bugfix/DEVSU-2131-fix-rapid-report-filter

.github/workflows/npm-test.yml

@@ -10,7 +10,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node: [14, 16, 18, 20]
+        node: [18, 20]
+        # TODO: readd node versions: node: [14, 16, 18, 20]
     name: node-${{ matrix.node }}
     services:
       postgres:

app/middleware/report.js

@@ -1,7 +1,6 @@
 const HTTP_STATUS = require('http-status-codes');
 const db = require('../models');
 const logger = require('../log');
-const cache = require('../cache');
 const aclMiddleware = require('./acl');
 const {hasAccessToNonProdReports} = require('../libs/helperFunctions');
 
@@ -29,48 +28,28 @@ module.exports = async (req, res, next, ident) => {
     },
   ];
 
-  // Check cache for report
-  const key = `/reports/${ident}`;
   let result;
 
   try {
-    result = await cache.get(key);
-  } catch (error) {
-    logger.error(`Error during report cache get ${error}`);
-  }
-
-  if (result) {
-    // Build Sequelize model from cached string without calling db
-    result = db.models.report.build(JSON.parse(result), {
-      raw: true,
-      isNewRecord: false,
+    result = await db.models.report.findOne({
+      where: {ident},
+      attributes: {exclude: ['config']},
       include,
     });
-  } else {
-    try {
-      result = await db.models.report.findOne({
-        where: {ident},
-        attributes: {exclude: ['config']},
-        include,
-      });
-    } catch (error) {
-      logger.error(`Error while trying to get report: ${ident} ${error}`);
-      return res.status(HTTP_STATUS.INTERNAL_SERVER_ERROR).json({error: {message: 'Error while trying to get report'}});
-    }
-
-    // Nothing found?
-    if (!result) {
-      logger.error(`Unable to find the requested report ${ident}`);
-      return res.status(HTTP_STATUS.NOT_FOUND).json({error: {message: 'Unable to find the requested report'}});
-    }
+  } catch (error) {
+    logger.error(`Error while trying to get report: ${ident} ${error}`);
+    return res.status(HTTP_STATUS.INTERNAL_SERVER_ERROR).json({error: {message: 'Error while trying to get report'}});
+  }
 
-    if (!hasAccessToNonProdReports(req.user) && result.state === 'nonproduction') {
-      logger.error(`User does not have non-production access to ${ident}`);
-      return res.status(HTTP_STATUS.FORBIDDEN).json({error: {message: 'User does not have access to Non-Production reports'}});
-    }
+  // Nothing found?
+  if (!result) {
+    logger.error(`Unable to find the requested report ${ident}`);
+    return res.status(HTTP_STATUS.NOT_FOUND).json({error: {message: 'Unable to find the requested report'}});
+  }
 
-    // Add result to cache
-    cache.set(key, JSON.stringify(result), 'EX', 14400);
+  if (!hasAccessToNonProdReports(req.user) && result.state === 'nonproduction') {
+    logger.error(`User does not have non-production access to ${ident}`);
+    return res.status(HTTP_STATUS.FORBIDDEN).json({error: {message: 'User does not have access to Non-Production reports'}});
   }
 
   // Add report to request

app/routes/report/variants.js

@@ -37,18 +37,18 @@ const therapeuticAssociationFilter = {
   matchedCancer: true,
   variantType: {[Op.and]: [
     {[Op.is]: literal('distinct from \'exp\'')},
-    {[Op.is]: literal('distinct from \'msi\'')},
-    {[Op.is]: literal('distinct from \'tmb\'')},
   ]},
-  [Op.or]: [
-    {
-      relevance: 'resistance',
-      iprEvidenceLevel: 'IPR-A',
-    },
-    {
-      relevance: 'sensitivity',
-    },
-  ],
+  [Op.and]: {
+    [Op.or]: [
+      {
+        relevance: 'resistance',
+        iprEvidenceLevel: 'IPR-A',
+      },
+      {
+        relevance: 'sensitivity',
+      },
+    ],
+  },
   // Regex filter for finding columns with 2 or more spaces that end with
   // mutation or mutations
   [Op.not]: {kbVariant: {[Op.regexp]: MUTATION_REGEX}},
@@ -58,14 +58,6 @@ const therapeuticAssociationFilter = {
 // 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.and]: [
     {[Op.is]: literal('distinct from \'exp\'')},
   ]},

test/routes/report/report.test.js

@@ -74,7 +74,7 @@ describe('/reports/{REPORTID}', () => {
   let totalReports;
   let reportDualProj;
 
