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CQL Execution VSAC Code Service

This project establishes a VSAC-enabled code service module for use with the CQL Execution Engine. This allows the CQL Execution Engine to execute CQL containing references to Value Sets that are published in the National Library of Medicine's (NLM) Value Set Authority Center (VSAC). Value Set references can be defined using a valid VSAC identifying URL for the value set, a URN, or the oid itself. For example:

valueset "Diabetes": 'https://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.103.12.1001'
// or valueset "Diabetes": 'urn:oid:2.16.840.1.113883.3.464.1003.103.12.1001'
// or valueset "Diabetes": '2.16.840.1.113883.3.464.1003.103.12.1001'

As of 1.1.1, this library supports Value Set versions, so the following is also supported:

valueset "Diabetes": 'https://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.103.12.1001' version '20190315'
// or valueset "Diabetes": 'urn:oid:2.16.840.1.113883.3.464.1003.103.12.1001' version '20190315'
// or valueset "Diabetes": '2.16.840.1.113883.3.464.1003.103.12.1001' version '20190315'

When using the canonical URL as a Value Set identifier, it is also possible to embed the version directly in the URL, using a vertical bar (|) to separate the identifier and version:

valueset "Diabetes": 'https://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.103.12.1001|20190315'

The embedded version, however, is only supported for the canonical URL form of value sets. It is not supported for URN or OID identifiers.

UMLS API Key Required

This library requires a valid UMLS API key. If you do not have an UMLS account, you can request one here: https://uts.nlm.nih.gov/license.html

SVS and FHIR APIs

The CQL Execution Code Service supports the Value Set Authority Center's SVS API and FHIR API. The SVS API is used by default, as our internal testing has shown it to be more performant than the FHIR API. The chosen API can be switched by passing in the useFHIR flag to the CodeService constructor.

Setting Up the Environment

To use this project, you should perform the following steps:

  1. Install Node.js
  2. Execute the following from this project's root directory: npm install

Using the VSAC Code Service

The Local Cache

The VSAC Code Service is constructed with a file path pointing to the location where the cache should be stored. If a file location is not passed into the constructor, it will default the cache to a folder called vsac_cache in the working directory. The cache is used to store value sets and their codes after retrieving them from VSAC. This prevents the code service from having to make multiple calls to VSAC for the same value set.

The second argument to the CodeService constructor is a boolean indicating if the code service should begin by loading existing value sets from the cache. If true, it will initialize the code service from the cache (if the cache exists and is populated). If false, ensureValueSetsWithAPIKey will re-download any value sets passed to it, overwriting the cache.

Using UMLS Credentials

Downloading value set definitions from VSAC requires a valid UMLS account. The code service's ensureValueSetsWithAPIKey function allows a UMLS API key to be passed in. Alternately, the UMLS API key can be provided via the UMLS_API_KEY environment variable.

Downloading Value Set Definitions

The ensureValueSetsWithAPIKey and ensureValueSetsInLibraryWithAPIKey functions are the only functions that attempt to download value sets from VSAC. Before they make a request to VSAC, they will check the cache. If the value set is already in the cache, they will not make a request to VSAC. Otherwise, they will use VSAC's SVS2 API or FHIR API to download the expanded codes from the value set.

The findValueSet and findValueSets functions (including the legacy findValueSetsByOid function) do not reach out to VSAC, so implementations should call ensureValueSetsInLibraryWithAPIKey or ensureValueSetsWithAPIKey before attempting to execute CQL. If ensureValueSetsWithAPIKey is used, the implementor is responsible for passing in the OIDs / versions that will be needed.

Breaking Changes in Version 2.0.0

Version 2.0.0 of the code service removes the old ensureValueSets and ensureValueSetsInLibrary methods that accepted a UMLS user name and password. As of Jan 1, 2021, VSAC no longer allows API authentication using username and password. Instead, implementations should now use ensureValueSetsWithAPIKey and ensureValueSetsInLibraryWithApiKey, each of which allows an API key to be passed in (or to be specified via the UMLS_API_KEY environment variables).

In addition, version 2.0.0 switched its communication library from request to node-fetch. This should be transparent in most cases, but some thrown errors may have a different format since they are thrown by node-fetch rather than request.

Example

The following is a simple example of setting up the VSAC Code Service, calling ensureValueSetsInLibraryWithApiKey, and passing the Code Service into the CQL Execution engine:

const vsac = require('cql-exec-vsac');

// Code setting up the CQL library, patient source, parameters, etc
// ...

// Set up the code service, loading from the cache if it exists
const codeService = new vsac.CodeService('/path/to/vsac_cache', true);
// Ensure value sets in the library and its dependencies, downloading any missing value sets
codeService.ensureValueSetsInLibraryWithApiKey(library, true, 'myUmlsApiKey')
.then(() => {
  // Value sets are loaded, so execute!
  const executor = new cql.Executor(lib, codeService, parameters);
  const results = executor.exec(patientSource);
  // Do something with results...
})
.catch( (err) => {
  // There was an error downloading the value sets!
  console.error('Error downloading value sets', err);
});

Testing the Code

To run the automated unit tests, execute the following command:

$ npm test

Linting the Code

To encourage quality and consistency within the code base, all code should pass eslint without any warnings. Many text editors can be configured to automatically flag eslint violations. We also provide an npm script for running eslint on the project. To check your code against eslint's rules, execute the following command:

$ npm run lint

To automatically fix code that violates eslint's rules:

$ npm run lint:fix

Prettier

To encourage quality and consistency within the code base, all code should also be formatted using Prettier. Many text editors can be configured to automatically reformat code using Prettier on save. We also provide an npm script for running prettier on the project. To check your code against Prettier's rules, execute the following command:

$ npm run prettier

To automatically fix any code that violates Prettier's rules:

$ npm run prettier:fix

Altogether Now!

To run the unit tests, linter, and prettier all in one shot, execute the following command:

$ npm run test:plus