diff --git a/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementNGSValidator.java b/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementNGSValidator.java index fc8182b4e..b07144d85 100644 --- a/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementNGSValidator.java +++ b/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"), diff --git a/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java b/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java index 35489efab..71e11329e 100644 --- a/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java +++ b/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"), diff --git a/project-management/src/test/groovy/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidatorSpec.groovy b/project-management/src/test/groovy/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidatorSpec.groovy index bbf1a3444..ee7b0f7b9 100644 --- a/project-management/src/test/groovy/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidatorSpec.groovy +++ b/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 validPXPProperties = Collections.unmodifiableList(["qbic sample id", "sample label", "organisation id", "facility", "instrument", + final static List 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"]) diff --git a/user-interface/src/main/bundles/README.md b/user-interface/src/main/bundles/README.md new file mode 100644 index 000000000..581b703fa --- /dev/null +++ b/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`: +``` + + true + +``` +- configure `jetty-maven-plugin`: +``` + + + true + + +``` + +Read more [about Vaadin development mode](https://vaadin.com/docs/next/configuration/development-mode/#pre-compiled-front-end-bundle-for-faster-start-up). \ No newline at end of file diff --git a/user-interface/src/main/bundles/dev.bundle b/user-interface/src/main/bundles/dev.bundle new file mode 100644 index 000000000..5fc763920 Binary files /dev/null and b/user-interface/src/main/bundles/dev.bundle differ diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementDetailsComponent.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementDetailsComponent.java index 400257d68..4c69f4c39 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementDetailsComponent.java +++ b/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 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 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); diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMain.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMain.java index 872ec09ad..70245f85f 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMain.java +++ b/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); } } diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/NGSMeasurementContentProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/NGSMeasurementContentProvider.java index b6cee5b56..cf1a7458f 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/NGSMeasurementContentProvider.java +++ b/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), diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/ProteomicsMeasurementContentProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/ProteomicsMeasurementContentProvider.java index 463a41dfd..8f00e1cdf 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/ProteomicsMeasurementContentProvider.java +++ b/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); diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java index f8158dcbd..ed7e8f886 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java +++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java @@ -31,7 +31,7 @@ public byte[] getContent() { } TSVBuilder 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()); diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java index 308737bc5..10d4efb3d 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java +++ b/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), diff --git a/user-interface/src/main/resources/templates/ngs_measurement_registration_sheet.xlsx b/user-interface/src/main/resources/templates/ngs_measurement_registration_sheet.xlsx index cf66ede87..24bb90dfe 100644 Binary files a/user-interface/src/main/resources/templates/ngs_measurement_registration_sheet.xlsx and b/user-interface/src/main/resources/templates/ngs_measurement_registration_sheet.xlsx differ diff --git a/user-interface/src/main/resources/templates/proteomics_measurement_registration_sheet.xlsx b/user-interface/src/main/resources/templates/proteomics_measurement_registration_sheet.xlsx index 32915b759..fa8406e3b 100644 Binary files a/user-interface/src/main/resources/templates/proteomics_measurement_registration_sheet.xlsx and b/user-interface/src/main/resources/templates/proteomics_measurement_registration_sheet.xlsx differ