Merge pull request #341 from qbicsoftware/development

* set duration to 3sec and change position (#333) * Introduce editor functionality to show a custom component within the spreadsheet only if user selects the cell. (#335) * WIP increase performance * Fix blinking issue for comboboxes * Add javadoc and fix header row * Fix Dialog loading * Fix rowcount accession and prefilling of cells for validation * Remove unnecessary duplicate unused checks since we already define the value during row addition * WIP fix dialog reload everything else works * Finally fixed! * Remove unused method * replaces red validation borders in spreadsheet by cell highlighting comparable to usual style * Update Javadocs * rename conversion methods * Fix SonarCloud Code Smell * unlock cells after validation * Fix copy past JD fail --------- Co-authored-by: wow-such-code <[email protected]> * Confirm experimental group deletion with the user when editing experimental variables (#334) * clean up code * add double-check confirmation dialog * address inspection warning * extract confirm dialog into new method * Fix typo Co-authored-by: Steffengreiner <[email protected]> * Fix switched JavaDocs Co-authored-by: steffengreiner <[email protected]> --------- Co-authored-by: Steffengreiner <[email protected]> * Inform User that row deletion is not possible if only one row remains in the spreadsheet. (#336) * Ensure user can't delete the last row * Inline method and ensure that the header row is never deleted * Fix typo in notification * Enables multiple experimental group addition (#328) * Save current work progress * Save work * Save work * Enable addition of multiple experimental groups * Reload experimental groups after registration * Enable experimental group edit * Save current work * Save the day * Finish styling * Clean up * More cleanup work * rename methods, extract methods Co-authored-by: steffengreiner <[email protected]> * Add all experimental groups or none Co-authored-by: steffengreiner <[email protected]> * rename method Co-authored-by: steffengreiner <[email protected]> * Exchange group input by existing component * address code review Co-authored-by: steffengreiner <[email protected]> * Add JavaDoc Co-authored-by: steffengreiner <[email protected]> * rename method Co-authored-by: steffengreiner <[email protected]> * address review * address review * remove duplicate css, group css selectors Co-authored-by: steffengreiner <[email protected]> * remove unused css Co-authored-by: steffengreiner <[email protected]> --------- Co-authored-by: Tobias Koch <[email protected]> Co-authored-by: steffengreiner <[email protected]> * Adds prefill option to sample batch registration (#338) * set experiment null on closing of dialog. reload after prefill to make prefill selection after back-button work * Fix reload of cells with prefilled information * Adapt JD * only remove prefill info if it is variable, correctly validate and remove validation errors * Extract reload into singular method * remove unused boolean flags * clear currently selected cell if experiment has changed * implement correct sorting for replicate labels --------- Co-authored-by: Steffengreiner <[email protected]> Co-authored-by: Tobias Koch <[email protected]> * Check if the cells contain valid values before validation (#337) * Check if the cells contain valid values before validation * add bracket missing due to merge --------- Co-authored-by: Tobias Koch <[email protected]> Co-authored-by: wow-such-code <[email protected]> * Batch registration is enqueued propely with jobrunnr (#340) * Fix missing replicate and specify job logging for add sample to batch job * Fix Job scheduling * Allow the user to edit experiment information via dialog (#339) * Provide edit functionality of an experiment * Provide JD and ensure that only valid values land in backend * Remove outdated dialog and propagate experiment creation correctly * Remove unused deletion methods * Remove unused css and update method name * address Code smell * address Code smell * Address code review part 1 * Fix faulty renaming of method * Extract methods from multiline lambda expression during experimentInformationDialog creation * Fix CSS * Propagate Experiment Information to components instead of reloading the page --------- Co-authored-by: Tobias Koch <[email protected]> Co-authored-by: wow-such-code <[email protected]> Co-authored-by: Sven F <[email protected]>
qbicsoftware · Aug 8, 2023 · 5e5e2b3 · 5e5e2b3
2 parents bfe2a5c + 877b1c7
commit 5e5e2b3
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Showing 46 changed files with 1,933 additions and 1,308 deletions.
diff --git a/projectmanagement/src/main/java/life/qbic/projectmanagement/application/DeletionService.java b/projectmanagement/src/main/java/life/qbic/projectmanagement/application/DeletionService.java
@@ -1,9 +1,10 @@
 package life.qbic.projectmanagement.application;
 
-import static java.util.Objects.*;
+import static java.util.Objects.requireNonNull;
+import static life.qbic.logging.service.LoggerFactory.logger;
 
