diff --git a/.gitignore b/.gitignore index 9b6e69c..a97d365 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ /.gradle /node_modules .DS_Store +coverage diff --git a/CREATING-TEST-CASES.md b/CREATING-TEST-CASES.md index 3d29321..1da3221 100644 --- a/CREATING-TEST-CASES.md +++ b/CREATING-TEST-CASES.md @@ -8,6 +8,9 @@ Each YAML file in the `tests` folder is a separate test case. Each file has the * **externalData**: A YAML [array](https://yaml.org/spec/1.2/spec.html#id2802662) of the names of other YAML files which may contain [anchored](https://yaml.org/spec/1.2/spec.html#id2785586) resource definitions which can be referenced below under the `data` section. See "Reusing Resources" below for more information. * **data**: A sequence (i.e., array) of the resource instances making up the test case (with the `Patient` resource as the first one). Can include YAML references to anchored resources defined in any YAML files listed under the `externalData` section. * **results**: A hash (i.e. object) for which each key corresponds to a CQL expression name and the value is the _expected_ result for that CQL expression. +* **skip**: Skip test case if true (optional, default false). +* **only**: Only run this test case if true (optional, default false). +* **parameters**: A hash (i.e. object) for which each key corresponds to a CQL library parameter name and the value is the input for execution. (optional, default none). The following is a very simple example of a test case for a fictional CQL library with inclusion criteria that the patient must be male, over 18, and have an Opiod prescription on record. It sets up test data for a 40 year-old male with an Oxycodone prescription and specifies that the `MeetsInclusionCriteria` CQL expression should evaluate to `true`. @@ -211,6 +214,8 @@ results: # The following indicates that these outputs should be arrays of length 1 ThirdCqlExpression: $should have length 1 FourthCqlExpression: $should have length 1 + # The following indicates that the output should contain a JSON subset, needs to be properly quoted and valid JSON + FifthCqlExpression: "$should include {\"LookbackPeriod\": 90}" ``` Currently only the `exist` and `have length` methods are supported. diff --git a/README.md b/README.md index afefe64..4d25fa5 100644 --- a/README.md +++ b/README.md @@ -136,6 +136,8 @@ The following configuration parameters are currently supported: * **dumpFiles**: * **enabled**: Indicates if test data and actual results should be dumped to files for debugging or testing; supports bundles, CQL Hooks requests, and Postman collections of CQL Hooks requests _(optional, boolean, default: false)_ * **path**: The file path to dump files to, if enabled _(optional, string, default: dump\_files)_ +* **skip**: Skip test folder if true _(optional, boolean, default: false)_. +* **only**: Only run this test folder if true _(optional, boolean, default: false)_. All file paths are relative to the location of the `cqlt.yaml` configuraton file unless the file path is absolute. @@ -289,6 +291,30 @@ CQLT Config: /path/to/my/cql/project/test/cqlt.yaml ``` +## Generating CQL library coverage reports + +Test coverage reports describing total number of expressions in the library, number of covered expressions, and list of uncovered expressions can be generated using the custom Mocha coverage reporter. Setup the additional script `test:coverage` in `package.json` as below. The reporter exports lcov formatted files and HTML to the `coverage` folder. + +```json +{ + "name": "my-cql-project", + "version": "1.0.0", + "scripts": { + "test": "./node_modules/.bin/mocha --reporter spec --recursive", + "test:coverage": "./node_modules/.bin/mocha --reporter ./src/exporters/coverage.js --recursive" + }, + "devDependencies": { + "mocha": "^5.2.0", + "cql-testing": "^1.0.0", + "cql-execution": "^1.3.7" + } +} +``` + +```sh +$ npm run test:coverage +``` + ## Generating FHIR Documentation The _FHIR_DSTU2.md_ and _FHIR_STU3.md_ documentation files are generated using the FHIR specification definitions and the corresponding _config.yaml_ files (in _src/fhir/${version}/_). Developers working on the CQL Testing Framework (i.e., developing the framework itself) can regenerate the documentation using the following command: diff --git a/bin/cql2elm.js b/bin/cql2elm.js index 7a33bc8..0f72346 100644 --- a/bin/cql2elm.js +++ b/bin/cql2elm.js @@ -3,6 +3,18 @@ const { platform, argv, cwd } = require('process'); const { join, resolve, sep } = require('path'); const { exec } = require('child_process'); +// ANSI escape codes for colors +const GREEN = '\x1b[32m'; +const RED = '\x1b[31m'; +const YELLOW = '\x1b[33m'; +const RESET = '\x1b[0m'; + +// List of strings to check for non-error output piped to stderr +const greenPrefixes = ['================================================================================', + 'TRANSLATE ', + 'Translation completed successfully.', 'ELM output written to: ']; +const yellowPrefixes = ['Translation completed with messages:', 'Warning:']; + let exeCmd = platform == 'win32' ? 'gradlew.bat' : './gradlew'; let inputArgs = argv; @@ -20,12 +32,32 @@ exec( cwd: resolve(join(__dirname, '..')) }, (error, stdout, stderr) => { + // Handle any errors from exec if (error) { console.error(error); return; } - // eslint-disable-next-line no-console - console.log(stdout); - console.error(stderr); + + // Output stdout in green + if (stdout) { + process.stdout.write(`${GREEN}${stdout}${RESET}`); + } + + // Handle stderr + if (stderr) { + const stderrLines = stderr.toString().split('\n'); + stderrLines.forEach(line => { + if (greenPrefixes.some(prefix => line.startsWith(prefix))) { + // Output lines starting with specified prefixes in green + process.stderr.write(`${GREEN}${line}${RESET}\n`); + } else if (yellowPrefixes.some(prefix => line.startsWith(prefix))) { + // Output warnings in yellow + process.stderr.write(`${YELLOW}${line}${RESET}\n`); + } else if (line.trim()) { + // Output other stderr data in red + process.stderr.write(`${RED}${line}${RESET}\n`); + } + }); + } } ); \ No newline at end of file diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar index 7f93135..a4b76b9 100644 Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 3fa8f86..94113f2 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,6 +1,6 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-8.11-bin.zip networkTimeout=10000 validateDistributionUrl=true zipStoreBase=GRADLE_USER_HOME diff --git a/gradlew b/gradlew index 1aa94a4..f5feea6 100755 --- a/gradlew +++ b/gradlew @@ -15,6 +15,8 @@ # See the License for the specific language governing permissions and # limitations under the License. # +# SPDX-License-Identifier: Apache-2.0 +# ############################################################################## # @@ -55,7 +57,7 @@ # Darwin, MinGW, and NonStop. # # (3) This script is generated from the Groovy template -# https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt # within the Gradle project. # # You can find Gradle at https://github.com/gradle/gradle/. @@ -84,7 +86,8 @@ done # shellcheck disable=SC2034 APP_BASE_NAME=${0##*/} # Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036) -APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit +APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s +' "$PWD" ) || exit # Use the maximum available, or set MAX_FD != -1 to use that value. MAX_FD=maximum diff --git a/gradlew.bat b/gradlew.bat index 6689b85..9b42019 100644 --- a/gradlew.bat +++ b/gradlew.bat @@ -13,6 +13,8 @@ @rem See the License for the specific language governing permissions and @rem limitations under the License. @rem +@rem SPDX-License-Identifier: Apache-2.0 +@rem @if "%DEBUG%"=="" @echo off @rem ########################################################################## @@ -43,11 +45,11 @@ set JAVA_EXE=java.exe %JAVA_EXE% -version >NUL 2>&1 if %ERRORLEVEL% equ 0 goto execute -echo. -echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. -echo. -echo Please set the JAVA_HOME variable in your environment to match the -echo location of your Java installation. +echo. 1>&2 +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2 +echo. 1>&2 +echo Please set the JAVA_HOME variable in your environment to match the 1>&2 +echo location of your Java installation. 1>&2 goto fail @@ -57,11 +59,11 @@ set JAVA_EXE=%JAVA_HOME%/bin/java.exe if exist "%JAVA_EXE%" goto execute -echo. -echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% -echo. -echo Please set the JAVA_HOME variable in your environment to match the -echo location of your Java installation. +echo. 1>&2 +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2 +echo. 1>&2 +echo Please set the JAVA_HOME variable in your environment to match the 1>&2 +echo location of your Java installation. 