Allows editing of experimental variables (#322)

Introduces editing functionality for experimental variables.

Co-authored-by: Tobias Koch <[email protected]>

commons/src/main/java/life/qbic/application/commons/ApplicationException.java

@@ -16,87 +16,19 @@
  */
 public class ApplicationException extends RuntimeException {
 
-  /**
-   * The error code of an ApplicationException. This code can be used to determine what kind of
-   * error occurred. This allows for the message of the ApplicationException to hold debug
-   * information and avoids string matching to search for the error message.
-   */
-  public enum ErrorCode {
-    GENERAL,
-    INVALID_EXPERIMENTAL_DESIGN,
-    INVALID_PROJECT_OBJECTIVE,
-    INVALID_PROJECT_TITLE,
-    INVALID_PROJECT_CODE,
-    DUPLICATE_PROJECT_CODE,
-    UNDEFINED_VARIABLE_LEVEL,
-    NO_SPECIES_DEFINED,
-    NO_SPECIMEN_DEFINED,
-    NO_ANALYTE_DEFINED,
-    ;
-
-    @Override
-    public String toString() {
-      return this.getClass().getSimpleName() + "." + this.name();
-    }
-
-  }
-
-  /**
-   * Error parameters to be used in error messages.
-   *
-   * @param value an ordered array of parameters
-   */
-  public record ErrorParameters(Object[] value) {
-
-    public static ErrorParameters create() {
-      return new ErrorParameters(new Object[]{});
-    }
-
-    public static ErrorParameters of(Object... parameters) {
-      return new ErrorParameters(parameters);
-    }
-
-    @Override
-    public boolean equals(Object o) {
-      if (this == o) {
-        return true;
-      }
-      if (o == null || getClass() != o.getClass()) {
-        return false;
-      }
-
-      ErrorParameters that = (ErrorParameters) o;
-
-      return Arrays.equals(value, that.value);
-    }
-
-    @Override
-    public int hashCode() {
-      return Arrays.hashCode(value);
-    }
-
-    @Override
-    public String toString() {
-      return new StringJoiner(", ", ErrorParameters.class.getSimpleName() + "[", "]")
-          .add("value=" + Arrays.toString(value))
-          .toString();
-    }
-  }
-
   private final ErrorCode errorCode;
-
   private final ErrorParameters errorParameters;
 
   public ApplicationException() {
-    this(ErrorCode.GENERAL, ErrorParameters.create());
+    this(ErrorCode.GENERAL, ErrorParameters.empty());
   }
 
   public ApplicationException(String message) {
-    this(message, ErrorCode.GENERAL, ErrorParameters.create());
+    this(message, ErrorCode.GENERAL, ErrorParameters.empty());
   }
 
   public ApplicationException(String message, Throwable cause) {
-    this(message, cause, ErrorCode.GENERAL, ErrorParameters.create());
+    this(message, cause, ErrorCode.GENERAL, ErrorParameters.empty());
   }
 
   public ApplicationException(ErrorCode errorCode, ErrorParameters errorParameters) {
@@ -132,14 +64,6 @@ public ApplicationException(String message, Throwable cause, boolean enableSuppr
     this.errorParameters = errorParameters;
   }
 
-  public ErrorCode errorCode() {
-    return errorCode;
-  }
-
-  public ErrorParameters errorParameters() {
-    return errorParameters;
-  }
-
   /**
    * Wraps the provided throwable into an ApplicationException and sets the provided error message.
    * <p>
@@ -185,6 +109,14 @@ public static ApplicationException wrapping(Throwable e) {
     }
   }
 
+  public ErrorCode errorCode() {
+    return errorCode;
+  }
+
+  public ErrorParameters errorParameters() {
+    return errorParameters;
+  }
+
   @Override
   public String toString() {
     return new StringJoiner(", ", ApplicationException.class.getSimpleName() + "[", "]")
@@ -193,4 +125,84 @@ public String toString() {
         .add("errorParameters=" + errorParameters)
         .toString();
   }
+
+  /**
+   * The error code of an ApplicationException. This code can be used to determine what kind of
+   * error occurred. This allows for the message of the ApplicationException to hold debug
+   * information and avoids string matching to search for the error message.
+   */
+  public enum ErrorCode {
+    GENERAL,
+    INVALID_EXPERIMENTAL_DESIGN,
+    INVALID_PROJECT_OBJECTIVE,
+    INVALID_PROJECT_TITLE,
+    INVALID_PROJECT_CODE,
+    DUPLICATE_PROJECT_CODE,
+    UNDEFINED_VARIABLE_LEVEL,
+    NO_SPECIES_DEFINED,
+    NO_SPECIMEN_DEFINED,
+    NO_ANALYTE_DEFINED,
+    ;
+
+    @Override
+    public String toString() {
+      return this.getClass().getSimpleName() + "." + this.name();
+    }
+
+  }
+
+  /**
+   * Error parameters to be used in error messages.
+   *
+   * @param value an ordered array of parameters
+   */
+  public record ErrorParameters(Object[] value) {
+
+    /**
+     * Creates a new instance of an empty error parameter array
+     *
+     * @return
+     * @since 1.0.0
+     */
+    public static ErrorParameters empty() {
+      return new ErrorParameters(new Object[]{});
+    }
+
+    /**
+     * Creates a new instance with the provided error parameters
+     *
+     * @param parameters the error parameters
+     * @return
+     * @since 1.0.0
+     */
+    public static ErrorParameters of(Object... parameters) {
+      return new ErrorParameters(parameters);
+    }
+
+    @Override
+    public boolean equals(Object o) {
+      if (this == o) {
+        return true;
+      }
+      if (o == null || getClass() != o.getClass()) {
+        return false;
+      }
+
+      ErrorParameters that = (ErrorParameters) o;
+
+      return Arrays.equals(value, that.value);
+    }
+
+    @Override
+    public int hashCode() {
+      return Arrays.hashCode(value);
+    }
+
+    @Override
+    public String toString() {
+      return new StringJoiner(", ", ErrorParameters.class.getSimpleName() + "[", "]")
+          .add("value=" + Arrays.toString(value))
+          .toString();
+    }
+  }
 }

