Merge branch 'development' into feature-642/#642-editing-registered-m…

…etadata-to-add-confounding-variables

project-management/src/main/java/life/qbic/projectmanagement/domain/model/measurement/NGSMeasurement.java

@@ -118,8 +118,8 @@ private static void evaluateMandatoryMetadata(NGSMethodMetadata method)
   }
 
   /**
-   * Creates a new pooled {@link NGSMeasurement} object instance, that describes an NGS measurement entity
-   * with many describing properties about provenance and instrumentation.
+   * Creates a new pooled {@link NGSMeasurement} object instance, that describes an NGS measurement
+   * entity with many describing properties about provenance and instrumentation.
    *
    * @param projectId                   the project id the measurement belongs to
    * @param samplePool                  the sample pool label the measurement represents
@@ -201,6 +201,17 @@ public void updateMethod(NGSMethodMetadata methodMetadata) {
     setMethod(methodMetadata);
   }
 
+  /**
+   * Convenience method to query if the measurement was derived from a single sample.
+   *
+   * @return true, if the measurement was performed on a single sample, else returns false if the
+   * measurement was derived from pooled samples
+   * @since 1.0.0
+   */
+  public boolean isSingleSampleMeasurement() {
+    return specificMetadata.size() <= 1;
+  }
+
 
   public MeasurementCode measurementCode() {
     return this.measurementCode;
@@ -209,6 +220,7 @@ public MeasurementCode measurementCode() {
   public MeasurementId measurementId() {
     return measurementId;
   }
+
   public ProjectId projectId() {
     return projectId;
   }

project-management/src/main/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsMeasurement.java

@@ -192,13 +192,14 @@ public void addSpecificMetadata(ProteomicsSpecificMeasurementMetadata specificMe
   }
 
   /**
-   * Convenience method to query if the measurement was derived from a pooled sample.
+   * Convenience method to query if the measurement was derived from a single Sample.
    *
-   * @return true, if the measurement was performed on a pooled sample, else returns false
+   * @return true, if the measurement was performed on a single Sample, else returns false if the
+   * measurement was derived from pooled samples
    * @since 1.0.0
    */
-  public boolean isPooledSampleMeasurement() {
-    return specificMetadata.size() > 1;
+  public boolean isSingleSampleMeasurement() {
+    return specificMetadata.size() <= 1;
   }
 
   public MeasurementCode measurementCode() {
@@ -253,7 +254,7 @@ public String lcmsMethod() {
   public Instant registrationDate() {
     return registration;
   }
-  
+
   public void updateMethod(ProteomicsMethodMetadata method) {
     setMethodMetadata(method);
     emitUpdatedEvent();
@@ -320,10 +321,6 @@ public int hashCode() {
     return measurementId != null ? measurementId.hashCode() : 0;
   }
 
-  public Optional<String> comment() {
-    return Optional.empty();
-  }
-
   public Optional<String> technicalReplicateName() {
     return Optional.ofNullable(technicalReplicateName);
   }

project-management/src/main/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsSpecificMeasurementMetadata.java

@@ -3,6 +3,7 @@
 import jakarta.persistence.Column;
 import jakarta.persistence.Embeddable;
 import java.util.Objects;
+import java.util.Optional;
 import life.qbic.projectmanagement.domain.model.sample.SampleId;
 
 /**
@@ -80,8 +81,8 @@ public String fractionName() {
     return fractionName;
   }
 
-  public String comment() {
-    return comment;
+  public Optional<String> comment() {
+    return comment.isBlank() ? Optional.empty() : Optional.of(comment);
   }
 
 }

user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementEditTemplate.java

@@ -167,6 +167,7 @@ public byte[] getContent() {
       }
 
       var startIndex = 1; // start in row number 2 with index 1 as the header row has number 1 index 0
+      var helperStopIndex = 1; //stop in row number 2 with index 1 as the header row has number 1 index 0
       int rowIndex = startIndex;
       for (NGSMeasurementEntry measurement : measurements) {
         Row row = getOrCreateRow(sheet, rowIndex);
@@ -195,7 +196,7 @@ public byte[] getContent() {
                 column.columnIndex(),
                 startIndex,
                 column.columnIndex(),
-                DEFAULT_GENERATED_ROW_COUNT - 1,
+                helperStopIndex,
                 helper.exampleValue(),
                 helper.description())
         );

user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementRegisterTemplate.java

