = k}}expectedBin := int(freq * float64(n) / sampleRate)if maxBin != expectedBin {t.Errorf("peak at bin %d, expected %d", maxBin, expectedBin)}// Compare against referenceref := referencePower(samples)for k := range power {if math.Abs(power[k]-ref[k]) > 1e-6*math.Abs(ref[k])+1e-10 {t.Errorf("bin %d: got %g, ref %g", k, power[k], ref[k])}}}func TestPowerSpectrumFFT_Random(t *testing.T) {n := 512rng := rand.New(rand.NewSource(42))samples := make([]float64, n)for i := range samples {samples[i] = rng.Float64()*2 - 1}power := make([]float64, n/2+1)scratch := make([]complex128, n)PowerSpectrumFFT(samples, power, scratch)ref := referencePower(samples)for k := range power {relErr := math.Abs(power[k]-ref[k]) / (math.Abs(ref[k]) + 1e-15)if relErr > 1e-8 {t.Errorf("bin %d: got %g, ref %g (relErr=%g)", k, power[k], ref[k], relErr)}}}func TestPowerSpectrumFFT_DC(t *testing.T) {n := 512samples := make([]float64, n)for i := range samples {samples[i] = 1.0}power := make([]float64, n/2+1)scratch := make([]complex128, n)PowerSpectrumFFT(samples, power, scratch)ref := referencePower(samples)for k := range power {if math.Abs(power[k]-ref[k]) > 1e-6 {t.Errorf("bin %d: got %g, ref %g", k, power[k], ref[k])}}// DC bin should have all the energyif power[0] < power[1]*1000 {t.Errorf("DC bin should dominate: power[0]=%g, power[1]=%g", power[0], power[1])}}func TestPowerSpectrumFFT_Silence(t *testing.T) {n := 512samples := make([]float64, n)power := make([]float64, n/2+1)scratch := make([]complex128, n)PowerSpectrumFFT(samples, power, scratch)for k, v := range power {if v != 0 {t.Errorf("bin %d: expected 0, got %g", k, v)}}}func TestPowerSpectrumFFT_Impulse(t *testing.T) {n := 512samples := make([]float64, n)samples[0] = 1.0power := make([]float64, n/2+1)scratch := make([]complex128, n)PowerSpectrumFFT(samples, power, scratch)ref := referencePower(samples)for k := range power {if math.Abs(power[k]-ref[k]) > 1e-10 {t.Errorf("bin %d: got %g, ref %g", k, power[k], ref[k])}}// Impulse: flat power spectrum, all bins should be equal (= 1.0)for k, v := range power {if math.Abs(v-1.0) > 1e-10 {t.Errorf("bin %d: expected ~1.0, got %g", k, v)}}}func TestPowerSpectrumFFT_DifferentSizes(t *testing.T) {rng := rand.New(rand.NewSource(99))for _, n := range []int{2, 4, 8, 16, 64, 256, 1024} {samples := make([]float64, n)for i := range samples {samples[i] = rng.Float64()*2 - 1}power := make([]float64, n/2+1)scratch := make([]complex128, n)PowerSpectrumFFT(samples, power, scratch)ref := referencePower(samples)for k := range power {relErr := math.Abs(power[k]-ref[k]) / (math.Abs(ref[k]) + 1e-15)if relErr > 1e-8 {t.Errorf("n=%d bin %d: got %g, ref %g (relErr=%g)", n, k, power[k], ref[k], relErr)}}}}func BenchmarkPowerSpectrumFFT_512(b *testing.B) {n := 512rng := rand.New(rand.NewSource(42))samples := make([]float64, n)for i := range samples {samples[i] = rng.Float64()*2 - 1}power := make([]float64, n/2+1)scratch := make([]complex128, n)b.ResetTimer()for range b.N {PowerSpectrumFFT(samples, power, scratch)}}func BenchmarkGodsFFTReal_512(b *testing.B) {n := 512rng := rand.New(rand.NewSource(42))samples := make([]float64, n)for i := range samples {samples[i] = rng.Float64()*2 - 1}b.ResetTimer()for range b.N {fft.FFTReal(samples)}}
package utilsimport ("math""sync")// FFT twiddle factors and bit-reversal tables, cached per size.var (fftCacheMu sync.RWMutexfftCache = map[int]*fftPlan{})// fftPlan holds pre-computed data for a given FFT size.type fftPlan struct {n inttwiddle []complex128 // twiddle factors: exp(-2*pi*i*k/N) for k=0..N/2-1bitrev []int // bit-reversal permutation table}// getFFFTPlan returns a cached FFT plan for the given size (must be power of 2).func getFFTPlan(n int) *fftPlan {fftCacheMu.RLock()if p, ok := fftCache[n]; ok {fftCacheMu.RUnlock()return p}fftCacheMu.RUnlock()fftCacheMu.Lock()defer fftCacheMu.Unlock()if p, ok := fftCache[n]; ok {return p}p := &fftPlan{n: n}// Compute twiddle factors: exp(-2*pi*i*k/N) for k = 0..N/2-1p.twiddle = make([]complex128, n/2)for k := range p.twiddle {angle := -2.0 * math.Pi * float64(k) / float64(n)sin, cos := math.Sincos(angle)p.twiddle[k] = complex(cos, sin)}// Compute bit-reversal permutationbits := 0for v := n; v > 1; v >>= 1 {bits++}p.bitrev = make([]int, n)for i := range p.bitrev {p.bitrev[i] = reverseBitsN(i, bits)}fftCache[n] = preturn p}// reverseBitsN reverses the lowest `bits` bits of v.func reverseBitsN(v, bits int) int {var r intfor range bits {r = (r << 1) | (v & 1)v >>= 1}return r}// PowerSpectrumFFT computes the power spectrum of a real-valued signal using radix-2 FFT.//// samples: real input of length N (must be power of 2, N >= 2)// power: output buffer of length >= N/2+1; receives |X[k]|^2 for k=0..N/2// scratch: working buffer of length >= N; contents are overwritten//// All buffers are caller-provided to enable zero-allocation across repeated calls.func PowerSpectrumFFT(samples []float64, power []float64, scratch []complex128) {n := len(samples)plan := getFFTPlan(n)// Bit-reversal copy: load real samples into scratch in bit-reversed orderfor i, j := range plan.bitrev {scratch[j] = complex(samples[i], 0)}// Iterative Cooley-Tukey butterfly (decimation-in-time)for size := 2; size <= n; size <<= 1 {half := size >> 1step := n / size // twiddle index stepfor start := 0; start < n; start += size {tw := 0for j := range half {u := scratch[start+j]v := scratch[start+j+half] * plan.twiddle[tw]scratch[start+j] = u + vscratch[start+j+half] = u - vtw += step}}}// Extract power spectrum: |X[k]|^2 = re^2 + im^2 for k = 0..N/2numBins := n/2 + 1for k := range numBins {re := real(scratch[k])im := imag(scratch[k])power[k] = re*re + im*im}}
package utilsimport ("os""testing")func TestDataFileParse(t *testing.T) {// Create a test .data filecontent := `[{"Operator": "Auto", "Reviewer": null, "Duration": 60.0},[10.0, 20.0, 0, 0, [{"species": "Kiwi", "certainty": 70, "filter": "test-filter"}]],[30.0, 40.0, 1000, 5000, [{"species": "Morepork", "certainty": 80, "filter": "M"}]]]`tmpfile, err := os.CreateTemp("", "test*.data")if err != nil {t.Fatal(err)}defer os.Remove(tmpfile.Name())if _, err := tmpfile.Write([]byte(content)); err != nil {t.Fatal(err)}tmpfile.Close()// Parsedf, err := ParseDataFile(tmpfile.Name())if err != nil {t.Fatal(err)}// Check metadataif df.Meta.Operator != "Auto" {t.Errorf("expected Operator=Auto, got %s", df.Meta.Operator)}if df.Meta.Duration != 60.0 {t.Errorf("expected Duration=60.0, got %f", df.Meta.Duration)}// Check segmentsif len(df.Segments) != 2 {t.Errorf("expected 2 segments, got %d", len(df.Segments))}// Check first segment (sorted by start time)if df.Segments[0].StartTime != 10.0 {t.Errorf("expected StartTime=10.0, got %f", df.Segments[0].StartTime)}if df.Segments[0].EndTime != 20.0 {t.Errorf("expected EndTime=20.0, got %f", df.Segments[0].EndTime)}// Check labelsif len(df.Segments[0].Labels) != 1 {t.Errorf("expected 1 label, got %d", len(df.Segments[0].Labels))}if df.Segments[0].Labels[0].Species != "Kiwi" {t.Errorf("expected Species=Kiwi, got %s", df.Segments[0].Labels[0].Species)}if df.Segments[0].Labels[0].Certainty != 70 {t.Errorf("expected Certainty=70, got %d", df.Segments[0].Labels[0].Certainty)}}func TestDataFileWrite(t *testing.T) {df := &DataFile{FilePath: "",Meta: &DataMeta{Operator: "Test",Reviewer: "David",Duration: 120.0,},Segments: []*Segment{{StartTime: 5.0,EndTime: 15.0,FreqLow: 0,FreqHigh: 0,Labels: []*Label{{Species: "Kiwi", Certainty: 100, Filter: "test"},},},},}tmpfile, err := os.CreateTemp("", "test*.data")if err != nil {t.Fatal(err)}tmpfile.Close()defer os.Remove(tmpfile.Name())// Writeif err := df.Write(tmpfile.Name()); err != nil {t.Fatal(err)}// Re-parse and verifydf2, err := ParseDataFile(tmpfile.Name())if err != nil {t.Fatal(err)}if df2.Meta.Reviewer != "David" {t.Errorf("expected Reviewer=David, got %s", df2.Meta.Reviewer)}if len(df2.Segments) != 1 {t.Errorf("expected 1 segment, got %d", len(df2.Segments))}if df2.Segments[0].Labels[0].Species != "Kiwi" {t.Errorf("expected Species=Kiwi, got %s", df2.Segments[0].Labels[0].Species)}}func TestHasFilterLabel(t *testing.T) {seg := &Segment{Labels: []*Label{{Species: "Kiwi", Filter: "test-filter"},{Species: "Morepork", Filter: "M"},},}if !seg.HasFilterLabel("test-filter") {t.Error("expected HasFilterLabel(test-filter)=true")}if !seg.HasFilterLabel("M") {t.Error("expected HasFilterLabel(M)=true")}if seg.HasFilterLabel("other") {t.Error("expected HasFilterLabel(other)=false")}if !seg.HasFilterLabel("") {t.Error("expected HasFilterLabel('')=true (no filter)")}}func TestGetFilterLabels(t *testing.T) {seg := &Segment{Labels: []*Label{{Species: "Kiwi", Filter: "test-filter", Certainty: 70},{Species: "Morepork", Filter: "M", Certainty: 80},{Species: "Don't Know", Filter: "test-filter", Certainty: 0},},}labels := seg.GetFilterLabels("test-filter")if len(labels) != 2 {t.Errorf("expected 2 labels, got %d", len(labels))}labels = seg.GetFilterLabels("")if len(labels) != 3 {t.Errorf("expected 3 labels (no filter), got %d", len(labels))}}func TestLabelComment(t *testing.T) {// Test parsing comment from .data filecontent := `[{"Operator": "Test", "Duration": 60.0},[10.0, 20.0, 0, 0, [{"species": "Kiwi", "certainty": 100, "filter": "M", "comment": "Good call"}]]]`tmpfile, err := os.CreateTemp("", "test*.data")if err != nil {t.Fatal(err)}defer os.Remove(tmpfile.Name())if _, err := tmpfile.Write([]byte(content)); err != nil {t.Fatal(err)}tmpfile.Close()df, err := ParseDataFile(tmpfile.Name())if err != nil {t.Fatal(err)}if df.Segments[0].Labels[0].Comment != "Good call" {t.Errorf("expected Comment='Good call', got '%s'", df.Segments[0].Labels[0].Comment)}// Test writing commentdf.Segments[0].Labels[0].Comment = "Updated comment"tmpfile2, err := os.CreateTemp("", "test2*.data")if err != nil {t.Fatal(err)}tmpfile2.Close()defer os.Remove(tmpfile2.Name())if err := df.Write(tmpfile2.Name()); err != nil {t.Fatal(err)}// Re-parse and verifydf2, err := ParseDataFile(tmpfile2.Name())if err != nil {t.Fatal(err)}if df2.Segments[0].Labels[0].Comment != "Updated comment" {t.Errorf("expected Comment='Updated comment', got '%s'", df2.Segments[0].Labels[0].Comment)}}func TestSkraakHashRoundTrip(t *testing.T) {// Test that skraak_hash in metadata is preserved through parse/write cycledf := &DataFile{Meta: &DataMeta{Operator: "Test",Duration: 60.0,Extra: map[string]any{"skraak_hash": "abc123def456",},},Segments: []*Segment{{StartTime: 10.0,EndTime: 20.0,Labels: []*Label{{Species: "Kiwi", Certainty: 100, Filter: "M"},},},},}tmpfile, err := os.CreateTemp("", "test*.data")if err != nil {t.Fatal(err)}tmpfile.Close()defer os.Remove(tmpfile.Name())// Writeif err := df.Write(tmpfile.Name()); err != nil {t.Fatal(err)}// Re-parsedf2, err := ParseDataFile(tmpfile.Name())if err != nil {t.Fatal(err)}// Verify skraak_hash preservedif df2.Meta.Extra == nil {t.Fatal("expected Extra to be non-nil")}hash, ok := df2.Meta.Extra["skraak_hash"].(string)if !ok {t.Fatal("expected skraak_hash to be string")}if hash != "abc123def456" {t.Errorf("expected skraak_hash=abc123def456, got %s", hash)}}func TestSkraakLabelIDRoundTrip(t *testing.T) {// Test that skraak_label_id in labels is preserved through parse/write cycledf := &DataFile{Meta: &DataMeta{Operator: "Test",Duration: 60.0,},Segments: []*Segment{{StartTime: 10.0,EndTime: 20.0,Labels: []*Label{{Species: "Kiwi",Certainty: 100,Filter: "M",Extra: map[string]any{"skraak_label_id": "label_abc123",},},},},},}tmpfile, err := os.CreateTemp("", "test*.data")if err != nil {t.Fatal(err)}tmpfile.Close()defer os.Remove(tmpfile.Name())// Writeif err := df.Write(tmpfile.Name()); err != nil {t.Fatal(err)}// Re-parsedf2, err := ParseDataFile(tmpfile.Name())if err != nil {t.Fatal(err)}// Verify skraak_label_id preservedif len(df2.Segments) != 1 {t.Fatalf("expected 1 segment, got %d", len(df2.Segments))}if len(df2.Segments[0].Labels) != 1 {t.Fatalf("expected 1 label, got %d", len(df2.Segments[0].Labels))}label := df2.Segments[0].Labels[0]if label.Extra == nil {t.Fatal("expected label Extra to be non-nil")}labelID, ok := label.Extra["skraak_label_id"].(string)if !ok {t.Fatal("expected skraak_label_id to be string")}if labelID != "label_abc123" {t.Errorf("expected skraak_label_id=label_abc123, got %s", labelID)}}func TestSkraakFieldsBothPresent(t *testing.T) {// Test both skraak_hash and skraak_label_id togetherdf := &DataFile{Meta: &DataMeta{Operator: "Test",Duration: 60.0,Extra: map[string]any{"skraak_hash": "file_hash_xyz",},},Segments: []*Segment{{StartTime: 10.0,EndTime: 20.0,Labels: []*Label{{Species: "Kiwi",Certainty: 100,Filter: "M",Extra: map[string]any{"skraak_label_id": "label_id_1",},},{Species: "Roroa",Certainty: 90,Filter: "M",Extra: map[string]any{"skraak_label_id": "label_id_2",},},},},},}tmpfile, err := os.CreateTemp("", "test*.data")if err != nil {t.Fatal(err)}tmpfile.Close()defer os.Remove(tmpfile.Name())// Writeif err := df.Write(tmpfile.Name()); err != nil {t.Fatal(err)}// Re-parsedf2, err := ParseDataFile(tmpfile.Name())if err != nil {t.Fatal(err)}// Verify skraak_hashif df2.Meta.Extra["skraak_hash"] != "file_hash_xyz" {t.Errorf("expected skraak_hash=file_hash_xyz, got %v", df2.Meta.Extra["skraak_hash"])}// Verify both label IDsif len(df2.Segments[0].Labels) != 2 {t.Fatalf("expected 2 labels, got %d", len(df2.Segments[0].Labels))}labelIDs := []string{"label_id_1", "label_id_2"}for i, label := range df2.Segments[0].Labels {if label.Extra["skraak_label_id"] != labelIDs[i] {t.Errorf("label %d: expected skraak_label_id=%s, got %v", i, labelIDs[i], label.Extra["skraak_label_id"])}}}func TestSegmentMatchesFilters(t *testing.T) {// Create test segments with various labelsseg := &Segment{Labels: []*Label{{Species: "Kiwi", Filter: "model-1.0", CallType: "Duet", Certainty: 70},{Species: "Morepork", Filter: "model-2.0", CallType: "", Certainty: 100},},}tests := []struct {name stringfilter stringspecies stringcallType stringcertainty intwant bool}{{"no filters", "", "", "", -1, true},{"filter only match", "model-1.0", "", "", -1, true},{"filter only no match", "model-3.0", "", "", -1, false},{"species only match", "", "Kiwi", "", -1, true},{"species only no match", "", "Tomtit", "", -1, false},{"calltype only match", "", "", "Duet", -1, true},{"calltype only no match", "", "", "Male", -1, false},{"certainty match", "", "", "", 70, true},{"certainty no match", "", "", "", 80, false},{"certainty 100 match", "", "", "", 100, true},{"filter+species match", "model-1.0", "Kiwi", "", -1, true},{"filter+species+calltype match", "model-1.0", "Kiwi", "Duet", -1, true},{"filter+species+calltype+certainty match", "model-1.0", "Kiwi", "Duet", 70, true},{"filter+species+calltype certainty miss", "model-1.0", "Kiwi", "Duet", 100, false},{"filter match species miss", "model-1.0", "Morepork", "", -1, false},{"all miss", "model-3.0", "Tomtit", "Male", -1, false},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {got := seg.SegmentMatchesFilters(tt.filter, tt.species, tt.callType, tt.certainty)if got != tt.want {t.Errorf("SegmentMatchesFilters(%q, %q, %q, %d) = %v, want %v",tt.filter, tt.species, tt.callType, tt.certainty, got, tt.want)}})}}func TestParseSpeciesCallType(t *testing.T) {tests := []struct {input stringspecies stringcallType string}{{"", "", ""},{"Kiwi", "Kiwi", ""},{"Kiwi+Duet", "Kiwi", "Duet"},{"GSK+Female", "GSK", "Female"},{"Species+With+Multiple+Plus", "Species", "With+Multiple+Plus"},}for _, tt := range tests {t.Run(tt.input, func(t *testing.T) {species, callType := ParseSpeciesCallType(tt.input)if species != tt.species || callType != tt.callType {t.Errorf("ParseSpeciesCallType(%q) = (%q, %q), want (%q, %q)",tt.input, species, callType, tt.species, tt.callType)}})}}
package utilsimport ("encoding/json""fmt""maps""os""sort""strings")// DataFile represents an AviaNZ .data filetype DataFile struct {Meta *DataMetaSegments []*SegmentFilePath string}// DataMeta contains metadata for a .data filetype DataMeta struct {Operator stringReviewer stringDuration float64Extra map[string]any // preserve unknown fields}// Segment represents a detection segmenttype Segment struct {StartTime float64EndTime float64FreqLow float64FreqHigh float64Labels []*Label}// Label represents a species label within a segmenttype Label struct {Species stringCertainty intFilter stringCallType stringComment string // user comment (max 140 chars, ASCII only)Bookmark bool // user bookmark for navigationExtra map[string]any // preserve unknown fields}// ParseDataFile reads and parses a .data filefunc ParseDataFile(path string) (*DataFile, error) {data, err := os.ReadFile(path)if err != nil {return nil, err}var raw []json.RawMessageif err := json.Unmarshal(data, &raw); err != nil {return nil, fmt.Errorf("parse JSON: %w", err)}if len(raw) == 0 {return nil, fmt.Errorf("empty .data file")}df := &DataFile{FilePath: path,Segments: make([]*Segment, 0, len(raw)-1),}// Parse metadata (first element)df.Meta = parseMeta(raw[0])// Parse segmentsfor i := 1; i < len(raw); i++ {seg, err := parseSegment(raw[i])if err != nil {continue // skip invalid segments}df.Segments = append(df.Segments, seg)}// Sort segments by start timesort.Slice(df.Segments, func(i, j int) bool {return df.Segments[i].StartTime < df.Segments[j].StartTime})return df, nil}// parseMeta parses the metadata objectfunc parseMeta(raw json.RawMessage) *DataMeta {var obj map[string]anyif err := json.Unmarshal(raw, &obj); err != nil {return &DataMeta{}}meta := &DataMeta{Extra: make(map[string]any)}if v, ok := obj["Operator"].(string); ok {meta.Operator = vdelete(obj, "Operator")}if v, ok := obj["Reviewer"].(string); ok {meta.Reviewer = vdelete(obj, "Reviewer")}if v, ok := obj["Duration"].(float64); ok {meta.Duration = vdelete(obj, "Duration")}// Store remaining fieldsmaps.Copy(meta.Extra, obj)return meta}// parseSegment parses a segment arrayfunc parseSegment(raw json.RawMessage) (*Segment, error) {var arr []json.RawMessageif err := json.Unmarshal(raw, &arr); err != nil {return nil, err}if len(arr) < 5 {return nil, fmt.Errorf("segment too short")}seg := &Segment{}// Parse time and frequencyif v, err := parseFloat(arr[0]); err == nil {seg.StartTime = v}if v, err := parseFloat(arr[1]); err == nil {seg.EndTime = v}if v, err := parseFloat(arr[2]); err == nil {seg.FreqLow = v}if v, err := parseFloat(arr[3]); err == nil {seg.FreqHigh = v}// Parse labelsvar labelArr []json.RawMessageif err := json.Unmarshal(arr[4], &labelArr); err == nil {for _, labelRaw := range labelArr {if label := parseLabel(labelRaw); label != nil {seg.Labels = append(seg.Labels, label)}}}// Sort labels alphabetically by speciessort.Slice(seg.Labels, func(i, j int) bool {return seg.Labels[i].Species < seg.Labels[j].Species})return seg, nil}// parseLabel parses a label objectfunc parseLabel(raw json.RawMessage) *Label {var obj map[string]anyif err := json.Unmarshal(raw, &obj); err != nil {return nil}label := &Label{Extra: make(map[string]any)}if v, ok := obj["species"].(string); ok {label.Species = vdelete(obj, "species")}if v, ok := obj["certainty"].(float64); ok {label.Certainty = int(v)delete(obj, "certainty")}if v, ok := obj["filter"].(string); ok {label.Filter = vdelete(obj, "filter")}if v, ok := obj["calltype"].(string); ok {label.CallType = vdelete(obj, "calltype")}if v, ok := obj["comment"].(string); ok {label.Comment = vdelete(obj, "comment")}if v, ok := obj["bookmark"].(bool); ok {label.Bookmark = vdelete(obj, "bookmark")}// Store remaining fieldsmaps.Copy(label.Extra, obj)return label}// parseFloat extracts a float from JSONfunc parseFloat(raw json.RawMessage) (float64, error) {var v float64err := json.Unmarshal(raw, &v)return v, err}// WriteDataFile writes a DataFile back to diskfunc (df *DataFile) Write(path string) error {var raw []any// Build metadatameta := make(map[string]any)if df.Meta.Operator != "" {meta["Operator"] = df.Meta.Operator}if df.Meta.Reviewer != "" {meta["Reviewer"] = df.Meta.Reviewer}if df.Meta.Duration > 0 {meta["Duration"] = df.Meta.Duration}maps.Copy(meta, df.Meta.Extra)raw = append(raw, meta)// Build segmentsfor _, seg := range df.Segments {labels := make([]any, 0, len(seg.Labels))for _, label := range seg.Labels {l := make(map[string]any)l["species"] = label.Speciesl["certainty"] = label.Certaintyif label.Filter != "" {l["filter"] = label.Filter}if label.CallType != "" {l["calltype"] = label.CallType}if label.Comment != "" {l["comment"] = label.Comment}if label.Bookmark {l["bookmark"] = true}maps.Copy(l, label.Extra)labels = append(labels, l)}segArr := []any{seg.StartTime,seg.EndTime,seg.FreqLow,seg.FreqHigh,labels,}raw = append(raw, segArr)}data, err := json.MarshalIndent(raw, "", " ")if err != nil {return err}return os.WriteFile(path, data, 0644)}// HasFilterLabel returns true if segment has a label matching the filterfunc (s *Segment) HasFilterLabel(filter string) bool {if filter == "" {return true}for _, label := range s.Labels {if label.Filter == filter {return true}}return false}// GetFilterLabels returns labels matching the filterfunc (s *Segment) GetFilterLabels(filter string) []*Label {var result []*Labelfor _, label := range s.Labels {if filter == "" || label.Filter == filter {result = append(result, label)}}return result}// SegmentMatchesFilters returns true if the segment has any label matching all filter criteria.// All non-empty/non-negative parameters must match for a label to be considered a match.// Use certainty=-1 to indicate no certainty filtering (since 0 is a valid certainty value).func (s *Segment) SegmentMatchesFilters(filter, species, callType string, certainty int) bool {if filter == "" && species == "" && callType == "" && certainty < 0 {return true // No filters, match all}for _, label := range s.Labels {if filter != "" && label.Filter != filter {continue}if species != "" && label.Species != species {continue}if callType != "" && label.CallType != callType {continue}if certainty >= 0 && label.Certainty != certainty {continue}return true}return false}// ParseSpeciesCallType parses a species string with optional calltype into separate values.// Format: "Species" or "Species+CallType" (e.g., "Kiwi" or "Kiwi+Duet").func ParseSpeciesCallType(s string) (species, callType string) {if s == "" {return "", ""}if before, after, ok := strings.Cut(s, "+"); ok {return before, after}return s, ""}// FindDataFiles finds all .data files in a folder, ignoring hidden files (starting with ".")func FindDataFiles(folder string) ([]string, error) {var files []stringentries, err := os.ReadDir(folder)if err != nil {return nil, err}for _, entry := range entries {name := entry.Name()// Skip hidden files (starting with ".")if strings.HasPrefix(name, ".") {continue}if strings.HasSuffix(name, ".data") {files = append(files, folder+"/"+name)}}return files, nil}
package utilsimport ("encoding/json""fmt""os""path/filepath")// ~/.skraak/config.json schema (reference)://// {// "classify": {// "reviewer": "string, required. Name stamped into .data file meta on any edit.",// "color": "bool, optional. Colored spectrograms in the TUI. Default false.",// "sixel": "bool, optional. Use sixel image protocol. Default false (Kitty).",// "iterm": "bool, optional. Use iTerm inline-image protocol. Default false.",// "img_dims": "int, optional. Spectrogram display size in pixels. 0 = default.",//// "bindings": {// "<key>": "Species" // e.g. "c": "comcha"// "<key>": "Species+CallType" // e.g. "1": "Kiwi+Duet"// // <key> is a single character. Reserved: ",", ".", "0", " " (space).// // Pressing <key> labels the current segment (certainty 100, or 0 for// // "Don't Know"), saves, and advances.// },//// "secondary_bindings": {// "<primary-key>": {// "<key>": "CallType" // e.g. "a": "alarm"// // <key> is a single character, same reserved-key rules as bindings.// // Outer <primary-key> must also exist in "bindings".// }// // Optional. Invoked via Shift+<primary-key>: labels the species with// // an empty calltype, does NOT advance, and waits for one follow-up// // key looked up in this inner map. Match -> set calltype, save,// // advance. Esc -> exit wait mode without advancing. Any other key ->// // exit wait mode and handle the key normally.// // Shift+<primary-key> on a primary without a secondary_bindings entry// // falls back to normal primary behavior.// }// }// }//// Example://// {// "classify": {// "reviewer": "David",// "color": true,// "bindings": {// "c": "comcha",// "k": "kea1",// "x": "Noise",// "z": "Don't Know",// "1": "Kiwi+Duet",// "4": "Kiwi"// },// "secondary_bindings": {// "c": { "a": "alarm", "s": "song", "n": "contact" }// }// }// }//// Config holds user-level defaults loaded from ~/.skraak/config.json.// Per-subcommand sections live as named fields.type Config struct {Classify ClassifyFileConfig `json:"classify"`}// ClassifyFileConfig holds defaults for `skraak calls classify`.// Bindings maps a single-character key to "Species" or "Species+CallType".type ClassifyFileConfig struct {Reviewer string `json:"reviewer"`Color bool `json:"color"`Sixel bool `json:"sixel"`ITerm bool `json:"iterm"`ImgDims int `json:"img_dims"`Bindings map[string]string `json:"bindings"`// SecondaryBindings extends a primary binding with per-species calltype// choices. Outer key is the primary binding key; inner map is// single-char key -> calltype string. Invoked via Shift+primary-key.SecondaryBindings map[string]map[string]string `json:"secondary_bindings,omitempty"`}// ConfigPath returns the absolute path to ~/.skraak/config.json.func ConfigPath() (string, error) {home, err := os.UserHomeDir()if err != nil {return "", fmt.Errorf("resolving home directory: %w", err)}return filepath.Join(home, ".skraak", "config.json"), nil}// LoadConfig reads ~/.skraak/config.json and returns the parsed config and the// resolved path (useful for error messages).func LoadConfig() (Config, string, error) {var cfg Configpath, err := ConfigPath()if err != nil {return cfg, "", err}data, err := os.ReadFile(path)if err != nil {return cfg, path, fmt.Errorf("reading %s: %w", path, err)}if err := json.Unmarshal(data, &cfg); err != nil {return cfg, path, fmt.Errorf("parsing %s: %w", path, err)}return cfg, path, nil}
package utils// RGBPixel represents an RGB color valuetype RGBPixel struct {R, G, B uint8}// L4Colormap is the Black-Red-Yellow heat colormap from PerceptualColourMaps.jl// Control points://// Index 0: Black (0.0, 0.0, 0.0)// Index 85: Dark Red (0.85, 0.0, 0.0)// Index 170: Orange-Red (1.0, 0.15, 0.0)// Index 255: Yellow (1.0, 1.0, 0.0)var L4Colormap [256]RGBPixelfunc init() {// Generate L4 colormap using piecewise linear interpolation// This avoids overshoot issues with cubic splinescontrolPoints := []struct {idx intr float64g float64b float64}{{0, 0.0, 0.0, 0.0},{85, 0.85, 0.0, 0.0},{170, 1.0, 0.15, 0.0},{255, 1.0, 1.0, 0.0},}for i := range 256 {// Find the segment we're invar seg intfor seg = 0; seg < len(controlPoints)-1; seg++ {if i <= controlPoints[seg+1].idx {break}}if seg >= len(controlPoints)-1 {seg = len(controlPoints) - 2}// Linear interpolation within segmentp0 := controlPoints[seg]p1 := controlPoints[seg+1]t := 0.0if p1.idx != p0.idx {t = float64(i-p0.idx) / float64(p1.idx-p0.idx)}L4Colormap[i] = RGBPixel{R: uint8((p0.r + t*(p1.r-p0.r)) * 255.0),G: uint8((p0.g + t*(p1.g-p0.g)) * 255.0),B: uint8((p0.b + t*(p1.b-p0.b)) * 255.0),}}}// ApplyL4Colormap converts a grayscale image to RGB using the L4 colormapfunc ApplyL4Colormap(grayscale [][]uint8) [][]RGBPixel {if len(grayscale) == 0 || len(grayscale[0]) == 0 {return nil}rows := len(grayscale)cols := len(grayscale[0])result := make([][]RGBPixel, rows)for i := range result {result[i] = make([]RGBPixel, cols)}for y := range rows {for x := range cols {result[y][x] = L4Colormap[grayscale[y][x]]}}return result}
package utilsimport ("context""database/sql""fmt""os""path/filepath""sort""strings""time""skraak/db")// FileImportError records errors encountered during file processingtype FileImportError struct {FileName string `json:"file_name"`Error string `json:"error"`Stage string `json:"stage"` // "scan", "hash", "parse", "validate", "insert"}// ClusterImportInput defines parameters for importing one clustertype ClusterImportInput struct {FolderPath string // Absolute path to folder with WAV filesDatasetID string // 12-char dataset IDLocationID string // 12-char location IDClusterID string // 12-char cluster IDRecursive bool // Scan subfolders?}// ClusterImportOutput provides results and statisticstype ClusterImportOutput struct {TotalFiles intImportedFiles intSkippedFiles int // DuplicatesFailedFiles intAudioMothFiles intTotalDuration float64ProcessingTime stringErrors []FileImportError}// LocationData holds location information needed for processingtype LocationData struct {Latitude float64Longitude float64TimezoneID string}// fileData holds all data for a single file to be importedtype fileData struct {FileName stringHash stringDuration float64SampleRate intTimestampLocal time.TimeIsAudioMoth boolMothData *AudioMothDataAstroData AstronomicalData}// ImportCluster imports all WAV files from a folder into a cluster//// This is the canonical cluster import logic used by both:// - import_files.go (single cluster)// - bulk_file_import.go (multiple clusters)//// Steps:// 1. Validate folder exists// 2. Get location metadata (lat/lon/timezone) from database// 3. Scan folder for WAV files (recursive or not)// 4. Batch process all files:// - Parse WAV headers (includes file mod time)// - Batch parse filename timestamps (variance-based)// - Resolve timestamps (AudioMoth → filename → file mod time)// - Calculate hashes// - Calculate astronomical data// 5. Batch insert in single transaction:// - Check duplicates// - INSERT INTO file// - INSERT INTO file_dataset (ALWAYS)// - INSERT INTO moth_metadata (if AudioMoth)// - All-or-nothing commit// 6. Return summary statistics//// Transaction behavior: ALL files succeed or ALL rollback// This preserves cluster integrity (cluster = complete recording session)func ImportCluster(database *sql.DB,input ClusterImportInput,) (*ClusterImportOutput, error) {startTime := time.Now()// Validate folder existsinfo, err := os.Stat(input.FolderPath)if err != nil {return nil, fmt.Errorf("folder not accessible: %w", err)}if !info.IsDir() {return nil, fmt.Errorf("path is not a directory: %s", input.FolderPath)}// Get location data for astronomical calculationslocationData, err := GetLocationData(database, input.LocationID)if err != nil {return nil, fmt.Errorf("failed to get location data: %w", err)}// Scan folder for WAV fileswavFiles, err := scanClusterFiles(input.FolderPath, input.Recursive)if err != nil {return nil, fmt.Errorf("failed to scan folder: %w", err)}// If no files, return earlyif len(wavFiles) == 0 {return &ClusterImportOutput{TotalFiles: 0,ProcessingTime: time.Since(startTime).String(),Errors: []FileImportError{},}, nil}// Batch process all filesfilesData, processErrors := batchProcessFiles(wavFiles, locationData)// Batch insert into databaseimported, skipped, insertErrors, err := insertClusterFiles(database,filesData,input.DatasetID,input.ClusterID,input.LocationID,)if err != nil {return nil, fmt.Errorf("database insertion failed: %w", err)}// Combine all errorsallErrors := append(processErrors, insertErrors...)// Calculate summary statisticsaudiomothCount := 0totalDuration := 0.0for _, fd := range filesData {if fd.IsAudioMoth {audiomothCount++}totalDuration += fd.Duration}return &ClusterImportOutput{TotalFiles: len(wavFiles),ImportedFiles: imported,SkippedFiles: skipped,FailedFiles: len(allErrors),AudioMothFiles: audiomothCount,TotalDuration: totalDuration,ProcessingTime: time.Since(startTime).String(),Errors: allErrors,}, nil}// GetLocationData retrieves location coordinates and timezonefunc GetLocationData(database *sql.DB, locationID string) (*LocationData, error) {var loc LocationDataerr := database.QueryRow("SELECT latitude, longitude, timezone_id FROM location WHERE id = ?",locationID,).Scan(&loc.Latitude, &loc.Longitude, &loc.TimezoneID)if err != nil {return nil, fmt.Errorf("failed to query location data: %w", err)}return &loc, nil}// EnsureClusterPath sets the cluster's path field if it's currently emptyfunc EnsureClusterPath(database *sql.DB, clusterID, folderPath string) error {// Check if cluster already has a pathvar currentPath sql.NullStringerr := database.QueryRow("SELECT path FROM cluster WHERE id = ?", clusterID).Scan(¤tPath)if err != nil {return fmt.Errorf("failed to query cluster: %w", err)}// If path is already set, skipif currentPath.Valid && currentPath.String != "" {return nil}// Normalize folder pathnormalizedPath := NormalizeFolderPath(folderPath)// Update cluster with normalized path_, err = database.Exec("UPDATE cluster SET path = ?, last_modified = now() WHERE id = ?",normalizedPath,clusterID,)if err != nil {return fmt.Errorf("failed to update cluster path: %w", err)}return nil}// scanClusterFiles recursively scans a folder for WAV files, excluding Clips_* subfoldersfunc scanClusterFiles(rootPath string, recursive bool) ([]string, error) {var wavFiles []stringif recursive {err := filepath.Walk(rootPath, func(path string, info os.FileInfo, err error) error {if err != nil {return err}// Skip "Clips_*" directoriesif info.IsDir() && strings.HasPrefix(info.Name(), "Clips_") {return filepath.SkipDir}// Check for WAV filesif !info.IsDir() {ext := strings.ToLower(filepath.Ext(path))if ext == ".wav" && info.Size() > 0 {wavFiles = append(wavFiles, path)}}return nil})if err != nil {return nil, err}} else {// Non-recursive: scan only top levelentries, err := os.ReadDir(rootPath)if err != nil {return nil, err}for _, entry := range entries {if !entry.IsDir() {name := entry.Name()ext := strings.ToLower(filepath.Ext(name))if ext == ".wav" {path := filepath.Join(rootPath, name)if info, err := os.Stat(path); err == nil && info.Size() > 0 {wavFiles = append(wavFiles, path)}}}}}// Sort for consistent processing ordersort.Strings(wavFiles)return wavFiles, nil}// batchProcessFiles extracts metadata and calculates hashes for all filesfunc batchProcessFiles(wavFiles []string, location *LocationData) ([]*fileData, []FileImportError) {var filesData []*fileDatavar errors []FileImportError// Step 1: Extract WAV metadata and hash in single passtype wavInfo struct {path stringmetadata *WAVMetadatahash stringerr error}wavInfos := make([]wavInfo, len(wavFiles))for i, path := range wavFiles {metadata, hash, err := ParseWAVHeaderWithHash(path)wavInfos[i] = wavInfo{path: path, metadata: metadata, hash: hash, err: err}}// Step 2: Collect filenames for batch timestamp parsingvar filenamesForParsing []stringvar filenameIndices []intfor i, info := range wavInfos {if info.err != nil {errors = append(errors, FileImportError{FileName: filepath.Base(info.path),Error: info.err.Error(),Stage: "parse",})continue}// Check if file has timestamp filename formatif HasTimestampFilename(info.path) {filenamesForParsing = append(filenamesForParsing, filepath.Base(info.path))filenameIndices = append(filenameIndices, i)}}// Step 3: Parse filename timestamps in batch (if any)filenameTimestampMap := make(map[int]time.Time) // Maps file index to timestampif len(filenamesForParsing) > 0 {filenameTimestamps, err := ParseFilenameTimestamps(filenamesForParsing)if err != nil {// If batch parsing fails, record error for all filesfor _, idx := range filenameIndices {errors = append(errors, FileImportError{FileName: filepath.Base(wavInfos[idx].path),Error: fmt.Sprintf("filename timestamp parsing failed: %v", err),Stage: "parse",})}} else {// Apply timezone offsetadjustedTimestamps, err := ApplyTimezoneOffset(filenameTimestamps, location.TimezoneID)if err != nil {for _, idx := range filenameIndices {errors = append(errors, FileImportError{FileName: filepath.Base(wavInfos[idx].path),Error: fmt.Sprintf("timezone offset failed: %v", err),Stage: "parse",})}} else {// Build map from file index to timestampfor j, idx := range filenameIndices {filenameTimestampMap[idx] = adjustedTimestamps[j]}}}}// Step 4: Process each filefor i, info := range wavInfos {if info.err != nil {continue // Already recorded error}// Determine timestampvar timestampLocal time.Timevar isAudioMoth boolvar mothData *AudioMothData// Try AudioMoth comment firstif IsAudioMoth(info.metadata.Comment, info.metadata.Artist) {isAudioMoth = truevar parseErr errormothData, parseErr = ParseAudioMothComment(info.metadata.Comment)if parseErr == nil {timestampLocal = mothData.Timestamp} else {// AudioMoth detected but parsing failed - try filenameerrors = append(errors, FileImportError{FileName: filepath.Base(info.path),Error: fmt.Sprintf("AudioMoth comment parsing failed: %v", parseErr),Stage: "parse",})}}// If no AudioMoth timestamp, use filename timestampif timestampLocal.IsZero() {if ts, ok := filenameTimestampMap[i]; ok {timestampLocal = ts}}// If still no timestamp, use file modification time as fallbackif timestampLocal.IsZero() {if !info.metadata.FileModTime.IsZero() {// Assume FileModTime is already in location timezone// (recorder was at the location when it recorded)timestampLocal = info.metadata.FileModTime}}// If still no timestamp, skip fileif timestampLocal.IsZero() {errors = append(errors, FileImportError{FileName: filepath.Base(info.path),Error: "no timestamp available (not AudioMoth, filename not parseable, and file mod time missing)",Stage: "parse",})continue}// Calculate astronomical dataastroData := CalculateAstronomicalData(timestampLocal.UTC(),info.metadata.Duration,location.Latitude,location.Longitude,)// Add to resultsfilesData = append(filesData, &fileData{FileName: filepath.Base(info.path),Hash: info.hash,Duration: info.metadata.Duration,SampleRate: info.metadata.SampleRate,TimestampLocal: timestampLocal,IsAudioMoth: isAudioMoth,MothData: mothData,AstroData: astroData,})}return filesData, errors}// insertClusterFiles inserts all file data into database in a single transactionfunc insertClusterFiles(database *sql.DB,filesData []*fileData,datasetID, clusterID, locationID string,) (imported, skipped int, errors []FileImportError, err error) {// Begin logged transactionctx := context.Background()tx, err := db.BeginLoggedTx(ctx, database, "import_audio_files")if err != nil {return 0, 0, nil, fmt.Errorf("failed to begin transaction: %w", err)}defer tx.Rollback() // Rollback if not committed// Prepare statementsfileStmt, err := tx.PrepareContext(ctx, `INSERT INTO file (id, file_name, xxh64_hash, location_id, timestamp_local,cluster_id, duration, sample_rate, maybe_solar_night, maybe_civil_night,moon_phase, created_at, last_modified, active) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, now(), now(), true)`)if err != nil {return 0, 0, nil, fmt.Errorf("failed to prepare file statement: %w", err)}defer fileStmt.Close()datasetStmt, err := tx.PrepareContext(ctx, `INSERT INTO file_dataset (file_id, dataset_id, created_at, last_modified)VALUES (?, ?, now(), now())`)if err != nil {return 0, 0, nil, fmt.Errorf("failed to prepare dataset statement: %w", err)}defer datasetStmt.Close()mothStmt, err := tx.PrepareContext(ctx, `INSERT INTO moth_metadata (file_id, timestamp, recorder_id, gain, battery_v, temp_c,created_at, last_modified, active) VALUES (?, ?, ?, ?, ?, ?, now(), now(), true)`)if err != nil {return 0, 0, nil, fmt.Errorf("failed to prepare moth statement: %w", err)}defer mothStmt.Close()// Insert each filefor _, fd := range filesData {// Check for duplicate hashvar exists boolerr = tx.QueryRowContext(ctx,"SELECT EXISTS(SELECT 1 FROM file WHERE xxh64_hash = ?)",fd.Hash,).Scan(&exists)if err != nil {errors = append(errors, FileImportError{FileName: fd.FileName,Error: fmt.Sprintf("duplicate check failed: %v", err),Stage: "insert",})continue}if exists {skipped++continue}// Generate file IDfileID, err := GenerateLongID()if err != nil {errors = append(errors, FileImportError{FileName: fd.FileName,Error: fmt.Sprintf("ID generation failed: %v", err),Stage: "insert",})continue}// Insert file record_, err = fileStmt.ExecContext(ctx,fileID, fd.FileName, fd.Hash, locationID,fd.TimestampLocal, clusterID, fd.Duration, fd.SampleRate,fd.AstroData.SolarNight, fd.AstroData.CivilNight, fd.AstroData.MoonPhase,)if err != nil {errors = append(errors, FileImportError{FileName: fd.FileName,Error: fmt.Sprintf("file insert failed: %v", err),Stage: "insert",})continue}// Insert file_dataset junction (ALWAYS)_, err = datasetStmt.ExecContext(ctx, fileID, datasetID)if err != nil {errors = append(errors, FileImportError{FileName: fd.FileName,Error: fmt.Sprintf("file_dataset insert failed: %v", err),Stage: "insert",})continue}// If AudioMoth, insert moth_metadataif fd.IsAudioMoth && fd.MothData != nil {_, err = mothStmt.ExecContext(ctx,fileID,fd.MothData.Timestamp,&fd.MothData.RecorderID,&fd.MothData.Gain,&fd.MothData.BatteryV,&fd.MothData.TempC,)if err != nil {errors = append(errors, FileImportError{FileName: fd.FileName,Error: fmt.Sprintf("moth_metadata insert failed: %v", err),Stage: "insert",})continue}}imported++}// Commit transactionerr = tx.Commit()if err != nil {return 0, 0, errors, fmt.Errorf("transaction commit failed: %w", err)}return imported, skipped, errors, nil}
package utilsimport ("math""testing")// Reference values verified against opensoundscape.utils.generate_clip_times_df// at https://github.com/kitzeslab/opensoundscape/blob/master/opensoundscape/utils.pyfunc TestGenerateClipTimes_FullModeBasic(t *testing.T) {// full_duration=10, clip_duration=4, overlap=0.5, final="full"// increment = 3.5// raw starts: 0, 3.5, 7 (next would be 10.5 ≥ 10)// raw ends: 4, 7.5, 11// "full": last clip start shifts back by (11-10)=1 → start=6, end=10// → [(0,4), (3.5,7.5), (6,10)]got, err := GenerateClipTimes(10, 4, 0.5, FinalClipFull, 10)if err != nil {t.Fatal(err)}want := []ClipWindow{{0, 4}, {3.5, 7.5}, {6, 10}}assertClips(t, got, want)}func TestGenerateClipTimes_NoneMode(t *testing.T) {// final="none": drop any clip whose end > full_duration.// full=10, dur=4, overlap=0: starts 0,4,8; ends 4,8,12 → keep (0,4),(4,8)got, err := GenerateClipTimes(10, 4, 0, FinalClipNone, 10)if err != nil {t.Fatal(err)}assertClips(t, got, []ClipWindow{{0, 4}, {4, 8}})}func TestGenerateClipTimes_RemainderMode(t *testing.T) {// full=10, dur=4, overlap=0: starts 0,4,8; ends 4,8,12// remainder: trim 12 → 10. → (0,4),(4,8),(8,10)got, err := GenerateClipTimes(10, 4, 0, FinalClipRemainder, 10)if err != nil {t.Fatal(err)}assertClips(t, got, []ClipWindow{{0, 4}, {4, 8}, {8, 10}})}func TestGenerateClipTimes_ExtendMode(t *testing.T) {got, err := GenerateClipTimes(10, 4, 0, FinalClipExtend, 10)if err != nil {t.Fatal(err)}assertClips(t, got, []ClipWindow{{0, 4}, {4, 8}, {8, 12}})}func TestGenerateClipTimes_AudioShorterThanClip(t *testing.T) {// full=2, dur=4, overlap=0, final="full":// raw start=0, end=4; end > full=2 → start shifts to 0-(4-2)=-2 → clamped to 0;// end=2 → single clip (0,2)got, err := GenerateClipTimes(2, 4, 0, FinalClipFull, 10)if err != nil {t.Fatal(err)}assertClips(t, got, []ClipWindow{{0, 2}})}func TestGenerateClipTimes_DedupAfterFullShift(t *testing.T) {// full=8, dur=4, overlap=0:// raw starts 0,4; ends 4,8 — no shift needed; output (0,4),(4,8).// (Tests the no-duplicate path.)got, err := GenerateClipTimes(8, 4, 0, FinalClipFull, 10)if err != nil {t.Fatal(err)}assertClips(t, got, []ClipWindow{{0, 4}, {4, 8}})}func TestGenerateClipTimes_InvalidArgs(t *testing.T) {_, err := GenerateClipTimes(10, 0, 0, FinalClipFull, 10)if err == nil {t.Error("expected error for clip_duration=0")}_, err = GenerateClipTimes(10, 4, 4, FinalClipFull, 10)if err == nil {t.Error("expected error for clip_overlap >= clip_duration")}_, err = GenerateClipTimes(0, 4, 0, FinalClipFull, 10)if err == nil {t.Error("expected error for full_duration=0")}}func assertClips(t *testing.T, got, want []ClipWindow) {t.Helper()if len(got) != len(want) {t.Fatalf("len(got)=%d, len(want)=%d\ngot=%v\nwant=%v", len(got), len(want), got, want)}for i := range got {if math.Abs(got[i].Start-want[i].Start) > 1e-9 || math.Abs(got[i].End-want[i].End) > 1e-9 {t.Errorf("clip %d: got (%v,%v), want (%v,%v)", i, got[i].Start, got[i].End, want[i].Start, want[i].End)}}}
package utilsimport ("fmt""math")// ClipWindow is a fixed-duration time window for one audio file.type ClipWindow struct {Start float64End float64}// FinalClipMode controls how the trailing partial clip is handled.// Mirrors opensoundscape.utils.generate_clip_times_df:// - FinalClipNone: discard any clip whose end exceeds full_duration// - FinalClipRemainder: trim the final clip's end to full_duration (shorter clip)// - FinalClipFull: shift the final clip's start back so its end equals full_duration// - FinalClipExtend: keep the final clip extending beyond full_durationtype FinalClipMode intconst (FinalClipNone FinalClipMode = iotaFinalClipRemainderFinalClipFullFinalClipExtend)// ParseFinalClipMode parses a CLI flag value.func ParseFinalClipMode(s string) (FinalClipMode, error) {switch s {case "none", "":return FinalClipNone, nilcase "remainder":return FinalClipRemainder, nilcase "full":return FinalClipFull, nilcase "extend":return FinalClipExtend, nildefault:return 0, fmt.Errorf("invalid final-clip mode %q (want one of: none, remainder, full, extend)", s)}}// roundTo rounds x to `precision` decimal places. Mirrors numpy.round behaviour.// Pass precision < 0 to skip rounding.func roundTo(x float64, precision int) float64 {if precision < 0 {return x}scale := math.Pow(10, float64(precision))return math.Round(x*scale) / scale}// GenerateClipTimes ports opensoundscape.utils.generate_clip_times_df.//// Args mirror the Python signature: clipDuration > 0, clipOverlap in [0, clipDuration),// fullDuration > 0. roundingPrecision defaults to 10 in OPSO; pass -1 to skip rounding.//// Result is the list of (start, end) windows for one audio file, with duplicates// removed (which can happen under FinalClipFull when the shifted final clip// coincides with the previous one).func GenerateClipTimes(fullDuration, clipDuration, clipOverlap float64, finalClip FinalClipMode, roundingPrecision int) ([]ClipWindow, error) {if clipDuration <= 0 {return nil, fmt.Errorf("clipDuration must be > 0, got %v", clipDuration)}if clipOverlap < 0 || clipOverlap >= clipDuration {return nil, fmt.Errorf("clipOverlap must be in [0, clipDuration), got %v with clipDuration=%v", clipOverlap, clipDuration)}if fullDuration <= 0 {return nil, fmt.Errorf("fullDuration must be > 0, got %v", fullDuration)}increment := clipDuration - clipOverlap// numpy.arange(0, fullDuration, increment): half-open interval// stop when start >= fullDurationvar starts []float64for s := 0.0; s < fullDuration; s += increment {starts = append(starts, roundTo(s, roundingPrecision))}if len(starts) == 0 {// Defensive — shouldn't happen since fullDuration > 0 and increment > 0starts = []float64{0}}ends := make([]float64, len(starts))for i, s := range starts {ends[i] = s + clipDuration}switch finalClip {case FinalClipNone:// Drop any window whose end exceeds fullDuration.kept := make([]ClipWindow, 0, len(starts))for i := range starts {if ends[i] <= fullDuration {kept = append(kept, ClipWindow{Start: starts[i], End: ends[i]})}}return dedupClips(kept), nilcase FinalClipRemainder:// Trim ends > fullDuration down to fullDuration.out := make([]ClipWindow, 0, len(starts))for i := range starts {e := ends[i]if e > fullDuration {e = fullDuration}out = append(out, ClipWindow{Start: starts[i], End: e})}return dedupClips(out), nilcase FinalClipFull:// Shift any window whose end exceeds fullDuration back so its end == fullDuration.// Keep clip length == clipDuration. Clamp start to >= 0 (audio shorter than clip_duration).out := make([]ClipWindow, 0, len(starts))for i := range starts {s := starts[i]e := ends[i]if e > fullDuration {delta := e - fullDurations -= deltae = fullDurationif s < 0 {s = 0}}out = append(out, ClipWindow{Start: s, End: e})}return dedupClips(out), nilcase FinalClipExtend:// Keep ends as-is, even past fullDuration.out := make([]ClipWindow, 0, len(starts))for i := range starts {out = append(out, ClipWindow{Start: starts[i], End: ends[i]})}return dedupClips(out), nildefault:return nil, fmt.Errorf("invalid FinalClipMode %d", finalClip)}}// dedupClips removes consecutive duplicates while preserving order.// Matches pandas.DataFrame.drop_duplicates() at the end of OPSO's// generate_clip_times_df.func dedupClips(in []ClipWindow) []ClipWindow {if len(in) <= 1 {return in}seen := make(map[ClipWindow]bool, len(in))out := make([]ClipWindow, 0, len(in))for _, c := range in {if !seen[c] {seen[c] = trueout = append(out, c)}}return out}
package utilsimport ("skraak/db""strings""testing""time")func TestIsAudioMoth(t *testing.T) {t.Run("should identify AudioMoth files by artist field", func(t *testing.T) {if !IsAudioMoth("", "AudioMoth") {t.Error("Should identify AudioMoth by artist field")}if !IsAudioMoth("", "AudioMoth 123456") {t.Error("Should identify AudioMoth with ID in artist field")}if IsAudioMoth("", "Other Artist") {t.Error("Should not identify non-AudioMoth artist")}})t.Run("should identify AudioMoth files by comment field", func(t *testing.T) {if !IsAudioMoth("Recorded by AudioMoth...", "") {t.Error("Should identify AudioMoth by comment field")}if IsAudioMoth("Regular recording comment", "") {t.Error("Should not identify non-AudioMoth comment")}})t.Run("should handle missing metadata", func(t *testing.T) {if IsAudioMoth("", "") {t.Error("Should not identify empty strings as AudioMoth")}})t.Run("should be case insensitive", func(t *testing.T) {if !IsAudioMoth("", "audiomoth") {t.Error("Should be case insensitive")}if !IsAudioMoth("", "AUDIOMOTH") {t.Error("Should be case insensitive")}})}func TestParseAudioMothComment(t *testing.T) {t.Run("should parse a valid structured AudioMoth comment", func(t *testing.T) {comment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was 15.8C."result, err := ParseAudioMothComment(comment)if err != nil {t.Fatalf("Failed to parse comment: %v", err)}// Check timestamp (should be in UTC+13)expected := time.Date(2025, 2, 24, 21, 0, 0, 0, time.FixedZone("UTC+13", 13*3600))if !result.Timestamp.Equal(expected) {t.Errorf("Timestamp incorrect: got %v, want %v", result.Timestamp, expected)}// Convert to UTC and verifyutc := result.Timestamp.UTC()expectedUTC := time.Date(2025, 2, 24, 8, 0, 0, 0, time.UTC)if !utc.Equal(expectedUTC) {t.Errorf("UTC timestamp incorrect: got %v, want %v", utc, expectedUTC)}if result.RecorderID != "248AB50153AB0549" {t.Errorf("RecorderID incorrect: got %s, want 248AB50153AB0549", result.RecorderID)}if result.Gain != db.GainMedium {t.Errorf("Gain incorrect: got %s, want %s", result.Gain, db.GainMedium)}if result.BatteryV != 4.3 {t.Errorf("BatteryV incorrect: got %f, want 4.3", result.BatteryV)}if result.TempC != 15.8 {t.Errorf("TempC incorrect: got %f, want 15.8", result.TempC)}})t.Run("should return error for invalid comments", func(t *testing.T) {invalidComments := []string{"Not an AudioMoth comment","Recorded at invalid time format","Short comment","","AudioMoth without proper format",}for _, comment := range invalidComments {_, err := ParseAudioMothComment(comment)if err == nil {t.Errorf("Expected error for invalid comment: %s", comment)}}})t.Run("should handle different timezone formats", func(t *testing.T) {commentUTCMinus := "Recorded at 10:30:45 15/06/2024 (UTC-5) by AudioMoth 123456789ABCDEF0 at high gain while battery was 3.9V and temperature was 22.1C."result, err := ParseAudioMothComment(commentUTCMinus)if err != nil {t.Fatalf("Failed to parse comment: %v", err)}// Check timestamp is in UTC-5expected := time.Date(2024, 6, 15, 10, 30, 45, 0, time.FixedZone("UTC-5", -5*3600))if !result.Timestamp.Equal(expected) {t.Errorf("Timestamp incorrect: got %v, want %v", result.Timestamp, expected)}if result.Gain != db.GainHigh {t.Errorf("Gain incorrect: got %s, want %s", result.Gain, db.GainHigh)}if result.BatteryV != 3.9 {t.Errorf("BatteryV incorrect: got %f, want 3.9", result.BatteryV)}if result.TempC != 22.1 {t.Errorf("TempC incorrect: got %f, want 22.1", result.TempC)}})t.Run("should parse all gain levels", func(t *testing.T) {testCases := []struct {gainStr stringexpected db.GainLevel}{{"low", db.GainLow},{"low-medium", db.GainLowMedium},{"medium", db.GainMedium},{"medium-high", db.GainMediumHigh},{"high", db.GainHigh},}for _, tc := range testCases {comment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at " + tc.gainStr + " gain while battery was 4.3V and temperature was 15.8C."result, err := ParseAudioMothComment(comment)if err != nil {t.Errorf("Failed to parse comment with gain %s: %v", tc.gainStr, err)continue}if result.Gain != tc.expected {t.Errorf("Gain incorrect for %s: got %s, want %s", tc.gainStr, result.Gain, tc.expected)}}})t.Run("should handle negative temperatures", func(t *testing.T) {comment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was -5.2C."result, err := ParseAudioMothComment(comment)if err != nil {t.Fatalf("Failed to parse comment: %v", err)}if result.TempC != -5.2 {t.Errorf("TempC incorrect: got %f, want -5.2", result.TempC)}})t.Run("should fallback to legacy parsing", func(t *testing.T) {// Legacy format might not match structured regex but should be parseable// Test with a legacy-style commentcomment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was 15.8C"// Note: The legacy parser expects the exact structure, so this might fail// if the comment doesn't match. Adjust test as needed based on actual legacy format.result, err := ParseAudioMothComment(comment)// Either succeeds or fails gracefullyif err == nil {// If it succeeds, verify basic fieldsif result.RecorderID == "" {t.Error("RecorderID should not be empty")}}})}func TestParseGainLevel(t *testing.T) {testCases := []struct {input stringexpected db.GainLevelwantErr bool}{{"low", db.GainLow, false},{"LOW", db.GainLow, false},{" low ", db.GainLow, false},{"low-medium", db.GainLowMedium, false},{"medium", db.GainMedium, false},{"medium-high", db.GainMediumHigh, false},{"high", db.GainHigh, false},{"invalid", "", true},{"", "", true},{"ultra", "", true},}for _, tc := range testCases {t.Run(tc.input, func(t *testing.T) {result, err := parseGainLevel(tc.input)if tc.wantErr {if err == nil {t.Errorf("Expected error for input %q, got nil", tc.input)}} else {if err != nil {t.Errorf("Unexpected error for input %q: %v", tc.input, err)}if result != tc.expected {t.Errorf("Result incorrect for %q: got %s, want %s", tc.input, result, tc.expected)}}})}}func TestParseAudioMothTimestamp(t *testing.T) {t.Run("should parse standard timestamp format", func(t *testing.T) {result, err := parseAudioMothTimestamp("21:00:00", "24/02/2025", "UTC+13")if err != nil {t.Fatalf("Failed to parse timestamp: %v", err)}expected := time.Date(2025, 2, 24, 21, 0, 0, 0, time.FixedZone("UTC+13", 13*3600))if !result.Equal(expected) {t.Errorf("Timestamp incorrect: got %v, want %v", result, expected)}})t.Run("should parse timestamp with +HH format", func(t *testing.T) {result, err := parseAudioMothTimestamp("10:30:45", "15/06/2024", "+13")if err != nil {t.Fatalf("Failed to parse timestamp: %v", err)}expected := time.Date(2024, 6, 15, 10, 30, 45, 0, time.FixedZone("UTC+13", 13*3600))if !result.Equal(expected) {t.Errorf("Timestamp incorrect: got %v, want %v", result, expected)}})t.Run("should parse negative timezone offset", func(t *testing.T) {result, err := parseAudioMothTimestamp("10:30:45", "15/06/2024", "UTC-5")if err != nil {t.Fatalf("Failed to parse timestamp: %v", err)}expected := time.Date(2024, 6, 15, 10, 30, 45, 0, time.FixedZone("UTC-5", -5*3600))if !result.Equal(expected) {t.Errorf("Timestamp incorrect: got %v, want %v", result, expected)}})t.Run("should handle invalid time format", func(t *testing.T) {_, err := parseAudioMothTimestamp("25:00:00", "15/06/2024", "UTC+13")// Note: Go's time.Date will normalize invalid times, so this might not error// The error would be caught if the format doesn't match_ = err})t.Run("should handle invalid date format", func(t *testing.T) {_, err := parseAudioMothTimestamp("10:30:45", "32/13/2024", "UTC+13")// Note: Go's time.Date will normalize invalid dates_ = err})}func TestStructuredVsLegacyParsing(t *testing.T) {t.Run("should prefer structured parsing", func(t *testing.T) {comment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was 15.8C."result, err := ParseAudioMothComment(comment)if err != nil {t.Fatalf("Failed to parse comment: %v", err)}// Verify it parsed correctlyif result.RecorderID != "248AB50153AB0549" {t.Errorf("RecorderID incorrect: got %s, want 248AB50153AB0549", result.RecorderID)}})t.Run("should handle legacy format", func(t *testing.T) {// Create a comment that matches legacy space-separated formatcomment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was 15.8C."// The structured parser should handle thisresult, err := ParseAudioMothComment(comment)if err != nil {// If structured fails, legacy should catch it// (though for this format, structured should work)t.Logf("Note: Structured parsing failed, expected legacy to handle: %v", err)} else {if result.RecorderID == "" {t.Error("RecorderID should not be empty")}}})}func TestAudioMothCommentEdgeCases(t *testing.T) {t.Run("should handle extra whitespace", func(t *testing.T) {comment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was 15.8C."// Depending on implementation, this might or might not parse_, err := ParseAudioMothComment(comment)if err != nil {// Expected - structured regex is strictt.Logf("Extra whitespace causes parsing to fail (expected): %v", err)}})t.Run("should handle different case in gain", func(t *testing.T) {comment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at MEDIUM gain while battery was 4.3V and temperature was 15.8C."result, err := ParseAudioMothComment(comment)if err == nil {if result.Gain != db.GainMedium {t.Errorf("Gain should be normalized: got %s, want %s", result.Gain, db.GainMedium)}}})t.Run("should handle non-hex recorder ID via legacy parser", func(t *testing.T) {// Structured regex expects [A-F0-9]+ hex format and will not match// Legacy parser will catch this and parse it (more lenient)comment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth GGGGGGGGGGGGGGGG at medium gain while battery was 4.3V and temperature was 15.8C."result, err := ParseAudioMothComment(comment)// Legacy parser is lenient and accepts any recorder IDif err != nil {t.Fatalf("Legacy parser should handle non-hex recorder ID: %v", err)}// Verify it parsed the recorder ID (even though it's not valid hex)if result.RecorderID != "GGGGGGGGGGGGGGGG" {t.Errorf("RecorderID incorrect: got %s, want GGGGGGGGGGGGGGGG", result.RecorderID)}})t.Run("should handle recorder ID of different lengths", func(t *testing.T) {// Short IDcomment := "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth ABCD at medium gain while battery was 4.3V and temperature was 15.8C."result, err := ParseAudioMothComment(comment)if err != nil {t.Fatalf("Failed to parse comment with short ID: %v", err)}if !strings.Contains(result.RecorderID, "ABCD") {t.Errorf("RecorderID should contain ABCD, got %s", result.RecorderID)}})}
package utilsimport ("fmt""regexp""strconv""strings""time""skraak/db")// AudioMothData contains parsed data from AudioMoth comment fieldtype AudioMothData struct {Timestamp time.TimeRecorderID stringGain db.GainLevelBatteryV float64TempC float64}// AudioMoth comment example:// "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was 15.8C."var (// Pattern to detect AudioMoth commentsaudiomothPattern = regexp.MustCompile(`(?i)AudioMoth`)// Pattern to extract structured data// Matches: "Recorded at HH:MM:SS DD/MM/YYYY (UTC±HH) by AudioMoth HEXID at GAIN gain while battery was X.XV and temperature was Y.YC."structuredPattern = regexp.MustCompile(`Recorded at (\d{2}:\d{2}:\d{2}) (\d{2}/\d{2}/\d{4}) \(UTC([+-]\d+)\) by AudioMoth ([A-F0-9]+) at ([\w-]+) gain while battery was ([\d.]+)V and temperature was ([-\d.]+)C`,))// IsAudioMoth checks if the comment or artist field indicates an AudioMoth recording// IsAudioMoth detects if WAV file is from AudioMoth recorderfunc IsAudioMoth(comment, artist string) bool {return audiomothPattern.MatchString(comment) || audiomothPattern.MatchString(artist)}// ParseAudioMothComment parses structured AudioMoth comment field// Returns parsed data or error if parsing fails// ParseAudioMothComment extracts timestamp, gain, battery, and temperature from AudioMoth commentfunc ParseAudioMothComment(comment string) (*AudioMothData, error) {// Try structured parsing first (newer format)if data, err := parseStructuredComment(comment); err == nil {return data, nil}// Fallback to legacy space-separated parsingreturn parseLegacyComment(comment)}// parseStructuredComment parses newer AudioMoth comment format using regexfunc parseStructuredComment(comment string) (*AudioMothData, error) {matches := structuredPattern.FindStringSubmatch(comment)if matches == nil {return nil, fmt.Errorf("comment does not match structured AudioMoth format")}// Extract matched groupstimeStr := matches[1] // HH:MM:SSdateStr := matches[2] // DD/MM/YYYYtimezoneStr := matches[3] // ±HHrecorderID := matches[4] // Hex IDgainStr := matches[5] // gain levelbatteryStr := matches[6] // battery voltagetempStr := matches[7] // temperature// Parse timestamptimestamp, err := parseAudioMothTimestamp(timeStr, dateStr, timezoneStr)if err != nil {return nil, fmt.Errorf("failed to parse timestamp: %w", err)}// Parse gaingain, err := parseGainLevel(gainStr)if err != nil {return nil, fmt.Errorf("failed to parse gain: %w", err)}// Parse battery voltagebatteryV, err := strconv.ParseFloat(batteryStr, 64)if err != nil {return nil, fmt.Errorf("failed to parse battery voltage: %w", err)}// Parse temperaturetempC, err := strconv.ParseFloat(tempStr, 64)if err != nil {return nil, fmt.Errorf("failed to parse temperature: %w", err)}return &AudioMothData{Timestamp: timestamp,RecorderID: recorderID,Gain: gain,BatteryV: batteryV,TempC: tempC,}, nil}// parseLegacyComment parses older AudioMoth comment format (space-separated)// Example: "Recorded at 21:00:00 24/02/2025 (UTC+13) by AudioMoth 248AB50153AB0549 at medium gain while battery was 4.3V and temperature was 15.8C."func parseLegacyComment(comment string) (*AudioMothData, error) {parts := strings.Fields(comment)if len(parts) < 10 {return nil, fmt.Errorf("comment has insufficient parts (got %d, need at least 10)", len(parts))}// 0-based indices after split by space:// parts[2] = "21:00:00" (time HH:MM:SS)// parts[3] = "24/02/2025" (date DD/MM/YYYY)// parts[4] = "(UTC+13)" (timezone offset)// parts[7] = "248AB50153AB0549" (moth ID)// parts[9] = "medium" (gain)// parts[len-5] = "4.3V" (battery voltage)// parts[len-1] = "15.8C." (temperature)timeStr := parts[2]dateStr := parts[3]timezoneStr := strings.Trim(parts[4], "()")recorderID := parts[7]gainStr := parts[9]// Parse timestamptimestamp, err := parseAudioMothTimestamp(timeStr, dateStr, timezoneStr)if err != nil {return nil, fmt.Errorf("failed to parse timestamp: %w", err)}// Parse gaingain, err := parseGainLevel(gainStr)if err != nil {return nil, fmt.Errorf("failed to parse gain: %w", err)}// Parse battery voltage (e.g., "4.3V")batteryStr := parts[len(parts)-5]batteryStr = strings.TrimSuffix(batteryStr, "V")batteryV, err := strconv.ParseFloat(batteryStr, 64)if err != nil {return nil, fmt.Errorf("failed to parse battery voltage: %w", err)}// Parse temperature (e.g., "15.8C." or "15.8C")tempStr := parts[len(parts)-1]tempStr = strings.TrimSuffix(tempStr, ".")tempStr = strings.TrimSuffix(tempStr, "C")tempC, err := strconv.ParseFloat(tempStr, 64)if err != nil {return nil, fmt.Errorf("failed to parse temperature: %w", err)}return &AudioMothData{Timestamp: timestamp,RecorderID: recorderID,Gain: gain,BatteryV: batteryV,TempC: tempC,}, nil}// parseAudioMothTimestamp parses AudioMoth timestamp from time, date, and timezone strings// timeStr: "HH:MM:SS"// dateStr: "DD/MM/YYYY"// timezoneStr: "UTC+13" or "+13"func parseAudioMothTimestamp(timeStr, dateStr, timezoneStr string) (time.Time, error) {// Parse time componentstimeParts := strings.Split(timeStr, ":")if len(timeParts) != 3 {return time.Time{}, fmt.Errorf("invalid time format: %s", timeStr)}hour, _ := strconv.Atoi(timeParts[0])minute, _ := strconv.Atoi(timeParts[1])second, _ := strconv.Atoi(timeParts[2])// Parse date componentsdateParts := strings.Split(dateStr, "/")if len(dateParts) != 3 {return time.Time{}, fmt.Errorf("invalid date format: %s", dateStr)}day, _ := strconv.Atoi(dateParts[0])month, _ := strconv.Atoi(dateParts[1])year, _ := strconv.Atoi(dateParts[2])// Parse timezone offsettimezoneStr = strings.TrimPrefix(timezoneStr, "UTC")offsetHours, err := strconv.Atoi(timezoneStr)if err != nil {return time.Time{}, fmt.Errorf("invalid timezone offset: %s", timezoneStr)}// Create fixed timezone locationoffsetSeconds := offsetHours * 3600loc := time.FixedZone(fmt.Sprintf("UTC%+d", offsetHours), offsetSeconds)// Construct timestamptimestamp := time.Date(year, time.Month(month), day, hour, minute, second, 0, loc)return timestamp, nil}// parseGainLevel converts string gain level to GainLevel enumfunc parseGainLevel(gainStr string) (db.GainLevel, error) {gainStr = strings.ToLower(strings.TrimSpace(gainStr))switch gainStr {case "low":return db.GainLow, nilcase "low-medium":return db.GainLowMedium, nilcase "medium":return db.GainMedium, nilcase "medium-high":return db.GainMediumHigh, nilcase "high":return db.GainHigh, nildefault:return "", fmt.Errorf("unknown gain level: %s", gainStr)}}
package utilsimport ("bytes""encoding/binary""math""sync""github.com/ebitengine/oto/v3")// AudioPlayer wraps oto for simple audio playback.// The oto context is created once and reused across plays.type AudioPlayer struct {ctx *oto.Contextmu sync.Mutexplayer *oto.Player}// NewAudioPlayer creates a new audio player with the given sample rate.// Only one AudioPlayer should exist per process (oto allows one context).func NewAudioPlayer(sampleRate int) (*AudioPlayer, error) {op := &oto.NewContextOptions{SampleRate: sampleRate,ChannelCount: 1,Format: oto.FormatSignedInt16LE,}ctx, readyChan, err := oto.NewContext(op)if err != nil {return nil, err}<-readyChanreturn &AudioPlayer{ctx: ctx}, nil}// Play stops any current playback and starts playing the given samples.// Samples are float64 in the range -1.0 to 1.0.// Playback is non-blocking — audio plays in the background.func (ap *AudioPlayer) Play(samples []float64, sampleRate int) {ap.PlayAtSpeed(samples, sampleRate, 1.0)}// PlayAtSpeed plays samples at the given speed (1.0 = normal, 0.5 = half speed).// Speed change is achieved by resampling the audio.// Playback is non-blocking — audio plays in the background.func (ap *AudioPlayer) PlayAtSpeed(samples []float64, sampleRate int, speed float64) {ap.mu.Lock()defer ap.mu.Unlock()// Stop previous playbackif ap.player != nil {ap.player.Pause()ap.player = nil}// Resample if speed is not normalif speed != 1.0 {samples = Resample(samples, speed)}// Convert float64 samples to signed int16 LE bytesbuf := make([]byte, len(samples)*2)for i, s := range samples {// Clamp to [-1.0, 1.0]if s > 1.0 {s = 1.0} else if s < -1.0 {s = -1.0}v := int16(math.Round(s * 32767.0))binary.LittleEndian.PutUint16(buf[i*2:], uint16(v))}ap.player = ap.ctx.NewPlayer(bytes.NewReader(buf))ap.player.Play()}// IsPlaying returns true if audio is currently playing.func (ap *AudioPlayer) IsPlaying() bool {ap.mu.Lock()defer ap.mu.Unlock()return ap.player != nil && ap.player.IsPlaying()}// Stop stops any current playback.func (ap *AudioPlayer) Stop() {ap.mu.Lock()defer ap.mu.Unlock()if ap.player != nil {ap.player.Pause()ap.player = nil}}// Close stops playback and releases the oto context.func (ap *AudioPlayer) Close() {ap.Stop()}
package utilsimport ("testing""time")// Test location: Auckland, New Zealand (approx coordinates)var testLocationAuckland = struct {lat float64lon float64}{lat: -36.8485,lon: 174.7633,}// Test location: London, UKvar testLocationLondon = struct {lat float64lon float64}{lat: 51.5074,lon: -0.1278,}func TestCalculateAstronomicalData(t *testing.T) {t.Run("should return valid types for all fields", func(t *testing.T) {// Winter midnight in Auckland (should be solar night)winterMidnight := parseTime(t, "2024-06-15T12:00:00Z") // UTC midnight = noon in Auckland (winter)duration := 60.0 // 1 minuteresult := CalculateAstronomicalData(winterMidnight, duration, testLocationAuckland.lat, testLocationAuckland.lon)// Check types existif result.MoonPhase < 0 || result.MoonPhase > 1 {t.Errorf("MoonPhase out of range: got %f, want 0-1", result.MoonPhase)}})t.Run("should return false for solar night during daytime hours", func(t *testing.T) {// Summer midday in Auckland (should NOT be solar night)summerMidday := parseTime(t, "2024-12-15T00:00:00Z") // UTC midnight = noon in Auckland (summer)duration := 60.0 // 1 minuteresult := CalculateAstronomicalData(summerMidday, duration, testLocationAuckland.lat, testLocationAuckland.lon)// During summer midday, should NOT be solar nightif result.SolarNight {t.Error("Expected SolarNight to be false during daytime")}if result.CivilNight {t.Error("Expected CivilNight to be false during daytime")}})t.Run("should handle different durations correctly", func(t *testing.T) {timestamp := parseTime(t, "2024-06-15T10:00:00Z")shortDuration := 30.0 // 30 secondslongDuration := 3600.0 // 1 hourshortResult := CalculateAstronomicalData(timestamp, shortDuration, testLocationAuckland.lat, testLocationAuckland.lon)longResult := CalculateAstronomicalData(timestamp, longDuration, testLocationAuckland.lat, testLocationAuckland.lon)// Both should have valid resultsif shortResult.MoonPhase < 0 || shortResult.MoonPhase > 1 {t.Errorf("Short duration moon phase out of range: %f", shortResult.MoonPhase)}if longResult.MoonPhase < 0 || longResult.MoonPhase > 1 {t.Errorf("Long duration moon phase out of range: %f", longResult.MoonPhase)}})t.Run("should calculate midpoint time correctly", func(t *testing.T) {// Test that the calculation uses the midpoint, not the start timestartTime := parseTime(t, "2024-06-15T10:00:00Z")duration := 7200.0 // 2 hours (midpoint would be 1 hour later)result := CalculateAstronomicalData(startTime, duration, testLocationAuckland.lat, testLocationAuckland.lon)// Should calculate based on 11:00 UTC, not 10:00 UTC// Just verify we get valid boolean results_ = result.SolarNight_ = result.CivilNight})t.Run("should handle different geographical locations", func(t *testing.T) {timestamp := parseTime(t, "2024-06-15T12:00:00Z") // UTC noonduration := 60.0aucklandResult := CalculateAstronomicalData(timestamp, duration, testLocationAuckland.lat, testLocationAuckland.lon)londonResult := CalculateAstronomicalData(timestamp, duration, testLocationLondon.lat, testLocationLondon.lon)// Both should have valid boolean results (don't compare values, just that they're boolean)_ = aucklandResult.SolarNight_ = londonResult.SolarNight// Results might differ due to different timezones and seasons// Auckland: UTC noon = midnight local (winter) = likely night// London: UTC noon = 1pm local (summer) = likely day})t.Run("should return valid moon phase values", func(t *testing.T) {timestamp := parseTime(t, "2024-06-15T12:00:00Z")duration := 60.0result := CalculateAstronomicalData(timestamp, duration, testLocationAuckland.lat, testLocationAuckland.lon)if result.MoonPhase < 0 || result.MoonPhase > 1 {t.Errorf("MoonPhase out of range: got %f, want 0-1", result.MoonPhase)}})t.Run("should handle edge cases with very short durations", func(t *testing.T) {timestamp := parseTime(t, "2024-06-15T12:00:00Z")duration := 0.1 // 0.1 secondsresult := CalculateAstronomicalData(timestamp, duration, testLocationAuckland.lat, testLocationAuckland.lon)if result.MoonPhase < 0 || result.MoonPhase > 1 {t.Errorf("MoonPhase out of range: got %f, want 0-1", result.MoonPhase)}})t.Run("should handle edge cases with very long durations", func(t *testing.T) {timestamp := parseTime(t, "2024-06-15T12:00:00Z")duration := 86400.0 // 24 hoursresult := CalculateAstronomicalData(timestamp, duration, testLocationAuckland.lat, testLocationAuckland.lon)if result.MoonPhase < 0 || result.MoonPhase > 1 {t.Errorf("MoonPhase out of range: got %f, want 0-1", result.MoonPhase)}})}func TestBooleanLogicValidation(t *testing.T) {t.Run("should never return invalid values for valid inputs", func(t *testing.T) {testCases := []string{"2024-06-15T06:00:00Z", // Dawn/dusk time"2024-06-15T12:00:00Z", // Midday/midnight"2024-06-15T18:00:00Z", // Evening/morning"2024-12-15T06:00:00Z", // Summer dawn/dusk"2024-12-15T12:00:00Z", // Summer midday/midnight"2024-12-15T18:00:00Z", // Summer evening/morning}for _, timestamp := range testCases {t.Run(timestamp, func(t *testing.T) {ts := parseTime(t, timestamp)result := CalculateAstronomicalData(ts, 60, testLocationAuckland.lat, testLocationAuckland.lon)// These should be proper boolean types_ = result.SolarNight_ = result.CivilNight// MoonPhase should be in valid rangeif result.MoonPhase < 0 || result.MoonPhase > 1 {t.Errorf("MoonPhase out of range: got %f, want 0-1", result.MoonPhase)}})}})t.Run("should return false for daytime recordings", func(t *testing.T) {// Test a known daytime period in Auckland (summer midday UTC)summerMidday := parseTime(t, "2024-12-15T00:30:00Z") // Should be daytime in Aucklandduration := 60.0result := CalculateAstronomicalData(summerMidday, duration, testLocationAuckland.lat, testLocationAuckland.lon)// The key test: false values should remain falseif result.SolarNight && result.CivilNight {// This would be unexpected during middayt.Logf("Note: Both SolarNight and CivilNight are true (may be valid depending on season)")}})t.Run("should return true for nighttime recordings", func(t *testing.T) {// Test a known nighttime period in Auckland (winter midnight UTC)winterMidnight := parseTime(t, "2024-06-15T12:30:00Z") // Should be nighttime in Aucklandduration := 60.0result := CalculateAstronomicalData(winterMidnight, duration, testLocationAuckland.lat, testLocationAuckland.lon)// The key test: true values should remain true_ = result.SolarNight_ = result.CivilNight})}func TestCalculateMidpointTime(t *testing.T) {t.Run("should calculate midpoint correctly", func(t *testing.T) {startTime := parseTime(t, "2024-06-15T10:00:00Z")duration := 3600.0 // 1 hourmidpoint := CalculateMidpointTime(startTime, duration)expected := parseTime(t, "2024-06-15T10:30:00Z")if !midpoint.Equal(expected) {t.Errorf("Midpoint incorrect: got %v, want %v", midpoint, expected)}})t.Run("should handle short durations", func(t *testing.T) {startTime := parseTime(t, "2024-06-15T10:00:00Z")duration := 10.0 // 10 secondsmidpoint := CalculateMidpointTime(startTime, duration)expected := parseTime(t, "2024-06-15T10:00:05Z")if !midpoint.Equal(expected) {t.Errorf("Midpoint incorrect: got %v, want %v", midpoint, expected)}})}// Helper function to parse time stringsfunc parseTime(t *testing.T, s string) time.Time {t.Helper()parsed, err := time.Parse(time.RFC3339, s)if err != nil {t.Fatalf("Failed to parse time %s: %v", s, err)}return parsed}
package utilsimport ("time""github.com/sixdouglas/suncalc")// AstronomicalData contains calculated astronomical data for a recordingtype AstronomicalData struct {SolarNight bool // True if recording midpoint is between sunset and sunriseCivilNight bool // True if recording midpoint is between dusk and dawn (6° below horizon)MoonPhase float64 // 0.00=New Moon, 0.25=First Quarter, 0.50=Full Moon, 0.75=Last Quarter}// CalculateAstronomicalData calculates astronomical data for a recording.// Uses the recording MIDPOINT time (not start time) for calculations.//// Parameters:// - timestampUTC: Recording start time in UTC// - durationSec: Recording duration in seconds// - lat, lon: Location coordinates in decimal degrees//// Returns:// - solarNight: true if recording midpoint is between sunset and sunrise// - civilNight: true if recording midpoint is between dusk and dawn// - moonPhase: 0.00-1.00 representing moon phase (0=New, 0.5=Full)func CalculateAstronomicalData(timestampUTC time.Time,durationSec float64,lat, lon float64,) AstronomicalData {// Calculate recording MIDPOINT (not start time)midpoint := timestampUTC.Add(time.Duration(durationSec/2) * time.Second)// Get solar times for midpoint datetimes := suncalc.GetTimes(midpoint, lat, lon)// Solar night: between sunset and sunrise// Note: Handle day/night transitions properlysunrise := times[suncalc.Sunrise].Valuesunset := times[suncalc.Sunset].ValuesolarNight := isBetweenSunTimes(midpoint, sunset, sunrise)// Civil night: between dusk and dawn (6° below horizon)dawn := times[suncalc.Dawn].Valuedusk := times[suncalc.Dusk].ValuecivilNight := isBetweenSunTimes(midpoint, dusk, dawn)// Moon phase: 0.00=New Moon, 0.25=First Quarter, 0.50=Full Moon, 0.75=Last QuartermoonIllum := suncalc.GetMoonIllumination(midpoint)moonPhase := moonIllum.Phasereturn AstronomicalData{SolarNight: solarNight,CivilNight: civilNight,MoonPhase: moonPhase,}}// isBetweenSunTimes determines if a time is between sunset/dusk and sunrise/dawn// Handles the case where the night period crosses midnightfunc isBetweenSunTimes(t, evening, morning time.Time) bool {// If evening time is before morning time (normal case: both on same day)// Then we're NOT in night period (daytime)if evening.Before(morning) {return false}// Otherwise, night period crosses midnight// Night is: after evening OR before morningreturn t.After(evening) || t.Before(morning)}// CalculateMidpointTime calculates the midpoint time of a recordingfunc CalculateMidpointTime(startTime time.Time, durationSec float64) time.Time {return startTime.Add(time.Duration(durationSec/2) * time.Second)}
package tuiimport ("fmt""image""os""path/filepath""sort""strings""time"tea "charm.land/bubbletea/v2""charm.land/lipgloss/v2""skraak/tools""skraak/utils")// playbackTickMsg is sent every 50ms while audio is playingtype playbackTickMsg struct{}// Stylesvar (titleStyle = lipgloss.NewStyle().Bold(true).Foreground(lipgloss.Color("15")).Background(lipgloss.Color("62")).Padding(0, 1)labelStyle = lipgloss.NewStyle().Foreground(lipgloss.Color("86"))errorStyle = lipgloss.NewStyle().Foreground(lipgloss.Color("196"))helpStyle = lipgloss.NewStyle().Foreground(lipgloss.Color("241"))helpDarkStyle = lipgloss.NewStyle().Foreground(lipgloss.Color("86"))commentBoxStyle = lipgloss.NewStyle().Border(lipgloss.RoundedBorder()).BorderForeground(lipgloss.Color("62")).Padding(0, 1))// wrapText wraps text at word boundaries to fit within maxWidth.// Returns multiple lines joined with newlines.func wrapText(text string, maxWidth int) string {if len(text) <= maxWidth {return text}lines := strings.Split(text, "\n")var result []stringfor _, line := range lines {if len(line) <= maxWidth {result = append(result, line)continue}// Wrap at word boundarieswords := strings.Fields(line)var currentLine stringfor _, word := range words {if len(currentLine)+len(word)+1 <= maxWidth {if currentLine == "" {currentLine = word} else {currentLine += " " + word}} else {if currentLine != "" {result = append(result, currentLine)}// If single word is longer than maxWidth, force break itif len(word) > maxWidth {result = append(result, word[:maxWidth])word = word[maxWidth:]}currentLine = word}}if currentLine != "" {result = append(result, currentLine)}}return strings.Join(result, "\n")}// Model holds TUI statetype Model struct {state *tools.ClassifyStateerr stringquitting boolbindingsHelp string // pre-computed bindings text// Comment dialog statecommentMode bool // true when comment dialog is opencommentText string // current input textcommentCursor int // cursor position in comment text// Clip dialog stateclipMode bool // true when clip dialog is openclipInput string // current prefix input// Shift+primary wait mode: when non-empty, the next keypress is looked up// in Config.SecondaryBindings[awaitingSecondaryFor] as a calltype key.awaitingSecondaryFor string// Image generation counter - incremented on each segment change,// used to discard stale inline images (sixel/iTerm).// Pointer so it survives BubbleTea's value-copy update cycle.imageGen *uint64}// New creates a new TUI modelfunc New(state *tools.ClassifyState) Model {// Pre-compute bindings help text, sorted letters a-z then digits 0-9// (other single-char keys sorted after).sorted := make([]tools.KeyBinding, len(state.Config.Bindings))copy(sorted, state.Config.Bindings)keyRank := func(k string) int {if len(k) == 0 {return 3}c := k[0]switch {case c >= 'a' && c <= 'z':return 0case c >= 'A' && c <= 'Z':return 1case c >= '0' && c <= '9':return 2default:return 3}}sort.SliceStable(sorted, func(i, j int) bool {ri, rj := keyRank(sorted[i].Key), keyRank(sorted[j].Key)if ri != rj {return ri < rj}return sorted[i].Key < sorted[j].Key})var bindings []stringfor _, b := range sorted {if b.CallType != "" {bindings = append(bindings, fmt.Sprintf("%s=%s/%s", b.Key, b.Species, b.CallType))} else {bindings = append(bindings, fmt.Sprintf("%s=%s", b.Key, b.Species))}}bindingsHelp := strings.Join(bindings, " ")gen := uint64(0)return Model{state: state,bindingsHelp: bindingsHelp,imageGen: &gen,}}func (m Model) protocol() utils.ImageProtocol {if m.state.Config.ITerm {return utils.ProtocolITerm}if m.state.Config.Sixel {return utils.ProtocolSixel}return utils.ProtocolKitty}// Init initializes the modelfunc (m Model) Init() tea.Cmd {return inlineImageCmd(m.state, m.protocol(), *m.imageGen, m.imageGen)}// Update handles messagesfunc (m Model) Update(msg tea.Msg) (tea.Model, tea.Cmd) {switch msg := msg.(type) {case tea.KeyPressMsg:return m.handleKey(msg)case playbackTickMsg:if m.state.Player == nil || !m.state.Player.IsPlaying() {return m, nil // done, triggers re-render to clear "Playing..." text}return m, playbackTick()}return m, nil}// segmentChangeCmd returns the appropriate command after a segment change.// Clears screen then generates and writes the spectrogram image asynchronously.func (m Model) segmentChangeCmd() tea.Cmd {(*m.imageGen)++gen := *m.imageGenreturn tea.Sequence(tea.ClearScreen, inlineImageCmd(m.state, m.protocol(), gen, m.imageGen))}func (m Model) handleKey(msg tea.KeyPressMsg) (tea.Model, tea.Cmd) {// If in comment mode, route to comment handlerif m.commentMode {return m.handleCommentKey(msg)}// If in clip mode, route to clip handlerif m.clipMode {return m.handleClipKey(msg)}m.err = ""key := msg.Key()// Secondary-wait mode: next keypress is interpreted as a calltype key// for the species we just labeled via Shift+primary.if m.awaitingSecondaryFor != "" {primary := m.awaitingSecondaryForm.awaitingSecondaryFor = ""// Esc cancels wait mode; species stays labeled without calltype,// segment does not advance.if key.Code == tea.KeyEscape || key.Code == tea.KeyEsc {return m, nil}s := msg.String()if len(s) == 1 {if callType, ok := m.state.Config.SecondaryBindings[primary][s]; ok {if m.state.Player != nil {m.state.Player.Stop()}m.state.ApplyCallTypeOnly(callType)if err := m.state.Save(); err != nil {m.err = err.Error()}if !m.state.NextSegment() {m.quitting = truereturn m, tea.Quit}return m, m.segmentChangeCmd()}}// Unknown key — fall through to normal handling of this keypress.}// Handle Enter key (main or numpad, check code to catch modifiers)if key.Code == tea.KeyEnter || key.Code == tea.KeyKpEnter {speed := 1.0if key.Mod&tea.ModShift != 0 {speed = 0.5}if errMsg := playCurrentSegmentAtSpeed(m.state, speed); errMsg != "" {m.err = errMsg}return m, playbackTick()}// Check for Escape key for quitif key.Code == tea.KeyEscape || key.Code == tea.KeyEsc {if m.state.Player != nil {m.state.Player.Stop()}m.quitting = truereturn m, tea.Quit}// Check for Space key (open comment dialog)if key.Code == tea.KeySpace {m.commentText = m.state.GetCurrentComment()m.commentCursor = len(m.commentText) // start at endm.commentMode = truereturn m, nil}// Check for Ctrl+S (save clip dialog)if msg.String() == "ctrl+s" {m.clipInput = ""m.clipMode = truereturn m, nil}switch msg.String() {case "ctrl+c":if m.state.Player != nil {m.state.Player.Stop()}m.quitting = truereturn m, tea.Quitcase ",", "left":// Previous segmentif m.state.Player != nil {m.state.Player.Stop()}m.state.PrevSegment()return m, m.segmentChangeCmd()case ".", "right":// Next segment (no edit)if m.state.Player != nil {m.state.Player.Stop()}if !m.state.NextSegment() {m.quitting = truereturn m, tea.Quit}return m, m.segmentChangeCmd()case "ctrl+d":// Toggle bookmarkm.state.ToggleBookmark()if err := m.state.Save(); err != nil {m.err = err.Error()}return m, nilcase "ctrl+,":// Previous bookmarkif m.state.Player != nil {m.state.Player.Stop()}if m.state.PrevBookmark() {return m, m.segmentChangeCmd()}m.err = "No bookmarks found"return m, nilcase "ctrl+.":// Next bookmarkif m.state.Player != nil {m.state.Player.Stop()}if m.state.NextBookmark() {return m, m.segmentChangeCmd()}m.err = "No bookmarks found"return m, nilcase "0":// Confirm existing label (upgrade certainty to 100)if m.state.Player != nil {m.state.Player.Stop()}if m.state.ConfirmLabel() {if err := m.state.Save(); err != nil {m.err = err.Error()return m, nil}}if !m.state.NextSegment() {m.quitting = truereturn m, tea.Quit}return m, m.segmentChangeCmd()default:// Check for bindings := msg.String()if len(s) == 1 {k := s// Shift+letter: if the lowercase primary has secondary bindings,// label species-only and enter wait mode. Otherwise map to the// lowercase equivalent and dispatch as a normal primary keypress.if key.Mod&tea.ModShift != 0 {lower := strings.ToLower(s)if lower != s {if m.state.HasSecondary(lower) {if result := m.state.ParseKeyBuffer(lower); result != nil {if m.state.Player != nil {m.state.Player.Stop()}m.state.ApplyBinding(&tools.BindingResult{Species: result.Species})if err := m.state.Save(); err != nil {m.err = err.Error()}m.awaitingSecondaryFor = lowerreturn m, nil}}k = lower}}if result := m.state.ParseKeyBuffer(k); result != nil {if m.state.Player != nil {m.state.Player.Stop()}m.state.ApplyBinding(result)if err := m.state.Save(); err != nil {m.err = err.Error()}if !m.state.NextSegment() {m.quitting = truereturn m, tea.Quit}return m, m.segmentChangeCmd()}}return m, nil}}// handleCommentKey handles key presses in comment modefunc (m Model) handleCommentKey(msg tea.KeyPressMsg) (tea.Model, tea.Cmd) {key := msg.Key()// Enter: save commentif key.Code == tea.KeyEnter {m.state.SetComment(m.commentText)if err := m.state.Save(); err != nil {m.err = err.Error()}m.commentMode = falsereturn m, nil}// Escape: cancelif key.Code == tea.KeyEscape || key.Code == tea.KeyEsc {m.commentMode = falsereturn m, nil}// Navigation and editing keys (check by code, not string)switch key.Code {case tea.KeyLeft:if m.commentCursor > 0 {m.commentCursor--}return m, nilcase tea.KeyRight:if m.commentCursor < len(m.commentText) {m.commentCursor++}return m, nilcase tea.KeySpace:if len(m.commentText) < 140 {m.commentText = m.commentText[:m.commentCursor] + " " + m.commentText[m.commentCursor:]m.commentCursor++}return m, nilcase tea.KeyBackspace:if m.commentCursor > 0 {m.commentText = m.commentText[:m.commentCursor-1] + m.commentText[m.commentCursor:]m.commentCursor--}return m, nilcase tea.KeyDelete:if m.commentCursor < len(m.commentText) {m.commentText = m.commentText[:m.commentCursor] + m.commentText[m.commentCursor+1:]}return m, nil}// Handle via string representation for ctrl combosswitch msg.String() {case "ctrl+u":m.commentText = ""m.commentCursor = 0return m, nilcase "ctrl+a":m.commentCursor = 0return m, nilcase "ctrl+e":m.commentCursor = len(m.commentText)return m, nil}// Printable ASCII character (space handled above via KeySpace)s := msg.String()if len(s) == 1 && s[0] >= 33 && s[0] <= 126 { // 33='!', 126='~' (space=32 handled above)if len(m.commentText) < 140 {m.commentText = m.commentText[:m.commentCursor] + s + m.commentText[m.commentCursor:]m.commentCursor++}return m, nil}return m, nil}// handleClipKey handles key presses in clip modefunc (m Model) handleClipKey(msg tea.KeyPressMsg) (tea.Model, tea.Cmd) {key := msg.Key()// Enter: save clipif key.Code == tea.KeyEnter {if m.clipInput == "" {m.clipMode = falsereturn m, nil}// Save the cliperr := saveClip(m.state, m.clipInput)if err != nil {m.err = err.Error()} else {m.err = "Clip saved: " + m.clipInput}m.clipMode = falsereturn m, nil}// Escape: cancelif key.Code == tea.KeyEscape || key.Code == tea.KeyEsc {m.clipMode = falsereturn m, nil}// Backspace: remove last characterif key.Code == tea.KeyBackspace {if len(m.clipInput) > 0 {m.clipInput = m.clipInput[:len(m.clipInput)-1]}return m, nil}// Printable characters: append to inputs := msg.String()if len(s) == 1 && s[0] >= 32 && s[0] <= 126 { // printable ASCIIif len(m.clipInput) < 64 {m.clipInput += s}return m, nil}return m, nil}// saveClip saves a clip of the current segment to the current working directoryfunc saveClip(state *tools.ClassifyState, prefix string) error {df := state.CurrentFile()seg := state.CurrentSegment()if df == nil || seg == nil {return fmt.Errorf("no segment selected")}// Get WAV pathwavPath := strings.TrimSuffix(df.FilePath, ".data")// Get basename without path and extensionbasename := wavPath[strings.LastIndex(wavPath, "/")+1:]basename = strings.TrimSuffix(basename, ".wav")// Calculate integer times for filenamestartInt := int(seg.StartTime)endInt := int(seg.EndTime)if seg.EndTime > float64(endInt) {endInt++ // ceil}// Build output paths (current working directory)cwd, err := os.Getwd()if err != nil {return fmt.Errorf("failed to get working directory: %w", err)}baseName := fmt.Sprintf("%s_%s_%d_%d", prefix, basename, startInt, endInt)pngPath := filepath.Join(cwd, baseName+".png")wavOutPath := filepath.Join(cwd, baseName+".wav")// Check if files already existif _, err := os.Stat(pngPath); err == nil {return fmt.Errorf("file already exists: %s", pngPath)}if _, err := os.Stat(wavOutPath); err == nil {return fmt.Errorf("file already exists: %s", wavOutPath)}// Read WAV samplessamples, sampleRate, err := utils.ReadWAVSamples(wavPath)if err != nil {return fmt.Errorf("failed to read WAV: %w", err)}// Extract segment samplessegSamples := utils.ExtractSegmentSamples(samples, sampleRate, seg.StartTime, seg.EndTime)if len(segSamples) == 0 {return fmt.Errorf("no samples in segment")}// Determine output sample rate (downsample if > 16kHz)outputSampleRate := sampleRateif sampleRate > utils.DefaultMaxSampleRate {segSamples = utils.ResampleRate(segSamples, sampleRate, utils.DefaultMaxSampleRate)outputSampleRate = utils.DefaultMaxSampleRate}// Generate spectrogram (224px, color)config := utils.DefaultSpectrogramConfig(outputSampleRate)spectrogram := utils.GenerateSpectrogram(segSamples, config)if spectrogram == nil {return fmt.Errorf("failed to generate spectrogram")}colorData := utils.ApplyL4Colormap(spectrogram)img := utils.CreateRGBImage(colorData)if img == nil {return fmt.Errorf("failed to create image")}resized := utils.ResizeImage(img, 224, 224)// Write PNGpngFile, err := os.Create(pngPath)if err != nil {return fmt.Errorf("failed to create PNG: %w", err)}if err := utils.WritePNG(resized, pngFile); err != nil {_ = pngFile.Close()return fmt.Errorf("failed to write PNG: %w", err)}if err := pngFile.Close(); err != nil {return fmt.Errorf("failed to close PNG: %w", err)}// Write WAVif err := utils.WriteWAVFile(wavOutPath, segSamples, outputSampleRate); err != nil {return fmt.Errorf("failed to write WAV: %w", err)}return nil}// playCurrentSegmentAtSpeed loads and plays the current segment's audio at the given speed.// speed=1.0 is normal, speed=0.5 is half speed.// Returns an error message string, or empty string on success.func playCurrentSegmentAtSpeed(state *tools.ClassifyState, speed float64) string {df := state.CurrentFile()seg := state.CurrentSegment()if df == nil || seg == nil {return ""}wavPath := strings.TrimSuffix(df.FilePath, ".data")samples, sampleRate, err := utils.ReadWAVSamples(wavPath)if err != nil {return fmt.Sprintf("audio: %v", err)}// Initialize player lazily on first playif state.Player == nil {player, err := utils.NewAudioPlayer(sampleRate)if err != nil {return fmt.Sprintf("audio init: %v", err)}state.Player = player}segSamples := utils.ExtractSegmentSamples(samples, sampleRate, seg.StartTime, seg.EndTime)if len(segSamples) > 0 {state.PlaybackSpeed = speedstate.Player.PlayAtSpeed(segSamples, sampleRate, speed)}return ""}// playbackTick returns a command that sends a playbackTickMsg after 50ms.func playbackTick() tea.Cmd {return tea.Tick(50*time.Millisecond, func(t time.Time) tea.Msg {return playbackTickMsg{}})}// View renders the TUIfunc (m Model) View() tea.View {if m.quitting {var b strings.Builder_ = utils.ClearImages(&b, m.protocol())b.WriteString("\nDone!\n")return tea.NewView(b.String())}var b strings.Builder// Header: file infodf := m.state.CurrentFile()seg := m.state.CurrentSegment()total := m.state.TotalSegments()current := m.state.CurrentSegmentNumber()if df == nil || seg == nil {return tea.NewView("\nNo segments to review.\n")}// Bindings help (wrap at 80 chars)const wrapWidth = 80b.WriteString(helpStyle.Render(wrapText(m.bindingsHelp, wrapWidth)))b.WriteString("\n")b.WriteString(helpDarkStyle.Render(wrapText("[esc]quit [,]prev [.]next [0]confirm [space]comment [ctrl+s]clip [ctrl+d]bookmark [ctrl+,]prev-bk [ctrl+.]next-bk [enter]play [shift+enter]½speed", wrapWidth)))b.WriteString("\n\n")// Progress barprogress := float64(current) / float64(total)barWidth := 30filled := int(progress * float64(barWidth))bar := strings.Repeat("█", filled) + strings.Repeat("░", barWidth-filled)// Title linewavFile := strings.TrimSuffix(df.FilePath, ".data")wavFile = wavFile[strings.LastIndex(wavFile, "/")+1:]b.WriteString(titleStyle.Render(fmt.Sprintf(" %s [%s] %d/%d Segments ", wavFile, bar, current, total)))b.WriteString("\n\n")// Segment infosegInfo := fmt.Sprintf("Segment: %.1fs - %.1fs (%.1fs)", seg.StartTime, seg.EndTime, seg.EndTime-seg.StartTime)if m.state.HasBookmark() {segInfo += " [BOOKMARKED]"}if m.awaitingSecondaryFor != "" {segInfo += " Waiting..."}if m.state.Player != nil && m.state.Player.IsPlaying() {if m.state.PlaybackSpeed == 0.5 {segInfo += " ▶ Playing 0.5x..."} else {segInfo += " ▶ Playing..."}}b.WriteString(segInfo)b.WriteString("\n\n")// LabelsfilterLabels := seg.GetFilterLabels(m.state.Config.Filter)if len(filterLabels) > 0 {b.WriteString(labelStyle.Render("Labels:"))b.WriteString("\n")for _, l := range filterLabels {fmt.Fprintf(&b, " • %s\n", tools.FormatLabels([]*utils.Label{l}, m.state.Config.Filter))}}b.WriteString("\n")// Clip dialog (when active)if m.clipMode {m.renderClipDialog(&b)return tea.NewView(b.String())}// Comment dialog (when active)if m.commentMode {m.renderCommentDialog(&b)return tea.NewView(b.String())}// Errorif m.err != "" {b.WriteString(errorStyle.Render(m.err))}v := tea.NewView(b.String())v.AltScreen = truereturn v}// renderCommentDialog renders the comment input dialogfunc (m Model) renderCommentDialog(b *strings.Builder) {// Build input line with cursor at correct positionbefore := m.commentText[:m.commentCursor]after := m.commentText[m.commentCursor:]inputLine := before + "█" + aftercharCount := fmt.Sprintf("%d/140", len(m.commentText))helpLine := "[enter]save [esc]cancel [←→]move [ctrl+u]clear [ctrl+a]start [ctrl+e]end"// Render boxcontent := fmt.Sprintf("Comment:\n%s\n%s\n%s", inputLine, charCount, helpLine)b.WriteString(commentBoxStyle.Render(content))}// renderClipDialog renders the clip prefix input dialogfunc (m Model) renderClipDialog(b *strings.Builder) {inputLine := m.clipInput + "█"helpLine := "[enter]save [esc]cancel"// Render boxcontent := fmt.Sprintf("Clip prefix:\n%s\n%s", inputLine, helpLine)b.WriteString(commentBoxStyle.Render(content))}// generateSpectrogramImage creates a resized spectrogram image from a segment.func generateSpectrogramImage(state *tools.ClassifyState, dataPath string, seg *utils.Segment) image.Image {imgSize := state.Config.ImageSizeif imgSize == 0 {imgSize = utils.SpectrogramDisplaySize}img, err := utils.GenerateSegmentSpectrogram(dataPath, seg.StartTime, seg.EndTime, state.Config.Color, imgSize)if err != nil {return nil}return img}// inlineImageCmd returns a tea.Cmd that generates and writes an inline image// directly to the terminal, bypassing BubbleTea's renderer.// gen is the generation at dispatch time; currentGen points to the live counter.// If they differ when the image is ready, a newer segment change has occurred// and this image is stale — discard it instead of writing.func inlineImageCmd(state *tools.ClassifyState, protocol utils.ImageProtocol, gen uint64, currentGen *uint64) tea.Cmd {return func() tea.Msg {df := state.CurrentFile()seg := state.CurrentSegment()if df == nil || seg == nil {return nil}img := generateSpectrogramImage(state, df.FilePath, seg)if img == nil {return nil}// Discard if a newer segment change has superseded this oneif *currentGen != gen {return nil}// Clear previous kitty images before writing new one.// Terminal write errors during render are non-recoverable; ignore._ = utils.ClearImages(os.Stdout, protocol)_, _ = fmt.Fprint(os.Stdout, "\r\n\r\n")_ = utils.WriteImage(img, os.Stdout, protocol)return nil}}
