[BI-2256] - Experimental Collaborator BI-API Changes

src/main/java/org/breedinginsight/api/model/v1/request/ExperimentCollaboratorRequest.java

@@ -0,0 +1,19 @@
+package org.breedinginsight.api.model.v1.request;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.*;
+
+import javax.validation.constraints.NotBlank;
+import java.util.UUID;
+
+@Getter
+@Setter
+@Builder
+@ToString
+@AllArgsConstructor
+@NoArgsConstructor
+@Introspected
+public class ExperimentCollaboratorRequest {
+    @NotBlank
+    private UUID userId;
+}

src/main/java/org/breedinginsight/api/model/v1/response/ExperimentalCollaboratorResponse.java

@@ -0,0 +1,44 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.breedinginsight.api.model.v1.response;
+
+import lombok.*;
+import lombok.experimental.Accessors;
+
+import javax.validation.constraints.NotBlank;
+import javax.validation.constraints.NotNull;
+import java.util.UUID;
+
+@Getter
+@Setter
+@Accessors(chain=true)
+@ToString
+@NoArgsConstructor
+@AllArgsConstructor
+public class ExperimentalCollaboratorResponse {
+    //collaboratorId is null in case where active=false
+    private UUID collaboratorId;
+    @NotNull
+    private Boolean active;
+    @NotBlank
+    private String name;
+    @NotBlank
+    private String email;
+    @NotBlank
+    private UUID userId;
+}

src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java

@@ -11,23 +11,35 @@
 import lombok.extern.slf4j.Slf4j;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.breedinginsight.api.auth.*;
+import org.breedinginsight.api.model.v1.request.ExperimentCollaboratorRequest;
 import org.breedinginsight.api.model.v1.request.SubEntityDatasetRequest;
+import org.breedinginsight.api.model.v1.response.DataResponse;
+import org.breedinginsight.api.model.v1.response.ExperimentalCollaboratorResponse;
 import org.breedinginsight.api.model.v1.response.Response;
+import org.breedinginsight.api.model.v1.response.metadata.Metadata;
+import org.breedinginsight.api.model.v1.response.metadata.Pagination;
+import org.breedinginsight.api.model.v1.response.metadata.Status;
+import org.breedinginsight.api.model.v1.response.metadata.StatusCode;
 import org.breedinginsight.brapi.v2.model.request.query.ExperimentExportQuery;
 import org.breedinginsight.brapi.v2.services.BrAPITrialService;
-import org.breedinginsight.model.Dataset;
-import org.breedinginsight.model.DatasetMetadata;
-import org.breedinginsight.model.DownloadFile;
-import org.breedinginsight.model.Program;
+import org.breedinginsight.dao.db.tables.pojos.ExperimentProgramUserRoleEntity;
+import org.breedinginsight.model.*;
+import org.breedinginsight.services.ExperimentalCollaboratorService;
 import org.breedinginsight.services.ProgramService;
+import org.breedinginsight.services.ProgramUserService;
+import org.breedinginsight.services.RoleService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.services.exceptions.UnprocessableEntityException;
+import org.breedinginsight.utilities.Utilities;
 import org.breedinginsight.utilities.response.mappers.ExperimentQueryMapper;
 
 import javax.inject.Inject;
 import javax.validation.Valid;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import java.util.UUID;
+import java.util.stream.Collectors;
 
 @Slf4j
 @Controller
@@ -36,12 +48,20 @@ public class ExperimentController {
     private final BrAPITrialService experimentService;
     private final ExperimentQueryMapper experimentQueryMapper;
     private final ProgramService programService;
+    private final ExperimentalCollaboratorService experimentalCollaboratorService;
+    private final SecurityService securityService;
+    private final ProgramUserService programUserService;
+    private final RoleService roleService;
 
