Updated loadBundles script for connectathon and add QICore ModelInfo (#…

…112)

* brought back loadBundles script. added QICore-ModelInfo to dbsetup

* a bit of post cthon clean up to loadbundles

* Moved load ecqm-content script to dbSetup.ts

* fix missing / in url replacement

---------

Co-authored-by: Elsa <eperelli@mitre.org>

docker-build.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+npm#!/bin/bash
 
 docker buildx build --platform linux/arm64,linux/amd64 -t tacoma/measure-repository-service:latest -f service.Dockerfile . --push
 docker buildx build --platform linux/arm64,linux/amd64 -t tacoma/measure-repository-app:latest -f app.Dockerfile . --push

service/.gitignore

@@ -4,3 +4,4 @@ node_modules
 .DS_Store
 cache
 ecqm-content-r4-2021
+ecqm-content-qicore-2024

service/README.md

@@ -58,6 +58,12 @@ To load multiple bundles from a directory, run the same script with the desired
 npm run db:loadBundle <path to directory>
 ```
 
+To load [ecqm-content-qicore-2024](https://github.com/cqframework/ecqm-content-qicore-2024) into your database, clone the repository in the service directory of this repository. Then you can run the following script:
+
+```
+npm run db:loadEcqmContent <optional service url, default: http://localhost:3000/4_0_1>
+```
+
 ### Bundle Upload Details
 
 Upon uploading a Measure resource, the Measure's main library is added to the `relatedArtifact` array with an [isOwned extension](https://build.fhir.org/ig/HL7/fhir-extensions/StructureDefinition-artifact-isOwned.html).

service/package.json

@@ -14,6 +14,7 @@
  "db:setup": "ts-node ./scripts/dbSetup.ts create",
  "db:loadBundle": "ts-node ./scripts/dbSetup.ts loadBundle",
  "db:postBundle": "ts-node ./scripts/dbSetup.ts postBundle",
+ "db:loadEcqmContent": "ts-node ./scripts/dbSetup.ts loadEcqmContent",
  "lint": "eslint \"./src/**/*.{js,ts}\"",
  "lint:fix": "eslint \"./src/**/*.{js,ts}\" --fix",
  "prettier": "prettier --check \"./src/**/*.{js,ts}\"",

service/scripts/dbSetup.ts

@@ -10,6 +10,123 @@ dotenv.config();
 
 const DB_URL = process.env.DATABASE_URL || 'mongodb://localhost:27017/measure-repository';
 const COLLECTION_NAMES = ['Measure', 'Library'];
+const ECQM_CONTENT_PATH = 'ecqm-content-qicore-2024/bundles/measure';
+const MEASURES_PATH = path.join(ECQM_CONTENT_PATH);
+
+/**
+ * Gets the paths for the bundles in ecqm-content-qicore-2024
+ */
+function getBundlePaths(): string[] {
+ const filePaths: string[] = [];
+
+ fs.readdirSync(MEASURES_PATH, { withFileTypes: true }).forEach(ent => {
+ // if this item is a directory, look for .json files under it
+ if (ent.isDirectory()) {
+ fs.readdirSync(path.join(MEASURES_PATH, ent.name), { withFileTypes: true }).forEach(subEnt => {
+ if (!subEnt.isDirectory() && subEnt.name.endsWith('.json')) {
+ filePaths.push(path.join(MEASURES_PATH, ent.name, subEnt.name));
+ }
+ });
+ }
+ });
+ return filePaths;
+}
+
+/**
+ * Changes the incorrect ecqi.healthit.gov references on the Libraries in
+ * ecqm-content-qicore-2024 to the correct madie.cms.gov references
+ */
+async function fixAndPutLibraries(bundle: fhir4.Bundle, url: string) {
+ const libraries: fhir4.Library[] = bundle.entry
+ ?.filter(entry => entry.resource?.resourceType === 'Library')
+ .map(entry => entry.resource as fhir4.Library) as fhir4.Library[];
+
+ for (const library of libraries) {
+ console.log(` Library ${library.id}`);
+ if (library.relatedArtifact) {
+ for (let index = 0; index < library.relatedArtifact.length; index++) {
+ const ra = library.relatedArtifact[index];
+ // if a related artifact is using a ecqi.healthit.gov reference it needs to be
+ // changed to a madie.cms.gov reference to match the urls the resources use
+ if (
+ (ra.type === 'depends-on' || ra.type === 'composed-of') &&
+ ra.resource?.startsWith('http://ecqi.healthit.gov/ecqms/Library')
+ ) {
+ const newRef = ra.resource.replace(
+ 'http://ecqi.healthit.gov/ecqms/Library/',