package toolsimport ("context""os""testing""skraak/db")// setupTestDB creates a temporary database with schema for testingfunc setupTestDB(t *testing.T) (string, func()) {t.Helper()// Create temp file path (but don't create the file - DuckDB will create it)tmpFile, err := os.CreateTemp("", "skraak_update_test_*.duckdb")if err != nil {t.Fatalf("Failed to create temp file: %v", err)}tmpPath := tmpFile.Name()tmpFile.Close()os.Remove(tmpPath) // Remove the empty file so DuckDB can create it fresh// Open database and run schemadatabase, err := db.OpenWriteableDB(tmpPath)if err != nil {t.Fatalf("Failed to open database: %v", err)}// Read and execute schemaschema, err := db.ReadSchemaSQL()if err != nil {database.Close()os.Remove(tmpPath)t.Fatalf("Failed to read schema: %v", err)}statements := db.ExtractDDLStatements(schema)for _, stmt := range statements {// Skip CREATE TABLE AS (ebird_taxonomy_v2024 was removed)if stmt.Type == "CREATE_TABLE_AS" {continue}_, err := database.Exec(stmt.SQL)if err != nil {database.Close()os.Remove(tmpPath)t.Fatalf("Failed to execute DDL: %v\nSQL: %s", err, stmt.SQL)}}database.Close()cleanup := func() {os.Remove(tmpPath)}return tmpPath, cleanup}// TestDatasetUpdatePreservesUnsetFields tests that update only modifies provided fieldsfunc TestDatasetUpdatePreservesUnsetFields(t *testing.T) {dbPath, cleanup := setupTestDB(t)defer cleanup()SetDBPath(dbPath)// Create a dataset with all fieldsname := "Test Dataset"dsType := "train"description := "Original description"createInput := DatasetInput{Name: &name,Type: &dsType,Description: &description,}ctx := context.Background()created, err := CreateOrUpdateDataset(ctx, createInput)if err != nil {t.Fatalf("Failed to create dataset: %v", err)}// Verify initial valuesif created.Dataset.Name != "Test Dataset" {t.Errorf("Expected name 'Test Dataset', got '%s'", created.Dataset.Name)}if created.Dataset.Type != "train" {t.Errorf("Expected type 'train', got '%s'", created.Dataset.Type)}if created.Dataset.Description == nil || *created.Dataset.Description != "Original description" {t.Errorf("Expected description 'Original description', got '%v'", created.Dataset.Description)}// Update only the description (nil for other fields)newDesc := "Updated description only"updateInput := DatasetInput{ID: &created.Dataset.ID,Description: &newDesc,// Name and Type are nil - should be preserved}updated, err := CreateOrUpdateDataset(ctx, updateInput)if err != nil {t.Fatalf("Failed to update dataset: %v", err)}// Verify only description changedif updated.Dataset.Name != "Test Dataset" {t.Errorf("Name should be preserved, got '%s'", updated.Dataset.Name)}if updated.Dataset.Type != "train" {t.Errorf("Type should be preserved, got '%s'", updated.Dataset.Type)}if updated.Dataset.Description == nil || *updated.Dataset.Description != "Updated description only" {t.Errorf("Description should be updated, got '%v'", updated.Dataset.Description)}}// TestLocationUpdatePreservesUnsetFields tests that update only modifies provided fieldsfunc TestLocationUpdatePreservesUnsetFields(t *testing.T) {dbPath, cleanup := setupTestDB(t)defer cleanup()SetDBPath(dbPath)// Create a dataset firstdsName := "Test Dataset"dsCreated, err := CreateOrUpdateDataset(context.Background(), DatasetInput{Name: &dsName})if err != nil {t.Fatalf("Failed to create dataset: %v", err)}// Create a location with all fieldsname := "Test Location"lat := -36.85lon := 174.76tz := "Pacific/Auckland"description := "Original description"createInput := LocationInput{DatasetID: &dsCreated.Dataset.ID,Name: &name,Latitude: &lat,Longitude: &lon,TimezoneID: &tz,Description: &description,}ctx := context.Background()created, err := CreateOrUpdateLocation(ctx, createInput)if err != nil {t.Fatalf("Failed to create location: %v", err)}// Verify initial valuesif created.Location.Name != "Test Location" {t.Errorf("Expected name 'Test Location', got '%s'", created.Location.Name)}if created.Location.TimezoneID != "Pacific/Auckland" {t.Errorf("Expected timezone 'Pacific/Auckland', got '%s'", created.Location.TimezoneID)}// Update only the description (nil for other fields)newDesc := "Updated description only"updateInput := LocationInput{ID: &created.Location.ID,Description: &newDesc,// Name, Latitude, Longitude, TimezoneID are nil - should be preserved}updated, err := CreateOrUpdateLocation(ctx, updateInput)if err != nil {t.Fatalf("Failed to update location: %v", err)}// Verify only description changedif updated.Location.Name != "Test Location" {t.Errorf("Name should be preserved, got '%s'", updated.Location.Name)}if updated.Location.Latitude != -36.85 {t.Errorf("Latitude should be preserved, got %f", updated.Location.Latitude)}if updated.Location.Longitude != 174.76 {t.Errorf("Longitude should be preserved, got %f", updated.Location.Longitude)}if updated.Location.TimezoneID != "Pacific/Auckland" {t.Errorf("TimezoneID should be preserved, got '%s'", updated.Location.TimezoneID)}if updated.Location.Description == nil || *updated.Location.Description != "Updated description only" {t.Errorf("Description should be updated, got '%v'", updated.Location.Description)}}// TestClusterUpdatePreservesUnsetFields tests that update only modifies provided fieldsfunc TestClusterUpdatePreservesUnsetFields(t *testing.T) {dbPath, cleanup := setupTestDB(t)defer cleanup()SetDBPath(dbPath)// Create dataset and locationdsName := "Test Dataset"dsCreated, err := CreateOrUpdateDataset(context.Background(), DatasetInput{Name: &dsName})if err != nil {t.Fatalf("Failed to create dataset: %v", err)}locName := "Test Location"lat, lon := -36.85, 174.76tz := "Pacific/Auckland"locCreated, err := CreateOrUpdateLocation(context.Background(), LocationInput{DatasetID: &dsCreated.Dataset.ID,Name: &locName,Latitude: &lat,Longitude: &lon,TimezoneID: &tz,})if err != nil {t.Fatalf("Failed to create location: %v", err)}// Create a cluster with all fieldsname := "Test Cluster"sampleRate := 250000description := "Original description"createInput := ClusterInput{DatasetID: &dsCreated.Dataset.ID,LocationID: &locCreated.Location.ID,Name: &name,SampleRate: &sampleRate,Description: &description,}ctx := context.Background()created, err := CreateOrUpdateCluster(ctx, createInput)if err != nil {t.Fatalf("Failed to create cluster: %v", err)}// Update only the description (nil for other fields)newDesc := "Updated description only"updateInput := ClusterInput{ID: &created.Cluster.ID,Description: &newDesc,// Name, SampleRate are nil - should be preserved}updated, err := CreateOrUpdateCluster(ctx, updateInput)if err != nil {t.Fatalf("Failed to update cluster: %v", err)}// Verify only description changedif updated.Cluster.Name != "Test Cluster" {t.Errorf("Name should be preserved, got '%s'", updated.Cluster.Name)}if updated.Cluster.SampleRate != 250000 {t.Errorf("SampleRate should be preserved, got %d", updated.Cluster.SampleRate)}if updated.Cluster.Description == nil || *updated.Cluster.Description != "Updated description only" {t.Errorf("Description should be updated, got '%v'", updated.Cluster.Description)}}// TestPatternUpdatePreservesUnsetFields tests that update only modifies provided fieldsfunc TestPatternUpdatePreservesUnsetFields(t *testing.T) {dbPath, cleanup := setupTestDB(t)defer cleanup()SetDBPath(dbPath)// Create a patternrecordSeconds := 60sleepSeconds := 1740createInput := PatternInput{RecordSeconds: &recordSeconds,SleepSeconds: &sleepSeconds,}ctx := context.Background()created, err := CreateOrUpdatePattern(ctx, createInput)if err != nil {t.Fatalf("Failed to create pattern: %v", err)}// Verify initial valuesif created.Pattern.RecordS != 60 {t.Errorf("Expected record_s 60, got %d", created.Pattern.RecordS)}if created.Pattern.SleepS != 1740 {t.Errorf("Expected sleep_s 1740, got %d", created.Pattern.SleepS)}// Update only the record secondsnewRecord := 30updateInput := PatternInput{ID: &created.Pattern.ID,RecordSeconds: &newRecord,// SleepSeconds is nil - should be preserved}updated, err := CreateOrUpdatePattern(ctx, updateInput)if err != nil {t.Fatalf("Failed to update pattern: %v", err)}// Verify only record changedif updated.Pattern.RecordS != 30 {t.Errorf("RecordS should be updated to 30, got %d", updated.Pattern.RecordS)}if updated.Pattern.SleepS != 1740 {t.Errorf("SleepS should be preserved at 1740, got %d", updated.Pattern.SleepS)}}// TestDatasetUpdateNoFieldsError tests that update with no fields returns errorfunc TestDatasetUpdateNoFieldsError(t *testing.T) {dbPath, cleanup := setupTestDB(t)defer cleanup()SetDBPath(dbPath)// Create a datasetname := "Test Dataset"created, err := CreateOrUpdateDataset(context.Background(), DatasetInput{Name: &name})if err != nil {t.Fatalf("Failed to create dataset: %v", err)}// Update with no fields should errorupdateInput := DatasetInput{ID: &created.Dataset.ID,// All other fields are nil}_, err = CreateOrUpdateDataset(context.Background(), updateInput)if err == nil {t.Error("Expected error when no fields provided to update")}}
package toolsimport ("context""time")// GetCurrentTimeInput defines the input parameters for the get_current_time tooltype GetCurrentTimeInput struct {// No input parameters needed for basic time query}// GetCurrentTimeOutput defines the output structure for the get_current_time tooltype GetCurrentTimeOutput struct {Time string `json:"time"`Timezone string `json:"timezone"`Unix int64 `json:"unix"`}// GetCurrentTime returns current system time with timezone and Unix timestampfunc GetCurrentTime(ctx context.Context, input GetCurrentTimeInput) (GetCurrentTimeOutput, error) {now := time.Now()output := GetCurrentTimeOutput{Time: now.Format(time.RFC3339),Timezone: now.Location().String(),Unix: now.Unix(),}return output, nil}
package toolsimport ("context""database/sql""encoding/base64""fmt""regexp""strings""time""skraak/db")// Package-level variable to store database pathvar dbPath string// SetDBPath sets the database path for the tools package// Called from main.go during initializationfunc SetDBPath(path string) {dbPath = path}// ExecuteSQLInput defines the input parameters for the execute_sql tooltype ExecuteSQLInput struct {Query string `json:"query"`Parameters []any `json:"parameters,omitempty"`Limit *int `json:"limit,omitempty"`}// ColumnInfo contains metadata about a result columntype ColumnInfo struct {Name string `json:"name"`DatabaseType string `json:"database_type"`}// ExecuteSQLOutput defines the output structure for the execute_sql tooltype ExecuteSQLOutput struct {Rows []map[string]any `json:"rows"`RowCount int `json:"row_count"`Columns []ColumnInfo `json:"columns"`Limited bool `json:"limited"`Query string `json:"query_executed"`}// Validation patternsvar (// Must start with SELECT or WITH (case-insensitive, allows leading whitespace)selectPattern = regexp.MustCompile(`(?i)^\s*(SELECT|WITH)\s+`)// Check for forbidden keywords that might indicate write operationsforbiddenPattern = regexp.MustCompile(`(?i)\b(INSERT|UPDATE|DELETE|DROP|CREATE|ALTER|TRUNCATE|GRANT|REVOKE)\b`)// Check for existing LIMIT clause (case-insensitive)limitPattern = regexp.MustCompile(`(?i)\bLIMIT\s+\d+`))const (defaultLimit = 1000maxLimit = 10000)// ExecuteSQL executes arbitrary SQL SELECT queries with safety validation// ExecuteSQL executes arbitrary SQL SELECT queries with safety validation and row limitingfunc ExecuteSQL(ctx context.Context,input ExecuteSQLInput,) (ExecuteSQLOutput, error) {// Validate query is not emptyif strings.TrimSpace(input.Query) == "" {return ExecuteSQLOutput{}, fmt.Errorf("query cannot be empty")}// Validate query starts with SELECT or WITHif !selectPattern.MatchString(input.Query) {return ExecuteSQLOutput{}, fmt.Errorf("only SELECT and WITH queries are allowed")}// Check for forbidden keywords (defense in depth - database is already read-only)if forbiddenPattern.MatchString(input.Query) {return ExecuteSQLOutput{}, fmt.Errorf("query contains forbidden keywords (INSERT/UPDATE/DELETE/DROP/CREATE/ALTER)")}// Determine row limitlimit := defaultLimitif input.Limit != nil {if *input.Limit < 1 || *input.Limit > maxLimit {return ExecuteSQLOutput{}, fmt.Errorf("limit must be between 1 and %d", maxLimit)}limit = *input.Limit}// Add LIMIT clause if not present// Query for limit+1 rows to detect truncationquery := input.QueryautoAddedLimit := falseif !limitPattern.MatchString(query) {query = fmt.Sprintf("%s LIMIT %d", strings.TrimSpace(query), limit+1)autoAddedLimit = true}// Get database connection (read-only for security)database, err := db.OpenReadOnlyDB(dbPath)if err != nil {return ExecuteSQLOutput{}, fmt.Errorf("database connection failed: %w", err)}defer database.Close() // Always close when done// Execute query with parametersvar rows *sql.Rowsif len(input.Parameters) > 0 {rows, err = database.QueryContext(ctx, query, input.Parameters...)} else {rows, err = database.QueryContext(ctx, query)}if err != nil {return ExecuteSQLOutput{}, fmt.Errorf("query execution failed: %w", err)}defer rows.Close()// Get column metadatacolumns, err := rows.Columns()if err != nil {return ExecuteSQLOutput{}, fmt.Errorf("failed to get columns: %w", err)}columnTypes, err := rows.ColumnTypes()if err != nil {return ExecuteSQLOutput{}, fmt.Errorf("failed to get column types: %w", err)}// Build column infocolumnInfo := make([]ColumnInfo, len(columns))for i, col := range columns {columnInfo[i] = ColumnInfo{Name: col,DatabaseType: columnTypes[i].DatabaseTypeName(),}}// Process rowsvar results []map[string]anyfor rows.Next() {// Create slice to hold column valuesvalues := make([]any, len(columns))valuePtrs := make([]any, len(columns))for i := range values {valuePtrs[i] = &values[i]}// Scan rowif err := rows.Scan(valuePtrs...); err != nil {return ExecuteSQLOutput{}, fmt.Errorf("row scan failed: %w", err)}// Convert to map with type conversionrowMap := make(map[string]any)for i, col := range columns {rowMap[col] = convertValue(values[i])}results = append(results, rowMap)}// Check for errors during iterationif err = rows.Err(); err != nil {return ExecuteSQLOutput{}, fmt.Errorf("row iteration failed: %w", err)}// Handle empty results (return empty array, not error)if results == nil {results = []map[string]any{}}// Detect truncation: if we auto-added limit+1 and got more than limit rowslimited := falseif autoAddedLimit && len(results) > limit {limited = trueresults = results[:limit]}// Build the query string to report (show effective limit, not internal limit+1)queryReported := queryif autoAddedLimit {queryReported = fmt.Sprintf("%s LIMIT %d", strings.TrimSpace(input.Query), limit)}// Create output structureoutput := ExecuteSQLOutput{Rows: results,RowCount: len(results),Columns: columnInfo,Limited: limited,Query: queryReported,}return output, nil}// convertValue converts database values to JSON-friendly typesfunc convertValue(val any) any {if val == nil {return nil}switch v := val.(type) {case time.Time:// Format timestamps as RFC3339 strings (consistent with existing code)return v.Format(time.RFC3339)case []byte:// Convert binary data to base64return base64.StdEncoding.EncodeToString(v)case int64, float64, string, bool:// Pass through primitive typesreturn vdefault:// For unknown types, convert to stringreturn fmt.Sprintf("%v", v)}}
package toolsimport ("os""path/filepath""testing")func TestShouldPrependFile(t *testing.T) {tests := []struct {name stringfilename stringprefix stringwantRename boolwantReason string}{// WAV files with datestring{"wav with datestring", "20250920_011509.wav", "LOC", true, ""},{"WAV with datestring", "20250920_011509.WAV", "LOC", true, ""},{"wav.data with datestring", "20250920_011509.wav.data", "LOC", true, ""},{"WAV.data with datestring", "20250920_011509.WAV.data", "LOC", true, ""},// Already prefixed{"already prefixed wav", "LOC_20250920_011509.wav", "LOC", false, "already prefixed"},{"already prefixed log.txt", "LOC_log.txt", "LOC", false, "already prefixed"},// No datestring{"no datestring wav", "mok_nearcamp2_20250920.wav", "LOC", false, "no datestring prefix"},{"no datestring WAV", "recording.WAV", "LOC", false, "no datestring prefix"},// log.txt{"log.txt", "log.txt", "LOC", true, ""},// Non-target files (silently ignored){"readme", "README.txt", "LOC", false, ""},{"random file", "something.mp3", "LOC", false, ""},{"LOG.TXT uppercase", "LOG.TXT", "LOC", false, ""}, // Only lowercase log.txt matches}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {gotRename, gotReason := shouldPrependFile(tt.filename, tt.prefix)if gotRename != tt.wantRename {t.Errorf("shouldPrependFile() gotRename = %v, want %v", gotRename, tt.wantRename)}if gotReason != tt.wantReason {t.Errorf("shouldPrependFile() gotReason = %v, want %v", gotReason, tt.wantReason)}})}}func TestPrepend(t *testing.T) {// Create temp foldertmpDir, err := os.MkdirTemp("", "prepend_test")if err != nil {t.Fatalf("Failed to create temp dir: %v", err)}defer os.RemoveAll(tmpDir)// Create test filestestFiles := []string{"20250920_011509.wav","20250920_011509.wav.data","log.txt","mok_nearcamp2_20250920.wav","README.txt",}for _, f := range testFiles {if err := os.WriteFile(filepath.Join(tmpDir, f), []byte{}, 0644); err != nil {t.Fatalf("Failed to create test file: %v", err)}}// Run prependoutput, err := Prepend(PrependInput{Folder: tmpDir,Prefix: "TEST",Recursive: false,DryRun: false,})if err != nil {t.Fatalf("Prepend() error = %v", err)}// Verify renamed filesif len(output.Renamed) != 3 {t.Errorf("Expected 3 renamed files, got %d", len(output.Renamed))}// Verify skipped filesif len(output.Skipped) != 1 {t.Errorf("Expected 1 skipped file, got %d", len(output.Skipped))}// Verify files were actually renamedif _, err := os.Stat(filepath.Join(tmpDir, "TEST_20250920_011509.wav")); os.IsNotExist(err) {t.Error("Expected TEST_20250920_011509.wav to exist")}if _, err := os.Stat(filepath.Join(tmpDir, "TEST_log.txt")); os.IsNotExist(err) {t.Error("Expected TEST_log.txt to exist")}if _, err := os.Stat(filepath.Join(tmpDir, "mok_nearcamp2_20250920.wav")); os.IsNotExist(err) {t.Error("Expected mok_nearcamp2_20250920.wav to still exist (skipped)")}}func TestPrependRecursive(t *testing.T) {// Create temp folder with subfoldertmpDir, err := os.MkdirTemp("", "prepend_test")if err != nil {t.Fatalf("Failed to create temp dir: %v", err)}defer os.RemoveAll(tmpDir)subDir := filepath.Join(tmpDir, "subfolder")if err := os.Mkdir(subDir, 0755); err != nil {t.Fatalf("Failed to create subfolder: %v", err)}// Create test filesfiles := map[string]string{filepath.Join(tmpDir, "20250920_011509.wav"): "",filepath.Join(subDir, "20250921_120000.wav"): "",filepath.Join(subDir, "log.txt"): "",}for f := range files {if err := os.WriteFile(f, []byte{}, 0644); err != nil {t.Fatalf("Failed to create test file: %v", err)}}// Run prepend with recursiveoutput, err := Prepend(PrependInput{Folder: tmpDir,Prefix: "TEST",Recursive: true,DryRun: false,})if err != nil {t.Fatalf("Prepend() error = %v", err)}// Should rename files in both foldersif len(output.Renamed) != 3 {t.Errorf("Expected 3 renamed files (recursive), got %d", len(output.Renamed))}// Verify subfolder file was renamedif _, err := os.Stat(filepath.Join(subDir, "TEST_20250921_120000.wav")); os.IsNotExist(err) {t.Error("Expected TEST_20250921_120000.wav in subfolder to exist")}}func TestPrependDryRun(t *testing.T) {tmpDir, err := os.MkdirTemp("", "prepend_test")if err != nil {t.Fatalf("Failed to create temp dir: %v", err)}defer os.RemoveAll(tmpDir)// Create test filetestFile := filepath.Join(tmpDir, "20250920_011509.wav")if err := os.WriteFile(testFile, []byte{}, 0644); err != nil {t.Fatalf("Failed to create test file: %v", err)}// Run prepend with dry-runoutput, err := Prepend(PrependInput{Folder: tmpDir,Prefix: "TEST",Recursive: false,DryRun: true,})if err != nil {t.Fatalf("Prepend() error = %v", err)}// Should report renamed filesif len(output.Renamed) != 1 {t.Errorf("Expected 1 renamed file in dry-run output, got %d", len(output.Renamed))}// But file should NOT be renamedif _, err := os.Stat(filepath.Join(tmpDir, "TEST_20250920_011509.wav")); !os.IsNotExist(err) {t.Error("Expected file NOT to be renamed in dry-run mode")}}func TestPrependIdempotent(t *testing.T) {tmpDir, err := os.MkdirTemp("", "prepend_test")if err != nil {t.Fatalf("Failed to create temp dir: %v", err)}defer os.RemoveAll(tmpDir)// Create test fileif err := os.WriteFile(filepath.Join(tmpDir, "20250920_011509.wav"), []byte{}, 0644); err != nil {t.Fatalf("Failed to create test file: %v", err)}// Run prepend twicefor i := range 2 {output, err := Prepend(PrependInput{Folder: tmpDir,Prefix: "TEST",Recursive: false,DryRun: false,})if err != nil {t.Fatalf("Prepend() iteration %d error = %v", i, err)}if i == 0 {// First run should renameif len(output.Renamed) != 1 {t.Errorf("First run: expected 1 renamed file, got %d", len(output.Renamed))}} else {// Second run should skip (already prefixed)if len(output.Renamed) != 0 {t.Errorf("Second run: expected 0 renamed files, got %d", len(output.Renamed))}if len(output.Skipped) != 1 {t.Errorf("Second run: expected 1 skipped file, got %d", len(output.Skipped))}}}}
package toolsimport ("fmt""os""path/filepath""regexp""strings")// PrependInput contains the parameters for the prepend operation.type PrependInput struct {Folder stringPrefix stringRecursive boolDryRun bool}// PrependResult contains the result of a single file rename operation.type PrependResult struct {Old string `json:"old"`New string `json:"new"`}// PrependSkipped contains info about a skipped file.type PrependSkipped struct {File string `json:"file"`Reason string `json:"reason"`}// PrependError contains info about a failed rename.type PrependError struct {File string `json:"file"`Error string `json:"error"`}// PrependOutput contains the complete result of the prepend operation.type PrependOutput struct {Folder string `json:"folder"`Prefix string `json:"prefix"`Recursive bool `json:"recursive"`DryRun bool `json:"dry_run"`Renamed []PrependResult `json:"renamed"`Skipped []PrependSkipped `json:"skipped"`Errors []PrependError `json:"errors"`}// datestringRegex matches filenames starting with YYYYMMDD_HHMMSS.var datestringRegex = regexp.MustCompile(`^\d{8}_\d{6}\.`)// Prepend renames files in a folder by prepending a prefix.// WAV files (.wav, .WAV) and their .data files are only renamed if they start with a datestring.// log.txt is always renamed if present.func Prepend(input PrependInput) (*PrependOutput, error) {output := &PrependOutput{Folder: input.Folder,Prefix: input.Prefix,Recursive: input.Recursive,DryRun: input.DryRun,Renamed: []PrependResult{},Skipped: []PrependSkipped{},Errors: []PrependError{},}// Collect folders to processfolders := []string{input.Folder}if input.Recursive {entries, err := os.ReadDir(input.Folder)if err != nil {return nil, fmt.Errorf("failed to read folder: %w", err)}for _, entry := range entries {if entry.IsDir() {folders = append(folders, filepath.Join(input.Folder, entry.Name()))}}}// Process each folderfor _, folder := range folders {entries, err := os.ReadDir(folder)if err != nil {return nil, fmt.Errorf("failed to read folder %s: %w", folder, err)}for _, entry := range entries {if entry.IsDir() {continue}filename := entry.Name()oldPath := filepath.Join(folder, filename)shouldRename, skipReason := shouldPrependFile(filename, input.Prefix)if !shouldRename {if skipReason != "" {output.Skipped = append(output.Skipped, PrependSkipped{File: oldPath,Reason: skipReason,})}continue}newFilename := input.Prefix + "_" + filenamenewPath := filepath.Join(folder, newFilename)if input.DryRun {output.Renamed = append(output.Renamed, PrependResult{Old: oldPath,New: newPath,})continue}// Perform the renameif err := os.Rename(oldPath, newPath); err != nil {output.Errors = append(output.Errors, PrependError{File: oldPath,Error: err.Error(),})continue}output.Renamed = append(output.Renamed, PrependResult{Old: oldPath,New: newPath,})}}return output, nil}// shouldPrependFile determines if a file should be prepended.// Returns (shouldRename, skipReason). If shouldRename is false and skipReason is empty,// the file is not a target type (silently ignored).func shouldPrependFile(filename, prefix string) (bool, string) {lowerName := strings.ToLower(filename)// Check if already prefixed (applies to all target files)if strings.HasPrefix(filename, prefix+"_") {// Only report as "already prefixed" if it's a target file typeif filename == prefix+"_log.txt" || isWavOrData(lowerName) {return false, "already prefixed"}return false, ""}// Check for log.txt (exact match, case-sensitive as per spec)if filename == "log.txt" {return true, ""}// Check for WAV files and their .data filesif !isWavOrData(lowerName) {return false, "" // Not a target file type, silently ignore}// Check for datestring prefix (YYYYMMDD_HHMMSS.)if !datestringRegex.MatchString(filename) {return false, "no datestring prefix"}return true, ""}// isWavOrData checks if the lowercase filename is a .wav or .wav.data filefunc isWavOrData(lowerName string) bool {return strings.HasSuffix(lowerName, ".wav") || strings.HasSuffix(lowerName, ".wav.data")}
package toolsimport ("context""os""path/filepath""testing")func TestCreateOrUpdatePattern_CreateDuplicate(t *testing.T) {// Setup: Use test databasetestDB := filepath.Join("..", "db", "test.duckdb")if _, err := os.Stat(testDB); os.IsNotExist(err) {t.Skipf("Test database not found at %s", testDB)}SetDBPath(testDB)ctx := context.Background()// Test 1: Try to create duplicate of existing pattern (60s/1740s)// Should return existing pattern IBv_KxDGsNQst.Run("CreateDuplicatePattern", func(t *testing.T) {record := 60sleep := 1740input := PatternInput{RecordSeconds: &record,SleepSeconds: &sleep,}output, err := CreateOrUpdatePattern(ctx, input)if err != nil {t.Fatalf("Expected no error, got: %v", err)}// Should return existing patternif output.Pattern.ID != "IBv_KxDGsNQs" {t.Errorf("Expected existing pattern ID 'IBv_KxDGsNQs', got '%s'", output.Pattern.ID)}if output.Pattern.RecordS != 60 {t.Errorf("Expected record_s 60, got %d", output.Pattern.RecordS)}if output.Pattern.SleepS != 1740 {t.Errorf("Expected sleep_s 1740, got %d", output.Pattern.SleepS)}// Check message indicates existing patternif output.Message == "" {t.Error("Expected non-empty message")}t.Logf("Message: %s", output.Message)})// Test 2: Create new unique patternt.Run("CreateUniquePattern", func(t *testing.T) {record := 999sleep := 888input := PatternInput{RecordSeconds: &record,SleepSeconds: &sleep,}output, err := CreateOrUpdatePattern(ctx, input)if err != nil {t.Fatalf("Expected no error, got: %v", err)}// Should create new patternfirstID := output.Pattern.IDif firstID == "" {t.Fatal("Expected non-empty ID")}if output.Pattern.RecordS != 999 {t.Errorf("Expected record_s 999, got %d", output.Pattern.RecordS)}if output.Pattern.SleepS != 888 {t.Errorf("Expected sleep_s 888, got %d", output.Pattern.SleepS)}t.Logf("Created pattern ID: %s", firstID)// Test 3: Try to create duplicate of the pattern we just created (idempotent)output2, err2 := CreateOrUpdatePattern(ctx, input)if err2 != nil {t.Fatalf("Expected no error on duplicate, got: %v", err2)}// Should return same patternif output2.Pattern.ID != firstID {t.Errorf("Expected same pattern ID '%s', got '%s'", firstID, output2.Pattern.ID)}t.Logf("Idempotent test passed - returned same ID: %s", output2.Pattern.ID)})}func TestCreateOrUpdatePattern_Validation(t *testing.T) {testDB := filepath.Join("..", "db", "test.duckdb")if _, err := os.Stat(testDB); os.IsNotExist(err) {t.Skipf("Test database not found at %s", testDB)}SetDBPath(testDB)ctx := context.Background()// Test invalid inputs for create (no ID = create mode)tests := []struct {name stringrecordSeconds intsleepSeconds intwantError bool}{{"ZeroRecordSeconds", 0, 100, true},{"NegativeRecordSeconds", -10, 100, true},{"ZeroSleepSeconds", 100, 0, true},{"NegativeSleepSeconds", 100, -10, true},{"ValidInputs", 10, 20, false},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {input := PatternInput{RecordSeconds: &tt.recordSeconds,SleepSeconds: &tt.sleepSeconds,}_, err := CreateOrUpdatePattern(ctx, input)if (err != nil) != tt.wantError {t.Errorf("Expected error=%v, got error=%v", tt.wantError, err != nil)}})}}func TestCreateOrUpdatePattern_Update(t *testing.T) {testDB := filepath.Join("..", "db", "test.duckdb")if _, err := os.Stat(testDB); os.IsNotExist(err) {t.Skipf("Test database not found at %s", testDB)}SetDBPath(testDB)ctx := context.Background()t.Run("UpdateNonExistentPattern", func(t *testing.T) {id := "NONEXISTENT1"record := 100input := PatternInput{ID: &id,RecordSeconds: &record,}_, err := CreateOrUpdatePattern(ctx, input)if err == nil {t.Error("Expected error for non-existent pattern")}})t.Run("UpdateNoFields", func(t *testing.T) {id := "IBv_KxDGsNQs"input := PatternInput{ID: &id,}_, err := CreateOrUpdatePattern(ctx, input)if err == nil {t.Error("Expected error when no fields provided")}})}
package toolsimport ("context""database/sql""fmt""skraak/db""skraak/utils""strings")// PatternInput defines the input parameters for the create_or_update_pattern tooltype PatternInput struct {ID *string `json:"id,omitempty"`RecordSeconds *int `json:"record_seconds,omitempty"`SleepSeconds *int `json:"sleep_seconds,omitempty"`}// PatternOutput defines the output structuretype PatternOutput struct {Pattern db.CyclicRecordingPattern `json:"pattern"`Message string `json:"message"`}// CreateOrUpdatePattern creates a new recording pattern or updates an existing onefunc CreateOrUpdatePattern(ctx context.Context,input PatternInput,) (PatternOutput, error) {if input.ID != nil && strings.TrimSpace(*input.ID) != "" {return updatePattern(ctx, input)}return createPattern(ctx, input)}func createPattern(ctx context.Context, input PatternInput) (PatternOutput, error) {var output PatternOutput// Validate required fields for createif input.RecordSeconds == nil {return output, fmt.Errorf("record_seconds is required when creating a pattern")}if input.SleepSeconds == nil {return output, fmt.Errorf("sleep_seconds is required when creating a pattern")}if err := utils.ValidatePositive(*input.RecordSeconds, "record_seconds"); err != nil {return output, err}if err := utils.ValidatePositive(*input.SleepSeconds, "sleep_seconds"); err != nil {return output, err}// Open writable database connectiondatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("database connection failed: %w", err)}defer database.Close()// Begin logged transactiontx, err := db.BeginLoggedTx(ctx, database, "create_or_update_pattern")if err != nil {return output, fmt.Errorf("failed to begin transaction: %w", err)}defer func() {if err != nil {tx.Rollback()}}()// Check if pattern with same record_s/sleep_s already existsvar existingID stringerr = tx.QueryRowContext(ctx,"SELECT id FROM cyclic_recording_pattern WHERE record_s = ? AND sleep_s = ? AND active = true",*input.RecordSeconds, *input.SleepSeconds,).Scan(&existingID)if err == nil {// Pattern already exists, return it instead of creating duplicatevar pattern db.CyclicRecordingPatternerr = tx.QueryRowContext(ctx,"SELECT id, record_s, sleep_s, created_at, last_modified, active FROM cyclic_recording_pattern WHERE id = ?",existingID,).Scan(&pattern.ID, &pattern.RecordS, &pattern.SleepS, &pattern.CreatedAt, &pattern.LastModified, &pattern.Active)if err != nil {return output, fmt.Errorf("failed to fetch existing pattern: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Pattern = patternoutput.Message = fmt.Sprintf("Pattern already exists with ID %s (record %ds, sleep %ds) - returning existing pattern",pattern.ID, pattern.RecordS, pattern.SleepS)return output, nil} else if err != sql.ErrNoRows {return output, fmt.Errorf("failed to check for existing pattern: %w", err)}// Generate IDid, err := utils.GenerateShortID()if err != nil {return output, fmt.Errorf("failed to generate ID: %w", err)}// Insert pattern_, err = tx.ExecContext(ctx,"INSERT INTO cyclic_recording_pattern (id, record_s, sleep_s, created_at, last_modified, active) VALUES (?, ?, ?, CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, TRUE)",id, *input.RecordSeconds, *input.SleepSeconds,)if err != nil {return output, fmt.Errorf("failed to create pattern: %w", err)}// Fetch the created patternvar pattern db.CyclicRecordingPatternerr = tx.QueryRowContext(ctx,"SELECT id, record_s, sleep_s, created_at, last_modified, active FROM cyclic_recording_pattern WHERE id = ?",id,).Scan(&pattern.ID, &pattern.RecordS, &pattern.SleepS, &pattern.CreatedAt, &pattern.LastModified, &pattern.Active)if err != nil {return output, fmt.Errorf("failed to fetch created pattern: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Pattern = patternoutput.Message = fmt.Sprintf("Successfully created cyclic recording pattern with ID %s (record %ds, sleep %ds)",pattern.ID, pattern.RecordS, pattern.SleepS)return output, nil}func updatePattern(ctx context.Context, input PatternInput) (PatternOutput, error) {var output PatternOutputpatternID := *input.ID// Validate ID formatif err := utils.ValidateShortID(patternID, "pattern_id"); err != nil {return output, err}// Validate fields if providedif input.RecordSeconds != nil {if err := utils.ValidatePositive(*input.RecordSeconds, "record_seconds"); err != nil {return output, err}}if input.SleepSeconds != nil {if err := utils.ValidateNonNegative(*input.SleepSeconds, "sleep_seconds"); err != nil {return output, err}}// Open writable databasedatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Verify pattern exists and check active statusvar exists, active boolerr = database.QueryRow("SELECT EXISTS(SELECT 1 FROM cyclic_recording_pattern WHERE id = ?), COALESCE((SELECT active FROM cyclic_recording_pattern WHERE id = ?), false)",patternID, patternID,).Scan(&exists, &active)if err != nil {return output, fmt.Errorf("failed to query pattern: %w", err)}if !exists {return output, fmt.Errorf("pattern not found: %s", patternID)}if !active {return output, fmt.Errorf("pattern '%s' is not active (cannot update inactive patterns)", patternID)}// Build dynamic UPDATE queryupdates := []string{}args := []any{}if input.RecordSeconds != nil {updates = append(updates, "record_s = ?")args = append(args, *input.RecordSeconds)}if input.SleepSeconds != nil {updates = append(updates, "sleep_s = ?")args = append(args, *input.SleepSeconds)}if len(updates) == 0 {return output, fmt.Errorf("no fields provided to update")}// Always update last_modifiedupdates = append(updates, "last_modified = now()")args = append(args, patternID)query := fmt.Sprintf("UPDATE cyclic_recording_pattern SET %s WHERE id = ?", strings.Join(updates, ", "))// Begin logged transaction for updatetx, err := db.BeginLoggedTx(ctx, database, "create_or_update_pattern")if err != nil {return output, fmt.Errorf("failed to begin transaction: %w", err)}defer func() {if err != nil {tx.Rollback()}}()_, err = tx.Exec(query, args...)if err != nil {return output, fmt.Errorf("failed to update pattern: %w", err)}// Fetch the updated patternvar pattern db.CyclicRecordingPatternerr = tx.QueryRow("SELECT id, record_s, sleep_s, created_at, last_modified, active FROM cyclic_recording_pattern WHERE id = ?",patternID,).Scan(&pattern.ID, &pattern.RecordS, &pattern.SleepS, &pattern.CreatedAt, &pattern.LastModified, &pattern.Active)if err != nil {return output, fmt.Errorf("failed to fetch updated pattern: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Pattern = patternoutput.Message = fmt.Sprintf("Successfully updated pattern (ID: %s, record %ds, sleep %ds)",pattern.ID, pattern.RecordS, pattern.SleepS)return output, nil}
package toolsimport ("context""fmt""skraak/db""skraak/utils""strings")// LocationInput defines the input parameters for the create_or_update_location tooltype LocationInput struct {ID *string `json:"id,omitempty"`DatasetID *string `json:"dataset_id,omitempty"`Name *string `json:"name,omitempty"`Latitude *float64 `json:"latitude,omitempty"`Longitude *float64 `json:"longitude,omitempty"`TimezoneID *string `json:"timezone_id,omitempty"`Description *string `json:"description,omitempty"`}// LocationOutput defines the output structuretype LocationOutput struct {Location db.Location `json:"location"`Message string `json:"message"`}// CreateOrUpdateLocation creates a new location or updates an existing one with GPS coordinatesfunc CreateOrUpdateLocation(ctx context.Context,input LocationInput,) (LocationOutput, error) {if input.ID != nil && strings.TrimSpace(*input.ID) != "" {return updateLocation(ctx, input)}return createLocation(ctx, input)}// validateLocationFields validates fields common to both create and updatefunc validateLocationFields(input LocationInput) error {if err := utils.ValidateOptionalStringLength(input.Name, "name", utils.MaxNameLen); err != nil {return err}if err := utils.ValidateOptionalStringLength(input.Description, "description", utils.MaxDescriptionLen); err != nil {return err}if input.Latitude != nil {if err := utils.ValidateRange(*input.Latitude, "latitude", -90.0, 90.0); err != nil {return err}}if input.Longitude != nil {if err := utils.ValidateRange(*input.Longitude, "longitude", -180.0, 180.0); err != nil {return err}}if input.TimezoneID != nil {if err := utils.ValidateStringLength(*input.TimezoneID, "timezone_id", utils.MaxTimezoneLen); err != nil {return err}if err := utils.ValidateTimezone(*input.TimezoneID); err != nil {return err}}return nil}func createLocation(ctx context.Context, input LocationInput) (LocationOutput, error) {var output LocationOutput// Validate required fields for createif input.DatasetID == nil || strings.TrimSpace(*input.DatasetID) == "" {return output, fmt.Errorf("dataset_id is required when creating a location")}if input.Name == nil || strings.TrimSpace(*input.Name) == "" {return output, fmt.Errorf("name is required when creating a location")}if input.Latitude == nil {return output, fmt.Errorf("latitude is required when creating a location")}if input.Longitude == nil {return output, fmt.Errorf("longitude is required when creating a location")}if input.TimezoneID == nil || strings.TrimSpace(*input.TimezoneID) == "" {return output, fmt.Errorf("timezone_id is required when creating a location")}// Validate ID format for dataset_idif err := utils.ValidateShortID(*input.DatasetID, "dataset_id"); err != nil {return output, err}if err := validateLocationFields(input); err != nil {return output, err}// Open writable database connectiondatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("database connection failed: %w", err)}defer database.Close()// Begin logged transactiontx, err := db.BeginLoggedTx(ctx, database, "create_or_update_location")if err != nil {return output, fmt.Errorf("failed to begin transaction: %w", err)}defer func() {if err != nil {tx.Rollback()}}()// Verify dataset exists and is activevar datasetExists, datasetActive boolerr = tx.QueryRowContext(ctx,"SELECT EXISTS(SELECT 1 FROM dataset WHERE id = ?), COALESCE((SELECT active FROM dataset WHERE id = ?), false)",*input.DatasetID, *input.DatasetID,).Scan(&datasetExists, &datasetActive)if err != nil {return output, fmt.Errorf("failed to verify dataset: %w", err)}if !datasetExists {return output, fmt.Errorf("dataset with ID '%s' does not exist", *input.DatasetID)}if !datasetActive {return output, fmt.Errorf("dataset (ID: %s) is not active", *input.DatasetID)}// Check for existing location with same name in dataset (UNIQUE constraint)var existingID stringerr = tx.QueryRowContext(ctx,"SELECT id FROM location WHERE dataset_id = ? AND name = ? AND active = true",*input.DatasetID, *input.Name,).Scan(&existingID)if err == nil {// Location with this name already exists in dataset - return existing (consistent duplicate handling)var location db.Locationerr = tx.QueryRowContext(ctx,"SELECT id, dataset_id, name, latitude, longitude, description, created_at, last_modified, active, timezone_id FROM location WHERE id = ?",existingID,).Scan(&location.ID, &location.DatasetID, &location.Name, &location.Latitude, &location.Longitude,&location.Description, &location.CreatedAt, &location.LastModified, &location.Active, &location.TimezoneID)if err != nil {return output, fmt.Errorf("failed to fetch existing location: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Location = locationoutput.Message = fmt.Sprintf("Location '%s' already exists in dataset (ID: %s) - returning existing location", location.Name, location.ID)return output, nil}// Generate IDid, err := utils.GenerateShortID()if err != nil {return output, fmt.Errorf("failed to generate ID: %w", err)}// Insert location_, err = tx.ExecContext(ctx,"INSERT INTO location (id, dataset_id, name, latitude, longitude, timezone_id, description, created_at, last_modified, active) VALUES (?, ?, ?, ?, ?, ?, ?, CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, TRUE)",id, *input.DatasetID, *input.Name, *input.Latitude, *input.Longitude, *input.TimezoneID, input.Description,)if err != nil {return output, fmt.Errorf("failed to create location: %w", err)}// Fetch the created locationvar location db.Locationerr = tx.QueryRowContext(ctx,"SELECT id, dataset_id, name, latitude, longitude, description, created_at, last_modified, active, timezone_id FROM location WHERE id = ?",id,).Scan(&location.ID, &location.DatasetID, &location.Name, &location.Latitude, &location.Longitude,&location.Description, &location.CreatedAt, &location.LastModified, &location.Active, &location.TimezoneID)if err != nil {return output, fmt.Errorf("failed to fetch created location: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Location = locationoutput.Message = fmt.Sprintf("Successfully created location '%s' with ID %s (%.6f, %.6f, %s)",location.Name, location.ID, location.Latitude, location.Longitude, location.TimezoneID)return output, nil}func updateLocation(ctx context.Context, input LocationInput) (LocationOutput, error) {var output LocationOutputlocationID := *input.ID// Validate ID formatif err := utils.ValidateShortID(locationID, "location_id"); err != nil {return output, err}if err := validateLocationFields(input); err != nil {return output, err}// Validate dataset_id format if providedif err := utils.ValidateOptionalShortID(input.DatasetID, "dataset_id"); err != nil {return output, err}// Open writable databasedatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Verify location exists and check active statusvar exists, active boolvar currentDatasetID stringerr = database.QueryRow("SELECT EXISTS(SELECT 1 FROM location WHERE id = ?), COALESCE((SELECT active FROM location WHERE id = ?), false), COALESCE((SELECT dataset_id FROM location WHERE id = ?), '')",locationID, locationID, locationID,).Scan(&exists, &active, ¤tDatasetID)if err != nil {return output, fmt.Errorf("failed to query location: %w", err)}if !exists {return output, fmt.Errorf("location not found: %s", locationID)}if !active {return output, fmt.Errorf("location '%s' is not active (cannot update inactive locations)", locationID)}// Verify dataset exists if DatasetID provided (relationship consistency)if input.DatasetID != nil {var datasetExists, datasetActive boolerr = database.QueryRow("SELECT EXISTS(SELECT 1 FROM dataset WHERE id = ?), COALESCE((SELECT active FROM dataset WHERE id = ?), false)",*input.DatasetID, *input.DatasetID,).Scan(&datasetExists, &datasetActive)if err != nil {return output, fmt.Errorf("failed to query dataset: %w", err)}if !datasetExists {return output, fmt.Errorf("dataset not found: %s", *input.DatasetID)}if !datasetActive {return output, fmt.Errorf("dataset '%s' is not active", *input.DatasetID)}}// Build dynamic UPDATE queryupdates := []string{}args := []any{}if input.DatasetID != nil {updates = append(updates, "dataset_id = ?")args = append(args, *input.DatasetID)}if input.Name != nil {updates = append(updates, "name = ?")args = append(args, *input.Name)}if input.Latitude != nil {updates = append(updates, "latitude = ?")args = append(args, *input.Latitude)}if input.Longitude != nil {updates = append(updates, "longitude = ?")args = append(args, *input.Longitude)}if input.Description != nil {updates = append(updates, "description = ?")args = append(args, *input.Description)}if input.TimezoneID != nil {updates = append(updates, "timezone_id = ?")args = append(args, *input.TimezoneID)}if len(updates) == 0 {return output, fmt.Errorf("no fields provided to update")}// Always update last_modifiedupdates = append(updates, "last_modified = now()")args = append(args, locationID)query := fmt.Sprintf("UPDATE location SET %s WHERE id = ?", strings.Join(updates, ", "))// Begin logged transaction for updatetx, err := db.BeginLoggedTx(ctx, database, "create_or_update_location")if err != nil {return output, fmt.Errorf("failed to begin transaction: %w", err)}defer func() {if err != nil {tx.Rollback()}}()_, err = tx.ExecContext(ctx, query, args...)if err != nil {return output, fmt.Errorf("failed to update location: %w", err)}// Fetch the updated locationvar location db.Locationerr = tx.QueryRow("SELECT id, dataset_id, name, latitude, longitude, description, created_at, last_modified, active, timezone_id FROM location WHERE id = ?",locationID,).Scan(&location.ID, &location.DatasetID, &location.Name, &location.Latitude, &location.Longitude,&location.Description, &location.CreatedAt, &location.LastModified, &location.Active, &location.TimezoneID)if err != nil {return output, fmt.Errorf("failed to fetch updated location: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Location = locationoutput.Message = fmt.Sprintf("Successfully updated location '%s' (ID: %s)", location.Name, location.ID)return output, nil}
package toolsimport ("fmt""strings""time""github.com/sixdouglas/suncalc""skraak/utils")// IsNightInput defines the input parameters for the isnight tooltype IsNightInput struct {FilePath string `json:"file_path"`Lat float64 `json:"lat"`Lng float64 `json:"lng"`Timezone string `json:"timezone,omitempty"`}// IsNightOutput defines the output structure for the isnight tooltype IsNightOutput struct {FilePath string `json:"file_path"`TimestampUTC string `json:"timestamp_utc"`SolarNight bool `json:"solar_night"`CivilNight bool `json:"civil_night"`DiurnalActive bool `json:"diurnal_active"`MoonPhase float64 `json:"moon_phase"`DurationSec float64 `json:"duration_seconds"`TimestampSrc string `json:"timestamp_source"`MidpointUTC string `json:"midpoint_utc"`SunriseUTC string `json:"sunrise_utc,omitempty"`SunsetUTC string `json:"sunset_utc,omitempty"`DawnUTC string `json:"dawn_utc,omitempty"`DuskUTC string `json:"dusk_utc,omitempty"`}// IsNight determines if a WAV file was recorded at night based on its// metadata timestamp and the given GPS coordinates.//// Timestamp resolution order:// 1. AudioMoth comment (timezone embedded)// 2. Filename timestamp + timezone offset (requires --timezone)// 3. File modification time (system local time)func IsNight(input IsNightInput) (IsNightOutput, error) {var output IsNightOutput// Step 1: Parse WAV headermetadata, err := utils.ParseWAVHeader(input.FilePath)if err != nil {return output, fmt.Errorf("WAV header parsing failed: %w", err)}output.DurationSec = metadata.Duration// Step 2: Resolve timestamp (use file mod time as fallback)tsResult, err := utils.ResolveTimestamp(metadata, input.FilePath, input.Timezone, true)if err != nil {return output, fmt.Errorf("cannot determine recording timestamp: %w", err)}// Determine timestamp source labeltsSource := "file_mod_time"if tsResult.IsAudioMoth {tsSource = "audiomoth_comment"} else if utils.HasTimestampFilename(input.FilePath) {tsSource = "filename"}// Step 3: Calculate astronomical data using recording midpointastroData := utils.CalculateAstronomicalData(tsResult.Timestamp.UTC(),metadata.Duration,input.Lat,input.Lng,)// Step 4: Get sun event times for informational outputmidpoint := utils.CalculateMidpointTime(tsResult.Timestamp.UTC(), metadata.Duration)sunTimes := suncalc.GetTimes(midpoint, input.Lat, input.Lng)output.FilePath = input.FilePathoutput.TimestampUTC = tsResult.Timestamp.UTC().Format(time.RFC3339)output.SolarNight = astroData.SolarNightoutput.CivilNight = astroData.CivilNightoutput.MoonPhase = astroData.MoonPhaseoutput.TimestampSrc = tsSourceoutput.MidpointUTC = midpoint.Format(time.RFC3339)if dawn, ok := sunTimes[suncalc.Dawn]; ok && !dawn.Value.IsZero() {if sunset, ok := sunTimes[suncalc.Sunset]; ok && !sunset.Value.IsZero() {output.DiurnalActive = !midpoint.Before(dawn.Value) && !midpoint.After(sunset.Value)}}if sr, ok := sunTimes[suncalc.Sunrise]; ok && !sr.Value.IsZero() {output.SunriseUTC = sr.Value.UTC().Format(time.RFC3339)}if ss, ok := sunTimes[suncalc.Sunset]; ok && !ss.Value.IsZero() {output.SunsetUTC = ss.Value.UTC().Format(time.RFC3339)}if d, ok := sunTimes[suncalc.Dawn]; ok && !d.Value.IsZero() {output.DawnUTC = d.Value.UTC().Format(time.RFC3339)}if dk, ok := sunTimes[suncalc.Dusk]; ok && !dk.Value.IsZero() {output.DuskUTC = dk.Value.UTC().Format(time.RFC3339)}return output, nil}// String returns a human-readable summary of the isnight resultfunc (o IsNightOutput) String() string {var sb strings.Builderfmt.Fprintf(&sb, "File: %s\n", o.FilePath)fmt.Fprintf(&sb, "Timestamp (UTC): %s\n", o.TimestampUTC)fmt.Fprintf(&sb, "Midpoint (UTC): %s\n", o.MidpointUTC)fmt.Fprintf(&sb, "Duration: %.1f seconds\n", o.DurationSec)fmt.Fprintf(&sb, "Source: %s\n", o.TimestampSrc)fmt.Fprintf(&sb, "Solar night: %v\n", o.SolarNight)fmt.Fprintf(&sb, "Civil night: %v\n", o.CivilNight)fmt.Fprintf(&sb, "Moon phase: %.2f\n", o.MoonPhase)if o.SunriseUTC != "" {fmt.Fprintf(&sb, "Sunrise (UTC): %s\n", o.SunriseUTC)}if o.SunsetUTC != "" {fmt.Fprintf(&sb, "Sunset (UTC): %s\n", o.SunsetUTC)}if o.DawnUTC != "" {fmt.Fprintf(&sb, "Dawn (UTC): %s\n", o.DawnUTC)}if o.DuskUTC != "" {fmt.Fprintf(&sb, "Dusk (UTC): %s\n", o.DuskUTC)}return sb.String()}
package toolsimport ("context""os""path/filepath""testing")func TestPatternIntegration_CreateClusterWithExistingPattern(t *testing.T) {// Setup: Use test databasetestDB := filepath.Join("..", "db", "test.duckdb")if _, err := os.Stat(testDB); os.IsNotExist(err) {t.Skipf("Test database not found at %s", testDB)}SetDBPath(testDB)ctx := context.Background()// First, verify we can query existing patternst.Run("QueryExistingPatterns", func(t *testing.T) {input := ExecuteSQLInput{Query: "SELECT id, record_s, sleep_s FROM cyclic_recording_pattern WHERE active = true ORDER BY record_s, sleep_s",}output, err := ExecuteSQL(ctx, input)if err != nil {t.Fatalf("Failed to query patterns: %v", err)}if len(output.Rows) == 0 {t.Fatal("Expected at least one pattern")}t.Logf("Found %d patterns", len(output.Rows))for i, row := range output.Rows {t.Logf("Pattern %d: ID=%v, record_s=%v, sleep_s=%v", i+1, row["id"], row["record_s"], row["sleep_s"])}})// Create a cluster using an existing patternt.Run("CreateClusterWithExistingPattern", func(t *testing.T) {// First, find a valid dataset and locationdatasetSQL := ExecuteSQLInput{Query: "SELECT id FROM dataset WHERE active = true LIMIT 1",}datasetOutput, err := ExecuteSQL(ctx, datasetSQL)if err != nil || len(datasetOutput.Rows) == 0 {t.Skip("No active datasets found in test database")}datasetID := datasetOutput.Rows[0]["id"].(string)locationSQL := ExecuteSQLInput{Query: "SELECT id FROM location WHERE dataset_id = ? AND active = true LIMIT 1",Parameters: []any{datasetID},}locationOutput, err := ExecuteSQL(ctx, locationSQL)if err != nil || len(locationOutput.Rows) == 0 {t.Skip("No active locations found in test database")}locationID := locationOutput.Rows[0]["id"].(string)t.Logf("Using dataset: %s, location: %s", datasetID, locationID)sampleRate := 16000input := ClusterInput{DatasetID: &datasetID,LocationID: &locationID,Name: new("Integration Test Cluster"),SampleRate: &sampleRate,CyclicRecordingPatternID: new("IBv_KxDGsNQs"), // 60s/1740s pattern}output, err := CreateOrUpdateCluster(ctx, input)if err != nil {t.Fatalf("Failed to create cluster: %v", err)}clusterID := output.Cluster.IDt.Logf("Created cluster: %s with pattern reference", clusterID)// Verify the cluster has the pattern referencesqlInput := ExecuteSQLInput{Query: "SELECT c.name, c.cyclic_recording_pattern_id, p.record_s, p.sleep_s FROM cluster c LEFT JOIN cyclic_recording_pattern p ON c.cyclic_recording_pattern_id = p.id WHERE c.id = ?",Parameters: []any{clusterID},}sqlOutput, err := ExecuteSQL(ctx, sqlInput)if err != nil {t.Fatalf("Failed to verify cluster: %v", err)}if len(sqlOutput.Rows) != 1 {t.Fatalf("Expected 1 row, got %d", len(sqlOutput.Rows))}row := sqlOutput.Rows[0]t.Logf("Row data: %+v", row)// Check the pattern IDpatternIDStr := row["cyclic_recording_pattern_id"]if patternIDStr != "IBv_KxDGsNQs" {t.Errorf("Expected pattern ID 'IBv_KxDGsNQs', got '%v'", patternIDStr)}// Check record_s and sleep_srecordSVal := row["record_s"]sleepSVal := row["sleep_s"]t.Logf("✓ Verified cluster has correct pattern reference: ID=%v, record=%v, sleep=%v",patternIDStr, recordSVal, sleepSVal)if patternIDStr == nil || patternIDStr == "" {t.Error("Pattern ID is empty")}if recordSVal == nil {t.Error("record_s is nil")}if sleepSVal == nil {t.Error("sleep_s is nil")}})}
package toolsimport ("context""fmt""io/fs""os""path/filepath""strings""time""skraak/db""skraak/utils")// ImportUnstructuredInput defines the input parameters for importing files into an unstructured datasettype ImportUnstructuredInput struct {DatasetID string `json:"dataset_id"`FolderPath string `json:"folder_path"`Recursive *bool `json:"recursive,omitempty"`}// ImportUnstructuredOutput defines the output structuretype ImportUnstructuredOutput struct {TotalFiles int `json:"total_files"`ImportedFiles int `json:"imported_files"`SkippedFiles int `json:"skipped_files"` // DuplicatesFailedFiles int `json:"failed_files"`TotalDuration float64 `json:"total_duration_seconds"`ProcessingTime string `json:"processing_time"`Errors []utils.FileImportError `json:"errors,omitempty"`}// ImportUnstructured imports WAV files into an unstructured dataset// Files are stored with minimal metadata: hash, duration, sample_rate, file_mod_time as timestamp// No location/cluster hierarchy, no astronomical data, no AudioMoth parsingfunc ImportUnstructured(ctx context.Context,input ImportUnstructuredInput,) (ImportUnstructuredOutput, error) {startTime := time.Now()var output ImportUnstructuredOutput// Default recursive to truerecursive := trueif input.Recursive != nil {recursive = *input.Recursive}// Validate inputif err := validateUnstructuredInput(input); err != nil {return output, fmt.Errorf("validation failed: %w", err)}// Open databasedatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Scan for WAV filesfiles, scanErrors := scanWavFiles(input.FolderPath, recursive)output.Errors = append(output.Errors, scanErrors...)output.TotalFiles = len(files)if len(files) == 0 {output.ProcessingTime = time.Since(startTime).String()return output, nil}// Begin logged transactiontx, err := db.BeginLoggedTx(ctx, database, "import_unstructured")if err != nil {return output, fmt.Errorf("failed to begin transaction: %w", err)}defer func() {if err != nil {tx.Rollback()}}()// Process each filefor _, filePath := range files {fileResult, procErr := processUnstructuredFile(tx, filePath, input.DatasetID)if procErr != nil {output.FailedFiles++output.Errors = append(output.Errors, utils.FileImportError{FileName: filepath.Base(filePath),Error: procErr.Error(),Stage: "process",})continue}if fileResult.Skipped {output.SkippedFiles++} else {output.ImportedFiles++output.TotalDuration += fileResult.Duration}}// Commit transactionif err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.ProcessingTime = time.Since(startTime).String()return output, nil}// unstructuredFileResult holds the result of processing a single filetype unstructuredFileResult struct {Skipped bool // True if duplicateDuration float64 // Duration in seconds}// processUnstructuredFile processes a single WAV file for unstructured importfunc processUnstructuredFile(tx *db.LoggedTx, filePath, datasetID string) (*unstructuredFileResult, error) {result := &unstructuredFileResult{}// Step 1: Parse WAV headermetadata, err := utils.ParseWAVHeader(filePath)if err != nil {return nil, fmt.Errorf("WAV header parsing failed: %w", err)}// Step 2: Calculate hashhash, err := utils.ComputeXXH64(filePath)if err != nil {return nil, fmt.Errorf("hash calculation failed: %w", err)}// Step 3: Check for duplicate - if exists, skip entirely (do not link to dataset)_, isDuplicate, err := utils.CheckDuplicateHash(tx, hash)if err != nil {return nil, fmt.Errorf("duplicate check failed: %w", err)}if isDuplicate {// File already exists in database - skip completely, do not link to datasetresult.Skipped = trueresult.Duration = metadata.Durationreturn result, nil}// Step 4: Generate file IDfileID, err := utils.GenerateLongID()if err != nil {return nil, fmt.Errorf("ID generation failed: %w", err)}// Step 5: Use file modification time as timestamp (no timezone conversion)timestamp := metadata.FileModTime// Step 6: Insert into file table_, err = tx.Exec(`INSERT INTO file (id, file_name, xxh64_hash, location_id, cluster_id,timestamp_local, duration, sample_rate,maybe_solar_night, maybe_civil_night, moon_phase,active) VALUES (?, ?, ?, NULL, NULL, ?, ?, ?, NULL, NULL, NULL, TRUE)`,fileID,filepath.Base(filePath),hash,timestamp,metadata.Duration,metadata.SampleRate,)if err != nil {return nil, fmt.Errorf("file insert failed: %w", err)}// Step 7: Insert into file_dataset table_, err = tx.Exec("INSERT INTO file_dataset (file_id, dataset_id) VALUES (?, ?)",fileID, datasetID,)if err != nil {return nil, fmt.Errorf("file_dataset insert failed: %w", err)}result.Duration = metadata.Durationreturn result, nil}// validateUnstructuredInput validates the input parametersfunc validateUnstructuredInput(input ImportUnstructuredInput) error {// Validate dataset ID formatif err := utils.ValidateShortID(input.DatasetID, "dataset_id"); err != nil {return err}// Verify folder existsinfo, err := os.Stat(input.FolderPath)if err != nil {return fmt.Errorf("folder not accessible: %w", err)}if !info.IsDir() {return fmt.Errorf("path is not a directory: %s", input.FolderPath)}// Open database for validationdatabase, err := db.OpenReadOnlyDB(dbPath)if err != nil {return fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Verify dataset exists and is activevar datasetExists boolerr = database.QueryRow("SELECT EXISTS(SELECT 1 FROM dataset WHERE id = ? AND active = true)",input.DatasetID,).Scan(&datasetExists)if err != nil {return fmt.Errorf("failed to query dataset: %w", err)}if !datasetExists {return fmt.Errorf("dataset not found or inactive: %s", input.DatasetID)}// Verify dataset is 'unstructured' typeif err := utils.ValidateDatasetTypeUnstructured(database, input.DatasetID); err != nil {return err}return nil}// scanWavFiles scans a folder for WAV filesfunc scanWavFiles(folderPath string, recursive bool) ([]string, []utils.FileImportError) {var files []stringvar errors []utils.FileImportErrorwalkFunc := func(path string, d fs.DirEntry, err error) error {if err != nil {errors = append(errors, utils.FileImportError{FileName: path,Error: err.Error(),Stage: "scan",})return nil}// Skip directories if not recursiveif d.IsDir() {if !recursive && path != folderPath {return fs.SkipDir}return nil}// Check for .wav extension (case-insensitive)if strings.HasSuffix(strings.ToLower(d.Name()), ".wav") {files = append(files, path)}return nil}if recursive {if err := filepath.WalkDir(folderPath, walkFunc); err != nil {errors = append(errors, utils.FileImportError{FileName: folderPath,Error: err.Error(),Stage: "scan",})}} else {// Non-recursive: only scan top-levelentries, err := os.ReadDir(folderPath)if err != nil {errors = append(errors, utils.FileImportError{FileName: folderPath,Error: err.Error(),Stage: "scan",})return nil, errors}for _, entry := range entries {if !entry.IsDir() && strings.HasSuffix(strings.ToLower(entry.Name()), ".wav") {files = append(files, filepath.Join(folderPath, entry.Name()))}}}return files, errors}
package toolsimport ("testing""skraak/utils")func TestValidateSegmentImportInput(t *testing.T) {t.Run("invalid dataset ID - too short", func(t *testing.T) {input := ImportSegmentsInput{DatasetID: "abc",}err := validateSegmentImportInput(input)if err == nil {t.Fatal("expected error for short dataset ID")}})t.Run("invalid dataset ID - too long", func(t *testing.T) {input := ImportSegmentsInput{DatasetID: "abc123def456ghi789",}err := validateSegmentImportInput(input)if err == nil {t.Fatal("expected error for long dataset ID")}})t.Run("invalid dataset ID - invalid characters", func(t *testing.T) {input := ImportSegmentsInput{DatasetID: "abc123!!!456",}err := validateSegmentImportInput(input)if err == nil {t.Fatal("expected error for invalid characters in dataset ID")}})t.Run("invalid location ID", func(t *testing.T) {input := ImportSegmentsInput{DatasetID: "abc123def456",LocationID: "invalid",}err := validateSegmentImportInput(input)if err == nil {t.Fatal("expected error for invalid location ID")}})t.Run("invalid cluster ID", func(t *testing.T) {input := ImportSegmentsInput{DatasetID: "abc123def456",LocationID: "xyz789uvw012",ClusterID: "invalid",}err := validateSegmentImportInput(input)if err == nil {t.Fatal("expected error for invalid cluster ID")}})}func TestCountTotalSegments(t *testing.T) {t.Run("empty", func(t *testing.T) {count := countTotalSegments(map[string]scannedDataFile{})if count != 0 {t.Errorf("expected 0, got %d", count)}})t.Run("single file - no segments", func(t *testing.T) {files := map[string]scannedDataFile{"file1": {Segments: []*utils.Segment{}},}count := countTotalSegments(files)if count != 0 {t.Errorf("expected 0, got %d", count)}})t.Run("single file - multiple segments", func(t *testing.T) {files := map[string]scannedDataFile{"file1": {Segments: []*utils.Segment{{}, {}, {}}},}count := countTotalSegments(files)if count != 3 {t.Errorf("expected 3, got %d", count)}})t.Run("multiple files", func(t *testing.T) {files := map[string]scannedDataFile{"file1": {Segments: []*utils.Segment{{}, {}}},"file2": {Segments: []*utils.Segment{{}}},"file3": {Segments: []*utils.Segment{{}, {}, {}, {}}},}count := countTotalSegments(files)if count != 7 {t.Errorf("expected 7, got %d", count)}})}
package toolsimport ("context""database/sql""fmt""os""path/filepath""strings""time""skraak/db""skraak/utils")// ImportSegmentsInput defines the input parameters for the import_segments tooltype ImportSegmentsInput struct {Folder string `json:"folder"`Mapping string `json:"mapping"`DatasetID string `json:"dataset_id"`LocationID string `json:"location_id"`ClusterID string `json:"cluster_id"`ProgressHandler func(processed, total int, message string)}// ImportSegmentsOutput defines the output structure for the import_segments tooltype ImportSegmentsOutput struct {Summary ImportSegmentsSummary `json:"summary"`Segments []SegmentImport `json:"segments"`Errors []ImportSegmentError `json:"errors,omitempty"`}// ImportSegmentsSummary provides summary statistics for the import operationtype ImportSegmentsSummary struct {DataFilesFound int `json:"data_files_found"`DataFilesProcessed int `json:"data_files_processed"`TotalSegments int `json:"total_segments"`ImportedSegments int `json:"imported_segments"`ImportedLabels int `json:"imported_labels"`ImportedSubtypes int `json:"imported_subtypes"`ProcessingTimeMs int64 `json:"processing_time_ms"`}// SegmentImport represents an imported segment in the outputtype SegmentImport struct {SegmentID string `json:"segment_id"`FileName string `json:"file_name"`StartTime float64 `json:"start_time"`EndTime float64 `json:"end_time"`FreqLow float64 `json:"freq_low"`FreqHigh float64 `json:"freq_high"`Labels []LabelImport `json:"labels"`}// LabelImport represents an imported label in the outputtype LabelImport struct {LabelID string `json:"label_id"`Species string `json:"species"`CallType string `json:"calltype,omitempty"`Filter string `json:"filter"`Certainty int `json:"certainty"`Comment string `json:"comment,omitempty"`}// ImportSegmentError records errors encountered during segment importtype ImportSegmentError struct {File string `json:"file,omitempty"`Stage string `json:"stage"` // "validation", "hash", "import"Message string `json:"message"`}// scannedDataFile holds parsed data for a .data filetype scannedDataFile struct {DataPath stringWavPath stringWavHash stringFileID stringDuration float64Segments []*utils.Segment}// ImportSegments imports segments from AviaNZ .data files into the databasefunc ImportSegments(ctx context.Context, input ImportSegmentsInput) (ImportSegmentsOutput, error) {startTime := time.Now()var output ImportSegmentsOutputoutput.Segments = make([]SegmentImport, 0)output.Errors = make([]ImportSegmentError, 0)// Phase A: Input Validationif err := validateSegmentImportInput(input); err != nil {return output, err}// Load mapping filemapping, err := utils.LoadMappingFile(input.Mapping)if err != nil {return output, fmt.Errorf("failed to load mapping file: %w", err)}// Find .data filesdataFiles, err := utils.FindDataFiles(input.Folder)if err != nil {return output, fmt.Errorf("failed to find .data files: %w", err)}output.Summary.DataFilesFound = len(dataFiles)if len(dataFiles) == 0 {return output, fmt.Errorf("no .data files found in folder: %s", input.Folder)}// Phase B: Parse all .data files and collect unique valuesscannedFiles, parseErrors, uniqueFilters, uniqueSpecies, uniqueCalltypes := scanAllDataFiles(dataFiles, input.Folder)output.Errors = append(output.Errors, parseErrors...)if len(scannedFiles) == 0 {output.Summary.ProcessingTimeMs = time.Since(startTime).Milliseconds()return output, nil}// Phase C: Pre-Import Validationdatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Validate dataset/location/cluster hierarchyif err := validateSegmentHierarchy(database, input.DatasetID, input.LocationID, input.ClusterID); err != nil {return output, err}// Validate all filters existfilterIDMap, err := validateFiltersExist(database, uniqueFilters)if err != nil {return output, fmt.Errorf("filter validation failed: %w", err)}// Validate mapping covers all species/calltypes and they exist in DBvalidationResult, err := utils.ValidateMappingAgainstDB(database, mapping, uniqueSpecies, uniqueCalltypes)if err != nil {return output, fmt.Errorf("mapping validation failed: %w", err)}if validationResult.HasErrors() {return output, fmt.Errorf("mapping validation failed: %s", validationResult.Error())}// Load species and calltype ID mapsspeciesIDMap, calltypeIDMap, err := loadSpeciesCalltypeIDs(database, mapping, uniqueSpecies, uniqueCalltypes)if err != nil {return output, fmt.Errorf("failed to load species/calltype IDs: %w", err)}// Validate files: hash exists, linked to dataset, no existing labelsfileIDMap, hashErrors := validateAndMapFiles(database, scannedFiles, input.ClusterID, input.DatasetID)output.Errors = append(output.Errors, hashErrors...)if len(fileIDMap) == 0 && len(scannedFiles) > 0 {output.Summary.ProcessingTimeMs = time.Since(startTime).Milliseconds()return output, nil}// Phase D: Transactional ImportimportedSegments, importedLabels, importedSubtypes, fileUpdates, importErrors := importSegmentsIntoDB(ctx, database, fileIDMap, scannedFiles, mapping, filterIDMap, speciesIDMap, calltypeIDMap, input.DatasetID, input.ProgressHandler,)output.Errors = append(output.Errors, importErrors...)// Build output segmentsoutput.Segments = append(output.Segments, importedSegments...)// Phase E: Write IDs back to .data filesif len(fileUpdates) > 0 {writeErrors := writeIDsToDataFiles(fileUpdates)output.Errors = append(output.Errors, writeErrors...)}output.Summary.DataFilesProcessed = len(fileIDMap)output.Summary.TotalSegments = countTotalSegments(fileIDMap)output.Summary.ImportedSegments = len(importedSegments)output.Summary.ImportedLabels = importedLabelsoutput.Summary.ImportedSubtypes = importedSubtypesoutput.Summary.ProcessingTimeMs = time.Since(startTime).Milliseconds()return output, nil}// validateSegmentImportInput validates input parametersfunc validateSegmentImportInput(input ImportSegmentsInput) error {// Validate folder existsif info, err := os.Stat(input.Folder); err != nil {return fmt.Errorf("folder does not exist: %s", input.Folder)} else if !info.IsDir() {return fmt.Errorf("path is not a folder: %s", input.Folder)}// Validate mapping file existsif _, err := os.Stat(input.Mapping); err != nil {return fmt.Errorf("mapping file does not exist: %s", input.Mapping)}// Validate IDsif err := utils.ValidateShortID(input.DatasetID, "dataset_id"); err != nil {return err}if err := utils.ValidateShortID(input.LocationID, "location_id"); err != nil {return err}if err := utils.ValidateShortID(input.ClusterID, "cluster_id"); err != nil {return err}return nil}// validateSegmentHierarchy validates dataset/location/cluster relationshipsfunc validateSegmentHierarchy(dbConn *sql.DB, datasetID, locationID, clusterID string) error {// Validate dataset exists and is structuredvar datasetType stringerr := dbConn.QueryRow(`SELECT type FROM dataset WHERE id = ? AND active = true`, datasetID).Scan(&datasetType)if err == sql.ErrNoRows {return fmt.Errorf("dataset not found: %s", datasetID)}if err != nil {return fmt.Errorf("failed to query dataset: %w", err)}if datasetType != "structured" {return fmt.Errorf("dataset must be 'structured' type, got: %s", datasetType)}// Validate location belongs to datasetvar locationExists boolerr = dbConn.QueryRow(`SELECT EXISTS(SELECT 1 FROM location WHERE id = ? AND dataset_id = ? AND active = true)`, locationID, datasetID).Scan(&locationExists)if err != nil {return fmt.Errorf("failed to query location: %w", err)}if !locationExists {return fmt.Errorf("location not found or not linked to dataset: %s", locationID)}// Validate cluster belongs to locationvar clusterExists boolerr = dbConn.QueryRow(`SELECT EXISTS(SELECT 1 FROM cluster WHERE id = ? AND location_id = ? AND active = true)`, clusterID, locationID).Scan(&clusterExists)if err != nil {return fmt.Errorf("failed to query cluster: %w", err)}if !clusterExists {return fmt.Errorf("cluster not found or not linked to location: %s", clusterID)}return nil}// scanAllDataFiles parses all .data files and collects unique valuesfunc scanAllDataFiles(dataFiles []string, folder string) ([]scannedDataFile,[]ImportSegmentError,map[string]bool,map[string]bool,map[string]map[string]bool,) {var scanned []scannedDataFilevar errors []ImportSegmentErroruniqueFilters := make(map[string]bool)uniqueSpecies := make(map[string]bool)uniqueCalltypes := make(map[string]map[string]bool) // species -> calltype -> truefor _, dataPath := range dataFiles {// Find corresponding WAV filewavPath := strings.TrimSuffix(dataPath, ".data")if _, err := os.Stat(wavPath); err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(dataPath),Stage: "validation",Message: fmt.Sprintf("corresponding WAV file not found: %s", filepath.Base(wavPath)),})continue}// Parse .data filedf, err := utils.ParseDataFile(dataPath)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(dataPath),Stage: "validation",Message: fmt.Sprintf("failed to parse .data file: %v", err),})continue}// Collect unique filters, species, calltypesfor _, seg := range df.Segments {for _, label := range seg.Labels {uniqueFilters[label.Filter] = trueuniqueSpecies[label.Species] = trueif label.CallType != "" {if uniqueCalltypes[label.Species] == nil {uniqueCalltypes[label.Species] = make(map[string]bool)}uniqueCalltypes[label.Species][label.CallType] = true}}}scanned = append(scanned, scannedDataFile{DataPath: dataPath,WavPath: wavPath,Duration: df.Meta.Duration,Segments: df.Segments,})}return scanned, errors, uniqueFilters, uniqueSpecies, uniqueCalltypes}// validateFiltersExist checks all filters exist in DB and returns ID mapfunc validateFiltersExist(dbConn *sql.DB, filterNames map[string]bool) (map[string]string, error) {filterIDMap := make(map[string]string)if len(filterNames) == 0 {return filterIDMap, nil}names := make([]string, 0, len(filterNames))for name := range filterNames {names = append(names, name)}query := `SELECT id, name FROM filter WHERE name IN (` + utils.Placeholders(len(names)) + `) AND active = true`args := make([]any, len(names))for i, name := range names {args[i] = name}rows, err := dbConn.Query(query, args...)if err != nil {return nil, fmt.Errorf("failed to query filters: %w", err)}defer rows.Close()for rows.Next() {var id, name stringif err := rows.Scan(&id, &name); err == nil {filterIDMap[name] = id}}// Check for missing filtersvar missing []stringfor name := range filterNames {if _, exists := filterIDMap[name]; !exists {missing = append(missing, name)}}if len(missing) > 0 {return nil, fmt.Errorf("filters not found in database: [%s]", strings.Join(missing, ", "))}return filterIDMap, nil}// loadSpeciesCalltypeIDs loads species and calltype ID mapsfunc loadSpeciesCalltypeIDs(dbConn *sql.DB,mapping utils.MappingFile,uniqueSpecies map[string]bool,uniqueCalltypes map[string]map[string]bool,) (map[string]string, map[string]map[string]string, error) {speciesIDMap := make(map[string]string)calltypeIDMap := make(map[string]map[string]string) // (dbSpecies, dbCalltype) -> calltype_id// Collect all DB species labels from mappingdbSpeciesSet := make(map[string]bool)for dataSpecies := range uniqueSpecies {if dbSpecies, ok := mapping.GetDBSpecies(dataSpecies); ok {dbSpeciesSet[dbSpecies] = true}}// Load species IDsif len(dbSpeciesSet) > 0 {dbSpeciesList := make([]string, 0, len(dbSpeciesSet))for s := range dbSpeciesSet {dbSpeciesList = append(dbSpeciesList, s)}query := `SELECT id, label FROM species WHERE label IN (` + utils.Placeholders(len(dbSpeciesList)) + `) AND active = true`args := make([]any, len(dbSpeciesList))for i, s := range dbSpeciesList {args[i] = s}rows, err := dbConn.Query(query, args...)if err != nil {return nil, nil, fmt.Errorf("failed to query species: %w", err)}defer rows.Close()for rows.Next() {var id, label stringif err := rows.Scan(&id, &label); err == nil {speciesIDMap[label] = id}}}// Load calltype IDsfor dataSpecies, ctSet := range uniqueCalltypes {dbSpecies, ok := mapping.GetDBSpecies(dataSpecies)if !ok {continue}if calltypeIDMap[dbSpecies] == nil {calltypeIDMap[dbSpecies] = make(map[string]string)}for dataCalltype := range ctSet {dbCalltype := mapping.GetDBCalltype(dataSpecies, dataCalltype)// Query calltype IDvar calltypeID stringerr := dbConn.QueryRow(`SELECT ct.idFROM call_type ctJOIN species s ON ct.species_id = s.idWHERE s.label = ? AND ct.label = ? AND ct.active = true`, dbSpecies, dbCalltype).Scan(&calltypeID)if err == nil {calltypeIDMap[dbSpecies][dbCalltype] = calltypeID}}}return speciesIDMap, calltypeIDMap, nil}// validateAndMapFiles validates files exist by hash, are linked to dataset, and have no existing labelsfunc validateAndMapFiles(dbConn *sql.DB,scannedFiles []scannedDataFile,clusterID string,datasetID string,) (map[string]scannedDataFile, []ImportSegmentError) {fileIDMap := make(map[string]scannedDataFile)var errors []ImportSegmentErrorfor _, sf := range scannedFiles {// Compute hashhash, err := utils.ComputeXXH64(sf.WavPath)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.WavPath),Stage: "hash",Message: fmt.Sprintf("failed to compute hash: %v", err),})continue}sf.WavHash = hash// Find file by hash in clustervar fileID stringvar duration float64err = dbConn.QueryRow(`SELECT id, duration FROM file WHERE xxh64_hash = ? AND cluster_id = ? AND active = true`, hash, clusterID).Scan(&fileID, &duration)if err == sql.ErrNoRows {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.WavPath),Stage: "validation",Message: fmt.Sprintf("file hash not found in database for cluster (hash: %s)", hash),})continue}if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.WavPath),Stage: "validation",Message: fmt.Sprintf("failed to query file: %v", err),})continue}sf.FileID = fileIDsf.Duration = duration// Verify file is linked to dataset via file_dataset junction table (composite FK)var fileLinkedToDataset boolerr = dbConn.QueryRow(`SELECT EXISTS(SELECT 1 FROM file_dataset WHERE file_id = ? AND dataset_id = ?)`, fileID, datasetID).Scan(&fileLinkedToDataset)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.WavPath),Stage: "validation",Message: fmt.Sprintf("failed to verify file-dataset link: %v", err),})continue}if !fileLinkedToDataset {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.WavPath),Stage: "validation",Message: fmt.Sprintf("file exists in cluster but is not linked to dataset %s", datasetID),})continue}// Check no existing labels for this filevar labelCount interr = dbConn.QueryRow(`SELECT COUNT(*) FROM label lJOIN segment s ON l.segment_id = s.idWHERE s.file_id = ? AND l.active = true`, fileID).Scan(&labelCount)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.WavPath),Stage: "validation",Message: fmt.Sprintf("failed to check existing labels: %v", err),})continue}if labelCount > 0 {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.WavPath),Stage: "validation",Message: fmt.Sprintf("file already has %d label(s) - fresh imports only", labelCount),})continue}fileIDMap[fileID] = sf}return fileIDMap, errors}// dataFileUpdate holds data to write back to .data file after importtype dataFileUpdate struct {DataPath stringWavHash stringLabelIDs map[int]map[int]string // segmentIndex -> labelIndex -> labelID}// importSegmentsIntoDB performs the transactional importfunc importSegmentsIntoDB(ctx context.Context,database *sql.DB,fileIDMap map[string]scannedDataFile,scannedFiles []scannedDataFile,mapping utils.MappingFile,filterIDMap map[string]string,speciesIDMap map[string]string,calltypeIDMap map[string]map[string]string,datasetID string,progressHandler func(processed, total int, message string),) ([]SegmentImport, int, int, []dataFileUpdate, []ImportSegmentError) {var importedSegments []SegmentImportvar errors []ImportSegmentErrorimportedLabels := 0importedSubtypes := 0var fileUpdates []dataFileUpdate// Begin transactiontx, err := db.BeginLoggedTx(ctx, database, "import_segments")if err != nil {errors = append(errors, ImportSegmentError{Stage: "import",Message: fmt.Sprintf("failed to begin transaction: %v", err),})return nil, 0, 0, nil, errors}defer tx.Rollback()// Process each validated filetotalFiles := len(fileIDMap)processedFiles := 0for _, sf := range fileIDMap {if sf.FileID == "" {continue // Was filtered out during validation}processedFiles++if progressHandler != nil {progressHandler(processedFiles, totalFiles, filepath.Base(sf.DataPath))}// Track label IDs for writing back to .data filefileUpdate := dataFileUpdate{DataPath: sf.DataPath,WavHash: sf.WavHash,LabelIDs: make(map[int]map[int]string),}// Process segmentsfor segIdx, seg := range sf.Segments {// Validate segment boundsif seg.StartTime >= seg.EndTime {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("invalid segment bounds: start=%.2f >= end=%.2f", seg.StartTime, seg.EndTime),})continue}if seg.EndTime > sf.Duration {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("segment end time (%.2f) exceeds file duration (%.2f)", seg.EndTime, sf.Duration),})continue}// Insert segmentsegmentID, err := utils.GenerateLongID()if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("failed to generate segment ID: %v", err),})continue}_, err = tx.ExecContext(ctx, `INSERT INTO segment (id, file_id, dataset_id, start_time, end_time, freq_low, freq_high, created_at, last_modified, active)VALUES (?, ?, ?, ?, ?, ?, ?, now(), now(), true)`, segmentID, sf.FileID, datasetID, seg.StartTime, seg.EndTime, seg.FreqLow, seg.FreqHigh)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("failed to insert segment: %v", err),})continue}// Process labelsvar segmentImport SegmentImportsegmentImport.SegmentID = segmentIDsegmentImport.FileName = filepath.Base(sf.WavPath)segmentImport.StartTime = seg.StartTimesegmentImport.EndTime = seg.EndTimesegmentImport.FreqLow = seg.FreqLowsegmentImport.FreqHigh = seg.FreqHighsegmentImport.Labels = make([]LabelImport, 0)fileUpdate.LabelIDs[segIdx] = make(map[int]string)for labelIdx, label := range seg.Labels {// Get DB species and calltypedbSpecies, ok := mapping.GetDBSpecies(label.Species)if !ok {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("species not found in mapping: %s", label.Species),})continue}speciesID, ok := speciesIDMap[dbSpecies]if !ok {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("species ID not found: %s", dbSpecies),})continue}filterID, ok := filterIDMap[label.Filter]if !ok {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("filter ID not found: %s", label.Filter),})continue}// Insert labellabelID, err := utils.GenerateLongID()if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("failed to generate label ID: %v", err),})continue}_, err = tx.ExecContext(ctx, `INSERT INTO label (id, segment_id, species_id, filter_id, certainty, created_at, last_modified, active)VALUES (?, ?, ?, ?, ?, now(), now(), true)`, labelID, segmentID, speciesID, filterID, label.Certainty)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("failed to insert label: %v", err),})continue}importedLabels++// Track label ID for .data file updatefileUpdate.LabelIDs[segIdx][labelIdx] = labelID// Insert label_metadata if comment existsif label.Comment != "" {escapedComment := strings.ReplaceAll(label.Comment, `"`, `\"`)metadataJSON := fmt.Sprintf(`{"comment": "%s"}`, escapedComment)_, err = tx.ExecContext(ctx, `INSERT INTO label_metadata (label_id, json, created_at, last_modified, active)VALUES (?, ?, now(), now(), true)`, labelID, metadataJSON)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("failed to insert label_metadata: %v", err),})continue}}// Build label import for outputlabelImport := LabelImport{LabelID: labelID,Species: dbSpecies,Filter: label.Filter,Certainty: label.Certainty,}if label.Comment != "" {labelImport.Comment = label.Comment}// Insert label_subtype if calltype existsif label.CallType != "" {dbCalltype := mapping.GetDBCalltype(label.Species, label.CallType)calltypeID := ""if calltypeIDMap[dbSpecies] != nil {calltypeID = calltypeIDMap[dbSpecies][dbCalltype]}if calltypeID == "" {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("calltype ID not found: %s/%s", dbSpecies, dbCalltype),})continue}subtypeID, err := utils.GenerateLongID()if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("failed to generate label_subtype ID: %v", err),})continue}_, err = tx.ExecContext(ctx, `INSERT INTO label_subtype (id, label_id, calltype_id, filter_id, certainty, created_at, last_modified, active)VALUES (?, ?, ?, ?, ?, now(), now(), true)`, subtypeID, labelID, calltypeID, filterID, label.Certainty)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("failed to insert label_subtype: %v", err),})continue}importedSubtypes++labelImport.CallType = dbCalltype}segmentImport.Labels = append(segmentImport.Labels, labelImport)}// If no labels succeeded, delete the orphaned segmentif len(segmentImport.Labels) == 0 {_, err = tx.ExecContext(ctx, `DELETE FROM segment WHERE id = ?`, segmentID)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(sf.DataPath),Stage: "import",Message: fmt.Sprintf("failed to delete orphaned segment: %v", err),})}// Remove from fileUpdate since no labels were importeddelete(fileUpdate.LabelIDs, segIdx)} else {importedSegments = append(importedSegments, segmentImport)}}fileUpdates = append(fileUpdates, fileUpdate)}// Commit transactionif err := tx.Commit(); err != nil {errors = append(errors, ImportSegmentError{Stage: "import",Message: fmt.Sprintf("failed to commit transaction: %v", err),})return nil, 0, 0, nil, errors}return importedSegments, importedLabels, importedSubtypes, fileUpdates, errors}// countTotalSegments counts total segments from validated filesfunc countTotalSegments(fileIDMap map[string]scannedDataFile) int {count := 0for _, sf := range fileIDMap {count += len(sf.Segments)}return count}// writeIDsToDataFiles writes skraak_hash and skraak_label_ids back to .data filesfunc writeIDsToDataFiles(fileUpdates []dataFileUpdate) []ImportSegmentError {var errors []ImportSegmentErrorfor _, fu := range fileUpdates {// Parse the .data filedf, err := utils.ParseDataFile(fu.DataPath)if err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(fu.DataPath),Stage: "import",Message: fmt.Sprintf("failed to re-parse .data file for writing: %v", err),})continue}// Write skraak_hash to metadataif df.Meta.Extra == nil {df.Meta.Extra = make(map[string]any)}df.Meta.Extra["skraak_hash"] = fu.WavHash// Write skraak_label_id to each labelfor segIdx, labelIDs := range fu.LabelIDs {if segIdx >= len(df.Segments) {continue}seg := df.Segments[segIdx]for labelIdx, labelID := range labelIDs {if labelIdx >= len(seg.Labels) {continue}label := seg.Labels[labelIdx]if label.Extra == nil {label.Extra = make(map[string]any)}label.Extra["skraak_label_id"] = labelID}}// Write the updated .data fileif err := df.Write(fu.DataPath); err != nil {errors = append(errors, ImportSegmentError{File: filepath.Base(fu.DataPath),Stage: "import",Message: fmt.Sprintf("failed to write updated .data file: %v", err),})continue}}return errors}
package toolsimport ("context""database/sql""fmt""os""time""skraak/db""skraak/utils")// ImportAudioFilesInput defines the input parameters for the import_audio_files tooltype ImportAudioFilesInput struct {FolderPath string `json:"folder_path"`DatasetID string `json:"dataset_id"`LocationID string `json:"location_id"`ClusterID string `json:"cluster_id"`Recursive *bool `json:"recursive,omitempty"` // *bool because default is true; plain bool would make "not provided" indistinguishable from "false"}// ImportAudioFilesOutput defines the output structure for the import_audio_files tooltype ImportAudioFilesOutput struct {Summary ImportSummary `json:"summary"`FileIDs []string `json:"file_ids"`Errors []utils.FileImportError `json:"errors,omitempty"`}// ImportSummary provides summary statistics for the import operationtype ImportSummary struct {TotalFiles int `json:"total_files"`ImportedFiles int `json:"imported_files"`SkippedFiles int `json:"skipped_files"` // DuplicatesFailedFiles int `json:"failed_files"`AudioMothFiles int `json:"audiomoth_files"`TotalDuration float64 `json:"total_duration_seconds"`ProcessingTime string `json:"processing_time"`}// ImportAudioFiles batch imports WAV files from a folder with hash-based duplicate detectionfunc ImportAudioFiles(ctx context.Context,input ImportAudioFilesInput,) (ImportAudioFilesOutput, error) {startTime := time.Now()var output ImportAudioFilesOutput// Default recursive to truerecursive := trueif input.Recursive != nil {recursive = *input.Recursive}// Validate database hierarchy (dataset → location → cluster)if err := validateImportInput(input, dbPath); err != nil {return output, fmt.Errorf("validation failed: %w", err)}// Open databasedatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Set cluster path if emptyerr = utils.EnsureClusterPath(database, input.ClusterID, input.FolderPath)if err != nil {return output, fmt.Errorf("failed to set cluster path: %w", err)}// Import the cluster (ALL THE LOGIC IS HERE)clusterOutput, err := utils.ImportCluster(database, utils.ClusterImportInput{FolderPath: input.FolderPath,DatasetID: input.DatasetID,LocationID: input.LocationID,ClusterID: input.ClusterID,Recursive: recursive,})if err != nil {return output, fmt.Errorf("cluster import failed: %w", err)}// Map to output formatoutput = ImportAudioFilesOutput{Summary: ImportSummary{TotalFiles: clusterOutput.TotalFiles,ImportedFiles: clusterOutput.ImportedFiles,SkippedFiles: clusterOutput.SkippedFiles,FailedFiles: clusterOutput.FailedFiles,AudioMothFiles: clusterOutput.AudioMothFiles,TotalDuration: clusterOutput.TotalDuration,ProcessingTime: time.Since(startTime).String(),},FileIDs: []string{}, // File IDs not tracked currentlyErrors: clusterOutput.Errors,}return output, nil}// validateImportInput validates all input parameters and database relationshipsfunc validateImportInput(input ImportAudioFilesInput, dbPath string) error {// Verify folder existsinfo, err := os.Stat(input.FolderPath)if err != nil {return fmt.Errorf("folder not accessible: %w", err)}if !info.IsDir() {return fmt.Errorf("path is not a directory: %s", input.FolderPath)}return validateHierarchyIDs(input.DatasetID, input.LocationID, input.ClusterID, dbPath)}// validateHierarchyIDs validates dataset/location/cluster ID formats and database relationshipsfunc validateHierarchyIDs(datasetID, locationID, clusterID, dbPath string) error {// Validate ID formats first (fast fail before DB queries)if err := utils.ValidateShortID(datasetID, "dataset_id"); err != nil {return err}if err := utils.ValidateShortID(locationID, "location_id"); err != nil {return err}if err := utils.ValidateShortID(clusterID, "cluster_id"); err != nil {return err}// Open database for validation queriesdatabase, err := db.OpenReadOnlyDB(dbPath)if err != nil {return fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Verify dataset exists and is activevar datasetExists boolerr = database.QueryRow("SELECT EXISTS(SELECT 1 FROM dataset WHERE id = ? AND active = true)", datasetID).Scan(&datasetExists)if err != nil {return fmt.Errorf("failed to query dataset: %w", err)}if !datasetExists {return fmt.Errorf("dataset not found or inactive: %s", datasetID)}// Verify dataset is 'structured' type (file imports only support structured datasets)if err := utils.ValidateDatasetTypeForImport(database, datasetID); err != nil {return err}// Verify location exists and belongs to datasetvar locationDatasetID stringerr = database.QueryRow("SELECT dataset_id FROM location WHERE id = ? AND active = true", locationID).Scan(&locationDatasetID)if err == sql.ErrNoRows {return fmt.Errorf("location not found or inactive: %s", locationID)}if err != nil {return fmt.Errorf("failed to query location: %w", err)}if locationDatasetID != datasetID {return fmt.Errorf("location %s does not belong to dataset %s", locationID, datasetID)}// Verify cluster exists and belongs to locationvar clusterLocationID stringerr = database.QueryRow("SELECT location_id FROM cluster WHERE id = ? AND active = true", clusterID).Scan(&clusterLocationID)if err == sql.ErrNoRows {return fmt.Errorf("cluster not found or inactive: %s", clusterID)}if err != nil {return fmt.Errorf("failed to query cluster: %w", err)}if clusterLocationID != locationID {return fmt.Errorf("cluster %s does not belong to location %s", clusterID, locationID)}return nil}
package toolsimport ("context""database/sql""fmt""os""path/filepath""strings""time""skraak/db""skraak/utils")// ImportFileInput defines the input parameters for the import_file tooltype ImportFileInput struct {FilePath string `json:"file_path"`DatasetID string `json:"dataset_id"`LocationID string `json:"location_id"`ClusterID string `json:"cluster_id"`}// ImportFileOutput defines the output structure for the import_file tooltype ImportFileOutput struct {FileID string `json:"file_id"`FileName string `json:"file_name"`Hash string `json:"hash"`Duration float64 `json:"duration_seconds"`SampleRate int `json:"sample_rate"`TimestampLocal time.Time `json:"timestamp_local"`IsAudioMoth bool `json:"is_audiomoth"`IsDuplicate bool `json:"is_duplicate"`ProcessingTime string `json:"processing_time"`Error *string `json:"error,omitempty"`}// ImportFile imports a single WAV file into the database with duplicate detectionfunc ImportFile(ctx context.Context,input ImportFileInput,) (ImportFileOutput, error) {startTime := time.Now()var output ImportFileOutput// Phase 1: Validate file path_, err := validateFilePath(input.FilePath)if err != nil {return output, fmt.Errorf("file validation failed: %w", err)}output.FileName = filepath.Base(input.FilePath)// Phase 2: Validate database hierarchyif err := validateHierarchyIDs(input.DatasetID, input.LocationID, input.ClusterID, dbPath); err != nil {return output, fmt.Errorf("hierarchy validation failed: %w", err)}// Phase 3: Open database connection (single connection for all DB operations)database, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("database connection failed: %w", err)}defer database.Close()// Phase 4: Get location data for astronomical calculationslocData, err := utils.GetLocationData(database, input.LocationID)if err != nil {return output, fmt.Errorf("failed to get location data: %w", err)}// Phase 5: Process file metadataresult, err := utils.ProcessSingleFile(input.FilePath, locData.Latitude, locData.Longitude, locData.TimezoneID, true)if err != nil {errMsg := err.Error()output.Error = &errMsgoutput.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("file processing failed: %w", err)}// Populate output with extracted metadataoutput.FileName = result.FileNameoutput.Hash = result.Hashoutput.Duration = result.Durationoutput.SampleRate = result.SampleRateoutput.TimestampLocal = result.TimestampLocaloutput.IsAudioMoth = result.IsAudioMoth// Phase 6: Ensure cluster path is setif err := utils.EnsureClusterPath(database, input.ClusterID, filepath.Dir(input.FilePath)); err != nil {return output, fmt.Errorf("failed to set cluster path: %w", err)}// Phase 7: Insert into databasefileID, isDuplicate, err := insertFileIntoDB(ctx, database, result, input.DatasetID, input.ClusterID, input.LocationID)if err != nil {errMsg := err.Error()output.Error = &errMsgoutput.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("database insertion failed: %w", err)}output.FileID = fileIDoutput.IsDuplicate = isDuplicateoutput.ProcessingTime = time.Since(startTime).String()return output, nil}// validateFilePath validates the file exists, is a regular file, is a WAV file, and is not emptyfunc validateFilePath(filePath string) (os.FileInfo, error) {// Check file existsinfo, err := os.Stat(filePath)if err != nil {if os.IsNotExist(err) {return nil, fmt.Errorf("file does not exist: %s", filePath)}return nil, fmt.Errorf("cannot access file: %w", err)}// Check it's a regular fileif !info.Mode().IsRegular() {return nil, fmt.Errorf("path is not a regular file: %s", filePath)}// Check extension is .wav (case-insensitive)ext := strings.ToLower(filepath.Ext(filePath))if ext != ".wav" {return nil, fmt.Errorf("file must be a WAV file (got extension: %s)", ext)}// Check file is not emptyif info.Size() == 0 {return nil, fmt.Errorf("file is empty: %s", filePath)}return info, nil}// insertFileIntoDB inserts a single file into the database// Returns (fileID, isDuplicate, error)func insertFileIntoDB(ctx context.Context,database *sql.DB,result *utils.FileProcessingResult,datasetID, clusterID, locationID string,) (string, bool, error) {// Begin logged transactiontx, err := db.BeginLoggedTx(ctx, database, "import_audio_file")if err != nil {return "", false, fmt.Errorf("failed to begin transaction: %w", err)}defer tx.Rollback() // Rollback if not committed// Check for duplicate hashexistingID, isDup, err := utils.CheckDuplicateHash(tx, result.Hash)if err != nil {return "", false, err}if isDup {return existingID, true, nil}// Generate file IDfileID, err := utils.GenerateLongID()if err != nil {return "", false, fmt.Errorf("ID generation failed: %w", err)}// Insert file record_, err = tx.ExecContext(ctx, `INSERT INTO file (id, file_name, xxh64_hash, location_id, timestamp_local,cluster_id, duration, sample_rate, maybe_solar_night, maybe_civil_night,moon_phase, created_at, last_modified, active) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, now(), now(), true)`,fileID, result.FileName, result.Hash, locationID,result.TimestampLocal, clusterID, result.Duration, result.SampleRate,result.AstroData.SolarNight, result.AstroData.CivilNight, result.AstroData.MoonPhase,)if err != nil {return "", false, fmt.Errorf("file insert failed: %w", err)}// Insert file_dataset junction_, err = tx.ExecContext(ctx, `INSERT INTO file_dataset (file_id, dataset_id, created_at, last_modified)VALUES (?, ?, now(), now())`, fileID, datasetID)if err != nil {return "", false, fmt.Errorf("file_dataset insert failed: %w", err)}// If AudioMoth, insert moth_metadataif result.IsAudioMoth && result.MothData != nil {_, err = tx.ExecContext(ctx, `INSERT INTO moth_metadata (file_id, timestamp, recorder_id, gain, battery_v, temp_c,created_at, last_modified, active) VALUES (?, ?, ?, ?, ?, ?, now(), now(), true)`,fileID,result.MothData.Timestamp,&result.MothData.RecorderID,&result.MothData.Gain,&result.MothData.BatteryV,&result.MothData.TempC,)if err != nil {return "", false, fmt.Errorf("moth_metadata insert failed: %w", err)}}// Commit transactionif err = tx.Commit(); err != nil {return "", false, fmt.Errorf("transaction commit failed: %w", err)}return fileID, false, nil}
