Merge remote-tracking branch 'origin/development' into feature/#720-p…

…ossibility-to-download-the-project-information

docs/processes/README.md

@@ -0,0 +1 @@
+diagrams have been created with: https://sequencediagram.org/

docs/processes/Sample_registration_process.txt

@@ -0,0 +1,24 @@
+title Sample Registration Process
+
+
+note over Client, Template Service: Provide experiment ID
+Client->Template Service:Request sample registration template
+Template Service->Experiment Service:Fetch experimental groups
+Experiment Service->Experiment Service:Load experimental groups
+Template Service<-Experiment Service:Return experimental groups
+Template Service->XLSXBuilder:Build template with selection choices
+Template Service<-XLSXBuilder:Return template
+Client<-Template Service: Return template
+Client->Client: Fill out template
+Client->Sample Registration Service: Register samples
+Sample Registration Service->Validation Service: Requests validation
+Validation Service->Validation Service: Validates
+Sample Registration Service<-Validation Service: Returns validation report
+Client<-Sample Registration Service: Notify about report
+Client->Client: Resolve potential conflicts
+Client->Sample Registration Service: Register sample batch
+Sample Registration Service->Sample Registration Service: Create new sample batch
+Sample Registration Service->Sample Registration Service: Create new samples with batch ID
+Sample Registration Service->Sample Registration Service: Update batch with sample IDs
+
+Client<-Sample Registration Service: Notify

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/ontology/TIBTerminologyServiceIntegration.java

@@ -173,15 +173,11 @@ public List<OntologyClass> query(String searchTerm, int offset, int limit)
   @Override
   public Optional<OntologyClass> searchByCurie(String curie) throws LookupException {
     try {
-      List<TibTerm> result = searchByOboId(curie, 0, 10);
-      if (result.isEmpty()) {
-        return Optional.empty();
-      }
-      return Optional.of(
-          result.stream().map(TIBTerminologyServiceIntegration::convert).toList().get(0));
+      return searchByOboIdExact(curie).map(TIBTerminologyServiceIntegration::convert);
     } catch (IOException e) {
       throw wrapIO(e);
     } catch (InterruptedException e) {
+      Thread.currentThread().interrupt();
       throw wrapInterrupted(e);
     } catch (Exception e) {
       throw wrapUnknown(e);
@@ -221,9 +217,12 @@ private List<TibTerm> fullSearch(String searchTerm, int offset, int limit)
       return List.of();
     }
     HttpRequest termSelectQuery = HttpRequest.newBuilder().uri(URI.create(
-            searchEndpointAbsoluteUrl.toString() + "?q=" + URLEncoder.encode(searchTerm,
-                StandardCharsets.UTF_8) + "&rows="
-                + limit + "&start=" + offset + "&ontology=" + createOntologyFilterQueryParameter()))
+            searchEndpointAbsoluteUrl.toString() + "?q="
+                + URLEncoder.encode(
+                searchTerm,
+                StandardCharsets.UTF_8)
+                + "&rows=" + limit + "&start=" + offset
+                + "&ontology=" + createOntologyFilterQueryParameter()))
         .header("Content-Type", "application/json").GET().build();
     var response = HTTP_CLIENT.send(termSelectQuery, BodyHandlers.ofString());
     return parseResponse(response);
@@ -278,15 +277,47 @@ private List<TibTerm> searchByOboId(String oboId, int offset, int limit)
       return List.of();
     }
     HttpRequest termSelectQuery = HttpRequest.newBuilder().uri(URI.create(
-            searchEndpointAbsoluteUrl.toString() + "?q=" + URLEncoder.encode(oboId,
-                StandardCharsets.UTF_8) + "&rows="
-                + limit + "&start=" + offset + "&ontology=" + createOntologyFilterQueryParameter()
-                + "&queryFields=obo_id"))
+            searchEndpointAbsoluteUrl.toString() + "?q="
+                + URLEncoder.encode(
+                //obo_id query field requires `:` separator instead of `_`
+                oboId.replace("_", ":"), StandardCharsets.UTF_8)
+                + "&queryFields=obo_id"
+                + "&rows=" + limit + "&start=" + offset
+                + "&ontology=" + createOntologyFilterQueryParameter()))
         .header("Content-Type", "application/json").GET().build();
     var response = HTTP_CLIENT.send(termSelectQuery, BodyHandlers.ofString());
     return parseResponse(response);
   }
 