1>&2 goto fail diff --git a/package-lock.json b/package-lock.json index 21312da..9a31bd6 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,6 +14,8 @@ "cql-exec-fhir": "^2.1.5", "cql-exec-vsac": "^2.2.0", "fs-extra": "^11.2.0", + "istanbul-lib-report": "^3.0.1", + "istanbul-reports": "^3.1.7", "js-yaml": "^4.1.0", "lodash": "^4.17.21", "mocha": "^10.6.0", @@ -28,7 +30,8 @@ "@eslint/js": "^9.6.0", "cql-execution": "^3.0.1", "eslint": "^9.6.0", - "globals": "^15.8.0" + "globals": "^15.8.0", + "sinon": "^19.0.2" }, "peerDependencies": { "cql-execution": ">=1.3.0" @@ -211,6 +214,55 @@ "node": ">= 8" } }, + "node_modules/@sinonjs/commons": { + "version": "3.0.1", + "resolved": "https://registry.npmjs.org/@sinonjs/commons/-/commons-3.0.1.tgz", + "integrity": "sha512-K3mCHKQ9sVh8o1C9cxkwxaOmXoAMlDxC1mYyHrjqOWEcBjYr76t96zL2zlj5dUGZ3HSw240X1qgH3Mjf1yJWpQ==", + "dev": true, + "license": "BSD-3-Clause", + "dependencies": { + "type-detect": "4.0.8" + } + }, + "node_modules/@sinonjs/fake-timers": { + "version": "13.0.5", + "resolved": "https://registry.npmjs.org/@sinonjs/fake-timers/-/fake-timers-13.0.5.tgz", + "integrity": "sha512-36/hTbH2uaWuGVERyC6da9YwGWnzUZXuPro/F2LfsdOsLnCojz/iSH8MxUt/FD2S5XBSVPhmArFUXcpCQ2Hkiw==", + "dev": true, + "license": "BSD-3-Clause", + "dependencies": { + "@sinonjs/commons": "^3.0.1" + } + }, + "node_modules/@sinonjs/samsam": { + "version": "8.0.2", + "resolved": "https://registry.npmjs.org/@sinonjs/samsam/-/samsam-8.0.2.tgz", + "integrity": 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"https://registry.npmjs.org/node-fetch/-/node-fetch-2.7.0.tgz", @@ -3119,6 +3388,12 @@ "integrity": "sha512-ojmeN0qd+y0jszEtoY48r0Peq5dwMEkIlCOu6Q5f41lfkswXuKtYrhgoTpLnyIcHm24Uhqx+5Tqm2InSwLhE6Q==", "dev": true }, + "path-to-regexp": { + "version": "8.2.0", + "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-8.2.0.tgz", + "integrity": "sha512-TdrF7fW9Rphjq4RjrW0Kp2AW0Ahwu9sRGTkS6bvDi0SCwZlEZYmcfDbEsTz8RVk0EHIS/Vd1bv3JhG+1xZuAyQ==", + "dev": true + }, "pathval": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/pathval/-/pathval-1.1.1.tgz", @@ -3253,6 +3528,28 @@ "integrity": "sha512-7++dFhtcx3353uBaq8DDR4NuxBetBzC7ZQOhmTQInHEd6bSrXdiEyzCvG07Z44UYdLShWUyXt5M/yhz8ekcb1A==", "dev": true }, + "sinon": { + "version": "19.0.2", + "resolved": "https://registry.npmjs.org/sinon/-/sinon-19.0.2.tgz", + "integrity": "sha512-euuToqM+PjO4UgXeLETsfQiuoyPXlqFezr6YZDFwHR3t4qaX0fZUe1MfPMznTL5f8BWrVS89KduLdMUsxFCO6g==", + "dev": true, + "requires": { + "@sinonjs/commons": "^3.0.1", + "@sinonjs/fake-timers": "^13.0.2", + "@sinonjs/samsam": "^8.0.1", + "diff": "^7.0.0", + "nise": "^6.1.1", + "supports-color": "^7.2.0" + }, + "dependencies": { + "diff": { + "version": "7.0.0", + "resolved": "https://registry.npmjs.org/diff/-/diff-7.0.0.tgz", + "integrity": "sha512-PJWHUb1RFevKCwaFA9RlG5tCd+FO5iRh9A8HEtkmBH2Li03iJriB6m6JIN4rGz3K3JLawI7/veA1xzRKP6ISBw==", + "dev": true + } + } + }, "stream": { "version": "0.0.2", "resolved": "https://registry.npmjs.org/stream/-/stream-0.0.2.tgz", diff --git a/package.json b/package.json index 30b2cc4..723a4c6 100644 --- a/package.json +++ b/package.json @@ -9,6 +9,7 @@ "test": "./node_modules/.bin/mocha --reporter spec --recursive", "test:watch": "npm test -- --watch", "test:debug": "./node_modules/.bin/mocha --inspect --inspect-brk --reporter spec --recursive", + "test:coverage": "./node_modules/.bin/mocha --reporter ./src/exporters/coverage.js --recursive", "lint": "./node_modules/.bin/eslint .", "lint:fix": "./node_modules/.bin/eslint . --fix", "doc": "node ./src/doc-gen.js" @@ -19,6 +20,8 @@ "cql-exec-fhir": "^2.1.5", "cql-exec-vsac": "^2.2.0", "fs-extra": "^11.2.0", + "istanbul-lib-report": "^3.0.1", + "istanbul-reports": "^3.1.7", "js-yaml": "^4.1.0", "lodash": "^4.17.21", "mocha": "^10.6.0", @@ -33,7 +36,8 @@ "@eslint/js": "^9.6.0", "cql-execution": "^3.0.1", "eslint": "^9.6.0", - "globals": "^15.8.0" + "globals": "^15.8.0", + "sinon": "^19.0.2" }, "bin": { "cql-to-elm": "bin/cql2elm.js" diff --git a/src/buildTestSuite.js b/src/buildTestSuite.js index 1860f85..c6ee6d9 100644 --- a/src/buildTestSuite.js +++ b/src/buildTestSuite.js @@ -31,7 +31,10 @@ function buildTestSuite(testCases, library, codeService, fhirVersion, config) { prefetchKeys = hooksExporter.extractPrefetchKeys(library); } const executor = new cql.Executor(library, codeService); - describe(libraryHandle, () => { + // Use describe.skip if the suite has skip: true, use describe.only if the suite has only: true, + // otherwise use describe + const describeFn = config.get('skip') ? describe.skip : config.get('only') ? describe.only : describe; + describeFn(libraryHandle, function() { let patientSource; before('Initialize FHIR patient source', () => { switch (fhirVersion) { @@ -77,11 +80,16 @@ function buildTestSuite(testCases, library, codeService, fhirVersion, config) { }); } + before('Initialize coverage report', () => { + this.emit('initCoverageReport', + { source: library.source.library, paths: config.get('library.paths')}); + }); + afterEach('Reset the patient source', () => patientSource.reset()); for (const testCase of testCases) { const testFunc = testCase.skip ? it.skip : testCase.only ? it.only : it; - testFunc(testCase.name, () => { + testFunc(testCase.name, function() { const dumpFileName = `${testCase.name.replace(/[\s/\\]/g, '_')}.json`; if (dumpBundlesPath) { const filePath = path.join(dumpBundlesPath, dumpFileName); @@ -98,12 +106,14 @@ function buildTestSuite(testCases, library, codeService, fhirVersion, config) { } } patientSource.loadBundles([testCase.bundle]); + executor.withParameters(testCase.parameters); return Promise.resolve(executor.exec(patientSource, executionDateTime)).then((results) => { if (dumpResultsPath) { const filePath = path.join(dumpResultsPath, dumpFileName); fs.writeFileSync(filePath, JSON.stringify(results, null, 2), 'utf8'); } const patientId = testCase.bundle.entry[0].resource.id; + this.test.emit('addLocalIdResultMap', results.localIdPatientResultsMap[patientId]); expect(results.patientResults[patientId]).to.exist; for (const expr of Object.keys(testCase.expected)) { checkResult(expr, results.patientResults[patientId][expr], testCase.expected[expr]); @@ -125,6 +135,10 @@ function checkResult(expr, actual, expected) { } else if (/^\$should have length (\d+)/.test(expectedString)) { let expectedLength = Number(expectedString.match(/^\$should have length (\d+)/)[1]); expect(actual, message).to.have.lengthOf(expectedLength); + } else if (/^\$should include (.+)/.test(expectedString)) { + let expectedJson = String(expectedString.match(/^\$should include (.+)/)[1]); + const simpleResult = simplifyResult(actual); + expect(simpleResult, message).to.deep.include(JSON.parse(expectedJson)); } else { // Anything else is not supported throw new Error(`Unsupported $should method: ${message}`); } @@ -150,10 +164,17 @@ function simplifyResult(result) { result2[key] = simplifyResult(result[key]); } return result2; - } else if (result != null && typeof result === 'object') { + } else if (result.constructor.name === 'FHIRObject') { + return result._json; + } else if (typeof result === 'object') { + let result2 = {}; for (const key of Object.keys(result)) { - result[key] = simplifyResult(result[key]); + if(result[key] !== undefined){ + // execution library is serializing uninitialized fields, skip these + result2[key] = simplifyResult(result[key]); + } } + return result2; } return result; } diff --git a/src/exporters/coverage.js b/src/exporters/coverage.js new file mode 100644 index 0000000..b94b49e --- /dev/null +++ b/src/exporters/coverage.js @@ -0,0 +1,172 @@ +const Mocha = require('mocha'); +const path = require('path'); +const libReport = require('istanbul-lib-report'); +const createMap = require('istanbul-lib-coverage').createCoverageMap; +const reports = require('istanbul-reports'); + +class LibraryCoverageReporter extends Mocha.reporters.Base { + constructor(runner) { + super(runner); + + let coverageReport = null; + const coverageReports = []; + + runner.on(Mocha.Runner.constants.EVENT_SUITE_BEGIN, (suite) => { + coverageReport = null; + suite.on('initCoverageReport', (library) => { + if (library) { + coverageReport = LibraryCoverageReporter.initCoverageReport(library.source, library.paths); + coverageReports.push(coverageReport); + } + }); + }); + + runner.on(Mocha.Runner.constants.EVENT_TEST_BEGIN, (test) => { + if (coverageReport) { + test.on('addLocalIdResultMap', (localIdResultsMap) => { + LibraryCoverageReporter.addLocalIdResultMap(localIdResultsMap, coverageReport); + }); + } + }); + + runner.on(Mocha.Runner.constants.EVENT_RUN_END, () => { + const coverage = []; + for (const coverageReport of coverageReports) { + if (coverageReport.paths == null || coverageReport.paths.length > 1) { + console.error('Library paths must be set to a single path'); + } + const coverageData = { + path: path.join(coverageReport.paths[0], `${coverageReport.library.id}.cql`), + statementMap: LibraryCoverageReporter.parseExpressonLocator(coverageReport.expressions), + fnMap: {}, + branchMap: {}, + s: coverageReport.covered, + f: {}, + b: {} + }; + coverage.push(coverageData); + } + LibraryCoverageReporter.writeReport(coverage, 'coverage'); + }); + } + + static parseExpressonLocator(originalObject) { + const parsedObject = {}; + + for (const key in originalObject) { + if (originalObject[key].locator) { + const locator = originalObject[key].locator; + const [start, end] = locator.split('-'); + const [startLine, startColumn] = start.includes(':') ? + start.split(':').map(Number) : [Number(start), 0]; + const [endLine, endColumn] = end !