Feature 1119/1119 implement api for creating experiments

project-management-infrastructure/src/test/groovy/life/qbic/projectmanagement/infrastructure/ontology/OntologyTermRepositorySpec.groovy → project-management-infrastructure/src/test/groovy/life/qbic/projectmanagement/infrastructure/ontology/OntologyTermV1RepositorySpec.groovy

@@ -7,7 +7,7 @@ import spock.lang.Specification
  *
  * @since 1.0.0
  */
-class OntologyTermRepositorySpec extends Specification{
+class OntologyTermV1RepositorySpec extends Specification {
 
     def "Given a one-word search, the correct ontology searchterm is created"() {
         given:

project-management/src/main/java/life/qbic/projectmanagement/application/VirtualThreadScheduler.java → project-management/src/main/java/life/qbic/application/commons/VirtualThreadScheduler.java

@@ -1,4 +1,4 @@
-package life.qbic.projectmanagement.application;
+package life.qbic.application.commons;
 
 import java.util.concurrent.Executor;
 import java.util.concurrent.Executors;

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

@@ -13,7 +13,7 @@
 import life.qbic.domain.concepts.DomainEventDispatcher;
 import life.qbic.domain.concepts.LocalDomainEventDispatcher;
 import life.qbic.projectmanagement.application.experiment.ExperimentInformationService.ExperimentCreatedDomainEventSubscriber;
-import life.qbic.projectmanagement.domain.model.OntologyTerm;
+import life.qbic.projectmanagement.domain.model.OntologyTermV1;
 import life.qbic.projectmanagement.domain.model.experiment.Experiment;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
 import life.qbic.projectmanagement.domain.model.project.Project;
@@ -54,11 +54,9 @@ public AddExperimentToProjectService(
   @PreAuthorize("hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE')")
   public Result<ExperimentId, RuntimeException> addExperimentToProject(ProjectId projectId,
       String experimentName,
-      List<OntologyTerm> species,
-      List<OntologyTerm> specimens,
-      List<OntologyTerm> analytes,
-      String speciesIconLabel,
-      String specimenIconLabel) {
+      List<OntologyTermV1> species,
+      List<OntologyTermV1> specimens,
+      List<OntologyTermV1> analytes) {
       requireNonNull(projectId, "project id must not be null during experiment creation");
       if (experimentName.isBlank()) {
         experimentName = "Unnamed Experiment";
@@ -91,7 +89,6 @@ public Result<ExperimentId, RuntimeException> addExperimentToProject(ProjectId p
           .onValue(exp -> exp.addAnalytes(analytes))
           .onValue(exp -> exp.addSpecies(species))
           .onValue(exp -> exp.addSpecimens(specimens))
-          .onValue(exp -> exp.setIconNames(speciesIconLabel, specimenIconLabel, "default"))
           .onValue(experiment -> {
             project.addExperiment(experiment);
             projectRepository.update(project);

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

@@ -18,11 +18,12 @@
 import java.util.function.UnaryOperator;
 import java.util.stream.Collectors;
 import life.qbic.application.commons.SortOrder;
+import life.qbic.application.commons.VirtualThreadScheduler;
 import life.qbic.logging.api.Logger;
 import life.qbic.logging.service.LoggerFactory;
+import life.qbic.projectmanagement.application.AddExperimentToProjectService;
 import life.qbic.projectmanagement.application.ProjectInformationService;
 import life.qbic.projectmanagement.application.ValidationResult;
-import life.qbic.projectmanagement.application.VirtualThreadScheduler;
 import life.qbic.projectmanagement.application.api.fair.ContactPoint;
 import life.qbic.projectmanagement.application.api.fair.DigitalObject;
 import life.qbic.projectmanagement.application.api.fair.DigitalObjectFactory;
@@ -37,6 +38,7 @@
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
 import life.qbic.projectmanagement.application.sample.SamplePreview;
 import life.qbic.projectmanagement.application.sample.SampleValidationService;
+import life.qbic.projectmanagement.domain.model.OntologyTermV1;
 import life.qbic.projectmanagement.domain.model.experiment.Experiment;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
 import life.qbic.projectmanagement.domain.model.project.Contact;
@@ -47,7 +49,6 @@
 import life.qbic.projectmanagement.domain.repository.ProjectRepository.ProjectNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.lang.NonNull;
-import org.springframework.security.access.AccessDeniedException;
 import org.springframework.security.core.context.SecurityContext;
 import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.stereotype.Service;
@@ -82,6 +83,7 @@ public class AsyncProjectServiceImpl implements AsyncProjectService {
   private final ExperimentInformationService experimentInformationService;
   private final TerminologyService terminologyService;
   private final SpeciesLookupService taxaService;
+  private final AddExperimentToProjectService addExperimentToProjectService;
 