     @Inject
-    public ExperimentController(BrAPITrialService experimentService, ExperimentQueryMapper experimentQueryMapper, ProgramService programService) {
+    public ExperimentController(BrAPITrialService experimentService, ExperimentQueryMapper experimentQueryMapper, ProgramService programService, ExperimentalCollaboratorService experimentalCollaboratorService, SecurityService securityService, ProgramUserService programUserService, RoleService roleService) {
         this.experimentService = experimentService;
         this.experimentQueryMapper = experimentQueryMapper;
         this.programService = programService;
+        this.experimentalCollaboratorService = experimentalCollaboratorService;
+        this.securityService = securityService;
+        this.programUserService = programUserService;
+        this.roleService = roleService;
     }
 
     @Get("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/export{?queryParams*}")
@@ -129,7 +149,7 @@ public HttpResponse<Response<Dataset>> createSubEntityDataset(
      * @param experimentId The UUID of the experiment.
      * @return An HttpResponse with a Response object containing a list of DatasetMetadata.
      * @throws DoesNotExistException if the program does not exist.
-     * @throws ApiException if an error occurs while retrieving the datasets.
+     * @throws ApiException if an error occurs while retrieving the datasets
      */
     @Get("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/datasets")
     @ExperimentCollaboratorSecured
@@ -148,4 +168,136 @@ public HttpResponse<Response<List<DatasetMetadata>>> getDatasets(
         return HttpResponse.ok(response);
 
