Edit templates for measurement registration (#832)

* WIP * wip * make it work * Extract behaviour * remove unused method * Adapt proteomics template Fixes the edit case and renames instrument to MS device fixes #786 * Make ngs row creation simpler Uses the enum and enhanced switch to make sure all columns are covered and removes complexity. * remove duplicate row creation for ngs * Rename `Instrument` to `MS Device` in template * Fix column name * Fix sheet locking Excel protected the visible sheet. I do not know why and can only speculate that some reordering was not complete. Creating the hidden sheet second solves the issue. * replace instrument by ms device for proteomics * correct spelling * fix jpa access * solves #747 add technical replicate * fix constructors in tests * use correct methods * Fix wrong imports Co-authored-by: steffengreiner <[email protected]> * move test Co-authored-by: steffengreiner <[email protected]> * Add QBIC_SAMPLE_ID Co-authored-by: steffengreiner <[email protected]> --------- Co-authored-by: steffengreiner <[email protected]>
qbicsoftware · Sep 17, 2024 · f99ebc2 · f99ebc2
1 parent 1f7f71b
commit f99ebc2
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Showing 17 changed files with 705 additions and 348 deletions.
diff --git a/...jectmanagement/infrastructure/experiment/measurement/MeasurementLookupImplementation.java b/...jectmanagement/infrastructure/experiment/measurement/MeasurementLookupImplementation.java
@@ -252,7 +252,7 @@ public static Specification<ProteomicsMeasurement> isOrganisationLabel(String fi
     public static Specification<ProteomicsMeasurement> isOntologyTermName(String filter) {
       return (root, query, builder) -> {
         Expression<String> function = builder.function("JSON_EXTRACT", String.class,
-            root.get("instrument"),
+            root.get("msDevice"),
             builder.literal("$.name"));
         return builder.like(function,
             "%" + filter + "%");
@@ -263,7 +263,7 @@ public static Specification<ProteomicsMeasurement> isOntologyTermLabel(String fi
       return (root, query, builder) ->
       {
         Expression<String> function = builder.function("JSON_EXTRACT", String.class,
-            root.get("instrument"), builder.literal("$.label"));
+            root.get("msDevice"), builder.literal("$.label"));
         return builder.like(function,
             "%" + filter + "%");
       };

diff --git a/...src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java b/...src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java
@@ -389,15 +389,20 @@ private Map<ProteomicsMeasurement, Collection<SampleIdCodeEntry>> buildPxP(
       throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ORGANISATION_ROR_ID);
     }
 
-    var instrumentQuery = resolveOntologyCURI(firstMetadataEntry.instrumentCURI());
-    if (instrumentQuery.isEmpty()) {
+    var msDeviceQuery = resolveOntologyCURI(firstMetadataEntry.msDeviceCURIE());
+    if (msDeviceQuery.isEmpty()) {
       throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ONTOLOGY_TERM);
     }
 
-    var method = new ProteomicsMethodMetadata(instrumentQuery.get(), firstMetadataEntry.facility(),
-        firstMetadataEntry.digestionMethod(), firstMetadataEntry.digestionEnzyme(),
-        firstMetadataEntry.enrichmentMethod(), firstMetadataEntry.lcColumn(),
-        firstMetadataEntry.lcmsMethod(), readInjectionVolume(firstMetadataEntry.injectionVolume()),
+    var method = new ProteomicsMethodMetadata(msDeviceQuery.get(),
+        firstMetadataEntry.technicalReplicateName(),
+        firstMetadataEntry.facility(),
+        firstMetadataEntry.digestionMethod(),
+        firstMetadataEntry.digestionEnzyme(),
+        firstMetadataEntry.enrichmentMethod(),
+        firstMetadataEntry.lcColumn(),
+        firstMetadataEntry.lcmsMethod(),
+        readInjectionVolume(firstMetadataEntry.injectionVolume()),
         firstMetadataEntry.labeling()
             .labelType());
 
@@ -611,12 +616,13 @@ private List<Result<MeasurementId, ErrorCode>> updateAllPxP(
         throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ORGANISATION_ROR_ID);
       }
 
-      var instrumentQuery = resolveOntologyCURI(measurementMetadata.instrumentCURI());
-      if (instrumentQuery.isEmpty()) {
+      var msDeviceQuery = resolveOntologyCURI(measurementMetadata.msDeviceCURIE());
+      if (msDeviceQuery.isEmpty()) {
         throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ONTOLOGY_TERM);
       }
 
