Update experiment API (#1065)

* Update experiment API

* Update JavaDoc

Co-authored-by: steffengreiner <steffen.greiner@qbic.uni-tuebingen.de>

---------

Co-authored-by: KochTobi <kochtobi@users.noreply.github.com>
Co-authored-by: steffengreiner <steffen.greiner@qbic.uni-tuebingen.de>

Author: KochTobi

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

@@ -35,7 +35,7 @@
 public interface AsyncProjectService {
 
   /**
-   * Submits a project update request and returns a reactive {@link Mono< ProjectUpdateResponse >}
+   * Submits a project update request and returns a reactive {@link Mono<ProjectUpdateResponse>}
    * object immediately.
    * <p>
    * The method implementation must be non-blocking.
@@ -65,7 +65,7 @@ public interface AsyncProjectService {
 
   /**
    * Submits an experiment update request and returns a reactive
-   * {@link Mono< ExperimentUpdateResponse >} object immediately.
+   * {@link Mono<ExperimentUpdateResponse>} object immediately.
    * <p>
    * The method is non-blocking.
    * <p>
@@ -92,7 +92,7 @@ public interface AsyncProjectService {
   Mono<ExperimentUpdateResponse> update(ExperimentUpdateRequest request);
 
   /**
-   * Submits a project creation request and returns a {@link Mono< ProjectCreationResponse >}
+   * Submits a project creation request and returns a {@link Mono<ProjectCreationResponse>}
    * immediately.
    * <p>
    * This implementation must be non-blocking.
@@ -244,8 +244,9 @@ sealed interface ProjectUpdateResponseBody permits FundingInformation, ProjectCo
 
   }
 
-  sealed interface ExperimentUpdateRequestBody permits ConfoundingVariables, ExperimentDescription,
-      ExperimentalGroups, ExperimentalVariables {
+  sealed interface ExperimentUpdateRequestBody permits ConfoundingVariableAdditions,
+      ConfoundingVariableDeletions, ConfoundingVariableUpdates, ExperimentDescription,
+      ExperimentalGroups, ExperimentalVariableAdditions, ExperimentalVariableDeletions {
 
   }
 
@@ -331,11 +332,54 @@ record FundingInformation(String grant, String grantId) implements ProjectUpdate
    * @param unit   the unit of the experimental variable. Can be null if no unit is set
    * @since 1.9.0
    */
-  record ExperimentalVariable(String name, Set<String> levels, @Nullable String unit) {
+  record ExperimentalVariable(Long id, String name, Set<String> levels, @Nullable String unit) {
 
     public ExperimentalVariable {
       levels = Set.copyOf(levels);
     }
+
+    @Override
+    public Set<String> levels() {
+      return Set.copyOf(levels);
+    }
+  }
+
+  /**
+   * Information about variables that should be created
+   *
+   * @param experimentalVariables
+   * @since 1.9.2
+   */
+  record ExperimentalVariableAdditions(List<ExperimentalVariable> experimentalVariables) implements
+      ExperimentUpdateRequestBody {
+
+    public ExperimentalVariableAdditions {
+      experimentalVariables = List.copyOf(experimentalVariables);
+    }
+
+    @Override
+    public List<ExperimentalVariable> experimentalVariables() {
+      return List.copyOf(experimentalVariables);
+    }
+  }
+
+
+  /**
+   * Information about variables that should be deleted
+   *
+   * @param experimentalVariables
+   */
+  record ExperimentalVariableDeletions(List<ExperimentalVariable> experimentalVariables) implements
+      ExperimentUpdateRequestBody {
+
+    public ExperimentalVariableDeletions {
+      experimentalVariables = List.copyOf(experimentalVariables);
+    }
+
+    @Override
+    public List<ExperimentalVariable> experimentalVariables() {
+      return List.copyOf(experimentalVariables);
+    }
   }
 
   /**
@@ -345,22 +389,29 @@ record ExperimentalVariable(String name, Set<String> levels, @Nullable String un
    * @since 1.9.0
    */
   record ExperimentalVariables(List<ExperimentalVariable> experimentalVariables) implements
-      ExperimentUpdateRequestBody, ExperimentUpdateResponseBody {
+      ExperimentUpdateResponseBody {
+
 
     public ExperimentalVariables {
       experimentalVariables = List.copyOf(experimentalVariables);
     }
+
+    @Override
+    public List<ExperimentalVariable> experimentalVariables() {
+      return List.copyOf(experimentalVariables);
+    }
   }
 
   /**
    * A level of an experimental variable
    *
+   * @param variableId   the identifier of the variable
    * @param variableName the name of the variable
    * @param levelValue   the value of the level
    * @param unit         the unit for the value of the level. Can be null if no unit is set
    * @since 1.9.0
    */
-  record VariableLevel(String variableName, String levelValue, @Nullable String unit) {
+  record VariableLevel(Long variableId, String variableName, String levelValue, @Nullable String unit) {
 
   }
 
@@ -421,17 +472,81 @@ record ExperimentDescription(String experimentName, Set<String> species, Set<Str
   }
 
