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]>
qbicsoftware · Aug 3, 2023 · bb93893 · bb93893
1 parent 8c521f4
commit bb93893
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Showing 14 changed files with 659 additions and 312 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
@@ -1,8 +1,10 @@
 package life.qbic.projectmanagement.application;
 
 import static java.util.Objects.requireNonNull;
+import static life.qbic.logging.service.LoggerFactory.logger;
 
 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;
@@ -18,6 +20,7 @@
 @Service
 public class DeletionService {
 
+  private static final Logger log = logger(DeletionService.class);
   private final ExperimentInformationService experimentInformationService;
 
   private final SampleInformationService sampleInformationService;
@@ -53,6 +56,20 @@ public Result<ExperimentId, ResponseCode> deleteAllExperimentalVariables(Experim
     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
@@ -261,19 +254,52 @@ 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 id the experiment identifier of the experiment the experimental groups are going to be
+   *           deleted.
+   * @since 1.0.0
+   */
+  public void deleteAllExperimentalGroups(ExperimentId id) {
+    Experiment experiment = loadExperimentById(id);
+    experiment.removeAllExperimentalGroups();
+    experimentRepository.update(experiment);
+  }
+
+  /**
+   * Adds experimental groups to an experiment
    *
-   * @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 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 boolean hasExperimentalGroup(ExperimentId experimentId) {
+  public Result<Collection<ExperimentalGroup>, ResponseCode> addExperimentalGroupsToExperiment(
+      ExperimentId experimentId, List<ExperimentalGroupDTO> experimentalGroupDTOS) {
     Experiment experiment = loadExperimentById(experimentId);
-    return !experiment.getExperimentalGroups().isEmpty();
+    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 record ExperimentalGroupDTO(Set<VariableLevel> levels, int sampleSize) {
+  /**
+   * 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/...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/vaadinfrontend/frontend/themes/datamanager/components/card.css b/vaadinfrontend/frontend/themes/datamanager/components/card.css
@@ -85,13 +85,32 @@
   max-width: 300px;
 }
 
-.experimental-group-card-collection {
+.experimental-group-card-collection .header {
+  justify-content: space-between;
+  display: flex;
+}
+
+.experimental-group-card-collection .content {
   display: flex;
   align-content: space-evenly;
   flex-flow: row wrap;
   gap: 1rem;
 }
 
+.experimental-group-card-collection .controls {
+  display: flex;
+  align-content: space-evenly;
+  flex-flow: row wrap;
+  gap: 0.5rem;
+}
+
+.experimental-group-card-collection {
+  display: block;
+  align-content: space-evenly;
+  flex-flow: row wrap;
+  gap: 1rem;
+}
+
 .experimental-group .header {
   display: flex;
   justify-content: space-between;

diff --git a/vaadinfrontend/frontend/themes/datamanager/components/custom.css b/vaadinfrontend/frontend/themes/datamanager/components/custom.css
@@ -33,3 +33,11 @@
 .error-text {
   color: var(--lumo-error-text-color);
 }
+
+vaadin-multi-select-combo-box::part(toggle-button)::before {
+  color: var(--lumo-primary-color);
+}
+
+vaadin-number-field::part(decrease-button), vaadin-number-field::part(increase-button) {
+  color: var(--lumo-primary-color);
+}
diff --git a/vaadinfrontend/frontend/themes/datamanager/components/dialog.css b/vaadinfrontend/frontend/themes/datamanager/components/dialog.css
@@ -2,6 +2,22 @@
   opacity: 0.05;
 }
 
+vaadin-dialog-overlay::part(content) {
+  padding: 1rem 4rem 3rem 4rem;
+}
+
+vaadin-dialog-overlay::part(footer) {
+  padding: 1rem 4rem 1rem 0;
+}
+
+vaadin-dialog-overlay::part(header) {
+  padding: 2rem 1rem 1rem 4rem;
+}
+
+vaadin-dialog-overlay::part(title) {
+  margin-inline-start: 0;
+}
+
 .batch-registration-dialog .stepper {
   width: 100%;
   height: 100%;
@@ -146,36 +162,55 @@ Used by both project creation and experiment creation dialog, thus the unique na
   width: 66%;
 }
 
-.experiment-group-dialog .group-input {
-  width: 100%;
+.experiment-group-dialog .number-field {
+  min-width: 175px;
 }
 
