Add support for confounding variables (#877)

* add todo to open PR * add mermaid plot * change to identifier * add sequence diagrams * update sql scripts * Pass schema validation * Fix order of statements * do not allow null values for measurement counts * refine diagram * update sql so it only creates missing tables * minimal example * add javadoc * wip * add confounding variables to templates * move the `@Transactional` aspect to the implementing class > The Spring team recommends that you annotate methods of concrete classes with the @transactional annotation, rather than relying on annotated methods in interfaces, even if the latter does work for interface-based and target-class proxies as of 5.0. https://docs.spring.io/spring-framework/reference/data-access/transaction/declarative/annotations.html * wip * wip * wip * Fix file size formatting * Fix connection testing for openbis * Add equals and hash code to Sample.java object * implement the update case for confounding variables * Implement sample/batch deletion * extract methods for measurement and sample creation in openbis * Fix merge breaks * fix test * update demo with detail box and cards * static import of Objects.requireNonNull * Add javadoc to HasBoundField.java * Extract StringBean * Add color and cursor classes * replace random by cursor * add missing flex-align-items-baseline * Add ConfoundingVariablesUserInput * Add info text and adjust gap * Add tab for confounding variables * update dev bundle * show existing confounding variables * add new confounding variables * Implement editing of confounding variables * Throw exception for duplicate columns * Prevent creation and rename of duplicate confounding variable * Prevent duplicate naming and accidental deletion * prettify frontend * Fix groups not being loaded * remove file * Address sonar cloud analysis of SampleRepositoryImpl.java * address further sonarcloud issues * Rename method Co-authored-by: Sven F. <[email protected]> * remove Propagation.REQUIRES_NEW I don't think we need a new transaction when creating samples Co-authored-by: Sven F. <[email protected]> * Replace Map#foreach with Collectors#toMap Co-authored-by: Sven F. <[email protected]> * Ask before deleting confounding variables Co-authored-by: Sven F. <[email protected]> --------- Co-authored-by: KochTobi <[email protected]> Co-authored-by: Sven F. <[email protected]>
qbicsoftware · Jan 28, 2025 · 7042182 · 7042182
1 parent 9addc37
commit 7042182
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diff --git a/...re/src/main/java/life/qbic/projectmanagement/infrastructure/batch/BatchJpaRepository.java b/...re/src/main/java/life/qbic/projectmanagement/infrastructure/batch/BatchJpaRepository.java
@@ -14,7 +14,7 @@
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
 import life.qbic.projectmanagement.domain.model.sample.Sample;
 import life.qbic.projectmanagement.domain.repository.BatchRepository;
-import life.qbic.projectmanagement.infrastructure.sample.QbicSampleRepository;
+import life.qbic.projectmanagement.infrastructure.sample.SampleJpaRepository;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 
@@ -31,11 +31,11 @@ public class BatchJpaRepository implements BatchRepository {
   private static final Logger log = logger(BatchJpaRepository.class);
 
   private final QbicBatchRepo qbicBatchRepo;
-  private final QbicSampleRepository qbicSampleRepository;
+  private final SampleJpaRepository qbicSampleRepository;
 
   @Autowired
   public BatchJpaRepository(QbicBatchRepo qbicBatchRepo,
-      QbicSampleRepository qbicSampleRepository) {
+      SampleJpaRepository qbicSampleRepository) {
     this.qbicBatchRepo = qbicBatchRepo;
     this.qbicSampleRepository = qbicSampleRepository;
   }

