remove unused code

Author: KochTobi

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

@@ -1,6 +1,5 @@
 package life.qbic.projectmanagement.infrastructure.experiment.measurement;
 
-import jakarta.persistence.criteria.Expression;
 import jakarta.persistence.criteria.Join;
 import java.util.Collection;
 import java.util.List;
@@ -27,22 +26,19 @@ public class MeasurementLookupImplementation implements MeasurementLookup {
 
   private final NGSMeasurementJpaRepo ngsMeasurementJpaRepo;
   private final ProteomicsMeasurementJpaRepo pxpMeasurementJpaRepo;
-  private final MeasurementDataRepo measurementDataRepo;
 
   public MeasurementLookupImplementation(NGSMeasurementJpaRepo ngsMeasurementJpaRepo,
-      ProteomicsMeasurementJpaRepo pxpMeasurementJpaRepo,
-      MeasurementDataRepo measurementDataRepo) {
+      ProteomicsMeasurementJpaRepo pxpMeasurementJpaRepo) {
     this.ngsMeasurementJpaRepo = ngsMeasurementJpaRepo;
     this.pxpMeasurementJpaRepo = pxpMeasurementJpaRepo;
-    this.measurementDataRepo = measurementDataRepo;
   }
 
   @Override
   public long countProteomicsMeasurementsBySampleIds(Collection<SampleId> sampleIds) {
     Specification<ProteomicsMeasurement> isDistinctSpec = ProteomicsMeasurementSpec.isDistinct();
     Specification<ProteomicsMeasurement> containsSampleId = ProteomicsMeasurementSpec.containsSampleId(
         sampleIds);
-    Specification<ProteomicsMeasurement> distinct = Specification.where(containsSampleId)
+    Specification<ProteomicsMeasurement> distinct = containsSampleId
         .and(isDistinctSpec);
     return pxpMeasurementJpaRepo.count(distinct);
   }
@@ -52,7 +48,7 @@ public long countNgsMeasurementsBySampleIds(Collection<SampleId> sampleIds) {
     Specification<NGSMeasurement> isDistinctSpec = NgsMeasurementSpec.isDistinct();
     Specification<NGSMeasurement> containsSampleId = NgsMeasurementSpec.containsSampleId(
         sampleIds);
-    Specification<NGSMeasurement> distinct = Specification.where(containsSampleId)
+    Specification<NGSMeasurement> distinct = containsSampleId
         .and(isDistinctSpec);
     return ngsMeasurementJpaRepo.count(distinct);
   }
@@ -75,73 +71,6 @@ public List<ProteomicsMeasurement> findProteomicsMeasurementsBySampleIds(String
         new OffsetBasedRequest(offset, limit, Sort.by(orders))).getContent();
   }
 
-  private Specification<ProteomicsMeasurement> generateProteomicsFilterSpecification(
-      Collection<SampleId> sampleIds, String filter) {
-    Specification<ProteomicsMeasurement> isBlankSpec = ProteomicsMeasurementSpec.isBlank(filter);
-    Specification<ProteomicsMeasurement> isDistinctSpec = ProteomicsMeasurementSpec.isDistinct();
-    Specification<ProteomicsMeasurement> containsSampleId = ProteomicsMeasurementSpec.containsSampleId(
-        sampleIds);
-    Specification<ProteomicsMeasurement> measurementCodeContains = ProteomicsMeasurementSpec.isMeasurementCode(
-        filter);
-    Specification<ProteomicsMeasurement> measurementLabelContains = ProteomicsMeasurementSpec.isMeasurementLabel(
-        filter);
-    Specification<ProteomicsMeasurement> measurementLabelingTypeContains = ProteomicsMeasurementSpec.isMeasurementLabelingType(
-        filter);
-    Specification<ProteomicsMeasurement> samplePoolGroupContains = ProteomicsMeasurementSpec.isSamplePoolGroup(
-        filter);
-    Specification<ProteomicsMeasurement> organisationLabelContains = ProteomicsMeasurementSpec.isOrganisationLabel(
-        filter);
-    Specification<ProteomicsMeasurement> ontologyNameContains = ProteomicsMeasurementSpec.isOntologyTermName(
-        filter);
-    Specification<ProteomicsMeasurement> ontologyLabelContains = ProteomicsMeasurementSpec.isOntologyTermLabel(
-        filter);
-    Specification<ProteomicsMeasurement> facilityContains = ProteomicsMeasurementSpec.isFacility(
-        filter);
-    Specification<ProteomicsMeasurement> fractionContains = ProteomicsMeasurementSpec.isFraction(
-        filter);
-    Specification<ProteomicsMeasurement> digestionMethodContains = ProteomicsMeasurementSpec.isDigestionMethod(
-        filter);
-    Specification<ProteomicsMeasurement> digestionEnzymeContains = ProteomicsMeasurementSpec.isDigestionEnzyme(
-        filter);
-    Specification<ProteomicsMeasurement> enrichmentMethodContains = ProteomicsMeasurementSpec.isEnrichmentMethod(
-        filter);
-    Specification<ProteomicsMeasurement> injectionVolumeContains = ProteomicsMeasurementSpec.isInjectionVolume(
-        filter);
-    Specification<ProteomicsMeasurement> lcColumnContains = ProteomicsMeasurementSpec.isLcColumn(
-        filter);
-    Specification<ProteomicsMeasurement> lcmsMethodContains = ProteomicsMeasurementSpec.isLcmsMethod(
-        filter);
-    Specification<ProteomicsMeasurement> registrationDateContains = ProteomicsMeasurementSpec.isRegistrationDate(
-        filter);
-    Specification<ProteomicsMeasurement> commentContains = ProteomicsMeasurementSpec.isComment(
-        filter);
-
-    Specification<ProteomicsMeasurement> filterSpecification =
-        Specification.anyOf(
-            commentContains,
-            digestionMethodContains,
-            digestionEnzymeContains,
-            enrichmentMethodContains,
-            facilityContains,
-            fractionContains,
-            injectionVolumeContains,
-            lcColumnContains,
-            lcmsMethodContains,
-            measurementCodeContains,
-            measurementLabelContains,
-            measurementLabelingTypeContains,
-            ontologyNameContains,
-            ontologyLabelContains,
-            organisationLabelContains,
-            registrationDateContains,
-            samplePoolGroupContains
-        );
-    return Specification.where(isBlankSpec)
-        .and(containsSampleId)
-        .and(filterSpecification)
-        .and(isDistinctSpec);
-  }
-
   @Override
   public List<NGSMeasurement> queryNGSMeasurementsBySampleIds(String filter,
       Collection<SampleId> sampleIds, int offset,
@@ -172,42 +101,6 @@ public List<NGSMeasurement> findNGSMeasurementsBySampleIds(
     return ngsMeasurementJpaRepo.findAll(NgsMeasurementSpec.containsSampleId(sampleIds));
   }
 
