Merge branch 'development' into add-token-encoder-interface

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

@@ -81,6 +81,8 @@ private Specification<ProteomicsMeasurement> generateProteomicsFilterSpecificati
         filter);
     Specification<ProteomicsMeasurement> facilityContains = ProteomicsMeasurementSpec.isFacility(
             filter);
+    Specification<ProteomicsMeasurement> fractionContains = ProteomicsMeasurementSpec.isFraction(
+        filter);
     Specification<ProteomicsMeasurement> digestionMethodContains = ProteomicsMeasurementSpec.isDigestionMethod(
             filter);
     Specification<ProteomicsMeasurement> digestionEnzymeContains = ProteomicsMeasurementSpec.isDigestionEnzyme(
@@ -93,6 +95,8 @@ private Specification<ProteomicsMeasurement> generateProteomicsFilterSpecificati
             filter);
     Specification<ProteomicsMeasurement> lcmsMethodContains = ProteomicsMeasurementSpec.isLcmsMethod(
             filter);
+    Specification<ProteomicsMeasurement> registrationDateContains = ProteomicsMeasurementSpec.isRegistrationDate(
+            filter);
     Specification<ProteomicsMeasurement> commentContains = ProteomicsMeasurementSpec.isComment(
             filter);
 
@@ -113,6 +117,7 @@ private Specification<ProteomicsMeasurement> generateProteomicsFilterSpecificati
             injectionVolumeContains,
             lcColumnContains,
             lcmsMethodContains,
+            registrationDateContains,
             commentContains);
     return Specification.where(isBlankSpec)
             .and(containsSampleId)
@@ -220,6 +225,11 @@ public static Specification<ProteomicsMeasurement> isFacility(String filter) {
               builder.like(root.get("facility"), "%" + filter + "%");
     }
 
+    public static Specification<ProteomicsMeasurement> isFraction(String filter) {
+      return (root, query, builder) ->
+          builder.like(root.get("fraction"), "%" + filter + "%");
+    }
+
     public static Specification<ProteomicsMeasurement> isDigestionMethod(String filter) {
       return (root, query, builder) ->
               builder.like(root.get("digestionMethod"), "%" + filter + "%");
@@ -270,10 +280,10 @@ public static Specification<ProteomicsMeasurement> isSamplePoolGroup(String filt
               builder.like(root.get("samplePool"), "%" + filter + "%");
     }
 
-//    public static Specification<ProteomicsMeasurement> isRegistrationDate(String filter){
-//      return (root, query, builder) ->
-//              builder.like(root.get("registration"), "%" + filter + "%");
-//    }
+    public static Specification<ProteomicsMeasurement> isRegistrationDate(String filter){
+      return (root, query, builder) ->
+          builder.like(root.get("registration").as(String.class), "%" + filter + "%");
+    }
   }
 
   private static class NgsMeasurementSpec {

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java

@@ -193,6 +193,8 @@ private Result<MeasurementId, ResponseCode> registerPxP(
 
     measurement.setLabeling(labelingMethod);
 
+    measurement.setFraction(metadata.fractionName());
+
     var parentCodes = sampleIdCodeEntries.stream().map(SampleIdCodeEntry::sampleCode).toList();
 
     var result = measurementDomainService.addProteomics(measurement, parentCodes);

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/NGSValidator.java → project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementNGSValidator.java

@@ -12,14 +12,17 @@
 import org.springframework.stereotype.Component;
 
 /**
- * <b><class short description - 1 Line!></b>
+ * <b>Measurement NGS Validator</b>
  *
- * <p><More detailed description - When to use, what it solves, etc.></p>
+ * <p>Validator employed to check the provided user input for a measurement in the ngs domain.
+ *    The validator checks the for the provision of mandatory information, and will return a ValidationResult
+ *    dependent on the presence or absence of data
+ * </p>
  *
- * @since <version tag>
  */
 @Component
-public class NGSValidator implements Validator<NGSMeasurementMetadata> {
+public class MeasurementNGSValidator implements
+    MeasurementValidator<NGSMeasurementMetadata> {
 
   private static final Set<String> NGS_PROPERTIES = new HashSet<>();
 
