Merge pull request #221 from bcgsc/release/v7.12.0

Release/v7.12.0

app/models/germlineSmallMutation/variants.js

@@ -200,6 +200,31 @@ module.exports = (sequelize, Sq) => {
       type: Sq.TEXT,
       allowNull: true,
     },
+    cglReviewResult: {
+      name: 'cglReviewResult',
+      field: 'cgl_review_result',
+      type: Sq.ENUM(['pathogenic', 'likely pathogenic', 'VUS', 'likely benign', 'benign']),
+    },
+    returnedToClinician: {
+      name: 'returnedToClinician',
+      field: 'returned_to_clinician',
+      type: Sq.ENUM(['yes', 'no']),
+    },
+    referralHcp: {
+      name: 'referralHcp',
+      field: 'referral_hcp',
+      type: Sq.ENUM(['yes', 'no']),
+    },
+    knownToHcp: {
+      name: 'knownToHcp',
+      field: 'known_to_hcp',
+      type: Sq.ENUM(['yes', 'no']),
+    },
+    reasonNoHcpReferral: {
+      name: 'reasonNoHcpReferral',
+      field: 'reason_no_hcp_referral',
+      type: Sq.TEXT,
+    },
   }, {
     ...DEFAULT_OPTIONS,
     tableName: 'germline_small_mutations_variant',

app/routes/report/index.js

@@ -26,6 +26,7 @@ const patientInformation = require('./patientInformation');
 const images = require('./image');
 const msi = require('./msi');
 const reportUser = require('./reportUser');
+const variants = require('./variants');
 
 const router = express.Router({mergeParams: true});
 
@@ -56,5 +57,6 @@ router.use('/genes', gene);
 router.use('/patient-information', patientInformation);
 router.use('/msi', msi);
 router.use('/user', reportUser);
+router.use('/variants', variants);
 
 module.exports = router;

app/routes/report/kbMatches.js

@@ -1,6 +1,6 @@
 const HTTP_STATUS = require('http-status-codes');
 const express = require('express');
-const {Op, literal} = require('sequelize');
+const {Op} = require('sequelize');
 
 const router = express.Router({mergeParams: true});
 
@@ -59,7 +59,7 @@ router.route('/:kbMatch([A-z0-9-]{36})')
 
 router.route('/')
   .get(async (req, res) => {
-    const {query: {matchedCancer, approvedTherapy, category, rapidTable}} = req;
+    const {query: {matchedCancer, approvedTherapy, category}} = req;
 
     // Check cache
     const key = generateKey(`/reports/${req.report.ident}/kb-matches`, req.query);
@@ -76,37 +76,12 @@ router.route('/')
     }
 
     try {
-      const therapeuticAssociationFilter = {
-        [Op.or]: [{iprEvidenceLevel: ['IPR-A', 'IPR-B']}],
-        category: 'therapeutic',
-        matchedCancer: true,
-        variantType: {[Op.is]: literal('distinct from \'exp\'')},
-      };
-
-      // PSQL natively ignores null on equal checks.
-      // Literal is used in order to accomodate NULL rows.
-      const cancerRelevanceFilter = {
-        [Op.not]: {
-          [Op.or]: [
-            {iprEvidenceLevel: {[Op.is]: literal('not distinct from \'IPR-A\'')}},
-            {iprEvidenceLevel: {[Op.is]: literal('not distinct from \'IPR-B\'')}},
-          ],
-          category: 'therapeutic',
-          matchedCancer: true,
-        },
-        variantType: {[Op.is]: literal('distinct from \'exp\'')},
-      };
-
       const results = await db.models.kbMatches.scope('public').findAll({
         where: {
           reportId: req.report.id,
           ...((category) ? {category: {[Op.in]: category.split(',')}} : {}),
           ...((typeof matchedCancer === 'boolean') ? {matchedCancer} : {}),
           ...((typeof approvedTherapy === 'boolean') ? {approvedTherapy} : {}),
-          ...((rapidTable === 'therapeuticAssociation')
-            ? therapeuticAssociationFilter : {}),
-          ...((rapidTable === 'cancerRelevance')
-            ? cancerRelevanceFilter : {}),
         },
         order: [['variantType', 'ASC'], ['variantId', 'ASC']],
       });

