Working example for sample registration

Author: sven1103

project-management/src/main/java/life/qbic/projectmanagement/application/api/AsyncProjectServiceImpl.java

@@ -31,6 +31,7 @@
 import life.qbic.projectmanagement.domain.model.sample.Sample;
 import life.qbic.projectmanagement.domain.model.sample.SampleId;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.lang.NonNull;
 import org.springframework.security.core.context.SecurityContext;
 import org.springframework.security.core.context.SecurityContextHolder;
@@ -67,7 +68,7 @@ public AsyncProjectServiceImpl(
       @Autowired SampleInformationService sampleInfoService,
       @Autowired Scheduler scheduler,
       @Autowired DigitalObjectFactory digitalObjectFactory,
-      @Autowired TemplateService templateService
+      @Autowired @Qualifier("templateServiceV2") TemplateService templateService
   ) {
     this.projectService = Objects.requireNonNull(projectService);
     this.sampleInfoService = Objects.requireNonNull(sampleInfoService);

project-management/src/main/java/life/qbic/projectmanagement/application/api/template/TemplateService.java

@@ -26,7 +26,7 @@
  *
  * @since <version tag>
  */
-@Service
+@Service("templateServiceV2")
 public class TemplateService {
 
   private final ExperimentInformationService experimentService;
@@ -45,9 +45,8 @@ public TemplateService(ExperimentInformationService experimentService,
   }
 
   /**
-   * Creates a {@link XSSFWorkbook} that contains a template
-   * {@link org.apache.poi.xssf.usermodel.XSSFSheet} that can be used to register one or more sample
-   * batches for an experiment.
+   * Creates a {@link DigitalObject} that contains a template in the provided {@link MimeType} that
+   * can be used to register one or more sample batches for an experiment.
    * <p>
    * The workbook contains two sheets. The first one is for the user input and contains cell with
    * data-validation, e.g. a list of available conditions in the experiment.
@@ -66,7 +65,8 @@ public TemplateService(ExperimentInformationService experimentService,
    *                     template shall be generated
    * @param experimentId the experiment id of the experiment to create the template for
    * @return a pre-configured template workbook
-   * @throws NoSuchExperimentException if no experiment with the provided id can be found.
+   * @throws NoSuchExperimentException    if no experiment with the provided id can be found.
+   * @throws UnsupportedMimeTypeException if there is no support for the requested {@link MimeType}
    * @since 1.5.0
    */
   @PreAuthorize(

user-interface/src/main/java/life/qbic/datamanager/files/export/sample/TemplateService.java

@@ -17,6 +17,7 @@
 import org.apache.poi.ss.usermodel.Workbook;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Service;
 

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

@@ -16,14 +16,15 @@
 import com.vaadin.flow.spring.annotation.SpringComponent;
 import com.vaadin.flow.spring.annotation.UIScope;
 import jakarta.annotation.security.PermitAll;
+import java.io.IOException;
 import java.io.Serial;
 import java.time.LocalDate;
 import java.util.ArrayList;
 import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.TimeUnit;
 import life.qbic.application.commons.ApplicationException;
 import life.qbic.application.commons.FileNameFormatter;
-import life.qbic.datamanager.files.export.download.WorkbookDownloadStreamProvider;
+import life.qbic.datamanager.files.export.download.ByteArrayDownloadStreamProvider;
 import life.qbic.datamanager.files.export.sample.TemplateService;
 import life.qbic.datamanager.views.AppRoutes.ProjectRoutes;
 import life.qbic.datamanager.views.Context;
@@ -44,6 +45,8 @@
 import life.qbic.projectmanagement.application.ProjectInformationService;
 import life.qbic.projectmanagement.application.ProjectOverview;
 import life.qbic.projectmanagement.application.api.AsyncProjectService;
+import life.qbic.projectmanagement.application.api.AsyncProjectService.AccessDeniedException;
+import life.qbic.projectmanagement.application.api.fair.DigitalObject;
 import life.qbic.projectmanagement.application.confounding.ConfoundingVariableService.ExperimentReference;
 import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
@@ -55,8 +58,8 @@
 import life.qbic.projectmanagement.domain.model.project.Project;
 import life.qbic.projectmanagement.domain.model.project.ProjectId;
 import life.qbic.projectmanagement.domain.model.sample.Sample;
-import org.apache.poi.ss.usermodel.Workbook;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.util.MimeType;
 
