fqm-e bump to 1.3.1 and update Docker setup

.eslintignore

@@ -0,0 +1,2 @@
+connectathon
+ecqm-content-r4-2021

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:14
+FROM node:16
 
 # Create app directory
 WORKDIR /usr/src/app

docker-compose.yml

@@ -19,7 +19,7 @@ services:
       NDJSON_WORKERS: 2
       REDIS_HOST: redis
       REDIS_PORT: 6379
-      VALIDATE: "false"
+      VALIDATE: 'false'
       VALIDATOR_HOST: validator
       VALIDATOR_PORT: 4567
     ports:
@@ -31,7 +31,7 @@ services:
     tty: true
 
   mongo:
-    image: mongo:4.4.4
+    image: mongo:6.0
     ports:
       - '27017'
     volumes:

package.json

@@ -34,7 +34,7 @@
     "cql-exec-fhir-mongo": "git+https://[email protected]/projecttacoma/cql-exec-fhir-mongo",
     "dotenv": "^10.0.0",
     "express": "^4.17.1",
-    "fqm-execution": "^1.0.5",
+    "fqm-execution": "^1.3.1",
     "lodash": "^4.17.21",
     "mongodb": "^4.1.3",
     "uuid": "^8.3.2",
@@ -54,4 +54,4 @@
       "./test/globalSetup.js"
     ]
   }
-}
+}

src/queue/execQueue.js

@@ -36,12 +36,18 @@ class ScaledCalculation {
     }
 
     this._measureBundle = measureBundle;
+    const measureEntry = measureBundle.entry.find(e => e.resource.resourceType === 'Measure');
+    if (measureEntry) {
+      this._measure = measureEntry.resource;
+    } else {
+      throw new Error('Measure resource was not found in bundle.');
+    }
     this._periodStart = periodStart;
     this._periodEnd = periodEnd;
 
     // Prepare the fqm-execution measure report builder
     try {
-      this._mrBuilder = new MeasureReportBuilder(this._measureBundle, {
+      this._mrBuilder = new MeasureReportBuilder(this._measure, {
         measurementPeriodStart: this._periodStart,
         measurementPeriodEnd: this._periodEnd,
         reportType: 'summary'

src/scripts/uploadPremadeBundles.js

@@ -2,6 +2,7 @@ const fs = require('fs');
 const path = require('path');
 const mongoUtil = require('../database/connection');
 const { createResource } = require('../database/dbOperations');
+const { randomUUID } = require('crypto');
 
 const ecqmContentR4Path = path.resolve(path.join(__dirname, '../../ecqm-content-r4-2021/bundles/measure/'));
 
@@ -84,7 +85,7 @@ async function main() {
   } else {
     try {
       if (!searchPattern) {
-        searchPattern = /^[A-Z].*-bundle.json$/;
+        searchPattern = /^[A-Z].*.json$/;
       }
       console.log(`Finding bundles in ecqm-content-r4-2021 repo at ${ecqmContentR4Path}.`);
       getEcqmBundleFiles(ecqmContentR4Path, searchPattern);
@@ -100,11 +101,21 @@ async function main() {
     // read each EXM bundle file
     const data = fs.readFileSync(filePath, 'utf8');
     if (data) {
-      console.log(`Uploading ${filePath.split('/').slice(-1)}...`);
       const bundle = JSON.parse(data);
+      if (bundle.resourceType !== 'Bundle') {
+        console.log(`Skipping ${filePath.split('/').slice(-1)} NOT A BUNDLE`);
+        continue;
+      }
+      //console.log(`Uploading ${filePath.split('/').slice(-1)}...`);
+
       // retrieve each resource and insert into database
       const uploads = bundle.entry.map(async res => {
         try {
+          // If there is no ID... make one probably MADiE Bundle Measure
+          if (!res.resource.id) {
+            res.resource.id = filePath.split('/').slice(-1)[0].split('-')[0] || randomUUID();
+            console.log(`Gave ${res.resource.resourceType} an ID of ${res.resource.id}`);
+          }
           await createResource(res.resource, res.resource.resourceType);
           resourcesUploaded += 1;
         } catch (e) {

src/services/measure.service.js

@@ -237,7 +237,7 @@ const evaluateMeasure = async (args, { req }) => {
   const { reportType, subject } = req.query;
 
   // If reportType is not specified, default to 'subject', but
-  // only if the 'subject' parameter is also specificed
+  // only if the 'subject' parameter is also specified
   if (reportType === 'subject' || (reportType == null && subject != null)) {
     logger.debug('Evaluating measure for individual');
     return evaluateMeasureForIndividual(args, { req });

src/util/bundleUtils.js

@@ -146,8 +146,12 @@ async function getDependentValueSets(lib) {
   }
 
   const depValueSetUrls = lib.relatedArtifact
-    .filter(ra => ra.type === 'depends-on' && ra.resource.includes('ValueSet'))
-    .map(ra => ra.resource);
+    .filter(
+      ra =>
+        ra.type === 'depends-on' &&
+        ((ra.resource && ra.resource.includes('ValueSet')) || (ra.url && ra.url.includes('ValueSet')))
+    )
+    .map(ra => ra.resource || ra.url);
 
   const valueSetGets = depValueSetUrls.map(async url => {
     const vsQuery = getQueryFromReference(url);
@@ -180,10 +184,10 @@ async function getAllDependentLibraries(lib) {
     .filter(
       ra =>
         ra.type === 'depends-on' &&
-        ra.resource.includes('Library') &&
+        (ra.resource?.includes('Library') || ra.url?.includes('Library')) &&
         ra.resource !== 'http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo|4.0.1'
     ) // exclude modelinfo dependency
-    .map(ra => ra.resource);
+    .map(ra => ra.resource || ra.url);
   // Obtain all libraries referenced in the related artifact, and recurse on their dependencies
   const libraryGets = depLibUrls.map(async url => {
     // Quick fix for invalid connectathon url references
@@ -225,7 +229,7 @@ function replaceReferences(entries) {
   // Add metadata for old IDs and newly created ones of POST entries
   entries.forEach(e => {
     logger.debug(`Replacing resourceIds for entry: ${JSON.stringify(e)}`);
-    if (e.request.method === 'POST') {
+    if (!e.request || e.request.method === 'POST') {
       e.isPost = true;
       e.oldId = e.resource.id;
       e.newId = uuidv4();

test/queue/execQueue.test.js

@@ -94,7 +94,7 @@ describe('execQueue', () => {
           '2019-01-01',
           '2019-12-31'
         );
-      }).toThrow('Could not prepare report builder:');
+      }).toThrow('Measure resource was not found in bundle.');
     });
 
     test('Throws an error if scaled calculation is disabled', () => {

test/services/base.service.test.js

@@ -80,8 +80,9 @@ describe('base.service', () => {
               url: expect.stringMatching(/\/4_0_1\/Patient\?page=1$/)
             }
           ]);
-          expect(response.body.entry[0].resource.id).toEqual(testPatient.id);
-          expect(response.body.entry[0].resource.resourceType).toEqual('Patient');
+          const testPatientEntry = response.body.entry.find(e => e.resource.id === testPatient.id);
+          expect(testPatientEntry).toBeDefined();
+          expect(testPatientEntry.resource.resourceType).toEqual('Patient');
         });
     });