-  private Specification<NGSMeasurement> generateNGSFilterSpecification(
-      Collection<SampleId> sampleIds, String filter) {
-    Specification<NGSMeasurement> isBlankSpec = NgsMeasurementSpec.isBlank(filter);
-    Specification<NGSMeasurement> isDistinctSpec = NgsMeasurementSpec.isDistinct();
-    Specification<NGSMeasurement> containsSampleId = NgsMeasurementSpec.containsSampleId(
-        sampleIds);
-    Specification<NGSMeasurement> measurementCodeContains = NgsMeasurementSpec.isMeasurementCode(
-        filter);
-    Specification<NGSMeasurement> sequencingReadTypeContains = NgsMeasurementSpec.isSequencingReadType(
-        filter);
-    Specification<NGSMeasurement> facilityContains = NgsMeasurementSpec.isFacility(filter);
-    Specification<NGSMeasurement> libraryKitContains = NgsMeasurementSpec.isLibraryKit(filter);
-    Specification<NGSMeasurement> flowCellContains = NgsMeasurementSpec.isFlowCell(filter);
-    Specification<NGSMeasurement> sequencingRunProtocolContains = NgsMeasurementSpec.isSequencingRunProtocol(
-        filter);
-    Specification<NGSMeasurement> indexI7Contains = NgsMeasurementSpec.isIndexI7(filter);
-    Specification<NGSMeasurement> indexI5Contains = NgsMeasurementSpec.isIndexI5(filter);
-    Specification<NGSMeasurement> registrationDateContains = NgsMeasurementSpec.isRegistrationDate(
-        filter);
-    Specification<NGSMeasurement> commentContains = NgsMeasurementSpec.isComment(
-        filter);
-    Specification<NGSMeasurement> filterSpecification = Specification.anyOf(
-        measurementCodeContains,
-        sequencingReadTypeContains,
-        facilityContains,
-        libraryKitContains,
-        flowCellContains,
-        sequencingRunProtocolContains,
-        indexI7Contains,
-        indexI5Contains,
-        registrationDateContains,
-        commentContains);
-    return Specification.where(isBlankSpec).and(containsSampleId).and(filterSpecification)
-        .and(isDistinctSpec);
-  }
-
 
   private static class ProteomicsMeasurementSpec {
 
@@ -232,119 +125,6 @@ public static Specification<ProteomicsMeasurement> containsSampleId(
       };
     }
 