== undefined ? + (end.includes(':') ? end.split(':').map(Number) : [Number(end), 0]) + : [startLine, startColumn]; + + parsedObject[key] = { + start: { line: startLine, column: startColumn > 0 ? startColumn - 1 : startColumn }, + end: { line: endLine, column: endColumn > 0 ? endColumn - 1 : endColumn } + }; + } + } + + return parsedObject; + } + + static writeReport(coverage, coveragePath) { + const coverageMap = createMap({}); + for (const coverageData of coverage) { + coverageMap.addFileCoverage(coverageData); + } + + // create a context for report generation + const context = libReport.createContext({ + dir: `${coveragePath}`, + // The summarizer to default to (may be overridden by some reports) + // values can be nested/flat/pkg. Defaults to 'pkg' + defaultSummarizer: 'nested', + coverageMap + }); + + // create an instance of the relevant report class, passing the + // report name e.g. json/html/html-spa/text + const report = reports.create('lcov', {}); + + // call execute to synchronously create and write the report to disk + report.execute(context); + } + + static initCoverageReport(librarySource, libraryPaths) { + const coverageReport = { + library: librarySource.identifier, + paths: libraryPaths + }; + coverageReport.expressions = this.extractLocalIdData(librarySource.statements.def); + coverageReport.covered = Object.keys(coverageReport.expressions).reduce((acc, key) => { + acc[key] = 0; + return acc; + }, {}); + return coverageReport; + } + + static extractLocalIdData(jsonArray) { + const resultObject = {}; + + function recursiveSearch(obj) { + if (typeof obj !== 'object' || obj === null) { + return; + } + + // Check if the current object has a 'localId' property + if (obj['localId']) { + const localId = obj.localId; + const extractedData = {}; + + // Iterate over the properties of the object + for (const key in obj) { + const value = obj[key]; + // Check if the value is a literal (not an object or array) + if (value !== null && typeof value !== 'object') { + extractedData[key] = value; + } + } + + // Check if 'locator' and 'type' is not null in the extracted data + // Skip types that don't require unit testing - alias, as, type specifiers, literals and property extractors + if (extractedData.locator !== undefined && extractedData.type !== undefined && + extractedData.alias === undefined && + (extractedData.type !== 'As' && !extractedData.type.includes('TypeSpecifier') && extractedData.type !== 'Literal' && extractedData.type !== 'Property') + ) { + resultObject[localId] = extractedData; + } + } + + // Recursively search through all properties of the object, skipping signature and resultTypeSpecifier + for (const key in obj) { + if (typeof obj[key] === 'object' && key !== 'signature' && key !== 'resultTypeSpecifier') { + recursiveSearch(obj[key]); + } + } + } + + // Iterate over each JSON object in the array + jsonArray.forEach(jsonObject => { + recursiveSearch(jsonObject); + }); + + return resultObject; + } + + static addLocalIdResultMap(localIdResultMap, coverageReport) { + if (localIdResultMap == null) { return; } + // Iterate over each key in the results map + for (const localId in localIdResultMap[coverageReport.library.id]) { + // Check if the key exists in the expressions map + if (coverageReport.expressions[localId]) { + coverageReport.covered[localId] += 1; + } + } + } +} + +module.exports = LibraryCoverageReporter; \ No newline at end of file diff --git a/src/loadConfig.js b/src/loadConfig.js index 67235b8..35b3a2a 100644 --- a/src/loadConfig.js +++ b/src/loadConfig.js @@ -107,6 +107,20 @@ function newConfig() { } } }, + skip: { + doc: 'Skip test folder if true', + format: 'Boolean', + default: false, + env: 'CQLT_SKIP', + arg: 'skip' + }, + only: { + doc: 'Only run this test folder if true', + format: 'Boolean', + default: false, + env: 'CQLT_ONLY', + arg: 'only' + } }); } diff --git a/src/loadYamlTestCases.js b/src/loadYamlTestCases.js index c71422d..a96cb81 100644 --- a/src/loadYamlTestCases.js +++ b/src/loadYamlTestCases.js @@ -41,14 +41,14 @@ function yamlToTestCases(yamlFilePath, fhirVersion) { // Get document as a string let docString = fs.readFileSync(yamlFilePath, 'utf8'); // Look for any referenced external data files - let matches = docString.match(/externalData:\s*(\[?-?\s*\w*\s*,?\]?)+/); + let matches = docString.match(/externalData:\s*(\[?-?\s*[\w./-]*\s*,?\]?)+/); matches = matches ? matches[0] : null; let extDataFiles = ['']; if (matches) { let matchNames = matches.split('['); if (matchNames.length == 1) { // There are no square brackets // This must be a block style array. - extDataFiles = matchNames[0].match(/(-\s*\w*)+/g); + extDataFiles = matchNames[0].match(/(-\s*[\w./-]*)+/g); extDataFiles = extDataFiles.map(file => file.replace(/-\s*/,'')); } else { // There are square brackets // This must be a flow style array @@ -70,6 +70,11 @@ function yamlToTestCases(yamlFilePath, fhirVersion) { } // Try to load the document + if(!docString.startsWith('---')){ + // eslint-disable-next-line no-console + console.log(`Ignoring potential external data file: ${yamlFilePath}`); + return []; + } const doc = yaml.load(docString); if (!doc.name) { if (!doc.data && !doc.results) { @@ -81,7 +86,7 @@ function yamlToTestCases(yamlFilePath, fhirVersion) { } const testName = doc.name; if (doc.skip) { - return new TestCase(testName, null, null, true); + return [new TestCase(testName, null, null, true)]; } // Handle the data @@ -114,12 +119,19 @@ function yamlToTestCases(yamlFilePath, fhirVersion) { } // Handle the patient - if (doc.data.length === 0 || doc.data[0].resourceType !== 'Patient') { + if (doc.data.length === 0) { console.warn(`${testName}: First element was not a patient. Inserting a patient element.`); doc.data = doc.data.unshift({ resourceType: 'Patient' }); } - const p = yaml2fhir(doc.data[0], null, fhirVersion); + let p = yaml2fhir(doc.data[0], null, fhirVersion); + + if (p.resourceType !== 'Patient') { + console.warn(`${testName}: First element was not a patient. Inserting a patient element.`); + doc.data = doc.data.unshift({ resourceType: 'Patient' }); + p = yaml2fhir(doc.data[0], null, fhirVersion); + } + addResource(p); for (let i = 1; i < doc.data.length; i++) { @@ -164,7 +176,7 @@ function yamlToTestCases(yamlFilePath, fhirVersion) { for (let i = 0; i < bundles.length; i++) { let iterateTestName = testName + (i > 0 ? ` (${i})` : ''); returnedTestCases.push( - new TestCase(iterateTestName, bundles[i], doc.results, false, doc.only) + new TestCase(iterateTestName, bundles[i], doc.results, false, doc.only, doc.parameters) ); } return returnedTestCases; diff --git a/src/testCase.js b/src/testCase.js index 96e839c..c4bb0f7 100644 --- a/src/testCase.js +++ b/src/testCase.js @@ -1,17 +1,19 @@ class TestCase { - constructor(name, bundle, expected, skip=false, only=false) { + constructor(name, bundle, expected, skip=false, only=false, parameters=null) { this._name = name; this._bundle = bundle; - this._expected = expected; + this._expected = expected; this._skip = skip; this._only = only; + this._parameters = parameters; } get name() { return this._name; } get bundle() { return this._bundle; } - get expected() { return this._expected; } + get expected() { return this._expected; } get skip() { return this._skip; } get only() { return this._only; } + get parameters() { return this._parameters; } } module.exports = TestCase; \ No newline at end of file diff --git a/test/buildTestSuite.test.js b/test/buildTestSuite.test.js new file mode 100644 index 0000000..0aa8c49 --- /dev/null +++ b/test/buildTestSuite.test.js @@ -0,0 +1,53 @@ +const buildTestSuite = require('../src/buildTestSuite'); +const loadConfig = require('../src/loadConfig'); +const sinon = require('sinon'); +const { expect } = require('chai'); +const path = require('path'); + +// Mock library and other dependencies +const mockLibrary = { + source: { + library: { + identifier: { + id: 'test', + version: '1.0' + } + } + } +}; + +describe('buildTestSuite', () => { + it('should use describe.skip when config.skip is true', () => { + const configPath = path.join(__dirname, 'config-skip.yaml'); + const config = loadConfig(configPath); + + const describeSpy = sinon.spy(global, 'describe'); + const describeSkipSpy = sinon.spy(global.describe, 'skip'); + + buildTestSuite([], mockLibrary, null, null, config); + + expect(describeSpy.called).to.be.false; + expect(describeSkipSpy.calledOnce).to.be.true; + expect(describeSkipSpy.calledWith('test_v1.0')).to.be.true; + + describeSpy.restore(); + describeSkipSpy.restore(); + }); + + it('should