Merge pull request #389 from qbicsoftware/development

Release PR

Author: KochTobi

database-connector/src/main/java/life/qbic/projectmanagement/experiment/persistence/SamplePreviewJpaRepository.java

@@ -73,11 +73,12 @@ private Specification<SamplePreview> generateExperimentIdandFilterSpecification(
     Specification<SamplePreview> speciesSpec = SamplePreviewSpecs.speciesContains(filter);
     Specification<SamplePreview> specimenSpec = SamplePreviewSpecs.specimenContains(filter);
     Specification<SamplePreview> analyteSpec = SamplePreviewSpecs.analyteContains(filter);
-    Specification<SamplePreview> analysisTypeSpec = SamplePreviewSpecs.analysisTypeContains(filter);
+    Specification<SamplePreview> analysisMethodContains = SamplePreviewSpecs.analysisMethodContains(
+        filter);
     Specification<SamplePreview> commentSpec = SamplePreviewSpecs.commentContains(filter);
     Specification<SamplePreview> containsFilterSpec = Specification.anyOf(sampleCodeSpec,
         sampleLabelSpec, batchLabelSpec, bioReplicateLabelSpec, conditionSpec, speciesSpec,
-        specimenSpec, analyteSpec, analysisTypeSpec, commentSpec);
+        specimenSpec, analyteSpec, analysisMethodContains, commentSpec);
     Specification<SamplePreview> isDistinctSpec = SamplePreviewSpecs.isDistinct();
     return Specification.where(experimentIdSpec).and(isBlankSpec)
         .and(containsFilterSpec)
@@ -163,9 +164,9 @@ public static Specification<SamplePreview> analyteContains(String filter) {
           builder.like(root.get("analyte"), "%" + filter + "%");
     }
 
-    public static Specification<SamplePreview> analysisTypeContains(String filter) {
+    public static Specification<SamplePreview> analysisMethodContains(String filter) {
       return (root, query, builder) ->
-          builder.like(root.get("analysisType"), "%" + filter + "%");
+          builder.like(root.get("analysisMethod"), "%" + filter + "%");
     }
 
     public static Specification<SamplePreview> commentContains(String filter) {

database-connector/src/main/java/life/qbic/projectmanagement/persistence/repository/AnalyteTermMapper.java

@@ -0,0 +1,25 @@
+package life.qbic.projectmanagement.persistence.repository;
+
+import java.util.Optional;
+
+/**
+ * <b>Analyte Term Mapper</b>
+ *
+ * <p>Enables the mapping of an analyte ontology term used in the data manager against a term
+ * provided by the mapper implementation. </p>
+ *
+ * @since 1.0.0
+ */
+public interface AnalyteTermMapper {
+
+  /**
+   * Tries to map a given term to a term of the mapper implementation
+   *
+   * @param term the term that the mapper should look-up and try to map
+   * @return an {@link Optional<String>} mapped term, is {@link Optional#empty()} if the look-up was
+   * unsuccessful.
+   * @since 1.0.0
+   */
+  Optional<String> mapFrom(String term);
+
+}

database-connector/src/main/java/life/qbic/projectmanagement/persistence/repository/OpenbisConnector.java

@@ -72,7 +72,7 @@ public class OpenbisConnector implements ExperimentalDesignVocabularyRepository,
   private static final String DEFAULT_EXPERIMENT_TYPE = "Q_SAMPLE_PREPARATION";
   private static final String DEFAULT_DELETION_REASON = "Commanded by data manager app";
 
-  private final AnalyteToOpenbisSampleTypeMapper analyteMapper = new AnalyteToOpenbisSampleTypeMapperImpl();
+  private final AnalyteTermMapper analyteMapper = new SimpleOpenBisTermMapper();
 
   // used by spring to wire it up
   private OpenbisConnector(@Value("${openbis.user.name}") String userName,
@@ -207,11 +207,11 @@ public void addSamplesToProject(Project project,
         sampleCreation.setSpaceId(new SpacePermId(DEFAULT_SPACE_CODE));
         Map<String, String> props = new HashMap<>();
 
-        props.put("Q_SECONDARY_NAME", sample.biologicalReplicateId().toString());
-        props.put("Q_EXTERNALDB_ID", sample.label());
+        props.put("Q_SECONDARY_NAME", sample.label());
+        props.put("Q_EXTERNALDB_ID", sample.sampleId().value());
         String analyteValue = sample.sampleOrigin().getAnalyte().value();
         String openBisSampleType = retrieveOpenBisAnalyteCode(analyteValue).or(
-                () -> analyteMapper.translateSampleTypeString(analyteValue))
+                () -> analyteMapper.mapFrom(analyteValue))
             .orElseThrow(() -> {
               logger("No mapping was found for " + analyteValue);
               return new MappingNotFoundException();
@@ -384,27 +384,4 @@ static class ConnectionException extends RuntimeException {
   static class MappingNotFoundException extends RuntimeException {
 
