From 517ef1c58c485fa2b18ddb4b7951217d56723531 Mon Sep 17 00:00:00 2001 From: Elsa Date: Mon, 26 Feb 2024 09:16:48 -0500 Subject: [PATCH 01/16] Initial dr comparison script work --- ColorectalCancerScreeningsDR.json | 1774 +++++++++++++++++ data-requirements/compare-output.ts | 71 + data-requirements/compare.sh | 72 + data-requirements/compare.ts | 72 + .../elm-parser-dr/BCSEHEDISMY2022.xml.json | 703 +++++++ .../BreastCancerScreeningsFHIR.xml.json | 1152 +++++++++++ .../CervicalCancerScreeningFHIR.xml.json | 552 +++++ .../ColorectalCancerScreeningsFHIR.xml.json | 1133 +++++++++++ ...WithPhysicianManagingDiabetesFHIR.xml.json | 373 ++++ ...emoglobinA1cHbA1cPoorControl9FHIR.xml.json | 892 +++++++++ ...hargedonAntithromboticTherapyFHIR.xml.json | 225 +++ .../elm-parser-dr/Exam125FHIR.xml.json | 1152 +++++++++++ .../elm-parser-dr/Exam130FHIR.xml.json | 1133 +++++++++++ .../elm-parser-dr/FHIR347.xml.json | 1277 ++++++++++++ ...lycemiainHospitalizedPatientsFHIR.xml.json | 182 ++ ...ospitalHarmSevereHypoglycemiaFHIR.xml.json | 142 ++ .../elm-parser-dr/HybridHWMFHIR.xml.json | 623 ++++++ .../elm-parser-dr/HybridHWRFHIR.xml.json | 768 +++++++ ...ousThromboembolismProphylaxisFHIR.xml.json | 998 ++++++++++ ...fferedbyPCPsincludingDentistsFHIR.xml.json | 399 ++++ ...fOpioidsConcurrentPrescribingFHIR.xml.json | 198 ++ data-requirements/elm-parser-for-ecqms | 1 + .../elm-parser-input/fhir_all.csv | 806 ++++++++ .../elm-parser-input/library/.gitignore | 4 + .../fqm-e-dr/BCSEHEDISMY2022-dr.json | 739 +++++++ .../BreastCancerScreeningsFHIR-dr.json | 1428 +++++++++++++ .../CervicalCancerScreeningFHIR-dr.json | 834 ++++++++ .../ColorectalCancerScreeningsFHIR-dr.json | 1774 +++++++++++++++++ ...nWithPhysicianManagingDiabetesFHIR-dr.json | 595 ++++++ ...HemoglobinA1cHbA1cPoorControl9FHIR-dr.json | 1128 +++++++++++ ...chargedonAntithromboticTherapyFHIR-dr.json | 443 ++++ data-requirements/fqm-e-dr/FHIR347-dr.json | 1189 +++++++++++ ...glycemiainHospitalizedPatientsFHIR-dr.json | 397 ++++ ...HospitalHarmSevereHypoglycemiaFHIR-dr.json | 288 +++ .../fqm-e-dr/HybridHWMFHIR-dr.json | 303 +++ .../fqm-e-dr/HybridHWRFHIR-dr.json | 313 +++ ...nousThromboembolismProphylaxisFHIR-dr.json | 1382 +++++++++++++ ...OfferedbyPCPsincludingDentistsFHIR-dr.json | 517 +++++ ...ofOpioidsConcurrentPrescribingFHIR-dr.json | 346 ++++ data-requirements/parse-dr.ts | 102 + data-requirements/parse-fhir-all.ts | 76 + package-lock.json | 182 ++ package.json | 3 + src/helpers/DataRequirementHelpers.ts | 1 + src/helpers/elm/RetrievesHelper.ts | 1 + src/types/Calculator.ts | 2 + 46 files changed, 26745 insertions(+) create mode 100644 ColorectalCancerScreeningsDR.json create mode 100644 data-requirements/compare-output.ts create mode 100755 data-requirements/compare.sh create mode 100644 data-requirements/compare.ts create mode 100644 data-requirements/elm-parser-dr/BCSEHEDISMY2022.xml.json create mode 100644 data-requirements/elm-parser-dr/BreastCancerScreeningsFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/CervicalCancerScreeningFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/ColorectalCancerScreeningsFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/DRCommunicationWithPhysicianManagingDiabetesFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/DiabetesHemoglobinA1cHbA1cPoorControl9FHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/DischargedonAntithromboticTherapyFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/Exam125FHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/Exam130FHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/FHIR347.xml.json create mode 100644 data-requirements/elm-parser-dr/HospitalHarmHyperglycemiainHospitalizedPatientsFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/HospitalHarmSevereHypoglycemiaFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/HybridHWMFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/HybridHWRFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/IntensiveCareUnitVenousThromboembolismProphylaxisFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/PrimaryCariesPreventionasOfferedbyPCPsincludingDentistsFHIR.xml.json