diff --git a/...e/qbic/projectmanagement/infrastructure/confounding/ConfoundingVariableJpaRepository.java b/...e/qbic/projectmanagement/infrastructure/confounding/ConfoundingVariableJpaRepository.java
@@ -0,0 +1,16 @@
+package life.qbic.projectmanagement.infrastructure.confounding;
+
+import java.util.Collection;
+import java.util.List;
+import life.qbic.projectmanagement.domain.model.confounding.jpa.ConfoundingVariableData;
+import org.springframework.data.repository.ListCrudRepository;
+
+public interface ConfoundingVariableJpaRepository extends
+    ListCrudRepository<ConfoundingVariableData, Long> {
+
+  long countByExperimentIdEquals(String experimentId);
+
+  List<ConfoundingVariableData> findAllByExperimentIdEquals(String experimentId);
+
+  boolean existsDistinctByIdIsIn(Collection<Long> ids);
+}
diff --git a/...c/projectmanagement/infrastructure/confounding/ConfoundingVariableLevelJpaRepository.java b/...c/projectmanagement/infrastructure/confounding/ConfoundingVariableLevelJpaRepository.java
@@ -0,0 +1,24 @@
+package life.qbic.projectmanagement.infrastructure.confounding;
+
+import java.util.List;
+import java.util.Optional;
+import life.qbic.projectmanagement.domain.model.confounding.jpa.ConfoundingVariableLevelData;
+import org.springframework.data.repository.ListCrudRepository;
+
+public interface ConfoundingVariableLevelJpaRepository extends
+    ListCrudRepository<ConfoundingVariableLevelData, Long> {
+
+  List<ConfoundingVariableLevelData> findAllBySampleIdEquals(String sampleId);
+
+  List<ConfoundingVariableLevelData> findAllByVariableIdEquals(long variableId);
+
+  List<ConfoundingVariableLevelData> findAllByVariableIdIn(List<Long> variableIds);
+
+  Optional<ConfoundingVariableLevelData> findBySampleIdEqualsAndVariableIdEquals(String sampleId,
+      long variableId);
+
+  long countByVariableIdEquals(long variableId);
+
+  void deleteAllByVariableIdEquals(long variableId);
+
+}
diff --git a/.../projectmanagement/infrastructure/confounding/ConfoundingVariableLevelRepositoryImpl.java b/.../projectmanagement/infrastructure/confounding/ConfoundingVariableLevelRepositoryImpl.java
@@ -0,0 +1,84 @@
+package life.qbic.projectmanagement.infrastructure.confounding;
+
+import java.util.List;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
+import life.qbic.projectmanagement.domain.model.confounding.jpa.ConfoundingVariableLevelData;
+import life.qbic.projectmanagement.domain.repository.ConfoundingVariableLevelRepository;
+import org.springframework.stereotype.Repository;
+
+/**
+ * The implementation of the {@link ConfoundingVariableLevelRepository} interface.
+ * Delegates method calls to the corresponding JPA repositories.
+ * @since 1.6.0
+ */
+@Repository
+public class ConfoundingVariableLevelRepositoryImpl implements ConfoundingVariableLevelRepository {
+
+  private final ConfoundingVariableLevelJpaRepository jpaRepository;
+
+  public ConfoundingVariableLevelRepositoryImpl(
+      ConfoundingVariableLevelJpaRepository jpaRepository) {
+    this.jpaRepository = jpaRepository;
+  }
+
+  @Override
+  public List<ConfoundingVariableLevelData> findAllForSample(String projectId, String sampleId) {
+    return jpaRepository.findAllBySampleIdEquals(sampleId);
+  }
+
+  @Override
+  public List<ConfoundingVariableLevelData> findAllForVariable(String projectId,
+      long variableId) {
+    return jpaRepository.findAllByVariableIdEquals(variableId);
+  }
+
+
+  @Override
+  public List<ConfoundingVariableLevelData> findAllForVariables(String projectId,
+      List<Long> variableIds) {
+    return jpaRepository.findAllByVariableIdIn(variableIds);
+  }
+
+  @Override
+  public Optional<ConfoundingVariableLevelData> findVariableLevelOfSample(String projectId,
+      String sampleId, long variableId) {
+    return jpaRepository.findBySampleIdEqualsAndVariableIdEquals(sampleId, variableId);
+  }
+
+
+  @Override
+  public <S extends ConfoundingVariableLevelData> S save(String projectId, S entity) {
+    return jpaRepository.save(entity);
+  }
+
+  @Override
+  public Optional<ConfoundingVariableLevelData> findById(String projectId, Long aLong) {
+    return jpaRepository.findById(aLong);
+  }
+
+  @Override
