Added: Resend export files to research environment

CHANGELOG.md

@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
-## [0.0.1 - 2024-07-01]
+## [0.0.1 - 2024-07-08]
 ### Added
 - First version of the project
 - Spring Application
@@ -139,3 +139,4 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 - Research environment project type
 - Upload file to Coder
 - Delete Coder workspace job
+- Resend export files to research environment

src/main/java/de/samply/app/ProjectManagerConst.java

@@ -108,6 +108,8 @@ public class ProjectManagerConst {
     public final static String SET_PROJECT_CONFIGURATION_ACTION = "SET_PROJECT_CONFIGURATION";
     public final static String FETCH_VISIBLE_PROJECT_BRIDGEHEADS_ACTION = "FETCH_VISIBLE_PROJECT_BRIDGEHEADS";
     public final static String FETCH_PROJECT_ROLES_ACTION = "FETCH_PROJECT_ROLES";
+    public final static String SEND_EXPORT_FILES_TO_RESEARCH_ENVIRONMENT_ACTION = "SEND_EXPORT_FILES_TO_RESEARCH_ENVIRONMENT";
+    public final static String ARE_EXPORT_FILES_TRANSFERRED_TO_RESEARCH_ENVIRONMENT_ACTION = "ARE_EXPORT_FILES_TRANSFERRED_TO_RESEARCH_ENVIRONMENT";
 
 
     // REST Services
@@ -176,6 +178,8 @@ public class ProjectManagerConst {
     public final static String SAVE_QUERY_IN_BRIDGEHEAD = "/save-query-in-bridgehead";
     public final static String SAVE_AND_EXECUTE_QUERY_IN_BRIDGEHEAD = "/save-and-execute-query-in-bridgehead";
     public final static String DOWNLOAD_AUTHENTICATION_SCRIPT = "/download-authentication-script";
+    public final static String SEND_EXPORT_FILES_TO_RESEARCH_ENVIRONMENT = "/send-export-files-to-research-environment";
+    public final static String ARE_EXPORT_FILES_TRANSFERRED_TO_RESEARCH_ENVIRONMENT = "/export-files-transferred-to-research-environment";
     public final static String EXISTS_AUTHENTICATION_SCRIPT = "/exists-authentication-script";
     public final static String FETCH_DATASHIELD_STATUS = "/datashield-status";
     public final static String FETCH_PUBLICATIONS = "/publications";

src/main/java/de/samply/app/ProjectManagerController.java

@@ -1046,6 +1046,34 @@ public ResponseEntity<String> saveAndExecuteQueryInBridgehead(
         return convertToResponseEntity(() -> this.projectBridgeheadService.scheduleSendQueryToBridgeheadAndExecute(projectCode, bridgehead));
     }
 
+    @RoleConstraints(projectRoles = {ProjectRole.DEVELOPER, ProjectRole.PILOT, ProjectRole.FINAL})
+    @StateConstraints(projectStates = {ProjectState.DEVELOP, ProjectState.PILOT, ProjectState.FINAL},
+            queryStates = {QueryState.FINISHED})
+    @ProjectConstraints(projectTypes = {ProjectType.RESEARCH_ENVIRONMENT, ProjectType.DATASHIELD})
+    @FrontendSiteModule(site = ProjectManagerConst.PROJECT_VIEW_SITE, module = ProjectManagerConst.EXPORT_MODULE)
+    @FrontendAction(action = ProjectManagerConst.SEND_EXPORT_FILES_TO_RESEARCH_ENVIRONMENT_ACTION)
+    @PostMapping(value = ProjectManagerConst.SEND_EXPORT_FILES_TO_RESEARCH_ENVIRONMENT)
+    public ResponseEntity<String> sendExportFilesToResearchEnvironment(
+            @ProjectCode @RequestParam(name = ProjectManagerConst.PROJECT_CODE) String projectCode,
+            @Bridgehead @RequestParam(name = ProjectManagerConst.BRIDGEHEAD) String bridgehead
+    ) {
+        return convertToResponseEntity(() -> exporterService.transferFileToResearchEnvironment(projectCode, bridgehead));
+    }
+
+    @RoleConstraints(projectRoles = {ProjectRole.DEVELOPER, ProjectRole.PILOT, ProjectRole.FINAL})
+    @StateConstraints(projectStates = {ProjectState.DEVELOP, ProjectState.PILOT, ProjectState.FINAL},
+            queryStates = {QueryState.FINISHED})
+    @ProjectConstraints(projectTypes = {ProjectType.RESEARCH_ENVIRONMENT, ProjectType.DATASHIELD})
+    @FrontendSiteModule(site = ProjectManagerConst.PROJECT_VIEW_SITE, module = ProjectManagerConst.EXPORT_MODULE)
+    @FrontendAction(action = ProjectManagerConst.ARE_EXPORT_FILES_TRANSFERRED_TO_RESEARCH_ENVIRONMENT_ACTION)
+    @PostMapping(value = ProjectManagerConst.ARE_EXPORT_FILES_TRANSFERRED_TO_RESEARCH_ENVIRONMENT)
+    public ResponseEntity<String> isExportFileTransferredToResearchEnvironment(
+            @ProjectCode @RequestParam(name = ProjectManagerConst.PROJECT_CODE) String projectCode,
+            @Bridgehead @RequestParam(name = ProjectManagerConst.BRIDGEHEAD) String bridgehead
+    ) {
+        return convertToResponseEntity(() -> exporterService.isExportFileTransferredToResearchEnvironment(projectCode, bridgehead));
+    }
+
     @RoleConstraints(projectRoles = {ProjectRole.DEVELOPER, ProjectRole.PILOT, ProjectRole.FINAL})
     @StateConstraints(projectStates = {ProjectState.DEVELOP, ProjectState.PILOT, ProjectState.FINAL})
     @ProjectConstraints(projectTypes = {ProjectType.DATASHIELD})