   public AsyncProjectServiceImpl(
       @Autowired ProjectInformationService projectService,
@@ -93,7 +95,8 @@ public AsyncProjectServiceImpl(
       @Autowired MeasurementValidationService measurementValidationService,
       @Autowired ExperimentInformationService experimentInformationService,
       @Autowired TerminologyService termService,
-      @Autowired SpeciesLookupService taxaService) {
+      @Autowired SpeciesLookupService taxaService,
+      AddExperimentToProjectService addExperimentToProjectService) {
     this.projectService = Objects.requireNonNull(projectService);
     this.sampleInfoService = Objects.requireNonNull(sampleInfoService);
     this.scheduler = Objects.requireNonNull(scheduler);
@@ -104,6 +107,7 @@ public AsyncProjectServiceImpl(
     this.experimentInformationService = Objects.requireNonNull(experimentInformationService);
     this.terminologyService = Objects.requireNonNull(termService);
     this.taxaService = Objects.requireNonNull(taxaService);
+    this.addExperimentToProjectService = Objects.requireNonNull(addExperimentToProjectService);
   }
 
   private static Retry defaultRetryStrategy() {
@@ -112,12 +116,12 @@ private static Retry defaultRetryStrategy() {
   }
 
   private static Set<OntologyTerm> convertToApi(
-      Collection<life.qbic.projectmanagement.domain.model.OntologyTerm> terms) {
+      Collection<OntologyTermV1> terms) {
     return terms.stream().map(AsyncProjectServiceImpl::convertToApi).collect(Collectors.toSet());
   }
 
   private static OntologyTerm convertToApi(
-      life.qbic.projectmanagement.domain.model.OntologyTerm term) {
+      OntologyTermV1 term) {
     return new OntologyTerm(term.getLabel(), term.getDescription(),
         Curie.parse(term.oboId().toString()),
         URI.create(term.getClassIri()), term.getOntologyAbbreviation());
@@ -131,12 +135,37 @@ private static OntologyTerm convertToApi(OntologyClass term) {
 
   @Override
   public Mono<ExperimentCreationResponse> create(ExperimentCreationRequest request) {
-    throw new RuntimeException("Not implemented");
+    var securityContext = SecurityContextHolder.getContext();
+    var call = Mono.fromSupplier(() -> {
+      Objects.requireNonNull(request.experimentDescription());
+      var species = request.experimentDescription().species().stream().map(
+          it -> new OntologyTermV1(it.label(), null, null,
+              null, null, null, null)).toList(); //todo replace with v2
+      var specimen = request.experimentDescription().specimen().stream().map(
+          it -> new OntologyTermV1(it.label(), null, null,
+              null, null, null, null)).toList(); //todo replace with v2
+      var analytes = request.experimentDescription().analytes().stream().map(
+          it -> new OntologyTermV1(it.label(), null, null,
+              null, null, null, null)).toList(); //todo replace with v2
+      ProjectId parse = ProjectId.parse(request.projectId());
+      String experimentName = request.experimentDescription().experimentName();
+
+      ExperimentId res = addExperimentToProjectService.addExperimentToProject(parse, experimentName,
+              species, specimen, analytes)
+          .valueOrElseThrow(e -> new RuntimeException(e));
+      return new ExperimentCreationResponse(request.projectId(), res.value(),
+          request.experimentDescription(), request.requestId());
+    });
+    return applySecurityContext(call)
+        .contextWrite(reactiveSecurity(securityContext))
+        .subscribeOn(VirtualThreadScheduler.getScheduler())
+        .retryWhen(defaultRetryStrategy());
   }
 
   @Override
   public Mono<ExperimentalGroupCreationResponse> create(ExperimentalGroupCreationRequest request) {
-    throw new RuntimeException("not implemented");
+//TODO implement
+    throw new RuntimeException("Not implemented");
   }
 
