Merge pull request #295 from bcgsc/release/v7.19.0

Release/v7.19.0

.github/workflows/npm-test.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node: [18, 20]
+        node: [16, 18, 20]
         # TODO: readd node versions: node: [14, 16, 18, 20]
     name: node-${{ matrix.node }}
     services:
@@ -40,8 +40,8 @@ jobs:
           # Maps port 6379 on service container to the host
           - 6379:6379
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-node@v3
         with:
           node-version: ${{ matrix.node }}
       - run: bash ./demo/restore_iprdb_dump.sh
@@ -73,11 +73,11 @@ jobs:
           IPR_TESTING_PASSWORD: iprdemo
           IPR_TESTING_USERNAME: iprdemo
           IPR_REDIS_HOST: localhost
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         with:
           yml: codecov.yml
           token: ${{ secrets.CODECOV_TOKEN }}
-          fail_if_ci_error: true
+          fail_ci_if_error: true
         if: matrix.node == 16
       - uses: EnricoMi/[email protected]
         with:
@@ -88,7 +88,7 @@ jobs:
     runs-on: ubuntu-latest
     name: docker build
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: build the API docker container
         run: |
           docker build --file Dockerfile --tag pori/ipr-api .

app/config.js

@@ -59,7 +59,10 @@ const DEFAULTS = {
       : 'iprdevdb.bcgsc.ca',
     port: 5432,
     name: DEFAULT_DB_NAME,
-    maxConn: 30,
+    poolMax: 20,
+    poolMin: 0,
+    poolAcquire: 60000,
+    poolIdle: 5000,
   },
   redis: {
     host: ENV === 'production'

app/index.js

@@ -70,8 +70,13 @@ const fetchRoutes = (initialRouter) => {
 
 const listen = async (port = null) => {
   const app = express(); // define app using express
-  logger.info(`starting http server on port ${port || conf.get('web:port')}`);
-  const server = http.createServer(app).listen(port || conf.get('web:port'));
+  port = process.env.PORT || conf.get('web:port');
+
+  if (process.env.NODE_ENV === 'test') {
+    port = 0;
+  }
+  logger.info(`starting http server on port ${port}`);
+  const server = http.createServer(app).listen(port);
   // TODO: https://www.bcgsc.ca/jira/browse/DEVSU-985 reduce when images are a separate upload
   app.use(express.json({limit: '100mb'}));
   app.use(boolParser());

app/libs/helperFunctions.js

@@ -82,8 +82,7 @@ const hasAccessToNonProdReports = (user) => {
   return user.groups.some((group) => {
     return group.name.toLowerCase() === 'admin'
     || group.name.toLowerCase() === 'manager'
-    || group.name.toLowerCase() === 'non-production access'
-    || group.name.toLowerCase() === 'demo';
+    || group.name.toLowerCase() === 'non-production access';
   });
 };
 
@@ -97,8 +96,21 @@ const hasAccessToUnreviewedReports = (user) => {
   return user.groups.some((group) => {
     return group.name.toLowerCase() === 'admin'
     || group.name.toLowerCase() === 'manager'
-    || group.name.toLowerCase() === 'unreviewed access'
-    || group.name.toLowerCase() === 'demo';
+    || group.name.toLowerCase() === 'unreviewed access';
+  });
+};
+
+/**
+ * Checks if user has access to germline repots
+ *
+ * @param {object} user - Sequelize user model
+ * @returns {boolean} - Returns a boolean indicating if the user has access to germline reports
+ */
+const hasAccessToGermlineReports = (user) => {
+  return user.groups.some((group) => {
+    return group.name.toLowerCase() === 'admin'
+    || group.name.toLowerCase() === 'manager'
+    || group.name.toLowerCase() === 'germline access';
   });
 };
 
@@ -164,6 +176,7 @@ module.exports = {
   hasAccess,
   hasAccessToNonProdReports,
   hasAccessToUnreviewedReports,
+  hasAccessToGermlineReports,
   hasMasterAccess,
   projectAccess,
   isIntersectionBy,

app/middleware/acl.js

@@ -1,7 +1,7 @@
 const {FORBIDDEN} = require('http-status-codes');
 const {pathToRegexp} = require('path-to-regexp');
 const {
-  isAdmin, isIntersectionBy, hasAccess, hasMasterAccess, projectAccess,
+  isAdmin, isIntersectionBy, hasAccess, hasMasterAccess, projectAccess, hasAccessToGermlineReports,
 } = require('../libs/helperFunctions');
 const {MASTER_REPORT_ACCESS, UPDATE_METHODS} = require('../constants');
 const logger = require('../log');
@@ -62,6 +62,14 @@ module.exports = async (req, res, next) => {
     await req.user.update({lastLoginAt: new Date()});
   }
 
