[JN-1467] doc request admin ux

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

@@ -0,0 +1,66 @@
+package bio.terra.pearl.api.admin.controller.file;
+
+import bio.terra.pearl.api.admin.api.ParticipantFileApi;
+import bio.terra.pearl.api.admin.service.auth.AuthUtilService;
+import bio.terra.pearl.api.admin.service.auth.context.PortalEnrolleeAuthContext;
+import bio.terra.pearl.api.admin.service.file.ParticipantFileExtService;
+import bio.terra.pearl.core.model.EnvironmentName;
+import bio.terra.pearl.core.model.admin.AdminUser;
+import bio.terra.pearl.core.model.file.ParticipantFile;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import jakarta.servlet.http.HttpServletRequest;
+import java.io.InputStream;
+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;
+
+@Controller
+public class ParticipantFileController implements ParticipantFileApi {
+  private final ParticipantFileExtService participantFileExtService;
+  private final HttpServletRequest request;
+  private final ObjectMapper objectMapper;
+  private final AuthUtilService authUtilService;
+
+  public ParticipantFileController(
+      ParticipantFileExtService participantFileExtService,
+      HttpServletRequest request,
+      ObjectMapper objectMapper,
+      AuthUtilService authUtilService) {
+    this.participantFileExtService = participantFileExtService;
+    this.request = request;
+    this.objectMapper = objectMapper;
+    this.authUtilService = authUtilService;
+  }
+
+  @Override
+  public ResponseEntity<Resource> download(
+      String portalShortcode,
+      String studyShortcode,
+      String envName,
+      String enrolleeShortcode,
+      String fileName) {
+    AdminUser adminUser = authUtilService.requireAdminUser(request);
+    PortalEnrolleeAuthContext authContext =
+        PortalEnrolleeAuthContext.of(
+            adminUser,
+            portalShortcode,
+            studyShortcode,
+            EnvironmentName.valueOf(envName),
+            enrolleeShortcode);
+
+    ParticipantFile participantFile = participantFileExtService.get(authContext, fileName);
+
+    InputStream content = participantFileExtService.downloadFile(authContext, 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));
+  }
+}

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

@@ -0,0 +1,39 @@
+package bio.terra.pearl.api.admin.service.file;
+
+import bio.terra.pearl.api.admin.service.auth.EnforcePortalEnrolleePermission;
+import bio.terra.pearl.api.admin.service.auth.context.PortalEnrolleeAuthContext;
+import bio.terra.pearl.core.model.file.ParticipantFile;
+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.InputStream;
+import org.springframework.stereotype.Service;
+
+@Service
+public class ParticipantFileExtService {
+
+  private final ParticipantFileService participantFileService;
+  private final FileStorageBackend fileStorageBackend;
+
+  public ParticipantFileExtService(
+      ParticipantFileService participantFileService,
+      FileStorageBackendProvider fileStorageBackendProvider) {
+    this.participantFileService = participantFileService;
+    this.fileStorageBackend = fileStorageBackendProvider.get();
+  }
+
+  @EnforcePortalEnrolleePermission(permission = "participant_data_view")
+  public InputStream downloadFile(PortalEnrolleeAuthContext authContext, String fileName) {
+    ParticipantFile participantFile = get(authContext, fileName);
+
+    return fileStorageBackend.downloadFile(participantFile.getExternalFileId());
+  }
+
+  @EnforcePortalEnrolleePermission(permission = "participant_data_view")
+  public ParticipantFile get(PortalEnrolleeAuthContext authContext, String fileName) {
+    return participantFileService
+        .findByEnrolleeIdAndFileName(authContext.getEnrollee().getId(), fileName)
+        .orElseThrow(() -> new NotFoundException("File not found"));
+  }
+}