src/main/java/de/samply/coder/CoderJob.java

@@ -13,7 +13,6 @@
 import org.springframework.stereotype.Component;
 
 import java.time.Instant;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 
@@ -49,10 +48,7 @@ public void manageCoderActiveUsers() {
             if (projectCoder.isEmpty()) {
                 this.coderService.createWorkspace(user);
             } else if (!projectCoder.get().isExportTransferred()) {
-                exporterService.transferFileToCoder(user.getProjectBridgehead(), projectCoder.get()).subscribe(result -> {
-                    projectCoder.get().setExportTransferred(true);
-                    this.projectCoderRepository.save(projectCoder.get());
-                });
+                exporterService.transferFileToResearchEnvironment(projectCoder.get());
             }
         });
     }

src/main/java/de/samply/db/repository/ProjectCoderRepository.java

@@ -14,4 +14,6 @@ public interface ProjectCoderRepository extends JpaRepository<ProjectCoder, Long
 
     Optional<ProjectCoder> findByProjectBridgeheadUserAndDeletedAtIsNull(ProjectBridgeheadUser projectBridgeheadUser);
 
+    Optional<ProjectCoder> findByProjectBridgeheadUser_ProjectBridgehead_BridgeheadAndProjectBridgeheadUser_ProjectBridgehead_Project_CodeAndProjectBridgeheadUser_Email(String bridgehead, String projectCode, String email);
+
 }

src/main/java/de/samply/exporter/ExporterService.java

@@ -8,6 +8,7 @@
 import de.samply.db.model.*;
 import de.samply.db.repository.ProjectBridgeheadDataShieldRepository;
 import de.samply.db.repository.ProjectBridgeheadRepository;
+import de.samply.db.repository.ProjectCoderRepository;
 import de.samply.exporter.focus.BeamRequest;
 import de.samply.exporter.focus.BeamService;
 import de.samply.exporter.focus.BeamServiceException;
@@ -16,6 +17,7 @@
 import de.samply.notification.OperationType;
 import de.samply.project.ProjectType;
 import de.samply.query.QueryState;
+import de.samply.security.SessionUser;
 import de.samply.utils.Base64Utils;
 import de.samply.utils.WebClientFactory;
 import jakarta.validation.constraints.NotNull;
@@ -41,11 +43,14 @@
 @Service
 @Slf4j
 public class ExporterService {
-    private final ProjectBridgeheadRepository projectBridgeheadRepository;
+
 
     private final BeamService beamService;
     private final WebClient webClient;
+    private final SessionUser sessionUser;
     private final ProjectBridgeheadDataShieldRepository projectBridgeheadDataShieldRepository;
+    private final ProjectBridgeheadRepository projectBridgeheadRepository;
+    private final ProjectCoderRepository projectCoderRepository;
     private final NotificationService notificationService;
     private final Set<String> exportTemplates;
     private final Set<String> datashieldTemplates;
@@ -73,11 +78,14 @@ public ExporterService(
             @Value(ProjectManagerConst.MAX_TIME_TO_WAIT_FOCUS_TASK_IN_MINUTES_SV) int maxTimeToWaitFocusTaskInMinutes,
             @Value(ProjectManagerConst.CODER_BEAM_ID_SUFFIX_SV) String coderBeamIdSuffix,
             @Value(ProjectManagerConst.CODER_TEST_FILE_BEAM_ID_SV) String testCoderFileBeamId,
+            SessionUser sessionUser,
             BeamService beamService,
             ProjectBridgeheadDataShieldRepository projectBridgeheadDataShieldRepository,
             NotificationService notificationService,
             WebClientFactory webClientFactory,
-            ProjectBridgeheadRepository projectBridgeheadRepository) {
+            ProjectBridgeheadRepository projectBridgeheadRepository,
+            ProjectCoderRepository projectCoderRepository) {
+        this.sessionUser = sessionUser;
         this.beamService = beamService;
         this.projectBridgeheadDataShieldRepository = projectBridgeheadDataShieldRepository;
         this.notificationService = notificationService;
@@ -90,6 +98,7 @@ public ExporterService(
         this.researchEnvironmentTemplates = researchEnvironmentTemplates;
         this.coderBeamIdSuffix = coderBeamIdSuffix;
         this.testCoderFileBeamId = testCoderFileBeamId;
+        this.projectCoderRepository = projectCoderRepository;
         this.webClient = webClientFactory.createWebClient(focusUrl);
         this.exporterApiKey = exporterApiKey;
         this.projectBridgeheadRepository = projectBridgeheadRepository;
@@ -113,18 +122,37 @@ public Mono<ExporterServiceResult> checkExecutionStatus(ProjectBridgehead projec
         return postRequest(projectBridgehead, generateFocusBody(projectBridgehead, taskType), taskType);
     }
 