-      var method = new ProteomicsMethodMetadata(instrumentQuery.get(),
+      var method = new ProteomicsMethodMetadata(msDeviceQuery.get(),
+          measurementMetadata.technicalReplicateName(),
           measurementMetadata.facility(),
           measurementMetadata.digestionMethod(), measurementMetadata.digestionEnzyme(),
           measurementMetadata.enrichmentMethod(), measurementMetadata.lcColumn(),
@@ -642,15 +648,20 @@ private List<Result<MeasurementId, ErrorCode>> updateAllPxP(
         throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ORGANISATION_ROR_ID);
       }
 
-      var instrumentQuery = resolveOntologyCURI(firstEntry.instrumentCURI());
-      if (instrumentQuery.isEmpty()) {
+      var msDeviceQuery = resolveOntologyCURI(firstEntry.msDeviceCURIE());
+      if (msDeviceQuery.isEmpty()) {
         throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ONTOLOGY_TERM);
       }
 
-      var method = new ProteomicsMethodMetadata(instrumentQuery.get(), firstEntry.facility(),
-          firstEntry.digestionMethod(), firstEntry.digestionEnzyme(),
-          firstEntry.enrichmentMethod(), firstEntry.lcColumn(),
-          firstEntry.lcmsMethod(), readInjectionVolume(firstEntry.injectionVolume()),
+      var method = new ProteomicsMethodMetadata(msDeviceQuery.get(),
+          firstEntry.technicalReplicateName(),
+          firstEntry.facility(),
+          firstEntry.digestionMethod(),
+          firstEntry.digestionEnzyme(),
+          firstEntry.enrichmentMethod(),
+          firstEntry.lcColumn(),
+          firstEntry.lcmsMethod(),
+          readInjectionVolume(firstEntry.injectionVolume()),
           firstEntry.labeling()
               .labelType());
 

diff --git a/...va/life/qbic/projectmanagement/application/measurement/ProteomicsMeasurementMetadata.java b/...va/life/qbic/projectmanagement/application/measurement/ProteomicsMeasurementMetadata.java
@@ -10,38 +10,26 @@
  *
  * @since 1.0.0
  */
-public record ProteomicsMeasurementMetadata(String measurementId,
-                                            SampleCode sampleCode,
-                                            String organisationId, String instrumentCURI,
-                                            String samplePoolGroup, String facility,
-                                            String fractionName,
-                                            String digestionEnzyme,
-                                            String digestionMethod, String enrichmentMethod,
-                                            String injectionVolume, String lcColumn,
-                                            String lcmsMethod, Labeling labeling,
-                                            String comment) implements MeasurementMetadata {
+public record ProteomicsMeasurementMetadata(
+    String measurementId,
+    SampleCode sampleCode,
+    String technicalReplicateName,
+    String organisationId,
+    String msDeviceCURIE,
+    String samplePoolGroup,
+    String facility,
+    String fractionName,
+    String digestionEnzyme,
+    String digestionMethod,
+    String enrichmentMethod,
+    String injectionVolume,
+    String lcColumn,
+    String lcmsMethod,
+    Labeling labeling,
+    String comment
+) implements MeasurementMetadata {
 
 
-  public static ProteomicsMeasurementMetadata copyWithNewProperties(SampleCode associatedSample,
-      Labeling labeling,
-      ProteomicsMeasurementMetadata metadata) {
-    return new ProteomicsMeasurementMetadata(metadata.measurementId(),
-        associatedSample,
-        metadata.organisationId(),
-        metadata.instrumentCURI(),
-        metadata.samplePoolGroup(),
-        metadata.facility(),
-        metadata.fractionName(),
-        metadata.digestionEnzyme(),
-        metadata.digestionMethod(),
-        metadata.enrichmentMethod(),
-        metadata.injectionVolume(),
-        metadata.lcColumn(),
-        metadata.lcmsMethod(),
-        labeling,
-        metadata.comment());
-  }
-
   @Override
   public Optional<String> assignedSamplePoolGroup() {
     return Optional.ofNullable(samplePoolGroup.isBlank() ? null : samplePoolGroup);
@@ -72,4 +60,5 @@ public boolean equals(Object o) {
   public int hashCode() {
     return measurementId.hashCode();
   }
+
 }
diff --git a/.../projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java b/.../projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java
@@ -102,7 +102,7 @@ public ValidationResult validate(ProteomicsMeasurementMetadata measurementMetada
     return validationPolicy.validateSampleId(measurementMetadata.sampleCode())
         .combine(validationPolicy.validateMandatoryDataProvided(measurementMetadata))
         .combine(validationPolicy.validateOrganisation(measurementMetadata.organisationId())
-            .combine(validationPolicy.validateInstrument(measurementMetadata.instrumentCURI())));
+            .combine(validationPolicy.validateMsDevice(measurementMetadata.msDeviceCURIE())));
   }
 
