Merge branch 'develop' into feature/DEVSU-2475-update-rapid-report-fi…

…lter
bcgsc · Nov 5, 2024 · 03b02e3 · 03b02e3
2 parents 936bec1 + c5e3691
commit 03b02e3
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Showing 4 changed files with 39 additions and 4 deletions.
diff --git a/app/models/reports/mutationBurden.js b/app/models/reports/mutationBurden.js
@@ -112,6 +112,16 @@ module.exports = (sequelize, Sq) => {
         description: 'somatic indels and SNVs per megabase in the genome',
       },
     },
+    svBurdenHidden: {
+      name: 'svBurdenHidden',
+      field: 'sv_burden_hidden',
+      type: Sq.BOOLEAN,
+      defaultValue: false,
+      allowNull: false,
+      jsonSchema: {
+        description: 'SV Burden Hidden',
+      },
+    },
   }, {
     ...DEFAULT_REPORT_OPTIONS,
     tableName: 'reports_mutation_burden',

diff --git a/migrations/20241021211045-DEVSU-2473-hide-sv-burden-by-default.js b/migrations/20241021211045-DEVSU-2473-hide-sv-burden-by-default.js
@@ -0,0 +1,22 @@
+const TABLE = 'reports_mutation_burden';
+
+module.exports = {
+  async up(queryInterface, Sq) {
+    return queryInterface.sequelize.transaction(async (transaction) => {
+      await queryInterface.addColumn(
+        TABLE,
+        'sv_burden_hidden',
+        {
+          type: Sq.BOOLEAN,
+          defaultValue: false,
+          allowNull: false,
+        },
+        {transaction},
+      );
+    });
+  },
+
+  async down() {
+    throw new Error('Not Implemented!');
+  },
+};
diff --git a/test/routes/report/mutationBurden.test.js b/test/routes/report/mutationBurden.test.js
@@ -23,7 +23,7 @@ const mutationBurdenProperties = [
   'ident', 'createdAt', 'updatedAt', 'role', 'codingSnvCount', 'truncatingSnvCount',
   'codingIndelsCount', 'frameshiftIndelsCount', 'qualitySvCount', 'qualitySvExpressedCount',
   'codingSnvPercentile', 'codingIndelPercentile', 'qualitySvPercentile',
-  'totalSnvCount', 'totalIndelCount', 'totalMutationsPerMb',
+  'totalSnvCount', 'totalIndelCount', 'totalMutationsPerMb', 'svBurdenHidden',
 ];
 
 const checkMutationBurden = (mutationObject) => {

diff --git a/test/testData/mockReportData.json b/test/testData/mockReportData.json
@@ -190,7 +190,8 @@
             "role": "primary",
             "totalSnvCount": 120,
             "totalIndelCount": 80,
-            "totalMutationsPerMb": 56.24
+            "totalMutationsPerMb": 56.24,
+            "svBurdenHidden": true
         },
         {
             "codingSnvCount": 4,
@@ -205,7 +206,8 @@
             "role": "primary",
             "totalSnvCount": 120,
             "totalIndelCount": 80,
-            "totalMutationsPerMb": 56.24
+            "totalMutationsPerMb": 56.24,
+            "svBurdenHidden": true
         },
         {
             "codingSnvCount": 4,
@@ -220,7 +222,8 @@
             "role": null,
             "totalSnvCount": 120,
             "totalIndelCount": 80,
-            "totalMutationsPerMb": 56.24
+            "totalMutationsPerMb": 56.24,
+            "svBurdenHidden": true
         }
     ],
     "tmburMutationBurden": {