+ 'https://madie.cms.gov/Library/'
+ );
+ console.log(` replacing ra ${ra.resource} with ${newRef}`);
+ ra.resource = newRef;
+ }
+ }
+ }
+ try {
+ console.log(` PUT ${url}/Library/${library.id}`);
+
+ const resp = await fetch(`${url}/Library/${library.id}`, {
+ method: 'PUT',
+ body: JSON.stringify(library),
+ headers: {
+ 'Content-Type': 'application/json+fhir'
+ }
+ });
+ console.log(` ${resp.status}`);
+ } catch (e) {
+ console.error(e);
+ }
+ }
+}
+
+/**
+ * Changes the Measures in ecqm-content-qicore-2024 to have status 'active'
+ * before being added to the database with a PUT
+ */
+async function putMeasure(bundle: fhir4.Bundle, url: string) {
+ const measure: fhir4.Measure = bundle.entry?.find(entry => entry.resource?.resourceType === 'Measure')
+ ?.resource as fhir4.Measure;
+
+ console.log(` Measure ${measure.id}`);
+ try {
+ console.log(` PUT ${url}/Measure/${measure.id}`);
+ measure.status = 'active';
+ const resp = await fetch(`${url}/Measure/${measure.id}`, {
+ method: 'PUT',
+ body: JSON.stringify(measure),
+ headers: {
+ 'Content-Type': 'application/json+fhir'
+ }
+ });
+ console.log(` ${resp.status}`);
+ if (resp.status >= 400) {
+ const responseBody = await resp.json();
+ if (responseBody.resourceType === 'OperationOutcome') {
+ console.log(JSON.stringify(responseBody, null, 2));
+ }
+ }
+ } catch (e) {
+ console.error(e);
+ }
+}
+
+/**
+ * Loads ecqm-content-qicore-2024 into the database
+ */
+async function loadEcqmContent(bundlePaths: string[], url: string) {
+ for (const path of bundlePaths) {
+ const bundle = JSON.parse(fs.readFileSync(path, 'utf8')) as fhir4.Bundle;
+ if (bundle.resourceType === 'Bundle') {
+ if (bundle?.entry) {
+ console.log('FILE' + path);
+ bundle.entry = modifyEntriesForUpload(bundle.entry);
+ await fixAndPutLibraries(bundle, url);
+ await putMeasure(bundle, url);
+ }
+ } else {
+ console.warn(`${path} is not a Bundle`);
+ }
+ }
+}
 
 async function createCollections() {
  await Connection.connect(DB_URL);
@@ -183,7 +300,7 @@ async function uploadBundleResources(filePath: string) {
  * Convenience modification of an array of entries to create isOwned relationships and coerce to status active.
  * This lets us massage existing data that may not have the appropriate properties needed for a Publishable Measure Repository
  */
-function modifyEntriesForUpload(entries: fhir4.BundleEntry<fhir4.FhirResource>[]) {
+export function modifyEntriesForUpload(entries: fhir4.BundleEntry<fhir4.FhirResource>[]) {
  // pre-process to find owned relationships
  const ownedUrls: string[] = [];
  const modifiedEntries = entries.map(ent => {
@@ -236,9 +353,14 @@ async function insertFHIRModelInfoLibrary() {
  const fhirModelInfo = fs.readFileSync('scripts/fixtures/Library-FHIR-ModelInfo.json', 'utf8');
  const fhirModelInfoLibrary: CRMIShareableLibrary = JSON.parse(fhirModelInfo);
 
+ const qicoreModelInfo = fs.readFileSync('scripts/fixtures/Library-QICore-ModelInfo.json', 'utf8');
+ const qicoreModelInfoLibrary: CRMIShareableLibrary = JSON.parse(qicoreModelInfo);
+
  const collection = Connection.db.collection<FhirArtifact>('Library');
  console.log(`Inserting Library/${fhirModelInfoLibrary.id} into database`);
  await collection.insertOne(fhirModelInfoLibrary);
+ console.log(`Inserting Library/${qicoreModelInfoLibrary.id} into database`);
+ await collection.insertOne(qicoreModelInfoLibrary);
 }
 
 if (process.argv[2] === 'delete') {
@@ -305,6 +427,16 @@ if (process.argv[2] === 'delete') {
  console.log('Done');
  })
  .catch(console.error);
+} else if (process.argv[2] === 'loadEcqmContent') {
+ let url = 'http://localhost:3000/4_0_1';
+ if (process.argv.length < 4) {
+ console.log('Defaulting service url to http://localhost:3000/4_0_1');
+ } else {
+ url = process.argv[3];
+ }
+
+ const bundlePaths = getBundlePaths();
+ loadEcqmContent(bundlePaths, url);
 } else {
  console.log('Usage: ts-node src/scripts/dbSetup.ts <create|delete|reset>');
 }