Merge branch 'master' into Release

HDRUK · Dec 16, 2021 · c650881 · c650881
2 parents 8d41bf7 + ad5eb4e
commit c650881
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Showing 10 changed files with 659 additions and 26 deletions.
diff --git a/migrations/1631621029553-update_publishers_uses5safes.js b/migrations/1631621029553-update_publishers_uses5safes.js
@@ -31,3 +31,4 @@ async function up() {
 async function down() {}
 
 module.exports = { up, down };
+
diff --git a/src/config/account.js b/src/config/account.js
@@ -1,7 +1,7 @@
 import { getUserByUserId } from '../resources/user/user.repository';
 import ga4ghUtils from '../resources/utilities/ga4gh.utils';
 import { to } from 'await-to-js';
-import _ from 'lodash';
+import { isNil } from 'lodash';
 
 const store = new Map();
 const logins = new Map();
@@ -29,8 +29,8 @@ class Account {
 			sub: this.accountId, // it is essential to always return a sub claim
 		};
 
-		let [, user] = await to(getUserByUserId(parseInt(this.accountId)));
-		if (!_.isNil(user)) {
+		let [err, user] = await to(getUserByUserId(parseInt(this.accountId)));
+		if (!isNil(user)) {
 			if (claimsToSend.includes('profile')) {
 				claim.firstname = user.firstname;
 				claim.lastname = user.lastname;

diff --git a/src/config/configuration.js b/src/config/configuration.js
@@ -27,13 +27,7 @@ export const clients = [
 		//response_types: ['code id_token'],
 		redirect_uris: process.env.MDWRedirectURI.split(',') || [''],
 		id_token_signed_response_alg: 'HS256',
-		post_logout_redirect_uris: [
-			'https://hdr.auth.metadata.works/logout',
-			'https://hdr.auth.metadata.works/auth/logout',
-			'https://hdruk-preprod-auth.metadata.works/auth/logout',
-			'http://localhost:8080/logout',
-			'http://localhost:8080/auth/logout',
-		],
+		post_logout_redirect_uris: ['https://hdruk-auth.metadata.works/auth/logout'],
 	},
 	{
 		//BC Platforms

diff --git a/src/config/db.js b/src/config/db.js
@@ -20,7 +20,7 @@ const connectToDatabase = async () => {
 			autoIndex: false, // Don't build indexes
 			poolSize: 10, // Maintain up to 10 socket connections
 			// If not connected, return errors immediately rather than waiting for reconnect
-			bufferMaxEntries: 0
+			bufferMaxEntries: 0,
 		});
 
 		console.log('MongoDB connected...');

diff --git a/src/resources/dataset/dataset.model.js b/src/resources/dataset/dataset.model.js
@@ -71,7 +71,7 @@ const datasetSchema = new Schema(
 			phenotypes: [],
 		},
 		datasetv2: {},
-		isLatestVersion: Boolean
+		isLatestVersion: Boolean,
 	},
 	{
 		timestamps: true,
@@ -115,15 +115,15 @@ datasetSchema.virtual('submittedDataAccessRequests', {
 });
 
 // Pre hook query middleware
-datasetSchema.pre('find', function() {
-    this.where({type: 'dataset'});
+datasetSchema.pre('find', function () {
+	this.where({ type: 'dataset' });
 });
 
-datasetSchema.pre('findOne', function() {
-    this.where({type: 'dataset'});
+datasetSchema.pre('findOne', function () {
+	this.where({ type: 'dataset' });
 });
 
 // Load entity class
 datasetSchema.loadClass(DatasetClass);
 
-export const Dataset = model('Dataset', datasetSchema, 'tools');
+export const Dataset = model('Dataset', datasetSchema, 'tools');
diff --git a/src/resources/dataset/datasetonboarding.controller.js b/src/resources/dataset/datasetonboarding.controller.js
@@ -269,11 +269,7 @@ module.exports = {
 					} else {
 						Data.findByIdAndUpdate(
 							{ _id: id },
-							{
-								structuralMetadata,
-								percentageCompleted,
-								'timestamps.updated': Date.now(),
-							},
+							{ structuralMetadata, percentageCompleted: data.percentageCompleted, 'timestamps.updated': Date.now() },
 							{ new: true }
 						).catch(err => {
 							console.error(err);
@@ -853,7 +849,7 @@ module.exports = {
 			return res.status(500).json({ success: false, message: 'Bulk upload of metadata failed', error: err.message });
 		}
 	},
-
+  
 	//POST api/v1/dataset-onboarding/duplicate/:id
 	duplicateDataset: async (req, res) => {
 		try {
@@ -897,3 +893,10 @@ module.exports = {
 		}
 	},
 };
+
+/* Sentry.addBreadcrumb({
+				category: 'Bulk Upload',
+				message: 'Unable to get metadata quality value ' + err.message,
+				level: Sentry.Severity.Error,
+			});
+			Sentry.captureException(err); */
diff --git a/src/resources/dataset/v1/dataset.service.js b/src/resources/dataset/v1/dataset.service.js
@@ -6,7 +6,7 @@ import { v4 as uuidv4 } from 'uuid';
 import { filtersService } from '../../filters/dependency';
 import { PublisherModel } from '../../publisher/publisher.model';
 import { metadataCatalogues, validateCatalogueParams } from '../dataset.util';
-import { isEmpty } from 'lodash';
+import { has, isEmpty } from 'lodash';
 
 let metadataQualityList = [],
 	phenotypesList = [],
Original file line number	Diff line number	Diff line change
Expand Up		@@ -31,3 +31,4 @@ async function up() {
		async function down() {}

		module.exports = { up, down };