   @Override

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

@@ -1,6 +1,6 @@
 package life.qbic.projectmanagement.application.batch;
 
-import life.qbic.projectmanagement.domain.model.OntologyTerm;
+import life.qbic.projectmanagement.domain.model.OntologyTermV1;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentalGroup;
 import life.qbic.projectmanagement.domain.model.sample.AnalysisMethod;
 import life.qbic.projectmanagement.domain.model.sample.SampleId;
@@ -29,8 +29,8 @@ public record SampleUpdateRequest(SampleId sampleId, SampleInformation sampleInf
    */
   public record SampleInformation(String sampleName, String biologicalReplicate,
                                   AnalysisMethod analysisMethod,
-                                  ExperimentalGroup experimentalGroup, OntologyTerm species,
-                                  OntologyTerm specimen, OntologyTerm analyte,
+                                  ExperimentalGroup experimentalGroup, OntologyTermV1 species,
+                                  OntologyTermV1 specimen, OntologyTermV1 analyte,
                                   String comment) {
 
   }

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

@@ -23,7 +23,7 @@
 import life.qbic.logging.service.LoggerFactory;
 import life.qbic.projectmanagement.application.DeletionService;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
-import life.qbic.projectmanagement.domain.model.OntologyTerm;
+import life.qbic.projectmanagement.domain.model.OntologyTermV1;
 import life.qbic.projectmanagement.domain.model.experiment.Experiment;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentalDesign.AddExperimentalGroupResponse.ResponseCode;
@@ -245,7 +245,7 @@ public List<Experiment> findAllForProject(ProjectId projectId) {
   @PreAuthorize(
       "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE') ")
   public void addSpeciesToExperiment(String projectId, ExperimentId experimentId,
-      OntologyTerm... species) {
+      OntologyTermV1... species) {
     Arrays.stream(species).forEach(Objects::requireNonNull);
     if (species.length < 1) {
       return;
@@ -274,7 +274,7 @@ public void addSpeciesToExperiment(String projectId, ExperimentId experimentId,
   @PreAuthorize(
       "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE') ")
   public void addSpecimenToExperiment(String projectId, ExperimentId experimentId,
-      OntologyTerm... specimens) {
+      OntologyTermV1... specimens) {
     Arrays.stream(specimens).forEach(Objects::requireNonNull);
     if (specimens.length < 1) {
       return;
@@ -303,7 +303,7 @@ public void addSpecimenToExperiment(String projectId, ExperimentId experimentId,
   @PreAuthorize(
       "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE') ")
   public void addAnalyteToExperiment(String projectId, ExperimentId experimentId,
-      OntologyTerm... analytes) {
+      OntologyTermV1... analytes) {
     Arrays.stream(analytes).forEach(Objects::requireNonNull);
     if (analytes.length < 1) {
       return;
@@ -452,7 +452,7 @@ public List<ExperimentalVariableInformation> addVariablesToExperiment(String pro
    * @param experimentId the Id of the experiment for which the analytes should be retrieved
    * @return a collection of analytes in the active experiment.
    */
-  public Collection<OntologyTerm> getAnalytesOfExperiment(ExperimentId experimentId) {
+  public Collection<OntologyTermV1> getAnalytesOfExperiment(ExperimentId experimentId) {
     Experiment experiment = loadExperimentById(experimentId);
     return experiment.getAnalytes();
   }
@@ -463,7 +463,7 @@ public Collection<OntologyTerm> getAnalytesOfExperiment(ExperimentId experimentI
    * @param experimentId the Id of the experiment for which the species should be retrieved
    * @return a collection of species in the active experiment.
    */
-  public Collection<OntologyTerm> getSpeciesOfExperiment(ExperimentId experimentId) {
+  public Collection<OntologyTermV1> getSpeciesOfExperiment(ExperimentId experimentId) {
     Experiment experiment = loadExperimentById(experimentId);
     return experiment.getSpecies();
   }
@@ -474,7 +474,7 @@ public Collection<OntologyTerm> getSpeciesOfExperiment(ExperimentId experimentId
    * @param experimentId the Id of the experiment for which the specimen should be retrieved
    * @return a collection of specimen in the active experiment.
    */
-  public Collection<OntologyTerm> getSpecimensOfExperiment(ExperimentId experimentId) {
+  public Collection<OntologyTermV1> getSpecimensOfExperiment(ExperimentId experimentId) {
     Experiment experiment = loadExperimentById(experimentId);
     return experiment.getSpecimens();
   }
@@ -532,10 +532,9 @@ public void deleteExperimentalGroupsWithIds(String projectId, ExperimentId id, L
     handleLocalEventCache(domainEventsCache);
   }
 
