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projecttacoma · Oct 1, 2024 · 6fec277 · 6fec277
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -3,19 +3,18 @@ on: [pull_request]
 
 jobs:
  build:
-
  runs-on: ubuntu-latest
 
  strategy:
  matrix:
- node-version: [12.x, 14.x]
+ node-version: [14.x, 16.x]
 
  steps:
- - uses: actions/checkout@v2
- - name: Use Node.js ${{ matrix.node-version }}
- uses: actions/setup-node@v1
- with:
- node-version: ${{ matrix.node-version }}
- - run: npm ci
- - run: npm run build --if-present
- - run: npm run check
+  - uses: actions/checkout@v2
+  - name: Use Node.js ${{ matrix.node-version }}
+  uses: actions/setup-node@v1
+  with:
+  node-version: ${{ matrix.node-version }}
+  - run: npm ci
+  - run: npm run build --if-present
+  - run: npm run check
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -4,20 +4,19 @@ on: [push]
 
 jobs:
  build:
-
  runs-on: ubuntu-latest
  timeout-minutes: 5
  env:
  REPO: https://github.com/projecttacoma/fqm-execution-service
  REMOTE_EXCLUDES_URL: https://raw.githubusercontent.com/projecttacoma/fqm-execution-service/master/.github/gitleaks.toml
  GITLEAKS_VERSION: v4.3.0
  steps:
- - name: Execute Gitleaks
- run: |
- #wget ${REMOTE_EXCLUDES_URL} -O gitleaks.toml
- curl -H 'Authorization: token ${{ secrets.ACCESS_TOKEN_GITLEAKS }}' ${REMOTE_EXCLUDES_URL} -o gitleaks.toml
- wget https://github.com/zricethezav/gitleaks/releases/download/${GITLEAKS_VERSION}/gitleaks-linux-amd64 -O gitleaks
- chmod +x gitleaks
- echo ${GITHUB_SHA}
- echo "gitleaks --repo=${REPO} -v --pretty --redact --commit=${GITHUB_SHA} --config=gitleaks.toml"
- ./gitleaks --repo=${REPO} -v --pretty --redact --commit=${GITHUB_SHA} --config=gitleaks.toml --access-token=${{ secrets.ACCESS_TOKEN_GITLEAKS }}
+  - name: Execute Gitleaks
+  run: |
+  #wget ${REMOTE_EXCLUDES_URL} -O gitleaks.toml
+  curl -H 'Authorization: token ${{ secrets.ACCESS_TOKEN_GITLEAKS }}' ${REMOTE_EXCLUDES_URL} -o gitleaks.toml
+  wget https://github.com/zricethezav/gitleaks/releases/download/${GITLEAKS_VERSION}/gitleaks-linux-amd64 -O gitleaks
+  chmod +x gitleaks
+  echo ${GITHUB_SHA}
+  echo "gitleaks --repo=${REPO} -v --pretty --redact --commit=${GITHUB_SHA} --config=gitleaks.toml"
+  ./gitleaks --repo=${REPO} -v --pretty --redact --commit=${GITHUB_SHA} --config=gitleaks.toml --access-token=${{ secrets.ACCESS_TOKEN_GITLEAKS }}
diff --git a/README.md b/README.md
@@ -8,103 +8,103 @@ Web service wrapper for [fqm-execution](https://github.com/projecttacoma/fqm-exe
 | ---------------------------------- | ------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------- |
 | `POST /calculate` | [RequestBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L5) | [ExecutionResult\[\]](https://github.com/projecttacoma/fqm-execution/blob/794b86ca80c3e0e9dd970c1e049724bf7c67e353/src/types/Calculator.ts#L54) |
 | `POST /calculateRaw` | [RequestBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L5) | [cql.Results](https://github.com/projecttacoma/fqm-execution/blob/master/src/types/CQLTypes.ts#L14) |
-| `POST /calculateMeasureReports` | [RequestBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L5) | [fhir4.MeasureReport\[\]](https://www.hl7.org/fhir/measurereport.html)  |
-| `POST /Measure/$care-gaps` | [RequestBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L5) | [fhir4.Bundle](https://www.hl7.org/fhir/bundle.html)  |
-| `POST /Measure/$data-requirements` | [DataRequirementsBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L13) | [fhir4.Library](https://www.hl7.org/fhir/library.html)  |
+| `POST /calculateMeasureReports` | [RequestBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L5) | [fhir4.MeasureReport\[\]](https://www.hl7.org/fhir/measurereport.html) |
+| `POST /Measure/$care-gaps` | [RequestBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L5) | [fhir4.Bundle](https://www.hl7.org/fhir/bundle.html) |
+| `POST /Measure/$data-requirements` | [DataRequirementsBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L13) | [fhir4.Library](https://www.hl7.org/fhir/library.html) |
 