app/routes/report/variants.js

@@ -0,0 +1,184 @@
+const HTTP_STATUS = require('http-status-codes');
+const express = require('express');
+
+const router = express.Router({mergeParams: true});
+
+const {Op, literal} = require('sequelize');
+const db = require('../../models');
+const logger = require('../../log');
+
+const {KB_PIVOT_MAPPING} = require('../../constants');
+
+const KBMATCHEXCLUDE = ['id', 'reportId', 'variantId', 'deletedAt', 'updatedBy'];
+const getVariants = async (tableName, variantType, reportId) => {
+  return db.models[tableName].scope('extended').findAll({
+    order: [['id', 'ASC']],
+    attributes: {
+      include: [[literal(`'${variantType}'`), 'variantType']],
+    },
+    where: {
+      reportId,
+    },
+    include: [
+      {
+        model: db.models.kbMatches,
+        attributes: {exclude: KBMATCHEXCLUDE},
+      },
+    ],
+  });
+};
+
+const therapeuticAssociationFilter = {
+  id: {[Op.ne]: null},
+  [Op.or]: [{iprEvidenceLevel: ['IPR-A', 'IPR-B']}],
+  category: 'therapeutic',
+  matchedCancer: true,
+  variantType: {[Op.is]: literal('distinct from \'exp\'')},
+};
+
+// PSQL natively ignores null on equal checks.
+// Literal is used in order to accomodate NULL rows.
+const cancerRelevanceFilter = {
+  id: {[Op.ne]: null},
+  [Op.not]: {
+    [Op.or]: [
+      {iprEvidenceLevel: {[Op.is]: literal('not distinct from \'IPR-A\'')}},
+      {iprEvidenceLevel: {[Op.is]: literal('not distinct from \'IPR-B\'')}},
+    ],
+    category: 'therapeutic',
+    matchedCancer: true,
+  },
+  variantType: {[Op.is]: literal('distinct from \'exp\'')},
+};
+
+const unknownSignificanceIncludes = ['mut'];
+
+const unknownSignificanceGeneFilter = {
+  [Op.or]: [{oncogene: true}, {tumourSuppressor: true}],
+};
+
+const getRapidReportVariants = async (tableName, variantType, reportId, rapidTable) => {
+  const therapeuticAssociationResults = await db.models[tableName].scope('extended').findAll({
+    order: [['id', 'ASC']],
+    attributes: {
+      include: [[literal(`'${variantType}'`), 'variantType']],
+    },
+    where: {
+      reportId,
+    },
+    include: [
+      {
+        model: db.models.kbMatches,
+        attributes: {exclude: KBMATCHEXCLUDE},
+        where: {...therapeuticAssociationFilter},
+      },
+    ],
+  });
+
+  if (rapidTable === 'therapeuticAssociation') {
+    return therapeuticAssociationResults;
+  }
+
+  const cancerRelevanceResultsFiltered = [];
+  const cancerRelevanceResults = await db.models[tableName].scope('extended').findAll({
+    order: [['id', 'ASC']],
+    attributes: {
+      include: [[literal(`'${variantType}'`), 'variantType']],
+    },
+    where: {
+      reportId,
+    },
+    include: [
+      {
+        model: db.models.kbMatches,
+        where: {...cancerRelevanceFilter},
+        attributes: {exclude: KBMATCHEXCLUDE},
+      },
+    ],
+  });
+
+  for (const row of cancerRelevanceResults) {
+    if (!(therapeuticAssociationResults.find(
+      (e) => {return e.ident === row.ident;},
+    ))) {
+      cancerRelevanceResultsFiltered.push(row);
+    }
+  }
+
+  if (rapidTable === 'cancerRelevance') {
+    return cancerRelevanceResultsFiltered;
+  }
+
+  const unknownSignificanceResultsFiltered = [];
+  let unknownSignificanceResults = [];
+
+  if (unknownSignificanceIncludes.includes(variantType)) {
+    unknownSignificanceResults = await db.models[tableName].scope('extended').findAll({
+      order: [['id', 'ASC']],
+      attributes: {
+        include: [[literal(`'${variantType}'`), 'variantType']],
+      },
+      where: {
+        reportId,
+      },
+      include: [
+        {
+          model: db.models.kbMatches,
+          attributes: {exclude: KBMATCHEXCLUDE},
+        },
+        {
+          model: db.models.genes.scope('minimal'),
+          as: 'gene',
+          where: unknownSignificanceGeneFilter,
+        },
+      ],
+    });
+  }
+
+  for (const row of unknownSignificanceResults) {
+    if (!(therapeuticAssociationResults.find(
+      (e) => {return e.ident === row.ident;},
+    )) && !(cancerRelevanceResultsFiltered.find(
+      (e) => {return e.ident === row.ident;},
+    ))) {
+      unknownSignificanceResultsFiltered.push(row);
+    }
+  }
+
+  return unknownSignificanceResultsFiltered;
+};
+
+// Routing for Alteration
+router.route('/')
+  .get(async (req, res) => {
+    // Get all variants for this report
+    // Cache was removed from this endpoint due to requiring multiple tables,
+    // increasing the chance of retrieving outdated data
+    const {query: {rapidTable}} = req;
+
+    try {
+      const variantTypes = Object.keys(KB_PIVOT_MAPPING);
+      const variantsArray = [];
+
+      for (const variantType of variantTypes) {
+        const tableName = KB_PIVOT_MAPPING[variantType];
+
+        if (rapidTable) {
+          variantsArray.push(await getRapidReportVariants(tableName, variantType, req.report.id, rapidTable));
+        } else {
+          variantsArray.push(await getVariants(tableName, variantType, req.report.id));
+        }
+      }
+
+      const results = variantsArray.flat(1);
+
+      return res.json(results);
+    } catch (error) {
+      logger.error(`Unable to retrieve variants ${error}`);
+      return res.status(HTTP_STATUS.INTERNAL_SERVER_ERROR).json({
+        error: {message: 'Unable to retrieve variants'},
+      });
+    }
+  });
+
+module.exports = router;