+  /**
+   * Queries the /search endpoint of the TIB terminology service, but filters any results by the
+   * terms `obo_id` property.
+   * <p>
+   *
+   * @param oboId the obo id to match exactly
+   * @return a list of matching terms.
+   * @throws IOException          if e.g. the service cannot be reached
+   * @throws InterruptedException the query is interrupted before succeeding
+   * @since 1.4.0
+   */
+  private Optional<TibTerm> searchByOboIdExact(String oboId)
+      throws IOException, InterruptedException {
+    if (oboId.isBlank()) { // avoid unnecessary API calls
+      return Optional.empty();
+    }
+    HttpRequest termSelectQuery = HttpRequest.newBuilder().uri(URI.create(
+            searchEndpointAbsoluteUrl.toString() + "?q="
+                + URLEncoder.encode(
+                //obo_id query field requires `:` separator instead of `_`
+                oboId.replace("_", ":"), StandardCharsets.UTF_8)
+                + "&queryFields=obo_id"
+                + "&exact=true"
+                + "&ontology=" + createOntologyFilterQueryParameter()))
+        .header("Content-Type", "application/json").GET().build();
+    var response = HTTP_CLIENT.send(termSelectQuery, BodyHandlers.ofString());
+    return parseResponse(response).stream().findFirst();
+  }
+
   /**
    * Parses the TIB service response object and returns the wrapped terms.
    *
@@ -310,5 +341,3 @@ private List<TibTerm> parseResponse(HttpResponse<String> response) {
     }
   }
 }
-
-

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

@@ -3,13 +3,17 @@
 import jakarta.persistence.criteria.Expression;
 import jakarta.persistence.criteria.Join;
 import jakarta.persistence.criteria.Predicate;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
 import life.qbic.application.commons.OffsetBasedRequest;
 import life.qbic.application.commons.SortOrder;
 import life.qbic.projectmanagement.application.sample.SamplePreview;
 import life.qbic.projectmanagement.application.sample.SamplePreviewLookup;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
+import life.qbic.projectmanagement.domain.model.sample.AnalysisMethod;
 import org.springframework.context.annotation.Scope;
 import org.springframework.data.domain.Sort;
 import org.springframework.data.domain.Sort.Order;
@@ -176,8 +180,13 @@ public static Specification<SamplePreview> analyteContains(String filter) {
     }
 
     public static Specification<SamplePreview> analysisMethodContains(String filter) {
-      return (root, query, builder) ->
-          builder.like(root.get("analysisMethod"), "%" + filter + "%");
+      return (root, query, builder) -> {
+        Set<String> matchingValues = Arrays.stream(AnalysisMethod.values())
+            .filter(method -> method.label().toUpperCase().contains(filter.toUpperCase()))
+            .map(AnalysisMethod::abbreviation)
+            .collect(Collectors.toUnmodifiableSet());
+        return root.get("analysisMethod").in(matchingValues);
+      };
     }
 
     public static Specification<SamplePreview> commentContains(String filter) {

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

@@ -16,9 +16,11 @@
 import life.qbic.projectmanagement.domain.model.batch.BatchId;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
 import life.qbic.projectmanagement.domain.model.project.Project;
+import life.qbic.projectmanagement.domain.model.project.ProjectId;
 import life.qbic.projectmanagement.domain.model.sample.Sample;
 import life.qbic.projectmanagement.domain.model.sample.SampleCode;
 import life.qbic.projectmanagement.domain.model.sample.SampleId;
+import life.qbic.projectmanagement.domain.repository.ProjectRepository;
 import life.qbic.projectmanagement.domain.repository.SampleRepository;
 import life.qbic.projectmanagement.domain.service.SampleDomainService.ResponseCode;
 import life.qbic.projectmanagement.infrastructure.sample.openbis.OpenbisConnector.SampleNotDeletedException;
@@ -48,34 +50,46 @@ public class SampleRepositoryImpl implements SampleRepository {
   private static final Logger log = logger(SampleRepositoryImpl.class);
   private final QbicSampleRepository qbicSampleRepository;
   private final QbicSampleDataRepo sampleDataRepo;
+  private final ProjectRepository projectRepository;
 
   @Autowired
   public SampleRepositoryImpl(QbicSampleRepository qbicSampleRepository,
-      QbicSampleDataRepo sampleDataRepo) {
-    this.qbicSampleRepository = qbicSampleRepository;
-    this.sampleDataRepo = sampleDataRepo;
+      QbicSampleDataRepo sampleDataRepo, ProjectRepository projectRepository) {
+    this.qbicSampleRepository = Objects.requireNonNull(qbicSampleRepository);
+    this.sampleDataRepo = Objects.requireNonNull(sampleDataRepo);
+    this.projectRepository = Objects.requireNonNull(projectRepository);
   }
 
