Merge pull request #226 from bcgsc/feature/DEVSU-1886-update-kbMatche…

…s-enum feature/DEVSU-1886-update-kbMatches
bcgsc · Feb 10, 2023 · 412cdd5 · 412cdd5
2 parents 0ea1d87 + eb9337a
commit 412cdd5
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Showing 6 changed files with 58 additions and 11 deletions.
diff --git a/app/constants.js b/app/constants.js
@@ -6,6 +6,7 @@ module.exports = {
     mut: 'smallMutations',
     exp: 'expressionVariants',
     protein: 'proteinVariants',
+    msi: 'msi',
   },
   KB_PIVOT_COLUMN: 'variantType',
   GENE_LINKED_VARIANT_MODELS: [

diff --git a/app/models/index.js b/app/models/index.js
@@ -207,6 +207,16 @@ analysisReports.hasMany(immuneCellTypes, {
   as: 'immuneCellTypes', foreignKey: 'reportId', onDelete: 'CASCADE', constraints: true,
 });
 
+// MSI
+const msi = require('./reports/msi')(sequelize, Sq);
+
+analysisReports.hasMany(msi, {
+  as: 'msi', foreignKey: 'reportId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
+});
+msi.belongsTo(analysisReports, {
+  as: 'report', foreignKey: 'reportId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
+});
+
 // Copy Number Analysis
 const copyVariants = require('./reports/copyVariants')(sequelize, Sq);
 
@@ -441,16 +451,6 @@ comparators.belongsTo(analysisReports, {
   as: 'report', foreignKey: 'reportId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
 });
 
-// MSI
-const msi = require('./reports/msi')(sequelize, Sq);
-
-analysisReports.hasMany(msi, {
-  as: 'msi', foreignKey: 'reportId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
-});
-msi.belongsTo(analysisReports, {
-  as: 'report', foreignKey: 'reportId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
-});
-
 // Images
 const image = require('./image')(sequelize, Sq);
 

diff --git a/app/models/reports/msi.js b/app/models/reports/msi.js
@@ -30,6 +30,11 @@ module.exports = (sequelize, Sq) => {
           exclude: ['id', 'reportId', 'deletedAt', 'updatedBy'],
         },
       },
+      extended: {
+        attributes: {
+          exclude: ['id', 'reportId', 'deletedAt', 'updatedBy'],
+        },
+      },
     },
   });
 

diff --git a/app/schemas/report/reportUpload/variant.js b/app/schemas/report/reportUpload/variant.js
@@ -50,6 +50,17 @@ const generateVariantUploadSchemas = (isJsonSchema) => {
     });
   });
 
+  variantSchemas.msi = schemaGenerator(db.models.msi, {
+    isJsonSchema,
+    baseUri: UPLOAD_BASE_URI,
+    properties: {
+      key: {
+        type: 'string', description: 'Unique identifier for this variant within this section used to link it to kb-matches',
+      },
+    },
+    isSubSchema: true,
+  });
+
   return variantSchemas;
 };
 

diff --git a/migrations/20230208194424-DEVSU-1886-update-kbMatches-enum.js b/migrations/20230208194424-DEVSU-1886-update-kbMatches-enum.js
@@ -0,0 +1,9 @@
+module.exports = {
+  up: async (queryInterface) => {
+    queryInterface.sequelize.query('ALTER TYPE enum_reports_kb_matches_variant_type ADD VALUE \'msi\'');
+  },
+
+  down: async () => {
+    throw new Error('Not Implemented!');
+  },
+};
diff --git a/test/testData/mockReportData.json b/test/testData/mockReportData.json
@@ -215,6 +215,26 @@
             "externalSource": "CIViC",
             "externalStatementId": "1234",
             "reviewStatus": "pending"
+        },
+        {
+            "category": "cancer predisposition",
+            "variantType": "msi",
+            "variant": "msi",
+            "kbVariant": "protein increased expression",
+            "disease": "colorectal cancer",
+            "relevance": "unfavourable",
+            "context": "lower overall survival",
+            "status": "na",
+            "reference": "12345678#",
+            "sample": "UPLOADPAT01-FFPE-1; UPLOADPAT01-FFPE-1_trans",
+            "evidenceLevel": "reported",
+            "matchedCancer": false,
+            "pmidRef": "yes",
+            "kbStatementId": "prognostic_unfavourable_lower overall survival_(ELV-PROT_ZNF703_increased expression,True,ns)_colorectal cancer_reported_pubmed_25017610",
+            "inferred": false,
+            "externalSource": "CIViC",
+            "externalStatementId": "1234",
+            "reviewStatus": "pending"
         }
     ],
     "genes": [
@@ -415,7 +435,8 @@
     "msi": [
         {
             "score": 19.5,
-            "kbCategory": "moderate"
+            "kbCategory": "moderate",
+            "key": "msi"
         }
     ],
     "project": "TEST",