fqm-execution - npm Package Compare versions

Comparing version 1.3.3 to 1.4.0

build/calculation/Calculator.js

@@ -37,6 +37,6 @@ "use strict";
 const MeasureReportBuilder_1 = __importDefault(require("./MeasureReportBuilder"));
-const GapsInCareHelpers = __importStar(require("../gaps/GapsReportBuilder"));
+const GapsReportBuilder = __importStar(require("./GapsReportBuilder"));
 const HTMLBuilder_1 = require("./HTMLBuilder");
-const QueryFilterParser_1 = require("../gaps/QueryFilterParser");
-const RetrievesHelper = __importStar(require("../gaps/RetrievesFinder"));
+const QueryFilterParser_1 = require("../helpers/elm/QueryFilterParser");
+const RetrievesHelper = __importStar(require("../helpers/elm/RetrievesHelper"));
 const CustomErrors_1 = require("../types/errors/CustomErrors");
@@ -48,3 +48,3 @@ const cql_execution_1 = require("cql-execution");
 const lodash_1 = __importStar(require("lodash"));
-const reportBuilderFactory_1 = require("../helpers/reportBuilderFactory");
+const ReportBuilderFactory_1 = require("../helpers/ReportBuilderFactory");
 /**
@@ -60,3 +60,3 @@ * Calculate measure against a set of patients. Returning detailed results for each patient and population group.
 async function calculate(measureBundle, patientBundles, options, valueSetCache = []) {
-    var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k;
+    var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m;
     // Ensure verboseCalculationResults defaults to true when not provided in options
@@ -72,4 +72,6 @@ options.verboseCalculationResults = (_a = options.verboseCalculationResults) !== null && _a !== void 0 ? _a : true;
     options.calculateClauseCoverage = (_d = options.calculateClauseCoverage) !== null && _d !== void 0 ? _d : true;
-    options.disableHTMLOrdering = (_e = options.disableHTMLOrdering) !== null && _e !== void 0 ? _e : false;
-    options.buildStatementLevelHTML = (_f = options.buildStatementLevelHTML) !== null && _f !== void 0 ? _f : false;
+    options.calculateClauseUncoverage = (_e = options.calculateClauseUncoverage) !== null && _e !== void 0 ? _e : false;
+    options.calculateCoverageDetails = (_f = options.calculateCoverageDetails) !== null && _f !== void 0 ? _f : false;
+    options.disableHTMLOrdering = (_g = options.disableHTMLOrdering) !== null && _g !== void 0 ? _g : false;
+    options.buildStatementLevelHTML = (_h = options.buildStatementLevelHTML) !== null && _h !== void 0 ? _h : false;
     const compositeMeasureResource = MeasureBundleHelpers.extractCompositeMeasure(measureBundle);
@@ -85,2 +87,4 @@ const isCompositeExecution = compositeMeasureResource != null;
     let groupClauseCoverageHTML;
+    let groupClauseUncoverageHTML;
+    let groupClauseCoverageDetails;
     let newValueSetCache = [...valueSetCache];
@@ -93,7 +97,7 @@ const allELM = [];
         // Set the measurement period start/end, but only if the caller didn't specify one
-        options.measurementPeriodStart = (_g = options.measurementPeriodStart) !== null && _g !== void 0 ? _g : measurementPeriod.measurementPeriodStart;
-        options.measurementPeriodEnd = (_h = options.measurementPeriodEnd) !== null && _h !== void 0 ? _h : measurementPeriod.measurementPeriodEnd;
+        options.measurementPeriodStart = (_j = options.measurementPeriodStart) !== null && _j !== void 0 ? _j : measurementPeriod.measurementPeriodStart;
+        options.measurementPeriodEnd = (_k = options.measurementPeriodEnd) !== null && _k !== void 0 ? _k : measurementPeriod.measurementPeriodEnd;
         const results = await Execution.execute(measure, measureBundle, patientSource, options, newValueSetCache, debugObject);
         if (!results.rawResults) {
-            throw new Error((_j = results.errorMessage) !== null && _j !== void 0 ? _j : 'something happened with no error message');
+            throw new Error((_l = results.errorMessage) !== null && _l !== void 0 ? _l : 'something happened with no error message');
         }
@@ -196,3 +200,4 @@ const rawResults = results.rawResults;
         if (!isCompositeExecution && options.calculateClauseCoverage) {
-            groupClauseCoverageHTML = (0, HTMLBuilder_1.generateClauseCoverageHTML)(measure, executedELM, executionResults, options.disableHTMLOrdering);
+            const coverage = (0, HTMLBuilder_1.generateClauseCoverageHTML)(measure, executedELM, executionResults, options);
+            groupClauseCoverageHTML = coverage.coverage;
             overallClauseCoverageHTML = '';
@@ -214,5 +219,23 @@ Object.entries(groupClauseCoverageHTML).forEach(([groupId, result]) => {
             });
+            // pull out uncoverage html
+            if (options.calculateClauseUncoverage && coverage.uncoverage) {
+                groupClauseUncoverageHTML = coverage.uncoverage;
+                if (debugObject && options.enableDebugOutput) {
+                    Object.entries(groupClauseUncoverageHTML).forEach(([groupId, result]) => {
+                        const debugUncoverageHTML = {
+                            name: `clause-uncoverage-${groupId}.html`,
+                            html: result
+                        };
+                        if (Array.isArray(debugObject.html)) {
+                            debugObject.html.push(debugUncoverageHTML);
+                        }
+                        else {
+                            debugObject.html = [debugUncoverageHTML];
+                        }
+                    });
+                }
+            }
             // don't necessarily need this file, but adding it for backwards compatibility
             if (debugObject && options.enableDebugOutput) {
-                (_k = debugObject.html) === null || _k === void 0 ? void 0 : _k.push({
+                (_m = debugObject.html) === null || _m === void 0 ? void 0 : _m.push({
                     name: 'overall-clause-coverage.html',
@@ -222,2 +245,9 @@ html: overallClauseCoverageHTML
             }
+            // grab coverage details
+            if (options.calculateCoverageDetails && coverage.details) {
+                groupClauseCoverageDetails = coverage.details;
+                if (debugObject && options.enableDebugOutput) {
+                    debugObject.coverageDetails = groupClauseCoverageDetails;
+                }
+            }
         }
@@ -236,3 +266,3 @@ }
     }
-    return Object.assign(Object.assign(Object.assign(Object.assign({ results: prunedExecutionResults, debugOutput: debugObject }, (options.returnELM && {
+    return Object.assign(Object.assign(Object.assign(Object.assign(Object.assign(Object.assign({ results: prunedExecutionResults, debugOutput: debugObject }, (options.returnELM && {
         elmLibraries: lodash_1.default.uniqWith(allELM, (libOne, libTwo) => libOne.library.identifier.id === libTwo.library.identifier.id &&
@@ -244,3 +274,3 @@ libOne.library.identifier.version === libOne.library.identifier.version),
         valueSetCache: lodash_1.default.uniqWith(newValueSetCache, (vsOne, vsTwo) => vsOne.url === vsTwo.url && vsOne.version === vsTwo.version)
-    })), (overallClauseCoverageHTML && { coverageHTML: overallClauseCoverageHTML })), (groupClauseCoverageHTML && { groupClauseCoverageHTML: groupClauseCoverageHTML }));
+    })), (overallClauseCoverageHTML && { coverageHTML: overallClauseCoverageHTML })), (groupClauseCoverageHTML && { groupClauseCoverageHTML: groupClauseCoverageHTML })), (groupClauseUncoverageHTML && { groupClauseUncoverageHTML: groupClauseUncoverageHTML })), (groupClauseCoverageDetails && { groupClauseCoverageDetails: groupClauseCoverageDetails }));
 }
@@ -306,3 +336,3 @@ exports.calculate = calculate;
     const { results, debugOutput } = calculationResults;
-    const builder = (0, reportBuilderFactory_1.getReportBuilder)(measureBundle, options);
+    const builder = (0, ReportBuilderFactory_1.getReportBuilder)(measureBundle, options);
     builder.addAllResults(results);
@@ -410,3 +440,3 @@ const report = builder.getReport();
                 // Add detailed info to queries based on clause results
-                const gapsRetrieves = GapsInCareHelpers.processQueriesForGaps(baseRetrieves, dr);
+                const gapsRetrieves = GapsReportBuilder.processQueriesForGaps(baseRetrieves, dr);
                 const grPromises = gapsRetrieves.map(async (retrieve) => {
@@ -423,8 +453,8 @@ // If the retrieves have a localId for the query and a known library name, we can get more info
                 await Promise.all(grPromises);
-                const { results: detailedGapsRetrieves, withErrors: reasonDetailErrors } = GapsInCareHelpers.calculateReasonDetail(gapsRetrieves, improvementNotation, dr);
+                const { results: detailedGapsRetrieves, withErrors: reasonDetailErrors } = GapsReportBuilder.calculateReasonDetail(gapsRetrieves, improvementNotation, dr);
                 errorLog.push(...reasonDetailErrors);
-                const { detectedIssues, withErrors: detectedIssueErrors } = GapsInCareHelpers.generateDetectedIssueResources(detailedGapsRetrieves, matchingMeasureReport, improvementNotation);
+                const { detectedIssues, withErrors: detectedIssueErrors } = GapsReportBuilder.generateDetectedIssueResources(detailedGapsRetrieves, matchingMeasureReport, improvementNotation);
                 errorLog.push(...detectedIssueErrors);
                 const patient = (_l = res.patientObject) === null || _l === void 0 ? void 0 : _l._json;
-                const gapsBundle = GapsInCareHelpers.generateGapsInCareBundle(detectedIssues, matchingMeasureReport, patient);
+                const gapsBundle = GapsReportBuilder.generateGapsInCareBundle(detectedIssues, matchingMeasureReport, patient);
                 result.push(gapsBundle);
@@ -431,0 +461,0 @@ if (debugOutput && options.enableDebugOutput) {

