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Author: sven1103

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

@@ -20,6 +20,8 @@
 import life.qbic.projectmanagement.application.api.fair.DigitalObject;
 import life.qbic.projectmanagement.application.api.fair.DigitalObjectFactory;
 import life.qbic.projectmanagement.application.api.fair.ResearchProject;
+import life.qbic.projectmanagement.application.api.template.TemplateService;
+import life.qbic.projectmanagement.application.authorization.ReactiveSecurityContextUtils;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
 import life.qbic.projectmanagement.application.sample.SamplePreview;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
@@ -58,14 +60,20 @@ public class AsyncProjectServiceImpl implements AsyncProjectService {
   private final Scheduler scheduler;
   private final SampleInformationService sampleInfoService;
   private final DigitalObjectFactory digitalObjectFactory;
+  private final TemplateService templateService;
 
-  public AsyncProjectServiceImpl(@Autowired ProjectInformationService projectService,
+  public AsyncProjectServiceImpl(
+      @Autowired ProjectInformationService projectService,
       @Autowired SampleInformationService sampleInfoService,
-      @Autowired Scheduler scheduler, @Autowired DigitalObjectFactory digitalObjectFactory) {
+      @Autowired Scheduler scheduler,
+      @Autowired DigitalObjectFactory digitalObjectFactory,
+      @Autowired TemplateService templateService
+  ) {
     this.projectService = Objects.requireNonNull(projectService);
     this.sampleInfoService = Objects.requireNonNull(sampleInfoService);
     this.scheduler = Objects.requireNonNull(scheduler);
     this.digitalObjectFactory = Objects.requireNonNull(digitalObjectFactory);
+    this.templateService = Objects.requireNonNull(templateService);
   }
 
   private static Retry defaultRetryStrategy() {
@@ -239,8 +247,12 @@ public Mono<Sample> findSample(String projectId, String sampleId) {
   @Override
   public Mono<DigitalObject> sampleRegistrationTemplate(String projectId, String experimentId,
       MimeType mimeType) {
-
-    throw new RuntimeException("not implemented");
+    SecurityContext securityContext = SecurityContextHolder.getContext();
+    return ReactiveSecurityContextUtils.applySecurityContext(Mono.fromCallable(
+            () -> templateService.sampleRegistrationTemplate(projectId, experimentId, mimeType)))
+        .subscribeOn(scheduler)
+        .transform(original -> ReactiveSecurityContextUtils.writeSecurityContext(original,
+            securityContext));
   }
 
   @Override

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

@@ -1,10 +1,10 @@
 package life.qbic.projectmanagement.application.api.template;
 
 import java.util.Arrays;
-import java.util.List;
 import java.util.Objects;
 import life.qbic.projectmanagement.application.api.AsyncProjectService.UnsupportedMimeTypeException;
 import life.qbic.projectmanagement.application.api.fair.DigitalObject;
+import life.qbic.projectmanagement.application.api.template.TemplateProvider.SampleRegistration;
 import life.qbic.projectmanagement.application.confounding.ConfoundingVariableService;
 import life.qbic.projectmanagement.application.confounding.ConfoundingVariableService.ConfoundingVariableInformation;
 import life.qbic.projectmanagement.application.confounding.ConfoundingVariableService.ExperimentReference;
@@ -91,11 +91,18 @@ private DigitalObject generateSampleRegistrationTemplate(String projectId, Strin
     var analytes = experiment.getAnalytes().stream().map(PropertyConversion::toString).toList();
     var analysisMethods = Arrays.stream(AnalysisMethod.values()).map(AnalysisMethod::abbreviation)
         .toList();
-    List<ConfoundingVariableInformation> confoundingVariables = confVariableService.listConfoundingVariablesForExperiment(
+    var confoundingVariables = confVariableService.listConfoundingVariablesForExperiment(
             projectId, new ExperimentReference(experimentId)).stream()
         .map(it -> new ConfoundingVariableInformation(it.id(), it.variableName()))
         .toList();
-    return null;
+    return templateProvider.getTemplate(new SampleRegistration(
+        analysisMethods,
+        conditions,
+        analytes,
+        species,
+        specimen,
+        confoundingVariables
+    ));
   }
 
   private boolean isSupportedMimeType(MimeType mimeType) {
@@ -104,6 +111,7 @@ private boolean isSupportedMimeType(MimeType mimeType) {
 
 
   static class NoSuchExperimentException extends RuntimeException {
+
     public NoSuchExperimentException() {
       super();
     }

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

@@ -11,6 +11,7 @@
 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.api.template.TemplateService;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
@@ -25,6 +26,7 @@ class AsyncProjectServiceImplTest {
   ProjectInformationService projectServiceMock = mock(ProjectInformationService.class);
   SampleInformationService sampleServiceMock = mock(SampleInformationService.class);
   DigitalObjectFactory digitalObjectFactory = mock(DigitalObjectFactory.class);
+  TemplateService templateService = mock(TemplateService.class);
 
   @BeforeEach
   void setUp() {
@@ -41,9 +43,13 @@ void afterEach() {
   @DisplayName("Test that the update completes for ProjectDesign")
   void updateProjectDesignCompletes() {
 
-    AsyncProjectServiceImpl underTest = new AsyncProjectServiceImpl(projectServiceMock,
+    AsyncProjectServiceImpl underTest = new AsyncProjectServiceImpl(
+        projectServiceMock,
         sampleServiceMock,
-        Schedulers.boundedElastic(), digitalObjectFactory);
+        Schedulers.boundedElastic(),
+        digitalObjectFactory,
+        templateService
+    );
 
     String projectId = UUID.randomUUID().toString();
     ProjectDesign requestBody = new ProjectDesign("neq title", "new objective");
@@ -72,9 +78,13 @@ void updateProjectDesignCompletes() {
   @DisplayName("Test that the update retries for ProjectDesign")
   void updateProjectDesignRepeats() {
 
-    AsyncProjectServiceImpl underTest = new AsyncProjectServiceImpl(projectServiceMock,
+    AsyncProjectServiceImpl underTest = new AsyncProjectServiceImpl(
+        projectServiceMock,
         sampleServiceMock,
-        Schedulers.boundedElastic(), digitalObjectFactory);
+        Schedulers.boundedElastic(),
+        digitalObjectFactory,
+        templateService
+    );
 
     String projectId = UUID.randomUUID().toString();
     ProjectDesign requestBody = new ProjectDesign("new title", "new objective");