Merge branch 'development' into feature/#784-evaluate-technical-feasa…

…bility-of-tib-terminology-service-integration-for-ontology-terms

project-management/src/main/java/life/qbic/projectmanagement/domain/model/experiment/repository/jpa/OntologyClassAttributeConverter.java

@@ -1,6 +1,7 @@
 package life.qbic.projectmanagement.domain.model.experiment.repository.jpa;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import jakarta.persistence.AttributeConverter;
 import jakarta.persistence.Converter;
@@ -11,7 +12,8 @@
 public class OntologyClassAttributeConverter implements
     AttributeConverter<OntologyTerm, String> {
 
-  private static final ObjectMapper objectMapper = new ObjectMapper();
+  private static final ObjectMapper objectMapper = new ObjectMapper().configure(
+      DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
   @Override
   public String convertToDatabaseColumn(OntologyTerm attribute) {

user-interface/frontend/themes/datamanager/components/div.css

@@ -55,6 +55,7 @@
   font-weight: normal;
   color: #2d2d2d;
   font-size: var(--lumo-font-size-s);
+  white-space: pre-line;
 }
 
 .disclaimer .disclaimer-title {

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

@@ -45,6 +45,7 @@
 import life.qbic.datamanager.views.projects.project.measurements.download.ProteomicsMeasurementContentProvider;
 import life.qbic.logging.api.Logger;
 import life.qbic.logging.service.LoggerFactory;
+import life.qbic.projectmanagement.application.ProjectInformationService;
 import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
 import life.qbic.projectmanagement.application.measurement.MeasurementService;
 import life.qbic.projectmanagement.application.measurement.MeasurementService.MeasurementDeletionException;
@@ -97,6 +98,7 @@ public class MeasurementMain extends Main implements BeforeEnterObserver {
   private final NGSMeasurementContentProvider ngsMeasurementContentProvider;
   private final DownloadProvider ngsDownloadProvider;
   private final DownloadProvider proteomicsDownloadProvider;
+  private final ProjectInformationService projectInformationService;
   private transient Context context;
 
   public MeasurementMain(
@@ -105,7 +107,8 @@ public MeasurementMain(
       @Autowired SampleInformationService sampleInformationService,
       @Autowired MeasurementService measurementService,
       @Autowired MeasurementPresenter measurementPresenter,
-      @Autowired MeasurementValidationService measurementValidationService) {
+      @Autowired MeasurementValidationService measurementValidationService,
+      ProjectInformationService projectInformationService) {
     Objects.requireNonNull(measurementTemplateListComponent);
     Objects.requireNonNull(measurementDetailsComponent);
     Objects.requireNonNull(measurementService);
@@ -133,7 +136,8 @@ public MeasurementMain(
     add(measurementDetailsComponent);
 
     measurementDetailsComponent.addListener(
-        selectionChangedEvent -> setSelectedMeasurementsInfo(selectionChangedEvent.getSource().getNumberOfSelectedMeasurements()));
+        selectionChangedEvent -> setSelectedMeasurementsInfo(
+            selectionChangedEvent.getSource().getNumberOfSelectedMeasurements()));
 
     add(ngsDownloadProvider);
     add(proteomicsDownloadProvider);
@@ -143,6 +147,7 @@ public MeasurementMain(
         getClass().getSimpleName(), System.identityHashCode(this),
         measurementTemplateListComponent.getClass().getSimpleName(),
         System.identityHashCode(measurementTemplateListComponent)));
+    this.projectInformationService = projectInformationService;
   }
 
   private static String convertErrorCodeToMessage(MeasurementService.ErrorCode errorCode) {
@@ -203,24 +208,25 @@ private void initSearchFieldAndButtonBar() {
 
   private void onDeleteMeasurementsClicked() {
     Optional<String> tabLabel = measurementDetailsComponent.getSelectedTabName();
-    if(tabLabel.isEmpty()) {
+    if (tabLabel.isEmpty()) {
       return;
     }
     String label = tabLabel.get();
-    if(label.equals("Proteomics")) {
+    if (label.equals("Proteomics")) {
       handlePtxDeletionRequest(measurementDetailsComponent.getSelectedProteomicsMeasurements());
     }
-    if(label.equals("Genomics")) {
+    if (label.equals("Genomics")) {
       handleNGSDeletionRequest(measurementDetailsComponent.getSelectedNGSMeasurements());
     }
   }
 