build/calculation/ClauseResultsBuilder.js

@@ -31,3 +31,3 @@ "use strict";
 exports.getSDEValues = exports.createOrSetResult = exports.setResult = exports.getResult = exports.hasResult = exports.findResult = exports.buildPopulationGroupRelevanceMap = exports.buildPopulationRelevanceMap = exports.buildPopulationRelevanceForAllEpisodes = exports.doesResultPass = exports.findResultForStatementClause = exports.setFinalResults = exports.prettyFHIRObject = exports.prettyConcept = exports.prettyCode = exports.prettyResult = exports.buildStatementAndClauseResults = exports.getStatementResult = exports.markStatementRelevant = exports.buildStatementRelevanceMap = void 0;
-const ClauseResultsHelpers = __importStar(require("./ClauseResultsHelpers"));
+const ClauseResultsHelpers = __importStar(require("../helpers/ClauseResultsHelpers"));
 const MeasureBundleHelpers = __importStar(require("../helpers/MeasureBundleHelpers"));
@@ -34,0 +34,0 @@ const ELMDependencyHelper = __importStar(require("../helpers/elm/ELMDependencyHelpers"));

build/calculation/HTMLBuilder.d.ts

 import { ELM } from '../types/ELMTypes';
-import { CalculationOptions, ClauseResult, DetailedPopulationGroupResult, ExecutionResult, StatementResult } from '../types/Calculator';
+import { CalculationOptions, ClauseCoverageDetails, ClauseResult, DetailedPopulationGroupResult, ExecutionResult, StatementResult } from '../types/Calculator';
 export declare const cqlLogicClauseTrueStyle: {
@@ -8,2 +8,3 @@ 'background-color': string;
     'border-bottom-style': string;
+    'border-bottom-width': string;
 };
@@ -15,2 +16,3 @@ export declare const cqlLogicClauseFalseStyle: {
     'border-bottom-style': string;
+    'border-bottom-width': string;
 };
@@ -20,4 +22,2 @@ export declare const cqlLogicClauseCoveredStyle: {
     color: string;
-    'border-bottom-color': string;
-    'border-bottom-style': string;
 };
@@ -27,5 +27,7 @@ export declare const cqlLogicUncoveredClauseStyle: {
     color: string;
-    'border-bottom-color': string;
-    'border-bottom-style': string;
 };
+export declare const cqlLogicUncoveredUncoverageClauseStyle: {
+    'background-color': string;
+    color: string;
+};
 /**
@@ -68,3 +70,7 @@ * Convert JS object to CSS Style string
  */
-export declare function generateClauseCoverageHTML(measure: fhir4.Measure, elmLibraries: ELM[], executionResults: ExecutionResult<DetailedPopulationGroupResult>[], disableHTMLOrdering?: boolean): Record<string, string>;
+export declare function generateClauseCoverageHTML<T extends CalculationOptions>(measure: fhir4.Measure, elmLibraries: ELM[], executionResults: ExecutionResult<DetailedPopulationGroupResult>[], options: T): {
+    coverage: Record<string, string>;
+    uncoverage?: Record<string, string>;
+    details?: Record<string, ClauseCoverageDetails>;
+};
 /**
@@ -77,2 +83,6 @@ * Calculates clause coverage as the percentage of relevant clauses with FinalResult.TRUE
  */
-export declare function calculateClauseCoverage(relevantStatements: StatementResult[], clauseResults: ClauseResult[]): string;
+export declare function calculateClauseCoverage(relevantStatements: StatementResult[], clauseResults: ClauseResult[]): {
+    percentage: string;
+    coveredClauses: ClauseResult[];
+    uncoveredClauses: ClauseResult[];
+};