use describe.only when config.only is true', () => { + const configPath = path.join(__dirname, 'config-only.yaml'); + const config = loadConfig(configPath); + + const describeSpy = sinon.spy(global, 'describe'); + const describeOnlySpy = sinon.spy(global.describe, 'only'); + + buildTestSuite([], mockLibrary, null, null, config); + + expect(describeSpy.called).to.be.false; + expect(describeOnlySpy.calledOnce).to.be.true; + expect(describeOnlySpy.calledWith('test_v1.0')).to.be.true; + + describeSpy.restore(); + describeOnlySpy.restore(); + }); +}); diff --git a/test/config-only.yaml b/test/config-only.yaml new file mode 100644 index 0000000..4e38959 --- /dev/null +++ b/test/config-only.yaml @@ -0,0 +1,8 @@ +--- +library: + name: FactorsToConsiderInManagingChronicPainFHIRv102Test +options: + date: "2018-12-10T00:00:00.0Z" + dumpFiles: + enabled: true +only: true diff --git a/test/config-skip.yaml b/test/config-skip.yaml new file mode 100644 index 0000000..3af8415 --- /dev/null +++ b/test/config-skip.yaml @@ -0,0 +1,8 @@ +--- +library: + name: FactorsToConsiderInManagingChronicPainFHIRv102Test +options: + date: "2018-12-10T00:00:00.0Z" + dumpFiles: + enabled: true +skip: true diff --git a/test/coverage.test.js b/test/coverage.test.js new file mode 100644 index 0000000..6d78756 --- /dev/null +++ b/test/coverage.test.js @@ -0,0 +1,112 @@ +const { expect } = require('chai'); +const fs = require('fs'); +const path = require('path'); +const LibraryCoverageReporter = require('../src/exporters/coverage'); + +describe('LibraryCoverageReporter', () => { + describe('initCoverageReport', function() { + it('should initialize the coverage report with the correct library and paths', function() { + // Read the librarySource from the JSON file + const librarySourcePath = path.join(__dirname, 'yaml', 'other', 'cql', 'OtherFHIRv401Test.json'); + const librarySource = JSON.parse(fs.readFileSync(librarySourcePath, 'utf8')); + + const libraryPaths = ['path1', 'path2']; + + const partialExpectedOutput = { + library: { + id: 'OtherFHIRv401Test', + version: '0.0.1', + }, + paths: ['path1', 'path2'] + }; + + const result = LibraryCoverageReporter.initCoverageReport(librarySource.library, libraryPaths); + + // Use include to partially match the expected output + expect(result).to.deep.include(partialExpectedOutput, 'includes the correct library and paths'); + + // Additional checks for expressions and covered + expect(result.expressions).to.include.keys(['216', '217']); + expect(result.covered).to.include.keys(['216', '217']); + expect(result.covered).to.deep.include({ 216: 0, 217: 0 }); + }); + }); + + describe('writeReport', () => { + it('should write Istanbul HTML report', () => { + const coverageData = { + path: 'test/yaml/other/cql/OtherFHIRv401Test.cql', + statementMap: { + '0': { + start: { line: 2, column: 0 }, + end: { line: 2, column: 29 } + }, + '1': { + start: { line: 3, column: 0 }, + end: { line: 3, column: 47 } + }, + '2': { + start: { line: 5, column: 0 }, + end: { line: 5, column: 47 } + } + }, + fnMap: {}, + branchMap: {}, + s: { + '0': 0, + '1': 0, + '2': 0 + }, + f: {}, + b: {} + }; + + LibraryCoverageReporter.writeReport([coverageData], 'coverage'); + }); + }); + + describe('parseExpressonLocator', function() { + it('should correctly parse various locator formats', function() { + const originalObject = { + key1: { locator: '1:5-2:10' }, // Line and column + key2: { locator: '3-4' }, // Line only + key3: { locator: '5:8' }, // Start line and column only + key4: { locator: '6' }, // Start line only + key5: { noLocator: 'value' }, // No locator + key6: { locator: '7:2-8:3' }, // Multiple keys with locators + key7: { locator: '9:4-10:5' } + }; + + const expectedOutput = { + key1: { + start: { line: 1, column: 4 }, + end: { line: 2, column: 9 } + }, + key2: { + start: { line: 3, column: 0 }, + end: { line: 4, column: 0 } + }, + key3: { + start: { line: 5, column: 7 }, + end: { line: 5, column: 7 } + }, + key4: { + start: { line: 6, column: 0 }, + end: { line: 6, column: 0 } + }, + // key5 is not included in expectedOutput as it has no locator + key6: { + start: { line: 7, column: 1 }, + end: { line: 8, column: 2 } + }, + key7: { + start: { line: 9, column: 3 }, + end: { line: 10, column: 4 } + } + }; + + const result = LibraryCoverageReporter.parseExpressonLocator(originalObject); + expect(result).to.deep.equal(expectedOutput, 'correctly parses various locator formats'); + }); + }); +}); \ No newline at end of file diff --git a/test/yaml/other/cql/FHIRHelpers-4.0.1.cql b/test/yaml/other/cql/FHIRHelpers-4.0.1.cql new file mode 100644 index 0000000..ce8608d --- /dev/null +++ b/test/yaml/other/cql/FHIRHelpers-4.0.1.cql @@ -0,0 +1,520 @@ +/* +@author: Bryn Rhodes +@description: This library defines functions to convert between FHIR + data types and CQL system-defined types, as well as functions to support + FHIRPath implementation. For more information, the FHIRHelpers wiki page: + https://github.com/cqframework/clinical_quality_language/wiki/FHIRHelpers +@allowFluent: true +*/ +library FHIRHelpers version '4.0.1' + +using FHIR version '4.0.1' + +define function ToInterval(period FHIR.Period): + if period is null then + null + else + if period."start" is null then + Interval(period."start".value, period."end".value] + else + Interval[period."start".value, period."end".value] + +define function ToCalendarUnit(unit System.String): + case unit + when 'ms' then 'millisecond' + when 's' then 'second' + when 'min' then 'minute' + when 'h' then 'hour' + when 'd' then 'day' + when 'wk' then 'week' + when 'mo' then 'month' + when 'a' then 'year' + else unit + end + +define function ToQuantity(quantity FHIR.Quantity): + case + when quantity is null then null + when quantity.value is null then null + when quantity.comparator is not null then + Message(null, true, 'FHIRHelpers.ToQuantity.ComparatorQuantityNotSupported', 'Error', 'FHIR Quantity value has a comparator and cannot be converted to a System.Quantity value.') + when quantity.system is null or quantity.system.value = 'http://unitsofmeasure.org' + or quantity.system.value = 'http://hl7.org/fhirpath/CodeSystem/calendar-units' then + System.Quantity { value: quantity.value.value, unit: ToCalendarUnit(Coalesce(quantity.code.value, quantity.unit.value, '1')) } + else + Message(null, true, 'FHIRHelpers.ToQuantity.InvalidFHIRQuantity', 'Error', 'Invalid FHIR Quantity code: ' & quantity.unit.value & ' (' & quantity.system.value & '|' & quantity.code.value & ')') + end + +define function ToQuantityIgnoringComparator(quantity FHIR.Quantity): + case + when quantity is null then null + when quantity.value is null then null + when quantity.system is null or quantity.system.value = 'http://unitsofmeasure.org' + or quantity.system.value = 'http://hl7.org/fhirpath/CodeSystem/calendar-units' then + System.Quantity { value: quantity.value.value, unit: ToCalendarUnit(Coalesce(quantity.code.value, quantity.unit.value, '1')) } + else + Message(null, true, 'FHIRHelpers.ToQuantity.InvalidFHIRQuantity', 'Error', 'Invalid FHIR Quantity code: ' & quantity.unit.value & ' (' & quantity.system.value & '|' & quantity.code.value & ')') + end + +define function ToInterval(quantity FHIR.Quantity): + if quantity is null then null else + case quantity.comparator.value + when '<' then + Interval[ + null, + ToQuantityIgnoringComparator(quantity) + ) + when '<=' then + Interval[ + null, + ToQuantityIgnoringComparator(quantity) + ] + when '>=' then + Interval[ + ToQuantityIgnoringComparator(quantity), + null + ] + when '>' then + Interval( + ToQuantityIgnoringComparator(quantity), + null + ] + else + Interval[ToQuantity(quantity), ToQuantity(quantity)] + end + +define function ToRatio(ratio FHIR.Ratio): + if ratio is null then + null + else + System.Ratio { numerator: ToQuantity(ratio.numerator), denominator: ToQuantity(ratio.denominator) } + +define function ToInterval(range FHIR.Range): + if range is null then + null + else + Interval[ToQuantity(range.low), ToQuantity(range.high)] + +define function ToCode(coding FHIR.Coding): + if coding is null then + null + else + System.Code { + code: coding.code.value, + system: coding.system.value, + version: coding.version.value, + display: coding.display.value + } + +define function ToConcept(concept FHIR.CodeableConcept): + if concept is null then + null + else + System.Concept { + codes: concept.coding C return ToCode(C), + display: concept.text.value + } + +define function ToValueSet(uri String): + if uri is null then + null + else + System.ValueSet { + id: uri + } + +define function reference(reference String): + if reference is null then + null + else + Reference { reference: string { value: reference } } + +define function ToValue(value Choice): + case + when value is base64Binary then (value as base64Binary).value + when value is boolean then (value as boolean).value + when value is canonical then (value as canonical).value + when value is code then (value as code).value + when value is