Merge pull request #845 from HDRUK/release-preprod/v3.1.0

Release preprod/v3.1.0

src/config/server.js

@@ -53,7 +53,7 @@ configuration.findAccount = Account.findAccount;
 const oidc = new Provider(process.env.api_url || 'http://localhost:3001', configuration);
 oidc.proxy = true;
 
-var domains = [/\.healthdatagateway\.org$/, process.env.homeURL];
+var domains = [/\.healthdatagateway\.org$/, /\.hdruk\.dev$/, process.env.homeURL];
 
 var rx = /^((http|https)+:\/\/[a-z]+)\.([^/]*)/;
 var arr = rx.exec(process.env.homeURL);

src/resources/auth/utils.js

@@ -127,18 +127,6 @@ const getTeams = async () => {
 	return teams;
 };
 
-const userIsTeamManager = () => async (req, res, next) => {
-	const { user, params } = req;
-
-	const members = await TeamModel.findOne({ _id: params.id }, { _id: 0, members: { $elemMatch: { memberid: user._id } } }).lean();
-	if (!isEmpty(members) && members.members[0].roles.includes(constants.roleTypes.MANAGER)) return next();
-
-	return res.status(401).json({
-		status: 'error',
-		message: 'Unauthorised to perform this action.',
-	});
-};
-
 const catchLoginErrorAndRedirect = (req, res, next) => {
 	if (req.auth.err || !req.auth.user) {
 		if (req.auth.err === 'loginError') {
@@ -214,6 +202,17 @@ const loginAndSignToken = (req, res, next) => {
 	});
 };
 
+const userIsTeamManager = () => async (req, res, next) => {
+	const { user, params } = req;
+	const members = await TeamModel.findOne({ _id: params.id }, { _id: 0, members: { $elemMatch: { memberid: user._id } } }).lean();
+	if ((!isEmpty(members) && members.members[0].roles.includes(constants.roleTypes.MANAGER)) || user.role === 'Admin') return next();
+
+	return res.status(401).json({
+		status: 'error',
+		message: 'Unauthorised to perform this action.',
+	});
+};
+
 function isUserMemberOfTeamById(user, teamId) {
 	let { teams } = user;
 	return teams.filter(team => !isNull(team.publisher)).some(team => team.publisher._id.equals(teamId));

src/resources/datarequest/datarequest.controller.js

@@ -476,6 +476,7 @@ export default class DataRequestController extends Controller {
 							dataRequestId: accessRecord._id,
 							createdDate: accessRecord.createdAt,
 							questionBank: accessRecord.questionAnswers,
+							files: accessRecord.files,
 						},
 						darIntegration: publisherDetails['dar-integration'],
 					};

src/resources/datarequest/schema/datarequest.schemas.route.js

@@ -7,6 +7,7 @@ import DatarequestschemaController from './datarequest.schema.controller';
 import { datarequestschemaService } from './dependency';
 import { utils } from '../../auth';
 import { ROLES } from '../../user/user.roles';
+import constants from '../../utilities/constants.util';
 
 const datarequestschemaController = new DatarequestschemaController(datarequestschemaService);
 
@@ -39,8 +40,9 @@ const authorizeUpdate = async (req, res, next) => {
 	}
 
 	const authorised = isUserMemberOfTeam(requestingUser, datarequestschema.publisher);
+	const isAdminUser = requestingUser.teams.map(team => team.type).includes(constants.teamTypes.ADMIN);
 
-	if (!authorised) {
+	if (!authorised && !isAdminUser) {
 		return res.status(401).json({
 			success: false,
 			message: 'You are not authorised to perform this action',

src/resources/dataset/datasetfiles/dummy.json

@@ -0,0 +1 @@
+{ "reasonForExistence": "I live so this folder will live" }

src/resources/message/message.controller.js

@@ -19,7 +19,7 @@ module.exports = {
 	// POST /api/v1/messages
 	createMessage: async (req, res) => {
 		try {
-			const { _id: createdBy, firstname, lastname } = req.user;
+			const { _id: createdBy, firstname, lastname, isServiceAccount = false } = req.user;
 			let { messageType = 'message', topic = '', messageDescription, relatedObjectIds, firstMessage } = req.body;
 			let topicObj = {};
 			let team, publisher, userType;
@@ -188,7 +188,7 @@ module.exports = {
 
 				// publish the message to GCP PubSub
 				const cacheEnabled = parseInt(process.env.CACHE_ENABLED) || 0;
-				if(cacheEnabled) {
+				if (cacheEnabled && !isServiceAccount) {
 					let publisherDetails = await PublisherModel.findOne({ _id: ObjectId(tools[0].publisher._id) }).lean();
 
 					if (publisherDetails['dar-integration']['enabled']) {

src/resources/publisher/publisher.controller.js

@@ -161,6 +161,19 @@ export default class PublisherController extends Controller {
 		}
 	}
 
