cqframework/cql-execution

Name: cql-execution

Owner: cqframework

Description: A coffeescript (soon-to-be-javascript) framework for executing CQL

Created: 2018-03-15 17:42:40.0

Updated: 2018-03-15 18:09:55.0

Pushed: 2018-03-20 20:32:25.0

Homepage: null

Size: 3809

Language: CoffeeScript

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README

CQL Execution Framework

The CQL Execution Framework is a set of CoffeeScript libraries that can execute CQL artifacts expressed as JSON ELM.

For more information, see the CQL Execution Framework Overview.

Project Configuration

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

1. Install Node.js
2. Install Yarn
3. Install CoffeeScript
4. Execute the following from the root directory: yarn install

To Execute Your CQL

Please note that while the CQL Execution Framework supports many aspects of CQL, it does not support everything in the CQL specification. You should check to see what is implemented before expecting it to work! For a working example, see src/example.

There are several steps involved to execture CQL. First, you must create a JSON representation of the ELM. For easiest integration, we will generate a coffee file using cql-to-elm:

1. Install the Java 8 SDK
2. Clone the clinical_quality_language repository to a location of your choice
3. cd ${path_to_clinical_quality_language}/Src/java (replacing ${path_to_clinical_quality_language} with the path to the local clone)
4. ./gradlew :cql-to-elm:installDist
5. ./cql-to-elm/build/install/cql-to-elm/bin/cql-to-elm --format=COFFEE --input ${path_to_cql} --output ${path_to_cql-execution}/src/

The above example puts the example CQL into the src directory to make things easy, but it doesn't have to go there. If you put it elsewhere, you'll need to compile it to javascript and modify the examples below with the new path (where applicable).

In the rest of the examples, we'll assume an age.cql file with the following contents (but of course you can use your own CQL):

ary AgeAtMP version '1'

g QUICK

meter MeasurementPeriod default Interval[DateTime(2013, 1, 1, 0, 0, 0, 0), DateTime(2014, 1, 1, 0, 0, 0, 0))

ext Patient

ne InDemographic:
AgeInYearsAt(start of MeasurementPeriod) >= 2 and AgeInYearsAt(start of MeasurementPeriod) < 18

Next, create a coffeescript file to execute the measure. This file will need to contain (or require) JSON patient representations for testing as well. Since our example CQL uses the QUICK data model, each patient is represented using a FHIR bundle. For ease of use, let's put the file in the src directory:

= require './cql'
ure = require './age'

= new cql.Library(measure)
utor = new cql.Executor(lib)
rce = new cql.PatientSource [ {
"resourceType": "Bundle",
"id": "example1",
"meta": {
  "versionId": "1",
  "lastUpdated": "2014-08-18T01:43:30Z"
},
"base": "http://example.com/base",
"entry" : [{
    "resource": {
    "id" : "1",
    "meta" :{ "profile" : ["patient-qicore-qicore-patient"]},
    "resourceType" : "Patient",
    "identifier": [{ "value": "1" }],
    "name": {"given":["John"], "family": ["Smith"]},
    "gender": "M",
    "birthDate" : "1980-02-17T06:15"}
    }
]
 {
"resourceType": "Bundle",
"id": "example1",
"meta": {
  "versionId": "1",
  "lastUpdated": "2014-08-18T01:43:30Z"
},
"base": "http://example.com/base",
"entry" : [{
    "resource": {
    "id" : "2",
    "meta" :{ "profile" : ["patient-qicore-qicore-patient"]},
    "resourceType" : "Patient",
    "identifier": [{ "value": "2" }],
    "name": {"given":["Sally"], "family": ["Smith"]},
    "gender": "F",
    "birthDate" : "2007-08-02T11:47"}
    }
]
]


lt = executor.exec(psource)
ole.log JSON.stringify(result, undefined, 2)

In the above file, we've assumed the JSON ELM coffeescript file for the measure is called age.coffee and is in the same directory as the file (and cql library). We've also assumed a couple of very simple patients. Let's call the file we just created age-exec.coffee.