@@ -33,7 +36,7 @@ public class NGSValidator implements Validator<NGSMeasurementMetadata> {
             "note"));
   }
   @Autowired
-  public NGSValidator(SampleInformationService sampleInformationService) {
+  public MeasurementNGSValidator(SampleInformationService sampleInformationService) {
     this.sampleInformationService = sampleInformationService;
   }
 

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/ProteomicsValidator.java → project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java

@@ -13,21 +13,24 @@
 import org.springframework.stereotype.Component;
 
 /**
- * <b><class short description - 1 Line!></b>
+ * <b>Measurement Proteomics Validator</b>
  *
- * <p><More detailed description - When to use, what it solves, etc.></p>
+ * <p>Validator employed to check the provided user input for a measurement in the proteomics domain.
+ *    The validator checks the for the provision of mandatory information, and will return a ValidationResult
+ *    dependent on the presence or absence of data
+ * </p>
  *
- * @since <version tag>
  */
 @Component
-public class ProteomicsValidator implements Validator<ProteomicsMeasurementMetadata> {
+public class MeasurementProteomicsValidator implements
+    MeasurementValidator<ProteomicsMeasurementMetadata> {
 
   protected final SampleInformationService sampleInformationService;
 
   protected final OntologyLookupService ontologyLookupService;
 
   @Autowired
-  public ProteomicsValidator(SampleInformationService sampleInformationService,
+  public MeasurementProteomicsValidator(SampleInformationService sampleInformationService,
       OntologyLookupService ontologyLookupService) {
     this.sampleInformationService = Objects.requireNonNull(sampleInformationService);
     this.ontologyLookupService = Objects.requireNonNull(ontologyLookupService);
@@ -129,7 +132,8 @@ ValidationResult validateSampleIds(Collection<SampleCode> sampleCodes) {
         return ValidationResult.withFailures(1,
             List.of("A measurement must contain at least one sample reference. Provided: none"));
       }
-      ValidationResult validationResult = ValidationResult.successful(0);
+      ValidationResult validationResult = ValidationResult.successful(
+          0);
       for (SampleCode sample : sampleCodes) {
         validationResult = validationResult.combine(validateSampleId(sample));
       }
@@ -158,33 +162,38 @@ ValidationResult validateInstrument(String instrument) {
       if (result.isPresent()) {
         return ValidationResult.successful(1);
       }
-      return ValidationResult.withFailures(1, List.of(UNKNOWN_INSTRUMENT_ID.formatted(instrument)));
+      return ValidationResult.withFailures(1,
+          List.of(UNKNOWN_INSTRUMENT_ID.formatted(instrument)));
     }
 
     ValidationResult validateMandatoryDataProvided(
         ProteomicsMeasurementMetadata measurementMetadata) {
       var validation = ValidationResult.successful(0);
       if (measurementMetadata.sampleCodes().isEmpty()) {
         validation = validation.combine(
-            ValidationResult.withFailures(1, List.of("Sample id: missing sample id reference")));
+            ValidationResult.withFailures(1,
+                List.of("Sample id: missing sample id reference")));
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }
       if (measurementMetadata.organisationId().isBlank()) {
         validation = validation.combine(
-            ValidationResult.withFailures(1, List.of("Organisation: missing mandatory metadata")));
+            ValidationResult.withFailures(1,
+                List.of("Organisation: missing mandatory metadata")));
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }
       if (measurementMetadata.instrumentCURI().isBlank()) {
         validation = validation.combine(
-            ValidationResult.withFailures(1, List.of("Instrument: missing mandatory metadata")));
+            ValidationResult.withFailures(1,
+                List.of("Instrument: missing mandatory metadata")));
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }
       if (measurementMetadata.facility().isBlank()) {
         validation = validation.combine(
-            ValidationResult.withFailures(1, List.of("Facility: missing mandatory meta;data")));
+            ValidationResult.withFailures(1,
+                List.of("Facility: missing mandatory metadata")));
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }
@@ -214,13 +223,15 @@ ValidationResult validateMandatoryDataProvided(
       }
       if (measurementMetadata.lcColumn().isBlank()) {
         validation = validation.combine(
-            ValidationResult.withFailures(1, List.of("LC Column: missing mandatory metadata")));
+            ValidationResult.withFailures(1,
+                List.of("LC Column: missing mandatory metadata")));
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }
       if (measurementMetadata.lcmsMethod().isBlank()) {
         validation = validation.combine(
-            ValidationResult.withFailures(1, List.of("LCMS Method: missing mandatory metadata")));
+            ValidationResult.withFailures(1,
+                List.of("LCMS Method: missing mandatory metadata")));
       } else {
         validation = validation.combine(ValidationResult.successful(1));
       }