   @Override
   public Result<Collection<Sample>, ResponseCode> addAll(Project project,
       Collection<Sample> samples) {
     String commaSeperatedSampleIds = buildCommaSeparatedSampleIds(
         samples.stream().map(Sample::sampleId).toList());
+    List<Sample> savedSamples;
     try {
-      this.qbicSampleRepository.saveAll(samples);
+      savedSamples = this.qbicSampleRepository.saveAll(samples);
     } catch (Exception e) {
       log.error("The samples:" + commaSeperatedSampleIds + "could not be saved", e);
       return Result.fromError(ResponseCode.REGISTRATION_FAILED);
     }
     try {
-      sampleDataRepo.addSamplesToProject(project, samples.stream().toList());
+      sampleDataRepo.addSamplesToProject(project, savedSamples);
     } catch (Exception e) {
       log.error("The samples:" + commaSeperatedSampleIds + "could not be stored in openBIS", e);
       log.error("Removing samples from repository, as well.");
-      qbicSampleRepository.deleteAll(samples);
+      qbicSampleRepository.deleteAll(savedSamples);
       return Result.fromError(ResponseCode.REGISTRATION_FAILED);
     }
-    return Result.fromValue(samples);
+    return Result.fromValue(savedSamples);
+  }
+
+  @Override
+  public Result<Collection<Sample>, ResponseCode> addAll(ProjectId projectId, Collection<Sample> samples) {
+    var projectQuery = projectRepository.find(projectId);
+    if (projectQuery.isPresent()) {
+      return addAll(projectQuery.get(), samples);
+    }
+    return Result.fromError(ResponseCode.REGISTRATION_FAILED);
   }
 
   private String buildCommaSeparatedSampleIds(Collection<SampleId> sampleIds) {
@@ -100,7 +114,7 @@ public void deleteAll(Project project,
 
   @Override
   public boolean isSampleRemovable(SampleId sampleId) {
-    SampleCode sampleCode = qbicSampleRepository.findById(sampleId).get().sampleCode();
+    SampleCode sampleCode = qbicSampleRepository.findById(sampleId).orElseThrow().sampleCode();
     return sampleDataRepo.canDeleteSample(sampleCode);
   }
 
@@ -134,6 +148,17 @@ public void updateAll(Project project,
     sampleDataRepo.updateAll(project, updatedSamples);
   }
 
+  @Transactional
+  @Override
+  public void updateAll(ProjectId projectId, Collection<Sample> updatedSamples) {
+    var projectQuery = projectRepository.find(projectId);
+    if (projectQuery.isPresent()) {
+      updateAll(projectQuery.get(), updatedSamples);
+    } else {
+      throw new SampleRepositoryException("Could not find project with id " + projectId.value());
+    }
+  }
+
   @Override
   public List<Sample> findSamplesBySampleId(List<SampleId> sampleId) {
     return qbicSampleRepository.findAllById(sampleId);

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

@@ -102,6 +102,13 @@ public Optional<Project> find(String projectId) throws IllegalArgumentException
     return find(ProjectId.parse(projectId));
   }
 
+  @PreAuthorize("hasPermission(#projectId,'life.qbic.projectmanagement.domain.model.project.Project','READ')")
+  public Optional<ProjectOverview> findOverview(ProjectId projectId) {
+    Objects.requireNonNull(projectId);
+    return projectOverviewLookup.query("", 0, 1, List.of(), List.of(projectId)).stream()
+        .findFirst();
+  }
+
   public boolean isProjectCodeUnique(String projectCode) throws IllegalArgumentException {
     return !projectRepository.existsProjectByProjectCode(ProjectCode.parse(projectCode));
   }

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

@@ -1,4 +1,4 @@
-package life.qbic.projectmanagement.application.measurement.validation;
+package life.qbic.projectmanagement.application;
 
 public class ValidationException extends RuntimeException {
 

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

@@ -1,4 +1,4 @@
-package life.qbic.projectmanagement.application.measurement.validation;
+package life.qbic.projectmanagement.application;
 
 import java.util.ArrayList;
 import java.util.Collection;
@@ -16,43 +16,32 @@
  */
 public class ValidationResult {
 