   private void handlePtxDeletionRequest(Set<ProteomicsMeasurement> measurements) {
-    if(measurements.isEmpty()) {
+    if (measurements.isEmpty()) {
       return;
     }
     MeasurementDeletionConfirmationNotification notification =
-        new MeasurementDeletionConfirmationNotification("Selected proteomics measurements will be deleted", measurements.size());
+        new MeasurementDeletionConfirmationNotification(
+            "Selected proteomics measurements will be deleted", measurements.size());
     notification.open();
     notification.addConfirmListener(event -> {
       deletePtxMeasurements(measurements);
@@ -230,11 +236,12 @@ private void handlePtxDeletionRequest(Set<ProteomicsMeasurement> measurements) {
   }
 
   private void handleNGSDeletionRequest(Set<NGSMeasurement> measurements) {
-    if(measurements.isEmpty()) {
+    if (measurements.isEmpty()) {
       return;
     }
     MeasurementDeletionConfirmationNotification notification =
-        new MeasurementDeletionConfirmationNotification("Selected genomics measurements will be deleted", measurements.size());
+        new MeasurementDeletionConfirmationNotification(
+            "Selected genomics measurements will be deleted", measurements.size());
     notification.open();
     notification.addConfirmListener(event -> {
       deleteNGSMeasurements(measurements);
@@ -245,7 +252,7 @@ private void handleNGSDeletionRequest(Set<NGSMeasurement> measurements) {
 
   private void deleteNGSMeasurements(Set<NGSMeasurement> measurements) {
     Result<Void, MeasurementDeletionException> result = measurementService.deleteNGSMeasurements(
-          context.projectId().orElseThrow(), measurements);
+        context.projectId().orElseThrow(), measurements);
     handleDeletionResults(result);
   }
 
@@ -326,7 +333,7 @@ private void openEditMeasurementDialog() {
 
   private void downloadMetadataForSelectedTab() {
     Optional<String> tabLabel = measurementDetailsComponent.getSelectedTabName();
-    if(tabLabel.isEmpty()) {
+    if (tabLabel.isEmpty()) {
       return;
     }
     switch (tabLabel.get()) {
@@ -356,7 +363,9 @@ private void downloadProteomicsMetadata() {
         .flatMap(Collection::stream)
         .sorted(Comparator.comparing(ProteomicsMeasurementEntry::measurementCode, natOrder)
             .thenComparing(ptx -> ptx.sampleInformation().sampleId(), natOrder)).toList();
-    proteomicsMeasurementContentProvider.setMeasurements(result);
+    proteomicsMeasurementContentProvider.setMeasurements(result,
+        projectInformationService.find(context.projectId().orElseThrow()).orElseThrow()
+            .getProjectCode().value());
     proteomicsDownloadProvider.trigger();
   }
 
@@ -373,7 +382,9 @@ private void downloadNGSMetadata() {
         // sort by measurement codes first, then by sample codes
         .sorted(Comparator.comparing(NGSMeasurementEntry::measurementCode, natOrder)
             .thenComparing(ngs -> ngs.sampleInformation().sampleId(), natOrder)).toList();
-    ngsMeasurementContentProvider.setMeasurements(result);
+    ngsMeasurementContentProvider.setMeasurements(result,
+        projectInformationService.find(context.projectId().orElseThrow()).orElseThrow()
+            .getProjectCode().value());
     ngsDownloadProvider.trigger();
   }
 
@@ -535,13 +546,13 @@ private void routeToRawData(ComponentEvent<?> componentEvent) {
   }
 
   private void setSelectedMeasurementsInfo(int selectedMeasurements) {
-      String text = "%s measurements are currently selected.".formatted(
-          String.valueOf(selectedMeasurements));
+    String text = "%s measurements are currently selected.".formatted(
+        String.valueOf(selectedMeasurements));
     if (selectedMeasurements > 0) {
       measurementsSelectedInfoBox.getStyle().setVisibility(Visibility.INITIAL);
     } else {
       measurementsSelectedInfoBox.getStyle().setVisibility(Visibility.HIDDEN);
     }
-      measurementsSelectedInfoBox.setText(text);
+    measurementsSelectedInfoBox.setText(text);
   }
 }

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

@@ -32,14 +32,16 @@
  */
 public class NGSMeasurementContentProvider implements DownloadContentProvider {
 