   }
-
-  public interface AnalyteToOpenbisSampleTypeMapper {
-
-    Optional<String> translateSampleTypeString(String analyte);
-  }
-
-  private class AnalyteToOpenbisSampleTypeMapperImpl implements
-      AnalyteToOpenbisSampleTypeMapper {
-
-    // dummy map needed once ontologies outside openBIS are used
-    private static final Map<String, String> analyteToSampleType;
-
-    static {
-      analyteToSampleType = new HashMap<>();
-      analyteToSampleType.put("RNA", "RNA");
-      analyteToSampleType.put("DNA", "DNA");
-    }
-
-    @Override
-    public Optional<String> translateSampleTypeString(String analyte) {
-      return Optional.ofNullable(analyte);
-    }
-  }
 }

database-connector/src/main/java/life/qbic/projectmanagement/persistence/repository/SimpleOpenBisTermMapper.java

@@ -0,0 +1,58 @@
+package life.qbic.projectmanagement.persistence.repository;
+
+import static life.qbic.logging.service.LoggerFactory.logger;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Optional;
+import life.qbic.logging.api.Logger;
+
+/**
+ * <b>Simple openBIS term mapper</b>
+ * <p>
+ * OpenBIS term mapper implementation of the {@link AnalyteTermMapper} interface.
+ * <p>
+ * Enables the client to lookup a possible mapping openBIS term for a given input analyte value.
+ *
+ * @since 1.0.0
+ */
+public class SimpleOpenBisTermMapper implements AnalyteTermMapper {
+
+  private static final Logger log = logger(SimpleOpenBisTermMapper.class);
+  private static final Map<String, String> ANALYTE_TO_SAMPLE_TYPE;
+
+  /*
+  EXTEND MAPPINGS TO OPENBIS TERMS HERE
+   */
+  static {
+    ANALYTE_TO_SAMPLE_TYPE = new HashMap<>();
+    ANALYTE_TO_SAMPLE_TYPE.put("AMPLICON", "AMPLICON");
+    ANALYTE_TO_SAMPLE_TYPE.put("CARBOHYDRATES", "CARBOHYDRATES");
+    ANALYTE_TO_SAMPLE_TYPE.put("CELL_LYSATE", "CELL_LYSATE");
+    ANALYTE_TO_SAMPLE_TYPE.put("CF_DNA", "CF_DNA");
+    ANALYTE_TO_SAMPLE_TYPE.put("DNA", "DNA");
+    ANALYTE_TO_SAMPLE_TYPE.put("GLYCANS", "GLYCANS");
+    ANALYTE_TO_SAMPLE_TYPE.put("GLYCOPEPTIDES", "GLYCOPEPTIDES");
+    ANALYTE_TO_SAMPLE_TYPE.put("LIPIDS", "LIPIDS");
+    ANALYTE_TO_SAMPLE_TYPE.put("M_RNA", "M_RNA");
+    ANALYTE_TO_SAMPLE_TYPE.put("PEPTIDES", "PEPTIDES");
+    ANALYTE_TO_SAMPLE_TYPE.put("PHOSPHOPEPTIDES", "PHOSPHOPEPTIDES");
+    ANALYTE_TO_SAMPLE_TYPE.put("PHOSPHOPROTEINS", "PHOSPHOPROTEINS");
+    ANALYTE_TO_SAMPLE_TYPE.put("PHOSPHOLIPIDS", "PHOSPHOLIPIDS");
+    ANALYTE_TO_SAMPLE_TYPE.put("PROTEINS", "PROTEINS");
+    ANALYTE_TO_SAMPLE_TYPE.put("RNA", "RNA");
+    ANALYTE_TO_SAMPLE_TYPE.put("R_RNA", "R_RNA");
+    ANALYTE_TO_SAMPLE_TYPE.put("SINGLE_NUCLEI", "SINGLE_NUCLEI");
+    ANALYTE_TO_SAMPLE_TYPE.put("SMALLMOLECULES", "SMALLMOLECULES");
+  }
+
+  @Override
+  public Optional<String> mapFrom(String term) {
+    try {
+      return Optional.of(ANALYTE_TO_SAMPLE_TYPE.get(term));
+    } catch (NullPointerException e) {
+      log.debug("Unknown analyte term '%s', cannot map to openBIS terminology.".formatted(term));
+      return Optional.empty();
+    }
+  }
+}

projectmanagement/src/main/java/life/qbic/projectmanagement/application/ProjectCreationService.java