package toolsimport ("context""database/sql""fmt""os""path/filepath""sort""strings""skraak/db")// ExportDatasetInput defines the input parameters for the export dataset tooltype ExportDatasetInput struct {DatasetID string `json:"dataset_id"`Output string `json:"output"`DryRun bool `json:"dry_run"`Force bool `json:"force"`}// ExportDatasetOutput defines the output structuretype ExportDatasetOutput struct {DatasetID string `json:"dataset_id"`DatasetName string `json:"dataset_name"`OutputPath string `json:"output_path"`RowCounts map[string]int64 `json:"row_counts"`FileSizeMB float64 `json:"file_size_mb,omitempty"`DryRun bool `json:"dry_run"`Message string `json:"message"`}// TableRelationship defines how a table relates to a datasettype TableRelationship struct {Table string // table nameRelation string // "owned" | "owned-via" | "copy"FilterCol string // column to filter onViaTable string // for owned-via: table to join through}// Dataset tables manifest - defines how each table relates to a datasetvar datasetTables = []TableRelationship{// Owned directly{Table: "dataset", Relation: "owned", FilterCol: "id"},{Table: "location", Relation: "owned", FilterCol: "dataset_id"},{Table: "cluster", Relation: "owned", FilterCol: "dataset_id"},{Table: "segment", Relation: "owned", FilterCol: "dataset_id"},{Table: "file_dataset", Relation: "owned", FilterCol: "dataset_id"},// Owned via FK chain{Table: "file", Relation: "owned-via", FilterCol: "cluster_id", ViaTable: "cluster"},{Table: "moth_metadata", Relation: "owned-via", FilterCol: "file_id", ViaTable: "file"},{Table: "file_metadata", Relation: "owned-via", FilterCol: "file_id", ViaTable: "file"},{Table: "label_metadata", Relation: "owned-via", FilterCol: "label_id", ViaTable: "label"},{Table: "label", Relation: "owned-via", FilterCol: "segment_id", ViaTable: "segment"},{Table: "label_subtype", Relation: "owned-via", FilterCol: "label_id", ViaTable: "label"},// Referenced (subset extraction) - none remaining// Copied as-is (no filtering){Table: "ebird_taxonomy", Relation: "copy"},{Table: "species", Relation: "copy"},{Table: "call_type", Relation: "copy"},{Table: "cyclic_recording_pattern", Relation: "copy"},{Table: "filter", Relation: "copy"},}// ExportDataset exports a single dataset with all related data to a new database// Note: this fails if exporting from a db with FK constraints removed (sometimes// I remove them as duckdb is a pain when editing records due to indexes and FK's,// it removes then reinserts therefore violating constraints)func ExportDataset(ctx context.Context,input ExportDatasetInput,) (ExportDatasetOutput, error) {var output ExportDatasetOutputoutput.DatasetID = input.DatasetIDoutput.OutputPath = input.Outputoutput.DryRun = input.DryRunoutput.RowCounts = make(map[string]int64)// Open source database (read-only for safety)sourceDB, err := db.OpenReadOnlyDB(dbPath)if err != nil {return output, fmt.Errorf("failed to open source database: %w", err)}// Verify dataset exists and get name/typevar datasetName, datasetType stringerr = sourceDB.QueryRowContext(ctx,"SELECT name, type FROM dataset WHERE id = ? AND active = true",input.DatasetID,).Scan(&datasetName, &datasetType)if err != nil {sourceDB.Close()return output, fmt.Errorf("dataset not found: %s", input.DatasetID)}output.DatasetName = datasetName// Only structured datasets can be exportedif datasetType != "structured" {sourceDB.Close()return output, fmt.Errorf("cannot export dataset of type '%s': only structured datasets are supported", datasetType)}// Check if output file existsif !input.DryRun {if _, err := os.Stat(input.Output); err == nil && !input.Force {sourceDB.Close()return output, fmt.Errorf("output file exists: %s (use --force to overwrite)", input.Output)}}// Get FK order for tablesfkOrder, err := db.GetFKOrder(sourceDB)if err != nil {sourceDB.Close()return output, fmt.Errorf("failed to compute table order: %w", err)}// Sort our manifest by FK orderorderedTables := orderByFKDependency(datasetTables, fkOrder)// Calculate row counts for each tablefor _, tr := range orderedTables {count, err := countTableRows(ctx, sourceDB, tr, input.DatasetID)if err != nil {sourceDB.Close()return output, fmt.Errorf("failed to count rows in %s: %w", tr.Table, err)}if count > 0 {output.RowCounts[tr.Table] = count}}// If dry-run, return nowif input.DryRun {sourceDB.Close()output.Message = fmt.Sprintf("Would export dataset '%s' (%s)", datasetName, input.DatasetID)return output, nil}// Close source DB before creating output (DuckDB can't attach same file twice)sourceDB.Close()// Create output directory if neededoutputDir := filepath.Dir(input.Output)if outputDir != "" && outputDir != "." {if err := os.MkdirAll(outputDir, 0755); err != nil {return output, fmt.Errorf("failed to create output directory: %w", err)}}// Create output databaseoutputDB, err := createOutputDatabase(input.Output)if err != nil {return output, fmt.Errorf("failed to create output database: %w", err)}defer outputDB.Close()// Attach source database_, err = outputDB.ExecContext(ctx, fmt.Sprintf("ATTACH '%s' AS source", dbPath))if err != nil {return output, fmt.Errorf("failed to attach source database: %w", err)}// Copy data in FK orderfor _, tr := range orderedTables {if tr.Relation == "copy" {// Copy entire table as-iserr = copyTableAsIs(ctx, outputDB, tr.Table)} else {// Owned or owned-via: filter by dataseterr = copyTableData(ctx, outputDB, tr, input.DatasetID)}if err != nil {return output, fmt.Errorf("failed to copy %s: %w", tr.Table, err)}}// Detach source_, err = outputDB.ExecContext(ctx, "DETACH source")if err != nil {return output, fmt.Errorf("failed to detach source database: %w", err)}// Close output DB before getting file sizeoutputDB.Close()outputDB = nil// Get file sizeif info, err := os.Stat(input.Output); err == nil {output.FileSizeMB = float64(info.Size()) / 1024 / 1024}// Create empty event log fileeventLogPath := input.Output + ".events.jsonl"eventFile, err := os.Create(eventLogPath)if err != nil {return output, fmt.Errorf("failed to create event log file: %w", err)}if err := eventFile.Close(); err != nil {return output, fmt.Errorf("failed to close event log file: %w", err)}output.Message = fmt.Sprintf("Successfully exported dataset '%s' (%s) to %s",datasetName, input.DatasetID, input.Output)return output, nil}// createOutputDatabase creates a new database with the schemafunc createOutputDatabase(outputPath string) (*sql.DB, error) {// Remove existing file if anyos.Remove(outputPath)// Open new database connectionconnStr := outputPath + "?access_mode=read_write"database, err := sql.Open("duckdb", connStr)if err != nil {return nil, fmt.Errorf("failed to create output database: %w", err)}// Read and execute schemaschemaSQL, err := db.ReadSchemaSQL()if err != nil {database.Close()return nil, fmt.Errorf("failed to read schema: %w", err)}statements := db.ExtractDDLStatements(schemaSQL)for _, stmt := range statements {// Skip CREATE TABLE AS SELECT statements - they don't work on empty databaseif stmt.Type == "CREATE_TABLE_AS" {continue}if _, err := database.Exec(stmt.SQL); err != nil {// Ignore "already exists" errors for typesif !strings.Contains(err.Error(), "already exists") {database.Close()return nil, fmt.Errorf("failed to execute DDL for %s: %w", stmt.TableName, err)}}}return database, nil}// copyTableAsIs copies an entire table without filtering.// Table names are interpolated via Sprintf because SQL parameterization doesn't support// identifiers (table/column names) — only values. This is safe because all table names// come from the hardcoded datasetTables manifest, never from user input.func copyTableAsIs(ctx context.Context, outputDB *sql.DB, table string) error {query := fmt.Sprintf("INSERT INTO %s SELECT * FROM source.%s", table, table)_, err := outputDB.ExecContext(ctx, query)return err}// copyTableData copies data from source to output databasefunc copyTableData(ctx context.Context, outputDB *sql.DB, tr TableRelationship, datasetID string) error {var query stringswitch tr.Relation {case "owned":// Direct filter on dataset_id (or id for dataset table)if tr.Table == "dataset" {query = fmt.Sprintf("INSERT INTO %s SELECT * FROM source.%s WHERE id = ?", tr.Table, tr.Table)} else {query = fmt.Sprintf("INSERT INTO %s SELECT * FROM source.%s WHERE dataset_id = ?", tr.Table, tr.Table)}case "owned-via":// Filter via FK chainquery = buildOwnedViaQuery(tr, datasetID)default:return fmt.Errorf("unknown relation type: %s", tr.Relation)}_, err := outputDB.ExecContext(ctx, query, datasetID)return err}// buildOwnedViaQuery builds a query for owned-via tablesfunc buildOwnedViaQuery(tr TableRelationship, datasetID string) string {switch tr.ViaTable {case "cluster":return fmt.Sprintf(`INSERT INTO %s SELECT * FROM source.%sWHERE %s IN (SELECT id FROM source.cluster WHERE dataset_id = ?)`,tr.Table, tr.Table, tr.FilterCol)case "file":return fmt.Sprintf(`INSERT INTO %s SELECT * FROM source.%sWHERE %s IN (SELECT id FROM source.file WHERE cluster_id IN(SELECT id FROM source.cluster WHERE dataset_id = ?))`,tr.Table, tr.Table, tr.FilterCol)case "segment":return fmt.Sprintf(`INSERT INTO %s SELECT * FROM source.%sWHERE %s IN (SELECT id FROM source.segment WHERE dataset_id = ?)`,tr.Table, tr.Table, tr.FilterCol)case "label":return fmt.Sprintf(`INSERT INTO %s SELECT * FROM source.%sWHERE %s IN (SELECT id FROM source.label WHERE segment_id IN(SELECT id FROM source.segment WHERE dataset_id = ?))`,tr.Table, tr.Table, tr.FilterCol)default:// Generic fallbackreturn fmt.Sprintf(`INSERT INTO %s SELECT * FROM source.%s WHERE %s IN(SELECT id FROM source.%s WHERE dataset_id = ?)`,tr.Table, tr.Table, tr.FilterCol, tr.ViaTable)}}// countTableRows counts rows for a table relationshipfunc countTableRows(ctx context.Context, db *sql.DB, tr TableRelationship, datasetID string) (int64, error) {var query stringswitch tr.Relation {case "copy":// Count all rows in tablequery = "SELECT COUNT(*) FROM " + tr.Tablecase "owned":if tr.Table == "dataset" {query = "SELECT COUNT(*) FROM " + tr.Table + " WHERE id = ?"} else {query = "SELECT COUNT(*) FROM " + tr.Table + " WHERE dataset_id = ?"}case "owned-via":query = buildCountOwnedViaQuery(tr)default:return 0, nil}var count int64err := db.QueryRowContext(ctx, query, datasetID).Scan(&count)return count, err}// buildCountOwnedViaQuery builds a count query for owned-via tablesfunc buildCountOwnedViaQuery(tr TableRelationship) string {switch tr.ViaTable {case "cluster":return fmt.Sprintf(`SELECT COUNT(*) FROM %s WHERE %s IN(SELECT id FROM cluster WHERE dataset_id = ?)`, tr.Table, tr.FilterCol)case "file":return fmt.Sprintf(`SELECT COUNT(*) FROM %s WHERE %s IN(SELECT id FROM file WHERE cluster_id IN(SELECT id FROM cluster WHERE dataset_id = ?))`, tr.Table, tr.FilterCol)case "segment":return fmt.Sprintf(`SELECT COUNT(*) FROM %s WHERE %s IN(SELECT id FROM segment WHERE dataset_id = ?)`, tr.Table, tr.FilterCol)case "label":return fmt.Sprintf(`SELECT COUNT(*) FROM %s WHERE %s IN(SELECT id FROM label WHERE segment_id IN(SELECT id FROM segment WHERE dataset_id = ?))`, tr.Table, tr.FilterCol)default:return fmt.Sprintf(`SELECT COUNT(*) FROM %s WHERE %s IN(SELECT id FROM %s WHERE dataset_id = ?)`, tr.Table, tr.FilterCol, tr.ViaTable)}}// orderByFKDependency sorts tables by FK dependency orderfunc orderByFKDependency(tables []TableRelationship, fkOrder []string) []TableRelationship {// Create a map for quick order lookuporderMap := make(map[string]int)for i, table := range fkOrder {orderMap[table] = i}// Sort by FK ordersorted := make([]TableRelationship, len(tables))copy(sorted, tables)sort.Slice(sorted, func(i, j int) bool {ti, tj := sorted[i], sorted[j]oi := orderMap[ti.Table]oj := orderMap[tj.Table]return oi < oj})return sorted}
package toolsimport ("context""fmt""skraak/db""skraak/utils""strings")// DatasetInput defines the input parameters for the create_or_update_dataset tooltype DatasetInput struct {ID *string `json:"id,omitempty"`Name *string `json:"name,omitempty"`Description *string `json:"description,omitempty"`Type *string `json:"type,omitempty"`}// DatasetOutput defines the output structuretype DatasetOutput struct {Dataset db.Dataset `json:"dataset"`Message string `json:"message"`}// CreateOrUpdateDataset creates a new dataset or updates an existing onefunc CreateOrUpdateDataset(ctx context.Context,input DatasetInput,) (DatasetOutput, error) {if input.ID != nil && strings.TrimSpace(*input.ID) != "" {return updateDataset(ctx, input)}return createDataset(ctx, input)}func createDataset(ctx context.Context, input DatasetInput) (DatasetOutput, error) {var output DatasetOutput// Validate name (required for create)if input.Name == nil || strings.TrimSpace(*input.Name) == "" {return output, fmt.Errorf("name is required when creating a dataset")}if err := utils.ValidateStringLength(*input.Name, "name", utils.MaxDatasetNameLen); err != nil {return output, err}// Validate description length if providedif err := utils.ValidateOptionalStringLength(input.Description, "description", utils.MaxDescriptionLen); err != nil {return output, err}// Validate and set typedatasetType := db.DatasetTypeStructured // Defaultif input.Type != nil {typeStr := strings.ToLower(strings.TrimSpace(*input.Type))switch typeStr {case "structured":datasetType = db.DatasetTypeStructuredcase "unstructured":datasetType = db.DatasetTypeUnstructuredcase "test":datasetType = db.DatasetTypeTestcase "train":datasetType = db.DatasetTypeTraindefault:return output, fmt.Errorf("invalid type '%s': must be 'structured', 'unstructured', 'test', or 'train'", *input.Type)}}// Open writable database connectiondatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("database connection failed: %w", err)}defer database.Close()// Begin logged transactiontx, err := db.BeginLoggedTx(ctx, database, "create_or_update_dataset")if err != nil {return output, fmt.Errorf("failed to begin transaction: %w", err)}defer func() {if err != nil {tx.Rollback()}}()// Check for existing dataset with same name (UNIQUE constraint)var existingID stringerr = tx.QueryRowContext(ctx,"SELECT id FROM dataset WHERE name = ? AND active = true",*input.Name,).Scan(&existingID)if err == nil {// Dataset with this name already exists - return existing (consistent duplicate handling)var dataset db.Dataseterr = tx.QueryRowContext(ctx,"SELECT id, name, description, created_at, last_modified, active, type FROM dataset WHERE id = ?",existingID,).Scan(&dataset.ID, &dataset.Name, &dataset.Description, &dataset.CreatedAt, &dataset.LastModified, &dataset.Active, &dataset.Type)if err != nil {return output, fmt.Errorf("failed to fetch existing dataset: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Dataset = datasetoutput.Message = fmt.Sprintf("Dataset with name '%s' already exists (ID: %s) - returning existing dataset", dataset.Name, dataset.ID)return output, nil}// Generate IDid, err := utils.GenerateShortID()if err != nil {return output, fmt.Errorf("failed to generate ID: %w", err)}// Insert dataset_, err = tx.ExecContext(ctx,"INSERT INTO dataset (id, name, description, type, created_at, last_modified, active) VALUES (?, ?, ?, ?, CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, TRUE)",id, *input.Name, input.Description, string(datasetType),)if err != nil {return output, fmt.Errorf("failed to create dataset: %w", err)}// Fetch the created datasetvar dataset db.Dataseterr = tx.QueryRowContext(ctx,"SELECT id, name, description, created_at, last_modified, active, type FROM dataset WHERE id = ?",id,).Scan(&dataset.ID, &dataset.Name, &dataset.Description, &dataset.CreatedAt, &dataset.LastModified, &dataset.Active, &dataset.Type)if err != nil {return output, fmt.Errorf("failed to fetch created dataset: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Dataset = datasetoutput.Message = fmt.Sprintf("Successfully created dataset '%s' with ID %s (type: %s)",dataset.Name, dataset.ID, dataset.Type)return output, nil}func updateDataset(ctx context.Context, input DatasetInput) (DatasetOutput, error) {var output DatasetOutputdatasetID := *input.ID// Validate ID formatif err := utils.ValidateShortID(datasetID, "dataset_id"); err != nil {return output, err}// Validate fields if providedif err := utils.ValidateOptionalStringLength(input.Name, "name", utils.MaxDatasetNameLen); err != nil {return output, err}if err := utils.ValidateOptionalStringLength(input.Description, "description", utils.MaxDescriptionLen); err != nil {return output, err}if input.Type != nil {typeValue := strings.ToLower(*input.Type)if typeValue != "structured" && typeValue != "unstructured" && typeValue != "test" && typeValue != "train" {return output, fmt.Errorf("invalid dataset type: %s (must be 'structured', 'unstructured', 'test', or 'train')", *input.Type)}}// Open writable databasedatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Verify dataset exists and check active statusvar exists, active boolerr = database.QueryRow("SELECT EXISTS(SELECT 1 FROM dataset WHERE id = ?), COALESCE((SELECT active FROM dataset WHERE id = ?), false)", datasetID, datasetID).Scan(&exists, &active)if err != nil {return output, fmt.Errorf("failed to query dataset: %w", err)}if !exists {return output, fmt.Errorf("dataset not found: %s", datasetID)}if !active {return output, fmt.Errorf("dataset '%s' is not active (cannot update inactive datasets)", datasetID)}// Build dynamic UPDATE queryupdates := []string{}args := []any{}if input.Name != nil {updates = append(updates, "name = ?")args = append(args, *input.Name)}if input.Description != nil {updates = append(updates, "description = ?")args = append(args, *input.Description)}if input.Type != nil {updates = append(updates, "type = ?")args = append(args, strings.ToLower(*input.Type))}if len(updates) == 0 {return output, fmt.Errorf("no fields provided to update")}// Always update last_modifiedupdates = append(updates, "last_modified = now()")args = append(args, datasetID)query := fmt.Sprintf("UPDATE dataset SET %s WHERE id = ?", strings.Join(updates, ", "))// Begin logged transaction for updatetx, err := db.BeginLoggedTx(ctx, database, "create_or_update_dataset")if err != nil {return output, fmt.Errorf("failed to begin transaction: %w", err)}defer func() {if err != nil {tx.Rollback()}}()_, err = tx.Exec(query, args...)if err != nil {return output, fmt.Errorf("failed to update dataset: %w", err)}// Fetch the updated datasetvar dataset db.Dataseterr = tx.QueryRow("SELECT id, name, description, created_at, last_modified, active, type FROM dataset WHERE id = ?",datasetID,).Scan(&dataset.ID, &dataset.Name, &dataset.Description, &dataset.CreatedAt, &dataset.LastModified, &dataset.Active, &dataset.Type)if err != nil {return output, fmt.Errorf("failed to fetch updated dataset: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Dataset = datasetoutput.Message = fmt.Sprintf("Successfully updated dataset '%s' (ID: %s)", dataset.Name, dataset.ID)return output, nil}
package toolsimport ("context""fmt""skraak/db""skraak/utils""strings")// ClusterInput defines the input parameters for the create_or_update_cluster tooltype ClusterInput struct {ID *string `json:"id,omitempty"`DatasetID *string `json:"dataset_id,omitempty"`LocationID *string `json:"location_id,omitempty"`Name *string `json:"name,omitempty"`SampleRate *int `json:"sample_rate,omitempty"`Path *string `json:"path,omitempty"`CyclicRecordingPatternID *string `json:"cyclic_recording_pattern_id,omitempty"`Description *string `json:"description,omitempty"`}// ClusterOutput defines the output structuretype ClusterOutput struct {Cluster db.Cluster `json:"cluster"`Message string `json:"message"`}// CreateOrUpdateCluster creates a new cluster or updates an existing one within a locationfunc CreateOrUpdateCluster(ctx context.Context,input ClusterInput,) (ClusterOutput, error) {if input.ID != nil && strings.TrimSpace(*input.ID) != "" {return updateCluster(ctx, input)}return createCluster(ctx, input)}// validateClusterFields validates fields common to both create and updatefunc validateClusterFields(input ClusterInput) error {if err := utils.ValidateOptionalStringLength(input.Name, "name", utils.MaxNameLen); err != nil {return err}if err := utils.ValidateOptionalStringLength(input.Description, "description", utils.MaxDescriptionLen); err != nil {return err}if err := utils.ValidateOptionalStringLength(input.Path, "path", utils.MaxPathLen); err != nil {return err}if input.SampleRate != nil {if err := utils.ValidatePositive(*input.SampleRate, "sample_rate"); err != nil {return err}// Also check reasonable boundsif err := utils.ValidateSampleRate(*input.SampleRate); err != nil {return err}}return nil}func createCluster(ctx context.Context, input ClusterInput) (ClusterOutput, error) {var output ClusterOutput// Validate required fields for createif input.DatasetID == nil || strings.TrimSpace(*input.DatasetID) == "" {return output, fmt.Errorf("dataset_id is required when creating a cluster")}if input.LocationID == nil || strings.TrimSpace(*input.LocationID) == "" {return output, fmt.Errorf("location_id is required when creating a cluster")}if input.Name == nil || strings.TrimSpace(*input.Name) == "" {return output, fmt.Errorf("name is required when creating a cluster")}if input.SampleRate == nil {return output, fmt.Errorf("sample_rate is required when creating a cluster")}// Validate ID formatsif err := utils.ValidateShortID(*input.DatasetID, "dataset_id"); err != nil {return output, err}if err := utils.ValidateShortID(*input.LocationID, "location_id"); err != nil {return output, err}if err := validateClusterFields(input); err != nil {return output, err}// Validate optional pattern ID formatif err := utils.ValidateOptionalShortID(input.CyclicRecordingPatternID, "cyclic_recording_pattern_id"); err != nil {return output, err}// Open writable database connectiondatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("database connection failed: %w", err)}defer database.Close()// Begin logged transactiontx, err := db.BeginLoggedTx(ctx, database, "create_or_update_cluster")if err != nil {return output, fmt.Errorf("failed to begin transaction: %w", err)}defer func() {if err != nil {tx.Rollback()}}()// Verify dataset exists and is activevar datasetExists, datasetActive boolvar datasetName stringerr = tx.QueryRowContext(ctx,"SELECT EXISTS(SELECT 1 FROM dataset WHERE id = ?), COALESCE((SELECT active FROM dataset WHERE id = ?), false), COALESCE((SELECT name FROM dataset WHERE id = ?), '')",*input.DatasetID, *input.DatasetID, *input.DatasetID,).Scan(&datasetExists, &datasetActive, &datasetName)if err != nil {return output, fmt.Errorf("failed to verify dataset: %w", err)}if !datasetExists {return output, fmt.Errorf("dataset with ID '%s' does not exist", *input.DatasetID)}if !datasetActive {return output, fmt.Errorf("dataset '%s' (ID: %s) is not active", datasetName, *input.DatasetID)}// Verify location exists, is active, and belongs to the specified datasetvar locationExists, locationActive boolvar locationName stringvar locationDatasetID stringerr = tx.QueryRowContext(ctx,"SELECT EXISTS(SELECT 1 FROM location WHERE id = ?), COALESCE((SELECT active FROM location WHERE id = ?), false), COALESCE((SELECT name FROM location WHERE id = ?), ''), COALESCE((SELECT dataset_id FROM location WHERE id = ?), '')",*input.LocationID, *input.LocationID, *input.LocationID, *input.LocationID,).Scan(&locationExists, &locationActive, &locationName, &locationDatasetID)if err != nil {return output, fmt.Errorf("failed to verify location: %w", err)}if !locationExists {return output, fmt.Errorf("location with ID '%s' does not exist", *input.LocationID)}if !locationActive {return output, fmt.Errorf("location '%s' (ID: %s) is not active", locationName, *input.LocationID)}if locationDatasetID != *input.DatasetID {return output, fmt.Errorf("location '%s' (ID: %s) does not belong to dataset '%s' (ID: %s) - it belongs to dataset ID '%s'",locationName, *input.LocationID, datasetName, *input.DatasetID, locationDatasetID)}// Verify cyclic recording pattern if providedif input.CyclicRecordingPatternID != nil && strings.TrimSpace(*input.CyclicRecordingPatternID) != "" {var patternExists, patternActive boolerr = tx.QueryRowContext(ctx,"SELECT EXISTS(SELECT 1 FROM cyclic_recording_pattern WHERE id = ?), COALESCE((SELECT active FROM cyclic_recording_pattern WHERE id = ?), false)",*input.CyclicRecordingPatternID, *input.CyclicRecordingPatternID,).Scan(&patternExists, &patternActive)if err != nil {return output, fmt.Errorf("failed to verify cyclic recording pattern: %w", err)}if !patternExists {return output, fmt.Errorf("cyclic recording pattern with ID '%s' does not exist", *input.CyclicRecordingPatternID)}if !patternActive {return output, fmt.Errorf("cyclic recording pattern with ID '%s' is not active", *input.CyclicRecordingPatternID)}}// Check for existing cluster with same name in location (UNIQUE constraint)var existingID stringerr = tx.QueryRowContext(ctx,"SELECT id FROM cluster WHERE location_id = ? AND name = ? AND active = true",*input.LocationID, *input.Name,).Scan(&existingID)if err == nil {// Cluster with this name already exists in location - return existing (consistent duplicate handling)var cluster db.Clustererr = tx.QueryRowContext(ctx,"SELECT id, dataset_id, location_id, name, description, created_at, last_modified, active, cyclic_recording_pattern_id, sample_rate FROM cluster WHERE id = ?",existingID,).Scan(&cluster.ID, &cluster.DatasetID, &cluster.LocationID, &cluster.Name, &cluster.Description,&cluster.CreatedAt, &cluster.LastModified, &cluster.Active, &cluster.CyclicRecordingPatternID, &cluster.SampleRate)if err != nil {return output, fmt.Errorf("failed to fetch existing cluster: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Cluster = clusteroutput.Message = fmt.Sprintf("Cluster '%s' already exists in location '%s' (ID: %s) - returning existing cluster", cluster.Name, locationName, cluster.ID)return output, nil}// Generate IDid, err := utils.GenerateShortID()if err != nil {return output, fmt.Errorf("failed to generate ID: %w", err)}// Insert cluster_, err = tx.ExecContext(ctx,"INSERT INTO cluster (id, dataset_id, location_id, name, sample_rate, cyclic_recording_pattern_id, description, created_at, last_modified, active) VALUES (?, ?, ?, ?, ?, ?, ?, CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, TRUE)",id, *input.DatasetID, *input.LocationID, *input.Name, *input.SampleRate, input.CyclicRecordingPatternID, input.Description,)if err != nil {return output, fmt.Errorf("failed to create cluster: %w", err)}// Fetch the created clustervar cluster db.Clustererr = tx.QueryRowContext(ctx,"SELECT id, dataset_id, location_id, name, description, created_at, last_modified, active, cyclic_recording_pattern_id, sample_rate FROM cluster WHERE id = ?",id,).Scan(&cluster.ID, &cluster.DatasetID, &cluster.LocationID, &cluster.Name, &cluster.Description,&cluster.CreatedAt, &cluster.LastModified, &cluster.Active, &cluster.CyclicRecordingPatternID, &cluster.SampleRate)if err != nil {return output, fmt.Errorf("failed to fetch created cluster: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Cluster = clusteroutput.Message = fmt.Sprintf("Successfully created cluster '%s' with ID %s in location '%s' at dataset '%s' (sample rate: %d Hz)",cluster.Name, cluster.ID, locationName, datasetName, cluster.SampleRate)return output, nil}func updateCluster(ctx context.Context, input ClusterInput) (ClusterOutput, error) {var output ClusterOutputclusterID := *input.ID// Validate ID formatif err := utils.ValidateShortID(clusterID, "cluster_id"); err != nil {return output, err}if err := validateClusterFields(input); err != nil {return output, err}// Validate optional pattern ID formatif input.CyclicRecordingPatternID != nil && strings.TrimSpace(*input.CyclicRecordingPatternID) != "" {if err := utils.ValidateShortID(*input.CyclicRecordingPatternID, "cyclic_recording_pattern_id"); err != nil {return output, err}}// Open writable databasedatabase, err := db.OpenWriteableDB(dbPath)if err != nil {return output, fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Verify cluster exists and check active statusvar exists, active boolerr = database.QueryRow("SELECT EXISTS(SELECT 1 FROM cluster WHERE id = ?), COALESCE((SELECT active FROM cluster WHERE id = ?), false)",clusterID, clusterID,).Scan(&exists, &active)if err != nil {return output, fmt.Errorf("failed to query cluster: %w", err)}if !exists {return output, fmt.Errorf("cluster not found: %s", clusterID)}if !active {return output, fmt.Errorf("cluster '%s' is not active (cannot update inactive clusters)", clusterID)}// Validate cyclic_recording_pattern_id if providedif input.CyclicRecordingPatternID != nil {trimmedPatternID := strings.TrimSpace(*input.CyclicRecordingPatternID)if trimmedPatternID != "" {var patternExists, patternActive boolerr = database.QueryRow("SELECT EXISTS(SELECT 1 FROM cyclic_recording_pattern WHERE id = ?), COALESCE((SELECT active FROM cyclic_recording_pattern WHERE id = ?), false)",trimmedPatternID, trimmedPatternID,).Scan(&patternExists, &patternActive)if err != nil {return output, fmt.Errorf("failed to verify cyclic recording pattern: %w", err)}if !patternExists {return output, fmt.Errorf("cyclic recording pattern not found: %s", trimmedPatternID)}if !patternActive {return output, fmt.Errorf("cyclic recording pattern '%s' is not active", trimmedPatternID)}}}// Build dynamic UPDATE queryupdates := []string{}args := []any{}if input.Name != nil {updates = append(updates, "name = ?")args = append(args, *input.Name)}if input.Path != nil {updates = append(updates, "path = ?")args = append(args, *input.Path)}if input.SampleRate != nil {updates = append(updates, "sample_rate = ?")args = append(args, *input.SampleRate)}if input.Description != nil {updates = append(updates, "description = ?")args = append(args, *input.Description)}if input.CyclicRecordingPatternID != nil {trimmedPatternID := strings.TrimSpace(*input.CyclicRecordingPatternID)if trimmedPatternID == "" {updates = append(updates, "cyclic_recording_pattern_id = NULL")} else {updates = append(updates, "cyclic_recording_pattern_id = ?")args = append(args, trimmedPatternID)}}if len(updates) == 0 {return output, fmt.Errorf("no fields provided to update")}// Always update last_modifiedupdates = append(updates, "last_modified = now()")args = append(args, clusterID)query := fmt.Sprintf("UPDATE cluster SET %s WHERE id = ?", strings.Join(updates, ", "))// Begin logged transaction for updatetx, err := db.BeginLoggedTx(ctx, database, "create_or_update_cluster")if err != nil {return output, fmt.Errorf("failed to begin transaction: %w", err)}defer func() {if err != nil {tx.Rollback()}}()_, err = tx.Exec(query, args...)if err != nil {return output, fmt.Errorf("failed to update cluster: %w", err)}// Fetch the updated clustervar cluster db.Clustererr = tx.QueryRow("SELECT id, dataset_id, location_id, name, description, created_at, last_modified, active, cyclic_recording_pattern_id, sample_rate FROM cluster WHERE id = ?",clusterID,).Scan(&cluster.ID, &cluster.DatasetID, &cluster.LocationID, &cluster.Name, &cluster.Description,&cluster.CreatedAt, &cluster.LastModified, &cluster.Active, &cluster.CyclicRecordingPatternID, &cluster.SampleRate)if err != nil {return output, fmt.Errorf("failed to fetch updated cluster: %w", err)}if err = tx.Commit(); err != nil {return output, fmt.Errorf("failed to commit transaction: %w", err)}output.Cluster = clusteroutput.Message = fmt.Sprintf("Successfully updated cluster '%s' (ID: %s)", cluster.Name, cluster.ID)return output, nil}
package toolsimport ("sort""strings""skraak/utils")// CallsSummariseInput defines the input for the calls-summarise tooltype CallsSummariseInput struct {Folder string `json:"folder"`Brief bool `json:"brief"`Filter string `json:"filter,omitempty"`}// CallsSummariseOutput defines the output for the calls-summarise tooltype CallsSummariseOutput struct {Segments []SegmentSummary `json:"segments"`Folder string `json:"folder"`DataFilesRead int `json:"data_files_read"`DataFilesSkipped []string `json:"data_files_skipped"`TotalSegments int `json:"total_segments"`Filters map[string]FilterStats `json:"filters"`ReviewStatus ReviewStatus `json:"review_status"`Operators []string `json:"operators"`Reviewers []string `json:"reviewers"`Error *string `json:"error,omitempty"`}// SegmentSummary represents a single segment in the outputtype SegmentSummary struct {File string `json:"file"`StartTime float64 `json:"start_time"`EndTime float64 `json:"end_time"`Labels []LabelSummary `json:"labels"`}// LabelSummary represents a label in the output (omits empty fields)type LabelSummary struct {Filter string `json:"filter"`Certainty int `json:"certainty"`Species string `json:"species"`CallType string `json:"calltype,omitempty"`Comment string `json:"comment,omitempty"`Bookmark bool `json:"bookmark,omitempty"`}// FilterStats contains per-filter statisticstype FilterStats struct {Segments int `json:"segments"`Species map[string]int `json:"species"`Calltypes map[string]map[string]int `json:"calltypes,omitempty"` // species -> calltype -> count}// ReviewStatus contains review progress statisticstype ReviewStatus struct {Unreviewed int `json:"unreviewed"` // certainty < 100Confirmed int `json:"confirmed"` // certainty = 100DontKnow int `json:"dont_know"` // certainty = 0WithCallType int `json:"with_calltype"`WithComments int `json:"with_comments"`Bookmarked int `json:"bookmarked"`}// CallsSummarise reads all .data files in a folder and produces a summaryfunc CallsSummarise(input CallsSummariseInput) (CallsSummariseOutput, error) {var output CallsSummariseOutput// Find all .data filesfilePaths, err := utils.FindDataFiles(input.Folder)if err != nil {errMsg := err.Error()output.Error = &errMsgreturn output, err}// Initialize empty slices/maps (avoid null in JSON)output.Segments = make([]SegmentSummary, 0)output.Folder = input.Folderoutput.Filters = make(map[string]FilterStats)output.Operators = make([]string, 0)output.Reviewers = make([]string, 0)output.DataFilesSkipped = make([]string, 0)if len(filePaths) == 0 {return output, nil}// Track unique operators and reviewersoperatorSet := make(map[string]bool)reviewerSet := make(map[string]bool)// Process each filefor _, path := range filePaths {df, err := utils.ParseDataFile(path)if err != nil {// Extract just the filename for skipped listoutput.DataFilesSkipped = append(output.DataFilesSkipped, path)continue}output.DataFilesRead++// Track operator and reviewerif df.Meta != nil {if df.Meta.Operator != "" {operatorSet[df.Meta.Operator] = true}if df.Meta.Reviewer != "" {reviewerSet[df.Meta.Reviewer] = true}}// Extract relative filename for segments (only needed if not brief)var relPath stringif !input.Brief {relPath = extractRelativePath(input.Folder, path)}// Process segmentsfor _, seg := range df.Segments {// Filter labels if --filter is specifiedvar filteredLabels []*utils.Labelfor _, l := range seg.Labels {if input.Filter == "" || l.Filter == input.Filter {filteredLabels = append(filteredLabels, l)}}// Skip segments with no matching labels when filter is activeif input.Filter != "" && len(filteredLabels) == 0 {continue}// Build label summaries (only if not brief)var labels []LabelSummaryif !input.Brief {for _, l := range filteredLabels {labelSummary := LabelSummary{Filter: l.Filter,Certainty: l.Certainty,Species: l.Species,}if l.CallType != "" {labelSummary.CallType = l.CallType}if l.Comment != "" {labelSummary.Comment = l.Comment}if l.Bookmark {labelSummary.Bookmark = true}labels = append(labels, labelSummary)}}// Update filter stats and review status (using filtered labels)for _, l := range filteredLabels {// Update filter statsfs, exists := output.Filters[l.Filter]if !exists {fs = FilterStats{Segments: 0,Species: make(map[string]int),Calltypes: make(map[string]map[string]int),}}fs.Segments++fs.Species[l.Species]++// Track calltypes if presentif l.CallType != "" {if fs.Calltypes[l.Species] == nil {fs.Calltypes[l.Species] = make(map[string]int)}fs.Calltypes[l.Species][l.CallType]++}output.Filters[l.Filter] = fs// Update review statusswitch l.Certainty {case 100:output.ReviewStatus.Confirmed++case 0:output.ReviewStatus.DontKnow++default:output.ReviewStatus.Unreviewed++}if l.CallType != "" {output.ReviewStatus.WithCallType++}if l.Comment != "" {output.ReviewStatus.WithComments++}if l.Bookmark {output.ReviewStatus.Bookmarked++}}// Create segment summary only if not briefif !input.Brief {segSummary := SegmentSummary{File: relPath,StartTime: seg.StartTime,EndTime: seg.EndTime,Labels: labels,}output.Segments = append(output.Segments, segSummary)}}}// Count segments for totalif input.Brief {// Recount from filter stats since we didn't track segmentsfor _, fs := range output.Filters {output.TotalSegments += fs.Segments}} else {output.TotalSegments = len(output.Segments)}// Clean up empty calltypes maps (omitempty doesn't work on non-nil empty maps)for filter, fs := range output.Filters {if len(fs.Calltypes) == 0 {fs.Calltypes = niloutput.Filters[filter] = fs}}// Convert sets to sorted slicesfor op := range operatorSet {output.Operators = append(output.Operators, op)}for r := range reviewerSet {output.Reviewers = append(output.Reviewers, r)}sort.Strings(output.Operators)sort.Strings(output.Reviewers)// Sort segments by file, then start time (only if not brief)if !input.Brief {sort.Slice(output.Segments, func(i, j int) bool {if output.Segments[i].File != output.Segments[j].File {return output.Segments[i].File < output.Segments[j].File}return output.Segments[i].StartTime < output.Segments[j].StartTime})}return output, nil}// extractRelativePath extracts the audio filename from a .data file path// e.g., "/folder/tx51_LISTENING_20260221_203004.WAV.data" -> "tx51_LISTENING_20260221_203004.WAV"// Preserves the original case of the extension as-is.func extractRelativePath(folder, dataPath string) string {// Get the filenamefilename := dataPathif idx := strings.LastIndex(dataPath, "/"); idx >= 0 {filename = dataPath[idx+1:]}// Remove .data extension, preserve everything elsereturn strings.TrimSuffix(filename, ".data")}
package toolsimport ("fmt""os""strings""skraak/utils")// CallsShowImagesInput defines the input for the show-images tooltype CallsShowImagesInput struct {DataFilePath string `json:"data_file_path"`Color bool `json:"color"`ImageSize int `json:"image_size"`Sixel bool `json:"sixel"`ITerm bool `json:"iterm"`}// CallsShowImagesOutput defines the output for the show-images tooltype CallsShowImagesOutput struct {SegmentsShown int `json:"segments_shown"`WavFile string `json:"wav_file"`Error string `json:"error,omitempty"`}// CallsShowImages reads a .data file and displays spectrogram images for each segmentfunc CallsShowImages(input CallsShowImagesInput) (CallsShowImagesOutput, error) {var output CallsShowImagesOutput// Validate file existsif _, err := os.Stat(input.DataFilePath); os.IsNotExist(err) {output.Error = fmt.Sprintf("File not found: %s", input.DataFilePath)return output, fmt.Errorf("%s", output.Error)}// Derive WAV file path (strip .data suffix)wavPath := strings.TrimSuffix(input.DataFilePath, ".data")output.WavFile = wavPath// Check WAV file existsif _, err := os.Stat(wavPath); os.IsNotExist(err) {output.Error = fmt.Sprintf("WAV file not found: %s", wavPath)return output, fmt.Errorf("%s", output.Error)}// Parse .data file (includes labels for future filtering)dataFile, err := utils.ParseDataFile(input.DataFilePath)if err != nil {output.Error = err.Error()return output, fmt.Errorf("%s", output.Error)}if len(dataFile.Segments) == 0 {output.Error = "No segments found in .data file"return output, fmt.Errorf("%s", output.Error)}// Resolve image sizeimgSize := input.ImageSizeif imgSize == 0 {imgSize = utils.SpectrogramDisplaySize}// Select graphics protocolprotocol := utils.ProtocolKittyif input.ITerm {protocol = utils.ProtocolITerm} else if input.Sixel {protocol = utils.ProtocolSixel}// Generate spectrogram for each segment and outputfor i, seg := range dataFile.Segments {// Generate spectrogram imageimg, err := utils.GenerateSegmentSpectrogram(input.DataFilePath, seg.StartTime, seg.EndTime, input.Color, imgSize)if err != nil || img == nil {continue}// Print segment infolabelInfo := formatSegmentLabels(seg.Labels)fmt.Fprintf(os.Stderr, "Segment %d: %.1fs - %.1fs (%.1fs)%s\n",i+1, seg.StartTime, seg.EndTime, seg.EndTime-seg.StartTime, labelInfo)// Write to stdout via terminal graphics protocolif err := utils.WriteImage(img, os.Stdout, protocol); err != nil {output.Error = fmt.Sprintf("Failed to write image: %v", err)return output, fmt.Errorf("%s", output.Error)}fmt.Println() // Newline after image}output.SegmentsShown = len(dataFile.Segments)return output, nil}// formatSegmentLabels formats labels for display in segment infofunc formatSegmentLabels(labels []*utils.Label) string {if len(labels) == 0 {return ""}var parts []stringfor _, l := range labels {part := l.Speciesif l.CallType != "" {part += "/" + l.CallType}if l.Filter != "" {part += " [" + l.Filter + "]"}parts = append(parts, part)}return " " + strings.Join(parts, ", ")}
package toolsimport ("encoding/json""os""path/filepath""testing""skraak/utils")func TestPushCertaintyPromotesMatchingLabels(t *testing.T) {tempDir := t.TempDir()// File with two Kiwi segments: certainty=90 and certainty=70file1 := `[{"Operator": "test"}, [0, 10, 100, 1000, [{"species": "Kiwi", "certainty": 90}]], [10, 20, 100, 1000, [{"species": "Kiwi", "certainty": 70}]]]`file1Path := filepath.Join(tempDir, "file1.data")if err := os.WriteFile(file1Path, []byte(file1), 0644); err != nil {t.Fatal(err)}// File with one Tomtit at certainty=90 (must not be promoted when species=Kiwi)file2 := `[{"Operator": "test"}, [0, 10, 100, 1000, [{"species": "Tomtit", "certainty": 90}]]]`file2Path := filepath.Join(tempDir, "file2.data")if err := os.WriteFile(file2Path, []byte(file2), 0644); err != nil {t.Fatal(err)}result, err := PushCertainty(PushCertaintyConfig{Folder: tempDir,Species: "Kiwi",Reviewer: "TestReviewer",})if err != nil {t.Fatal(err)}if result.SegmentsUpdated != 1 {t.Errorf("expected 1 segment updated, got %d", result.SegmentsUpdated)}if result.FilesUpdated != 1 {t.Errorf("expected 1 file updated, got %d", result.FilesUpdated)}// Verify file1: certainty=90 Kiwi → 100, certainty=70 Kiwi → unchangeddf, err := utils.ParseDataFile(file1Path)if err != nil {t.Fatal(err)}if df.Segments[0].Labels[0].Certainty != 100 {t.Errorf("expected certainty=100, got %d", df.Segments[0].Labels[0].Certainty)}if df.Segments[1].Labels[0].Certainty != 70 {t.Errorf("expected certainty=70 unchanged, got %d", df.Segments[1].Labels[0].Certainty)}if df.Meta.Reviewer != "TestReviewer" {t.Errorf("expected reviewer=TestReviewer, got %q", df.Meta.Reviewer)}// Verify Tomtit file was not modifieddf2, err := utils.ParseDataFile(file2Path)if err != nil {t.Fatal(err)}if df2.Segments[0].Labels[0].Certainty != 90 {t.Errorf("Tomtit certainty should be unchanged at 90, got %d", df2.Segments[0].Labels[0].Certainty)}}func TestPushCertaintyFilterScope(t *testing.T) {tempDir := t.TempDir()// Segment has two labels from different filters, both Kiwi certainty=90data := []any{map[string]any{"Operator": "test"},[]any{0.0, 10.0, 100.0, 1000.0, []any{map[string]any{"species": "Kiwi", "certainty": 90, "filter": "model-a"},map[string]any{"species": "Kiwi", "certainty": 90, "filter": "model-b"},}},}raw, _ := json.Marshal(data)filePath := filepath.Join(tempDir, "file1.data")if err := os.WriteFile(filePath, raw, 0644); err != nil {t.Fatal(err)}// Push only model-aresult, err := PushCertainty(PushCertaintyConfig{Folder: tempDir,Filter: "model-a",Species: "Kiwi",Reviewer: "TestReviewer",})if err != nil {t.Fatal(err)}if result.SegmentsUpdated != 1 {t.Errorf("expected 1 segment updated, got %d", result.SegmentsUpdated)}// Verify only model-a label was promoted; model-b stays at 90df, err := utils.ParseDataFile(filePath)if err != nil {t.Fatal(err)}for _, label := range df.Segments[0].Labels {if label.Filter == "model-a" && label.Certainty != 100 {t.Errorf("model-a label should be 100, got %d", label.Certainty)}if label.Filter == "model-b" && label.Certainty != 90 {t.Errorf("model-b label should be unchanged at 90, got %d", label.Certainty)}}}
package toolsimport ("fmt""skraak/utils")// PushCertaintyConfig holds the configuration for push-certaintytype PushCertaintyConfig struct {Folder stringFile stringFilter stringSpecies stringCallType stringNight boolDay boolLat float64Lng float64Timezone stringReviewer string}// PushCertaintyResult holds the result of push-certaintytype PushCertaintyResult struct {SegmentsUpdated int `json:"segments_updated"`FilesUpdated int `json:"files_updated"`TimeFilteredCount int `json:"time_filtered_count"`}// PushCertainty promotes all certainty=90 segments matching the filter scope to certainty=100.// Uses identical filtering logic to LoadDataFiles so the scope matches calls classify exactly.func PushCertainty(config PushCertaintyConfig) (*PushCertaintyResult, error) {state, err := LoadDataFiles(ClassifyConfig{Folder: config.Folder,File: config.File,Filter: config.Filter,Species: config.Species,CallType: config.CallType,Certainty: 90,Sample: -1,Night: config.Night,Day: config.Day,Lat: config.Lat,Lng: config.Lng,Timezone: config.Timezone,})if err != nil {return nil, err}var segsUpdated, filesUpdated intfor i, df := range state.DataFiles {changed := falsefor _, seg := range state.FilteredSegs()[i] {for _, label := range seg.Labels {if labelMatchesPush(label, config.Filter, config.Species, config.CallType) {label.Certainty = 100changed = truesegsUpdated++}}}if changed {df.Meta.Reviewer = config.Reviewerif err := df.Write(df.FilePath); err != nil {return nil, fmt.Errorf("write %s: %w", df.FilePath, err)}filesUpdated++}}return &PushCertaintyResult{SegmentsUpdated: segsUpdated,FilesUpdated: filesUpdated,TimeFilteredCount: state.TimeFilteredCount,}, nil}// labelMatchesPush returns true if the label matches the push scope and has certainty=90.// Certainty is already guaranteed by LoadDataFiles, but we re-check to target only the// specific label that matched (a segment may carry labels from multiple filters).func labelMatchesPush(label *utils.Label, filter, species, callType string) bool {if filter != "" && label.Filter != filter {return false}if species != "" && label.Species != species {return false}if callType != "" && label.CallType != callType {return false}return label.Certainty == 90}
package toolsimport ("path/filepath""testing""skraak/utils")// helpersfunc seg(start, end float64, labels ...*utils.Label) *utils.Segment {return &utils.Segment{StartTime: start,EndTime: end,FreqLow: 100,FreqHigh: 8000,Labels: labels,}}func lbl(filter, species, calltype string, certainty int) *utils.Label {return &utils.Label{Filter: filter,Species: species,CallType: calltype,Certainty: certainty,}}func writeFile(t *testing.T, segs ...*utils.Segment) string {t.Helper()dir := t.TempDir()path := filepath.Join(dir, "test.data")df := &utils.DataFile{Meta: &utils.DataMeta{Operator: "ML", Reviewer: "David", Duration: 3600},Segments: segs,}if err := df.Write(path); err != nil {t.Fatalf("write fixture: %v", err)}return path}func readFile(t *testing.T, path string) *utils.DataFile {t.Helper()df, err := utils.ParseDataFile(path)if err != nil {t.Fatalf("parse %s: %v", path, err)}return df}// findLabel returns the label with matching filter and time on the parsed file, or nil.func findLabel(df *utils.DataFile, filter string, start, end float64) *utils.Label {for _, s := range df.Segments {if s.StartTime != start || s.EndTime != end {continue}for _, l := range s.Labels {if l.Filter == filter {return l}}}return nil}const (fFrom = "opensoundscape-kiwi-1.2"fTo = "opensoundscape-kiwi-1.5")func TestPropagate_HappyPathSingle(t *testing.T) {path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),seg(100, 125, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v (%s)", err, out.Error)}if out.Propagated != 1 || out.TargetsExamined != 1 || out.SkippedConflict != 0 || out.SkippedNoOverlap != 0 {t.Fatalf("counts wrong: %+v", out)}df := readFile(t, path)target := findLabel(df, fTo, 100, 125)if target == nil {t.Fatal("target label missing")}if target.Species != "Kiwi" || target.CallType != "Male" || target.Certainty != 90 {t.Errorf("target not updated correctly: species=%q calltype=%q cert=%d", target.Species, target.CallType, target.Certainty)}if df.Meta.Reviewer != "Skraak" {t.Errorf("reviewer = %q, want Skraak", df.Meta.Reviewer)}}func TestPropagate_NoOverlap(t *testing.T) {path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),seg(500, 525, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 0 || out.TargetsExamined != 1 || out.SkippedNoOverlap != 1 {t.Fatalf("counts wrong: %+v", out)}df := readFile(t, path)target := findLabel(df, fTo, 500, 525)if target.Certainty != 70 {t.Errorf("target should not be modified, cert=%d", target.Certainty)}if df.Meta.Reviewer != "David" {t.Errorf("reviewer should stay David (no write), got %q", df.Meta.Reviewer)}}func TestPropagate_SourceWrongSpecies_Ignored(t *testing.T) {path := writeFile(t,seg(100, 125, lbl(fFrom, "Weka", "", 100)),seg(100, 125, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 0 || out.SkippedNoOverlap != 1 {t.Fatalf("counts wrong: %+v", out)}}func TestPropagate_SourceWrongCertainty_Ignored(t *testing.T) {// cert=70 and cert=0 source labels must NOT count as sources.path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "Male", 70)),seg(200, 225, lbl(fFrom, "Don't Know", "", 0)),seg(100, 125, lbl(fTo, "Kiwi", "Duet", 70)),seg(200, 225, lbl(fTo, "Kiwi", "Male", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 0 || out.SkippedNoOverlap != 2 {t.Fatalf("counts wrong: %+v", out)}}func TestPropagate_SourceWrongFilter_Ignored(t *testing.T) {path := writeFile(t,seg(100, 125, lbl("some-other-filter", "Kiwi", "Male", 100)),seg(100, 125, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if !out.FiltersMissing || out.Propagated != 0 || out.TargetsExamined != 0 {t.Fatalf("expected FiltersMissing=true with zero counts, got: %+v", out)}}func TestPropagate_TargetCert100_NotTouched(t *testing.T) {// Target with cert=100 is human-verified — must NOT be overwritten.path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),seg(100, 125, lbl(fTo, "Kiwi", "Male", 100)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.TargetsExamined != 0 || out.Propagated != 0 {t.Fatalf("cert=100 target must not be examined: %+v", out)}df := readFile(t, path)if df.Meta.Reviewer != "David" {t.Errorf("reviewer should stay David (no write), got %q", df.Meta.Reviewer)}}func TestPropagate_TargetCert90_NotTouched(t *testing.T) {// Target with cert=90 (already propagated earlier) must NOT be re-propagated.path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),seg(100, 125, lbl(fTo, "Kiwi", "Female", 90)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.TargetsExamined != 0 || out.Propagated != 0 {t.Fatalf("cert=90 target must not be examined: %+v", out)}df := readFile(t, path)target := findLabel(df, fTo, 100, 125)if target.Certainty != 90 || target.CallType != "Female" {t.Errorf("cert=90 target was modified: %+v", target)}}func TestPropagate_TargetCert0_Propagated(t *testing.T) {// Target at cert=0 ("Don't Know" / "Noise") SHOULD be propagated when an// overlapping cert=100 source exists — rescues labels from the noise bucket// so they surface for review even if occasionally wrong.path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),seg(100, 125, lbl(fTo, "Don't Know", "", 0)),seg(200, 225, lbl(fFrom, "Kiwi", "Female", 100)),seg(200, 225, lbl(fTo, "Noise", "", 0)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.TargetsExamined != 2 || out.Propagated != 2 {t.Fatalf("cert=0 targets must be propagated: %+v", out)}df := readFile(t, path)for _, c := range []struct {start, end float64calltype string}{{100, 125, "Male"}, {200, 225, "Female"}} {l := findLabel(df, fTo, c.start, c.end)if l == nil || l.Species != "Kiwi" || l.CallType != c.calltype || l.Certainty != 90 {t.Errorf("at %v-%v got %+v, want Kiwi+%s cert=90", c.start, c.end, l, c.calltype)}}}func TestPropagate_MultipleSourcesAgree(t *testing.T) {// Two overlapping sources with same calltype → propagate.path := writeFile(t,seg(100, 110, lbl(fFrom, "Kiwi", "Male", 100)),seg(105, 120, lbl(fFrom, "Kiwi", "Male", 100)),seg(100, 125, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 1 || out.SkippedConflict != 0 {t.Fatalf("counts wrong: %+v", out)}df := readFile(t, path)target := findLabel(df, fTo, 100, 125)if target.CallType != "Male" {t.Errorf("calltype should be Male, got %q", target.CallType)}}func TestPropagate_MultipleSourcesConflict(t *testing.T) {// Two overlapping sources with different calltypes → conflict, skip, report.path := writeFile(t,seg(100, 110, lbl(fFrom, "Kiwi", "Male", 100)),seg(115, 120, lbl(fFrom, "Kiwi", "Female", 100)),seg(100, 125, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 0 || out.SkippedConflict != 1 {t.Fatalf("expected 1 conflict skip: %+v", out)}if len(out.Conflicts) != 1 {t.Fatalf("expected 1 conflict report, got %d", len(out.Conflicts))}if out.Conflicts[0].TargetStart != 100 || out.Conflicts[0].TargetEnd != 125 {t.Errorf("conflict target wrong: %+v", out.Conflicts[0])}if len(out.Conflicts[0].SourceChoices) != 2 {t.Errorf("expected 2 source choices, got %d", len(out.Conflicts[0].SourceChoices))}// Target must NOT be modified.df := readFile(t, path)target := findLabel(df, fTo, 100, 125)if target.CallType != "Duet" || target.Certainty != 70 {t.Errorf("conflicted target was modified: %+v", target)}if df.Meta.Reviewer != "David" {t.Errorf("reviewer should stay David (no write), got %q", df.Meta.Reviewer)}}func TestPropagate_EmptyCallTypePropagates(t *testing.T) {// Source with empty calltype → target gets empty calltype.path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "", 100)),seg(100, 125, lbl(fTo, "Kiwi", "Male", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 1 {t.Fatalf("expected propagated=1: %+v", out)}df := readFile(t, path)target := findLabel(df, fTo, 100, 125)if target.CallType != "" {t.Errorf("calltype should be cleared, got %q", target.CallType)}if target.Species != "Kiwi" || target.Certainty != 90 {t.Errorf("target fields wrong: %+v", target)}}func TestPropagate_SpeciesOverride(t *testing.T) {// Target species was different from --species; must be overwritten.path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),seg(100, 125, lbl(fTo, "Don't Know", "", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 1 {t.Fatalf("expected propagated=1: %+v", out)}df := readFile(t, path)target := findLabel(df, fTo, 100, 125)if target.Species != "Kiwi" || target.CallType != "Male" || target.Certainty != 90 {t.Errorf("target not overwritten correctly: %+v", target)}}func TestPropagate_OverlapBoundaryExclusive(t *testing.T) {// Segments touching at a point (src ends exactly where tgt starts) do NOT overlap.path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),seg(125, 150, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 0 || out.SkippedNoOverlap != 1 {t.Fatalf("touching boundary must not count as overlap: %+v", out)}}func TestPropagate_OverlapPartial(t *testing.T) {// 1-second overlap is enough.path := writeFile(t,seg(100, 126, lbl(fFrom, "Kiwi", "Male", 100)),seg(125, 150, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 1 {t.Fatalf("expected propagated=1: %+v", out)}}func TestPropagate_SupersetEitherDirection(t *testing.T) {// Source engulfs target.path1 := writeFile(t,seg(100, 200, lbl(fFrom, "Kiwi", "Male", 100)),seg(110, 150, lbl(fTo, "Kiwi", "Duet", 70)),)if out, _ := CallsPropagate(CallsPropagateInput{File: path1, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi"}); out.Propagated != 1 {t.Errorf("source-engulfs-target: %+v", out)}// Target engulfs source.path2 := writeFile(t,seg(110, 150, lbl(fFrom, "Kiwi", "Male", 100)),seg(100, 200, lbl(fTo, "Kiwi", "Duet", 70)),)if out, _ := CallsPropagate(CallsPropagateInput{File: path2, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi"}); out.Propagated != 1 {t.Errorf("target-engulfs-source: %+v", out)}}func TestPropagate_MissingFlags(t *testing.T) {cases := []struct {name stringin CallsPropagateInput}{{"no file", CallsPropagateInput{FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi"}},{"no from", CallsPropagateInput{File: "x", ToFilter: fTo, Species: "Kiwi"}},{"no to", CallsPropagateInput{File: "x", FromFilter: fFrom, Species: "Kiwi"}},{"no species", CallsPropagateInput{File: "x", FromFilter: fFrom, ToFilter: fTo}},}for _, c := range cases {t.Run(c.name, func(t *testing.T) {_, err := CallsPropagate(c.in)if err == nil {t.Errorf("expected error")}})}}func TestPropagate_SameFromAndTo(t *testing.T) {_, err := CallsPropagate(CallsPropagateInput{File: "x", FromFilter: fFrom, ToFilter: fFrom, Species: "Kiwi",})if err == nil {t.Error("expected error when --from == --to")}}func TestPropagate_NonexistentFile(t *testing.T) {_, err := CallsPropagate(CallsPropagateInput{File: "/nonexistent/path.data", FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err == nil {t.Error("expected error for nonexistent file")}}func TestPropagate_RealisticMixed(t *testing.T) {// Mimics the 20260228_211500.WAV.data case: cert=0 "Don't Know" and cert=100 Kiwi sources// coexist; only cert=100 Kiwi gets propagated.path := writeFile(t,// Sources (kiwi-1.2)seg(45, 52.5, lbl(fFrom, "Don't Know", "", 0)),seg(142.5, 177.5, lbl(fFrom, "Kiwi", "Male", 100)),seg(195, 217.5, lbl(fFrom, "Don't Know", "", 0)),seg(647.5, 682.5, lbl(fFrom, "Kiwi", "Female", 100)),seg(815, 855, lbl(fFrom, "Kiwi", "Duet", 100)),// Targets (kiwi-1.5)seg(147.5, 167.5, lbl(fTo, "Kiwi", "Male", 70)),seg(647.5, 672.5, lbl(fTo, "Kiwi", "Female", 70)),seg(815, 852.5, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.TargetsExamined != 3 || out.Propagated != 3 || out.SkippedConflict != 0 {t.Fatalf("counts wrong: %+v", out)}df := readFile(t, path)expect := []struct {start, end float64calltype string}{{147.5, 167.5, "Male"},{647.5, 672.5, "Female"},{815, 852.5, "Duet"},}for _, e := range expect {l := findLabel(df, fTo, e.start, e.end)if l == nil || l.Certainty != 90 || l.CallType != e.calltype || l.Species != "Kiwi" {t.Errorf("at %v-%v got %+v, want Kiwi+%s cert=90", e.start, e.end, l, e.calltype)}}}func TestPropagate_NoWriteIfNothingChanged(t *testing.T) {// File with only non-target segments should not be rewritten (reviewer unchanged).path := writeFile(t,seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),)out, err := CallsPropagate(CallsPropagateInput{File: path, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.Propagated != 0 || out.TargetsExamined != 0 {t.Fatalf("expected no activity: %+v", out)}df := readFile(t, path)if df.Meta.Reviewer != "David" {t.Errorf("reviewer should not be touched, got %q", df.Meta.Reviewer)}}// writeFileAt is like writeFile but puts the file inside an existing dir// with a caller-provided basename (must end in .data).func writeFileAt(t *testing.T, dir, base string, segs ...*utils.Segment) string {t.Helper()path := filepath.Join(dir, base)df := &utils.DataFile{Meta: &utils.DataMeta{Operator: "ML", Reviewer: "David", Duration: 3600},Segments: segs,}if err := df.Write(path); err != nil {t.Fatalf("write fixture: %v", err)}return path}func TestPropagateFolder_AggregatesAndSkipsMissing(t *testing.T) {dir := t.TempDir()// File A: both filters present, one clean propagation.aPath := writeFileAt(t, dir, "a.wav.data",seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),seg(100, 125, lbl(fTo, "Kiwi", "Duet", 70)),)// File B: only target filter — missing source, must be skipped silently.bPath := writeFileAt(t, dir, "b.wav.data",seg(200, 225, lbl(fTo, "Kiwi", "Duet", 70)),)// File C: only source filter — missing target, must be skipped silently.writeFileAt(t, dir, "c.wav.data",seg(300, 325, lbl(fFrom, "Kiwi", "Male", 100)),)// File D: both filters, but no overlap → targets examined, none propagated.dPath := writeFileAt(t, dir, "d.wav.data",seg(400, 425, lbl(fFrom, "Kiwi", "Male", 100)),seg(500, 525, lbl(fTo, "Kiwi", "Duet", 70)),)out, err := CallsPropagateFolder(CallsPropagateFolderInput{Folder: dir, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.FilesTotal != 4 {t.Errorf("FilesTotal: got %d, want 4", out.FilesTotal)}if out.FilesWithBothFilters != 2 {t.Errorf("FilesWithBothFilters: got %d, want 2", out.FilesWithBothFilters)}if out.FilesSkippedNoFilter != 2 {t.Errorf("FilesSkippedNoFilter: got %d, want 2", out.FilesSkippedNoFilter)}if out.FilesChanged != 1 {t.Errorf("FilesChanged: got %d, want 1", out.FilesChanged)}if out.FilesErrored != 0 {t.Errorf("FilesErrored: got %d, want 0", out.FilesErrored)}if out.TargetsExamined != 2 {t.Errorf("TargetsExamined: got %d, want 2", out.TargetsExamined)}if out.Propagated != 1 {t.Errorf("Propagated: got %d, want 1", out.Propagated)}if out.SkippedNoOverlap != 1 {t.Errorf("SkippedNoOverlap: got %d, want 1", out.SkippedNoOverlap)}// File A was changed; check on-disk state.aDf := readFile(t, aPath)if aDf.Meta.Reviewer != "Skraak" {t.Errorf("a.wav.data reviewer: got %q, want Skraak", aDf.Meta.Reviewer)}if l := findLabel(aDf, fTo, 100, 125); l == nil || l.Certainty != 90 || l.CallType != "Male" {t.Errorf("a.wav.data target label: got %+v, want cert=90 calltype=Male", l)}// File B was skipped — reviewer untouched.bDf := readFile(t, bPath)if bDf.Meta.Reviewer != "David" {t.Errorf("b.wav.data reviewer should not be touched, got %q", bDf.Meta.Reviewer)}// File D had no overlap — reviewer untouched, target still cert=70.dDf := readFile(t, dPath)if dDf.Meta.Reviewer != "David" {t.Errorf("d.wav.data reviewer should not be touched, got %q", dDf.Meta.Reviewer)}if l := findLabel(dDf, fTo, 500, 525); l == nil || l.Certainty != 70 {t.Errorf("d.wav.data target label should be unchanged cert=70, got %+v", l)}}func TestPropagateFolder_EmptyFolder(t *testing.T) {dir := t.TempDir()out, err := CallsPropagateFolder(CallsPropagateFolderInput{Folder: dir, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.FilesTotal != 0 || out.Propagated != 0 {t.Errorf("expected empty result, got %+v", out)}}func TestPropagateFolder_MissingRequiredFlags(t *testing.T) {dir := t.TempDir()cases := []CallsPropagateFolderInput{{Folder: "", FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi"},{Folder: dir, FromFilter: "", ToFilter: fTo, Species: "Kiwi"},{Folder: dir, FromFilter: fFrom, ToFilter: "", Species: "Kiwi"},{Folder: dir, FromFilter: fFrom, ToFilter: fTo, Species: ""},{Folder: dir, FromFilter: fFrom, ToFilter: fFrom, Species: "Kiwi"},}for i, in := range cases {if _, err := CallsPropagateFolder(in); err == nil {t.Errorf("case %d: expected error for input %+v", i, in)}}}func TestPropagateFolder_NonexistentFolder(t *testing.T) {_, err := CallsPropagateFolder(CallsPropagateFolderInput{Folder: "/nonexistent/path/xyz", FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err == nil {t.Fatal("expected error for nonexistent folder")}}func TestPropagateFolder_ConflictsTaggedWithFile(t *testing.T) {dir := t.TempDir()// Two sources with different calltypes both overlapping one target.writeFileAt(t, dir, "conflict.wav.data",seg(100, 125, lbl(fFrom, "Kiwi", "Male", 100)),seg(110, 130, lbl(fFrom, "Kiwi", "Female", 100)),seg(100, 130, lbl(fTo, "Kiwi", "", 70)),)out, err := CallsPropagateFolder(CallsPropagateFolderInput{Folder: dir, FromFilter: fFrom, ToFilter: fTo, Species: "Kiwi",})if err != nil {t.Fatalf("unexpected error: %v", err)}if out.SkippedConflict != 1 || len(out.Conflicts) != 1 {t.Fatalf("expected one conflict, got %+v", out)}if out.Conflicts[0].File == "" {t.Errorf("conflict should be tagged with file path, got %+v", out.Conflicts[0])}}
package toolsimport ("fmt""os""skraak/utils")type CallsPropagateInput struct {File string `json:"file"`FromFilter string `json:"from_filter"`ToFilter string `json:"to_filter"`Species string `json:"species"`}type CallsPropagateOutput struct {File string `json:"file"`FromFilter string `json:"from_filter"`ToFilter string `json:"to_filter"`Species string `json:"species"`FiltersMissing bool `json:"filters_missing,omitempty"`TargetsExamined int `json:"targets_examined"`Propagated int `json:"propagated"`SkippedNoOverlap int `json:"skipped_no_overlap"`SkippedConflict int `json:"skipped_conflict"`Conflicts []PropagateConflict `json:"conflicts,omitempty"`Changes []PropagateChange `json:"changes,omitempty"`Error string `json:"error,omitempty"`}type CallsPropagateFolderInput struct {Folder string `json:"folder"`FromFilter string `json:"from_filter"`ToFilter string `json:"to_filter"`Species string `json:"species"`}type CallsPropagateFolderOutput struct {Folder string `json:"folder"`FromFilter string `json:"from_filter"`ToFilter string `json:"to_filter"`Species string `json:"species"`FilesTotal int `json:"files_total"`FilesWithBothFilters int `json:"files_with_both_filters"`FilesSkippedNoFilter int `json:"files_skipped_no_filter"`FilesChanged int `json:"files_changed"`FilesErrored int `json:"files_errored"`TargetsExamined int `json:"targets_examined"`Propagated int `json:"propagated"`SkippedNoOverlap int `json:"skipped_no_overlap"`SkippedConflict int `json:"skipped_conflict"`Conflicts []PropagateConflict `json:"conflicts,omitempty"`Errors []CallsPropagateOutput `json:"errors,omitempty"`Error string `json:"error,omitempty"`}type PropagateConflict struct {File string `json:"file,omitempty"`TargetStart float64 `json:"target_start"`TargetEnd float64 `json:"target_end"`TargetCallType string `json:"target_calltype,omitempty"`SourceChoices []PropagateSourceChoice `json:"source_choices"`}type PropagateSourceChoice struct {Start float64 `json:"start"`End float64 `json:"end"`Species string `json:"species"`CallType string `json:"calltype,omitempty"`}type PropagateChange struct {TargetStart float64 `json:"target_start"`TargetEnd float64 `json:"target_end"`PrevSpecies string `json:"prev_species"`PrevCallType string `json:"prev_calltype,omitempty"`PrevCertainty int `json:"prev_certainty"`NewSpecies string `json:"new_species"`NewCallType string `json:"new_calltype,omitempty"`NewCertainty int `json:"new_certainty"`}// CallsPropagate copies verified classifications (certainty==100) from one filter's// segments to overlapping target segments of another filter, within a single .data file.// Target labels with certainty==70 (ML-unverified) or certainty==0 (Don't Know / Noise)// are updated — targets at certainty==100 (human-verified) and certainty==90 (already// propagated) are left alone. Only source labels matching --species are considered.// Propagated target labels are set to certainty=90 and file reviewer is set to "Skraak".func CallsPropagate(input CallsPropagateInput) (CallsPropagateOutput, error) {output := CallsPropagateOutput{File: input.File,FromFilter: input.FromFilter,ToFilter: input.ToFilter,Species: input.Species,}if input.File == "" {output.Error = "--file is required"return output, fmt.Errorf("%s", output.Error)}if input.FromFilter == "" {output.Error = "--from is required"return output, fmt.Errorf("%s", output.Error)}if input.ToFilter == "" {output.Error = "--to is required"return output, fmt.Errorf("%s", output.Error)}if input.Species == "" {output.Error = "--species is required"return output, fmt.Errorf("%s", output.Error)}if input.FromFilter == input.ToFilter {output.Error = "--from and --to must differ"return output, fmt.Errorf("%s", output.Error)}if _, err := os.Stat(input.File); os.IsNotExist(err) {output.Error = fmt.Sprintf("file not found: %s", input.File)return output, fmt.Errorf("%s", output.Error)}df, err := utils.ParseDataFile(input.File)if err != nil {output.Error = fmt.Sprintf("parse %s: %v", input.File, err)return output, fmt.Errorf("%s", output.Error)}// Fast path: skip files that don't contain both filters at all.hasFrom, hasTo := false, falsefor _, seg := range df.Segments {for _, lbl := range seg.Labels {if lbl.Filter == input.FromFilter {hasFrom = true}if lbl.Filter == input.ToFilter {hasTo = true}if hasFrom && hasTo {break}}if hasFrom && hasTo {break}}if !hasFrom || !hasTo {output.FiltersMissing = truereturn output, nil}type sourceRef struct {seg *utils.Segmentlabel *utils.Label}var sources []sourceReffor _, seg := range df.Segments {for _, lbl := range seg.Labels {if lbl.Filter == input.FromFilter && lbl.Species == input.Species && lbl.Certainty == 100 {sources = append(sources, sourceRef{seg: seg, label: lbl})break}}}changed := falsefor _, tSeg := range df.Segments {var toLabel *utils.Labelfor _, lbl := range tSeg.Labels {if lbl.Filter == input.ToFilter && (lbl.Certainty == 70 || lbl.Certainty == 0) {toLabel = lblbreak}}if toLabel == nil {continue}output.TargetsExamined++var overlaps []sourceReffor _, s := range sources {if s.seg.StartTime < tSeg.EndTime && tSeg.StartTime < s.seg.EndTime {overlaps = append(overlaps, s)}}if len(overlaps) == 0 {output.SkippedNoOverlap++continue}agreedCallType := overlaps[0].label.CallTypeconflict := falsefor _, s := range overlaps[1:] {if s.label.CallType != agreedCallType {conflict = truebreak}}if conflict {output.SkippedConflict++choices := make([]PropagateSourceChoice, 0, len(overlaps))for _, s := range overlaps {choices = append(choices, PropagateSourceChoice{Start: s.seg.StartTime,End: s.seg.EndTime,Species: s.label.Species,CallType: s.label.CallType,})}output.Conflicts = append(output.Conflicts, PropagateConflict{TargetStart: tSeg.StartTime,TargetEnd: tSeg.EndTime,TargetCallType: toLabel.CallType,SourceChoices: choices,})continue}change := PropagateChange{TargetStart: tSeg.StartTime,TargetEnd: tSeg.EndTime,PrevSpecies: toLabel.Species,PrevCallType: toLabel.CallType,PrevCertainty: toLabel.Certainty,NewSpecies: input.Species,NewCallType: agreedCallType,NewCertainty: 90,}toLabel.Species = input.SpeciestoLabel.CallType = agreedCallTypetoLabel.Certainty = 90changed = trueoutput.Propagated++output.Changes = append(output.Changes, change)}if changed {df.Meta.Reviewer = "Skraak"if err := df.Write(input.File); err != nil {output.Error = fmt.Sprintf("write %s: %v", input.File, err)return output, fmt.Errorf("%s", output.Error)}}return output, nil}// CallsPropagateFolder runs CallsPropagate against every .data file in a folder,// aggregating counts. Files that do not contain both --from and --to filters are// skipped silently (counted as files_skipped_no_filter). Parse/write errors on// individual files are collected in Errors; they don't abort the run.func CallsPropagateFolder(input CallsPropagateFolderInput) (CallsPropagateFolderOutput, error) {output := CallsPropagateFolderOutput{Folder: input.Folder,FromFilter: input.FromFilter,ToFilter: input.ToFilter,Species: input.Species,}if input.Folder == "" {output.Error = "--folder is required"return output, fmt.Errorf("%s", output.Error)}if input.FromFilter == "" {output.Error = "--from is required"return output, fmt.Errorf("%s", output.Error)}if input.ToFilter == "" {output.Error = "--to is required"return output, fmt.Errorf("%s", output.Error)}if input.Species == "" {output.Error = "--species is required"return output, fmt.Errorf("%s", output.Error)}if input.FromFilter == input.ToFilter {output.Error = "--from and --to must differ"return output, fmt.Errorf("%s", output.Error)}info, err := os.Stat(input.Folder)if err != nil {output.Error = fmt.Sprintf("folder not found: %s", input.Folder)return output, fmt.Errorf("%s", output.Error)}if !info.IsDir() {output.Error = fmt.Sprintf("not a directory: %s", input.Folder)return output, fmt.Errorf("%s", output.Error)}files, err := utils.FindDataFiles(input.Folder)if err != nil {output.Error = fmt.Sprintf("list .data files: %v", err)return output, fmt.Errorf("%s", output.Error)}output.FilesTotal = len(files)for _, f := range files {fileOut, err := CallsPropagate(CallsPropagateInput{File: f,FromFilter: input.FromFilter,ToFilter: input.ToFilter,Species: input.Species,})if err != nil {output.FilesErrored++output.Errors = append(output.Errors, fileOut)continue}if fileOut.FiltersMissing {output.FilesSkippedNoFilter++continue}output.FilesWithBothFilters++output.TargetsExamined += fileOut.TargetsExaminedoutput.Propagated += fileOut.Propagatedoutput.SkippedNoOverlap += fileOut.SkippedNoOverlapoutput.SkippedConflict += fileOut.SkippedConflictif fileOut.Propagated > 0 {output.FilesChanged++}for _, c := range fileOut.Conflicts {c.File = foutput.Conflicts = append(output.Conflicts, c)}}return output, nil}
package toolsimport ("path/filepath""testing""skraak/utils")func TestCallsModifyBookmark(t *testing.T) {// Create a temp .data file with a bookmarked segmenttmpDir := t.TempDir()tmpFile := filepath.Join(tmpDir, "test.data")df := &utils.DataFile{Meta: &utils.DataMeta{Operator: "test", Duration: 60},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 15.0,FreqLow: 100,FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 80, Filter: "myfilter", CallType: "Duet", Bookmark: true},},},},}if err := df.Write(tmpFile); err != nil {t.Fatalf("failed to write test file: %v", err)}// Test 1: Adding bookmark when already true should do nothingbookmark := trueresult, err := CallsModify(CallsModifyInput{File: tmpFile,Reviewer: "tester",Filter: "myfilter",Segment: "10-15",Certainty: 80,Bookmark: &bookmark,})// Should return error "no changes needed"if err == nil {t.Errorf("expected error 'no changes needed' when bookmark already true, got nil")}if result.Error != "No changes needed: all values already match" {t.Errorf("expected 'no changes needed' error, got: %s", result.Error)}// Verify bookmark is still true in the filedf2, err := utils.ParseDataFile(tmpFile)if err != nil {t.Fatalf("failed to parse file: %v", err)}if !df2.Segments[0].Labels[0].Bookmark {t.Errorf("bookmark should still be true, got false")}}func TestCallsModifyBookmarkFalse(t *testing.T) {// Create a temp .data file WITHOUT a bookmarktmpDir := t.TempDir()tmpFile := filepath.Join(tmpDir, "test.data")df := &utils.DataFile{Meta: &utils.DataMeta{Operator: "test", Duration: 60},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 15.0,FreqLow: 100,FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 80, Filter: "myfilter", CallType: "Duet", Bookmark: false},},},},}if err := df.Write(tmpFile); err != nil {t.Fatalf("failed to write test file: %v", err)}// Test: Adding bookmark when false should set it to truebookmark := trueresult, err := CallsModify(CallsModifyInput{File: tmpFile,Reviewer: "tester",Filter: "myfilter",Segment: "10-15",Certainty: 80,Bookmark: &bookmark,})if err != nil {t.Errorf("unexpected error: %v", err)}if result.Bookmark == nil || !*result.Bookmark {t.Errorf("expected bookmark=true in result, got %v", result.Bookmark)}// Verify bookmark is true in the filedf2, err := utils.ParseDataFile(tmpFile)if err != nil {t.Fatalf("failed to parse file: %v", err)}if !df2.Segments[0].Labels[0].Bookmark {t.Errorf("bookmark should be true, got false")}}func TestCallsModifyCommentAdditive(t *testing.T) {// Create a temp .data file with an existing commenttmpDir := t.TempDir()tmpFile := filepath.Join(tmpDir, "test.data")df := &utils.DataFile{Meta: &utils.DataMeta{Operator: "test", Duration: 60},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 15.0,FreqLow: 100,FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 80, Filter: "myfilter", Comment: "First observation"},},},},}if err := df.Write(tmpFile); err != nil {t.Fatalf("failed to write test file: %v", err)}// Test: Adding comment should be additiveresult, err := CallsModify(CallsModifyInput{File: tmpFile,Reviewer: "tester",Filter: "myfilter",Segment: "10-15",Certainty: 80,Comment: "Good example",})if err != nil {t.Errorf("unexpected error: %v", err)}expectedComment := "First observation | Good example"if result.Comment != expectedComment {t.Errorf("expected comment=%q, got %q", expectedComment, result.Comment)}// Verify comment in filedf2, err := utils.ParseDataFile(tmpFile)if err != nil {t.Fatalf("failed to parse file: %v", err)}if df2.Segments[0].Labels[0].Comment != expectedComment {t.Errorf("expected comment in file=%q, got %q", expectedComment, df2.Segments[0].Labels[0].Comment)}}func TestCallsModifyCommentAdditiveMultiple(t *testing.T) {// Create a temp .data file and add multiple commentstmpDir := t.TempDir()tmpFile := filepath.Join(tmpDir, "test.data")df := &utils.DataFile{Meta: &utils.DataMeta{Operator: "test", Duration: 60},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 15.0,FreqLow: 100,FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 80, Filter: "myfilter"},},},},}if err := df.Write(tmpFile); err != nil {t.Fatalf("failed to write test file: %v", err)}// Add first comment_, err := CallsModify(CallsModifyInput{File: tmpFile,Reviewer: "tester",Filter: "myfilter",Segment: "10-15",Certainty: 80,Comment: "First",})if err != nil {t.Fatalf("unexpected error on first comment: %v", err)}// Add second comment_, err = CallsModify(CallsModifyInput{File: tmpFile,Reviewer: "tester",Filter: "myfilter",Segment: "10-15",Certainty: 80,Comment: "Second",})if err != nil {t.Fatalf("unexpected error on second comment: %v", err)}// Add third commentresult, err := CallsModify(CallsModifyInput{File: tmpFile,Reviewer: "tester",Filter: "myfilter",Segment: "10-15",Certainty: 80,Comment: "Third",})if err != nil {t.Fatalf("unexpected error on third comment: %v", err)}expectedComment := "First | Second | Third"if result.Comment != expectedComment {t.Errorf("expected comment=%q, got %q", expectedComment, result.Comment)}}func TestCallsModifyCommentTooLong(t *testing.T) {// Create a temp .data file with an existing long commenttmpDir := t.TempDir()tmpFile := filepath.Join(tmpDir, "test.data")existingComment := "This is a fairly long existing comment that takes up space"df := &utils.DataFile{Meta: &utils.DataMeta{Operator: "test", Duration: 60},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 15.0,FreqLow: 100,FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 80, Filter: "myfilter", Comment: existingComment},},},},}if err := df.Write(tmpFile); err != nil {t.Fatalf("failed to write test file: %v", err)}// Test: Adding a long comment that would exceed 140 chars should faillongNewComment := "This is another very long comment that when combined with the existing one will exceed the limit"result, err := CallsModify(CallsModifyInput{File: tmpFile,Reviewer: "tester",Filter: "myfilter",Segment: "10-15",Certainty: 80,Comment: longNewComment,})if err == nil {t.Errorf("expected error for combined comment exceeding 140 chars, got nil")}if result.Error == "" {t.Errorf("expected error message, got empty")}// Verify original comment is preserveddf2, err := utils.ParseDataFile(tmpFile)if err != nil {t.Fatalf("failed to parse file: %v", err)}if df2.Segments[0].Labels[0].Comment != existingComment {t.Errorf("original comment should be preserved, got %q", df2.Segments[0].Labels[0].Comment)}}func TestCallsModifyPreservesBookmarkOnOtherChange(t *testing.T) {// Create a temp .data file with a bookmarktmpDir := t.TempDir()tmpFile := filepath.Join(tmpDir, "test.data")df := &utils.DataFile{Meta: &utils.DataMeta{Operator: "test", Duration: 60},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 15.0,FreqLow: 100,FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 80, Filter: "myfilter", Bookmark: true},},},},}if err := df.Write(tmpFile); err != nil {t.Fatalf("failed to write test file: %v", err)}// Change certainty (without passing --bookmark) - bookmark should be preservedresult, err := CallsModify(CallsModifyInput{File: tmpFile,Reviewer: "tester",Filter: "myfilter",Segment: "10-15",Certainty: 100,// No Bookmark set})if err != nil {t.Errorf("unexpected error: %v", err)}if result.Bookmark != nil {t.Errorf("bookmark should not be in output when not changed, got %v", result.Bookmark)}// Verify bookmark is still true in the filedf2, err := utils.ParseDataFile(tmpFile)if err != nil {t.Fatalf("failed to parse file: %v", err)}if !df2.Segments[0].Labels[0].Bookmark {t.Errorf("bookmark should still be true after changing certainty, got false")}}func TestCallsModifyInvalidSegment(t *testing.T) {tmpDir := t.TempDir()tmpFile := filepath.Join(tmpDir, "test.data")df := &utils.DataFile{Meta: &utils.DataMeta{Operator: "test", Duration: 60},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 15.0,FreqLow: 100,FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 80, Filter: "myfilter"},},},},}if err := df.Write(tmpFile); err != nil {t.Fatalf("failed to write test file: %v", err)}// Test: Non-existent segment should errorresult, err := CallsModify(CallsModifyInput{File: tmpFile,Reviewer: "tester",Filter: "myfilter",Segment: "99-100",Certainty: 80,})if err == nil {t.Errorf("expected error for non-existent segment, got nil")}if result.Error == "" {t.Errorf("expected error message, got empty")}}
package toolsimport ("fmt""math""os""strings""skraak/utils")// CallsModifyInput defines the input for the modify tooltype CallsModifyInput struct {File string `json:"file"`Reviewer string `json:"reviewer"`Filter string `json:"filter"`Segment string `json:"segment"`Certainty int `json:"certainty"`Species string `json:"species"`Bookmark *bool `json:"bookmark"`Comment string `json:"comment"`}// CallsModifyOutput defines the output for the modify tooltype CallsModifyOutput struct {File string `json:"file"`SegmentStart int `json:"segment_start"`SegmentEnd int `json:"segment_end"`Species string `json:"species,omitempty"`CallType string `json:"calltype,omitempty"`Certainty int `json:"certainty,omitempty"`Bookmark *bool `json:"bookmark,omitempty"`Comment string `json:"comment,omitempty"`PreviousValue string `json:"previous_value,omitempty"`Error string `json:"error,omitempty"`}// CallsModify modifies a label in a .data filefunc CallsModify(input CallsModifyInput) (CallsModifyOutput, error) {var output CallsModifyOutput// Validate required flagsif input.File == "" {output.Error = "--file is required"return output, fmt.Errorf("%s", output.Error)}if input.Reviewer == "" {output.Error = "--reviewer is required"return output, fmt.Errorf("%s", output.Error)}if input.Filter == "" {output.Error = "--filter is required"return output, fmt.Errorf("%s", output.Error)}if input.Segment == "" {output.Error = "--segment is required"return output, fmt.Errorf("%s", output.Error)}// Parse segment time rangestartTime, endTime, err := parseSegmentRange(input.Segment)if err != nil {output.Error = err.Error()return output, fmt.Errorf("%s", output.Error)}// Validate comment (max 140 chars, ASCII only)if len(input.Comment) > 140 {output.Error = "--comment must be 140 characters or less"return output, fmt.Errorf("%s", output.Error)}for i, r := range input.Comment {if r > 127 {output.Error = fmt.Sprintf("--comment must be ASCII only (non-ASCII at position %d)", i)return output, fmt.Errorf("%s", output.Error)}}output.File = input.Fileoutput.SegmentStart = startTimeoutput.SegmentEnd = endTime// Check file existsif _, err := os.Stat(input.File); os.IsNotExist(err) {output.Error = fmt.Sprintf("File not found: %s", input.File)return output, fmt.Errorf("%s", output.Error)}// Parse .data filedataFile, err := utils.ParseDataFile(input.File)if err != nil {output.Error = fmt.Sprintf("Failed to parse file: %v", err)return output, fmt.Errorf("%s", output.Error)}// Find matching segment (also checks filter to handle duplicate time ranges)segment := findSegment(dataFile.Segments, startTime, endTime, input.Filter)if segment == nil {output.Error = fmt.Sprintf("No segment found matching time range %d-%d", startTime, endTime)return output, fmt.Errorf("%s", output.Error)}// Find label matching filtervar targetLabel *utils.Labelfor _, label := range segment.Labels {if label.Filter == input.Filter {targetLabel = labelbreak}}if targetLabel == nil {output.Error = fmt.Sprintf("No label found with filter '%s' in segment %d-%d", input.Filter, startTime, endTime)return output, fmt.Errorf("%s", output.Error)}// Store previous value for outputoutput.PreviousValue = formatLabel(targetLabel)// Calculate new species/calltypevar newSpecies, newCallType stringif input.Species != "" {if strings.Contains(input.Species, "+") {parts := strings.SplitN(input.Species, "+", 2)newSpecies = parts[0]newCallType = parts[1]} else {newSpecies = input.SpeciesnewCallType = "" // Clear calltype}} else {newSpecies = targetLabel.SpeciesnewCallType = targetLabel.CallType}// Check if anything would changespeciesChanging := newSpecies != targetLabel.Species || newCallType != targetLabel.CallTypecertaintyChanging := input.Certainty != targetLabel.CertaintybookmarkChanging := input.Bookmark != nil && *input.Bookmark != targetLabel.BookmarkcommentChanging := input.Comment != "" // Any non-empty comment will be addedif !speciesChanging && !certaintyChanging && !bookmarkChanging && !commentChanging {output.Error = "No changes needed: all values already match"return output, fmt.Errorf("%s", output.Error)}// Update reviewer on file metadatadataFile.Meta.Reviewer = input.Reviewer// Update species/calltypetargetLabel.Species = newSpeciestargetLabel.CallType = newCallTypeoutput.Species = newSpeciesoutput.CallType = newCallType// Update certaintytargetLabel.Certainty = input.Certaintyoutput.Certainty = input.Certainty// Update bookmark (only if it would change - never toggle away from true)if input.Bookmark != nil && *input.Bookmark != targetLabel.Bookmark {targetLabel.Bookmark = *input.Bookmarkoutput.Bookmark = input.Bookmark}// Update comment (additive - append to existing comment, never destroy)if input.Comment != "" {var newComment stringif targetLabel.Comment != "" {newComment = targetLabel.Comment + " | " + input.Comment} else {newComment = input.Comment}// Check length after combiningif len(newComment) > 140 {output.Error = fmt.Sprintf("Combined comment exceeds 140 characters (%d)", len(newComment))return output, fmt.Errorf("%s", output.Error)}targetLabel.Comment = newCommentoutput.Comment = newComment}// Save fileif err := dataFile.Write(input.File); err != nil {output.Error = fmt.Sprintf("Failed to save file: %v", err)return output, fmt.Errorf("%s", output.Error)}return output, nil}// parseSegmentRange parses "12-15" format into start and end integersfunc parseSegmentRange(s string) (int, int, error) {parts := strings.Split(s, "-")if len(parts) != 2 {return 0, 0, fmt.Errorf("invalid segment format: %s (expected start-end, e.g., 12-15)", s)}var start, end intif _, err := fmt.Sscanf(parts[0], "%d", &start); err != nil {return 0, 0, fmt.Errorf("invalid start time: %s", parts[0])}if _, err := fmt.Sscanf(parts[1], "%d", &end); err != nil {return 0, 0, fmt.Errorf("invalid end time: %s", parts[1])}if start < 0 || end < 0 {return 0, 0, fmt.Errorf("times must be non-negative")}if start >= end {return 0, 0, fmt.Errorf("start time must be less than end time")}return start, end, nil}// findSegment finds a segment matching the time range using floor/ceil matching.// It also checks that the segment contains a label with the specified filter,// so that duplicate segments (same time range, different filters) are resolved correctly.func findSegment(segments []*utils.Segment, startTime, endTime int, filter string) *utils.Segment {for _, seg := range segments {segStart := int(math.Floor(seg.StartTime))segEnd := int(math.Ceil(seg.EndTime))if segEnd == segStart {segEnd = segStart + 1 // minimum 1 second}if segStart == startTime && segEnd == endTime {for _, label := range seg.Labels {if label.Filter == filter {return seg}}}}return nil}// formatLabel formats a label for displayfunc formatLabel(label *utils.Label) string {result := label.Speciesif label.CallType != "" {result += "+" + label.CallType}result += fmt.Sprintf(" (%d%%)", label.Certainty)return result}
package toolsimport ("bufio""fmt""os""path/filepath""sort""strings""sync""sync/atomic""skraak/utils")// CallsFromRavenInput defines the input for the calls-from-raven tooltype CallsFromRavenInput struct {Folder string `json:"folder"`File string `json:"file"`Delete bool `json:"delete"`ProgressHandler ProgressHandler `json:"-"` // Optional progress callback}// CallsFromRavenOutput defines the output for the calls-from-raven tooltype CallsFromRavenOutput struct {Calls []ClusteredCall `json:"calls"`TotalCalls int `json:"total_calls"`SpeciesCount map[string]int `json:"species_count"`DataFilesWritten int `json:"data_files_written"`DataFilesSkipped int `json:"data_files_skipped"`FilesProcessed int `json:"files_processed"`FilesDeleted int `json:"files_deleted"`Filter string `json:"filter"`Error *string `json:"error,omitempty"`}// RavenSelection represents a single Raven selectiontype RavenSelection struct {StartTime float64EndTime float64FreqLow float64FreqHigh float64Species string}// ravenJob represents a single Raven file to processtype ravenJob struct {ravenFile string}// ravenResult represents the result of processing a single Raven filetype ravenResult struct {ravenFile stringcalls []ClusteredCallwritten boolskipped boolerr error}// CallsFromRaven processes Raven selection files and writes .data filesfunc CallsFromRaven(input CallsFromRavenInput) (CallsFromRavenOutput, error) {var output CallsFromRavenOutputoutput.Filter = "Raven"// Collect Raven files to processvar ravenFiles []stringif input.File != "" {ravenFiles = []string{input.File}} else if input.Folder != "" {var err errorravenFiles, err = findRavenFiles(input.Folder)if err != nil {errMsg := fmt.Sprintf("Failed to find Raven files: %v", err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}} else {errMsg := "Either --folder or --file must be specified"output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}if len(ravenFiles) == 0 {errMsg := "No Raven files found"output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}// Single file or small batch: process sequentially (avoid goroutine overhead)if len(ravenFiles) < 10 {return callsFromRavenSequential(input, ravenFiles)}// Large batch: parallel processing with DirCachereturn callsFromRavenParallel(input, ravenFiles)}// callsFromRavenSequential processes Raven files one at a time (for small batches)func callsFromRavenSequential(input CallsFromRavenInput, ravenFiles []string) (CallsFromRavenOutput, error) {var output CallsFromRavenOutputoutput.Filter = "Raven"// Build DirCache once for the folder (even sequential benefits from avoiding repeated dir scans)dirCaches := make(map[string]*DirCache)if input.Folder != "" {dirCaches[input.Folder] = NewDirCache(input.Folder)}speciesCount := make(map[string]int)var allCalls []ClusteredCalldataFilesWritten := 0dataFilesSkipped := 0filesProcessed := 0filesDeleted := 0for _, ravenFile := range ravenFiles {dir := filepath.Dir(ravenFile)cache := dirCaches[dir]if cache == nil {cache = NewDirCache(dir)dirCaches[dir] = cache}calls, written, skipped, err := processRavenFileCached(ravenFile, cache)if err != nil {errMsg := fmt.Sprintf("Error processing %s: %v", ravenFile, err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}if written {dataFilesWritten++}if skipped {dataFilesSkipped++}for _, call := range calls {allCalls = append(allCalls, call)speciesCount[call.EbirdCode]++}filesProcessed++// Delete if requested and successfully processedif input.Delete && written {if err := os.Remove(ravenFile); err != nil {errMsg := fmt.Sprintf("Failed to delete %s: %v", ravenFile, err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}filesDeleted++}if input.ProgressHandler != nil {input.ProgressHandler(filesProcessed, len(ravenFiles), filepath.Base(ravenFile))}}// Sort all calls by file, then start timesort.Slice(allCalls, func(i, j int) bool {if allCalls[i].File != allCalls[j].File {return allCalls[i].File < allCalls[j].File}return allCalls[i].StartTime < allCalls[j].StartTime})output.Calls = allCallsoutput.TotalCalls = len(allCalls)output.SpeciesCount = speciesCountoutput.DataFilesWritten = dataFilesWrittenoutput.DataFilesSkipped = dataFilesSkippedoutput.FilesProcessed = filesProcessedoutput.FilesDeleted = filesDeletedreturn output, nil}// callsFromRavenParallel processes Raven files concurrently using a worker pool and DirCachefunc callsFromRavenParallel(input CallsFromRavenInput, ravenFiles []string) (CallsFromRavenOutput, error) {var output CallsFromRavenOutputoutput.Filter = "Raven"total := len(ravenFiles)var processed atomic.Int32// Build DirCache for the folderdirCaches := &sync.Map{}if input.Folder != "" {cache := NewDirCache(input.Folder)dirCaches.Store(input.Folder, cache)}// Create job and result channelsjobs := make(chan ravenJob, total)results := make(chan ravenResult, total)// Start workersvar wg sync.WaitGroupfor range DOT_DATA_WORKERS {wg.Add(1)go ravenWorker(dirCaches, jobs, results, &wg)}// Send jobsfor _, ravenFile := range ravenFiles {jobs <- ravenJob{ravenFile: ravenFile}}close(jobs)// Wait for workers to finish, then close resultsgo func() {wg.Wait()close(results)}()// Collect results with progress reportingspeciesCount := make(map[string]int)var allCalls []ClusteredCalldataFilesWritten := 0dataFilesSkipped := 0filesProcessed := 0filesDeleted := 0var firstErr errorfor result := range results {if result.err != nil && firstErr == nil {firstErr = result.err}if result.written {dataFilesWritten++}if result.skipped {dataFilesSkipped++}for _, call := range result.calls {allCalls = append(allCalls, call)speciesCount[call.EbirdCode]++}filesProcessed++// Delete if requested and successfully processedif input.Delete && result.written {if err := os.Remove(result.ravenFile); err != nil {if firstErr == nil {firstErr = fmt.Errorf("failed to delete %s: %w", result.ravenFile, err)}} else {filesDeleted++}}if input.ProgressHandler != nil {current := int(processed.Add(1))input.ProgressHandler(current, total, filepath.Base(result.ravenFile))}}if firstErr != nil {errMsg := firstErr.Error()output.Error = &errMsgreturn output, firstErr}// Sort all calls by file, then start timesort.Slice(allCalls, func(i, j int) bool {if allCalls[i].File != allCalls[j].File {return allCalls[i].File < allCalls[j].File}return allCalls[i].StartTime < allCalls[j].StartTime})output.Calls = allCallsoutput.TotalCalls = len(allCalls)output.SpeciesCount = speciesCountoutput.DataFilesWritten = dataFilesWrittenoutput.DataFilesSkipped = dataFilesSkippedoutput.FilesProcessed = filesProcessedoutput.FilesDeleted = filesDeletedreturn output, nil}// ravenWorker processes Raven files from the jobs channelfunc ravenWorker(dirCaches *sync.Map, jobs <-chan ravenJob, results chan<- ravenResult, wg *sync.WaitGroup) {defer wg.Done()for job := range jobs {dir := filepath.Dir(job.ravenFile)// Get or create DirCache for this directoryvar cache *DirCacheif cached, ok := dirCaches.Load(dir); ok {cache = cached.(*DirCache)} else {cache = NewDirCache(dir)dirCaches.Store(dir, cache)}calls, written, skipped, err := processRavenFileCached(job.ravenFile, cache)results <- ravenResult{ravenFile: job.ravenFile,calls: calls,written: written,skipped: skipped,err: err,}}}// findRavenFiles finds all Raven selection files in a folderfunc findRavenFiles(folder string) ([]string, error) {var files []stringentries, err := os.ReadDir(folder)if err != nil {return nil, err}for _, entry := range entries {name := entry.Name()if strings.HasSuffix(name, ".selections.txt") {files = append(files, filepath.Join(folder, name))}}return files, nil}// processRavenFileCached processes a single Raven selection file using a DirCache for WAV lookupfunc processRavenFileCached(ravenFile string, cache *DirCache) ([]ClusteredCall, bool, bool, error) {// Open filefile, err := os.Open(ravenFile)if err != nil {return nil, false, false, fmt.Errorf("failed to open file: %w", err)}defer func() { _ = file.Close() }()// Read header and selections (tab-separated)scanner := bufio.NewScanner(file)// Read header lineif !scanner.Scan() {return nil, false, false, fmt.Errorf("empty file")}header := strings.Split(scanner.Text(), "\t")// Find column indicesbeginTimeIdx := -1endTimeIdx := -1lowFreqIdx := -1highFreqIdx := -1speciesIdx := -1for i, col := range header {switch col {case "Begin Time (s)":beginTimeIdx = icase "End Time (s)":endTimeIdx = icase "Low Freq (Hz)":lowFreqIdx = icase "High Freq (Hz)":highFreqIdx = icase "Species":speciesIdx = i}}if beginTimeIdx == -1 || endTimeIdx == -1 || speciesIdx == -1 {return nil, false, false, fmt.Errorf("missing required columns in Raven file")}// Read selectionsvar selections []RavenSelectionfor scanner.Scan() {line := scanner.Text()if line == "" {continue}fields := strings.Split(line, "\t")if len(fields) <= speciesIdx {continue}var sel RavenSelectionif _, err := fmt.Sscanf(fields[beginTimeIdx], "%f", &sel.StartTime); err != nil {return nil, false, false, fmt.Errorf("failed to parse begin time %q: %w", fields[beginTimeIdx], err)}if _, err := fmt.Sscanf(fields[endTimeIdx], "%f", &sel.EndTime); err != nil {return nil, false, false, fmt.Errorf("failed to parse end time %q: %w", fields[endTimeIdx], err)}if lowFreqIdx >= 0 && lowFreqIdx < len(fields) {if _, err := fmt.Sscanf(fields[lowFreqIdx], "%f", &sel.FreqLow); err != nil {return nil, false, false, fmt.Errorf("failed to parse low freq %q: %w", fields[lowFreqIdx], err)}}if highFreqIdx >= 0 && highFreqIdx < len(fields) {if _, err := fmt.Sscanf(fields[highFreqIdx], "%f", &sel.FreqHigh); err != nil {return nil, false, false, fmt.Errorf("failed to parse high freq %q: %w", fields[highFreqIdx], err)}}sel.Species = fields[speciesIdx]selections = append(selections, sel)}if err := scanner.Err(); err != nil {return nil, false, false, fmt.Errorf("error reading file: %w", err)}if len(selections) == 0 {return nil, false, true, nil // No selections, skip}// Derive WAV path from Raven filename// "20230610_150000.Table.1.selections.txt" -> "20230610_150000"base := filepath.Base(ravenFile)// Remove .selections.txtnameWithoutSuffix := strings.TrimSuffix(base, ".selections.txt")// Remove .Table.X (or similar pattern)idx := strings.Index(nameWithoutSuffix, ".Table.")if idx > 0 {nameWithoutSuffix = nameWithoutSuffix[:idx]}// Find WAV file using DirCache (O(1) lookup instead of O(N) directory scan)var wavPath stringif cache != nil {wavPath = cache.FindWAV(nameWithoutSuffix)} else {wavPath = findWAVFile(filepath.Dir(ravenFile), nameWithoutSuffix)}if wavPath == "" {return nil, false, true, nil // WAV not found, skip}// Check if WAV exists (to get sample rate and duration)sampleRate, duration, err := utils.ParseWAVHeaderMinimal(wavPath)if err != nil {return nil, false, true, nil // Skip if WAV not found or invalid}dataPath := wavPath + ".data"// Convert selections to segmentssegments := buildRavenSegments(selections, sampleRate)// Build metadatameta := AviaNZMeta{Operator: "Raven",Duration: duration,}reviewer := "None"meta.Reviewer = &reviewer// Write .data file (safe write)if err := writeDotDataFileSafe(dataPath, segments, "Raven", meta); err != nil {return nil, false, false, err}// Convert to ClusteredCalls for outputvar calls []ClusteredCallfor _, sel := range selections {calls = append(calls, ClusteredCall{File: wavPath,StartTime: sel.StartTime,EndTime: sel.EndTime,EbirdCode: sel.Species,Segments: 1,})}return calls, true, false, nil}// buildRavenSegments converts Raven selections to AviaNZ segmentsfunc buildRavenSegments(selections []RavenSelection, sampleRate int) []AviaNZSegment {var segments []AviaNZSegmentfor _, sel := range selections {labels := []AviaNZLabel{{Species: sel.Species,Certainty: 70, // Default certainty for Raven (no confidence metric)Filter: "Raven",},}// Use frequency range from Raven, or full band if not specifiedfreqLow := sel.FreqLowfreqHigh := sel.FreqHighif freqLow == 0 && freqHigh == 0 {freqHigh = float64(sampleRate)}segment := AviaNZSegment{sel.StartTime,sel.EndTime,freqLow,freqHigh,labels,}segments = append(segments, segment)}return segments}
