[JN-1409] Document library [participant UX]

.github/workflows/java-ci.yml

@@ -96,7 +96,7 @@ jobs:
   # Run DSP App Sec Trivy Scanner on PRs
   dispatch-trivy:
     needs: [ build ]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     if: github.event_name == 'pull_request'
 
@@ -110,7 +110,7 @@ jobs:
 
   dispatch-tag:
     needs: [ build ]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     # Only tag a new release if prior steps were successful and triggering commit is a merge to mainline
     if: success() && github.ref == 'refs/heads/development'

.github/workflows/java-publish.yml

@@ -12,7 +12,7 @@ env:
 
 jobs:
   get-version-tag:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       tag: ${{ steps.tag.outputs.tag }}
     steps:
@@ -29,7 +29,7 @@ jobs:
     permissions:
       contents: 'read'
       id-token:  'write'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       tag: ${{ steps.build-publish.outputs.published-image }}
     steps:
@@ -64,7 +64,7 @@ jobs:
     permissions:
       contents: 'read'
       id-token:  'write'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       tag: ${{ steps.build-publish.outputs.published-image }}
     steps:
@@ -119,7 +119,7 @@ jobs:
       id-token: 'write'
 
   notify-upon-completion:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: always()
     needs: [set-version-in-dev, get-version-tag]
     steps:

.github/workflows/juniper-eng-infra-upload-image.yml

@@ -11,7 +11,7 @@ env:
 
 jobs:
   get-version-tag:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       tag: ${{ steps.tag.outputs.tag }}
     steps:
@@ -28,7 +28,7 @@ jobs:
     permissions:
       contents: 'read'
       id-token:  'write'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       tag: ${{ steps.juniper-eng-build-publish.outputs.published-image }}
     steps:
@@ -50,7 +50,7 @@ jobs:
     permissions:
       contents: 'read'
       id-token:  'write'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       tag: ${{ steps.juniper-eng-build-publish.outputs.published-image }}
     steps:

.github/workflows/require-ticket.yml

@@ -6,7 +6,7 @@ on:
 
 jobs:
   require_ticket:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - name: Check for ticket in PR title
         id: validate

.github/workflows/sonar.yaml

@@ -10,7 +10,7 @@ on:
 jobs:
   sonar-java:
     name: SonarCloud Java
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
         with:
@@ -50,7 +50,7 @@ jobs:
 
   sonar-typescript:
     name: SonarCloud TypeScript
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         subproject: ['ui-admin', 'ui-core', 'ui-participant']

.github/workflows/tag.yml

@@ -10,7 +10,7 @@ on:
 
 jobs:
   tag-job:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       tag: ${{ steps.tag.outputs.tag }}
     steps:

api-participant/src/main/java/bio/terra/pearl/api/participant/controller/file/ParticipantFileController.java

