diff --git a/.eslintignore b/.eslintignore new file mode 100644 index 00000000..d88e1020 --- /dev/null +++ b/.eslintignore @@ -0,0 +1,2 @@ +connectathon +ecqm-content-r4-2021 \ No newline at end of file diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 092132d1..a616f5e6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -8,7 +8,7 @@ jobs: strategy: matrix: node-version: [16.x] - mongodb-version: ['5.0'] + mongodb-version: ['6.0'] steps: - uses: actions/checkout@v2 @@ -48,7 +48,7 @@ jobs: strategy: matrix: node-version: [16.x] - mongodb-version: ['5.0'] + mongodb-version: ['6.0'] steps: - uses: actions/checkout@v2 diff --git a/Dockerfile b/Dockerfile index c0a5c0b6..0e547015 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM node:14 +FROM node:16 # Create app directory WORKDIR /usr/src/app diff --git a/README.md b/README.md index 395c43ff..887248af 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ Test server for executing FHIR-based Electronic Clinical Quality Measures (eCQMs ### Prerequisites - [Node.js >=16.0.0](https://nodejs.org/en/) -- [MongoDB >= 5.0](https://www.mongodb.com) +- [MongoDB >= 6.0](https://www.mongodb.com) - [Git](https://git-scm.com/) - [Docker](https://docs.docker.com/get-docker/) - [Redis](https://redis.com/break-the-data-matrix/) diff --git a/docker-compose.yml b/docker-compose.yml index 89f3d6ba..0f83c4de 100644 --- a/docker-compose.yml +++ b/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: diff --git a/package-lock.json b/package-lock.json index 82580d6e..f0746efc 100644 --- a/package-lock.json +++ b/package-lock.json @@ -19,7 +19,7 @@ "cql-exec-fhir-mongo": "git+https://git@github.com/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", @@ -85,10 +85,27 @@ "resolved": "https://registry.npmjs.org/@asymmetrik/sof-scope-checker/-/sof-scope-checker-1.0.7.tgz", "integrity": "sha512-QzLGDRMaVX/R/iAqQu4MuDV29d/0mvSyT1i4p/C3Xi5sSQXPtSa8e/uUChBfpPGOdbIQv1Uv84tkRifRKUKtZA==" }, + "node_modules/@aws-crypto/crc32": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/@aws-crypto/crc32/-/crc32-3.0.0.tgz", + "integrity": "sha512-IzSgsrxUcsrejQbPVilIKy16kAT52EwB6zSaI+M3xxIhKh5+aldEyvI+z6erM7TCLB2BJsFrtHjp6/4/sr+3dA==", + "optional": true, + "dependencies": { + "@aws-crypto/util": "^3.0.0", + "@aws-sdk/types": "^3.222.0", + "tslib": "^1.11.1" + } + }, + "node_modules/@aws-crypto/crc32/node_modules/tslib": { + "version": "1.14.1", + "resolved": "https://registry.npmjs.org/tslib/-/tslib-1.14.1.tgz", + "integrity": 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"resolved": "https://registry.npmjs.org/semver/-/semver-7.3.8.tgz", - "integrity": "sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A==", + "version": "7.5.4", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.4.tgz", + "integrity": "sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA==", "dev": true, "requires": { "lru-cache": "^6.0.0" @@ -17436,9 +18024,9 @@ } }, "tough-cookie": { - "version": "4.1.2", - "resolved": "https://registry.npmjs.org/tough-cookie/-/tough-cookie-4.1.2.tgz", - "integrity": "sha512-G9fqXWoYFZgTc2z8Q5zaHy/vJMjm+WV0AkAeHxVCQiEB1b+dGvWzFW6QV07cY5jQ5gRkeid2qIkzkxUnmoQZUQ==", + "version": "4.1.3", + "resolved": "https://registry.npmjs.org/tough-cookie/-/tough-cookie-4.1.3.tgz", + "integrity": "sha512-aX/y5pVRkfRnfmuX+OdbSdXvPe6ieKX/G2s7e98f4poJHnqH3281gDPm/metm6E/WRamfx7WC4HUqkWHfQHprw==", "dev": true, "requires": { "psl": "^1.1.33", @@ -17462,10 +18050,9 @@ 