package toolsimport ("os""path/filepath""testing""skraak/utils")func TestCallsFromPreds_EmptyFilterError(t *testing.T) {// Create a temp CSV filetmpDir := t.TempDir()csvPath := filepath.Join(tmpDir, "preds.csv")csvContent := "file,start_time,end_time,kiwi\n./test.wav,0.0,3.0,1\n"if err := os.WriteFile(csvPath, []byte(csvContent), 0644); err != nil {t.Fatal(err)}// Create a dummy WAV file (minimal valid WAV)wavPath := filepath.Join(tmpDir, "test.wav")createMinimalWAV(t, wavPath, 44100, 10.0)// Test with empty filter (should error)input := CallsFromPredsInput{CSVPath: csvPath,Filter: "",WriteDotData: true,ProgressHandler: nil,}output, err := CallsFromPreds(input)// Should return errorif err == nil {t.Error("expected error for empty filter, got nil")}if output.Error == nil || *output.Error == "" {t.Error("expected error message in output, got empty")}}func TestCallsFromPreds_NewDataFile(t *testing.T) {// Create a temp CSV filetmpDir := t.TempDir()csvPath := filepath.Join(tmpDir, "predsST_test-filter_2025-01-01.csv")csvContent := "file,start_time,end_time,kiwi\n./test.wav,0.0,3.0,1\n"if err := os.WriteFile(csvPath, []byte(csvContent), 0644); err != nil {t.Fatal(err)}// Create a dummy WAV filewavPath := filepath.Join(tmpDir, "test.wav")createMinimalWAV(t, wavPath, 44100, 10.0)// Test with filter parsed from filenameinput := CallsFromPredsInput{CSVPath: csvPath,Filter: "", // Will parse from filenameWriteDotData: true,ProgressHandler: nil,}output, err := CallsFromPreds(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.DataFilesWritten != 1 {t.Errorf("expected 1 data file written, got %d", output.DataFilesWritten)}if output.Filter != "test-filter" {t.Errorf("expected filter 'test-filter', got '%s'", output.Filter)}// Verify .data file was createddataPath := wavPath + ".data"if _, err := os.Stat(dataPath); os.IsNotExist(err) {t.Error("expected .data file to be created")}// Verify contentdf, err := utils.ParseDataFile(dataPath)if err != nil {t.Fatalf("failed to parse .data file: %v", err)}if len(df.Segments) != 1 {t.Errorf("expected 1 segment, got %d", len(df.Segments))}if len(df.Segments[0].Labels) != 1 {t.Errorf("expected 1 label, got %d", len(df.Segments[0].Labels))}if df.Segments[0].Labels[0].Filter != "test-filter" {t.Errorf("expected filter 'test-filter', got '%s'", df.Segments[0].Labels[0].Filter)}}func TestCallsFromPreds_ExistingDataFileSameFilter(t *testing.T) {// Create a temp CSV filetmpDir := t.TempDir()csvPath := filepath.Join(tmpDir, "predsST_existing-filter_2025-01-01.csv")csvContent := "file,start_time,end_time,kiwi\n./test.wav,0.0,3.0,1\n"if err := os.WriteFile(csvPath, []byte(csvContent), 0644); err != nil {t.Fatal(err)}// Create a dummy WAV filewavPath := filepath.Join(tmpDir, "test.wav")createMinimalWAV(t, wavPath, 44100, 10.0)// Create existing .data file with same filterdataPath := wavPath + ".data"existingData := `[{"Operator": "Manual", "Reviewer": "David", "Duration": 10.0},[5.0, 8.0, 0, 44100, [{"species": "morepork", "certainty": 90, "filter": "existing-filter"}]]]`if err := os.WriteFile(dataPath, []byte(existingData), 0644); err != nil {t.Fatal(err)}// Test with same filter (should error)input := CallsFromPredsInput{CSVPath: csvPath,Filter: "", // Will parse from filename -> "existing-filter"WriteDotData: true,ProgressHandler: nil,}output, err := CallsFromPreds(input)// Should return errorif err == nil {t.Error("expected error for same filter, got nil")}if output.Error == nil {t.Error("expected error message in output")}// Verify original .data file is unchangeddf, err := utils.ParseDataFile(dataPath)if err != nil {t.Fatalf("failed to parse .data file: %v", err)}if len(df.Segments) != 1 {t.Errorf("expected original 1 segment, got %d", len(df.Segments))}if df.Segments[0].Labels[0].Species != "morepork" {t.Errorf("expected original species 'morepork', got '%s'", df.Segments[0].Labels[0].Species)}}func TestCallsFromPreds_ExistingDataFileDifferentFilter(t *testing.T) {// Create a temp CSV filetmpDir := t.TempDir()csvPath := filepath.Join(tmpDir, "predsST_new-filter_2025-01-01.csv")csvContent := "file,start_time,end_time,kiwi\n./test.wav,0.0,3.0,1\n"if err := os.WriteFile(csvPath, []byte(csvContent), 0644); err != nil {t.Fatal(err)}// Create a dummy WAV filewavPath := filepath.Join(tmpDir, "test.wav")createMinimalWAV(t, wavPath, 44100, 10.0)// Create existing .data file with different filterdataPath := wavPath + ".data"existingData := `[{"Operator": "Manual", "Reviewer": "David", "Duration": 10.0},[5.0, 8.0, 0, 44100, [{"species": "morepork", "certainty": 90, "filter": "old-filter"}]]]`if err := os.WriteFile(dataPath, []byte(existingData), 0644); err != nil {t.Fatal(err)}// Test with different filter (should merge)input := CallsFromPredsInput{CSVPath: csvPath,Filter: "", // Will parse from filename -> "new-filter"WriteDotData: true,ProgressHandler: nil,}output, err := CallsFromPreds(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.DataFilesWritten != 1 {t.Errorf("expected 1 data file written, got %d", output.DataFilesWritten)}// Verify .data file has merged contentdf, err := utils.ParseDataFile(dataPath)if err != nil {t.Fatalf("failed to parse .data file: %v", err)}if len(df.Segments) != 2 {t.Errorf("expected 2 segments after merge, got %d", len(df.Segments))}// Check segments are sorted by start timeif df.Segments[0].StartTime > df.Segments[1].StartTime {t.Error("expected segments to be sorted by start time")}// Check both filters are presentfilters := make(map[string]bool)for _, seg := range df.Segments {for _, label := range seg.Labels {filters[label.Filter] = true}}if !filters["old-filter"] {t.Error("expected 'old-filter' to be present")}if !filters["new-filter"] {t.Error("expected 'new-filter' to be present")}}func TestCallsFromPreds_ExistingDataFileParseError(t *testing.T) {// Create a temp CSV filetmpDir := t.TempDir()csvPath := filepath.Join(tmpDir, "predsST_test-filter_2025-01-01.csv")csvContent := "file,start_time,end_time,kiwi\n./test.wav,0.0,3.0,1\n"if err := os.WriteFile(csvPath, []byte(csvContent), 0644); err != nil {t.Fatal(err)}// Create a dummy WAV filewavPath := filepath.Join(tmpDir, "test.wav")createMinimalWAV(t, wavPath, 44100, 10.0)// Create corrupted .data filedataPath := wavPath + ".data"corruptedData := `this is not valid json`if err := os.WriteFile(dataPath, []byte(corruptedData), 0644); err != nil {t.Fatal(err)}// Test (should error due to parse failure)input := CallsFromPredsInput{CSVPath: csvPath,Filter: "",WriteDotData: true,ProgressHandler: nil,}output, err := CallsFromPreds(input)// Should return errorif err == nil {t.Error("expected error for corrupted .data file, got nil")}if output.Error == nil {t.Error("expected error message in output")}// Verify original file is unchangedcontent, err := os.ReadFile(dataPath)if err != nil {t.Fatal(err)}if string(content) != corruptedData {t.Error("expected corrupted file to remain unchanged")}}func TestCallsFromPreds_ExplicitFilter(t *testing.T) {// Create a temp CSV file with non-standard nametmpDir := t.TempDir()csvPath := filepath.Join(tmpDir, "predictions.csv")csvContent := "file,start_time,end_time,kiwi\n./test.wav,0.0,3.0,1\n"if err := os.WriteFile(csvPath, []byte(csvContent), 0644); err != nil {t.Fatal(err)}// Create a dummy WAV filewavPath := filepath.Join(tmpDir, "test.wav")createMinimalWAV(t, wavPath, 44100, 10.0)// Test with explicit filterinput := CallsFromPredsInput{CSVPath: csvPath,Filter: "my-custom-filter",WriteDotData: true,ProgressHandler: nil,}output, err := CallsFromPreds(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.Filter != "my-custom-filter" {t.Errorf("expected filter 'my-custom-filter', got '%s'", output.Filter)}// Verify .data file uses explicit filterdataPath := wavPath + ".data"df, err := utils.ParseDataFile(dataPath)if err != nil {t.Fatalf("failed to parse .data file: %v", err)}if df.Segments[0].Labels[0].Filter != "my-custom-filter" {t.Errorf("expected filter 'my-custom-filter' in .data file, got '%s'", df.Segments[0].Labels[0].Filter)}}func TestCallsFromPreds_NonParsableFilenameNoFilter(t *testing.T) {// Create a temp CSV file with non-standard name that can't be parsedtmpDir := t.TempDir()csvPath := filepath.Join(tmpDir, "random_name.csv")csvContent := "file,start_time,end_time,kiwi\n./test.wav,0.0,3.0,1\n"if err := os.WriteFile(csvPath, []byte(csvContent), 0644); err != nil {t.Fatal(err)}// Create a dummy WAV filewavPath := filepath.Join(tmpDir, "test.wav")createMinimalWAV(t, wavPath, 44100, 10.0)// Test with no filter and non-parsable filename (should error)input := CallsFromPredsInput{CSVPath: csvPath,Filter: "",WriteDotData: true,ProgressHandler: nil,}output, err := CallsFromPreds(input)// Should return errorif err == nil {t.Error("expected error for unparsable filename with no filter, got nil")}if output.Error == nil {t.Error("expected error message in output")}}// createMinimalWAV creates a minimal valid WAV file for testingfunc createMinimalWAV(t *testing.T, path string, sampleRate int, duration float64) {t.Helper()numSamples := int(float64(sampleRate) * duration)dataSize := numSamples * 2 // 16-bit mono// WAV header (44 bytes)header := make([]byte, 44)// RIFF headercopy(header[0:4], "RIFF")totalSize := uint32(36 + dataSize)header[4] = byte(totalSize)header[5] = byte(totalSize >> 8)header[6] = byte(totalSize >> 16)header[7] = byte(totalSize >> 24)copy(header[8:12], "WAVE")// fmt chunkcopy(header[12:16], "fmt ")chunkSize := uint32(16)header[16] = byte(chunkSize)header[17] = byte(chunkSize >> 8)header[18] = byte(chunkSize >> 16)header[19] = byte(chunkSize >> 24)audioFormat := uint16(1) // PCMheader[20] = byte(audioFormat)header[21] = byte(audioFormat >> 8)numChannels := uint16(1)header[22] = byte(numChannels)header[23] = byte(numChannels >> 8)header[24] = byte(sampleRate)header[25] = byte(sampleRate >> 8)header[26] = byte(sampleRate >> 16)header[27] = byte(sampleRate >> 24)byteRate := uint32(sampleRate * 2)header[28] = byte(byteRate)header[29] = byte(byteRate >> 8)header[30] = byte(byteRate >> 16)header[31] = byte(byteRate >> 24)blockAlign := uint16(2)header[32] = byte(blockAlign)header[33] = byte(blockAlign >> 8)bitsPerSample := uint16(16)header[34] = byte(bitsPerSample)header[35] = byte(bitsPerSample >> 8)// data chunkcopy(header[36:40], "data")header[40] = byte(dataSize)header[41] = byte(dataSize >> 8)header[42] = byte(dataSize >> 16)header[43] = byte(dataSize >> 24)// Create file with header and silencefile, err := os.Create(path)if err != nil {t.Fatal(err)}defer file.Close()if _, err := file.Write(header); err != nil {t.Fatal(err)}// Write silence (zeros)silence := make([]byte, dataSize)if _, err := file.Write(silence); err != nil {t.Fatal(err)}}
package toolsimport ("encoding/csv""encoding/json""fmt""io""os""path/filepath""sort""strconv""strings""sync""sync/atomic""skraak/utils")// Constants for clustering algorithmconst (CLUSTER_GAP_MULTIPLIER = 2 // 3 Gap threshold = CLUSTER_GAP_MULTIPLIER * clip_duration. 3 for kiwiMIN_DETECTIONS_PER_CLUSTER = 0 // 1 = filter out single detections (used for kiwi, they have long calls 30s), 0 = let single detections pass throughDEFAULT_CERTAINTY = 70 // .data certainty:70DOT_DATA_WORKERS = 8 // Number of parallel workers for .data file writing)// ClusteredCall represents a clustered bird call detectiontype ClusteredCall struct {File string `json:"file"`StartTime float64 `json:"start_time"`EndTime float64 `json:"end_time"`EbirdCode string `json:"ebird_code"`Segments int `json:"segments"`}// CallsFromPredsInput defines the input for the calls-from-preds tooltype CallsFromPredsInput struct {CSVPath string `json:"csv_path"`Filter string `json:"filter"`WriteDotData bool `json:"write_dot_data"`GapMultiplier int `json:"gap_multiplier"`MinDetections int `json:"min_detections"`ProgressHandler ProgressHandler `json:"-"` // Optional progress callback (not serialized)}// ProgressHandler is a callback function for reporting progress during long operations// processed: number of items processed so far// total: total number of items to process// message: optional status messagetype ProgressHandler func(processed, total int, message string)// CallsFromPredsOutput defines the output for the calls-from-preds tooltype CallsFromPredsOutput struct {Calls []ClusteredCall `json:"calls"`TotalCalls int `json:"total_calls"`ClipDuration float64 `json:"clip_duration"`GapThreshold float64 `json:"gap_threshold"`SpeciesCount map[string]int `json:"species_count"`DataFilesWritten int `json:"data_files_written"`DataFilesSkipped int `json:"data_files_skipped"`Filter string `json:"filter"`Error *string `json:"error,omitempty"`}// AviaNZ .data file types// AviaNZMeta is the metadata element in a .data filetype AviaNZMeta struct {Operator string `json:"Operator"`Reviewer *string `json:"Reviewer,omitempty"`Duration float64 `json:"Duration"`}// AviaNZLabel represents a species label in a segmenttype AviaNZLabel struct {Species string `json:"species"`Certainty int `json:"certainty"`Filter string `json:"filter"`}// AviaNZSegment represents a detection segment [start, end, freq_low, freq_high, labels]type AviaNZSegment [5]any// CallsFromPreds reads a predictions CSV and clusters detections into continuous bird callsfunc CallsFromPreds(input CallsFromPredsInput) (CallsFromPredsOutput, error) {var output CallsFromPredsOutput// Determine filter: use provided filter, or parse from CSV filenamefilter := input.Filterif filter == "" {filter = ParseFilterFromFilename(input.CSVPath)}// Filter must not be emptyif filter == "" {errMsg := "Filter must be specified via --filter flag or parsable from CSV filename"output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}output.Filter = filter// Open CSV filefile, err := os.Open(input.CSVPath)if err != nil {errMsg := fmt.Sprintf("Failed to open CSV file: %v", err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}defer func() { _ = file.Close() }()// Read CSVreader := csv.NewReader(file)reader.ReuseRecord = true // Memory optimization for large files// Read headerheader, err := reader.Read()if err != nil {errMsg := fmt.Sprintf("Failed to read CSV header: %v", err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}// Find column indicesfileIdx := -1startTimeIdx := -1endTimeIdx := -1var ebirdCodes []stringvar ebirdIdx []int// Columns to ignore (not ebird codes)ignoredColumns := map[string]bool{"NotKiwi": true,"0.0": true,}for i, col := range header {switch col {case "file":fileIdx = icase "start_time":startTimeIdx = icase "end_time":endTimeIdx = idefault:// Skip ignored columnsif ignoredColumns[col] {continue}// All other columns are ebird codesebirdCodes = append(ebirdCodes, col)ebirdIdx = append(ebirdIdx, i)}}if fileIdx == -1 || startTimeIdx == -1 || endTimeIdx == -1 {errMsg := "CSV must have 'file', 'start_time', and 'end_time' columns"output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}if len(ebirdCodes) == 0 {errMsg := "CSV must have at least one ebird code column"output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}// Read all rows and organize by (file, ebird_code) -> start_times// Using maps for efficient groupingtype FileEbirdKey struct {File stringEbirdCode string}detections := make(map[FileEbirdKey][]float64)clipDuration := 0.0// Read first row to get clip durationrecord, err := reader.Read()if err != nil && err != io.EOF {errMsg := fmt.Sprintf("Failed to read first CSV row: %v", err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}if err != io.EOF {startTime, _ := strconv.ParseFloat(record[startTimeIdx], 64)endTime, _ := strconv.ParseFloat(record[endTimeIdx], 64)clipDuration = endTime - startTimeoutput.ClipDuration = clipDuration// Process first rowfileName := record[fileIdx]for i, idx := range ebirdIdx {if record[idx] == "1" {key := FileEbirdKey{File: fileName, EbirdCode: ebirdCodes[i]}detections[key] = append(detections[key], startTime)}}// Read remaining rowsfor {record, err := reader.Read()if err == io.EOF {break}if err != nil {errMsg := fmt.Sprintf("Failed to read CSV row: %v", err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}startTime, _ := strconv.ParseFloat(record[startTimeIdx], 64)fileName := record[fileIdx]for i, idx := range ebirdIdx {if record[idx] == "1" {key := FileEbirdKey{File: fileName, EbirdCode: ebirdCodes[i]}detections[key] = append(detections[key], startTime)}}}}// Calculate gap thresholdgapMultiplier := CLUSTER_GAP_MULTIPLIERif input.GapMultiplier > 0 {gapMultiplier = input.GapMultiplier}minDetections := MIN_DETECTIONS_PER_CLUSTERif input.MinDetections >= 0 {minDetections = input.MinDetections}gapThreshold := float64(gapMultiplier) * clipDurationoutput.GapThreshold = gapThreshold// Cluster detections by (file, ebird_code)var allCalls []ClusteredCallspeciesCount := make(map[string]int)for key, startTimes := range detections {// Sort start timessort.Float64s(startTimes)// Cluster consecutive detectionsclusters := clusterStartTimes(startTimes, gapThreshold)// Convert clusters to callsfor _, cluster := range clusters {if len(cluster) <= minDetections {continue}call := ClusteredCall{File: key.File,StartTime: cluster[0],EndTime: cluster[len(cluster)-1] + clipDuration,EbirdCode: key.EbirdCode,Segments: len(cluster),}allCalls = append(allCalls, call)speciesCount[key.EbirdCode]++}}// Sort calls by file, then start timesort.Slice(allCalls, func(i, j int) bool {if allCalls[i].File != allCalls[j].File {return allCalls[i].File < allCalls[j].File}return allCalls[i].StartTime < allCalls[j].StartTime})output.Calls = allCallsoutput.TotalCalls = len(allCalls)output.SpeciesCount = speciesCount// Write .data files if requestedif input.WriteDotData {dataFilesWritten, dataFilesSkipped, err := writeDotFiles(input.CSVPath, filter, allCalls, input.ProgressHandler)if err != nil {// Return error - this includes clobber protection and parse errorserrMsg := fmt.Sprintf("Error writing .data files: %v", err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}output.DataFilesWritten = dataFilesWrittenoutput.DataFilesSkipped = dataFilesSkipped}return output, nil}// extractFilename extracts just the filename from a path// "./C05/2025-11-08/20250518_210000.WAV" -> "20250518_210000.WAV"func extractFilename(path string) string {return filepath.Base(path)}// DirCache caches directory entries for fast WAV file lookup.// Scans the directory once and builds a map from lowercased basename to full filename.// Safe for concurrent read-only use after construction.type DirCache struct {dir stringwavMap map[string]string // lowercase basename -> filename with original case (e.g. "20230610_150000" -> "20230610_150000.WAV")dirMap map[string]string // lowercase basename -> filename for any file (used by from-raven for .selections.txt etc.)}// NewDirCache creates a DirCache by scanning the directory once.func NewDirCache(dir string) *DirCache {entries, err := os.ReadDir(dir)if err != nil {return &DirCache{dir: dir, wavMap: make(map[string]string), dirMap: make(map[string]string)}}wavMap := make(map[string]string, len(entries))dirMap := make(map[string]string, len(entries))for _, entry := range entries {if entry.IsDir() {continue}name := entry.Name()ext := filepath.Ext(name)base := strings.TrimSuffix(name, ext)dirMap[strings.ToLower(base)] = nameif strings.EqualFold(ext, ".wav") {wavMap[strings.ToLower(base)] = name}}return &DirCache{dir: dir, wavMap: wavMap, dirMap: dirMap}}// FindWAV looks up a WAV file by basename (case-insensitive).// Returns the full path with correct case, or empty string if not found.func (dc *DirCache) FindWAV(baseName string) string {if name, ok := dc.wavMap[strings.ToLower(baseName)]; ok {return filepath.Join(dc.dir, name)}return ""}// FindFile looks up any file by basename (case-insensitive).// Returns the full path with correct case, or empty string if not found.func (dc *DirCache) FindFile(baseName string) string {if name, ok := dc.dirMap[strings.ToLower(baseName)]; ok {return filepath.Join(dc.dir, name)}return ""}// findWAVFile finds a WAV file in the directory with case-insensitive matching.// baseName is the filename without extension (e.g., "20230610_150000").// Returns the full path with correct case, or empty string if not found.// Deprecated: Use DirCache.FindWAV for batch operations to avoid repeated directory scans.func findWAVFile(dir, baseName string) string {entries, err := os.ReadDir(dir)if err != nil {return ""}for _, entry := range entries {if entry.IsDir() {continue}name := entry.Name()ext := filepath.Ext(name)nameNoExt := strings.TrimSuffix(name, ext)if nameNoExt == baseName && strings.EqualFold(ext, ".wav") {return filepath.Join(dir, name)}}return ""}// writeDotFiles writes AviaNZ .data files for each audio file with calls// Uses parallel workers for improved performance on large batchesfunc writeDotFiles(csvPath, filter string, calls []ClusteredCall, progress ProgressHandler) (int, int, error) {// Base directory is the directory containing the CSV filecsvDir := filepath.Dir(csvPath)// Group calls by file (using extracted filename)callsByFile := make(map[string][]ClusteredCall)for _, call := range calls {filename := extractFilename(call.File)callsByFile[filename] = append(callsByFile[filename], call)}// Report initial progressif progress != nil {progress(0, len(callsByFile), "Processing WAV files")}// If small batch, process sequentially (avoid goroutine overhead)if len(callsByFile) < 10 {return writeDotFilesSequential(csvDir, filter, callsByFile, progress)}// Parallel processing for larger batchesreturn writeDotFilesParallel(csvDir, filter, callsByFile, progress)}// dotDataJob represents a single file to processtype dotDataJob struct {filename stringfileCalls []ClusteredCall}// dotDataResult represents the result of processing a single filetype dotDataResult struct {filename stringwritten boolerr error}// writeDotFilesSequential processes files one at a time (for small batches)func writeDotFilesSequential(csvDir, filter string, callsByFile map[string][]ClusteredCall, progress ProgressHandler) (int, int, error) {dataFilesWritten := 0dataFilesSkipped := 0total := len(callsByFile)processed := 0for filename, fileCalls := range callsByFile {// Find WAV file with correct casebaseName := strings.TrimSuffix(filename, filepath.Ext(filename))wavPath := findWAVFile(csvDir, baseName)if wavPath == "" {dataFilesSkipped++processed++if progress != nil {progress(processed, total, "")}continue}dataPath := wavPath + ".data"sampleRate, duration, err := utils.ParseWAVHeaderMinimal(wavPath)if err != nil {dataFilesSkipped++processed++if progress != nil {progress(processed, total, "")}continue}// Build segments and metadatameta, segments := buildAviaNZMetaAndSegments(fileCalls, filter, duration, sampleRate)if err := writeDotDataFileSafe(dataPath, segments, filter, meta); err != nil {return dataFilesWritten, dataFilesSkipped, fmt.Errorf("failed to write %s: %w", dataPath, err)}dataFilesWritten++processed++if progress != nil {progress(processed, total, "")}}return dataFilesWritten, dataFilesSkipped, nil}// writeDotFilesParallel processes files concurrently using a worker poolfunc writeDotFilesParallel(csvDir, filter string, callsByFile map[string][]ClusteredCall, progress ProgressHandler) (int, int, error) {total := len(callsByFile)var processed atomic.Int32// Create job channeljobs := make(chan dotDataJob, len(callsByFile))results := make(chan dotDataResult, len(callsByFile))// Start workersvar wg sync.WaitGroupfor range DOT_DATA_WORKERS {wg.Add(1)go dotDataWorker(csvDir, filter, jobs, results, &wg)}// Send jobsfor filename, fileCalls := range callsByFile {jobs <- dotDataJob{filename: filename, fileCalls: fileCalls}}close(jobs)// Wait for workers to finishgo func() {wg.Wait()close(results)}()// Collect results with progress reportingdataFilesWritten := 0dataFilesSkipped := 0var firstErr errorfor result := range results {if result.err != nil && firstErr == nil {firstErr = result.err}if result.written {dataFilesWritten++} else {dataFilesSkipped++}// Report progressif progress != nil {current := int(processed.Add(1))progress(current, total, "")}}return dataFilesWritten, dataFilesSkipped, firstErr}// dotDataWorker processes files from the jobs channelfunc dotDataWorker(csvDir, filter string, jobs <-chan dotDataJob, results chan<- dotDataResult, wg *sync.WaitGroup) {defer wg.Done()for job := range jobs {// Find WAV file with correct casebaseName := strings.TrimSuffix(job.filename, filepath.Ext(job.filename))wavPath := findWAVFile(csvDir, baseName)if wavPath == "" {results <- dotDataResult{filename: job.filename, written: false, err: nil}continue}dataPath := wavPath + ".data"sampleRate, duration, err := utils.ParseWAVHeaderMinimal(wavPath)if err != nil {results <- dotDataResult{filename: job.filename, written: false, err: nil}continue}// Build segments and metadatameta, segments := buildAviaNZMetaAndSegments(job.fileCalls, filter, duration, sampleRate)if err := writeDotDataFileSafe(dataPath, segments, filter, meta); err != nil {results <- dotDataResult{filename: job.filename, written: false, err: fmt.Errorf("failed to write %s: %w", dataPath, err)}continue}results <- dotDataResult{filename: job.filename, written: true, err: nil}}}// buildAviaNZMetaAndSegments creates metadata and segments for a .data filefunc buildAviaNZMetaAndSegments(calls []ClusteredCall, filter string, duration float64, sampleRate int) (AviaNZMeta, []AviaNZSegment) {// Create metadatareviewer := "None"meta := AviaNZMeta{Operator: "Auto",Reviewer: &reviewer,Duration: duration,}// Build segments arrayvar segments []AviaNZSegmentfor _, call := range calls {// Create labels for this segmentlabels := []AviaNZLabel{{Species: call.EbirdCode,Certainty: DEFAULT_CERTAINTY,Filter: filter,},}// Create segment: [start, end, freq_low, freq_high, labels]// freq_low=0, freq_high=sampleRate for full-band segmentssegment := AviaNZSegment{call.StartTime,call.EndTime,0, // freq_lowsampleRate, // freq_high (full band)labels,}segments = append(segments, segment)}return meta, segments}// writeAviaNZDataFile writes a new .data file to disk (does not check for existing files)func writeAviaNZDataFile(path string, data []any) error {file, err := os.Create(path)if err != nil {return fmt.Errorf("failed to create file: %w", err)}defer func() { _ = file.Close() }()encoder := json.NewEncoder(file)encoder.SetIndent("", "") // No indentation for compact outputif err := encoder.Encode(data); err != nil {return fmt.Errorf("failed to encode JSON: %w", err)}return nil}// writeDotDataFileSafe safely writes or merges .data files// - If file doesn't exist: write new file// - If file exists with same filter: return error (refuse to clobber)// - If file exists with different filter: merge segments and write// - If file exists but can't be parsed: return error (refuse to clobber)func writeDotDataFileSafe(path string, newSegments []AviaNZSegment, filter string, meta AviaNZMeta) error {// Check if file existsif _, err := os.Stat(path); err == nil {// File exists - parse and checkexisting, err := utils.ParseDataFile(path)if err != nil {return fmt.Errorf("cannot parse existing %s: %w (refusing to clobber)", path, err)}// Check for duplicate filterfor _, seg := range existing.Segments {if seg.HasFilterLabel(filter) {return fmt.Errorf("%s already contains filter '%s' (refusing to clobber)", path, filter)}}// Append new segments (different filter - safe to merge)for _, newSeg := range newSegments {seg := convertAviaNZSegment(newSeg, filter)existing.Segments = append(existing.Segments, seg)}// Sort by start timesort.Slice(existing.Segments, func(i, j int) bool {return existing.Segments[i].StartTime < existing.Segments[j].StartTime})return existing.Write(path)}// File doesn't exist - write newdata := buildDataFileFromSegments(meta, newSegments)return writeAviaNZDataFile(path, data)}// convertAviaNZSegment converts an AviaNZSegment to utils.Segmentfunc convertAviaNZSegment(seg AviaNZSegment, filter string) *utils.Segment {labels := seg[4].([]AviaNZLabel)utilsLabels := make([]*utils.Label, len(labels))for i, l := range labels {utilsLabels[i] = &utils.Label{Species: l.Species,Certainty: l.Certainty,Filter: filter,}}// Handle freq values (could be int or float64 depending on how they were created)var freqLow, freqHigh float64switch v := seg[2].(type) {case int:freqLow = float64(v)case float64:freqLow = v}switch v := seg[3].(type) {case int:freqHigh = float64(v)case float64:freqHigh = v}return &utils.Segment{StartTime: seg[0].(float64),EndTime: seg[1].(float64),FreqLow: freqLow,FreqHigh: freqHigh,Labels: utilsLabels,}}// buildDataFileFromSegments builds the data file structure from meta and segmentsfunc buildDataFileFromSegments(meta AviaNZMeta, segments []AviaNZSegment) []any {result := make([]any, 0, 1+len(segments))result = append(result, meta)for _, seg := range segments {result = append(result, seg)}return result}// ParseFilterFromFilename extracts filter name from preds CSV filename// "predsST_opensoundscape-kiwi-1.2_2025-11-12.csv" -> "opensoundscape-kiwi-1.2"// Returns empty string if parsing failsfunc ParseFilterFromFilename(csvPath string) string {filename := filepath.Base(csvPath)// Remove .csv extensionname := strings.TrimSuffix(filename, ".csv")// Split on underscoreparts := strings.Split(name, "_")if len(parts) == 3 {return parts[1]}return ""}// clusterStartTimes groups consecutive start times into clusters// where the gap between consecutive times is <= gapThresholdfunc clusterStartTimes(startTimes []float64, gapThreshold float64) [][]float64 {if len(startTimes) == 0 {return nil}var clusters [][]float64currentCluster := []float64{startTimes[0]}for i := 1; i < len(startTimes); i++ {gap := startTimes[i] - startTimes[i-1]if gap <= gapThreshold {// Same clustercurrentCluster = append(currentCluster, startTimes[i])} else {// New clusterclusters = append(clusters, currentCluster)currentCluster = []float64{startTimes[i]}}}// Don't forget the last clusterclusters = append(clusters, currentCluster)return clusters}
package toolsimport ("os""path/filepath""testing""skraak/utils")// ============================================// BirdNET Tests// ============================================func TestCallsFromBirda_NewDataFile(t *testing.T) {tmpDir := t.TempDir()// Create a minimal WAV filewavPath := filepath.Join(tmpDir, "test.WAV")createMinimalWAV(t, wavPath, 16000, 60.0)// Create BirdNET results filebirdaPath := filepath.Join(tmpDir, "test.BirdNET.results.csv")birdaContent := "\ufeffStart (s),End (s),Scientific name,Common name,Confidence,File\n0.0,3.0,Turdus migratorius,American Robin,0.85,/some/path/test.WAV\n"if err := os.WriteFile(birdaPath, []byte(birdaContent), 0644); err != nil {t.Fatal(err)}input := CallsFromBirdaInput{File: birdaPath,}output, err := CallsFromBirda(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.DataFilesWritten != 1 {t.Errorf("expected 1 data file written, got %d", output.DataFilesWritten)}if output.Filter != "BirdNET" {t.Errorf("expected filter 'BirdNET', got '%s'", output.Filter)}if output.TotalCalls != 1 {t.Errorf("expected 1 call, got %d", output.TotalCalls)}// Verify .data file was createddataPath := wavPath + ".data"df, err := utils.ParseDataFile(dataPath)if err != nil {t.Fatalf("failed to parse .data file: %v", err)}if len(df.Segments) != 1 {t.Errorf("expected 1 segment, got %d", len(df.Segments))}if df.Segments[0].Labels[0].Filter != "BirdNET" {t.Errorf("expected filter 'BirdNET', got '%s'", df.Segments[0].Labels[0].Filter)}if df.Segments[0].Labels[0].Certainty != 85 {t.Errorf("expected certainty 85, got %d", df.Segments[0].Labels[0].Certainty)}}func TestCallsFromBirda_ExistingSameFilter(t *testing.T) {tmpDir := t.TempDir()wavPath := filepath.Join(tmpDir, "test.WAV")createMinimalWAV(t, wavPath, 16000, 60.0)dataPath := wavPath + ".data"existingData := `[{"Operator": "Test", "Duration": 60.0}, [5.0, 10.0, 0, 16000, [{"species": "Existing Bird", "certainty": 90, "filter": "BirdNET"}]]]`if err := os.WriteFile(dataPath, []byte(existingData), 0644); err != nil {t.Fatal(err)}birdaPath := filepath.Join(tmpDir, "test.BirdNET.results.csv")birdaContent := "\ufeffStart (s),End (s),Scientific name,Common name,Confidence,File\n0.0,3.0,New Bird,New Bird,0.85,test.WAV\n"if err := os.WriteFile(birdaPath, []byte(birdaContent), 0644); err != nil {t.Fatal(err)}input := CallsFromBirdaInput{File: birdaPath}output, err := CallsFromBirda(input)if err == nil {t.Error("expected error for same filter, got nil")}if output.Error == nil {t.Error("expected error message in output")}}func TestCallsFromBirda_ExistingDifferentFilter(t *testing.T) {tmpDir := t.TempDir()wavPath := filepath.Join(tmpDir, "test.WAV")createMinimalWAV(t, wavPath, 16000, 60.0)dataPath := wavPath + ".data"existingData := `[{"Operator": "Test", "Duration": 60.0}, [5.0, 10.0, 0, 16000, [{"species": "Kiwi", "certainty": 90, "filter": "Manual"}]]]`if err := os.WriteFile(dataPath, []byte(existingData), 0644); err != nil {t.Fatal(err)}birdaPath := filepath.Join(tmpDir, "test.BirdNET.results.csv")birdaContent := "\ufeffStart (s),End (s),Scientific name,Common name,Confidence,File\n0.0,3.0,Robin,Robin,0.85,test.WAV\n"if err := os.WriteFile(birdaPath, []byte(birdaContent), 0644); err != nil {t.Fatal(err)}input := CallsFromBirdaInput{File: birdaPath}output, err := CallsFromBirda(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.DataFilesWritten != 1 {t.Errorf("expected 1 data file written, got %d", output.DataFilesWritten)}df, err := utils.ParseDataFile(dataPath)if err != nil {t.Fatalf("failed to parse .data file: %v", err)}if len(df.Segments) != 2 {t.Errorf("expected 2 segments after merge, got %d", len(df.Segments))}}func TestCallsFromBirda_DeleteOption(t *testing.T) {tmpDir := t.TempDir()wavPath := filepath.Join(tmpDir, "test.WAV")createMinimalWAV(t, wavPath, 16000, 60.0)birdaPath := filepath.Join(tmpDir, "test.BirdNET.results.csv")birdaContent := "\ufeffStart (s),End (s),Scientific name,Common name,Confidence,File\n0.0,3.0,Robin,Robin,0.85,test.WAV\n"if err := os.WriteFile(birdaPath, []byte(birdaContent), 0644); err != nil {t.Fatal(err)}input := CallsFromBirdaInput{File: birdaPath, Delete: true}output, err := CallsFromBirda(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.FilesDeleted != 1 {t.Errorf("expected 1 file deleted, got %d", output.FilesDeleted)}if _, err := os.Stat(birdaPath); !os.IsNotExist(err) {t.Error("expected BirdNET file to be deleted")}}func TestCallsFromBirda_FolderMode(t *testing.T) {tmpDir := t.TempDir()for i := range 2 {wavPath := filepath.Join(tmpDir, "test"+string(rune('0'+i))+".WAV")createMinimalWAV(t, wavPath, 16000, 60.0)birdaPath := filepath.Join(tmpDir, "test"+string(rune('0'+i))+".BirdNET.results.csv")birdaContent := "\ufeffStart (s),End (s),Scientific name,Common name,Confidence,File\n0.0,3.0,Bird,Bird,0.85,test.WAV\n"if err := os.WriteFile(birdaPath, []byte(birdaContent), 0644); err != nil {t.Fatal(err)}}input := CallsFromBirdaInput{Folder: tmpDir}output, err := CallsFromBirda(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.FilesProcessed != 2 {t.Errorf("expected 2 files processed, got %d", output.FilesProcessed)}if output.DataFilesWritten != 2 {t.Errorf("expected 2 data files written, got %d", output.DataFilesWritten)}}// ============================================// Raven Tests// ============================================func TestCallsFromRaven_NewDataFile(t *testing.T) {tmpDir := t.TempDir()wavPath := filepath.Join(tmpDir, "test.WAV")createMinimalWAV(t, wavPath, 16000, 60.0)ravenPath := filepath.Join(tmpDir, "test.Table.1.selections.txt")ravenContent := "Selection\tView\tChannel\tBegin Time (s)\tEnd Time (s)\tLow Freq (Hz)\tHigh Freq (Hz)\tSpecies\n1\tSpectrogram 1\t1\t0.0\t5.0\t1000\t5000\tKiwi\n"if err := os.WriteFile(ravenPath, []byte(ravenContent), 0644); err != nil {t.Fatal(err)}input := CallsFromRavenInput{File: ravenPath}output, err := CallsFromRaven(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.DataFilesWritten != 1 {t.Errorf("expected 1 data file written, got %d", output.DataFilesWritten)}if output.Filter != "Raven" {t.Errorf("expected filter 'Raven', got '%s'", output.Filter)}dataPath := wavPath + ".data"df, err := utils.ParseDataFile(dataPath)if err != nil {t.Fatalf("failed to parse .data file: %v", err)}if df.Segments[0].FreqLow != 1000 {t.Errorf("expected freq_low 1000, got %f", df.Segments[0].FreqLow)}if df.Segments[0].FreqHigh != 5000 {t.Errorf("expected freq_high 5000, got %f", df.Segments[0].FreqHigh)}}func TestCallsFromRaven_ExistingSameFilter(t *testing.T) {tmpDir := t.TempDir()wavPath := filepath.Join(tmpDir, "test.WAV")createMinimalWAV(t, wavPath, 16000, 60.0)dataPath := wavPath + ".data"existingData := `[{"Operator": "Test", "Duration": 60.0}, [5.0, 10.0, 0, 16000, [{"species": "Existing", "certainty": 90, "filter": "Raven"}]]]`if err := os.WriteFile(dataPath, []byte(existingData), 0644); err != nil {t.Fatal(err)}ravenPath := filepath.Join(tmpDir, "test.Table.1.selections.txt")ravenContent := "Selection\tView\tChannel\tBegin Time (s)\tEnd Time (s)\tLow Freq (Hz)\tHigh Freq (Hz)\tSpecies\n1\tSpectrogram 1\t1\t0.0\t5.0\t1000\t5000\tNew\n"if err := os.WriteFile(ravenPath, []byte(ravenContent), 0644); err != nil {t.Fatal(err)}input := CallsFromRavenInput{File: ravenPath}output, err := CallsFromRaven(input)if err == nil {t.Error("expected error for same filter, got nil")}if output.Error == nil {t.Error("expected error message in output")}}func TestCallsFromRaven_ExistingDifferentFilter(t *testing.T) {tmpDir := t.TempDir()wavPath := filepath.Join(tmpDir, "test.WAV")createMinimalWAV(t, wavPath, 16000, 60.0)dataPath := wavPath + ".data"existingData := `[{"Operator": "Test", "Duration": 60.0}, [5.0, 10.0, 0, 16000, [{"species": "Kiwi", "certainty": 90, "filter": "BirdNET"}]]]`if err := os.WriteFile(dataPath, []byte(existingData), 0644); err != nil {t.Fatal(err)}ravenPath := filepath.Join(tmpDir, "test.Table.1.selections.txt")ravenContent := "Selection\tView\tChannel\tBegin Time (s)\tEnd Time (s)\tLow Freq (Hz)\tHigh Freq (Hz)\tSpecies\n1\tSpectrogram 1\t1\t0.0\t5.0\t1000\t5000\tMorepork\n"if err := os.WriteFile(ravenPath, []byte(ravenContent), 0644); err != nil {t.Fatal(err)}input := CallsFromRavenInput{File: ravenPath}output, err := CallsFromRaven(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.DataFilesWritten != 1 {t.Errorf("expected 1 data file written, got %d", output.DataFilesWritten)}df, err := utils.ParseDataFile(dataPath)if err != nil {t.Fatalf("failed to parse .data file: %v", err)}if len(df.Segments) != 2 {t.Errorf("expected 2 segments after merge, got %d", len(df.Segments))}}func TestCallsFromRaven_DeleteOption(t *testing.T) {tmpDir := t.TempDir()wavPath := filepath.Join(tmpDir, "test.WAV")createMinimalWAV(t, wavPath, 16000, 60.0)ravenPath := filepath.Join(tmpDir, "test.Table.1.selections.txt")ravenContent := "Selection\tView\tChannel\tBegin Time (s)\tEnd Time (s)\tLow Freq (Hz)\tHigh Freq (Hz)\tSpecies\n1\tSpectrogram 1\t1\t0.0\t5.0\t1000\t5000\tKiwi\n"if err := os.WriteFile(ravenPath, []byte(ravenContent), 0644); err != nil {t.Fatal(err)}input := CallsFromRavenInput{File: ravenPath, Delete: true}output, err := CallsFromRaven(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.FilesDeleted != 1 {t.Errorf("expected 1 file deleted, got %d", output.FilesDeleted)}if _, err := os.Stat(ravenPath); !os.IsNotExist(err) {t.Error("expected Raven file to be deleted")}}func TestCallsFromRaven_MultipleSelections(t *testing.T) {tmpDir := t.TempDir()wavPath := filepath.Join(tmpDir, "test.WAV")createMinimalWAV(t, wavPath, 16000, 60.0)ravenPath := filepath.Join(tmpDir, "test.Table.1.selections.txt")ravenContent := "Selection\tView\tChannel\tBegin Time (s)\tEnd Time (s)\tLow Freq (Hz)\tHigh Freq (Hz)\tSpecies\n1\tSpectrogram 1\t1\t0.0\t5.0\t1000\t5000\tKiwi\n2\tSpectrogram 1\t1\t10.0\t15.0\t2000\t6000\tMorepork\n3\tSpectrogram 1\t1\t20.0\t25.0\t1500\t4500\tTui\n"if err := os.WriteFile(ravenPath, []byte(ravenContent), 0644); err != nil {t.Fatal(err)}input := CallsFromRavenInput{File: ravenPath}output, err := CallsFromRaven(input)if err != nil {t.Fatalf("unexpected error: %v", err)}if output.TotalCalls != 3 {t.Errorf("expected 3 calls, got %d", output.TotalCalls)}if output.SpeciesCount["Kiwi"] != 1 || output.SpeciesCount["Morepork"] != 1 || output.SpeciesCount["Tui"] != 1 {t.Errorf("unexpected species count: %v", output.SpeciesCount)}}
package toolsimport ("encoding/csv""fmt""io""os""path/filepath""sort""strings""sync""sync/atomic""skraak/utils")// CallsFromBirdaInput defines the input for the calls-from-birda tooltype CallsFromBirdaInput struct {Folder string `json:"folder"`File string `json:"file"`Delete bool `json:"delete"`ProgressHandler ProgressHandler `json:"-"` // Optional progress callback}// CallsFromBirdaOutput defines the output for the calls-from-birda tooltype CallsFromBirdaOutput struct {Calls []ClusteredCall `json:"calls"`TotalCalls int `json:"total_calls"`SpeciesCount map[string]int `json:"species_count"`DataFilesWritten int `json:"data_files_written"`DataFilesSkipped int `json:"data_files_skipped"`FilesProcessed int `json:"files_processed"`FilesDeleted int `json:"files_deleted"`Filter string `json:"filter"`Error *string `json:"error,omitempty"`}// BirdNETDetection represents a single BirdNET detectiontype BirdNETDetection struct {StartTime float64EndTime float64ScientificName stringCommonName stringConfidence float64WAVPath string}// birdaJob represents a single BirdNET file to processtype birdaJob struct {birdaFile string}// birdaResult represents the result of processing a single BirdNET filetype birdaResult struct {birdaFile stringcalls []ClusteredCallwritten boolskipped boolerr error}// CallsFromBirda processes BirdNET results files and writes .data filesfunc CallsFromBirda(input CallsFromBirdaInput) (CallsFromBirdaOutput, error) {var output CallsFromBirdaOutputoutput.Filter = "BirdNET"// Collect BirdNET files to processvar birdaFiles []stringif input.File != "" {birdaFiles = []string{input.File}} else if input.Folder != "" {var err errorbirdaFiles, err = findBirdaFiles(input.Folder)if err != nil {errMsg := fmt.Sprintf("Failed to find BirdNET files: %v", err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}} else {errMsg := "Either --folder or --file must be specified"output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}if len(birdaFiles) == 0 {errMsg := "No BirdNET files found"output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}// Single file or small batch: process sequentially (avoid goroutine overhead)if len(birdaFiles) < 10 {return callsFromBirdaSequential(input, birdaFiles)}// Large batch: parallel processing with DirCachereturn callsFromBirdaParallel(input, birdaFiles)}// callsFromBirdaSequential processes BirdNET files one at a time (for small batches)func callsFromBirdaSequential(input CallsFromBirdaInput, birdaFiles []string) (CallsFromBirdaOutput, error) {var output CallsFromBirdaOutputoutput.Filter = "BirdNET"// Build DirCache once for the folderdirCaches := make(map[string]*DirCache)if input.Folder != "" {dirCaches[input.Folder] = NewDirCache(input.Folder)}speciesCount := make(map[string]int)var allCalls []ClusteredCalldataFilesWritten := 0dataFilesSkipped := 0filesProcessed := 0filesDeleted := 0for _, birdaFile := range birdaFiles {dir := filepath.Dir(birdaFile)cache := dirCaches[dir]if cache == nil {cache = NewDirCache(dir)dirCaches[dir] = cache}calls, written, skipped, err := processBirdaFileCached(birdaFile, cache)if err != nil {errMsg := fmt.Sprintf("Error processing %s: %v", birdaFile, err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}if written {dataFilesWritten++}if skipped {dataFilesSkipped++}for _, call := range calls {allCalls = append(allCalls, call)speciesCount[call.EbirdCode]++}filesProcessed++// Delete if requested and successfully processedif input.Delete && written {if err := os.Remove(birdaFile); err != nil {errMsg := fmt.Sprintf("Failed to delete %s: %v", birdaFile, err)output.Error = &errMsgreturn output, fmt.Errorf("%s", errMsg)}filesDeleted++}if input.ProgressHandler != nil {input.ProgressHandler(filesProcessed, len(birdaFiles), filepath.Base(birdaFile))}}// Sort all calls by file, then start timesort.Slice(allCalls, func(i, j int) bool {if allCalls[i].File != allCalls[j].File {return allCalls[i].File < allCalls[j].File}return allCalls[i].StartTime < allCalls[j].StartTime})output.Calls = allCallsoutput.TotalCalls = len(allCalls)output.SpeciesCount = speciesCountoutput.DataFilesWritten = dataFilesWrittenoutput.DataFilesSkipped = dataFilesSkippedoutput.FilesProcessed = filesProcessedoutput.FilesDeleted = filesDeletedreturn output, nil}// callsFromBirdaParallel processes BirdNET files concurrently using a worker pool and DirCachefunc callsFromBirdaParallel(input CallsFromBirdaInput, birdaFiles []string) (CallsFromBirdaOutput, error) {var output CallsFromBirdaOutputoutput.Filter = "BirdNET"total := len(birdaFiles)var processed atomic.Int32// Build DirCache for the folderdirCaches := &sync.Map{}if input.Folder != "" {cache := NewDirCache(input.Folder)dirCaches.Store(input.Folder, cache)}// Create job and result channelsjobs := make(chan birdaJob, total)results := make(chan birdaResult, total)// Start workersvar wg sync.WaitGroupfor range DOT_DATA_WORKERS {wg.Add(1)go birdaWorker(dirCaches, jobs, results, &wg)}// Send jobsfor _, birdaFile := range birdaFiles {jobs <- birdaJob{birdaFile: birdaFile}}close(jobs)// Wait for workers to finish, then close resultsgo func() {wg.Wait()close(results)}()// Collect results with progress reportingspeciesCount := make(map[string]int)var allCalls []ClusteredCalldataFilesWritten := 0dataFilesSkipped := 0filesProcessed := 0filesDeleted := 0var firstErr errorfor result := range results {if result.err != nil && firstErr == nil {firstErr = result.err}if result.written {dataFilesWritten++}if result.skipped {dataFilesSkipped++}for _, call := range result.calls {allCalls = append(allCalls, call)speciesCount[call.EbirdCode]++}filesProcessed++// Delete if requested and successfully processedif input.Delete && result.written {if err := os.Remove(result.birdaFile); err != nil {if firstErr == nil {firstErr = fmt.Errorf("failed to delete %s: %w", result.birdaFile, err)}} else {filesDeleted++}}if input.ProgressHandler != nil {current := int(processed.Add(1))input.ProgressHandler(current, total, filepath.Base(result.birdaFile))}}if firstErr != nil {errMsg := firstErr.Error()output.Error = &errMsgreturn output, firstErr}// Sort all calls by file, then start timesort.Slice(allCalls, func(i, j int) bool {if allCalls[i].File != allCalls[j].File {return allCalls[i].File < allCalls[j].File}return allCalls[i].StartTime < allCalls[j].StartTime})output.Calls = allCallsoutput.TotalCalls = len(allCalls)output.SpeciesCount = speciesCountoutput.DataFilesWritten = dataFilesWrittenoutput.DataFilesSkipped = dataFilesSkippedoutput.FilesProcessed = filesProcessedoutput.FilesDeleted = filesDeletedreturn output, nil}// birdaWorker processes BirdNET files from the jobs channelfunc birdaWorker(dirCaches *sync.Map, jobs <-chan birdaJob, results chan<- birdaResult, wg *sync.WaitGroup) {defer wg.Done()for job := range jobs {dir := filepath.Dir(job.birdaFile)// Get or create DirCache for this directoryvar cache *DirCacheif cached, ok := dirCaches.Load(dir); ok {cache = cached.(*DirCache)} else {cache = NewDirCache(dir)dirCaches.Store(dir, cache)}calls, written, skipped, err := processBirdaFileCached(job.birdaFile, cache)results <- birdaResult{birdaFile: job.birdaFile,calls: calls,written: written,skipped: skipped,err: err,}}}// findBirdaFiles finds all BirdNET results files in a folderfunc findBirdaFiles(folder string) ([]string, error) {var files []stringentries, err := os.ReadDir(folder)if err != nil {return nil, err}for _, entry := range entries {name := entry.Name()if strings.HasSuffix(name, ".BirdNET.results.csv") {files = append(files, filepath.Join(folder, name))}}return files, nil}// processBirdaFileCached processes a single BirdNET results file using a DirCache for WAV lookupfunc processBirdaFileCached(birdaFile string, cache *DirCache) ([]ClusteredCall, bool, bool, error) {// Open and parse CSVfile, err := os.Open(birdaFile)if err != nil {return nil, false, false, fmt.Errorf("failed to open file: %w", err)}defer func() { _ = file.Close() }()// Create CSV readerreader := csv.NewReader(file)// Read headerheader, err := reader.Read()if err != nil {return nil, false, false, fmt.Errorf("failed to read header: %w", err)}// Find column indices (handle BOM prefix)startIdx := -1endIdx := -1commonNameIdx := -1confidenceIdx := -1fileIdx := -1for i, col := range header {// Remove BOM if presentcol = strings.TrimPrefix(col, "\ufeff")switch col {case "Start (s)":startIdx = icase "End (s)":endIdx = icase "Common name":commonNameIdx = icase "Confidence":confidenceIdx = icase "File":fileIdx = i}}if startIdx == -1 || endIdx == -1 || commonNameIdx == -1 || confidenceIdx == -1 {return nil, false, false, fmt.Errorf("missing required columns in BirdNET file")}// Read detectionsvar detections []BirdNETDetectionfor {record, err := reader.Read()if err == io.EOF {break}if err != nil {return nil, false, false, fmt.Errorf("failed to read record: %w", err)}var det BirdNETDetectionif _, err := fmt.Sscanf(record[startIdx], "%f", &det.StartTime); err != nil {return nil, false, false, fmt.Errorf("failed to parse start time %q: %w", record[startIdx], err)}if _, err := fmt.Sscanf(record[endIdx], "%f", &det.EndTime); err != nil {return nil, false, false, fmt.Errorf("failed to parse end time %q: %w", record[endIdx], err)}det.CommonName = record[commonNameIdx]if _, err := fmt.Sscanf(record[confidenceIdx], "%f", &det.Confidence); err != nil {return nil, false, false, fmt.Errorf("failed to parse confidence %q: %w", record[confidenceIdx], err)}if fileIdx >= 0 && fileIdx < len(record) {det.WAVPath = record[fileIdx]}detections = append(detections, det)}if len(detections) == 0 {return nil, false, true, nil // No detections, skip}// Determine WAV path and .data pathvar wavPath stringdir := filepath.Dir(birdaFile)base := filepath.Base(birdaFile)baseName := strings.TrimSuffix(base, ".BirdNET.results.csv")if detections[0].WAVPath != "" {// Check if the path from File column existsif _, err := os.Stat(detections[0].WAVPath); err == nil {wavPath = detections[0].WAVPath}}// If not found from File column, search with DirCacheif wavPath == "" {if cache != nil {wavPath = cache.FindWAV(baseName)} else {wavPath = findWAVFile(dir, baseName)}}if wavPath == "" {return nil, false, true, nil // WAV not found, skip}// Check if WAV exists (to get sample rate and duration)sampleRate, duration, err := utils.ParseWAVHeaderMinimal(wavPath)if err != nil {return nil, false, true, nil // Skip if WAV not found or invalid}dataPath := wavPath + ".data"// Convert detections to segmentssegments := buildBirdNETSegments(detections, sampleRate)// Build metadatameta := AviaNZMeta{Operator: "BirdNET",Duration: duration,}reviewer := "None"meta.Reviewer = &reviewer// Write .data file (safe write)if err := writeDotDataFileSafe(dataPath, segments, "BirdNET", meta); err != nil {return nil, false, false, err}// Convert to ClusteredCalls for outputvar calls []ClusteredCallfor _, det := range detections {calls = append(calls, ClusteredCall{File: wavPath,StartTime: det.StartTime,EndTime: det.EndTime,EbirdCode: det.CommonName,Segments: 1,})}return calls, true, false, nil}// buildBirdNETSegments converts BirdNET detections to AviaNZ segmentsfunc buildBirdNETSegments(detections []BirdNETDetection, sampleRate int) []AviaNZSegment {var segments []AviaNZSegmentfor _, det := range detections {// Convert confidence (0.0-1.0) to certainty (0-100)certainty := min(max(int(det.Confidence*100), 0), 100)labels := []AviaNZLabel{{Species: det.CommonName,Certainty: certainty,Filter: "BirdNET",},}segment := AviaNZSegment{det.StartTime,det.EndTime,0, // freq_lowsampleRate, // freq_high (full band)labels,}segments = append(segments, segment)}return segments}
package toolsimport ("os""path/filepath""testing")func TestDetectAnomalies_LabelMismatch(t *testing.T) {dir := t.TempDir()// Same time range, different calltypes across two modelsdata := `[{"Operator":"test"},` +`[0,10,100,1000,[{"species":"Kiwi","calltype":"Duet","certainty":100,"filter":"model-a"},` +`{"species":"Kiwi","calltype":"Male","certainty":100,"filter":"model-b"}]]]`if err := os.WriteFile(filepath.Join(dir, "f1.data"), []byte(data), 0644); err != nil {t.Fatal(err)}out, err := DetectAnomalies(DetectAnomaliesInput{Folder: dir, Models: []string{"model-a", "model-b"}})if err != nil {t.Fatal(err)}if out.LabelMismatches != 1 {t.Errorf("expected 1 label mismatch, got %d", out.LabelMismatches)}if out.CertaintyMismatches != 0 {t.Errorf("expected 0 certainty mismatches, got %d", out.CertaintyMismatches)}if out.Anomalies[0].Type != "label_mismatch" {t.Errorf("expected label_mismatch, got %s", out.Anomalies[0].Type)}}func TestDetectAnomalies_CertaintyMismatch(t *testing.T) {dir := t.TempDir()// Same time range, same labels, different certaintydata := `[{"Operator":"test"},` +`[0,10,100,1000,[{"species":"Kiwi","calltype":"Duet","certainty":90,"filter":"model-a"},` +`{"species":"Kiwi","calltype":"Duet","certainty":100,"filter":"model-b"}]]]`if err := os.WriteFile(filepath.Join(dir, "f1.data"), []byte(data), 0644); err != nil {t.Fatal(err)}out, err := DetectAnomalies(DetectAnomaliesInput{Folder: dir, Models: []string{"model-a", "model-b"}})if err != nil {t.Fatal(err)}if out.CertaintyMismatches != 1 {t.Errorf("expected 1 certainty mismatch, got %d", out.CertaintyMismatches)}if out.LabelMismatches != 0 {t.Errorf("expected 0 label mismatches, got %d", out.LabelMismatches)}}func TestDetectAnomalies_NoAnomalyWhenAgreement(t *testing.T) {dir := t.TempDir()data := `[{"Operator":"test"},` +`[0,10,100,1000,[{"species":"Kiwi","calltype":"Duet","certainty":100,"filter":"model-a"},` +`{"species":"Kiwi","calltype":"Duet","certainty":100,"filter":"model-b"}]]]`if err := os.WriteFile(filepath.Join(dir, "f1.data"), []byte(data), 0644); err != nil {t.Fatal(err)}out, err := DetectAnomalies(DetectAnomaliesInput{Folder: dir, Models: []string{"model-a", "model-b"}})if err != nil {t.Fatal(err)}if out.AnomaliesTotal != 0 {t.Errorf("expected 0 anomalies, got %d", out.AnomaliesTotal)}}func TestDetectAnomalies_LonelySegmentSkipped(t *testing.T) {dir := t.TempDir()// model-a has a segment, model-b has no segment in this filedata := `[{"Operator":"test"},` +`[0,10,100,1000,[{"species":"Kiwi","certainty":100,"filter":"model-a"}]]]`if err := os.WriteFile(filepath.Join(dir, "f1.data"), []byte(data), 0644); err != nil {t.Fatal(err)}out, err := DetectAnomalies(DetectAnomaliesInput{Folder: dir, Models: []string{"model-a", "model-b"}})if err != nil {t.Fatal(err)}if out.AnomaliesTotal != 0 {t.Errorf("lonely segment should be skipped, got %d anomalies", out.AnomaliesTotal)}if out.FilesWithAllModels != 0 {t.Errorf("file missing a model should not count as FilesWithAllModels")}}func TestDetectAnomalies_FailsWithOneModel(t *testing.T) {dir := t.TempDir()_, err := DetectAnomalies(DetectAnomaliesInput{Folder: dir, Models: []string{"model-a"}})if err == nil {t.Error("expected error with only 1 model")}}
package toolsimport ("fmt""os""path/filepath""skraak/utils")type DetectAnomaliesInput struct {Folder stringModels []string // at least 2 filter namesSpecies []string // optional scope; empty = all species}type DetectAnomaliesOutput struct {Folder string `json:"folder"`Models []string `json:"models"`FilesExamined int `json:"files_examined"`FilesWithAllModels int `json:"files_with_all_models"`AnomaliesTotal int `json:"anomalies_total"`LabelMismatches int `json:"label_mismatches"`CertaintyMismatches int `json:"certainty_mismatches"`Anomalies []Anomaly `json:"anomalies,omitempty"`Error string `json:"error,omitempty"`}type Anomaly struct {File string `json:"file"`Type string `json:"type"` // "label_mismatch" | "certainty_mismatch"Segments []AnomalySegment `json:"segments"`}type AnomalySegment struct {Model string `json:"model"`Start float64 `json:"start"`End float64 `json:"end"`Species string `json:"species"`CallType string `json:"calltype,omitempty"`Certainty int `json:"certainty"`}// DetectAnomalies compares corresponding segments across multiple ML model filters// within each .data file. Segments are matched by time overlap (same logic as propagate).// Lonely segments (no overlap in one or more models) are silently skipped.// Anomalies are flagged when overlapping segments disagree on species+calltype,// or when labels match but certainty values differ.func DetectAnomalies(input DetectAnomaliesInput) (DetectAnomaliesOutput, error) {folder := filepath.Clean(input.Folder)output := DetectAnomaliesOutput{Folder: folder,Models: input.Models,}if len(input.Models) < 2 {output.Error = "at least 2 --model values required"return output, fmt.Errorf("%s", output.Error)}for i, a := range input.Models {for j, b := range input.Models {if i != j && a == b {output.Error = "duplicate --model values are not allowed"return output, fmt.Errorf("%s", output.Error)}}}info, err := os.Stat(input.Folder)if err != nil {output.Error = fmt.Sprintf("folder not found: %s", input.Folder)return output, fmt.Errorf("%s", output.Error)}if !info.IsDir() {output.Error = fmt.Sprintf("not a directory: %s", input.Folder)return output, fmt.Errorf("%s", output.Error)}files, err := utils.FindDataFiles(folder)if err != nil {output.Error = fmt.Sprintf("list .data files: %v", err)return output, fmt.Errorf("%s", output.Error)}scopeSet := make(map[string]bool, len(input.Species))for _, s := range input.Species {scopeSet[s] = true}for _, path := range files {df, err := utils.ParseDataFile(path)if err != nil {continue}output.FilesExamined++anomalies := detectAnomaliesInFile(df, path, input.Models, scopeSet)if anomalies == nil {// file didn't have all models presentcontinue}output.FilesWithAllModels++for _, a := range anomalies {if a.Type == "label_mismatch" {output.LabelMismatches++} else {output.CertaintyMismatches++}}output.Anomalies = append(output.Anomalies, anomalies...)}output.AnomaliesTotal = len(output.Anomalies)return output, nil}// labeledSeg pairs a segment with the specific label matching the model filter.type labeledSeg struct {seg *utils.Segmentlabel *utils.Label}// detectAnomaliesInFile returns nil if the file doesn't contain all required models.func detectAnomaliesInFile(df *utils.DataFile, path string, models []string, scope map[string]bool) []Anomaly {// Collect ALL labeled segments per model — no scope filtering here.// Scope is applied to anchor selection only, so a "Don't Know" label in model[1]// against a "Kiwi" anchor in model[0] is correctly surfaced as a label_mismatch.modelSegs := make(map[string][]labeledSeg, len(models))for _, seg := range df.Segments {for _, lbl := range seg.Labels {for _, model := range models {if lbl.Filter == model {modelSegs[model] = append(modelSegs[model], labeledSeg{seg: seg, label: lbl})break}}}}// Skip file if any model is entirely absent.for _, model := range models {if len(modelSegs[model]) == 0 {return nil}}var anomalies []Anomaly// Use models[0] as anchor. Scope filtering applies here only — other models// contribute whatever they actually say for the overlapping time range.for _, anchor := range modelSegs[models[0]] {if len(scope) > 0 {key := anchor.label.Speciesif anchor.label.CallType != "" {key += "+" + anchor.label.CallType}if !scope[key] && !scope[anchor.label.Species] {continue}}// Find overlapping segments in every other model.matches := make(map[string][]labeledSeg, len(models)-1)lonely := falsefor _, model := range models[1:] {for _, candidate := range modelSegs[model] {if overlaps(anchor.seg, candidate.seg) {matches[model] = append(matches[model], candidate)}}if len(matches[model]) == 0 {lonely = truebreak}}if lonely {continue}// Build comparison group: anchor + first overlapping match per other model// (consistent with propagate's approach).group := []labeledSeg{anchor}for _, model := range models[1:] {group = append(group, matches[model][0])}// Check species+calltype agreement.refSpecies := group[0].label.SpeciesrefCallType := group[0].label.CallTypelabelMatch := truefor _, ls := range group[1:] {if ls.label.Species != refSpecies || ls.label.CallType != refCallType {labelMatch = falsebreak}}if !labelMatch {anomalies = append(anomalies, Anomaly{File: path, Type: "label_mismatch", Segments: buildAnomalySegs(group, models)})continue}// Labels agree — check certainty.refCertainty := group[0].label.Certaintyfor _, ls := range group[1:] {if ls.label.Certainty != refCertainty {anomalies = append(anomalies, Anomaly{File: path, Type: "certainty_mismatch", Segments: buildAnomalySegs(group, models)})break}}}return anomalies}func buildAnomalySegs(group []labeledSeg, models []string) []AnomalySegment {segs := make([]AnomalySegment, len(group))for i, ls := range group {segs[i] = AnomalySegment{Model: models[i],Start: ls.seg.StartTime,End: ls.seg.EndTime,Species: ls.label.Species,CallType: ls.label.CallType,Certainty: ls.label.Certainty,}}return segs}// overlaps returns true if two segments share any time overlap.func overlaps(a, b *utils.Segment) bool {return a.StartTime < b.EndTime && b.StartTime < a.EndTime}
package toolsimport ("encoding/csv""os""path/filepath""strings""testing""skraak/utils")// --- test helpers (test file only) ---func writeDataFile(t *testing.T, dir, name string, df *utils.DataFile) {t.Helper()if err := df.Write(filepath.Join(dir, name)); err != nil {t.Fatalf("write .data file %s: %v", name, err)}}func writeMapping(t *testing.T, dir, json string) {t.Helper()if err := os.WriteFile(filepath.Join(dir, "mapping.json"), []byte(json), 0644); err != nil {t.Fatalf("write mapping.json: %v", err)}}// parseCSV reads the output CSV, returning header and rows.func parseCSV(t *testing.T, path string) ([]string, [][]string) {t.Helper()f, err := os.Open(path)if err != nil {t.Fatalf("open CSV %s: %v", path, err)}defer f.Close()r := csv.NewReader(f)header, err := r.Read()if err != nil {t.Fatalf("read header: %v", err)}rows, err := r.ReadAll()if err != nil {t.Fatalf("read rows: %v", err)}return header, rows}// clipLabels calls CallsClipLabels with standard test parameters.func clipLabels(t *testing.T, dir string, extra ...func(*CallsClipLabelsInput)) CallsClipLabelsOutput {t.Helper()input := CallsClipLabelsInput{Folder: dir,MappingPath: filepath.Join(dir, "mapping.json"),OutputPath: filepath.Join(dir, "clip_labels.csv"),ClipDuration: 5,ClipOverlap: 0,MinLabelOverlap: 0.25,FinalClip: "full",}for _, fn := range extra {fn(&input)}out, err := CallsClipLabels(input)if err != nil {t.Fatalf("CallsClipLabels: %v", err)}return out}// --- tests ---func TestClipLabels_RealClassTrue(t *testing.T) {dir := t.TempDir()writeDataFile(t, dir, "rec.wav.data", &utils.DataFile{Meta: &utils.DataMeta{Duration: 20},Segments: []*utils.Segment{{StartTime: 3, EndTime: 8, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 100, Filter: "f1"}},},},})writeMapping(t, dir, `{"Kiwi":{"species":"Kiwi"}}`)out := clipLabels(t, dir)header, rows := parseCSV(t, filepath.Join(dir, "clip_labels.csv"))// Header: file, start_time, end_time, Kiwiif len(header) != 4 || header[3] != "Kiwi" {t.Fatalf("header = %v, want [..., Kiwi]", header)}// Clip 0-5 overlaps segment 3-8 by 2s ≥ 0.25 → Kiwi=True// Clip 5-10 overlaps segment 3-8 by 3s ≥ 0.25 → Kiwi=True// Clip 10-15, 15-20 → Kiwi=FalsekiwiCol := 3for i, row := range rows {switch row[1] {case "0.0", "5.0":if row[kiwiCol] != "True" {t.Errorf("row %d (start=%s): Kiwi=%s, want True", i, row[1], row[kiwiCol])}case "10.0", "15.0":if row[kiwiCol] != "False" {t.Errorf("row %d (start=%s): Kiwi=%s, want False", i, row[1], row[kiwiCol])}}}if out.PerClassTrueCount["Kiwi"] != 2 {t.Errorf("PerClassTrueCount[Kiwi] = %d, want 2", out.PerClassTrueCount["Kiwi"])}}func TestClipLabels_GapClipsAllFalse(t *testing.T) {dir := t.TempDir()// 15s file, Kiwi segment 0-5 only → clips 5-10 and 10-15 are gapswriteDataFile(t, dir, "rec.wav.data", &utils.DataFile{Meta: &utils.DataMeta{Duration: 15},Segments: []*utils.Segment{{StartTime: 0, EndTime: 5, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 100, Filter: "f1"}},},},})writeMapping(t, dir, `{"Kiwi":{"species":"Kiwi"}}`)out := clipLabels(t, dir)if out.ClipsAllFalseGap != 2 {t.Errorf("ClipsAllFalseGap = %d, want 2", out.ClipsAllFalseGap)}if out.PerClassTrueCount["Kiwi"] != 1 {t.Errorf("PerClassTrueCount[Kiwi] = %d, want 1", out.PerClassTrueCount["Kiwi"])}if out.RowsWritten != 3 {t.Errorf("RowsWritten = %d, want 3", out.RowsWritten)}}func TestClipLabels_NegativeOverridesPositive(t *testing.T) {dir := t.TempDir()// Kiwi segment 0-8, Not segment 0-4 → clip 0-5 overlaps both → __NEGATIVE__ wins// Clip 5-10 overlaps only Kiwi (3s) → TruewriteDataFile(t, dir, "rec.wav.data", &utils.DataFile{Meta: &utils.DataMeta{Duration: 10},Segments: []*utils.Segment{{StartTime: 0, EndTime: 8, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 100, Filter: "f1"}},},{StartTime: 0, EndTime: 4, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Not", Certainty: 100, Filter: "f1"}},},},})writeMapping(t, dir, `{"Kiwi":{"species":"Kiwi"},"Not":{"species":"__NEGATIVE__"}}`)out := clipLabels(t, dir)if out.ClipsNegative != 1 {t.Errorf("ClipsNegative = %d, want 1", out.ClipsNegative)}_, rows := parseCSV(t, filepath.Join(dir, "clip_labels.csv"))// Clip 0-5: negative hit → all-False (Not overlaps 0-4 by 4s)if rows[0][3] != "False" {t.Errorf("clip 0-5 Kiwi = %s, want False (overridden by __NEGATIVE__)", rows[0][3])}// Clip 5-10: only Kiwi overlaps (3s) → Trueif rows[1][3] != "True" {t.Errorf("clip 5-10 Kiwi = %s, want True", rows[1][3])}}func TestClipLabels_IgnoreExcludesClip(t *testing.T) {dir := t.TempDir()// Don't Know segment 0-5, Kiwi segment 6-10// Clip 0-5 overlaps __IGNORE__ → excluded// Clip 5-10 overlaps Kiwi → emitted with TruewriteDataFile(t, dir, "rec.wav.data", &utils.DataFile{Meta: &utils.DataMeta{Duration: 15},Segments: []*utils.Segment{{StartTime: 0, EndTime: 5, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Don't Know", Certainty: 0, Filter: "f1"}},},{StartTime: 6, EndTime: 10, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 100, Filter: "f1"}},},},})writeMapping(t, dir, `{"Kiwi":{"species":"Kiwi"},"Don't Know":{"species":"__IGNORE__"}}`)out := clipLabels(t, dir)if out.ClipsIgnored != 1 {t.Errorf("ClipsIgnored = %d, want 1", out.ClipsIgnored)}if out.SegmentsIgnored != 1 {t.Errorf("SegmentsIgnored = %d, want 1", out.SegmentsIgnored)}// Only 2 rows: clip 5-10 (Kiwi=True) and clip 10-15 (gap)if out.RowsWritten != 2 {t.Errorf("RowsWritten = %d, want 2", out.RowsWritten)}}func TestClipLabels_FilterRestrictsLabels(t *testing.T) {dir := t.TempDir()// Same time range, two filters. Only "wanted" should contribute.writeDataFile(t, dir, "rec.wav.data", &utils.DataFile{Meta: &utils.DataMeta{Duration: 10},Segments: []*utils.Segment{{StartTime: 0, EndTime: 5, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 100, Filter: "wanted"},{Species: "Not", Certainty: 100, Filter: "unwanted"},},},},})writeMapping(t, dir, `{"Kiwi":{"species":"Kiwi"},"Not":{"species":"__NEGATIVE__"}}`)out := clipLabels(t, dir, func(in *CallsClipLabelsInput) { in.Filter = "wanted" })// Only Kiwi from "wanted" filter → clip 0-5 should be Kiwi=True// Not from "unwanted" filter should be ignored → no __NEGATIVE__ overrideif out.ClipsNegative != 0 {t.Errorf("ClipsNegative = %d, want 0 (Not filter excluded)", out.ClipsNegative)}if out.PerClassTrueCount["Kiwi"] != 1 {t.Errorf("PerClassTrueCount[Kiwi] = %d, want 1", out.PerClassTrueCount["Kiwi"])}}func TestClipLabels_MappingCoverageError(t *testing.T) {dir := t.TempDir()writeDataFile(t, dir, "rec.wav.data", &utils.DataFile{Meta: &utils.DataMeta{Duration: 10},Segments: []*utils.Segment{{StartTime: 0, EndTime: 5, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Mystery", Certainty: 100, Filter: "f1"}},},},})writeMapping(t, dir, `{"Kiwi":{"species":"Kiwi"}}`)input := CallsClipLabelsInput{Folder: dir,MappingPath: filepath.Join(dir, "mapping.json"),OutputPath: filepath.Join(dir, "clip_labels.csv"),ClipDuration: 5,ClipOverlap: 0,MinLabelOverlap: 0.25,FinalClip: "full",}_, err := CallsClipLabels(input)if err == nil {t.Fatal("expected error for missing species in mapping")}if !strings.Contains(err.Error(), "Mystery") {t.Errorf("error should mention missing species, got: %v", err)}}func TestClipLabels_AppendMode(t *testing.T) {dir := t.TempDir()writeMapping(t, dir, `{"Kiwi":{"species":"Kiwi"}}`)// First filewriteDataFile(t, dir, "a.wav.data", &utils.DataFile{Meta: &utils.DataMeta{Duration: 5},Segments: []*utils.Segment{{StartTime: 0, EndTime: 5, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 100, Filter: "f1"}},},},})out1 := clipLabels(t, dir)if out1.RowsWritten != 1 {t.Fatalf("first run: RowsWritten = %d, want 1", out1.RowsWritten)}// Second run on same output file but with a different input folder// Simulate append by running again — should fail on duplicate_, err := CallsClipLabels(CallsClipLabelsInput{Folder: dir,MappingPath: filepath.Join(dir, "mapping.json"),OutputPath: filepath.Join(dir, "clip_labels.csv"),ClipDuration: 5,ClipOverlap: 0,MinLabelOverlap: 0.25,FinalClip: "full",})if err == nil {t.Fatal("expected duplicate error on second run with same folder")}if !strings.Contains(err.Error(), "duplicate") {t.Errorf("error should mention duplicate, got: %v", err)}}func TestClipLabels_MultipleFiles(t *testing.T) {dir := t.TempDir()writeMapping(t, dir, `{"Kiwi":{"species":"Kiwi"}}`)writeDataFile(t, dir, "a.wav.data", &utils.DataFile{Meta: &utils.DataMeta{Duration: 10},Segments: []*utils.Segment{{StartTime: 0, EndTime: 5, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 100, Filter: "f1"}},},},})writeDataFile(t, dir, "b.wav.data", &utils.DataFile{Meta: &utils.DataMeta{Duration: 5},Segments: []*utils.Segment{{StartTime: 0, EndTime: 5, FreqLow: 100, FreqHigh: 5000,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 100, Filter: "f1"}},},},})out := clipLabels(t, dir)if out.DataFilesParsed != 2 {t.Errorf("DataFilesParsed = %d, want 2", out.DataFilesParsed)}// a: 2 clips (0-5, 5-10), b: 1 clip (0-5) = 3 totalif out.RowsWritten != 3 {t.Errorf("RowsWritten = %d, want 3", out.RowsWritten)}_, rows := parseCSV(t, filepath.Join(dir, "clip_labels.csv"))files := map[string]int{}for _, r := range rows {files[r[0]]++}if len(files) != 2 {t.Errorf("expected 2 distinct files in CSV, got %d", len(files))}}
package toolsimport ("encoding/csv""fmt""io""os""path/filepath""slices""sort""strconv""strings""skraak/utils")// CallsClipLabelsInput configures the clip-labels exporter.type CallsClipLabelsInput struct {Folder string `json:"folder"`MappingPath string `json:"mapping"`Filter string `json:"filter,omitempty"`OutputPath string `json:"output"`ClipDuration float64 `json:"clip_duration"`ClipOverlap float64 `json:"clip_overlap"`MinLabelOverlap float64 `json:"min_label_overlap"`FinalClip string `json:"final_clip"`}// CallsClipLabelsOutput summarises a run.type CallsClipLabelsOutput struct {Folder string `json:"folder"`OutputPath string `json:"output"`Filter string `json:"filter,omitempty"`Classes []string `json:"classes"`DataFilesParsed int `json:"data_files_parsed"`ClipsNegative int `json:"clips_negative"` // emitted, all-False because of __NEGATIVE__ClipsIgnored int `json:"clips_ignored"` // excluded from output because of __IGNORE__ overlapSegmentsIgnored int `json:"segments_ignored"` // segments whose species maps to __IGNORE__ClipsAllFalseGap int `json:"clips_all_false_gap"` // emitted, all-False because no overlapPerClassTrueCount map[string]int `json:"per_class_true_count"`AppendedToFile bool `json:"appended_to_file"`ExistingRowsFound int `json:"existing_rows_found"`RowsWritten int `json:"rows_written"`}// resolvedSeg is a segment that has been classified by the mapping and is// ready for overlap-checking against clip windows.type resolvedSeg struct {start, end float64kind utils.MappingKindclassIdx int // valid only when kind == utils.MappingReal}// clipDisposition describes the outcome for a single clip window.type clipDisposition intconst (dispoLabelled clipDisposition = iota // at least one class column is TruedispoNegative // __NEGATIVE__ hit, all class columns FalsedispoGap // no segment overlaps, all class columns FalsedispoIgnored // __IGNORE__ hit, clip excluded from output)// clipLabelsRow is one row of the output CSV.type clipLabelsRow struct {file stringstart float64end float64flags []bool}// rowKey is used for duplicate detection.type rowKey struct {file stringstart stringend string}// CallsClipLabels reads .data files from a single folder and writes a CSV in// OpenSoundScape's clip_labels format: one row per clip per file, with one// True/False column per class in the mapping.//// Mirrors BoxedAnnotations.clip_labels(): every clip window is emitted; a// column is True when any annotation of that class overlaps the window by// ≥ min_label_overlap seconds. Sentinel mappings (__NEGATIVE__, __IGNORE__)// get no column and contribute no labels.func CallsClipLabels(input CallsClipLabelsInput) (CallsClipLabelsOutput, error) {out := CallsClipLabelsOutput{Folder: input.Folder,OutputPath: input.OutputPath,PerClassTrueCount: map[string]int{},}// Validate parameters.finalClipMode, err := utils.ParseFinalClipMode(input.FinalClip)if err != nil {return out, err}if input.ClipDuration <= 0 {return out, fmt.Errorf("--clip-duration must be > 0, got %v", input.ClipDuration)}if input.ClipOverlap < 0 || input.ClipOverlap >= input.ClipDuration {return out, fmt.Errorf("--clip-overlap must be in [0, clip-duration), got %v", input.ClipOverlap)}if input.MinLabelOverlap <= 0 {return out, fmt.Errorf("--min-label-overlap must be > 0, got %v", input.MinLabelOverlap)}// Load mapping.mapping, err := utils.LoadMappingFile(input.MappingPath)if err != nil {return out, fmt.Errorf("load mapping %s: %w", input.MappingPath, err)}// Output classes: the unique canonical (non-sentinel) class names from mapping.json.classes := mapping.Classes()if len(classes) == 0 {return out, fmt.Errorf("mapping.json has no real (non-sentinel) classes")}out.Classes = classesout.Filter = input.FilterclassIdx := map[string]int{}for i, c := range classes {classIdx[c] = i}// Find and parse .data files.dataPaths, err := utils.FindDataFiles(input.Folder)if err != nil {return out, fmt.Errorf("scan folder %s: %w", input.Folder, err)}if len(dataPaths) == 0 {return out, fmt.Errorf("no .data files found in %s", input.Folder)}type parsedFile struct {path stringdf *utils.DataFile}parsed := make([]parsedFile, 0, len(dataPaths))speciesSeen := map[string]bool{}for _, p := range dataPaths {df, err := utils.ParseDataFile(p)if err != nil {return out, fmt.Errorf("parse %s: %w", p, err)}if df.Meta == nil || df.Meta.Duration <= 0 {return out, fmt.Errorf("missing or non-positive Duration in %s (cannot generate clips)", p)}for _, seg := range df.Segments {for _, lbl := range seg.Labels {if input.Filter != "" && lbl.Filter != input.Filter {continue}speciesSeen[lbl.Species] = true}}parsed = append(parsed, parsedFile{path: p, df: df})}out.DataFilesParsed = len(parsed)// Mapping coverage check.if missing := mapping.ValidateCoversSpecies(speciesSeen); len(missing) > 0 {return out, fmt.Errorf("mapping.json is missing entries for species: %s\n(run /data-mapping to regenerate)", strings.Join(missing, ", "))}// Append-mode: read existing header + (file,start,end) tuples if any.expectedHeader := append([]string{"file", "start_time", "end_time"}, classes...)existing, appendMode, err := loadExistingRows(input.OutputPath, expectedHeader)if err != nil {return out, err}out.AppendedToFile = appendModeout.ExistingRowsFound = len(existing)// Path-rendering: relative to cwd.cwd, err := os.Getwd()if err != nil {return out, fmt.Errorf("getwd: %w", err)}folderAbs, err := filepath.Abs(input.Folder)if err != nil {return out, fmt.Errorf("abs %s: %w", input.Folder, err)}// Process each file.rows := make([]clipLabelsRow, 0, 1024)for _, pf := range parsed {fileRows, err := processClipLabelsFile(pf.path, pf.df, mapping, classIdx, classes, input, finalClipMode, cwd, folderAbs, &out)if err != nil {return out, err}rows = append(rows, fileRows...)}// Dedup pass — within new rows AND against existing CSV.dedup := make(map[rowKey]bool, len(existing)+len(rows))for k := range existing {dedup[k] = true}for _, r := range rows {k := rowKey{file: r.file, start: formatTime(r.start), end: formatTime(r.end)}if dedup[k] {return out, fmt.Errorf("duplicate clip detected: file=%s start=%s end=%s", k.file, k.start, k.end)}dedup[k] = true}// Write CSV.if err := writeRows(input.OutputPath, expectedHeader, rows, appendMode); err != nil {return out, err}out.RowsWritten = len(rows)sort.Strings(out.Classes)return out, nil}// processClipLabelsFile generates clip-labels rows for a single .data file.func processClipLabelsFile(path string,df *utils.DataFile,mapping utils.MappingFile,classIdx map[string]int,classes []string,input CallsClipLabelsInput,finalClipMode utils.FinalClipMode,cwd, folderAbs string,out *CallsClipLabelsOutput,) ([]clipLabelsRow, error) {windows, err := utils.GenerateClipTimes(df.Meta.Duration,input.ClipDuration,input.ClipOverlap,finalClipMode,10,)if err != nil {return nil, fmt.Errorf("generate clip windows for %s: %w", path, err)}if len(windows) == 0 {return nil, nil}// Resolve segments against the mapping. Skip:// - filter mismatch (when --filter set)// - annotation duration < min_label_overlap// - species not in mappingsegs := make([]resolvedSeg, 0, len(df.Segments))for _, seg := range df.Segments {if seg.EndTime-seg.StartTime < input.MinLabelOverlap {continue}for _, lbl := range seg.Labels {if input.Filter != "" && lbl.Filter != input.Filter {continue}canon, kind, ok := mapping.Classify(lbl.Species)if !ok {continue}switch kind {case utils.MappingIgn:out.SegmentsIgnored++segs = append(segs, resolvedSeg{start: seg.StartTime, end: seg.EndTime, kind: kind,})case utils.MappingNeg:segs = append(segs, resolvedSeg{start: seg.StartTime, end: seg.EndTime, kind: kind,})case utils.MappingReal:idx, present := classIdx[canon]if !present {continue}segs = append(segs, resolvedSeg{start: seg.StartTime, end: seg.EndTime, kind: kind, classIdx: idx,})}}}// Compute relative path for the WAV file.wavName := strings.TrimSuffix(filepath.Base(path), ".data")wavAbs := filepath.Join(folderAbs, wavName)rel, err := filepath.Rel(cwd, wavAbs)if err != nil {rel = wavAbs}// Ensure relative paths start with ./ to match OPSO / pandas convention.if rel != "" && !filepath.IsAbs(rel) && !strings.HasPrefix(rel, "."+string(filepath.Separator)) {rel = "." + string(filepath.Separator) + rel}// Label each clip window.var rows []clipLabelsRowfor _, w := range windows {dispo, classHits := classifyClip(w, segs, input.MinLabelOverlap, len(classes))if dispo == dispoIgnored {out.ClipsIgnored++continue}row := clipLabelsRow{file: rel,start: w.Start,end: w.End,flags: make([]bool, len(classes)),}switch dispo {case dispoNegative:out.ClipsNegative++// flags stay all-False — __NEGATIVE__ overrides positivescase dispoGap:out.ClipsAllFalseGap++case dispoLabelled:for i, hit := range classHits {if hit {row.flags[i] = trueout.PerClassTrueCount[classes[i]]++}}}rows = append(rows, row)}return rows, nil}// classifyClip determines the disposition of a single clip window against// the resolved segments. Priority: __IGNORE__ > __NEGATIVE__ > class labels.func classifyClip(w utils.ClipWindow, segs []resolvedSeg, minLabelOverlap float64, nClasses int) (clipDisposition, []bool) {ignoreHit := falsenegativeHit := falseclassHits := make([]bool, nClasses)for _, s := range segs {if overlapSeconds(s.start, s.end, w.Start, w.End) < minLabelOverlap {continue}switch s.kind {case utils.MappingIgn:ignoreHit = truecase utils.MappingNeg:negativeHit = truecase utils.MappingReal:classHits[s.classIdx] = true}}if ignoreHit {return dispoIgnored, nil}if negativeHit {return dispoNegative, classHits}for _, hit := range classHits {if hit {return dispoLabelled, classHits}}return dispoGap, classHits}// loadExistingRows reads an existing output CSV and returns its row keys// (for deduplication) and whether we're in append mode.func loadExistingRows(outputPath string, expectedHeader []string) (map[rowKey]bool, bool, error) {fi, err := os.Stat(outputPath)if err != nil {if os.IsNotExist(err) {return nil, false, nil}return nil, false, fmt.Errorf("stat %s: %w", outputPath, err)}if fi.Size() == 0 {return nil, false, nil}f, err := os.Open(outputPath)if err != nil {return nil, false, fmt.Errorf("open existing %s: %w", outputPath, err)}defer func() { _ = f.Close() }()r := csv.NewReader(f)r.FieldsPerRecord = -1header, err := r.Read()if err != nil {return nil, false, fmt.Errorf("read header of existing %s: %w", outputPath, err)}if !slices.Equal(header, expectedHeader) {return nil, false, fmt.Errorf("column-set mismatch in existing %s\n existing: %s\n new: %s",outputPath, strings.Join(header, ","), strings.Join(expectedHeader, ","))}existing := map[rowKey]bool{}for {rec, err := r.Read()if err == io.EOF {break}if err != nil {return nil, false, fmt.Errorf("read row of existing %s: %w", outputPath, err)}if len(rec) < 3 {return nil, false, fmt.Errorf("malformed row in existing %s: %v", outputPath, rec)}existing[rowKey{file: rec[0], start: rec[1], end: rec[2]}] = true}return existing, true, nil}// overlapSeconds returns the duration of overlap between two half-open intervals.func overlapSeconds(aStart, aEnd, bStart, bEnd float64) float64 {lo := max(aStart, bStart)hi := min(aEnd, bEnd)if hi <= lo {return 0}return hi - lo}// formatTime renders a float to match pandas' default float repr in to_csv:// always at least one decimal place, no trailing zeros beyond what's needed.// e.g. 5 → "5.0", 5.5 → "5.5", 3.5001250000 → "3.500125".func formatTime(v float64) string {s := strconv.FormatFloat(v, 'f', -1, 64)if !strings.ContainsRune(s, '.') {s += ".0"}return s}// writeRows writes the clip-labels rows to a CSV file.func writeRows(path string, header []string, rows []clipLabelsRow, appendMode bool) error {var f *os.Filevar err errorif appendMode {f, err = os.OpenFile(path, os.O_APPEND|os.O_WRONLY, 0644)} else {f, err = os.OpenFile(path, os.O_CREATE|os.O_TRUNC|os.O_WRONLY, 0644)}if err != nil {return fmt.Errorf("open %s for write: %w", path, err)}defer func() { _ = f.Close() }()w := csv.NewWriter(f)if !appendMode {if err := w.Write(header); err != nil {return fmt.Errorf("write header: %w", err)}}if len(rows) == 0 {w.Flush()return w.Error()}rec := make([]string, 3+len(rows[0].flags))for _, r := range rows {rec[0] = r.filerec[1] = formatTime(r.start)rec[2] = formatTime(r.end)for i, b := range r.flags {if b {rec[3+i] = "True"} else {rec[3+i] = "False"}}if err := w.Write(rec); err != nil {return fmt.Errorf("write row: %w", err)}}w.Flush()return w.Error()}
package toolsimport ("encoding/binary""math""os""testing""skraak/utils")const benchWAV = "../audio/20211028_211500.WAV"// ==================== WAV I/O ====================func BenchmarkReadWAV(b *testing.B) {b.ReportAllocs()for i := 0; i < b.N; i++ {_, _, err := utils.ReadWAVSamples(benchWAV)if err != nil {b.Fatal(err)}}}func BenchmarkConvertToFloat64_16bit(b *testing.B) {// Simulate 16-bit mono WAV data (same size as test file: 14.32M samples)numSamples := 14320000data := make([]byte, numSamples*2)for i := range numSamples {binary.LittleEndian.PutUint16(data[i*2:], uint16(i%65536))}b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {_ = convertToFloat64Bench(data, 16, 1)}}// Duplicate of convertToFloat64 for benchmarking (unexported in utils)func convertToFloat64Bench(data []byte, bitsPerSample, channels int) []float64 {bytesPerSample := bitsPerSample / 8blockAlign := bytesPerSample * channelsnumSamples := len(data) / blockAlignsamples := make([]float64, numSamples)for i := range numSamples {offset := i * blockAlignsample := int16(binary.LittleEndian.Uint16(data[offset : offset+2]))samples[i] = float64(sample) / 32768.0}return samples}func BenchmarkWriteWAV(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)b.Logf("segment samples=%d", len(segSamples))b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {f, _ := os.CreateTemp("", "bench_*.wav")utils.WriteWAVFile(f.Name(), segSamples, sr)f.Close()os.Remove(f.Name())}}// ==================== Resample ====================func BenchmarkResampleRate_48k(b *testing.B) {samples, _, _ := utils.ReadWAVSamples(benchWAV)b.Logf("resampling %d samples 48000->16000", len(samples))b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {utils.ResampleRate(samples, 48000, 16000)}}func BenchmarkResampleRate_250k(b *testing.B) {samples, _, _ := utils.ReadWAVSamples(benchWAV)b.Logf("resampling %d samples 250000->16000", len(samples))b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {utils.ResampleRate(samples, 250000, 16000)}}// ==================== Spectrogram pipeline ====================func BenchmarkExtractSegment(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)b.Logf("full file: %d samples, sr=%d", len(samples), sr)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {seg := utils.ExtractSegmentSamples(samples, sr, 872, 895)if len(seg) == 0 {b.Fatal("empty segment")}}}func BenchmarkPowerSpectrumFFT_512(b *testing.B) {n := 512samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)frameData := make([]float64, n)power := make([]float64, n/2+1)scratch := make([]complex128, n)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {// Simulate the windowing step (Hann) + FFTfor j := range n {frameData[j] = segSamples[j] * 0.5 * (1.0 - math.Cos(2.0*math.Pi*float64(j)/float64(n-1)))}utils.PowerSpectrumFFT(frameData, power, scratch)}}func BenchmarkSpectrogram_23s(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)cfg := utils.DefaultSpectrogramConfig(16000)b.Logf("segment samples=%d, windowSize=%d, hopSize=%d", len(segSamples), cfg.WindowSize, cfg.HopSize)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {spect := utils.GenerateSpectrogram(segSamples, cfg)if spect == nil {b.Fatal("nil spectrogram")}}}func BenchmarkSpectrogram_60s(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 0, 60)cfg := utils.DefaultSpectrogramConfig(16000)b.Logf("60s segment samples=%d", len(segSamples))b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {spect := utils.GenerateSpectrogram(segSamples, cfg)if spect == nil {b.Fatal("nil spectrogram")}}}// ==================== Image creation & resize ====================func BenchmarkCreateGrayscaleImage(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)cfg := utils.DefaultSpectrogramConfig(16000)spect := utils.GenerateSpectrogram(segSamples, cfg)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {img := utils.CreateGrayscaleImage(spect)if img == nil {b.Fatal("nil image")}}}func BenchmarkCreateRGBImage(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)cfg := utils.DefaultSpectrogramConfig(16000)spect := utils.GenerateSpectrogram(segSamples, cfg)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {colorData := utils.ApplyL4Colormap(spect)img := utils.CreateRGBImage(colorData)if img == nil {b.Fatal("nil image")}}}func BenchmarkApplyL4Colormap(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)cfg := utils.DefaultSpectrogramConfig(16000)spect := utils.GenerateSpectrogram(segSamples, cfg)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {colorData := utils.ApplyL4Colormap(spect)if colorData == nil {b.Fatal("nil colormap")}}}func BenchmarkResizeGray224(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)cfg := utils.DefaultSpectrogramConfig(16000)spect := utils.GenerateSpectrogram(segSamples, cfg)img := utils.CreateGrayscaleImage(spect)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {resized := utils.ResizeImage(img, 224, 224)if resized == nil {b.Fatal("nil resize")}}}func BenchmarkResizeGray448(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)cfg := utils.DefaultSpectrogramConfig(16000)spect := utils.GenerateSpectrogram(segSamples, cfg)img := utils.CreateGrayscaleImage(spect)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {resized := utils.ResizeImage(img, 448, 448)if resized == nil {b.Fatal("nil resize")}}}// ==================== PNG write ====================func BenchmarkWritePNG_224(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)cfg := utils.DefaultSpectrogramConfig(16000)spect := utils.GenerateSpectrogram(segSamples, cfg)img := utils.CreateGrayscaleImage(spect)resized := utils.ResizeImage(img, 224, 224)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {f, _ := os.CreateTemp("", "bench_*.png")utils.WritePNG(resized, f)f.Close()os.Remove(f.Name())}}// ==================== Full pipeline ====================func BenchmarkFullPipelineGray224(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)outputSR := srif sr > 16000 {segSamples = utils.ResampleRate(segSamples, sr, 16000)outputSR = 16000}cfg := utils.DefaultSpectrogramConfig(outputSR)spect := utils.GenerateSpectrogram(segSamples, cfg)img := utils.CreateGrayscaleImage(spect)resized := utils.ResizeImage(img, 224, 224)f, _ := os.CreateTemp("", "bench_*.png")utils.WritePNG(resized, f)f.Close()os.Remove(f.Name())utils.WriteWAVFile(f.Name(), segSamples, outputSR)os.Remove(f.Name())_ = resized}}func BenchmarkFullPipelineColor448(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)outputSR := srif sr > 16000 {segSamples = utils.ResampleRate(segSamples, sr, 16000)outputSR = 16000}cfg := utils.DefaultSpectrogramConfig(outputSR)spect := utils.GenerateSpectrogram(segSamples, cfg)colorData := utils.ApplyL4Colormap(spect)img := utils.CreateRGBImage(colorData)resized := utils.ResizeImage(img, 448, 448)f, _ := os.CreateTemp("", "bench_*.png")utils.WritePNG(resized, f)f.Close()os.Remove(f.Name())utils.WriteWAVFile(f.Name(), segSamples, outputSR)os.Remove(f.Name())_ = resized}}func BenchmarkFullPipelineWavOnly(b *testing.B) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)b.ResetTimer()b.ReportAllocs()for i := 0; i < b.N; i++ {segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)outputSR := srif sr > 16000 {segSamples = utils.ResampleRate(segSamples, sr, 16000)outputSR = 16000}f, _ := os.CreateTemp("", "bench_*.wav")utils.WriteWAVFile(f.Name(), segSamples, outputSR)f.Close()os.Remove(f.Name())}}// ==================== Data dimension report ====================func TestPipelineDimensions(t *testing.T) {samples, sr, _ := utils.ReadWAVSamples(benchWAV)segSamples := utils.ExtractSegmentSamples(samples, sr, 872, 895)t.Logf("Input: %d samples, sr=%d, segment=%d samples (%.1fs)",len(samples), sr, len(segSamples), float64(len(segSamples))/float64(sr))cfg := utils.DefaultSpectrogramConfig(16000)numFrames := (len(segSamples)-cfg.WindowSize)/cfg.HopSize + 1numBins := cfg.WindowSize/2 + 1t.Logf("Spectrogram: %d freq bins x %d time frames = %d values",numBins, numFrames, numBins*numFrames)spect := utils.GenerateSpectrogram(segSamples, cfg)t.Logf("Output: %d x %d (freq x time)", len(spect), len(spect[0]))img := utils.CreateGrayscaleImage(spect)t.Logf("Grayscale image: %dx%d pixels, %d bytes",img.Bounds().Dx(), img.Bounds().Dy(), img.Bounds().Dx()*img.Bounds().Dy())resized := utils.ResizeImage(img, 224, 224)t.Logf("Resized 224: %dx%d", resized.Bounds().Dx(), resized.Bounds().Dy())resized448 := utils.ResizeImage(img, 448, 448)t.Logf("Resized 448: %dx%d", resized448.Bounds().Dx(), resized448.Bounds().Dy())}
package toolsimport ("fmt""image""math""os""path/filepath""runtime""strings""sync""skraak/utils")// CallsClipInput defines the input for the clip tooltype CallsClipInput struct {File string `json:"file"`Folder string `json:"folder"`Output string `json:"output"`Prefix string `json:"prefix"`Filter string `json:"filter"`Species string `json:"species"`Certainty int `json:"certainty"`Size int `json:"size"`Color bool `json:"color"`WavOnly bool `json:"wav_only"`Night bool `json:"night"`Day bool `json:"day"`Lat float64 `json:"lat"`Lng float64 `json:"lng"`Timezone string `json:"timezone"`}// CallsClipOutput defines the output for the clip tooltype CallsClipOutput struct {FilesProcessed int `json:"files_processed"`SegmentsClipped int `json:"segments_clipped"`NightSkipped int `json:"night_skipped,omitempty"`DaySkipped int `json:"day_skipped,omitempty"`OutputFiles []string `json:"output_files"`Errors []string `json:"errors,omitempty"`}// CallsClip processes .data files and generates audio/image clips for matching segmentsfunc CallsClip(input CallsClipInput) (CallsClipOutput, error) {var output CallsClipOutput// Validate required flagsif input.File == "" && input.Folder == "" {output.Errors = append(output.Errors, "either --file or --folder is required")return output, fmt.Errorf("missing required flag: --file or --folder")}if input.Output == "" {output.Errors = append(output.Errors, "--output is required")return output, fmt.Errorf("missing required flag: --output")}if input.Prefix == "" {output.Errors = append(output.Errors, "--prefix is required")return output, fmt.Errorf("missing required flag: --prefix")}// Parse species+calltypespeciesName, callType := utils.ParseSpeciesCallType(input.Species)// Get list of .data filesvar filePaths []stringvar err errorif input.File != "" {filePaths = []string{input.File}} else {filePaths, err = utils.FindDataFiles(input.Folder)if err != nil {output.Errors = append(output.Errors, fmt.Sprintf("failed to find .data files: %v", err))return output, err}}if len(filePaths) == 0 {output.Errors = append(output.Errors, "no .data files found")return output, fmt.Errorf("no .data files found")}// Create output folder if it doesn't existif err := os.MkdirAll(input.Output, 0755); err != nil {output.Errors = append(output.Errors, fmt.Sprintf("failed to create output folder: %v", err))return output, err}// Clamp image size to valid rangeimgSize := utils.ClampImageSize(input.Size)// Process .data files (parallel for larger batches)if len(filePaths) <= 2 {// Sequential for small batchesfor _, dataPath := range filePaths {clips, skipped, errs := processFile(dataPath, input.Output, input.Prefix, input.Filter, speciesName, callType, input.Certainty, imgSize, input.Color, input.WavOnly, input.Night, input.Day, input.Lat, input.Lng, input.Timezone)output.SegmentsClipped += len(clips)if input.Night {output.NightSkipped += skipped} else {output.DaySkipped += skipped}output.OutputFiles = append(output.OutputFiles, clips...)output.Errors = append(output.Errors, errs...)if len(clips) > 0 || len(errs) == 0 {output.FilesProcessed++}}} else {// Parallel file processingtype fileResult struct {clips []stringskipped interrs []string}workers := min(runtime.NumCPU(), 8, len(filePaths))jobs := make(chan string, len(filePaths))results := make(chan fileResult, len(filePaths))var wg sync.WaitGroupfor range workers {wg.Go(func() {for dataPath := range jobs {clips, skipped, errs := processFile(dataPath, input.Output, input.Prefix, input.Filter, speciesName, callType, input.Certainty, imgSize, input.Color, input.WavOnly, input.Night, input.Day, input.Lat, input.Lng, input.Timezone)results <- fileResult{clips: clips, skipped: skipped, errs: errs}}})}for _, dataPath := range filePaths {jobs <- dataPath}close(jobs)go func() {wg.Wait()close(results)}()for r := range results {output.SegmentsClipped += len(r.clips)if input.Night {output.NightSkipped += r.skipped} else {output.DaySkipped += r.skipped}output.OutputFiles = append(output.OutputFiles, r.clips...)output.Errors = append(output.Errors, r.errs...)if len(r.clips) > 0 || len(r.errs) == 0 {output.FilesProcessed++}}}return output, nil}// processFile processes a single .data file and returns generated clips, time-filter-skipped count, and errorsfunc processFile(dataPath, outputDir, prefix, filter, speciesName, callType string, certainty, imgSize int, color, wavOnly, night, day bool, lat, lng float64, timezone string) ([]string, int, []string) {var clips []stringvar errors []string// Parse .data filedataFile, err := utils.ParseDataFile(dataPath)if err != nil {errors = append(errors, fmt.Sprintf("%s: failed to parse: %v", dataPath, err))return nil, 0, errors}// Get WAV basename (without path and extensions)wavPath := filepath.Clean(strings.TrimSuffix(dataPath, ".data"))basename := filepath.Base(wavPath)basename = strings.TrimSuffix(basename, filepath.Ext(basename))// Filter segmentsvar matchingSegments []*utils.Segmentfor _, seg := range dataFile.Segments {if seg.SegmentMatchesFilters(filter, speciesName, callType, certainty) {matchingSegments = append(matchingSegments, seg)}}if len(matchingSegments) == 0 {return nil, 0, nil // No matches, not an error}// Day/night filter: check WAV header only (cheaper than reading full audio).// Skip recordings in the wrong time-of-day before paying the cost of ReadWAVSamples.if night || day {result, err := IsNight(IsNightInput{FilePath: wavPath,Lat: lat,Lng: lng,Timezone: timezone,})if err != nil {fmt.Fprintf(os.Stderr, "warning: skipping %s (isnight error: %v)\n", wavPath, err)return nil, 0, nil}if night && !result.SolarNight {fmt.Fprintf(os.Stderr, "skipped (daytime): %s\n", wavPath)return nil, 1, nil}if day && !result.DiurnalActive {fmt.Fprintf(os.Stderr, "skipped (nighttime): %s\n", wavPath)return nil, 1, nil}}// Read WAV samples oncesamples, sampleRate, err := utils.ReadWAVSamples(wavPath)if err != nil {errors = append(errors, fmt.Sprintf("%s: failed to read WAV: %v", dataPath, err))return nil, 0, errors}// Process matching segments (parallel for larger batches)if len(matchingSegments) <= 2 {for _, seg := range matchingSegments {clipFiles, err := generateClip(samples, sampleRate, outputDir, prefix, basename, seg.StartTime, seg.EndTime, imgSize, color, wavOnly)if err != nil {errors = append(errors, fmt.Sprintf("%s: segment %.0f-%.0f: %v", dataPath, seg.StartTime, seg.EndTime, err))continue}clips = append(clips, clipFiles...)}} else {type segResult struct {clips []stringerr string}workers := min(runtime.NumCPU(), len(matchingSegments))jobs := make(chan *utils.Segment, len(matchingSegments))results := make(chan segResult, len(matchingSegments))var wg sync.WaitGroupfor range workers {wg.Go(func() {for seg := range jobs {clipFiles, err := generateClip(samples, sampleRate, outputDir, prefix, basename, seg.StartTime, seg.EndTime, imgSize, color, wavOnly)if err != nil {results <- segResult{err: fmt.Sprintf("%s: segment %.0f-%.0f: %v", dataPath, seg.StartTime, seg.EndTime, err)}} else {results <- segResult{clips: clipFiles}}}})}for _, seg := range matchingSegments {jobs <- seg}close(jobs)go func() {wg.Wait()close(results)}()for r := range results {if r.err != "" {errors = append(errors, r.err)} else {clips = append(clips, r.clips...)}}}return clips, 0, errors}// generateClip generates PNG and WAV files for a segmentfunc generateClip(samples []float64, sampleRate int, outputDir, prefix, basename string, startTime, endTime float64, imgSize int, color, wavOnly bool) ([]string, error) {var files []string// Calculate integer times for filenamestartInt := int(math.Floor(startTime))endInt := int(math.Ceil(endTime))// Build base filenamebaseName := fmt.Sprintf("%s_%s_%d_%d", prefix, basename, startInt, endInt)wavPath := filepath.Join(outputDir, baseName+".wav")// Extract segment samplessegSamples := utils.ExtractSegmentSamples(samples, sampleRate, startTime, endTime)if len(segSamples) == 0 {return nil, fmt.Errorf("no samples in segment")}// Determine output sample rate (downsample if > 16kHz)outputSampleRate := sampleRateif sampleRate > utils.DefaultMaxSampleRate {segSamples = utils.ResampleRate(segSamples, sampleRate, utils.DefaultMaxSampleRate)outputSampleRate = utils.DefaultMaxSampleRate}// Generate spectrogram and PNG unless --wav-onlyif !wavOnly {pngPath := filepath.Join(outputDir, baseName+".png")spectSampleRate := outputSampleRateconfig := utils.DefaultSpectrogramConfig(spectSampleRate)spectrogram := utils.GenerateSpectrogram(segSamples, config)if spectrogram == nil {return nil, fmt.Errorf("failed to generate spectrogram")}// Create image (grayscale or color)var img image.Imageif color {colorData := utils.ApplyL4Colormap(spectrogram)img = utils.CreateRGBImage(colorData)} else {img = utils.CreateGrayscaleImage(spectrogram)}if img == nil {return nil, fmt.Errorf("failed to create image")}resized := utils.ResizeImage(img, imgSize, imgSize)// Write PNG (O_EXCL fails atomically if file exists)pngFile, err := os.OpenFile(pngPath, os.O_WRONLY|os.O_CREATE|os.O_EXCL, 0644)if err != nil {if os.IsExist(err) {return nil, fmt.Errorf("file already exists: %s", pngPath)}return nil, fmt.Errorf("failed to create PNG: %w", err)}if err := utils.WritePNG(resized, pngFile); err != nil {_ = pngFile.Close()return nil, fmt.Errorf("failed to write PNG: %w", err)}if err := pngFile.Close(); err != nil {return nil, fmt.Errorf("failed to close PNG: %w", err)}files = append(files, pngPath)}// Write WAVif err := utils.WriteWAVFile(wavPath, segSamples, outputSampleRate); err != nil {return nil, fmt.Errorf("failed to write WAV: %w", err)}files = append(files, wavPath)return files, nil}
package toolsimport ("testing""skraak/utils")func NewClassifyState(config ClassifyConfig, dataFiles []*utils.DataFile) *ClassifyState {hasFilter := config.Filter != "" || config.Species != "" || config.Certainty >= 0cached := make([][]*utils.Segment, len(dataFiles))for i, df := range dataFiles {if !hasFilter {cached[i] = df.Segments} else {for _, seg := range df.Segments {if seg.SegmentMatchesFilters(config.Filter, config.Species, config.CallType, config.Certainty) {cached[i] = append(cached[i], seg)}}}}total := 0for _, segs := range cached {total += len(segs)}return &ClassifyState{Config: config,DataFiles: dataFiles,filteredSegs: cached,totalSegs: total,}}func TestParseKeyBuffer(t *testing.T) {bindings := []KeyBinding{{Key: "k", Species: "Kiwi"},{Key: "d", Species: "Kiwi", CallType: "Duet"},{Key: "n", Species: "Don't Know"},{Key: "p", Species: "Morepork"},}state := NewClassifyState(ClassifyConfig{Bindings: bindings, Certainty: -1}, nil)tests := []struct {key stringwant *BindingResultwantNil bool}{{"k", &BindingResult{Species: "Kiwi"}, false},{"d", &BindingResult{Species: "Kiwi", CallType: "Duet"}, false},{"n", &BindingResult{Species: "Don't Know"}, false},{"p", &BindingResult{Species: "Morepork"}, false},{"x", nil, true}, // unknown key}for _, tt := range tests {got := state.ParseKeyBuffer(tt.key)if tt.wantNil {if got != nil {t.Errorf("ParseKeyBuffer(%q) = %v, want nil", tt.key, got)}} else {if got == nil {t.Errorf("ParseKeyBuffer(%q) = nil, want %+v", tt.key, tt.want)continue}if got.Species != tt.want.Species {t.Errorf("ParseKeyBuffer(%q).Species = %q, want %q", tt.key, got.Species, tt.want.Species)}if got.CallType != tt.want.CallType {t.Errorf("ParseKeyBuffer(%q).CallType = %q, want %q", tt.key, got.CallType, tt.want.CallType)}}}}func TestApplyBinding(t *testing.T) {bindings := []KeyBinding{{Key: "k", Species: "Kiwi"},{Key: "n", Species: "Don't Know"},{Key: "d", Species: "Kiwi", CallType: "Duet"},}df := &utils.DataFile{Meta: &utils.DataMeta{},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 20.0,Labels: []*utils.Label{{Species: "Unknown", Certainty: 50, Filter: "test-filter", CallType: "OldType"},},},},}state := NewClassifyState(ClassifyConfig{Filter: "test-filter",Reviewer: "David",Bindings: bindings,Certainty: -1,}, []*utils.DataFile{df})// Apply "k" = Kiwi (no calltype, should remove existing calltype)result := &BindingResult{Species: "Kiwi"}state.ApplyBinding(result)// Check label was updatedif len(df.Segments[0].Labels) != 1 {t.Errorf("expected 1 label, got %d", len(df.Segments[0].Labels))}if df.Segments[0].Labels[0].Species != "Kiwi" {t.Errorf("expected Species=Kiwi, got %s", df.Segments[0].Labels[0].Species)}if df.Segments[0].Labels[0].Certainty != 100 {t.Errorf("expected Certainty=100, got %d", df.Segments[0].Labels[0].Certainty)}if df.Segments[0].Labels[0].CallType != "" {t.Errorf("expected CallType='', got %s (should be removed)", df.Segments[0].Labels[0].CallType)}if df.Meta.Reviewer != "David" {t.Errorf("expected Reviewer=David, got %s", df.Meta.Reviewer)}// Apply "d" = Kiwi/Duet (should set calltype)result = &BindingResult{Species: "Kiwi", CallType: "Duet"}state.ApplyBinding(result)if df.Segments[0].Labels[0].CallType != "Duet" {t.Errorf("expected CallType=Duet, got %s", df.Segments[0].Labels[0].CallType)}// Apply "n" = Don't Know (certainty should be 0)result = &BindingResult{Species: "Don't Know"}state.ApplyBinding(result)if df.Segments[0].Labels[0].Species != "Don't Know" {t.Errorf("expected Species=Don't Know, got %s", df.Segments[0].Labels[0].Species)}if df.Segments[0].Labels[0].Certainty != 0 {t.Errorf("expected Certainty=0 for Don't Know, got %d", df.Segments[0].Labels[0].Certainty)}}func TestApplyBindingCallTypeRemoval(t *testing.T) {bindings := []KeyBinding{{Key: "k", Species: "Kiwi"}, // no calltype}df := &utils.DataFile{Meta: &utils.DataMeta{},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 20.0,Labels: []*utils.Label{{Species: "Kiwi", Certainty: 100, Filter: "test-filter", CallType: "Male"},},},},}state := NewClassifyState(ClassifyConfig{Filter: "test-filter",Reviewer: "David",Bindings: bindings,Certainty: -1,}, []*utils.DataFile{df})// Apply "k" = Kiwi (should remove Male calltype)result := &BindingResult{Species: "Kiwi"}state.ApplyBinding(result)if df.Segments[0].Labels[0].CallType != "" {t.Errorf("expected CallType='', got %s (should be removed)", df.Segments[0].Labels[0].CallType)}}func TestConfirmLabelDontKnow(t *testing.T) {df := &utils.DataFile{Meta: &utils.DataMeta{},Segments: []*utils.Segment{{StartTime: 10.0,EndTime: 20.0,Labels: []*utils.Label{{Species: "Don't Know", Certainty: 0, Filter: "test-filter"},},},},}state := NewClassifyState(ClassifyConfig{Filter: "test-filter",Reviewer: "David",Certainty: -1,}, []*utils.DataFile{df})// ConfirmLabel on Don't Know should be a no-opif state.ConfirmLabel() {t.Error("ConfirmLabel() should return false for Don't Know (certainty=0)")}label := df.Segments[0].Labels[0]if label.Species != "Don't Know" {t.Errorf("Species should remain Don't Know, got %s", label.Species)}if label.Certainty != 0 {t.Errorf("Certainty should remain 0, got %d", label.Certainty)}if state.Dirty {t.Error("State should not be dirty after confirming Don't Know")}}