@@ -0,0 +1,122 @@
+package bio.terra.pearl.api.participant.controller.file;
+
+import bio.terra.pearl.api.participant.api.ParticipantFileApi;
+import bio.terra.pearl.api.participant.service.RequestUtilService;
+import bio.terra.pearl.api.participant.service.file.ParticipantFileExtService;
+import bio.terra.pearl.core.model.EnvironmentName;
+import bio.terra.pearl.core.model.file.ParticipantFile;
+import bio.terra.pearl.core.model.participant.ParticipantUser;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import jakarta.servlet.http.HttpServletRequest;
+import java.io.InputStream;
+import java.util.List;
+import org.springframework.core.io.InputStreamResource;
+import org.springframework.core.io.Resource;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.multipart.MultipartFile;
+
+@Controller
+public class ParticipantFileController implements ParticipantFileApi {
+  private final ParticipantFileExtService participantFileExtService;
+  private final HttpServletRequest request;
+  private final ObjectMapper objectMapper;
+  private final RequestUtilService requestUtilService;
+
+  public ParticipantFileController(
+      ParticipantFileExtService participantFileExtService,
+      HttpServletRequest request,
+      ObjectMapper objectMapper,
+      RequestUtilService requestUtilService) {
+    this.participantFileExtService = participantFileExtService;
+    this.request = request;
+    this.objectMapper = objectMapper;
+    this.requestUtilService = requestUtilService;
+  }
+
+  @Override
+  public ResponseEntity<Resource> download(
+      String portalShortcode,
+      String envName,
+      String studyShortcode,
+      String enrolleeShortcode,
+      String fileName) {
+    ParticipantUser participantUser = requestUtilService.requireUser(request);
+
+    ParticipantFile participantFile =
+        participantFileExtService.get(
+            portalShortcode,
+            EnvironmentName.valueOf(envName),
+            participantUser,
+            enrolleeShortcode,
+            fileName);
+
+    InputStream content =
+        participantFileExtService.downloadFile(
+            portalShortcode,
+            EnvironmentName.valueOf(envName),
+            participantUser,
+            enrolleeShortcode,
+            fileName);
+
+    MediaType mediaType;
+    try {
+      mediaType = MediaType.parseMediaType(participantFile.getFileType());
+    } catch (Exception e) {
+      mediaType = MediaType.APPLICATION_OCTET_STREAM;
+    }
+
+    return ResponseEntity.ok().contentType(mediaType).body(new InputStreamResource(content));
+  }
+
+  @Override
+  public ResponseEntity<Object> upload(
+      String portalShortcode,
+      String envName,
+      String studyShortcode,
+      String enrolleeShortcode,
+      MultipartFile participantFile) {
+    ParticipantUser participantUser = requestUtilService.requireUser(request);
+
+    ParticipantFile created =
+        participantFileExtService.uploadFile(
+            portalShortcode,
+            EnvironmentName.valueOf(envName),
+            participantUser,
+            enrolleeShortcode,
+            participantFile);
+
+    return ResponseEntity.ok(created);
+  }
+
+  @Override
+  public ResponseEntity<Object> list(
+      String portalShortcode, String envName, String studyShortcode, String enrolleeShortcode) {
+    ParticipantUser participantUser = requestUtilService.requireUser(request);
+
+    List<ParticipantFile> participantFiles =
+        participantFileExtService.list(
+            portalShortcode, EnvironmentName.valueOf(envName), participantUser, enrolleeShortcode);
+    return ResponseEntity.ok(participantFiles);
+  }
+
+  @Override
+  public ResponseEntity<Object> delete(
+      String portalShortcode,
+      String envName,
+      String studyShortcode,
+      String enrolleeShortcode,
+      String fileName) {
+    ParticipantUser participantUser = requestUtilService.requireUser(request);
+
+    participantFileExtService.delete(
+        portalShortcode,
+        EnvironmentName.valueOf(envName),
+        participantUser,
+        enrolleeShortcode,
+        fileName);
+
+    return ResponseEntity.noContent().build();
+  }
+}

api-participant/src/main/java/bio/terra/pearl/api/participant/service/file/ParticipantFileExtService.java