-  private static final String FILE_NAME = "ngs_measurements.xlsx";
+  private static final String FILE_NAME_SUFFIX = "ngs_measurements.xlsx";
   private static final Logger log = logger(NGSMeasurementContentProvider.class);
   private static final byte[] DARK_GREY = {119, 119, 119};
   private static final byte[] LIGHT_GREY = {(byte) 220, (byte) 220, (byte) 220};
   private static CellStyle readOnlyCellStyle;
   private static CellStyle readOnlyHeaderStyle;
   private static CellStyle boldStyle;
   private final List<NGSMeasurementEntry> measurements = new LinkedList<>();
+  private static final String DEFAULT_FILE_NAME_PREFIX = "QBiC";
+  private String fileNamePrefix = DEFAULT_FILE_NAME_PREFIX ;
 
   private static void setAutoWidth(Sheet sheet) {
     for (int col = 0; col <= NGSMeasurementColumns.values().length; col++) {
@@ -135,9 +137,10 @@ private static void createMeasurementEntry(NGSMeasurementEntry ngsMeasurementEnt
     setCellStyle(commentCol, NGSMeasurementColumns.COMMENT.readOnly());
   }
 
-  public void setMeasurements(List<NGSMeasurementEntry> measurements) {
+  public void setMeasurements(List<NGSMeasurementEntry> measurements, String fileNamePrefix) {
     this.measurements.clear();
     this.measurements.addAll(measurements);
+    this.fileNamePrefix = fileNamePrefix.trim();
   }
 
   private void defineBoldStyle(Workbook workbook) {
@@ -207,7 +210,7 @@ public byte[] getContent() {
 
   @Override
   public String getFileName() {
-    return FILE_NAME;
+    return String.join("_" , fileNamePrefix, FILE_NAME_SUFFIX);
   }
 
   /**

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

@@ -31,11 +31,13 @@
  */
 public class ProteomicsMeasurementContentProvider implements DownloadContentProvider {
 
-  private static final String FILE_NAME = "proteomics_measurements.xlsx";
+  private static final String FILE_NAME_SUFFIX = "proteomics_measurements.xlsx";
   private static final Logger log = logger(ProteomicsMeasurementContentProvider.class);
   private static final byte[] DARK_GREY = {119, 119, 119};
   private static final byte[] LIGHT_GREY = {(byte) 220, (byte) 220, (byte) 220};
   private final List<ProteomicsMeasurementEntry> measurements = new LinkedList<>();
+  private static final String DEFAULT_FILE_NAME_PREFIX = "QBiC";
+  private String fileNamePrefix = DEFAULT_FILE_NAME_PREFIX;
 
   private static void setAutoWidth(Sheet sheet) {
     for (int col = 0; col <= 18; col++) {
@@ -139,9 +141,10 @@ private static void createMeasurementEntry(ProteomicsMeasurementEntry pxpEntry,
     entry.createCell(18).setCellValue(pxpEntry.comment());
   }
 
-  public void setMeasurements(List<ProteomicsMeasurementEntry> measurements) {
+  public void setMeasurements(List<ProteomicsMeasurementEntry> measurements, String fileNamePrefix) {
     this.measurements.clear();
     this.measurements.addAll(measurements);
+    this.fileNamePrefix = fileNamePrefix;
   }
 
   @Override
@@ -202,6 +205,6 @@ public byte[] getContent() {
 
   @Override
   public String getFileName() {
-    return FILE_NAME;
+    return String.join("_", fileNamePrefix, FILE_NAME_SUFFIX);
   }
 }

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataMain.java

@@ -30,6 +30,7 @@
 import life.qbic.datamanager.views.projects.project.experiments.ExperimentMainLayout;
 import life.qbic.logging.api.Logger;
 import life.qbic.logging.service.LoggerFactory;
+import life.qbic.projectmanagement.application.ProjectInformationService;
 import life.qbic.projectmanagement.application.dataset.RawDataService;
 import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
 import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
@@ -73,21 +74,27 @@ public class RawDataMain extends Main implements BeforeEnterObserver {
   private final Disclaimer registerMeasurementsDisclaimer;
   private final Disclaimer noRawDataRegisteredDisclaimer;
   private final String rawDataSourceURL;
+  private final String documentationUrl;
+  private final ProjectInformationService projectInformationService;
   private transient Context context;
 
