Merge branch 'feature/#680-move-from-the-spreadsheet-component-for-sa…

…mple-batch-registration-to-xlsx-upload' of github.com:qbicsoftware/data-manager-app into feature/#680-move-from-the-spreadsheet-component-for-sample-batch-registration-to-xlsx-upload

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);
@@ -283,16 +279,45 @@ private List<TibTerm> searchByOboId(String oboId, int offset, int limit)
     HttpRequest termSelectQuery = HttpRequest.newBuilder().uri(URI.create(
             searchEndpointAbsoluteUrl.toString() + "?q="
                 + URLEncoder.encode(
-                oboId.replace("_", ":") + "&queryFields=obo_id",
                 //obo_id query field requires `:` separator instead of `_`
-                StandardCharsets.UTF_8)
+                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.
    *

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

@@ -65,21 +65,22 @@ 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
@@ -113,7 +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);
   }
 
@@ -147,6 +148,7 @@ public void updateAll(Project project,
     sampleDataRepo.updateAll(project, updatedSamples);
   }
 
+  @Transactional
   @Override
   public void updateAll(ProjectId projectId, Collection<Sample> updatedSamples) {
     var projectQuery = projectRepository.find(projectId);

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/sample/SampleRegistrationServiceV2.java

@@ -8,6 +8,7 @@
 import java.util.concurrent.CompletableFuture;
 import java.util.function.Function;
 import java.util.stream.Collectors;
+import life.qbic.projectmanagement.application.DeletionService;
 import life.qbic.projectmanagement.application.api.SampleCodeService;
 import life.qbic.projectmanagement.application.batch.BatchRegistrationService;
 import life.qbic.projectmanagement.domain.model.batch.BatchId;
@@ -37,13 +38,16 @@ public class SampleRegistrationServiceV2 {
   private final BatchRegistrationService batchRegistrationService;
   private final SampleRepository sampleRepository;
   private final SampleCodeService sampleCodeService;
+  private final DeletionService deletionService;
 
   @Autowired
   public SampleRegistrationServiceV2(BatchRegistrationService batchRegistrationService,
-      SampleRepository sampleRepository, SampleCodeService sampleCodeService) {
+      SampleRepository sampleRepository, SampleCodeService sampleCodeService,
+      DeletionService deletionService) {
     this.batchRegistrationService = Objects.requireNonNull(batchRegistrationService);
     this.sampleRepository = Objects.requireNonNull(sampleRepository);
     this.sampleCodeService = Objects.requireNonNull(sampleCodeService);
+    this.deletionService = Objects.requireNonNull(deletionService);
   }
 
   @PreAuthorize("hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE')")
@@ -59,24 +63,29 @@ public CompletableFuture<Void> registerSamples(Collection<SampleMetadata> sample
     try {
       var sampleIds = registerSamples(sampleMetadata, batchId, projectId);
       batchRegistrationService.addSamplesToBatch(sampleIds, batchId, projectId);
-    } catch (Exception e) {
+    } catch (RuntimeException e) {
       rollbackSampleRegistration(batchId);
-      throw new RegistrationException("Sample batch registration failed");
+      deletionService.deleteSamples(projectId, batchId,
+          sampleMetadata.stream().map(SampleMetadata::sampleId).map(SampleId::parse).toList());
+      deletionService.deleteBatch(projectId, batchId);
+      throw e;
     }
     return CompletableFuture.completedFuture(null);
   }
 
   @PreAuthorize("hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE')")
   @Async
   public CompletableFuture<Void> updateSamples(
-      Collection<SampleMetadata> sampleRegistrationRequests, ProjectId projectId) throws RegistrationException {
+      Collection<SampleMetadata> sampleRegistrationRequests, ProjectId projectId)
+      throws RegistrationException {
     var samples = fetchSamples(
         sampleRegistrationRequests.stream().map(SampleMetadata::sampleCode).map(SampleCode::create)
             .toList());
-    var sampleBySampleCode = samples.stream().collect(Collectors.toMap(sample -> sample.sampleCode().code(), Function.identity()));
+    var sampleBySampleCode = samples.stream()
+        .collect(Collectors.toMap(sample -> sample.sampleCode().code(), Function.identity()));
     var updatedSamples = updateSamples(sampleBySampleCode, sampleRegistrationRequests);
     sampleRepository.updateAll(projectId, updatedSamples);
-    return CompletableFuture.completedFuture( null);
+    return CompletableFuture.completedFuture(null);
   }
 
