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mcode-cql

Prerequisites

Users also need to configure a .env file, defining the following values:

TRANSLATION_SERVICE_URL=http://example.com  # 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'
...

Provisional values are provided in the .env.example file. To start with these values, simply copy these contents into a new file called .env.

See the cql-testing-harness library for a detailed description of the environment.

Test Script

To run the tests,

yarn test

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 ./test

To only do steps 2. and 3. above without starting a new container:

yarn test -n

Unit Tests

The unit tests will make assertions based on the execution results of the mCODE CQL for a given patient. Before any unit tests are run, the CQL is executed using cql-execution and cql-exec-fhir, and the execution results are stored in a variable to be used for assertions in the unit tests.

To run only the unit tests with the existing ELM in the OUTPUT_ELM directory (and not re-translate the CQL):

yarn test:unit

CQL Translation

To only translate the CQL and not do the rest of the build/test steps, spin up a cql-translation-service docker container and run the translate script:

docker run --name cql-translation-service --rm -d -p 8080:8080 cqframework/cql-translation-service:v1.5.2
yarn translate

To stop the docker container once translation is complete, run the following command:

docker stop cql-translation-service

The default URL used for the translation service is http://localhost:8080/cql/translator, however that can be configured by setting the TRANSLATION_SERVICE_URL node environment variable. This variable can be set by modifying the TRANSLATION_SERVICE_URL value in your .env file, or by providing a new value at runtime like so:

TRANSLATION_SERVICE_URL=http://example.com/cql/translator yarn translate

When translating CQL with a custom URL, yarn test should be run with the -n flag to prevent the testing harness from starting a new docker container.