date then (value as date).value + when value is dateTime then (value as dateTime).value + when value is decimal then (value as decimal).value + when value is id then (value as id).value + when value is instant then (value as instant).value + when value is integer then (value as integer).value + when value is markdown then (value as markdown).value + when value is oid then (value as oid).value + when value is positiveInt then (value as positiveInt).value + when value is string then (value as string).value + when value is time then (value as time).value + when value is unsignedInt then (value as unsignedInt).value + when value is uri then (value as uri).value + when value is url then (value as url).value + when value is uuid then (value as uuid).value + when value is Age then ToQuantity(value as Age) + when value is CodeableConcept then ToConcept(value as CodeableConcept) + when value is Coding then ToCode(value as Coding) + when value is Count then ToQuantity(value as Count) + when value is Distance then ToQuantity(value as Distance) + when value is Duration then ToQuantity(value as Duration) + when value is Quantity then ToQuantity(value as Quantity) + when value is Range then ToInterval(value as Range) + when value is Period then ToInterval(value as Period) + when value is Ratio then ToRatio(value as Ratio) + else value as Choice + end + +define function resolve(reference String) returns Resource: external +define function resolve(reference Reference) returns Resource: external +define function reference(resource Resource) returns Reference: external +define function extension(element Element, url String) returns List: external +define function extension(resource DomainResource, url String) returns List: external +define function modifierExtension(element BackboneElement, url String) returns List: external +define function modifierExtension(resource DomainResource, url String) returns List: external +define function hasValue(element Element) returns Boolean: external +define function getValue(element Element) returns Any: external +define function ofType(identifier String) returns List: external +define function is(identifier String) returns Boolean: external +define function as(identifier String) returns Any: external +define function elementDefinition(element Element) returns ElementDefinition: external +define function slice(element Element, url String, name String) returns List: external +define function checkModifiers(resource Resource) returns Resource: external +define function checkModifiers(resource Resource, modifier String) returns Resource: external +define function checkModifiers(element Element) returns Element: external +define function checkModifiers(element Element, modifier String) returns Element: external +define function conformsTo(resource Resource, structure String) returns Boolean: external +define function memberOf(code code, valueSet String) returns Boolean: external +define function memberOf(coding Coding, valueSet String) returns Boolean: external +define function memberOf(concept CodeableConcept, valueSet String) returns Boolean: external +define function subsumes(coding Coding, subsumedCoding Coding) returns Boolean: external +define function subsumes(concept CodeableConcept, subsumedConcept CodeableConcept) returns Boolean: external +define function subsumedBy(coding Coding, subsumingCoding Coding) returns Boolean: external +define function subsumedBy(concept CodeableConcept, subsumingConcept CodeableConcept) returns Boolean: external +define function htmlChecks(element Element) returns Boolean: external + +define function ToString(value AccountStatus): value.value +define function ToString(value ActionCardinalityBehavior): value.value +define function ToString(value ActionConditionKind): value.value +define function ToString(value ActionGroupingBehavior): value.value +define function ToString(value ActionParticipantType): value.value +define function ToString(value ActionPrecheckBehavior): value.value +define function ToString(value ActionRelationshipType): value.value +define function ToString(value ActionRequiredBehavior): value.value +define function ToString(value ActionSelectionBehavior): value.value +define function ToString(value ActivityDefinitionKind): value.value +define function ToString(value ActivityParticipantType): value.value +define function ToString(value AddressType): value.value +define function ToString(value AddressUse): value.value +define function ToString(value AdministrativeGender): value.value +define function ToString(value AdverseEventActuality): value.value +define function ToString(value AggregationMode): value.value +define function ToString(value AllergyIntoleranceCategory): value.value +define function ToString(value AllergyIntoleranceCriticality): value.value +define function ToString(value AllergyIntoleranceSeverity): value.value +define function ToString(value AllergyIntoleranceType): value.value +define function ToString(value AppointmentStatus): value.value +define function ToString(value AssertionDirectionType): value.value +define function ToString(value AssertionOperatorType): value.value +define function ToString(value AssertionResponseTypes): value.value +define function ToString(value AuditEventAction): value.value +define function ToString(value AuditEventAgentNetworkType): value.value +define function ToString(value AuditEventOutcome): value.value +define function ToString(value BindingStrength): value.value +define function ToString(value BiologicallyDerivedProductCategory): value.value +define function ToString(value BiologicallyDerivedProductStatus): value.value +define function ToString(value BiologicallyDerivedProductStorageScale): value.value +define function ToString(value BundleType): value.value +define function ToString(value CapabilityStatementKind): value.value +define function ToString(value CarePlanActivityKind): value.value +define function ToString(value CarePlanActivityStatus): value.value +define function ToString(value CarePlanIntent): value.value +define function ToString(value CarePlanStatus): value.value +define function ToString(value CareTeamStatus): value.value +define function ToString(value CatalogEntryRelationType): value.value +define function ToString(value ChargeItemDefinitionPriceComponentType): value.value +define function ToString(value ChargeItemStatus): value.value +define function ToString(value ClaimResponseStatus): value.value +define function ToString(value ClaimStatus): value.value +define function ToString(value ClinicalImpressionStatus): value.value +define function ToString(value CodeSearchSupport): value.value +define function ToString(value CodeSystemContentMode): value.value +define function ToString(value CodeSystemHierarchyMeaning): value.value +define function ToString(value CommunicationPriority): value.value +define function ToString(value CommunicationRequestStatus): value.value +define function ToString(value CommunicationStatus): value.value +define function ToString(value CompartmentCode): value.value +define function ToString(value CompartmentType): value.value +define function ToString(value CompositionAttestationMode): value.value +define function ToString(value CompositionStatus): value.value +define function ToString(value ConceptMapEquivalence): value.value +define function ToString(value ConceptMapGroupUnmappedMode): value.value +define function ToString(value ConditionalDeleteStatus): value.value +define function ToString(value ConditionalReadStatus): value.value +define function ToString(value ConsentDataMeaning): value.value +define function ToString(value ConsentProvisionType): value.value +define function ToString(value ConsentState): value.value +define function ToString(value ConstraintSeverity): value.value +define function ToString(value ContactPointSystem): value.value +define function ToString(value ContactPointUse): value.value +define function ToString(value ContractPublicationStatus): value.value +define function ToString(value ContractStatus): value.value +define function ToString(value ContributorType): value.value +define function ToString(value CoverageStatus): value.value +define function ToString(value CurrencyCode): value.value +define function ToString(value DayOfWeek): value.value +define function ToString(value DaysOfWeek): value.value +define function ToString(value DetectedIssueSeverity): value.value +define function ToString(value DetectedIssueStatus): value.value +define function ToString(value DeviceMetricCalibrationState): value.value +define function ToString(value DeviceMetricCalibrationType): value.value +define function ToString(value DeviceMetricCategory): value.value +define function ToString(value DeviceMetricColor): value.value +define function ToString(value DeviceMetricOperationalStatus): value.value +define function ToString(value DeviceNameType): value.value +define function ToString(value DeviceRequestStatus): value.value +define function