@@ -110,6 +110,7 @@ public byte[] getContent() {
       }
 
       var startIndex = 1; // start in row number 2 with index 1 as the header row has number 1 index 0
+      var helperStopIndex = 1; //stop in row number 2 with index 1 as the header row has number 1 index 0
       // make sure to create the visible sheet first
       Sheet hiddenSheet = workbook.createSheet("hidden");
       Name sequencingReadTypeArea = createOptionArea(hiddenSheet,
@@ -128,7 +129,7 @@ public byte[] getContent() {
                 column.columnIndex(),
                 startIndex,
                 column.columnIndex(),
-                DEFAULT_GENERATED_ROW_COUNT - 1,
+                helperStopIndex,
                 helper.exampleValue(),
                 helper.description()));
       }

user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementEditTemplate.java

@@ -172,6 +172,7 @@ public byte[] getContent() {
       }
 
       var startIndex = 1; // start in row number 2 with index 1 skipping the header in the first row
+      var helperStopIndex = 1; //stop in row number 2 with index 1 as the header row has number 1 index 0
       var rowIndex = startIndex;
 
       for (ProteomicsMeasurementEntry pxpEntry : measurements) {
@@ -199,7 +200,7 @@ public byte[] getContent() {
                 column.columnIndex(),
                 startIndex,
                 column.columnIndex(),
-                DEFAULT_GENERATED_ROW_COUNT - 1,
+                helperStopIndex,
                 helper.exampleValue(),
                 helper.description())
         );

user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementRegisterTemplate.java

@@ -123,7 +123,7 @@ public byte[] getContent() {
       }
 
       var startIndex = 1; // start in row number 2 with index 1 skipping the header in the first row
-
+      var helperStopIndex = 1; //stop in row number 2 with index 1 as the header row has number 1 index 0
       // make sure to create the visible sheet first
       Sheet hiddenSheet = workbook.createSheet("hidden");
       Name digestionMethodArea = createOptionArea(hiddenSheet, "Digestion Method",
@@ -141,7 +141,7 @@ public byte[] getContent() {
                 column.columnIndex(),
                 startIndex,
                 column.columnIndex(),
-                DEFAULT_GENERATED_ROW_COUNT - 1,
+                helperStopIndex,
                 helper.exampleValue(),
                 helper.description())
         );

user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchRegistrationTemplate.java

@@ -129,6 +129,7 @@ public static XSSFWorkbook createRegistrationTemplate(List<String> conditions,
     }
 
     var startIndex = 1; //start in the second row with index 1.
+    var helperStopIndex = 1; //stop in the second row with index 1
 
     var hiddenSheet = workbook.createSheet("hidden");
     Name analysisToBePerformedOptions = createOptionArea(hiddenSheet, "Analysis to be performed",
@@ -175,7 +176,7 @@ public static XSSFWorkbook createRegistrationTemplate(List<String> conditions,
               column.columnIndex(),
               startIndex,
               column.columnIndex(),
-              MAX_ROW_INDEX_TO,
+              helperStopIndex,
               helper.exampleValue(),
               helper.description())
       );

user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchUpdateTemplate.java

@@ -131,6 +131,7 @@ public static XSSFWorkbook createUpdateTemplate(List<Sample> samples, List<Strin
     }
 
     var startIndex = 1; //start in the second row with index 1.
+    var helperStopIndex = 1; //stop in the second row with index 1.
     int rowIndex = startIndex;
     for (Sample sample : samples) {
       Row row = getOrCreateRow(sheet, rowIndex);
@@ -187,7 +188,7 @@ public static XSSFWorkbook createUpdateTemplate(List<Sample> samples, List<Strin
               column.columnIndex(),
               startIndex,
               column.columnIndex(),
-              MAX_ROW_INDEX_TO,
+              helperStopIndex,
               helper.exampleValue(),
               helper.description())
       );

user-interface/src/main/java/life/qbic/datamanager/views/demo/ComponentDemo.java

@@ -1,9 +1,11 @@
 package life.qbic.datamanager.views.demo;
 