   /**
-   * A list of confounding variable information. Can be used in
+   * A list of confounding variable information for variable addition. Can be used in
+   * {@link #update(ExperimentUpdateRequest)}
+   *
+   * @param confoundingVariables the variable information
+   */
+  record ConfoundingVariableAdditions(
+      List<ConfoundingVariableInformation> confoundingVariables) implements
+      ExperimentUpdateRequestBody {
+
+    public ConfoundingVariableAdditions {
+      confoundingVariables = List.copyOf(confoundingVariables);
+    }
+
+    @Override
+    public List<ConfoundingVariableInformation> confoundingVariables() {
+      return List.copyOf(confoundingVariables);
+    }
+  }
+
+  /**
+   * A list of confounding variable information for variable update. Can be used in
+   * {@link #update(ExperimentUpdateRequest)}
+   *
+   * @param confoundingVariables the variable information
+   */
+  record ConfoundingVariableDeletions(
+      List<ConfoundingVariableInformation> confoundingVariables) implements
+      ExperimentUpdateRequestBody {
+
+    public ConfoundingVariableDeletions {
+      confoundingVariables = List.copyOf(confoundingVariables);
+    }
+
+    @Override
+    public List<ConfoundingVariableInformation> confoundingVariables() {
+      return List.copyOf(confoundingVariables);
+    }
+  }
+
+  /**
+   * A list of confounding variable information for variable deletion. Can be used in
    * {@link #update(ExperimentUpdateRequest)}
    *
    * @param confoundingVariables the variable information
    */
+  record ConfoundingVariableUpdates(
+      List<ConfoundingVariableInformation> confoundingVariables) implements
+      ExperimentUpdateRequestBody {
+
+    public ConfoundingVariableUpdates {
+      confoundingVariables = List.copyOf(confoundingVariables);
+    }
+
+    @Override
+    public List<ConfoundingVariableInformation> confoundingVariables() {
+      return List.copyOf(confoundingVariables);
+    }
+  }
+
+  /**
+   * A list of confounding variable information.
+   *
+   * @param confoundingVariables the variable information
+   */
   record ConfoundingVariables(List<ConfoundingVariableInformation> confoundingVariables) implements
-      ExperimentUpdateRequestBody, ExperimentUpdateResponseBody {
+      ExperimentUpdateResponseBody {
 
     public ConfoundingVariables {
       confoundingVariables = List.copyOf(confoundingVariables);
     }
+
+    @Override
+    public List<ConfoundingVariableInformation> confoundingVariables() {
+      return List.copyOf(confoundingVariables);
+    }
   }
 
 

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

@@ -1,8 +1,8 @@
 package life.qbic.projectmanagement.application.api;
 
 import static life.qbic.projectmanagement.application.authorization.ReactiveSecurityContextUtils.applySecurityContext;
-import static life.qbic.projectmanagement.application.authorization.ReactiveSecurityContextUtils.applySecurityContextMany;
 import static life.qbic.projectmanagement.application.authorization.ReactiveSecurityContextUtils.writeSecurityContext;
+import static life.qbic.projectmanagement.application.authorization.ReactiveSecurityContextUtils.applySecurityContextMany;
 import static life.qbic.projectmanagement.application.authorization.ReactiveSecurityContextUtils.writeSecurityContextMany;
 
 import java.nio.ByteBuffer;
@@ -12,6 +12,7 @@
 import life.qbic.logging.api.Logger;
 import life.qbic.logging.service.LoggerFactory;
 import life.qbic.projectmanagement.application.ProjectInformationService;
+import life.qbic.projectmanagement.application.sample.SampleIdCodeEntry;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
 import life.qbic.projectmanagement.application.sample.SamplePreview;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
@@ -164,17 +165,17 @@ public Mono<Sample> findSample(String projectId, String sampleId) {
   public Mono<ExperimentUpdateResponse> update(
       ExperimentUpdateRequest request) {
     Mono<ExperimentUpdateResponse> response = switch (request.body()) {
-      case ExperimentalVariables experimentalVariables ->
-          updateExperimentalVariables(request.projectId(), request.experimentId(),
-              experimentalVariables);
+
       case ExperimentDescription experimentDescription ->
           updateExperimentDescription(request.projectId(), request.experimentId(),
               experimentDescription);
 
-      case ConfoundingVariables confoundingVariables ->
-          updateConfoundingVariables(request.projectId(), request.experimentId(),
-              confoundingVariables);
       case ExperimentalGroups experimentalGroups -> unknownRequest();
+      case ConfoundingVariableAdditions confoundingVariableAdditions -> unknownRequest();
+      case ConfoundingVariableDeletions confoundingVariableDeletions -> unknownRequest();
+      case ConfoundingVariableUpdates confoundingVariableUpdates -> unknownRequest();
+      case ExperimentalVariableAdditions experimentalVariableAdditions -> unknownRequest();
+      case ExperimentalVariableDeletions experimentalVariableDeletions -> unknownRequest();
     };
 
     SecurityContext securityContext = SecurityContextHolder.getContext();
@@ -187,26 +188,13 @@ private <T> Mono<T> unknownRequest() {
     return Mono.error(() -> new UnknownRequestException("Invalid request body"));
   }
 
-  private Mono<ExperimentUpdateResponse> updateConfoundingVariables(String projectId,
-      String experimentId,
-      ConfoundingVariables confoundingVariables) {
-    //TODO implement
-    throw new RuntimeException("Not implemented");
-  }
-
   private Mono<ExperimentUpdateResponse> updateExperimentDescription(String projectId,
       String experimentId,
       ExperimentDescription experimentDescription) {
     //TODO implement
     throw new RuntimeException("Not implemented");
   }
 
-  private Mono<ExperimentUpdateResponse> updateExperimentalVariables(String projectId,
-      String experimentId, ExperimentalVariables experimentalVariables) {
-    //TODO implement
-    throw new RuntimeException("Not implemented");
-  }
-
 
   private Mono<ProjectUpdateResponse> updateProjectDesign(String projectId, ProjectDesign design,
       String requestId) {