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/ValidationService.java → project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementValidationService.java

@@ -19,35 +19,37 @@
  * @since 1.0.0
  */
 @Service
-public class ValidationService {
+public class MeasurementValidationService {
 
-  private final NGSValidator ngsValidator;
+  private final MeasurementNGSValidator measurementNgsValidator;
 
-  private final ProteomicsValidator pxValidator;
+  private final MeasurementProteomicsValidator pxpValidator;
 
   @Autowired
-  public ValidationService(NGSValidator ngsValidator, ProteomicsValidator pxValidator) {
-    this.ngsValidator = ngsValidator;
-    this.pxValidator = pxValidator;
+  public MeasurementValidationService(MeasurementNGSValidator measurementNgsValidator,
+      MeasurementProteomicsValidator pxpValidator) {
+    this.measurementNgsValidator = measurementNgsValidator;
+    this.pxpValidator = pxpValidator;
   }
 
   public ValidationResult validateNGS(NGSMeasurementMetadata ngsMeasurementMetadata) {
-    return ngsValidator.validate(ngsMeasurementMetadata);
+    return measurementNgsValidator.validate(ngsMeasurementMetadata);
   }
 
-  public ValidationResult validateProteomics(ProteomicsMeasurementMetadata pxMeasurementMetadata) {
-    return pxValidator.validate(pxMeasurementMetadata);
+  public ValidationResult validateProteomics(
+      ProteomicsMeasurementMetadata pxMeasurementMetadata) {
+    return pxpValidator.validate(pxMeasurementMetadata);
   }
 
   public Optional<Domain> inferDomainByPropertyTypes(Collection<String> propertyTypes) {
     return Optional.ofNullable(determinDomain(propertyTypes));
   }
 
   private static Domain determinDomain(Collection<String> propertyTypes) {
-    if (NGSValidator.isNGS(propertyTypes)) {
+    if (MeasurementNGSValidator.isNGS(propertyTypes)) {
       return Domain.NGS;
     }
-    if (ProteomicsValidator.isProteomics(propertyTypes)) {
+    if (MeasurementProteomicsValidator.isProteomics(propertyTypes)) {
       return Domain.PROTEOMICS;
     }
     return null;

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementValidator.java

@@ -0,0 +1,18 @@
+package life.qbic.projectmanagement.application.measurement.validation;
+
+import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
+
+/**
+ * <b>Measurement Validator</b>
+ *
+ * <p>Validation interface employed to check the provided user input for a measurement.
+ *    Implementations of this interface are supposed to be domain specific and will
+ *    return a ValidationResult dependent on the presence or absence of data
+ * </p>
+ *
+ */
+public interface MeasurementValidator<T extends MeasurementMetadata> {
+
+  ValidationResult validate(T measurementMetadata);
+
+}

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/ValidationResult.java

@@ -7,11 +7,12 @@
 import java.util.stream.Stream;
 