create mode 100644 data-requirements/elm-parser-dr/SafeUseofOpioidsConcurrentPrescribingFHIR.xml.json create mode 160000 data-requirements/elm-parser-for-ecqms create mode 100644 data-requirements/elm-parser-input/fhir_all.csv create mode 100644 data-requirements/elm-parser-input/library/.gitignore create mode 100644 data-requirements/fqm-e-dr/BCSEHEDISMY2022-dr.json create mode 100644 data-requirements/fqm-e-dr/BreastCancerScreeningsFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/CervicalCancerScreeningFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/ColorectalCancerScreeningsFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/DRCommunicationWithPhysicianManagingDiabetesFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/DiabetesHemoglobinA1cHbA1cPoorControl9FHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/DischargedonAntithromboticTherapyFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/FHIR347-dr.json create mode 100644 data-requirements/fqm-e-dr/HospitalHarmHyperglycemiainHospitalizedPatientsFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/HospitalHarmSevereHypoglycemiaFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/HybridHWMFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/HybridHWRFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/IntensiveCareUnitVenousThromboembolismProphylaxisFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/PrimaryCariesPreventionasOfferedbyPCPsincludingDentistsFHIR-dr.json create mode 100644 data-requirements/fqm-e-dr/SafeUseofOpioidsConcurrentPrescribingFHIR-dr.json create mode 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"display": "Library FrailtyLTI", + "resource": "http://ecqi.healthit.gov/ecqms/Library/AdvancedIllnessandFrailtyExclusionECQMFHIR4|5.17.000" + }, + { + "type": "depends-on", + "display": "Library PalliativeCare", + "resource": "http://ecqi.healthit.gov/ecqms/Library/PalliativeCareFHIR|0.6.000" + }, + { + "type": "depends-on", + "display": "Value set Annual Wellness Visit", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.526.3.1240" + }, + { + "type": "depends-on", + "display": "Value set Colonoscopy", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1020" + }, + { + "type": "depends-on", + "display": "Value set CT Colonography", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1038" + }, + { + "type": "depends-on", + "display": "Value set Discharged to Health Care Facility for Hospice Care", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.207" + }, + { + "type": "depends-on", + "display": "Value set Discharged to Home for Hospice Care", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.209" + }, + { + "type": "depends-on", + "display": "Value set Fecal Occult Blood Test (FOBT)", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1011" + }, + { + "type": "depends-on", + "display": "Value set FIT DNA", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1039" + }, + { + "type": "depends-on", + "display": "Value set Flexible Sigmoidoscopy", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1010" + }, + { + "type": "depends-on", + "display": "Value set Home Healthcare Services", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1016" + }, + { + "type": "depends-on", + "display": "Value set Malignant Neoplasm of Colon", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1001" + }, + { + "type": "depends-on", + "display": "Value set Office Visit", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1001" + }, + { + "type": "depends-on", + "display": "Value set Online Assessments", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1089" + }, + { + "type": "depends-on", + "display": "Value