-import java.util.Objects;
 import life.qbic.application.commons.Result;
+import life.qbic.logging.api.Logger;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
 import life.qbic.projectmanagement.domain.project.experiment.ExperimentId;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -19,8 +20,8 @@
 @Service
 public class DeletionService {
 
+  private static final Logger log = logger(DeletionService.class);
   private final ExperimentInformationService experimentInformationService;
-
   private final SampleInformationService sampleInformationService;
 
   @Autowired
@@ -47,13 +48,27 @@ public Result<ExperimentId, ResponseCode> deleteAllExperimentalVariables(Experim
     if (queryResult.isError()) {
       return Result.fromError(ResponseCode.QUERY_FAILED);
     }
-    if (queryResult.isValue() && queryResult.getValue().size() > 0) {
+    if (queryResult.isValue() && !queryResult.getValue().isEmpty()) {
       return Result.fromError(ResponseCode.SAMPLES_STILL_ATTACHED_TO_EXPERIMENT);
     }
     experimentInformationService.deleteAllExperimentalVariables(id);
     return Result.fromValue(id);
   }
 
+  public Result<ExperimentId, ResponseCode> deleteAllExperimentalGroups(ExperimentId id) {
+    var queryResult = sampleInformationService.retrieveSamplesForExperiment(id);
+    if (queryResult.isError()) {
+      log.debug("experiment (%s) converting %s to %s".formatted(id, queryResult.getError(),
+          ResponseCode.QUERY_FAILED));
+      return Result.fromError(ResponseCode.QUERY_FAILED);
+    }
+    if (queryResult.isValue() && !queryResult.getValue().isEmpty()) {
+      return Result.fromError(ResponseCode.SAMPLES_STILL_ATTACHED_TO_EXPERIMENT);
+    }
+    experimentInformationService.deleteAllExperimentalGroups(id);
+    return Result.fromValue(id);
+  }
+
   public enum ResponseCode {
     SAMPLES_STILL_ATTACHED_TO_EXPERIMENT, QUERY_FAILED
   }

diff --git a/...t/src/main/java/life/qbic/projectmanagement/application/ExperimentInformationService.java b/...t/src/main/java/life/qbic/projectmanagement/application/ExperimentInformationService.java
@@ -6,7 +6,6 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
-import java.util.Set;
 import life.qbic.application.commons.ApplicationException;
 import life.qbic.application.commons.Result;
 import life.qbic.logging.api.Logger;
@@ -74,7 +73,7 @@ public Result<ExperimentalGroup, ResponseCode> addExperimentalGroupToExperiment(
 
     Experiment activeExperiment = loadExperimentById(experimentId);
     Result<ExperimentalGroup, ResponseCode> result = activeExperiment.addExperimentalGroup(
-        experimentalGroup.levels(), experimentalGroup.sampleSize());
+        experimentalGroup.levels(), experimentalGroup.replicateCount());
     if (result.isValue()) {
       experimentRepository.update(activeExperiment);
     }
@@ -100,15 +99,9 @@ public List<ExperimentalGroup> experimentalGroupsFor(ExperimentId experimentId)
     return experiment.getExperimentalGroups().stream().toList();
   }
 
-  public void deleteExperimentGroup(ExperimentId experimentId, long groupId) {
-    Experiment experiment = loadExperimentById(experimentId);
-    experiment.removeExperimentGroup(groupId);
-    experimentRepository.update(experiment);
-  }
-
   /**
-   * <b>ATTENTION!</b> This will remove all existing experimental variables and all defined experimental
-   * groups in a give experiment!
+   * <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
@@ -119,6 +112,7 @@ public void deleteAllExperimentalVariables(ExperimentId experimentId) {
     experiment.removeAllExperimentalVariables();
     experimentRepository.update(experiment);
   }
+
   /**
    * Returns a list of experiment for a given project.
    *
@@ -261,19 +255,62 @@ public List<ExperimentalVariable> getVariablesOfExperiment(ExperimentId experime
   }
 