build/calculation/HTMLBuilder.js

@@ -6,3 +6,3 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.calculateClauseCoverage = exports.generateClauseCoverageHTML = exports.generateHTML = exports.sortStatements = exports.objToCSS = exports.cqlLogicUncoveredClauseStyle = exports.cqlLogicClauseCoveredStyle = exports.cqlLogicClauseFalseStyle = exports.cqlLogicClauseTrueStyle = void 0;
+exports.calculateClauseCoverage = exports.generateClauseCoverageHTML = exports.generateHTML = exports.sortStatements = exports.objToCSS = exports.cqlLogicUncoveredUncoverageClauseStyle = exports.cqlLogicUncoveredClauseStyle = exports.cqlLogicClauseCoveredStyle = exports.cqlLogicClauseFalseStyle = exports.cqlLogicClauseTrueStyle = void 0;
 const handlebars_1 = __importDefault(require("handlebars"));
@@ -18,3 +18,4 @@ const Enums_1 = require("../types/Enums");
     'border-bottom-color': '#20744c',
-    'border-bottom-style': 'solid'
+    'border-bottom-style': 'solid',
+    'border-bottom-width': '0.35em'
 };
@@ -25,16 +26,17 @@ exports.cqlLogicClauseFalseStyle = {
     'border-bottom-color': '#a63b12',
-    'border-bottom-style': 'double'
+    'border-bottom-style': 'double',
+    'border-bottom-width': '0.35em'
 };
 exports.cqlLogicClauseCoveredStyle = {
     'background-color': '#daeaf5',
-    color: '#004e82',
-    'border-bottom-color': '#006cb4',
-    'border-bottom-style': 'dashed'
+    color: '#004e82'
 };
 exports.cqlLogicUncoveredClauseStyle = {
     'background-color': 'white',
-    color: 'black',
-    'border-bottom-color': 'white',
-    'border-bottom-style': 'solid'
+    color: 'black'
 };
+exports.cqlLogicUncoveredUncoverageClauseStyle = {
+    'background-color': '#edd8d0',
+    color: '#a63b12'
+};
 /**
@@ -86,2 +88,16 @@ * Convert JS object to CSS Style string
 });
+// apply highlighting style to uncovered clauses
+handlebars_1.default.registerHelper('highlightUncoverage', (localId, context) => {
+    const libraryName = context.data.root.libraryName;
+    if (context.data.root.uncoveredClauses.some(result => result.libraryName === libraryName && result.localId === localId)) {
+        // Mark with red styling if clause is found in uncoverage list
+        return objToCSS(exports.cqlLogicUncoveredUncoverageClauseStyle);
+    }
+    else if (context.data.root.coveredClauses.some(result => result.libraryName === libraryName && result.localId === localId)) {
+        // Mark with white (clear out styling) if the clause is in coverage list
+        return objToCSS(exports.cqlLogicUncoveredClauseStyle);
+    }
+    // If this clause has no results then it should not be styled
+    return '';
+});
 /**
@@ -164,3 +180,3 @@ * Sort statements into population, then non-functions, then functions
         if (matchingExpression.annotation) {
-            const statementHTML = main(Object.assign({ libraryName: s.libraryName, statementName: s.statementName, clauseResults: clauseResults }, matchingExpression.annotation[0].s));
+            const statementHTML = main(Object.assign(Object.assign({ libraryName: s.libraryName, statementName: s.statementName, clauseResults: clauseResults }, matchingExpression.annotation[0].s), { highlightLogic: true }));
             overallHTML += statementHTML;
@@ -188,5 +204,7 @@ if (options === null || options === void 0 ? void 0 : options.buildStatementLevelHTML) {
  */
-function generateClauseCoverageHTML(measure, elmLibraries, executionResults, disableHTMLOrdering) {
+function generateClauseCoverageHTML(measure, elmLibraries, executionResults, options) {
     const groupResultLookup = {};
-    const htmlGroupLookup = {};
+    const coverageHtmlGroupLookup = {};
+    const uncoverageHtmlGroupLookup = {};
+    const coverageDetailsGroupLookup = {};
     // get the detailed result for each group within each patient and add it
@@ -214,3 +232,3 @@ // to the key in groupResults that matches the groupId
         const uniqueRelevantStatements = flattenedStatementResults.filter(s => s.relevance !== Enums_1.Relevance.NA);
-        if (!disableHTMLOrdering) {
+        if (!options.disableHTMLOrdering) {
             sortStatements(measure, groupId, uniqueRelevantStatements);
@@ -237,12 +255,42 @@ }
         });
-        let htmlString = `<div><h2> ${groupId} Clause Coverage: ${calculateClauseCoverage(uniqueRelevantStatements, flattenedClauseResults)}%</h2>`;
+        const clauseCoverage = calculateClauseCoverage(uniqueRelevantStatements, flattenedClauseResults);
+        const uniqueCoverageClauses = clauseCoverage.coveredClauses.concat(clauseCoverage.uncoveredClauses);
+        // setup initial html for coverage
+        let coverageHtmlString = `<div><h2> ${groupId} Clause Coverage: ${clauseCoverage.percentage}%</h2>`;
+        // setup initial html for uncoverage
+        let uncoverageHtmlString = '';
+        if (options.calculateClauseUncoverage) {
+            uncoverageHtmlString = `<div><h2> ${groupId} Clause Uncoverage: ${clauseCoverage.uncoveredClauses.length} of ${clauseCoverage.coveredClauses.length + clauseCoverage.uncoveredClauses.length} clauses</h2>`;
+        }
         // generate HTML clauses using hbs template for each annotation
         statementAnnotations.forEach(a => {
-            const res = main(Object.assign(Object.assign({ libraryName: a.libraryName, statementName: a.statementName, clauseResults: flattenedClauseResults }, a.annotation[0].s), { highlightCoverage: true }));
-            htmlString += res;
+            coverageHtmlString += main(Object.assign(Object.assign({ libraryName: a.libraryName, statementName: a.statementName, clauseResults: uniqueCoverageClauses }, a.annotation[0].s), { highlightCoverage: true }));
+            // calculate for uncoverage
+            if (options.calculateClauseUncoverage) {
+                uncoverageHtmlString += main(Object.assign(Object.assign({ libraryName: a.libraryName, statementName: a.statementName, uncoveredClauses: clauseCoverage.uncoveredClauses, coveredClauses: clauseCoverage.coveredClauses }, a.annotation[0].s), { highlightUncoverage: true }));
+            }
         });
-        htmlString += '</div>';
-        htmlGroupLookup[groupId] = htmlString;
+        coverageHtmlString += '</div>';
+        uncoverageHtmlString += '</div>';
+        coverageHtmlGroupLookup[groupId] = coverageHtmlString;
+        if (options.calculateClauseUncoverage) {
+            uncoverageHtmlGroupLookup[groupId] = uncoverageHtmlString;
+        }
+        // If details on coverage are requested, tally them up and add them to the map.
+        if (options.calculateCoverageDetails) {
+            coverageDetailsGroupLookup[groupId] = {
+                totalClauseCount: clauseCoverage.coveredClauses.length + clauseCoverage.uncoveredClauses.length,
+                coveredClauseCount: clauseCoverage.coveredClauses.length,
+                uncoveredClauseCount: clauseCoverage.uncoveredClauses.length,
+                uncoveredClauses: clauseCoverage.uncoveredClauses.map(uncoveredClause => {
+                    return {
+                        localId: uncoveredClause.localId,
+                        libraryName: uncoveredClause.libraryName,
+                        statementName: uncoveredClause.statementName
+                    };
+                })
+            };
+        }
     });
-    return htmlGroupLookup;
+    return Object.assign(Object.assign({ coverage: coverageHtmlGroupLookup }, (options.calculateClauseUncoverage && { uncoverage: uncoverageHtmlGroupLookup })), (options.calculateCoverageDetails && { details: coverageDetailsGroupLookup }));
 }
@@ -263,5 +311,12 @@ exports.generateClauseCoverageHTML = generateClauseCoverageHTML;
     const coveredClauses = (0, lodash_1.uniqWith)(allRelevantClauses.filter(clause => clause.final === Enums_1.FinalResult.TRUE), (c1, c2) => c1.libraryName === c2.libraryName && c1.localId === c2.localId);
-    return ((coveredClauses.length / allUniqueClauses.length) * 100).toPrecision(3);
+    const uncoveredClauses = allUniqueClauses.filter(c => {
+        return !coveredClauses.find(coveredC => c.libraryName === coveredC.libraryName && c.localId === coveredC.localId);
+    });
+    return {
+        percentage: ((coveredClauses.length / allUniqueClauses.length) * 100).toPrecision(3),
+        coveredClauses,
+        uncoveredClauses
+    };
 }
 exports.calculateClauseCoverage = calculateClauseCoverage;
 //# sourceMappingURL=HTMLBuilder.js.map