set Preventive Care Services - Established Office Visit, 18 and Up", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1025" + }, + { + "type": "depends-on", + "display": "Value set Preventive Care Services-Initial Office Visit, 18 and Up", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1023" + }, + { + "type": "depends-on", + "display": "Value set Telephone Visits", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1080" + }, + { + "type": "depends-on", + "display": "Value set Total Colectomy", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1019" + }, + { + "type": "depends-on", + "display": "Value set Total Colectomy ICD9", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.11.1136" + } + ] +} \ No newline at end of file diff --git a/data-requirements/compare-output.ts b/data-requirements/compare-output.ts new file mode 100644 index 00000000..b12f5b22 --- /dev/null +++ b/data-requirements/compare-output.ts @@ -0,0 +1,71 @@ +import fs from 'fs'; +import * as _ from 'lodash'; + +/** + * The purpose of this script is to comparison the output of the current fqm-execution (1.3.3) data-requirements JSON output + * to the current data-requirements JSON output of the elm-parser-for-ecqms fhir_review branch + */ + +// Get the JSON data-requirements output for a single measure from fqm-execution (put JSON file into fqm-e-input directory) +const fqmEDataRequirementsLibrary = JSON.parse( + fs.readFileSync('./fqm-e-input/ColorectalCancerScreeningsDR.json', 'utf8') +) as fhir4.Library; +const fqmEDataRequirements = fqmEDataRequirementsLibrary?.dataRequirement as fhir4.DataRequirement[]; + +// Get the JSON data-requirements output for a single measure from elm-parser-for-ecqms (put JSON file into elm-parser-input directory) +const elmParserDataRequirementsLibrary = JSON.parse( + fs.readFileSync('./elm-parser-input/library/ColorectalCancerScreeningsFHIR.xml.json', 'utf8') +) as fhir4.Library; +const elmPaserDataRequirements = elmParserDataRequirementsLibrary?.dataRequirement as fhir4.DataRequirement[]; + +// Group data requirements in each file by type in Record +let fqmEData: Record = {}; +fqmEDataRequirements.forEach(dr => { + if (fqmEData[dr.type]) { + fqmEData[dr.type].push(dr); + } else { + fqmEData[dr.type] = [dr]; + } +}); + +// Sort the data requirements by type alphabetically +let sortedFqmEData: Record = {}; + +Object.keys(fqmEData) + .sort() + .forEach(key => { + sortedFqmEData[key] = fqmEData[key]; + }); + +// Print the fqm-execution results to the console +console.log('------FQM-EXECUTION------'); + +_.forEach(sortedFqmEData, function (value, key) { + console.log(key, value.length); +}); + +// Group data requirements in each file by type in Record +let elmParserData: Record = {}; +elmPaserDataRequirements.forEach(dr => { + if (elmParserData[dr.type]) { + elmParserData[dr.type].push(dr); + } else { + elmParserData[dr.type] = [dr]; + } +}); + +// Sort the data requirements by type alphabetically +let sortedElmParserData: Record = {}; + +Object.keys(elmParserData) + .sort() + .forEach(key => { + sortedElmParserData[key] = elmParserData[key]; + }); + +// Print the fqm-execution results to the console +console.log('------ELM-PARSER------'); + +_.forEach(sortedElmParserData, function (value, key) { + console.log(key, value.length); +}); diff --git a/data-requirements/compare.sh b/data-requirements/compare.sh new file mode 100755 index 00000000..46dfe09d --- /dev/null +++ b/data-requirements/compare.sh @@ -0,0 +1,72 @@ +#!