 /**
  * Sample Information Main Component
@@ -74,6 +77,8 @@ public class SampleInformationMain extends Main implements BeforeEnterObserver {
 
   public static final String PROJECT_ID_ROUTE_PARAMETER = "projectId";
   public static final String EXPERIMENT_ID_ROUTE_PARAMETER = "experimentId";
+  private static final MimeType OPEN_XML = MimeType.valueOf(
+      "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
   @Serial
   private static final long serialVersionUID = 3778218989387044758L;
   private static final Logger log = LoggerFactory.logger(SampleInformationMain.class);
@@ -96,6 +101,7 @@ public class SampleInformationMain extends Main implements BeforeEnterObserver {
   private final transient TemplateService templateService;
   private final transient SampleRegistrationServiceV2 sampleRegistrationServiceV2;
   private final transient AsyncProjectService asyncProjectService;
+  private final MessageSourceNotificationFactory messageSourceNotificationFactory;
   private transient Context context;
 
   public SampleInformationMain(@Autowired ExperimentInformationService experimentInformationService,
@@ -108,7 +114,9 @@ public SampleInformationMain(@Autowired ExperimentInformationService experimentI
       CancelConfirmationDialogFactory cancelConfirmationDialogFactory,
       MessageSourceNotificationFactory notificationFactory,
       SampleValidationService sampleValidationService,
-      TemplateService templateService, SampleRegistrationServiceV2 sampleRegistrationServiceV2) {
+      TemplateService templateService,
+      SampleRegistrationServiceV2 sampleRegistrationServiceV2,
+      MessageSourceNotificationFactory messageSourceNotificationFactory) {
     this.downloadComponent = new DownloadComponent();
 
     this.experimentInformationService = requireNonNull(experimentInformationService,
@@ -155,6 +163,7 @@ public SampleInformationMain(@Autowired ExperimentInformationService experimentI
         sampleDetailsComponent.getClass().getSimpleName(),
         System.identityHashCode(sampleDetailsComponent)));
     add(downloadComponent);
+    this.messageSourceNotificationFactory = messageSourceNotificationFactory;
   }
 
   private static boolean noExperimentGroupsInExperiment(Experiment experiment) {
@@ -195,21 +204,52 @@ private void downloadSampleMetadata() {
         .map(ProjectOverview::projectCode).orElseThrow();
     var experimentName = experimentInformationService.find(projectId.value(), experimentId)
         .map(Experiment::getName).orElseThrow();
-    downloadComponent.trigger(new WorkbookDownloadStreamProvider() {
-      @Override
-      public String getFilename() {
-        return FileNameFormatter.formatWithTimestampedContext(LocalDate.now(), projectCode,
-            experimentName,
-            "sample information",
-            "xlsx");
-      }
 
-      @Override
-      public Workbook getWorkbook() {
-        return templateService.sampleBatchInformationXLSXTemplate(projectId.value(),
-            experimentId.value());
-      }
-    });
+    asyncProjectService.sampleRegistrationTemplate(projectId.value(), experimentId.value(),
+        OPEN_XML).doOnSuccess(resource ->
+        triggerDownload(resource,
+            FileNameFormatter.formatWithTimestampedContext(LocalDate.now(), projectCode,
+                experimentName,
+                "sample information",
+                "xlsx")
+        )).doOnError(this::handleError).subscribe();
+  }
+
+  private void handleError(Throwable throwable) {
+    switch (throwable) {
+      case AccessDeniedException ignored:
+        handleAccessDeniedError();
+        return;
+      default:
+        handleUnexpectedError(throwable);
+    }
+  }
+
+  private void handleUnexpectedError(Throwable throwable) {
+    throw new ApplicationException("We are sorry, an unexpected error occurred.", throwable);
+  }
+
+  private void handleAccessDeniedError() {
+    getUI().ifPresent(ui -> ui.access(() -> messageSourceNotificationFactory.toast("access.denied.message", new Object[]{}, getLocale()).open()));
+  }
+
+  private void triggerDownload(DigitalObject resource, String filename) {
+    getUI().ifPresent(
+        ui -> ui.access(() -> downloadComponent.trigger(new ByteArrayDownloadStreamProvider() {
+          @Override
+          public byte[] getBytes() {
+            try (var content = resource.content()) {
+              return content.readAllBytes();
+            } catch (IOException e) {
+              throw new RuntimeException(e);
+            }
+          }
+
+          @Override
+          public String getFilename() {
+            return filename;
+          }
+        })));
   }
 