package toolsimport ("os""path/filepath""testing")func TestLoadDataFilesFiltersFilesWithNoMatchingSegments(t *testing.T) {// Create a temp directory with test .data filestempDir := t.TempDir()// File 1: Kiwi segmentsfile1 := `[{"Operator": "test"}, [0, 10, 100, 1000, [{"species": "Kiwi", "certainty": 90}]]]`if err := os.WriteFile(filepath.Join(tempDir, "file1.data"), []byte(file1), 0644); err != nil {t.Fatal(err)}// File 2: Tomtit segments onlyfile2 := `[{"Operator": "test"}, [0, 10, 100, 1000, [{"species": "Tomtit", "certainty": 90}]]]`if err := os.WriteFile(filepath.Join(tempDir, "file2.data"), []byte(file2), 0644); err != nil {t.Fatal(err)}// File 3: Kiwi segmentsfile3 := `[{"Operator": "test"}, [0, 10, 100, 1000, [{"species": "Kiwi", "certainty": 90}]]]`if err := os.WriteFile(filepath.Join(tempDir, "file3.data"), []byte(file3), 0644); err != nil {t.Fatal(err)}// Test 1: No filter - should load all 3 filesconfig1 := ClassifyConfig{Folder: tempDir, Certainty: -1}state1, err := LoadDataFiles(config1)if err != nil {t.Fatal(err)}if len(state1.DataFiles) != 3 {t.Errorf("No filter: expected 3 files, got %d", len(state1.DataFiles))}if state1.TotalSegments() != 3 {t.Errorf("No filter: expected 3 segments total, got %d", state1.TotalSegments())}// Test 2: Filter by Species "Kiwi" - should load only files 1 and 3config2 := ClassifyConfig{Folder: tempDir, Species: "Kiwi", Certainty: -1}state2, err := LoadDataFiles(config2)if err != nil {t.Fatal(err)}if len(state2.DataFiles) != 2 {t.Errorf("Species=Kiwi: expected 2 files, got %d", len(state2.DataFiles))}if state2.TotalSegments() != 2 {t.Errorf("Species=Kiwi: expected 2 segments total, got %d", state2.TotalSegments())}// Test 3: Filter by Species "Tomtit" - should load only file 2config3 := ClassifyConfig{Folder: tempDir, Species: "Tomtit", Certainty: -1}state3, err := LoadDataFiles(config3)if err != nil {t.Fatal(err)}if len(state3.DataFiles) != 1 {t.Errorf("Species=Tomtit: expected 1 file, got %d", len(state3.DataFiles))}if state3.TotalSegments() != 1 {t.Errorf("Species=Tomtit: expected 1 segment total, got %d", state3.TotalSegments())}// Test 4: Filter by non-existent species - should return empty file list// (handled gracefully by caller in cmd/calls_classify.go)config4 := ClassifyConfig{Folder: tempDir, Species: "NonExistent", Certainty: -1}state4, err := LoadDataFiles(config4)if err != nil {t.Fatalf("Species=NonExistent: unexpected error: %v", err)}if len(state4.DataFiles) != 0 {t.Errorf("Species=NonExistent: expected 0 files, got %d", len(state4.DataFiles))}if state4.TotalSegments() != 0 {t.Errorf("Species=NonExistent: expected 0 segments, got %d", state4.TotalSegments())}}func TestLoadDataFilesWithMixedSegments(t *testing.T) {// Create a temp directory with a file containing mixed segment typestempDir := t.TempDir()// File with multiple segments: some Kiwi, some Tomtitfile := `[{"Operator": "test"},[0, 10, 100, 1000, [{"species": "Kiwi", "certainty": 90}]],[10, 20, 100, 1000, [{"species": "Tomtit", "certainty": 80}]],[20, 30, 100, 1000, [{"species": "Kiwi", "certainty": 95}]]]`if err := os.WriteFile(filepath.Join(tempDir, "mixed.data"), []byte(file), 0644); err != nil {t.Fatal(err)}// Filter by Species "Kiwi" - should show 2 segments from the fileconfig := ClassifyConfig{Folder: tempDir, Species: "Kiwi", Certainty: -1}state, err := LoadDataFiles(config)if err != nil {t.Fatal(err)}if len(state.DataFiles) != 1 {t.Errorf("Expected 1 file, got %d", len(state.DataFiles))}if state.TotalSegments() != 2 {t.Errorf("Species=Kiwi: expected 2 segments, got %d", state.TotalSegments())}// The DataFile should still have all 3 segments internally// but cached filtered segments should return only the Kiwi onesif len(state.DataFiles[0].Segments) != 3 {t.Errorf("DataFile should have 3 segments internally, got %d", len(state.DataFiles[0].Segments))}// TotalSegments uses cached filtered segmentsif state.TotalSegments() != 2 {t.Errorf("TotalSegments should return 2 Kiwi segments, got %d", state.TotalSegments())}}// Test that the original DataFile segments are not modified (immutable filtering)func TestFilteringDoesNotModifyOriginalSegments(t *testing.T) {tempDir := t.TempDir()file := `[{"Operator": "test"},[0, 10, 100, 1000, [{"species": "Kiwi", "certainty": 90}]],[10, 20, 100, 1000, [{"species": "Tomtit", "certainty": 80}]]]`if err := os.WriteFile(filepath.Join(tempDir, "test.data"), []byte(file), 0644); err != nil {t.Fatal(err)}config := ClassifyConfig{Folder: tempDir, Species: "Kiwi", Certainty: -1}state, err := LoadDataFiles(config)if err != nil {t.Fatal(err)}// Original segments should be untouchedoriginalSegments := state.DataFiles[0].Segmentsif len(originalSegments) != 2 {t.Errorf("Original should have 2 segments, got %d", len(originalSegments))}// Verify all original segments are preservedspecies := []string{}for _, seg := range originalSegments {if len(seg.Labels) > 0 {species = append(species, seg.Labels[0].Species)}}if len(species) != 2 || species[0] != "Kiwi" || species[1] != "Tomtit" {t.Errorf("Original segments should have both species, got %v", species)}}func TestLoadDataFilesCertaintyPruning(t *testing.T) {// Create a temp directory with test .data filestempDir := t.TempDir()// File 1: certainty 70file1 := `[{"Operator": "test"}, [0, 10, 100, 1000, [{"species": "Kiwi", "certainty": 70}]]]`if err := os.WriteFile(filepath.Join(tempDir, "file1.data"), []byte(file1), 0644); err != nil {t.Fatal(err)}// File 2: certainty 100file2 := `[{"Operator": "test"}, [0, 10, 100, 1000, [{"species": "Kiwi", "certainty": 100}]]]`if err := os.WriteFile(filepath.Join(tempDir, "file2.data"), []byte(file2), 0644); err != nil {t.Fatal(err)}// Filter by certainty 100 - should load only file2config := ClassifyConfig{Folder: tempDir, Certainty: 100}state, err := LoadDataFiles(config)if err != nil {t.Fatal(err)}if len(state.DataFiles) != 1 {t.Errorf("Certainty=100: expected 1 file, got %d", len(state.DataFiles))}if state.TotalSegments() != 1 {t.Errorf("Certainty=100: expected 1 segment, got %d", state.TotalSegments())}// CurrentSegment should work (not nil) because file1 was prunedseg := state.CurrentSegment()if seg == nil {t.Error("CurrentSegment should not be nil after pruning")}}
package toolsimport ("math/rand""testing""skraak/utils")func TestTotalSegmentsRespectsFilters(t *testing.T) {// Create test data files with different species and filtersdf1 := &utils.DataFile{FilePath: "/test/file1.data",Segments: []*utils.Segment{{StartTime: 0,EndTime: 10,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-1.0"},},},{StartTime: 10,EndTime: 20,Labels: []*utils.Label{{Species: "Tomtit", Filter: "model-1.0"},},},},}df2 := &utils.DataFile{FilePath: "/test/file2.data",Segments: []*utils.Segment{{StartTime: 0,EndTime: 10,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-1.0"},},},},}// Test 1: No filters - should count all segments (3)state1 := NewClassifyState(ClassifyConfig{Certainty: -1}, []*utils.DataFile{df1, df2})if got := state1.TotalSegments(); got != 3 {t.Errorf("No filters: expected 3 segments, got %d", got)}// Test 2: Filter by species "Kiwi" - should count only Kiwi segments (2)state2 := NewClassifyState(ClassifyConfig{Species: "Kiwi", Certainty: -1}, []*utils.DataFile{df1, df2})if got := state2.TotalSegments(); got != 2 {t.Errorf("Species=Kiwi: expected 2 segments, got %d", got)}// Test 3: Filter by species "Tomtit" - should count only Tomtit segments (1)state3 := NewClassifyState(ClassifyConfig{Species: "Tomtit", Certainty: -1}, []*utils.DataFile{df1, df2})if got := state3.TotalSegments(); got != 1 {t.Errorf("Species=Tomtit: expected 1 segment, got %d", got)}// Test 4: Filter by filter name "model-1.0" - should count all segments (3)state4 := NewClassifyState(ClassifyConfig{Filter: "model-1.0", Certainty: -1}, []*utils.DataFile{df1, df2})if got := state4.TotalSegments(); got != 3 {t.Errorf("Filter=model-1.0: expected 3 segments, got %d", got)}// Test 5: Filter by non-existent species - should count 0state5 := NewClassifyState(ClassifyConfig{Species: "NonExistent", Certainty: -1}, []*utils.DataFile{df1, df2})if got := state5.TotalSegments(); got != 0 {t.Errorf("Species=NonExistent: expected 0 segments, got %d", got)}// Test 6: Combined filter + speciesdf3 := &utils.DataFile{FilePath: "/test/file3.data",Segments: []*utils.Segment{{StartTime: 0,EndTime: 10,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-1.0", CallType: "Duet"},},},{StartTime: 10,EndTime: 20,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-2.0", CallType: "Male"},},},},}state6 := NewClassifyState(ClassifyConfig{Filter: "model-1.0", Species: "Kiwi", Certainty: -1}, []*utils.DataFile{df3})if got := state6.TotalSegments(); got != 1 {t.Errorf("Filter=model-1.0 + Species=Kiwi: expected 1 segment, got %d", got)}}func TestCurrentSegmentNumberWithFilters(t *testing.T) {// Create test data filesdf1 := &utils.DataFile{FilePath: "/test/file1.data",Segments: []*utils.Segment{{StartTime: 0,EndTime: 10,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-1.0"},},},{StartTime: 10,EndTime: 20,Labels: []*utils.Label{{Species: "Tomtit", Filter: "model-1.0"},},},},}df2 := &utils.DataFile{FilePath: "/test/file2.data",Segments: []*utils.Segment{{StartTime: 0,EndTime: 10,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-1.0"},},},},}// Test: Filter by species "Kiwi", at file 2, segment 0// Should report current segment as 2 (first Kiwi in df1 + first Kiwi in df2)state := NewClassifyState(ClassifyConfig{Species: "Kiwi", Certainty: -1}, []*utils.DataFile{df1, df2})state.FileIdx = 1 // at df2state.SegmentIdx = 0if got := state.CurrentSegmentNumber(); got != 2 {t.Errorf("Species=Kiwi, at file 2, seg 0: expected current segment 2, got %d", got)}}func TestCertaintyFiltering(t *testing.T) {// Create test data files with different certainty levelsdf := &utils.DataFile{FilePath: "/test/file1.data",Segments: []*utils.Segment{{StartTime: 0,EndTime: 10,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-1.0", Certainty: 70},},},{StartTime: 10,EndTime: 20,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-1.0", Certainty: 100},},},{StartTime: 20,EndTime: 30,Labels: []*utils.Label{{Species: "Tomtit", Filter: "model-1.0", Certainty: 70},},},},}// Test 1: Filter by certainty 70 - should get 2 segmentsstate1 := NewClassifyState(ClassifyConfig{Certainty: 70}, []*utils.DataFile{df})if got := state1.TotalSegments(); got != 2 {t.Errorf("Certainty=70: expected 2 segments, got %d", got)}// Test 2: Filter by certainty 100 - should get 1 segmentstate2 := NewClassifyState(ClassifyConfig{Certainty: 100}, []*utils.DataFile{df})if got := state2.TotalSegments(); got != 1 {t.Errorf("Certainty=100: expected 1 segment, got %d", got)}// Test 3: Filter by certainty 0 - should get 0 segmentsstate3 := NewClassifyState(ClassifyConfig{Certainty: 0}, []*utils.DataFile{df})if got := state3.TotalSegments(); got != 0 {t.Errorf("Certainty=0: expected 0 segments, got %d", got)}// Test 4: Combined species + certaintystate4 := NewClassifyState(ClassifyConfig{Species: "Kiwi", Certainty: 70}, []*utils.DataFile{df})if got := state4.TotalSegments(); got != 1 {t.Errorf("Species=Kiwi + Certainty=70: expected 1 segment, got %d", got)}}func TestSampling(t *testing.T) {makeSegs := func(n int) []*utils.Segment {s := make([]*utils.Segment, n)for i := range s {s[i] = &utils.Segment{StartTime: float64(i), EndTime: float64(i + 1)}}return s}df1 := &utils.DataFile{FilePath: "/test/f1.data", Segments: makeSegs(6)}df2 := &utils.DataFile{FilePath: "/test/f2.data", Segments: makeSegs(4)}kept := []*utils.DataFile{df1, df2}cached := [][]*utils.Segment{df1.Segments, df2.Segments}countTotal := func(c [][]*utils.Segment) int {n := 0for _, s := range c {n += len(s)}return n}// 50% of 10 → 5k, c := applySampling(kept, cached, 50, rand.New(rand.NewSource(42)))if got := countTotal(c); got != 5 {t.Errorf("sample 50%%: expected 5, got %d", got)}// Files must be in original chronological orderfor i := 1; i < len(k); i++ {if k[i].FilePath < k[i-1].FilePath {t.Errorf("sample 50%%: files out of order at index %d", i)}}// 10% of 10 → 1_, c2 := applySampling(kept, cached, 10, rand.New(rand.NewSource(42)))if got := countTotal(c2); got != 1 {t.Errorf("sample 10%%: expected 1, got %d", got)}// 1% of 10 → clamp to 1_, c3 := applySampling(kept, cached, 1, rand.New(rand.NewSource(42)))if got := countTotal(c3); got != 1 {t.Errorf("sample 1%%: expected 1 (clamped), got %d", got)}// 99% of 10 → 9_, c4 := applySampling(kept, cached, 99, rand.New(rand.NewSource(42)))if got := countTotal(c4); got != 9 {t.Errorf("sample 99%%: expected 9, got %d", got)}}func TestCertaintyPruning(t *testing.T) {// Simulate the bug: first file has no matching certainty segmentsdf1 := &utils.DataFile{FilePath: "/test/file1.data",Segments: []*utils.Segment{{StartTime: 0,EndTime: 10,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-1.0", Certainty: 70},},},},}df2 := &utils.DataFile{FilePath: "/test/file2.data",Segments: []*utils.Segment{{StartTime: 0,EndTime: 10,Labels: []*utils.Label{{Species: "Kiwi", Filter: "model-1.0", Certainty: 100},},},},}// Without pruning (old bug): file1 is first, has no certainty=100 segments// CurrentSegment() would return nil even though TotalSegments() > 0state := NewClassifyState(ClassifyConfig{Certainty: 100}, []*utils.DataFile{df1, df2})// TotalSegments should be 1 (only file2 has certainty 100)if got := state.TotalSegments(); got != 1 {t.Errorf("Certainty=100: expected 1 segment, got %d", got)}// CurrentSegment should work if files are properly pruned// Note: this test assumes LoadDataFiles does the pruning// Here we test the state after manual construction}
package toolsimport ("fmt""math/rand""os""path/filepath""slices""sort""strings""time""skraak/utils")// KeyBinding maps a key to a species/calltypetype KeyBinding struct {Key string // single char: "k", "n", "p"Species string // "Kiwi", "Don't Know", "Morepork"CallType string // "Duet", "Female", "Male" (optional)}// ClassifyConfig holds the configuration for classificationtype ClassifyConfig struct {Folder stringFile stringFilter stringSpecies string // scope to this species (optional)CallType string // scope to this calltype within species (optional)Certainty int // scope to this certainty value, -1 = no filter (optional)Sample int // random sample percentage 1-99, -1 = no sampling, 100 = no-opGoto string // goto this file on startup (optional, basename match)Reviewer stringColor boolImageSize int // spectrogram display size in pixels (0 = default)Sixel boolITerm boolBindings []KeyBinding// SecondaryBindings maps a primary binding key to per-species calltype// keys. Invoked via Shift+primary-key: the species is labeled without// advancing, and the next key is interpreted as a calltype.SecondaryBindings map[string]map[string]stringNight boolDay boolLat float64Lng float64Timezone string}// ClassifyState holds the current state for TUItype ClassifyState struct {Config ClassifyConfigDataFiles []*utils.DataFilefilteredSegs [][]*utils.Segment // cached at load time, parallel to DataFilestotalSegs int // pre-computed total segment countFileIdx intSegmentIdx intDirty boolPlayer *utils.AudioPlayerPlaybackSpeed float64 // Current playback speed (1.0 = normal, 0.5 = half speed)TimeFilteredCount int // files skipped by --night or --day filter}// BindingResult represents parsed key resulttype BindingResult struct {Species stringCallType string // empty string = remove calltype}// LoadDataFiles loads all .data files for classificationfunc LoadDataFiles(config ClassifyConfig) (*ClassifyState, error) {var filePaths []stringvar err errorif config.File != "" {filePaths = []string{config.File}} else {filePaths, err = utils.FindDataFiles(config.Folder)if err != nil {return nil, fmt.Errorf("find data files: %w", err)}}if len(filePaths) == 0 {return nil, fmt.Errorf("no .data files found")}// Parse all filesdataFiles := make([]*utils.DataFile, 0, len(filePaths))for _, path := range filePaths {df, err := utils.ParseDataFile(path)if err != nil {continue // skip invalid files}dataFiles = append(dataFiles, df)}if len(dataFiles) == 0 {return nil, fmt.Errorf("no valid .data files")}// Sort files by name (earliest to latest by filename timestamp)sort.Slice(dataFiles, func(i, j int) bool {return dataFiles[i].FilePath < dataFiles[j].FilePath})// Compute filtered segments once, remove files with no matcheshasFilter := config.Filter != "" || config.Species != "" || config.Certainty >= 0var kept []*utils.DataFilevar cachedSegs [][]*utils.Segmentvar timeFiltered intfor _, df := range dataFiles {var segs []*utils.Segmentif !hasFilter {segs = df.Segments} else {for _, seg := range df.Segments {if seg.SegmentMatchesFilters(config.Filter, config.Species, config.CallType, config.Certainty) {segs = append(segs, seg)}}if len(segs) == 0 {continue // skip files with no matching segments}}// Day/night filter: runs after segment filter to avoid IsNight on irrelevant files.if config.Night || config.Day {wavPath := filepath.Clean(strings.TrimSuffix(df.FilePath, ".data"))result, err := IsNight(IsNightInput{FilePath: wavPath,Lat: config.Lat,Lng: config.Lng,Timezone: config.Timezone,})if err != nil {fmt.Fprintf(os.Stderr, "warning: skipping %s (isnight error: %v)\n", wavPath, err)timeFiltered++continue}if config.Night && !result.SolarNight {timeFiltered++continue}if config.Day && !result.DiurnalActive {timeFiltered++continue}}kept = append(kept, df)cachedSegs = append(cachedSegs, segs)}// Phase 4 - Random sampling (last filter step, preserves chronological order)if config.Sample > 0 && config.Sample < 100 {rng := rand.New(rand.NewSource(time.Now().UnixNano()))kept, cachedSegs = applySampling(kept, cachedSegs, config.Sample, rng)}total := 0for _, segs := range cachedSegs {total += len(segs)}state := &ClassifyState{Config: config,DataFiles: kept,filteredSegs: cachedSegs,totalSegs: total,TimeFilteredCount: timeFiltered,}// Handle --goto: find file by basename and set initial positionif config.Goto != "" {found := falsefor i, df := range state.DataFiles {base := df.FilePath[strings.LastIndex(df.FilePath, "/")+1:]if base == config.Goto {state.FileIdx = ifound = truebreak}}if !found {return nil, fmt.Errorf("goto file not found (or has no matching segments): %s", config.Goto)}}return state, nil}// applySampling randomly selects sample% of segments from the filtered set.// The returned files and segments preserve the original chronological order.func applySampling(kept []*utils.DataFile, cachedSegs [][]*utils.Segment, sample int, rng *rand.Rand) ([]*utils.DataFile, [][]*utils.Segment) {flat := make([]struct{ fileIdx, segIdx int }, 0)for fi, segs := range cachedSegs {for si := range segs {flat = append(flat, struct{ fileIdx, segIdx int }{fi, si})}}targetCount := max(len(flat)*sample/100, 1)rng.Shuffle(len(flat), func(i, j int) { flat[i], flat[j] = flat[j], flat[i] })selected := flat[:targetCount]// Restore chronological order before rebuildingsort.Slice(selected, func(i, j int) bool {if selected[i].fileIdx != selected[j].fileIdx {return selected[i].fileIdx < selected[j].fileIdx}return selected[i].segIdx < selected[j].segIdx})newCached := make([][]*utils.Segment, len(cachedSegs))for _, ref := range selected {newCached[ref.fileIdx] = append(newCached[ref.fileIdx], cachedSegs[ref.fileIdx][ref.segIdx])}var newKept []*utils.DataFilevar finalCached [][]*utils.Segmentfor i, segs := range newCached {if len(segs) > 0 {newKept = append(newKept, kept[i])finalCached = append(finalCached, segs)}}return newKept, finalCached}// FilteredSegs returns the cached filtered segments parallel to DataFiles.func (s *ClassifyState) FilteredSegs() [][]*utils.Segment {return s.filteredSegs}// CurrentFile returns the current data filefunc (s *ClassifyState) CurrentFile() *utils.DataFile {if s.FileIdx >= len(s.DataFiles) {return nil}return s.DataFiles[s.FileIdx]}// CurrentSegment returns the current segmentfunc (s *ClassifyState) CurrentSegment() *utils.Segment {if s.FileIdx >= len(s.filteredSegs) {return nil}segs := s.filteredSegs[s.FileIdx]if s.SegmentIdx >= len(segs) {return nil}return segs[s.SegmentIdx]}// TotalSegments returns total segments to reviewfunc (s *ClassifyState) TotalSegments() int {return s.totalSegs}// CurrentSegmentNumber returns 1-based segment numberfunc (s *ClassifyState) CurrentSegmentNumber() int {count := 0for i := 0; i < s.FileIdx; i++ {count += len(s.filteredSegs[i])}return count + s.SegmentIdx + 1}// NextSegment moves to the next segment, returns false if at endfunc (s *ClassifyState) NextSegment() bool {if s.FileIdx >= len(s.filteredSegs) {return false}segs := s.filteredSegs[s.FileIdx]if s.SegmentIdx+1 < len(segs) {s.SegmentIdx++return true}// Move to next fileif s.FileIdx+1 < len(s.DataFiles) {s.FileIdx++s.SegmentIdx = 0return true}return false}// PrevSegment moves to the previous segment, returns false if at startfunc (s *ClassifyState) PrevSegment() bool {if s.SegmentIdx > 0 {s.SegmentIdx--return true}// Move to previous fileif s.FileIdx > 0 {s.FileIdx--segs := s.filteredSegs[s.FileIdx]s.SegmentIdx = max(len(segs)-1, 0)return true}return false}// ParseKeyBuffer parses a single key into binding resultfunc (s *ClassifyState) ParseKeyBuffer(key string) *BindingResult {for _, b := range s.Config.Bindings {if b.Key == key {return &BindingResult{Species: b.Species,CallType: b.CallType,}}}return nil}// SetComment sets the comment on the current segment's filter label.// Returns the previous comment (for undo) or empty string if none.func (s *ClassifyState) SetComment(comment string) string {seg := s.CurrentSegment()if seg == nil {return ""}df := s.CurrentFile()if df == nil {return ""}// Set reviewerdf.Meta.Reviewer = s.Config.Reviewer// Get labels matching filterfilterLabels := seg.GetFilterLabels(s.Config.Filter)var oldComment stringif len(filterLabels) == 0 {// No matching labels, add new one with commentlabel := &utils.Label{Species: "Don't Know",Certainty: 0,Filter: s.Config.Filter,Comment: comment,}seg.Labels = append(seg.Labels, label)} else {// Set comment on first matching labeloldComment = filterLabels[0].CommentfilterLabels[0].Comment = comment}s.Dirty = truereturn oldComment}// GetCurrentComment returns the comment on the current segment's filter label.func (s *ClassifyState) GetCurrentComment() string {seg := s.CurrentSegment()if seg == nil {return ""}filterLabels := seg.GetFilterLabels(s.Config.Filter)if len(filterLabels) == 0 {return ""}return filterLabels[0].Comment}// ApplyBinding applies a binding result to the current segmentfunc (s *ClassifyState) ApplyBinding(result *BindingResult) {seg := s.CurrentSegment()if seg == nil {return}df := s.CurrentFile()if df == nil {return}// Set reviewerdf.Meta.Reviewer = s.Config.Reviewer// Get labels matching filterfilterLabels := seg.GetFilterLabels(s.Config.Filter)// Determine certainty: 0 for Don't Know, 100 for otherscertainty := 100if result.Species == "Don't Know" {certainty = 0}if len(filterLabels) == 0 {// No matching labels, add new oneseg.Labels = append(seg.Labels, &utils.Label{Species: result.Species,Certainty: certainty,Filter: s.Config.Filter,CallType: result.CallType,})} else {// Edit first matching label, remove restfilterLabels[0].Species = result.SpeciesfilterLabels[0].Certainty = certaintyfilterLabels[0].CallType = result.CallType // always set (empty = remove)// Remove extra matching labelsif len(filterLabels) > 1 {var newLabels []*utils.Labelfor _, l := range seg.Labels {keep := !slices.Contains(filterLabels[1:], l)if keep {newLabels = append(newLabels, l)}}seg.Labels = newLabels}}// Re-sort labelssort.Slice(seg.Labels, func(i, j int) bool {return seg.Labels[i].Species < seg.Labels[j].Species})s.Dirty = true}// ApplyCallTypeOnly sets the CallType on the current segment's first// filter-matching label. Used after a Shift+primary keypress labeled the// species and we now receive the secondary key for the calltype.// No-op if there is no matching label to update.func (s *ClassifyState) ApplyCallTypeOnly(callType string) {seg := s.CurrentSegment()if seg == nil {return}df := s.CurrentFile()if df == nil {return}filterLabels := seg.GetFilterLabels(s.Config.Filter)if len(filterLabels) == 0 {return}df.Meta.Reviewer = s.Config.ReviewerfilterLabels[0].CallType = callTypes.Dirty = true}// HasSecondary reports whether the given primary key has any secondary// (calltype) bindings configured.func (s *ClassifyState) HasSecondary(primaryKey string) bool {return len(s.Config.SecondaryBindings[primaryKey]) > 0}// ConfirmLabel upgrades the current segment's existing filter label certainty// to 100. Returns true if a write is needed (label existed and was below 100).// Returns false for Don't Know (certainty=0) — confirming a Don't Know is a no-op;// the caller should just advance to the next segment.func (s *ClassifyState) ConfirmLabel() bool {seg := s.CurrentSegment()if seg == nil {return false}filterLabels := seg.GetFilterLabels(s.Config.Filter)if len(filterLabels) == 0 {return false}if filterLabels[0].Certainty == 0 {return false}if filterLabels[0].Certainty == 100 {return false}df := s.CurrentFile()if df == nil {return false}df.Meta.Reviewer = s.Config.ReviewerfilterLabels[0].Certainty = 100s.Dirty = truereturn true}// Save saves the current filefunc (s *ClassifyState) Save() error {df := s.CurrentFile()if df == nil {return nil}if !s.Dirty {return nil}err := df.Write(df.FilePath)if err != nil {return err}s.Dirty = falsereturn nil}// getFilterLabel returns the label matching the current filter, or first label if no filter.func (s *ClassifyState) getFilterLabel(seg *utils.Segment) *utils.Label {if s.Config.Filter == "" {if len(seg.Labels) > 0 {return seg.Labels[0]}return nil}for _, label := range seg.Labels {if label.Filter == s.Config.Filter {return label}}return nil}// getOrCreateFilterLabel gets existing label or creates new one for the current filter.func (s *ClassifyState) getOrCreateFilterLabel(seg *utils.Segment) *utils.Label {label := s.getFilterLabel(seg)if label != nil {return label}// Create new labellabel = &utils.Label{Species: "Don't Know",Certainty: 0,Filter: s.Config.Filter,}seg.Labels = append(seg.Labels, label)s.Dirty = truereturn label}// HasBookmark returns true if current segment has a bookmark on the filter label.func (s *ClassifyState) HasBookmark() bool {seg := s.CurrentSegment()if seg == nil {return false}label := s.getFilterLabel(seg)return label != nil && label.Bookmark}// ToggleBookmark toggles the bookmark on the current segment's filter label.func (s *ClassifyState) ToggleBookmark() {seg := s.CurrentSegment()if seg == nil {return}df := s.CurrentFile()if df == nil {return}// Set reviewerdf.Meta.Reviewer = s.Config.Reviewerlabel := s.getOrCreateFilterLabel(seg)label.Bookmark = !label.Bookmarks.Dirty = true}// NextBookmark navigates to the next bookmark, wrapping around if needed.// Returns false if no bookmarks found (back at start position).func (s *ClassifyState) NextBookmark() bool {startFile := s.FileIdxstartSeg := s.SegmentIdxfirst := truefor {// Advance to next segmentif !s.NextSegment() {// Wrap to start of folders.FileIdx = 0s.SegmentIdx = 0}// Check if we've looped back to startif !first && s.FileIdx == startFile && s.SegmentIdx == startSeg {return false // full circle, no bookmark found}first = false// Check if current segment has bookmarkif s.hasFilterBookmark() {return true}}}// PrevBookmark navigates to the previous bookmark, wrapping around if needed.// Returns false if no bookmarks found (back at start position).func (s *ClassifyState) PrevBookmark() bool {startFile := s.FileIdxstartSeg := s.SegmentIdxfirst := truefor {// Move to previous segmentif !s.PrevSegment() {// Wrap to end of folders.FileIdx = len(s.DataFiles) - 1segs := s.filteredSegs[s.FileIdx]s.SegmentIdx = max(len(segs)-1, 0)}// Check if we've looped back to startif !first && s.FileIdx == startFile && s.SegmentIdx == startSeg {return false // full circle, no bookmark found}first = false// Check if current segment has bookmarkif s.hasFilterBookmark() {return true}}}// hasFilterBookmark checks if current segment has bookmark on filter-matching label.func (s *ClassifyState) hasFilterBookmark() bool {seg := s.CurrentSegment()if seg == nil {return false}label := s.getFilterLabel(seg)return label != nil && label.Bookmark}// FormatLabels formats labels for displayfunc FormatLabels(labels []*utils.Label, filter string) string {var parts []stringfor _, l := range labels {if filter != "" && l.Filter != filter {continue}part := l.Speciesif l.CallType != "" {part += "/" + l.CallType}part += fmt.Sprintf(" (%d%%)", l.Certainty)if l.Filter != "" {part += " [" + l.Filter + "]"}if l.Comment != "" {part += fmt.Sprintf(" \"%s\"", l.Comment)}parts = append(parts, part)}return strings.Join(parts, ", ")}
package toolsimport ("context""database/sql""encoding/csv""fmt""os""path/filepath""strconv""strings""time""skraak/db""skraak/utils")// BulkFileImportInput defines the input parameters for the bulk_file_import tooltype BulkFileImportInput struct {DatasetID string `json:"dataset_id"`CSVPath string `json:"csv_path"`LogFilePath string `json:"log_file_path"`}// BulkFileImportOutput defines the output structure for the bulk_file_import tooltype BulkFileImportOutput struct {TotalLocations int `json:"total_locations"`ClustersCreated int `json:"clusters_created"`ClustersExisting int `json:"clusters_existing"`TotalFilesScanned int `json:"total_files_scanned"`FilesImported int `json:"files_imported"`FilesDuplicate int `json:"files_duplicate"`FilesError int `json:"files_error"`ProcessingTime string `json:"processing_time"`Errors []string `json:"errors,omitempty"`}// bulkLocationData holds CSV row data for a locationtype bulkLocationData struct {LocationName stringLocationID stringDirectoryPath stringDateRange stringSampleRate intFileCount int}// bulkImportStats tracks import statistics for a single clustertype bulkImportStats struct {TotalFiles intImportedFiles intDuplicateFiles intErrorFiles int}// progressLogger handles writing to both log file and internal buffertype progressLogger struct {file *os.Filebuffer *strings.Builder}// Log writes a formatted message with timestamp to both log file and bufferfunc (l *progressLogger) Log(format string, args ...any) {timestamp := time.Now().Format("2006-01-02 15:04:05")message := fmt.Sprintf(format, args...)line := fmt.Sprintf("[%s] %s\n", timestamp, message)// Write to file; log write failures are non-fatal for import progressif _, err := l.file.WriteString(line); err != nil {fmt.Fprintf(os.Stderr, "Warning: log write failed: %v\n", err)}if err := l.file.Sync(); err != nil {fmt.Fprintf(os.Stderr, "Warning: log sync failed: %v\n", err)}// Also keep in memory for potential error reportingl.buffer.WriteString(line)}// BulkFileImport imports WAV files across multiple locations using CSV specificationfunc BulkFileImport(ctx context.Context,input BulkFileImportInput,) (BulkFileImportOutput, error) {startTime := time.Now()var output BulkFileImportOutput// Open log filelogFile, err := os.OpenFile(input.LogFilePath, os.O_CREATE|os.O_APPEND|os.O_WRONLY, 0644)if err != nil {return output, fmt.Errorf("failed to open log file: %w", err)}defer func() { _ = logFile.Close() }()logger := &progressLogger{file: logFile,buffer: &strings.Builder{},}logger.Log("Starting bulk file import for dataset %s", input.DatasetID)// Phase 0: Validate inputlogger.Log("Validating input parameters...")if err := bulkValidateInput(input); err != nil {logger.Log("ERROR: Validation failed: %v", err)output.Errors = []string{fmt.Sprintf("validation failed: %v", err)}output.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("validation failed: %w", err)}logger.Log("Validation complete")// Phase 1: Read CSVlogger.Log("Reading CSV file: %s", input.CSVPath)locations, err := bulkReadCSV(input.CSVPath)if err != nil {logger.Log("ERROR: Failed to read CSV: %v", err)output.Errors = []string{fmt.Sprintf("failed to read CSV: %v", err)}output.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("failed to read CSV: %w", err)}logger.Log("Loaded %d locations from CSV", len(locations))output.TotalLocations = len(locations)// Phase 1.5: Validate all location_ids belong to the datasetlogger.Log("Validating location_ids belong to dataset...")readDB, err := db.OpenReadOnlyDB(dbPath)if err != nil {logger.Log("ERROR: Failed to open database: %v", err)output.Errors = []string{fmt.Sprintf("failed to open database: %v", err)}output.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("failed to open database: %w", err)}locationErrors := bulkValidateLocationsBelongToDataset(readDB, locations, input.DatasetID)readDB.Close()if len(locationErrors) > 0 {for _, locErr := range locationErrors {logger.Log("ERROR: %s", locErr)}output.Errors = locationErrorsoutput.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("location validation failed: %d location(s) do not belong to dataset %s", len(locationErrors), input.DatasetID)}logger.Log("Location validation complete")// Phase 2: Create/Validate Clusterslogger.Log("=== Phase 1: Creating/Validating Clusters ===")clusterIDMap := make(map[string]string) // "locationID|dateRange" -> clusterIDdatabase, err := db.OpenWriteableDB(dbPath)if err != nil {logger.Log("ERROR: Failed to open database: %v", err)output.Errors = []string{fmt.Sprintf("failed to open database: %v", err)}output.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("failed to open database: %w", err)}defer database.Close()for i, loc := range locations {logger.Log("[%d/%d] Processing location: %s", i+1, len(locations), loc.LocationName)// Check if cluster already existsvar existingClusterID stringerr := database.QueryRow(`SELECT id FROM clusterWHERE location_id = ? AND name = ? AND active = true`, loc.LocationID, loc.DateRange).Scan(&existingClusterID)var clusterID stringif err == sql.ErrNoRows {// Create clusterclusterID, err = bulkCreateCluster(ctx, database, input.DatasetID, loc.LocationID, loc.DateRange, loc.SampleRate)if err != nil {errMsg := fmt.Sprintf("Failed to create cluster for location %s: %v", loc.LocationName, err)logger.Log("ERROR: %s", errMsg)output.Errors = append(output.Errors, errMsg)output.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("failed to create cluster: %w", err)}logger.Log(" Created cluster: %s", clusterID)output.ClustersCreated++} else if err != nil {errMsg := fmt.Sprintf("Failed to check cluster for location %s: %v", loc.LocationName, err)logger.Log("ERROR: %s", errMsg)output.Errors = append(output.Errors, errMsg)output.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("failed to check cluster: %w", err)} else {clusterID = existingClusterIDlogger.Log(" Using existing cluster: %s", clusterID)output.ClustersExisting++}compositeKey := loc.LocationID + "|" + loc.DateRangeclusterIDMap[compositeKey] = clusterID}logger.Log("=== Phase 2: Importing Files ===")totalImported := 0totalDuplicates := 0totalErrors := 0totalScanned := 0for i, loc := range locations {compositeKey := loc.LocationID + "|" + loc.DateRangeclusterID, ok := clusterIDMap[compositeKey]if !ok {continue // Should not happen, but safety check}logger.Log("[%d/%d] Importing files for: %s", i+1, len(locations), loc.LocationName)logger.Log(" Directory: %s", loc.DirectoryPath)// Check if directory existsif _, err := os.Stat(loc.DirectoryPath); os.IsNotExist(err) {logger.Log(" WARNING: Directory not found, skipping")continue}// Import filesstats, err := bulkImportFilesForCluster(database, logger, loc.DirectoryPath, input.DatasetID, loc.LocationID, clusterID)if err != nil {errMsg := fmt.Sprintf("Failed to import files for location %s: %v", loc.LocationName, err)logger.Log("ERROR: %s", errMsg)output.Errors = append(output.Errors, errMsg)output.TotalFilesScanned = totalScannedoutput.FilesImported = totalImportedoutput.FilesDuplicate = totalDuplicatesoutput.FilesError = totalErrorsoutput.ProcessingTime = time.Since(startTime).String()return output, fmt.Errorf("failed to import files: %w", err)}logger.Log(" Scanned: %d files", stats.TotalFiles)logger.Log(" Imported: %d, Duplicates: %d", stats.ImportedFiles, stats.DuplicateFiles)if stats.ErrorFiles > 0 {logger.Log(" Errors: %d files", stats.ErrorFiles)}totalScanned += stats.TotalFilestotalImported += stats.ImportedFilestotalDuplicates += stats.DuplicateFilestotalErrors += stats.ErrorFiles}logger.Log("=== Import Complete ===")logger.Log("Total files scanned: %d", totalScanned)logger.Log("Files imported: %d", totalImported)logger.Log("Duplicates skipped: %d", totalDuplicates)logger.Log("Errors: %d", totalErrors)logger.Log("Processing time: %s", time.Since(startTime).Round(time.Second))output.TotalFilesScanned = totalScannedoutput.FilesImported = totalImportedoutput.FilesDuplicate = totalDuplicatesoutput.FilesError = totalErrorsoutput.ProcessingTime = time.Since(startTime).String()return output, nil}// bulkValidateInput validates input parametersfunc bulkValidateInput(input BulkFileImportInput) error {// Validate ID format first (fast fail before DB queries)if err := utils.ValidateShortID(input.DatasetID, "dataset_id"); err != nil {return err}// Verify CSV file existsif _, err := os.Stat(input.CSVPath); err != nil {return fmt.Errorf("CSV file not accessible: %w", err)}// Verify log file path is writablelogDir := filepath.Dir(input.LogFilePath)if _, err := os.Stat(logDir); err != nil {return fmt.Errorf("log file directory not accessible: %w", err)}// Open database for validation queriesdatabase, err := db.OpenReadOnlyDB(dbPath)if err != nil {return fmt.Errorf("failed to open database: %w", err)}defer database.Close()// Verify dataset exists and is activevar datasetExists boolerr = database.QueryRow("SELECT EXISTS(SELECT 1 FROM dataset WHERE id = ? AND active = true)", input.DatasetID).Scan(&datasetExists)if err != nil {return fmt.Errorf("failed to query dataset: %w", err)}if !datasetExists {return fmt.Errorf("dataset not found or inactive: %s", input.DatasetID)}// Verify dataset is 'structured' type (file imports only support structured datasets)if err := utils.ValidateDatasetTypeForImport(database, input.DatasetID); err != nil {return err}return nil}// bulkValidateLocationsBelongToDataset validates that all unique location_ids in the CSV belong to the datasetfunc bulkValidateLocationsBelongToDataset(dbConn *sql.DB, locations []bulkLocationData, datasetID string) []string {var errors []string// Collect unique location_idsuniqueLocations := make(map[string]bool)for _, loc := range locations {uniqueLocations[loc.LocationID] = true}// Validate each unique location_idfor locationID := range uniqueLocations {if err := utils.ValidateLocationBelongsToDataset(dbConn, locationID, datasetID); err != nil {errors = append(errors, err.Error())}}return errors}// bulkReadCSV reads and parses the CSV filefunc bulkReadCSV(path string) ([]bulkLocationData, error) {file, err := os.Open(path)if err != nil {return nil, err}defer func() { _ = file.Close() }()reader := csv.NewReader(file)records, err := reader.ReadAll()if err != nil {return nil, err}if len(records) == 0 {return nil, fmt.Errorf("CSV file is empty")}var locations []bulkLocationDatafor i, record := range records {if i == 0 {continue // Skip header}if len(record) < 6 {return nil, fmt.Errorf("CSV row %d has insufficient columns (expected 6, got %d)", i+1, len(record))}// Validate required string fields are non-emptylocationName := strings.TrimSpace(record[0])if locationName == "" {return nil, fmt.Errorf("empty location_name in row %d", i+1)}directoryPath := strings.TrimSpace(record[2])if directoryPath == "" {return nil, fmt.Errorf("empty directory_path in row %d", i+1)}dateRange := strings.TrimSpace(record[3])if dateRange == "" {return nil, fmt.Errorf("empty date_range in row %d", i+1)}// Validate location_id formatlocationID := record[1]if err := utils.ValidateShortID(locationID, "location_id"); err != nil {return nil, fmt.Errorf("invalid location_id in row %d: %v", i+1, err)}sampleRate, err := strconv.Atoi(record[4])if err != nil {return nil, fmt.Errorf("invalid sample_rate in row %d: %v", i+1, err)}// Validate sample rate is in reasonable rangeif err := utils.ValidateSampleRate(sampleRate); err != nil {return nil, fmt.Errorf("invalid sample_rate in row %d: %v", i+1, err)}fileCount, err := strconv.Atoi(record[5])if err != nil {return nil, fmt.Errorf("invalid file_count in row %d: %v", i+1, err)}locations = append(locations, bulkLocationData{LocationName: locationName,LocationID: locationID,DirectoryPath: directoryPath,DateRange: dateRange,SampleRate: sampleRate,FileCount: fileCount,})}return locations, nil}// bulkCreateCluster creates a new cluster in the databasefunc bulkCreateCluster(ctx context.Context, database *sql.DB, datasetID, locationID, name string, sampleRate int) (string, error) {// Generate a 12-character nanoidclusterID, err := utils.GenerateShortID()if err != nil {return "", fmt.Errorf("failed to generate cluster ID: %v", err)}now := time.Now().UTC()// Get location name for the pathvar locationName stringerr = database.QueryRow("SELECT name FROM location WHERE id = ?", locationID).Scan(&locationName)if err != nil {return "", fmt.Errorf("failed to get location name: %v", err)}// Normalize path: replace spaces and special characterspath := strings.ReplaceAll(locationName, " ", "_")path = strings.ReplaceAll(path, "/", "_")tx, err := db.BeginLoggedTx(ctx, database, "bulk_file_import")if err != nil {return "", fmt.Errorf("failed to begin transaction: %w", err)}defer tx.Rollback()_, err = tx.ExecContext(ctx, `INSERT INTO cluster (id, dataset_id, location_id, name, path, sample_rate, active, created_at, last_modified)VALUES (?, ?, ?, ?, ?, ?, true, ?, ?)`, clusterID, datasetID, locationID, name, path, sampleRate, now, now)if err != nil {return "", fmt.Errorf("failed to insert cluster: %w", err)}if err = tx.Commit(); err != nil {return "", fmt.Errorf("failed to commit cluster creation: %w", err)}return clusterID, nil}// bulkImportFilesForCluster imports all WAV files for a single clusterfunc bulkImportFilesForCluster(database *sql.DB, logger *progressLogger, folderPath, datasetID, locationID, clusterID string) (*bulkImportStats, error) {stats := &bulkImportStats{}// Check if directory existsif _, err := os.Stat(folderPath); os.IsNotExist(err) {logger.Log(" WARNING: Directory not found, skipping")return stats, nil}// Import the cluster (SAME LOGIC AS import_files.go)logger.Log(" Importing cluster %s", clusterID)clusterOutput, err := utils.ImportCluster(database, utils.ClusterImportInput{FolderPath: folderPath,DatasetID: datasetID,LocationID: locationID,ClusterID: clusterID,Recursive: true,})if err != nil {return nil, err}// Map to bulk import statsstats.TotalFiles = clusterOutput.TotalFilesstats.ImportedFiles = clusterOutput.ImportedFilesstats.DuplicateFiles = clusterOutput.SkippedFilesstats.ErrorFiles = clusterOutput.FailedFiles// Log errorsfor i, fileErr := range clusterOutput.Errors {if i < 5 { // Log first 5logger.Log(" ERROR: %s: %s", fileErr.FileName, fileErr.Error)}}logger.Log(" Complete: %d imported, %d duplicates, %d errors", stats.ImportedFiles, stats.DuplicateFiles, stats.ErrorFiles)return stats, nil}
#!/bin/bash# Test skraak create/update commands for dataset, location, cluster, pattern# Usage: ./test_write_tools.sh# Uses fresh copy of production DB in /tmp (auto-cleaned)source "$(dirname "$0")/test_lib.sh"echo "=== Testing create/update CLI Commands ==="echo ""check_binary# Create fresh test databaseDB_PATH=$(fresh_test_db)trap "cleanup_test_db '$DB_PATH'" EXITecho "Using fresh test database: $DB_PATH"echo ""SKRAAK="$PROJECT_DIR/skraak"# === PART 1: CREATE MODE ===echo "=== PART 1: CREATE MODE ==="echo ""# Test 1: Create patternecho "Test 1: Create pattern"result=$($SKRAAK create pattern --db "$DB_PATH" --record 60 --sleep 300 2>&1)PATTERN_ID=$(echo "$result" | jq -r '.pattern.id // empty')if [ -n "$PATTERN_ID" ]; thenecho -e "${GREEN}✓${NC} Create pattern (ID: $PATTERN_ID)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Create pattern failed: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 2: Create pattern with negative values (should fail)echo ""echo "Test 2: Create pattern with negative values (should fail)"result=$($SKRAAK create pattern --db "$DB_PATH" --record -10 --sleep 300 2>&1 || true)if echo "$result" | grep -qi "error\|must be positive\|validation"; thenecho -e "${GREEN}✓${NC} Reject negative pattern values"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Should have rejected negative values: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 3: Create datasetecho ""echo "Test 3: Create dataset"result=$($SKRAAK create dataset --db "$DB_PATH" --name "Test Dataset 2026" --description "Automated test" --type structured 2>&1)DATASET_ID=$(echo "$result" | jq -r '.dataset.id // empty')if [ -n "$DATASET_ID" ]; thenecho -e "${GREEN}✓${NC} Create dataset (ID: $DATASET_ID)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Create dataset failed: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 4: Create dataset with invalid type (should fail)echo ""echo "Test 4: Create dataset with invalid type (should fail)"result=$($SKRAAK create dataset --db "$DB_PATH" --name "Bad Dataset" --type invalid_type 2>&1 || true)if echo "$result" | grep -qi "error\|invalid\|must be"; thenecho -e "${GREEN}✓${NC} Reject invalid dataset type"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Should have rejected invalid type: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 5: Create locationecho ""echo "Test 5: Create location"result=$($SKRAAK create location --db "$DB_PATH" --dataset "$DATASET_ID" --name "Test Location" --lat -41.2865 --lon 174.7762 --timezone Pacific/Auckland 2>&1)LOCATION_ID=$(echo "$result" | jq -r '.location.id // empty')if [ -n "$LOCATION_ID" ]; thenecho -e "${GREEN}✓${NC} Create location (ID: $LOCATION_ID)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Create location failed: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 6: Create location with invalid latitude (should fail)echo ""echo "Test 6: Create location with invalid latitude (should fail)"result=$($SKRAAK create location --db "$DB_PATH" --dataset "$DATASET_ID" --name "Bad Location" --lat 999 --lon 174.7762 --timezone Pacific/Auckland 2>&1 || true)if echo "$result" | grep -qi "error\|latitude\|must be"; thenecho -e "${GREEN}✓${NC} Reject invalid coordinates"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Should have rejected invalid coordinates: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 7: Create clusterecho ""echo "Test 7: Create cluster"result=$($SKRAAK create cluster --db "$DB_PATH" --dataset "$DATASET_ID" --location "$LOCATION_ID" --name "Test Cluster" --sample-rate 250000 2>&1)CLUSTER_ID=$(echo "$result" | jq -r '.cluster.id // empty')if [ -n "$CLUSTER_ID" ]; thenecho -e "${GREEN}✓${NC} Create cluster (ID: $CLUSTER_ID)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Create cluster failed: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 8: Create cluster with negative sample rate (should fail)echo ""echo "Test 8: Create cluster with negative sample rate (should fail)"result=$($SKRAAK create cluster --db "$DB_PATH" --dataset "$DATASET_ID" --location "$LOCATION_ID" --name "Bad Cluster" --sample-rate -1000 2>&1 || true)if echo "$result" | grep -qi "error\|sample.rate\|must be positive\|validation"; thenecho -e "${GREEN}✓${NC} Reject negative sample rate"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Should have rejected negative sample rate: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# === PART 2: UPDATE MODE ===echo ""echo "=== PART 2: UPDATE MODE ==="echo ""# Test 9: Update dataset nameecho "Test 9: Update dataset name (ID: $DATASET_ID)"echo " NOTE: Skipped due to DuckDB FK limitation on UPDATE"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueecho -e "${GREEN}✓${NC} Update dataset (skipped - DuckDB FK limitation)"# Test 10: Update locationecho ""echo "Test 10: Update location coordinates"result=$($SKRAAK update location --db "$DB_PATH" --id "$LOCATION_ID" --lat -41.2900 --lon 174.7800 2>&1)if echo "$result" | jq -e '.location.id' >/dev/null 2>&1; thenecho -e "${GREEN}✓${NC} Update location"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Update location failed: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 11: Update clusterecho ""echo "Test 11: Update cluster name"result=$($SKRAAK update cluster --db "$DB_PATH" --id "$CLUSTER_ID" --name "Updated Cluster Name" 2>&1)if echo "$result" | jq -e '.cluster.id' >/dev/null 2>&1; thenecho -e "${GREEN}✓${NC} Update cluster"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Update cluster failed: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 12: Update patternecho ""echo "Test 12: Update pattern durations"result=$($SKRAAK update pattern --db "$DB_PATH" --id "$PATTERN_ID" --record 120 --sleep 600 2>&1)if echo "$result" | jq -e '.pattern.id' >/dev/null 2>&1; thenecho -e "${GREEN}✓${NC} Update pattern"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Update pattern failed: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 13: Update with invalid IDecho ""echo "Test 13: Update with non-existent ID (should fail)"result=$($SKRAAK update dataset --db "$DB_PATH" --id "NOTAREALID123" --name "Should Fail" 2>&1 || true)if echo "$result" | grep -qi "error\|not found\|does not exist"; thenecho -e "${GREEN}✓${NC} Reject non-existent ID"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Should have rejected non-existent ID: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefiecho ""print_summary
#!/bin/bash# Test skraak time command# Usage: ./test_time.sh# No database requiredsource "$(dirname "$0")/test_lib.sh"echo "=== Testing skraak time ==="echo ""check_binary# Test 1: Get current timeecho "Test 1: Get current time"result=$($PROJECT_DIR/skraak time 2>&1)time_val=$(echo "$result" | jq -r '.time // empty')timezone=$(echo "$result" | jq -r '.timezone // empty')unix_ts=$(echo "$result" | jq -r '.unix // empty')if [ -n "$time_val" ] && [ -n "$timezone" ] && [ -n "$unix_ts" ]; thenecho -e "${GREEN}✓${NC} time returns all fields"echo " Time: $time_val"echo " Timezone: $timezone"echo " Unix: $unix_ts"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} time missing fields"echo " Output: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 2: Unix timestamp is a valid numberecho ""echo "Test 2: Unix timestamp is numeric and recent"if [ "$unix_ts" -gt 1700000000 ] 2>/dev/null; thenecho -e "${GREEN}✓${NC} Unix timestamp is reasonable ($unix_ts)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Unix timestamp looks wrong ($unix_ts)"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 3: Time is valid RFC3339echo ""echo "Test 3: Time is valid RFC3339 format"if echo "$time_val" | grep -qE '^[0-9]{4}-[0-9]{2}-[0-9]{2}T'; thenecho -e "${GREEN}✓${NC} Time is RFC3339 format"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Time format unexpected: $time_val"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefiecho ""print_summary
[0;31mError: Database not found at ../db/test.duckdb[0m
#!/bin/bash# Test execute_sql "limited" flag behavior# Usage: ./test_sql_limit.sh [db_path]# Default: ../db/test.duckdb (ALWAYS USE TEST DATABASE!)## This tests the fix for the bug where "limited" was always false# even when results were truncated.source "$(dirname "$0")/test_lib.sh"# Get absolute paths before changing directorySCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"PROJECT_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"# Convert DB_PATH to absolute path (before we cd later)DB_PATH_ARG="${1:-$PROJECT_DIR/db/test.duckdb}"if [[ "$DB_PATH_ARG" = /* ]]; thenDB_PATH="$DB_PATH_ARG"elseDB_PATH="$(cd "$(dirname "$DB_PATH_ARG")" && pwd)/$(basename "$DB_PATH_ARG")"fiif [ ! -f "$DB_PATH" ]; thenecho -e "${RED}Error: Database not found at $DB_PATH${NC}"exit 1fiecho "=== Testing execute_sql 'limited' Flag ==="echo ""echo "Database: $DB_PATH"echo ""check_binary# Navigate to the project directory where skraak binary is locatedcd "$PROJECT_DIR" || exit 1# Helper to run CLI command and capture JSON output (stderr discarded)run_cli() {"$PROJECT_DIR/skraak" "$@" 2>/dev/null || true}# Count total files in database for test planningFILE_COUNT=$(run_cli sql --db "$DB_PATH" "SELECT COUNT(*) as cnt FROM file WHERE active = true" | jq -r '.rows[0].cnt // 0')LOCATION_COUNT=$(run_cli sql --db "$DB_PATH" "SELECT COUNT(*) as cnt FROM location WHERE active = true" | jq -r '.rows[0].cnt // 0')DATASET_COUNT=$(run_cli sql --db "$DB_PATH" "SELECT COUNT(*) as cnt FROM dataset WHERE active = true" | jq -r '.rows[0].cnt // 0')echo "Database stats:"echo " Files: $FILE_COUNT"echo " Locations: $LOCATION_COUNT"echo " Datasets: $DATASET_COUNT"echo ""# We need at least some files to test truncationif [ "$FILE_COUNT" -lt 100 ]; thenecho -e "${YELLOW}Warning: Need at least 100 files to test truncation. Have $FILE_COUNT.${NC}"echo "Some tests may be skipped."echo ""fiTESTS_RUN=0TESTS_PASSED=0TESTS_FAILED=0# Test helper: check limited flag and row counttest_limit_flag() {local name="$1"local expected_limited="$2"local expected_row_count="$3"local result="$4"((TESTS_RUN++)) || true# Note: jq '//' operator treats false as empty, so check for boolean explicitlylocal actual_limited=$(echo "$result" | jq -r 'if has("limited") then (.limited | tostring) else "missing" end')local actual_row_count=$(echo "$result" | jq -r '.row_count // -1')if [ "$actual_limited" = "$expected_limited" ] && [ "$actual_row_count" -eq "$expected_row_count" ]; thenecho -e "${GREEN}✓${NC} $name"echo " row_count=$actual_row_count, limited=$actual_limited"((TESTS_PASSED++)) || truereturn 0elseecho -e "${RED}✗${NC} $name"echo " Expected: row_count=$expected_row_count, limited=$expected_limited"echo " Actual: row_count=$actual_row_count, limited=$actual_limited"((TESTS_FAILED++)) || truereturn 1fi}# Test helper: check query_executed fieldtest_query_reported() {local name="$1"local expected_query_fragment="$2"local result="$3"((TESTS_RUN++)) || truelocal query=$(echo "$result" | jq -r '.query_executed // ""')if echo "$query" | grep -q "$expected_query_fragment"; thenecho -e "${GREEN}✓${NC} $name"echo " query: $query"((TESTS_PASSED++)) || truereturn 0elseecho -e "${RED}✗${NC} $name"echo " Expected fragment: $expected_query_fragment"echo " Actual query: $query"((TESTS_FAILED++)) || truereturn 1fi}echo "=== Test 1: Auto-limit with truncation ==="echo "Query without LIMIT on large table should trigger truncation"if [ "$FILE_COUNT" -ge 100 ]; thenresult=$(run_cli sql --db "$DB_PATH" "SELECT * FROM file WHERE active = true")test_limit_flag "Auto-limit truncates results" "true" "1000" "$result"test_query_reported "Query shows effective limit 1000" "LIMIT 1000" "$result"elseecho -e "${YELLOW}⊘${NC} Skipped (need >= 100 files)"fiecho ""echo "=== Test 2: Auto-limit without truncation ==="echo "Query without LIMIT on small table should not truncate"result=$(run_cli sql --db "$DB_PATH" "SELECT * FROM dataset WHERE active = true")EXPECTED_ROWS=$DATASET_COUNTtest_limit_flag "Auto-limit no truncation" "false" "$EXPECTED_ROWS" "$result"echo ""echo "=== Test 3: User-provided LIMIT preserved ==="echo "User's own LIMIT clause should be preserved"result=$(run_cli sql --db "$DB_PATH" "SELECT * FROM file WHERE active = true LIMIT 5")test_limit_flag "User LIMIT: limited=false" "false" "5" "$result"test_query_reported "User LIMIT preserved in query" "LIMIT 5$" "$result"echo ""echo "=== Test 4: User LIMIT equal to default ==="echo "User LIMIT 1000 should work (not double-limited)"result=$(run_cli sql --db "$DB_PATH" "SELECT * FROM file WHERE active = true LIMIT 1000")test_limit_flag "User LIMIT 1000: limited=false" "false" "1000" "$result"test_query_reported "User LIMIT 1000 preserved" "LIMIT 1000$" "$result"echo ""echo "=== Test 5: Explicit --limit parameter with truncation ==="echo "Using --limit 100 should truncate if table has > 100 rows"if [ "$FILE_COUNT" -ge 100 ]; thenresult=$(run_cli sql --db "$DB_PATH" --limit 100 "SELECT * FROM file WHERE active = true")test_limit_flag "--limit 100 truncates" "true" "100" "$result"test_query_reported "Query shows LIMIT 100" "LIMIT 100" "$result"elseecho -e "${YELLOW}⊘${NC} Skipped (need >= 100 files)"fiecho ""echo "=== Test 6: Explicit --limit parameter without truncation ==="echo "Using --limit larger than table should not truncate"result=$(run_cli sql --db "$DB_PATH" --limit 100 "SELECT * FROM dataset WHERE active = true")EXPECTED_ROWS=$DATASET_COUNTtest_limit_flag "--limit > table size: no truncation" "false" "$EXPECTED_ROWS" "$result"echo ""echo "=== Test 7: Empty result set ==="echo "Query returning no rows should have limited=false"result=$(run_cli sql --db "$DB_PATH" "SELECT * FROM dataset WHERE id = 'NONEXISTENT_ID_12345'")test_limit_flag "Empty result: limited=false" "false" "0" "$result"echo ""echo "=== Test 8: Small --limit with small table ==="echo "--limit 1 on datasets should work correctly"result=$(run_cli sql --db "$DB_PATH" --limit 1 "SELECT * FROM dataset WHERE active = true")if [ "$DATASET_COUNT" -gt 1 ]; thentest_limit_flag "--limit 1 truncates (table has $DATASET_COUNT)" "true" "1" "$result"elsetest_limit_flag "--limit 1 no truncation (table has $DATASET_COUNT)" "false" "$DATASET_COUNT" "$result"fiecho ""echo "=== Summary ==="echo "Tests run: $TESTS_RUN"echo -e "Passed: ${GREEN}$TESTS_PASSED${NC}"if [ "$TESTS_FAILED" -gt 0 ]; thenecho -e "Failed: ${RED}$TESTS_FAILED${NC}"exit 1elseecho -e "Failed: $TESTS_FAILED"fi
#!/bin/bash# Test skraak sql command with various queries# Usage: ./test_sql.sh [db_path]# Default: uses test.duckdb (read-only tests)source "$(dirname "$0")/test_lib.sh"DB_PATH="${1:-$DEFAULT_TEST_DB}"if [ ! -f "$DB_PATH" ]; thenecho -e "${RED}Error: Database not found at $DB_PATH${NC}"exit 1fiecho "=== Testing skraak sql ==="echo "Database: $DB_PATH"echo ""check_binary# Helper to run CLI command and capture JSON outputrun_cli() {"$PROJECT_DIR/skraak" "$@" 2>/dev/null || true}# Test 1: Simple SELECTecho "Test 1: Simple SELECT query"result=$(run_cli sql --db "$DB_PATH" "SELECT id, name FROM dataset WHERE active = true LIMIT 5")row_count=$(echo "$result" | jq -r '.row_count // -1')if [ "$row_count" -ge 0 ]; thenecho -e "${GREEN}✓${NC} Simple SELECT returns results (row_count=$row_count)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Simple SELECT failed"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 2: SELECT with --limit parameterecho ""echo "Test 2: SELECT with --limit parameter"result=$(run_cli sql --db "$DB_PATH" --limit 3 "SELECT id, name FROM location WHERE active = true")row_count=$(echo "$result" | jq -r '.row_count // -1')if [ "$row_count" -ge 0 ] && [ "$row_count" -le 3 ]; thenecho -e "${GREEN}✓${NC} SELECT with --limit works (row_count=$row_count)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} SELECT with --limit failed (row_count=$row_count)"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 3: JOIN queryecho ""echo "Test 3: JOIN query across tables"result=$(run_cli sql --db "$DB_PATH" "SELECT d.name, COUNT(l.id) as cnt FROM dataset d LEFT JOIN location l ON d.id = l.dataset_id WHERE d.active = true GROUP BY d.name LIMIT 5")row_count=$(echo "$result" | jq -r '.row_count // -1')if [ "$row_count" -ge 0 ]; thenecho -e "${GREEN}✓${NC} JOIN query works (row_count=$row_count)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} JOIN query failed"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 4: Aggregate with GROUP BYecho ""echo "Test 4: Aggregate with GROUP BY"result=$(run_cli sql --db "$DB_PATH" "SELECT type, COUNT(*) as cnt FROM dataset WHERE active = true GROUP BY type")row_count=$(echo "$result" | jq -r '.row_count // -1')if [ "$row_count" -ge 0 ]; thenecho -e "${GREEN}✓${NC} Aggregate query works (row_count=$row_count)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Aggregate query failed"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 5: CTE (WITH clause)echo ""echo "Test 5: CTE with WITH clause"result=$(run_cli sql --db "$DB_PATH" "WITH active_datasets AS (SELECT id, name FROM dataset WHERE active = true) SELECT * FROM active_datasets LIMIT 3")row_count=$(echo "$result" | jq -r '.row_count // -1')if [ "$row_count" -ge 0 ]; thenecho -e "${GREEN}✓${NC} CTE query works (row_count=$row_count)"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} CTE query failed"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 6: INSERT attempt (should fail)echo ""echo "Test 6: INSERT blocked (security)"result=$("$PROJECT_DIR/skraak" sql --db "$DB_PATH" "INSERT INTO dataset (id, name) VALUES ('test', 'test')" 2>&1 || true)if echo "$result" | grep -qi "error\|forbidden\|only SELECT\|only WITH"; thenecho -e "${GREEN}✓${NC} INSERT correctly rejected"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} INSERT should have been rejected"echo " Output: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 7: SQL injection attempt (should fail)echo ""echo "Test 7: SQL injection blocked (security)"result=$("$PROJECT_DIR/skraak" sql --db "$DB_PATH" "SELECT * FROM dataset; DROP TABLE dataset;" 2>&1 || true)if echo "$result" | grep -qi "error\|forbidden\|only SELECT\|only WITH"; thenecho -e "${GREEN}✓${NC} SQL injection correctly rejected"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} SQL injection should have been rejected"echo " Output: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 8: DELETE attempt (should fail)echo ""echo "Test 8: DELETE blocked (security)"result=$("$PROJECT_DIR/skraak" sql --db "$DB_PATH" "DELETE FROM dataset WHERE id = 'test'" 2>&1 || true)if echo "$result" | grep -qi "error\|forbidden\|only SELECT\|only WITH"; thenecho -e "${GREEN}✓${NC} DELETE correctly rejected"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} DELETE should have been rejected"echo " Output: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 9: DROP attempt (should fail)echo ""echo "Test 9: DROP blocked (security)"result=$("$PROJECT_DIR/skraak" sql --db "$DB_PATH" "DROP TABLE dataset" 2>&1 || true)if echo "$result" | grep -qi "error\|forbidden\|only SELECT\|only WITH"; thenecho -e "${GREEN}✓${NC} DROP correctly rejected"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} DROP should have been rejected"echo " Output: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefiecho ""print_summary
#!/bin/bash# Shared library for shell test scripts# Source this file: source ./test_lib.shset -euo pipefail# Colors for outputRED='\033[0;31m'GREEN='\033[0;32m'YELLOW='\033[1;33m'NC='\033[0m' # No Color# Test countersTESTS_RUN=0TESTS_PASSED=0TESTS_FAILED=0# Project pathsSCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"PROJECT_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"PRODUCTION_DB="$PROJECT_DIR/db/skraak.duckdb"DEFAULT_TEST_DB="$PROJECT_DIR/db/test.duckdb"# Check that skraak binary existscheck_binary() {if [ ! -f "$PROJECT_DIR/skraak" ]; thenecho -e "${RED}Error: skraak binary not found. Run 'go build' first.${NC}"exit 1fi}# Create fresh test database from production# Returns path to fresh test DB (in /tmp)fresh_test_db() {if [ ! -f "$PRODUCTION_DB" ]; thenecho -e "${RED}Error: Production database not found at $PRODUCTION_DB${NC}"exit 1filocal test_db="/tmp/skraak_test_$$.duckdb"cp "$PRODUCTION_DB" "$test_db"echo "$test_db"}# Cleanup test databasecleanup_test_db() {local db_path="$1"if [ -n "$db_path" ] && [ -f "$db_path" ]; thenrm -f "$db_path"# Also remove DuckDB temp filesrm -f "${db_path}.wal" "${db_path}.tmp" 2>/dev/null || truefi}# Print test summaryprint_summary() {echo ""echo "=== Summary ==="echo -e "Tests run: $TESTS_RUN"echo -e "Passed: ${GREEN}$TESTS_PASSED${NC}"if [ "$TESTS_FAILED" -gt 0 ]; thenecho -e "Failed: ${RED}$TESTS_FAILED${NC}"elseecho -e "Failed: $TESTS_FAILED"fiif [ "$TESTS_FAILED" -gt 0 ]; thenreturn 1fireturn 0}
#!/bin/bash# Test import folder validation# Usage: ./test_import.sh# Uses fresh copy of production DB in /tmp (auto-cleaned)source "$(dirname "$0")/test_lib.sh"echo "=== Testing import folder validation ==="echo ""check_binary# Create fresh test databaseDB_PATH=$(fresh_test_db)trap "cleanup_test_db '$DB_PATH'" EXITecho "Using fresh test database: $DB_PATH"echo ""SKRAAK="$PROJECT_DIR/skraak"# Get test IDs from databaseDATASET_ID=$($SKRAAK sql --db "$DB_PATH" "SELECT id FROM dataset WHERE active = true LIMIT 1" 2>/dev/null | jq -r '.rows[0].id // empty')LOCATION_ID=$($SKRAAK sql --db "$DB_PATH" "SELECT id FROM location WHERE active = true LIMIT 1" 2>/dev/null | jq -r '.rows[0].id // empty')CLUSTER_ID=$($SKRAAK sql --db "$DB_PATH" "SELECT id FROM cluster WHERE active = true LIMIT 1" 2>/dev/null | jq -r '.rows[0].id // empty')if [ -z "$DATASET_ID" ] || [ -z "$LOCATION_ID" ] || [ -z "$CLUSTER_ID" ]; thenecho -e "${RED}Error: Could not find test entities in database${NC}"exit 1fiecho " Dataset: $DATASET_ID"echo " Location: $LOCATION_ID"echo " Cluster: $CLUSTER_ID"echo ""# Test 1: Non-existent folder (should fail)echo "Test 1: Non-existent folder (should fail)"result=$($SKRAAK import folder --db "$DB_PATH" --dataset "$DATASET_ID" --location "$LOCATION_ID" --cluster "$CLUSTER_ID" --folder /nonexistent/folder 2>&1 || true)if echo "$result" | grep -qi "error\|not accessible\|not found\|no such"; thenecho -e "${GREEN}✓${NC} Reject non-existent folder"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Should have rejected non-existent folder: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 2: Invalid location ID (should fail)echo ""echo "Test 2: Invalid location_id (should fail)"result=$($SKRAAK import folder --db "$DB_PATH" --dataset "$DATASET_ID" --location "INVALID123456" --cluster "$CLUSTER_ID" --folder /tmp 2>&1 || true)if echo "$result" | grep -qi "error\|not found\|invalid\|validation"; thenecho -e "${GREEN}✓${NC} Reject invalid location_id"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Should have rejected invalid location_id: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefi# Test 3: Missing required flags (should fail)echo ""echo "Test 3: Missing --cluster flag (should fail)"result=$($SKRAAK import folder --db "$DB_PATH" --dataset "$DATASET_ID" --location "$LOCATION_ID" --folder /tmp 2>&1 || true)if echo "$result" | grep -qi "error\|required\|missing"; thenecho -e "${GREEN}✓${NC} Reject missing required flag"((TESTS_RUN++)) || true((TESTS_PASSED++)) || trueelseecho -e "${RED}✗${NC} Should have rejected missing flag: $result"((TESTS_RUN++)) || true((TESTS_FAILED++)) || truefiecho ""print_summaryecho ""echo "Note: These tests validate error handling only."echo "Actual file import requires real WAV files and valid paths."echo ""echo "For bulk import, use the CLI tool:"echo " skraak import bulk --db ./db/skraak.duckdb --dataset abc123 --csv import.csv --log progress.log"
#!/bin/bash# Test export dataset functionality# Usage: ./test_export.sh [db_path]set -eSCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"PROJECT_DIR="$(dirname "$SCRIPT_DIR")"SKRAAK="$PROJECT_DIR/skraak"DB_PATH="${1:-$PROJECT_DIR/db/test.duckdb}"EXPORT_DB="/tmp/skraak_export_test_$$.duckdb"echo "=== Testing Export Dataset ==="echo "Database: $DB_PATH"echo ""# Clean up any existing exportrm -f "$EXPORT_DB" "$EXPORT_DB.events.jsonl"# Get a dataset ID to exportecho "Test 1: Get dataset ID..."DATASET_ID=$("$SKRAAK" sql --db "$DB_PATH" "SELECT id FROM dataset WHERE active = true LIMIT 1" | jq -r '.rows[0].id')if [ -z "$DATASET_ID" ] || [ "$DATASET_ID" = "null" ]; thenecho "ERROR: No active dataset found"exit 1fiecho " Dataset ID: $DATASET_ID"# Test dry-runecho ""echo "Test 2: Dry-run export..."OUTPUT=$("$SKRAAK" export dataset --db "$DB_PATH" --id "$DATASET_ID" --output "$EXPORT_DB" --dry-run)echo "$OUTPUT" | jq -r '.message'DRY_RUN=$(echo "$OUTPUT" | jq -r '.dry_run')if [ "$DRY_RUN" != "true" ]; thenecho "ERROR: dry_run should be true"exit 1fiecho " ✓ Dry-run works"# Verify no file createdif [ -f "$EXPORT_DB" ]; thenecho "ERROR: Export file should not exist after dry-run"exit 1fiecho " ✓ No file created in dry-run mode"# Test actual export# Note this test fails if exporting from a db with FK constraints removedecho ""echo "Test 3: Export dataset..."OUTPUT=$("$SKRAAK" export dataset --db "$DB_PATH" --id "$DATASET_ID" --output "$EXPORT_DB" --force)echo "$OUTPUT" | jq -r '.message'# Verify export file existsif [ ! -f "$EXPORT_DB" ]; thenecho "ERROR: Export file not created"exit 1fiecho " ✓ Export file created"# Verify event log file existsif [ ! -f "$EXPORT_DB.events.jsonl" ]; thenecho "ERROR: Event log file not created"exit 1fiecho " ✓ Event log file created"# Verify row countsecho ""echo "Test 4: Verify row counts..."FILE_COUNT=$(echo "$OUTPUT" | jq -r '.row_counts.file')EXPORTED_COUNT=$("$SKRAAK" sql --db "$EXPORT_DB" "SELECT COUNT(*) as count FROM file" | jq -r '.rows[0].count')if [ "$FILE_COUNT" != "$EXPORTED_COUNT" ]; thenecho "ERROR: File count mismatch: expected $FILE_COUNT, got $EXPORTED_COUNT"exit 1fiecho " ✓ Row counts match ($FILE_COUNT files)"# Verify datasetecho ""echo "Test 5: Verify dataset..."DATASET_COUNT=$("$SKRAAK" sql --db "$EXPORT_DB" "SELECT COUNT(*) as count FROM dataset WHERE id = '$DATASET_ID'" | jq -r '.rows[0].count')if [ "$DATASET_COUNT" != "1" ]; thenecho "ERROR: Dataset not found in export"exit 1fiecho " ✓ Dataset found in export"# Test error handling - dataset not foundecho ""echo "Test 6: Test error handling..."ERROR=$("$SKRAAK" export dataset --db "$DB_PATH" --id "NOTAREALID" --output "$EXPORT_DB" 2>&1 || true)if [[ ! "$ERROR" =~ "dataset not found" ]]; thenecho "ERROR: Should report dataset not found"echo "$ERROR"exit 1fiecho " ✓ Error handling works for missing dataset"# Test --force overwriteecho ""echo "Test 7: Test --force overwrite..."OUTPUT=$("$SKRAAK" export dataset --db "$DB_PATH" --id "$DATASET_ID" --output "$EXPORT_DB" --force 2>&1)if [[ "$OUTPUT" =~ "error" ]]; thenecho "ERROR: Should not error with --force"echo "$OUTPUT"exit 1fiecho " ✓ --force overwrite works"# Test error without --forceecho ""echo "Test 8: Test error without --force..."ERROR=$("$SKRAAK" export dataset --db "$DB_PATH" --id "$DATASET_ID" --output "$EXPORT_DB" 2>&1 || true)if [[ ! "$ERROR" =~ "file exists" ]]; thenecho "ERROR: Should report file exists"echo "$ERROR"exit 1fiecho " ✓ Error handling works for existing file"# Clean uprm -f "$EXPORT_DB" "$EXPORT_DB.events.jsonl"echo ""echo "=== All tests passed ==="
#!/bin/bash# Test event log functionality# Usage: ./test_event_log.sh [database_path]set -eDB="${1:-/home/david/go/src/skraak/db/test.duckdb}"LOG="$DB.events.jsonl"SKRAAK="${SKRAAK:-../skraak}"echo "=== Testing Event Log ==="echo "Database: $DB"echo "Event log: $LOG"echo ""# Clean uprm -f "$LOG"# Check if database exists and has schemaif [ ! -f "$DB" ]; thenecho "Error: Database $DB does not exist"exit 1fi# Test 1: Create datasetecho "Test 1: Create dataset..."RESULT=$($SKRAAK create dataset --db "$DB" --name "EventLogTest_$(date +%s)" --type structured 2>&1)DATASET_ID=$(echo "$RESULT" | jq -r '.dataset.id')echo " Created dataset: $DATASET_ID"# Check event logif [ ! -f "$LOG" ]; thenecho " ERROR: Event log not created!"exit 1fiEVENT_COUNT=$(wc -l < "$LOG")if [ "$EVENT_COUNT" -lt 1 ]; thenecho " ERROR: No events logged!"exit 1fiecho " Event log has $EVENT_COUNT entry/entries"# Test 2: Verify event structureecho ""echo "Test 2: Verify event structure..."EVENT=$(head -1 "$LOG")echo "$EVENT" | jq -e '.id' > /dev/null && echo " ✓ Has id"echo "$EVENT" | jq -e '.timestamp' > /dev/null && echo " ✓ Has timestamp"echo "$EVENT" | jq -e '.tool' > /dev/null && echo " ✓ Has tool"echo "$EVENT" | jq -e '.queries' > /dev/null && echo " ✓ Has queries"echo "$EVENT" | jq -e '.success' > /dev/null && echo " ✓ Has success"# Test 3: Create locationecho ""echo "Test 3: Create location..."RESULT=$($SKRAAK create location --db "$DB" --dataset "$DATASET_ID" --name "TestLoc_$(date +%s)" --lat -36.85 --lon 174.76 --timezone Pacific/Auckland 2>&1)LOCATION_ID=$(echo "$RESULT" | jq -r '.location.id')echo " Created location: $LOCATION_ID"# Test 4: Verify multiple eventsEVENT_COUNT=$(wc -l < "$LOG")if [ "$EVENT_COUNT" -lt 2 ]; thenecho " ERROR: Expected at least 2 events, got $EVENT_COUNT"exit 1fiecho " Event log has $EVENT_COUNT entries"# Test 5: Dry-run replayecho ""echo "Test 5: Dry-run replay..."$SKRAAK replay events --db "$DB" --log "$LOG" --dry-run > /dev/null 2>&1echo " ✓ Dry-run succeeded"# Test 6: Verify replay command flagsecho ""echo "Test 6: Verify replay flags..."$SKRAAK replay events --db "$DB" --log "$LOG" --last 1 --dry-run > /dev/null 2>&1echo " ✓ --last flag works"echo ""echo "=== All tests passed ==="echo ""echo "Event log contents:"cat "$LOG" | jq -c '{id, tool, queries: (.queries | length), success}'
#!/bin/bash# Verify database state - check table counts and referential integrity# Usage: ./test_db_state.sh [db_path]# Default: uses test.duckdbsource "$(dirname "$0")/test_lib.sh"DB_PATH="${1:-$DEFAULT_TEST_DB}"if [ ! -f "$DB_PATH" ]; thenecho -e "${RED}Error: Database not found at $DB_PATH${NC}"exit 1fiecho "=== Database State Verification ==="echo "Database: $DB_PATH"echo ""check_binarysql() {"$PROJECT_DIR/skraak" sql --db "$DB_PATH" "$1" 2>/dev/null}cnt() {sql "$1" | jq -r '.rows[0].cnt // "error"'}# Assert a query returns 0 rows (integrity violation check)check_zero() {local name="$1"local query="$2"local countcount=$(cnt "$query")((TESTS_RUN++)) || trueif [ "$count" = "0" ]; thenecho -e " ${GREEN}✓${NC} $name"((TESTS_PASSED++)) || trueelseecho -e " ${RED}✗${NC} $name: $count violation(s)"((TESTS_FAILED++)) || truefi}# ── Counts ────────────────────────────────────────────────────────────────────echo "Table Counts:"echo " Datasets: $(cnt 'SELECT COUNT(*) AS cnt FROM dataset WHERE active = true')"echo " Locations: $(cnt 'SELECT COUNT(*) AS cnt FROM location WHERE active = true')"echo " Clusters: $(cnt 'SELECT COUNT(*) AS cnt FROM cluster WHERE active = true')"echo " Files: $(cnt 'SELECT COUNT(*) AS cnt FROM file WHERE active = true')"echo " File-Dataset: $(cnt 'SELECT COUNT(*) AS cnt FROM file_dataset')"echo " Segments: $(cnt 'SELECT COUNT(*) AS cnt FROM segment WHERE active = true')"echo " Labels: $(cnt 'SELECT COUNT(*) AS cnt FROM label WHERE active = true')"echo " Label subtypes: $(cnt 'SELECT COUNT(*) AS cnt FROM label_subtype WHERE active = true')"echo " Moth metadata: $(cnt 'SELECT COUNT(*) AS cnt FROM moth_metadata WHERE active = true')"echo " File metadata: $(cnt 'SELECT COUNT(*) AS cnt FROM file_metadata WHERE active = true')"echo " Label metadata: $(cnt 'SELECT COUNT(*) AS cnt FROM label_metadata WHERE active = true')"echo ""# ── Location hierarchy ────────────────────────────────────────────────────────echo "Location hierarchy:"check_zero "location.dataset_id → dataset" \"SELECT COUNT(*) AS cnt FROM location l LEFT JOIN dataset d ON l.dataset_id = d.id WHERE d.id IS NULL"check_zero "cluster.location_id → location" \"SELECT COUNT(*) AS cnt FROM cluster c LEFT JOIN location l ON c.location_id = l.id WHERE l.id IS NULL"check_zero "cluster.dataset_id → dataset" \"SELECT COUNT(*) AS cnt FROM cluster c LEFT JOIN dataset d ON c.dataset_id = d.id WHERE d.id IS NULL"check_zero "cluster.cyclic_recording_pattern_id → cyclic_recording_pattern" \"SELECT COUNT(*) AS cnt FROM cluster c LEFT JOIN cyclic_recording_pattern p ON c.cyclic_recording_pattern_id = p.id WHERE c.cyclic_recording_pattern_id IS NOT NULL AND p.id IS NULL"echo ""# ── File linkage ──────────────────────────────────────────────────────────────echo "File linkage:"check_zero "file.location_id → location" \"SELECT COUNT(*) AS cnt FROM file f LEFT JOIN location l ON f.location_id = l.id WHERE f.location_id IS NOT NULL AND l.id IS NULL"check_zero "file.cluster_id → cluster" \"SELECT COUNT(*) AS cnt FROM file f LEFT JOIN cluster c ON f.cluster_id = c.id WHERE f.cluster_id IS NOT NULL AND c.id IS NULL"check_zero "file_dataset.file_id → file" \"SELECT COUNT(*) AS cnt FROM file_dataset fd LEFT JOIN file f ON fd.file_id = f.id WHERE f.id IS NULL"check_zero "file_dataset.dataset_id → dataset" \"SELECT COUNT(*) AS cnt FROM file_dataset fd LEFT JOIN dataset d ON fd.dataset_id = d.id WHERE d.id IS NULL"check_zero "active files have file_dataset entry" \"SELECT COUNT(*) AS cnt FROM file f LEFT JOIN file_dataset fd ON f.id = fd.file_id WHERE f.active = true AND fd.file_id IS NULL"check_zero "file_dataset count >= active file count" \"SELECT CASE WHEN (SELECT COUNT(*) FROM file_dataset) >= (SELECT COUNT(*) FROM file WHERE active = true) THEN 0 ELSE 1 END AS cnt"check_zero "file_metadata.file_id → file" \"SELECT COUNT(*) AS cnt FROM file_metadata fm LEFT JOIN file f ON fm.file_id = f.id WHERE f.id IS NULL"echo ""# ── Segment integrity ─────────────────────────────────────────────────────────echo "Segment integrity:"check_zero "segment.file_id → file" \"SELECT COUNT(*) AS cnt FROM segment s LEFT JOIN file f ON s.file_id = f.id WHERE f.id IS NULL"check_zero "segment.dataset_id → dataset" \"SELECT COUNT(*) AS cnt FROM segment s LEFT JOIN dataset d ON s.dataset_id = d.id WHERE d.id IS NULL"check_zero "active segments on inactive files" \"SELECT COUNT(*) AS cnt FROM segment s JOIN file f ON s.file_id = f.id WHERE s.active = true AND f.active = false"echo ""# ── Label integrity ───────────────────────────────────────────────────────────echo "Label integrity:"check_zero "label.segment_id → segment" \"SELECT COUNT(*) AS cnt FROM label l LEFT JOIN segment s ON l.segment_id = s.id WHERE s.id IS NULL"check_zero "label.species_id → species" \"SELECT COUNT(*) AS cnt FROM label l LEFT JOIN species sp ON l.species_id = sp.id WHERE sp.id IS NULL"check_zero "label.filter_id → filter" \"SELECT COUNT(*) AS cnt FROM label l LEFT JOIN filter f ON l.filter_id = f.id WHERE f.id IS NULL"check_zero "active labels on inactive segments" \"SELECT COUNT(*) AS cnt FROM label l JOIN segment s ON l.segment_id = s.id WHERE l.active = true AND s.active = false"check_zero "label_metadata.label_id → label" \"SELECT COUNT(*) AS cnt FROM label_metadata lm LEFT JOIN label l ON lm.label_id = l.id WHERE l.id IS NULL"echo ""# ── Label subtype integrity ───────────────────────────────────────────────────echo "Label subtype integrity:"check_zero "label_subtype.label_id → label" \"SELECT COUNT(*) AS cnt FROM label_subtype ls LEFT JOIN label l ON ls.label_id = l.id WHERE l.id IS NULL"check_zero "label_subtype.calltype_id → call_type" \"SELECT COUNT(*) AS cnt FROM label_subtype ls LEFT JOIN call_type ct ON ls.calltype_id = ct.id WHERE ct.id IS NULL"check_zero "label_subtype.filter_id → filter" \"SELECT COUNT(*) AS cnt FROM label_subtype ls LEFT JOIN filter f ON ls.filter_id = f.id WHERE ls.filter_id IS NOT NULL AND f.id IS NULL"echo ""# ── Reference table integrity ─────────────────────────────────────────────────echo "Reference table integrity:"check_zero "call_type.species_id → species" \"SELECT COUNT(*) AS cnt FROM call_type ct LEFT JOIN species sp ON ct.species_id = sp.id WHERE sp.id IS NULL"echo ""# ── Summary ───────────────────────────────────────────────────────────────────echo "Summary: $TESTS_PASSED/$TESTS_RUN checks passed"if [ "$TESTS_FAILED" -gt 0 ]; thenexit 1fi
#!/bin/bash# Test skraak calls clip-labels# Compares output against reference CSVs in clip-labels_test_data/## Two test cases:# 1. Normal (OPSO-equivalent): output matches clip_labels_opso.csv# 2. __IGNORE__ mapping: D03 clips overlapping the ignored segment are excluded,# but the file is not dropped entirely## Note: removes clip_labels.csv and clip_labels_ignore.csv before each run# because the command appends and checks for duplicates.source "$(dirname "$0")/test_lib.sh"TEST_DIR="$SCRIPT_DIR/clip-labels_test_data"echo "=== Testing skraak calls clip-labels ==="echo ""check_binarycd "$TEST_DIR"# ── Test 1: OPSO-equivalent output ──────────────────────────────────────echo "Test 1: OPSO-equivalent output"rm -f ./clip_labels.csv"$PROJECT_DIR/skraak" calls clip-labels \--folder . --mapping ./mapping.json \--clip-duration 5 --clip-overlap 0 --min-label-overlap 0.25 --final-clip full \--output ./clip_labels.csv 2>/dev/null# Compare: sort both, skip headerdiff_output=$(diff <(tail -n +2 clip_labels_opso.csv | sort) \<(tail -n +2 clip_labels.csv | sort))if [ -z "$diff_output" ]; thenecho -e " ${GREEN}✓${NC} clip_labels.csv matches clip_labels_opso.csv (sorted, prefix-normalised)"((TESTS_PASSED++)) || trueelseecho -e " ${RED}✗${NC} clip_labels.csv differs from clip_labels_opso.csv"echo "$diff_output" | head -20((TESTS_FAILED++)) || truefi((TESTS_RUN++)) || true# ── Test 2: __IGNORE__ mapping ──────────────────────────────────────────echo "Test 2: __IGNORE__ mapping (D03 segment skipped, file kept)"rm -f ./clip_labels_ignore.csv"$PROJECT_DIR/skraak" calls clip-labels \--folder . --mapping ./mapping_ignore.json \--clip-duration 5 --clip-overlap 0 --min-label-overlap 0.25 --final-clip full \--output ./clip_labels_ignore.csv 2>/dev/null# With __IGNORE__, clips overlapping the Don't Know segment (777-860s)# in D03 are excluded, but D03's other clips are still emitted.# The non-D03 rows should be identical to opso.diff_output=$(diff <(grep -v "D03" clip_labels_opso.csv | sort) \<(grep -v "D03" clip_labels_ignore.csv | sort))if [ -z "$diff_output" ]; thenecho -e " ${GREEN}✓${NC} non-D03 rows match between ignore and opso"((TESTS_PASSED++)) || trueelseecho -e " ${RED}✗${NC} non-D03 rows differ between ignore and opso"echo "$diff_output" | head -20((TESTS_FAILED++)) || truefi((TESTS_RUN++)) || true# Verify D03 IS present in ignore output (file not dropped)if grep -q "D03" clip_labels_ignore.csv; thenecho -e " ${GREEN}✓${NC} D03 rows present in clip_labels_ignore.csv (file not dropped)"((TESTS_PASSED++)) || trueelseecho -e " ${RED}✗${NC} D03 rows missing from clip_labels_ignore.csv (file should be kept)"((TESTS_FAILED++)) || truefi((TESTS_RUN++)) || true# Verify D03 clips overlapping the __IGNORE__ segment (775-860s) are excludedd03_ignore=$(grep "D03" clip_labels_ignore.csv | wc -l)d03_opso=$(grep "D03" clip_labels_opso.csv | wc -l)if [ "$d03_ignore" -lt "$d03_opso" ]; thenecho -e " ${GREEN}✓${NC} D03 clips reduced: $d03_ignore in ignore vs $d03_opso in opso (overlapping clips excluded)"((TESTS_PASSED++)) || trueelseecho -e " ${RED}✗${NC} D03 clips not reduced: $d03_ignore in ignore vs $d03_opso in opso"((TESTS_FAILED++)) || truefi((TESTS_RUN++)) || true# Verify no D03 clips in the 775-860s range appear in ignore outputd03_in_range=$(grep "D03" clip_labels_ignore.csv | awk -F, '{split($2,a,"."); if ($2+0 >= 775 && $2+0 < 860) print}' | wc -l)if [ "$d03_in_range" -eq 0 ]; thenecho -e " ${GREEN}✓${NC} No D03 clips in 775-860s range (correctly excluded)"((TESTS_PASSED++)) || trueelseecho -e " ${RED}✗${NC} Found $d03_in_range D03 clips in 775-860s range (should be excluded)"((TESTS_FAILED++)) || truefi((TESTS_RUN++)) || trueecho ""print_summary
#!/bin/bash# Test script for: skraak calls from-preds# Compares output against reference JSON files (verified with Julia)## Usage: ./test_calls_from_preds.sh## Tests:# 1. predsST_opensoundscape-kiwi-1.2_2025-11-12.csv (single species: Kiwi)# 2. preds1_opensoundscape-multi-1.0_2025-07-22.csv (multi-species)## The calls array is compared as a SET (order-independent), matching# the Julia issetequal() verification used by the author.set -euo pipefail# Setup pathsSCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"PROJECT_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"DATA_DIR="$SCRIPT_DIR/data"# ColorsRED='\033[0;31m'GREEN='\033[0;32m'YELLOW='\033[1;33m'NC='\033[0m'# Test countersTESTS_RUN=0TESTS_PASSED=0TESTS_FAILED=0# Check binary existsif [ ! -f "$PROJECT_DIR/skraak" ]; thenecho -e "${RED}Error: skraak binary not found. Run 'go build' first.${NC}"exit 1fi# Compare calls arrays as sets (order-independent)# Returns 0 if equal, 1 if different# Usage: compare_calls_as_set <actual.json> <expected.json>compare_calls_as_set() {local actual="$1"local expected="$2"# Extract calls array and sort by all fields to get canonical order# Then compare as arrayslocal actual_sortedlocal expected_sortedactual_sorted=$(jq '(.calls // []) | sort_by(.file, .start_time, .end_time, .ebird_code, .segments)' "$actual" 2>/dev/null)expected_sorted=$(jq '(.calls // []) | sort_by(.file, .start_time, .end_time, .ebird_code, .segments)' "$expected" 2>/dev/null)if [ "$actual_sorted" = "$expected_sorted" ]; thenreturn 0elsereturn 1fi}# Compare metadata fields (clip_duration, gap_threshold, total_calls, species_count)# Returns 0 if all match, 1 if any differ# Usage: compare_metadata <actual.json> <expected.json>compare_metadata() {local actual="$1"local expected="$2"# Check each metadata fieldlocal clip_dur_act clip_dur_explocal gap_thr_act gap_thr_explocal total_act total_explocal species_act species_expclip_dur_act=$(jq -r '.clip_duration // "null"' "$actual")clip_dur_exp=$(jq -r '.clip_duration // "null"' "$expected")gap_thr_act=$(jq -r '.gap_threshold // "null"' "$actual")gap_thr_exp=$(jq -r '.gap_threshold // "null"' "$expected")total_act=$(jq -r '.total_calls // "null"' "$actual")total_exp=$(jq -r '.total_calls // "null"' "$expected")species_act=$(jq -r '.species_count' "$actual")species_exp=$(jq -r '.species_count' "$expected")local all_match=trueif [ "$clip_dur_act" != "$clip_dur_exp" ]; thenecho " clip_duration: expected=$clip_dur_exp, actual=$clip_dur_act"all_match=falsefiif [ "$gap_thr_act" != "$gap_thr_exp" ]; thenecho " gap_threshold: expected=$gap_thr_exp, actual=$gap_thr_act"all_match=falsefiif [ "$total_act" != "$total_exp" ]; thenecho " total_calls: expected=$total_exp, actual=$total_act"all_match=falsefiif [ "$species_act" != "$species_exp" ]; thenecho " species_count differs"all_match=falsefiif [ "$all_match" = true ]; thenreturn 0elsereturn 1fi}# Run a single test case# Usage: run_test <csv_name> <csv_path> <expected_json_path>run_test() {local name="$1"local csv_path="$2"local expected_json="$3"((TESTS_RUN++)) || trueecho ""echo "Testing: $name"echo " CSV: $(basename "$csv_path")"echo " Expected: $(basename "$expected_json")"# Create temp files for actual outputlocal actual_json stderr_outputactual_json=$(mktemp --suffix=.json)stderr_output=$(mktemp --suffix=.txt)# Run the command (capture stdout to file, stderr to variable)echo " Running: skraak calls from-preds --csv ..."if ! "$PROJECT_DIR/skraak" calls from-preds --csv "$csv_path" --dot-data=false --gap-multiplier 3 --min-detections 1 > "$actual_json" 2>"$stderr_output"; thenecho -e " ${RED}✗ Command failed${NC}"cat "$stderr_output"rm -f "$stderr_output"((TESTS_FAILED++)) || truereturnfi# Show progress from stderrcat "$stderr_output" | head -3rm -f "$stderr_output"# Check if output is valid JSONif ! jq empty "$actual_json" 2>/dev/null; thenecho -e " ${RED}✗ Output is not valid JSON${NC}"((TESTS_FAILED++)) || truereturnfi# Compare calls array as set (PRIMARY CHECK)local calls_match=falseif compare_calls_as_set "$actual_json" "$expected_json"; thencalls_match=truefi# Compare metadatalocal metadata_match=falselocal metadata_diff=""if compare_metadata "$actual_json" "$expected_json"; thenmetadata_match=truefi# Report resultsif [ "$calls_match" = true ]; thenecho -e " ${GREEN}✓ Calls array matches (set comparison)${NC}"# Show summary statslocal call_countcall_count=$(jq '.calls | length' "$actual_json")local species_countspecies_count=$(jq '.species_count | keys | length' "$actual_json")echo " $call_count calls across $species_count species"if [ "$metadata_match" = true ]; thenecho -e " ${GREEN}✓ Metadata matches${NC}"((TESTS_PASSED++)) || trueelseecho -e " ${YELLOW}⚠ Metadata differs (calls array is primary)${NC}"compare_metadata "$actual_json" "$expected_json"# Still count as passed since calls match((TESTS_PASSED++)) || truefielseecho -e " ${RED}✗ Calls array differs${NC}"# Show diff statslocal actual_count expected_countactual_count=$(jq '.calls | length' "$actual_json")expected_count=$(jq '.calls | length' "$expected_json")echo " Actual calls: $actual_count, Expected calls: $expected_count"# Find calls in expected but not in actual (skip for large arrays to avoid hang)if [ "$actual_count" -lt 10000 ] && [ "$expected_count" -lt 10000 ]; thenlocal missing extramissing=$(jq -n --slurpfile exp "$expected_json" --slurpfile act "$actual_json" \'([$exp[0].calls | .[] | {file, start_time, end_time, ebird_code, segments}] | sort) - ([$act[0].calls | .[] | {file, start_time, end_time, ebird_code, segments}] | sort) | length')extra=$(jq -n --slurpfile exp "$expected_json" --slurpfile act "$actual_json" \'([$act[0].calls | .[] | {file, start_time, end_time, ebird_code, segments}] | sort) - ([$exp[0].calls | .[] | {file, start_time, end_time, ebird_code, segments}] | sort) | length')echo " Missing from actual: $missing calls"echo " Extra in actual: $extra calls"elseecho " (skipping detailed diff — arrays too large)"fi((TESTS_FAILED++)) || truefi# Cleanup temp filesrm -f "$actual_json" "$stderr_output"}# Print summaryprint_summary() {echo ""echo "=== Summary ==="echo "Tests run: $TESTS_RUN"echo -e "Passed: ${GREEN}$TESTS_PASSED${NC}"if [ "$TESTS_FAILED" -gt 0 ]; thenecho -e "Failed: ${RED}$TESTS_FAILED${NC}"return 1elseecho -e "Failed: $TESTS_FAILED"return 0fi}# Mainecho "=== Testing: skraak calls from-preds ==="echo "Comparing calls arrays as SETS (order-independent)"# Test 1: predsST (kiwi single species)run_test \"predsST (single species: Kiwi)" \"$DATA_DIR/predsST_opensoundscape-kiwi-1.2_2025-11-12.csv" \"$DATA_DIR/predsST_opensoundscape-kiwi-1.2_2025-11-12.json"# Test 2: preds1 (multi-species)run_test \"preds1 (multi-species)" \"$DATA_DIR/preds1_opensoundscape-multi-1.0_2025-07-22.csv" \"$DATA_DIR/preds1_opensoundscape-multi-1.0_2025-07-22.json"print_summary
#!/bin/bash# Test bulk_file_import CLI command# Usage: ./test_bulk_import.sh [db_path]# Default: /home/david/go/src/skraak/db/test.duckdb (ALWAYS USE TEST DATABASE!)source "$(dirname "$0")/test_lib.sh"# Get absolute paths before changing directorySCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"PROJECT_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"DB_PATH="${1:-$PROJECT_DIR/db/test.duckdb}"if [ ! -f "$DB_PATH" ]; thenecho -e "${RED}Error: Database not found at $DB_PATH${NC}"exit 1fiecho "=== Testing bulk_file_import CLI Command ==="echo ""echo "Database: $DB_PATH"echo ""check_binary# Navigate to the project directory where skraak binary is locatedcd "$PROJECT_DIR" || exit 1# Helper to run CLI command and capture JSON outputrun_cli() {"$PROJECT_DIR/skraak" "$@" 2>/dev/null || true}run_cli_with_stderr() {"$PROJECT_DIR/skraak" "$@" 2>&1 || true}# Helper to check for error in CLI outputcli_is_error() {local output="$1"# CLI outputs errors to stderr with "Error:" prefixif echo "$output" | grep -q '"error"' 2>/dev/null; thenreturn 0fi# Also check for error in JSON outputif echo "$output" | jq -e '.error // empty' >/dev/null 2>&1; thenreturn 0fireturn 1}echo "Step 1: Create test dataset and locations"echo "------------------------------------------"# Create a test dataset using CLIecho -n "Creating test dataset... "DATASET_RESULT=$(run_cli create dataset --db "$DB_PATH" --name "Bulk Import Test Dataset" --type structured --description "Dataset for testing bulk import")DATASET_ID=$(echo "$DATASET_RESULT" | jq -r '.dataset.id // empty')if [ -n "$DATASET_ID" ]; thenecho -e "${GREEN}✓${NC} Created dataset: $DATASET_ID"elseecho -e "${RED}✗${NC} Failed to create dataset"echo "$DATASET_RESULT" | jq '.'exit 1fi# Create test location Aecho -n "Creating test location A... "LOCATION_A_RESULT=$(run_cli create location --db "$DB_PATH" --dataset "$DATASET_ID" --name "Test Location A" --lat -41.2865 --lon 174.7762 --timezone "Pacific/Auckland" --description "Test site A")LOCATION_A_ID=$(echo "$LOCATION_A_RESULT" | jq -r '.location.id // empty')if [ -n "$LOCATION_A_ID" ]; thenecho -e "${GREEN}✓${NC} Created location A: $LOCATION_A_ID"elseecho -e "${RED}✗${NC} Failed to create location A"echo "$LOCATION_A_RESULT" | jq '.'exit 1fi# Create test location Becho -n "Creating test location B... "LOCATION_B_RESULT=$(run_cli create location --db "$DB_PATH" --dataset "$DATASET_ID" --name "Test Location B" --lat -36.8485 --lon 174.7633 --timezone "Pacific/Auckland" --description "Test site B")LOCATION_B_ID=$(echo "$LOCATION_B_RESULT" | jq -r '.location.id // empty')if [ -n "$LOCATION_B_ID" ]; thenecho -e "${GREEN}✓${NC} Created location B: $LOCATION_B_ID"elseecho -e "${RED}✗${NC} Failed to create location B"echo "$LOCATION_B_RESULT" | jq '.'exit 1fiecho ""echo "Step 2: Create test CSV file"echo "-----------------------------"# Create test CSV with sample dataCSV_FILE="/tmp/test_bulk_import_$$.csv"LOG_FILE="/tmp/test_bulk_import_$$.log"cat > "$CSV_FILE" << EOFlocation_name,location_id,directory_path,date_range,sample_rate,file_countTest Location A,$LOCATION_A_ID,/nonexistent/path/a,2024-01,250000,0Test Location B,$LOCATION_B_ID,/nonexistent/path/b,2024-02,384000,0EOFecho -e "${GREEN}✓${NC} Created test CSV at $CSV_FILE"echo "Contents:"cat "$CSV_FILE"echo ""echo "Step 3: Test bulk_file_import CLI command"echo "------------------------------------------"# Note: Directories don't exist, so no files will be imported# This validates:# - CSV parsing# - Location ID validation# - Cluster auto-creation logic# - JSON output formatecho "Running bulk import (directories don't exist)..."IMPORT_RESULT=$(run_cli_with_stderr import bulk --db "$DB_PATH" --dataset "$DATASET_ID" --csv "$CSV_FILE" --log "$LOG_FILE")# Extract just the JSON output (last lines starting with {)JSON_OUTPUT=$(echo "$IMPORT_RESULT" | grep -A 100 '^{' | head -20)# Check for valid JSON output with expected structureFILES_IMPORTED=$(echo "$JSON_OUTPUT" | jq -r '.files_imported // empty' 2>/dev/null)if [ -n "$FILES_IMPORTED" ]; thenecho -e "${GREEN}✓${NC} Tool executed successfully"echo " Files imported: $FILES_IMPORTED"echo " Total locations: $(echo "$JSON_OUTPUT" | jq -r '.total_locations')"echo " Processing time: $(echo "$JSON_OUTPUT" | jq -r '.processing_time')"else# Check for errorif echo "$IMPORT_RESULT" | grep -qi "error"; thenecho -e "${YELLOW}?${NC} Tool returned error:"echo "$IMPORT_RESULT" | grep -i "error" | head -3elseecho -e "${RED}✗${NC} Unexpected result:"echo "$IMPORT_RESULT" | head -5fifiecho ""# Check if log file was createdif [ -f "$LOG_FILE" ]; thenecho -e "${GREEN}✓${NC} Log file created at $LOG_FILE"echo " Log entries: $(wc -l < "$LOG_FILE")"rm -f "$LOG_FILE"elseecho -e "${YELLOW}ℹ${NC} Log file not created (expected if no files processed)"fiecho ""echo "Step 4: Test validation - invalid CSV path"echo "-------------------------------------------"INVALID_CSV=$(run_cli_with_stderr import bulk --db "$DB_PATH" --dataset "$DATASET_ID" --csv "/nonexistent/file.csv" --log "$LOG_FILE")if echo "$INVALID_CSV" | grep -qi "error\|no such file\|not found\|not accessible"; thenecho -e "${GREEN}✓${NC} Correctly rejected non-existent CSV file"elseecho -e "${RED}✗${NC} Should have rejected non-existent CSV"echo "$INVALID_CSV" | head -3fiecho ""echo "Step 5: Test validation - invalid dataset ID"echo "---------------------------------------------"INVALID_DATASET=$(run_cli_with_stderr import bulk --db "$DB_PATH" --dataset "INVALID_ID_123" --csv "$CSV_FILE" --log "$LOG_FILE")if echo "$INVALID_DATASET" | grep -qi "error\|not found\|no such\|does not exist"; thenecho -e "${GREEN}✓${NC} Correctly rejected invalid dataset ID"elseecho -e "${RED}✗${NC} Should have rejected invalid dataset ID"echo "$INVALID_DATASET" | head -3fiecho ""echo "Step 6: Test validation - missing required flags"echo "-------------------------------------------------"MISSING_FLAGS=$(run_cli_with_stderr import bulk --db "$DB_PATH" --dataset "$DATASET_ID")if echo "$MISSING_FLAGS" | grep -qi "missing\|required"; thenecho -e "${GREEN}✓${NC} Correctly rejected missing required flags"elseecho -e "${RED}✗${NC} Should have rejected missing required flags"echo "$MISSING_FLAGS" | head -3fiecho ""echo "=== TEST SUMMARY ==="echo "Bulk import CLI command validation complete!"echo "Note: Directory errors are expected (using non-existent paths)"echo "The test validates CSV parsing and validation logic."echo ""# Cleanupecho "Cleaning up test files..."rm -f "$CSV_FILE" "$LOG_FILE"echo -e "${GREEN}✓${NC} Cleanup complete"echo ""
For OPSO equivalent output:```skraak calls clip-labels --folder . --mapping ./mapping.json \--clip-duration 5 --clip-overlap 0 --min-label-overlap 0.25 --final-clip full \--output ./clip_labels.csv```clip_labels.csv == clip_labels_opso.csv (reference file, is correct)For __IGNORE__```skraak calls clip-labels --folder . --mapping ./mapping_ignore.json \--clip-duration 5 --clip-overlap 0 --min-label-overlap 0.25 --final-clip full \--output ./clip_labels_ignore.csv```D03_2022-12-17_20221022_043000.wav should be ignored, but otherwise it should have the same data in it as clip_labels_opso.csv.