-  private final int validatedEntries;
 
   private final List<String> warnings;
 
   private final List<String> failures;
 
   private ValidationResult() {
-    this.validatedEntries = 0;
     this.warnings = Collections.emptyList();
     this.failures = Collections.emptyList();
   }
 
-  private ValidationResult(int validatedEntries) {
-    this.validatedEntries = validatedEntries;
-    this.warnings = Collections.emptyList();
-    this.failures = Collections.emptyList();
-  }
-
-  private ValidationResult(int validatedEntries, Collection<String> warnings,
+  private ValidationResult(Collection<String> warnings,
       Collection<String> failures) {
-    this.validatedEntries = validatedEntries;
     this.warnings = warnings.stream().toList();
     this.failures = failures.stream().toList();
   }
 
-  public static ValidationResult successful(int validatedEntries) {
-    return new ValidationResult(validatedEntries);
+  public static ValidationResult successful() {
+    return new ValidationResult();
   }
 
-  public static ValidationResult withFailures(int validatedEntries,
-      Collection<String> failureReports) {
-    return new ValidationResult(validatedEntries, new ArrayList<>(), failureReports);
+  public static ValidationResult withFailures(Collection<String> failureReports) {
+    return new ValidationResult(new ArrayList<>(), failureReports);
   }
 
-  public static ValidationResult successful(int validatedEntries,
-      Collection<String> warnings) {
-    return new ValidationResult(validatedEntries, warnings, new ArrayList<>());
+  public static ValidationResult successful(Collection<String> warnings) {
+    return new ValidationResult(warnings, new ArrayList<>());
   }
 
 
@@ -79,20 +68,12 @@ public Collection<String> failures() {
     return failures.stream().toList();
   }
 
-  public int failedEntries() {
-    return failures.size();
-  }
-
-  public int validatedEntries() {
-    return validatedEntries;
-  }
-
   public boolean containsWarnings() {
     return !warnings.isEmpty();
   }
 
   public ValidationResult combine(ValidationResult otherResult) {
-    return new ValidationResult(this.validatedEntries + otherResult.validatedEntries,
+    return new ValidationResult(
         Stream.concat(this.warnings.stream(), otherResult.warnings.stream()).toList(),
         Stream.concat(this.failures.stream(), otherResult.failures.stream()).toList());
   }

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

@@ -0,0 +1,17 @@
+package life.qbic.projectmanagement.application;
+
+import java.util.Objects;
+
+/**
+ * <b><class short description - 1 Line!></b>
+ *
+ * <p><More detailed description - When to use, what it solves, etc.></p>
+ *
+ * @since <version tag>
+ */
+public record ValidationResultWithPayload<T>(ValidationResult validationResult, T payload) {
+
+  public ValidationResultWithPayload {
+    Objects.requireNonNull(validationResult);
+  }
+}

project-management/src/main/java/life/qbic/projectmanagement/application/batch/BatchRegistrationService.java

@@ -89,6 +89,21 @@ public Result<BatchId, ResponseCode> registerBatch(String label, boolean isPilot
     return Result.fromValue(result.getValue());
   }
 
+  @PreAuthorize("hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE')")
+  public Result<BatchId, ResponseCode> addSamplesToBatch(Collection<SampleId> sampleIds, BatchId batchId, ProjectId projectId) {
+    var batchQuery = batchRepository.find(batchId);
+    if (batchQuery.isEmpty()) {
+      log.error("No batch with id found: " + batchId);
+      return Result.fromError(ResponseCode.BATCH_UPDATE_FAILED);
+    }
+    var batch = batchQuery.get();
+    for (SampleId sampleId : sampleIds) {
+      batch.addSample(sampleId);
+    }
+    batchRepository.update(batch);
+    return Result.fromValue(batchId);
+  }
+
   public Result<BatchId, ResponseCode> addSampleToBatch(SampleId sampleId, BatchId batchId) {
     var random = new Random();
     while (true) {
@@ -197,6 +212,10 @@ public Result<BatchId, ResponseCode> editBatch(BatchId batchId, String batchLabe
     return Result.fromValue(batch.batchId());
   }
 
+  public void deleteBatch(BatchId batchId) {
+    batchRepository.deleteById(batchId);
+  }
+
   private void dispatchSuccessfulBatchUpdate(BatchId batchId, ProjectId projectId) {
     BatchUpdated batchUpdated = BatchUpdated.create(batchId, projectId);
     DomainEventDispatcher.instance().dispatch(batchUpdated);