   private void onRegisterBatchClicked() {
@@ -225,7 +265,7 @@ private void onRegisterBatchClicked() {
     ProjectOverview projectOverview = projectInformationService.findOverview(projectId)
         .orElseThrow();
     RegisterSampleBatchDialog registerSampleBatchDialog = new RegisterSampleBatchDialog(
-        sampleValidationService, templateService, experimentId.value(),
+        sampleValidationService, asyncProjectService, messageSourceNotificationFactory, experimentId.value(),
         projectId.value(), projectOverview.projectCode());
     UI ui = UI.getCurrent();
     registerSampleBatchDialog.addConfirmListener(event -> {

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/RegisterSampleBatchDialog.java

@@ -13,39 +13,45 @@
 import com.vaadin.flow.component.textfield.TextField;
 import com.vaadin.flow.shared.Registration;
 import java.io.IOException;
+import java.time.LocalDate;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.TimeUnit;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 import life.qbic.application.commons.ApplicationException;
-import life.qbic.datamanager.download.DownloadContentProvider.XLSXDownloadContentProvider;
-import life.qbic.datamanager.download.DownloadProvider;
 import life.qbic.application.commons.FileNameFormatter;
-import life.qbic.datamanager.files.export.sample.TemplateService;
+import life.qbic.datamanager.files.export.download.ByteArrayDownloadStreamProvider;
 import life.qbic.datamanager.files.parsing.MetadataParser.ParsingException;
 import life.qbic.datamanager.files.parsing.ParsingResult;
 import life.qbic.datamanager.files.parsing.SampleInformationExtractor;
 import life.qbic.datamanager.files.parsing.SampleInformationExtractor.SampleInformationForNewSample;
 import life.qbic.datamanager.files.parsing.xlsx.XLSXParser;
 import life.qbic.datamanager.views.general.WizardDialogWindow;
+import life.qbic.datamanager.views.general.download.DownloadComponent;
 import life.qbic.datamanager.views.general.upload.UploadWithDisplay;
 import life.qbic.datamanager.views.general.upload.UploadWithDisplay.FileType;
 import life.qbic.datamanager.views.general.upload.UploadWithDisplay.SucceededEvent;
 import life.qbic.datamanager.views.general.upload.UploadWithDisplay.UploadedData;
+import life.qbic.datamanager.views.notifications.MessageSourceNotificationFactory;
 import life.qbic.logging.api.Logger;
 import life.qbic.logging.service.LoggerFactory;
 import life.qbic.projectmanagement.application.ValidationResult;
 import life.qbic.projectmanagement.application.ValidationResultWithPayload;
+import life.qbic.projectmanagement.application.api.AsyncProjectService;
+import life.qbic.projectmanagement.application.api.AsyncProjectService.AccessDeniedException;
 import life.qbic.projectmanagement.application.api.SampleMetadata;
+import life.qbic.projectmanagement.application.api.fair.DigitalObject;
 import life.qbic.projectmanagement.application.sample.SampleValidationService;
-import org.apache.poi.ss.usermodel.Workbook;
+import org.springframework.util.MimeType;
 
 public class RegisterSampleBatchDialog extends WizardDialogWindow {
-
+  private static final MimeType OPEN_XML = MimeType.valueOf(
+      "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
   private final List<SampleMetadata> validatedSampleMetadata;
   private final TextField batchNameField;
   private static final Logger log = LoggerFactory.logger(RegisterSampleBatchDialog.class);
@@ -55,17 +61,22 @@ public class RegisterSampleBatchDialog extends WizardDialogWindow {
   private final Div succeededView;
   private static final int MAX_FILE_SIZE = 25 * 1024 * 1024;
   private final UploadWithDisplay uploadWithDisplay;
+  private transient final MessageSourceNotificationFactory messageFactory;
+  private final DownloadComponent downloadComponent;
 