migrations/20221202195545-DEVSU-1891-add-columns-to-germline-report.js

@@ -0,0 +1,47 @@
+const GSM_TABLE = 'germline_small_mutations_variant';
+
+module.exports = {
+  up: async (queryInterface, Sq) => {
+    return queryInterface.sequelize.transaction(async (transaction) => {
+      await queryInterface.addColumn(
+        GSM_TABLE,
+        'cgl_review_result',
+        {type: Sq.ENUM(['pathogenic', 'likely pathogenic', 'VUS', 'likely benign', 'benign']),
+          defaultValue: null},
+        {transaction},
+      );
+      await queryInterface.addColumn(
+        GSM_TABLE,
+        'returned_to_clinician',
+        {type: Sq.ENUM(['yes', 'no']),
+          defaultValue: null},
+        {transaction},
+      );
+      await queryInterface.addColumn(
+        GSM_TABLE,
+        'referral_hcp',
+        {type: Sq.ENUM(['yes', 'no']),
+          defaultValue: null},
+        {transaction},
+      );
+      await queryInterface.addColumn(
+        GSM_TABLE,
+        'known_to_hcp',
+        {type: Sq.ENUM(['yes', 'no']),
+          defaultValue: null},
+        {transaction},
+      );
+      await queryInterface.addColumn(
+        GSM_TABLE,
+        'reason_no_hcp_referral',
+        {type: Sq.TEXT,
+          defaultValue: null},
+        {transaction},
+      );
+    });
+  },
+
+  down: async () => {
+    throw new Error('Not Implemented!');
+  },
+};

package.json

@@ -1,7 +1,7 @@
 {
   "private": true,
   "name": "ipr-api",
-  "version": "7.11.2",
+  "version": "7.12.0",
   "description": "Integrated Pipeline Reports API",
   "main": "bin/server.js",
   "scripts": {