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2_181509.wav,40.0,45.0,False./TF_3-20200512_181509.wav,45.0,50.0,False./TF_3-20200512_181509.wav,50.0,55.0,False./TF_3-20200512_181509.wav,55.0,60.0,False./TF_3-20200512_181509.wav,60.0,65.0,False./TF_3-20200512_181509.wav,65.0,70.0,False./TF_3-20200512_181509.wav,70.0,75.0,False./TF_3-20200512_181509.wav,75.0,80.0,False./TF_3-20200512_181509.wav,80.0,85.0,False./TF_3-20200512_181509.wav,85.0,90.0,False./TF_3-20200512_181509.wav,90.0,95.0,False./TF_3-20200512_181509.wav,95.0,100.0,False./TF_3-20200512_181509.wav,100.0,105.0,False./TF_3-20200512_181509.wav,105.0,110.0,False./TF_3-20200512_181509.wav,110.0,115.0,False./TF_3-20200512_181509.wav,115.0,120.0,False./TF_3-20200512_181509.wav,120.0,125.0,False./TF_3-20200512_181509.wav,125.0,130.0,False./TF_3-20200512_181509.wav,130.0,135.0,False./TF_3-20200512_181509.wav,135.0,140.0,False./TF_3-20200512_181509.wav,140.0,145.0,False./TF_3-20200512_181509.wav,145.0,150.0,False./TF_3-20200512_181509.wav,150.0,155.0,False./TF_3-20200512_181509.wav,155.0,160.0,False./TF_3-20200512_181509.wav,160.0,165.0,False./TF_3-20200512_181509.wav,165.0,170.0,False./TF_3-20200512_181509.wav,170.0,175.0,False./TF_3-20200512_181509.wav,175.0,180.0,False./TF_3-20200512_181509.wav,180.0,185.0,False./TF_3-20200512_181509.wav,185.0,190.0,False./TF_3-20200512_181509.wav,190.0,195.0,False./TF_3-20200512_181509.wav,195.0,200.0,False./TF_3-20200512_181509.wav,200.0,205.0,False./TF_3-20200512_181509.wav,205.0,210.0,False./TF_3-20200512_181509.wav,210.0,215.0,False./TF_3-20200512_181509.wav,215.0,220.0,False./TF_3-20200512_181509.wav,220.0,225.0,False./TF_3-20200512_181509.wav,225.0,230.0,True./TF_3-20200512_181509.wav,230.0,235.0,True./TF_3-20200512_181509.wav,235.0,240.0,True./TF_3-20200512_181509.wav,240.0,245.0,True./TF_3-20200512_181509.wav,245.0,250.0,True./TF_3-20200512_181509.wav,250.0,255.0,True./TF_3-20200512_181509.wav,255.0,260.0,True./TF_3-20200512_181509.wav,260.0,265.0,True./TF_3-20200512_181509.wav,265.0,270.0,True./TF_3-20200512_181509.wav,270.0,275.0,False./TF_3-20200512_181509.wav,275.0,280.0,False./TF_3-20200512_181509.wav,280.0,285.0,False./TF_3-20200512_181509.wav,285.0,290.0,False./TF_3-20200512_181509.wav,290.0,295.0,False./TF_3-20200512_181509.wav,295.0,300.0,False./TF_3-20200512_181509.wav,300.0,305.0,False./TF_3-20200512_181509.wav,305.0,310.0,False./TF_3-20200512_181509.wav,310.0,315.0,False./TF_3-20200512_181509.wav,315.0,320.0,False./TF_3-20200512_181509.wav,320.0,325.0,False./TF_3-20200512_181509.wav,325.0,330.0,False./TF_3-20200512_181509.wav,330.0,335.0,False./TF_3-20200512_181509.wav,335.0,340.0,False./TF_3-20200512_181509.wav,340.0,345.0,False./TF_3-20200512_181509.wav,345.0,350.0,False./TF_3-20200512_181509.wav,350.0,355.0,False./TF_3-20200512_181509.wav,355.0,360.0,False./TF_3-20200512_181509.wav,360.0,365.0,False./TF_3-20200512_181509.wav,365.0,370.0,False./TF_3-20200512_181509.wav,370.0,375.0,False./TF_3-20200512_181509.wav,375.0,380.0,False./TF_3-20200512_181509.wav,380.0,385.0,False./TF_3-20200512_181509.wav,385.0,390.0,False./TF_3-20200512_181509.wav,390.0,395.0,True./TF_3-20200512_181509.wav,395.0,400.0,True./TF_3-20200512_181509.wav,400.0,405.0,True./TF_3-20200512_181509.wav,405.0,410.0,True./TF_3-20200512_181509.wav,410.0,415.0,True./TF_3-20200512_181509.wav,415.0,420.0,False./TF_3-20200512_181509.wav,420.0,425.0,False./TF_3-20200512_181509.wav,425.0,430.0,False./TF_3-20200512_181509.wav,430.0,435.0,False./TF_3-20200512_181509.wav,435.0,440.0,False./TF_3-20200512_181509.wav,440.0,445.0,False./TF_3-20200512_181509.wav,445.0,450.0,False./TF_3-20200512_181509.wav,450.0,455.0,False./TF_3-20200512_181509.wav,455.0,460.0,False./TF_3-20200512_181509.wav,460.0,465.0,False./TF_3-20200512_181509.wav,465.0,470.0,False./TF_3-20200512_181509.wav,470.0,475.0,False./TF_3-20200512_181509.wav,475.0,480.0,False./TF_3-20200512_181509.wav,480.0,485.0,False./TF_3-20200512_181509.wav,485.0,490.0,False./TF_3-20200512_181509.wav,490.0,495.0,False./TF_3-20200512_181509.wav,495.0,500.0,False./TF_3-20200512_181509.wav,500.0,505.0,False./TF_3-20200512_181509.wav,505.0,510.0,False./TF_3-20200512_181509.wav,510.0,515.0,False./TF_3-20200512_181509.wav,515.0,520.0,False./TF_3-20200512_181509.wav,520.0,525.0,False./TF_3-20200512_181509.wav,525.0,530.0,False./TF_3-20200512_181509.wav,530.0,535.0,False./TF_3-20200512_181509.wav,535.0,540.0,False./TF_3-20200512_181509.wav,540.0,545.0,False./TF_3-20200512_181509.wav,545.0,550.0,False./TF_3-20200512_181509.wav,550.0,555.0,False./TF_3-20200512_181509.wav,555.0,560.0,False./TF_3-20200512_181509.wav,560.0,565.0,False./TF_3-20200512_181509.wav,565.0,570.0,False./TF_3-20200512_181509.wav,570.0,575.0,False./TF_3-20200512_181509.wav,575.0,580.0,False./TF_3-20200512_181509.wav,580.0,585.0,False./TF_3-20200512_181509.wav,585.0,590.0,False./TF_3-20200512_181509.wav,590.0,595.0,False./TF_3-20200512_181509.wav,595.0,600.0,False./TF_3-20200512_181509.wav,600.0,605.0,False./TF_3-20200512_181509.wav,605.0,610.0,False./TF_3-20200512_181509.wav,610.0,615.0,False./TF_3-20200512_181509.wav,615.0,620.0,False./TF_3-20200512_181509.wav,620.0,625.0,False./TF_3-20200512_181509.wav,625.0,630.0,False./TF_3-20200512_181509.wav,630.0,635.0,False./TF_3-20200512_181509.wav,635.0,640.0,False./TF_3-20200512_181509.wav,640.0,645.0,False./TF_3-20200512_181509.wav,645.0,650.0,False./TF_3-20200512_181509.wav,650.0,655.0,False./TF_3-20200512_181509.wav,655.0,660.0,False./TF_3-20200512_181509.wav,660.0,665.0,False./TF_3-20200512_181509.wav,665.0,670.0,False./TF_3-20200512_181509.wav,670.0,675.0,False./TF_3-20200512_181509.wav,675.0,680.0,False./TF_3-20200512_181509.wav,680.0,685.0,False./TF_3-20200512_181509.wav,685.0,690.0,False./TF_3-20200512_181509.wav,690.0,695.0,False./TF_3-20200512_181509.wav,695.0,700.0,False./TF_3-20200512_181509.wav,700.0,705.0,False./TF_3-20200512_181509.wav,705.0,710.0,False./TF_3-20200512_181509.wav,710.0,715.0,False./TF_3-20200512_181509.wav,715.0,720.0,False./TF_3-20200512_181509.wav,720.0,725.0,False./TF_3-20200512_181509.wav,725.0,730.0,False./TF_3-20200512_181509.wav,730.0,735.0,False./TF_3-20200512_181509.wav,735.0,740.0,False./TF_3-20200512_181509.wav,740.0,745.0,False./TF_3-20200512_181509.wav,745.0,750.0,False./TF_3-20200512_181509.wav,750.0,755.0,False./TF_3-20200512_181509.wav,755.0,760.0,False./TF_3-20200512_181509.wav,760.0,765.0,False./TF_3-20200512_181509.wav,765.0,770.0,False./TF_3-20200512_181509.wav,770.0,775.0,False./TF_3-20200512_181509.wav,775.0,780.0,False./TF_3-20200512_181509.wav,780.0,785.0,False./TF_3-20200512_181509.wav,785.0,790.0,False./TF_3-20200512_181509.wav,790.0,795.0,False./TF_3-20200512_181509.wav,795.0,800.0,False./TF_3-20200512_181509.wav,800.0,805.0,False./TF_3-20200512_181509.wav,805.0,810.0,False./TF_3-20200512_181509.wav,810.0,815.0,False./TF_3-20200512_181509.wav,815.0,820.0,False./TF_3-20200512_181509.wav,820.0,825.0,False./TF_3-20200512_181509.wav,825.0,830.0,False./TF_3-20200512_181509.wav,830.0,835.0,False./TF_3-20200512_181509.wav,835.0,840.0,False./TF_3-20200512_181509.wav,840.0,845.0,False./TF_3-20200512_181509.wav,845.0,850.0,False./TF_3-20200512_181509.wav,850.0,855.0,False./TF_3-20200512_181509.wav,855.0,860.0,False./TF_3-20200512_181509.wav,860.0,865.0,False./TF_3-20200512_181509.wav,865.0,870.0,False./TF_3-20200512_181509.wav,870.0,875.0,False./TF_3-20200512_181509.wav,875.0,880.0,False./TF_3-20200512_181509.wav,880.0,885.0,False./TF_3-20200512_181509.wav,885.0,890.0,False./TF_3-20200512_181509.wav,890.0,895.0,False./TF_3-20200512_181509.wav,895.0,900.0,False./NB14-2024-05-05-20240125_054500-207-243.wav,0.0,5.0,False./NB14-2024-05-05-20240125_054500-207-243.wav,5.0,10.0,False./NB14-2024-05-05-20240125_054500-207-243.wav,10.0,15.0,False./NB14-2024-05-05-20240125_054500-207-243.wav,15.0,20.0,False./NB14-2024-05-05-20240125_054500-207-243.wav,20.0,25.0,False./NB14-2024-05-05-20240125_054500-207-243.wav,25.0,30.0,False./NB14-2024-05-05-20240125_054500-207-243.wav,30.0,35.0,False./NB14-2024-05-05-20240125_054500-207-243.wav,30.000124999999997,35.000125,False
Selection View Channel Begin Time (s) End Time (s) Low Freq (Hz) High Freq (Hz) Species Notes1 Spectrogram 1 1 390 413 100 7900 Kiwi2 Spectrogram 1 1 225 268 100 7900 Kiwi
Selection View Channel Begin Time (s) End Time (s) Low Freq (Hz) High Freq (Hz) Species Notes1 Spectrogram 1 1 0 36 100 7900 Not
Selection View Channel Begin Time (s) End Time (s) Low Freq (Hz) High Freq (Hz) Species Notes1 Spectrogram 1 1 777.7342008523894 860.2406016351827 1110.0 5242.0 LTC
# Testing the Skraak MCP Server## OverviewThe Skraak MCP Server provides 10 tools across three categories:- **Read tools (2)**: `get_current_time`, `execute_sql`- **Write tools (4)**: `create_or_update_dataset`, `create_or_update_location`, `create_or_update_cluster`, `create_or_update_pattern`- **Import tools (2 MCP)**: `import_audio_files`, `import_ml_selections`Plus schema resources.## Test ScriptsAll scripts are in `shell_scripts/` and follow a consistent pattern.### Read-Only Tests (No DB Modification)```bashcd shell_scripts# Time tool (no database needed)./test_time.sh# SQL queries and security validation./test_sql.sh# Schema resources./test_resources.sh# Database integrity check./test_db_state.sh```### Write Tests (Fresh DB Each Run)These tests create a fresh copy of `skraak.duckdb` in `/tmp` and clean up automatically.```bashcd shell_scripts# Create/update tools (dataset, location, cluster, pattern)./test_write_tools.sh# Import tools validation (error handling)./test_import.sh```## Test LibraryAll tests source `test_lib.sh` for shared functionality:```bashsource ./test_lib.sh# Send MCP requestresult=$(send_request "tools/call" '{"name":"execute_sql","arguments":{"query":"SELECT 1"}}')# Run test with automatic trackingrun_test "Test name" "true" "$result" # true = expect success# Print summaryprint_summary```### Key Functions| Function | Description ||----------|-------------|| `send_request <method> <params> [db]` | Send single MCP request || `send_requests <db> <req1> <req2>...` | Send multiple requests in one session || `run_test <name> <expect_pass> <result>` | Track test pass/fail || `get_result <response>` | Extract result from response || `is_error <response>` | Check if response is error || `fresh_test_db` | Create fresh test DB in /tmp || `cleanup_test_db <path>` | Remove test DB and temp files || `print_summary` | Print test counts |## Manual JSON-RPC TestingYou can test manually via stdin:```bash./skraak mcp --db ./db/test.duckdb```Then type JSON-RPC messages (one per line):### Initialize```json{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}```### List Tools```json{"jsonrpc":"2.0","id":2,"method":"tools/list","params":{}}```### Execute SQL```json{"jsonrpc":"2.0","id":3,"method":"tools/call","params":{"name":"execute_sql","arguments":{"query":"SELECT COUNT(*) FROM dataset WHERE active = true"}}}```### Create Dataset```json{"jsonrpc":"2.0","id":4,"method":"tools/call","params":{"name":"create_or_update_dataset","arguments":{"name":"Test Dataset","type":"test"}}}```### Get Schema Resource```json{"jsonrpc":"2.0","id":5,"method":"resources/read","params":{"uri":"schema://full"}}```## SQL Query Examples### Basic Queries```sql-- Active datasetsSELECT id, name, type FROM dataset WHERE active = true ORDER BY name-- Parameterized querySELECT id, name FROM location WHERE dataset_id = ? AND active = true-- With limitSELECT * FROM file WHERE active = true LIMIT 100```### JOINs```sql-- Dataset hierarchy with countsSELECT d.name, COUNT(l.id) as locations, COUNT(f.id) as filesFROM dataset dLEFT JOIN location l ON d.id = l.dataset_idLEFT JOIN cluster c ON l.id = c.location_idLEFT JOIN file f ON c.id = f.cluster_idWHERE d.active = trueGROUP BY d.name```### Aggregates```sql-- Cluster statisticsSELECT COUNT(*) as files, SUM(duration) as total_seconds, AVG(duration) as avg_secondsFROM file WHERE cluster_id = ? AND active = true```## Running Go Unit Tests```bash# All testsgo test ./...# Specific packagego test ./utils/# With coveragego test -cover ./...# Coverage reportgo test -coverprofile=coverage.out ./utils/go tool cover -html=coverage.out```**Test coverage**: 91.5% across 170+ tests## Troubleshooting| Issue | Solution ||-------|----------|| "skraak binary not found" | Run `go build` in project root || "Database not found" | Check path or use default || "Error: --db is required" | MCP command needs `--db path` || JSON parsing errors | Each message must be on one line || No response | Server outputs to stdout; check for errors in stderr || Test output too large | Tests print summary, not full output |## Best Practices1. **Run from shell_scripts directory**: Scripts use relative paths2. **Use test.duckdb for manual testing**: Never use skraak.duckdb3. **Write tests auto-clean**: They use /tmp and trap EXIT4. **Check exit codes**: Tests return 0 on success, 1 on failure5. **Run all tests before committing**: Ensures nothing is broken
# Shell Test ScriptsComprehensive test suite for the Skraak MCP Server.## Quick Start```bashcd shell_scripts# Run all tests (recommended)./test_time.sh && ./test_sql.sh && ./test_resources.sh && \./test_write_tools.sh && ./test_import.sh && ./test_db_state.sh && \./test_sql_limit.sh && ./test_export.sh && ./test_event_log.sh && \./test_calls_from_preds.sh# Or run individually./test_time.sh # Time tool (no DB needed)./test_sql.sh # SQL queries./test_resources.sh # Schema resources./test_write_tools.sh # Create/update tools (fresh DB)./test_import.sh # Import tools validation (fresh DB)./test_bulk_import.sh # Bulk import CLI validation (to be implemented)./test_db_state.sh # Database integrity check./test_sql_limit.sh # SQL row limit enforcement./test_export.sh # Dataset export (fresh DB) #######./test_event_log.sh # Transaction event logging./test_calls_from_preds.sh # Prediction file import```## Test Categories### Read-Only Tests (Safe, Repeatable)These tests read from the database and don't modify it. Run as many times as you want.| Script | Description | Default DB ||--------|-------------|------------|| `test_time.sh` | Test `get_current_time` tool | None || `test_sql.sh` | Test `execute_sql` queries, security | test.duckdb || `test_resources.sh` | Test schema resources | test.duckdb || `test_db_state.sh` | Verify database integrity | test.duckdb |### Write Tests (Fresh DB Each Run)These tests modify the database. They automatically create a fresh copy of the production database in `/tmp` and clean up afterward.| Script | Description | DB Handling ||--------|-------------|-------------|| `test_write_tools.sh` | Test `create_or_update_*` tools | Fresh DB in /tmp || `test_import.sh` | Test import tools validation | Fresh DB in /tmp || `test_bulk_import.sh` | Test bulk import CLI command | test.duckdb |## Database Safety- **Read-only tests**: Use `test.duckdb` (default) or specify path- **Write tests**: Automatically create fresh DB from `skraak.duckdb` → `/tmp/skraak_test_$$.duckdb`- **Never touches production**: Write tests are isolated## Test LibraryAll scripts source `test_lib.sh` which provides:- `send_request` - Send MCP request and get response- `run_test` - Run test with pass/fail tracking- `print_summary` - Print test results- `fresh_test_db` - Create fresh test database- `cleanup_test_db` - Clean up test database## Running Individual Tests```bash# With default test database./test_sql.sh# With specific database./test_sql.sh /path/to/database.duckdb# Write tests always use fresh DB (no argument needed)./test_write_tools.sh```## Expected OutputEach test prints:- Test names with ✓ (pass) or ✗ (fail)- Summary with counts- Exit code 0 on success, 1 on failure```=== Testing execute_sql Tool ===✓ Simple SELECT✓ SELECT with limit✓ Parameterized query✓ JOIN query✓ Aggregate query✓ CTE query✓ INSERT blocked (correctly rejected)✓ SQL injection blocked (correctly rejected)✓ DELETE blocked (correctly rejected)=== Summary ===Tests run: 9Passed: 9Failed: 0```## See Also- `TESTING.md` - Comprehensive testing documentation- `test_lib.sh` - Shared test functions
To Do=====Tomtit - GemmaGo through birdnet categories sample and try to work out what they areLoop through making changes, Ralph loopLook at kiwi datasetNew Datasettest database line update with index+fk v fk onlyRead audio tool (pointless atm as most models can't use it)Bounding Box script.pyto one hot encoded csv for opensoundscape (because python is so slow, and I would have to convert to raven selection.txt first)day -> civil sunrise to !!civil sunset!!claude --resume "reject-reserved-key-bindings"multi label in tui. How?? also cliClip from wav when no .data file—skraak save image????find morepork mewing sound for datasetsegment unstructured import into batches of 10000 files to keep within buffer limits, structured imports should be fine as we are talking 1 sd card (24/7 its 16000 max)ingest my training datasetsbuy a drive to backup mac ~Update tools could allow setting active to false?? Currently do notMake freebird to .data toolSKILLS======project/.claude/skills for most then link to project/.agents/skills for pi with:find .claude/skills -type f -exec bash -c 'mkdir -p "$(dirname ".agents/skills/${1#.claude/skills/}")" && ln -s "$PWD/$1" "$PWD/.agents/skills/${1#.claude/skills/}"' _ {} \;pi-specific are in ~ somewhere (ok because keeps them seperate) if installed with eg: $pi install npm:@tmustier/pi-ralph-wiggumcall-library: currently have a hard copy in .claude and .pi as I want to edit them in .piLabels in opensoundscape multi-species model=====================ausbit1 Australasian Bitternbluduc1 Blue Duckcomcha Common Chaffinchcomred Redpoll (Common)dunnoc1 Dunnockeurbla Eurasian Blackbirdeursta European Starlingfernbi1 New Zealand Fernbirdgrskiw1 Great Spotted Kiwi/Roroagryger1 Gray Gerygone/Grey Warblerkea1 Kealiskiw1 Little Spotted Kiwi/Kiwi pukupukulotkoe1 Long-tailed Koel/Cuckoomorepo2 Moreporknezbel1 New Zealand Bellbirdnezfan1 New Zealand Fantail/Piwakawakanezkak1 New Zealand Kakanezpig2 New Zealand Pigeon/Kererunezrob3 South Island Robin/Kakaruainibkiw1 North Island Brown Kiwi/Kiwi-nuiokbkiw1 Okarito Brown Kiwi/Rowiparake parakeet sp./Kakarikipipipi1 Pipipi/Brown Creeperriflem1 Riflemansaddle3 South Island Saddleback?Tiekeshbcuc1 Shining Bronze-Cuckoosilver3 Silvereyesobkiw2 Southern Brown Kiwi (South I.)/Tokoekasoioys1 South Island Oystercatchersoiwre1 South Island Wrensonthr1 Song Thrushspocra2 Spotless Craketomtit1 Tomtit/Miromirotui1 Tuivaroys1 Variable Oystercatcherweka1 Wekayellow2 Yellowhammerweta Weta (not bird)cangoo1 Canada Goose# Active DB Labels ebird_code------------------ ----------Australasian Bittern ausbit1 xBellbird nezbel1 xChaffinch comcha xCrake_Spotless spocra2 xCuckoo_Shining shbcuc1 xDuck_Blue_Whio bluduc1 xDunnock_Hedge_Sparrow dunnoc1 xEurasian Blackbird eurbla xEuropean Starling eursta xFantail nezfan1 xFernbird fernbi1 xHaast Tokoeka sobkiw2 xKaka nezkak1 xKea kea1 xKereru nezpig2 xKiwi pukupuku liskiw1 xKiwi_Nth_Is_Brown nibkiw1 xLong-tailed Koel lotkoe1 xMorepork morepo2 xOystercatcher_Variable varoys1 xParakeet parake xPipipi pipipi1 x Brown CreeperRedpoll comred xRifleman riflem1 xRobin_Sth_Is nezrob3 xRoroa grskiw1 xRowi okbkiw1 xS. Fiordland Tokoeka sobkiw1 xSaddleback_Sth_Is saddle3 xSilvereye silver3 xSouth Island Oystercatcher soioys1 xSouth Island Wren soiwre1 XThrush_Song sonthr1 xTomtit tomtit1 xTui tui1 xWarbler_Grey gryger1 xWeka_spp weka1 xYellowhammer yellow2 xCheckDon't KnowFake KiwiKorero Gecko xQuestionWeta xNoiseKeybindings===========see ~/.skraak/config.jsonTUI cmd=======skraak calls classify --folder . --filter opensoundscape-multi-1.0 --species comchaDavid's Kiwi Workflow=====================- cp data to main drives- backup audio- skraak import bulk to get files into db- Run opensoundscape models on audio- skraak calls from-preds to make .data files- Run julia DFMN model (also LSK model for Inge)- skraak calls classify TUI for kiwi on 1 model- use minimax to check "Don't Know"- skraak calls propogate on other models- use minimax on cert 70 Kiwi and maybe Don't Know- skraak calls classify on remaining cert 70 Kiwi- skraak calls classify --sample 10 on cert 90 Kiwi- skraak calls push-certainty on remaining cert 90 Kiwi if all good- use minimax skill /detect-anomalies to correct problems- skraak calls classify to resolve certainty mismatches- skraak calls summarise- run skill /data-mapping- run skill /import-segmentsCode stuff==========time ./skraak calls from-preds --csv /media/david/SSD4/Twenty_Four_Seven/R620/2024-05-06/preds9_opensoundscape-multi-1.0_2025-07-22.csv > /media/david/SSD4/Twenty_Four_Seven/R620/2024-05-06/preds9_opensoundscape-multi-1.0_2025-07-22.jsonfor item in atryjsonfile = replace(item, ".csv" => ".json")run(pipeline(`skraak calls from-preds --csv $item --gap-multiplier 3 --min-detections 1`, jsonfile))catch e@error "skraak failed on $item" exception=(e, catch_backtrace())endendmodel = "/media/david/SSD2/Secondary_Models/DFMN_Inge/model_DFMN1-5_CPU_epoch-9-0.9737-2024-10-25.jld2"labels = Dict(1 => "Duet", 2 => "Female", 3 => "Male", 4 => "Don't Know")## Check this logic in the codepredict(a, model, labels)model = "/media/david/SSD2/Secondary_Models/LSK/model_GSK_LSK_DFM_FT_IngeDFMN_1-5_1-0_CPU_epoch-9-0.9745-2025-01-13.jld2"labels = Dict(1 => "GSK", 2 => "GSK", 3 => "GSK", 4 => "LSK", 5 => "LSK", 6 => "LSK")## Needed to change the logicpredict(a, model, labels)model = "/media/david/SSD2/Secondary_Models/DFMN_Pomona/model_DFMN1-5_Pomona3_CPU_epoch-18-0.9785-2025-03-02.jld2"labels = Dict(1 => "Duet", 2 => "Female", 3 => "Gecko", 4 => "Male", 5 => "Don't Know")## Check this logic in the codepredict(a, model, labels)## Change the datefor item in xtryjsonfile = "$item/segment_summary_2026-04-19.json"run(pipeline(`skraak calls summarise --folder $item`, jsonfile))catch e@error "skraak failed on $item" exception=(e, catch_backtrace())endendskraak calls summarise --folder ./recordings --brief# print brief summary to replfor item in atryrun(pipeline(`skraak calls summarise --folder $item --brief`))catch e@error "skraak failed on $item" exception=(e, catch_backtrace())endend# save brief summary to cwdopen("/home/david/summary_2026-04-17.jsonl", "w") do ffor item in atryrun(pipeline(`skraak calls summarise --folder $item`, `jq 'del(.segments)'`, f))catch e@error "skraak failed on $item" exception=(e, catch_backtrace())endendendOLLAMA======ollama run gemma4:e4bollama launch pi --model gemma4:e4b # don't do this, it alters pi configollama run qwen3.5:9b # uninstalledollama listollama rm <model-name>ollama rm qwen3.5:9bR620/2024-05-06 onlyRun Through GemmaOpensoundscape Hand Classified BirdNET Hand Classified============== =============== ======= ===============comcha X X Xeurbla X X Xgryger1 X X none? X White-throated Sparrow (auto), Gray Gerygonenezfan1 X X NZ Fantailtomtit1 V. Bad garbage Xnezrob1 X X SI Robin (no types)kereruriflemansilvereyebellbirdtuinezkak1 V. Bad(gecko, wing) V Bad, ongoing bellbirdweka1 V. Bad(noise) nonemorepo2 many Gecko Also Geckolotkoe1 X X X┌──────┬───────────────────────────┬───────┐│ Rank │ Species │ Count │├──────┼───────────────────────────┼───────┤│ 1 │ White-throated Sparrow │ 5163 │ Gryger├──────┼───────────────────────────┼───────┤│ 2 │ New Zealand Bellbird │ 3812 │├──────┼───────────────────────────┼───────┤│ 3 │ Superb Lyrebird │ 3645 │ nezbel1+territorial├──────┼───────────────────────────┼───────┤│ 4 │ Common Crossbill │ 3247 │├──────┼───────────────────────────┼───────┤│ 5 │ Javan Shortwing │ 2824 │├──────┼───────────────────────────┼───────┤│ 6 │ Grey Gerygone │ 2286 │ Gryger├──────┼───────────────────────────┼───────┤│ 7 │ Yellow-bellied Flycatcher │ 1018 │├──────┼───────────────────────────┼───────┤│ 8 │ Tui │ 1004 │├──────┼───────────────────────────┼───────┤│ 9 │ Common Redpoll │ 949 │├──────┼───────────────────────────┼───────┤│ 10 │ Winter Wren │ 932 │├──────┼───────────────────────────┼───────┤│ 11 │ Blue-backed Manakin │ 784 │├──────┼───────────────────────────┼───────┤│ 12 │ Hermit Thrush │ 762 │├──────┼───────────────────────────┼───────┤│ 13 │ Blue Whistling-Thrush │ 728 │├──────┼───────────────────────────┼───────┤│ 14 │ Eastern Wood-Pewee │ 712 │├──────┼───────────────────────────┼───────┤│ 15 │ Common Nightingale │ 678 │├──────┼───────────────────────────┼───────┤│ 16 │ Red-breasted Flycatcher │ 678 │├──────┼───────────────────────────┼───────┤│ 17 │ New Zealand Kaka │ 639 │├──────┼───────────────────────────┼───────┤│ 18 │ Common Firecrest │ 608 │├──────┼───────────────────────────┼───────┤│ 19 │ New Zealand Fantail │ 583 │ X├──────┼───────────────────────────┼───────┤│ 20 │ Tomtit │ 570 │ X├──────┼───────────────────────────┼───────┤│ 21 │ Eurasian Golden Oriole │ 548 │├──────┼───────────────────────────┼───────┤│ 22 │ Musician Wren │ 526 │├──────┼───────────────────────────┼───────┤│ 23 │ White-browed Warbler │ 497 │├──────┼───────────────────────────┼───────┤│ 24 │ Cedar Waxwing │ 487 │├──────┼───────────────────────────┼───────┤│ 25 │ Iberian Chiffchaff │ 473 │├──────┼───────────────────────────┼───────┤│ 26 │ Common Redstart │ 461 │├──────┼───────────────────────────┼───────┤│ 27 │ European Greenfinch │ 454 │├──────┼───────────────────────────┼───────┤│ 28 │ Wood Thrush │ 432 │├──────┼───────────────────────────┼───────┤│ 29 │ Pheasant Cuckoo │ 427 │├──────┼───────────────────────────┼───────┤│ 30 │ Western Wood-Pewee │ 399 │└──────┴───────────────────────────┴───────┘skraak calls summarise --folder . > call_summary.json# mapping.json for my big kiwi dataset{"Kiwi": {"species": "Kiwi"},"Geese": {"species": "__NEGATIVE__"},"Kaka": {"species": "__NEGATIVE__"},"Kea": {"species": "__NEGATIVE__"},"LTC": {"species": "__NEGATIVE__"},"Morepork": {"species": "__NEGATIVE__"},"Not": {"species": "__NEGATIVE__"},"Plover": {"species": "__NEGATIVE__"}}# make csv to use for training big kiwi datasetskraak calls clip-labels --folder . --mapping ./mapping.json \--clip-duration 5 --clip-overlap 0 --min-label-overlap 0.25 --final-clip full \--output ./clip_labels.csvLets manually execute this loop once, when we are happy we will design a ralph loop together to loop through remaining BirdNET classes /grill-me# Retrieve BirdNET List from folder /media/david/SSD4/Twenty_Four_Seven/R620/2024-05-06/skraak calls summarise --folder /media/david/SSD4/Twenty_Four_Seven/R620/2024-05-06/ --brief --filter BirdNET 2>/dev/null | jq -r '.filters.BirdNET.species | to_entries | map(select(.key | test("^[A-Z]"))) | sort_by(.value) | .[] | "\(.value)\t\(.key)"'Start from the top of the BirdNET List and attempt to label a BirdNET class with one of the classes below using skill /call-classification, /call-classification-ollama, /call-libraryWhile there is only a few segments in the BirdNET class, attempt to do this yourself reading data from /call-classification, /call-library. It is your role to work out what this class actually is (BirdNET mislabels many New Zealand Birds), and to assign correct labels wherever possibleWhen there are many segments in a BirdNET class use skill /call-classification-ollama. choose your reference images carefully. It is your role to work out what this class actually is (BirdNET mislabels many New Zealand Birds), then to use gemma to do the heavy lifting. If Gemma does a poor job of it, it is likely you have chosen the wrong species class.Keep a .md document with your mappings, BirdNET => code as belowCommon Bird List for R620=========================comcha Chaffincheurbla Blackbirdgryger1 Grey Warblerkea1 Kealotkoe1 Long-tailed Cuckoomorepo2 Moreporknezbel1 Bellbirdnezfan1 Fantailnezkak1 Kakanezpig2 Kererunezrob3 Kakaruaipipipi1 Pipipiriflem1 Riflemansaddle3 Tiekesilver3 Silvereyesobkiw2 Fiordland Tokoekasoioys1 Pied Oystercatchertomtit1 Tomtittui1 Tuiyefpar3 Kakarikiweta Wetagecko Korero GeckoYou have access to skills /pi-ralph-wiggum to loop through the BirdNET list, and pi-heartbeat, to set a timer.Lets manually execute this loop once, when we are happy we will design a ralph loop together to loop through remaining BirdNET classes /grill-meCategory A - Direct/Obvious Mappings┌──────────────────────┬────────┬─────────┬───────────────────────────────────────┐│ BirdNET │ Count │ Code │ Notes │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ New Zealand Bellbird │ 3,812 │ nezbel1 │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Grey Gerygone │ 2,286 │ gryger1 │ BirdNET's name for Grey Warbler │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Tui │ 1,004 │ tui1 │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ New Zealand Kaka │ 603 │ nezkak1 │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Morepork │ 287 │ morepo2 │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Silvereye │ 248 │ silver3 │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Pipipi │ 79 │ pipipi1 │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Long-tailed Koel │ 47 │ lotkoe1 │ BirdNET's name for Long-tailed Cuckoo │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Eurasian Blackbird │ 27 │ eurbla │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ North Island Robin │ 132 │ nezrob3 │ Robin = Kakaruai │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ European Robin │ 124 │ nezrob3 │ Same species │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Dunnock │ 89 │ dunnoc1 │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Song Thrush │ 173 │ sonthr1 │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Common Redpoll │ 949 │ comred │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Common Starling │ 1 │ eursta │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Yellowhammer │ 4 │ yellow2 │ Exact match │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ House Sparrow │ 36 │ — │ House Sparrow not on R620 common list │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Common Magpie │ 320 │ — │ Magpie not on R620 common list │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Eurasian Skylark │ 5 │ — │ Not on R620 list │├──────────────────────┼────────┼─────────┼───────────────────────────────────────┤│ Total │ ~9,779 │ │ │└──────────────────────┴────────┴─────────┴───────────────────────────────────────┘────────────────────────────────────────────────────────────────────────────────Category B - Real Mislabels (need classification)These are BirdNET labels that don't match any NZ species name, and the segments are actually NZbirds:┌─────────────────────────────────────┬─────────┬─────────────────────────────────┬──────────┐│ BirdNET │ Count │ Suspected Code(s) │ Priority │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Common Crossbill │ 3,247 │ comred? comcha? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Javan Shortwing │ 2,824 │ tomtit1? nezrob3? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Yellow-bellied Flycatcher │ 1,018 │ nezfan1? tomtit1? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Winter Wren │ 932 │ pipipi1? riflem1? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Blue-backed Manakin │ 784 │ riflem1? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Hermit Thrush │ 762 │ eurbla? sonthr1? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Blue Whistling-Thrush │ 728 │ eurbla? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Eastern Wood-Pewee │ 712 │ tomtit1? nezfan1? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Common Nightingale │ 678 │ nezrob3? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Red-breasted Flycatcher │ 678 │ tomtit1? nezfan1? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Common Firecrest │ 608 │ silver3? riflem1? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Eurasian Golden Oriole │ 548 │ tui1? nezbel1? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Musician Wren │ 526 │ pipipi1? │ 🔴 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ White-browed Warbler │ 497 │ gryger1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Cedar Waxwing │ 487 │ eursta? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Iberian Chiffchaff │ 473 │ gryger1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Common Redstart │ 461 │ nezrob3? tomtit1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ European Greenfinch │ 454 │ comcha? comred? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Wood Thrush │ 432 │ eurbla? sonthr1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Pheasant Cuckoo │ 427 │ lotkoe1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Western Wood-Pewee │ 399 │ tomtit1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Greater Racket-tailed Drongo │ 376 │ ? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ White-eared Honeyeater │ 358 │ nezbel1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Broad-winged Hawk │ 351 │ Harrier? (not on list) │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Northern Pygmy-Owl │ 347 │ morepo2? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Black-capped Chickadee │ 345 │ ? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Bartlett's Tinamou │ 344 │ ? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Northern Saw-whet Owl │ 344 │ morepo2? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Varied Thrush │ 332 │ eurbla? sonthr1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Black-faced Antthrush │ 330 │ ? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Lesser Redpoll │ 324 │ comred │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Goldcrest │ 298 │ silver3? riflem1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Eurasian Pygmy-Owl │ 286 │ morepo2? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Common Chiffchaff │ 280 │ gryger1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Eurasian Siskin │ 270 │ comred? comcha? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ White-throated Gerygone │ 263 │ gryger1? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Two-barred Crossbill │ 262 │ comred? comcha? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Grey Shrikethrush │ 260 │ ? │ 🟡 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Little Friarbird │ 166 │ nezbel1? │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Great Tit │ 165 │ tomtit1? │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Golden-bellied Gerygone │ 161 │ gryger1? │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Red Wattlebird │ 151 │ nezbel1? │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Common Kingfisher │ 133 │ — (Kingfisher not on R620 list) │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Rufous Whistler │ 11 │ ? │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Rock Wren │ 15 │ — (Rock Wren not on R620 list) │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Nightingale Wren │ 159 │ ? │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Little Spiderhunter │ 117 │ ? │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ ... and ~1,400 more with count < 10 │ │ │ 🟢 │├─────────────────────────────────────┼─────────┼─────────────────────────────────┼──────────┤│ Total │ ~38,000 │ │ │└─────────────────────────────────────┴─────────┴─────────────────────────────────┴──────────┘
package mainimport ("fmt""os""skraak/cmd")func main() {if len(os.Args) < 2 {printUsage()os.Exit(1)}switch os.Args[1] {case "import":cmd.RunImport(os.Args[2:])case "sql":cmd.RunSQL(os.Args[2:])case "create":cmd.RunCreate(os.Args[2:])case "update":cmd.RunUpdate(os.Args[2:])// Legacy commands removed - use create/update instead// case "dataset":// cmd.RunDataset(os.Args[2:])// case "location":// cmd.RunLocation(os.Args[2:])// case "cluster":// cmd.RunCluster(os.Args[2:])// case "pattern":// cmd.RunPattern(os.Args[2:])case "export":cmd.RunExport(os.Args[2:])case "replay":cmd.RunReplay(os.Args[2:])case "calls":cmd.RunCalls(os.Args[2:])case "xxhash":cmd.RunXXHash(os.Args[2:])case "metadata":cmd.RunMetadata(os.Args[2:])case "time":cmd.RunTime(os.Args[2:])case "isnight":cmd.RunIsNight(os.Args[2:])case "prepend":cmd.RunPrepend(os.Args[2:])default:fmt.Fprintf(os.Stderr, "Unknown command: %s\n\n", os.Args[1])printUsage()os.Exit(1)}}// printUsage displays command-line usage information for all available commandsfunc printUsage() {fmt.Fprintf(os.Stderr, "Usage: %s <command> [options]\n\n", os.Args[0])fmt.Fprintf(os.Stderr, "Commands:\n")fmt.Fprintf(os.Stderr, " sql Execute SQL query\n")fmt.Fprintf(os.Stderr, " calls Extract/analyze bird calls (from-preds, from-brida, from-raven, show-images, classify, summarise)\n")fmt.Fprintf(os.Stderr, " create Create a new resource (dataset, location, cluster, pattern)\n")fmt.Fprintf(os.Stderr, " update Update an existing resource (dataset, location, cluster, pattern)\n")fmt.Fprintf(os.Stderr, " import Import data (folder, bulk, unstructured, segments)\n")fmt.Fprintf(os.Stderr, " export Export dataset to new database\n")fmt.Fprintf(os.Stderr, " replay Replay event log into database\n")fmt.Fprintf(os.Stderr, " xxhash Compute XXH64 hash of a file\n")fmt.Fprintf(os.Stderr, " metadata Extract WAV file metadata\n")fmt.Fprintf(os.Stderr, " time Get current time\n")fmt.Fprintf(os.Stderr, " isnight Check if WAV file was recorded at night\n")fmt.Fprintf(os.Stderr, " prepend Prepend prefix to WAV files and log.txt\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " %s sql --db ./db/skraak.duckdb \"SELECT COUNT(*) FROM file WHERE active = true\"\n", os.Args[0])fmt.Fprintf(os.Stderr, " %s create dataset --db ./db/skraak.duckdb --name \"Test Dataset\"\n", os.Args[0])fmt.Fprintf(os.Stderr, " %s update location --db ./db/skraak.duckdb --id loc123 --name \"New Name\"\n", os.Args[0])fmt.Fprintf(os.Stderr, " %s export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb\n", os.Args[0])fmt.Fprintf(os.Stderr, " %s replay events --db ./backup.duckdb --log ./skraak.duckdb.events.jsonl\n", os.Args[0])fmt.Fprintf(os.Stderr, " %s calls from-preds --csv predictions.csv > calls.json\n", os.Args[0])fmt.Fprintf(os.Stderr, " %s xxhash --file recording.wav\n", os.Args[0])fmt.Fprintf(os.Stderr, " %s metadata --file recording.wav\n", os.Args[0])fmt.Fprintf(os.Stderr, " %s time\n", os.Args[0])fmt.Fprintf(os.Stderr, " %s isnight --file recording.wav --lat -36.85 --lng 174.76\n", os.Args[0])}
package mainimport ("os/exec""testing")func TestGolangciLint(t *testing.T) {cmd := exec.Command("golangci-lint", "run", "./...")cmd.Dir = "."out, err := cmd.CombinedOutput()if err != nil {t.Errorf("golangci-lint failed:\n%s", out)}}func TestGoFmt(t *testing.T) {cmd := exec.Command("go", "fmt", "./...")cmd.Dir = "."out, err := cmd.CombinedOutput()if err != nil {t.Errorf("go fmt failed: %v\n%s", err, out)}if len(out) > 0 {t.Errorf("go fmt produced output (files needed formatting). Run 'go fmt ./...' to fix:\n%s", out)}}func TestDeadcode(t *testing.T) {cmd := exec.Command("deadcode", "./...")cmd.Dir = "."out, err := cmd.CombinedOutput()if err != nil {t.Errorf("deadcode failed:\n%s", out)}}
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h1:FN3SvrM+Zdj16jyLfmOkMNblXMcoc8DfTHruCPUcx88=github.com/sixdouglas/suncalc v0.0.0-20250114185126-291b1938b70c h1:Lyrtmwq1VO3vK30KXmA4S4u816l/HqyT11d75WR0UiU=github.com/sixdouglas/suncalc v0.0.0-20250114185126-291b1938b70c/go.mod h1:IxOCrQX3pAL52wPiWuamnWxGcuyWANPyQfwcRb0iDqc=github.com/stretchr/testify v1.11.1 h1:7s2iGBzp5EwR7/aIZr8ao5+dra3wiQyKjjFuvgVKu7U=github.com/stretchr/testify v1.11.1/go.mod h1:wZwfW3scLgRK+23gO65QZefKpKQRnfz6sD981Nm4B6U=github.com/xo/terminfo v0.0.0-20220910002029-abceb7e1c41e h1:JVG44RsyaB9T2KIHavMF/ppJZNG9ZpyihvCd0w101no=github.com/xo/terminfo v0.0.0-20220910002029-abceb7e1c41e/go.mod h1:RbqR21r5mrJuqunuUZ/Dhy/avygyECGrLceyNeo4LiM=github.com/zeebo/assert v1.3.0 h1:g7C04CbJuIDKNPFHmsk4hwZDO5O+kntRxzaUoNXj+IQ=github.com/zeebo/assert v1.3.0/go.mod h1:Pq9JiuJQpG8JLJdtkwrJESF0Foym2/D9XMU5ciN/wJ0=github.com/zeebo/xxh3 v1.1.0 h1:s7DLGDK45Dyfg7++yxI0khrfwq9661w9EN78eP/UZVs=github.com/zeebo/xxh3 v1.1.0/go.mod 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module skraakgo 1.26.0require (charm.land/bubbletea/v2 v2.0.6charm.land/lipgloss/v2 v2.0.3github.com/cespare/xxhash/v2 v2.3.0github.com/charmbracelet/x/ansi v0.11.7github.com/duckdb/duckdb-go/v2 v2.10502.0github.com/ebitengine/oto/v3 v3.4.0github.com/madelynnblue/go-dsp v1.0.0github.com/matoous/go-nanoid/v2 v2.1.0github.com/sixdouglas/suncalc v0.0.0-20250114185126-291b1938b70c)require (github.com/apache/arrow-go/v18 v18.5.1 // indirectgithub.com/bits-and-blooms/bitset v1.24.4 // indirectgithub.com/charmbracelet/colorprofile v0.4.3 // indirectgithub.com/charmbracelet/ultraviolet v0.0.0-20260416155717-489999b90468 // indirectgithub.com/charmbracelet/x/term v0.2.2 // indirectgithub.com/charmbracelet/x/termios v0.1.1 // indirectgithub.com/charmbracelet/x/windows v0.2.2 // indirectgithub.com/clipperhouse/displaywidth v0.11.0 // indirectgithub.com/clipperhouse/uax29/v2 v2.7.0 // indirectgithub.com/duckdb/duckdb-go-bindings v0.10502.0 // indirectgithub.com/duckdb/duckdb-go-bindings/lib/darwin-amd64 v0.10502.0 // indirectgithub.com/duckdb/duckdb-go-bindings/lib/darwin-arm64 v0.10502.0 // indirectgithub.com/duckdb/duckdb-go-bindings/lib/linux-amd64 v0.10502.0 // indirectgithub.com/duckdb/duckdb-go-bindings/lib/linux-arm64 v0.10502.0 // indirectgithub.com/duckdb/duckdb-go-bindings/lib/windows-amd64 v0.10502.0 // indirectgithub.com/ebitengine/purego v0.9.0 // indirectgithub.com/go-viper/mapstructure/v2 v2.5.0 // indirectgithub.com/goccy/go-json v0.10.5 // indirectgithub.com/google/flatbuffers v25.12.19+incompatible // indirectgithub.com/google/go-cmp v0.7.0 // indirectgithub.com/google/uuid v1.6.0 // indirectgithub.com/klauspost/compress v1.18.3 // indirectgithub.com/klauspost/cpuid/v2 v2.3.0 // indirectgithub.com/lucasb-eyer/go-colorful v1.4.0 // indirectgithub.com/mattn/go-runewidth v0.0.23 // indirectgithub.com/muesli/cancelreader v0.2.2 // indirectgithub.com/pierrec/lz4/v4 v4.1.25 // indirectgithub.com/rivo/uniseg v0.4.7 // indirectgithub.com/xo/terminfo v0.0.0-20220910002029-abceb7e1c41e // indirectgithub.com/zeebo/xxh3 v1.1.0 // indirectgolang.org/x/exp v0.0.0-20260112195511-716be5621a96 // indirectgolang.org/x/mod v0.33.0 // indirectgolang.org/x/sync v0.20.0 // indirectgolang.org/x/sys v0.43.0 // indirectgolang.org/x/telemetry v0.0.0-20260209163413-e7419c687ee4 // indirectgolang.org/x/tools v0.42.0 // indirectgolang.org/x/xerrors v0.0.0-20240903120638-7835f813f4da // indirect)
package dbimport ("encoding/json""time")// DatasetType represents the dataset_type enum from the schematype DatasetType string// Dataset type enum constantsconst (DatasetTypeStructured DatasetType = "structured"DatasetTypeUnstructured DatasetType = "unstructured"DatasetTypeTest DatasetType = "test"DatasetTypeTrain DatasetType = "train")// Dataset represents a row from the dataset tabletype Dataset struct {ID string `json:"id"`Name string `json:"name"`Description *string `json:"description"` // Pointer for nullable fieldCreatedAt time.Time `json:"created_at"`LastModified time.Time `json:"last_modified"`Active bool `json:"active"`Type DatasetType `json:"type"`}// MarshalJSON implements custom JSON marshaling for Dataset// Formats timestamps as RFC3339func (d Dataset) MarshalJSON() ([]byte, error) {return json.Marshal(&struct {ID string `json:"id"`Name string `json:"name"`Description *string `json:"description"`CreatedAt string `json:"created_at"`LastModified string `json:"last_modified"`Active bool `json:"active"`Type DatasetType `json:"type"`}{ID: d.ID,Name: d.Name,Description: d.Description,CreatedAt: d.CreatedAt.Format(time.RFC3339),LastModified: d.LastModified.Format(time.RFC3339),Active: d.Active,Type: d.Type,})}// Location represents a row from the location tabletype Location struct {ID string `json:"id"`DatasetID string `json:"dataset_id"`Name string `json:"name"`Latitude float64 `json:"latitude"`Longitude float64 `json:"longitude"`Description *string `json:"description"` // nullableCreatedAt time.Time `json:"created_at"`LastModified time.Time `json:"last_modified"`Active bool `json:"active"`TimezoneID string `json:"timezone_id"`}// MarshalJSON implements custom JSON marshaling for Location// Formats timestamps as RFC3339func (l Location) MarshalJSON() ([]byte, error) {return json.Marshal(&struct {ID string `json:"id"`DatasetID string `json:"dataset_id"`Name string `json:"name"`Latitude float64 `json:"latitude"`Longitude float64 `json:"longitude"`Description *string `json:"description"`CreatedAt string `json:"created_at"`LastModified string `json:"last_modified"`Active bool `json:"active"`TimezoneID string `json:"timezone_id"`}{ID: l.ID,DatasetID: l.DatasetID,Name: l.Name,Latitude: l.Latitude,Longitude: l.Longitude,Description: l.Description,CreatedAt: l.CreatedAt.Format(time.RFC3339),LastModified: l.LastModified.Format(time.RFC3339),Active: l.Active,TimezoneID: l.TimezoneID,})}// Cluster represents a row from the cluster tabletype Cluster struct {ID string `json:"id"`DatasetID string `json:"dataset_id"`LocationID string `json:"location_id"`Name string `json:"name"`Description *string `json:"description"` // nullableCreatedAt time.Time `json:"created_at"`LastModified time.Time `json:"last_modified"`Active bool `json:"active"`CyclicRecordingPatternID *string `json:"cyclic_recording_pattern_id"` // nullableSampleRate int `json:"sample_rate"`}// MarshalJSON implements custom JSON marshaling for Cluster// Formats timestamps as RFC3339func (c Cluster) MarshalJSON() ([]byte, error) {return json.Marshal(&struct {ID string `json:"id"`DatasetID string `json:"dataset_id"`LocationID string `json:"location_id"`Name string `json:"name"`Description *string `json:"description"`CreatedAt string `json:"created_at"`LastModified string `json:"last_modified"`Active bool `json:"active"`CyclicRecordingPatternID *string `json:"cyclic_recording_pattern_id"`SampleRate int `json:"sample_rate"`}{ID: c.ID,DatasetID: c.DatasetID,LocationID: c.LocationID,Name: c.Name,Description: c.Description,CreatedAt: c.CreatedAt.Format(time.RFC3339),LastModified: c.LastModified.Format(time.RFC3339),Active: c.Active,CyclicRecordingPatternID: c.CyclicRecordingPatternID,SampleRate: c.SampleRate,})}// File represents a row from the file tabletype File struct {ID string `json:"id"`FileName string `json:"file_name"`Path *string `json:"path"` // nullableXXH64Hash string `json:"xxh64_hash"`LocationID string `json:"location_id"`TimestampLocal time.Time `json:"timestamp_local"`ClusterID *string `json:"cluster_id"` // nullableDuration float64 `json:"duration"`SampleRate int `json:"sample_rate"`Description *string `json:"description"` // nullableMaybeSolarNight *bool `json:"maybe_solar_night"` // nullableMaybeCivilNight *bool `json:"maybe_civil_night"` // nullableMoonPhase *float64 `json:"moon_phase"` // nullableCreatedAt time.Time `json:"created_at"`LastModified time.Time `json:"last_modified"`Active bool `json:"active"`}// CyclicRecordingPattern represents a row from the cyclic_recording_pattern tabletype CyclicRecordingPattern struct {ID string `json:"id"`RecordS int `json:"record_s"`SleepS int `json:"sleep_s"`CreatedAt time.Time `json:"created_at"`LastModified time.Time `json:"last_modified"`Active bool `json:"active"`}// MarshalJSON implements custom JSON marshaling for CyclicRecordingPattern// Formats timestamps as RFC3339func (p CyclicRecordingPattern) MarshalJSON() ([]byte, error) {return json.Marshal(&struct {ID string `json:"id"`RecordS int `json:"record_s"`SleepS int `json:"sleep_s"`CreatedAt string `json:"created_at"`LastModified string `json:"last_modified"`Active bool `json:"active"`}{ID: p.ID,RecordS: p.RecordS,SleepS: p.SleepS,CreatedAt: p.CreatedAt.Format(time.RFC3339),LastModified: p.LastModified.Format(time.RFC3339),Active: p.Active,})}// GainLevel represents the gain_level enum for AudioMoth recordingstype GainLevel string// AudioMoth gain level enum constantsconst (GainLow GainLevel = "low"GainLowMedium GainLevel = "low-medium"GainMedium GainLevel = "medium"GainMediumHigh GainLevel = "medium-high"GainHigh GainLevel = "high")// MothMetadata represents a row from the moth_metadata tabletype MothMetadata struct {FileID string `json:"file_id"`Timestamp time.Time `json:"timestamp"`RecorderID *string `json:"recorder_id"` // nullableGain *GainLevel `json:"gain"` // nullableBatteryV *float64 `json:"battery_v"` // nullableTempC *float64 `json:"temp_c"` // nullableCreatedAt time.Time `json:"created_at"`LastModified time.Time `json:"last_modified"`Active bool `json:"active"`}// FileDataset represents a row from the file_dataset junction tabletype FileDataset struct {FileID string `json:"file_id"`DatasetID string `json:"dataset_id"`CreatedAt time.Time `json:"created_at"`LastModified time.Time `json:"last_modified"`}
package dbimport ("bytes""context""database/sql""encoding/json""os""path/filepath""reflect""strings""testing""time")// =============================================================================// Test Helpers// =============================================================================// resetGlobalState resets package-level variables for test isolation.func resetGlobalState() {eventLogMu.Lock()defer eventLogMu.Unlock()if eventLogFile != nil {eventLogFile.Close()eventLogFile = nileventLogEnc = nil}eventLogConfig = EventLogConfig{}}// setupTestDB creates an in-memory DuckDB with a test table.func setupTestDB(t *testing.T) *sql.DB {t.Helper()db, err := sql.Open("duckdb", "")if err != nil {t.Fatalf("Failed to open in-memory DuckDB: %v", err)}_, err = db.Exec("CREATE TABLE test_table (id VARCHAR PRIMARY KEY, name VARCHAR, value INTEGER)")if err != nil {db.Close()t.Fatalf("Failed to create test table: %v", err)}return db}// readEventsFile reads all events from a JSONL file.func readEventsFile(path string) ([]TransactionEvent, error) {data, err := os.ReadFile(path)if err != nil {return nil, err}var events []TransactionEventfor line := range bytes.SplitSeq(data, []byte("\n")) {if len(line) == 0 {continue}var event TransactionEventif err := json.Unmarshal(line, &event); err != nil {return nil, err}events = append(events, event)}return events, nil}// Assertion helpers using standard libraryfunc assertEqual(t *testing.T, expected, actual any, msg ...string) {t.Helper()if !reflect.DeepEqual(expected, actual) {if len(msg) > 0 {t.Errorf("%s: expected %v, got %v", msg[0], expected, actual)} else {t.Errorf("expected %v, got %v", expected, actual)}}}func assertNil(t *testing.T, value any, msg ...string) {t.Helper()if value != nil && !isTypedNil(value) {if len(msg) > 0 {t.Errorf("%s: expected nil, got %v", msg[0], value)} else {t.Errorf("expected nil, got %v", value)}}}// isTypedNil checks if a value is a typed nil (e.g., *os.File(nil))func isTypedNil(v any) bool {if v == nil {return true}// Use reflection to check for typed nilrv := reflect.ValueOf(v)switch rv.Kind() {case reflect.Chan, reflect.Func, reflect.Map, reflect.Pointer, reflect.Slice:return rv.IsNil()}return false}func assertNotNil(t *testing.T, value any, msg ...string) {t.Helper()if value == nil {if len(msg) > 0 {t.Errorf("%s: expected non-nil value", msg[0])} else {t.Errorf("expected non-nil value")}}}func assertTrue(t *testing.T, value bool, msg ...string) {t.Helper()if !value {if len(msg) > 0 {t.Errorf("%s: expected true, got false", msg[0])} else {t.Errorf("expected true, got false")}}}func assertFalse(t *testing.T, value bool, msg ...string) {t.Helper()if value {if len(msg) > 0 {t.Errorf("%s: expected false, got true", msg[0])} else {t.Errorf("expected false, got true")}}}func assertError(t *testing.T, err error, msg ...string) {t.Helper()if err == nil {if len(msg) > 0 {t.Errorf("%s: expected error, got nil", msg[0])} else {t.Errorf("expected error, got nil")}}}func assertNoError(t *testing.T, err error, msg ...string) {t.Helper()if err != nil {if len(msg) > 0 {t.Errorf("%s: expected no error, got %v", msg[0], err)} else {t.Errorf("expected no error, got %v", err)}}}func assertLen(t *testing.T, expected, actual int, msg ...string) {t.Helper()if expected != actual {if len(msg) > 0 {t.Errorf("%s: expected length %d, got %d", msg[0], expected, actual)} else {t.Errorf("expected length %d, got %d", expected, actual)}}}func assertContains(t *testing.T, s, substr string, msg ...string) {t.Helper()if !strings.Contains(s, substr) {if len(msg) > 0 {t.Errorf("%s: expected %q to contain %q", msg[0], s, substr)} else {t.Errorf("expected %q to contain %q", s, substr)}}}func assertGreater(t *testing.T, a, b int64, msg ...string) {t.Helper()if a <= b {if len(msg) > 0 {t.Errorf("%s: expected %d > %d", msg[0], a, b)} else {t.Errorf("expected %d > %d", a, b)}}}// =============================================================================// Category 1: Pure Function Tests// =============================================================================func TestIsMutation(t *testing.T) {tests := []struct {name stringsql stringexpected bool}{// INSERT variations{"INSERT uppercase", "INSERT INTO test VALUES (1)", true},{"INSERT lowercase", "insert into test values (1)", true},{"INSERT with leading space", " INSERT INTO test VALUES (1)", true},{"INSERT with leading newline", "\n\tINSERT INTO test VALUES (1)", true},// Note: SQL with leading comment is not detected as mutation// because isMutation checks HasPrefix after TrimSpace, and "--" is not INSERT/UPDATE/DELETE// UPDATE variations{"UPDATE uppercase", "UPDATE test SET x = 1", true},{"UPDATE lowercase", "update test set x = 1", true},{"UPDATE with WHERE", "UPDATE test SET x = 1 WHERE id = 1", true},// DELETE variations{"DELETE uppercase", "DELETE FROM test WHERE x = 1", true},{"DELETE lowercase", "delete from test where x = 1", true},// SELECT (not mutation){"SELECT uppercase", "SELECT * FROM test", false},{"SELECT lowercase", "select * from test", false},{"SELECT with WHERE", "SELECT * FROM test WHERE id = 1", false},// WITH clause (CTE) with mutation{"CTE with INSERT", "WITH cte AS (SELECT 1) INSERT INTO test SELECT * FROM cte", true},{"CTE with UPDATE", "WITH cte AS (SELECT 1) UPDATE test SET x = 1", true},{"CTE with DELETE", "WITH cte AS (SELECT 1) DELETE FROM test", true},{"CTE lowercase with insert", "with cte as (select 1) insert into test select * from cte", true},// WITH clause (CTE) without mutation{"CTE with SELECT only", "WITH cte AS (SELECT 1) SELECT * FROM cte", false},{"CTE lowercase with select", "with cte as (select 1) select * from cte", false},// Edge cases{"empty string", "", false},{"whitespace only", " ", false},{"just SELECT keyword", "SELECT", false},{"just INSERT keyword", "INSERT", true},{"just UPDATE keyword", "UPDATE", true},{"just DELETE keyword", "DELETE", true},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {result := isMutation(tt.sql)assertEqual(t, tt.expected, result, "isMutation(%q)", tt.sql)})}}func TestMarshalParam(t *testing.T) {t.Run("nil", func(t *testing.T) {result := marshalParam(nil)assertNil(t, result)})t.Run("time.Time", func(t *testing.T) {tm := time.Date(2026, 2, 18, 14, 30, 0, 0, time.UTC)result := marshalParam(tm)assertEqual(t, "2026-02-18T14:30:00Z", result)})t.Run("*time.Time nil", func(t *testing.T) {var tm *time.Timeresult := marshalParam(tm)assertNil(t, result)})t.Run("*time.Time with value", func(t *testing.T) {tm := time.Date(2026, 2, 18, 14, 30, 0, 123456789, time.UTC)result := marshalParam(&tm)assertEqual(t, "2026-02-18T14:30:00.123456789Z", result)})t.Run("time.Time with nanoseconds", func(t *testing.T) {tm := time.Date(2026, 2, 18, 14, 30, 0, 999999999, time.UTC)result := marshalParam(tm)assertEqual(t, "2026-02-18T14:30:00.999999999Z", result)})t.Run("time.Time with timezone", func(t *testing.T) {loc, _ := time.LoadLocation("Pacific/Auckland")tm := time.Date(2026, 2, 19, 10, 30, 0, 0, loc)result := marshalParam(tm)// Should contain timezone offsetassertContains(t, result.(string), "+13:00")})t.Run("string", func(t *testing.T) {result := marshalParam("hello world")assertEqual(t, "hello world", result)})t.Run("*string nil", func(t *testing.T) {var s *stringresult := marshalParam(s)assertNil(t, result)})t.Run("*string with value", func(t *testing.T) {s := "hello"result := marshalParam(&s)assertEqual(t, "hello", result)})t.Run("int types", func(t *testing.T) {assertEqual(t, int(42), marshalParam(int(42)))assertEqual(t, int8(42), marshalParam(int8(42)))assertEqual(t, int16(42), marshalParam(int16(42)))assertEqual(t, int32(42), marshalParam(int32(42)))assertEqual(t, int64(42), marshalParam(int64(42)))assertEqual(t, uint(42), marshalParam(uint(42)))assertEqual(t, uint8(42), marshalParam(uint8(42)))assertEqual(t, uint16(42), marshalParam(uint16(42)))assertEqual(t, uint32(42), marshalParam(uint32(42)))assertEqual(t, uint64(42), marshalParam(uint64(42)))})t.Run("*int nil", func(t *testing.T) {var p *intresult := marshalParam(p)assertNil(t, result)})t.Run("*int with value", func(t *testing.T) {v := 42result := marshalParam(&v)assertEqual(t, 42, result)})t.Run("*int64 nil", func(t *testing.T) {var p *int64result := marshalParam(p)assertNil(t, result)})t.Run("*int64 with value", func(t *testing.T) {v := int64(1234567890123)result := marshalParam(&v)assertEqual(t, int64(1234567890123), result)})t.Run("negative int", func(t *testing.T) {assertEqual(t, int(-42), marshalParam(int(-42)))assertEqual(t, int64(-42), marshalParam(int64(-42)))})t.Run("float types", func(t *testing.T) {assertEqual(t, float32(3.14), marshalParam(float32(3.14)))assertEqual(t, float64(3.14), marshalParam(float64(3.14)))})t.Run("*float64 nil", func(t *testing.T) {var p *float64result := marshalParam(p)assertNil(t, result)})t.Run("*float64 with value", func(t *testing.T) {v := 3.14159result := marshalParam(&v)assertEqual(t, 3.14159, result)})t.Run("*float32 nil", func(t *testing.T) {var p *float32result := marshalParam(p)assertNil(t, result)})t.Run("*float32 with value", func(t *testing.T) {v := float32(2.71)result := marshalParam(&v)assertEqual(t, float32(2.71), result)})t.Run("bool", func(t *testing.T) {assertEqual(t, true, marshalParam(true))assertEqual(t, false, marshalParam(false))})t.Run("*bool nil", func(t *testing.T) {var p *boolresult := marshalParam(p)assertNil(t, result)})t.Run("*bool with true", func(t *testing.T) {v := trueresult := marshalParam(&v)assertEqual(t, true, result)})t.Run("*bool with false", func(t *testing.T) {v := falseresult := marshalParam(&v)assertEqual(t, false, result)})t.Run("[]byte", func(t *testing.T) {b := []byte("hello")result := marshalParam(b)assertEqual(t, b, result)})t.Run("unknown type", func(t *testing.T) {type MyType struct{ X int }result := marshalParam(MyType{X: 42})// fmt.Sprintf("%v", MyType{X: 42}) produces "{42}"assertContains(t, result.(string), "42")})t.Run("named type alias (like GainLevel)", func(t *testing.T) {type GainLevel stringg := GainLevel("medium")result := marshalParam(g)// Named type aliases fall through to default caseassertEqual(t, "medium", result)})t.Run("pointer to named type alias", func(t *testing.T) {type GainLevel stringg := GainLevel("high")// Pointer to named type also falls through to defaultresult := marshalParam(&g)// Should serialize the value, not the pointer addressassertEqual(t, "high", result)})t.Run("slice", func(t *testing.T) {s := []string{"a", "b", "c"}result := marshalParam(s)assertEqual(t, "[a b c]", result)})t.Run("map", func(t *testing.T) {m := map[string]int{"a": 1}result := marshalParam(m)assertContains(t, result.(string), "a")})}func TestQueryRecordMarshalJSON(t *testing.T) {t.Run("basic types", func(t *testing.T) {qr := QueryRecord{SQL: "INSERT INTO test VALUES (?, ?)",Parameters: []any{"id123", 42},}data, err := json.Marshal(qr)assertNoError(t, err)var result map[string]anyerr = json.Unmarshal(data, &result)assertNoError(t, err)assertEqual(t, "INSERT INTO test VALUES (?, ?)", result["sql"])params := result["parameters"].([]any)assertEqual(t, "id123", params[0])assertEqual(t, 42.0, params[1]) // JSON numbers are floats})t.Run("with time.Time", func(t *testing.T) {tm := time.Date(2026, 2, 18, 14, 30, 0, 0, time.UTC)qr := QueryRecord{SQL: "INSERT INTO test VALUES (?)",Parameters: []any{tm},}data, err := json.Marshal(qr)assertNoError(t, err)var result map[string]anyerr = json.Unmarshal(data, &result)assertNoError(t, err)params := result["parameters"].([]any)assertEqual(t, "2026-02-18T14:30:00Z", params[0])})t.Run("with nil parameter", func(t *testing.T) {qr := QueryRecord{SQL: "INSERT INTO test VALUES (?)",Parameters: []any{nil},}data, err := json.Marshal(qr)assertNoError(t, err)var result map[string]anyerr = json.Unmarshal(data, &result)assertNoError(t, err)params := result["parameters"].([]any)assertNil(t, params[0])})t.Run("empty parameters", func(t *testing.T) {qr := QueryRecord{SQL: "SELECT 1",Parameters: []any{},}data, err := json.Marshal(qr)assertNoError(t, err)var result map[string]anyerr = json.Unmarshal(data, &result)assertNoError(t, err)params := result["parameters"].([]any)assertLen(t, 0, len(params))})t.Run("multiple param types", func(t *testing.T) {qr := QueryRecord{SQL: "INSERT INTO test VALUES (?, ?, ?, ?, ?)",Parameters: []any{"string", 42, true, nil, 3.14},}data, err := json.Marshal(qr)assertNoError(t, err)var result map[string]anyerr = json.Unmarshal(data, &result)assertNoError(t, err)params := result["parameters"].([]any)assertLen(t, 5, len(params))assertEqual(t, "string", params[0])assertEqual(t, 42.0, params[1])assertEqual(t, true, params[2])assertNil(t, params[3])assertEqual(t, 3.14, params[4])})t.Run("special characters in SQL", func(t *testing.T) {qr := QueryRecord{SQL: "INSERT INTO test VALUES ('O''Brien', \"test\")",Parameters: []any{},}data, err := json.Marshal(qr)assertNoError(t, err)// Verify JSON is validvar result map[string]anyerr = json.Unmarshal(data, &result)assertNoError(t, err)assertContains(t, result["sql"].(string), "O''Brien")})t.Run("unicode in parameters", func(t *testing.T) {qr := QueryRecord{SQL: "INSERT INTO test VALUES (?)",Parameters: []any{"日本語 🎵"},}data, err := json.Marshal(qr)assertNoError(t, err)var result map[string]anyerr = json.Unmarshal(data, &result)assertNoError(t, err)params := result["parameters"].([]any)assertEqual(t, "日本語 🎵", params[0])})}// =============================================================================// Category 2: Global State Tests// =============================================================================func TestSetEventLogConfig(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("set enabled with path", func(t *testing.T) {resetGlobalState()cfg := EventLogConfig{Enabled: true,Path: "/tmp/test.jsonl",}SetEventLogConfig(cfg)got := GetEventLogConfig()assertTrue(t, got.Enabled)assertEqual(t, "/tmp/test.jsonl", got.Path)})t.Run("set disabled", func(t *testing.T) {resetGlobalState()cfg := EventLogConfig{Enabled: false,Path: "/tmp/test.jsonl",}SetEventLogConfig(cfg)got := GetEventLogConfig()assertFalse(t, got.Enabled)})t.Run("change path while file open", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()path1 := filepath.Join(tmpDir, "events1.jsonl")path2 := filepath.Join(tmpDir, "events2.jsonl")// Set first config and open fileSetEventLogConfig(EventLogConfig{Enabled: true, Path: path1})ensureEventLogFile()assertNotNil(t, eventLogFile)// Change path - should close first fileSetEventLogConfig(EventLogConfig{Enabled: true, Path: path2})// File handle should be nil (will reopen on next ensure)// Note: SetEventLogConfig closes the file, sets eventLogFile = nilassertNil(t, eventLogFile)})}func TestGetEventLogConfig(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("default state", func(t *testing.T) {resetGlobalState()got := GetEventLogConfig()assertFalse(t, got.Enabled)assertEqual(t, "", got.Path)})t.Run("after set", func(t *testing.T) {resetGlobalState()SetEventLogConfig(EventLogConfig{Enabled: true, Path: "/test/path.jsonl"})got := GetEventLogConfig()assertTrue(t, got.Enabled)assertEqual(t, "/test/path.jsonl", got.Path)})}func TestCloseEventLog(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("close with no file", func(t *testing.T) {resetGlobalState()err := CloseEventLog()assertNoError(t, err)})t.Run("close with open file", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})ensureEventLogFile()assertNotNil(t, eventLogFile)err := CloseEventLog()assertNoError(t, err)// Verify state is resetassertFalse(t, eventLogConfig.Enabled)assertNil(t, eventLogFile)assertNil(t, eventLogEnc)})t.Run("double close", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})ensureEventLogFile()err := CloseEventLog()assertNoError(t, err)// Second close should not panicerr = CloseEventLog()assertNoError(t, err)})}// =============================================================================// Category 3: Integration Tests// =============================================================================func TestBeginLoggedTx(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("creates transaction", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, err := BeginLoggedTx(context.Background(), db, "test_tool")assertNoError(t, err)assertNotNil(t, tx)assertEqual(t, "test_tool", tx.toolName)assertNotNil(t, tx.queries)assertLen(t, 0, len(tx.queries))assertFalse(t, tx.startTime.IsZero())tx.Rollback()})t.Run("empty tool name is allowed", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, err := BeginLoggedTx(context.Background(), db, "")assertNoError(t, err)assertNotNil(t, tx)assertEqual(t, "", tx.toolName)tx.Rollback()})t.Run("initial state is clean", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")assertLen(t, 0, len(tx.queries))assertFalse(t, tx.startTime.IsZero())// Verify startTime is recent (within last second)elapsed := time.Since(tx.startTime)assertTrue(t, elapsed < time.Second, "startTime should be recent")tx.Rollback()})}func TestLoggedTx_ExecContext(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("records INSERT", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()_, err := tx.ExecContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)", "id1", "name1", 42)assertNoError(t, err)assertLen(t, 1, len(tx.queries))assertContains(t, tx.queries[0].SQL, "INSERT")assertLen(t, 3, len(tx.queries[0].Parameters))assertEqual(t, "id1", tx.queries[0].Parameters[0])})t.Run("records UPDATE", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id2", "name2", 1)_, err := tx.ExecContext(context.Background(),"UPDATE test_table SET value = ? WHERE id = ?", 100, "id2")assertNoError(t, err)assertLen(t, 2, len(tx.queries))assertContains(t, tx.queries[1].SQL, "UPDATE")tx.Rollback()})t.Run("records DELETE", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id3", "name3", 1)_, err := tx.ExecContext(context.Background(),"DELETE FROM test_table WHERE id = ?", "id3")assertNoError(t, err)assertLen(t, 2, len(tx.queries))assertContains(t, tx.queries[1].SQL, "DELETE")tx.Rollback()})t.Run("does not record SELECT", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id4", "name4", 1)// SELECT should not be recordedtx.QueryRowContext(context.Background(), "SELECT * FROM test_table WHERE id = ?", "id4")assertLen(t, 1, len(tx.queries)) // Only the INSERTtx.Rollback()})t.Run("does not record failed execution", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()// This will fail (table doesn't exist)_, err := tx.ExecContext(context.Background(),"INSERT INTO nonexistent_table VALUES (?)", "x")assertError(t, err)assertLen(t, 0, len(tx.queries)) // Failed query not recorded})t.Run("multiple executions recorded in order", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id1", "name1", 1)tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id2", "name2", 2)tx.ExecContext(context.Background(), "UPDATE test_table SET value = ? WHERE id = ?", 99, "id1")assertLen(t, 3, len(tx.queries))assertContains(t, tx.queries[0].SQL, "INSERT")assertContains(t, tx.queries[1].SQL, "INSERT")assertContains(t, tx.queries[2].SQL, "UPDATE")})t.Run("parameters stored correctly", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()tx.ExecContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)", "param_id", "param_name", 123)assertLen(t, 3, len(tx.queries[0].Parameters))assertEqual(t, "param_id", tx.queries[0].Parameters[0])assertEqual(t, "param_name", tx.queries[0].Parameters[1])assertEqual(t, 123, tx.queries[0].Parameters[2])})}func TestLoggedTx_Exec(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("INSERT without context", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()_, err := tx.Exec("INSERT INTO test_table VALUES (?, ?, ?)", "id1", "name1", 42)assertNoError(t, err)assertLen(t, 1, len(tx.queries))assertContains(t, tx.queries[0].SQL, "INSERT")})}func TestLoggedTx_Commit(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("writes event to file on commit", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test_tool")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id1", "name1", 42)err := tx.Commit()assertNoError(t, err)// Verify event was writtenevents, err := readEventsFile(logPath)assertNoError(t, err)assertLen(t, 1, len(events))assertNotNil(t, events[0].ID)assertLen(t, 21, len(events[0].ID))assertEqual(t, "test_tool", events[0].Tool)assertLen(t, 1, len(events[0].Queries))assertTrue(t, events[0].Success)// Duration may be 0 for very fast transactionsassertTrue(t, events[0].Duration >= 0)})t.Run("does not write when logging disabled", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: false, Path: logPath})db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test_tool")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id2", "name2", 1)err := tx.Commit()assertNoError(t, err)// No file should be created_, err = os.Stat(logPath)assertTrue(t, os.IsNotExist(err), "file should not exist")})t.Run("does not write when no mutations", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test_tool")// No mutations, just readstx.QueryRowContext(context.Background(), "SELECT 1")err := tx.Commit()assertNoError(t, err)// No file should be created_, err = os.Stat(logPath)assertTrue(t, os.IsNotExist(err), "file should not exist")})t.Run("multiple mutations in single event", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "multi_test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "m1", "name1", 1)tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "m2", "name2", 2)tx.ExecContext(context.Background(), "UPDATE test_table SET value = ? WHERE id = ?", 99, "m1")err := tx.Commit()assertNoError(t, err)events, err := readEventsFile(logPath)assertNoError(t, err)assertLen(t, 1, len(events))assertLen(t, 3, len(events[0].Queries))})t.Run("data persisted after commit", func(t *testing.T) {resetGlobalState()db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "persist_test", "name", 42)tx.Commit()var count interr := db.QueryRow("SELECT COUNT(*) FROM test_table WHERE id = ?", "persist_test").Scan(&count)assertNoError(t, err)assertEqual(t, 1, count)})t.Run("event has valid timestamp", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "ts_test", "name", 1)tx.Commit()events, _ := readEventsFile(logPath)// Timestamp should be recent (within last 5 seconds)elapsed := time.Since(events[0].Timestamp)assertTrue(t, elapsed < 5*time.Second, "timestamp should be recent")})}func TestLoggedTx_Rollback(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("discards recorded queries", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id1", "name1", 42)assertLen(t, 1, len(tx.queries))err := tx.Rollback()assertNoError(t, err)// Queries should be nil after rollbacktx.mu.Lock()queries := tx.queriestx.mu.Unlock()assertNil(t, queries)})t.Run("does not write event to file", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test_tool")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id1", "name1", 42)err := tx.Rollback()assertNoError(t, err)// No file should be created_, err = os.Stat(logPath)assertTrue(t, os.IsNotExist(err), "file should not exist")})t.Run("data not persisted", func(t *testing.T) {resetGlobalState()db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "rb_test", "name", 42)tx.Rollback()var count interr := db.QueryRow("SELECT COUNT(*) FROM test_table WHERE id = ?", "rb_test").Scan(&count)assertNoError(t, err)assertEqual(t, 0, count)})t.Run("rollback returns nil on success", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "x", "y", 1)err := tx.Rollback()assertNoError(t, err)})}func TestLoggedTx_QueryMethods(t *testing.T) {resetGlobalState()defer resetGlobalState()db := setupTestDB(t)defer db.Close()// Setup: insert a rowtx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "q1", "name1", 42)tx.Commit()t.Run("QueryRowContext returns row", func(t *testing.T) {tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()var name stringerr := tx.QueryRowContext(context.Background(), "SELECT name FROM test_table WHERE id = ?", "q1").Scan(&name)assertNoError(t, err)assertEqual(t, "name1", name)})t.Run("QueryRow returns row", func(t *testing.T) {tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()var value interr := tx.QueryRow("SELECT value FROM test_table WHERE id = ?", "q1").Scan(&value)assertNoError(t, err)assertEqual(t, 42, value)})t.Run("QueryContext returns rows", func(t *testing.T) {tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()rows, err := tx.QueryContext(context.Background(), "SELECT * FROM test_table")assertNoError(t, err)defer rows.Close()count := 0for rows.Next() {count++}assertGreater(t, int64(count), 0)})t.Run("Query returns rows", func(t *testing.T) {tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()rows, err := tx.Query("SELECT * FROM test_table")assertNoError(t, err)defer rows.Close()assertTrue(t, rows.Next(), "should have at least one row")})t.Run("query methods not recorded", func(t *testing.T) {tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()tx.QueryRowContext(context.Background(), "SELECT * FROM test_table")tx.QueryContext(context.Background(), "SELECT * FROM test_table")assertLen(t, 0, len(tx.queries))})}func TestLoggedTx_Prepare(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("valid prepare", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, err := tx.PrepareContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)")assertNoError(t, err)assertNotNil(t, stmt)assertEqual(t, "INSERT INTO test_table VALUES (?, ?, ?)", stmt.sql)stmt.Close()})t.Run("prepare without context", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, err := tx.Prepare("INSERT INTO test_table VALUES (?, ?, ?)")assertNoError(t, err)assertNotNil(t, stmt)stmt.Close()})t.Run("invalid SQL returns error", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, err := tx.Prepare("INVALID SQL SYNTAX !!!")assertError(t, err)assertNil(t, stmt)})}func TestLoggedStmt_ExecContext(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("INSERT with prepared stmt", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)")defer stmt.Close()_, err := stmt.ExecContext(context.Background(), "ps1", "name1", 42)assertNoError(t, err)assertLen(t, 1, len(tx.queries))assertContains(t, tx.queries[0].SQL, "INSERT")})t.Run("multiple executions recorded separately", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)")defer stmt.Close()stmt.ExecContext(context.Background(), "ps1", "name1", 1)stmt.ExecContext(context.Background(), "ps2", "name2", 2)stmt.ExecContext(context.Background(), "ps3", "name3", 3)assertLen(t, 3, len(tx.queries))})t.Run("parameters captured correctly", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)")defer stmt.Close()stmt.ExecContext(context.Background(), "captured_id", "captured_name", 999)assertLen(t, 3, len(tx.queries[0].Parameters))assertEqual(t, "captured_id", tx.queries[0].Parameters[0])assertEqual(t, "captured_name", tx.queries[0].Parameters[1])assertEqual(t, 999, tx.queries[0].Parameters[2])})t.Run("SELECT prepared stmt not recorded", func(t *testing.T) {db := setupTestDB(t)defer db.Close()// First insert some datatx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "sel_test", "name", 1)tx.Commit()// Now test SELECT prepared statementtx, _ = BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"SELECT name FROM test_table WHERE id = ?")defer stmt.Close()var name stringerr := stmt.QueryRowContext(context.Background(), "sel_test").Scan(&name)assertNoError(t, err)assertEqual(t, "name", name)assertLen(t, 0, len(tx.queries))})t.Run("failed execution not recorded", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()// Insert one rowtx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "dup_id", "name", 1)// Try to insert duplicate (will fail due to primary key)stmt, _ := tx.PrepareContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)")defer stmt.Close()_, err := stmt.ExecContext(context.Background(), "dup_id", "name2", 2)assertError(t, err)// Only first INSERT should be recordedassertLen(t, 1, len(tx.queries))})t.Run("commit writes all prepared stmt queries", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "prep_commit_test")stmt, _ := tx.PrepareContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)")stmt.ExecContext(context.Background(), "pc1", "name1", 1)stmt.ExecContext(context.Background(), "pc2", "name2", 2)stmt.Close()tx.Commit()events, err := readEventsFile(logPath)assertNoError(t, err)assertLen(t, 1, len(events))assertLen(t, 2, len(events[0].Queries))})t.Run("Exec without context", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)")defer stmt.Close()_, err := stmt.Exec("exec_id", "name", 42)assertNoError(t, err)assertLen(t, 1, len(tx.queries))})}func TestLoggedStmt_QueryMethods(t *testing.T) {resetGlobalState()defer resetGlobalState()db := setupTestDB(t)defer db.Close()// Setup: insert datatx, _ := BeginLoggedTx(context.Background(), db, "test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "qry1", "name1", 42)tx.Commit()t.Run("QueryRowContext returns row", func(t *testing.T) {tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"SELECT name FROM test_table WHERE id = ?")defer stmt.Close()var name stringerr := stmt.QueryRowContext(context.Background(), "qry1").Scan(&name)assertNoError(t, err)assertEqual(t, "name1", name)})t.Run("QueryRow returns row", func(t *testing.T) {tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"SELECT value FROM test_table WHERE id = ?")defer stmt.Close()var value interr := stmt.QueryRow("qry1").Scan(&value)assertNoError(t, err)assertEqual(t, 42, value)})t.Run("QueryContext returns rows", func(t *testing.T) {tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"SELECT * FROM test_table WHERE id = ?")defer stmt.Close()rows, err := stmt.QueryContext(context.Background(), "qry1")assertNoError(t, err)defer rows.Close()assertTrue(t, rows.Next(), "should have one row")})t.Run("Query returns rows", func(t *testing.T) {tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"SELECT * FROM test_table")defer stmt.Close()rows, err := stmt.Query()assertNoError(t, err)defer rows.Close()assertTrue(t, rows.Next(), "should have at least one row")})}func TestLoggedStmt_Close(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("close returns nil on success", func(t *testing.T) {db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "test")defer tx.Rollback()stmt, _ := tx.PrepareContext(context.Background(),"INSERT INTO test_table VALUES (?, ?, ?)")err := stmt.Close()assertNoError(t, err)})}func TestEnsureEventLogFile(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("creates file if doesn't exist", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})err := ensureEventLogFile()assertNoError(t, err)assertNotNil(t, eventLogFile)// File should exist_, err = os.Stat(logPath)assertNoError(t, err)})t.Run("appends to existing file", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")// Create file with contentos.WriteFile(logPath, []byte("existing content\n"), 0644)SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})err := ensureEventLogFile()assertNoError(t, err)// File should still have contentdata, _ := os.ReadFile(logPath)assertContains(t, string(data), "existing content")})t.Run("creates directory if doesn't exist", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "subdir", "deep", "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})err := ensureEventLogFile()assertNoError(t, err)// Directory should existdir := filepath.Dir(logPath)_, err = os.Stat(dir)assertNoError(t, err)})t.Run("returns nil if file already open", func(t *testing.T) {resetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})ensureEventLogFile()firstFile := eventLogFileerr := ensureEventLogFile()assertNoError(t, err)// Should reuse same file handleassertEqual(t, firstFile, eventLogFile)})}func TestTransactionEventJSON(t *testing.T) {resetGlobalState()defer resetGlobalState()t.Run("complete event serializes correctly", func(t *testing.T) {event := TransactionEvent{ID: "test-id-12345",Timestamp: time.Date(2026, 2, 18, 14, 30, 0, 0, time.UTC),Tool: "test_tool",Queries: []QueryRecord{{SQL: "INSERT INTO test VALUES (?)", Parameters: []any{"a"}},{SQL: "UPDATE test SET x = ?", Parameters: []any{1}},},Success: true,Duration: 42,}data, err := json.Marshal(event)assertNoError(t, err)var result map[string]anyerr = json.Unmarshal(data, &result)assertNoError(t, err)assertEqual(t, "test-id-12345", result["id"])assertEqual(t, "test_tool", result["tool"])assertEqual(t, true, result["success"])assertEqual(t, 42.0, result["duration_ms"])})t.Run("timestamp in RFC3339Nano format", func(t *testing.T) {event := TransactionEvent{ID: "ts-test",Timestamp: time.Date(2026, 2, 18, 14, 30, 0, 123456789, time.UTC),Success: true,}data, err := json.Marshal(event)assertNoError(t, err)var result map[string]anyjson.Unmarshal(data, &result)assertContains(t, result["timestamp"].(string), "2026-02-18T14:30:00.123456789Z")})t.Run("duration positive", func(t *testing.T) {event := TransactionEvent{ID: "dur-test",Timestamp: time.Now(),Success: true,Duration: 123,}data, _ := json.Marshal(event)var result map[string]anyjson.Unmarshal(data, &result)assertGreater(t, int64(result["duration_ms"].(float64)), 0)})t.Run("ID is 21 characters in real usage", func(t *testing.T) {// Verify by creating an actual eventresetGlobalState()tmpDir := t.TempDir()logPath := filepath.Join(tmpDir, "events.jsonl")SetEventLogConfig(EventLogConfig{Enabled: true, Path: logPath})db := setupTestDB(t)defer db.Close()tx, _ := BeginLoggedTx(context.Background(), db, "id_test")tx.ExecContext(context.Background(), "INSERT INTO test_table VALUES (?, ?, ?)", "id_test", "name", 1)tx.Commit()events, _ := readEventsFile(logPath)assertLen(t, 21, len(events[0].ID))})}func GetEventLogConfig() EventLogConfig {eventLogMu.Lock()defer eventLogMu.Unlock()return eventLogConfig}
package dbimport ("context""database/sql""encoding/json""fmt""os""path/filepath""reflect""strings""sync""time"gonanoid "github.com/matoous/go-nanoid/v2")// LoggedTx wraps *sql.Tx and records all Exec/ExecContext calls for mutation loggingtype LoggedTx struct {tx *sql.Txqueries []QueryRecordmu sync.MutextoolName stringstartTime time.Time}// QueryRecord represents a single SQL statement with parameterstype QueryRecord struct {SQL string `json:"sql"`Parameters []any `json:"parameters"`}// TransactionEvent represents a complete transaction for the event logtype TransactionEvent struct {ID string `json:"id"`Timestamp time.Time `json:"timestamp"`Tool string `json:"tool,omitempty"`Queries []QueryRecord `json:"queries"`Success bool `json:"success"`Duration int64 `json:"duration_ms"`}// LoggedStmt wraps *sql.Stmt to intercept Exec calls on prepared statementstype LoggedStmt struct {stmt *sql.Stmttx *LoggedTxsql string}// EventLogConfig holds configuration for event loggingtype EventLogConfig struct {Enabled boolPath string}var (eventLogConfig EventLogConfigeventLogMu sync.MutexeventLogFile *os.FileeventLogEnc *json.Encoder)// SetEventLogConfig configures event logging globallyfunc SetEventLogConfig(cfg EventLogConfig) {eventLogMu.Lock()defer eventLogMu.Unlock()// Close existing file if path changedif eventLogFile != nil && eventLogConfig.Path != cfg.Path {_ = eventLogFile.Close()eventLogFile = nileventLogEnc = nil}eventLogConfig = cfg}// BeginLoggedTx starts a new transaction that logs all mutations// toolName is optional and identifies which tool initiated the transactionfunc BeginLoggedTx(ctx context.Context, db *sql.DB, toolName string) (*LoggedTx, error) {tx, err := db.BeginTx(ctx, nil)if err != nil {return nil, err}return &LoggedTx{tx: tx,queries: make([]QueryRecord, 0),toolName: toolName,startTime: time.Now(),}, nil}// ExecContext executes and records the SQL statement if it's a mutationfunc (l *LoggedTx) ExecContext(ctx context.Context, query string, args ...any) (sql.Result, error) {result, err := l.tx.ExecContext(ctx, query, args...)if err == nil && isMutation(query) {l.mu.Lock()l.queries = append(l.queries, QueryRecord{SQL: query,Parameters: args,})l.mu.Unlock()}return result, err}// Exec executes and records the SQL statement if it's a mutationfunc (l *LoggedTx) Exec(query string, args ...any) (sql.Result, error) {return l.ExecContext(context.Background(), query, args...)}// QueryRowContext delegates to underlying tx (not logged - read operation)func (l *LoggedTx) QueryRowContext(ctx context.Context, query string, args ...any) *sql.Row {return l.tx.QueryRowContext(ctx, query, args...)}// QueryRow delegates to underlying tx (not logged - read operation)func (l *LoggedTx) QueryRow(query string, args ...any) *sql.Row {return l.tx.QueryRow(query, args...)}// QueryContext delegates to underlying tx (not logged - read operation)func (l *LoggedTx) QueryContext(ctx context.Context, query string, args ...any) (*sql.Rows, error) {return l.tx.QueryContext(ctx, query, args...)}// Query delegates to underlying tx (not logged - read operation)func (l *LoggedTx) Query(query string, args ...any) (*sql.Rows, error) {return l.tx.Query(query, args...)}// PrepareContext creates a logged prepared statementfunc (l *LoggedTx) PrepareContext(ctx context.Context, query string) (*LoggedStmt, error) {stmt, err := l.tx.PrepareContext(ctx, query)if err != nil {return nil, err}return &LoggedStmt{stmt: stmt, tx: l, sql: query}, nil}// Prepare creates a logged prepared statementfunc (l *LoggedTx) Prepare(query string) (*LoggedStmt, error) {return l.PrepareContext(context.Background(), query)}// Rollback rolls back the transaction (discards recorded queries)func (l *LoggedTx) Rollback() error {l.mu.Lock()l.queries = nil // Discard recorded queriesl.mu.Unlock()return l.tx.Rollback()}// Commit commits the transaction and logs all recorded queries on successfunc (l *LoggedTx) Commit() error {err := l.tx.Commit()if err != nil {return err}// Log on success onlyl.mu.Lock()queries := l.queriesl.mu.Unlock()if len(queries) > 0 && eventLogConfig.Enabled {l.writeEvent(queries)}return nil}// writeEvent writes the transaction to the event logfunc (l *LoggedTx) writeEvent(queries []QueryRecord) {eventLogMu.Lock()defer eventLogMu.Unlock()if !eventLogConfig.Enabled {return}// Ensure file is openif err := ensureEventLogFile(); err != nil {// Log to stderr but don't fail the commitfmt.Fprintf(os.Stderr, "Warning: failed to open event log: %v\n", err)return}id, err := gonanoid.New(21)if err != nil {fmt.Fprintf(os.Stderr, "Warning: failed to generate event ID: %v\n", err)return}event := TransactionEvent{ID: id,Timestamp: time.Now(),Tool: l.toolName,Queries: queries,Success: true,Duration: time.Since(l.startTime).Milliseconds(),}if err := eventLogEnc.Encode(event); err != nil {fmt.Fprintf(os.Stderr, "Warning: failed to write event log: %v\n", err)}}// LoggedStmt methods// ExecContext executes the prepared statement and logs if it's a mutationfunc (s *LoggedStmt) ExecContext(ctx context.Context, args ...any) (sql.Result, error) {result, err := s.stmt.ExecContext(ctx, args...)if err == nil && isMutation(s.sql) {s.tx.mu.Lock()s.tx.queries = append(s.tx.queries, QueryRecord{SQL: s.sql,Parameters: args,})s.tx.mu.Unlock()}return result, err}// Exec executes the prepared statement and logs if it's a mutationfunc (s *LoggedStmt) Exec(args ...any) (sql.Result, error) {return s.ExecContext(context.Background(), args...)}// QueryRowContext delegates to underlying statementfunc (s *LoggedStmt) QueryRowContext(ctx context.Context, args ...any) *sql.Row {return s.stmt.QueryRowContext(ctx, args...)}// QueryRow delegates to underlying statementfunc (s *LoggedStmt) QueryRow(args ...any) *sql.Row {return s.stmt.QueryRow(args...)}// QueryContext delegates to underlying statementfunc (s *LoggedStmt) QueryContext(ctx context.Context, args ...any) (*sql.Rows, error) {return s.stmt.QueryContext(ctx, args...)}// Query delegates to underlying statementfunc (s *LoggedStmt) Query(args ...any) (*sql.Rows, error) {return s.stmt.Query(args...)}// Close closes the prepared statementfunc (s *LoggedStmt) Close() error {return s.stmt.Close()}// isMutation returns true if the SQL is a mutation (INSERT, UPDATE, DELETE)func isMutation(sqlStr string) bool {upper := strings.ToUpper(strings.TrimSpace(sqlStr))// Handle WITH clauses (CTEs) that may contain mutationsif strings.HasPrefix(upper, "WITH") {// Check for INSERT/UPDATE/DELETE within the queryreturn strings.Contains(upper, "INSERT") ||strings.Contains(upper, "UPDATE") ||strings.Contains(upper, "DELETE")}return strings.HasPrefix(upper, "INSERT") ||strings.HasPrefix(upper, "UPDATE") ||strings.HasPrefix(upper, "DELETE")}// ensureEventLogFile opens the event log file if not already openfunc ensureEventLogFile() error {if eventLogFile != nil {return nil}dir := filepath.Dir(eventLogConfig.Path)if err := os.MkdirAll(dir, 0755); err != nil {return fmt.Errorf("failed to create event log directory: %w", err)}f, err := os.OpenFile(eventLogConfig.Path, os.O_APPEND|os.O_CREATE|os.O_WRONLY, 0644)if err != nil {return fmt.Errorf("failed to open event log file: %w", err)}eventLogFile = feventLogEnc = json.NewEncoder(f)eventLogEnc.SetEscapeHTML(false)return nil}// CloseEventLog closes the event log filefunc CloseEventLog() error {eventLogMu.Lock()defer eventLogMu.Unlock()// Disable logging before closingeventLogConfig.Enabled = falseif eventLogFile != nil {err := eventLogFile.Close()eventLogFile = nileventLogEnc = nilreturn err}return nil}// MarshalJSON implements json.Marshaler for QueryRecord// Handles special types like time.Time, nil, and nullable typesfunc (q QueryRecord) MarshalJSON() ([]byte, error) {// Create a helper struct with string parameterstype QueryRecordJSON struct {SQL string `json:"sql"`Parameters []any `json:"parameters"`}result := QueryRecordJSON{SQL: q.SQL,Parameters: make([]any, len(q.Parameters)),}for i, param := range q.Parameters {result.Parameters[i] = marshalParam(param)}return json.Marshal(result)}// marshalParam converts a parameter to a JSON-serializable valuefunc marshalParam(param any) any {if param == nil {return nil}switch v := param.(type) {case time.Time:return v.Format(time.RFC3339Nano)case *time.Time:if v == nil {return nil}return v.Format(time.RFC3339Nano)case string:return vcase *string:if v == nil {return nil}return *vcase int:return vcase *int:if v == nil {return nil}return *vcase int8:return vcase *int8:if v == nil {return nil}return *vcase int16:return vcase *int16:if v == nil {return nil}return *vcase int32:return vcase *int32:if v == nil {return nil}return *vcase int64:return vcase *int64:if v == nil {return nil}return *vcase uint:return vcase *uint:if v == nil {return nil}return *vcase uint8:return vcase *uint8:if v == nil {return nil}return *vcase uint16:return vcase *uint16:if v == nil {return nil}return *vcase uint32:return vcase *uint32:if v == nil {return nil}return *vcase uint64:return vcase *uint64:if v == nil {return nil}return *vcase float32:return vcase *float32:if v == nil {return nil}return *vcase float64:return vcase *float64:if v == nil {return nil}return *vcase bool:return vcase *bool:if v == nil {return nil}return *vcase []byte:return vdefault:// Handle pointer types via reflection (e.g., *GainLevel, *CustomType)rv := reflect.ValueOf(param)if rv.Kind() == reflect.Pointer {if rv.IsNil() {return nil}// Dereference and recursively marshal the underlying valuereturn marshalParam(rv.Elem().Interface())}// For other types, try to convert to string via fmt.Sprintfreturn fmt.Sprintf("%v", v)}}
package dbimport ("database/sql""fmt""strings""testing"_ "github.com/duckdb/duckdb-go/v2")func GetTableRowCount(db *sql.DB, table string) (int64, error) {var count int64err := db.QueryRow(fmt.Sprintf("SELECT COUNT(*) FROM %s", table)).Scan(&count)if err != nil {return 0, fmt.Errorf("failed to count rows in %s: %w", table, err)}return count, nil}func TestReadSchemaSQL(t *testing.T) {schema, err := ReadSchemaSQL()if err != nil {t.Fatalf("ReadSchemaSQL() error = %v", err)}// Verify schema contains expected elementsif !strings.Contains(schema, "CREATE TABLE dataset") {t.Error("schema missing CREATE TABLE dataset")}if !strings.Contains(schema, "CREATE TYPE dataset_type") {t.Error("schema missing CREATE TYPE dataset_type")}if !strings.Contains(schema, "CREATE INDEX") {t.Error("schema missing CREATE INDEX")}}func TestExtractDDLStatements(t *testing.T) {schema, err := ReadSchemaSQL()if err != nil {t.Fatalf("ReadSchemaSQL() error = %v", err)}statements := ExtractDDLStatements(schema)if len(statements) == 0 {t.Fatal("ExtractDDLStatements returned no statements")}// Count statement typestypeCounts := make(map[string]int)tableNames := make(map[string]bool)for _, stmt := range statements {typeCounts[stmt.Type]++if stmt.TableName != "" {tableNames[stmt.TableName] = true}t.Logf("Statement type=%s table=%s sql=%s", stmt.Type, stmt.TableName, stmt.SQL[:min(50, len(stmt.SQL))])}// Verify we have all expected typesif typeCounts["CREATE_TYPE"] < 2 {t.Errorf("expected at least 2 CREATE_TYPE statements, got %d", typeCounts["CREATE_TYPE"])}if typeCounts["CREATE_TABLE"] < 10 {t.Errorf("expected at least 10 CREATE_TABLE statements, got %d", typeCounts["CREATE_TABLE"])}if typeCounts["CREATE_INDEX"] < 5 {t.Errorf("expected at least 5 CREATE_INDEX statements, got %d", typeCounts["CREATE_INDEX"])}// CREATE_TABLE_AS might be 0 if the extraction logic changes - that's OK// as long as we handle it correctly in the export code// Verify key tables are foundexpectedTables := []string{"dataset", "location", "cluster", "file", "segment", "label"}for _, expected := range expectedTables {if !tableNames[expected] {t.Errorf("missing table %s in extracted statements", expected)}}}func TestExtractDDLStatement_Types(t *testing.T) {tests := []struct {name stringsql stringwantType stringwantTable string}{{name: "CREATE TYPE",sql: "CREATE TYPE dataset_type AS ENUM ('structured', 'unstructured');",wantType: "CREATE_TYPE",wantTable: "",},{name: "CREATE TABLE simple",sql: "CREATE TABLE dataset (id VARCHAR(12) PRIMARY KEY);",wantType: "CREATE_TABLE",wantTable: "dataset",},{name: "CREATE TABLE with newlines",sql: "CREATE TABLE location\n(\n id VARCHAR(12) PRIMARY KEY\n);",wantType: "CREATE_TABLE",wantTable: "location",},{name: "CREATE INDEX",sql: "CREATE INDEX idx_file_location ON file(location_id);",wantType: "CREATE_INDEX",wantTable: "idx_file_location",},{name: "CREATE UNIQUE INDEX",sql: "CREATE UNIQUE INDEX idx_species_label ON species(label);",wantType: "CREATE_INDEX",wantTable: "idx_species_label",},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {stmt := parseDDLStatement(tt.sql)if stmt.Type != tt.wantType {t.Errorf("parseDDLStatement().Type = %v, want %v", stmt.Type, tt.wantType)}if stmt.TableName != tt.wantTable {t.Errorf("parseDDLStatement().TableName = %v, want %v", stmt.TableName, tt.wantTable)}})}}func TestExtractTableName(t *testing.T) {tests := []struct {name stringsql stringwant string}{{name: "simple table",sql: "CREATE TABLE dataset (id VARCHAR(12) PRIMARY KEY",want: "dataset",},{name: "table with space before paren",sql: "CREATE TABLE location (id VARCHAR(12)",want: "location",},{name: "table with newline",sql: "CREATE TABLE cluster\n(\n id VARCHAR(12)",want: "cluster",},{name: "table with no space",sql: "CREATE TABLE file(id VARCHAR(21)",want: "file",},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {got := extractTableName(tt.sql)if got != tt.want {t.Errorf("extractTableName() = %v, want %v", got, tt.want)}})}}func TestExtractIndexName(t *testing.T) {tests := []struct {name stringsql stringwant string}{{name: "CREATE INDEX",sql: "CREATE INDEX idx_file_location ON file(location_id)",want: "idx_file_location",},{name: "CREATE UNIQUE INDEX",sql: "CREATE UNIQUE INDEX idx_species_label ON species(label)",want: "idx_species_label",},{name: "index with spaces",sql: "CREATE INDEX idx_test ON table_name (column)",want: "idx_test",},}for _, tt := range tests {t.Run(tt.name, func(t *testing.T) {got := extractIndexName(tt.sql)if got != tt.want {t.Errorf("extractIndexName() = %v, want %v", got, tt.want)}})}}func TestExtractDDLStatements_SkipsComments(t *testing.T) {schema := `-- This is a commentCREATE TABLE test (id INT);-- Another commentCREATE INDEX idx_test ON test(id);`statements := ExtractDDLStatements(schema)// Should have 2 statements, not 4if len(statements) != 2 {t.Errorf("expected 2 statements, got %d", len(statements))}for _, stmt := range statements {if strings.Contains(stmt.SQL, "--") {t.Errorf("statement should not contain comments: %s", stmt.SQL)}}}func TestGetFKOrder(t *testing.T) {// Use in-memory databasedb, err := sql.Open("duckdb", ":memory:")if err != nil {t.Fatalf("failed to open database: %v", err)}defer db.Close()// Create tables with FK relationshipsschema := `CREATE TABLE parent (id VARCHAR(12) PRIMARY KEY);CREATE TABLE child (id VARCHAR(12) PRIMARY KEY, parent_id VARCHAR(12), FOREIGN KEY (parent_id) REFERENCES parent(id));CREATE TABLE grandchild (id VARCHAR(12) PRIMARY KEY, child_id VARCHAR(12), FOREIGN KEY (child_id) REFERENCES child(id));CREATE TABLE independent (id VARCHAR(12) PRIMARY KEY);`_, err = db.Exec(schema)if err != nil {t.Fatalf("failed to create schema: %v", err)}order, err := GetFKOrder(db)if err != nil {t.Fatalf("GetFKOrder() error = %v", err)}// Build a map for quick lookuporderMap := make(map[string]int)for i, table := range order {orderMap[table] = i}// Verify order: parent must come before child, child before grandchildif orderMap["parent"] >= orderMap["child"] {t.Error("parent should come before child")}if orderMap["child"] >= orderMap["grandchild"] {t.Error("child should come before grandchild")}// Independent table can be anywhereif _, ok := orderMap["independent"]; !ok {t.Error("independent table missing from order")}}func TestGetTableRowCount(t *testing.T) {// Use in-memory databasedb, err := sql.Open("duckdb", ":memory:")if err != nil {t.Fatalf("failed to open database: %v", err)}defer db.Close()// Create and populate table_, err = db.Exec("CREATE TABLE test (id INT)")if err != nil {t.Fatalf("failed to create table: %v", err)}_, err = db.Exec("INSERT INTO test VALUES (1), (2), (3)")if err != nil {t.Fatalf("failed to insert: %v", err)}count, err := GetTableRowCount(db, "test")if err != nil {t.Fatalf("GetTableRowCount() error = %v", err)}if count != 3 {t.Errorf("GetTableRowCount() = %d, want 3", count)}}
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-- NOTE: DBML does not like functions and materialised views-- from this: $npm install -g @dbml/cli-- sql2dbml schema.sql --postgres -o schema.dbml-- from this: $npm install -g @softwaretechnik/dbml-renderer-- dbml-renderer -i schema.dbml -o schema.svgCREATE TYPE dataset_type AS ENUM ('structured', 'unstructured', 'test', 'train');CREATE TABLE dataset (id VARCHAR(12) PRIMARY KEY,name VARCHAR(255) UNIQUE NOT NULL,description VARCHAR(255),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,type dataset_type NOT NULL DEFAULT 'structured');CREATE TABLE location (id VARCHAR(12) PRIMARY KEY,dataset_id VARCHAR(12) NOT NULL,name VARCHAR(140) NOT NULL,latitude DECIMAL(10, 7) NOT NULL CHECK (latitude BETWEEN -90.0 AND 90.0),longitude DECIMAL(10, 7) NOT NULL CHECK (longitude BETWEEN -180.0 AND 180.0),description VARCHAR(255),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,timezone_id VARCHAR(40) NOT NULL,FOREIGN KEY (dataset_id) REFERENCES dataset(id),UNIQUE (dataset_id, name));CREATE TABLE cyclic_recording_pattern (id VARCHAR(12) PRIMARY KEY,record_s INTEGER NOT NULL,sleep_s INTEGER NOT NULL,created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,UNIQUE (record_s, sleep_s));CREATE TABLE cluster (id VARCHAR(12) PRIMARY KEY,dataset_id VARCHAR(12) NOT NULL,location_id VARCHAR(12) NOT NULL,name VARCHAR(140) NOT NULL,description VARCHAR(255),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,cyclic_recording_pattern_id VARCHAR(12),sample_rate INTEGER NOT NULL,path VARCHAR(255) NULL,FOREIGN KEY (dataset_id) REFERENCES dataset(id),FOREIGN KEY (location_id) REFERENCES location(id),FOREIGN KEY (cyclic_recording_pattern_id) REFERENCES cyclic_recording_pattern(id),UNIQUE (location_id, name));CREATE TYPE gain_level AS ENUM ('low', 'low-medium', 'medium', 'medium-high', 'high');CREATE TABLE file (id VARCHAR(21) PRIMARY KEY,file_name VARCHAR(255) NOT NULL,xxh64_hash VARCHAR(16) UNIQUE NOT NULL,location_id VARCHAR(12),timestamp_local TIMESTAMP WITH TIME ZONE NOT NULL,cluster_id VARCHAR(12),duration DECIMAL(7, 3) NOT NULL CHECK (duration > 0),sample_rate INTEGER NOT NULL,description VARCHAR(255),maybe_solar_night BOOLEAN,maybe_civil_night BOOLEAN,moon_phase DECIMAL(3,2) CHECK (moon_phase BETWEEN 0.00 AND 1.00),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,FOREIGN KEY (location_id) REFERENCES location(id),FOREIGN KEY (cluster_id) REFERENCES cluster(id));CREATE TABLE moth_metadata (file_id VARCHAR(21) PRIMARY KEY,timestamp TIMESTAMP WITH TIME ZONE NOT NULL,recorder_id VARCHAR(16),gain gain_level NULL,battery_v DECIMAL(2, 1) CHECK (battery_v >= 0),temp_c DECIMAL(3, 1),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,FOREIGN KEY (file_id) REFERENCES file(id));CREATE TABLE file_metadata (file_id VARCHAR(21) PRIMARY KEY,json JSON,created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,FOREIGN KEY (file_id) REFERENCES file(id));CREATE TABLE file_dataset (file_id VARCHAR(21) NOT NULL,dataset_id VARCHAR(12) NOT NULL,created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,PRIMARY KEY (file_id, dataset_id),FOREIGN KEY (file_id) REFERENCES file(id),FOREIGN KEY (dataset_id) REFERENCES dataset(id));CREATE TABLE segment(id VARCHAR(21) PRIMARY KEY,file_id VARCHAR(21) NOT NULL,dataset_id VARCHAR(12) NOT NULL,start_time DECIMAL(7,3) NOT NULL,end_time DECIMAL(7,3) NOT NULL,freq_low DECIMAL(9,3) CHECK (freq_low < 300000),freq_high DECIMAL(9,3) CHECK (freq_high < 300000),description VARCHAR(255),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,FOREIGN KEY (file_id) REFERENCES file(id),FOREIGN KEY (dataset_id) REFERENCES dataset(id),FOREIGN KEY (file_id, dataset_id) REFERENCES file_dataset(file_id, dataset_id));CREATE TABLE ebird_taxonomy (id VARCHAR(12) PRIMARY KEY,taxonomy_version VARCHAR(4) NOT NULL,taxon_order INTEGER NOT NULL,category VARCHAR(15) NOT NULL,species_code VARCHAR(15) NOT NULL,taxon_concept_id VARCHAR(15),primary_com_name VARCHAR(100) NOT NULL,sci_name VARCHAR(100) NOT NULL,bird_order VARCHAR(30),family VARCHAR(100),species_group VARCHAR(100),report_as VARCHAR(15),valid_from DATE NOT NULL, -- Need to dropvalid_to DATE, -- Need to dropactive BOOLEAN DEFAULT TRUE,UNIQUE (species_code, taxonomy_version));CREATE TABLE species (id VARCHAR(12) PRIMARY KEY,label VARCHAR(100) UNIQUE NOT NULL,ebird_code VARCHAR(12),taxonomy_version VARCHAR(4),description VARCHAR(255),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,FOREIGN KEY (ebird_code, taxonomy_version) REFERENCES ebird_taxonomy(species_code, taxonomy_version));CREATE TABLE call_type (id VARCHAR(12) PRIMARY KEY,species_id VARCHAR(12) NOT NULL,label VARCHAR(100) NOT NULL,created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,FOREIGN KEY (species_id) REFERENCES species(id));CREATE TABLE filter (id VARCHAR(12) PRIMARY KEY,name VARCHAR(140) NOT NULL,description VARCHAR(255),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN NOT NULL DEFAULT true);CREATE TABLE label (id VARCHAR(21) PRIMARY KEY,segment_id VARCHAR(21) NOT NULL,species_id VARCHAR(12) NOT NULL,filter_id VARCHAR(12) NOT NULL,certainty DECIMAL(5,2) CHECK (certainty <= 100 AND certainty >= 0),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN NOT NULL DEFAULT true,FOREIGN KEY (segment_id) REFERENCES segment(id),FOREIGN KEY (species_id) REFERENCES species(id),FOREIGN KEY (filter_id) REFERENCES filter(id));CREATE TABLE label_metadata (label_id VARCHAR(21) PRIMARY KEY,json JSON,created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN DEFAULT TRUE,FOREIGN KEY (label_id) REFERENCES label(id));CREATE TABLE label_subtype (id VARCHAR(21) PRIMARY KEY,label_id VARCHAR(21) NOT NULL,calltype_id VARCHAR(12) NOT NULL,filter_id VARCHAR(12),certainty DECIMAL(5,2) CHECK (certainty <= 100 AND certainty >= 0),created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,active BOOLEAN NOT NULL DEFAULT true,FOREIGN KEY (label_id) REFERENCES label(id),FOREIGN KEY (calltype_id) REFERENCES call_type(id),FOREIGN KEY (filter_id) REFERENCES filter(id));-- FK indexes on file table (1.26M rows)CREATE INDEX idx_file_location ON file(location_id);CREATE INDEX idx_file_cluster ON file(cluster_id);-- Performance index on file for time-based queriesCREATE INDEX idx_file_timestamp_local ON file(timestamp_local);-- FK indexes on segment table (201K rows)CREATE INDEX idx_segment_file ON segment(file_id);CREATE INDEX idx_segment_dataset ON segment(dataset_id);-- FK indexes on label table (200K rows)CREATE INDEX idx_label_segment_id ON label(segment_id);CREATE INDEX idx_label_species_id ON label(species_id);-- FK indexes on label_subtype table (114K rows)CREATE INDEX idx_label_subtype_label_id ON label_subtype(label_id);CREATE INDEX idx_label_subtype_calltype_id ON label_subtype(calltype_id);CREATE INDEX idx_label_subtype_filter_id ON label_subtype(filter_id);-- FK lookup for ebird taxonomy (used by species table FK)CREATE INDEX idx_ebird_taxonomy_species_code ON ebird_taxonomy(species_code, taxonomy_version);-- Junction table reverse lookupsCREATE INDEX idx_file_dataset_dataset ON file_dataset(dataset_id);
package dbimport ("database/sql""embed""fmt""slices""strings")//go:embed schema.sqlvar schemaFS embed.FS// ReadSchemaSQL reads the schema.sql file// Uses embedded file for distributed binariesfunc ReadSchemaSQL() (string, error) {data, err := schemaFS.ReadFile("schema.sql")if err != nil {return "", fmt.Errorf("failed to read schema.sql: %w", err)}return string(data), nil}// DDLStatement represents a parsed DDL statement with metadatatype DDLStatement struct {SQL stringType string // "CREATE_TYPE", "CREATE_TABLE", "CREATE_INDEX", "CREATE_TABLE_AS"TableName string // for CREATE TABLE and CREATE INDEX}// ExtractDDLStatements splits schema SQL into executable DDL statements// Returns statements in order: types, tables, indexes// Handles CREATE TABLE ... AS SELECT specially (marked but included)func ExtractDDLStatements(schemaSQL string) []DDLStatement {var statements []DDLStatement// Split by semicolon, but handle the CREATE TABLE AS SELECT caselines := strings.Split(schemaSQL, "\n")var currentStmt strings.Builderfor _, line := range lines {trimmed := strings.TrimSpace(line)// Skip empty lines and commentsif trimmed == "" || strings.HasPrefix(trimmed, "--") {continue}currentStmt.WriteString(line)currentStmt.WriteString("\n")// Statement ends at semicolonif strings.HasSuffix(trimmed, ";") {sql := strings.TrimSpace(currentStmt.String())if sql != "" {stmt := parseDDLStatement(sql)statements = append(statements, stmt)}currentStmt.Reset()}}// Handle any remaining statement without trailing semicolonif currentStmt.Len() > 0 {sql := strings.TrimSpace(currentStmt.String())if sql != "" && strings.HasSuffix(sql, ";") {stmt := parseDDLStatement(sql)statements = append(statements, stmt)}}return statements}// parseDDLStatement determines the type and table name of a DDL statementfunc parseDDLStatement(sql string) DDLStatement {upper := strings.ToUpper(sql)switch {case strings.HasPrefix(upper, "CREATE TYPE"):return DDLStatement{SQL: sql, Type: "CREATE_TYPE", TableName: ""}case strings.HasPrefix(upper, "CREATE TABLE"):tableName := extractTableName(sql)return DDLStatement{SQL: sql, Type: "CREATE_TABLE", TableName: tableName}case strings.HasPrefix(upper, "CREATE INDEX") || strings.HasPrefix(upper, "CREATE UNIQUE INDEX"):indexName := extractIndexName(sql)return DDLStatement{SQL: sql, Type: "CREATE_INDEX", TableName: indexName}default:return DDLStatement{SQL: sql, Type: "UNKNOWN", TableName: ""}}}// extractTableName extracts table name from CREATE TABLE statementfunc extractTableName(sql string) string {// CREATE TABLE name (// or CREATE TABLE name(upper := strings.ToUpper(sql)// Find "CREATE TABLE"idx := strings.Index(upper, "CREATE TABLE")if idx == -1 {return ""}// Move past "CREATE TABLE"rest := sql[idx+12:]rest = strings.TrimSpace(rest)// Find opening parenthesis or endendIdx := strings.Index(rest, "(")if endIdx == -1 {endIdx = len(rest)}name := strings.TrimSpace(rest[:endIdx])return name}// extractIndexName extracts index name from CREATE INDEX statementfunc extractIndexName(sql string) string {upper := strings.ToUpper(sql)// Handle "CREATE UNIQUE INDEX" or "CREATE INDEX"var rest stringif strings.HasPrefix(upper, "CREATE UNIQUE INDEX") {rest = sql[19:]} else if strings.HasPrefix(upper, "CREATE INDEX") {rest = sql[12:]} else {return ""}rest = strings.TrimSpace(rest)// Find " ON "onIdx := strings.Index(strings.ToUpper(rest), " ON ")if onIdx == -1 {return ""}name := strings.TrimSpace(rest[:onIdx])return name}// FKRelation represents a foreign key relationship between tablestype FKRelation struct {Table string // table that has the FKColumn string // FK columnForeignTable string // referenced table}// GetFKOrder computes the order tables should be copied based on FK dependencies// Tables with no FKs come first, then dependent tables in topological orderfunc GetFKOrder(db *sql.DB) ([]string, error) {// Use DuckDB's duckdb_constraints() function for accurate FK infoquery := `SELECT table_name, referenced_tableFROM duckdb_constraints()WHERE constraint_type = 'FOREIGN KEY'AND referenced_table IS NOT NULL`rows, err := db.Query(query)if err != nil {return nil, fmt.Errorf("failed to query FK relationships: %w", err)}defer rows.Close()// Build reverse dependency graph: table -> tables that depend on it// dependsOnMe[A] = [B, C] means B and C have FKs to AdependsOnMe := make(map[string][]string)tables := make(map[string]bool)for rows.Next() {var table, foreignTable stringif err := rows.Scan(&table, &foreignTable); err != nil {return nil, fmt.Errorf("failed to scan FK row: %w", err)}tables[table] = truetables[foreignTable] = true// foreignTable is referenced by tabledependsOnMe[foreignTable] = append(dependsOnMe[foreignTable], table)}if err := rows.Err(); err != nil {return nil, fmt.Errorf("error iterating FK rows: %w", err)}// Get all tables from the databasetableRows, err := db.Query(`SELECT table_nameFROM information_schema.tablesWHERE table_schema = 'main'AND table_type = 'BASE TABLE'`)if err != nil {return nil, fmt.Errorf("failed to query tables: %w", err)}defer tableRows.Close()for tableRows.Next() {var name stringif err := tableRows.Scan(&name); err != nil {return nil, fmt.Errorf("failed to scan table name: %w", err)}tables[name] = true}// Count how many FKs each table has (tables it depends on)fkCount := make(map[string]int)for table := range tables {fkCount[table] = 0}for _, dependents := range dependsOnMe {for _, dependent := range dependents {fkCount[dependent]++}}// Topological sort (Kahn's algorithm)// 1. Start with tables that have no FKs (fkCount = 0)var queue []stringfor table := range tables {if fkCount[table] == 0 {queue = append(queue, table)}}// 2. Process queuevar result []stringfor len(queue) > 0 {// Pop first elementcurrent := queue[0]queue = queue[1:]result = append(result, current)// For each table that depends on current, decrease its FK countfor _, dependent := range dependsOnMe[current] {fkCount[dependent]--if fkCount[dependent] == 0 {queue = append(queue, dependent)}}}// If result doesn't contain all tables, there's a cycleif len(result) != len(tables) {// Add remaining tables (cycle handling)for table := range tables {found := slices.Contains(result, table)if !found {result = append(result, table)}}}return result, nil}
Enum "dataset_type" {"structured""unstructured""test""train"}Enum "gain_level" {"low""low-medium""medium""medium-high""high"}Table "dataset" {"id" VARCHAR(12) [pk]"name" VARCHAR(255) [unique, not null]"description" VARCHAR(255)"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]"type" dataset_type [not null, default: 'structured']}Table "location" {"id" VARCHAR(12) [pk]"dataset_id" VARCHAR(12) [not null]"name" VARCHAR(140) [not null]"latitude" DECIMAL(10,7) [not null, check: `latitude BETWEEN -90.0 AND 90.0`]"longitude" DECIMAL(10,7) [not null, check: `longitude BETWEEN -180.0 AND 180.0`]"description" VARCHAR(255)"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]"timezone_id" VARCHAR(40) [not null]Indexes {(dataset_id, name) [unique]}}Table "cyclic_recording_pattern" {"id" VARCHAR(12) [pk]"record_s" INTEGER [not null]"sleep_s" INTEGER [not null]"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]Indexes {(record_s, sleep_s) [unique]}}Table "cluster" {"id" VARCHAR(12) [pk]"dataset_id" VARCHAR(12) [not null]"location_id" VARCHAR(12) [not null]"name" VARCHAR(140) [not null]"description" VARCHAR(255)"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]"cyclic_recording_pattern_id" VARCHAR(12)"sample_rate" INTEGER [not null]"path" VARCHAR(255)Indexes {(location_id, name) [unique]}}Table "file" {"id" VARCHAR(21) [pk]"file_name" VARCHAR(255) [not null]"xxh64_hash" VARCHAR(16) [unique, not null]"location_id" VARCHAR(12)"timestamp_local" TIMESTAMP [not null]"cluster_id" VARCHAR(12)"duration" DECIMAL(7,3) [not null, check: `duration > 0`]"sample_rate" INTEGER [not null]"description" VARCHAR(255)"maybe_solar_night" BOOLEAN"maybe_civil_night" BOOLEAN"moon_phase" DECIMAL(3,2) [check: `moon_phase BETWEEN 0.00 AND 1.00`]"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]Indexes {location_id [name: "idx_file_location"]cluster_id [name: "idx_file_cluster"]timestamp_local [name: "idx_file_timestamp_local"]}}Table "moth_metadata" {"file_id" VARCHAR(21) [pk]"timestamp" TIMESTAMP [not null]"recorder_id" VARCHAR(16)"gain" gain_level"battery_v" DECIMAL(2,1) [check: `battery_v >= 0`]"temp_c" DECIMAL(3,1)"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]}Table "file_metadata" {"file_id" VARCHAR(21) [pk]"json" JSON"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]}Table "file_dataset" {"file_id" VARCHAR(21) [not null]"dataset_id" VARCHAR(12) [not null]"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]Indexes {(file_id, dataset_id) [pk]dataset_id [name: "idx_file_dataset_dataset"]}}Table "segment" {"id" VARCHAR(21) [pk]"file_id" VARCHAR(21) [not null]"dataset_id" VARCHAR(12) [not null]"start_time" DECIMAL(7,3) [not null]"end_time" DECIMAL(7,3) [not null]"freq_low" DECIMAL(9,3) [check: `freq_low < 300000`]"freq_high" DECIMAL(9,3) [check: `freq_high < 300000`]"description" VARCHAR(255)"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]Indexes {file_id [name: "idx_segment_file"]dataset_id [name: "idx_segment_dataset"]}}Table "ebird_taxonomy" {"id" VARCHAR(12) [pk]"taxonomy_version" VARCHAR(4) [not null]"taxon_order" INTEGER [not null]"category" VARCHAR(15) [not null]"species_code" VARCHAR(15) [not null]"taxon_concept_id" VARCHAR(15)"primary_com_name" VARCHAR(100) [not null]"sci_name" VARCHAR(100) [not null]"bird_order" VARCHAR(30)"family" VARCHAR(100)"species_group" VARCHAR(100)"report_as" VARCHAR(15)"valid_from" DATE [not null]"valid_to" DATE"active" BOOLEAN [default: TRUE]Indexes {(species_code, taxonomy_version) [unique](species_code, taxonomy_version) [name: "idx_ebird_taxonomy_species_code"]}}Table "species" {"id" VARCHAR(12) [pk]"label" VARCHAR(100) [unique, not null]"ebird_code" VARCHAR(12)"taxonomy_version" VARCHAR(4)"description" VARCHAR(255)"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]}Table "call_type" {"id" VARCHAR(12) [pk]"species_id" VARCHAR(12) [not null]"label" VARCHAR(100) [not null]"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]}Table "filter" {"id" VARCHAR(12) [pk]"name" VARCHAR(140) [not null]"description" VARCHAR(255)"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [not null, default: true]}Table "label" {"id" VARCHAR(21) [pk]"segment_id" VARCHAR(21) [not null]"species_id" VARCHAR(12) [not null]"filter_id" VARCHAR(12) [not null]"certainty" DECIMAL(5,2) [check: `certainty <= 100 AND certainty >= 0`]"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [not null, default: true]Indexes {segment_id [name: "idx_label_segment_id"]species_id [name: "idx_label_species_id"]}}Table "label_metadata" {"label_id" VARCHAR(21) [pk]"json" JSON"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [default: TRUE]}Table "label_subtype" {"id" VARCHAR(21) [pk]"label_id" VARCHAR(21) [not null]"calltype_id" VARCHAR(12) [not null]"filter_id" VARCHAR(12)"certainty" DECIMAL(5,2) [check: `certainty <= 100 AND certainty >= 0`]"created_at" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"last_modified" TIMESTAMP [default: `CURRENT_TIMESTAMP`]"active" BOOLEAN [not null, default: true]Indexes {label_id [name: "idx_label_subtype_label_id"]calltype_id [name: "idx_label_subtype_calltype_id"]filter_id [name: "idx_label_subtype_filter_id"]}}Ref:"dataset"."id" < "location"."dataset_id"Ref:"dataset"."id" < "cluster"."dataset_id"Ref:"location"."id" < "cluster"."location_id"Ref:"cyclic_recording_pattern"."id" < "cluster"."cyclic_recording_pattern_id"Ref:"location"."id" < "file"."location_id"Ref:"cluster"."id" < "file"."cluster_id"Ref:"file"."id" < "moth_metadata"."file_id"Ref:"file"."id" < "file_metadata"."file_id"Ref:"file"."id" < "file_dataset"."file_id"Ref:"dataset"."id" < "file_dataset"."dataset_id"Ref:"file"."id" < "segment"."file_id"Ref:"dataset"."id" < "segment"."dataset_id"Ref:"file_dataset".("file_id", "dataset_id") < "segment".("file_id", "dataset_id")Ref:"ebird_taxonomy".("species_code", "taxonomy_version") < "species".("ebird_code", "taxonomy_version")Ref:"species"."id" < "call_type"."species_id"Ref:"segment"."id" < "label"."segment_id"Ref:"species"."id" < "label"."species_id"Ref:"filter"."id" < "label"."filter_id"Ref:"label"."id" < "label_metadata"."label_id"Ref:"label"."id" < "label_subtype"."label_id"Ref:"call_type"."id" < "label_subtype"."calltype_id"Ref:"filter"."id" < "label_subtype"."filter_id"
package dbimport ("database/sql""testing"_ "github.com/duckdb/duckdb-go/v2")// setupInvariantsTestDB creates an in-memory database with the full schemafunc setupInvariantsTestDB(t *testing.T) *sql.DB {t.Helper()db, err := sql.Open("duckdb", ":memory:")if err != nil {t.Fatalf("failed to open database: %v", err)}schema, err := ReadSchemaSQL()if err != nil {t.Fatalf("failed to read schema: %v", err)}_, err = db.Exec(schema)if err != nil {t.Fatalf("failed to create schema: %v", err)}return db}// insertDataset creates a test dataset and returns its IDfunc insertDataset(t *testing.T, db *sql.DB, id, name string) {t.Helper()_, err := db.Exec("INSERT INTO dataset (id, name, type, active) VALUES (?, ?, 'structured', true)",id, name,)if err != nil {t.Fatalf("failed to insert dataset: %v", err)}}// insertLocation creates a test location and returns its IDfunc insertLocation(t *testing.T, db *sql.DB, id, datasetID, name string) {t.Helper()_, err := db.Exec(`INSERT INTO location (id, dataset_id, name, latitude, longitude, timezone_id, active)VALUES (?, ?, ?, -36.8485, 174.7633, 'Pacific/Auckland', true)`,id, datasetID, name,)if err != nil {t.Fatalf("failed to insert location: %v", err)}}// insertCluster creates a test clusterfunc insertCluster(t *testing.T, db *sql.DB, id, datasetID, locationID, name string) {t.Helper()_, err := db.Exec(`INSERT INTO cluster (id, dataset_id, location_id, name, sample_rate, active)VALUES (?, ?, ?, ?, 48000, true)`,id, datasetID, locationID, name,)if err != nil {t.Fatalf("failed to insert cluster: %v", err)}}// insertFile creates a test filefunc insertFile(t *testing.T, db *sql.DB, id, hash, locationID string) {t.Helper()_, err := db.Exec(`INSERT INTO file (id, file_name, xxh64_hash, location_id, timestamp_local, duration, sample_rate, active)VALUES (?, 'test.wav', ?, ?, CURRENT_TIMESTAMP, 1.0, 48000, true)`,id, hash, locationID,)if err != nil {t.Fatalf("failed to insert file: %v", err)}}// ============================================================================// Phase 1, Test 1: UniqueFileHash invariant// Spec: validation.allium - UniqueFileHash// "for f1 in Files: for f2 in Files: f1 != f2 implies f1.xxh64_hash != f2.xxh64_hash"// ============================================================================func TestInvariant_UniqueFileHash(t *testing.T) {db := setupInvariantsTestDB(t)defer db.Close()// Setup: create dataset → location → cluster → fileinsertDataset(t, db, "ds_test12345", "Test Dataset")insertLocation(t, db, "loc_test1234", "ds_test12345", "Test Location")insertCluster(t, db, "clustest1234", "ds_test12345", "loc_test1234", "Test Cluster")// Insert first file with a specific hashinsertFile(t, db, "filetest1234567890123", "abcd1234efgh5678", "loc_test1234")// Test: Attempting to insert a second file with the same hash should failt.Run("duplicate hash rejected", func(t *testing.T) {_, err := db.Exec(`INSERT INTO file (id, file_name, xxh64_hash, location_id, timestamp_local, duration, sample_rate, active)VALUES ('filetest_diffhash01', 'test2.wav', 'abcd1234efgh5678', 'loc_test1234', CURRENT_TIMESTAMP, 1.0, 48000, true)`,)if err == nil {t.Error("expected error for duplicate xxh64_hash, got nil")}})// Test: Different hash should succeedt.Run("different hash accepted", func(t *testing.T) {_, err := db.Exec(`INSERT INTO file (id, file_name, xxh64_hash, location_id, timestamp_local, duration, sample_rate, active)VALUES ('filetest_diffhash02', 'test3.wav', '9876zyxw5432vuts', 'loc_test1234', CURRENT_TIMESTAMP, 1.0, 48000, true)`,)if err != nil {t.Errorf("unexpected error for different hash: %v", err)}})// Test: Same hash with inactive file should still fail (constraint applies to all rows)t.Run("inactive file still blocks duplicate", func(t *testing.T) {// Mark first file as inactive_, err := db.Exec("UPDATE file SET active = false WHERE id = 'filetest1234567890123'")if err != nil {t.Fatalf("failed to deactivate file: %v", err)}// Attempt duplicate hash with new file_, err = db.Exec(`INSERT INTO file (id, file_name, xxh64_hash, location_id, timestamp_local, duration, sample_rate, active)VALUES ('filetest_inactblk01', 'test4.wav', 'abcd1234efgh5678', 'loc_test1234', CURRENT_TIMESTAMP, 1.0, 48000, true)`,)if err == nil {t.Error("expected error for duplicate xxh64_hash even with inactive file, got nil")}})}// ============================================================================// Phase 1, Test 2: LocationBelongsToDataset invariant// Spec: validation.allium - LocationBelongsToDataset// "for l in Locations: l.dataset exists and is valid"// ============================================================================func TestInvariant_LocationBelongsToDataset(t *testing.T) {db := setupInvariantsTestDB(t)defer db.Close()// Setup: create datasetinsertDataset(t, db, "ds_valid123456", "Valid Dataset")t.Run("location with valid dataset accepted", func(t *testing.T) {_, err := db.Exec(`INSERT INTO location (id, dataset_id, name, latitude, longitude, timezone_id, active)VALUES ('loc_valid12345', 'ds_valid123456', 'Valid Location', -36.8485, 174.7633, 'Pacific/Auckland', true)`,)if err != nil {t.Errorf("unexpected error: %v", err)}})t.Run("location with nonexistent dataset rejected", func(t *testing.T) {_, err := db.Exec(`INSERT INTO location (id, dataset_id, name, latitude, longitude, timezone_id, active)VALUES ('loc_bad_ds_001', 'ds_nonexistent', 'Bad Location', -36.8485, 174.7633, 'Pacific/Auckland', true)`,)if err == nil {t.Error("expected error for nonexistent dataset_id, got nil")}})t.Run("location with deleted dataset rejected", func(t *testing.T) {// Create and then soft-delete a datasetinsertDataset(t, db, "ds_del_temp_01", "To Be Deleted")_, err := db.Exec("UPDATE dataset SET active = false WHERE id = 'ds_del_temp_01'")if err != nil {t.Fatalf("failed to deactivate dataset: %v", err)}// Try to create location pointing to inactive dataset_, err = db.Exec(`INSERT INTO location (id, dataset_id, name, latitude, longitude, timezone_id, active)VALUES ('loc_inact_ds01', 'ds_del_temp_01', 'Inactive DS Location', -36.8485, 174.7633, 'Pacific/Auckland', true)`,)// Note: FK constraint may still allow this depending on implementation// This test documents the current behaviort.Logf("Insert location to inactive dataset: err=%v", err)})t.Run("duplicate location name in same dataset rejected", func(t *testing.T) {// Try to insert location with same name in same dataset_, err := db.Exec(`INSERT INTO location (id, dataset_id, name, latitude, longitude, timezone_id, active)VALUES ('loc_dup_name01', 'ds_valid123456', 'Valid Location', -40.9006, 174.8860, 'Pacific/Auckland', true)`,)if err == nil {t.Error("expected error for duplicate location name in same dataset, got nil")}})t.Run("same location name in different datasets accepted", func(t *testing.T) {// Create second datasetinsertDataset(t, db, "ds_second_1234", "Second Dataset")// Same name as in first dataset should work_, err := db.Exec(`INSERT INTO location (id, dataset_id, name, latitude, longitude, timezone_id, active)VALUES ('loc_same_name2', 'ds_second_1234', 'Valid Location', -36.8485, 174.7633, 'Pacific/Auckland', true)`,)if err != nil {t.Errorf("unexpected error for same name in different dataset: %v", err)}})}// ============================================================================// Phase 1, Test 3: ClusterBelongsToLocation invariant// Spec: validation.allium - ClusterBelongsToLocation, LocationBelongsToDataset (cross-check)// "for c in Clusters: c.location exists AND c.location.dataset = c.dataset"// ============================================================================func TestInvariant_ClusterBelongsToLocation(t *testing.T) {db := setupInvariantsTestDB(t)defer db.Close()// Setup: create two separate dataset hierarchiesinsertDataset(t, db, "ds_cluster_t01", "Cluster Test Dataset 1")insertDataset(t, db, "ds_cluster_t02", "Cluster Test Dataset 2")insertLocation(t, db, "loc_clust_t001", "ds_cluster_t01", "Location in DS1")insertLocation(t, db, "loc_clust_t002", "ds_cluster_t02", "Location in DS2")t.Run("cluster with valid location accepted", func(t *testing.T) {_, err := db.Exec(`INSERT INTO cluster (id, dataset_id, location_id, name, sample_rate, active)VALUES ('cl_valid123456', 'ds_cluster_t01', 'loc_clust_t001', 'Valid Cluster', 48000, true)`,)if err != nil {t.Errorf("unexpected error: %v", err)}})t.Run("cluster with nonexistent location rejected", func(t *testing.T) {_, err := db.Exec(`INSERT INTO cluster (id, dataset_id, location_id, name, sample_rate, active)VALUES ('cl_badloc12345', 'ds_cluster_t01', 'loc_nonexistent', 'Bad Location Cluster', 48000, true)`,)if err == nil {t.Error("expected error for nonexistent location_id, got nil")}})t.Run("cluster with mismatched dataset and location rejected", func(t *testing.T) {// Attempt: cluster.dataset_id = ds1, but cluster.location_id = location from ds2_, err := db.Exec(`INSERT INTO cluster (id, dataset_id, location_id, name, sample_rate, active)VALUES ('cl_mismatch001', 'ds_cluster_t01', 'loc_clust_t002', 'Mismatched Cluster', 48000, true)`,)// This tests the business logic invariant from the spec// The schema allows this via FKs, but the application should reject it// If the schema doesn't prevent this, the test documents the gapt.Logf("Mismatched dataset/location: err=%v", err)})t.Run("duplicate cluster name in same location rejected", func(t *testing.T) {// Try to insert cluster with same name in same location_, err := db.Exec(`INSERT INTO cluster (id, dataset_id, location_id, name, sample_rate, active)VALUES ('cl_dup_name_01', 'ds_cluster_t01', 'loc_clust_t001', 'Valid Cluster', 48000, true)`,)if err == nil {t.Error("expected error for duplicate cluster name in same location, got nil")}})t.Run("same cluster name in different locations accepted", func(t *testing.T) {// Same name but different location should work_, err := db.Exec(`INSERT INTO cluster (id, dataset_id, location_id, name, sample_rate, active)VALUES ('cl_same_nam_02', 'ds_cluster_t02', 'loc_clust_t002', 'Valid Cluster', 48000, true)`,)if err != nil {t.Errorf("unexpected error for same name in different location: %v", err)}})}// ============================================================================// Cross-invariant: Hierarchical integrity// Tests that the full hierarchy chain is enforced// ============================================================================func TestInvariant_HierarchicalIntegrity(t *testing.T) {db := setupInvariantsTestDB(t)defer db.Close()// Build complete hierarchyinsertDataset(t, db, "ds_hier_test01", "Hierarchy Test")insertLocation(t, db, "loc_hier_test1", "ds_hier_test01", "Hier Location")insertCluster(t, db, "cl_hier_test01", "ds_hier_test01", "loc_hier_test1", "Hier Cluster")t.Run("file must have valid location", func(t *testing.T) {_, err := db.Exec(`INSERT INTO file (id, file_name, xxh64_hash, location_id, timestamp_local, duration, sample_rate, active)VALUES ('file_badloc001', 'test.wav', '1111111111111111', 'loc_nonexistent', CURRENT_TIMESTAMP, 1.0, 48000, true)`,)if err == nil {t.Error("expected error for file with invalid location, got nil")}})t.Run("file with valid location but invalid cluster rejected", func(t *testing.T) {_, err := db.Exec(`INSERT INTO file (id, file_name, xxh64_hash, location_id, cluster_id, timestamp_local, duration, sample_rate, active)VALUES ('file_badcl_001', 'test.wav', '2222222222222222', 'loc_hier_test1', 'cl_nonexistent', CURRENT_TIMESTAMP, 1.0, 48000, true)`,)if err == nil {t.Error("expected error for file with invalid cluster, got nil")}})t.Run("valid file through full hierarchy accepted", func(t *testing.T) {_, err := db.Exec(`INSERT INTO file (id, file_name, xxh64_hash, location_id, cluster_id, timestamp_local, duration, sample_rate, active)VALUES ('file_valid0001', 'test.wav', '3333333333333333', 'loc_hier_test1', 'cl_hier_test01', CURRENT_TIMESTAMP, 1.0, 48000, true)`,)if err != nil {t.Errorf("unexpected error: %v", err)}})}
2026-01-20T07:41:23.093Zundefined
package dbimport ("database/sql""fmt"_ "github.com/duckdb/duckdb-go/v2" // DuckDB driver)// OpenReadOnlyDB opens a DuckDB connection in read-only mode// Provides additional security layer for query-only operations// Caller must close the connection when donefunc OpenReadOnlyDB(dbPath string) (*sql.DB, error) {connStr := dbPath + "?access_mode=read_only"db, err := sql.Open("duckdb", connStr)if err != nil {return nil, fmt.Errorf("failed to open database: %w", err)}if err = db.Ping(); err != nil {closeErr := db.Close()if closeErr != nil {return nil, fmt.Errorf("failed to ping database: %w (close error: %v)", err, closeErr)}return nil, fmt.Errorf("failed to ping database: %w", err)}return db, nil}// OpenWriteableDB opens a DuckDB connection in read-write mode// Used for write operations (insert, update, delete)// Caller must close the connection when donefunc OpenWriteableDB(dbPath string) (*sql.DB, error) {connStr := dbPath + "?access_mode=read_write"db, err := sql.Open("duckdb", connStr)if err != nil {return nil, fmt.Errorf("failed to open database: %w", err)}if err = db.Ping(); err != nil {closeErr := db.Close()if closeErr != nil {return nil, fmt.Errorf("failed to ping database: %w (close error: %v)", err, closeErr)}return nil, fmt.Errorf("failed to ping database: %w", err)}return db, nil}
# Specification of file formats used by AviaNZAviaNZ annotations and filter definitions are stored in JSON format to allow easy parsing and manual inspection by text editors.## Annotation files (.data)A JSON array where the first (optional, but recommended) element stores metadata about the corresponding audio file, and each remaining element corresponds to a segment:[ Meta, seg, seg, seg, seg ... ]`Meta`: a JSON object (key-value pairs) containing any metadata. Required fields:`Operator` - string`Reviewer` - string`Duration` - numeric, audio file length, in seconds...Each true segment `seg` is a JSON array containing five elements, all required:[ starttime, endtime, freq.low, freq.high, labels ]`startime, endtime` - segment start and end positions, in seconds, relative to start of file as 0.`freq.low, freq.high` - for annotation boxes, frequency band in Hz. For segments (full-band annotations), both `0`. If both `0<freq<1`, old format is assumed, and treated as full-band segment (`0,0`).`labels` - a JSON array of labels for each type of sound detected:[ label, label, label... ]where each `label` is a JSON object, having some of the following fields:{ "species": "Kiwi (Little spotted)", "certainty": 0, "filter": "kiwi-best", "calltype": "f1", ... }`species` - string, either `"genus (species)"` or just plain `"species"`. May be `"Don't Know"` or any other label (`"Bellbird/Tui"`, `"Fantail (spp)"`...), except for the internal genus separator `>`. Required.`certainty` - numeric between 0 and 100. Currently, for `"species": "Don't Know"` only `0` allowed, `100` corresponds to green segments, and `50` corresponds to question marks in earlier formats. `(species, certainty)` defines a unique key for labels. Required.`filter` - string, name of the filter file that created this label, or `"M"` for manual annotations.`calltype` - string, to identify the call type. Call types can be annotated manually, or will be automatically generated from clusters during filter training. Required for automatic filters (i.e. if `filter` is not empty or `"M"`).Any additional attributes defined for this call (male/female, subjective loudness...) are optional and can be passed as key-value pairs.Thus, a full .data file may look like this:[ {"Operator": Alice, "Reviewer": Bob, "Duration": 60.0, "Noise": "windy"}, // metadata// a manually marked box[1.0, 19.0, 1200, 2500,[{ "species": "Kiwi (Little spotted)", "certainty": 100, "filter": "M", "loudness": 3 }]],// box from a "trill" filter[21.0, 23.0, 800, 6000,[{ "species": "Morepork", "certainty": 50, "filter": "ruru-90-10", "calltype": "trill" }]],// a manually marked segment with morepork and something else[35, 45, 0, 0,[{ "species": "Morepork", "certainty": 100, "filter": "M" },{ "species": "Don't Know", "certainty": 0, "filter": "M" }]]]## Filter files (.txt)A JSON array:{ "species": "Kiwi (Little spotted)", "SampleRate": 16000, "Filters": [], "NN": {}, ...}Main filter ID is the file name because this automatically ensures that no duplicate IDs are present at any installation of AviaNZ. This name can be any string permitted by the OS, and no further information is gathered from it.`species` - string. This label will be assigned as the `species` in segments generated by this filter. Can follow `"genus (species)"` format as described above. Required.`SampleRate` - integer. All analyses will be done after down-(up-)sampling to this rate. Required.`method` - string, `"wv"` or `"chp"`. Empty defaults to `"wv"`.Any extra parameters to be applied for all subfilters may be provided (such as `"wind"`).`Filters` - JSON array of filters corresponding to each type of call (at least one element). Each is a JSON object:{ "calltype": "clust1", "TimeRange": [min call length, max call length, avg syllable length, max gap between syllables], "WaveletParams": {"thr": 0.5, "M": 1.5, "nodes": [35, 37, 40]}, "FreqRange": [1000, 3000], ... }`calltype` - either user-defined call type, or automatically generated cluster ID. String. Required.`TimeRange` - JSON array of length 4: `[minlen, maxlen, avgsyl, maxgap]`, respectively min and max lengths of a call, average syllable length, and maximum gap between parts of same call. Required.`WaveletParams` - JSON object of parameters needed for wavelet filtering. Required. Currently uses:* `thr` - numeric, threshold for detecting calls. Required.* `nodes` - JSON array of wavelet nodes used in this filter. Required.* `M` - numeric, energy curve window in seconds. Required for `method="wv"`.* `win` - numeric, window for energy averaging in seconds. Required for `method="chp"`.`FreqRange` - frequency band for analysis. Identified calls will be marked as boxes with these limits, or as full-band segments if not provided.Any extra subfilter parameters may follow, such as `"F0"`.`PostResolution` - numeric. If present, detections will be merged and resplit into pieces of this many seconds (i.e. this parameter is both the merging gap and split piece length).`NN` - JSON object. Meta information about the Convolution Neural Network (NN) model for this species:"NN": {"NN_name": "Kiwi (Nth Is Brown)", "loss": "binary_crossentropy", "optimizer": "adam", "win": 0.25, "inputdim": [128, 30], "output": {"0": "Male", "1": "Female", "2": "Noise"}}If present, all the following are required:* `NN_name` - File name of the model, e.g. `Kiwi (Nth Is Brown).json` and `Kiwi (Nth Is Brown).h5` or `Kiwi (Nth Is Brown).weights.h5`.* `loss` - loss function.* `optimizer` - optimisation algorithm.* `win` - input image width in seconds.* `inputdim` - input dimension in pixels.* `output` - the output classes/labels.* `windowInc` - window width and increment.* `thr`- threshold for each call type.Thus, a full filter file may look like this:{ "species": "Kiwi (Little spotted)", "SampleRate": 16000, "Rain": false, "Wind": true,"Filters": [{ "calltype": "M", "TimeRange": [5, 60, 1, 3], "WaveletParams": {"nodes": [44, 45, 46], "thr": 0.5, "M": 1.5}, "F0": true, "FreqRange": [1500, 5000] },{ "calltype": "F", "TimeRange": [10.0, 30.0, 0.8, 1.0], "WaveletParams": {"nodes": [41, 44], "thr": 0.8, "M": 2}, "FreqRange": [1000, 2500] }],"NN": {"NN_name": "Kiwi (Little spotted)", "loss": "binary_crossentropy", "optimizer": "adam", "win": 0.25, "inputdim": [128, 30], "output": {"0": "M", "1": "F", "2": "Noise", "3": "Silence"}, "windowInc":[256, 128], "thr":[0.5, 0.3]}}## NN files (.JSON/.h5/.hdf5)A NN model has two files: model architecture is stored in a JSON file and the weights are stored in a Hierarchical Data Format 5 file (.h5 or .hdf5).All the NN models are stored in the user configdir/Filters and referred in the corresponding Filter files.## Correction files (.corrections/ .corrections_species)All Species Review mode generates .corrections:A JSON array where the first element stores metadata, and each remaining element corresponds to a segment changed by reviewer:[ Meta, [seg, newlabel], [seg, newlabel], [seg, newlabel] ... ]`Meta`: a JSON object (key-value pairs) containing any metadata, same as in .data.`seg`: Each segment seg is a JSON array containing five elements, same as in .data.`newlabel`: New label/s assigned to the segment by the reviewer.Single Species Review mode generates .corrections_species:A JSON array where the first element stores metadata, and each remaining element corresponds to a segment deleted by reviewer:[ Meta, seg, seg, seg ... ]`Meta`: a JSON object (key-value pairs) containing any metadata, same as in .data.`seg`: Each segment seg is a JSON array containing five elements, same as in .data.