   private void setValidatedSampleMetadata(List<SampleMetadata> validatedSampleMetadata) {
     this.validatedSampleMetadata.clear();
     this.validatedSampleMetadata.addAll(validatedSampleMetadata);
   }
 
   public RegisterSampleBatchDialog(SampleValidationService sampleValidationService,
-      TemplateService templateService,
+      AsyncProjectService service, MessageSourceNotificationFactory messageFactory,
       String experimentId,
       String projectId,
       String projectCode) {
+    this.messageFactory = Objects.requireNonNull(messageFactory);
+    this.downloadComponent = new DownloadComponent();
+
 
     setHeaderTitle("Register Sample Batch");
     setConfirmButtonLabel("Register");
@@ -86,7 +97,7 @@ public RegisterSampleBatchDialog(SampleValidationService sampleValidationService
     batchNameField.setErrorMessage("Please provide a name for your batch.");
     batchNameField.setPlaceholder("Please enter a name for your batch");
 
-    Div downloadMetadataSection = setupDownloadMetadataSection(templateService, experimentId,
+    Div downloadMetadataSection = setupDownloadMetadataSection(service, experimentId,
         projectId, projectCode);
 
     validatedSampleMetadata = new ArrayList<>();
@@ -110,7 +121,25 @@ public RegisterSampleBatchDialog(SampleValidationService sampleValidationService
     inProgressView.setVisible(false);
     failedView.setVisible(false);
     succeededView.setVisible(false);
-    add(initialView, inProgressView, failedView, succeededView);
+    add(initialView, inProgressView, failedView, succeededView, downloadComponent);
+  }
+
+  private void handleError(Throwable throwable) {
+    switch (throwable) {
+      case AccessDeniedException ignored:
+        handleAccessDeniedError();
+        return;
+      default:
+        handleUnexpectedError(throwable);
+    }
+  }
+
+  private void handleUnexpectedError(Throwable throwable) {
+    throw new ApplicationException("We are sorry, an unexpected error occurred.", throwable);
+  }
+
+  private void handleAccessDeniedError() {
+    getUI().ifPresent(ui -> ui.access(() -> messageFactory.toast("access.denied.message", new Object[]{}, getLocale()).open()));
   }
 
   private void onUploadSucceeded(SampleValidationService sampleValidationService,
@@ -209,24 +238,36 @@ private void onUploadSucceeded(SampleValidationService sampleValidationService,
 
   }
 
-  private Div setupDownloadMetadataSection(TemplateService templateService, String experimentId,
+  private void triggerDownload(DigitalObject resource, String filename) {
+    getUI().ifPresent(
+        ui -> ui.access(() -> downloadComponent.trigger(new ByteArrayDownloadStreamProvider() {
+          @Override
+          public byte[] getBytes() {
+            try (var content = resource.content()) {
+              return content.readAllBytes();
+            } catch (IOException e) {
+              throw new RuntimeException(e);
+            }
+          }
+
+          @Override
+          public String getFilename() {
+            return filename;
+          }
+        })));
+  }
+
+  private Div setupDownloadMetadataSection(AsyncProjectService service, String experimentId,
       String projectId, String projectCode) {
     Button downloadTemplate = new Button("Download metadata template");
     downloadTemplate.addClassName("download-metadata-button");
     downloadTemplate.addClickListener(buttonClickEvent -> {
-      try (Workbook workbook = templateService.sampleBatchRegistrationXLSXTemplate(
-          projectId,
-          experimentId)) {
-        var filename = FileNameFormatter.formatWithVersion(
-            projectCode + "_sample metadata registration template",
-            1, "xlsx");
-        var downloadProvider = new DownloadProvider(
-            new XLSXDownloadContentProvider(filename, workbook));
-        add(downloadProvider);
-        downloadProvider.trigger();
-      } catch (IOException e) {
-        throw new ApplicationException(e.getMessage(), e);
-      }
+      service.sampleRegistrationTemplate(projectId, experimentId,
+          OPEN_XML).doOnSuccess(resource ->
+          triggerDownload(resource,
+              FileNameFormatter.formatWithTimestampedSimple(LocalDate.now(), projectCode, " sample metadata template",
+                  "xlsx")
+          )).doOnError(this::handleError).subscribe();
     });
     Div text = new Div();
     text.addClassName("download-metadata-text");