api-admin/src/main/resources/api/openapi.yml

@@ -2049,6 +2049,27 @@ paths:
                 format: binary
         '500':
           $ref: '#/components/responses/ServerError'
+  /api/portals/v1/{portalShortcode}/studies/{studyShortcode}/env/{envName}/enrollees/{enrolleeShortcode}/file/{fileName}:
+    get:
+      summary: Returns the binary file data for the file of the given shortcode
+      tags: [ participantFile ]
+      operationId: download
+      parameters:
+        - *portalShortcodeParam
+        - *studyShortcodeParam
+        - *envNameParam
+        - *enrolleeShortcodeParam
+        - { name: fileName, in: path, required: true, schema: { type: string } }
+      responses:
+        '200':
+          description: file data. Note that "version" supports both integers and the string 'latest' to get the most recent
+          content:
+            application/*: # any file type
+              schema:
+                type: string
+                format: binary
+        '500':
+          $ref: '#/components/responses/ServerError'
   /api/portals/v1/{portalShortcode}/studies/{studyShortcode}/env/{envName}/enrolleesWithKits:
     get:
       summary: Gets a list of enrollees with tasks and kit requests

core/src/main/java/bio/terra/pearl/core/dao/file/ParticipantFileDao.java

@@ -0,0 +1,63 @@
+package bio.terra.pearl.core.dao.file;
+
+import bio.terra.pearl.core.dao.BaseJdbiDao;
+import bio.terra.pearl.core.model.file.ParticipantFile;
+import org.jdbi.v3.core.Jdbi;
+import org.springframework.stereotype.Component;
+
+import java.util.List;
+import java.util.Optional;
+import java.util.UUID;
+
+@Component
+public class ParticipantFileDao extends BaseJdbiDao<ParticipantFile> {
+    public ParticipantFileDao(Jdbi jdbi) {
+        super(jdbi);
+    }
+
+    @Override
+    protected Class<ParticipantFile> getClazz() {
+        return ParticipantFile.class;
+    }
+
+    public List<ParticipantFile> findBySurveyResponseId(UUID surveyResponseId) {
+        return jdbi.withHandle(handle ->
+                handle.createQuery("""
+                                select file.* from %s file
+                                inner join participant_file_survey_response file_response on file.id = file_response.participant_file_id
+                                where file_response.survey_response_id = :surveyResponseId
+                                """.formatted(tableName))
+                        .bind("surveyResponseId", surveyResponseId)
+                        .mapTo(clazz)
+                        .stream()
+                        .toList()
+        );
+    }
+
+    public List<ParticipantFile> findByEnrolleeId(UUID enrolleeId) {
+        return findAllByProperty("enrollee_id", enrolleeId);
+    }
+
+    public void deleteByEnrolleeId(UUID enrolleeId) {
+        deleteByProperty("enrollee_id", enrolleeId);
+    }
+
+    public Optional<ParticipantFile> findByEnrolleeIdAndFileName(UUID enrolleeId, String fileName) {
+        return findByTwoProperties("enrollee_id", enrolleeId, "file_name", fileName);
+    }
+
+    public List<ParticipantFile> findAllByFileNameForEnrollee(UUID enrolleeId, List<String> participantFileNames) {
+        return jdbi.withHandle(handle ->
+                handle.createQuery("""
+                                select * from %s
+                                where enrollee_id = :enrolleeId
+                                and file_name in (<fileNames>)
+                                """.formatted(tableName))
+                        .bind("enrolleeId", enrolleeId)
+                        .bindList("fileNames", participantFileNames)
+                        .mapTo(clazz)
+                        .stream()
+                        .toList()
+        );
+    }
+}

core/src/main/java/bio/terra/pearl/core/dao/file/ParticipantFileSurveyResponseDao.java

@@ -0,0 +1,40 @@
+package bio.terra.pearl.core.dao.file;
+
+import bio.terra.pearl.core.dao.BaseJdbiDao;
+import bio.terra.pearl.core.model.survey.ParticipantFileSurveyResponse;
+import org.jdbi.v3.core.Jdbi;
+import org.springframework.stereotype.Component;
+
+import java.util.List;
+import java.util.UUID;
+
+@Component
+public class ParticipantFileSurveyResponseDao extends BaseJdbiDao<ParticipantFileSurveyResponse> {
+    public ParticipantFileSurveyResponseDao(Jdbi jdbi) {
+        super(jdbi);
+    }
+
+    @Override
+    protected Class<ParticipantFileSurveyResponse> getClazz() {
+        return ParticipantFileSurveyResponse.class;
+    }
+
+    public List<ParticipantFileSurveyResponse> findBySurveyResponseId(UUID surveyResponseId) {
+        return findAllByProperty("survey_response_id", surveyResponseId);
+    }
+
+    public void deleteByEnrolleeId(UUID enrolleeId) {
+        jdbi.withHandle(handle ->
+                handle.createUpdate("""
+                                    delete from participant_file_survey_response file_response
+                                    where id IN (
+                                        select inner_file_response.id from participant_file_survey_response inner_file_response 
+                                        inner join participant_file inner_file on inner_file_response.participant_file_id = inner_file.id 
+                                        where inner_file.enrollee_id = :enrolleeId
+                                    );
+                                """)
+                        .bind("enrolleeId", enrolleeId)
+                        .execute()
+        );
+    }
+}