@@ -0,0 +1,128 @@
+package bio.terra.pearl.api.participant.service.file;
+
+import bio.terra.pearl.api.participant.service.AuthUtilService;
+import bio.terra.pearl.core.model.EnvironmentName;
+import bio.terra.pearl.core.model.file.ParticipantFile;
+import bio.terra.pearl.core.model.participant.Enrollee;
+import bio.terra.pearl.core.model.participant.ParticipantUser;
+import bio.terra.pearl.core.service.exception.NotFoundException;
+import bio.terra.pearl.core.service.file.ParticipantFileService;
+import bio.terra.pearl.core.service.file.backends.FileStorageBackend;
+import bio.terra.pearl.core.service.file.backends.FileStorageBackendProvider;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
+import java.util.Set;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.stereotype.Service;
+import org.springframework.web.multipart.MultipartFile;
+
+@Service
+@Slf4j
+public class ParticipantFileExtService {
+
+  private final ParticipantFileService participantFileService;
+  private final AuthUtilService authUtilService;
+  private final FileStorageBackend fileStorageBackend;
+
+  public ParticipantFileExtService(
+      ParticipantFileService participantFileService,
+      AuthUtilService authUtilService,
+      FileStorageBackendProvider fileStorageBackendProvider) {
+    this.participantFileService = participantFileService;
+    this.authUtilService = authUtilService;
+    this.fileStorageBackend = fileStorageBackendProvider.get();
+  }
+
+  public ParticipantFile get(
+      String portalShortcode,
+      EnvironmentName envName,
+      ParticipantUser participantUser,
+      String enrolleeShortcode,
+      String fileName) {
+    authUtilService.authParticipantToPortal(participantUser.getId(), portalShortcode, envName);
+    Enrollee enrollee =
+        authUtilService.authParticipantUserToEnrollee(participantUser.getId(), enrolleeShortcode);
+    return participantFileService
+        .findByEnrolleeIdAndFileName(enrollee.getId(), fileName)
+        .orElseThrow(() -> new NotFoundException("Could not find file"));
+  }
+
+  public InputStream downloadFile(
+      String portalShortcode,
+      EnvironmentName envName,
+      ParticipantUser participantUser,
+      String enrolleeShortcode,
+      String fileName) {
+    authUtilService.authParticipantToPortal(participantUser.getId(), portalShortcode, envName);
+    Enrollee enrollee =
+        authUtilService.authParticipantUserToEnrollee(participantUser.getId(), enrolleeShortcode);
+    ParticipantFile participantFile =
+        participantFileService
+            .findByEnrolleeIdAndFileName(enrollee.getId(), fileName)
+            .orElseThrow(() -> new NotFoundException("Could not find file"));
+
+    return fileStorageBackend.downloadFile(participantFile.getExternalFileId());
+  }
+
+  public ParticipantFile uploadFile(
+      String portalShortcode,
+      EnvironmentName envName,
+      ParticipantUser participantUser,
+      String enrolleeShortcode,
+      MultipartFile file) {
+    authUtilService.authParticipantToPortal(participantUser.getId(), portalShortcode, envName);
+    Enrollee enrollee =
+        authUtilService.authParticipantUserToEnrollee(participantUser.getId(), enrolleeShortcode);
+
+    try {
+      return participantFileService.uploadFileAndCreate(
+          ParticipantFile.builder()
+              .enrolleeId(enrollee.getId())
+              .fileName(getFileName(file.getOriginalFilename()))
+              .fileType(file.getContentType())
+              .build(),
+          file.getInputStream());
+    } catch (IOException e) {
+      throw new RuntimeException("Error uploading file");
+    }
+  }
+
+  public List<ParticipantFile> list(
+      String portalShortcode,
+      EnvironmentName envName,
+      ParticipantUser participantUser,
+      String enrolleeShortcode) {
+    authUtilService.authParticipantToPortal(participantUser.getId(), portalShortcode, envName);
+    Enrollee enrollee =
+        authUtilService.authParticipantUserToEnrollee(participantUser.getId(), enrolleeShortcode);
+    return participantFileService.findByEnrolleeId(enrollee.getId());
+  }
+
+  // Returns the name of the file without the preceding path
+  public String getFileName(String fileName) {
+    if (fileName == null) {
+      return "";
+    }
+    String[] split = fileName.split("\\[/\\\\]");
+    return split[split.length - 1];
+  }
+
+  public void delete(
+      String portalShortcode,
+      EnvironmentName envName,
+      ParticipantUser participantUser,
+      String enrolleeShortcode,
+      String fileName) {
+    authUtilService.authParticipantToPortal(participantUser.getId(), portalShortcode, envName);
+    Enrollee enrollee =
+        authUtilService.authParticipantUserToEnrollee(participantUser.getId(), enrolleeShortcode);
+    ParticipantFile participantFile =
+        participantFileService
+            .findByEnrolleeIdAndFileName(enrollee.getId(), fileName)
+            .orElseThrow(() -> new NotFoundException("Could not find file"));
+
+    participantFileService.delete(participantFile.getId(), Set.of());
+    fileStorageBackend.deleteFile(participantFile.getExternalFileId());
+  }
+}