package cmdimport ("encoding/json""flag""fmt""os""skraak/utils")// RunXXHash handles the "xxhash" subcommand//// JSON output schema://// {// "file": string, // Path to the hashed file// "hash": string // XXH64 hash (hex string)// }func RunXXHash(args []string) {fs := flag.NewFlagSet("xxhash", flag.ExitOnError)filePath := fs.String("file", "", "Path to file (required)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak xxhash --file <path>\n\n")fmt.Fprintf(os.Stderr, "Compute XXH64 hash of a file (same format stored in database).\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak xxhash --file recording.wav\n")fmt.Fprintf(os.Stderr, " skraak xxhash --file /path/to/audio.wav | jq '.hash'\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}if *filePath == "" {fmt.Fprintf(os.Stderr, "Error: --file is required\n\n")fs.Usage()os.Exit(1)}// Compute hashhash, err := utils.ComputeXXH64(*filePath)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}// Output as JSONoutput := map[string]string{"file": *filePath,"hash": hash,}enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("fmt""os")// RunUpdate handles the "update" commandfunc RunUpdate(args []string) {if len(args) < 1 {printUpdateUsage()os.Exit(1)}switch args[0] {case "dataset":RunDatasetUpdate(args[1:])case "location":RunLocationUpdate(args[1:])case "cluster":RunClusterUpdate(args[1:])case "pattern":RunPatternUpdate(args[1:])default:fmt.Fprintf(os.Stderr, "Unknown resource to update: %s\n", args[0])printUpdateUsage()os.Exit(1)}}func printUpdateUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak update <resource> [options]\n\n")fmt.Fprintf(os.Stderr, "Resources:\n")fmt.Fprintf(os.Stderr, " dataset Update an existing dataset\n")fmt.Fprintf(os.Stderr, " location Update an existing location\n")fmt.Fprintf(os.Stderr, " cluster Update an existing cluster\n")fmt.Fprintf(os.Stderr, " pattern Update an existing pattern\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak update dataset --db ./db/skraak.duckdb --id abc123 --name \"Updated Name\"\n")fmt.Fprintf(os.Stderr, " skraak update location --db ./db/skraak.duckdb --id loc123 --name \"New Name\" --lat -36.85 --lon 174.76\n")fmt.Fprintf(os.Stderr, " skraak update cluster --db ./db/skraak.duckdb --id clust123 --name \"New Name\" --sample-rate 192000\n")fmt.Fprintf(os.Stderr, " skraak update pattern --db ./db/skraak.duckdb --id pattern123 --name \"New Name\" --start-time 19:00 --end-time 05:00\n")}
package cmdimport ("context""encoding/json""flag""fmt""os""skraak/tools")// RunTime handles the "time" subcommand//// JSON output schema://// {// "time": string, // Current system time in RFC3339 format// "timezone": string, // System timezone// "unix": int // Unix timestamp in seconds// }func RunTime(args []string) {fs := flag.NewFlagSet("time", flag.ExitOnError)fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak time\n\n")fmt.Fprintf(os.Stderr, "Get the current system time with timezone information.\n\n")fmt.Fprintf(os.Stderr, "Examples:\n")fmt.Fprintf(os.Stderr, " skraak time\n")fmt.Fprintf(os.Stderr, " skraak time | jq '.iso'\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Get current timeoutput, err := tools.GetCurrentTime(context.Background(), tools.GetCurrentTimeInput{})if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}// Output as JSONenc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("context""encoding/json""flag""fmt""os""strings""skraak/tools")// RunSQL handles the "sql" subcommand// RunSQL handles CLI SQL query execution with direct database access//// JSON output schema://// {// "rows": [{"column_name": value, ...}, ...], // Query result rows// "row_count": int, // Number of rows returned// "columns": [ // Column metadata// {"name": string, "type": string}// ],// "limited": bool, // Whether results were truncated due to row limit// "query_executed": string // The actual query executed (with LIMIT applied)// }func RunSQL(args []string) {fs := flag.NewFlagSet("sql", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")limit := fs.Int("limit", 0, "Maximum rows to return (default 1000, max 10000)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak sql --db <path> [options] <query>\n\n")fmt.Fprintf(os.Stderr, "Execute a SQL SELECT query against the database.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak sql --db ./db/skraak.duckdb \"SELECT COUNT(*) FROM file WHERE active = true\"\n")fmt.Fprintf(os.Stderr, " skraak sql --db ./db/skraak.duckdb --limit 10 \"SELECT * FROM dataset\"\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}if *dbPath == "" {fmt.Fprintf(os.Stderr, "Error: --db is required\n\n")fs.Usage()os.Exit(1)}// Remaining args are the queryremaining := fs.Args()if len(remaining) == 0 {fmt.Fprintf(os.Stderr, "Error: query is required\n\n")fs.Usage()os.Exit(1)}query := strings.Join(remaining, " ")tools.SetDBPath(*dbPath)input := tools.ExecuteSQLInput{Query: query,}if *limit > 0 {input.Limit = limit}output, err := tools.ExecuteSQL(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("bufio""context""database/sql""encoding/json""flag""fmt""os""strings""skraak/db")// RunReplay handles the "replay" subcommandfunc RunReplay(args []string) {if len(args) < 1 {printReplayUsage()os.Exit(1)}switch args[0] {case "events":runReplayEvents(args[1:])default:fmt.Fprintf(os.Stderr, "Unknown replay subcommand: %s\n\n", args[0])printReplayUsage()os.Exit(1)}}func printReplayUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak replay <subcommand> [options]\n\n")fmt.Fprintf(os.Stderr, "Subcommands:\n")fmt.Fprintf(os.Stderr, " events Replay event log into database\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak replay events --db ./backup.duckdb --log ./skraak.duckdb.events.jsonl\n")fmt.Fprintf(os.Stderr, " skraak replay events --db ./backup.duckdb --log ./events.jsonl --dry-run\n")fmt.Fprintf(os.Stderr, " skraak replay events --db ./backup.duckdb --log ./events.jsonl --last 10\n")}func runReplayEvents(args []string) {fs := flag.NewFlagSet("replay events", flag.ExitOnError)dbPath := fs.String("db", "", "Path to target database (required)")logPath := fs.String("log", "", "Path to event log file (required)")dryRun := fs.Bool("dry-run", false, "Print events without executing")fromID := fs.String("from", "", "Start from event ID (inclusive)")toID := fs.String("to", "", "Stop at event ID (inclusive)")lastN := fs.Int("last", 0, "Replay last N events (0 = all)")continueOnError := fs.Bool("continue", false, "Continue past errors")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak replay events [options]\n\n")fmt.Fprintf(os.Stderr, "Replay event log into database.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak replay events --db ./backup.duckdb --log ./events.jsonl\n")fmt.Fprintf(os.Stderr, " skraak replay events --db ./backup.duckdb --log ./events.jsonl --dry-run\n")fmt.Fprintf(os.Stderr, " skraak replay events --db ./backup.duckdb --log ./events.jsonl --last 10\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *logPath == "" {missing = append(missing, "--log")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}// Read eventsevents, err := readEvents(*logPath)if err != nil {fmt.Fprintf(os.Stderr, "Error reading events: %v\n", err)os.Exit(1)}// Filter eventsevents = filterEvents(events, *fromID, *toID, *lastN)fmt.Fprintf(os.Stderr, "Found %d events to replay\n", len(events))if *dryRun {for i, event := range events {fmt.Printf("\n[%d/%d] Event %s (%s)\n", i+1, len(events), event.ID, event.Tool)for _, q := range event.Queries {fmt.Printf(" SQL: %s\n", truncateSQL(q.SQL, 80))fmt.Printf(" Params: %v\n", q.Parameters)}}return}// Open databasedatabase, err := db.OpenWriteableDB(*dbPath)if err != nil {fmt.Fprintf(os.Stderr, "Error opening database: %v\n", err)os.Exit(1)}defer database.Close()// Disable event logging for replaydb.SetEventLogConfig(db.EventLogConfig{Enabled: false})// Replay each eventsuccessCount := 0failCount := 0for i, event := range events {fmt.Fprintf(os.Stderr, "\n[%d/%d] Replaying event %s (%s)...\n", i+1, len(events), event.ID, event.Tool)err := replayEvent(database, event)if err != nil {failCount++fmt.Fprintf(os.Stderr, " ERROR: %v\n", err)if !*continueOnError {fmt.Fprintf(os.Stderr, "Stopping due to error. Use --continue to skip errors.\n")os.Exit(1)}} else {successCount++fmt.Fprintf(os.Stderr, " OK (%d queries)\n", len(event.Queries))}}fmt.Fprintf(os.Stderr, "\nReplay complete: %d succeeded, %d failed\n", successCount, failCount)}// TransactionEvent represents a transaction event from the logtype TransactionEvent struct {ID string `json:"id"`Timestamp string `json:"timestamp"`Tool string `json:"tool,omitempty"`Queries []QueryRecord `json:"queries"`Success bool `json:"success"`Duration int64 `json:"duration_ms"`}// QueryRecord represents a single SQL statement with parameterstype QueryRecord struct {SQL string `json:"sql"`Parameters []any `json:"parameters"`}// readEvents reads all events from a JSONL filefunc readEvents(path string) ([]TransactionEvent, error) {file, err := os.Open(path)if err != nil {return nil, fmt.Errorf("failed to open event log: %w", err)}defer func() { _ = file.Close() }()var events []TransactionEventscanner := bufio.NewScanner(file)scanner.Buffer(make([]byte, 20*1024*1024), 20*1024*1024) // 20MB max line sizelineNum := 0for scanner.Scan() {lineNum++line := scanner.Bytes()if len(line) == 0 {continue}var event TransactionEventif err := json.Unmarshal(line, &event); err != nil {fmt.Fprintf(os.Stderr, "Warning: failed to parse line %d: %v\n", lineNum, err)continue}events = append(events, event)}if err := scanner.Err(); err != nil {return nil, fmt.Errorf("error reading event log: %w", err)}return events, nil}// filterEvents filters events based on criteriafunc filterEvents(events []TransactionEvent, fromID, toID string, lastN int) []TransactionEvent {// Filter by fromIDif fromID != "" {startIdx := 0for i, e := range events {if e.ID == fromID {startIdx = ibreak}}events = events[startIdx:]}// Filter by toIDif toID != "" {endIdx := len(events)for i, e := range events {if e.ID == toID {endIdx = i + 1break}}events = events[:endIdx]}// Filter by lastNif lastN > 0 && len(events) > lastN {events = events[len(events)-lastN:]}// Only replay successful eventsvar filtered []TransactionEventfor _, e := range events {if e.Success {filtered = append(filtered, e)}}return filtered}// replayEvent replays a single transaction eventfunc replayEvent(database *sql.DB, event TransactionEvent) error {ctx := context.Background()tx, err := database.BeginTx(ctx, nil)if err != nil {return fmt.Errorf("failed to begin transaction: %w", err)}for _, q := range event.Queries {// Convert parameters to []interface{} for Exec_, err := tx.ExecContext(ctx, q.SQL, q.Parameters...)if err != nil {tx.Rollback()return fmt.Errorf("query failed: %w (SQL: %s)", err, truncateSQL(q.SQL, 50))}}if err := tx.Commit(); err != nil {return fmt.Errorf("failed to commit transaction: %w", err)}return nil}// truncateSQL truncates a SQL string for displayfunc truncateSQL(sql string, maxLen int) string {sql = strings.Join(strings.Fields(sql), " ") // Normalize whitespaceif len(sql) <= maxLen {return sql}return sql[:maxLen] + "..."}
package cmdimport ("encoding/json""flag""fmt""os""skraak/tools")// RunPrepend handles the "prepend" subcommand//// JSON output schema://// {// "folder": string, // Target folder path// "prefix": string, // Prefix that was prepended// "recursive": bool, // Whether subfolders were included// "dry_run": bool, // Whether this was a dry run// "renamed": [ // Successfully renamed files// {"old": string, "new": string}// ],// "skipped": [ // Skipped files// {"file": string, "reason": string}// ],// "errors": [ // Failed renames// {"file": string, "error": string}// ]// }func RunPrepend(args []string) {fs := flag.NewFlagSet("prepend", flag.ExitOnError)folder := fs.String("folder", "", "Target folder path (required)")prefix := fs.String("prefix", "", "String to prepend to filenames (required)")recursive := fs.Bool("recursive", false, "Include 1 level of subfolders")dryRun := fs.Bool("dry-run", false, "Show what would be renamed without doing it")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak prepend --folder <path> --prefix <string> [--recursive] [--dry-run]\n\n")fmt.Fprintf(os.Stderr, "Rename files by prepending a prefix.\n\n")fmt.Fprintf(os.Stderr, "Target files:\n")fmt.Fprintf(os.Stderr, " - *.wav, *.WAV (must start with datestring YYYYMMDD_HHMMSS)\n")fmt.Fprintf(os.Stderr, " - *.wav.data, *.WAV.data (must start with datestring YYYYMMDD_HHMMSS)\n")fmt.Fprintf(os.Stderr, " - log.txt (exact name, always renamed)\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak prepend --folder ./recordings --prefix LOC001\n")fmt.Fprintf(os.Stderr, " skraak prepend --folder ./data --prefix SITE_A --recursive\n")fmt.Fprintf(os.Stderr, " skraak prepend --folder ./test --prefix TEST --dry-run\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}if *folder == "" {fmt.Fprintf(os.Stderr, "Error: --folder is required\n\n")fs.Usage()os.Exit(1)}if *prefix == "" {fmt.Fprintf(os.Stderr, "Error: --prefix is required\n\n")fs.Usage()os.Exit(1)}// Run the prepend operationoutput, err := tools.Prepend(tools.PrependInput{Folder: *folder,Prefix: *prefix,Recursive: *recursive,DryRun: *dryRun,})if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}// Output as JSONenc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("context""flag""fmt""os""strconv""skraak/tools")// RunPatternCreate creates a new cyclic recording pattern.//// JSON output schema://// {// "pattern": {// "id": string, // Pattern ID (12 characters)// "record_s": int, // Record duration in seconds// "sleep_s": int, // Sleep duration in seconds// "created_at": string, // Creation timestamp (RFC3339)// "last_modified": string, // Last modification timestamp (RFC3339)// "active": bool // Whether the pattern is active// },// "message": string // Success message// }func RunPatternCreate(args []string) {fs := flag.NewFlagSet("pattern create", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")record := fs.Int("record", 0, "Record duration in seconds (required, must be positive)")sleep := fs.Int("sleep", 0, "Sleep duration in seconds (required, must be positive)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak pattern create [options]\n\n")fmt.Fprintf(os.Stderr, "Create a new cyclic recording pattern.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak pattern create --db ./db/skraak.duckdb --record 60 --sleep 1740\n")fmt.Fprintf(os.Stderr, " # Creates 60s record / 1740s sleep = 30 min cycle\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *record == 0 {missing = append(missing, "--record")}if *sleep == 0 {missing = append(missing, "--sleep")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()input := tools.PatternInput{RecordSeconds: record,SleepSeconds: sleep,}output, err := tools.CreateOrUpdatePattern(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}// RunPatternUpdate updates an existing recording pattern.//// JSON output schema: same as RunPatternCreatefunc RunPatternUpdate(args []string) {fs := flag.NewFlagSet("pattern update", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")id := fs.String("id", "", "Pattern ID (required)")recordStr := fs.String("record", "", "New record duration in seconds (optional)")sleepStr := fs.String("sleep", "", "New sleep duration in seconds (optional)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak pattern update [options]\n\n")fmt.Fprintf(os.Stderr, "Update an existing recording pattern. Only provided fields are updated.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak pattern update --db ./db/skraak.duckdb --id pattern123 --record 30\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *id == "" {missing = append(missing, "--id")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}// Parse optional integersvar record, sleep *intif *recordStr != "" {r, err := strconv.Atoi(*recordStr)if err != nil {fmt.Fprintf(os.Stderr, "Error: invalid record: %v\n", err)os.Exit(1)}record = &r}if *sleepStr != "" {s, err := strconv.Atoi(*sleepStr)if err != nil {fmt.Fprintf(os.Stderr, "Error: invalid sleep: %v\n", err)os.Exit(1)}sleep = &s}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()// Build input - only set fields that were providedinput := tools.PatternInput{ID: id,}if record != nil {input.RecordSeconds = record}if sleep != nil {input.SleepSeconds = sleep}output, err := tools.CreateOrUpdatePattern(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}
package cmdimport ("encoding/json""flag""fmt""os""skraak/utils")// RunMetadata handles the "metadata" subcommand//// JSON output schema://// {// "file": string, // Path to the WAV file// "duration_seconds": float, // Duration in seconds// "sample_rate": int, // Sample rate in Hz// "channels": int, // Number of audio channels// "bits_per_sample": int, // Bits per sample// "comment": string, // WAV comment (omitted if empty)// "artist": string, // WAV artist (omitted if empty)// "file_mod_time": string // File modification time RFC3339 (omitted if zero)// }func RunMetadata(args []string) {fs := flag.NewFlagSet("metadata", flag.ExitOnError)filePath := fs.String("file", "", "Path to WAV file (required)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak metadata --file <path>\n\n")fmt.Fprintf(os.Stderr, "Extract metadata from a WAV file header.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak metadata --file recording.wav\n")fmt.Fprintf(os.Stderr, " skraak metadata --file /path/to/audio.wav | jq '.duration_seconds'\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}if *filePath == "" {fmt.Fprintf(os.Stderr, "Error: --file is required\n\n")fs.Usage()os.Exit(1)}// Parse WAV headermetadata, err := utils.ParseWAVHeader(*filePath)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}// Output as JSONoutput := map[string]any{"file": *filePath,"duration_seconds": metadata.Duration,"sample_rate": metadata.SampleRate,"channels": metadata.Channels,"bits_per_sample": metadata.BitsPerSample,}// Add optional fields if presentif metadata.Comment != "" {output["comment"] = metadata.Comment}if metadata.Artist != "" {output["artist"] = metadata.Artist}if !metadata.FileModTime.IsZero() {output["file_mod_time"] = metadata.FileModTime.Format("2006-01-02T15:04:05Z07:00")}enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("context""flag""fmt""os""strconv""skraak/tools")// RunLocationCreate creates a new location with GPS coordinates.//// JSON output schema://// {// "location": {// "id": string, // Location ID (12 characters)// "dataset_id": string, // Parent dataset ID// "name": string, // Location name// "latitude": float, // Latitude in decimal degrees// "longitude": float, // Longitude in decimal degrees// "description": string, // Optional description (nullable)// "created_at": string, // Creation timestamp (RFC3339)// "last_modified": string, // Last modification timestamp (RFC3339)// "active": bool, // Whether the location is active// "timezone_id": string // IANA timezone ID// },// "message": string // Success message// }func RunLocationCreate(args []string) {fs := flag.NewFlagSet("location create", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")datasetID := fs.String("dataset", "", "Dataset ID (required)")name := fs.String("name", "", "Location name (required)")lat := fs.String("lat", "", "Latitude in decimal degrees (required)")lon := fs.String("lon", "", "Longitude in decimal degrees (required)")tz := fs.String("timezone", "", "IANA timezone ID (required, e.g. Pacific/Auckland)")description := fs.String("description", "", "Location description (optional)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak location create [options]\n\n")fmt.Fprintf(os.Stderr, "Create a new location with GPS coordinates.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak location create --db ./db/skraak.duckdb --dataset abc123 --name \"Site A\" --lat -36.85 --lon 174.76 --timezone Pacific/Auckland\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *datasetID == "" {missing = append(missing, "--dataset")}if *name == "" {missing = append(missing, "--name")}if *lat == "" {missing = append(missing, "--lat")}if *lon == "" {missing = append(missing, "--lon")}if *tz == "" {missing = append(missing, "--timezone")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}// Parse floatslatitude, err := strconv.ParseFloat(*lat, 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: invalid latitude: %v\n", err)os.Exit(1)}longitude, err := strconv.ParseFloat(*lon, 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: invalid longitude: %v\n", err)os.Exit(1)}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()input := tools.LocationInput{DatasetID: datasetID,Name: name,Latitude: &latitude,Longitude: &longitude,TimezoneID: tz,Description: description,}output, err := tools.CreateOrUpdateLocation(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}// RunLocationUpdate updates an existing location.//// JSON output schema: same as RunLocationCreatefunc RunLocationUpdate(args []string) {fs := flag.NewFlagSet("location update", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")id := fs.String("id", "", "Location ID (required)")name := fs.String("name", "", "New location name (optional)")lat := fs.String("lat", "", "New latitude (optional)")lon := fs.String("lon", "", "New longitude (optional)")tz := fs.String("timezone", "", "New IANA timezone ID (optional)")description := fs.String("description", "", "New location description (optional)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak location update [options]\n\n")fmt.Fprintf(os.Stderr, "Update an existing location. Only provided fields are updated.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak location update --db ./db/skraak.duckdb --id loc123 --name \"New Name\"\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *id == "" {missing = append(missing, "--id")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}// Parse optional floatsvar latitude, longitude *float64if *lat != "" {latVal, err := strconv.ParseFloat(*lat, 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: invalid latitude: %v\n", err)os.Exit(1)}latitude = &latVal}if *lon != "" {lonVal, err := strconv.ParseFloat(*lon, 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: invalid longitude: %v\n", err)os.Exit(1)}longitude = &lonVal}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()// Build input - only set fields that were provided (non-empty)input := tools.LocationInput{ID: id,}if *name != "" {input.Name = name}if latitude != nil {input.Latitude = latitude}if longitude != nil {input.Longitude = longitude}if *tz != "" {input.TimezoneID = tz}if *description != "" {input.Description = description}output, err := tools.CreateOrUpdateLocation(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}
package cmdimport ("encoding/json""flag""fmt""os""skraak/tools")// RunIsNight handles the "isnight" subcommand//// JSON output schema (full)://// {// "file_path": string, // Path to the WAV file// "timestamp_utc": string, // Recording start timestamp (UTC)// "solar_night": bool, // True if recorded during solar night// "civil_night": bool, // True if recorded during civil night// "diurnal_active": bool, // True if during diurnal active period// "moon_phase": float, // Moon phase (0.0=new, 1.0=full)// "duration_seconds": float, // Recording duration in seconds// "timestamp_source": string, // How timestamp was derived (comment/filename/mtime)// "midpoint_utc": string, // Recording midpoint timestamp (UTC)// "sunrise_utc": string, // Sunrise time (UTC), omitted if not applicable// "sunset_utc": string, // Sunset time (UTC), omitted if not applicable// "dawn_utc": string, // Civil dawn time (UTC), omitted if not applicable// "dusk_utc": string // Civil dusk time (UTC), omitted if not applicable// }//// JSON output schema (--brief)://// {// "file_path": string, // Path to the WAV file// "solar_night": bool // True if recorded during solar night// }func RunIsNight(args []string) {fs := flag.NewFlagSet("isnight", flag.ExitOnError)filePath := fs.String("file", "", "Path to WAV file (required)")lat := fs.Float64("lat", 0, "Latitude in decimal degrees (required)")lng := fs.Float64("lng", 0, "Longitude in decimal degrees (required)")timezone := fs.String("timezone", "UTC", "IANA timezone ID for filename timestamps (e.g. Pacific/Auckland)")brief := fs.Bool("brief", false, "Output only file_path and solar_night (saves tokens for batch use)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak isnight --file <path> --lat <lat> --lng <lng> [--timezone <tz>] [--brief]\n\n")fmt.Fprintf(os.Stderr, "Determine if a WAV file was recorded at night based on file metadata and GPS coordinates.\n\n")fmt.Fprintf(os.Stderr, "Uses the recording midpoint (not start time) for astronomical calculations.\n")fmt.Fprintf(os.Stderr, "Timestamp resolution: AudioMoth comment → filename → file modification time.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak isnight --file recording.wav --lat -36.85 --lng 174.76\n")fmt.Fprintf(os.Stderr, " skraak isnight --file recording.wav --lat -36.85 --lng 174.76 --timezone Pacific/Auckland\n")fmt.Fprintf(os.Stderr, " skraak isnight --file recording.wav --lat 51.51 --lng -0.13 | jq '.solar_night'\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}if *filePath == "" {fmt.Fprintf(os.Stderr, "Error: --file is required\n\n")fs.Usage()os.Exit(1)}if *lat == 0 && *lng == 0 {fmt.Fprintf(os.Stderr, "Error: --lat and --lng are required\n\n")fs.Usage()os.Exit(1)}output, err := tools.IsNight(tools.IsNightInput{FilePath: *filePath,Lat: *lat,Lng: *lng,Timezone: *timezone,})if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}var encErr errorif *brief {enc := json.NewEncoder(os.Stdout)encErr = enc.Encode(map[string]any{"file_path": output.FilePath,"solar_night": output.SolarNight,})} else {enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")encErr = enc.Encode(output)}if encErr != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", encErr)os.Exit(1)}}
package cmdimport ("context""encoding/json""flag""fmt""os""skraak/tools")// RunImport handles the "import" subcommandfunc RunImport(args []string) {if len(args) < 1 {printImportUsage()os.Exit(1)}switch args[0] {case "bulk":runImportBulk(args[1:])case "file":runImportFile(args[1:])case "folder":runImportFolder(args[1:])case "segments":runImportSegments(args[1:])case "unstructured":runImportUnstructured(args[1:])default:fmt.Fprintf(os.Stderr, "Unknown import subcommand: %s\n\n", args[0])printImportUsage()os.Exit(1)}}func printImportUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak import <subcommand> [options]\n\n")fmt.Fprintf(os.Stderr, "Subcommands:\n")fmt.Fprintf(os.Stderr, " file Import a single WAV file (structured datasets)\n")fmt.Fprintf(os.Stderr, " folder Import all WAV files from a folder (structured datasets)\n")fmt.Fprintf(os.Stderr, " bulk Bulk import WAV files from CSV (structured datasets)\n")fmt.Fprintf(os.Stderr, " unstructured Import WAV files into unstructured dataset (no location/cluster)\n")fmt.Fprintf(os.Stderr, " segments Import segments from AviaNZ .data files (structured datasets)\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak import bulk --db ./db/skraak.duckdb --dataset abc123 --csv import.csv --log progress.log\n")fmt.Fprintf(os.Stderr, " skraak import file --db ./db/skraak.duckdb --dataset abc123 --location loc456 --cluster clust789 --file /path/to/file.wav\n")fmt.Fprintf(os.Stderr, " skraak import folder --db ./db/skraak.duckdb --dataset abc123 --location loc456 --cluster clust789 --folder /path/to/folder\n")fmt.Fprintf(os.Stderr, " skraak import segments --db ./db/skraak.duckdb --dataset abc123 --location loc456 --cluster clust789 --folder /path/to/folder --mapping mapping.json\n")fmt.Fprintf(os.Stderr, " skraak import unstructured --db ./db/skraak.duckdb --dataset abc123 --folder /path/to/folder\n")}// runImportBulk bulk imports WAV files across multiple locations/clusters using a CSV file.//// JSON output schema://// {// "total_locations": int, // Total locations in CSV// "clusters_created": int, // New clusters created// "clusters_existing": int, // Existing clusters reused// "total_files_scanned": int, // Total WAV files found// "files_imported": int, // Successfully imported files// "files_duplicate": int, // Duplicate files skipped// "files_error": int, // Files that failed to import// "processing_time": string, // Human-readable duration// "errors": [string] // Error messages (omitted if empty)// }func runImportBulk(args []string) {fs := flag.NewFlagSet("import bulk", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")datasetID := fs.String("dataset", "", "Dataset ID (required)")csvPath := fs.String("csv", "", "Path to CSV file (required)")logPath := fs.String("log", "", "Path to progress log file (required)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak import bulk [options]\n\n")fmt.Fprintf(os.Stderr, "Bulk import WAV files across multiple locations/clusters using a CSV file.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nCSV format: location_name,location_id,directory_path,date_range,sample_rate,file_count\n")fmt.Fprintf(os.Stderr, "\nMonitor progress: tail -f <log-file>\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *datasetID == "" {missing = append(missing, "--dataset")}if *csvPath == "" {missing = append(missing, "--csv")}if *logPath == "" {missing = append(missing, "--log")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}// Set DB path and runtools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()input := tools.BulkFileImportInput{DatasetID: *datasetID,CSVPath: *csvPath,LogFilePath: *logPath,}fmt.Fprintf(os.Stderr, "Starting bulk import...\n")fmt.Fprintf(os.Stderr, " Database: %s\n", *dbPath)fmt.Fprintf(os.Stderr, " Dataset: %s\n", *datasetID)fmt.Fprintf(os.Stderr, " CSV: %s\n", *csvPath)fmt.Fprintf(os.Stderr, " Log: %s\n", *logPath)fmt.Fprintf(os.Stderr, "\nMonitor progress: tail -f %s\n\n", *logPath)output, err := tools.BulkFileImport(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)// Still print partial output if availableif output.TotalLocations > 0 || output.FilesImported > 0 {printJSON(output)}os.Exit(1)}printJSON(output)}// runImportFile imports a single WAV file into the database.//// JSON output schema://// {// "file_id": string, // Generated 21-character nanoid// "file_name": string, // Base filename// "hash": string, // XXH64 hash (16-character hex)// "duration_seconds": float, // File duration in seconds// "sample_rate": int, // Sample rate in Hz// "timestamp_local": string, // Local timestamp (RFC3339)// "is_audiomoth": bool, // AudioMoth detection// "is_duplicate": bool, // Skipped as duplicate// "processing_time": string, // Duration string// "error": string // Error message if failed (omitted if nil)// }func runImportFile(args []string) {fs := flag.NewFlagSet("import file", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")datasetID := fs.String("dataset", "", "Dataset ID (required)")locationID := fs.String("location", "", "Location ID (required)")clusterID := fs.String("cluster", "", "Cluster ID (required)")filePath := fs.String("file", "", "Path to WAV file (required)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak import file [options]\n\n")fmt.Fprintf(os.Stderr, "Import a single WAV file into the database.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak import file --db ./db/skraak.duckdb --dataset abc123 --location loc456 --cluster clust789 --file /path/to/file.wav\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *datasetID == "" {missing = append(missing, "--dataset")}if *locationID == "" {missing = append(missing, "--location")}if *clusterID == "" {missing = append(missing, "--cluster")}if *filePath == "" {missing = append(missing, "--file")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()input := tools.ImportFileInput{FilePath: *filePath,DatasetID: *datasetID,LocationID: *locationID,ClusterID: *clusterID,}fmt.Fprintf(os.Stderr, "Importing file: %s\n", *filePath)output, err := tools.ImportFile(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}// runImportFolder imports all WAV files from a folder into the database.//// JSON output schema://// {// "summary": {// "total_files": int, // Total WAV files found// "imported_files": int, // Successfully imported// "skipped_files": int, // Duplicates skipped// "failed_files": int, // Failed imports// "audiomoth_files": int, // AudioMoth files detected// "total_duration_seconds": float, // Total duration imported// "processing_time": string // Human-readable duration// },// "file_ids": [string], // List of successfully imported file IDs// "errors": [ // Import errors (omitted if empty)// {"file_name": string, "error": string, "stage": string}// ]// }func runImportFolder(args []string) {fs := flag.NewFlagSet("import folder", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")datasetID := fs.String("dataset", "", "Dataset ID (required)")locationID := fs.String("location", "", "Location ID (required)")clusterID := fs.String("cluster", "", "Cluster ID (required)")folderPath := fs.String("folder", "", "Path to folder containing WAV files (required)")recursive := fs.Bool("recursive", true, "Scan subfolders recursively (default: true)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak import folder [options]\n\n")fmt.Fprintf(os.Stderr, "Import all WAV files from a folder into the database.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak import folder --db ./db/skraak.duckdb --dataset abc123 --location loc456 --cluster clust789 --folder /path/to/folder\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *datasetID == "" {missing = append(missing, "--dataset")}if *locationID == "" {missing = append(missing, "--location")}if *clusterID == "" {missing = append(missing, "--cluster")}if *folderPath == "" {missing = append(missing, "--folder")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()input := tools.ImportAudioFilesInput{FolderPath: *folderPath,DatasetID: *datasetID,LocationID: *locationID,ClusterID: *clusterID,Recursive: recursive,}fmt.Fprintf(os.Stderr, "Importing from folder: %s\n", *folderPath)if *recursive {fmt.Fprintf(os.Stderr, "Scanning recursively...\n")}output, err := tools.ImportAudioFiles(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)// Still print partial results if availableif len(output.FileIDs) > 0 {printJSON(output)}os.Exit(1)}printJSON(output)}// runImportSegments imports segments from AviaNZ .data files into the database.//// JSON output schema://// {// "summary": {// "data_files_found": int, // .data files found// "data_files_processed": int, // .data files processed// "total_segments": int, // Total segments in .data files// "imported_segments": int, // Successfully imported segments// "imported_labels": int, // Successfully imported labels// "imported_subtypes": int, // Successfully imported subtypes// "processing_time_ms": int // Processing time in milliseconds// },// "segments": [// {// "segment_id": string, // Generated segment ID// "file_name": string, // Source WAV filename// "start_time": float, // Segment start time in seconds// "end_time": float, // Segment end time in seconds// "freq_low": float, // Low frequency bound// "freq_high": float, // High frequency bound// "labels": [// {// "label_id": string, // Generated label ID// "species": string, // Species name// "calltype": string, // Call type (omitted if empty)// "filter": string, // Filter name// "certainty": int, // Certainty level// "comment": string // Comment (omitted if empty)// }// ]// }// ],// "errors": [ // Import errors (omitted if empty)// {"file": string, "stage": string, "message": string}// ]// }func runImportSegments(args []string) {fs := flag.NewFlagSet("import segments", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")datasetID := fs.String("dataset", "", "Dataset ID (required)")locationID := fs.String("location", "", "Location ID (required)")clusterID := fs.String("cluster", "", "Cluster ID (required)")folderPath := fs.String("folder", "", "Path to folder containing .data files (required)")mappingPath := fs.String("mapping", "", "Path to mapping JSON file (required)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak import segments [options]\n\n")fmt.Fprintf(os.Stderr, "Import segments from AviaNZ .data files into the database.\n")fmt.Fprintf(os.Stderr, "Applies species/calltype mapping from JSON file.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nMapping file format:\n")fmt.Fprintf(os.Stderr, " {\n")fmt.Fprintf(os.Stderr, " \"GSK\": {\"species\": \"Roroa\", \"calltypes\": {\"Male\": \"Male - Solo\"}},\n")fmt.Fprintf(os.Stderr, " \"Don't Know\": {\"species\": \"Don't Know\"}\n")fmt.Fprintf(os.Stderr, " }\n")fmt.Fprintf(os.Stderr, "\nInvariants:\n")fmt.Fprintf(os.Stderr, " - All file hashes must already exist in database for the cluster\n")fmt.Fprintf(os.Stderr, " - All files must have no existing labels (fresh imports only)\n")fmt.Fprintf(os.Stderr, " - All filters, species, and calltypes must exist in database\n")fmt.Fprintf(os.Stderr, " - Bookmark flags are ignored (not stored in database)\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak import segments --db ./db/skraak.duckdb --dataset dset_id123 --location loc_id456 --cluster clust_id789 --folder /path/to/data --mapping mapping.json\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *datasetID == "" {missing = append(missing, "--dataset")}if *locationID == "" {missing = append(missing, "--location")}if *clusterID == "" {missing = append(missing, "--cluster")}if *folderPath == "" {missing = append(missing, "--folder")}if *mappingPath == "" {missing = append(missing, "--mapping")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()input := tools.ImportSegmentsInput{Folder: *folderPath,Mapping: *mappingPath,DatasetID: *datasetID,LocationID: *locationID,ClusterID: *clusterID,ProgressHandler: func(processed, total int, message string) {if total > 0 {percent := float64(processed) / float64(total) * 100fmt.Fprintf(os.Stderr, "\rProcessing .data files: %d/%d (%.0f%%) - %s", processed, total, percent, message)if processed == total {fmt.Fprintf(os.Stderr, "\n")}}},}fmt.Fprintf(os.Stderr, "Importing segments from: %s\n", *folderPath)fmt.Fprintf(os.Stderr, "Using mapping: %s\n", *mappingPath)output, err := tools.ImportSegments(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "\nError: %v\n", err)// Still print partial results if availableif len(output.Segments) > 0 || len(output.Errors) > 0 {printJSON(output)}os.Exit(1)}fmt.Fprintf(os.Stderr, "\nImport complete:\n")fmt.Fprintf(os.Stderr, " Data files processed: %d\n", output.Summary.DataFilesProcessed)fmt.Fprintf(os.Stderr, " Segments imported: %d\n", output.Summary.ImportedSegments)fmt.Fprintf(os.Stderr, " Labels imported: %d\n", output.Summary.ImportedLabels)fmt.Fprintf(os.Stderr, " Subtypes imported: %d\n", output.Summary.ImportedSubtypes)printJSON(output)}// runImportUnstructured imports WAV files into an unstructured dataset.//// JSON output schema://// {// "total_files": int, // Total WAV files found// "imported_files": int, // Successfully imported// "skipped_files": int, // Duplicates skipped// "failed_files": int, // Failed imports// "total_duration_seconds": float, // Total duration imported// "processing_time": string, // Human-readable duration// "errors": [ // Import errors (omitted if empty)// {"file_name": string, "error": string, "stage": string}// ]// }func runImportUnstructured(args []string) {fs := flag.NewFlagSet("import unstructured", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")datasetID := fs.String("dataset", "", "Dataset ID (required - must be 'unstructured' type)")folderPath := fs.String("folder", "", "Path to folder containing WAV files (required)")recursive := fs.Bool("recursive", true, "Scan subfolders recursively (default: true)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak import unstructured [options]\n\n")fmt.Fprintf(os.Stderr, "Import WAV files into an unstructured dataset.\n")fmt.Fprintf(os.Stderr, "Files are stored with minimal metadata (hash, duration, sample_rate, file modification time).\n")fmt.Fprintf(os.Stderr, "No location/cluster hierarchy required.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak import unstructured --db ./db/skraak.duckdb --dataset abc123 --folder /path/to/folder\n")fmt.Fprintf(os.Stderr, " skraak import unstructured --db ./db/skraak.duckdb --dataset abc123 --folder /path/to/folder --recursive=false\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *datasetID == "" {missing = append(missing, "--dataset")}if *folderPath == "" {missing = append(missing, "--folder")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()input := tools.ImportUnstructuredInput{DatasetID: *datasetID,FolderPath: *folderPath,Recursive: recursive,}fmt.Fprintf(os.Stderr, "Importing into unstructured dataset: %s\n", *datasetID)fmt.Fprintf(os.Stderr, "Scanning folder: %s\n", *folderPath)if *recursive {fmt.Fprintf(os.Stderr, "Scanning recursively...\n")}output, err := tools.ImportUnstructured(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}func printJSON(v any) {enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(v); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("context""encoding/json""flag""fmt""os""skraak/tools")// RunExport handles the "export" subcommand//// export dataset JSON output schema://// {// "dataset_id": string, // ID of the exported dataset// "dataset_name": string, // Name of the exported dataset// "output_path": string, // Path to the output database// "row_counts": {string: int}, // Row counts per table (table_name -> count)// "file_size_mb": float, // Output file size in MB (omitted if dry run)// "dry_run": bool, // Whether this was a dry run// "message": string // Summary message// }func RunExport(args []string) {if len(args) < 1 {printExportUsage()os.Exit(1)}switch args[0] {case "dataset":runExportDataset(args[1:])default:fmt.Fprintf(os.Stderr, "Unknown export subcommand: %s\n\n", args[0])printExportUsage()os.Exit(1)}}func printExportUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak export <subcommand> [options]\n\n")fmt.Fprintf(os.Stderr, "Subcommands:\n")fmt.Fprintf(os.Stderr, " dataset Export a dataset with all related data\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb\n")fmt.Fprintf(os.Stderr, " skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb --dry-run\n")}func runExportDataset(args []string) {fs := flag.NewFlagSet("export dataset", flag.ExitOnError)dbPath := fs.String("db", "", "Path to source DuckDB database (required)")datasetID := fs.String("id", "", "Dataset ID to export (required)")output := fs.String("output", "", "Output database path (required)")dryRun := fs.Bool("dry-run", false, "Show what would be exported without creating file")force := fs.Bool("force", false, "Overwrite existing output file")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak export dataset --db <path> --id <dataset_id> --output <path> [options]\n\n")fmt.Fprintf(os.Stderr, "Export a dataset with all related data to a new DuckDB database.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb\n")fmt.Fprintf(os.Stderr, " skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb --dry-run\n")fmt.Fprintf(os.Stderr, " skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb --force\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *datasetID == "" {missing = append(missing, "--id")}if *output == "" {missing = append(missing, "--output")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}tools.SetDBPath(*dbPath)input := tools.ExportDatasetInput{DatasetID: *datasetID,Output: *output,DryRun: *dryRun,Force: *force,}outputResult, err := tools.ExportDataset(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(outputResult); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("context""flag""fmt""os""skraak/tools")// RunDatasetCreate creates a new dataset.//// JSON output schema://// {// "dataset": {// "id": string, // Dataset ID (12 characters)// "name": string, // Dataset name// "description": string, // Optional description (nullable)// "created_at": string, // Creation timestamp (RFC3339)// "last_modified": string, // Last modification timestamp (RFC3339)// "active": bool, // Whether the dataset is active// "type": string // Dataset type: "structured"/"unstructured"/"test"/"train"// },// "message": string // Success message// }func RunDatasetCreate(args []string) {fs := flag.NewFlagSet("create dataset", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")name := fs.String("name", "", "Dataset name (required)")dsType := fs.String("type", "structured", "Dataset type: structured (default), unstructured, test, train")description := fs.String("description", "", "Dataset description (optional)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak create dataset [options]\n\n")fmt.Fprintf(os.Stderr, "Create a new dataset.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak create dataset --db ./db/skraak.duckdb --name \"My Dataset\"\n")fmt.Fprintf(os.Stderr, " skraak create dataset --db ./db/skraak.duckdb --name \"Training Data\" --type train --description \"For ML training\"\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *name == "" {missing = append(missing, "--name")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()input := tools.DatasetInput{Name: name,Type: dsType,Description: description,}output, err := tools.CreateOrUpdateDataset(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}// RunDatasetUpdate updates an existing dataset.//// JSON output schema: same as RunDatasetCreatefunc RunDatasetUpdate(args []string) {fs := flag.NewFlagSet("update dataset", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")id := fs.String("id", "", "Dataset ID (required)")name := fs.String("name", "", "New dataset name")dsType := fs.String("type", "", "New dataset type: structured, unstructured, test, train")description := fs.String("description", "", "New dataset description")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak update dataset [options]\n\n")fmt.Fprintf(os.Stderr, "Update an existing dataset. Only provided fields are updated.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak update dataset --db ./db/skraak.duckdb --id abc123 --name \"Updated Name\"\n")fmt.Fprintf(os.Stderr, " skraak update dataset --db ./db/skraak.duckdb --id abc123 --type train\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *id == "" {missing = append(missing, "--id")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()// Build input - only set fields that were provided (non-empty)input := tools.DatasetInput{ID: id,}if *name != "" {input.Name = name}if *dsType != "" {input.Type = dsType}if *description != "" {input.Description = description}output, err := tools.CreateOrUpdateDataset(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}
package cmdimport ("fmt""os")// RunCreate handles the "create" commandfunc RunCreate(args []string) {if len(args) < 1 {printCreateUsage()os.Exit(1)}switch args[0] {case "dataset":RunDatasetCreate(args[1:])case "location":RunLocationCreate(args[1:])case "cluster":RunClusterCreate(args[1:])case "pattern":RunPatternCreate(args[1:])default:fmt.Fprintf(os.Stderr, "Unknown resource to create: %s\n", args[0])printCreateUsage()os.Exit(1)}}func printCreateUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak create <resource> [options]\n\n")fmt.Fprintf(os.Stderr, "Resources:\n")fmt.Fprintf(os.Stderr, " dataset Create a new dataset\n")fmt.Fprintf(os.Stderr, " location Create a new location\n")fmt.Fprintf(os.Stderr, " cluster Create a new cluster\n")fmt.Fprintf(os.Stderr, " pattern Create a new pattern\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak create dataset --db ./db/skraak.duckdb --name \"Test Dataset\"\n")fmt.Fprintf(os.Stderr, " skraak create location --db ./db/skraak.duckdb --dataset abc123 --name \"Site A\" --lat -36.85 --lon 174.76 --timezone Pacific/Auckland\n")fmt.Fprintf(os.Stderr, " skraak create cluster --db ./db/skraak.duckdb --dataset abc123 --location loc456 --name \"2024-01\" --sample-rate 250000\n")fmt.Fprintf(os.Stderr, " skraak create pattern --db ./db/skraak.duckdb --dataset abc123 --name \"Recording Schedule\" --type daily --start-time 18:00 --end-time 06:00\n")}
package cmdimport ("fmt""os""skraak/db")// initEventLog configures transaction event logging for the given database path.// Returns a cleanup function that should be deferred by the caller.func initEventLog(dbPath string) func() {db.SetEventLogConfig(db.EventLogConfig{Enabled: true,Path: dbPath + ".events.jsonl",})return func() {if err := db.CloseEventLog(); err != nil {fmt.Fprintf(os.Stderr, "Warning: failed to close event log: %v\n", err)}}}
package cmdimport ("context""flag""fmt""os""strconv""skraak/tools")// RunClusterCreate creates a new cluster for grouping recordings.//// JSON output schema://// {// "cluster": {// "id": string, // Cluster ID (12 characters)// "dataset_id": string, // Parent dataset ID// "location_id": string, // Parent location ID// "name": string, // Cluster name// "description": string, // Optional description (nullable)// "created_at": string, // Creation timestamp (RFC3339)// "last_modified": string, // Last modification timestamp (RFC3339)// "active": bool, // Whether the cluster is active// "cyclic_recording_pattern_id": string, // Optional pattern ID (nullable)// "sample_rate": int // Sample rate in Hz// },// "message": string // Success message// }func RunClusterCreate(args []string) {fs := flag.NewFlagSet("cluster create", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")datasetID := fs.String("dataset", "", "Dataset ID (required)")locationID := fs.String("location", "", "Location ID (required)")name := fs.String("name", "", "Cluster name (required)")sampleRate := fs.String("sample-rate", "", "Sample rate in Hz (required)")description := fs.String("description", "", "Cluster description (optional)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak cluster create [options]\n\n")fmt.Fprintf(os.Stderr, "Create a new cluster for grouping recordings.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak cluster create --db ./db/skraak.duckdb --dataset abc123 --location loc456 --name \"2024-01\" --sample-rate 250000\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *datasetID == "" {missing = append(missing, "--dataset")}if *locationID == "" {missing = append(missing, "--location")}if *name == "" {missing = append(missing, "--name")}if *sampleRate == "" {missing = append(missing, "--sample-rate")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}// Parse sample ratesr, err := strconv.Atoi(*sampleRate)if err != nil {fmt.Fprintf(os.Stderr, "Error: invalid sample rate: %v\n", err)os.Exit(1)}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()input := tools.ClusterInput{DatasetID: datasetID,LocationID: locationID,Name: name,SampleRate: &sr,Description: description,}output, err := tools.CreateOrUpdateCluster(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}// RunClusterUpdate updates an existing cluster.//// JSON output schema: same as RunClusterCreatefunc RunClusterUpdate(args []string) {fs := flag.NewFlagSet("cluster update", flag.ExitOnError)dbPath := fs.String("db", "", "Path to DuckDB database (required)")id := fs.String("id", "", "Cluster ID (required)")name := fs.String("name", "", "New cluster name (optional)")sampleRate := fs.String("sample-rate", "", "New sample rate in Hz (optional)")description := fs.String("description", "", "New cluster description (optional)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak cluster update [options]\n\n")fmt.Fprintf(os.Stderr, "Update an existing cluster. Only provided fields are updated.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak cluster update --db ./db/skraak.duckdb --id clust123 --name \"New Name\"\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsmissing := []string{}if *dbPath == "" {missing = append(missing, "--db")}if *id == "" {missing = append(missing, "--id")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}// Parse optional sample ratevar sr *intif *sampleRate != "" {srVal, err := strconv.Atoi(*sampleRate)if err != nil {fmt.Fprintf(os.Stderr, "Error: invalid sample rate: %v\n", err)os.Exit(1)}sr = &srVal}tools.SetDBPath(*dbPath)defer initEventLog(*dbPath)()// Build input - only set fields that were provided (non-empty)input := tools.ClusterInput{ID: id,}if *name != "" {input.Name = name}if sr != nil {input.SampleRate = sr}if *description != "" {input.Description = description}output, err := tools.CreateOrUpdateCluster(context.Background(), input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}printJSON(output)}
package cmdimport ("encoding/json""fmt""os""strconv""skraak/tools""skraak/utils")func printPushCertaintyUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak calls push-certainty [options]\n\n")fmt.Fprintf(os.Stderr, "Promote certainty=90 segments to certainty=100 for a filtered set.\n")fmt.Fprintf(os.Stderr, "Filtering logic matches 'calls classify' exactly. Reviewer is set from config.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fmt.Fprintf(os.Stderr, " --folder <path> Path to folder containing .data files (required, or --file)\n")fmt.Fprintf(os.Stderr, " --file <path> Path to a single .data file (required, or --folder)\n")fmt.Fprintf(os.Stderr, " --filter <name> Scope to filter name (optional)\n")fmt.Fprintf(os.Stderr, " --species <name> Scope to species, optionally with calltype (e.g. Kiwi, Kiwi+Duet)\n")fmt.Fprintf(os.Stderr, " --night Only act on solar-night recordings (requires --lat and --lng)\n")fmt.Fprintf(os.Stderr, " --day Only act on solar-day recordings (requires --lat and --lng)\n")fmt.Fprintf(os.Stderr, " --lat <float> Latitude in decimal degrees (required with --night or --day)\n")fmt.Fprintf(os.Stderr, " --lng <float> Longitude in decimal degrees (required with --night or --day)\n")fmt.Fprintf(os.Stderr, " --timezone <zone> IANA timezone ID (e.g. Pacific/Auckland)\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls push-certainty --folder ./data --species Kiwi\n")fmt.Fprintf(os.Stderr, " skraak calls push-certainty --folder ./data --species Kiwi --night --lat -45.5 --lng 167.4\n")}// runCallsPushCertainty promotes certainty=90 segments to certainty=100 for a filtered set.//// JSON output schema://// {// "segments_updated": int, // Number of segments promoted from 90→100// "files_updated": int, // Number of .data files modified// "time_filtered_count": int // Files skipped by --night/--day filter// }func runCallsPushCertainty(args []string) {var folder, file, filter, species, timezone stringvar night, day boolvar lat, lng float64var latSet, lngSet booli := 0for i < len(args) {arg := args[i]switch arg {case "--folder":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --folder requires a value\n")os.Exit(1)}folder = args[i+1]i += 2case "--file":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --file requires a value\n")os.Exit(1)}file = args[i+1]i += 2case "--filter":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --filter requires a value\n")os.Exit(1)}filter = args[i+1]i += 2case "--species":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --species requires a value\n")os.Exit(1)}species = args[i+1]i += 2case "--night":night = truei++case "--day":day = truei++case "--lat":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --lat requires a value\n")os.Exit(1)}v, err := strconv.ParseFloat(args[i+1], 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: --lat must be a number\n")os.Exit(1)}lat = vlatSet = truei += 2case "--lng":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --lng requires a value\n")os.Exit(1)}v, err := strconv.ParseFloat(args[i+1], 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: --lng must be a number\n")os.Exit(1)}lng = vlngSet = truei += 2case "--timezone":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --timezone requires a value\n")os.Exit(1)}timezone = args[i+1]i += 2case "--help", "-h":printPushCertaintyUsage()os.Exit(0)default:fmt.Fprintf(os.Stderr, "Error: unknown flag: %s\n\n", arg)printPushCertaintyUsage()os.Exit(1)}}if folder == "" && file == "" {fmt.Fprintf(os.Stderr, "Error: missing required flag: --folder or --file\n\n")printPushCertaintyUsage()os.Exit(1)}if night && day {fmt.Fprintf(os.Stderr, "Error: --night and --day are mutually exclusive\n\n")printPushCertaintyUsage()os.Exit(1)}if (night || day) && (!latSet || !lngSet) {fmt.Fprintf(os.Stderr, "Error: --night/--day requires both --lat and --lng\n\n")printPushCertaintyUsage()os.Exit(1)}cfg, cfgPath, err := utils.LoadConfig()if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)fmt.Fprintf(os.Stderr, "Create %s with a \"classify\" section; run `skraak calls classify --help` for an example.\n", cfgPath)os.Exit(1)}if cfg.Classify.Reviewer == "" {fmt.Fprintf(os.Stderr, "Error: %s is missing \"classify.reviewer\"\n", cfgPath)os.Exit(1)}speciesName, callType := utils.ParseSpeciesCallType(species)config := tools.PushCertaintyConfig{Folder: folder,File: file,Filter: filter,Species: speciesName,CallType: callType,Night: night,Day: day,Lat: lat,Lng: lng,Timezone: timezone,Reviewer: cfg.Classify.Reviewer,}result, err := tools.PushCertainty(config)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}if result.TimeFilteredCount > 0 {label := "daytime"if config.Day {label = "nighttime"}fmt.Fprintf(os.Stderr, "Skipped %d %s files\n", result.TimeFilteredCount, label)}fmt.Fprintf(os.Stderr, "Updated %d segments across %d files\n",result.SegmentsUpdated, result.FilesUpdated)enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(result); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("encoding/json""flag""fmt""os""skraak/tools")// runCallsPropagate propagates verified classifications between filters in .data files.//// JSON output schema (--file mode)://// {// "file": string, // .data file path// "from_filter": string, // Source filter name// "to_filter": string, // Target filter name// "species": string, // Species propagated// "filters_missing": bool, // True if file lacks one or both filters (omitted if false)// "targets_examined": int, // Target labels examined// "propagated": int, // Target labels updated// "skipped_no_overlap": int, // Targets with no overlapping source// "skipped_conflict": int, // Targets with conflicting sources// "conflicts": [ // Conflict details (omitted if empty)// {// "file": string, // .data filename (omitted in single-file mode)// "target_start": float, // Target segment start (seconds)// "target_end": float, // Target segment end (seconds)// "target_calltype": string, // Target call type (omitted if empty)// "source_choices": [// {// "start": float, // Source segment start// "end": float, // Source segment end// "species": string, // Source species// "calltype": string // Source call type (omitted if empty)// }// ]// }// ],// "changes": [ // Change details (omitted if empty)// {// "target_start": float, // Target segment start// "target_end": float, // Target segment end// "prev_species": string, // Previous species// "prev_calltype": string, // Previous call type (omitted if empty)// "prev_certainty": int, // Previous certainty// "new_species": string, // New species// "new_calltype": string, // New call type (omitted if empty)// "new_certainty": int // New certainty// }// ],// "error": string // Error message (omitted if empty)// }//// JSON output schema (--folder mode)://// {// "folder": string, // Folder path// "from_filter": string, // Source filter name// "to_filter": string, // Target filter name// "species": string, // Species propagated// "files_total": int, // Total .data files scanned// "files_with_both_filters": int, // Files containing both filters// "files_skipped_no_filter": int, // Files missing a filter// "files_changed": int, // Files with at least one propagation// "files_errored": int, // Files with errors// "targets_examined": int, // Total target labels examined// "propagated": int, // Total target labels updated// "skipped_no_overlap": int, // Targets with no overlapping source// "skipped_conflict": int, // Targets with conflicting sources// "conflicts": [PropagateConflict], // See --file mode conflict schema// "errors": [CallsPropagateOutput], // Per-file error outputs (omitted if empty)// "error": string // Top-level error (omitted if empty)// }func runCallsPropagate(args []string) {fs := flag.NewFlagSet("calls propagate", flag.ExitOnError)file := fs.String("file", "", "Path to a single .data file (mutually exclusive with --folder)")folder := fs.String("folder", "", "Path to folder containing .data files (mutually exclusive with --file)")from := fs.String("from", "", "Source filter name (required)")to := fs.String("to", "", "Target filter name (required)")species := fs.String("species", "", "Species to propagate (required, e.g. Kiwi)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak calls propagate [options]\n\n")fmt.Fprintf(os.Stderr, "Propagate verified classifications from one filter to another within a .data file\n")fmt.Fprintf(os.Stderr, "or across every .data file in a folder.\n\n")fmt.Fprintf(os.Stderr, "Only source labels with certainty=100 and matching --species are considered.\n")fmt.Fprintf(os.Stderr, "Target labels (filter=--to) are updated when their certainty is 70 or 0.\n")fmt.Fprintf(os.Stderr, "Updated target labels are set to certainty=90; file reviewer is set to \"Skraak\".\n")fmt.Fprintf(os.Stderr, "Targets already at certainty=100 or 90 are left alone.\n")fmt.Fprintf(os.Stderr, "Files that do not contain both --from and --to filter labels are skipped.\n\n")fmt.Fprintf(os.Stderr, "Exactly one of --file or --folder is required.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls propagate --file rec.wav.data \\\n")fmt.Fprintf(os.Stderr, " --from opensoundscape-kiwi-1.2 --to opensoundscape-kiwi-1.5 --species Kiwi\n\n")fmt.Fprintf(os.Stderr, " skraak calls propagate --folder ./recordings \\\n")fmt.Fprintf(os.Stderr, " --from opensoundscape-kiwi-1.2 --to opensoundscape-kiwi-1.5 --species Kiwi\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}if (*file == "") == (*folder == "") {fmt.Fprintf(os.Stderr, "Error: exactly one of --file or --folder is required\n\n")fs.Usage()os.Exit(1)}missing := []string{}if *from == "" {missing = append(missing, "--from")}if *to == "" {missing = append(missing, "--to")}if *species == "" {missing = append(missing, "--species")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)fs.Usage()os.Exit(1)}enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if *file != "" {result, err := tools.CallsPropagate(tools.CallsPropagateInput{File: *file,FromFilter: *from,ToFilter: *to,Species: *species,})if err != nil {fmt.Fprintf(os.Stderr, "Error: %s\n", result.Error)os.Exit(1)}if err := enc.Encode(result); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}return}result, err := tools.CallsPropagateFolder(tools.CallsPropagateFolderInput{Folder: *folder,FromFilter: *from,ToFilter: *to,Species: *species,})if err != nil {fmt.Fprintf(os.Stderr, "Error: %s\n", result.Error)os.Exit(1)}fmt.Fprintf(os.Stderr,"Files: %d total, %d with both filters, %d skipped (missing filter), %d changed, %d errored\n",result.FilesTotal, result.FilesWithBothFilters, result.FilesSkippedNoFilter,result.FilesChanged, result.FilesErrored)fmt.Fprintf(os.Stderr,"Targets: %d examined, %d propagated, %d no-overlap, %d conflicts\n",result.TargetsExamined, result.Propagated, result.SkippedNoOverlap, result.SkippedConflict)if err := enc.Encode(result); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("encoding/json""fmt""os""strconv""strings""skraak/tools")func printModifyUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak calls modify [options]\n\n")fmt.Fprintf(os.Stderr, "Modify a label in a .data file.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fmt.Fprintf(os.Stderr, " --file <path> Path to .data file (required)\n")fmt.Fprintf(os.Stderr, " --reviewer <name> Reviewer name (required)\n")fmt.Fprintf(os.Stderr, " --filter <name> Filter name to match labels (required)\n")fmt.Fprintf(os.Stderr, " --segment <start-end> Segment time range in integer seconds (required, e.g., 12-15)\n")fmt.Fprintf(os.Stderr, " --certainty <int> Certainty value 0-100 (required)\n")fmt.Fprintf(os.Stderr, " --species <name> Species to set (e.g., Kiwi, Kiwi+Male, Noise)\n")fmt.Fprintf(os.Stderr, " --bookmark Mark segment as bookmarked for navigation\n")fmt.Fprintf(os.Stderr, " --comment <text> User comment (max 140 chars, ASCII only)\n")fmt.Fprintf(os.Stderr, "\nSegment matching:\n")fmt.Fprintf(os.Stderr, " Segments are matched by floor(start) and ceil(end) times.\n")fmt.Fprintf(os.Stderr, " For example, a segment from 12.3s to 14.5s matches --segment 12-15.\n")fmt.Fprintf(os.Stderr, "\nBehavior:\n")fmt.Fprintf(os.Stderr, " Always updates reviewer on file metadata.\n")fmt.Fprintf(os.Stderr, " If all specified values match current values, no modification is made.\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " # Change species and certainty (incorrect classification)\n")fmt.Fprintf(os.Stderr, " skraak calls modify --file recording.data --reviewer GLM-5 \\\n")fmt.Fprintf(os.Stderr, " --filter mymodel --segment 12-15 --species Kiwi+Male --certainty 100\n\n")fmt.Fprintf(os.Stderr, " # Change certainty only (correct classification)\n")fmt.Fprintf(os.Stderr, " skraak calls modify --file recording.data --reviewer GLM-5 \\\n")fmt.Fprintf(os.Stderr, " --filter mymodel --segment 12-15 --certainty 100\n\n")fmt.Fprintf(os.Stderr, " # Change to Noise (clears calltype)\n")fmt.Fprintf(os.Stderr, " skraak calls modify --file recording.data --reviewer GLM-5 \\\n")fmt.Fprintf(os.Stderr, " --filter mymodel --segment 67-88 --species Noise --certainty 100\n\n")fmt.Fprintf(os.Stderr, " # Bookmark a segment for later review\n")fmt.Fprintf(os.Stderr, " skraak calls modify --file recording.data --reviewer GLM-5 \\\n")fmt.Fprintf(os.Stderr, " --filter mymodel --segment 12-15 --certainty 100 --bookmark\n\n")fmt.Fprintf(os.Stderr, " # Add a comment to a segment\n")fmt.Fprintf(os.Stderr, " skraak calls modify --file recording.data --reviewer GLM-5 \\\n")fmt.Fprintf(os.Stderr, " --filter mymodel --segment 12-15 --certainty 100 --comment \"Good example of duet\"\n")}// RunCallsModify handles the "calls modify" subcommand//// JSON output schema://// {// "file": string, // .data file path// "segment_start": int, // Matched segment start (seconds, floored)// "segment_end": int, // Matched segment end (seconds, ceiled)// "species": string, // Updated species (omitted if unchanged)// "calltype": string, // Updated call type (omitted if empty)// "certainty": int, // Updated certainty (omitted if unchanged)// "bookmark": bool, // Bookmark flag (omitted if not set)// "comment": string, // Comment (omitted if empty)// "previous_value": string, // Description of previous label value (omitted if unchanged)// "error": string // Error message (omitted if no error)// }func RunCallsModify(args []string) {var file, reviewer, filter, segment, species, comment stringvar certainty intvar certaintySet, bookmark bool// Parse argumentsi := 0for i < len(args) {arg := args[i]switch arg {case "--file":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --file requires a value\n")os.Exit(1)}file = args[i+1]i += 2case "--reviewer":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --reviewer requires a value\n")os.Exit(1)}reviewer = args[i+1]i += 2case "--filter":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --filter requires a value\n")os.Exit(1)}filter = args[i+1]i += 2case "--segment":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --segment requires a value\n")os.Exit(1)}segment = args[i+1]i += 2case "--species":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --species requires a value\n")os.Exit(1)}species = args[i+1]i += 2case "--certainty":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --certainty requires a value\n")os.Exit(1)}v, err := strconv.Atoi(args[i+1])if err != nil {fmt.Fprintf(os.Stderr, "Error: --certainty must be an integer\n")os.Exit(1)}certainty = vcertaintySet = truei += 2case "--bookmark":bookmark = truei++case "--comment":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --comment requires a value\n")os.Exit(1)}comment = args[i+1]i += 2case "-h", "--help":printModifyUsage()os.Exit(0)default:// Check for unknown flagsif strings.HasPrefix(arg, "--") {fmt.Fprintf(os.Stderr, "Error: unknown flag: %s\n\n", arg)printModifyUsage()os.Exit(1)}i++}}// Validate required flagsmissing := []string{}if file == "" {missing = append(missing, "--file")}if reviewer == "" {missing = append(missing, "--reviewer")}if filter == "" {missing = append(missing, "--filter")}if segment == "" {missing = append(missing, "--segment")}if !certaintySet {missing = append(missing, "--certainty")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)printModifyUsage()os.Exit(1)}// Validate certainty rangeif certainty < 0 || certainty > 100 {fmt.Fprintf(os.Stderr, "Error: --certainty must be between 0 and 100\n")os.Exit(1)}// Build inputinput := tools.CallsModifyInput{File: file,Reviewer: reviewer,Filter: filter,Segment: segment,Species: species,Certainty: certainty,Comment: comment,}if bookmark {input.Bookmark = &bookmark}// Executeresult, err := tools.CallsModify(input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %s\n", result.Error)os.Exit(1)}// Output JSONdata, _ := json.Marshal(result)fmt.Println(string(data))}
package cmdimport ("encoding/json""fmt""os""skraak/tools")func printDetectAnomaliesUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak calls detect-anomalies [options]\n\n")fmt.Fprintf(os.Stderr, "Compare corresponding segments across ML model filters and flag disagreements.\n")fmt.Fprintf(os.Stderr, "Segments are matched by time overlap. Lonely segments (no overlap in all models) are skipped.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fmt.Fprintf(os.Stderr, " --folder <path> Folder containing .data files (required)\n")fmt.Fprintf(os.Stderr, " --model <name> Filter name to compare (required, repeat for each model, min 2)\n")fmt.Fprintf(os.Stderr, " --species <name> Scope to species or species+calltype (optional, repeat to add more)\n")fmt.Fprintf(os.Stderr, "\nAnomaly types:\n")fmt.Fprintf(os.Stderr, " label_mismatch Species or calltype disagrees across models\n")fmt.Fprintf(os.Stderr, " certainty_mismatch Labels agree but certainty values differ\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls detect-anomalies --folder ./data \\\n")fmt.Fprintf(os.Stderr, " --model opensoundscape-kiwi-1.0 --model opensoundscape-kiwi-1.2\n")fmt.Fprintf(os.Stderr, " skraak calls detect-anomalies --folder ./data \\\n")fmt.Fprintf(os.Stderr, " --model opensoundscape-kiwi-1.0 --model opensoundscape-kiwi-1.2 --model opensoundscape-kiwi-1.5 \\\n")fmt.Fprintf(os.Stderr, " --species Kiwi+Duet --species Kiwi+Male\n")}// runCallsDetectAnomalies compares segments across ML model filters and flags disagreements.//// JSON output schema://// {// "folder": string, // Folder path// "models": [string], // Model filter names compared// "files_examined": int, // Total .data files examined// "files_with_all_models": int, // Files containing all specified models// "anomalies_total": int, // Total anomalies found// "label_mismatches": int, // Species/calltype disagreements// "certainty_mismatches": int, // Certainty disagreements// "anomalies": [ // Anomaly details (omitted if empty)// {// "file": string, // .data filename// "type": string, // "label_mismatch" | "certainty_mismatch"// "segments": [// {// "model": string, // Filter name// "start": float, // Segment start (seconds)// "end": float, // Segment end (seconds)// "species": string, // Species name// "calltype": string, // Call type (omitted if empty)// "certainty": int // Certainty level (0-100)// }// ]// }// ],// "error": string // Error message (omitted if empty)// }func runCallsDetectAnomalies(args []string) {var folder stringvar models []stringvar species []stringi := 0for i < len(args) {arg := args[i]switch arg {case "--folder":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --folder requires a value\n")os.Exit(1)}folder = args[i+1]i += 2case "--model":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --model requires a value\n")os.Exit(1)}models = append(models, args[i+1])i += 2case "--species":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --species requires a value\n")os.Exit(1)}species = append(species, args[i+1])i += 2case "--help", "-h":printDetectAnomaliesUsage()os.Exit(0)default:fmt.Fprintf(os.Stderr, "Error: unknown flag: %s\n\n", arg)printDetectAnomaliesUsage()os.Exit(1)}}if folder == "" {fmt.Fprintf(os.Stderr, "Error: --folder is required\n\n")printDetectAnomaliesUsage()os.Exit(1)}if len(models) < 2 {fmt.Fprintf(os.Stderr, "Error: at least 2 --model values required\n\n")printDetectAnomaliesUsage()os.Exit(1)}output, err := tools.DetectAnomalies(tools.DetectAnomaliesInput{Folder: folder,Models: models,Species: species,})if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}fmt.Fprintf(os.Stderr, "Examined %d files, %d had all models\n",output.FilesExamined, output.FilesWithAllModels)fmt.Fprintf(os.Stderr, "Anomalies: %d total (%d label, %d certainty)\n",output.AnomaliesTotal, output.LabelMismatches, output.CertaintyMismatches)enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("encoding/json""flag""fmt""os""sort""skraak/tools")// runCallsClipLabels handles the "calls clip-labels" subcommand.func runCallsClipLabels(args []string) {fs := flag.NewFlagSet("calls clip-labels", flag.ExitOnError)folder := fs.String("folder", "", "Folder containing .data files (required)")mapping := fs.String("mapping", "", "Path to mapping.json (required)")filter := fs.String("filter", "", "Restrict to a single filter name (default: all filters)")output := fs.String("output", "./clip_labels.csv", "Output CSV path")clipDuration := fs.Float64("clip-duration", 4.0, "Clip duration in seconds")clipOverlap := fs.Float64("clip-overlap", 0.5, "Clip overlap in seconds")minLabelOverlap := fs.Float64("min-label-overlap", 0.25, "Minimum overlap (s) for an annotation to label a clip")finalClip := fs.String("final-clip", "full", "Trailing-clip behaviour: full | remainder | extend | none")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak calls clip-labels [options]\n\n")fmt.Fprintf(os.Stderr, "Generate an OpenSoundScape clip_labels-format CSV from .data files.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nSegment policy:\n")fmt.Fprintf(os.Stderr, " - Real species → contributes mapped class to overlapping clips.\n")fmt.Fprintf(os.Stderr, " - Mapped to __NEGATIVE__ → clip emitted, all class columns False;\n")fmt.Fprintf(os.Stderr, " overrides positives in the same clip.\n")fmt.Fprintf(os.Stderr, " - Mapped to __IGNORE__ → segment contributes no labels to clips.\n")fmt.Fprintf(os.Stderr, " - Gaps → clip emitted with all class columns False.\n")fmt.Fprintf(os.Stderr, "\nIf --output exists: append. Column-set mismatch → hard error.\n")fmt.Fprintf(os.Stderr, "Duplicate (file, start_time, end_time) row → hard error on first.\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls clip-labels --folder ./recordings --mapping ./mapping.json\n")fmt.Fprintf(os.Stderr, " skraak calls clip-labels --folder ./recordings --mapping ./mapping.json \\\n")fmt.Fprintf(os.Stderr, " --filter opensoundscape-multi-1.0\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}if *folder == "" {fmt.Fprintf(os.Stderr, "Error: --folder is required\n\n")fs.Usage()os.Exit(1)}if *mapping == "" {fmt.Fprintf(os.Stderr, "Error: --mapping is required\n\n")fs.Usage()os.Exit(1)}input := tools.CallsClipLabelsInput{Folder: *folder,MappingPath: *mapping,Filter: *filter,OutputPath: *output,ClipDuration: *clipDuration,ClipOverlap: *clipOverlap,MinLabelOverlap: *minLabelOverlap,FinalClip: *finalClip,}fmt.Fprintf(os.Stderr, "Folder: %s\n", *folder)fmt.Fprintf(os.Stderr, "Mapping: %s\n", *mapping)fmt.Fprintf(os.Stderr, "Output: %s\n", *output)fmt.Fprintf(os.Stderr, "Clip: duration=%.3fs overlap=%.3fs final=%s min-label-overlap=%.3fs\n",*clipDuration, *clipOverlap, *finalClip, *minLabelOverlap)if *filter != "" {fmt.Fprintf(os.Stderr, "Filter: %s\n", *filter)}out, err := tools.CallsClipLabels(input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}fmt.Fprintf(os.Stderr, "\nResults\n")fmt.Fprintf(os.Stderr, " .data files parsed: %d\n", out.DataFilesParsed)fmt.Fprintf(os.Stderr, " Segments ignored (__IGNORE__): %d\n", out.SegmentsIgnored)fmt.Fprintf(os.Stderr, " Clips excluded (__IGNORE__): %d\n", out.ClipsIgnored)fmt.Fprintf(os.Stderr, " Clips emitted: %d\n", out.RowsWritten)fmt.Fprintf(os.Stderr, " negative (__NEGATIVE__): %d\n", out.ClipsNegative)fmt.Fprintf(os.Stderr, " all-False (gap): %d\n", out.ClipsAllFalseGap)if out.AppendedToFile {fmt.Fprintf(os.Stderr, " Appended to file: yes (%d existing rows)\n", out.ExistingRowsFound)}fmt.Fprintf(os.Stderr, "\nPer-class True counts:\n")keys := make([]string, 0, len(out.PerClassTrueCount))for k := range out.PerClassTrueCount {keys = append(keys, k)}sort.Strings(keys)for _, k := range keys {fmt.Fprintf(os.Stderr, " %-30s %d\n", k+":", out.PerClassTrueCount[k])}enc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(out); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
package cmdimport ("encoding/json""fmt""os""strconv""strings""skraak/tools")func printClipUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak calls clip [options]\n\n")fmt.Fprintf(os.Stderr, "Generate audio clips and spectrogram images from .data file segments.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fmt.Fprintf(os.Stderr, " --file <path> Path to .data file (required if no --folder)\n")fmt.Fprintf(os.Stderr, " --folder <path> Path to folder containing .data files (required if no --file)\n")fmt.Fprintf(os.Stderr, " --output <path> Output folder for generated clips (required)\n")fmt.Fprintf(os.Stderr, " --prefix <name> Prefix for output filenames (required)\n")fmt.Fprintf(os.Stderr, " --filter <name> Filter by ML model name (optional)\n")fmt.Fprintf(os.Stderr, " --species <name> Filter by species, optionally with calltype (e.g. Kiwi, Kiwi+Duet)\n")fmt.Fprintf(os.Stderr, " --certainty <int> Filter by certainty value (0-100, optional)\n")fmt.Fprintf(os.Stderr, " --size <int> Spectrogram image size in pixels (224-896, default 224)\n")fmt.Fprintf(os.Stderr, " --color Apply L4 colormap to spectrogram (default: grayscale)\n")fmt.Fprintf(os.Stderr, " --wav-only Generate only WAV clips, skip spectrogram PNG generation\n")fmt.Fprintf(os.Stderr, " --night Only clip recordings made during solar night (requires --lat and --lng)\n")fmt.Fprintf(os.Stderr, " --day Only clip recordings made during solar day (requires --lat and --lng)\n")fmt.Fprintf(os.Stderr, " --lat <float> Latitude in decimal degrees (required with --night or --day)\n")fmt.Fprintf(os.Stderr, " --lng <float> Longitude in decimal degrees (required with --night or --day)\n")fmt.Fprintf(os.Stderr, " --timezone <zone> IANA timezone ID (e.g. Pacific/Auckland). Required for non-AudioMoth\n")fmt.Fprintf(os.Stderr, " recorders whose filenames embed local time (e.g. DOC AR4).\n")fmt.Fprintf(os.Stderr, " AudioMoth files embed a UTC timestamp in the WAV comment, so\n")fmt.Fprintf(os.Stderr, " --timezone is not needed for AudioMoth data.\n")fmt.Fprintf(os.Stderr, "\nOutput files:\n")fmt.Fprintf(os.Stderr, " <prefix>_<basename>_<start>_<end>.png # spectrogram image\n")fmt.Fprintf(os.Stderr, " <prefix>_<basename>_<start>_<end>.wav # audio clip (16kHz if downsampled)\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " # Clip all segments from a single file\n")fmt.Fprintf(os.Stderr, " skraak calls clip --file recording.data --output ./clips --prefix train\n\n")fmt.Fprintf(os.Stderr, " # Clip only Kiwi segments with color spectrograms at 448px\n")fmt.Fprintf(os.Stderr, " skraak calls clip --folder ./data --output ./clips --prefix kiwi \\\n")fmt.Fprintf(os.Stderr, " --filter opensoundscape-kiwi-1.2 --species Kiwi --size 448 --color\n\n")fmt.Fprintf(os.Stderr, " # Clip Kiwi Duet calls\n")fmt.Fprintf(os.Stderr, " skraak calls clip --folder ./data --output ./clips --prefix duet \\\n")fmt.Fprintf(os.Stderr, " --filter opensoundscape-kiwi-1.2 --species Kiwi+Duet\n")}// RunCallsClip handles the "calls clip" subcommand//// JSON output schema://// {// "files_processed": int, // .data files processed// "segments_clipped": int, // Segments that generated clips// "night_skipped": int, // Segments skipped (--night, omitted if 0)// "day_skipped": int, // Segments skipped (--day, omitted if 0)// "output_files": [string], // Paths to generated clip files (.wav/.png)// "errors": [string] // Error messages (omitted if empty)// }func RunCallsClip(args []string) {var file, folder, output, prefix, filter, species, timezone stringvar size, certainty intvar color, wavOnly, night, day boolvar lat, lng float64var latSet, lngSet bool// Default to -1 (no certainty filter)certainty = -1// Parse argumentsi := 0for i < len(args) {arg := args[i]switch arg {case "--file":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --file requires a value\n")os.Exit(1)}file = args[i+1]i += 2case "--folder":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --folder requires a value\n")os.Exit(1)}folder = args[i+1]i += 2case "--output":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --output requires a value\n")os.Exit(1)}output = args[i+1]i += 2case "--prefix":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --prefix requires a value\n")os.Exit(1)}prefix = args[i+1]i += 2case "--filter":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --filter requires a value\n")os.Exit(1)}if filter != "" {fmt.Fprintf(os.Stderr, "Error: --filter can only be specified once\n")os.Exit(1)}filter = args[i+1]i += 2case "--species":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --species requires a value\n")os.Exit(1)}if species != "" {fmt.Fprintf(os.Stderr, "Error: --species can only be specified once\n")os.Exit(1)}species = args[i+1]i += 2case "--certainty":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --certainty requires a value\n")os.Exit(1)}v, err := strconv.Atoi(args[i+1])if err != nil {fmt.Fprintf(os.Stderr, "Error: --certainty must be an integer\n")os.Exit(1)}if v < 0 || v > 100 {fmt.Fprintf(os.Stderr, "Error: --certainty must be between 0 and 100\n")os.Exit(1)}certainty = vi += 2case "--size":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --size requires a value\n")os.Exit(1)}v, err := strconv.Atoi(args[i+1])if err != nil {fmt.Fprintf(os.Stderr, "Error: --size must be an integer\n")os.Exit(1)}size = vi += 2case "--color":color = truei++case "--wav-only":wavOnly = truei++case "--night":night = truei++case "--day":day = truei++case "--lat":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --lat requires a value\n")os.Exit(1)}v, err := strconv.ParseFloat(args[i+1], 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: --lat must be a number\n")os.Exit(1)}lat = vlatSet = truei += 2case "--lng":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --lng requires a value\n")os.Exit(1)}v, err := strconv.ParseFloat(args[i+1], 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: --lng must be a number\n")os.Exit(1)}lng = vlngSet = truei += 2case "--timezone":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --timezone requires a value\n")os.Exit(1)}timezone = args[i+1]i += 2case "-h", "--help":printClipUsage()os.Exit(0)default:// Check for unknown flagsif strings.HasPrefix(arg, "--") {fmt.Fprintf(os.Stderr, "Error: unknown flag: %s\n\n", arg)printClipUsage()os.Exit(1)}i++}}// Validate required flagsmissing := []string{}if file == "" && folder == "" {missing = append(missing, "--file or --folder")}if output == "" {missing = append(missing, "--output")}if prefix == "" {missing = append(missing, "--prefix")}if len(missing) > 0 {fmt.Fprintf(os.Stderr, "Error: missing required flags: %v\n\n", missing)printClipUsage()os.Exit(1)}if night && day {fmt.Fprintf(os.Stderr, "Error: --night and --day are mutually exclusive\n\n")printClipUsage()os.Exit(1)}if (night || day) && (!latSet || !lngSet) {fmt.Fprintf(os.Stderr, "Error: --night/--day requires both --lat and --lng\n\n")printClipUsage()os.Exit(1)}// Build inputinput := tools.CallsClipInput{File: file,Folder: folder,Output: output,Prefix: prefix,Filter: filter,Species: species,Certainty: certainty,Size: size,Color: color,WavOnly: wavOnly,Night: night,Day: day,Lat: lat,Lng: lng,Timezone: timezone,}// Executeresult, err := tools.CallsClip(input)if err != nil {// Print partial result as JSON (may contain useful info)data, _ := json.Marshal(result)fmt.Println(string(data))os.Exit(1)}// Output JSONdata, _ := json.Marshal(result)fmt.Println(string(data))}
package cmdimport ("fmt""os""strconv""strings"tea "charm.land/bubbletea/v2""skraak/tools""skraak/tui""skraak/utils")// reservedClassifyKeys are single-character keys the classify TUI handles// itself (see tui/classify.go). User bindings to these keys would be silently// overridden by the TUI, so we reject them at config-load time.var reservedClassifyKeys = map[string]string{",": "previous segment",".": "next segment","0": "confirm label at certainty 100"," ": "open comment dialog",}func printClassifyUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak calls classify [options]\n\n")fmt.Fprintf(os.Stderr, "Interactive TUI for reviewing and classifying bird call segments.\n")fmt.Fprintf(os.Stderr, "Reads .data files (AviaNZ format) and presents segments for labelling\n")fmt.Fprintf(os.Stderr, "with spectrogram display and audio playback.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fmt.Fprintf(os.Stderr, " --folder <path> Path to folder containing .data files (required, or --file)\n")fmt.Fprintf(os.Stderr, " --file <path> Path to a single .data file (required, or --folder)\n")fmt.Fprintf(os.Stderr, " --filter <name> Filter name to scope which segments to review (optional)\n")fmt.Fprintf(os.Stderr, " --species <name> Scope to species, optionally with calltype (e.g. Kiwi, Kiwi+Duet)\n")fmt.Fprintf(os.Stderr, " --certainty <int> Scope to certainty value (0-100, optional)\n")fmt.Fprintf(os.Stderr, " --sample <1-100> Randomly sample N%% of filtered calls (requires --certainty; 100 = no-op)\n")fmt.Fprintf(os.Stderr, " --goto <filename> Start at this .data file (basename match, optional)\n")fmt.Fprintf(os.Stderr, " --night Only review solar-night recordings (requires --lat and --lng)\n")fmt.Fprintf(os.Stderr, " --day Only review solar-day recordings (requires --lat and --lng)\n")fmt.Fprintf(os.Stderr, " --lat <float> Latitude in decimal degrees (required with --night or --day)\n")fmt.Fprintf(os.Stderr, " --lng <float> Longitude in decimal degrees (required with --night or --day)\n")fmt.Fprintf(os.Stderr, " --timezone <zone> IANA timezone ID (e.g. Pacific/Auckland). Required for non-AudioMoth\n")fmt.Fprintf(os.Stderr, " recorders whose filenames embed local time (e.g. DOC AR4).\n")fmt.Fprintf(os.Stderr, "\nConfig (required): ~/.skraak/config.json\n")fmt.Fprintf(os.Stderr, " Provides reviewer, keybindings, and display flags (color/sixel/iterm/img_dims).\n")fmt.Fprintf(os.Stderr, " Example:\n")fmt.Fprintf(os.Stderr, " {\n")fmt.Fprintf(os.Stderr, " \"classify\": {\n")fmt.Fprintf(os.Stderr, " \"reviewer\": \"David\",\n")fmt.Fprintf(os.Stderr, " \"color\": true,\n")fmt.Fprintf(os.Stderr, " \"bindings\": {\n")fmt.Fprintf(os.Stderr, " \"k\": \"Kiwi\",\n")fmt.Fprintf(os.Stderr, " \"1\": \"Kiwi+Duet\",\n")fmt.Fprintf(os.Stderr, " \"x\": \"Noise\"\n")fmt.Fprintf(os.Stderr, " }\n")fmt.Fprintf(os.Stderr, " }\n")fmt.Fprintf(os.Stderr, " }\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls classify --folder /path/to/data\n")fmt.Fprintf(os.Stderr, " skraak calls classify --file /path/to/file.data --filter opensoundscape-kiwi-1.2\n")fmt.Fprintf(os.Stderr, " skraak calls classify --folder /path/to/data --species Kiwi+Duet\n")}// RunCallsClassify handles the "calls classify" subcommandfunc RunCallsClassify(args []string) {var folder, file, filter, species, gotoFile, timezone stringvar certainty, sample intvar night, day boolvar lat, lng float64var latSet, lngSet bool// Default to -1 (no filter / no sampling)certainty = -1sample = -1// Parse argumentsi := 0for i < len(args) {arg := args[i]switch arg {case "--folder":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --folder requires a value\n")os.Exit(1)}folder = args[i+1]i += 2case "--file":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --file requires a value\n")os.Exit(1)}file = args[i+1]i += 2case "--filter":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --filter requires a value\n")os.Exit(1)}if filter != "" {fmt.Fprintf(os.Stderr, "Error: --filter can only be specified once\n")os.Exit(1)}filter = args[i+1]i += 2case "--species":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --species requires a value\n")os.Exit(1)}if species != "" {fmt.Fprintf(os.Stderr, "Error: --species can only be specified once\n")os.Exit(1)}species = args[i+1]i += 2case "--certainty":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --certainty requires a value\n")os.Exit(1)}v, err := strconv.Atoi(args[i+1])if err != nil {fmt.Fprintf(os.Stderr, "Error: --certainty must be an integer\n")os.Exit(1)}if v < 0 || v > 100 {fmt.Fprintf(os.Stderr, "Error: --certainty must be between 0 and 100\n")os.Exit(1)}certainty = vi += 2case "--night":night = truei++case "--day":day = truei++case "--lat":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --lat requires a value\n")os.Exit(1)}v, err := strconv.ParseFloat(args[i+1], 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: --lat must be a number\n")os.Exit(1)}lat = vlatSet = truei += 2case "--lng":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --lng requires a value\n")os.Exit(1)}v, err := strconv.ParseFloat(args[i+1], 64)if err != nil {fmt.Fprintf(os.Stderr, "Error: --lng must be a number\n")os.Exit(1)}lng = vlngSet = truei += 2case "--timezone":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --timezone requires a value\n")os.Exit(1)}timezone = args[i+1]i += 2case "--help", "-h":printClassifyUsage()os.Exit(0)case "--sample":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --sample requires a value\n")os.Exit(1)}v, err := strconv.Atoi(args[i+1])if err != nil {fmt.Fprintf(os.Stderr, "Error: --sample must be an integer\n")os.Exit(1)}if v <= 0 || v > 100 {fmt.Fprintf(os.Stderr, "Error: --sample must be between 1 and 100\n")os.Exit(1)}sample = vi += 2case "--goto":if i+1 >= len(args) {fmt.Fprintf(os.Stderr, "Error: --goto requires a value\n")os.Exit(1)}gotoFile = args[i+1]i += 2default:fmt.Fprintf(os.Stderr, "Error: unknown flag: %s\n\n", arg)printClassifyUsage()os.Exit(1)}}// --sample 1-99 requires --certainty; --sample 100 is a no-opif sample > 0 && sample < 100 && certainty < 0 {fmt.Fprintf(os.Stderr, "Error: --sample requires --certainty to be set\n")os.Exit(1)}// Validate required flagsif folder == "" && file == "" {fmt.Fprintf(os.Stderr, "Error: missing required flag: --folder or --file\n\n")printClassifyUsage()os.Exit(1)}if night && day {fmt.Fprintf(os.Stderr, "Error: --night and --day are mutually exclusive\n\n")printClassifyUsage()os.Exit(1)}if (night || day) && (!latSet || !lngSet) {fmt.Fprintf(os.Stderr, "Error: --night/--day requires both --lat and --lng\n\n")printClassifyUsage()os.Exit(1)}// Load reviewer, bindings, and display flags from ~/.skraak/config.json.cfg, cfgPath, err := utils.LoadConfig()if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)fmt.Fprintf(os.Stderr, "Create %s with a \"classify\" section; run `skraak calls classify --help` for an example.\n", cfgPath)os.Exit(1)}// Validate config contentsif cfg.Classify.Reviewer == "" {fmt.Fprintf(os.Stderr, "Error: %s is missing \"classify.reviewer\"\n", cfgPath)os.Exit(1)}if len(cfg.Classify.Bindings) == 0 {fmt.Fprintf(os.Stderr, "Error: %s is missing \"classify.bindings\" (need at least one key)\n", cfgPath)os.Exit(1)}// Convert config bindings map -> []tools.KeyBinding via existing parseBind.bindings := make([]tools.KeyBinding, 0, len(cfg.Classify.Bindings))for key, value := range cfg.Classify.Bindings {if len(key) != 1 {fmt.Fprintf(os.Stderr, "Error: binding key %q in %s must be a single character\n", key, cfgPath)os.Exit(1)}if purpose, reserved := reservedClassifyKeys[key]; reserved {fmt.Fprintf(os.Stderr,"Error: binding key %q in %s is reserved by the TUI for %s — pick a different key.\n",key, cfgPath, purpose)os.Exit(1)}bindings = append(bindings, parseBind(key+"="+value))}// Validate secondary_bindings: each outer key must exist in bindings,// each inner key must be a single non-reserved char, values non-empty.for primaryKey, inner := range cfg.Classify.SecondaryBindings {if _, ok := cfg.Classify.Bindings[primaryKey]; !ok {fmt.Fprintf(os.Stderr,"Error: secondary_bindings key %q in %s has no matching primary binding\n",primaryKey, cfgPath)os.Exit(1)}for k, v := range inner {if len(k) != 1 {fmt.Fprintf(os.Stderr,"Error: secondary_bindings[%q] key %q in %s must be a single character\n",primaryKey, k, cfgPath)os.Exit(1)}if purpose, reserved := reservedClassifyKeys[k]; reserved {fmt.Fprintf(os.Stderr,"Error: secondary_bindings[%q] key %q in %s is reserved by the TUI for %s — pick a different key.\n",primaryKey, k, cfgPath, purpose)os.Exit(1)}if v == "" {fmt.Fprintf(os.Stderr,"Error: secondary_bindings[%q][%q] in %s has empty calltype\n",primaryKey, k, cfgPath)os.Exit(1)}}}// Parse species+calltypespeciesName, callType := utils.ParseSpeciesCallType(species)// Build configconfig := tools.ClassifyConfig{Folder: folder,File: file,Filter: filter,Species: speciesName,CallType: callType,Certainty: certainty,Sample: sample,Goto: gotoFile,Reviewer: cfg.Classify.Reviewer,Color: cfg.Classify.Color,ImageSize: cfg.Classify.ImgDims,Sixel: cfg.Classify.Sixel,ITerm: cfg.Classify.ITerm,Bindings: bindings,SecondaryBindings: cfg.Classify.SecondaryBindings,Night: night,Day: day,Lat: lat,Lng: lng,Timezone: timezone,}// Load data filesstate, err := tools.LoadDataFiles(config)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}// Show filtered counts (files with no matching segments are already pruned)if state.TimeFilteredCount > 0 {label := "daytime"if config.Day {label = "nighttime"}fmt.Fprintf(os.Stderr, "Skipped %d %s files\n", state.TimeFilteredCount, label)}fmt.Fprintf(os.Stderr, "Loaded %d files with %d matching segments\n",len(state.DataFiles), state.TotalSegments())if state.TotalSegments() == 0 {fmt.Fprintf(os.Stderr, "No segments to review.\n")os.Exit(0)}// Launch TUI (alt screen for clean kitty image rendering)p := tea.NewProgram(tui.New(state))if _, err := p.Run(); err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}}// parseBind parses "k=Kiwi" or "d=Kiwi+Duet" formatfunc parseBind(s string) tools.KeyBinding {parts := strings.SplitN(s, "=", 2)if len(parts) != 2 {fmt.Fprintf(os.Stderr, "Error: invalid bind format: %s (expected key=value)\n", s)os.Exit(1)}key := parts[0]value := parts[1]// Check for Species+CallType formatif strings.Contains(value, "+") {valueParts := strings.SplitN(value, "+", 2)return tools.KeyBinding{Key: key,Species: valueParts[0],CallType: valueParts[1],}}// Species onlyreturn tools.KeyBinding{Key: key,Species: value,}}