database-connector/src/main/java/life/qbic/projectmanagement/experiment/persistence/SampleJpaRepository.java

@@ -70,7 +70,7 @@ public Result<Collection<Sample>, SampleInformationService.ResponseCode> findSam
     } catch (Exception e) {
       log.error(
           "Retrieving Samples for experiment with id " + experimentId.value() + " failed: " + e);
-      return Result.fromError(SampleInformationService.ResponseCode.SAMPLES_NOT_FOUND);
+      return Result.fromError(SampleInformationService.ResponseCode.QUERY_FAILED);
     }
     return Result.fromValue(samples);
   }

projectmanagement/src/main/java/life/qbic/projectmanagement/application/DeletionService.java

@@ -0,0 +1,62 @@
+package life.qbic.projectmanagement.application;
+
+import static java.util.Objects.*;
+
+import java.util.Objects;
+import life.qbic.application.commons.Result;
+import life.qbic.projectmanagement.application.sample.SampleInformationService;
+import life.qbic.projectmanagement.domain.project.experiment.ExperimentId;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+/**
+ * <b>Deletion Service</b>
+ *
+ * <p>Service that orchestrates deletion use cases in the application</p>
+ *
+ * @since 1.0.0
+ */
+@Service
+public class DeletionService {
+
+  private final ExperimentInformationService experimentInformationService;
+
+  private final SampleInformationService sampleInformationService;
+
+  @Autowired
+  public DeletionService(ExperimentInformationService experimentInformationService,
+      SampleInformationService sampleInformationService) {
+    this.experimentInformationService = requireNonNull(experimentInformationService,
+        "experimentInformationService must not be null");
+    this.sampleInformationService = requireNonNull(sampleInformationService,
+        "sampleInformationService must not be null");
+  }
+
+  /**
+   * Deletes all experiment variables and groups in a given experiment.
+   * <p>
+   * Will contain an error, if samples are available and attached to the experiment. In this case,
+   * no variables and groups will be deleted.
+   *
+   * @param id the experiment id
+   * @return a result containing the experiment id on success or an error {@link ResponseCode}
+   * @since 1.0.0
+   */
+  public Result<ExperimentId, ResponseCode> deleteAllExperimentalVariables(ExperimentId id) {
+    var queryResult = sampleInformationService.retrieveSamplesForExperiment(id);
+    if (queryResult.isError()) {
+      return Result.fromError(ResponseCode.QUERY_FAILED);
+    }
+    if (queryResult.isValue() && queryResult.getValue().size() > 0) {
+      return Result.fromError(ResponseCode.SAMPLES_STILL_ATTACHED_TO_EXPERIMENT);
+    }
+    experimentInformationService.deleteAllExperimentalVariables(id);
+    return Result.fromValue(id);
+  }
+
+  public enum ResponseCode {
+    SAMPLES_STILL_ATTACHED_TO_EXPERIMENT, QUERY_FAILED
+  }
+
+
+}

projectmanagement/src/main/java/life/qbic/projectmanagement/application/ExperimentInformationService.java

@@ -100,9 +100,18 @@ public void deleteExperimentGroup(ExperimentId experimentId, long groupId) {
     experimentRepository.update(experiment);
   }
 
-
-  public record ExperimentalGroupDTO(Set<VariableLevel> levels, int sampleSize) {
-
+  /**
+   * <b>ATTENTION!</b> This will remove all existing experimental variables and all defined experimental
+   * groups in a give experiment!
+   *
+   * @param experimentId the experiment reference to delete the experimental variables from
+   * @since 1.0.0
+   */
+  public void deleteAllExperimentalVariables(ExperimentId experimentId) {
+    Experiment experiment = loadExperimentById(experimentId);
+    experiment.removeAllExperimentalGroups();
+    experiment.removeAllExperimentalVariables();
+    experimentRepository.update(experiment);
   }
 
   /**
@@ -196,7 +205,6 @@ public Collection<Analyte> getAnalytesOfExperiment(ExperimentId experimentId) {
     return experiment.getAnalytes();
   }
 
-
   /**
    * Retrieve all species of an experiment.
    *
@@ -244,4 +252,8 @@ public boolean hasExperimentalGroup(ExperimentId experimentId) {
     return !experiment.getExperimentalGroups().isEmpty();
   }
 
+  public record ExperimentalGroupDTO(Set<VariableLevel> levels, int sampleSize) {
+
+  }
+
 }

projectmanagement/src/main/java/life/qbic/projectmanagement/application/sample/SampleInformationService.java

@@ -68,6 +68,6 @@ public int countPreviews(ExperimentId experimentId, String filter) {
   }
 
   public enum ResponseCode {
-    SAMPLES_NOT_FOUND
+    QUERY_FAILED
   }
 }