ToString(value DeviceUseStatementStatus): value.value +define function ToString(value DiagnosticReportStatus): value.value +define function ToString(value DiscriminatorType): value.value +define function ToString(value DocumentConfidentiality): value.value +define function ToString(value DocumentMode): value.value +define function ToString(value DocumentReferenceStatus): value.value +define function ToString(value DocumentRelationshipType): value.value +define function ToString(value EligibilityRequestPurpose): value.value +define function ToString(value EligibilityRequestStatus): value.value +define function ToString(value EligibilityResponsePurpose): value.value +define function ToString(value EligibilityResponseStatus): value.value +define function ToString(value EnableWhenBehavior): value.value +define function ToString(value EncounterLocationStatus): value.value +define function ToString(value EncounterStatus): value.value +define function ToString(value EndpointStatus): value.value +define function ToString(value EnrollmentRequestStatus): value.value +define function ToString(value EnrollmentResponseStatus): value.value +define function ToString(value EpisodeOfCareStatus): value.value +define function ToString(value EventCapabilityMode): value.value +define function ToString(value EventTiming): value.value +define function ToString(value EvidenceVariableType): value.value +define function ToString(value ExampleScenarioActorType): value.value +define function ToString(value ExplanationOfBenefitStatus): value.value +define function ToString(value ExposureState): value.value +define function ToString(value ExtensionContextType): value.value +define function ToString(value FHIRAllTypes): value.value +define function ToString(value FHIRDefinedType): value.value +define function ToString(value FHIRDeviceStatus): value.value +define function ToString(value FHIRResourceType): value.value +define function ToString(value FHIRSubstanceStatus): value.value +define function ToString(value FHIRVersion): value.value +define function ToString(value FamilyHistoryStatus): value.value +define function ToString(value FilterOperator): value.value +define function ToString(value FlagStatus): value.value +define function ToString(value GoalLifecycleStatus): value.value +define function ToString(value GraphCompartmentRule): value.value +define function ToString(value GraphCompartmentUse): value.value +define function ToString(value GroupMeasure): value.value +define function ToString(value GroupType): value.value +define function ToString(value GuidanceResponseStatus): value.value +define function ToString(value GuidePageGeneration): value.value +define function ToString(value GuideParameterCode): value.value +define function ToString(value HTTPVerb): value.value +define function ToString(value IdentifierUse): value.value +define function ToString(value IdentityAssuranceLevel): value.value +define function ToString(value ImagingStudyStatus): value.value +define function ToString(value ImmunizationEvaluationStatus): value.value +define function ToString(value ImmunizationStatus): value.value +define function ToString(value InvoicePriceComponentType): value.value +define function ToString(value InvoiceStatus): value.value +define function ToString(value IssueSeverity): value.value +define function ToString(value IssueType): value.value +define function ToString(value LinkType): value.value +define function ToString(value LinkageType): value.value +define function ToString(value ListMode): value.value +define function ToString(value ListStatus): value.value +define function ToString(value LocationMode): value.value +define function ToString(value LocationStatus): value.value +define function ToString(value MeasureReportStatus): value.value +define function ToString(value MeasureReportType): value.value +define function ToString(value MediaStatus): value.value +define function ToString(value MedicationAdministrationStatus): value.value +define function ToString(value MedicationDispenseStatus): value.value +define function ToString(value MedicationKnowledgeStatus): value.value +define function ToString(value MedicationRequestIntent): value.value +define function ToString(value MedicationRequestPriority): value.value +define function ToString(value MedicationRequestStatus): value.value +define function ToString(value MedicationStatementStatus): value.value +define function ToString(value MedicationStatus): value.value +define function ToString(value MessageSignificanceCategory): value.value +define function ToString(value Messageheader_Response_Request): value.value +define function ToString(value MimeType): value.value +define function ToString(value NameUse): value.value +define function ToString(value NamingSystemIdentifierType): value.value +define function ToString(value NamingSystemType): value.value +define function ToString(value NarrativeStatus): value.value +define function ToString(value NoteType): value.value +define function ToString(value NutritiionOrderIntent): value.value +define function ToString(value NutritionOrderStatus): value.value +define function ToString(value ObservationDataType): value.value +define function ToString(value ObservationRangeCategory): value.value +define function ToString(value ObservationStatus): value.value +define function ToString(value OperationKind): value.value +define function ToString(value OperationParameterUse): value.value +define function ToString(value OrientationType): value.value +define function ToString(value ParameterUse): value.value +define function ToString(value ParticipantRequired): value.value +define function ToString(value ParticipantStatus): value.value +define function ToString(value ParticipationStatus): value.value +define function ToString(value PaymentNoticeStatus): value.value +define function ToString(value PaymentReconciliationStatus): value.value +define function ToString(value ProcedureStatus): value.value +define function ToString(value PropertyRepresentation): value.value +define function ToString(value PropertyType): value.value +define function ToString(value ProvenanceEntityRole): value.value +define function ToString(value PublicationStatus): value.value +define function ToString(value QualityType): value.value +define function ToString(value QuantityComparator): value.value +define function ToString(value QuestionnaireItemOperator): value.value +define function ToString(value QuestionnaireItemType): value.value +define function ToString(value QuestionnaireResponseStatus): value.value +define function ToString(value ReferenceHandlingPolicy): value.value +define function ToString(value ReferenceVersionRules): value.value +define function ToString(value ReferredDocumentStatus): value.value +define function ToString(value RelatedArtifactType): value.value +define function ToString(value RemittanceOutcome): value.value +define function ToString(value RepositoryType): value.value +define function ToString(value RequestIntent): value.value +define function ToString(value RequestPriority): value.value +define function ToString(value RequestStatus): value.value +define function ToString(value ResearchElementType): value.value +define function ToString(value ResearchStudyStatus): value.value +define function ToString(value ResearchSubjectStatus): value.value +define function ToString(value ResourceType): value.value +define function ToString(value ResourceVersionPolicy): value.value +define function ToString(value ResponseType): value.value +define function ToString(value RestfulCapabilityMode): value.value +define function ToString(value RiskAssessmentStatus): value.value +define function ToString(value SPDXLicense): value.value +define function ToString(value SearchComparator): value.value +define function ToString(value SearchEntryMode): value.value +define function ToString(value SearchModifierCode): value.value +define function ToString(value SearchParamType): value.value +define function ToString(value SectionMode): value.value +define function ToString(value SequenceType): value.value +define function ToString(value ServiceRequestIntent): value.value +define function ToString(value ServiceRequestPriority): value.value +define function ToString(value ServiceRequestStatus): value.value +define function ToString(value SlicingRules): value.value +define function ToString(value SlotStatus): value.value +define function ToString(value SortDirection): value.value +define function ToString(value SpecimenContainedPreference): value.value +define function ToString(value SpecimenStatus): value.value +define function ToString(value Status): value.value +define function ToString(value StrandType): value.value +define function ToString(value StructureDefinitionKind): value.value +define function ToString(value StructureMapContextType): value.value +define function ToString(value StructureMapGroupTypeMode): value.value +define function ToString(value StructureMapInputMode): value.value +define