+import com.vaadin.flow.component.UI;
 import com.vaadin.flow.component.Unit;
 import com.vaadin.flow.component.button.Button;
 import com.vaadin.flow.component.html.Div;
 import com.vaadin.flow.component.icon.VaadinIcon;
+import com.vaadin.flow.component.progressbar.ProgressBar;
 import com.vaadin.flow.component.textfield.TextField;
 import com.vaadin.flow.data.binder.Binder;
 import com.vaadin.flow.data.value.ValueChangeMode;
@@ -18,6 +20,7 @@
 import life.qbic.datamanager.views.general.Card;
 import life.qbic.datamanager.views.general.DetailBox;
 import life.qbic.datamanager.views.general.DetailBox.Header;
+import java.util.concurrent.CompletableFuture;
 import life.qbic.datamanager.views.general.dialog.AppDialog;
 import life.qbic.datamanager.views.general.dialog.DialogBody;
 import life.qbic.datamanager.views.general.dialog.DialogFooter;
@@ -31,6 +34,8 @@
 import life.qbic.datamanager.views.general.dialog.stepper.StepperDisplay;
 import life.qbic.datamanager.views.general.icon.IconFactory;
 import life.qbic.datamanager.views.projects.project.info.SimpleParagraph;
+import life.qbic.datamanager.views.notifications.MessageSourceNotificationFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Profile;
 import org.springframework.lang.NonNull;
 import org.springframework.stereotype.Component;
@@ -53,9 +58,13 @@ public class ComponentDemo extends Div {
   public static final String HEADING_3 = "heading-3";
   public static final String GAP_04 = "gap-04";
   public static final String FLEX_VERTICAL = "flex-vertical";
+  public static final String NORMAL_BODY_TEXT = "normal-body-text";
   Div title = new Div("Data Manager - Component Demo");
+  private final MessageSourceNotificationFactory messageFactory;
 
-  public ComponentDemo() {
+  @Autowired
+  public ComponentDemo(MessageSourceNotificationFactory messageSourceNotificationFactory) {
+    this.messageFactory = Objects.requireNonNull(messageSourceNotificationFactory);
     title.addClassName("heading-1");
     addClassNames("padding-left-right-07", "padding-top-bottom-04");
     add(title);
@@ -66,6 +75,7 @@ public ComponentDemo() {
     add(detailBoxShowCase());
     add(dialogShowCase());
     add(cardShowCase());
+    add(toastShowCase());
   }
 
   private static Div clickableShowCase() {
@@ -101,7 +111,7 @@ private static Div headingShowcase() {
       heading.addClassName("heading-" + i);
       heading.setText("Heading " + i);
       Div description = new Div();
-      description.addClassName("normal-body-text");
+      description.addClassName(NORMAL_BODY_TEXT);
       description.setText("CSS class: %s".formatted(".heading-" + i));
       container.add(heading, description);
     }
@@ -243,6 +253,49 @@ private static Div dialogShowCase(AppDialog dialog, String dialogType) {
     return content;
   }
 
+  private Div toastShowCase() {
+    var title = new Div("Toast it!");
+    title.addClassName(HEADING_2);
+    var description = new Div(
+        "Let's see how toasts work and also how to use them when we want to indicate a background task to the user.");
+    description.addClassName(NORMAL_BODY_TEXT);
+    var content = new Div();
+    content.addClassNames(FLEX_VERTICAL, GAP_04);
+
+    content.add(title);
+    content.add(description);
+
+    var button = new Button("Show Toast");
+
+    content.add(button);
+
+    button.addClickListener(e ->
+    {
+      var progressBar = new ProgressBar();
+      progressBar.setIndeterminate(true);
+      var toast = messageFactory.pendingTaskToast("task.in-progress", new Object[]{"Doing something really heavy here"}, getLocale());
+      var succeededToast = messageFactory.toast("task.finished", new Object[]{"Heavy Task #1"},  getLocale());
+      toast.open();
+      var ui = UI.getCurrent();
+      CompletableFuture.runAsync(() -> {
+        try {
+          Thread.sleep(5000);
+
+        } catch (InterruptedException ex) {
+          Thread.currentThread().interrupt();
+        }
+      }).thenRunAsync(() -> {
+        ui.access(() -> {
+              toast.close();
+              succeededToast.open();
+            }
+        );
+      });
+    });
+    content.add(button);
+    return content;
+  }
+
   private static Div detailBoxShowCase() {
     Div container = new Div();
     container.add(createHeading2("Detail Box"));
@@ -337,7 +390,7 @@ private static Div cardShowCase() {
   private static class BodyFontStyles {
 
