Merge pull request #301 from bcgsc/release/v7.20.0

Release/v7.20.0
bcgsc · Feb 13, 2024 · bdb0825 · bdb0825
2 parents b96c08b + 83862c4
commit bdb0825
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Showing 14 changed files with 367 additions and 82 deletions.
diff --git a/app/middleware/acl.js b/app/middleware/acl.js
@@ -88,12 +88,16 @@ module.exports = async (req, res, next) => {
   if (req.report) {
     // check if user is bound to report depending on report type
     let boundUser;
-    if (req.report.biofxAssigned) {
-      boundUser = req.report.biofxAssigned.ident === req.user.ident;
-    } else {
-      boundUser = req.report.users.some((reportUser) => {
-        return reportUser.user.ident === req.user.ident;
-      }) || req.report.createdBy?.ident === req.user.ident;
+    try {
+      if (req.report.biofxAssigned) {
+        boundUser = req.report.biofxAssigned.ident === req.user.ident;
+      } else {
+        boundUser = req.report.users.some((reportUser) => {
+          return reportUser.user.ident === req.user.ident;
+        }) || req.report.createdBy?.ident === req.user.ident;
+      }
+    } catch {
+      logger.error('Error while retrieving bound user');
     }
 
     // If the user doesn't have access to the project this report

diff --git a/app/models/reports/kbMatches.js b/app/models/reports/kbMatches.js
@@ -56,10 +56,6 @@ module.exports = (sequelize, Sq) => {
     sample: {
       type: Sq.TEXT,
     },
-    inferred: {
-      type: Sq.BOOLEAN,
-      defaultValue: false,
-    },
     evidenceLevel: {
       name: 'evidenceLevel',
       field: 'evidence_level',

diff --git a/app/models/reports/mutationBurden.js b/app/models/reports/mutationBurden.js
@@ -13,8 +13,8 @@ module.exports = (sequelize, Sq) => {
       },
     },
     role: {
-      type: Sq.ENUM(['primary', 'secondary', 'tertiary', 'quaternary']),
-      allowNull: false,
+      type: Sq.ENUM(['primary', 'secondary', 'tertiary', 'quaternary', null]),
+      defaultValue: null,
     },
     codingSnvCount: {
       name: 'codingSnvCount',
@@ -115,18 +115,6 @@ module.exports = (sequelize, Sq) => {
   }, {
     ...DEFAULT_REPORT_OPTIONS,
     tableName: 'reports_mutation_burden',
-    indexes: [
-      ...DEFAULT_REPORT_OPTIONS.indexes,
-      {
-        unique: true,
-        fields: ['report_id', 'role'],
-        where: {
-          deleted_at: {
-            [Sq.Op.eq]: null,
-          },
-        },
-      },
-    ],
     scopes: {
       public: {
         attributes: {

diff --git a/app/routes/report/immuneCellTypes.js b/app/routes/report/immuneCellTypes.js
@@ -9,9 +9,13 @@ const cache = require('../../cache');
 
 const schemaGenerator = require('../../schemas/schemaGenerator');
 const validateAgainstSchema = require('../../libs/validateAgainstSchema');
-const {REPORT_UPDATE_BASE_URI} = require('../../constants');
+const {REPORT_UPDATE_BASE_URI, REPORT_CREATE_BASE_URI} = require('../../constants');
+const {REPORT_EXCLUDE} = require('../../schemas/exclude');
 
 // Generate schema's
+const createSchema = schemaGenerator(db.models.immuneCellTypes, {
+  baseUri: REPORT_CREATE_BASE_URI, exclude: REPORT_EXCLUDE,
+});
 const updateSchema = schemaGenerator(db.models.immuneCellTypes, {
   baseUri: REPORT_UPDATE_BASE_URI, nothingRequired: true,
 });
@@ -105,6 +109,30 @@ router.route('/')
         error: {message: 'Unable to retrieve immune cell types'},
       });
     }
+  })
+  .post(async (req, res) => {
+    try {
+      // validate against the model
+      validateAgainstSchema(createSchema, req.body);
+    } catch (error) {
+      const message = `There was an error validating the Immune Cell Type create request ${error}`;
+      logger.error(message);
+      return res.status(HTTP_STATUS.BAD_REQUEST).json({error: {message}});
+    }
+
+    try {
+      // Add new Immune Cell Type to report
+      const result = await db.models.immuneCellTypes.create({
+        ...req.body,
+        reportId: req.report.id,
+      });
+      return res.status(HTTP_STATUS.CREATED).json(result.view('public'));
+    } catch (error) {
+      logger.error(`Unable to create new Immune Cell Type ${error}`);
+      return res.status(HTTP_STATUS.INTERNAL_SERVER_ERROR).json({
+        error: {message: 'Unable to create new Immune Cell Type'},
+      });
+    }
   });
 
 module.exports = router;
diff --git a/app/routes/report/tmburMutationBurden.js b/app/routes/report/tmburMutationBurden.js
@@ -32,7 +32,7 @@ router.use('/', async (req, res, next) => {
     });
   }
 
-  if (!result) {
+  if (!result && req.method !== 'POST') {
     logger.error(`Unable to find Tmbur Mutation Burden for report ${req.report.ident}`);
     return res.status(HTTP_STATUS.NOT_FOUND).json({
       error: {message: `Unable to find Tmbur Mutation Burden for report ${req.report.ident}`},