@@ -11,6 +11,7 @@
 import life.qbic.application.commons.Result;
 import life.qbic.logging.api.Logger;
 import life.qbic.projectmanagement.domain.project.Contact;
+import life.qbic.projectmanagement.domain.project.Funding;
 import life.qbic.projectmanagement.domain.project.OfferIdentifier;
 import life.qbic.projectmanagement.domain.project.Project;
 import life.qbic.projectmanagement.domain.project.ProjectCode;
@@ -55,7 +56,8 @@ public Result<Project, ApplicationException> createProject(String sourceOffer,
       String objective,
       Contact principalInvestigator,
       Contact responsiblePerson,
-      Contact projectManager) {
+      Contact projectManager,
+      Funding funding) {
     if (Objects.isNull(principalInvestigator)) {
       return Result.fromError(new ApplicationException("principal investigator is null"));
     }
@@ -65,7 +67,7 @@ public Result<Project, ApplicationException> createProject(String sourceOffer,
 
     try {
       Project project = createProject(code, title, objective, projectManager,
-          principalInvestigator, responsiblePerson);
+          principalInvestigator, responsiblePerson, funding);
       Optional.ofNullable(sourceOffer)
           .flatMap(it -> it.isBlank() ? Optional.empty() : Optional.of(it))
           .ifPresent(offerIdentifier -> project.linkOffer(OfferIdentifier.of(offerIdentifier)));
@@ -77,7 +79,7 @@ public Result<Project, ApplicationException> createProject(String sourceOffer,
 
   private Project createProject(String code, String title, String objective,
       Contact projectManager,
-      Contact principalInvestigator, Contact responsiblePerson) {
+      Contact principalInvestigator, Contact responsiblePerson, Funding funding) {
     ProjectIntent intent = getProjectIntent(title, objective);
     ProjectCode projectCode;
     try {
@@ -93,7 +95,7 @@ private Project createProject(String code, String title, String objective,
           ErrorParameters.of(code, ProjectCode.getPREFIX(), ProjectCode.getLENGTH()));
     }
 
-    var registrationResult = projectDomainService.registerProject(intent, projectCode, projectManager, principalInvestigator, responsiblePerson);
+    var registrationResult = projectDomainService.registerProject(intent, projectCode, projectManager, principalInvestigator, responsiblePerson, funding);
 
     if (registrationResult.isError() && registrationResult.getError().equals(ResponseCode.PROJECT_REGISTRATION_FAILED)) {
       throw new ApplicationException("Project registration failed.", ErrorCode.GENERAL, ErrorParameters.of(code));

projectmanagement/src/main/java/life/qbic/projectmanagement/application/ProjectInformationService.java

@@ -9,6 +9,7 @@
 import life.qbic.logging.service.LoggerFactory;
 import life.qbic.projectmanagement.application.api.ProjectPreviewLookup;
 import life.qbic.projectmanagement.domain.project.Contact;
+import life.qbic.projectmanagement.domain.project.Funding;
 import life.qbic.projectmanagement.domain.project.Project;
 import life.qbic.projectmanagement.domain.project.ProjectId;
 import life.qbic.projectmanagement.domain.project.ProjectObjective;
@@ -110,4 +111,18 @@ public void stateObjective(ProjectId projectId, String objective) {
     project.stateObjective(projectObjective);
     projectRepository.update(project);
   }
+
+  public void addFunding(ProjectId projectId, String label, String referenceId) {
+    Funding funding = Funding.of(label, referenceId);
+    var project = loadProject(projectId);
+    project.setFunding(funding);
+    projectRepository.update(project);
+
+  }
+
+  public void removeFunding(ProjectId projectId) {
+    var project = loadProject(projectId);
+    project.removeFunding();
+    projectRepository.update(project);
+  }
 }

projectmanagement/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java

@@ -45,8 +45,8 @@ public class SamplePreview {
   @Column(name = "label")
   private String sampleLabel;
   private String comment;
-  @Column(name = "analysis_type")
-  private String analysisType;
+  @Column(name = "analysis_method")
+  private String analysisMethod;
   @OneToOne(cascade = CascadeType.ALL)
   @JoinColumn(name = "experimentalGroupId")
   private ExperimentalGroup experimentalGroup;
@@ -61,7 +61,7 @@ protected SamplePreview() {
   private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampleCode,
       String batchLabel, String bioReplicateLabel,
       String sampleLabel, ExperimentalGroup experimentalGroup, String species, String specimen,
-      String analyte, String analysisType, String comment) {
+      String analyte, String analysisMethod, String comment) {
     Objects.requireNonNull(experimentId);
     Objects.requireNonNull(sampleId);
     Objects.requireNonNull(sampleCode);
@@ -82,9 +82,9 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl
     this.species = species;
     this.specimen = specimen;
     this.analyte = analyte;
+    this.analysisMethod = analysisMethod;
     // optional columns
     this.comment = comment;
-    this.analysisType = analysisType;
   }
 
