Add support for confounding variables

docs/processes/project-lifecycles.md

@@ -0,0 +1,17 @@
+#bla
+
+blubb
+
+```mermaid
+flowchart TB
+    start((Start))
+    cproject["Service call for create project"]
+    cprojectDB["Create the project in the data base"]
+    cprojectOpBis["Create the project in OpenBIS"]
+    start --> cproject
+    cproject --> cprojectDB
+    cprojectDB --> cprojectOpBis
+    cprojectOpBis -- rollback -->cprojectDB
+
+    cprojectDB -- rollback --> start 
+```

project-management-infrastructure/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;
   }

project-management-infrastructure/src/main/java/life/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);
+}

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

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

project-management-infrastructure/src/main/java/life/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);
+  }
+}

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/QbicSampleDataRepo.java → project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/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.

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/QbicSampleRepository.java → project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/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);