Now we must compile it to javascript in the lib directory. There is a simple Cakefile build script for this (cake is installed with coffeescript):

1. cd ${path_to_cql-execution}
2. cake build

Now we can execute the measure using Node.js:

1. cd ${path_to_cql-execution}/lib
2. node age-exec

If all is well, it should print the result object to standard out.

To Run the CQL Execution Unit Tests

Execute yarn test or cake test.

To Develop Tests

Many of the tests require JSON ELM data. It is much easier to write CQL rather than JSON ELM, so test authors should create test data by adding new CQL to test/data/cql-test-data.txt. Some conventions are followed to make testing easier. The following is an example of some test data:

// @Test: And
define AllTrue = true and true
define AllFalse = false and false
define SomeTrue = true and false

The // @Test: And indicates the name of the test suite it applies to (“And”). The group of statements that follows the # And represents the CQL Library that will be supplied as test data to the “And” test suite.

To convert the CQL to CoffeeScript containing the JSON ELM representation, execute cake build-test-data. This will use the java cql-to-elm project to generate the test/data/cql-test-data.coffee file containing the following exported variable declaration:

And
ary TestSnippet version '1'
g QUICK
ext Patient
ne AllTrue = true and true
ne AllFalse = false and false
ne SomeTrue = true and false


le.exports.And = {
library" : {
  "identifier" : {
     "id" : "TestSnippet",
     "version" : "1"
  },
  "dataModels" : {
     "modelReference" : [ {
        "referencedModel" : {
           "value" : "http://org.hl7.fhir"
        }
     } ]
  },
  "statements" : {
     "def" : [ {
        "name" : "AllTrue",
        "context" : "Patient",
        "expression" : {
           "type" : "And",
           "operand" : [ {
              "valueType" : "{http://www.w3.org/2001/XMLSchema}bool",
              "value" : "true",
              "type" : "Literal"
           }, {
              "valueType" : "{http://www.w3.org/2001/XMLSchema}bool",
              "value" : "true",
              "type" : "Literal"
           } ]
        }
     }, {
        "name" : "AllFalse",
        "context" : "Patient",
        "expression" : {
           "type" : "And",
           "operand" : [ {
              "valueType" : "{http://www.w3.org/2001/XMLSchema}bool",
              "value" : "false",
              "type" : "Literal"
           }, {
              "valueType" : "{http://www.w3.org/2001/XMLSchema}bool",
              "value" : "false",
              "type" : "Literal"
           } ]
        }
     }, {
        "name" : "SomeTrue",
        "context" : "Patient",
        "expression" : {
           "type" : "And",
           "operand" : [ {
              "valueType" : "{http://www.w3.org/2001/XMLSchema}bool",
              "value" : "true",
              "type" : "Literal"
           }, {
              "valueType" : "{http://www.w3.org/2001/XMLSchema}bool",
              "value" : "false",
              "type" : "Literal"
           } ]
        }
     } ]
  }

Notice that since the CQL didn't declare a library name/version, a data model, or a context, default values were inserted into the CQL at generation time. Now this CQL can be used in a test defined in test/cql-exec-test.coffee. For example:

ribe 'And', ->
eforeEach ->
setup @

 'should have type: And', ->
@allTrue.type.should.equal 'And'

 'should execute allTrue as true', ->
@allTrue.exec(@ctx).should.be.true

 'should execute allFalse as false', ->
@allFalse.exec(@ctx).should.be.false

 'should execute someTrue as false', ->
@someTrue.exec(@ctx).should.be.false

The test suite above uses Mocha and Should.js. The setup @ sets up the test case by creating @lib (representing the CqlLibrary instance of the test data), creating @ctx (representing a Context for execution), and creating local variables for each defined concept (in this case, @allTrue, @allFalse, and @someTrue).

Watching For Changes

Rather than continually having to run cake build-test-data after every modification to the test data text file, you can setup a process to watch for changes and regenerate the cql-test-data.coffee file every time it detects changes in the source text file. Simply execute cake watch-test-data.

To watch for all changes (Coffeescript and CQL), use:

cake watch-all