   private List<Sample> updateSamples(Map<String, Sample> samples,
@@ -85,7 +94,8 @@ private List<Sample> updateSamples(Map<String, Sample> samples,
     for (SampleMetadata sampleMetadata : sampleRegistrationRequests) {
       var sampleForUpdate = samples.get(sampleMetadata.sampleCode());
       sampleForUpdate.setLabel(sampleMetadata.sampleName());
-      var sampleOrigin = SampleOrigin.create(sampleMetadata.species(), sampleMetadata.specimen(), sampleMetadata.analyte());
+      var sampleOrigin = SampleOrigin.create(sampleMetadata.species(), sampleMetadata.specimen(),
+          sampleMetadata.analyte());
       sampleForUpdate.setSampleOrigin(sampleOrigin);
       sampleForUpdate.setExperimentalGroupId(sampleMetadata.experimentalGroupId());
       sampleForUpdate.setAnalysisMethod(sampleMetadata.analysisToBePerformed());
@@ -108,15 +118,19 @@ private Sample fetchSample(SampleCode sampleCode) throws UnknownSampleException
     return sampleQuery.get();
   }
 
-  private Collection<SampleId> registerSamples(Collection<SampleMetadata> sampleMetadata, BatchId batchId,
+  private Collection<SampleId> registerSamples(Collection<SampleMetadata> sampleMetadata,
+      BatchId batchId,
       ProjectId projectId)
       throws RegistrationException {
     var samplesToRegister = new ArrayList<Sample>();
     var sampleCodes = generateSampleCodes(sampleMetadata.size(), projectId).iterator();
     for (SampleMetadata sample : sampleMetadata) {
       samplesToRegister.add(buildSample(sample, batchId, sampleCodes.next()));
     }
-    return sampleRepository.addAll(projectId, samplesToRegister).getValue().stream().map(Sample::sampleId).toList();
+    return sampleRepository.addAll(projectId, samplesToRegister)
+        .valueOrElseThrow(e -> new RegistrationException("Could not register samples: " + e.name()))
+        .stream().map(Sample::sampleId)
+        .toList();
   }
 
   private Sample buildSample(SampleMetadata sample, BatchId batchId, SampleCode sampleCode) {

user-interface/src/main/java/life/qbic/datamanager/parser/sample/RegisterColumn.java

@@ -12,18 +12,19 @@
  */
 public enum RegisterColumn {
 
-  ANALYSIS("Analysis to be performed", 0, false),
-  SAMPLE_NAME("Sample Name", 1, false),
-  BIOLOGICAL_REPLICATE("Biological Replicate", 2, false),
-  CONDITION("Condition", 3, false),
-  SPECIES("Species", 4, false),
-  ANALYTE("Analyte", 5, false),
-  SPECIMEN("Specimen", 6, false),
-  COMMENT("Comment", 7, false);
+  ANALYSIS("Analysis to be performed", 0, false, true),
+  SAMPLE_NAME("Sample Name", 1, false, true),
+  BIOLOGICAL_REPLICATE("Biological Replicate", 2, false, false),
+  CONDITION("Condition", 3, false, true),
+  SPECIES("Species", 4, false, true),
+  ANALYTE("Analyte", 5, false, true),
+  SPECIMEN("Specimen", 6, false, true),
+  COMMENT("Comment", 7, false, false);
 
   private final String headerName;
   private final int columnIndex;
   private final boolean readOnly;
+  private final boolean mandatory;
 
   public static int maxColumnIndex() {
     return Arrays.stream(values())
@@ -35,11 +36,13 @@ public static int maxColumnIndex() {
    * @param headerName  the name in the header
    * @param columnIndex the index of the column this property is in
    * @param readOnly    is the property read only
+   * @param mandatory
    */
-  RegisterColumn(String headerName, int columnIndex, boolean readOnly) {
+  RegisterColumn(String headerName, int columnIndex, boolean readOnly, boolean mandatory) {
     this.headerName = headerName;
     this.columnIndex = columnIndex;
     this.readOnly = readOnly;
+    this.mandatory = mandatory;
   }
 
   public String headerName() {
@@ -50,8 +53,11 @@ public int columnIndex() {
     return columnIndex;
   }
 