+  try {
+    if (req.query.clinician_view && hasMasterAccess(req.user)) {
+      req.user.groups = [{name: 'Clinician'}];
+    }
+  } catch {
+    logger.error('Clinician View error: Using users normal group');
+  }
+
   // Check if user is an admin
   if (isAdmin(req.user)) {
     return next();
@@ -70,6 +78,13 @@ module.exports = async (req, res, next) => {
   // Get route
   const [route] = req.originalUrl.split('?');
 
+  if (!hasAccessToGermlineReports(req.user) && route.includes('/germline-small-mutation-reports')) {
+    logger.error('User does not have germline access');
+    return res.status(
+      FORBIDDEN,
+    ).json({error: {message: 'User does not have access to Germline reports'}});
+  }
+
   if (req.report) {
     // check if user is bound to report depending on report type
     let boundUser;
@@ -93,6 +108,18 @@ module.exports = async (req, res, next) => {
         error: {message: 'You do not have the correct permissions to access this'},
       });
     }
+
+    // If user is trying to make an update and the report is completed
+    // and they dont have update permissions, throw an error
+    if (UPDATE_METHODS.includes(req.method)
+      && req.report.state === 'completed'
+      && !(hasAccess(req.user, MASTER_REPORT_ACCESS))
+    ) {
+      logger.error(`User: ${req.user.username} is trying to make a ${req.method} request to ${req.originalUrl} - Report is marked as complete`);
+      return res.status(FORBIDDEN).json({
+        error: {message: 'Report is marked as completed and update has been restricted'},
+      });
+    }
   } else {
     // See if route exists in special cases
     const spCase = SPECIAL_CASES.find((value) => {

app/middleware/germlineSmallMutation/reports.js

@@ -75,7 +75,7 @@ module.exports = async (req, res, next, ident) => {
       return res.status(HTTP_STATUS.FORBIDDEN).json({error: {message: 'User does not have access to Non-Production reports'}});
     }
 
-    if (!hasAccessToUnreviewedReports(req.user) && (result.state !== 'reviewed' && result.state !== 'archived')) {
+    if (!hasAccessToUnreviewedReports(req.user) && (result.state !== 'reviewed' && result.state !== 'completed')) {
       logger.error(`User does not have unreviewed access to ${ident}`);
       return res.status(HTTP_STATUS.FORBIDDEN).json({error: {message: 'User does not have access to Unreviewed reports'}});
     }

app/middleware/report.js

@@ -48,7 +48,7 @@ module.exports = async (req, res, next, ident) => {
     return res.status(HTTP_STATUS.NOT_FOUND).json({error: {message: 'Unable to find the requested report'}});
   }
 
-  if (!hasAccessToUnreviewedReports(req.user) && (result.state !== 'reviewed' && result.state !== 'archived')) {
+  if (!hasAccessToUnreviewedReports(req.user) && (result.state !== 'reviewed' && result.state !== 'completed')) {
     logger.error(`User does not have unreviewed access to ${ident}`);
     return res.status(HTTP_STATUS.FORBIDDEN).json({error: {message: 'User does not have access to Unreviewed reports'}});
   }

app/models/base.js

@@ -171,6 +171,20 @@ const DEFAULT_REPORT_OPTIONS = {
             transaction: options.transaction,
             userId: options.userId,
           }),
+        // If report is state "reviewed" change to "ready"
+        (!changed || includesAll(updateExclude, changed)) ? Promise.resolve(true)
+          : instance.sequelize.models.report.update({
+            state: 'ready',
+          }, {
+            where: {
+              id: (modelName === 'report') ? instance.id : instance.reportId,
+              state: 'reviewed',
+            },
+            individualHooks: true,
+            paranoid: true,
+            transaction: options.transaction,
+            userId: options.userId,
+          }),
       ]);
     },
     afterCreate: async (instance, options = {}) => {

app/models/germlineSmallMutation/reports.js

@@ -48,7 +48,7 @@ module.exports = (sequelize, Sq) => {
       defaultValue: false,
     },
     state: {
-      type: Sq.ENUM('ready', 'active', 'uploaded', 'signedoff', 'archived', 'reviewed', 'nonproduction', null),
+      type: Sq.ENUM('ready', 'active', 'uploaded', 'signedoff', 'completed', 'reviewed', 'nonproduction', null),
       defaultValue: 'uploaded',
     },
   }, {