   /**
@@ -106,17 +106,17 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl
    *                          preview
    * @param analyte           the {@link Analyte} for the {@link Sample} associated with this
    *                          preview
-   * @param analysisType      the type of analysis to be performed for this {@link Sample}
+   * @param analysisMethod    the analysis method to be performed for this {@link Sample}
    * @param comment           an optional comment pertaining to the associated {@link Sample}
    * @return the sample preview
    */
   public static SamplePreview create(ExperimentId experimentId, SampleId sampleId,
       String sampleCode,
       String batchLabel, String bioReplicateLabel,
       String sampleLabel, ExperimentalGroup experimentalGroup, String species, String specimen,
-      String analyte, String analysisType, String comment) {
+      String analyte, String analysisMethod, String comment) {
     return new SamplePreview(experimentId, sampleId, sampleCode, batchLabel, bioReplicateLabel,
-        sampleLabel, experimentalGroup, species, specimen, analyte, analysisType, comment);
+        sampleLabel, experimentalGroup, species, specimen, analyte, analysisMethod, comment);
   }
 
   public ExperimentId experimentId() {
@@ -154,9 +154,11 @@ public String specimen() {
   public String analyte() {
     return analyte;
   }
-  public String analysisType() {
-    return analysisType;
+
+  public String analysisMethod() {
+    return analysisMethod;
   }
+
   public String comment() {
     return comment;
   }
@@ -181,15 +183,15 @@ public boolean equals(Object o) {
         that.sampleLabel)
         && Objects.equals(species, that.species) && Objects.equals(specimen,
         that.specimen) && Objects.equals(analyte, that.analyte) && Objects.equals(
-        experimentalGroup, that.experimentalGroup) && Objects.equals(analysisType,
-        that.analysisType) && Objects.equals(comment, that.comment);
+        experimentalGroup, that.experimentalGroup) && Objects.equals(analysisMethod,
+        that.analysisMethod) && Objects.equals(comment, that.comment);
   }
 
   @Override
   public int hashCode() {
     return Objects.hash(experimentId, sampleCode, sampleId, batchLabel, bioReplicateLabel,
         sampleLabel,
-        species, specimen, analyte, experimentalGroup, analysisType, comment);
+        species, specimen, analyte, experimentalGroup, analysisMethod, comment);
   }
 
   @Override
@@ -204,7 +206,7 @@ public String toString() {
         ", species='" + species + '\'' +
         ", specimen='" + specimen + '\'' +
         ", analyte='" + analyte + '\'' +
-        ", analysisType='" + analysisType + '\'' +
+        ", analysisType='" + analysisMethod + '\'' +
         ", comment='" + comment + '\'' +
         ", conditions=" + experimentalGroup +
         '}';

projectmanagement/src/main/java/life/qbic/projectmanagement/domain/project/Funding.java

@@ -0,0 +1,64 @@
+package life.qbic.projectmanagement.domain.project;
+
+import jakarta.persistence.Embeddable;
+import java.util.Objects;
+
+/**
+ * A small business value object representing information about funding.
+ * <p>
+ * Funding is described by a free-text label and a funding body's reference identifier.
+ * <p>
+ * For example:
+ * <ul>
+ *   <li>SFB (label)</li>
+ *   <li>SFB 1101 (reference id)</li>
+ * </ul>
+ *
+ * @since 1.0.0
+ */
+@Embeddable
+public class Funding {
+
+  private String grant;
+
+  private String grantId;
+
+  protected Funding() {
+
+  }
+
+  private Funding(String grant, String grantId) {
+    this.grant = grant;
+    this.grantId = grantId;
+  }
+
+  public static Funding of(String grant, String grantId) {
+    return new Funding(grant, grantId);
+  }
+
+  public String grant() {
+    return this.grant;
+  }
+
+  public String grantId() {
+    return this.grantId;
+  }
+
+  @Override
+  public boolean equals(Object o) {
+    if (this == o) {
+      return true;
+    }
+    if (o == null || getClass() != o.getClass()) {
+      return false;
+    }
+    Funding funding = (Funding) o;
+    return Objects.equals(grant, funding.grant) && Objects.equals(grantId,
+        funding.grantId);
+  }
+
+  @Override
+  public int hashCode() {
+    return Objects.hash(grant, grantId);
+  }
+}