Implement experiment query API (#1125)

Implements the reactive API for querying experimental information.

Wires the async service call in the UI and renders information about species, specimen and analyte dynamically.

Author: sven1103

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

@@ -814,6 +814,18 @@ record OntologyTerm(String label, Curie oboId, URI id) {
    */
   record Curie(String idSpace, String localId) {
 
+    public static Curie parse(String value) {
+      requireNonNull(value);
+      if (value.contains(":")) {
+        var parts = value.split(":");
+        return new Curie(parts[0], parts[1]);
+      }
+      throw new IllegalArgumentException("Invalid Curie: " + value);
+    }
+
+    public String toString() {
+      return idSpace + ":" + localId;
+    }
   }
 
   /**

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

@@ -6,14 +6,18 @@
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.net.URI;
 import java.nio.ByteBuffer;
 import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.Collection;
 import java.util.List;
 import java.util.Objects;
+import java.util.Set;
 import java.util.concurrent.Callable;
 import java.util.function.Function;
 import java.util.function.UnaryOperator;
+import java.util.stream.Collectors;
 import life.qbic.application.commons.SortOrder;
 import life.qbic.logging.api.Logger;
 import life.qbic.logging.service.LoggerFactory;
@@ -27,6 +31,7 @@
 import life.qbic.projectmanagement.application.api.template.TemplateService;
 import life.qbic.projectmanagement.application.authorization.ReactiveSecurityContextUtils;
 import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
+import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
 import life.qbic.projectmanagement.application.experiment.ExperimentInformationService.ExperimentalVariableAddition;
 import life.qbic.projectmanagement.application.measurement.validation.MeasurementValidationService;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
@@ -99,6 +104,17 @@ private static Retry defaultRetryStrategy() {
         .doBeforeRetry(retrySignal -> log.warn("Operation failed (" + retrySignal + ")"));
   }
 
+  private static Set<OntologyTerm> convertToApi(
+      Collection<life.qbic.projectmanagement.domain.model.OntologyTerm> terms) {
+    return terms.stream().map(AsyncProjectServiceImpl::convertToApi).collect(Collectors.toSet());
+  }
+
+  private static OntologyTerm convertToApi(
+      life.qbic.projectmanagement.domain.model.OntologyTerm term) {
+    return new OntologyTerm(term.getLabel(), Curie.parse(term.oboId().toString()),
+        URI.create(term.getOntologyIri()));
+  }
+
   @Override
   public Mono<ProjectUpdateResponse> update(@NonNull ProjectUpdateRequest request)
       throws UnknownRequestException, RequestFailedException, AccessDeniedException {
@@ -168,7 +184,20 @@ public Flux<ByteBuffer> roCrateSummary(String projectId) {
 
   @Override
   public Flux<ExperimentDescription> getExperiments(String projectId) {
-    throw new RuntimeException("Not yet implemented");
+    var securityContext = SecurityContextHolder.getContext();
+    return applySecurityContextMany(Flux.fromIterable(
+            () -> experimentInformationService.findAllForProject(ProjectId.parse(projectId)).iterator())
+        .map(e -> e.experimentId())
+        .flatMap(id -> {
+          var analytes = experimentInformationService.getAnalytesOfExperiment(id);
+          var specimen = experimentInformationService.getSpecimensOfExperiment(id);
+          var species = experimentInformationService.getSpeciesOfExperiment(id);
+          var experimentName = experimentInformationService.find(projectId, id)
+              .map(Experiment::getName).orElse("not available");
+          return Mono.just(new ExperimentDescription(experimentName, convertToApi(species),
+              convertToApi(specimen), convertToApi(analytes)));
+        })).subscribeOn(VirtualThreadScheduler.getScheduler())
+        .contextWrite(reactiveSecurity(securityContext));
   }
 
   // Requires the SecurityContext to work
@@ -315,7 +344,8 @@ public Mono<DigitalObject> sampleRegistrationTemplate(String projectId, String e
   }
 