 <!-- Note: linked line numbers may be inaccurate as code is updated -->
 
 ### Request Inputs
 
 The input to each of the endpoints listed above is expected to be a JSON object, which conforms to the type format specified in [RequestBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L5), or in [DataRequirementsBody](https://github.com/projecttacoma/fqm-execution-service/blob/master/src/types/server-types.ts#L13). This object contains 3 properties:
 
--  `measure`: a FHIR `Bundle` resource containing the `Measure` object, `Library` objects for every CQL/ELM library used in the measure, 
-  as well as `ValueSet` objects with code expansions included.
+- `measure`: a FHIR `Bundle` resource containing the `Measure` object, `Library` objects for every CQL/ELM library used in the measure,
+ as well as `ValueSet` objects with code expansions included.
 
-  -  NOTE: `ValueSet` objects are not needed for `/Measure/$data-requirements`.
+ - NOTE: `ValueSet` objects are not needed for `/Measure/$data-requirements`.
 
--  `patients`: an array of FHIR `Bundle` resources, each of which contains the `Patient` object and any required clinical resources (`Condition`, `Medication`, etc.)
-  for measure calculation. This must be an array, even if only one patient is provided.
+- `patients`: an array of FHIR `Bundle` resources, each of which contains the `Patient` object and any required clinical resources (`Condition`, `Medication`, etc.)
+ for measure calculation. This must be an array, even if only one patient is provided.
 
-  -  NOTE: `/Measure/$care-gaps` only accepts 1 patient in this array currently.
-  -  NOTE: `/Measure/$data-requirements` does not accept `Patient` resources.
+ - NOTE: `/Measure/$care-gaps` only accepts 1 patient in this array currently.
+ - NOTE: `/Measure/$data-requirements` does not accept `Patient` resources.
 
--  `options`: an optional object containing Calculation Options, each of which is listed below, with its default.
+- `options`: an optional object containing Calculation Options, each of which is listed below, with its default.
 
-  -  NOTE: `/Measure/$data-requirements` does not accept an `options` resource.
+ - NOTE: `/Measure/$data-requirements` does not accept an `options` resource.
 
