Merge branch 'develop' into feature/DEVSU-2824-add-mutation-signature-search

Author: bnguyen-bcgsc

app/libs/createReport.js

@@ -148,6 +148,7 @@ const createReportObservedVariantAnnotationSection = async (reportId, sectionCon
         variantType: record.variantType,
         variantId: record.variantId,
         annotations: record.annotations,
+        flags: record.flags,
       };
 
       const annotation = await db.models.observedVariantAnnotations.create({

app/models/reports/observedVariantAnnotations.js

@@ -37,6 +37,11 @@ module.exports = (sequelize, Sq) => {
         },
       },
     },
+    flags: {
+      name: 'flags',
+      field: 'flags',
+      type: Sq.ARRAY(Sq.TEXT),
+    },
   }, {
     ...DEFAULT_REPORT_OPTIONS,
     tableName: 'reports_observed_variant_annotations',

app/routes/report/observedVariantAnnotations.js

@@ -20,7 +20,7 @@ const createSchema = schemaGenerator(db.models.observedVariantAnnotations, {
 // we only want to allow updates to annotations
 const updateSchema = schemaGenerator(db.models.observedVariantAnnotations, {
   baseUri: REPORT_UPDATE_BASE_URI,
-  required: ['annotations'],
+  required: ['annotations', 'flags'],
   exclude: ['variantType', 'variantId', 'ident', 'createdAt'],
 });
 

app/routes/report/variants.js

@@ -548,9 +548,11 @@ router.route('/set-summary-table/')
       if (!annotationMatch) {
         const newAnnotation = {...(annotation.annotations || {})};
         newAnnotation.rapidReportTableTag = req.body.rapidTable;
+        const newFlags = req.body.flags ?? null;
         try {
           await db.models.observedVariantAnnotations.update({
             annotations: newAnnotation,
+            flags: newFlags,
           }, {where: {id: annotation.id}});
         } catch (error) {
           logger.error(`Unable to create update observed variant annotation ${error}`);
@@ -566,6 +568,7 @@ router.route('/set-summary-table/')
           variantId: req.body.variantId,
           variantType: req.body.variantType,
           annotations: {rapidReportTableTag: req.body.rapidTable},
+          flags: req.body.flags ?? null,
           reportId: req.report.id,
         });
       } catch (error) {

migrations/v8.3.1/20260204193421-DEVSU-2828-add-flags-observed-variant-annotations.js

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

test/routes/report/observedVariantAnnotations.test.js

@@ -101,13 +101,15 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
           variantType: 'cnv',
           variantIdent: variant.ident,
           annotations: {rapidReportTableTag: 'cancerRelevance'},
+          flags: ['test'],
         })
         .expect(StatusCodes.CREATED);
 
       const checkVar = await getVariantByIdent(variant.ident, rapidReportIdent.ident);
       const annotation = checkVar.observedVariantAnnotation;
       expect(annotation.variantType).toEqual('cnv');
       expect(annotation.annotations.rapidReportTableTag).toEqual('cancerRelevance');
+      expect(annotation.flags).toEqual(['test']);
     });
 
     test('Does not create new annotation with no matching variant - OK', async () => {
@@ -119,6 +121,7 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
           variantType: 'mut',
           variantIdent: 'hello',
           annotations: {rapidReportTableTag: 'therapeuticAssociation'},
+          flags: ['test'],
         })
         .expect(StatusCodes.BAD_REQUEST);
     });
@@ -132,6 +135,7 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
           variantType: 'test',
           variantIdent: 'hello',
           annotations: {rapidReportTableTag: 'therapeuticAssociation'},
+          flags: ['test'],
         })
         .expect(StatusCodes.BAD_REQUEST);
     });
@@ -157,6 +161,7 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
           variantType: 'mut',
           variantIdent: variant.ident,
           annotations: {rapidReportTableTag: 'therapeuticAssociation'},
+          flags: ['test'],
         })
         .expect(StatusCodes.CREATED);
 
@@ -168,6 +173,7 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
           variantType: 'mut',
           variantIdent: variant.ident,
           annotations: {rapidReportTableTag: 'cancerRelevance'},
+          flags: ['test'],
         })
         .expect(StatusCodes.CONFLICT);
     });
@@ -198,32 +204,36 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
           variantType: 'mut',
           variantIdent: origVariant.ident,
           annotations,
+          flags: ['test'],
         })
         .expect(StatusCodes.CREATED);
-      console.log('here in test at 205');
 
       // get the created variant annotation and check it's correct
       const createdVar = await getVariantByIdent(origVariant.ident, rapidReportIdent.ident);
       expect(createdVar.observedVariantAnnotation.annotations.secondTag).toEqual(annotations.secondTag);
       expect(createdVar.observedVariantAnnotation.annotations.rapidReportTableTag).toEqual(annotations.rapidReportTableTag);
+      expect(createdVar.observedVariantAnnotation.flags).toEqual(['test']);
 
       // do the update
       const updatedSecondTag = 'testValue2';
       annotations.secondTag = updatedSecondTag;
+      const updatedFlags = ['updated'];
 
       await request
         .put(`/api/reports/${rapidReportIdent.ident}/observed-variant-annotations/${createdVar.observedVariantAnnotation.ident}`)
         .auth(username, password)
         .type('json')
         .send({
           annotations,
+          flags: updatedFlags,
         })
         .expect(StatusCodes.OK);
 
       // get the new variant data
       const updatedVar = await getVariantByIdent(origVariant.ident, rapidReportIdent.ident);
       expect(updatedVar.observedVariantAnnotation.annotations.secondTag).toEqual(updatedSecondTag);
       expect(updatedVar.observedVariantAnnotation.annotations.rapidReportTableTag).toEqual(annotations.rapidReportTableTag);
+      expect(updatedVar.observedVariantAnnotation.flags).toEqual(updatedFlags);
     });
   });
 
@@ -260,6 +270,7 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
           variantType,
           variantIdent: record.ident,
           annotations,
+          flags: ['test'],
         })
         .expect(StatusCodes.CREATED);
 
@@ -275,6 +286,7 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
         .expect(StatusCodes.OK);
       const record2 = res2.body;
       expect(record2.observedVariantAnnotation.annotations.testTag).toEqual(annotations.testTag);
+      expect(record2.observedVariantAnnotation.flags).toEqual(['test']);
     });
 
     test('Annotations delivered with variants endpt - OK', async () => {
@@ -305,6 +317,7 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
           variantType: record.variantType,
           variantIdent: record.ident,
           annotations,
+          flags: ['test'],
         })
         .expect(StatusCodes.CREATED);
 
@@ -317,6 +330,7 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
         return variant.ident === record.ident;
       })[0];
       expect(updatedRecord.observedVariantAnnotation.annotations.testTag).toEqual(annotations.testTag);
+      expect(updatedRecord.observedVariantAnnotation.flags).toEqual(['test']);
     });
 
     // skipping test as rapid report tagging now works through different endpoint
@@ -346,6 +360,7 @@ describe('/reports/{REPORTID}/observed-variant-annotations', () => {
           variantType: record.variantType,
           variantIdent: record.ident,
           annotations: {rapidReportTableTag: 'cancerRelevance', testTag: 'testValue'},
+          flags: ['test'],
         })
         .expect(StatusCodes.CREATED);