     }
+
+    /**
+     * Adds a record to the experiment_program_user_role table
+     * @param programId The UUID of the program
+     * @param experimentId The UUID of the experiment
+     * @param request ExperimentalCollaboratorRequest containing the UUID of the bi user to add as a collaborator to the experiemnt
+     * @return HttpResponse containing the newly created ExperimentProgramUserRoleEntity
+     */
+    @Post("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/collaborators")
+    @ProgramSecured(roles = {ProgramSecuredRole.PROGRAM_ADMIN, ProgramSecuredRole.SYSTEM_ADMIN})
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse<Response<ExperimentProgramUserRoleEntity>> createExperimentalCollaborator(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("experimentId") UUID experimentId,
+            @Body @Valid ExperimentCollaboratorRequest request
+    ) {
+        try {
+            //Check if program exists
+            Optional<Program> programOptional = programService.getById(programId);
+            if (programOptional.isEmpty()) {
+                return HttpResponse.status(HttpStatus.NOT_FOUND, "Program does not exist");
+            }
+
+            //Check if program user exists
+            Optional<ProgramUser> programUserOptional = programUserService.getProgramUserbyId(programId, request.getUserId());
+            if (programUserOptional.isEmpty()) {
+                return HttpResponse.status(HttpStatus.NOT_FOUND, "Program user does not exist");
+            }
+
+            //get active user creating the collaborator
+            AuthenticatedUser createdByUser = securityService.getUser();
+            UUID programUserId = programUserOptional.get().getId();
+            UUID createdByUserId = createdByUser.getId();
+            Response<ExperimentProgramUserRoleEntity> response = new Response(experimentalCollaboratorService.createExperimentalCollaborator(programUserId,experimentId,createdByUserId));
+            return HttpResponse.ok(response);
+        } catch (Exception e){
+            log.info(e.getMessage());
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        }
+
+    }
+
+    /**
+     * Returns an array of collaborators for given experiment filterable using the active query parameter
+     * @param programId The UUID of the program
+     * @param experimentId The UUID of the experiment
+     * @param active true if querying for collaborators added as a collaborator to the experiment, false if querying for collaborators not added
+     * @return list of ExperimentalCollaboratorResponse
+     *  Response includes name and email as a convenience to the front end to avoid making another api call
+     */
+    @Get("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/collaborators{?active}")
+    @ProgramSecured(roles = {ProgramSecuredRole.PROGRAM_ADMIN, ProgramSecuredRole.SYSTEM_ADMIN})
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse<Response<DataResponse<List<ExperimentalCollaboratorResponse>>>> getExperimentalCollaborators(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("experimentId") UUID experimentId,
+            @QueryValue(defaultValue = "true") Boolean active
+    ) {
+        try {
+            //Get experimental collaborators associated with the experiment
+            List<ExperimentProgramUserRoleEntity> collaborators = experimentalCollaboratorService.getExperimentalCollaborators(experimentId);
+            List<UUID> activeCollaboratorIds = collaborators.stream().map((ExperimentProgramUserRoleEntity::getProgramUserRoleId)).collect(Collectors.toList());
+
+            //Get roleId for experimental collaborator role
+            Role experimentalCollabRole = roleService.getRoleByDomain(ProgramSecuredRole.EXPERIMENTAL_COLLABORATOR.toString()).get();
+            UUID roleId = experimentalCollabRole.getId();
+
+            //Get all program users with experimental collaborator role
+            List<ProgramUser> collabRoleUsers = programUserService.getProgramUsersByRole(programId, roleId);
+            List<ExperimentalCollaboratorResponse> collaboratorResponses = new ArrayList<>();
+
+            for (ProgramUser collabRoleUser : collabRoleUsers) {
+                UUID collaboratorId = null;
+                //check if user is an active collaborator for this experiment
+                Boolean isThisExpCollab = activeCollaboratorIds.contains(collabRoleUser.getId());
+                if (isThisExpCollab) {
+                    collaboratorId = collaborators.get(activeCollaboratorIds.indexOf(collabRoleUser.getId())).getId();
+                }
+
+                //If active, want to retrieve experimental collaborators added to the experiment
+                //If not active, want to retrieve experimental collaborators not added to the experiment
+                if ((active && isThisExpCollab) || (!active && !isThisExpCollab)) {
+                    ExperimentalCollaboratorResponse collabResponse = new ExperimentalCollaboratorResponse();
+                    collabResponse.setActive(active);
+                    collabResponse.setEmail(collabRoleUser.getUser().getEmail());
+                    collabResponse.setName(collabRoleUser.getUser().getName());
+                    collabResponse.setUserId(collabRoleUser.getUserId());
+                    collabResponse.setCollaboratorId(collaboratorId);
+                    collaboratorResponses.add(collabResponse);
+                }
+            }
+
+            List<Status> metadataStatus = new ArrayList<>();
+            metadataStatus.add(new Status(StatusCode.INFO, "Successful Query"));
+            //TODO: paging
+            Pagination pagination = new Pagination(collaborators.size(), collaborators.size(), 1, 0);
+            Metadata metadata = new Metadata(pagination, metadataStatus);
+
+            Response<DataResponse<List<ExperimentalCollaboratorResponse>>> response = new Response(metadata, new DataResponse<>(collaboratorResponses));
+            return HttpResponse.ok(response);
+        } catch (Exception e) {
+            log.info(e.getMessage(), e);
+            HttpResponse response = HttpResponse.serverError();
+            return response;
+        }
+
+    }
+
+    /**
+     * Removes record from experiment_program_user_role table
+     * @param programId The UUID of the program
+     * @param experimentId The UUID of the experiment
+     * @param collaboratorId The UUID of the collaborator, referring to a unique experiment-program user role combo in the experiment_program_user_role table
+     * @return A Http Response
+     */
+    @Delete("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/collaborators/{collaboratorId}")
+    @ProgramSecured(roles = {ProgramSecuredRole.PROGRAM_ADMIN, ProgramSecuredRole.SYSTEM_ADMIN})
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse deleteExperimentalCollaborator(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("experimentId") UUID experimentId,
+            @PathVariable("collaboratorId") UUID collaboratorId
+    ) {
+        try {
+            experimentalCollaboratorService.deleteExperimentalCollaborator(collaboratorId);
+            return HttpResponse.ok();
+        } catch (Exception e) {
+            log.error("Error deleting experimental collaborator.\n\tprogramId: " + programId +  "\n\texperimentId: " + experimentId + "\n\tcollaboratorId: " + collaboratorId);
+            throw e;
+        }
+
+    }
 }

src/main/java/org/breedinginsight/daos/ExperimentalCollaboratorDAO.java

@@ -50,7 +50,7 @@ public ExperimentalCollaboratorDAO(Configuration config, DSLContext dsl) {
         this.dsl = dsl;
     }
 