/bin/bash + +RED='\033[0;31m' +GREEN='\033[0;32m' +NC='\033[0m' + +VERBOSE=false + +# Potentailly add data-requirement type option to just look at one type ? +# Also maybe include a verbose option ? +function usage() { + cat <] [-v|--verbose] + + Options: + -dr/--data-requirement: Data requirement type to specifically compare + -v/--verbose: Use verbose comparison. +USAGE + exit 1 +} + +# Clone the elm-parser-for-ecqms in the data-requirements directory if it hasn't been +if [ ! -d "elm-parser-for-ecqms" ]; then + git clone https://github.com/projecttacoma/elm-parser-for-ecqms.git + git fetch --all + cd elm-parser-for-ecqms + git checkout "fhir_review" + ruby parse_elm.rb --bundle fhir + cd .. + mkdir elm-parser-dr + SOURCE_DIR="elm-parser-for-ecqms/data_requirements/library" + TARGET_DIR="elm-parser-dr" + + # Move all files from source to target directory + mv "$SOURCE_DIR"/* "$TARGET_DIR" + echo "Files moved successfully" +fi + +echo "Gathering data-requirements output from fqm-execution using the measure bundle from ecqm-content-r4-2021" + +npx ts-node compare.ts + +# The following code directly compares the Library data requirements outputs of both fqm-execution and elm-parser-for-ecqms +# The problem with this is that the JSON is structured slightly differently so it may not even be helpful +FAILURES=() +for file in "fqm-e-dr"/*; do + BASE_PATH="$(basename "$file")" + BASE_NAME=${BASE_PATH%"-dr.json"*} + + FQM_E_DR=$file + ELM_PARSER_DR="elm-parser-dr/${BASE_NAME}.xml.json" + + if ! test -f "$FQM_E_DR"; then + echo -e "${RED}FAIL${NC}: $FQM_E_DR does not exist" + FAILURES+=("$FQM_E_DR") + fi + + if ! test -f "$ELM_PARSER_DR"; then + echo -e "${RED}FAIL${NC}: $ELM_PARSER_DR does not exist" + FAILURES+=("$ELM_PARSER_DR") + fi + + if cmp --silent $FQM_E_DR $ELM_PARSER_DR; then + echo -e "${GREEN}PASS${NC}: $BASE_NAME" + else + echo -e "${RED}FAIL${NC}: $FQM_E_DR and $ELM_PARSER_DR are different" + FAILURES+=("$BASE_NAME") + fi +done + +echo "Finished" \ No newline at end of file diff --git a/data-requirements/compare.ts b/data-requirements/compare.ts new file mode 100644 index 00000000..25b522fa --- /dev/null +++ b/data-requirements/compare.ts @@ -0,0 +1,72 @@ +import fs from 'fs'; +import path from 'path'; +import { Calculator } from '../src'; + +const RESET = '\x1b[0m'; +const FG_YELLOW = '\x1b[33m'; +const FG_GREEN = '\x1b[32m'; + +const ECQM_CONTENT_BASE_PATH = path.join(__dirname, '../regression/ecqm-content-r4-2021/bundles/measure'); + +async function main() { + if (fs.existsSync('./fqm-e-dr')) { + fs.rmSync('./fqm-e-dr', { recursive: true }); + } + + fs.mkdirSync('./fqm-e-dr'); + + const allDirs = fs.readdirSync(ECQM_CONTENT_BASE_PATH).map(f => ({ + shortName: f, + fullPath: path.join(ECQM_CONTENT_BASE_PATH, f) + })); + + for (const dir of allDirs) { + const basePath = dir.fullPath; + + // It is assumed that the bundle lives under the base directory with `-bundle.json added to the extension + const measureBundle = JSON.parse( + fs.readFileSync(path.join(basePath, `${dir.shortName}-bundle.json`), 'utf8') + ) as fhir4.Bundle; + + // try to calculate the data requirements for the measure bundle + try { + const { results } = await Calculator.calculateDataRequirements(measureBundle, {}); + + fs.writeFileSync(`./fqm-e-dr/${dir.shortName}-dr.json`, JSON.stringify(results, undefined, 2), 'utf8'); + console.log(`${FG_GREEN}%s${RESET}: Results written to ./fqm-e-dr/${dir.shortName}-dr.json`, 'SUCCESS'); + } catch (e) { + if (e instanceof Error) { + fs.writeFileSync( + `./fqm-e-dr/${dir.shortName}-dr.json`, + JSON.stringify({ error: e.message }, undefined, 2), + 'utf8' + ); + console.log( + `${FG_YELLOW}%s${RESET}: Results written to ./fqm-e-dr/${dir.shortName}-dr.json`, + 'EXECUTION ERROR' + ); + } + } + + // In the following code, I would like to go through the data-requirements library outputs, take just the data-requirements + // array, sort them and put them in their own files + // const fqmEDataReqs = ( + // JSON.parse(fs.readFileSync(`./fqm-e-dr/${dir.shortName}-drLib.json`, 'utf8')) as fhir4.Library + // ).dataRequirement; + + // if (!fs.existsSync(`./elm-parser-dr/${dir.shortName}.xml.json`)) continue; + + // const elmParserDataReqs = ( + // JSON.parse(fs.readFileSync(`./elm-parser-dr/${dir.shortName}.xml.json`, 