-  public boolean readOnly() {
+  public boolean isReadOnly() {
     return readOnly;
   }
 
+  public boolean isMandatory() {
+    return mandatory;
+  }
 }

user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchRegistrationTemplate.java

@@ -70,9 +70,14 @@ public static XSSFWorkbook createRegistrationTemplate(List<String> conditions,
     Row header = getOrCreateRow(sheet, 0);
     for (RegisterColumn column : RegisterColumn.values()) {
       var cell = XLSXTemplateHelper.getOrCreateCell(header, column.columnIndex());
-      cell.setCellValue(column.headerName());
+
       cell.setCellStyle(boldCellStyle);
-      if (column.readOnly()) {
+      if (column.isMandatory()) {
+        cell.setCellValue(column.headerName() + "*");
+      } else {
+        cell.setCellValue(column.headerName());
+      }
+      if (column.isReadOnly()) {
         cell.setCellStyle(readOnlyHeaderStyle);
       }
     }

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java

@@ -48,6 +48,7 @@
 import life.qbic.logging.service.LoggerFactory;
 import life.qbic.projectmanagement.application.DeletionService;
 import life.qbic.projectmanagement.application.ProjectInformationService;
+import life.qbic.projectmanagement.application.ProjectOverview;
 import life.qbic.projectmanagement.application.batch.BatchRegistrationService;
 import life.qbic.projectmanagement.application.batch.SampleUpdateRequest;
 import life.qbic.projectmanagement.application.batch.SampleUpdateRequest.SampleInformation;
@@ -222,30 +223,38 @@ private void downloadSampleMetadata() {
   }
 
   private void onRegisterBatchClicked() {
-    Experiment experiment = context.experimentId()
-        .flatMap(
-            id -> experimentInformationService.find(context.projectId().orElseThrow().value(), id))
+    ProjectId projectId = context.projectId().orElseThrow();
+    ExperimentId experimentId = context.experimentId().orElseThrow();
+
+    Experiment experiment = experimentInformationService.find(projectId.value(), experimentId)
         .orElseThrow();
+
     if (experiment.getExperimentalGroups().isEmpty()) {
       return;
     }
+    ProjectOverview projectOverview = projectInformationService.findOverview(projectId)
+        .orElseThrow();
     RegisterSampleBatchDialog registerSampleBatchDialog = new RegisterSampleBatchDialog(
-        sampleValidationService, templateService,
-        context.experimentId().map(ExperimentId::value).orElseThrow(),
-        context.projectId().map(ProjectId::value).orElseThrow());
+        sampleValidationService, templateService, experimentId.value(),
+        projectId.value(), projectOverview.projectCode());
     registerSampleBatchDialog.addConfirmListener(event -> {
       event.getSource().taskInProgress("Register the sample batch metadata",
           "It may take about a minute for the registration task to complete.");
       UI ui = event.getSource().getUI().orElseThrow();
       CompletableFuture<Void> registrationTask = sampleRegistrationServiceV2.registerSamples(
               event.validatedSampleMetadata(),
-              context.projectId()
-                  .orElseThrow(), event.batchName(), event.isPilot())
+              projectId, event.batchName(), false)
           .orTimeout(5, TimeUnit.MINUTES);
       registrationTask
-          .thenRun(() -> ui.access(() -> event.getSource().close()))
-          .exceptionally(e -> null /*TODO show failed*/);
-      event.getSource().close();
+          .thenRun(() -> ui.access(() -> {
+            event.getSource().taskSucceeded("", ""); //todo label and description
+          }))
+          .exceptionally(e -> {
+            ui.access(() -> {
+              event.getSource().taskFailed("", ""); //todo label and description s
+            });
+            return null;
+          });
     });
     registerSampleBatchDialog.addCancelListener(
         event -> showCancelConfirmationDialog(event.getSource()));