build/cli.js

@@ -77,2 +77,4 @@ #!/usr/bin/env node
     else if (commander_1.program.outputType === 'detailed') {
+        calcOptions.calculateClauseUncoverage = true;
+        calcOptions.calculateCoverageDetails = true;
         result = await (0, Calculator_1.calculate)(measureBundle, patientBundles, calcOptions, valueSetCache);
@@ -192,2 +194,5 @@ }
             }
+            if (debugOutput === null || debugOutput === void 0 ? void 0 : debugOutput.coverageDetails) {
+                (0, DebugHelpers_1.dumpObject)(debugOutput.coverageDetails, 'coverageDetails.json');
+            }
             // Dump ELM
@@ -194,0 +199,0 @@ if (debugOutput === null || debugOutput === void 0 ? void 0 : debugOutput.elm) {

build/helpers/DataRequirementHelpers.d.ts

 import { CalculationOptions, DataTypeQuery, DRCalculationOutput } from '../types/Calculator';
 import { GracefulError } from '../types/errors/GracefulError';
-import { EqualsFilter, InFilter, DuringFilter, AnyFilter, Filter } from '../types/QueryFilterTypes';
 import { ELM, ELMIdentifier } from '../types/ELMTypes';
@@ -8,9 +7,2 @@ import { ExtractedLibrary } from '../types/CQLTypes';
 /**
- * Take any nesting of base filters and AND filters and flatten into one list
- *
- * @param filter the root filter to flatten
- * @returns a list of all filters used by this query at one level
- */
-export declare function flattenFilters(filter: AnyFilter): AnyFilter[];
-/**
  * Returns a FHIR library containing data requirements, given a root library
@@ -20,23 +12,2 @@ */
 /**
- * Map an EqualsFilter or InFilter into a FHIR DataRequirement codeFilter
- *
- * @param filter the filter to translate
- * @returns codeFilter to be put on the DataRequirement
- */
-export declare function generateDetailedCodeFilter(filter: EqualsFilter | InFilter, dataType?: string): fhir4.DataRequirementCodeFilter | null;
-/**
- * Map a during filter into a FHIR DataRequirement dateFilter
- *
- * @param filter the "during" filter to map
- * @returns dateFilter for the dateFilter list of dataRequirement
- */
-export declare function generateDetailedDateFilter(filter: DuringFilter): fhir4.DataRequirementDateFilter;
-/**
- * Map a filter into a FHIR DataRequirement valueFilter extension
- *
- * @param filter the filter to map
- * @returns extension for the valueFilter list of dataRequirement
- */
-export declare function generateDetailedValueFilter(filter: Filter): fhir4.Extension | GracefulError;
-/**
  * Creates query string for the data requirement using either the code filter code or valueSet and
@@ -57,10 +28,2 @@ * the specified endpoint, and adds a fhirQueryPattern extension to the data requirement that
 /**
- * Given a fhir dataType as a string and an attribute as a string, returns the url which outlines
- * the code system used to define the valid inputs for the given attribute for the given dataType
- * @param dataType
- * @param attribute
- * @returns string url for code system
- */
-export declare function codeLookup(dataType: string, attribute: string): string | null;
-/**
  * Extracts the measurement period information from either the options or effective period (in that order depending on presence)
@@ -82,1 +45,9 @@ * and populates a parameters object including the extracted info to be passed into the parseQueryInfo function
 export declare function getFlattenedRelatedArtifacts(measureBundle: fhir4.Bundle, rootLibRef?: string): fhir4.RelatedArtifact[];
+/**
+ *
+ * @param q The query which contains the filters to add to the data requirement
+ * @param dataRequirement Data requirement to add date filters to
+ * @param withErrors Errors object which will eventually be returned to the user if populated
+ * @returns void, but populated the dataRequirement filters
+ */
+export declare function addFiltersToDataRequirement(q: DataTypeQuery, dataRequirement: fhir4.DataRequirement, withErrors: GracefulError[]): void;