'utf8')) as fhir4.Library + // ).dataRequirement; + + // fs.writeFileSync(`./fqm-e-dr/${dir.shortName}-dr.json`, JSON.stringify(fqmEDataReqs, undefined, 2), 'utf8'); + // fs.writeFileSync( + // `./elm-parser-dr/${dir.shortName}-dr.json`, + // JSON.stringify(elmParserDataReqs, undefined, 2), + // 'utf8' + // ); + } +} + +main().then(() => console.log('done')); diff --git a/data-requirements/elm-parser-dr/BCSEHEDISMY2022.xml.json b/data-requirements/elm-parser-dr/BCSEHEDISMY2022.xml.json new file mode 100644 index 00000000..b9ccb8ff --- /dev/null +++ b/data-requirements/elm-parser-dr/BCSEHEDISMY2022.xml.json @@ -0,0 +1,703 @@ +{ + "name": "BCSEHEDISMY2022.xml", + "status": "draft", + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/library-type", + "code": "module-definition" + } + ] + }, + "dataRequirement": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", + "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1329" + } + ], + "type": "Condition", + "mustSupport": [ + "code", + "clinicalStatus", + "onset", + "abatement" + ], + "codeFilter": [ + { + "path": "code", + "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1329" + } + ] + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", + "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1330" + } + ], + "type": "Condition", + "mustSupport": [ + "code", + "clinicalStatus", + "onset", + "abatement" + ], + "codeFilter": [ + { + "path": "code", + "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1330" + } + ] + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", + "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1465" + } + ], + "type": "Condition", + "mustSupport": [ + "code" + ], + "codeFilter": [ + { + "path": "code", + "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1465" + } + ] + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", + "valueString": "Condition?code=Z51.5" + } + ], + "type": "Condition", + "mustSupport": [ + "clinicalStatus", + "code", + "onset", + "abatement" + ], + "codeFilter": [ + { + "path": "code", + "code": [ + { + "system": "ICD-10", + "code": "Z51.5" + } + ] + } + ] + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", + "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1531" + } + ], + "type": "Condition", + "mustSupport": [ + "clinicalStatus", + "code", + "onset", + "abatement" + ], + "codeFilter": [ + { + "path": "code", + "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1531" + } + ] + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", + "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1331" + } + ], + "type": "Condition", + "mustSupport": [ + "code", 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"http://ecqi.healthit.gov/ecqms/Library/FHIRHelpers|4.0.001" + }, + { + "type": "depends-on", + "display": "Code system ConditionClinicalStatusCodes", + "resource": "http://terminology.hl7.org/CodeSystem/condition-clinical" + }, + { + "type": "depends-on", + "display": "Code system AllergyIntoleranceClinicalStatusCodes", + "resource": "http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical" + }, + { + "type": "depends-on", + "display": "Code system AllergyIntoleranceVerificationStatusCodes", + "resource": "http://terminology.hl7.org/CodeSystem/allergyintolerance-verification" + }, + { + "type": "depends-on", + "display": "Code system Diagnosis Role", + "resource": "http://terminology.hl7.org/CodeSystem/diagnosis-role" + }, + { + "type": "depends-on", + "display": "Code system LOINC", + "resource": "http://loinc.org" + }, + { + "type": "depends-on", + "display": "Code system MedicationRequestCategory", + "resource": "http://terminology.hl7.org/CodeSystem/medicationrequest-category" + }, + { + "type": "depends-on", + "display": "Code system ConditionVerificationStatusCodes", + "resource": "http://terminology.hl7.org/CodeSystem/condition-ver-status" + }, + { + "type": "depends-on", + "display": "Code