Merge branch 'develop' into feature/DEVSU-2656-email-notification

Author: sshugsc

app/libs/createReport.js

@@ -21,6 +21,7 @@ const EXCLUDE_SECTIONS = new Set([
   'ReportUserFilter',
   'users',
   'kbMatchedStatements',
+  'observedVariantAnnotations',
 ]);
 
 /**
@@ -126,6 +127,42 @@ const createStatementMatching = async (reportId, content, createdKbMatches, tran
   }
 };
 
+/**
+ * Creates a new section for the report with the provided data
+ *
+ * @param {Number} reportId - The id of the report this section belongs to
+ * @param {Array|Object} sectionContent - The record or records to be created for this section
+ * @param {object} options - Options for creating report sections
+ * @property {object} options.transaction - Transaction to run bulkCreate under
+ *
+ * @returns {undefined}
+ */
+const createReportObservedVariantAnnotationSection = async (reportId, sectionContent, options = {}) => {
+  const records = Array.isArray(sectionContent)
+    ? sectionContent
+    : [sectionContent];
+  const retvals = [];
+  try {
+    for (const record of records) {
+      const annotationData = {
+        variantType: record.variantType,
+        variantId: record.variantId,
+        annotations: record.annotations,
+      };
+
+      const annotation = await db.models.observedVariantAnnotations.create({
+        reportId,
+        ...annotationData,
+      }, options);
+      annotation.dataValues.variant = record.variant;
+      retvals.push(annotation.dataValues);
+    }
+    return retvals;
+  } catch (error) {
+    throw new Error(`Unable to create section observedVariantAnnotation: ${error.message || error}`);
+  }
+};
+
 /**
  * Given the content for a report to be created, pull gene names from
  * the variant sections and create the genes which will be used as
@@ -237,10 +274,8 @@ const createReportVariantsSection = async (reportId, genesRecordsByName, modelNa
       keyCheck.add(key);
     }
   }
-
   try {
     if (modelName === 'structuralVariants') {
-      // add the gene FK associations
       records = await db.models[modelName].bulkCreate(sectionContent.map(({
         key, gene1, gene2, ...newEntry
       }) => {
@@ -252,7 +287,6 @@ const createReportVariantsSection = async (reportId, genesRecordsByName, modelNa
         };
       }), options);
     } else {
-      // add the gene FK association
       records = await db.models[modelName].bulkCreate(sectionContent.map(({key, gene, ...newEntry}) => {
         return {
           ...newEntry,
@@ -264,7 +298,6 @@ const createReportVariantsSection = async (reportId, genesRecordsByName, modelNa
   } catch (error) {
     throw new Error(`Unable to create variant section (${modelName}) ${error.message || error}`);
   }
-
   const mapping = {};
   for (let i = 0; i < sectionContent.length; i++) {
     if (sectionContent[i].key) {
@@ -277,7 +310,6 @@ const createReportVariantsSection = async (reportId, genesRecordsByName, modelNa
 const createReportVariantSections = async (report, content, transaction) => {
   // create the genes first since they will need to be linked to the variant records
   const geneDefns = await createReportGenes(report, content, {transaction});
-
   // create the variants and create a mapping from their input 'key' value to the new records
   const variantMapping = {};
   const variantPromises = Object.keys(KB_PIVOT_MAPPING).map(async (variantType) => {
@@ -287,16 +319,14 @@ const createReportVariantSections = async (report, content, transaction) => {
     if (!Array.isArray(content[variantModel]) && typeof content[variantModel] === 'object') {
       content[variantModel] = [content[variantModel]];
     }
-
     const mapping = await createReportVariantsSection(report.id, geneDefns, variantModel, content[variantModel] || [], {transaction});
+
     variantMapping[variantType] = mapping;
   });
-
   // create the probe results (linked to gene but not to kbMatches)
   variantPromises.push(createReportVariantsSection(report.id, geneDefns, 'probeResults', content.probeResults || [], {transaction}));
 
   await Promise.all(variantPromises);
-
   // then the kb matches which must be linked to the variants
   const kbMatches = (content.kbMatches || []).map(({variant, variantType, ...match}) => {
     if (variantMapping[variantType] === undefined) {
@@ -313,6 +343,19 @@ const createReportVariantSections = async (report, content, transaction) => {
   const createdKbMatches = await createReportKbMatchSection(report.id, 'kbMatches', kbMatches, {transaction});
 
   await createStatementMatching(report.id, content, createdKbMatches, transaction);
+  // then the observed variant annotations which must be linked to the variants
+
+  const observedVariantAnnotations = (content.observedVariantAnnotations || []).map(({variant, variantType, ...annotation}) => {
+    if (variantMapping[variantType] === undefined) {
+      throw new Error(`cannot link annotations to variant type ${variantType} as none were specified`);
+    }
+    if (variantMapping[variantType][variant] === undefined) {
+      throw new Error(`invalid link (variant=${variant}) variant definition does not exist`);
+    }
+    return {...annotation, variantId: variantMapping[variantType][variant], variantType, variant};
+  });
+
+  await createReportObservedVariantAnnotationSection(report.id, observedVariantAnnotations, {transaction});
 };
 
 /**

app/models/index.js

@@ -424,6 +424,13 @@ for (const [pivotValue, modelName] of Object.entries(KB_PIVOT_MAPPING)) {
   });
 }
 