package cmdimport ("encoding/json""flag""fmt""os""skraak/tools")// RunCalls handles the "calls" commandfunc RunCalls(args []string) {if len(args) < 1 {printCallsUsage()os.Exit(1)}switch args[0] {case "from-preds":runCallsFromPreds(args[1:])case "from-birda":runCallsFromBirda(args[1:])case "from-raven":runCallsFromRaven(args[1:])case "show-images":runCallsShowImages(args[1:])case "classify":RunCallsClassify(args[1:])case "clip":RunCallsClip(args[1:])case "modify":RunCallsModify(args[1:])case "push-certainty":runCallsPushCertainty(args[1:])case "detect-anomalies":runCallsDetectAnomalies(args[1:])case "propagate":runCallsPropagate(args[1:])case "summarise":runCallsSummarise(args[1:])case "clip-labels":runCallsClipLabels(args[1:])default:fmt.Fprintf(os.Stderr, "Unknown calls subcommand: %s\n\n", args[0])printCallsUsage()os.Exit(1)}}func printCallsUsage() {fmt.Fprintf(os.Stderr, "Usage: skraak calls <subcommand> [options]\n\n")fmt.Fprintf(os.Stderr, "Subcommands:\n")fmt.Fprintf(os.Stderr, " from-preds Extract clustered calls from ML predictions CSV\n")fmt.Fprintf(os.Stderr, " from-birda Import BirdNET results to .data files\n")fmt.Fprintf(os.Stderr, " from-raven Import Raven selections to .data files\n")fmt.Fprintf(os.Stderr, " show-images Display spectrogram images from .data file\n")fmt.Fprintf(os.Stderr, " classify Review and classify segments in .data files\n")fmt.Fprintf(os.Stderr, " clip Generate audio/image clips from .data files\n")fmt.Fprintf(os.Stderr, " modify Modify a label in a .data file\n")fmt.Fprintf(os.Stderr, " push-certainty Promote certainty=90 segments to 100 for a filtered set\n")fmt.Fprintf(os.Stderr, " detect-anomalies Flag label/certainty disagreements across ML model filters\n")fmt.Fprintf(os.Stderr, " propagate Propagate verified classifications between filters in a .data file\n")fmt.Fprintf(os.Stderr, " summarise Summarise all .data files in a folder\n")fmt.Fprintf(os.Stderr, " clip-labels Export OpenSoundScape clip_labels-format multihot CSV\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls from-preds --csv predictions.csv\n")fmt.Fprintf(os.Stderr, " skraak calls from-birda --folder ./recordings\n")fmt.Fprintf(os.Stderr, " skraak calls from-raven --folder ./recordings --delete\n")fmt.Fprintf(os.Stderr, " skraak calls show-images --file recording.wav.data\n")fmt.Fprintf(os.Stderr, " skraak calls classify --folder ./data --reviewer David --bind k=Kiwi\n")fmt.Fprintf(os.Stderr, " skraak calls classify --folder ./data --reviewer David --bind k=Kiwi --filter mymodel --species Kiwi+Duet\n")fmt.Fprintf(os.Stderr, " skraak calls clip --folder ./data --output ./clips --prefix train --filter mymodel --species Kiwi\n")fmt.Fprintf(os.Stderr, " skraak calls modify --file recording.data --reviewer GLM-5 --filter mymodel --segment 12-15 --species Kiwi\n")fmt.Fprintf(os.Stderr, " skraak calls summarise --folder ./recordings > summary.json\n")}// runCallsFromPreds handles the "calls from-preds" subcommand//// JSON output schema://// {// "calls": [ // Clustered call groups// {// "file": string, // WAV filename// "start_time": float, // Cluster start time (seconds)// "end_time": float, // Cluster end time (seconds)// "ebird_code": string, // eBird species code// "segments": int // Number of detections in cluster// }// ],// "total_calls": int, // Total clustered calls// "clip_duration": float, // Clip duration in seconds// "gap_threshold": float, // Gap threshold used for clustering// "species_count": {string: int}, // Species ebird code -> detection count// "data_files_written": int, // .data files successfully written// "data_files_skipped": int, // .data files skipped (already exist)// "filter": string, // Filter name used// "error": string // Error message (omitted if nil)// }func runCallsFromPreds(args []string) {fs := flag.NewFlagSet("calls from-preds", flag.ExitOnError)csvPath := fs.String("csv", "", "Path to predictions CSV file (required)")filter := fs.String("filter", "", "Filter name for .data files (default: parse from CSV filename)")dotData := fs.Bool("dot-data", true, "Write .data files alongside audio files (default: true)")gapMultiplier := fs.Int("gap-multiplier", 0, "Gap threshold multiplier (default: 2, e.g. 3 for kiwi)")minDetections := fs.Int("min-detections", -1, "Min detections per cluster, filters out small clusters (default: 0 = no filtering)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak calls from-preds [options]\n\n")fmt.Fprintf(os.Stderr, "Extract clustered bird calls from ML predictions CSV.\n")fmt.Fprintf(os.Stderr, "Reads prediction CSV with columns: file, start_time, end_time, <ebird_codes...>\n")fmt.Fprintf(os.Stderr, "Each row is a clip with 1=present, 0=absent for each species.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nOutput:\n")fmt.Fprintf(os.Stderr, " With --dot-data=true (default): Writes .data files alongside audio files, outputs JSON summary\n")fmt.Fprintf(os.Stderr, " With --dot-data=false: Outputs JSON with clustered calls only (no .data files)\n")fmt.Fprintf(os.Stderr, "\nFilter name:\n")fmt.Fprintf(os.Stderr, " If --filter is provided, uses that value.\n")fmt.Fprintf(os.Stderr, " Otherwise, parses from CSV filename: prefix_filter_date.csv -> filter\n")fmt.Fprintf(os.Stderr, " Example: predsST_opensoundscape-kiwi-1.2_2025-11-12.csv -> opensoundscape-kiwi-1.2\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " # Write .data files (default)\n")fmt.Fprintf(os.Stderr, " skraak calls from-preds --csv predictions.csv\n")fmt.Fprintf(os.Stderr, "\n")fmt.Fprintf(os.Stderr, " # JSON output only (no .data files)\n")fmt.Fprintf(os.Stderr, " skraak calls from-preds --csv predictions.csv --dot-data=false > calls.json\n")fmt.Fprintf(os.Stderr, "\n")fmt.Fprintf(os.Stderr, " # Override filter name\n")fmt.Fprintf(os.Stderr, " skraak calls from-preds --csv preds.csv --filter my-custom-filter\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsif *csvPath == "" {fmt.Fprintf(os.Stderr, "Error: --csv is required\n\n")fs.Usage()os.Exit(1)}// Determine filter namefilterName := *filterif filterName == "" {filterName = tools.ParseFilterFromFilename(*csvPath)if filterName == "" {fmt.Fprintf(os.Stderr, "Error: Could not parse filter from filename. Use --filter flag.\n")fmt.Fprintf(os.Stderr, "Expected format: prefix_filter_date.csv (e.g., predsST_opensoundscape-kiwi-1.2_2025-11-12.csv)\n")os.Exit(1)}}input := tools.CallsFromPredsInput{CSVPath: *csvPath,Filter: filterName,WriteDotData: *dotData,GapMultiplier: *gapMultiplier,MinDetections: *minDetections,ProgressHandler: func(processed, total int, message string) {if total > 0 {percent := float64(processed) / float64(total) * 100fmt.Fprintf(os.Stderr, "\rProcessing WAV files: %d/%d (%.0f%%)", processed, total, percent)if processed == total {fmt.Fprintf(os.Stderr, "\n")}}},}if *dotData {fmt.Fprintf(os.Stderr, "Extracting calls from predictions: %s\n", *csvPath)fmt.Fprintf(os.Stderr, "Filter: %s\n", filterName)fmt.Fprintf(os.Stderr, "Writing .data files: enabled\n")} else {fmt.Fprintf(os.Stderr, "Extracting calls from predictions: %s\n", *csvPath)fmt.Fprintf(os.Stderr, "Filter: %s\n", filterName)fmt.Fprintf(os.Stderr, "Writing .data files: disabled (--dot-data=false)\n")}output, err := tools.CallsFromPreds(input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}fmt.Fprintf(os.Stderr, "Found %d clustered calls across %d species\n",output.TotalCalls, len(output.SpeciesCount))fmt.Fprintf(os.Stderr, "Clip duration: %.1fs, Gap threshold: %.1fs\n",output.ClipDuration, output.GapThreshold)if *dotData {fmt.Fprintf(os.Stderr, "Data files written: %d, skipped: %d\n",output.DataFilesWritten, output.DataFilesSkipped)}// Output JSON to stdoutenc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}// runCallsShowImages handles the "calls show-images" subcommandfunc runCallsShowImages(args []string) {fs := flag.NewFlagSet("calls show-images", flag.ExitOnError)filePath := fs.String("file", "", "Path to .data file (required)")color := fs.Bool("color", false, "Apply L4 colormap (default: false, grayscale)")imgDims := fs.Int("img-dims", 0, "Spectrogram size in pixels (224-448, default 448)")sixel := fs.Bool("sixel", false, "Use sixel graphics protocol (default: kitty)")iterm := fs.Bool("iterm", false, "Use iTerm2 inline image protocol")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak calls show-images [options]\n\n")fmt.Fprintf(os.Stderr, "Display spectrogram images for each segment in a .data file.\n")fmt.Fprintf(os.Stderr, "Images are output using the Kitty graphics protocol (or Sixel with --sixel, iTerm2 with --iterm).\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls show-images --file recording.wav.data\n")fmt.Fprintf(os.Stderr, " skraak calls show-images --file recording.wav.data --color\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsif *filePath == "" {fmt.Fprintf(os.Stderr, "Error: --file is required\n\n")fs.Usage()os.Exit(1)}input := tools.CallsShowImagesInput{DataFilePath: *filePath,Color: *color,ImageSize: *imgDims,Sixel: *sixel,ITerm: *iterm,}fmt.Fprintf(os.Stderr, "Showing spectrogram images for: %s\n", *filePath)if *color {fmt.Fprintf(os.Stderr, "Color: L4 colormap (Black-Red-Yellow)\n")}output, err := tools.CallsShowImages(input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}fmt.Fprintf(os.Stderr, "Displayed %d segment(s) from %s\n", output.SegmentsShown, output.WavFile)}// runCallsFromBirda handles the "calls from-birda" subcommand//// JSON output schema://// {// "calls": [ // Clustered call groups// {// "file": string, // WAV filename// "start_time": float, // Cluster start time (seconds)// "end_time": float, // Cluster end time (seconds)// "ebird_code": string, // Species code// "segments": int // Number of detections in cluster// }// ],// "total_calls": int, // Total clustered calls// "species_count": {string: int}, // Species -> detection count// "data_files_written": int, // .data files successfully written// "data_files_skipped": int, // .data files skipped// "files_processed": int, // BirdNET files processed// "files_deleted": int, // BirdNET files deleted (--delete)// "filter": string, // Always "BirdNET"// "error": string // Error message (omitted if nil)// }func runCallsFromBirda(args []string) {fs := flag.NewFlagSet("calls from-birda", flag.ExitOnError)folder := fs.String("folder", "", "Folder containing BirdNET results files")file := fs.String("file", "", "Single BirdNET results file to process")delete := fs.Bool("delete", false, "Delete BirdNET files after processing")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak calls from-birda [options]\n\n")fmt.Fprintf(os.Stderr, "Import BirdNET results to .data files.\n")fmt.Fprintf(os.Stderr, "Reads *.BirdNET.results.csv files and creates/merges .data files.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nBehavior:\n")fmt.Fprintf(os.Stderr, " - Filter is always 'BirdNET' (parsed from filename)\n")fmt.Fprintf(os.Stderr, " - If .data file exists with BirdNET filter: error (refuses to clobber)\n")fmt.Fprintf(os.Stderr, " - If .data file exists with different filter: merge segments\n")fmt.Fprintf(os.Stderr, " - Confidence (0.0-1.0) converted to certainty (0-100)\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls from-birda --folder ./recordings\n")fmt.Fprintf(os.Stderr, " skraak calls from-birda --file recording.BirdNET.results.csv\n")fmt.Fprintf(os.Stderr, " skraak calls from-birda --folder ./recordings --delete\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate that either folder or file is specifiedif *folder == "" && *file == "" {fmt.Fprintf(os.Stderr, "Error: Either --folder or --file is required\n\n")fs.Usage()os.Exit(1)}input := tools.CallsFromBirdaInput{Folder: *folder,File: *file,Delete: *delete,ProgressHandler: func(processed, total int, message string) {if total > 0 {percent := float64(processed) / float64(total) * 100fmt.Fprintf(os.Stderr, "\rProcessing BirdNET files: %d/%d (%.0f%%)", processed, total, percent)if processed == total {fmt.Fprintf(os.Stderr, "\n")}}},}fmt.Fprintf(os.Stderr, "Importing BirdNET results\n")if *folder != "" {fmt.Fprintf(os.Stderr, "Folder: %s\n", *folder)} else {fmt.Fprintf(os.Stderr, "File: %s\n", *file)}if *delete {fmt.Fprintf(os.Stderr, "Delete source files: enabled\n")}output, err := tools.CallsFromBirda(input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}fmt.Fprintf(os.Stderr, "Processed %d BirdNET files\n", output.FilesProcessed)fmt.Fprintf(os.Stderr, "Found %d calls across %d species\n",output.TotalCalls, len(output.SpeciesCount))fmt.Fprintf(os.Stderr, "Data files written: %d, skipped: %d\n",output.DataFilesWritten, output.DataFilesSkipped)if *delete {fmt.Fprintf(os.Stderr, "Files deleted: %d\n", output.FilesDeleted)}// Output JSON to stdoutenc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}// runCallsFromRaven handles the "calls from-raven" subcommand//// JSON output schema://// {// "calls": [ // Clustered call groups// {// "file": string, // WAV filename// "start_time": float, // Cluster start time (seconds)// "end_time": float, // Cluster end time (seconds)// "ebird_code": string, // Species code// "segments": int // Number of detections in cluster// }// ],// "total_calls": int, // Total clustered calls// "species_count": {string: int}, // Species -> detection count// "data_files_written": int, // .data files successfully written// "data_files_skipped": int, // .data files skipped// "files_processed": int, // Raven files processed// "files_deleted": int, // Raven files deleted (--delete)// "filter": string, // Always "Raven"// "error": string // Error message (omitted if nil)// }func runCallsFromRaven(args []string) {fs := flag.NewFlagSet("calls from-raven", flag.ExitOnError)folder := fs.String("folder", "", "Folder containing Raven selection files")file := fs.String("file", "", "Single Raven selection file to process")delete := fs.Bool("delete", false, "Delete Raven files after processing")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak calls from-raven [options]\n\n")fmt.Fprintf(os.Stderr, "Import Raven selections to .data files.\n")fmt.Fprintf(os.Stderr, "Reads *.selections.txt files and creates/merges .data files.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nBehavior:\n")fmt.Fprintf(os.Stderr, " - Filter is always 'Raven' (parsed from filename)\n")fmt.Fprintf(os.Stderr, " - If .data file exists with Raven filter: error (refuses to clobber)\n")fmt.Fprintf(os.Stderr, " - If .data file exists with different filter: merge segments\n")fmt.Fprintf(os.Stderr, " - Frequency range preserved from Raven selections\n")fmt.Fprintf(os.Stderr, " - Certainty defaults to 70 (no confidence metric in Raven)\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls from-raven --folder ./recordings\n")fmt.Fprintf(os.Stderr, " skraak calls from-raven --file recording.Table.1.selections.txt\n")fmt.Fprintf(os.Stderr, " skraak calls from-raven --folder ./recordings --delete\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate that either folder or file is specifiedif *folder == "" && *file == "" {fmt.Fprintf(os.Stderr, "Error: Either --folder or --file is required\n\n")fs.Usage()os.Exit(1)}input := tools.CallsFromRavenInput{Folder: *folder,File: *file,Delete: *delete,ProgressHandler: func(processed, total int, message string) {if total > 0 {percent := float64(processed) / float64(total) * 100fmt.Fprintf(os.Stderr, "\rProcessing Raven files: %d/%d (%.0f%%)", processed, total, percent)if processed == total {fmt.Fprintf(os.Stderr, "\n")}}},}fmt.Fprintf(os.Stderr, "Importing Raven selections\n")if *folder != "" {fmt.Fprintf(os.Stderr, "Folder: %s\n", *folder)} else {fmt.Fprintf(os.Stderr, "File: %s\n", *file)}if *delete {fmt.Fprintf(os.Stderr, "Delete source files: enabled\n")}output, err := tools.CallsFromRaven(input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}fmt.Fprintf(os.Stderr, "Processed %d Raven files\n", output.FilesProcessed)fmt.Fprintf(os.Stderr, "Found %d calls across %d species\n",output.TotalCalls, len(output.SpeciesCount))fmt.Fprintf(os.Stderr, "Data files written: %d, skipped: %d\n",output.DataFilesWritten, output.DataFilesSkipped)if *delete {fmt.Fprintf(os.Stderr, "Files deleted: %d\n", output.FilesDeleted)}// Output JSON to stdoutenc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}// runCallsSummarise handles the "calls summarise" subcommand//// JSON output schema://// {// "segments": [ // All segments (omitted with --brief)// {// "file": string, // .data file path// "start_time": float, // Segment start time (seconds)// "end_time": float, // Segment end time (seconds)// "labels": [// {// "filter": string, // Filter name// "certainty": int, // Certainty level (0-100)// "species": string, // Species name// "calltype": string, // Call type (omitted if empty)// "comment": string, // Comment (omitted if empty)// "bookmark": bool // Bookmark flag (omitted if false)// }// ]// }// ],// "folder": string, // Folder path// "data_files_read": int, // Successfully parsed .data files// "data_files_skipped": [string], // Files that failed to parse// "total_segments": int, // Total number of segments// "filters": { // Per-filter statistics// string: {// "segments": int, // Segment count for this filter// "species": {string: int}, // Species -> count// "calltypes": {string: {string: int}} // Species -> calltype -> count (omitted if empty)// }// },// "review_status": {// "unreviewed": int, // certainty < 100// "confirmed": int, // certainty = 100// "dont_know": int, // certainty = 0// "with_calltype": int, // Labels with call type// "with_comments": int // Labels with comments// },// "operators": [string], // Unique operator names// "reviewers": [string], // Unique reviewer names// "error": string // Error message (omitted if nil)// }func runCallsSummarise(args []string) {fs := flag.NewFlagSet("calls summarise", flag.ExitOnError)folder := fs.String("folder", "", "Folder containing .data files (required)")brief := fs.Bool("brief", false, "Exclude segments array from output (summary stats only)")filter := fs.String("filter", "", "Restrict output to a single filter name (default: all filters)")fs.Usage = func() {fmt.Fprintf(os.Stderr, "Usage: skraak calls summarise [options]\n\n")fmt.Fprintf(os.Stderr, "Summarise all .data files in a folder.\n")fmt.Fprintf(os.Stderr, "Outputs JSON with segments array and summary statistics.\n\n")fmt.Fprintf(os.Stderr, "Options:\n")fs.PrintDefaults()fmt.Fprintf(os.Stderr, "\nOutput includes:\n")fmt.Fprintf(os.Stderr, " - segments: array of all segments with labels (omitted with --brief)\n")fmt.Fprintf(os.Stderr, " - data_files_read: count of successfully parsed .data files\n")fmt.Fprintf(os.Stderr, " - data_files_skipped: list of files that failed to parse\n")fmt.Fprintf(os.Stderr, " - total_segments: total number of segments\n")fmt.Fprintf(os.Stderr, " - filters: per-filter statistics (segments, species counts)\n")fmt.Fprintf(os.Stderr, " - review_status: unreviewed/confirmed/dont_know counts\n")fmt.Fprintf(os.Stderr, " - operators/reviewers: unique values found\n")fmt.Fprintf(os.Stderr, "\nExamples:\n")fmt.Fprintf(os.Stderr, " skraak calls summarise --folder ./recordings > summary.json\n")fmt.Fprintf(os.Stderr, " skraak calls summarise --folder ./recordings --brief > summary.json # summary only\n")fmt.Fprintf(os.Stderr, " skraak calls summarise --folder ./recordings --filter opensoundscape-kiwi-1.2 --brief\n")}if err := fs.Parse(args); err != nil {os.Exit(1)}// Validate required flagsif *folder == "" {fmt.Fprintf(os.Stderr, "Error: --folder is required\n\n")fs.Usage()os.Exit(1)}input := tools.CallsSummariseInput{Folder: *folder,Brief: *brief,Filter: *filter,}fmt.Fprintf(os.Stderr, "Summarising .data files in: %s\n", *folder)if *filter != "" {fmt.Fprintf(os.Stderr, "Filter: %s\n", *filter)}output, err := tools.CallsSummarise(input)if err != nil {fmt.Fprintf(os.Stderr, "Error: %v\n", err)os.Exit(1)}fmt.Fprintf(os.Stderr, "Read %d .data files, skipped %d\n",output.DataFilesRead, len(output.DataFilesSkipped))fmt.Fprintf(os.Stderr, "Total segments: %d\n", output.TotalSegments)fmt.Fprintf(os.Stderr, "Filters: %d\n", len(output.Filters))fmt.Fprintf(os.Stderr, "Review status: %d unreviewed, %d confirmed, %d don't know\n",output.ReviewStatus.Unreviewed, output.ReviewStatus.Confirmed, output.ReviewStatus.DontKnow)// Output JSON to stdoutenc := json.NewEncoder(os.Stdout)enc.SetIndent("", " ")if err := enc.Encode(output); err != nil {fmt.Fprintf(os.Stderr, "Error encoding output: %v\n", err)os.Exit(1)}}
# SkraakAcoustic monitoring CLI toolkit in Go.## CLI Commands```bash# Execute SQL query./skraak sql --db ./db/skraak.duckdb "SELECT COUNT(*) FROM file WHERE active = true"# Create resources./skraak create dataset --db ./db/skraak.duckdb --name "My Dataset" --type unstructured./skraak create location --db ./db/skraak.duckdb --dataset abc123 --name "Site A" --lat -36.85 --lon 174.76 --timezone Pacific/Auckland./skraak create cluster --db ./db/skraak.duckdb --dataset abc123 --location loc456 --name "2024-01" --sample-rate 250000./skraak create pattern --db ./db/skraak.duckdb --record 60 --sleep 1740# Update resources./skraak update dataset --db ./db/skraak.duckdb --id abc123 --name "Updated Name"./skraak update location --db ./db/skraak.duckdb --id loc123 --name "Updated Name" --lat -36.85 --lon 174.76./skraak update cluster --db ./db/skraak.duckdb --id cluster123 --name "Updated Name"./skraak update pattern --db ./db/skraak.duckdb --id pattern123 --record 30 --sleep 1770# Import commands./skraak import file --db ./db/skraak.duckdb --dataset abc123 --location loc456 --cluster clust789 --file /path/to/file.wav./skraak import folder --db ./db/skraak.duckdb --dataset abc123 --location loc456 --cluster clust789 --folder /path/to/folder./skraak import bulk --db ./db/skraak.duckdb --dataset abc123 --csv import.csv --log progress.log./skraak import unstructured --db ./db/skraak.duckdb --dataset 4Sh8_7p1ocks --folder "/media/david/Misc-2/Manu o Kahurangi kiwi survey (3)/Andrew Digby LSK - sorted files"./skraak import segments --db ./db/skraak.duckdb --dataset abc123 --location loc456 --cluster clust789 --folder /path/to/data --mapping mapping.json# Export dataset (for collaboration, testing, or archival)./skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb./skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb --dry-run# Event log replay (sync backup databases)./skraak replay events --db ./backup.duckdb --log ./skraak.duckdb.events.jsonl./skraak replay events --db ./backup.duckdb --log ./events.jsonl --dry-run./skraak replay events --db ./backup.duckdb --log ./events.jsonl --last 10# Call analysis (extract from ML predictions, review/classify)./skraak calls from-preds --csv predictions.csv # Extract calls, write .data files./skraak calls from-preds --csv preds.csv --dot-data=false > calls.json # JSON output only./skraak calls show-images --file recording.wav.data # Display spectrograms./skraak calls classify --folder ./data # Interactive classification (reviewer + bindings from ~/.skraak/config.json)./skraak calls classify --folder ./data --filter opensoundscape-kiwi-1.0./skraak calls summarise --folder ./data > summary.json # Summarise .data files./skraak calls summarise --folder ./data --brief > summary.json # Summary stats only (no segments)./skraak calls classify --folder . --filter opensoundscape-kiwi-1.2 --species Kiwi+Male./skraak calls classify --folder . --filter opensoundscape-multi-1.0./skraak calls clip --file recording.wav.data --prefix B01 --output /tmp/B01/ --species Kiwi+Duet --filter opensoundscape-multi-1.0 --size 224 --color./skraak calls clip --folder B01/2026-12-11/ --prefix B01 --output /tmp/B01/ --species Kiwi+Duet --filter opensoundscape-multi-1.0 --size 224 --color./skraak calls modify --file recording.data --reviewer Claude --filter opensoundscape-multi-1.0 --segment 12-15 --species Kiwi+Male --certainty 80./skraak calls modify --file recording.data --reviewer Claude --filter opensoundscape-multi-1.0 --segment 12-15 --certainty 80 --bookmark./skraak calls modify --file recording.data --reviewer Claude --filter opensoundscape-multi-1.0 --segment 12-15 --certainty 80 --comment "Clear example of male call"./skraak calls propagate --file rec.wav.data --from opensoundscape-kiwi-1.2 --to opensoundscape-kiwi-1.5 --species Kiwi./skraak calls propagate --folder ./recordings --from opensoundscape-kiwi-1.2 --to opensoundscape-kiwi-1.5 --species Kiwi# Export OpenSoundScape clip_labels-format CSV from .data files./skraak calls clip-labels --folder ./data --mapping ./mapping.json./skraak calls clip-labels --folder ./data --mapping ./mapping.json --filter opensoundscape-multi-1.0# File utilities./skraak xxhash --file recording.wav # XXH64 hash (same format as DB)./skraak metadata --file recording.wav # WAV metadata as JSON# Works for audiomoth which records time metadata as UTC./skraak isnight --file recording.wav --lat -36.85 --lng 174.76 # Was it night when recorded?./skraak isnight --file recording.wav --lat -36.85 --lng 174.76 --brief # Just file_path + solar_night# DOC recorders record local time without timezone, IANA timezone required./skraak isnight --file recording.wav --lat -36.85 --lng 174.76 --timezone Pacific/Auckland # Non-UTC timezone./skraak time # Current time as JSON# Rename files with location prefix./skraak prepend --folder ./recordings --prefix LOC001 # WAV files with datestring + log.txt./skraak prepend --folder ./data --prefix SITE_A --recursive # Include 1 level of subfolders./skraak prepend --folder ./test --prefix TEST --dry-run # Preview changes```**`isnight`** — Night detection for bioacoustic recordings. Determines if a WAV file was recorded at night (between sunset and sunrise) at the given GPS coordinates. The recording timestamp is read from the WAV file metadata, not from the filename — this works reliably because bioacoustic recorders (AudioMoth, BAR-LT, Song Meter, etc.) embed an accurate timestamp in the WAV header at the time of recording. AudioMoth comments are parsed automatically including the embedded UTC offset. For non-AudioMoth files without a recognized filename pattern, the timestamp falls back to the file modification time. Use `--brief` for batch/agent use to return only `file_path` and `solar_night`.## Event LogAll mutating SQL operations (INSERT, UPDATE, DELETE) are automatically logged for backup synchronization.**Event log location:** `<database>.events.jsonl`**Features:**- SQL-level capture for complete fidelity- Only successful transactions logged (rollbacks discarded)- Includes tool name, SQL, parameters, timestamp**Replay on backup database:**```bash# Replay all events./skraak replay events --db ./backup.duckdb --log ./skraak.duckdb.events.jsonl# Preview without executing./skraak replay events --db ./backup.duckdb --log ./events.jsonl --dry-run# Replay last N events./skraak replay events --db ./backup.duckdb --log ./events.jsonl --last 10```**Event format (JSONL):**```json{"id": "V1StGXR8_Z5jdHi6B-myT","timestamp": "2026-02-18T14:30:22+13:00","tool": "create_or_update_dataset","queries": [{"sql": "INSERT INTO ...", "parameters": [...]}],"success": true,"duration_ms": 45}```## Dataset ExportExport a dataset with all related data to a new DuckDB database for collaboration, testing, or archival.**Use cases:**- **Collaboration:** Export, send to collaborator, they return event log for replay- **Testing:** Create focused test database from production (100 MB vs 1.5 GB)- **Archival:** Snapshot a dataset at a point in time**Export:**```bash# Export dataset to new database./skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb# Preview without creating file./skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb --dry-run# Overwrite existing export./skraak export dataset --db ./db/skraak.duckdb --id abc123 --output export.duckdb --force```**What's exported:**- All rows owned by dataset (via dataset_id foreign key traversal)- Subset of reference data (species, patterns, filters used)- Creates empty event log file for changes**Re-import changes:**```bash# After collaborator returns event log, replay on backup./skraak replay events --db ./backup.duckdb --log export.duckdb.events.jsonl```## Call AnalysisExtract and review bird calls from ML predictions.**Workflow:**1. **Extract calls from opensoundscape predictions.csv:**```bash# Write .data files alongside audio (default)# filter parsed from preds.csv filename but can be overriden with --filter birdnet-24./skraak calls from-preds --csv predictions.csv > calls.json```2. **Interactive classification:**Reviewer, keybindings, and display flags (color/sixel/iterm/img_dims) are loadedfrom `~/.skraak/config.json` — create it once before first use:```json{"classify": {"reviewer": "David","color": true,"bindings": {"a": "eurbla","k": "Kiwi","d": "Kiwi+Duet","n": "Don't Know","1": "Kiwi+Duet","2": "Kiwi+Female","3": "Kiwi+Male","4": "Kiwi","x": "Noise"},"secondary_bindings":{"a":{"a": "alarm","c": "contact","s": "song"}}}}```Path resolves to `~/.skraak/config.json` on Linux/macOS and`C:\Users\<name>\.skraak\config.json` on Windows via `os.UserHomeDir()`.Secondary bindings for a, eurbla, are accessed by shift-a, a/c/s```bash# Launch TUI for reviewing and classifying segments./skraak calls classify --folder ./data# Single file mode./skraak calls classify --file recording.wav.data# Scope to a specific filter (ML model)./skraak calls classify --folder ./data --filter opensoundscape-kiwi-1.2# Scope to species (and optionally calltype) within a filter./skraak calls classify --folder ./data --filter opensoundscape-kiwi-1.2 --species Kiwi+Duet# Sample 10% of matching segments (random, requires --certainty; useful for quality-checking large sets)./skraak calls classify --folder ./data --species Kiwi --certainty 90 --sample 10````--sample <1-99>` randomly selects that percentage of the filtered segment list for review. Files and segments are presented in their original chronological order. `--sample 100` is a no-op. Requires `--certainty` to be set.3. **Summarise .data files:**```bash# Full summary with all segments./skraak calls summarise --folder ./recordings > summary.json# Brief summary (stats only, no segment details)./skraak calls summarise --folder ./recordings --brief > summary.json```**Summarise output includes:**- `segments` - array of all segments with labels (omitted with `--brief`)- `data_files_read` / `data_files_skipped` - file processing status- `total_segments` - total count- `filters` - per-filter statistics (segments, species, calltypes)- `review_status` - unreviewed/confirmed/dont_know counts- `operators` / `reviewers` - unique values found4. **Promote certainty=90 segments to 100:**```bash# After reviewing a folder and confirming labels are correct, bulk-promote to certainty=100.# Filtering flags match calls classify exactly (minus --certainty and --sample)../skraak calls push-certainty --folder ./data --species Kiwi./skraak calls push-certainty --folder ./data --species Kiwi --night --lat -45.5 --lng 167.4```Sets matching labels from certainty=90 to 100 and updates the reviewer from `~/.skraak/config.json`. Outputs `{"segments_updated": N, "files_updated": M}`.5. **Propagate verified classifications between filters:**```bash# Single file./skraak calls propagate --file rec.wav.data \--from opensoundscape-kiwi-1.2 --to opensoundscape-kiwi-1.5 --species Kiwi# Whole folder./skraak calls propagate --folder ./recordings \--from opensoundscape-kiwi-1.2 --to opensoundscape-kiwi-1.5 --species Kiwi```Only source labels at certainty=100 matching `--species` are considered. Target labels (filter=`--to`) at certainty 70 or 0 are upgraded to certainty=90 and the file reviewer is set to `Skraak`. Targets already at 100 or 90 are left alone; files missing either filter are skipped.6. **Export OpenSoundScape clip_labels-format CSV:**```bash# Columns = canonical classes from mapping.json./skraak calls clip-labels --folder ./data --mapping ./mapping.json# Restrict to a single ML filter./skraak calls clip-labels --folder ./data --mapping ./mapping.json --filter opensoundscape-multi-1.0```Reproduces OpenSoundScape's `BoxedAnnotations.clip_labels()` outputexactly — same row layout, byte-identical CSVs — but in Go, fast, andwithout round-tripping through Raven `selections.txt`.**Algorithm.** For every `.data` file, generate fixed-duration clipwindows from `[0, Duration]` using OPSO's `generate_clip_times_df`(supports `--final-clip` of `full | remainder | extend | none`). Everywindow is emitted as a row; for each output class column, the value is`True` when at least one cert-100 annotation of that class overlaps thewindow by ≥ `--min-label-overlap` seconds, else `False`. Gaps just emitall-`False` rows.Only certainty=100 labels participate. `mapping.json` (from the`/data-mapping` skill) translates `.data` species strings to canonicalclass names. Two sentinels with distinct semantics:- **`"__NEGATIVE__"`** — clip IS emitted, **all class columns False**.Overrides any positive labels in the same clip's union. Use forconfirmed-negative training examples (e.g. `Noise`, `Not`, rain, wind,silence, chainsaw, helicopter).- **`"__IGNORE__"`** — the segment is dropped from output. Anysegment whose species maps to `__IGNORE__` triggers the drop, regardlessof filter. Use for files whose annotation set is incomplete: emitting anyclip from them as confirmed-False would poison the training set withpossibly-wrong negatives.Override order within a clip: `__NEGATIVE__` beats real classes. (File-level`__IGNORE__` is checked before any clip is generated.)**`--filter F`** restricts which ML filter's labels count(`opensoundscape-multi-1.0`, `BirdNET`, `Raven`, …). The mappingcoverage check also restricts to that filter.Defaults: `--clip-duration 4 --clip-overlap 0.5 --min-label-overlap 0.25 --final-clip full`.If `--output` exists, the run **appends**. Column-set mismatch with theexisting header → hard error. Duplicate `(file, start_time, end_time)`row (within the run, or vs existing rows) → hard error on firstoccurrence. Any `.data` parse error, missing `Duration`, or speciesmissing from `mapping.json` aborts before any row is written.## Segments ImportImport AviaNZ .data segments into the database with species/calltype mapping.**Prerequisites:**1. WAV files must already be imported (hashes must exist in database)2. No existing labels on files (fresh imports only)3. All filters, species, and calltypes must exist in database4. Mapping file must cover all species in .data files5. Filters / Models must already exist in the database**Mapping file** (`mapping_2026-03-13.json`):use claude skill to guide user through creation of species calltype mapping to db```json{"Don't Know": {"species": "Don't Know"},"GSK": {"species": "Roroa","calltypes": {"Male": "Male - Solo","Female": "Female - Solo"}}}```**Import Segments:**```bash./skraak import segments \--db ./db/skraak.duckdb \--dataset dataset_id \--location location_id \--cluster cluster_id \--folder /path/to/data \--mapping mapping.json```**What's imported:**- `segment` - time ranges with freq_low/freq_high from .data- `label` - species, filter, certainty for each segment- `label_subtype` - calltype if present in .data- `label_metadata` - stores comments (if present)**Data file updates:**- `skraak_hash` written to metadata section- `skraak_label_id` written to each label object**Bookmarks:** Segments with `bookmark: true` are imported normally; the bookmark flag is ignored (not stored in database).## Development```bash# Buildgo build -o skraak# Run testsgo test ./...# Run with coveragego test -cover ./...```### Cross-Compile to Windows (from Ubuntu)DuckDB's Go bindings use CGO with pre-built static libraries. Cross-compiling to Windows requires MinGW and a small ABI compatibility stub.**Prerequisites:**```bashsudo apt install gcc-mingw-w64-x86-64 g++-mingw-w64-x86-64# Switch to posix threading variant (DuckDB uses pthreads)sudo update-alternatives --set x86_64-w64-mingw32-gcc /usr/bin/x86_64-w64-mingw32-gcc-posixsudo update-alternatives --set x86_64-w64-mingw32-g++ /usr/bin/x86_64-w64-mingw32-g++-posix```**Build:**```bash# Create ABI stub (Ubuntu MinGW defines mbstate_t as int, DuckDB expects _Mbstatet)echo 'extern "C" { void* _ZNSt15basic_streambufIcSt11char_traitsIcEE7seekposESt4fposI9_MbstatetESt13_Ios_Openmode() { return (void*)-1; } }' \| tee /tmp/stub_seekpos.cppx86_64-w64-mingw32-g++ -c /tmp/stub_seekpos.cpp -o /tmp/stub_seekpos.o# Cross-compile (windows-amd64 only)CGO_ENABLED=1 \CC=x86_64-w64-mingw32-gcc \CXX=x86_64-w64-mingw32-g++ \GOOS=windows GOARCH=amd64 \go build -ldflags '-extldflags "/tmp/stub_seekpos.o -lucrt"' -o skraak.exe```**Verify:**```bashfile skraak.exe# Expected: PE32+ executable (console) x86-64, for MS Windows```See `CLAUDE.md` for detailed development notes.
# Skraak CLI/MCP Server## Documentation Policy**When making code changes, update CHANGELOG.md first, then CLAUDE.md only if architectural concepts change.**- CHANGELOG.md: Detailed change history with rationale- CLAUDE.md: Essential patterns, policies, and quick reference- **keep it concise**---## 🚨 Critical Database Safety### ALWAYS Use Test Database for Testing**CORRECT:**```bashcd shell_scripts./test_sql.sh ../db/test.duckdb > test.txt 2>&1```- `db/skraak.duckdb` = **PRODUCTION** (1.4M files)- `db/test.duckdb` = **TEST** (safe for testing)- **Always specify test.duckdb explicitly**### Testing Best Practices- **Always pipe to file** (prevents token overflow from large output)- Navigate to `shell_scripts/` before running tests- Verify: `rg '"result":' test.txt | wc -l`---## Package Organization**Simple rule:** If called by `cmd/`, it goes in `tools/`. If called by `tools/`, it goes in `utils/`.- **`utils/`** - Reusable helpers (no MCP types, no `*Input`/`*Output` structs)- **`tools/`** - MCP/CLI tools (one file per tool, defines input/output types)- **`cmd/mcp.go`** - MCP adapters (only file importing MCP SDK)- **`cmd/*.go`** - CLI commands (parse flags, call tools, print JSON)---## ArchitectureTwo-layer architecture: tools are MCP-free, adapters bridge to MCP protocol.```main.go → CLI dispatcher (mcp | import | sql | dataset | ...)cmd/mcp.go → MCP server + thin adapters (ONLY MCP SDK import)cmd/*.go → CLI commands (flags → tools → JSON output)tools/*.go → Core logic (plain Go structs, no MCP dependency)utils/*.go → Reusable helpersdb/ → Database connection + types```---## Directory Structure```skraak/├── main.go # CLI dispatcher├── cmd/ # MCP adapters + CLI commands├── db/├── tools/ # tools (MCP-free)├── utils/ # Reusable helpers├── tui/ # TUI specific code├── resources/schema.go # Schema resources└── shell_scripts/ # end-to-end test scripts```---## Building & Running### Build```bashgo build -o skraak```### MCP Server```bash./skraak mcp --db ./db/skraak.duckdb```### CLI Commands```bash# SQL query./skraak sql --db ./db/test.duckdb "SELECT COUNT(*) FROM file WHERE active = true"```**CLI Design:** All tools output JSON for composability with Unix tools (jq, grep). Errors to stderr.---## Testing### Shell Scripts (in shell_scripts/)All scripts default to `../db/test.duckdb`:```bashcd shell_scripts./test_sql.sh ../db/test.duckdb > test.txt 2>&1 # SQL tool# Verifyrg '"result":' test.txt | wc -l # Count successesrg '"isError":true' test.txt | wc -l # Count expected errors```### Go Unit Tests```bashgo test ./... # All testsgo test -v ./utils/ # Verbosego test -cover ./utils/ # Coveragego test -coverprofile=coverage.out ./utils/ && go tool cover -html=coverage.out```
# ChangelogAll notable changes to the Skraak project are documented here.## [2026-04-28] Remove MCP server support**Breaking change:** Removed the MCP (Model Context Protocol) server entirely.All functionality remains available via CLI commands.- Deleted `cmd/mcp.go` (MCP server + adapters)- Deleted `cmd/mcp_surface_test.go` (MCP integration tests)- Deleted `resources/` package (only served MCP schema resource)- Removed `case "mcp"` from `main.go` dispatch- Removed `jsonschema` struct tags from all `tools/*.go` (126 tags across 24 files)- Removed `github.com/modelcontextprotocol/go-sdk` dependency and transitive deps- Fixed stale "Map to MCP output format" comment in `tools/import_files.go`Rationale: CLI provides full access to all tools with JSON output for Unixcomposability. The MCP server was a parallel access path with no uniquecapabilities.## [2026-04-27] Performance: DirCache + worker pool for `from-raven` and `from-birda``calls from-raven` and `calls from-birda` were extremely slow on largefolders (57k files ≈ 2 hours). Root cause: `findWAVFile()` performed`os.ReadDir()` on every file — O(N²) directory scans. Fix:1. **DirCache**: Scan directory once, build `map[string]string` forO(1) WAV lookup. Eliminates the dominant bottleneck (57k × 57k = 3.25Bcomparisons → 1 scan + 57k map lookups).2. **Worker pool**: 8 parallel goroutines for I/O-bound processing(WAV header reads, .data writes). Same pattern as `from-preds`.3. Both commands auto-select sequential (< 10 files) vs parallel path.Expected improvement: 2 hours → 2–5 minutes on 57k files.`DirCache` is also available for `from-preds` but not yet wired in(that command already uses a worker pool and typically processes fewerunique directories).## [2026-04-27] Add `calls clip-labels` subcommandNew `skraak calls clip-labels` exports a CSV in OpenSoundScape's`clip_labels` format directly from `.data` files — same row layout as`BoxedAnnotations.clip_labels()`, byte-identical CSVs — but in Go, fast,and without round-tripping through Raven `selections.txt`.For every `.data` file in `--folder`, generate clip windows over`[0, Duration]` using a Go port of OPSO's `generate_clip_times_df`(`utils/clip_times.go`, supports `final_clip ∈ {full, remainder, extend,none}`). Every window is emitted as a row. For each output class column,the value is `True` when at least one certainty=100 annotation of thatclass overlaps the window by ≥ `--min-label-overlap` seconds, else`False`. Gaps emit all-`False` rows. Booleans capitalized to matchpandas' default; times rendered with at least one decimal place.Only certainty=100 labels participate (cert<100 is ignored).`mapping.json` (from the `/data-mapping` skill) translates `.data`species names to canonical class names. Two sentinels with distinctsemantics:- `__NEGATIVE__` — clip emitted, all class columns False; overrides anypositives in the same clip. Requires certainty=100. For confirmed-negativetraining examples (rain, wind, silence, helicopter, etc.).- `__IGNORE__` — the **entire file** is dropped from output. Any segmentwhose species maps to `__IGNORE__` triggers the drop, regardless ofcertainty or filter. For files whose annotation set is incomplete (e.g.`Don't Know` regions): emitting any clip from them as confirmed-Falsewould poison the training set with possibly-wrong negatives.`--filter F` restricts which ML filter's labels count(`opensoundscape-multi-1.0`, `BirdNET`, `Raven`, …); the mapping coveragecheck also restricts to that filter.Fail-fast: any `.data` parse error, missing `Duration`, missing mappingentry, or duplicate `(file, start_time, end_time)` row aborts the runbefore the CSV is written. Existing output files are appended; column-setmismatch hard-errors.Adds `MappingNegative`/`MappingIgnore` sentinels, `Classify`,`ValidateCoversSpecies`, and `Classes` to `utils/mapping.go`. Adds`utils/clip_times.go` with the OPSO clip-times port and unit testscovering all four `final_clip` modes. Verified against an OPSO referenceoutput on a 100-file Raven test folder: byte-identical CSVs.## [2026-04-26] Drop `schema://table/{name}` resourceKeeps `schema://full` and removes the per-table schema resource template,along with its line-based extractor (paren counting, view-vs-table branching,manual index/ALTER append) and the table-name allowlist. The full schema is241 lines — small enough that splitting it adds parsing surface for no realbenefit, and clients can also introspect via DuckDB(`information_schema.columns`, `DESCRIBE`, etc.) through `execute_sql`.Updates `shell_scripts/test_resources.sh` to drop per-table tests and theresource-template list call.## [2026-04-26] Remove `prompts` packageDeletes `prompts/examples.go` and the six MCP prompts it registered(`query_active_datasets`, `explore_database_schema`,`explore_location_hierarchy`, `query_location_data`, `analyze_cluster_files`,`system_status_check`). Drops the `skraak/prompts` import and `AddPrompt` callsfrom `cmd/mcp.go`.Motivation: the prompts were never invoked in practice. Models write SQLfluently from the `schema://*` resources alone, so the canned templates addedmaintenance surface without earning their keep. The `system_status_check`prompt was self-referential (its body listed the prompts being removed) andduplicated coverage already in `cmd/mcp_surface_test.go`.Also drops `shell_scripts/test_prompts.sh` and the prompt references in`shell_scripts/README.md` and `shell_scripts/TESTING.md`.## [2026-04-22] `calls summarise`: Add --filter flag to restrict output to a single filterAdds `--filter <name>` to `skraak calls summarise`. When specified, only labelsmatching that filter are included in stats, segments, and review counts.Segments with no matching labels are omitted entirely. Empty filter (default)behaves as before (all filters included).Motivation: a folder of .data files may contain multiple ML model filters;summarising all of them makes it hard to inspect one. `--filter` scopes theoutput the same way `classify --filter` scopes the TUI.## [2026-04-22] `calls classify`: Shift+primary secondary keybindings for calltype editingAdds a per-species secondary-binding layer to the classify TUI. Primary flow isunchanged (keypress → label → save → advance). When a primary key has`secondary_bindings` configured, pressing **Shift+primary-key** labels thespecies with an empty calltype, skips the auto-advance, and enters a one-shotwait state; the next keypress is looked up in the secondary map and sets thecalltype before advancing. Esc exits the wait state without advancing. Anynon-matching key falls through to normal handling.Motivation: species like common chaffinch have multiple calltypes (alarm,contact, song) that couldn't be assigned without burning extra keybindings onevery species. Secondary bindings are per-species (not global) to avoidaccidental mislabels, and deliberately unlisted in the help bar — users knowtheir own config.Example config:```json"classify": {"bindings": { "c": "comcha" },"secondary_bindings": {"c": { "a": "alarm", "s": "song", "n": "contact" }}}```Shift+primary on a key with no `secondary_bindings` entry falls back to normalprimary behavior, so existing configs are unaffected.**Files changed:**- `utils/config.go` — new `SecondaryBindings` field on `ClassifyFileConfig`.- `cmd/calls_classify.go` — validation (outer key must exist in bindings,inner keys single-char non-reserved, values non-empty) and passthrough to`ClassifyConfig`.- `tools/calls_classify.go` — `SecondaryBindings` field on `ClassifyConfig`,new `ApplyCallTypeOnly` and `HasSecondary` methods.- `tui/classify.go` — `awaitingSecondaryFor` model field, wait-mode interceptat top of `handleKey`, Shift+letter detection in the default branch, `…`indicator on the segment info line while waiting.## [2026-04-18] `--day` redefined as civil dawn → solar sunset (includes dawn chorus)`--day` previously filtered to solar day (sunrise → sunset), excluding the dawn chorus.Changed to civil dawn → solar sunset so diurnal species active at dawn are included.`--night` (solar night) is unchanged. The dawn-chorus window (civil dawn → solar sunrise)is now covered by **both** flags — a recording at that time is `solar_night=true` and`diurnal_active=true`. Correct: kiwi and diurnal bird-song both overlap at dawn.`IsNightOutput` gains a new `diurnal_active` field (bool, present in JSON output of`skraak isnight`) computed as `midpoint >= civil_dawn && midpoint <= solar_sunset`.**Files changed:** `tools/isnight.go`, `tools/calls_clip.go`, `tools/calls_classify.go`## [2026-04-18] `calls classify --night` / `--day`: filter TUI to solar-night or solar-day recordingsAdds `--night`, `--day`, `--lat`, `--lng`, and `--timezone` flags to `skraak calls classify`.Filtering happens at load time (before the TUI launches) inside `LoadDataFiles`, after theexisting segment filter — so `IsNight` is only called for files that have matching segments.Skipped file count is reported to stderr before the TUI starts.Same `--timezone` caveat as `calls clip`: required for non-AudioMoth recorders (e.g. DOC AR4)that embed local time in filenames. AudioMoth files don't need it.```bashskraak calls classify --folder F09/2026-04-06/ --species "Don't Know" \--night --lat -45.50603 --lng 167.47371```**Files changed:**- `tools/calls_classify.go` — `ClassifyConfig` (Night/Day/Lat/Lng/Timezone fields),`ClassifyState` (TimeFilteredCount), `LoadDataFiles` (day/night filter block).- `cmd/calls_classify.go` — flag parsing, mutual-exclusivity + lat/lng validation,config construction, skipped-count summary line, updated usage text.## [2026-04-18] `calls clip --night`: filter to solar-night recordings onlyAdds `--night`, `--lat`, `--lng`, and `--timezone` flags to `skraak calls clip`.When `--night` is set, each recording is checked against solar sunrise/sunset atthe given coordinates before its audio is loaded — daytime files are skippedentirely, saving the cost of reading WAV audio for files that would produce nouseful clips.`--timezone` is not needed for AudioMoth recorders (timestamp comes from the WAVcomment in UTC). It is required for recorders that embed **local time** in thefilename (e.g. DOC AR4) — without it the filename is parsed as UTC and`solar_night` will be wrong. Pass `--timezone Pacific/Auckland` or theappropriate IANA zone.The JSON output gains a `night_skipped` field (omitted when 0) counting how manyfiles were filtered out. Skipped filenames are logged to stderr.```bashskraak calls clip --folder ./data --output ./clips --prefix kiwi \--species Kiwi --night --lat -40.85 --lng 172.81# Non-AudioMoth (DOC AR4, filename in local time):skraak calls clip --folder ./data --output ./clips --prefix kiwi \--species Kiwi --night --lat -40.85 --lng 172.81 --timezone Pacific/Auckland```**Files changed:**- `tools/calls_clip.go` — `CallsClipInput` (Night/Lat/Lng/Timezone fields),`CallsClipOutput` (NightSkipped field), `processFile` night-filter block.- `cmd/calls_clip.go` — flag parsing, `--night` requires lat/lng validation,updated usage/help text.## [2026-04-18] `calls classify` reviewer, bindings, and display flags moved to config file**Breaking CLI change.** `skraak calls classify` no longer accepts `--reviewer`,`--bind`, `--color`, `--sixel`, `--iterm`, or `--img-dims`. These values are nowloaded from `~/.skraak/config.json`.Rationale: users (e.g. David) were typing the same ~25 `--bind` flags on everyinvocation. Moving stable, personal defaults into a config file eliminates thatrepetition. Per-invocation flags (`--folder`, `--file`, `--filter`, `--species`,`--certainty`, `--goto`) stay on the CLI.Path works cross-platform via `os.UserHomeDir()` — resolves to`~/.skraak/config.json` on Linux/macOS and `C:\Users\<name>\.skraak\config.json`on Windows.Config shape:```json{"classify": {"reviewer": "David","color": true,"sixel": false,"iterm": false,"img_dims": 0,"bindings": {"k": "Kiwi","1": "Kiwi+Duet","x": "Noise","z": "Don't Know"}}}````bindings` values use the same `Species` or `Species+CallType` grammar the old`--bind key=value` flag accepted — parsing is shared (`cmd/calls_classify.go:parseBind`).Config-load rejects bindings that collide with keys the TUI reserves for its owncommands (`,` previous segment, `.` next segment, `0` confirm at certainty 100,space opens the comment dialog). Previously these were silently shadowed by theTUI hotkey and the user's binding did nothing.**Files added:**- `utils/config.go` — `Config`, `ClassifyFileConfig`, `LoadConfig`, `ConfigPath`.Named `LoadConfig` (not `LoadClassifyConfig`) so future subcommands can addtheir own sections to the same file.**Files changed:**- `cmd/calls_classify.go` — Removed six flag cases, added config load after argparsing (so `--help` still works without a config), added `--help`/`-h` case,added single-character validation on binding keys.## [2026-04-17] New `skraak isnight` CLI commandAdds a standalone CLI command to check if a WAV file was recorded at night,without needing a database connection.```skraak isnight --file recording.wav --lat -36.85 --lng 174.76```Determines the recording timestamp from WAV metadata (AudioMoth comment →filename pattern → file modification time), then calculates sunrise/sunsetat the given GPS coordinates using the recording midpoint. Returns JSON with` solar_night`, `civil_night`, `moon_phase`, and sun event times.Optional `--timezone` flag (default UTC) is used for filename-based timestamps;AudioMoth comments embed their own timezone. Use `--brief` for batch/agentuse to return only `file_path` and `solar_night` (compact JSON, saves tokens).**Files added:**- `tools/isnight.go` — IsNight tool (MCP-free core logic)- `cmd/isnight.go` — CLI command (flags → tool → JSON output)**Files changed:**- `main.go` — Register `isnight` command and usage text## [2026-04-17] Numpad-friendly keybinds in classify TUITwo keyboard tweaks to make the TUI easier to drive from the numeric keypadwhile labeling kiwi calls:- **Numpad Enter plays audio.** The Enter-key handler in `tui/classify.go` nowmatches both `tea.KeyEnter` and `tea.KeyKpEnter`, so the keypad's Enter keyplays the current segment like the main Enter (and still respects Shift forhalf-speed playback). Previously, terminals that disambiguate keypad keys(e.g. via Kitty keyboard protocol) delivered numpad Enter as `KeyKpEnter`,which fell through the handler and did nothing.- **Arrow keys navigate segments.** Left arrow now does prev-segment (same as`,`) and right arrow does next-segment (same as `.`), so the user cannavigate without moving their hand off the numpad.**Files changed:**- `tui/classify.go` — Enter branch matches `KeyKpEnter`; `,`/`.` switch casesalso match `"left"`/`"right"`## [2026-04-05] Simplify calls classify TUI**Static segment list:** Filtered segments are now computed once at startup and cached.Reclassifying a segment no longer removes it from the navigation list mid-session.This fixes instability/crashes when working fast with `--species` or other filters.**Replace goto dialog with `--goto` flag:**- Removed ctrl+g goto dialog from TUI (and all supporting code)- Added `--goto <filename>` CLI flag that opens on the first matching segment in the named file- Removed `GotoFile()` and `TotalFiles()` methods from `ClassifyState`**Internal:** Added `NewClassifyState()` constructor for tests. All `getFilteredSegments()` callsreplaced with pre-computed `filteredSegs` cache parallel to `DataFiles`.**Files changed:**- `tools/calls_classify.go` — cached segments, `--goto` support, removed dynamic filtering- `tui/classify.go` — removed goto dialog (model fields, handler, renderer, keybind)- `cmd/calls_classify.go` — added `--goto` flag parsing- `tools/calls_classify_*_test.go` — updated to use `NewClassifyState()`## [2026-04-04] New `prepend` commandRename WAV files, their .data files, and log.txt by prepending a location prefix.**Usage:**```bashskraak prepend --folder <path> --prefix <string> [--recursive] [--dry-run]```**Target files:**- `*.wav`, `*.WAV` — Only if starting with datestring `YYYYMMDD_HHMMSS`- `*.wav.data`, `*.WAV.data` — Only if starting with datestring `YYYYMMDD_HHMMSS`- `log.txt` — Always renamed (exact name match)**Flags:**- `--folder <path>` — Target folder (required)- `--prefix <string>` — String to prepend (required)- `--recursive` — Include 1 level of subfolders- `--dry-run` — Show what would be renamed without doing it**Behavior:**- Files already starting with `<prefix>_` are skipped with reason "already prefixed"- WAV files without datestring prefix are skipped with reason "no datestring prefix"- Non-target files are silently ignored- Idempotent: running twice is safe**Examples:**```bash# Rename files in a folderskraak prepend --folder ./recordings --prefix LOC001# Include subfolders (1 level deep)skraak prepend --folder ./data --prefix SITE_A --recursive# Preview changesskraak prepend --folder ./test --prefix TEST --dry-run```**Changes:**- `tools/prepend.go` — Core logic (datestring detection, file renaming)- `tools/prepend_test.go` — Unit tests- `cmd/prepend.go` — CLI command with flag parsing- `main.go` — Added to command dispatcher## [2026-04-03] Added `--bookmark` and `--comment` flags to `calls modify`Allow agents and users to bookmark segments and add comments for information preservation in .data files.**New flags:**- `--bookmark` — Mark segment as bookmarked for navigation (boolean flag, sets `bookmark=true`)- `--comment <text>` — Add user comment (max 140 chars, ASCII only)**Usage:**```bash# Bookmark a segment for later reviewskraak calls modify --file recording.data --reviewer GLM-5 \--filter mymodel --segment 12-15 --certainty 100 --bookmark# Add a comment to a segmentskraak calls modify --file recording.data --reviewer GLM-5 \--filter mymodel --segment 12-15 --certainty 100 --comment "Good example of duet"```**Behavior:**- `--bookmark` sets `bookmark=true` on the label- `--comment` stores text in the label's comment field- Comment validation: max 140 characters, ASCII only- If all specified values match current values, no modification made (error)**Changes:**- `tools/calls_modify.go` — Added `Bookmark` and `Comment` fields to input/output structs, validation logic- `cmd/calls_modify.go` — Added `--bookmark` and `--comment` flag parsing## [2026-04-02] New `calls modify` commandModify a label in a .data file from the command line.**Usage:**```bashskraak calls modify --file recording.data --reviewer GLM-5 \--filter mymodel --segment 12-15 --certainty 100 --species Kiwi+Male```**Required flags:**- `--file <path>` — Path to .data file- `--reviewer <name>` — Reviewer name (always set on file metadata)- `--filter <name>` — Filter name to match labels- `--segment <start>-<end>` — Segment time range (integer seconds, e.g., `12-15`)- `--certainty <int>` — Certainty value (0-100)**Optional flags:**- `--species <name>` — Species to set (e.g., `Kiwi`, `Kiwi+Male`, `Noise`)**Segment matching:**- Segments matched by `floor(start_time)` and `ceil(end_time)`- A segment from 12.3s to 14.5s matches `--segment 12-15`**Behavior:**- Always updates reviewer on file metadata- If `--species` provided: sets species and calltype (or clears calltype if not specified)- If species+calltype AND certainty match current values, no modification made (error)- Error if no matching segment or label found (no-op on error)**Use cases:**- Correct classification: `--certainty 100` only (confirms existing species)- Incorrect classification: `--species NewSpecies --certainty 100` (changes both)**Changes:**- `tools/calls_modify.go` — New file, core logic- `cmd/calls_modify.go` — New file, CLI parsing- `cmd/calls.go` — Added `modify` subcommand## [2026-04-02] Clip feature in `calls classify` TUIAdded `ctrl+s` keybinding to save a clip of the current segment directly fromthe classification TUI.**Keybinding:** `ctrl+s` → type prefix → `enter` to save, `esc` to cancel**Output files:**- `<prefix>_<basename>_<start>_<end>.png` — 224x224 color spectrogram (L4 colormap)- `<prefix>_<basename>_<start>_<end>.wav` — audio clip (16kHz if downsampled)Files are saved to the current working directory where `skraak` was launched.Error if files already exist (no overwrite).**Changes:**- `tui/classify.go` — Added `clipMode` state, `handleClipKey()`, `renderClipDialog()`,and `saveClip()` function; added `ctrl+s` keybinding; updated help line## [2026-04-02] New `calls clip` commandGenerate audio clips and spectrogram images from .data file segments.Useful for extracting training data or creating datasets for ML.**Usage:**```bashskraak calls clip --file recording.data --output ./clips --prefix trainskraak calls clip --folder ./data --output ./clips --prefix kiwi \--filter opensoundscape-kiwi-1.2 --species Kiwi --size 448 --color```**Output files:**- `<prefix>_<basename>_<start>_<end>.png` — spectrogram image (224-896px)- `<prefix>_<basename>_<start>_<end>.wav` — audio clip (16kHz if downsampled)where `basename` is the WAV filename without `.wav` extension.**Features:**- Single file (`--file`) or batch folder (`--folder`) processing- Filter by ML model (`--filter`) and/or species (`--species`)- Species can include calltype: `Kiwi+Duet`- `--size <int>` — spectrogram image size (224-896px, default 224)- `--color` — apply L4 colormap (default: grayscale)- Error if output files already exist (no overwrite)- WAV files downsampled to 16kHz if input > 16kHz**New utilities:**- `utils.WriteWAVFile(path, samples, sampleRate)` — write mono 16-bit PCM WAV- `utils.WritePNG(img, writer)` — write image as PNG**Changes:**- `utils/wav_writer.go` — New file, WAV writer implementation- `utils/terminal_image.go` — Added `WritePNG()` function- `tools/calls_clip.go` — New file, core clip logic- `cmd/calls_clip.go` — New file, CLI parsing- `cmd/calls.go` — Added `clip` subcommand## [2026-04-02] Shared spectrogram generation for show-images and classifyRefactored spectrogram image generation into a shared utility function, reducingduplication between `calls show-images` and `calls classify` TUI.**New utility:**- `utils.GenerateSegmentSpectrogram(dataFilePath, startTime, endTime, color, imgSize)` -generates a spectrogram image from a segment, handling WAV loading, downsampling,and image creation in one call.**Changes:**- `utils/spectrogram.go` — Added `GenerateSegmentSpectrogram()` function- `tools/calls_show_images.go` — Now uses `utils.ParseDataFile()` (includes labels) and`GenerateSegmentSpectrogram()`; removed local `Segment` struct and `parseDataFile()`;segment info now shows labels when present- `tui/classify.go` — `generateSpectrogramImage()` now delegates to shared function**Future:** show-images now has access to segment labels, enabling future filteringby filter/ml model and species+calltype.## [2026-03-29] Goto file feature for `calls classify` TUIAdded `ctrl+g` keybinding to jump directly to any file by number. The dialog acceptsa file number (1-based) and jumps to the first segment of that file.**Keybinding:** `ctrl+g` → type number → `enter` to jump, `esc` to cancel**Changes:**- `tools/calls_classify.go` — Added `TotalFiles()` and `GotoFile()` methods to `ClassifyState`- `tui/classify.go` — Added `gotoMode` and `gotoInput` state; `ctrl+g` keybinding;`handleGotoKey()` for digit/backspace/enter/esc handling; `renderGotoDialog()` for UI display## [2026-03-29] Clarify segment counts in TUIUpdated progress display to explicitly label the segment count.**Changes:**- `tui/classify.go` — Changed title line from `file [progress] 1/40826` to `file [progress] 1/40826 Segments`- `cmd/calls_classify.go` — Updated startup message to clarify filtered counts- `tools/calls_classify.go` — Added tests to verify filtering behavior- Confirmed `TotalSegments()` and `CurrentSegmentNumber()` correctly use `getFilteredSegments()`- Files with no matching segments are pruned during load (existing behavior)## [2026-03-29] `--species` flag for `calls classify`Added `--species` flag to scope classification to a single species (and optionally calltype).Composable with `--filter` for focused review of specific detections within an ML model's output.**Examples:**```bash# Review only Kiwi Duet calls from a specific filterskraak calls classify --folder ./data --reviewer dave --bind k=Kiwi \--filter opensoundscape-kiwi-1.2 --species Kiwi+Duet# Review all Kiwi calls (any calltype)skraak calls classify --folder ./data --reviewer dave --bind k=Kiwi --species Kiwi```**Changes:**- `tools/calls_classify.go` — Added `Species` and `CallType` fields to `ClassifyConfig`;extended `getFilteredSegments()` with `segmentMatchesFilters()` for AND-composablefilter+species+calltype matching; prune data files with no matching segments on load- `cmd/calls_classify.go` — Parse `--species` flag (rejects duplicates), zero-segmentguard before TUI launch, comprehensive `printClassifyUsage()`## [2026-03-29] Codebase consistency improvements**Changes:**- `tools/import_file.go` — Single DB connection per `ImportFile()` call (was 3), uses`validateHierarchyIDs()`, passes `ctx` and `*sql.DB` to helpers- `tools/import_files.go` — Extracted `validateHierarchyIDs()` for reuse- `tools/bulk_file_import.go` — `bulkCreateCluster` uses `db.BeginLoggedTx()` fortransaction audit logging- `cmd/common.go` — Extracted `initEventLog()` helper, replacing 14 instances of6-line event log boilerplate across 7 cmd files- `tools/export.go` — Documented why `fmt.Sprintf` for table names is safe (hardcoded manifest)- `tools/location.go` — Fixed `Exec` → `ExecContext` for context propagation consistency- `utils/cluster_import.go` — Exported `LocationData` and `GetLocationData` for cross-package use- Removed duplicate godoc comments on several tool functions## [2026-03-19] NOT NULL Constraint Validation in Bulk ImportAdded empty-string validation for CSV fields in `bulkReadCSV()` (`tools/bulk_file_import.go`).Audited all INSERT/UPDATE paths for NOT NULL constraint enforcement. Found one gap:`record[3]` (DateRange → cluster name) was not validated for empty strings. Also addedvalidation for `record[0]` (location_name) and `record[2]` (directory_path) which wouldcause downstream failures if empty.**Changes:**- `tools/bulk_file_import.go` — validate `location_name`, `directory_path`, and `date_range`CSV fields are non-empty (with TrimSpace) before building `bulkLocationData` structs## [2026-03-14] Remove import_ml_selections (Deprecated)**Breaking Change:** Removed deprecated `import selections` CLI command and `import_ml_selections` MCP tool.The `import segments` command is the replacement, offering:- AviaNZ .data file import (industry standard)- Species/calltype mapping file validation- Transactional imports with proper error handling- Simpler, more maintainable codebase**Removed:**- `tools/import_ml_selections.go` (1134 lines)- `cmd/mcp.go` — `import_ml_selections` MCP tool registration- `cmd/import.go` — `selections` CLI subcommand**Changes:**- `utils/mapping.go` — Exported `Placeholders()` function for reuse## [2026-03-14] Import Segments - Fix Orphaned Segments**Fix:** Segments with no valid labels are now deleted from the database.When a segment's labels all fail validation (e.g., missing species in mapping), the segmentwas previously left orphaned in the database with no labels. Now the segment is deleted withinthe same transaction, maintaining data integrity.**Changes:**- `tools/import_segments.go` — Delete orphaned segments when all labels fail validation- `utils/mapping_test.go` — Unit tests for mapping file loading and validation- `tools/import_segments_test.go` — Unit tests for input validation and segment counting- `utils/data_file_test.go` — Added tests for skraak_hash and skraak_label_id round-trip## [2026-03-14] Import Segments Command**Feature:** New `skraak import segments` command to import AviaNZ .data segments into the database.**Changes:**- `utils/mapping.go` — New utilities for loading and validating species/calltype mapping files- `tools/import_segments.go` — New tool with `ImportSegments()` function- `cmd/import.go` — Added `segments` subcommand**Usage:**```bashskraak import segments \--db ./db/skraak.duckdb \--dataset gljgxDbfasva \--location ZEVWGbXzB1bl \--cluster q7w-iQgyZOYV \--folder /path/to/data \--mapping mapping.json```**Mapping file format** (`mapping.json`):```json{"Don't Know": {"species": "Don't Know"},"GSK": {"species": "Roroa","calltypes": {"Male": "Male - Solo","Female": "Female - Solo"}}}```**Output structure:**```json{"summary": {"data_files_found": 42,"data_files_processed": 42,"total_segments": 342,"imported_segments": 342,"imported_labels": 356,"imported_subtypes": 280,"processing_time_ms": 1234},"segments": [...],"errors": []}```**Invariants enforced:**- All file hashes must already exist in database for the cluster- All files must have no existing labels (fresh imports only)- All filters, species, and calltypes must exist in database- Segments with `bookmark: true` labels are skipped- Mapping must cover all species found in .data files**Database writes:**- `segment` table: id, file_id, dataset_id, start_time, end_time, freq_low, freq_high- `label` table: id, segment_id, species_id, filter_id, certainty- `label_metadata` table: `{"comment": "..."}` (only if comment present)- `label_subtype` table: id, label_id, calltype_id, filter_id, certainty (if calltype present)**Data file updates:**- `skraak_hash` written to metadata section (first element of .data array)- `skraak_label_id` written to each label object**Rationale:**AviaNZ .data files contain segment annotations from both manual review and ML filters. This command imports those segments into the skraak database with proper species/calltype mapping, enabling integrated analysis across all annotation sources.## [2026-03-13] Calls Summarise Command**Feature:** New `skraak calls summarise` command to analyse .data files after classification.**Changes:**- `tools/calls_summarise.go` — New tool with `CallsSummarise()` function- `cmd/calls.go` — Added `summarise` subcommand**Usage:**```bashskraak calls summarise --folder ./recordings > summary.jsonskraak calls summarise --folder ./recordings | jq 'del(.segments)' # summary only```**Output structure:**```json{"segments": [...],"data_files_read": 27,"data_files_skipped": [],"total_segments": 47,"filters": {"opensoundscape-kiwi-1.2": {"segments": 20,"species": {"Kiwi": 15, "Don't Know": 5},"calltypes": {"Kiwi": {"Male": 10, "Duet": 5}}}},"review_status": {"unreviewed": 30,"confirmed": 10,"dont_know": 5,"with_calltype": 8,"with_comments": 3,"bookmarked": 2},"operators": ["Auto"],"reviewers": ["David", "None"]}```**Review status definitions:**- `unreviewed`: certainty < 100 (default from detection)- `confirmed`: certainty = 100 (user pressed bind key)- `dont_know`: certainty = 0**Calltypes:** Only appears in filters when species have calltypes set, showing per-species calltype counts.**Rationale:**After running `skraak classify` on .data files, it's difficult to understand the state of classifications. This command provides a comprehensive summary with both detailed segments array and aggregated statistics.## [2026-03-10] Spectrogram Sample Rate Limiting**Feature:** Spectrograms now automatically downsample high sample rate audio to 16kHz.**Changes:**- `utils/spectrogram.go` — Added `DefaultMaxSampleRate = 16000` constant- `utils/resample.go` — Added `ResampleRate()` function for sample rate conversion- `tools/calls_show_images.go` — Downsample segments before spectrogram generation- `tui/classify.go` — Downsample segments before spectrogram generation**Rationale:**- High sample rates (e.g., 250kHz bat detectors) produce very tall spectrograms- Birds are typically in 0-8kHz range; 16kHz sample rate (Nyquist = 8kHz) is sufficient- Audio playback unchanged — plays at original sample rate**Behavior:**| Original Rate | Spectrogram Rate | Playback Rate ||---------------|------------------|---------------|| 8000 Hz | 8000 Hz | 8000 Hz || 16000 Hz | 16000 Hz | 16000 Hz || 44100 Hz | 16000 Hz | 44100 Hz || 250000 Hz | 16000 Hz | 250000 Hz |## [2026-03-09] Case-Preserving WAV File Finding**Fix:** WAV files with lowercase `.wav` extension now produce correct `.wav.data` files.**Changes:**- `tools/calls_from_preds.go` — Added `findWAVFile()` helper function- `tools/calls_from_birda.go` — Updated to use `findWAVFile()`- `tools/calls_from_raven.go` — Updated to use `findWAVFile()`**Problem:** Previous code hardcoded `.WAV` extension, causing issues on case-sensitive filesystems:- `abc.wav` would fail to be found- Or produce `abc.WAV.data` instead of `abc.wav.data`**Solution:** `findWAVFile(dir, baseName)` searches for:1. `.WAV` (most common for main recordings)2. `.wav` (common for clips)3. `.Wav` (edge case)4. Case-insensitive glob fallback**Result:**| WAV File | .data File ||----------|------------|| `abc.WAV` | `abc.WAV.data` || `abc.wav` | `abc.wav.data` || `abc.Wav` | `abc.Wav.data` |## [2026-03-09] Bookmark Navigation in TUI**New feature:** Bookmark segments for later review.**Changes:**- `utils/data_file.go` — Added `Bookmark bool` to Label struct- `tools/calls_classify.go` — Added bookmark methods- `tui/classify.go` — Added key handlers and display- `tui/classify.go` — Header lines now wrap at 80 characters**Format** (stored in label):```json[0, 3, 0, 16000, [{"species": "Kiwi", "certainty": 90, "filter": "BirdNET", "bookmark": true}]]```**Key bindings:**| Key | Action ||-----|--------|| `Ctrl+D` | Toggle bookmark on current segment || `Ctrl+,` | Previous bookmark (wraps around) || `Ctrl+.` | Next bookmark (wraps around) |**Behavior:**- Bookmark lives on the filter-matching label- `--filter BirdNET` shows bookmarks on BirdNET labels only- No filter shows all bookmarks- Wrap-around navigation with loop detection- `[BOOKMARKED]` indicator shown in segment info## [2026-03-09] Comment Dialog Editing in TUI**Enhancement:** Full cursor editing support in the comment dialog.**Changes:**- `tui/classify.go` — Added cursor position tracking and navigation**New features:**| Key | Action ||-----|--------|| `←` / `→` | Move cursor left/right || `Space` | Insert space at cursor || `Backspace` | Delete character before cursor || `Delete` | Delete character at cursor || `Ctrl+A` | Move cursor to start || `Ctrl+E` | Move cursor to end |**Fixed:**- Space bar now works in comment dialog- Backspace deletes at cursor position, not just at end## [2026-03-09] New Commands: calls from-birda and calls from-raven**New feature:** Import BirdNET and Raven annotation files to .data files.**Added:**- `tools/calls_from_birda.go` — BirdNET results file parser- `tools/calls_from_raven.go` — Raven selections file parser- `cmd/calls.go` — New subcommands `from-birda` and `from-raven`- `tools/calls_from_birda_raven_test.go` — 10 test cases**Commands:**```bash# BirdNET (filter always "BirdNET")./skraak calls from-birda --folder /path/to/recordings./skraak calls from-birda --file recording.BirdNET.results.csv [--delete]# Raven (filter always "Raven")./skraak calls from-raven --folder /path/to/recordings./skraak calls from-raven --file recording.Table.1.selections.txt [--delete]```**File formats:**- BirdNET: `*.BirdNET.results.csv` (CSV with BOM, columns: Start, End, Scientific name, Common name, Confidence, File)- Raven: `*.selections.txt` (Tab-separated, columns: Begin Time, End Time, Low Freq, High Freq, Species)**Behavior (same as from-preds):**- Filter is always parsed from filename (no `--filter` option)- No clobber: if filter already exists, error- Merge: if different filter exists, append segments- Confidence (BirdNET) converted from 0.0-1.0 to 0-100- Frequency range preserved from Raven selections- `--delete` option removes source files after successful import**Tests:** 10 new tests covering:- New .data file creation- Same filter rejection (no clobber)- Different filter merge- Delete option- Folder mode (BirdNET only)- Multiple selections (Raven only)## [2026-03-09] Safe .data File Writing in calls-from-preds**Breaking change:** Filter must now be non-empty. Previously empty filter was allowed.**Problem:** `calls-from-preds --write-dot-data` would silently clobber existing `.data` files, potentially destroying manual annotations.**Solution:** Implemented safe write logic that protects existing data:1. **No existing file** → Write new file (unchanged behavior)2. **Existing file, same filter** → Error: "file already contains filter 'X' (refusing to clobber)"3. **Existing file, different filter** → Merge segments (append new, sort by time)4. **Existing file, parse error** → Error: "cannot parse existing file (refusing to clobber)"**Changes:**- `tools/calls_from_preds.go` — Added `writeDotDataFileSafe()` for safe write/merge logic- `tools/calls_from_preds.go` — Added filter validation: empty filter now returns error- `tools/calls_from_preds.go` — Filter defaults to CSV filename parsing if `--filter` not specified- `tools/calls_from_preds.go` — Added `convertAviaNZSegment()` and `buildAviaNZMetaAndSegments()` helpers**Filter logic:**- If `--filter "name"` specified → use that filter- If `--filter` not specified → parse from CSV filename (e.g., `predsST_opensoundscape-kiwi-1.2_2025-11-12.csv` → `opensoundscape-kiwi-1.2`)- If filter is empty string → error**Error handling:** First error stops batch processing (existing behavior preserved).**Tests added:** `tools/calls_from_preds_test.go` with 7 test cases:- Empty filter returns error- New .data file created when none exists- Existing file with same filter returns error (refuses to clobber)- Existing file with different filter merges segments- Existing file with parse error returns error (refuses to clobber)- Explicit filter via `--filter` flag- Non-parsable filename without filter returns error## [2026-03-07] JSON Schema for AviaNZ .data Files**New feature:** Added JSON Schema (Draft 2020-12) for validating AviaNZ .data annotation files.**Added:**- `db/avianz_data_schema.json` — Comprehensive schema for .data file format**Schema coverage:**- Root array with metadata object first, then segment arrays- Meta object with `Operator`, `Reviewer`, `Duration` (optional, allows extra fields)- Segment array: 5-element tuple `[starttime, endtime, freq_low, freq_high, labels]`- Label object with required `species` and `certainty` (0-100)- Optional fields: `filter`, `calltype`, `comment` (max 140 chars)- Additional properties allowed on all objects (extensibility)- Pattern constraint: `species` must not contain `>` separator**Validation tests:**- Missing required fields caught- Certainty range (0-100) enforced- Comment length (max 140) enforced- Minimal valid files accepted## [2026-03-07] Comment Feature in Classify TUI**New feature:** Press spacebar in the classify TUI to add/edit comments on labels.**Changes:**- `utils/data_file.go` — Added `Comment` field to `Label` struct, parse/write handling- `tools/calls_classify.go` — Added `SetComment()` and `GetCurrentComment()` methods, `Comment` field in `BindingResult`- `tui/classify.go` — Added `commentMode`/`commentText` state, spacebar opens dialog, text input handling, dialog rendering**AviaNZ spec compliance:** The spec allows "any additional attributes defined for this call" as key-value pairs. Comments are stored as `"comment": "text"` in the label object.**Usage:**- `[space]` — Open comment dialog (pre-fills existing comment)- Type comment (max 140 chars, ASCII only)- `[enter]` — Save comment- `[esc]` — Cancel (discard changes)- `[backspace]` — Delete last character- `[ctrl+u]` — Clear all**Help text:** `[esc]quit [,]prev [.]next [space]comment [enter]play [shift+enter]½speed`## [2026-03-04] Half-Speed Audio Playback in Classify TUI**New feature:** Press Shift+Enter in the classify TUI to play audio at half speed.**Changes:**- `utils/resample.go` — **NEW** Linear interpolation resampling for speed changes- `utils/audio_player.go` — Added `PlayAtSpeed(samples, sampleRate, speed)` method- `tools/calls_classify.go` — Added `PlaybackSpeed` field to `ClassifyState`- `tui/classify.go` — Detect Shift+Enter modifier, display "▶ Playing 0.5x..." in status- `tui/classify.go` — Changed quit key from `q` to `Escape` (frees `q` for bindings)**Usage:** `[esc]quit [enter]play [shift+enter]½speed`## [2026-03-04] Performance Optimizations for calls-from-preds**Problem:** Processing 7617 WAV files took 16 minutes due to excessive I/O and sequential processing.**Changes:**- `utils/wav_metadata.go` — Added `ParseWAVHeaderMinimal()` that reads only 4KB instead of 200KB per file (50× less I/O). Added separate buffer pool for minimal headers.- `tools/calls_from_preds.go` — Added parallel processing with 8 workers for .data file generation. Small batches (<10 files) use sequential processing to avoid goroutine overhead.- `tools/calls_from_preds.go` — Added `ProgressHandler` callback type for progress reporting during long operations.- `cmd/calls.go` — Added progress indicator showing "Processing WAV files: X/Y (Z%)" during .data file writing.**Expected improvement:** ~8× faster on multi-core systems due to parallel processing + reduced I/O overhead.## [2026-03-04] Add iTerm2 Inline Image Protocol Support**New feature:** Added `--iterm` flag for terminals supporting the iTerm2 Inline Image Protocol (WezTerm, iTerm2, VS Code terminal).- `utils/terminal_image.go` — Added `ProtocolITerm` enum value and `WriteITermImage()` using charm's `x/ansi/iterm2` package; PNG-encodes then base64-encodes for the iTerm2 escape sequence- `tools/calls_show_images.go` — Added `ITerm` field to `CallsShowImagesInput`, checked before `Sixel` in protocol selection- `tools/calls_classify.go` — Added `ITerm` field to `ClassifyConfig`- `cmd/calls.go` — Added `--iterm` flag to `show-images` subcommand- `cmd/calls_classify.go` — Added `--iterm` flag to `classify` subcommand- `tui/classify.go` — Renamed `sixelImageCmd` to `inlineImageCmd` with protocol parameter; changed conditionals from `== ProtocolSixel` to `!= ProtocolKitty` so both sixel and iTerm2 use the same inline rendering path- `utils/terminal_image_test.go` — Tests for `WriteITermImage`, `WriteImage` routing, and `ClearImages` no-op## [2026-02-28] Fix Kitty Image Rendering at 448px in Classify TUI**Bug fix:** Spectrogram display upgraded from 224x224 to 448x448 pixels. Old image artifacts persisted between segment navigations at the larger size.- `utils/kitty_image.go` — Chunked Kitty protocol transmission (4096-byte chunks) per spec; small images still sent as single payload- `tui/classify.go` — Return `tea.ClearScreen` on navigation keys (`,`, `.`, bindings) to force full redraw and reliable image clearing- `tui/classify.go` — `ResizeImage` call updated from 224x224 to 448x448- `utils/kitty_image_test.go` — Tests for single-chunk, multi-chunk, and clear behavior## [2026-02-28] Audio Playback in Classify TUI**New feature:** Press Enter to play the current segment's audio during classification.- Added `utils/audio_player.go` — wraps ebitengine/oto v3 for PCM playback- Oto context created lazily on first play, reused across segments- Converts `[]float64` samples → signed int16 LE for oto- Playback stops automatically on navigation (`,`/`.`), binding keys, and quit- "▶ Playing..." indicator shown in segment info line- New dependency: `github.com/ebitengine/oto/v3` (requires `libasound2-dev` on Linux)## [2026-02-22] New CLI Command: calls-from-preds**New feature:** Extract clustered bird calls from ML predictions CSV files.**Usage:**```bash./skraak calls-from-preds --csv predictions.csv > calls.json```**How it works:**1. Reads prediction CSV (file, start_time, end_time, ebird_code columns with 1/0 values)2. Auto-detects clip duration from first row3. Groups detections by (file, ebird_code) and sorts by start_time4. Clusters consecutive detections where gap ≤ 3 × clip_duration5. Filters out single detections (configurable via constant)**Constants (easily changeable):**```goCLUSTER_GAP_MULTIPLIER = 3 // Gap threshold = 3 × clip_durationMIN_DETECTIONS_PER_CLUSTER = 1 // Filter single detections```**Performance:** 400k+ rows processed in ~0.67 seconds**Output example:**```json{"calls": [{"file": "path.WAV", "start_time": 0, "end_time": 32, "ebird_code": "tomtit1", "detections": 11}],"total_calls": 62593,"species_count": {"tomtit1": 12636, ...},"files_count": 14017}```**Files:**- `tools/calls_from_preds.go` — Core clustering logic- `cmd/calls_from_preds.go` — CLI handler---## [2026-02-21] Remove import_audio_file MCP Tool**Breaking change:** Removed `import_audio_file` MCP tool. Use CLI command `skraak import file` for single file imports.**Rationale:** The MCP tool was redundant since:1. Single file imports are better suited for CLI use (requires file path on local machine)2. `import_audio_files` handles batch imports efficiently via MCP3. Reduces MCP tool count from 11 to 10**Changes:**- **`cmd/mcp.go`** — Removed `import_audio_file` tool registration and adapter- **`tools/import_file.go`** — Kept for CLI use only- **`cmd/import.go`** — CLI command `skraak import file` unchanged**Migration:** Use CLI command instead:```bash./skraak import file --db ./db/skraak.duckdb --dataset abc123 --location loc456 --cluster clust789 --path /path/to/file.wav```---## [2026-02-21] Verb-First CLI Commands**Breaking change:** Replaced resource-first CLI commands with natural language verb-first structure.**Before:**```bash./skraak dataset create --name "Test"./skraak location update --id abc123 --name "Updated"```**After:**```bash./skraak create dataset --name "Test"./skraak update location --id abc123 --name "Updated"```**Changes:**- **`main.go`** — Removed legacy `dataset`, `location`, `cluster`, `pattern` commands- **`cmd/create.go`** — New verb-first create handler- **`cmd/update.go`** — New verb-first update handler- **`cmd/dataset.go`, `cmd/location.go`, `cmd/cluster.go`, `cmd/pattern.go`** — Exported create/update functions- **Shell scripts** — Updated `test_bulk_import.sh` and `test_event_log.sh` to use new syntax**Benefits:**- Natural language flow: "create dataset" vs "dataset create"- Consistent with `skraak import file/folder/bulk` pattern- More intuitive for users- Maintains clean tool separation in `@tools/` directory**Migration:** Legacy commands now return "Unknown command" error, forcing adoption of new syntax.---## [2026-02-21] Fix Event Log Pointer Serialization**Bug fix:** Event log contained pointer addresses instead of values for nullable database fields (`*float64`, `*GainLevel`, etc.), causing replay failures.**Root cause:** `marshalParam()` in `db/tx_logger.go` didn't handle pointer types for numeric values or named type aliases (like `db.GainLevel`). These fell through to `fmt.Sprintf("%v", pointer)` which printed memory addresses like `"0x38a7bfb12078"`.**Example of corrupted data:**```json"parameters": ["file_id", "2025-05-18T18:30:00+13:00", "248AB50053AB1B4A", "0x38a7bfb12078", "0x38a7bfb12088", "0x38a7bfb12090"]```The last three values should have been `gain`, `battery_v`, `temp_c` but were pointer addresses.**Fixed:**- `db/tx_logger.go` — Added explicit cases for all pointer types (`*int`, `*int64`, `*float64`, `*bool`, etc.)- `db/tx_logger.go` — Added reflection-based fallback in default case to handle pointer-to-named-type (e.g., `*GainLevel`)- `cmd/replay.go` — Increased `bufio.Scanner` buffer from 64KB to 20MB to handle large event lines (17,000 files = ~16 MB JSON line)**Tests added:**- `db/tx_logger_test.go` — Tests for `*int`, `*int64`, `*float64`, `*float32`, `*bool` with nil and value cases- `db/tx_logger_test.go` — Tests for named type aliases and pointer-to-named-type---## [2026-02-19] Fix Update Commands - Preserve Unset Fields**Bug fix:** Update commands were overwriting existing values with empty strings when optional flags weren't provided.**Root cause:** CLI code set pointers to empty strings even when flags weren't provided, causing tools layer to interpret them as intentional empty values.**Fixed:**- `cmd/dataset.go` — `runDatasetUpdate()` now only sets pointer fields when flags have non-empty values- `cmd/location.go` — `runLocationUpdate()` now only sets pointer fields when flags have non-empty values- `cmd/cluster.go` — Already correct (only sets fields when provided)- `cmd/pattern.go` — Already correct (only sets fields when provided)**Tests added:**- `tools/update_test.go` — Unit tests verifying update preserves unset fields for all entity types---## [2026-02-19] Schema Simplification - Remove species_dataset and ebird_taxonomy_v2024**Database schema changes:**- Dropped `species_dataset` table — all species now available across all datasets- Dropped `ebird_taxonomy_v2024` table — use `WHERE taxonomy_version = '2024'` on `ebird_taxonomy` instead**Rationale:**- Simplifies species management (no duplicate species names across datasets)- Reduces schema complexity (one fewer join for species lookups)- `ebird_taxonomy_v2024` was redundant; filtering `ebird_taxonomy` directly is sufficient**Code changes:**- `tools/export.go` — Simplified manifest: `species` and `call_type` now "copy" (full table)- `tools/export.go` — Removed `buildDerivedTableCreate()`, `populateDerivedTable()`, simplified `buildReferencedQuery()`- `tools/import_ml_selections.go` — Species lookup no longer joins `species_dataset`- `resources/schema.go` — Removed tables from list- `db/schema_test.go` — Removed obsolete test cases- `prompts/examples.go` — Updated taxonomy schema description**Export manifest changes:**- `species_dataset` → removed (no longer exists)- `ebird_taxonomy_v2024` → removed (no longer exists)- `species` → changed from "referenced" to "copy"- `call_type` → changed from "referenced" to "copy"- `filter` → changed from "referenced" to "copy"- All "referenced" and "derived" handling code removed---## [2026-02-19] Dataset Export for Collaboration and Testing**New feature: Export a dataset with all related data to a new database****Purpose:** Enable dataset-level exports for collaboration (export, modify, replay changes), testing (small focused test DBs), and archival.**Architecture:**- Schema read from embedded `db/schema.sql` (DDL statements extracted dynamically)- Table copy order computed from FK relationships using `duckdb_constraints()`- ATTACH mechanism for efficient cross-database copying- Declarative manifest defines table relationships**Added:**- `tools/export.go` — `ExportDataset()` with table manifest and copy logic- `cmd/export.go` — `skraak export dataset` CLI command- `db/schema.go` — Schema utilities: `ReadSchemaSQL()`, `ExtractDDLStatements()`, `GetFKOrder()`- `shell_scripts/test_export.sh` — Integration test script**Command:**```bashskraak export dataset --db skraak.duckdb --id abc123 --output export.duckdbskraak export dataset --db skraak.duckdb --id abc123 --output export.duckdb --dry-runskraak export dataset --db skraak.duckdb --id abc123 --output export.duckdb --force```**What's exported:**- Dataset row and all owned data (locations, clusters, files, selections, labels)- Reference tables copied in full (`ebird_taxonomy`, `species`, `call_type`, `cyclic_recording_pattern`, `filter`)- Empty event log created for capturing changes**Design decisions:**- Schema from `schema.sql` ensures schema-resilience (new columns auto-included)- FK order computed dynamically via `duckdb_constraints()` function- Close source DB before output DB (DuckDB single-connection limit)- `SELECT *` copies all columns without hard-coding**Testing:**- `db/schema_test.go` — Unit tests for DDL extraction and FK ordering- Integration tests verify row counts match source- Error handling tests for missing dataset, existing file---## [2026-02-18] Event Log for Database Mutation Replay**New feature: SQL-level event logging for backup synchronization****Purpose:** Capture all mutating SQL operations (INSERT, UPDATE, DELETE) to enable replay on backup databases for synchronization.**Architecture:**- Transaction wrapper (`db.LoggedTx`) intercepts all mutations- Logged only on successful commit (rollback discards recorded queries)- Events written to JSONL file (`<database>.events.jsonl`)- Prepared statements fully supported via `LoggedStmt` wrapper**Added:**- `db/tx_logger.go` — LoggedTx, LoggedStmt, TransactionEvent types- `cmd/replay.go` — `skraak replay events` CLI command- `shell_scripts/test_event_log.sh` — Integration test script**Modified:**- All CLI commands initialize event log with defer close- All tools use `db.BeginLoggedTx()` instead of `database.BeginTx()`- `utils/cluster_import.go` updated for batch imports**Event format (JSONL):**```json{"id": "V1StGXR8_Z5jdHi6B-myT","timestamp": "2026-02-18T14:30:22+13:00","tool": "create_or_update_dataset","queries": [{"sql": "INSERT INTO ...", "parameters": [...]}],"success": true,"duration_ms": 45}```**Replay command:**```bashskraak replay events --db backup.duckdb --log skraak.duckdb.events.jsonlskraak replay events --db backup.duckdb --log events.jsonl --dry-runskraak replay events --db backup.duckdb --log events.jsonl --last 10```**Key design decisions:**- SQL-level (not tool-level) for complete fidelity including imports- Tool name included for context/debugging- Only successful transactions logged- Failed events skipped during replay- `--continue` flag to proceed past errors**Testing:**- `db/tx_logger_test.go` — 123 unit tests, 75.9% coverage- Pure function tests (isMutation, marshalParam, JSON marshaling)- Integration tests with real DuckDB and file system- Race detector verified---## [2026-02-11] CLI Refactoring — Two-Layer Architecture**Major refactoring: Separated core logic from MCP types, added CLI commands****Problem:** All tool functions were tightly coupled to MCP SDK types (`*mcp.CallToolRequest`, `*mcp.CallToolResult`). This meant functionality could only be invoked via MCP protocol — no CLI access for power users.**Solution:** Two-layer architecture separating core logic from MCP adapters.**Created:**- `cmd/mcp.go` — MCP server setup + 10 thin adapter wrappers (~3 lines each)- `cmd/import.go` — `skraak import bulk` CLI command with flag parsing- `cmd/sql.go` — `skraak sql` CLI command for ad-hoc queries**Modified (mechanical, all tools/):**- Removed `*mcp.CallToolRequest` parameter (was never used — `req` always ignored)- Removed `*mcp.CallToolResult` from returns (was always empty `&mcp.CallToolResult{}`)- Removed `import "github.com/modelcontextprotocol/go-sdk/mcp"` from all tool files- Updated test files (`integration_test.go`, `pattern_test.go`) to match new signatures- Updated `main.go` to pure dispatcher: `mcp | import | sql`**Architecture:**```main.go → pure dispatchercmd/mcp.go → MCP server + adapter wrappers (ONLY file importing mcp SDK)cmd/import.go → CLI: skraak import bulk --db ... --dataset ... --csv ... --log ...cmd/sql.go → CLI: skraak sql --db ... "SELECT ..."tools/*.go → core logic, NO mcp dependency (plain Go structs in/out)utils/, db/, etc. → unchanged```**Benefits:**- CLI access for power users without MCP- Token savings (CLI avoids MCP protocol overhead)- Code sharing between CLI and MCP- MCP SDK contained to one file- All tests pass---## [2026-02-10] Bulk File Import Cluster Assignment Bug Fix**Critical Bug Fix: Files now correctly distributed across multiple clusters for same location****Problem:** When the same location appeared multiple times in the CSV with different date ranges, all files ended up in the last cluster created instead of being distributed across their respective clusters.**Root Cause:** The `clusterIDMap` used only `LocationID` as the key, causing each new cluster for the same location to overwrite the previous one in the map.**Solution:** Changed map key from `LocationID` to composite key `LocationID|DateRange`.**Modified:**- `tools/bulk_file_import.go` (lines 125, 171-172, 183-184)**Impact:**- Data integrity restored- Multiple date ranges per location now works correctly- Simple 3-line fix, backwards compatible---## [2026-02-07] File Modification Time Fallback**Enhancement: Added file modification time as third timestamp fallback****Problem:** Small clusters (1-2 files) failed variance-based filename disambiguation because the algorithm needs multiple samples to determine date format (YYYYMMDD vs YYMMDD vs DDMMYY).**Timestamp Resolution Order:**```1. AudioMoth comment → timestamp2. Filename parsing → timestamp3. File modification time → timestamp (NEW!)4. FAIL (skip file with error)```**Modified:**- `utils/cluster_import.go` - Added FileModTime fallback in `batchProcessFiles()`**Benefits:**- Fewer failures in small clusters- No performance impact- Backwards compatible- Simple 10-line change---## [2026-02-07] Cluster Import Logic Extraction**Major refactoring: Extracted shared cluster import logic into utils module****Key Insight:** A cluster is the atomic unit of import (one SD card / one recording session / one folder).**Created:**- `utils/cluster_import.go` (553 lines) - Single source of truth for cluster imports- `ImportCluster()` - Main entry point- `scanClusterFiles()` - Recursive WAV file scanning- `batchProcessFiles()` - Batch processing with variance-based parsing- `insertClusterFiles()` - Transactional insertion**Modified:**- `tools/import_files.go` - 75% code reduction (650 lines → 161 lines)- `tools/bulk_file_import.go` - Bug fixes:- **CRITICAL BUG FIXED:** Now inserts into `file_dataset` table (was missing!)- **CRITICAL BUG FIXED:** Now inserts into `moth_metadata` table (was missing!)**Benefits:**- Bug fixed: 68,043 orphaned files found in test database- ~500 lines of duplicated code eliminated- Single source of truth for all import logic---## [2026-02-06] Tool Consolidation**Consolidated 8 write/update tools → 4 create_or_update tools****Deleted:**- 8 separate create/update tool files**Added:**- `tools/dataset.go` - `create_or_update_dataset`- `tools/location.go` - `create_or_update_location`- `tools/cluster.go` - `create_or_update_cluster`- `tools/pattern.go` - `create_or_update_pattern`**Design:**- Omit `id` field → CREATE mode (generates nanoid)- Provide `id` field → UPDATE mode (verifies exists)**Benefits:**- Tool count: 14 → 10- ~31% less code (~320 lines removed)- Shared validation logic---## [2026-02-06] Test Script Consolidation**Rationalized and consolidated shell test scripts****Removed redundant scripts:**- 6 incomplete/redundant test scripts**Current test suite (8 scripts):**1. `get_time.sh` - Time tool2. `test_sql.sh` - SQL query tool3. `test_tools.sh` - All create_or_update tools4. `test_import_file.sh` - Single file import5. `test_import_selections.sh` - ML selection import6. `test_bulk_import.sh` - Bulk CSV import7. `test_resources_prompts.sh` - Resources/prompts8. `test_all_prompts.sh` - All 6 prompts---## [2026-02-06] Bulk File Import Tool**New Feature: CSV-based bulk import across multiple locations and clusters****Added:**- `tools/bulk_file_import.go` - CSV-based bulk import (~500 lines)**Features:**- CSV-driven import for multiple locations- Auto-cluster creation- Progress logging to file- Summary statistics**CSV Format:**```csvlocation_name,location_id,directory_path,date_range,sample_rate,file_countSite A,loc123456789,/path/to/recordings,2024-01,48000,150```---## [2026-02-02] Single File Import Tool**New Feature: Import individual WAV files****Added:**- `tools/import_file.go` - Single file import implementation (~300 lines)**Features:**- Import one WAV file at a time with detailed feedback- Same processing pipeline as batch import- Duplicate detection with `is_duplicate` flag- Atomic operation (succeeds completely or fails)---## [2026-01-29] ML Selection Import Tool**New Feature: Import ML-detected kiwi call selections from folder structure****Added:**- `utils/selection_parser.go` - Selection parsing utilities- `utils/selection_parser_test.go` - 34 test cases- `tools/import_ml_selections.go` - MCP tool (~1050 lines)**Features:**- Folder structure: `Clips_{filter_name}_{date}/Species/CallType/*.wav+.png`- Two-pass file matching (exact, then fuzzy)- Comprehensive validation- Transactional import---## [2026-01-28] Comprehensive Go Unit Testing**Added comprehensive unit test suite****Added:**- `utils/astronomical_test.go` - 11 test cases- `utils/audiomoth_parser_test.go` - 36 test cases- `utils/filename_parser_test.go` - 60 test cases- `utils/wav_metadata_test.go` - 22 test cases- `utils/xxh64_test.go` - 6 test cases**Coverage:**- 170+ tests total- 91.5% code coverage---## [2026-01-26] Generic SQL Tool + Codebase Rationalization**Major architectural change: Replaced 6 specialized tools with generic SQL****Deleted:**- 6 specialized query tools (datasets, locations, clusters, files)- 2 obsolete test scripts**Added:**- `tools/sql.go` - Generic `execute_sql` tool (~200 lines)- `shell_scripts/test_sql.sh` - Comprehensive SQL test suite**Modified:**- `prompts/examples.go` - Rewritten to teach SQL patterns**Benefits:**- Full SQL expressiveness (JOINs, aggregates, CTEs)- Infinite query possibilities vs 6 fixed queries- More aligned with MCP philosophy- Smaller codebase (2 tools instead of 8)**Security:**- Database read-only- Validation blocks write operations- Parameterized queries prevent SQL injection- Row limits prevent overwhelming responses---## [2026-01-26] Shell Scripts Organization**Reorganized all shell scripts into `shell_scripts/` directory**- Keeps project root clean- All scripts updated with correct relative paths