Merge branch 'develop' into bugfix/DEVSU-2524-reorder-graphkb-evidenc…

…e-levels

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}];
       }
 

app/libs/getUser.js

@@ -76,7 +76,7 @@ const getUser = async (req, res) => {
   }
   // Check for IPR access
   if (!decoded.realm_access.roles.includes(nconf.get('keycloak:role'))) {
-    return res.status(HTTP_STATUS.FORBIDDEN).json({message: 'IPR Access Error'});
+    return res.status(HTTP_STATUS.FORBIDDEN).json({message: 'IPR Access Error: Keycloak role missing'});
   }
   const username = decoded.preferred_username;
   const expiry = decoded.exp;

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'],
+        },
+      ],
     },
   );
 };

app/models/reports/mutationBurden.js

@@ -116,7 +116,7 @@ module.exports = (sequelize, Sq) => {
       name: 'svBurdenHidden',
       field: 'sv_burden_hidden',
       type: Sq.BOOLEAN,
-      defaultValue: false,
+      defaultValue: true,
       allowNull: false,
       jsonSchema: {
         description: 'SV Burden Hidden',

app/models/reports/report.js

@@ -26,6 +26,11 @@ module.exports = (sequelize, Sq) => {
       field: 'hrdetect_score',
       type: Sq.FLOAT,
     },
+    intersectTmbScore: {
+      name: 'intersectTmbScore',
+      field: 'intersect_tmb_score',
+      type: Sq.FLOAT,
+    },
     alternateIdentifier: {
       name: 'alternateIdentifier',
       field: 'alternate_identifier',

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}`;

app/schemas/report/reportUpload/kbMatches.js

@@ -13,6 +13,7 @@ module.exports = (isJsonSchema) => {
         type: 'array', description: 'kbMatched statement object',
       },
       category: {type: 'string', description: 'legacy kbMatch loading'},
+      approvedTherapy: {type: 'boolean', description: 'legacy kbMatch loading'},
       disease: {type: 'string', description: 'legacy kbMatch loading'},
       relevance: {type: 'string', description: 'legacy kbMatch loading'},
       context: {type: 'string', description: 'legacy kbMatch loading'},

migrations/20241106215517-DEVSU-2462-new-report-field.js

@@ -0,0 +1,20 @@
+const TABLE = 'reports';
+
+module.exports = {
+  async up(queryInterface, Sq) {
+    return queryInterface.sequelize.transaction(async (transaction) => {
+      await queryInterface.addColumn(
+        TABLE,
+        'intersect_tmb_score',
+        {
+          type: Sq.FLOAT,
+        },
+        {transaction},
+      );
+    });
+  },
+
+  async down() {
+    throw new Error('Not Implemented!');
+  },
+};

migrations/20241107001943-DEVSU-2473-default-hidesvburden-true.js

@@ -0,0 +1,22 @@
+const TABLE = 'reports_mutation_burden';
+
+module.exports = {
+  async up(queryInterface, Sq) {
+    return queryInterface.sequelize.transaction(async (transaction) => {
+      await queryInterface.changeColumn(
+        TABLE,
+        'sv_burden_hidden',
+        {
+          type: Sq.BOOLEAN,
+          defaultValue: true,
+          allowNull: false,
+        },
+        {transaction},
+      );
+    });
+  },
+
+  async down() {
+    throw new Error('Not Implemented!');
+  },
+};

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!');
+  },
+};

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!');
+  },
+};

test/routes/report/report.test.js

@@ -29,6 +29,7 @@ const checkReport = (report) => {
     'biopsyDate', 'biopsyName', 'presentationDate', 'kbDiseaseMatch',
     'kbUrl', 'pediatricIds', 'captiv8Score', 'appendix', 'hrdetectScore',
     'legacyReportFilepath', 'legacyPresentationFilepath', 'signatures',
+    'intersectTmbScore',
   ].forEach((element) => {
     expect(report).toHaveProperty(element);
   });

test/routes/report/reportAsync.test.js

@@ -27,6 +27,7 @@ const checkReport = (report) => {
     'state', 'expression_matrix', 'alternateIdentifier', 'ageOfConsent',
     'biopsyDate', 'biopsyName', 'presentationDate', 'kbDiseaseMatch',
     'kbUrl', 'pediatricIds', 'captiv8Score', 'hrdetectScore', 'appendix',
+    'intersectTmbScore',
   ].forEach((element) => {
     expect(report).toHaveProperty(element);
   });

test/routes/report/signatureVariants.test.js

@@ -124,7 +124,7 @@ describe('/reports/{REPORTID}/sigv', () => {
     });
 
     afterEach(async () => {
-      await db.models.signatureVariants.destroy({where: {ident: sigvUpdate.ident}, force: true});
+      await db.models.signatureVariants.destroy({where: {ident: sigvUpdate.ident}});
     });
 
     test('/{sigv} - 200 Success', async () => {
@@ -169,7 +169,7 @@ describe('/reports/{REPORTID}/sigv', () => {
     });
 
     afterEach(async () => {
-      await db.models.signatureVariants.destroy({where: {ident: sigvDelete.ident}, force: true});
+      await db.models.signatureVariants.destroy({where: {ident: sigvDelete.ident}});
     });
 
     test('/{sigv} - 204 No content', async () => {
@@ -201,7 +201,7 @@ describe('/reports/{REPORTID}/sigv', () => {
   afterAll(async () => {
     // delete newly created report and all of it's components
     // indirectly by hard deleting newly created patient
-    report.destroy({force: true});
+    report.destroy();
   });
 });
 

test/testData/mockReportData.json

@@ -2,6 +2,7 @@
     "template": "genomic",
     "captiv8Score": 20,
     "hrdetectScore": 10.5,
+    "intersectTmbScore": 9.75,
     "appendix": "this is an example of an appendix",
     "sampleInfo": [
         {
@@ -255,6 +256,7 @@
             "variantType": "exp",
             "variant": "hash12345678",
             "kbVariant": "protein increased expression",
+            "kbVariantId": "123321",
             "category": "cancer predisposition",
             "disease": "colorectal cancer",
             "relevance": "unfavourable",
@@ -268,7 +270,8 @@
             "kbStatementId": "prognostic_unfavourable_lower overall survival_(ELV-PROT_ZNF703_increased expression,True,ns)_colorectal cancer_reported_pubmed_25017610",
             "externalSource": "CIViC",
             "externalStatementId": "1234",
-            "reviewStatus": "pending"
+            "reviewStatus": "pending",
+            "approvedTherapy": true
         },
         {
             "variantType": "msi",