Edit templates for measurement registration

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/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 + "%");
  };

project-management/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());
 

project-management/src/main/java/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();
  }
+
 }

project-management/src/main/java/life/qbic/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));
  }

project-management/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");
  }

project-management/src/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);
+ }
 }

project-management/src/main/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
+) {
 
 }