   @Override
-  public Mono<DigitalObject> sampleUpdateTemplate(String projectId, String experimentId, String batchId,
+  public Mono<DigitalObject> sampleUpdateTemplate(String projectId, String experimentId,
+      String batchId,
       MimeType mimeType) {
     SecurityContext securityContext = SecurityContextHolder.getContext();
     return applySecurityContext(Mono.fromCallable(
@@ -542,7 +572,8 @@ private Mono<ProjectDeletionResponse> delete(String projectId, String requestId,
         return Mono.error(new AccessDeniedException(ACCESS_DENIED));
       } catch (Exception e) {
         log.error("Unexpected exception deleting funding information", e);
-        return Mono.error(new RequestFailedException("Unexpected exception deleting funding information"));
+        return Mono.error(
+            new RequestFailedException("Unexpected exception deleting funding information"));
       }
     });
   }
@@ -605,20 +636,20 @@ private Mono<ExperimentUpdateResponse> addExperimentalVariables(
   private Mono<ProjectUpdateResponse> update(ProjectId projectId, String requestId,
       ProjectDesign design) {
     return
-       Mono.<ProjectUpdateResponse>create(sink -> {
-          try {
-            projectService.updateTitle(projectId, design.title());
-            projectService.updateObjective(projectId, design.objective());
-            sink.success(new ProjectUpdateResponse(projectId.value(), design, requestId));
-          } catch (IllegalArgumentException e) {
-            sink.error(new RequestFailedException("Invalid project id: " + projectId));
-          } catch (org.springframework.security.access.AccessDeniedException e) {
-            sink.error(new AccessDeniedException(ACCESS_DENIED));
-          } catch (RuntimeException e) {
-            sink.error(new RequestFailedException("Update project design failed", e));
-          }
-        }
-    );
+        Mono.<ProjectUpdateResponse>create(sink -> {
+              try {
+                projectService.updateTitle(projectId, design.title());
+                projectService.updateObjective(projectId, design.objective());
+                sink.success(new ProjectUpdateResponse(projectId.value(), design, requestId));
+              } catch (IllegalArgumentException e) {
+                sink.error(new RequestFailedException("Invalid project id: " + projectId));
+              } catch (org.springframework.security.access.AccessDeniedException e) {
+                sink.error(new AccessDeniedException(ACCESS_DENIED));
+              } catch (RuntimeException e) {
+                sink.error(new RequestFailedException("Update project design failed", e));
+              }
+            }
+        );
   }
 
 }

project-management/src/main/java/life/qbic/projectmanagement/domain/model/OntologyTerm.java

@@ -34,6 +34,8 @@ public class OntologyTerm implements Serializable {
   private String description;
   @JsonProperty("classIri")
   private String classIri;
+  @JsonProperty("oboId")
+  private OboId realOboId;
 
   public OntologyTerm() {
   }
@@ -106,10 +108,21 @@ public void setDescription(String description) {
     this.description = description;
   }
 
+  @Deprecated(since = "1.10.0", forRemoval = true)
   public String getOboId() {
     return oboId;
   }
 
+  public OboId oboId() {
+    // Legacy support for CURIE specification violation
+    return Objects.requireNonNullElseGet(realOboId, () -> OboId.parse(oboId, "_"));
+  }
+
+  public void setOboId(OboId oboId) {
+    this.realOboId = Objects.requireNonNull(oboId);
+  }
+
+  @Deprecated(since = "1.10.0", forRemoval = true)
   public void setOboId(String oboId) {
     this.oboId = oboId;
   }
@@ -162,4 +175,26 @@ public String toString() {
         .add("classIri='" + classIri + "'")
         .toString();
   }
+
+  public record OboId(String idSpace, String localId) {
+    static OboId parse(String id) {
+      if (id == null || id.isEmpty()) {
+        throw new IllegalArgumentException("OboId cannot be null or empty");
+      }
+      String[] parts = id.split(":");
+      return new OboId(parts[0], parts[1]);
+    }
+
+    static OboId parse(String id, String separator) {
+      if (id == null || id.isEmpty()) {
+        throw new IllegalArgumentException("OboId cannot be null or empty");
+      }
+      String[] parts = id.split(separator);
+      return new OboId(parts[0], parts[1]);
+    }
+
+    public String toString() {
+      return idSpace + ":" + localId;
+    }
+  }
 }

project-management/src/test/groovy/life/qbic/projectmanagement/application/api/AsyncProjectServiceImplTest.java

@@ -23,6 +23,8 @@
 import life.qbic.projectmanagement.application.api.AsyncProjectService.ProjectDesign;
 import life.qbic.projectmanagement.application.api.AsyncProjectService.ProjectUpdateRequest;
 import life.qbic.projectmanagement.application.api.fair.DigitalObjectFactory;
+import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
+import life.qbic.projectmanagement.application.measurement.validation.MeasurementValidationService;
 import life.qbic.projectmanagement.application.api.template.TemplateService;
 import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
 import life.qbic.projectmanagement.application.measurement.validation.MeasurementValidationService;
@@ -49,6 +51,7 @@ class AsyncProjectServiceImplTest {
   MeasurementValidationService measurementValidationService = mock(
       MeasurementValidationService.class);
   TemplateService templateService = mock(TemplateService.class);
+  ExperimentInformationService experimentInformationService = mock(ExperimentInformationService.class);
   ExperimentInformationService experimentInformationServiceMock = mock(
       ExperimentInformationService.class);