function ToString(value StructureMapModelMode): value.value +define function ToString(value StructureMapSourceListMode): value.value +define function ToString(value StructureMapTargetListMode): value.value +define function ToString(value StructureMapTransform): value.value +define function ToString(value SubscriptionChannelType): value.value +define function ToString(value SubscriptionStatus): value.value +define function ToString(value SupplyDeliveryStatus): value.value +define function ToString(value SupplyRequestStatus): value.value +define function ToString(value SystemRestfulInteraction): value.value +define function ToString(value TaskIntent): value.value +define function ToString(value TaskPriority): value.value +define function ToString(value TaskStatus): value.value +define function ToString(value TestReportActionResult): value.value +define function ToString(value TestReportParticipantType): value.value +define function ToString(value TestReportResult): value.value +define function ToString(value TestReportStatus): value.value +define function ToString(value TestScriptRequestMethodCode): value.value +define function ToString(value TriggerType): value.value +define function ToString(value TypeDerivationRule): value.value +define function ToString(value TypeRestfulInteraction): value.value +define function ToString(value UDIEntryType): value.value +define function ToString(value UnitsOfTime): value.value +define function ToString(value Use): value.value +define function ToString(value VariableType): value.value +define function ToString(value VisionBase): value.value +define function ToString(value VisionEyes): value.value +define function ToString(value VisionStatus): value.value +define function ToString(value XPathUsageType): value.value +define function ToString(value base64Binary): value.value +define function ToBoolean(value boolean): value.value +define function ToDate(value date): value.value +define function ToDateTime(value dateTime): value.value +define function ToDecimal(value decimal): value.value +define function ToDateTime(value instant): value.value +define function ToInteger(value integer): value.value +define function ToString(value string): value.value +define function ToTime(value time): value.value +define function ToString(value uri): value.value +define function ToString(value xhtml): value.value diff --git a/test/yaml/other/cql/FHIRHelpers-4.0.1.json b/test/yaml/other/cql/FHIRHelpers-4.0.1.json new file mode 100644 index 0000000..37a0cff --- /dev/null +++ b/test/yaml/other/cql/FHIRHelpers-4.0.1.json @@ -0,0 +1,42985 @@ +{ + "library" : { + "localId" : "0", + "annotation" : [ { + "translatorVersion" : "3.12.0", + "translatorOptions" : "EnableAnnotations,EnableLocators,EnableResultTypes,DisableListDemotion,DisableListPromotion", + "signatureLevel" : "All", + "type" : "CqlToElmInfo" + }, { + "message" : "An operand identifier [reference] is hiding another identifier of the same name.", + "errorType" : "semantic", + "errorSeverity" : "warning", + "type" : "CqlToElmError" + }, { + "message" : "An operand identifier [reference] is hiding another identifier of the same name.", + "errorType" : "semantic", + "errorSeverity" : "warning", + "type" : "CqlToElmError" + }, { + "message" : "An operand identifier [reference] is hiding another identifier of the same name.", + "errorType" : "semantic", + "errorSeverity" : "warning", + "type" : "CqlToElmError" + }, { + "type" : "Annotation", + "t" : [ { + "name" : "author", + "value" : "Bryn Rhodes" + }, { + "name" : "description", + "value" : "This library defines functions to convert between FHIR\n data types and CQL system-defined types, as well as functions to support\n FHIRPath implementation. For more information, the FHIRHelpers wiki page:\n https://github.com/cqframework/clinical_quality_language/wiki/FHIRHelpers" + }, { + "name" : "allowFluent", + "value" : "true" + } ], + "s" : { + "r" : "7019", + "s" : [ { + "value" : [ "/*\n@author: Bryn Rhodes\n@description: This library defines functions to convert between FHIR\n data types and CQL system-defined types, as well as functions to support\n FHIRPath implementation. For more information, the FHIRHelpers wiki page:\n https://github.com/cqframework/clinical_quality_language/wiki/FHIRHelpers\n@allowFluent: true\n*/\n","library FHIRHelpers version '4.0.1'" ] + } ] + } + } ], + "identifier" : { + "id" : "FHIRHelpers", + "version" : "4.0.1" + }, + "schemaIdentifier" : { + "id" : "urn:hl7-org:elm", + "version" : "r1" + }, + "usings" : { + "def" : [ { + "localId" : "1", + "localIdentifier" : "System", + "uri" : "urn:hl7-org:elm-types:r1" + }, { + "localId" : "206", + "locator" : "11:1-11:26", + "localIdentifier" : "FHIR", + "uri" : "http://hl7.org/fhir", + "version" : "4.0.1", + "annotation" : [ { + "type" : "Annotation", + "s" : { + "r" : "206", + "s" : [ { + "value" : [ "","using " ] + }, { + "s" : [ { + "value" : [ "FHIR" ] + } ] + }, { + "value" : [ " version '4.0.1'" ] + } ] + } + } ] + } ] + }, + "statements" : { + "def" : [ { + "localId" : "207", + "locator" : "13:1-20:62", + "name" : "ToInterval", + "context" : "Unfiltered", + "accessLevel" : 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+ } ] + }, { + "value" : [ "." ] + }, { + "r" : "221", + "s" : [ { + "value" : [ "\"start\"" ] + } ] + } ] + }, { + "value" : [ "." ] + }, { + "r" : "222", + "s" : [ { + "value" : [ "value" ] + } ] + } ] + }, { + "value" : [ ", " ] + }, { + "r" : "225", + "s" : [ { + "r" : "224", + "s" : [ { + "r" : "223", + "s" : [ { + "value" : [ "period" ] + } ] + }, { + "value" : [ "." ] + }, { + "r" : "224", + "s" : [ { + "value" : [ "\"end\"" ] + } ] + } ] + }, { + "value" : [ "." ] + }, { + "r" : "225", + "s" : [ { + "value" : [ "value" ] + } ] + } ] + }, { + "value" : [ "]" ] + } ] + }, { + "value" : [ "\n else\n " ] + }, { + "r" : "235", + "s" : [ { + "value" : [ "Interval[" ] + }, { + "r" : "231", + "s" : [ { + "r" : "230", + "s" : [ { + "r" : "229", + "s" : [ { + "value" : [ "period" ] + } ] + }, { + "value" : [ "." ] + }, { + "r" : "230", + "s" : [ { + "value" : [ "\"start\"" ] + } ] + } ] + }, { + "value" : [ "." ] + }, { + "r" : "231", + "s" : [ { + "value" : [ "value" ] + } ] + } ] + }, 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"520:32-520:36", + "resultTypeName" : "{http://hl7.org/fhir}xhtml", + "name" : "{http://hl7.org/fhir}xhtml", + "type" : "NamedTypeSpecifier" + } + } ] + } ] + } + } +} + diff --git a/test/yaml/other/cql/OtherFHIRv401Test.cql b/test/yaml/other/cql/OtherFHIRv401Test.cql new file mode 100644 index 0000000..fe6ab59 --- /dev/null +++ b/test/yaml/other/cql/OtherFHIRv401Test.cql @@ -0,0 +1,18 @@ +library OtherFHIRv401Test version '0.0.1' + +using FHIR version '4.0.1' + +include FHIRHelpers version '4.0.1' called FHIRHelpers + +parameter "LookbackPeriod" default 180 + +context Patient + +define "TestParamAndIncludeSubset": + { + LookbackPeriod: "LookbackPeriod", + Ignore: 'some other output' + } + +define AbatementAge: + First([Condition] C).abatement as Age \ No newline at end of file diff --git a/test/yaml/other/cql/OtherFHIRv401Test.json b/test/yaml/other/cql/OtherFHIRv401Test.json new file mode 100644 index 0000000..804827b --- /dev/null +++ b/test/yaml/other/cql/OtherFHIRv401Test.json @@ -0,0 +1,420 @@ +{ + "library" : { + "localId" : "0", + "annotation" : [ { + "translatorVersion" : "3.12.0", + "translatorOptions" : "EnableAnnotations,EnableLocators,EnableResultTypes,DisableListDemotion,DisableListPromotion", + "signatureLevel" : "All", + "type" : "CqlToElmInfo" + }, { + "type" : "Annotation", + "s" : { + "r" : "230", + "s" : [ { + "value" : [ "","library OtherFHIRv401Test version '0.0.1'" ] + } ] + } + } ], + "identifier" : { + "id" : "OtherFHIRv401Test", + "version" : "0.0.1" + }, + "schemaIdentifier" : { + "id" : "urn:hl7-org:elm", + "version" : "r1" + }, + "usings" : { + "def" : [ { + "localId" : "1", + "localIdentifier" : "System", + "uri" : "urn:hl7-org:elm-types:r1" + }, { + "localId" : "206", + "locator" : "3:1-3:26", + "localIdentifier" : "FHIR", + "uri" : "http://hl7.org/fhir", + "version" : "4.0.1", + "annotation" : [ { + "type" : "Annotation", + "s" : { + "r" : "206", + "s" : [ { + "value" : [ "","using " ] + }, { + "s" : [ { + "value" : [ "FHIR" ] + } ] + }, { + "value" : [ " version '4.0.1'" ] + } ] + } + } ] + } ] + }, + "includes" : { + "def" : [ { + "localId" : "207", + "locator" : "5:1-5:54", + "localIdentifier" : "FHIRHelpers", + "path" : "FHIRHelpers", + "version" : "4.0.1", + "annotation" : [ { + "type" : "Annotation", + "s" : { + "r" : "207", + "s" : [ { + "value" : [ "","include " ] + }, { + "s" : [ { + "value" : [ "FHIRHelpers" ] + } ] + }, { + "value" : [ " version ","'4.0.1'"," called ","FHIRHelpers" ] + } ] + } + } ] + } ] + }, + "parameters" : { + "def" : [ { + "localId" : "208", + "locator" : "7:1-7:38", + "resultTypeName" : "{urn:hl7-org:elm-types:r1}Integer", + "name" : "LookbackPeriod", + "accessLevel" : "Public", + "annotation" : [ { + "type" : "Annotation", + "s" : { + "r" : "208", + "s" : [ { + "r" : "209", + "value" : [ "","parameter ","\"LookbackPeriod\""," default ","180" ] + } ] + } + } ], + "default" : { + "localId" : "209", + "locator" : "7:36-7:38", + "resultTypeName" : "{urn:hl7-org:elm-types:r1}Integer", + "valueType" : "{urn:hl7-org:elm-types:r1}Integer", + "value" : "180", + "type" : "Literal" + } + } ] + }, + "contexts" : { + "def" : [ { + "localId" : "213", + "locator" : "9:1-9:15", + "name" : "Patient" + } ] + }, + "statements" : { + "def" : [ { + "localId" : "211", + "locator" : "9:1-9:15", + "name" : "Patient", + "context" : "Patient", + "expression" : { + "localId" : "212", + "type" : "SingletonFrom", + "signature" : [ ], + "operand" : { + "localId" : "210", + "locator" : "9:1-9:15", + "dataType" : "{http://hl7.org/fhir}Patient", + "templateId" : "http://hl7.org/fhir/StructureDefinition/Patient", + "type" : "Retrieve", + "include" : [ ], + "codeFilter" : [ ], + "dateFilter" : [ ], + "otherFilter" : [ ] + } + } + }, { + "localId" : "215", + "locator" : "11:1-15:5", + "name" : "TestParamAndIncludeSubset", + "context" : "Patient", + "accessLevel" : "Public", + "annotation" : [ { + "type" : "Annotation", + "s" : { + "r" : "215", + "s" : [ { + "value" : [ "","define ","\"TestParamAndIncludeSubset\"",":\n " ] + }, { + "r" : "216", + "s" : [ { + "value" : [ "{\n " ] + }, { + "s" : [ { + "value" : [ "LookbackPeriod",": " ] + }, { + "r" : "217", + "s" : [ { + "value" : [ "\"LookbackPeriod\"" ] + } ] + } ] + }, { + "value" : [ ",\n " ] + }, { + "s" : [ { + "value" : [ "Ignore",": " ] + }, { + "r" : "218", + "s" : [ { + "value" : [ "'some other output'" ] + } ] + } ] + }, { + "value" : [ "\n }" ] + } ] + } ] + } + } ], + "resultTypeSpecifier" : { + "localId" : "224", + "type" : "TupleTypeSpecifier", + "element" : [ { + "localId" : "225", + "name" : "LookbackPeriod", + "elementType" : { + "localId" : "226", + "name" : "{urn:hl7-org:elm-types:r1}Integer", + "type" : "NamedTypeSpecifier" + } + }, { + "localId" : "227", + "name" : "Ignore", + "elementType" : { + "localId" : "228", + "name" : "{urn:hl7-org:elm-types:r1}String", + "type" : "NamedTypeSpecifier" + } + } ] + }, + "expression" : { + "localId" : "216", + "locator" : "12:5-15:5", + "type" : "Tuple", + "resultTypeSpecifier" : { + "localId" : "219", + "type" : "TupleTypeSpecifier", + "element" : [ { + "localId" : "220", + "name" : "LookbackPeriod", + "elementType" : { + "localId" : "221", + "name" : "{urn:hl7-org:elm-types:r1}Integer", + "type" : "NamedTypeSpecifier" + } + }, { + "localId" : "222", + "name" : "Ignore", + "elementType" : { + "localId" : "223", + "name" : "{urn:hl7-org:elm-types:r1}String", + "type" : "NamedTypeSpecifier" + } + } ] + }, + "element" : [ { + "name" : "LookbackPeriod", + "value" : { + "localId" : "217", + "locator" : "13:23-13:38", + "resultTypeName" : "{urn:hl7-org:elm-types:r1}Integer", + "name" : "LookbackPeriod", + "type" : "ParameterRef" + } + }, { + "name" : "Ignore", + "value" : { + "localId" : "218", + "locator" : "14:15-14:33", + "resultTypeName" : "{urn:hl7-org:elm-types:r1}String", + "valueType" : "{urn:hl7-org:elm-types:r1}String", + "value" : "some other output", + "type" : "Literal" + } + } ] + } + }, { + "localId" : "230", + "locator" : "17:1-18:39", + "resultTypeName" : "{http://hl7.org/fhir}Age", + "name" : "AbatementAge", + "context" : "Patient", + "accessLevel" : "Public", + "annotation" : [ { + "type" : "Annotation", + "s" : { + "r" : "230", + "s" : [ { + "value" : [ "","define ","AbatementAge",":\n " ] + }, { + "r" : "231", + "s" : [ { + "r" : "250", + "s" : [ { + "r" : "247", + "s" : [ { + "value" : [ "First","(" ] + }, { + "r" : "240", + "s" : [ { + "s" : [ { + "r" : "232", + "s" : [ { + "r" : "233", + "s" : [ { + "r" : "233", + "s" : [ { + "value" : [ "[","Condition","]" ] + } ] + } ] + }, { + "value" : [ " ","C" ] + } ] + } ] + } ] + }, { + "value" : [ ")" ] + } ] + }, { + "value" : [ "." ] + }, { + "r" : "250", + "s" : [ { + "value" : [ "abatement" ] + } ] + } ] + }, { + "value" : [ " as " ] + }, { + "r" : "263", + "s" : [ { + "value" : [ "Age" ] + } ] + } ] + } ] + } + } ], + "expression" : { + "localId" : "231", + "locator" : "18:3-18:39", + "resultTypeName" : "{http://hl7.org/fhir}Age", + "strict" : false, + "type" : "As", + "signature" : [ ], + "operand" : { + "localId" : "250", + "locator" : "18:3-18:32", + "path" : "abatement", + "type" : "Property", + "resultTypeSpecifier" : { + "localId" : "257", + "type" : "ChoiceTypeSpecifier", + "type" : [ ], + "choice" : [ { + "localId" : "258", + "name" : "{http://hl7.org/fhir}dateTime", + "type" : "NamedTypeSpecifier" + }, { + "localId" : "259", + "name" : "{http://hl7.org/fhir}Age", + "type" : "NamedTypeSpecifier" + }, { + "localId" : "260", + "name" : "{http://hl7.org/fhir}Period", + "type" : "NamedTypeSpecifier" + }, { + "localId" : "261", + "name" : "{http://hl7.org/fhir}Range", + "type" : "NamedTypeSpecifier" + }, { + "localId" : "262", + "name" : "{http://hl7.org/fhir}string", + "type" : "NamedTypeSpecifier" + } ] + }, + "source" : { + "localId" : "247", + "locator" : "18:3-18:22", + "resultTypeName" : "{http://hl7.org/fhir}Condition", + "type" : "First", + "signature" : [ { + "localId" : "248", + "type" : "ListTypeSpecifier", + "elementType" : { + "localId" : "249", + "name" : "{http://hl7.org/fhir}Condition", + "type" : "NamedTypeSpecifier" + } + } ], + "source" : { + "localId" : "240", + "locator" : "18:9-18:21", + "type" : "Query", + "resultTypeSpecifier" : { + "localId" : "241", + "type" : "ListTypeSpecifier", + "elementType" : { + "localId" : "242", + "name" : "{http://hl7.org/fhir}Condition", + "type" : "NamedTypeSpecifier" + } + }, + "source" : [ { + "localId" : "232", + "locator" : "18:9-18:21", + "alias" : "C", + "resultTypeSpecifier" : { + "localId" : "238", + "type" : "ListTypeSpecifier", + "elementType" : { + "localId" : "239", + "name" : "{http://hl7.org/fhir}Condition", + "type" : "NamedTypeSpecifier" + } + }, + "expression" : { + "localId" : "233", + "locator" : "18:9-18:19", + "dataType" : "{http://hl7.org/fhir}Condition", + "templateId" : "http://hl7.org/fhir/StructureDefinition/Condition", + "type" : "Retrieve", + "resultTypeSpecifier" : { + "localId" : "236", + "type" : "ListTypeSpecifier", + "elementType" : { + "localId" : "237", + "name" : "{http://hl7.org/fhir}Condition", + "type" : "NamedTypeSpecifier" + } + }, + "include" : [ ], + "codeFilter" : [ ], + "dateFilter" : [ ], + "otherFilter" : [ ] + } + } ], + "let" : [ ], + "relationship" : [ ] + } + } + }, + "asTypeSpecifier" : { + "localId" : "263", + "locator" : "18:37-18:39", + "resultTypeName" : "{http://hl7.org/fhir}Age", + "name" : "{http://hl7.org/fhir}Age", + "type" : "NamedTypeSpecifier" + } + } + } ] + } + } +} + diff --git a/test/yaml/other/cqlt.yaml b/test/yaml/other/cqlt.yaml new file mode 100644 index 0000000..2454443 --- /dev/null +++ b/test/yaml/other/cqlt.yaml @@ -0,0 +1,7 @@ +--- +library: + name: OtherFHIRv401Test +options: + date: "2018-12-10T00:00:00.0Z" + dumpFiles: + enabled: true diff --git a/test/yaml/other/reusable_resources.yml b/test/yaml/other/reusable_resources.yml new file mode 100644 index 0000000..543e7f3 --- /dev/null +++ b/test/yaml/other/reusable_resources.yml @@ -0,0 +1,6 @@ +reusable_resources: + - &reusablePatient + resourceType: Patient + name: Fuller Jackson + gender: male + birthDate: 1954-02-16 \ No newline at end of file diff --git a/test/yaml/other/tests/fhir_object.yaml b/test/yaml/other/tests/fhir_object.yaml new file mode 100644 index 0000000..75d325e --- /dev/null +++ b/test/yaml/other/tests/fhir_object.yaml @@ -0,0 +1,37 @@ +--- +name: Test fhir object serialization + + +data: + - + resourceType: Patient + name: Fuller Jackson + gender: male + birthDate: 1954-02-16 + - + resourceType: Condition + clinicalStatus: + coding: + - system: http://terminology.hl7.org/CodeSystem/condition-clinical + code: inactive + verificationStatus: + coding: + - system: http://terminology.hl7.org/CodeSystem/condition-ver-status + code: confirmed + code: + coding: + - system: http://snomed.info/sct + code: 77941000119104 + display: History of radiation therapy to chest + abatementAge: + value: 15 + unit: years + system: http://unitsofmeasure.org + code: a + +results: + AbatementAge: + value: 15 + unit: years + system: http://unitsofmeasure.org + code: a \ No newline at end of file diff --git a/test/yaml/other/tests/reusable_example_1.yaml b/test/yaml/other/tests/reusable_example_1.yaml new file mode 100644 index 0000000..3b16944 --- /dev/null +++ b/test/yaml/other/tests/reusable_example_1.yaml @@ -0,0 +1,15 @@ +--- +name: Test reusable resources with relative path, reusable patient, and should include + +externalData: + - ../reusable_resources + +data: + - *reusablePatient + +parameters: + LookbackPeriod: 90 + +results: + # To check for subset rather than deep equals, needs to be properly quoted and valid JSON + TestParamAndIncludeSubset: "$should include {\"LookbackPeriod\": 90}" \ No newline at end of file