+	async updateDataUseWidget(req, res) {
+		try {
+			await this.publisherService.updateDataUseWidget(req.params.id, req.body).then(() => {
+				return res.status(200).json({ success: true });
+			});
+		} catch (err) {
+			return res.status(500).json({
+				success: false,
+				message: 'An error occurred updating data use widget settings',
+			});
+		}
+	}
+
 	async updateDataRequestModalContent(req, res) {
 		try {
 			await this.publisherService.updateDataRequestModalContent(req.params.id, req.user.id, req.body.content).then(() => {

src/resources/publisher/publisher.model.js

@@ -41,6 +41,14 @@ const PublisherSchema = new Schema(
 			accessRequestCost: String,
 			dataUseLimitation: [String],
 			dataUseRequirements: [String],
+			dataUse: {
+				widget: {
+					enabled: { type: Boolean, default: false },
+					accepted: { type: Boolean, default: false },
+					acceptedByUserId: String,
+					acceptedDate: Date,
+				},
+			},
 			questionBank: {
 				enabled: { type: Boolean, default: false },
 			},

src/resources/publisher/publisher.route.js

@@ -4,6 +4,7 @@ import passport from 'passport';
 import { logger } from '../utilities/logger';
 import PublisherController from './publisher.controller';
 import { publisherService, workflowService, dataRequestService, amendmentService } from './dependency';
+import { userIsTeamManager } from '../auth/utils';
 import { utils } from '../auth';
 
 const logCategory = 'Publisher';
@@ -55,6 +56,12 @@ router.get(
 	(req, res) => publisherController.getPublisherWorkflows(req, res)
 );
 
+// @route   PATCH /api/publishers/:id/dataUseWidget
+// @desc	Update data use widget settings (terms and conditions)
+// @access  Public
+router.patch('/:id/dataUseWidget', passport.authenticate('jwt'), utils.userIsTeamManager(), (req, res) =>
+	publisherController.updateDataUseWidget(req, res)
+);
 router.patch('/dataRequestModalContent/:id', passport.authenticate('jwt'), utils.userIsTeamManager(), (req, res) =>
 	publisherController.updateDataRequestModalContent(req, res)
 );

src/resources/publisher/publisher.service.js

@@ -95,6 +95,22 @@ export default class PublisherService {
 		return filteredApplications;
 	}
 
+	async updateDataUseWidget(publisherId, content) {
+		const publisher = await this.publisherRepository.getPublisher(publisherId);
+		const data = { ...publisher.publisherDetails.dataUse.widget, ...content };
+		await this.publisherRepository.updateByQuery(
+			{ _id: publisherId },
+			{
+				'publisherDetails.dataUse': {
+					widget: {
+						...data,
+						acceptedDate: Date.now(),
+					},
+				},
+			}
+		);
+	}
+
 	async update(document, body = {}) {
 		return this.publisherRepository.update(document, body);
 	}

src/resources/questionbank/questionbank.route.js

@@ -6,6 +6,7 @@ import { questionbankService } from './dependency';
 import { datarequestschemaService } from './../datarequest/schema/dependency';
 import { logger } from '../utilities/logger';
 import { isUserMemberOfTeamById, isUserMemberOfTeamByName } from '../auth/utils';
+import constants from '../utilities/constants.util';
 
 const router = express.Router();
 const questionbankController = new QuestionbankController(questionbankService);
@@ -24,8 +25,9 @@ const authorizeViewRequest = (req, res, next) => {
 	const { publisherId } = req.params;
 
 	const authorised = isUserMemberOfTeamById(requestingUser, publisherId);
+	const isAdminUser = requestingUser.teams.map(team => team.type).includes(constants.teamTypes.ADMIN);
 
-	if (!authorised) {
+	if (!authorised && !isAdminUser) {
 		return res.status(401).json({
 			success: false,
 			message: 'You are not authorised to perform this action',
@@ -57,8 +59,9 @@ const authorizePostRequest = async (req, res, next) => {
 	}
 
 	const authorised = isUserMemberOfTeamByName(requestingUser, dataRequestSchema.publisher);
+	const isAdminUser = requestingUser.teams.map(team => team.type).includes(constants.teamTypes.ADMIN);
 
-	if (!authorised) {
+	if (!authorised && !isAdminUser) {
 		return res.status(401).json({
 			success: false,
 			message: 'You are not authorised to perform this action',
@@ -82,7 +85,7 @@ router.get(
 	(req, res) => questionbankController.getQuestionbank(req, res)
 );
 
