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]>
qbicsoftware · Aug 4, 2023 · 021081f · 021081f
1 parent bb93893
commit 021081f
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Showing 6 changed files with 95 additions and 9 deletions.
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/...ain/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java b/...ain/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java
@@ -85,6 +85,8 @@ public class SampleDetailsComponent extends PageArea implements Serializable {
   public final Button registerButton = new Button("Register");
   private final Button metadataDownloadButton = new Button("Download Metadata");
   private final TabSheet sampleExperimentTabSheet = new TabSheet();
+
+  //This should be rebuilt from scratch to avoid reset issues if it was opened before
   private final BatchRegistrationDialog batchRegistrationDialog = new BatchRegistrationDialog();
   private static final Logger log = getLogger(SampleDetailsComponent.class);
   private final transient SampleDetailsComponentHandler sampleDetailsComponentHandler;

diff --git a/...datamanager/views/projects/project/samples/registration/batch/BatchInformationLayout.java b/...datamanager/views/projects/project/samples/registration/batch/BatchInformationLayout.java
@@ -2,6 +2,7 @@
 
 import com.vaadin.flow.component.button.Button;
 import com.vaadin.flow.component.button.ButtonVariant;
+import com.vaadin.flow.component.checkbox.Checkbox;
 import com.vaadin.flow.component.html.Div;
 import com.vaadin.flow.component.html.Span;
 import com.vaadin.flow.component.icon.Icon;
@@ -30,6 +31,7 @@ public class BatchInformationLayout extends Div {
 
   public final TextField batchNameField = new TextField("Batch Name");
   public final RadioButtonGroup<MetadataType> dataTypeSelection = new RadioButtonGroup<>();
+  public final Checkbox prefillSelection = new Checkbox("Prefill complete sample batch");
   public final Button cancelButton = new Button("Cancel");
   public final Button nextButton = new Button("Next");
   public final Select<Experiment> experimentSelect = new Select<>();
@@ -62,7 +64,7 @@ private void initBatchLayout() {
 
   private void initDataTypeLayout() {
     Div dataTypeLayout = new Div();
-    dataTypeLayout.addClassName("data-type-information");
+    dataTypeLayout.addClassName("prefill-information");
     Span dataTypeHeader = new Span("Type of Data");
     dataTypeHeader.addClassName("title");
     dataTypeLayout.add(dataTypeHeader);
@@ -72,6 +74,12 @@ private void initDataTypeLayout() {
     dataTypeLayout.add(dataTypeDescription);
     initDataTypeSelection();
     dataTypeLayout.add(dataTypeSelection);
+
+    Div prefillDescription = new Div();
+    prefillDescription.add(
+        "If you want to register a complete batch (all possible permutations of conditions and replicates), some information can be prefilled.");
+    dataTypeLayout.add(prefillDescription);
+    dataTypeLayout.add(prefillSelection);
     add(dataTypeLayout);
   }
 
@@ -139,6 +147,7 @@ private void reset() {
 
     private void resetChildValues() {
       dataTypeSelection.setValue(MetadataType.TRANSCRIPTOMICS_GENOMICS);
+      prefillSelection.setValue(false);
       experimentSelect.clear();
       batchNameField.clear();
     }

diff --git a/...atamanager/views/projects/project/samples/registration/batch/BatchRegistrationDialog.java b/...atamanager/views/projects/project/samples/registration/batch/BatchRegistrationDialog.java
@@ -139,14 +139,22 @@ private void setTabSelectionListener() {
     }
 
     private void generateSampleRegistrationLayout() {
-      //We only reload the spreadsheet if the user selects an experiment and switches back in the tabSheet to select a different one
+      //we always set the batch name, as it can change without affecting the rest of the spreadsheet
+      sampleSpreadsheetLayout.setBatchName(batchInformationLayout.batchNameField.getValue());
+      //we need to reset the layout, if the experiment has changed
       if (hasExperimentInformationChanged()) {
         sampleSpreadsheetLayout.resetLayout();
       }
-      sampleSpreadsheetLayout.setBatchName(batchInformationLayout.batchNameField.getValue());
-      sampleSpreadsheetLayout.setExperiment(batchInformationLayout.experimentSelect.getValue());
-      sampleSpreadsheetLayout.generateSampleRegistrationSheet(
-          batchInformationLayout.dataTypeSelection.getValue());
+      //We need to build the spreadsheet upon initialization or if the user changed the experiment
+      if (sampleSpreadsheetLayout.getExperiment() == null || hasExperimentInformationChanged()) {
+        sampleSpreadsheetLayout.setExperiment(batchInformationLayout.experimentSelect.getValue());
+        sampleSpreadsheetLayout.generateSampleRegistrationSheet(
+            batchInformationLayout.dataTypeSelection.getValue());
+      }
+      //With the spreadsheet prepared, we can fill the prefilled information in the spreadsheet
+      sampleSpreadsheetLayout.prefillConditionsAndReplicates(
+          batchInformationLayout.prefillSelection.getValue());
+      sampleSpreadsheetLayout.reloadSpreadsheet();
     }
 
     private boolean hasExperimentInformationChanged() {
@@ -200,6 +208,7 @@ public void resetAndClose() {
     }
 