   public RawDataMain(@Autowired RawDataDetailsComponent rawDataDetailsComponent,
       @Autowired RawDataDownloadInformationComponent rawDataDownloadInformationComponent,
       @Autowired ExperimentInformationService experimentInformationService,
       @Autowired MeasurementService measurementService,
       @Autowired RawDataService rawDataService,
-      @Value("${server.download.api.measurement.url}") String dataSourceURL) {
+      @Value("${server.download.api.measurement.url}") String dataSourceURL,
+      @Value("${qbic.communication.documentation.url}") String documentationUrl,
+      @Autowired ProjectInformationService projectInformationService) {
+    this.projectInformationService = Objects.requireNonNull(projectInformationService);
     this.rawdataDetailsComponent = Objects.requireNonNull(rawDataDetailsComponent);
     this.rawDataDownloadInformationComponent = Objects.requireNonNull(
         rawDataDownloadInformationComponent);
     this.experimentInformationService = Objects.requireNonNull(experimentInformationService);
     this.measurementService = Objects.requireNonNull(measurementService);
     this.rawDataService = Objects.requireNonNull(rawDataService);
     this.rawDataSourceURL = Objects.requireNonNull(dataSourceURL);
+    this.documentationUrl = Objects.requireNonNull(documentationUrl);
     registerMeasurementsDisclaimer = createNoMeasurementsRegisteredDisclaimer();
     registerMeasurementsDisclaimer.addClassName("no-measurements-registered-disclaimer");
     noRawDataRegisteredDisclaimer = createNoRawDataRegisteredDisclaimer();
@@ -157,7 +164,10 @@ private void handleUrlDownload(ComponentEvent<?> event) {
     var currentExperiment = experimentInformationService.find(
             context.projectId().orElseThrow().value(), context.experimentId().orElseThrow())
         .orElseThrow();
-    urlDownloadFormatter.updateContext(currentExperiment, downloadUrls);
+    var currentProjectCode = projectInformationService.find(context.projectId().orElseThrow())
+        .orElseThrow().getProjectCode().value();
+    urlDownloadFormatter.updateContext(downloadUrls,
+        String.join("_", currentProjectCode, currentExperiment.getName().replace(" ", "_")));
     urlDownload.trigger();
   }
 
@@ -242,14 +252,22 @@ private Disclaimer createNoMeasurementsRegisteredDisclaimer() {
 
   private Disclaimer createNoRawDataRegisteredDisclaimer() {
     Disclaimer noRawDataRegistered = Disclaimer.createWithTitle(
-        "No Raw Data available",
-        "There is currently no raw data registered for the measurements within this experiment",
-        "Register Measurements");
+        "Register your raw data first",
+        "Raw data should be registered before you can view and download raw data files.\n"
+            + "You can refer to our documentation to register raw data for your measurements.",
+        "View Documentation");
     noRawDataRegistered.addDisclaimerConfirmedListener(
-        this::routeToMeasurementCreation);
+        this::routeToRawDataDocumentation);
     return noRawDataRegistered;
   }
 
+  private void routeToRawDataDocumentation(ComponentEvent<?> componentEvent) {
+    if (componentEvent.isFromClient()) {
+      componentEvent.getSource().getUI().ifPresent(ui -> ui.getPage()
+          .open(documentationUrl, "_blank"));
+    }
+  }
+
   private void routeToMeasurementCreation(ComponentEvent<?> componentEvent) {
     if (componentEvent.isFromClient()) {
       String currentExperimentId = context.experimentId().orElseThrow().value();

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataURLContentProvider.java

@@ -17,6 +17,8 @@ public class RawDataURLContentProvider implements DownloadContentProvider {
   private Experiment experiment;
   private List<RawDataURL> rawDataUrls;
   private static final String FILE_SUFFIX = "rawdata_urls.txt";
+  private static final String DEFAULT_FILE_PREFIX = "QBiC";
+  private String fileNamePrefix = DEFAULT_FILE_PREFIX;
 
   @Override
   public byte[] getContent() {
@@ -28,22 +30,14 @@ public byte[] getContent() {
     return textFileBuilder.getRowString().getBytes(StandardCharsets.UTF_8);
   }
 
-  public void updateContext(Experiment experiment, List<RawDataURL> rawDataUrls) {
-    this.experiment = experiment;
+  public void updateContext(List<RawDataURL> rawDataUrls, String fileNamePrefix) {
+    this.fileNamePrefix = fileNamePrefix;
     this.rawDataUrls = rawDataUrls;
   }
 
-  /**
-   * Provides the file name in the following format: CURRENTTIMESTAMP.EXPERIMENTNAME.FILESUFFIX.
-   * CURRENTTIMESTAMP is provided in the format "yyyy-MM-dd"
-   * EXPERIMENTNAME is provided with at most 15 characters and replacing whitespace values with underscore
-   * FILESUFFIX is set to "rawdata_urls.txt"
-   */
   @Override
   public String getFileName() {
-    return String.format("%s.%s.%s",
-        LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd")),
-        fileNamePrefixFromExperimentName(experiment.getName()), FILE_SUFFIX);
+    return String.join("_", fileNamePrefix, FILE_SUFFIX);
   }
 
   private String fileNamePrefixFromExperimentName(String experimentName) {