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"sha512-BN22B5eaMMI9UMtjrGd5g5eCYPpCPDUy0FJXbYsaT5zYxjFOckS53SQDE3pWkVoWpHXVb3BrYcEN4Twa55B5cA==" }, "wordwrap": { "version": "1.0.0", @@ -17916,8 +18503,7 @@ "yallist": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz", - "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==", - "dev": true + "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==" }, "yargs": { "version": "16.2.0", diff --git a/package.json b/package.json index 2a90311e..f8b6a18e 100644 --- a/package.json +++ b/package.json @@ -34,7 +34,7 @@ "cql-exec-fhir-mongo": "git+https://git@github.com/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" ] } -} +} \ No newline at end of file diff --git a/src/queue/execQueue.js b/src/queue/execQueue.js index 7b383b2a..f563e105 100644 --- a/src/queue/execQueue.js +++ b/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' diff --git a/src/scripts/uploadPremadeBundles.js b/src/scripts/uploadPremadeBundles.js index 13c93d53..518b83f8 100644 --- a/src/scripts/uploadPremadeBundles.js +++ b/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 { v4: uuidv4 } = require('uuid'); const ecqmContentR4Path = path.resolve(path.join(__dirname, '../../ecqm-content-r4-2021/bundles/measure/')); @@ -97,14 +98,27 @@ async function main() { let filesUploaded = 0; let resourcesUploaded = 0; for (const filePath of bundleFiles) { - // read each EXM bundle file + // read each 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; + } + + // uncomment if you want to see every bundle found that this script is processing + //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. This probably is a MADiE Export Measure resource. Try to grab the first + // chunk from the filename looking for the `-` to hopefully get `CMSXXXFHIR` otherwise use a random ID + if (!res.resource.id) { + res.resource.id = filePath.split('/').slice(-1)[0].split('-')[0] || uuidv4(); + console.log(`Gave ${res.resource.resourceType} an ID of ${res.resource.id}`); + } await createResource(res.resource, res.resource.resourceType); resourcesUploaded += 1; } catch (e) { diff --git a/src/services/measure.service.js b/src/services/measure.service.js index fcbcd2c9..8c6294ce 100644 --- a/src/services/measure.service.js +++ b/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 }); diff --git a/src/util/bundleUtils.js b/src/util/bundleUtils.js index 1ecb0139..c5e0d5ec 100644 --- a/src/util/bundleUtils.js +++ b/src/util/bundleUtils.js @@ -146,7 +146,7 @@ async function getDependentValueSets(lib) { } const depValueSetUrls = lib.relatedArtifact - .filter(ra => ra.type === 'depends-on' && ra.resource.includes('ValueSet')) + .filter(ra => ra.type === 'depends-on' && ra.resource?.includes('ValueSet')) .map(ra => ra.resource); const valueSetGets = depValueSetUrls.map(async url => { @@ -180,7 +180,7 @@ async function getAllDependentLibraries(lib) { .filter( ra => ra.type === 'depends-on' && - ra.resource.includes('Library') && + ra.resource?.includes('Library') && ra.resource !== 'http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo|4.0.1' ) // exclude modelinfo dependency .map(ra => ra.resource); diff --git a/test/queue/execQueue.test.js b/test/queue/execQueue.test.js index 035b1136..6a5ad74e 100644 --- a/test/queue/execQueue.test.js +++ b/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', () => { diff --git a/test/services/base.service.test.js b/test/services/base.service.test.js index cbb9184d..0f6dac10 100644 --- a/test/services/base.service.test.js +++ b/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'); }); });