   /**
-   * Checks if the provided ExperimentId contains an experimental Group
+   * Deletes all experimental groups in a given experiment.
+   * <p>
+   * This method does not check if samples are already.
    *
-   * @param experimentId the {@link ExperimentId} of the {@link Experiment} which should be checked
-   *                     if it contains an {@link ExperimentalGroup}
-   * @return a boolean indicating if the experiment contains an {@link ExperimentalGroup}
+   * @param id the experiment identifier of the experiment the experimental groups are going to be
+   *           deleted.
+   * @since 1.0.0
    */
-  public boolean hasExperimentalGroup(ExperimentId experimentId) {
-    Experiment experiment = loadExperimentById(experimentId);
-    return !experiment.getExperimentalGroups().isEmpty();
+  public void deleteAllExperimentalGroups(ExperimentId id) {
+    Experiment experiment = loadExperimentById(id);
+    experiment.removeAllExperimentalGroups();
+    experimentRepository.update(experiment);
   }
 
-  public record ExperimentalGroupDTO(Set<VariableLevel> levels, int sampleSize) {
+  /**
+   * Adds experimental groups to an experiment
+   *
+   * @param experimentId          the experiment to add the groups to
+   * @param experimentalGroupDTOS the group information
+   * @return either the collection of added groups or an appropriate response code
+   */
+  public Result<Collection<ExperimentalGroup>, ResponseCode> addExperimentalGroupsToExperiment(
+      ExperimentId experimentId, List<ExperimentalGroupDTO> experimentalGroupDTOS) {
+    Experiment experiment = loadExperimentById(experimentId);
+    List<ExperimentalGroup> addedGroups = new ArrayList<>();
+    for (ExperimentalGroupDTO experimentalGroupDTO : experimentalGroupDTOS) {
+      Result<ExperimentalGroup, ResponseCode> result = experiment.addExperimentalGroup(
+          experimentalGroupDTO.levels(),
+          experimentalGroupDTO.replicateCount());
+      if (result.isError()) {
+        return Result.fromError(result.getError());
+      } else {
+        addedGroups.add(result.getValue());
+      }
+    }
+    experimentRepository.update(experiment);
+    return Result.fromValue(addedGroups);
+  }
 
+  public void editExperimentInformation(ExperimentId experimentId, String experimentName,
+      List<Species> species, List<Specimen> specimens, List<Analyte> analytes) {
+    Experiment experiment = loadExperimentById(experimentId);
+    experiment.setName(experimentName);
+    experiment.setSpecies(species);
+    experiment.setAnalytes(analytes);
+    experiment.setSpecimens(specimens);
+    experimentRepository.update(experiment);
   }
 
+  /**
+   * Information about an experimental group
+   *
+   * @param levels         the levels in the condition of the group
+   * @param replicateCount the number of biological replicates
+   */
+  public record ExperimentalGroupDTO(Collection<VariableLevel> levels, int replicateCount) {
+
+  }
 }
diff --git a/.../src/main/java/life/qbic/projectmanagement/application/policy/SampleRegisteredPolicy.java b/.../src/main/java/life/qbic/projectmanagement/application/policy/SampleRegisteredPolicy.java
@@ -22,7 +22,7 @@ public class SampleRegisteredPolicy {
   /**
    * Creates an instance of a {@link SampleRegisteredPolicy} object.
    * <p>
-   * All directives will be created an subscribed upon instantiation.
+   * All directives will be created and subscribed upon instantiation.
    *
    * @param addSampleToBatch directive to update the affected sample
    *                         {@link life.qbic.projectmanagement.domain.project.sample.Batch}

diff --git a/.../main/java/life/qbic/projectmanagement/application/policy/directive/AddSampleToBatch.java b/.../main/java/life/qbic/projectmanagement/application/policy/directive/AddSampleToBatch.java
@@ -1,13 +1,17 @@
 package life.qbic.projectmanagement.application.policy.directive;
 
+import static life.qbic.logging.service.LoggerFactory.logger;
+
 import life.qbic.domain.concepts.DomainEvent;
 import life.qbic.domain.concepts.DomainEventSubscriber;
+import life.qbic.logging.api.Logger;
 import life.qbic.projectmanagement.application.batch.BatchRegistrationService;
 import life.qbic.projectmanagement.domain.project.sample.BatchId;
 import life.qbic.projectmanagement.domain.project.sample.SampleId;
 import life.qbic.projectmanagement.domain.project.sample.event.SampleRegistered;
+import org.jobrunr.jobs.annotations.Job;
 import org.jobrunr.scheduling.JobScheduler;
-
+import org.springframework.stereotype.Component;
 /**
  * <b>Directive: Add Sample to Batch</b>
  * <p>
@@ -16,8 +20,10 @@
  *
  * @since 1.0.0
  */
+@Component
 public class AddSampleToBatch implements DomainEventSubscriber<SampleRegistered> {
 
