Add support for detections datasets

CI-CMG · Aug 5, 2024 · bb3a86c · bb3a86c
1 parent ff63d07
commit bb3a86c
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Showing 11 changed files with 246 additions and 10 deletions.
diff --git a/pace-data/src/main/java/edu/colorado/cires/pace/data/object/dataset/base/BasePackage.java b/pace-data/src/main/java/edu/colorado/cires/pace/data/object/dataset/base/BasePackage.java
@@ -36,7 +36,7 @@ public abstract class BasePackage<T> implements AbstractObject, TimeRange, Calib
   private final Path otherPath;
   private final Path documentsPath;
   private final Path calibrationDocumentsPath;
-  private final Path navigationPath;
+  private final Path navigationPath; // TODO: Remove this
   @NotNull
   private final Path sourcePath;
 

diff --git a/.../colorado/cires/pace/data/object/dataset/base/metadata/location/MobileMarineLocation.java b/.../colorado/cires/pace/data/object/dataset/base/metadata/location/MobileMarineLocation.java
@@ -15,6 +15,8 @@ public class MobileMarineLocation implements MarineLocation {
   private final String vessel;
   @NotBlank
   private final String locationDerivationDescription;
+
+  // TODO: Add file list (List<Path>)
 
   @Override
   public MobileMarineLocation setSeaArea(String seaArea) {

diff --git a/...data/object/dataset/base/metadata/location/translator/MobileMarineLocationTranslator.java b/...data/object/dataset/base/metadata/location/translator/MobileMarineLocationTranslator.java
@@ -12,5 +12,6 @@ public class MobileMarineLocationTranslator implements LocationDetailTranslator
   private final String seaArea;
   private final String vessel;
   private final String locationDerivationDescription;
+  // TODO: Add file list mapping (String, value is semi-colon delimited): file-1.txt;file-2.txt;file-3.txt
 
 }
diff --git a/...du/colorado/cires/pace/data/object/dataset/base/metadata/translator/DataQualityEntry.java b/...du/colorado/cires/pace/data/object/dataset/base/metadata/translator/DataQualityEntry.java
@@ -4,6 +4,7 @@
 import edu.colorado.cires.pace.data.object.dataset.base.metadata.QualityLevel;
 import edu.colorado.cires.pace.data.object.dataset.base.metadata.TimeRange;
 import java.time.LocalDateTime;
+import java.util.Collections;
 import java.util.List;
 import lombok.Builder;
 import lombok.Data;
@@ -20,6 +21,7 @@ public class DataQualityEntry implements TimeRange, FrequencyRange {
   private final Float maxFrequency;
   private final QualityLevel qualityLevel;
   private final String comments;
-  private final List<Integer> channelNumbers;
+  @Builder.Default
+  private final List<Integer> channelNumbers = Collections.emptyList();
 
 }
diff --git a/...du/colorado/cires/pace/data/object/dataset/passivePacker/PassivePackerDatasetDetails.java b/...du/colorado/cires/pace/data/object/dataset/passivePacker/PassivePackerDatasetDetails.java
@@ -39,6 +39,8 @@ public class PassivePackerDatasetDetails {
   private final String modelEnd;
   private final String frequency;
   private final String dataComment;
+  private final String species;
+  private final String scientificName;
 
 
 }
diff --git a/pace-packaging/src/test/java/edu/colorado/cires/pace/packaging/PassivePackerFactory.java b/pace-packaging/src/test/java/edu/colorado/cires/pace/packaging/PassivePackerFactory.java
@@ -47,12 +47,14 @@
 import edu.colorado.cires.pace.data.object.dataset.soundClips.SoundClipsPackage;
 import edu.colorado.cires.pace.data.object.dataset.soundLevelMetrics.SoundLevelMetricsPackage;
 import edu.colorado.cires.pace.data.object.dataset.soundPropagationModels.SoundPropagationModelsPackage;
+import edu.colorado.cires.pace.data.object.detectionType.DetectionType;
 import edu.colorado.cires.pace.data.object.position.Position;
 import edu.colorado.cires.pace.data.object.sensor.audio.AudioSensor;
 import edu.colorado.cires.pace.data.object.sensor.base.Sensor;
 import edu.colorado.cires.pace.data.object.sensor.depth.DepthSensor;
 import edu.colorado.cires.pace.data.object.sensor.other.OtherSensor;
 import edu.colorado.cires.pace.datastore.DatastoreException;
+import edu.colorado.cires.pace.repository.DetectionTypeRepository;
 import edu.colorado.cires.pace.repository.NotFoundException;
 import edu.colorado.cires.pace.repository.OrganizationRepository;
 import edu.colorado.cires.pace.repository.PersonRepository;
@@ -73,11 +75,14 @@ public class PassivePackerFactory {
   private final PersonRepository personRepository;
   private final OrganizationRepository organizationRepository;
   private final SensorRepository sensorRepository;
+  private final DetectionTypeRepository detectionTypeRepository;
 