build/helpers/DataRequirementHelpers.js

@@ -26,3 +26,3 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getFlattenedRelatedArtifacts = exports.createIntervalFromEndpoints = exports.extractDataRequirementsMeasurementPeriod = exports.codeLookup = exports.generateDataRequirement = exports.addFhirQueryPatternToDataRequirements = exports.generateDetailedValueFilter = exports.generateDetailedDateFilter = exports.generateDetailedCodeFilter = exports.getDataRequirements = exports.flattenFilters = void 0;
+exports.addFiltersToDataRequirement = exports.getFlattenedRelatedArtifacts = exports.createIntervalFromEndpoints = exports.extractDataRequirementsMeasurementPeriod = exports.generateDataRequirement = exports.addFhirQueryPatternToDataRequirements = exports.getDataRequirements = void 0;
 const PatientParameters_1 = require("../compartment-definition/PatientParameters");
@@ -32,5 +32,4 @@ const SearchParameters_1 = require("../compartment-definition/SearchParameters");
 const CustomErrors_1 = require("../types/errors/CustomErrors");
-const GapsInCareHelpers = __importStar(require("../gaps/GapsReportBuilder"));
-const QueryFilterParser_1 = require("../gaps/QueryFilterParser");
-const RetrievesHelper = __importStar(require("../gaps/RetrievesFinder"));
+const QueryFilterParser_1 = require("./elm/QueryFilterParser");
+const RetrievesHelper = __importStar(require("./elm/RetrievesHelper"));
 const lodash_1 = require("lodash");
@@ -42,21 +41,2 @@ const cql_execution_1 = require("cql-execution");
 /**
- * Take any nesting of base filters and AND filters and flatten into one list
- *
- * @param filter the root filter to flatten
- * @returns a list of all filters used by this query at one level
- */
-function flattenFilters(filter) {
-    if (filter.type !== 'and') {
-        return [filter];
-    }
-    else {
-        const a = [];
-        filter.children.forEach(c => {
-            a.push(...flattenFilters(c));
-        });
-        return a;
-    }
-}
-exports.flattenFilters = flattenFilters;
-/**
  * Returns a FHIR library containing data requirements, given a root library
@@ -101,3 +81,3 @@ */
         const dr = generateDataRequirement(retrieve);
-        GapsInCareHelpers.addFiltersToDataRequirement(retrieve, dr, withErrors);
+        addFiltersToDataRequirement(retrieve, dr, withErrors);
         addFhirQueryPatternToDataRequirements(dr);
@@ -120,100 +100,2 @@ return dr;
 /**
- * Map an EqualsFilter or InFilter into a FHIR DataRequirement codeFilter
- *
- * @param filter the filter to translate
- * @returns codeFilter to be put on the DataRequirement
- */
-function generateDetailedCodeFilter(filter, dataType) {
-    var _a;
-    const system = dataType ? codeLookup(dataType, filter.attribute) : null;
-    if (filter.type === 'equals') {
-        const equalsFilter = filter;
-        if (typeof equalsFilter.value === 'string') {
-            return {
-                path: equalsFilter.attribute,
-                code: [
-                    Object.assign({ code: equalsFilter.value }, (system && { system: system }))
-                ]
-            };
-        }
-    }
-    else if (filter.type === 'in') {
-        const inFilter = filter;
-        if ((_a = inFilter.valueList) === null || _a === void 0 ? void 0 : _a.every(v => typeof v === 'string')) {
-            return {
-                path: inFilter.attribute,
-                code: inFilter.valueList.map(v => (Object.assign({ code: v }, (system && { system: system }))))
-            };
-        }
-        else if (filter.valueCodingList) {
-            return {
-                path: filter.attribute,
-                code: filter.valueCodingList
-            };
-        }
-    }
-    return null;
-}
-exports.generateDetailedCodeFilter = generateDetailedCodeFilter;
-/**
- * Map a during filter into a FHIR DataRequirement dateFilter
- *
- * @param filter the "during" filter to map
- * @returns dateFilter for the dateFilter list of dataRequirement
- */
-function generateDetailedDateFilter(filter) {
-    return {
-        path: filter.attribute,
-        valuePeriod: { start: filter.valuePeriod.start, end: filter.valuePeriod.end }
-    };
-}
-exports.generateDetailedDateFilter = generateDetailedDateFilter;
-/**
- * Map a filter into a FHIR DataRequirement valueFilter extension
- *
- * @param filter the filter to map
- * @returns extension for the valueFilter list of dataRequirement
- */
-function generateDetailedValueFilter(filter) {
-    if (filter.type === 'notnull' || filter.type === 'isnull') {
-        const nullFilter = filter;
-        return {
-            url: 'http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-valueFilter',
-            extension: [
-                { url: 'path', valueString: nullFilter.attribute },
-                { url: 'comparator', valueCode: 'eq' },
-                { url: 'value', valueString: nullFilter.type === 'notnull' ? 'not null' : 'null' }
-            ]
-        };
-    }
-    else if (filter.type === 'value') {
-        const valueFilter = filter;
-        const valueExtension = {
-            url: 'value',
-            valueBoolean: valueFilter.valueBoolean,
-            valueInteger: valueFilter.valueInteger,
-            valueString: valueFilter.valueString,
-            valueQuantity: valueFilter.valueQuantity,
-            valueRange: valueFilter.valueRange,
-            valueRatio: valueFilter.valueRatio
-        };
-        return {
-            url: 'http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-valueFilter',
-            extension: [
