Replace sample label by sample name (#768)

* rename sample label to sample name

* restart actions

* adapt test to new header

* don't show label if 0 measurements are selected

* add bundles precompile

* restore original gitignore

* Refactor SamplePage UI to current Prototype (#702)

* Remove batch view button from batchregistration component

* Fix sample grid layout

* WIP in progress

* Update column width of batch component and remove unnecessary logic in BatchDetailsComponent

* Update column width of sample grid and remove unnecessary logic in SampleDetailsComponent

* Allow user to filter via organismId while searching for samples in SampleInformationMain

* Update CSS to behave similar to MeasurementMain

* Move search and download logic into samplemain and remove unnecessary logic and components

* Remove unused logger

* Make columns resizable, change sample label to name in spreadsheet and freeze action and id column

* Reset search field value if page is refreshed due to any reason (project switch etc.)

* rename sample ids field

---------

Co-authored-by: wow-such-code <[email protected]>
Co-authored-by: Tobias Koch <[email protected]>
Co-authored-by: Steffengreiner <[email protected]>

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementNGSValidator.java

@@ -118,7 +118,7 @@ public ValidationResult validateUpdate(NGSMeasurementMetadata metadata, ProjectI
 
   public enum NGS_PROPERTY {
     QBIC_SAMPLE_ID("qbic sample id"),
-    SAMPLE_LABEL("sample label"),
+    SAMPLE_LABEL("sample name"),
     ORGANISATION_ID("organisation id"),
     FACILITY("facility"),
     INSTRUMENT("instrument"),

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java

@@ -129,7 +129,7 @@ public ValidationResult validateUpdate(ProteomicsMeasurementMetadata metadata,
 
   public enum PROTEOMICS_PROPERTY {
     QBIC_SAMPLE_ID("qbic sample id"),
-    SAMPLE_LABEL("sample label"),
+    SAMPLE_LABEL("sample name"),
     ORGANISATION_ID("organisation id"),
     FACILITY("facility"),
     INSTRUMENT("instrument"),

project-management/src/test/groovy/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidatorSpec.groovy

@@ -47,7 +47,7 @@ class MeasurementMeasurementProteomicsValidatorSpec extends Specification {
 
     final ProjectInformationService projectInformationService = Mock(ProjectInformationService.class)
 
-    final static List<String> validPXPProperties = Collections.unmodifiableList(["qbic sample id", "sample label", "organisation id", "facility", "instrument",
+    final static List<String> validPXPProperties = Collections.unmodifiableList(["qbic sample id", "sample name", "organisation id", "facility", "instrument",
                                                     "sample pool group", "cycle/fraction name", "digestion method", "digestion enzyme",
                                                     "enrichment method", "injection volume (uL)", "lc column",
                                                     "lcms method", "labeling type", "label", "comment"])

user-interface/src/main/bundles/README.md

@@ -0,0 +1,32 @@
+This directory is automatically generated by Vaadin and contains the pre-compiled 
+frontend files/resources for your project (frontend development bundle).
+
+It should be added to Version Control System and committed, so that other developers
+do not have to compile it again.
+
+Frontend development bundle is automatically updated when needed:
+- an npm/pnpm package is added with @NpmPackage or directly into package.json
+- CSS, JavaScript or TypeScript files are added with @CssImport, @JsModule or @JavaScript
+- Vaadin add-on with front-end customizations is added
+- Custom theme imports/assets added into 'theme.json' file
+- Exported web component is added.
+
+If your project development needs a hot deployment of the frontend changes, 
+you can switch Flow to use Vite development server (default in Vaadin 23.3 and earlier versions):
+- set `vaadin.frontend.hotdeploy=true` in `application.properties`
+- configure `vaadin-maven-plugin`:
+```
+   <configuration>
+       <frontendHotdeploy>true</frontendHotdeploy>
+   </configuration>
+```
+- configure `jetty-maven-plugin`:
+```
+   <configuration>
+       <systemProperties>
+           <vaadin.frontend.hotdeploy>true</vaadin.frontend.hotdeploy>
+       </systemProperties>
+   </configuration>
+```
+
+Read more [about Vaadin development mode](https://vaadin.com/docs/next/configuration/development-mode/#pre-compiled-front-end-bundle-for-faster-start-up).