+  public long countLevelsOfVariable(String projectId, long variableId) {
+    return jpaRepository.countByVariableIdEquals(variableId);
+  }
+
+  @Override
+  public void deleteById(String projectId, Long aLong) {
+    jpaRepository.deleteById(aLong);
+  }
+
+  @Override
+  public void deleteAllForSample(String projectId, String sampleId) {
+    List<ConfoundingVariableLevelData> allBySampleIdEquals = jpaRepository.findAllBySampleIdEquals(
+        sampleId);
+    Set<Long> levelIds = allBySampleIdEquals.stream().map(ConfoundingVariableLevelData::getId)
+        .collect(Collectors.toSet());
+    jpaRepository.deleteAllById(levelIds);
+  }
+
+  @Override
+  public void deleteAllForVariable(String projectId, long variableId) {
+    jpaRepository.deleteAllByVariableIdEquals(variableId);
+  }
+}
diff --git a/.../qbic/projectmanagement/infrastructure/confounding/ConfoundingVariableRepositoryImpl.java b/.../qbic/projectmanagement/infrastructure/confounding/ConfoundingVariableRepositoryImpl.java
@@ -0,0 +1,69 @@
+package life.qbic.projectmanagement.infrastructure.confounding;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Optional;
+import life.qbic.projectmanagement.domain.model.confounding.jpa.ConfoundingVariableData;
+import life.qbic.projectmanagement.domain.repository.ConfoundingVariableRepository;
+import org.springframework.stereotype.Repository;
+
+/**
+ * The implementation of the {@link ConfoundingVariableRepository} interface.
+ * Delegates method calls to the corresponding JPA repositories.
+ * @since 1.6.0
+ */
+@Repository
+public class ConfoundingVariableRepositoryImpl implements ConfoundingVariableRepository {
+
+  private final ConfoundingVariableJpaRepository jpaRepository;
+
+  public ConfoundingVariableRepositoryImpl(ConfoundingVariableJpaRepository jpaRepository) {
+    this.jpaRepository = jpaRepository;
+  }
+
+  @Override
+  public <S extends ConfoundingVariableData> List<S> saveAll(String projectId,
+      Iterable<S> entities) {
+    return jpaRepository.saveAll(entities);
+  }
+
+  @Override
+  public List<ConfoundingVariableData> findAll(String projectId, String experimentId) {
+    return jpaRepository.findAllByExperimentIdEquals(experimentId);
+  }
+
+  @Override
+  public List<ConfoundingVariableData> findAllById(String projectId, Iterable<Long> longs) {
+    return jpaRepository.findAllById(longs);
+  }
+
+  @Override
+  public boolean existsAllById(String projectId, Collection<Long> longs) {
+    return jpaRepository.existsDistinctByIdIsIn(longs);
+  }
+
+  @Override
+  public <S extends ConfoundingVariableData> S save(String projectId, S entity) {
+    return jpaRepository.save(entity);
+  }
+
+  @Override
+  public Optional<ConfoundingVariableData> findById(String projectId, Long aLong) {
+    return jpaRepository.findById(aLong);
+  }
+
+  @Override
+  public long countVariablesOfExperiment(String projectId, String experimentId) {
+    return jpaRepository.countByExperimentIdEquals(experimentId);
+  }
+
+  @Override
+  public void deleteById(String projectId, Long aLong) {
+    jpaRepository.deleteById(aLong);
+  }
+
+  @Override
+  public void deleteAllById(String projectId, Iterable<Long> longs) {
+    jpaRepository.deleteAllById(longs);
+  }
+}
diff --git a/...astructure/sample/QbicSampleDataRepo.java → ...tructure/sample/SampleDataRepository.java b/...astructure/sample/QbicSampleDataRepo.java → ...tructure/sample/SampleDataRepository.java
@@ -15,7 +15,7 @@
  *
  * @since 1.0.0
  */
-public interface QbicSampleDataRepo {
+public interface SampleDataRepository {
 
   /**
    * Creates a reference to one or more {@link Sample}s in the data repository to connect project data.

diff --git a/...tructure/sample/QbicSampleRepository.java → ...structure/sample/SampleJpaRepository.java b/...tructure/sample/QbicSampleRepository.java → ...structure/sample/SampleJpaRepository.java
@@ -9,7 +9,7 @@
 import life.qbic.projectmanagement.domain.model.sample.SampleId;
 import org.springframework.data.jpa.repository.JpaRepository;
 
-public interface QbicSampleRepository extends JpaRepository<Sample, SampleId> {
+public interface SampleJpaRepository extends JpaRepository<Sample, SampleId> {
 
   Collection<Sample> findAllByExperimentId(ExperimentId experimentId);