-  public PassivePackerFactory(PersonRepository personRepository, OrganizationRepository organizationRepository, SensorRepository sensorRepository) {
+  public PassivePackerFactory(PersonRepository personRepository, OrganizationRepository organizationRepository, SensorRepository sensorRepository,
+      DetectionTypeRepository detectionTypeRepository) {
     this.personRepository = personRepository;
     this.organizationRepository = organizationRepository;
     this.sensorRepository = sensorRepository;
+    this.detectionTypeRepository = detectionTypeRepository;
   }
 
   public PassivePackerPackage createPackage(Package aPackage) throws NotFoundException, DatastoreException {
@@ -115,6 +120,10 @@ public PassivePackerPackage createPackage(Package aPackage) throws NotFoundExcep
       passivePackerPackage = passivePackerPackage.toBuilder()
           .qualityDetails(getQualityDetails(soundLevelMetricsPackage))
           .build();
+    } else if (aPackage instanceof DetectionsPackage detectionsPackage) {
+      passivePackerPackage = passivePackerPackage.toBuilder()
+          .qualityDetails(getQualityDetails(detectionsPackage))
+          .build();
     }
 
     return passivePackerPackage;
@@ -234,7 +243,7 @@ private String getDeployType(LocationDetail locationDetail) {
     return null;
   }
 
-  private PassivePackerDatasetDetails getDatasetDetails(Package aPackage) {
+  private PassivePackerDatasetDetails getDatasetDetails(Package aPackage) throws NotFoundException, DatastoreException {
     PassivePackerDatasetDetails datasetDetails = PassivePackerDatasetDetails.builder()
         .type(aPackage.getProcessingLevel().name())
         .subType(subtypeFromPackage(aPackage))
@@ -284,6 +293,35 @@ private PassivePackerDatasetDetails getDatasetDetails(Package aPackage) {
           .modelEnd(serializeDateTime(soundPropagationModelsPackage.getEndTime()))
           .frequency(String.valueOf(soundPropagationModelsPackage.getModeledFrequency()))
           .build();
+    } else if (aPackage instanceof DetectionsPackage detectionsPackage) {
+      String sourceName = detectionsPackage.getSoundSource();
+      String species = null;
+      String scientificName = null;
+
+      if (sourceName != null) {
+        DetectionType detectionType = detectionTypeRepository.getByUniqueField(sourceName);
+
+        species = detectionType.getSource();
+        scientificName = detectionType.getScienceName();
+      }
+
+      datasetDetails = datasetDetails.toBuilder()
+          .dataFiles(String.valueOf(detectionsPackage.getSourcePath()))
+          .analysisStart(serializeDateTime(detectionsPackage.getStartTime()))
+          .analysisEnd(serializeDateTime(detectionsPackage.getEndTime()))
+          .analysisTimeZone(String.valueOf(detectionsPackage.getAnalysisTimeZone()))
+          .analysisEffort(String.valueOf(detectionsPackage.getAnalysisEffort()))
+          .minAnalysisFrequency(String.valueOf(detectionsPackage.getMinFrequency()))
+          .maxAnalysisFrequency(String.valueOf(detectionsPackage.getMaxFrequency()))
+          .analysisSampleRate(String.valueOf(detectionsPackage.getSampleRate()))
+          .species(species)
+          .scientificName(scientificName)
+          .softwareName(detectionsPackage.getSoftwareNames())
+          .softwareVersion(detectionsPackage.getSoftwareVersions())
+          .protocolReference(detectionsPackage.getSoftwareProtocolCitation())
+          .processingStatement(detectionsPackage.getSoftwareProcessingDescription())
+          .softwareStatement(detectionsPackage.getSoftwareDescription())
+          .build();
     }
 
     return datasetDetails;
@@ -337,7 +375,7 @@ private PassivePackerCalibrationInfo getCalibrationInfo(Package aPackage) {
     }
 