-                { url: 'path', valueString: valueFilter.attribute },
-                { url: 'comparator', valueCode: valueFilter.comparator },
-                // Remove undefineds
-                JSON.parse(JSON.stringify(valueExtension))
-            ]
-        };
-    }
-    else if (filter === null || filter === void 0 ? void 0 : filter.withError) {
-        return filter.withError;
-    }
-    else {
-        return { message: `Detailed value filter is not yet supported for filter type ${filter.type}` };
-    }
-}
-exports.generateDetailedValueFilter = generateDetailedValueFilter;
-/**
  * Creates query string for the data requirement using either the code filter code or valueSet and
@@ -347,38 +229,2 @@ * the specified endpoint, and adds a fhirQueryPattern extension to the data requirement that
 /**
- * Given a fhir dataType as a string and an attribute as a string, returns the url which outlines
- * the code system used to define the valid inputs for the given attribute for the given dataType
- * @param dataType
- * @param attribute
- * @returns string url for code system
- */
-function codeLookup(dataType, attribute) {
-    const validDataTypes = ['Observation', 'Procedure', 'Encounter', 'MedicationRequest'];
-    if (!validDataTypes.includes(dataType)) {
-        return null;
-    }
-    else if (dataType === 'Observation' && attribute === 'status') {
-        return 'http://hl7.org/fhir/observation-status';
-    }
-    else if (dataType === 'Procedure' && attribute === 'status') {
-        return 'http://hl7.org/fhir/event-status';
-    }
-    else if (dataType === 'Encounter' && attribute === 'status') {
-        return 'http://hl7.org/fhir/encounter-status';
-    }
-    else if (dataType === 'MedicationRequest') {
-        switch (attribute) {
-            case 'status':
-                return 'http://hl7.org/fhir/CodeSystem/medicationrequest-status';
-            case 'intent':
-                return 'http://hl7.org/fhir/CodeSystem/medicationrequest-intent';
-            case 'priority':
-                return 'http://hl7.org/fhir/request-priority';
-            default:
-                return null;
-        }
-    }
-    return null;
-}
-exports.codeLookup = codeLookup;
-/**
  * Extracts the measurement period information from either the options or effective period (in that order depending on presence)
@@ -491,2 +337,66 @@ * and populates a parameters object including the extracted info to be passed into the parseQueryInfo function
 exports.getFlattenedRelatedArtifacts = getFlattenedRelatedArtifacts;
+/**
+ *
+ * @param q The query which contains the filters to add to the data requirement
+ * @param dataRequirement Data requirement to add date filters to
+ * @param withErrors Errors object which will eventually be returned to the user if populated
+ * @returns void, but populated the dataRequirement filters
+ */
+function addFiltersToDataRequirement(q, dataRequirement, withErrors) {
+    if (q.queryInfo) {
+        const relevantSource = q.queryInfo.sources.find(source => source.resourceType === q.dataType);
+        // if a source cannot be found that matches, exit the function
+        if (relevantSource) {
+            const detailedFilters = (0, QueryFilterParser_1.flattenFilters)(q.queryInfo.filter);
+            detailedFilters.forEach(df => {
+                // DuringFilter, etc. inherit from attribute filter (and have alias on them)
+                if (relevantSource.alias === df.alias) {
+                    if (df.type === 'equals' || df.type === 'in') {
+                        const cf = (0, QueryFilterParser_1.generateDetailedCodeFilter)(df, q.dataType);
+                        if (cf !== null) {
+                            if (dataRequirement.codeFilter) {
+                                dataRequirement.codeFilter.push(cf);
+                            }
+                            else {
+                                dataRequirement.codeFilter = [cf];
+                            }
+                        }
+                    }
+                    else if (df.type === 'during') {
+                        const dateFilter = (0, QueryFilterParser_1.generateDetailedDateFilter)(df);
+                        if (dataRequirement.dateFilter) {
+                            dataRequirement.dateFilter.push(dateFilter);
+                        }
+                        else {
+                            dataRequirement.dateFilter = [dateFilter];
+                        }
+                    }
+                    else {
+                        const valueFilter = (0, QueryFilterParser_1.generateDetailedValueFilter)(df);
+                        if (didEncounterDetailedValueFilterErrors(valueFilter)) {
+                            withErrors.push(valueFilter);
+                        }
+                        else if (valueFilter) {
+                            if (dataRequirement.extension) {
+                                dataRequirement.extension.push(valueFilter);
+                            }
+                            else {
+                                dataRequirement.extension = [valueFilter];
+                            }
+                        }
+                    }
+                }
+            });
+        }
+    }
+}
+exports.addFiltersToDataRequirement = addFiltersToDataRequirement;
+function didEncounterDetailedValueFilterErrors(tbd) {
+    if (tbd.message) {
+        return true;
+    }
+    else {
+        return false;
+    }
+}
 //# sourceMappingURL=DataRequirementHelpers.js.map

