Merge pull request #557 from qbicsoftware/development

Release 0.40.0

Author: Steffengreiner

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/experiment/measurement/MeasurementDataRepo.java

@@ -1,6 +1,10 @@
 package life.qbic.projectmanagement.infrastructure.experiment.measurement;
 
+import java.util.Collection;
 import java.util.List;
+import java.util.Map;
+import life.qbic.projectmanagement.application.sample.SampleIdCodeEntry;
+import life.qbic.projectmanagement.domain.model.measurement.MeasurementCode;
 import life.qbic.projectmanagement.domain.model.measurement.NGSMeasurement;
 import life.qbic.projectmanagement.domain.model.measurement.ProteomicsMeasurement;
 import life.qbic.projectmanagement.domain.model.sample.SampleCode;
@@ -16,6 +20,16 @@ public interface MeasurementDataRepo {
 
   void addNGSMeasurement(NGSMeasurement ngsMeasurement, List<SampleCode> sampleCodes);
 
-  void addProtemicsMeasurement(ProteomicsMeasurement proteomicsMeasurement, List<SampleCode> sampleCodes);
+  void addProteomicsMeasurement(ProteomicsMeasurement proteomicsMeasurement, List<SampleCode> sampleCodes);
 
+  void deleteProteomicsMeasurements(List<ProteomicsMeasurement> measurements);
+  void deleteNGSMeasurements(List<NGSMeasurement> measurements);
+
+  void saveAllProteomics(
+      Map<ProteomicsMeasurement, Collection<SampleIdCodeEntry>> proteomicsMeasurementsMapping);
+
+  void saveAllNGS(
+      Map<NGSMeasurement, Collection<SampleIdCodeEntry>> ngsMeasurementsMapping);
+
+  boolean hasDataAttached(List<MeasurementCode> measurements);
 }

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/experiment/measurement/MeasurementLookupImplementation.java

@@ -1,7 +1,6 @@
 package life.qbic.projectmanagement.infrastructure.experiment.measurement;
 
 import jakarta.persistence.criteria.Expression;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import life.qbic.application.commons.OffsetBasedRequest;
@@ -150,21 +149,15 @@ public List<NGSMeasurement> queryNGSMeasurementsBySampleIds(String filter,
   }
 
   @Override
-  public List<MeasurementMetadata> retrieveAllMeasurementsWithSampleIds(Collection<SampleId> sampleIds) {
-    Specification<NGSMeasurement> ngsContainsSampleId = NgsMeasurementSpec.containsSampleId(
-        sampleIds);
-    Specification<ProteomicsMeasurement> proteomicsContainsSampleId = ProteomicsMeasurementSpec.containsSampleId(
-        sampleIds);
-    List<MeasurementMetadata> measurements = new ArrayList<>();
-    measurements.addAll(ngsMeasurementJpaRepo.findAll(ngsContainsSampleId));
-    measurements.addAll(pxpMeasurementJpaRepo.findAll(proteomicsContainsSampleId));
-    return measurements;
+  public List<ProteomicsMeasurement> findProteomicsMeasurementsBySampleIds(
+      Collection<SampleId> sampleIds) {
+    return pxpMeasurementJpaRepo.findAll(ProteomicsMeasurementSpec.containsSampleId(sampleIds));
   }
 
   @Override
-  public List<ProteomicsMeasurement> findProteomicsMeasurementsBySampleIds(
+  public List<NGSMeasurement> findNGSMeasurementsBySampleIds(
       Collection<SampleId> sampleIds) {
-    return pxpMeasurementJpaRepo.findAll(ProteomicsMeasurementSpec.containsSampleId(sampleIds));
+    return ngsMeasurementJpaRepo.findAll(NgsMeasurementSpec.containsSampleId(sampleIds));
   }
 
   private Specification<NGSMeasurement> generateNGSFilterSpecification(

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/experiment/measurement/MeasurementRepositoryImplementation.java

@@ -4,9 +4,14 @@
 
 import java.util.Collection;
 import java.util.List;
+import java.util.Map;
 import java.util.Optional;
+import java.util.Set;
 import life.qbic.application.commons.Result;
 import life.qbic.logging.api.Logger;
+import life.qbic.projectmanagement.application.measurement.MeasurementService.DeletionErrorCode;
+import life.qbic.projectmanagement.application.measurement.MeasurementService.MeasurementDeletionException;
+import life.qbic.projectmanagement.application.sample.SampleIdCodeEntry;
 import life.qbic.projectmanagement.domain.model.measurement.MeasurementCode;
 import life.qbic.projectmanagement.domain.model.measurement.NGSMeasurement;
 import life.qbic.projectmanagement.domain.model.measurement.ProteomicsMeasurement;
@@ -68,7 +73,7 @@ public Result<ProteomicsMeasurement, ResponseCode> save(
       return Result.fromError(ResponseCode.FAILED);
     }
     try {
-      measurementDataRepo.addProtemicsMeasurement(measurement, sampleCodes);
+      measurementDataRepo.addProteomicsMeasurement(measurement, sampleCodes);
     } catch (RuntimeException e) {
       log.error("Saving proteomics measurement in data repo failed for measurement "
           + measurement.measurementCode().value(), e);
@@ -80,24 +85,126 @@ public Result<ProteomicsMeasurement, ResponseCode> save(
   }
 
