cql-testing-harness v0.0.4

cql-testing-harness

A utility for translating, executing, and testing CQL libraries.

Prerequisites

• Docker
• Node.js

Users also need to configure a .env file in your CQL repository, defining the following values:

TRANSLATION_SERVICE_URL='http://localhost:8080/cql/translator'  # An endpoint exposing a CQL translation service
INPUT_CQL='./cql'                                               # Folder(s) containing all CQL to translate
VALUESETS='./valuesets'                                         # Folder where CQL-dependent valuesets live
OUTPUT_ELM='./output-elm'                                       # Folder where translated ELM will be saved
PATIENTS='./test/fixtures/patients'                             # Folder storing patient files used as test fixtures

The INPUT_CQL value can take multiple directories, separated by a comma, in order to tell the testing harness to look in more than one directory for CQL files.

INPUT_CQL='cqlDir1,cqlDir2,cqlDir3'
...

Usage

Install the testing harness into your project:

npm install --save cql-testing-harness

This will allow your project to access the testing scripts, as well as the exported utilities for executing your CQL.

Scripts

test-cql

test-cql [-n] [-t path/to/test/directory]

• -n: When this option is included, the script will not start a new cql-translation-service docker container. When using this option, ensure you have an instance of the translation service running on your machine at the URL specified in .env
• -t: This option allows you to specify a specific directory or pattern that jest should use to run the tests. If omitted, the script will use jest's default which is any file that ends in .test.js

This script will do the following:

1. Start a cql-translation-service docker container
2. Translate all CQL in theINPUT_CQL directory into ELM JSON and write it to OUTPUT_ELM. This will only occur if CQL files in the INPUT_CQL have changed and the ELM needs to be updated
3. Run the unit tests present in the specified test directory

translate-cql

translate-cql

This script will only do step 2. from above: translate all CQL in theINPUT_CQL directory into ELM JSON and write it to OUTPUT_ELM. This will only occur if CQL files in the INPUT_CQL have changed and the ELM needs to be updated

Utilities

Fixture Loading

loadJSONFromDirectory(pathToDir): loads all JSON files in pathToDir and returns the contents as an array

• pathToDir (string): absolute path to the directory containing the JSON files

loadJSONFixture(pathToFixture): loads the JSON file present at pathToFixture and returns the parsed contents

• pathToFixture (string): absolute path to the JSON file

defaultLoadElm(): loads the ELM JSON present at the OUTPUT_ELM value specified in .env

defaultLoadPatients(): loads all of the patient bundle JSONs present at the PATIENTS value specified in .env

defaultLoadValuesets(): loads all of the ValueSet JSON files present at the VALUESETS value specified in .env

CQL Execution Utilities

mapValueSets(valueSetResources): converts the list of FHIR ValueSet JSON content into a cql-execution CodeService

• valueSetResources (Array<FHIR ValueSet JSON>): Array of parsed FHIR ValueSet JSON objects

execute(elmJSONs, patientBundles, valueSetMap, libraryID): executes the provided ELM against the list of patient records and returns execution results.

• elmJSONs: Array of ELM JSON content
• patientBundles: Array of parsed patient bundle JSON
• valueSetMap: a CQL CodeService object for all of the ValueSets needed in the CQL library (can be obtained using mapValueSets from above)
• libraryID: The identifier of the "main" ELM library that is the root of your CQL repository

Full Example

1. Setup .env with necessary content

   # .env contents
   TRANSLATION_SERVICE_URL='http://localhost:8080/cql/translator'  # An endpoint exposing a CQL translation service
   INPUT_CQL='./cql'                                               # Folder(s) containing all CQL to translate
   VALUESETS='./valuesets'                                         # Folder where CQL-dependent valuesets live
   OUTPUT_ELM='./output-elm'                                       # Folder where translated ELM will be saved
   PATIENTS='./test/fixtures/patients'                             # Folder storing patient files used as test fixtures

2. Install cql-testing-harness

   npm install --save cql-testing-harness

3. Create a test for your CQL:

   /* example.test.js */
   
   const dotenv = require('dotenv');
   const {
     defaultLoadElm,
     defaultLoadPatients,
     defaultLoadValuesets,
     mapValueSets,
     execute,
   } = require('cql-testing-harness');
   
   // Initialize the env variables
   dotenv.config();
   
   let executionResults;
   beforeAll(() => {
     // Set up necessary data for cql-execution
     const valueSets = defaultLoadValuesets();
     const valueSetMap = mapValueSets(valueSets);
     const elm = defaultLoadElm();
     const patientBundles = defaultLoadPatients();
   
     executionResults = execute(elm, patientBundles, valueSetMap, 'ExampleLibrary');
   });
   
   test('Example Tests', () => {
     expect(executionResults).toBeDefined();
   });

4. Create script(s) for running the tests/doing translation in package.json

   "scripts": {
     "test": "test-cql -t path/to/test/directory",
     "translate": "translate-cql"
     ...
   }
   ...

5. Run the test script to translate the CQL into ELM and get the execution results to use in unit test assertions:

   npm run test

   Example output:

   > test-cql -t ./test
   > Starting cql-translation-service
   1a792ea3a528d707379e2e0c4d6842e317792167812eeb1b6df86a35c5fc1caf
   > Waiting for server
   ..> Translating CQL
   Wrote ELM to output-elm/example.json
   > Running unit tests
    PASS  test/example.test.js
     ✓ Example Tests (2 ms)
   
   Test Suites: 1 passed, 1 total
   Tests:       1 passed, 1 total
   Snapshots:   0 total
   Time:        2.06 s
   Ran all test suites matching /.\/test/i.
   > Stopping cql-translation-service
   cql-translation-service