+observedVariantAnnotations.belongsTo(analysisReports, {
+  as: 'report', foreignKey: 'reportId', targetKey: 'id', onDelete: 'CASCADE', constraints: true, foreignKeyConstraint: true,
+});
+analysisReports.hasMany(observedVariantAnnotations, {
+  as: 'observedVariantAnnotations', foreignKey: 'reportId', onDelete: 'CASCADE', constraints: true, foreignKeyConstraint: true,
+});
+
 // Presentation Data
 const presentation = {};
 presentation.discussion = require('./reports/genomic/presentation/discussion.model')(sequelize, Sq);

app/schemas/report/reportUpload/index.js

@@ -2,6 +2,7 @@ const db = require('../../../models');
 const {BASE_EXCLUDE} = require('../../exclude');
 const variantSchemas = require('./variant');
 const kbMatchesSchema = require('./kbMatches');
+const observedVariantAnnotationsSchema = require('./observedVariantAnnotations');
 const schemaGenerator = require('../../schemaGenerator');
 const {UPLOAD_BASE_URI} = require('../../../constants');
 
@@ -68,7 +69,7 @@ const generateReportUploadSchema = (isJsonSchema) => {
     presentationSlides, users, projects, ...associations
   } = db.models.report.associations;
 
-  schema.definitions = {...variantSchemas(isJsonSchema), kbMatches: kbMatchesSchema(isJsonSchema)};
+  schema.definitions = {...variantSchemas(isJsonSchema), kbMatches: kbMatchesSchema(isJsonSchema), observedVariantAnnotations: observedVariantAnnotationsSchema(isJsonSchema)};
 
   // add all associated schemas
   Object.values(associations).forEach((association) => {
@@ -86,7 +87,6 @@ const generateReportUploadSchema = (isJsonSchema) => {
       schema.definitions[model] = generatedSchema;
     }
   });
-
   return schema;
 };
 

app/schemas/report/reportUpload/observedVariantAnnotations.js

@@ -0,0 +1,18 @@
+const db = require('../../../models');
+const schemaGenerator = require('../../schemaGenerator');
+const {REPORT_EXCLUDE} = require('../../exclude');
+
+module.exports = (isJsonSchema) => {
+  return schemaGenerator(db.models.observedVariantAnnotations, {
+    isJsonSchema,
+    properties: {
+      variant: {
+        type: 'string', description: 'the variant key linking this to one of the variant records',
+      },
+      annotations: {type: 'object', description: 'json annotations'},
+    },
+    isSubSchema: true,
+    exclude: [...REPORT_EXCLUDE, 'variantId'],
+    required: ['variant'],
+  });
+};

test/reportUpload.test.js

@@ -226,6 +226,19 @@ describe('Tests for uploading a report and all of its components', () => {
     expect(totalExpectedStatements).toEqual(kbStatements.length);
   });
 
+  test('ObservedVariantAnnotations are linked correctly to observed variants', async () => {
+    const muts = await db.models.smallMutations.findAll({where: {report_id: reportId}});
+    const test3mut = muts.filter((mut) => {
+      return mut.hgvsProtein === 'ZFP36L2:p.Q111del-test3';
+    })[0];
+    const annotations = await db.models.observedVariantAnnotations.findAll({where: {report_id: reportId}});
+    const test3annotation = annotations.filter((ann) => {
+      return ann.annotations.isThisAnObservedVariantAnnotationsTest;
+    })[0];
+    expect(test3annotation.variantType).toEqual('mut');
+    expect(test3annotation.variantId).toEqual(test3mut.id);
+  });
+
   test('One variant record created for each input kbmatch record', async () => {
     const variants = mockReportData.kbMatches;
     expect(variants.length).toEqual(kbVariants.length);

test/testData/mockReportData.json

@@ -494,6 +494,15 @@
             "kbStatementRelated": true
         }
     ],
+    "observedVariantAnnotations": [
+        {
+            "variant": "test3",
+            "variantType": "mut",
+            "annotations": {
+                "isThisAnObservedVariantAnnotationsTest": true
+            }
+        }
+    ],
     "smallMutations": [
         {
             "gene": "ZFP36L2",
@@ -552,6 +561,34 @@
             "library": "TEST LIBRARY",
             "selected": false,
             "key": "test1"
+        },
+        {
+            "gene": "ZFP36L2",
+            "transcript": "ENST00000282388",
+            "proteinChange": "p.Q999del",
+            "startPosition": 43451739,
+            "endPosition": 43451739,
+            "chromosome": "2",
+            "refSeq": "CCTG",
+            "altSeq": "C",
+            "zygosity": "sub [0/3]",
+            "tumourRefCount": 583,
+            "tumourAltCount": 4,
+            "tumourDepth": 590,
+            "rnaRefCount": 400,
+            "rnaAltCount": 15,
+            "rnaDepth": 415,
+            "normalRefCount": 40,
+            "normalAltCount": 0,
+            "normalDepth": 40,
+            "ncbiBuild": "GRCh37",
+            "hgvsProtein": "ZFP36L2:p.Q111del-test3",
+            "germline": false,
+            "tumourRefCopies": 60,
+            "tumourAltCopies": 20,
+            "library": "TEST LIBRARY",
+            "selected": false,
+            "key": "test3"
         }
     ],
     "mutationSignature": [