-  @Transactional
   /**
    * Updates experimental groups in a given experiment.
-   *
+   * <p>
    * Compares the provided list of experimental groups of an experiment with the persistent state.
    * Removes groups from the experiment that are not in the new list, adds groups that are not in
    * the experiment yet and updates the other groups of the experiment.
@@ -545,6 +544,7 @@ public void deleteExperimentalGroupsWithIds(String projectId, ExperimentId id, L
    * @param experimentalGroupDTOS  the new list of experimental groups including all updates
    * @since 1.0.0
    */
+  @Transactional
   @PreAuthorize(
       "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE') ")
   public void updateExperimentalGroupsOfExperiment(String projectId, ExperimentId experimentId,
@@ -600,8 +600,7 @@ private List<Long> getGroupIdsToDelete(List<ExperimentalGroup> existingGroups,
       "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE') ")
   public void editExperimentInformation(String projectId, ExperimentId experimentId,
       String experimentName,
-      List<OntologyTerm> species, List<OntologyTerm> specimens, List<OntologyTerm> analytes,
-      String speciesIconName, String specimenIconName) {
+      List<OntologyTermV1> species, List<OntologyTermV1> specimens, List<OntologyTermV1> analytes) {
 
     List<DomainEvent> domainEventsCache = new ArrayList<>();
     var localDomainEventDispatcher = LocalDomainEventDispatcher.instance();
@@ -614,7 +613,6 @@ public void editExperimentInformation(String projectId, ExperimentId experimentI
     experiment.setSpecies(species);
     experiment.setSpecimens(specimens);
     experiment.setAnalytes(analytes);
-    experiment.setIconNames(speciesIconName, specimenIconName, "default");
     experimentRepository.update(experiment);
 
     handleLocalEventCache(domainEventsCache);

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

@@ -25,7 +25,7 @@
 import life.qbic.projectmanagement.application.ontology.TerminologyService;
 import life.qbic.projectmanagement.application.sample.SampleIdCodeEntry;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
-import life.qbic.projectmanagement.domain.model.OntologyTerm;
+import life.qbic.projectmanagement.domain.model.OntologyTermV1;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
 import life.qbic.projectmanagement.domain.model.measurement.MeasurementCode;
 import life.qbic.projectmanagement.domain.model.measurement.MeasurementId;
@@ -778,7 +778,7 @@ private boolean allMeasurementCodesExist(List<String> measurementCode) {
         .allMatch(measurementRepository::existsMeasurement);
   }
 
-  private Optional<OntologyTerm> resolveOntologyCURI(String ontologyCURI) {
+  private Optional<OntologyTermV1> resolveOntologyCURI(String ontologyCURI) {
     return terminologyService.findByCurie(ontologyCURI);
   }
 

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

@@ -2,7 +2,7 @@
 
 import java.util.List;
 import java.util.Optional;
-import life.qbic.projectmanagement.domain.model.OntologyTerm;
+import life.qbic.projectmanagement.domain.model.OntologyTermV1;
 
 /**
  * <b>API for ontology term selection or lookup for autocomplete use cases</b>
@@ -18,7 +18,7 @@ public interface TerminologySelect {
    * <p>
    * <b>NOTE!</b>
    * <p>
-   * The resulting {@link OntologyTerm} objects are not guaranteed to contain values for properties
+   * The resulting {@link OntologyTermV1} objects are not guaranteed to contain values for properties
    * like "description". This depends highly on the implementation, use the
    * {@link TerminologySelect#search(String, int, int)} method for a rich search.
    *
@@ -44,7 +44,7 @@ public interface TerminologySelect {
   Optional<OntologyClass> searchByCurie(String curie) throws LookupException;
 
   /**
-   * Searches for possible matching ontology terms. This search returns rich {@link OntologyTerm}
+   * Searches for possible matching ontology terms. This search returns rich {@link OntologyTermV1}
    * objects, and should be used when information for properties like "description" needs to be
    * used.
    *