build/helpers/reportBuilderFactory.js

@@ -9,3 +9,3 @@ "use strict";
 const MeasureReportBuilder_1 = __importDefault(require("../calculation/MeasureReportBuilder"));
-const MeasureBundleHelpers_1 = require("../helpers/MeasureBundleHelpers");
+const MeasureBundleHelpers_1 = require("./MeasureBundleHelpers");
 function getReportBuilder(measureBundle, options) {
@@ -20,2 +20,2 @@ const compositeMeasureResource = (0, MeasureBundleHelpers_1.extractCompositeMeasure)(measureBundle);
 exports.getReportBuilder = getReportBuilder;
-//# sourceMappingURL=reportBuilderFactory.js.map
+//# sourceMappingURL=ReportBuilderFactory.js.map

build/index.d.ts

@@ -6,3 +6,3 @@ export * as Calculator from './calculation/Calculator';
 export * as MeasureBundleHelpers from './helpers/MeasureBundleHelpers';
-export * as RetrievesFinder from './gaps/RetrievesFinder';
+export * as RetrievesFinder from './helpers/elm/RetrievesHelper';
 export { ValueSetResolver } from './execution/ValueSetResolver';
@@ -9,0 +9,0 @@ /**

build/index.js

@@ -39,3 +39,3 @@ "use strict";
 exports.MeasureBundleHelpers = __importStar(require("./helpers/MeasureBundleHelpers"));
-exports.RetrievesFinder = __importStar(require("./gaps/RetrievesFinder"));
+exports.RetrievesFinder = __importStar(require("./helpers/elm/RetrievesHelper"));
 var ValueSetResolver_1 = require("./execution/ValueSetResolver");
@@ -42,0 +42,0 @@ Object.defineProperty(exports, "ValueSetResolver", { enumerable: true, get: function () { return ValueSetResolver_1.ValueSetResolver; } });