 #### Calculation Options
 
 The options that we support for calculation are as follows:
-| option  | type  | optional? |  description  |
-| :--------------------- | :-----: | :-------: |  :-------------------------------------------------------------------------- |
-| includeClauseResults  | boolean |  yes  |  Option to include clause results. Defaults to false. |
-| includePrettyResults  | boolean |  yes  |  Option to include pretty results on statement results. Defaults to false. |
-| includeHighlighting  | boolean |  yes  |  Include highlighting in MeasureReport narrative. Defaults to false. |
-| measurementPeriodStart | string  | yes  |  Start of measurement period. Defaults to the period provided in the `Measure` resource|
-| measurementPeriodEnd  | string  | yes  |  End of measurement period. Defaults to the period provided in the `Measure` resource |
-| calculateSDEs  | boolean |  yes  |  Include Supplemental Data Elementss in calculation. Defaults to false. |
-| calculateHTML  | boolean |  yes  |  Include HTML structure for highlighting. Defaults to false. |
-| reportType  | string  | yes  | Type of MeasureReport to generate: "summary" or "individual". Defaults to "individual".|
+| option | type | optional? | description |
+| :--------------------- | :-----: | :-------: | :-------------------------------------------------------------------------- |
+| includeClauseResults | boolean | yes | Option to include clause results. Defaults to false. |
+| includePrettyResults | boolean | yes | Option to include pretty results on statement results. Defaults to false. |
+| includeHighlighting | boolean | yes | Include highlighting in MeasureReport narrative. Defaults to false. |
+| measurementPeriodStart | string | yes | Start of measurement period. Defaults to the period provided in the `Measure` resource|
+| measurementPeriodEnd | string | yes | End of measurement period. Defaults to the period provided in the `Measure` resource |
+| calculateSDEs | boolean | yes | Include Supplemental Data Elementss in calculation. Defaults to false. |
+| calculateHTML | boolean | yes | Include HTML structure for highlighting. Defaults to false. |
+| reportType | string | yes | Type of MeasureReport to generate: "summary" or "individual". Defaults to "individual".|
 
 These types will be passed through to the calculation service, and will be used in the execution of the measure.
 
 ### Request Outputs
 
 Each request output has a different output format, based on the data being conveyed:
 
--  `/calculate`: an array of `ExecutionResult` objects. Each `ExecutionResult` object contains:
+- `/calculate`: an array of `ExecutionResult` objects. Each `ExecutionResult` object contains:
 
-  -  `patient`: the ID of the patient this object is associated with
+ - `patient`: the ID of the patient this object is associated with
 
-  -  `detailedResults`, a map of `group`s to an object which contains population-, statement-, and clause-level results for that group, as well as the html
+ - `detailedResults`, a map of `group`s to an object which contains population-, statement-, and clause-level results for that group, as well as the html
 
-  for that group (if requested by the provided options)
+ for that group (if requested by the provided options)
 
-  -  `evaluatedResource`: an array of the FHIR resources used in the calculation of the measure for this patient
+ - `evaluatedResource`: an array of the FHIR resources used in the calculation of the measure for this patient
 
-  - `supplementalData`: if requested by the provided options, an array containing the raw and HTML structure results for each 
-  supplemental data element in the measure, calculated for the specified patient
+ - `supplementalData`: if requested by the provided options, an array containing the raw and HTML structure results for each
+ supplemental data element in the measure, calculated for the specified patient
 
--  `/calculateRaw`: a `cql.Result` object, which contains: 
+- `/calculateRaw`: a `cql.Result` object, which contains:
 
-  -  `patientResults`: A map of patient IDs to Statement-level results for that patient
+ - `patientResults`: A map of patient IDs to Statement-level results for that patient
 
-  -  A Statement-level result describes the results of one CQL Statement for this patient, including the name, the Library and ID of the Statement,
-  the relevance of a given Statement to a patient population, and the actual result from the patient. See below for an example:
+ - A Statement-level result describes the results of one CQL Statement for this patient, including the name, the Library and ID of the Statement,
+ the relevance of a given Statement to a patient population, and the actual result from the patient. See below for an example:
 
-  ```json
-  {
-  "libraryName": "EXM130",
-  "statementName": "Denominator",
-  "localId": "37",
-  "final": "TRUE",
-  "relevance": "TRUE",
-  "raw": true,
-  "pretty": "true"
-  }
-  ```
+ ```json
+ {
+ "libraryName": "EXM130",
+ "statementName": "Denominator",
+ "localId": "37",
+ "final": "TRUE",
+ "relevance": "TRUE",
+ "raw": true,
+ "pretty": "true"
+ }
+ ```
 
-  -  For more information on Clinical Quality Language (CQL) and Expression Logical Model (ELM) formats, see [the CQL specification](https://cql.hl7.org/)
+ - For more information on Clinical Quality Language (CQL) and Expression Logical Model (ELM) formats, see [the CQL specification](https://cql.hl7.org/)
 
-  -  `localIdPatientResultsMap`: A map of patient IDs to the raw results from every clause in every `Library` in the `Measure` resource.
+ - `localIdPatientResultsMap`: A map of patient IDs to the raw results from every clause in every `Library` in the `Measure` resource.
 
