Multiple enhancements for cancer screening CDS

.gitignore

@@ -4,3 +4,4 @@
 /.gradle
 /node_modules
 .DS_Store
+coverage

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.

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:

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`);
+        }
+      });
+    }
   }
 );

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