     static String[] fontStyles = new String[]{
-        "normal-body-text",
+        NORMAL_BODY_TEXT,
         "small-body-text",
         "extra-small-body-text",
         "field-label-text",
@@ -354,7 +407,8 @@ private static class ExampleUserInput extends Div implements UserInput {
     Binder<StringBean> binder;
 
     ExampleUserInput(String prefill) {
-      var dialogSection = DialogSection.with("User Input Validation", "Try correct and incorrect input values in the following field.");
+      var dialogSection = DialogSection.with("User Input Validation",
+          "Try correct and incorrect input values in the following field.");
       originalValue = prefill;
       var textField = new TextField();
       textField.setLabel("Correct input is 'Riddikulus'");

user-interface/src/main/java/life/qbic/datamanager/views/notifications/MessageSourceNotificationFactory.java

@@ -6,6 +6,7 @@
 import com.vaadin.flow.component.Component;
 import com.vaadin.flow.component.Html;
 import com.vaadin.flow.component.html.Span;
+import com.vaadin.flow.component.progressbar.ProgressBar;
 import com.vaadin.flow.router.RouteParameters;
 import com.vaadin.flow.spring.annotation.SpringComponent;
 import java.time.Duration;
@@ -17,8 +18,8 @@
 import org.springframework.context.NoSuchMessageException;
 
 /**
- * Notifications created by this factory can be shown to the user.
- * There are multiply types of notifications.
+ * Notifications created by this factory can be shown to the user. There are multiply types of
+ * notifications.
  * <ul>
  *   <li>Toast notification</li>
  *   <li>Notification dialog</li>
@@ -33,8 +34,8 @@
 @SpringComponent
 public class MessageSourceNotificationFactory {
 
-  private static final Logger log = logger(MessageSourceNotificationFactory.class);
   public static final Object[] EMPTY_PARAMETERS = new Object[]{};
+  private static final Logger log = logger(MessageSourceNotificationFactory.class);
   private static final String DEFAULT_CONFIRM_TEXT = "Okay";
   private static final NotificationLevel DEFAULT_LEVEL = NotificationLevel.INFO;
   private static final MessageType DEFAULT_MESSAGE_TYPE = MessageType.HTML;
@@ -109,6 +110,34 @@ public Toast routingToast(String key, Object[] messageArgs, Object[] routeArgs,
     return toast.withRouting(linkText, navigationTarget, routeParameters);
   }
 
+  /**
+   * Creates a toast that indicates a pending task. The display duration is set to
+   * {@link Duration#ZERO}, since it is the client's job to close the toast explicitly after the
+   * pending task has finished.
+   * <p>
+   * The following message keys have to be present:
+   * <ul>
+   *   <li>{@code <key>.message.type}
+   *   <li>{@code <key>.message.text}
+   *   <li>{@code <key>.routing.link.text}
+   * </ul>
+   * <p>
+   * For more information please see toast-notifications.properties
+   *
+   * @param key         the key for the messages
+   * @param messageArgs the parameters shown in the message
+   * @param locale      the locale for which to load the message
+   * @return a Toast with loaded content
+   * @see #toast(String, Object[], Locale)
+   */
+  public Toast pendingTaskToast(String key, Object[] messageArgs, Locale locale) {
+    var toast = toast(key, messageArgs, locale);
+    var progressBar = new ProgressBar();
+    progressBar.setIndeterminate(true);
+    toast.setDuration(Duration.ZERO);
+    return toast.add(progressBar);
+  }
+
   /**
    * Creates a dialog notification with the contents found for the message key. This method produces
    * a notification dialog with the link text read from the message properties file.