-.experiment-group-dialog .group-input .layout {
-  display: flex;
-  flex-direction: row;
-  gap: var(--lumo-space-m);
+.experiment-group-dialog .experimental-group-entry {
+  display: grid;
+  grid: auto auto auto / 1fr 175px auto;
+  column-gap: 1rem;
+  align-items: baseline;
 }
 
-.experiment-group-dialog .group-input .layout .combo-box {
-  width: 100%;
+.experiment-group-dialog vaadin-icon{
+  cursor: pointer;
+  color: var(--lumo-primary-color);
 }
 
-.experiment-group-dialog .group-input .layout .number-field {
-  width: 150px;
+.experiment-group-dialog .header{
+  font-weight: bold;
 }
 
 .experiment-variable-dialog .content {
-  padding: var(--lumo-space-m);
-  gap: var(--lumo-space-m);
   display: flex;
   flex-direction: column;
 }
 
+.experiment-group-dialog .add-new-group-action {
+  display: flex;
+  column-gap: 1rem;
+  color: var(--lumo-primary-color)
+}
+
+.experiment-group-dialog .content {
+  display: grid;
+  gap: 1.5rem;
+}
+
+.experiment-group-dialog .content .group-collection {
+  display: grid;
+  gap: 1rem;
+}
+
+
+.experiment-group-dialog .add-new-group-action span{
+  cursor: pointer;
+}
+
 .experiment-variable-dialog .content .variables {
   display: flex;
   flex-direction: column;
-  gap: var(--lumo-space-m);
-  padding: var(--lumo-space-m);
 }
 
 .experiment-variable-dialog .content .variables .header {
@@ -185,9 +220,10 @@ Used by both project creation and experiment creation dialog, thus the unique na
 .experiment-variable-dialog .content .row {
   display: flex;
   align-items: center;
-  gap: var(--lumo-space-m);
+  gap: var(--lumo-space-l);
 }
 
 .experiment-variable-dialog .content .row vaadin-icon {
   cursor: pointer;
+  color: var(--lumo-primary-color);
 }
diff --git a/vaadinfrontend/src/main/java/life/qbic/datamanager/views/general/AddEvent.java b/vaadinfrontend/src/main/java/life/qbic/datamanager/views/general/AddEvent.java
@@ -0,0 +1,30 @@
+package life.qbic.datamanager.views.general;
+
+import com.vaadin.flow.component.Component;
+import com.vaadin.flow.component.ComponentEvent;
+import java.io.Serial;
+
+/**
+ * <b>Add event</b>
+ * <p>
+ * Indicates that a user wants to add information to a component
+ *
+ * @since 1.0.0
+ */
+public class AddEvent<T extends Component> extends ComponentEvent<T> {
+
+  @Serial
+  private static final long serialVersionUID = 9114334039868158765L;
+
+  /**
+   * Creates a new event using the given source and indicator whether the event originated from the
+   * client side or the server side.
+   *
+   * @param source     the source component
+   * @param fromClient <code>true</code> if the event originated from the client
+   *                   side, <code>false</code> otherwise
+   */
+  public AddEvent(T source, boolean fromClient) {
+    super(source, fromClient);
+  }
+}
diff --git a/vaadinfrontend/src/main/java/life/qbic/datamanager/views/general/EditEvent.java b/vaadinfrontend/src/main/java/life/qbic/datamanager/views/general/EditEvent.java
@@ -0,0 +1,31 @@
+package life.qbic.datamanager.views.general;
+
+
+import com.vaadin.flow.component.Component;
+import com.vaadin.flow.component.ComponentEvent;
+import java.io.Serial;
+
+/**
+ * <b>Edit Event</b>
+ *
+ * <p>Indicates that a user wants to edit information in a component.</p>
+ *
+ * @since 1.0.0
+ */
+public class EditEvent<T extends Component> extends ComponentEvent<T> {
+
+  @Serial
+  private static final long serialVersionUID = -1033061739347133861L;
+
+  /**
+   * Creates a new event using the given source and indicator whether the event originated from the
+   * client side or the server side.
+   *
+   * @param source     the source component
+   * @param fromClient <code>true</code> if the event originated from the client
+   *                   side, <code>false</code> otherwise
+   */
+  public EditEvent(T source, boolean fromClient) {
+    super(source, fromClient);
+  }
+}