-// @route   POST /api/v1/questionbanks
+// @route   POST /api/v1/questionbank/schemaId
 // @desc    Activate a draft schema creating a jsonSchema from masterSchema
 // @access  Public
 router.post('/:schemaId', passport.authenticate('jwt'), validatePostRequest, authorizePostRequest, (req, res) =>

src/resources/search/search.repository.js

@@ -313,14 +313,27 @@ export async function getObjectResult(type, searchAll, searchQuery, startIndex,
 					'datasetv2.summary.publisher.name': 1,
 					'datasetv2.summary.publisher.logo': 1,
 					'datasetv2.summary.publisher.memberOf': 1,
+					'datasetv2.provenance.temporal.accrualPeriodicity': 1, 
 
 					'persons.id': 1,
 					'persons.firstname': 1,
 					'persons.lastname': 1,
 
 					activeflag: 1,
 					counter: 1,
-					'datasetfields.metadataquality.weighted_quality_score': 1,
+
+					'datasetfields.metadataquality.weighted_quality_score': {
+						$convert: {
+							input: '$datasetfields.metadataquality.weighted_quality_score',
+							to: 'double',
+							onError: 0,
+							onNull: 0,
+						},
+					},
+
+					'datasetfields.metadataquality.weighted_quality_rating': 1,
+					'datasetfields.metadataquality.weighted_error_percent': 1,
+					'datasetfields.metadataquality.weighted_completeness_percent': 1,
 
 					latestUpdate: '$timestamps.updated',
 					relatedresources: {

src/resources/team/team.controller.js

@@ -583,6 +583,7 @@ const getTeamsList = async (req, res) => {
 				'publisherDetails.name': 1,
 				'publisherDetails.memberOf': 1,
 				'publisherDetails.questionBank.enabled': 1,
+				'publisherDetails.dataUse.widget.enabled': 1,
 			})
 			.populate('users', { firstname: 1, lastname: 1 })
 			.sort({ updatedAt: -1 })
@@ -693,6 +694,7 @@ const addTeam = async (req, res) => {
 
 		publisher.name = `${inputSanitizer.removeNonBreakingSpaces(memberOf)} > ${inputSanitizer.removeNonBreakingSpaces(name)}`;
 		publisher.publisherDetails = {
+			...publisher.publisherDetails,
 			name: inputSanitizer.removeNonBreakingSpaces(name),
 			memberOf: inputSanitizer.removeNonBreakingSpaces(memberOf),
 			contactPoint: inputSanitizer.removeNonBreakingSpaces(contactPoint),
@@ -722,7 +724,8 @@ const addTeam = async (req, res) => {
 		// 11. Send email and notification to managers
 		await createNotifications(constants.notificationTypes.TEAMADDED, { recipients }, name, req.user, publisherId);
 
-		return res.status(200).json({ success: true, _id: newTeam._id });
+		return res.status(200).json(newPublisher);
+
 	} catch (err) {
 		console.error(err.message);
 		return res.status(500).json({

src/resources/utilities/cloudStorage.util.js

@@ -7,7 +7,7 @@ export const fileStatus = {
 	UPLOADED: 'UPLOADED',
 	ERROR: 'ERROR',
 	SCANNED: 'SCANNED',
-	QUARANTINED: 'QUARANTINED'
+	QUARANTINED: 'QUARANTINED',
 };
 
 export const processFile = (file, id, uniqueId) =>

src/utils/datasetonboarding.util.js

@@ -884,8 +884,10 @@ const createNotifications = async (type, context) => {
 			team = await TeamModel.findOne({ _id: context.datasetv2.summary.publisher.identifier }).lean();
 
 			for (let member of team.members) {
-				if ((Array.isArray(member.roles) && member.roles.some(role => ['manager', 'metadata_editor'].includes(role)))
-				 || (typeof member.roles === 'string' && ['manager', 'metadata_editor'].includes(member.roles))) {
+				if (
+					(Array.isArray(member.roles) && member.roles.some(role => ['manager', 'metadata_editor'].includes(role))) ||
+					(typeof member.roles === 'string' && ['manager', 'metadata_editor'].includes(member.roles))
+				) {
 					teamMembers.push(member.memberid);
 				}
 			}
@@ -958,14 +960,10 @@ const createNotifications = async (type, context) => {
 			};
 
 			html = emailGenerator.generateMetadataOnboardingRejected(options);
-			let subject = (options.isFederated) ? 'Your federated dataset has been rejected and requires review' : 'Your dataset version has been reviewed and rejected';
-			emailGenerator.sendEmail(
-				teamMembersDetails,
-				constants.hdrukEmail, 
-				subject,
-				html,
-				false
-			);
+			let subject = options.isFederated
+				? 'Your federated dataset has been rejected and requires review'
+				: 'Your dataset version has been reviewed and rejected';
+			emailGenerator.sendEmail(teamMembersDetails, constants.hdrukEmail, subject, html, false);
 			break;
 		case constants.notificationTypes.DATASETDUPLICATED:
 			// 1. Get user removed