   @Override
-  public Optional<ProteomicsMeasurement> find(String measurementCode) {
+  public Optional<ProteomicsMeasurement> findProteomicsMeasurement(String measurementCode) {
     try {
       var code = MeasurementCode.parse(measurementCode);
       return pxpMeasurementJpaRepo.findProteomicsMeasurementByMeasurementCode(code);
     } catch (IllegalArgumentException e) {
       log.error("Illegal measurement code: " + measurementCode, e);
       return Optional.empty();
     }
+  }
+
+  @Override
+  public void deleteAllProteomics(Set<ProteomicsMeasurement> measurements) {
+    if(measurements.isEmpty()) {
+      return;
+    }
+    List<MeasurementCode> measurementCodes = measurements.stream()
+        .map(ProteomicsMeasurement::measurementCode).toList();
+    if(measurementDataRepo.hasDataAttached(measurementCodes)) {
+      throw new MeasurementDeletionException(DeletionErrorCode.DATA_ATTACHED);
+    }
+    try {
+      deleteAllPtx(measurements.stream().toList());
+    } catch (Exception e) {
+      log.error("Measurement deletion failed due to " + e.getMessage());
+      throw new MeasurementDeletionException(DeletionErrorCode.FAILED);
+    }
+  }
+
+  @Override
+  public void deleteAllNGS(Set<NGSMeasurement> measurements) {
+    if(measurements.isEmpty()) {
+      return;
+    }
+    List<MeasurementCode> measurementCodes = measurements.stream()
+        .map(NGSMeasurement::measurementCode).toList();
+    if(measurementDataRepo.hasDataAttached(measurementCodes)) {
+      throw new MeasurementDeletionException(DeletionErrorCode.DATA_ATTACHED);
+    }
+    try {
+      deleteAllNGS(measurements.stream().toList());
+    } catch (Exception e) {
+      log.error("Measurement deletion failed due to " + e.getMessage());
+      throw new MeasurementDeletionException(DeletionErrorCode.FAILED);
+    }
+  }
+
+  private void deleteAllPtx(List<ProteomicsMeasurement> measurements) {
+    pxpMeasurementJpaRepo.deleteAll(measurements);
+    measurementDataRepo.deleteProteomicsMeasurements(measurements);
+  }
 
+  private void deleteAllNGS(List<NGSMeasurement> measurements) {
+    ngsMeasurementJpaRepo.deleteAll(measurements);
+    measurementDataRepo.deleteNGSMeasurements(measurements);
+  }
+
+  @Override
+  public Optional<NGSMeasurement> findNGSMeasurement(String measurementCode) {
+    try {
+      var code = MeasurementCode.parse(measurementCode);
+      return ngsMeasurementJpaRepo.findNGSMeasurementByMeasurementCode(code);
+    } catch (IllegalArgumentException e) {
+      log.error("Illegal measurement code: " + measurementCode, e);
+      return Optional.empty();
+    }
   }
 
   @Override
-  public void update(ProteomicsMeasurement measurement) {
+  public void updateProteomics(ProteomicsMeasurement measurement) {
     pxpMeasurementJpaRepo.save(measurement);
   }
 
   @Override
-  public void updateAll(Collection<ProteomicsMeasurement> measurements) {
+  public void updateNGS(NGSMeasurement measurement) {
+    ngsMeasurementJpaRepo.save(measurement);
+  }
+
+  @Override
+  public void updateAllProteomics(Collection<ProteomicsMeasurement> measurements) {
     pxpMeasurementJpaRepo.saveAll(measurements);
   }
+
+  @Override
+  public void updateAllNGS(Collection<NGSMeasurement> measurements) {
+    ngsMeasurementJpaRepo.saveAll(measurements);
+  }
+
+  @Override
+  public void saveAllProteomics(
+      Map<ProteomicsMeasurement, Collection<SampleIdCodeEntry>> proteomicsMeasurementsMapping) {
+    try {
+      pxpMeasurementJpaRepo.saveAll(proteomicsMeasurementsMapping.keySet());
+    } catch (RuntimeException e) {
+      log.error("Saving proteomics measurement failed", e);
+      throw e;
+    }
+    try {
+      measurementDataRepo.saveAllProteomics(proteomicsMeasurementsMapping);
+    } catch (RuntimeException e) {
+      log.error("Saving proteomics measurement in data repo failed", e);
+      pxpMeasurementJpaRepo.deleteAll(proteomicsMeasurementsMapping.keySet());
+      throw e;
+    }
+  }
+
+  @Override
+  public void saveAllNGS(
+      Map<NGSMeasurement, Collection<SampleIdCodeEntry>> ngsMeasurementsMapping) {
+    try {
+      ngsMeasurementJpaRepo.saveAll(ngsMeasurementsMapping.keySet());
+    } catch (RuntimeException e) {
+      log.error("Saving ngs measurement failed", e);
+      throw e;
+    }
+    try {
+      measurementDataRepo.saveAllNGS(ngsMeasurementsMapping);
+    } catch (RuntimeException e) {
+      log.error("Saving ngs measurement in data repo failed", e);
+      ngsMeasurementJpaRepo.deleteAll(ngsMeasurementsMapping.keySet());
+      throw e;
+    }
+  }
 }

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/experiment/measurement/NGSMeasurementJpaRepo.java

@@ -1,5 +1,7 @@
 package life.qbic.projectmanagement.infrastructure.experiment.measurement;
 
+import java.util.Optional;
+import life.qbic.projectmanagement.domain.model.measurement.MeasurementCode;
 import life.qbic.projectmanagement.domain.model.measurement.MeasurementId;
 import life.qbic.projectmanagement.domain.model.measurement.NGSMeasurement;
 import org.springframework.data.jpa.domain.Specification;
@@ -16,4 +18,7 @@ public interface NGSMeasurementJpaRepo
 
   @Override
   long count(Specification<NGSMeasurement> spec);
+
+  Optional<NGSMeasurement> findNGSMeasurementByMeasurementCode(
+      MeasurementCode measurementCode);
 }