build/templates/clause.d.ts

@@ -1,2 +0,2 @@
-declare const _default: "{{~#if @root.highlightCoverage~}}\n<span{{#if r}} data-ref-id=\"{{r}}\" style=\"{{highlightCoverage r}}\"{{/if}}>\n{{~#if value ~}}\n{{ concat value }}\n{{~/if ~}}\n{{~#if s~}}\n{{~#each s~}}\n{{> clause ~}}\n{{~/each ~}}\n{{~/if~}}\n</span>\n{{~else~}}\n<span{{#if r}} data-ref-id=\"{{r}}\" style=\"{{highlightClause r}}\"{{/if}}>\n{{~#if value ~}}\n{{ concat value }}\n{{~/if ~}}\n{{~#if s~}}\n{{~#each s~}}\n{{> clause ~}}\n{{~/each ~}}\n{{~/if~}}\n</span>\n{{~/if~}}";
+declare const _default: "{{~#if @root.highlightCoverage~}}\n<span{{#if r}} data-ref-id=\"{{r}}\" style=\"{{highlightCoverage r}}\"{{/if}}>\n{{~#if value ~}}\n{{ concat value }}\n{{~/if ~}}\n{{~#if s~}}\n{{~#each s~}}\n{{> clause ~}}\n{{~/each ~}}\n{{~/if~}}\n</span>\n{{~else~}}\n{{~#if @root.highlightUncoverage~}}\n<span{{#if r}} data-ref-id=\"{{r}}\" style=\"{{highlightUncoverage r}}\"{{/if}}>\n{{~#if value ~}}\n{{ concat value }}\n{{~/if ~}}\n{{~#if s~}}\n{{~#each s~}}\n{{> clause ~}}\n{{~/each ~}}\n{{~/if~}}\n</span>\n{{~else~}}\n<span{{#if r}} data-ref-id=\"{{r}}\" style=\"{{highlightClause r}}\"{{/if}}>\n{{~#if value ~}}\n{{ concat value }}\n{{~/if ~}}\n{{~#if s~}}\n{{~#each s~}}\n{{> clause ~}}\n{{~/each ~}}\n{{~/if~}}\n</span>\n{{~/if~}}\n{{~/if~}}";
 export default _default;

build/templates/clause.js

@@ -15,2 +15,14 @@ "use strict";
 {{~else~}}
+{{~#if @root.highlightUncoverage~}}
+<span{{#if r}} data-ref-id="{{r}}" style="{{highlightUncoverage r}}"{{/if}}>
+{{~#if value ~}}
+{{ concat value }}
+{{~/if ~}}
+{{~#if s~}}
+{{~#each s~}}
+{{> clause ~}}
+{{~/each ~}}
+{{~/if~}}
+</span>
+{{~else~}}
 <span{{#if r}} data-ref-id="{{r}}" style="{{highlightClause r}}"{{/if}}>
@@ -26,3 +38,4 @@ {{~#if value ~}}
 </span>
+{{~/if~}}
 {{~/if~}}`;
 //# sourceMappingURL=clause.js.map

build/templates/main.d.ts

@@ -1,2 +0,2 @@
-declare const _default: "<pre style=\"tab-size: 2; border-bottom-width: 4px; line-height: 1.4\"\n  data-library-name=\"{{ libraryName }}\" data-statement-name=\"{{ statementName }}\">\n<code>\n{{> clause}}\n</code>\n</pre>";
+declare const _default: "<pre style=\"tab-size: 2 {{~#if @root.highlightLogic~}}; line-height: 1.51em{{~/if~}}\"\n  data-library-name=\"{{ libraryName }}\" data-statement-name=\"{{ statementName }}\">\n<code>\n{{> clause}}\n</code>\n</pre>";
 export default _default;

build/templates/main.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = `<pre style="tab-size: 2; border-bottom-width: 4px; line-height: 1.4"
+exports.default = `<pre style="tab-size: 2 {{~#if @root.highlightLogic~}}; line-height: 1.51em{{~/if~}}"
   data-library-name="{{ libraryName }}" data-statement-name="{{ statementName }}">
@@ -5,0 +5,0 @@ <code>

build/types/Calculator.d.ts

@@ -26,2 +26,6 @@ import { PopulationType, FinalResult, Relevance, CareGapReasonCode } from './Enums';
     calculateClauseCoverage?: boolean;
+    /** Include HTML structure with clause uncoverage highlighting. Highlights what is not covered */
+    calculateClauseUncoverage?: boolean;
+    /** Include details about the clause coverage. Total clause count, total covered count, info on uncovered clauses. */
+    calculateCoverageDetails?: boolean;
     /** Enable debug output including CQL, ELM, results */
@@ -334,2 +338,3 @@ enableDebugOutput?: boolean;
     };
+    coverageDetails?: Record<string, ClauseCoverageDetails>;
 }
@@ -361,4 +366,19 @@ export interface CalculatorFunctionOutput {
     groupClauseCoverageHTML?: Record<string, string>;
+    groupClauseUncoverageHTML?: Record<string, string>;
+    groupClauseCoverageDetails?: Record<string, ClauseCoverageDetails>;
 }
 /**
+ * Details on clause coverage for group calculation.
+ */
+export interface ClauseCoverageDetails {
+    totalClauseCount: number;
+    coveredClauseCount: number;
+    uncoveredClauseCount: number;
+    uncoveredClauses: {
+        libraryName: string;
+        statementName: string;
+        localId: string;
+    }[];
+}
+/**
  * dataType for calculateMeasureReports() function
@@ -365,0 +385,0 @@ */

package.json

 {
   "name": "fqm-execution",
-  "version": "1.3.3",
+  "version": "1.4.0",
   "description": "FHIR Quality Measure Execution",
@@ -5,0 +5,0 @@ "main": "build/index.js",

No alert changes

Improved metrics

Total package byte prevSize

1454222

increased by17.87%

Number of package files

141

increased by9.3%

Lines of code

20317

increased by16.68%

Number of lines in readme file

1327

increased by7.19%

No dependency changes