-  beforeEach(async () => {
+  beforeAll(async () => {
     // Get genomic template
     const template = await db.models.template.findOne({where: {name: 'genomic'}});
     // Create Report and associate projects
@@ -549,12 +549,13 @@ describe('/reports/{REPORTID}', () => {
   });
 
   // delete report
-  afterEach(async () => {
+  afterAll(async () => {
     await db.models.report.destroy({where: {id: report.id}, force: true});
     await db.models.report.destroy({where: {id: reportReady.id}, force: true});
     await db.models.report.destroy({where: {id: reportReviewed.id}, force: true});
     await db.models.report.destroy({where: {id: reportArchived.id}, force: true});
     await db.models.report.destroy({where: {id: reportNonProduction.id}, force: true});
+    await db.models.report.destroy({where: {id: reportNonProduction.id}, force: true});
   }, LONGER_TIMEOUT);
 });
 

test/routes/report/variants.test.js

@@ -157,7 +157,7 @@ describe('/reports/{REPORTID}/kb-matches', () => {
 
   // delete report
   afterAll(async () => {
-    // await db.models.report.destroy({where: {ident: rapidReportIdent}, force: true});
+    await db.models.report.destroy({where: {ident: rapidReportIdent}, force: true});
   }, LONGER_TIMEOUT);
 });
 

test/testData/mockRapidReportData.json

@@ -17,7 +17,7 @@
             "category": "therapeutic",
             "variantType": "cnv",
             "variant": "TA",
-            "iprEvidenceLevel": "IPR-B",
+            "iprEvidenceLevel": "IPR-A",
             "kbVariant": "this should be in table 1",
             "matchedCancer": true,
             "relevance": "resistance",
@@ -43,6 +43,16 @@
             "relevance": "resistance",
             "evidenceLevel": "table 2"
         },
+        {
+            "category": "therapeutic",
+            "variantType": "cnv",
+            "variant": "CR",
+            "iprEvidenceLevel": "IPR-D",
+            "kbVariant": "geneX specific mutation 7",
+            "matchedCancer": true,
+            "relevance": "sensitivity",
+            "evidenceLevel": "table 2"
+        },
         {
             "category": "therapeutic",
             "variantType": "cnv",
@@ -71,20 +81,24 @@
             "evidenceLevel": "table 2"
         },
         {
-            "category": "unknown",
+            "category": "therapeutic",
             "variantType": "msi",
             "variant": "msi",
             "iprEvidenceLevel": "IPR-A",
-            "kbVariant": "also should be table 2",
-            "evidenceLevel": "table 2"
+            "matchedCancer": true,
+            "relevance": "sensitivity",
+            "kbVariant": "also should be table 1",
+            "evidenceLevel": "table 1"
         },
         {
-            "category": "unknown",
+            "category": "therapeutic",
             "variantType": "tmb",
             "variant": "tmb",
             "iprEvidenceLevel": "IPR-A",
+            "matchedCancer": true,
+            "relevance": "sensitivity",
             "kbVariant": "geneX specific mutation 2",
-            "evidenceLevel": "table 2"
+            "evidenceLevel": "table 1"
         },
         {
             "category": "therapeutic",
@@ -243,13 +257,13 @@
     ],
     "tmburMutationBurden": {
         "key": "tmb",
-        "displayName": "table 2"
+        "displayName": "table 1"
     },
     "msi": [
         {
             "score": 100,
             "key": "msi",
-            "displayName": "table 2"
+            "displayName": "table 1"
         },
         {
             "score": 15,