-    //If no filter was provided return all proteomicsMeasurement
-    public static Specification<ProteomicsMeasurement> isBlank(String filter) {
-      return (root, query, builder) -> {
-        if (filter != null && filter.isBlank()) {
-          return builder.conjunction();
-        }
-        return null;
-      };
-    }
-
-    public static Specification<ProteomicsMeasurement> isOrganisationLabel(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("organisation").get("label"), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isOntologyTermName(String filter) {
-      return (root, query, builder) -> {
-        Expression<String> function = builder.function("JSON_EXTRACT", String.class,
-            root.get("msDevice"),
-            builder.literal("$.name"));
-        return builder.like(function,
-            "%" + filter + "%");
-      };
-    }
-
-    public static Specification<ProteomicsMeasurement> isOntologyTermLabel(String filter) {
-      return (root, query, builder) ->
-      {
-        Expression<String> function = builder.function("JSON_EXTRACT", String.class,
-            root.get("msDevice"), builder.literal("$.label"));
-        return builder.like(function,
-            "%" + filter + "%");
-      };
-    }
-
-    public static Specification<ProteomicsMeasurement> isMeasurementCode(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("measurementCode").as(String.class), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isFacility(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("facility"), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isFraction(String filter) {
-      return (root, query, builder) -> {
-        Join<?, ?> sampleSpecificMetadata = root.join("specificMetadata");
-        return builder.like(sampleSpecificMetadata.get("fractionName").as(String.class),
-            "%" + filter + "%");
-      };
-    }
-
-    public static Specification<ProteomicsMeasurement> isDigestionMethod(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("digestionMethod"), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isDigestionEnzyme(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("digestionEnzyme"), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isEnrichmentMethod(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("enrichmentMethod"), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isInjectionVolume(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("injectionVolume").as(String.class), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isLcColumn(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("lcColumn"), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isLcmsMethod(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("lcmsMethod"), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isComment(String filter) {
-      return (root, query, builder) -> {
-        Join<?, ?> sampleSpecificMetadata = root.join("specificMetadata");
-        return builder.like(sampleSpecificMetadata.get("comment").as(String.class),
-            "%" + filter + "%");
-      };
-    }
-
-    public static Specification<ProteomicsMeasurement> isMeasurementLabel(String filter) {
-      return (root, query, builder) -> {
-        Join<?, ?> sampleSpecificMetadata = root.join("specificMetadata");
-        return builder.like(sampleSpecificMetadata.get("label").as(String.class),
-            "%" + filter + "%");
-      };
-    }
-
-    public static Specification<ProteomicsMeasurement> isMeasurementLabelingType(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("labelType"), "%" + filter + "%");
-    }
-
-    public static Specification<ProteomicsMeasurement> isSamplePoolGroup(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("samplePool"), "%" + 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 {
@@ -369,74 +149,5 @@ public static Specification<NGSMeasurement> containsSampleId(
         return sampleSpecificMetadata.get("measuredSample").in(sampleIds);
       };
     }
-
-    //If no filter was provided return all proteomicsMeasurement
-    public static Specification<NGSMeasurement> isBlank(String filter) {
-      return (root, query, builder) -> {
-        if (filter != null && filter.isBlank()) {
-          return builder.conjunction();
-        }
-        return null;
-      };
-    }
-
-    public static Specification<NGSMeasurement> isMeasurementCode(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("measurementCode").as(String.class), "%" + filter + "%");
-    }
-
-    public static Specification<NGSMeasurement> isFacility(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("facility"), "%" + filter + "%");
-    }
-
-    public static Specification<NGSMeasurement> isSequencingReadType(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("sequencingReadType"), "%" + filter + "%");
-    }
-
-    public static Specification<NGSMeasurement> isLibraryKit(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("libraryKit"), "%" + filter + "%");
-    }
-
-    public static Specification<NGSMeasurement> isFlowCell(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("flowCell"), "%" + filter + "%");
-    }
-
-    public static Specification<NGSMeasurement> isSequencingRunProtocol(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("sequencingRunProtocol"), "%" + filter + "%");
-    }
-
-    public static Specification<NGSMeasurement> isIndexI7(String filter) {
-      return (root, query, builder) -> {
-        Join<?, ?> sampleSpecificMetadata = root.join("specificMetadata");
-        return builder.like(sampleSpecificMetadata.get("indexI7").as(String.class),
-            "%" + filter + "%");
-      };
-    }
-
-    public static Specification<NGSMeasurement> isIndexI5(String filter) {
-      return (root, query, builder) -> {
-        Join<?, ?> sampleSpecificMetadata = root.join("specificMetadata");
-        return builder.like(sampleSpecificMetadata.get("indexI5").as(String.class),
-            "%" + filter + "%");
-      };
-    }
-
-    public static Specification<NGSMeasurement> isRegistrationDate(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("registration").as(String.class), "%" + filter + "%");
-    }
-
-    public static Specification<NGSMeasurement> isComment(String filter) {
-      return (root, query, builder) -> {
-        Join<?, ?> sampleSpecificMetadata = root.join("specificMetadata");
-        return builder.like(sampleSpecificMetadata.get("comment").as(String.class),
-            "%" + filter + "%");
-      };
-    }
   }
 }