+  private static final Logger log = logger(AddSampleToBatch.class);
   private final BatchRegistrationService batchRegistrationService;
 
   private final JobScheduler jobScheduler;
@@ -38,7 +44,8 @@ public void handleEvent(SampleRegistered event) {
     jobScheduler.enqueue(() -> addSampleToBatch(event.registeredSample(), event.assignedBatch()));
   }
 
-  protected void addSampleToBatch(SampleId sample, BatchId batch) throws RuntimeException {
+  @Job(name = "Add_Sample_To_Batch")
+  public void addSampleToBatch(SampleId sample, BatchId batch) throws RuntimeException {
     batchRegistrationService.addSampleToBatch(sample, batch).onError(responseCode -> {
       throw new RuntimeException(
           String.format("Adding sample %s to batch %s failed, response code was %s ", sample, batch,

diff --git a/...e/qbic/projectmanagement/application/policy/directive/CreateNewSampleStatisticsEntry.java b/...e/qbic/projectmanagement/application/policy/directive/CreateNewSampleStatisticsEntry.java
@@ -12,6 +12,7 @@
 import life.qbic.projectmanagement.domain.project.ProjectId;
 import life.qbic.projectmanagement.domain.project.event.ProjectRegisteredEvent;
 import life.qbic.projectmanagement.domain.project.repository.ProjectRepository;
+import org.jobrunr.jobs.annotations.Job;
 import org.jobrunr.scheduling.JobScheduler;
 import org.springframework.stereotype.Component;
 
@@ -50,6 +51,7 @@ public void handleEvent(ProjectRegisteredEvent event) {
     jobScheduler.enqueue(() -> createSampleStatisticsEntry(event.createdProject()));
   }
 
+  @Job(name = "Create_Sample_Statistics_Entry")
   public void createSampleStatisticsEntry(String projectId) throws RuntimeException {
     var id = ProjectId.parse(projectId);
     if (sampleStatisticsEntryMissing(id)) {

diff --git a/...c/main/java/life/qbic/projectmanagement/application/sample/SampleRegistrationService.java b/...c/main/java/life/qbic/projectmanagement/application/sample/SampleRegistrationService.java
@@ -50,7 +50,7 @@ public Result<Collection<Sample>, ResponseCode> registerSamples(
             Collection<SampleRegistrationRequest> sampleRegistrationRequests, ProjectId projectId) {
         Objects.requireNonNull(sampleRegistrationRequests);
         Objects.requireNonNull(projectId);
-        if (sampleRegistrationRequests.size() < 1) {
+        if (sampleRegistrationRequests.isEmpty()) {
             return Result.fromError(ResponseCode.NO_SAMPLES_DEFINED);
         }
         Map<SampleCode, SampleRegistrationRequest> sampleCodesToRegistrationRequests = new HashMap<>();

diff --git a/.../main/java/life/qbic/projectmanagement/domain/project/experiment/BiologicalReplicate.java b/.../main/java/life/qbic/projectmanagement/domain/project/experiment/BiologicalReplicate.java
@@ -5,6 +5,7 @@
 import jakarta.persistence.Entity;
 import java.io.Serial;
 import java.io.Serializable;
+import java.util.Comparator;
 import java.util.Objects;
 
 /**
@@ -102,4 +103,22 @@ public boolean equals(Object o) {
   public String toString() {
     return "BiologicalReplicate{" + "id=" + id + ", label='" + label + '\'' + '}';
   }
+
+  /**
+   * Provides sorting functionality for labels ending in numbers, e.g. label1 < label2 < label10.
+   * This is based on label length and only works for labels starting with the same letters.
+   */
+  public static class LexicographicLabelComparator implements Comparator<BiologicalReplicate> {
+
+    @Override
+    public int compare(BiologicalReplicate r1, BiologicalReplicate r2) {
+      int l1 = r1.label.length();
+      int l2 = r2.label.length();
+      if (l1 == l2) {
+        return r1.label.compareTo(r2.label);
+      } else {
+        return l1-l2;
+      }
+    }
+  }
 }
diff --git a/...ement/src/main/java/life/qbic/projectmanagement/domain/project/experiment/Experiment.java b/...ement/src/main/java/life/qbic/projectmanagement/domain/project/experiment/Experiment.java
@@ -9,7 +9,9 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
-import java.util.Set;
+import life.qbic.application.commons.ApplicationException;
+import life.qbic.application.commons.ApplicationException.ErrorCode;
+import life.qbic.application.commons.ApplicationException.ErrorParameters;
 import life.qbic.application.commons.Result;
 import life.qbic.projectmanagement.domain.project.experiment.ExperimentalDesign.AddExperimentalGroupResponse.ResponseCode;
 import life.qbic.projectmanagement.domain.project.experiment.exception.ConditionExistsException;
@@ -40,6 +42,7 @@ public class Experiment {
 