-  -  `patientEvaluatedRecords`: A map of patient IDs to the evaluated records for that patient
+ - `patientEvaluatedRecords`: A map of patient IDs to the evaluated records for that patient
 
--  `/Measure/$care-gaps`: a FHIR `Bundle` resource, which contains:
+- `/Measure/$care-gaps`: a FHIR `Bundle` resource, which contains:
 
-  -  a `Composition` resource containing the actual Gaps in Care report
+ - a `Composition` resource containing the actual Gaps in Care report
 
-  -  a `MeasureReport` resource containing the individual measure results for the patient passed in
+ - a `MeasureReport` resource containing the individual measure results for the patient passed in
 
-  - a set of `DetectedIssue` resources, one for each gap in the measure. Each `DetectedIssue` resource represents a particular gap in care, 
-  and will contain one or more `GuidanceResponse` resources detailing the data that could close that gap.
+ - a set of `DetectedIssue` resources, one for each gap in the measure. Each `DetectedIssue` resource represents a particular gap in care,
+ and will contain one or more `GuidanceResponse` resources detailing the data that could close that gap.
 
-  -  See [this fqm-execution wiki page](https://github.com/projecttacoma/fqm-execution/wiki/Gaps-In-Care) for more detail on the gaps-in-care
-  methodology, and how to interpret this output.
+ - See [this fqm-execution wiki page](https://github.com/projecttacoma/fqm-execution/wiki/Gaps-In-Care) for more detail on the gaps-in-care
+ methodology, and how to interpret this output.
 
--  `/Measure/$data-requirements`: a FHIR module-definition `Library` resource, which contains:
-  -  a `dataRequirement` array, with resources for each `datatype`/`valueSet` combination required.
+- `/Measure/$data-requirements`: a FHIR module-definition `Library` resource, which contains:
+ - a `dataRequirement` array, with resources for each `datatype`/`valueSet` combination required.
 
 ### Calculator Architecture
 

diff --git a/src/app.ts b/src/app.ts
@@ -107,7 +107,11 @@ app.post('/calculate', async (req, res) => {
  patients,
  options || {} // options are optional, so this defaults to an empty Object
  );
- return res.json({ results: calculateResult.results, groupClauseCoverageDetails: calculateResult.groupClauseCoverageDetails, withErrors: calculateResult.withErrors });
+ return res.json({
+ results: calculateResult.results,
+ groupClauseCoverageDetails: calculateResult.groupClauseCoverageDetails,
+ withErrors: calculateResult.withErrors
+ });
  } catch (error) {
  logger.log({
  level: 'error',

diff --git a/test/app.test.ts b/test/app.test.ts
@@ -62,9 +62,7 @@ const mockDataRequirementsResult: { results: fhir4.Library; debugOutput?: Calcul
 };
 
 const DataRequirementsSpy = jest.spyOn(Calculator, 'calculateDataRequirements');
-when(DataRequirementsSpy)
- .calledWith(mockMeasureBundle)
- .mockReturnValue(Promise.resolve(mockDataRequirementsResult));
+when(DataRequirementsSpy).calledWith(mockMeasureBundle).mockReturnValue(Promise.resolve(mockDataRequirementsResult));
 
 test('data requirements calculate', async () => {
  const response = await request(app)
@@ -102,7 +100,10 @@ test('measure reports calculate', async () => {
  expect(response.body.results).toEqual(mockMeasureReportResult.results);
 });
 
-const mockResult: { results: CalculatorTypes.ExecutionResult<PopulationGroupResult>[]; debugOutput?: CalculatorTypes.DebugOutput } = {
+const mockResult: {
+ results: CalculatorTypes.ExecutionResult<PopulationGroupResult>[];
+ debugOutput?: CalculatorTypes.DebugOutput;
+} = {
  results: [
  {
  patientId: ''