system SNOMEDCT", + "resource": "http://snomed.info/sct" + }, + { + "type": "depends-on", + "display": "Code system RoleCode", + "resource": "http://terminology.hl7.org/CodeSystem/v3-RoleCode" + }, + { + "type": "depends-on", + "display": "Value set Emergency Department Visit", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.292" + }, + { + "type": "depends-on", + "display": "Value set Encounter Inpatient", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.666.5.307" + }, + { + "type": "depends-on", + "display": "Value set Observation Services", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.143" + }, + { + "type": "depends-on", + "display": "Value set Present on Admission or Clinically Undetermined", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1147.197" + }, + { + "type": "depends-on", + "display": "Value set Ethnicity", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837" + }, + { + "type": "depends-on", + "display": "Value set ONC Administrative Sex", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1" + }, + { + "type": "depends-on", + "display": "Value set Payer", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.3591" + }, + { + "type": "depends-on", + "display": "Value set Race", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.836" + }, + { + "type": "depends-on", + "display": "Library SDE", + "resource": "http://ecqi.healthit.gov/ecqms/Library/SupplementalDataElementsFHIR4|2.0.000" + }, + { + "type": "depends-on", + "display": "Library Global", + "resource": "http://ecqi.healthit.gov/ecqms/Library/MATGlobalCommonFunctionsFHIR4|6.1.000" + }, + { + "type": "depends-on", + "display": "Value set All Primary and Secondary Cancer", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.161" + }, + { + "type": "depends-on", + "display": "Value set Discharge To Acute Care Facility", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.87" + }, + { + "type": "depends-on", + "display": "Value set Hospice Care Referral or Admission", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1116.365" + }, + { + "type": "depends-on", + "display": "Value set Palliative or Hospice Care", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.600.1.1579" + }, + { + "type": "depends-on", + "display": "Value set Patient Expired", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.309" + }, + { + "type": "depends-on", + "display": "Value set Schedule II & III Opioid Medications", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.165" + }, + { + "type": "depends-on", + "display": "Value set Schedule IV Benzodiazepines", + "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1125.1" + } + ] +} \ No newline at end of file diff --git a/data-requirements/parse-dr.ts b/data-requirements/parse-dr.ts new file mode 100644 index 00000000..9553b41d --- /dev/null +++ b/data-requirements/parse-dr.ts @@ -0,0 +1,102 @@ +import { DataRequirement } from 'fhir/r4'; +import fs from 'fs'; +import * as _ from 'lodash'; + +type DataRequirementType = { + 'Data Type': string; + 'Template Id': string; + 'Data Type Value Set'?: string; + 'Data Type Value OID': string; + Attribute: string; +}; + +let sortedFqmEData: Record = {}; + +// Get Data Requirements from fqm-execution output +const fqmEDRLib = JSON.parse( + fs.readFileSync('./fqm-e-input/ColorectalCancerScreeningsDR.json', 'utf8') +) as fhir4.Library; + +// Group data requirements by type in Record +let fqmEData: Record = {}; +fqmEDRLib.dataRequirement?.forEach(dr => { + if (fqmEData[dr.type]) { + fqmEData[dr.type].push(dr); + } else { + fqmEData[dr.type] = [dr]; + } +}); + +// Sort the data requirements by type alphabetically +Object.keys(fqmEData) + .sort() + .forEach(key => { + sortedFqmEData[key] = fqmEData[key]; + }); + +// Print the fqm-execution results to the console +console.log('------FQM-EXECUTION------'); + +_.forEach(sortedFqmEData, function (value, key) { + console.log(key, value.length); +}); + +// Get Data Requirements from the elm-parser output of fhir_all.csv +const elmParserDR = JSON.parse( + fs.readFileSync('./elm-parser-json/all/ColorectalCancerScreeningsFHIR.json', 'utf8') +) as DataRequirementType[]; + +// Group data requirements by type in Record +let elmParserData: Record = {}; +elmParserDR.forEach(dr => { + if (elmParserData[dr['Data Type']]) { + elmParserData[dr['Data Type']].push(dr); + } else { + elmParserData[dr['Data Type']] = [dr]; + } +}); + +// Sort the data requirements by type alphabetically +let sortedData: Record = {}; +Object.keys(elmParserData) + .sort() + .forEach(key => { + sortedData[key] = elmParserData[key]; + }); + +// Print the elm-parser results to the console +console.log('------ELM-PARSER-FHIR-ALL------'); + +_.forEach(sortedData, function (value, key) { + console.log(key, value.length); +}); + +// Get Data Requirements from th elm-parser by_measure output +const elmParserByMeasureDR = JSON.parse( + fs.readFileSync('./elm-parser-json/by_measure/ColorectalCancerScreeningsFHIR.json', 'utf8') +) as DataRequirementType[]; + +// Group data requirements by type in Record +let elmParserByMeasureData: Record = {}; +elmParserByMeasureDR.forEach(dr => { + if (elmParserByMeasureData[dr['Data Type']]) { + elmParserByMeasureData[dr['Data Type']].push(dr); + } else { + elmParserByMeasureData[dr['Data Type']] = [dr]; + } +}); + +// Sort the data requirements by type alphabetically +let sortedByMeasureData: Record = {}; +Object.keys(elmParserByMeasureData) + .sort() + .forEach(key => { + sortedByMeasureData[key] = elmParserByMeasureData[key]; + }); + +// Print the elm-parser results to the console +console.log('------ELM-PARSER-BY-MEASURE------'); + +_.forEach(sortedByMeasureData, function (value, key) { + console.log(key, value.length); +}); diff --git a/data-requirements/parse-fhir-all.ts b/data-requirements/parse-fhir-all.ts new file mode 100644 index 00000000..04b42372 --- /dev/null +++ b/data-requirements/parse-fhir-all.ts @@ -0,0 +1,76 @@ +import fs from 'fs'; +import Papa from 'papaparse'; +import * as csv from 'fast-csv'; + +// create directory for by_measure outputs if it doesn't exist +if (!fs.existsSync('./elm-parser-input/by_measure_all')) { + fs.mkdirSync('./elm-parser-input/by_measure_all'); +} + +if (!fs.existsSync('./elm-parser-json')) { + fs.mkdirSync('./elm-parser-json'); +} + +if (!fs.existsSync('./elm-parser-json/all')) { + fs.mkdirSync('./elm-parser-json/all'); +} + +if (!fs.existsSync('./elm-parser-json/by_measure')) { + fs.mkdirSync('./elm-parser-json/by_measure'); +} + +// Go through fhir_all.csv and split measures into their own csv files in the by_measure directory +const fhirAllFile = fs.createReadStream('./elm-parser-input/fhir_all.csv'); +Papa.parse(fhirAllFile, { + header: true, + delimiter: '|', + complete: (results: any) => { + const groups: Record = {}; + results.data.forEach((row: any) => { + const attribute = row['Measure']; + if (!groups[attribute]) { + groups[attribute] = []; + } + groups[attribute].push(row); + }); + for (const attribute in groups) { + const ws = fs.createWriteStream(`./elm-parser-input/by_measure_all/${attribute}.csv`); + csv.write(groups[attribute], { headers: true }).pipe(ws); + } + } +}); + +// Go through each of the csv files in elm_parser_input/by_measure_all and convert them to JSON +fs.readdirSync('./elm-parser-input/by_measure_all').forEach(file => { + const fileStream = fs.createReadStream(`./elm-parser-input/by_measure_all/${file}`); + Papa.parse(fileStream, { + header: true, + delimiter: ',', + complete: (results: any) => { + const fileName = file.split('.')