app/models/index.js

@@ -17,7 +17,10 @@ const sequelize = new Sq(
     schema: dbSettings.schema,
     logging: null,
     pool: {
-      max: dbSettings.maxConn,
+      max: dbSettings.poolMax,
+      min: dbSettings.poolMin,
+      acquire: dbSettings.poolAcquire,
+      idle: dbSettings.poolIdle,
     },
   },
 );

app/models/reports/genes.js

@@ -31,14 +31,14 @@ module.exports = (sequelize, Sq) => {
       type: Sq.BOOLEAN,
       defaultValue: false,
     },
-    cancerGene: {
-      name: 'cancerGene',
-      field: 'cancer_gene',
+    cancerGeneListMatch: {
+      name: 'cancerGeneListMatch',
+      field: 'cancer_gene_list_match',
       type: Sq.BOOLEAN,
     },
-    cancerRelated: {
-      name: 'cancerRelated',
-      field: 'cancer_related',
+    kbStatementRelated: {
+      name: 'kbStatementRelated',
+      field: 'kb_statement_related',
       type: Sq.BOOLEAN,
       defaultValue: false,
     },

app/models/reports/report.js

@@ -88,6 +88,9 @@ module.exports = (sequelize, Sq) => {
     config: {
       type: Sq.TEXT,
     },
+    appendix: {
+      type: Sq.TEXT,
+    },
     reportVersion: {
       type: Sq.STRING,
       defaultValue: null,
@@ -97,7 +100,7 @@ module.exports = (sequelize, Sq) => {
       defaultValue: null,
     },
     state: {
-      type: Sq.ENUM('ready', 'active', 'uploaded', 'signedoff', 'archived', 'reviewed', 'nonproduction'),
+      type: Sq.ENUM('ready', 'active', 'uploaded', 'signedoff', 'completed', 'reviewed', 'nonproduction'),
       defaultValue: 'ready',
       allowNull: false,
     },

app/routes/germlineSmallMutation/export.download.js

@@ -82,7 +82,7 @@ router.get('/batch/download', async (req, res) => {
               }),
             },
             state: {
-              [Op.in]: ['reviewed', 'active', 'archived'],
+              [Op.in]: ['reviewed', 'active', 'completed'],
             },
           },
           required: true,

app/routes/germlineSmallMutation/reports.js

@@ -130,7 +130,7 @@ router.route('/')
     if (!hasAccessToUnreviewedReports(req.user)) {
       opts.where = {
         ...opts.where,
-        state: ['reviewed', 'archived'],
+        state: ['reviewed', 'completed'],
       };
     }
 

app/routes/report/kbMatches.js

@@ -6,9 +6,6 @@ const router = express.Router({mergeParams: true});
 
 const db = require('../../models');
 const logger = require('../../log');
-const cache = require('../../cache');
-
-const {generateKey} = require('../../libs/cacheFunctions');
 const {KB_PIVOT_MAPPING} = require('../../constants');
 
 // Middleware for kbMatches
@@ -61,20 +58,6 @@ router.route('/')
   .get(async (req, res) => {
     const {query: {matchedCancer, approvedTherapy, category, iprEvidenceLevel}} = req;
 
-    // Check cache
-    const key = generateKey(`/reports/${req.report.ident}/kb-matches`, req.query);
-
-    try {
-      const cacheResults = await cache.get(key);
-
-      if (cacheResults) {
-        res.type('json');
-        return res.send(cacheResults);
-      }
-    } catch (error) {
-      logger.error(`Error while checking cache for kb matches ${error}`);
-    }
-
     try {
       const results = await db.models.kbMatches.scope('public').findAll({
         where: {
@@ -87,10 +70,6 @@ router.route('/')
         order: [['variantType', 'ASC'], ['variantId', 'ASC']],
       });
 
-      if (key) {
-        cache.set(key, JSON.stringify(results), 'EX', 14400);
-      }
-
       return res.json(results);
     } catch (error) {
       logger.error(`Unable to get kb matches ${error}`);

app/routes/report/report.js

@@ -236,7 +236,7 @@ router.route('/')
     if (!hasAccessToUnreviewedReports(req.user)) {
       opts.where = {
         ...opts.where,
-        state: ['reviewed', 'archived'],
+        state: ['reviewed', 'completed'],
       };
     }
 

app/routes/report/variants.js

@@ -70,7 +70,7 @@ const unknownSignificanceIncludes = ['mut'];
 const signatureVariant = ['tmb', 'msi'];
 
 const unknownSignificanceGeneFilter = {
-  [Op.or]: [{oncogene: true}, {tumourSuppressor: true}, {cancerGene: true}],
+  [Op.or]: [{oncogene: true}, {tumourSuppressor: true}, {cancerGeneListMatch: true}],
 };
 
 const getRapidReportVariants = async (tableName, variantType, reportId, rapidTable) => {