Merge branch 'develop' into feat/DEVSU-2473-hide-sv-burden-by-default

bcgsc · Nov 19, 2024 · b10c22c · b10c22c
2 parents fcc5465 + 3e72a3d
commit b10c22c
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diff --git a/app/libs/createReport.js b/app/libs/createReport.js
@@ -76,12 +76,14 @@ const createReportKbMatchSection = async (reportId, modelName, sectionContent, o
           variantType: record.variantType,
           variantId: record.variantId,
           kbVariant: record.kbVariant,
+          kbVariantId: record.kbVariantId,
         };
 
         const statementCopy = {...record};
         delete statementCopy.variantType;
         delete statementCopy.variantId;
         delete statementCopy.kbVariant;
+        delete statementCopy.kbVariantId;
         statementData = [{...statementCopy}];
       }
 

diff --git a/app/models/reports/kbMatchJoin.js b/app/models/reports/kbMatchJoin.js
@@ -38,6 +38,16 @@ module.exports = (sequelize, Sq) => {
           },
         },
       },
+      indexes: [
+        {
+          name: 'idx_kb_match_id_join',
+          fields: ['kb_match_id'],
+        },
+        {
+          name: 'idx_kb_matched_statement_id_join',
+          fields: ['kb_matched_statement_id'],
+        },
+      ],
     },
   );
 };
diff --git a/app/routes/variantText/variantText.js b/app/routes/variantText/variantText.js
@@ -203,6 +203,10 @@ router.route('/')
       delete req.body.project;
       delete req.body.template;
 
+      if (typeof req.body.cancerType === 'string') {
+        req.body.cancerType = [req.body.cancerType];
+      }
+
       await validateAgainstSchema(createSchema, req.body);
     } catch (error) {
       const message = `Error while validating variant text create request ${error}`;

diff --git a/migrations/20241112210700-DEVSU-2457-fix-id-sequence.js b/migrations/20241112210700-DEVSU-2457-fix-id-sequence.js
@@ -0,0 +1,10 @@
+module.exports = {
+  up: async (queryInterface) => {
+    // eslint-disable-next-line max-len
+    queryInterface.sequelize.query('SELECT setval(\'reports_kb_matches_id_seq\', (SELECT MAX(id) FROM reports_kb_matches) + 1);');
+  },
+
+  down: async () => {
+    throw new Error('Not Implemented!');
+  },
+};
diff --git a/migrations/20241112211455-DEVSU-2483-add-kb-match-index.js b/migrations/20241112211455-DEVSU-2483-add-kb-match-index.js
@@ -0,0 +1,14 @@
+module.exports = {
+  up: async (queryInterface) => {
+    await queryInterface.addIndex('reports_kb_match_join', ['kb_match_id'], {
+      name: 'idx_kb_match_id_join',
+    });
+    await queryInterface.addIndex('reports_kb_match_join', ['kb_matched_statement_id'], {
+      name: 'idx_kb_matched_statement_id_join',
+    });
+  },
+
+  down: async () => {
+    throw new Error('Not Implemented!');
+  },
+};
diff --git a/test/testData/mockReportData.json b/test/testData/mockReportData.json
@@ -256,6 +256,7 @@
             "variantType": "exp",
             "variant": "hash12345678",
             "kbVariant": "protein increased expression",
+            "kbVariantId": "123321",
             "category": "cancer predisposition",
             "disease": "colorectal cancer",
             "relevance": "unfavourable",