     PassivePackerCalibrationInfo calibrationInfo = PassivePackerCalibrationInfo.builder()
-        .calDate(String.valueOf(calDate))
+        .calDate(calDate == null ? null : String.valueOf(calDate))
         .calState(calState)
         .calDocsPath(aPackage.getCalibrationDocumentsPath().toString())
         .comment(aPackage.getCalibrationDescription())
@@ -350,7 +388,8 @@ private PassivePackerCalibrationInfo getCalibrationInfo(Package aPackage) {
           .gain(String.valueOf(audioDataPackage.getGain()))
           .calDate2(calDate2 == null ? null : String.valueOf(calDate2))
           .build();
-    } else if (aPackage instanceof SoundClipsPackage || aPackage instanceof SoundLevelMetricsPackage || aPackage instanceof SoundPropagationModelsPackage) {
+    } else if (aPackage instanceof SoundClipsPackage || aPackage instanceof SoundLevelMetricsPackage 
+        || aPackage instanceof SoundPropagationModelsPackage || aPackage instanceof DetectionsPackage) {
       calibrationInfo = calibrationInfo.toBuilder()
           .calState(aPackage.getPreDeploymentCalibrationDate() != null ? "Calibration applied before processing" : "Not calibrated / not applicable")
           .calDate(null)

diff --git a/pace-packaging/src/test/java/edu/colorado/cires/pace/packaging/PassivePackerFactoryTest.java b/pace-packaging/src/test/java/edu/colorado/cires/pace/packaging/PassivePackerFactoryTest.java
@@ -27,15 +27,18 @@
 import edu.colorado.cires.pace.data.object.dataset.base.metadata.location.StationaryMarineLocation;
 import edu.colorado.cires.pace.data.object.dataset.base.metadata.location.StationaryTerrestrialLocation;
 import edu.colorado.cires.pace.data.object.dataset.base.metadata.translator.DataQualityEntry;
+import edu.colorado.cires.pace.data.object.dataset.detections.DetectionsPackage;
 import edu.colorado.cires.pace.data.object.dataset.passivePacker.PassivePackerPackage;
 import edu.colorado.cires.pace.data.object.dataset.soundClips.SoundClipsPackage;
 import edu.colorado.cires.pace.data.object.dataset.soundLevelMetrics.SoundLevelMetricsPackage;
 import edu.colorado.cires.pace.data.object.dataset.soundPropagationModels.SoundPropagationModelsPackage;
+import edu.colorado.cires.pace.data.object.detectionType.DetectionType;
 import edu.colorado.cires.pace.data.object.position.Position;
 import edu.colorado.cires.pace.data.object.sensor.audio.AudioSensor;
 import edu.colorado.cires.pace.data.object.sensor.depth.DepthSensor;
 import edu.colorado.cires.pace.data.object.sensor.other.OtherSensor;
 import edu.colorado.cires.pace.datastore.DatastoreException;
+import edu.colorado.cires.pace.repository.DetectionTypeRepository;
 import edu.colorado.cires.pace.repository.NotFoundException;
 import edu.colorado.cires.pace.repository.OrganizationRepository;
 import edu.colorado.cires.pace.repository.PersonRepository;
@@ -58,13 +61,15 @@ class PassivePackerFactoryTest {
 
   private final ObjectMapper objectMapper = SerializationUtils.createObjectMapper()
       .configure(SerializationFeature.FAIL_ON_UNWRAPPED_TYPE_IDENTIFIERS, false) // for testing only
+      .configure(SerializationFeature.ORDER_MAP_ENTRIES_BY_KEYS, true)
       .setPropertyNamingStrategy(PropertyNamingStrategies.UPPER_SNAKE_CASE);
 
   private final PersonRepository personRepository = mock(PersonRepository.class);
   private final OrganizationRepository organizationRepository = mock(OrganizationRepository.class);
   private final SensorRepository sensorRepository = mock(SensorRepository.class);
+  private final DetectionTypeRepository detectionTypeRepository = mock(DetectionTypeRepository.class);
 