-    public ExperimentProgramUserRoleEntity create(UUID experimentId, UUID programUserRoleId, UUID userId) {
+    public ExperimentProgramUserRoleEntity create(UUID experimentId, UUID programUserRoleId, UUID createdByUserId) {
         return dsl.insertInto(EXPERIMENT_PROGRAM_USER_ROLE)
                 .columns(EXPERIMENT_PROGRAM_USER_ROLE.EXPERIMENT_ID,
                         EXPERIMENT_PROGRAM_USER_ROLE.PROGRAM_USER_ROLE_ID,
@@ -60,9 +60,9 @@ public ExperimentProgramUserRoleEntity create(UUID experimentId, UUID programUse
                         EXPERIMENT_PROGRAM_USER_ROLE.UPDATED_AT)
                 .values(experimentId,
                         programUserRoleId,
-                        userId,
+                        createdByUserId,
                         OffsetDateTime.now(),
-                        userId,
+                        createdByUserId,
                         OffsetDateTime.now())
                 .returning(EXPERIMENT_PROGRAM_USER_ROLE.fields())
                 .fetchOneInto(ExperimentProgramUserRoleEntity.class);

src/main/java/org/breedinginsight/services/ExperimentalCollaboratorService.java

@@ -37,8 +37,8 @@ public ExperimentalCollaboratorService(ExperimentalCollaboratorDAO experimentalC
         this.experimentalCollaboratorDAO = experimentalCollaboratorDAO;
     }
 
-    public ExperimentProgramUserRoleEntity createExperimentalCollaborator(UUID programUserRoleId, UUID experimentId, UUID userId) {
-        return this.experimentalCollaboratorDAO.create(experimentId, programUserRoleId, userId);
+    public ExperimentProgramUserRoleEntity createExperimentalCollaborator(UUID programUserRoleId, UUID experimentId, UUID createdByUserId) {
+        return this.experimentalCollaboratorDAO.create(experimentId, programUserRoleId, createdByUserId);
     }
 
     public List<ExperimentProgramUserRoleEntity> getExperimentalCollaborators(UUID experimentId) {
@@ -47,7 +47,7 @@ public List<ExperimentProgramUserRoleEntity> getExperimentalCollaborators(UUID e
     }
 
     public void deleteExperimentalCollaborator(UUID collaboratorId) {
-        // Note: collaboratorId is the PK of the experiment_program_user_role table.
+        // Note: collaboratorId is the primary key of the experiment_program_user_role table.
         this.experimentalCollaboratorDAO.deleteById(collaboratorId);
     }
 }

src/main/java/org/breedinginsight/services/RoleService.java

@@ -17,6 +17,9 @@
 
 package org.breedinginsight.services;
 
+import io.micronaut.http.HttpResponse;
+import io.micronaut.http.HttpStatus;
+import io.micronaut.http.MediaType;
 import lombok.extern.slf4j.Slf4j;
 import org.breedinginsight.dao.db.tables.daos.RoleDao;
 import org.breedinginsight.dao.db.tables.pojos.RoleEntity;
@@ -66,4 +69,13 @@ public List<Role> getRolesByIds(List<UUID> roleIds) {
         return roles;
     }
 
+    public Optional<Role> getRoleByDomain(String domain) {
+        RoleEntity role = dao.fetchByDomain(domain).get(0);
+        if (role == null) {
+            return Optional.empty();
+        }
+
+        return Optional.of(new Role(role));
+    }
+
 }