 /**
- * <b><class short description - 1 Line!></b>
+ * <b>Validation Result</b>
  *
- * <p><More detailed description - When to use, what it solves, etc.></p>
+ * <p>Validation Result in a measurement context which contains an extendable collection of Strings
+ * indicating failure or warnings occurring during the measurement validation
+ * </p>
  *
- * @since <version tag>
  */
 public class ValidationResult {
 
@@ -49,7 +50,8 @@ public static ValidationResult withFailures(int validatedEntries,
     return new ValidationResult(validatedEntries, new ArrayList<>(), failureReports);
   }
 
-  public static ValidationResult successful(int validatedEntries, Collection<String> warnings) {
+  public static ValidationResult successful(int validatedEntries,
+      Collection<String> warnings) {
     return new ValidationResult(validatedEntries, warnings, new ArrayList<>());
   }
 

project-management/src/main/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsMeasurement.java

@@ -14,7 +14,6 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
-import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
@@ -197,6 +196,10 @@ public void setLabeling(Collection<ProteomicsLabeling> labeling) {
     this.labeling = Set.copyOf(labeling.stream().toList());
   }
 
+  public void setFraction(String fraction) {
+    this.fraction = fraction;
+  }
+
   /**
    * Convenience method to query if the measurement was derived from a pooled sample.
    *
@@ -243,6 +246,10 @@ public String enrichmentMethod() {
     return enrichmentMethod;
   }
 
+  public Optional<String> fraction() {
+    return Optional.ofNullable(fraction.isBlank() ? null : fraction);
+  }
+
   public int injectionVolume() {
     return injectionVolume;
   }

project-management/src/test/groovy/life/qbic/projectmanagement/application/measurement/validation/NGSValidatorSpec.groovy → project-management/src/test/groovy/life/qbic/projectmanagement/application/measurement/validation/MeasurementNGSValidatorSpec.groovy

@@ -2,14 +2,14 @@ package life.qbic.projectmanagement.application.measurement.validation
 
 import spock.lang.Specification
 
-class NGSValidatorSpec extends Specification {
+class MeasurementNGSValidatorSpec extends Specification {
 
     def "Given a valid NGS measurement metadata property collection, pass the validation"() {
         given:
         def validNGSproperties = ["qbic sample id", "organisation id", "facility", "instrument", "sequencing read type", "library kit", "flow cell", "run protocol", "index i5", "index i7", "note"]
 
         when:
-        def isNGSMetadata = NGSValidator.isNGS(validNGSproperties)
+        def isNGSMetadata = MeasurementNGSValidator.isNGS(validNGSproperties)
 
         then:
         isNGSMetadata
@@ -21,7 +21,7 @@ class NGSValidatorSpec extends Specification {
         def missingProperties= ["organism id", "facility", "instrument", "sequencing read type", "library kit", "flow cell", "run protocol", "index i5", "index i7", "note"]
 
         when:
-        def isNGSMetadata = NGSValidator.isNGS(missingProperties)
+        def isNGSMetadata = MeasurementNGSValidator.isNGS(missingProperties)
 
         then:
         !isNGSMetadata
@@ -32,7 +32,7 @@ class NGSValidatorSpec extends Specification {
         def missingProperties= []
 
         when:
-        def isNGSMetadata = NGSValidator.isNGS(missingProperties)
+        def isNGSMetadata = MeasurementNGSValidator.isNGS(missingProperties)
 
         then:
         !isNGSMetadata
@@ -43,7 +43,7 @@ class NGSValidatorSpec extends Specification {
         def chaosCasing= ["QbiC SaMpLe ID", "organisation ID", "FACiLity", "Instrument", "sequencing read type", "library kit", "flow cell", "run protocol", "index i5", "index i7", "note"]
 
         when:
-        def isNGSMetadata = NGSValidator.isNGS(chaosCasing)
+        def isNGSMetadata = MeasurementNGSValidator.isNGS(chaosCasing)
 
         then:
         isNGSMetadata