-  private final PassivePackerFactory factory = new PassivePackerFactory(personRepository, organizationRepository, sensorRepository);
+  private final PassivePackerFactory factory = new PassivePackerFactory(personRepository, organizationRepository, sensorRepository, detectionTypeRepository);
 
   @BeforeEach
   void beforeEach() throws NotFoundException, DatastoreException {
@@ -110,6 +115,11 @@ void beforeEach() throws NotFoundException, DatastoreException {
             .sensorType("sensor type")
             .properties("sensor properties")
         .build());
+
+    when(detectionTypeRepository.getByUniqueField("Blue whale")).thenReturn(DetectionType.builder()
+            .source("Blue whale")
+            .scienceName("Balaenoptera musculus")
+        .build());
   }
 
   @Test
@@ -255,6 +265,62 @@ void testCPODPrePostDeploymentCalibrated() throws IOException, NotFoundException
         )
     );
   }
+
+  @Test
+  void testDetections() throws NotFoundException, DatastoreException, IOException {
+    assertEquals(
+        objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(
+            objectMapper.readValue(new File("src/test/resources/detections.json"), PassivePackerPackage.class)
+        ),
+        objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(
+            factory.createPackage(createDetectionsPackage(createStationaryMarineLocation(), null))
+        )
+    );
+  }
+
+  private Package createDetectionsPackage(LocationDetail locationDetail, LocalDate preDeploymentCalibrationDate) {
+    return createBasePackage(locationDetail).toInheritingType(DetectionsPackage.builder()).toBuilder()
+        .processingLevel(ProcessingLevel.Product)
+        .preDeploymentCalibrationDate(preDeploymentCalibrationDate)
+        .postDeploymentCalibrationDate(null)
+        .soundSource("Blue whale")
+        .qualityAnalyst("Chuck Anderson")
+        .qualityEntries(List.of(
+            DataQualityEntry.builder()
+                .qualityLevel(QualityLevel.good)
+                .minFrequency(0f)
+                .maxFrequency(500f)
+                .startTime(LocalDateTime.of(2011, 1, 1, 13, 0, 0))
+                .endTime(LocalDateTime.of(2011, 1, 1, 15, 0,0))
+                .comments("quality comments")
+                .channelNumbers(List.of(1, 2))
+                .build(),
+            DataQualityEntry.builder()
+                .qualityLevel(QualityLevel.unusable)
+                .minFrequency(1f)
+                .maxFrequency(20f)
+                .startTime(LocalDateTime.of(2011, 1, 6, 13, 0, 0))
+                .endTime(LocalDateTime.of(2012, 1, 8, 13, 0, 0))
+                .comments("quality comments 2")
+                .channelNumbers(List.of(2))
+                .build()
+        )).qualityAnalysisMethod("quality method")
+        .qualityAnalysisObjectives("quality objectives")
+        .qualityAssessmentDescription("quality assessment description")
+        .startTime(LocalDateTime.of(2010, 1, 1, 13, 0, 0))
+        .endTime(LocalDateTime.of(2011, 1, 2, 13, 0, 0))
+        .analysisTimeZone(6)
+        .analysisEffort(20)
+        .minFrequency(200f)
+        .maxFrequency(400f)
+        .sampleRate(20000f)
+        .softwareNames("software name")
+        .softwareVersions("software version")
+        .softwareProtocolCitation("protocol citation")
+        .softwareDescription("software statement")
+        .softwareProcessingDescription("software processing description")
+        .build();
+  }
 
   private Package createSoundPropagationModelsPackage(LocationDetail locationDetail, LocalDate preDeploymentCalibrationDate) {
     return createBasePackage(locationDetail).toInheritingType(SoundPropagationModelsPackage.builder()).toBuilder()
@@ -285,7 +351,7 @@ private Package createSoundClipsPackage(LocationDetail locationDetail, LocalDate
         .softwareProcessingDescription("software processing description")
         .processingLevel(ProcessingLevel.Product)
         .audioStartTime(LocalDateTime.of(2010, 1, 1, 13, 0, 0))
-        .audioEndTime(LocalDateTime.of(2010, 1, 1, 13, 10, 0))
+        .audioEndTime(LocalDateTime.of(2010, 1, 1, 13, 30, 0))
         .build();
   }