     private void reset() {
+
       batchInformationLayout.reset();
       sampleSpreadsheetLayout.resetLayout();
       tabStepper.setSelectedTab(batchInformationTab);

diff --git a/...ager/views/projects/project/samples/registration/batch/SampleRegistrationSpreadsheet.java b/...ager/views/projects/project/samples/registration/batch/SampleRegistrationSpreadsheet.java
@@ -22,6 +22,7 @@
 import java.util.stream.StreamSupport;
 import life.qbic.application.commons.Result;
 import life.qbic.projectmanagement.domain.project.experiment.BiologicalReplicate;
+import life.qbic.projectmanagement.domain.project.experiment.BiologicalReplicate.LexicographicLabelComparator;
 import life.qbic.projectmanagement.domain.project.experiment.BiologicalReplicateId;
 import life.qbic.projectmanagement.domain.project.experiment.Condition;
 import life.qbic.projectmanagement.domain.project.experiment.Experiment;
@@ -99,8 +100,10 @@ public void addSheetToSpreadsheet(MetadataType metaDataType) {
     setSpreadsheetComponentFactory(dropdownCellFactory);
     //initialise first rows based on known sample size
     addRowsForInitialSamples(numberOfSamples);
+  }
+
+  public void reloadSpreadsheet() {
     refreshAllCellValues();
-    //Only reloads based on first row and first column with index = 1, meaning row and column style has to be refreshed manually
     reloadVisibleCellContents();
   }
 
@@ -477,7 +480,10 @@ public Result<Void, InvalidSpreadsheetInput> areInputsValid() {
         if (SpreadsheetMethods.cellToStringOrNull(cell).isBlank()) {
           invalidCells.add(cell);
         } else {
-          validCells.add(cell);
+          // if a background color was set, but the cell is valid, we need to change the style
+          if(cell.getCellStyle().getFillBackgroundColorColor()!=null) {
+            validCells.add(cell);
+          }
         }
       }
     }
@@ -521,7 +527,7 @@ private void highlightInvalidCells(Collection<Cell> invalidCells) {
       cell.setCellStyle(invalidStyle);
     }
     //We need to refresh the cells so the style change takes effect.
-    this.refreshCells(invalidCells);
+    refreshCells(invalidCells);
   }
 
   /**
@@ -588,6 +594,36 @@ private BiologicalReplicateId retrieveBiologicalReplicateId(String replicateLabe
     return biologicalReplicateId;
   }
 
+  public void prefillConditionsAndReplicates(boolean isPrefilled) {
+    int conditionColIndex = header.indexOf(SamplesheetHeaderName.CONDITION);
+    int replicateColIndex = header.indexOf(SamplesheetHeaderName.BIOLOGICAL_REPLICATE_ID);
+    int rowIndex = 0;
+    Set<String> conditions = conditionsToReplicates.keySet();
+    for(String condition : conditions) {
+      List<String> sortedLabels = conditionsToReplicates.get(condition).stream()
+          .sorted(new LexicographicLabelComparator()).map(BiologicalReplicate::label).toList();
+      for (String label : sortedLabels) {
+        rowIndex++;
+        Cell replicateCell = this.getCell(rowIndex, replicateColIndex);
+        Cell conditionCell = this.getCell(rowIndex, conditionColIndex);
+        if (isPrefilled) {
+          //prefill cells
+          replicateCell.setCellValue(label);
+          conditionCell.setCellValue(condition);
+        } else {
+          //remove prefilled info, except if there is only one condition
+          replicateCell.setCellValue("");
+          String neutralValue = "";
+          if (conditions.size() == 1) {
+            neutralValue = condition;
+          }
+          conditionCell.setCellValue(neutralValue);
+          replicateCell.setCellValue("");
+        }
+      }
+    }
+  }
+
   /**
    * Record containing the provided mandatory specific information for the genomic
    * {@link MetadataType} sheet

diff --git a/...atamanager/views/projects/project/samples/registration/batch/SampleSpreadsheetLayout.java b/...atamanager/views/projects/project/samples/registration/batch/SampleSpreadsheetLayout.java
@@ -112,7 +112,13 @@ public void generateSampleRegistrationSheet(MetadataType metaDataType) {
   }
 
   public void resetLayout() {
+    sampleRegistrationSpreadsheet.getCellSelectionManager().clear();
     sampleInformationLayoutHandler.reset();
+    experiment = null;
+  }
+
+  public void reloadSpreadsheet() {
+    sampleRegistrationSpreadsheet.reloadSpreadsheet();
   }
 
   public void setBatchName(String text) {
@@ -137,6 +143,10 @@ public ExperimentId getExperiment() {
     return experiment;
   }
 
+  public void prefillConditionsAndReplicates(boolean isPrefilled) {
+    sampleRegistrationSpreadsheet.prefillConditionsAndReplicates(isPrefilled);
+  }
+
   private class SampleInformationLayoutHandler implements Serializable {
 
     @Serial
@@ -149,6 +159,7 @@ private void reset() {
     private void resetChildValues() {
       resetInstructions();
       resetSpreadSheet();
+      hideErrorInstructions();
     }
 
     private void resetInstructions() {