   /**
@@ -121,17 +121,18 @@ public ValidationResult validateUpdate(ProteomicsMeasurementMetadata metadata,
         .combine(validationPolicy.validateMeasurementCode(metadata.measurementIdentifier().orElse(""))
             .combine(validationPolicy.validateMandatoryDataForUpdate(metadata))
             .combine(validationPolicy.validateOrganisation(metadata.organisationId())
-                .combine(validationPolicy.validateInstrument(metadata.instrumentCURI())
+                .combine(validationPolicy.validateMsDevice(metadata.msDeviceCURIE())
                     .combine(
                         validationPolicy.validateDigestionMethod(metadata.digestionMethod())))));
   }
 
   public enum PROTEOMICS_PROPERTY {
     QBIC_SAMPLE_ID("qbic sample id"),
     SAMPLE_LABEL("sample name"),
+    TECHNICAL_REPLICATE_NAME("technical replicate"),
     ORGANISATION_ID("organisation id"),
     FACILITY("facility"),
-    INSTRUMENT("instrument"),
+    MS_DEVICE("ms device"),
     SAMPLE_POOL_GROUP("sample pool group"),
     CYCLE_FRACTION_NAME("cycle/fraction name"),
     DIGESTION_METHOD("digestion method"),
@@ -180,6 +181,10 @@ public static boolean isDigestionMethod(String input) {
     public String getName() {
       return name;
     }
+
+    public static List<String> getOptions() {
+      return Arrays.stream(values()).map(DigestionMethod::getName).toList();
+    }
   }
 
   private class ValidationPolicy {
@@ -188,7 +193,7 @@ private class ValidationPolicy {
 
     private static final String UNKNOWN_ORGANISATION_ID_MESSAGE = "The organisation ID does not seem to be a ROR ID: \"%s\"";
 
-    private static final String UNKNOWN_INSTRUMENT_ID = "Unknown instrument id: \"%s\"";
+    private static final String UNKNOWN_MS_DEVICE_ID = "Unknown ms device id: \"%s\"";
 
     private static final String UNKNOWN_DIGESTION_METHOD = "Unknown digestion method: \"%s\"";
 
@@ -242,13 +247,13 @@ ValidationResult validateMeasurementCode(String measurementCode) {
               List.of("Measurement Code: Unknown measurement for id '%s'".formatted(measurementCode))));
     }
 
-    ValidationResult validateInstrument(String instrument) {
-      var result = terminologyService.findByCurie(instrument);
+    ValidationResult validateMsDevice(String msDevice) {
+      var result = terminologyService.findByCurie(msDevice);
       if (result.isPresent()) {
         return ValidationResult.successful(1);
       }
       return ValidationResult.withFailures(1,
-          List.of(UNKNOWN_INSTRUMENT_ID.formatted(instrument)));
+          List.of(UNKNOWN_MS_DEVICE_ID.formatted(msDevice)));
     }
 
     ValidationResult validateDigestionMethod(String digestionMethod) {
@@ -273,9 +278,9 @@ ValidationResult validateMandatoryDataForUpdate(ProteomicsMeasurementMetadata me
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }
-      if (metadata.instrumentCURI().isBlank()) {
+      if (metadata.msDeviceCURIE().isBlank()) {
         validation = validation.combine(
-            ValidationResult.withFailures(1, List.of("Instrument: missing mandatory metadata")));
+            ValidationResult.withFailures(1, List.of("MS Device: missing mandatory metadata")));
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }
@@ -323,10 +328,10 @@ ValidationResult validateMandatoryDataProvided(
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }
-      if (metadata.instrumentCURI().isBlank()) {
+      if (metadata.msDeviceCURIE().isBlank()) {
         validation = validation.combine(
             ValidationResult.withFailures(1,
-                List.of("Instrument: missing mandatory metadata")));
+                List.of("MS Device: missing mandatory metadata")));
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }

diff --git a/...nt/src/main/java/life/qbic/projectmanagement/domain/model/measurement/NGSMeasurement.java b/...nt/src/main/java/life/qbic/projectmanagement/domain/model/measurement/NGSMeasurement.java
@@ -18,8 +18,8 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
-import life.qbic.domain.concepts.LocalDomainEventDispatcher;
 import java.util.Set;
+import life.qbic.domain.concepts.LocalDomainEventDispatcher;
 import life.qbic.projectmanagement.domain.Organisation;
 import life.qbic.projectmanagement.domain.model.OntologyTerm;
 import life.qbic.projectmanagement.domain.model.measurement.event.MeasurementCreatedEvent;
@@ -93,7 +93,7 @@ private NGSMeasurement(MeasurementId measurementId, ProjectId projectId,
     this.measurementId = measurementId;
     this.projectId = requireNonNull(projectId, "projectId must not be null");
     this.organisation = requireNonNull(organisation, "organisation must not be null");
-    this.instrument = requireNonNull(method.instrument(), "instrument must not be null");
+    this.instrument = requireNonNull(method.instrument(), "msDevice must not be null");
     this.measurementCode = requireNonNull(measurementCode, "measurement code must not be null");
     this.facility = requireNonNull(method.facility(), "facility must not be null");
     this.sequencingReadType = requireNonNull(method.sequencingReadType(),
@@ -136,7 +136,7 @@ public static NGSMeasurement createWithPool(ProjectId projectId, String samplePo
       throws IllegalArgumentException {
     requireNonNull(measurementCode, "measurement Code must not be null");
     requireNonNull(method, "method must not be null");
-    requireNonNull(method.instrument(), "instrument must not be null");
+    requireNonNull(method.instrument(), "msDevice must not be null");
     if (samplePool.isBlank()) {
       throw new IllegalArgumentException("Sample Pool: no value provided");
     }

diff --git a/...main/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsMeasurement.java b/...main/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsMeasurement.java
@@ -57,7 +57,10 @@ public class ProteomicsMeasurement {
   private MeasurementId measurementId;
 
   @Column(name = "instrument", columnDefinition = "longtext CHECK (json_valid(`instrument`))")
-  private OntologyTerm instrument;
+  private OntologyTerm msDevice;
+
+  @Column(name = "technicalReplicateName")
+  private String technicalReplicateName;
 
   @Column(name = "samplePool")
   private String samplePool = "";
@@ -127,8 +130,8 @@ private static void evaluateMandatorySpecificMetadata(
 
   private static void evaluateMandatoryMetadata(ProteomicsMethodMetadata method)
       throws IllegalArgumentException {
-    if (method.instrument() == null) {
-      throw new IllegalArgumentException("Instrument: Missing metadata.");
+    if (method.msDevice() == null) {
+      throw new IllegalArgumentException("MS Device: Missing metadata.");
     }
     if (method.facility().isBlank()) {
       throw new IllegalArgumentException("Facility: Missing metadata");
@@ -157,7 +160,7 @@ public static ProteomicsMeasurement create(ProjectId projectId,
       MeasurementCode measurementCode, Organisation organisation, ProteomicsMethodMetadata method,
       Collection<ProteomicsSpecificMeasurementMetadata> proteomicsSpecificMeasurementMetadata)
       throws IllegalArgumentException {
-    requireNonNull(method.instrument());
+    requireNonNull(method.msDevice());
     requireNonNull(measurementCode);
     requireNonNull(proteomicsSpecificMeasurementMetadata);
     if (!measurementCode.isMSDomain()) {
@@ -215,8 +218,8 @@ public Collection<SampleId> measuredSamples() {
         .toList();
   }
 
-  public OntologyTerm instrument() {
-    return instrument;
+  public OntologyTerm msDevice() {
+    return msDevice;
   }
 
   public Organisation organisation() {
@@ -257,7 +260,8 @@ public void updateMethod(ProteomicsMethodMetadata method) {
   }
 
   private void setMethodMetadata(ProteomicsMethodMetadata methodMetadata) {
-    this.instrument = methodMetadata.instrument();
+    this.msDevice = methodMetadata.msDevice();
+    this.technicalReplicateName = methodMetadata.technicalReplicate();
     this.facility = methodMetadata.facility();
     this.digestionMethod = methodMetadata.digestionMethod();
     this.digestionEnzyme = methodMetadata.digestionEnzyme();
@@ -319,4 +323,8 @@ public int hashCode() {
   public Optional<String> comment() {
     return Optional.empty();
   }
+
+  public Optional<String> technicalReplicateName() {
+    return Optional.ofNullable(technicalReplicateName);
+  }
 }
diff --git a/...n/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsMethodMetadata.java b/...n/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsMethodMetadata.java
@@ -9,10 +9,17 @@
  *
  * @since 1.0.0
  */
-public record ProteomicsMethodMetadata(OntologyTerm instrument, String facility,
-                                       String digestionMethod,
-                                       String digestionEnzyme, String enrichmentMethod,
-                                       String lcColumn, String lcmsMethod, int injectionVolume,
-                                       String labelType) {
+public record ProteomicsMethodMetadata(
+    OntologyTerm msDevice,
+    String technicalReplicate,
+    String facility,
+    String digestionMethod,
+    String digestionEnzyme,
+    String enrichmentMethod,
+    String lcColumn,
+    String lcmsMethod,
+    int injectionVolume,
+    String labelType
+) {
 
 }