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) Valu
npm install cql-exec-vsacThis 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.
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
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.
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
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 byensureValueSetsWithAPIKey
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, will re-download any value sets passed to it,
overwriting the cache.
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 beUMLS_API_KEY
provided via the environment variable.
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 outensureValueSetsInLibraryWithAPIKey
to VSAC, so implementations should call or ensureValueSetsWithAPIKey beforeensureValueSetsWithAPIKey
attempting to execute CQL. If is used, the implementor is responsible for passing in the
OIDs / versions that will be needed.
Version 2.0.0 of the code service removes the old ensureValueSets and ensureValueSetsInLibrary methods thatensureValueSetsWithAPIKey
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 and ensureValueSetsInLibraryWithApiKey,UMLS_API_KEY
each of which allows an API key to be passed in (or to be specified via the 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_.
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:
`js
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);
});
`
To run the automated unit tests, execute the following command:
`
$ npm test
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
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
To run the unit tests, linter, and prettier all in one shot, execute the following command:
`
$ npm run test:plus