core/src/main/java/bio/terra/pearl/core/dao/survey/SurveyResponseDao.java

@@ -1,8 +1,8 @@
 package bio.terra.pearl.core.dao.survey;
 
 import bio.terra.pearl.core.dao.BaseMutableJdbiDao;
-import bio.terra.pearl.core.dao.fileupload.ParticipantFileDao;
-import bio.terra.pearl.core.model.fileupload.ParticipantFile;
+import bio.terra.pearl.core.dao.file.ParticipantFileDao;
+import bio.terra.pearl.core.model.file.ParticipantFile;
 import bio.terra.pearl.core.model.survey.Answer;
 import bio.terra.pearl.core.model.survey.SurveyResponse;
 import org.jdbi.v3.core.Jdbi;
@@ -41,6 +41,7 @@ public List<SurveyResponse> findByEnrolleeIdWithAnswers(UUID enrolleeId) {
         Map<UUID, SurveyResponse> responseById = new HashMap<>();
         for (SurveyResponse response : responses) {
             responseById.put(response.getId(), response);
+            attachParticipantFiles(response);
         }
         for (Answer answer : answers) {
             responseById.get(answer.getSurveyResponseId()).getAnswers().add(answer);
@@ -52,6 +53,7 @@ public Optional<SurveyResponse> findOneWithAnswers(UUID responseId) {
         Optional<SurveyResponse> responseOpt = find(responseId);
         responseOpt.ifPresent(response -> {
             attachAnswers(response);
+            attachParticipantFiles(response);
         });
         return responseOpt;
     }

core/src/main/java/bio/terra/pearl/core/model/fileupload/ParticipantFile.java → core/src/main/java/bio/terra/pearl/core/model/file/ParticipantFile.java

@@ -1,4 +1,4 @@
-package bio.terra.pearl.core.model.fileupload;
+package bio.terra.pearl.core.model.file;
 
 import bio.terra.pearl.core.model.BaseEntity;
 import lombok.Getter;

core/src/main/java/bio/terra/pearl/core/model/participant/Enrollee.java

@@ -1,6 +1,7 @@
 package bio.terra.pearl.core.model.participant;
 
 import bio.terra.pearl.core.model.BaseEntity;
+import bio.terra.pearl.core.model.file.ParticipantFile;
 import bio.terra.pearl.core.model.study.StudyEnvAttached;
 import bio.terra.pearl.core.model.survey.PreEnrollmentResponse;
 import bio.terra.pearl.core.model.survey.SurveyResponse;
@@ -50,4 +51,6 @@ public class Enrollee extends BaseEntity implements StudyEnvAttached {
     private List<KitRequestDto> kitRequests = new ArrayList<>();
     @Builder.Default
     private List<EnrolleeRelation> relations = new ArrayList<>();
+    @Builder.Default
+    private List<ParticipantFile> files = new ArrayList<>();
 }

core/src/main/java/bio/terra/pearl/core/model/survey/SurveyResponse.java

@@ -2,7 +2,7 @@
 
 import bio.terra.pearl.core.model.BaseEntity;
 import bio.terra.pearl.core.model.audit.ResponsibleEntity;
-import bio.terra.pearl.core.model.fileupload.ParticipantFile;
+import bio.terra.pearl.core.model.file.ParticipantFile;
 import lombok.Builder;
 import lombok.Getter;
 import lombok.NoArgsConstructor;

core/src/main/java/bio/terra/pearl/core/service/fileupload/FileStorageConfig.java → core/src/main/java/bio/terra/pearl/core/service/file/FileStorageConfig.java

@@ -1,4 +1,4 @@
-package bio.terra.pearl.core.service.fileupload;
+package bio.terra.pearl.core.service.file;
 
 import lombok.Getter;
 import lombok.Setter;