-    public Mono<ExporterServiceResult> transferFileToCoder(ProjectBridgehead projectBridgehead, ProjectCoder projectCoder) {
-        log.info("Transfering file to Coder for project " + projectBridgehead.getProject().getCode() + " in bridgehead " + projectBridgehead.getBridgehead());
-        return postRequest(projectBridgehead, generateTransferFileBeamRequest(projectBridgehead, projectCoder), TaskType.FILE_TRANSFER);
+    public void transferFileToResearchEnvironment(@NotNull String projectCode, @NotNull String bridgehead) {
+        Optional<ProjectCoder> projectCoder = this.projectCoderRepository.findByProjectBridgeheadUser_ProjectBridgehead_BridgeheadAndProjectBridgeheadUser_ProjectBridgehead_Project_CodeAndProjectBridgeheadUser_Email(bridgehead, projectCode, sessionUser.getEmail());
+        if (projectCoder.isEmpty()) {
+            throw new ExporterServiceException("Project " + projectCode + " for bridgehead " + bridgehead + " for user " + sessionUser.getEmail() + " not found");
+        }
+        transferFileToResearchEnvironment(projectCoder.get());
+    }
+
+    public boolean isExportFileTransferredToResearchEnvironment(@NotNull String projectCode, @NotNull String bridgehead) {
+        Optional<ProjectCoder> projectCoder = this.projectCoderRepository.findByProjectBridgeheadUser_ProjectBridgehead_BridgeheadAndProjectBridgeheadUser_ProjectBridgehead_Project_CodeAndProjectBridgeheadUser_Email(bridgehead, projectCode, sessionUser.getEmail());
+        if (projectCoder.isEmpty()) {
+            throw new ExporterServiceException("Project " + projectCode + " for bridgehead " + bridgehead + " for user " + sessionUser.getEmail() + " not found");
+        }
+        return projectCoder.get().isExportTransferred();
+    }
+
+    public void transferFileToResearchEnvironment(ProjectCoder projectCoder) {
+        log.info("Transfering file to Coder for project " + projectCoder.getProjectBridgeheadUser().getProjectBridgehead().getProject().getCode() + " in bridgehead " + projectCoder.getProjectBridgeheadUser().getProjectBridgehead().getBridgehead());
+        postRequest(projectCoder.getProjectBridgeheadUser().getProjectBridgehead(), generateTransferFileBeamRequest(projectCoder), TaskType.FILE_TRANSFER).subscribe(result -> {
+            projectCoder.setExportTransferred(true);
+            this.projectCoderRepository.save(projectCoder);
+        });
     }
 
-    private BeamRequest generateTransferFileBeamRequest(ProjectBridgehead projectBridgehead, ProjectCoder projectCoder) {
-        return beamService.generateExporterFileTransferBeamRequest(projectBridgehead.getBridgehead(),
-                projectBridgehead.getExporterExecutionId(), fetchCoderFileBeamId(projectCoder));
+    private BeamRequest generateTransferFileBeamRequest(ProjectCoder projectCoder) {
+        return beamService.generateExporterFileTransferBeamRequest(projectCoder.getProjectBridgeheadUser().getProjectBridgehead().getBridgehead(),
+                projectCoder.getProjectBridgeheadUser().getProjectBridgehead().getExporterExecutionId(), fetchCoderFileBeamId(projectCoder));
     }
 
     private String fetchCoderFileBeamId(ProjectCoder projectCoder) {
-        if (testCoderFileBeamId != null){
+        if (testCoderFileBeamId != null) {
             return testCoderFileBeamId;
         }
         return projectCoder.getAppId() + ((coderBeamIdSuffix.startsWith(".")) ? "" : ".") + coderBeamIdSuffix;