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementDetailsComponent.java

@@ -198,7 +198,7 @@ private void createNGSMeasurementGrid() {
           expandSpan.addClickListener(event -> measurementPooledSamplesDialog.open());
           return expandSpan;
         })
-        .setHeader("Sample IDs")
+        .setHeader("Samples")
         .setAutoWidth(true);
     ngsMeasurementGrid.addColumn(NGSMeasurement::facility)
         .setHeader("Facility")
@@ -289,7 +289,7 @@ private void createProteomicsGrid() {
           expandSpan.addClickListener(event -> measurementPooledSamplesDialog.open());
           return expandSpan;
         })
-        .setHeader("Sample IDs")
+        .setHeader("Samples")
         .setAutoWidth(true);
     proteomicsMeasurementGrid.addComponentColumn(
             proteomicsMeasurement -> renderOrganisation(proteomicsMeasurement.organisation()))
@@ -525,7 +525,7 @@ private void setPooledProteomicSampleDetails(
       Grid<ProteomicsSpecificMeasurementMetadata> sampleDetailsGrid = new Grid<>();
       sampleDetailsGrid.addColumn(
               metadata -> retrieveSampleById(metadata.measuredSample()).orElseThrow().label())
-          .setHeader("Sample Label")
+          .setHeader("Sample Name")
           .setTooltipGenerator(
               metadata -> retrieveSampleById(metadata.measuredSample()).orElseThrow().label())
           .setAutoWidth(true);
@@ -558,7 +558,7 @@ private void setPooledNgsSampleDetails(
       Grid<NGSSpecificMeasurementMetadata> sampleDetailsGrid = new Grid<>();
       sampleDetailsGrid.addColumn(
               metadata -> retrieveSampleById(metadata.measuredSample()).orElseThrow().label())
-          .setHeader("Sample Label")
+          .setHeader("Sample Name")
           .setTooltipGenerator(
               metadata -> retrieveSampleById(metadata.measuredSample()).orElseThrow().label())
           .setAutoWidth(true);

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMain.java

@@ -536,6 +536,7 @@ private void routeToRawData(ComponentEvent<?> componentEvent) {
   private void setSelectedMeasurementsInfo(int selectedMeasurements) {
       String text = "%s measurements are currently selected.".formatted(
           String.valueOf(selectedMeasurements));
+      measurementsSelectedInfoBox.setVisible(selectedMeasurements > 0);
       measurementsSelectedInfoBox.setText(text);
   }
 }

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/NGSMeasurementContentProvider.java

@@ -224,7 +224,7 @@ enum NGSMeasurementColumns {
     SAMPLEID("QBiC Sample Id", 1,
         true),
     SAMPLELABEL(
-        "Sample label", 2,
+        "Sample Name", 2,
         true),
     POOLGROUP("Sample Pool Group", 3,
         true),

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/ProteomicsMeasurementContentProvider.java

@@ -53,7 +53,7 @@ private static void formatHeader(Row header, CellStyle readOnlyHeader, CellStyle
     h2.setCellStyle(readOnlyHeader);
 
     var h3 = header.createCell(2);
-    h3.setCellValue("Sample label");
+    h3.setCellValue("Sample Name");
     h3.setCellStyle(readOnlyHeader);
 
     var h4 = header.createCell(3);

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java

@@ -31,7 +31,7 @@ public byte[] getContent() {
     }
     TSVBuilder<SamplePreview> tsvBuilder = new TSVBuilder<>(samples);
     tsvBuilder.addColumn("Sample ID", SamplePreview::sampleCode);
-    tsvBuilder.addColumn("Label", SamplePreview::sampleLabel);
+    tsvBuilder.addColumn("Sample Name", SamplePreview::sampleLabel);
     tsvBuilder.addColumn("Organism ID", SamplePreview::organismId);
     tsvBuilder.addColumn("Batch", SamplePreview::batchLabel);
     tsvBuilder.addColumn("Species", sample -> sample.species().getLabel());

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java

@@ -161,7 +161,7 @@ public String getFileName() {
   enum SamplePreviewColumn {
 
     SAMPLE_ID("Sample ID", 0),
-    LABEL("Label", 1),
+    LABEL("Sample Name", 1),
     ORGANISM_ID("Organism ID", 2),
     BATCH("Batch", 3),
     SPECIES("Species", 4),