   @Embedded
   private ExperimentalDesign experimentalDesign;
+
   @ElementCollection(targetClass = Analyte.class)
   private List<Analyte> analytes = new ArrayList<>();
   @ElementCollection(targetClass = Species.class)
@@ -259,4 +262,50 @@ public List<ExperimentalGroup> getExperimentalGroups() {
   public void removeExperimentGroup(long groupId) {
     experimentalDesign.removeExperimentalGroup(groupId);
   }
+
+  /**
+   * Sets the name of the experiment.
+   */
+  public void setName(String name) {
+    if (name.isEmpty()) {
+      throw new ApplicationException("An Experiment must have a name");
+    }
+    this.name = name;
+  }
+
+  /**
+   * Sets the list of {@link Species}for an experiment.
+   */
+  public void setSpecies(
+      List<Species> species) {
+    if (species == null || species.isEmpty()) {
+      throw new ApplicationException(ErrorCode.NO_SPECIES_DEFINED,
+          ErrorParameters.of(species));
+    }
+    this.species = species;
+  }
+
+  /**
+   * Sets the list of {@link Species} for an experiment.
+   */
+  public void setSpecimens(
+      List<Specimen> specimens) {
+    if (specimens == null || specimens.isEmpty()) {
+      throw new ApplicationException(ErrorCode.NO_SPECIMEN_DEFINED,
+          ErrorParameters.of(specimens));
+    }
+    this.specimens = specimens;
+  }
+
+  /**
+   * Sets the list of {@link Analyte} for an experiment.
+   */
+  public void setAnalytes(
+      List<Analyte> analytes) {
+    if (analytes == null || analytes.isEmpty()) {
+      throw new ApplicationException(ErrorCode.NO_ANALYTE_DEFINED,
+          ErrorParameters.of(analytes));
+    }
+    this.analytes = analytes;
+  }
 }
diff --git a/...c/main/java/life/qbic/projectmanagement/domain/project/experiment/ExperimentalDesign.java b/...c/main/java/life/qbic/projectmanagement/domain/project/experiment/ExperimentalDesign.java
@@ -177,7 +177,7 @@ boolean isConditionDefined(Condition condition) {
   }
 
   Result<VariableName, Exception> addVariable(String variableName, List<ExperimentalValue> levels) {
-    if (levels.size() < 1) {
+    if (levels.isEmpty()) {
       return Result.fromError(new IllegalArgumentException(
           "No levels were defined for " + variableName));
     }
@@ -197,7 +197,7 @@ Result<VariableName, Exception> addVariable(String variableName, List<Experiment
   }
 
     public void removeAllExperimentalVariables() throws IllegalStateException {
-      if (experimentalGroups.size() > 0) {
+      if (!experimentalGroups.isEmpty()) {
         throw new IllegalStateException("Cannot delete experimental variables referenced by an experimental group.");
       }
       this.variables.clear();

diff --git a/projectmanagement/src/main/java/life/qbic/projectmanagement/domain/project/sample/Batch.java b/projectmanagement/src/main/java/life/qbic/projectmanagement/domain/project/sample/Batch.java
@@ -1,9 +1,12 @@
 package life.qbic.projectmanagement.domain.project.sample;
 
+import jakarta.persistence.CollectionTable;
 import jakarta.persistence.Column;
 import jakarta.persistence.ElementCollection;
 import jakarta.persistence.EmbeddedId;
 import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
@@ -21,6 +24,7 @@
 public class Batch {
 
   @EmbeddedId
+  @Column(name = "id")
   private BatchId id;
 
   @Column(name = "batchLabel")
@@ -29,7 +33,8 @@ public class Batch {
   @Column(name = "isPilot")
   private boolean pilot;
 
-  @ElementCollection(targetClass = SampleId.class)
+  @ElementCollection(targetClass = SampleId.class, fetch = FetchType.EAGER)
+  @CollectionTable(name = "sample_batches_sampleid", joinColumns = @JoinColumn(name = "batch_id"))
   private List<SampleId> sampleIds;
 
   protected Batch() {