[0]; + fs.writeFileSync(`./elm-parser-json/all/${fileName}.json`, JSON.stringify(results.data, null, 2), 'utf8'); + } + }); +}); + +// Go through each of the csv files in elm_parser_input/by_measure and convert them to JSON +fs.readdirSync('elm-parser-input/by_measure').forEach(file => { + const fileStream = fs.createReadStream(`elm-parser-input/by_measure/${file}`); + Papa.parse(fileStream, { + header: false, + delimiter: '|', + complete: (results: any) => { + let jsonResults: any[] = []; + results.data.forEach((row: any) => { + jsonResults.push({ + 'Data Type': row[0], + 'Template Id': row[1], + 'Data Type Value OID': row[2], + Attribute: row[3] + }); + }); + const fileName = file.split('.')[0]; + fs.writeFileSync(`./elm-parser-json/by_measure/${fileName}.json`, JSON.stringify(jsonResults, null, 2), 'utf8'); + } + }); +}); diff --git a/package-lock.json b/package-lock.json index 27800ceb..4e446506 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,9 +14,11 @@ "commander": "^6.1.0", "cql-exec-fhir": "^2.1.3", "cql-execution": "^3.0.1", + "fast-csv": "^5.0.1", "handlebars": "^4.7.7", "lodash": "^4.17.21", "moment": "^2.29.4", + "papaparse": "^5.4.1", "uuid": "^8.3.1" }, "bin": { @@ -27,6 +29,7 @@ "@types/jest": "^26.0.5", "@types/lodash": "^4.14.170", "@types/node": "^14.0.23", + "@types/papaparse": "^5.3.14", "@types/uuid": "^8.3.0", "@typescript-eslint/eslint-plugin": "^5.45.0", "@typescript-eslint/parser": "^5.45.0", @@ -933,6 +936,31 @@ "node": "^10.12.0 || >=12.0.0" } }, + "node_modules/@fast-csv/format": { + "version": "5.0.0", + "resolved": "https://registry.npmjs.org/@fast-csv/format/-/format-5.0.0.tgz", + "integrity": "sha512-IyMpHwYIOGa2f0BJi6Wk55UF0oBA5urdIydoEDYxPo88LFbeb3Yr4rgpu98OAO1glUWheSnNtUgS80LE+/dqmw==", + 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+10922,11 @@ "integrity": "sha512-jttmRe7bRse52OsWIMDLaXxWqRAmtIUccAQ3garviCqJjafXOfNMO0yMfNpdD6zbGaTU0P5Nz7e7gAT6cKmJRw==", "dev": true }, + "lodash.uniq": { + "version": "4.5.0", + "resolved": "https://registry.npmjs.org/lodash.uniq/-/lodash.uniq-4.5.0.tgz", + "integrity": "sha512-xfBaXQd9ryd9dlSDvnvI0lvxfLJlYAZzXomUYzLKtUeOQvOP5piqAWuGtrhWeqaXK9hhoM/iyJc5AV+XfsX3HQ==" + }, "log-symbols": { "version": "5.1.0", "resolved": "https://registry.npmjs.org/log-symbols/-/log-symbols-5.1.0.tgz", @@ -11097,6 +11274,11 @@ "integrity": "sha512-R4nPAVTAU0B9D35/Gk3uJf/7XYbQcyohSKdvAxIRSNghFl4e71hVoGnBNQz9cWaXxO2I10KTC+3jMdvvoKw6dQ==", "dev": true }, + "papaparse": { + "version": "5.4.1", + "resolved": "https://registry.npmjs.org/papaparse/-/papaparse-5.4.1.tgz", + "integrity": "sha512-HipMsgJkZu8br23pW15uvo6sib6wne/4woLZPlFf3rpDyMe9ywEXUsuD7+6K9PRkJlVT51j/sCOYDKGGS3ZJrw==" + }, "parent-module": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz", diff --git a/package.json b/package.json index e16ffa61..e51da80a 100644 --- a/package.json +++ b/package.json @@ -16,9 +16,11 @@ "commander": "^6.1.0", "cql-exec-fhir": "^2.1.3", "cql-execution": "^3.0.1", + "fast-csv": "^5.0.1", "handlebars": "^4.7.7", "lodash": "^4.17.21", "moment": "^2.29.4", + "papaparse": "^5.4.1", "uuid": "^8.3.1" }, "devDependencies": { @@ -26,6 +28,7 @@ "@types/jest": "^26.0.5", "@types/lodash": "^4.14.170", "@types/node": "^14.0.23", + "@types/papaparse": "^5.3.14", "@types/uuid": "^8.3.0", "@typescript-eslint/eslint-plugin": "^5.45.0", "@typescript-eslint/parser": "^5.45.0", diff --git a/src/helpers/DataRequirementHelpers.ts b/src/helpers/DataRequirementHelpers.ts index 01d2c7cc..52ce4e52 100644 --- a/src/helpers/DataRequirementHelpers.ts +++ b/src/helpers/DataRequirementHelpers.ts @@ -58,6 +58,7 @@ export async function getDataRequirements( if (retrieve.queryLocalId && retrieve.queryLibraryName && parameters['Measurement Period']) { const library = elmJSONs.find(lib => lib.library.identifier.id === retrieve.queryLibraryName); if (library) { + // use something else here, perhaps parseDRInfo retrieve.queryInfo = await parseQueryInfo( library, elmJSONs, diff --git a/src/helpers/elm/RetrievesHelper.ts b/src/helpers/elm/RetrievesHelper.ts index 2a3f0734..547d2872 100644 --- a/src/helpers/elm/RetrievesHelper.ts +++ b/src/helpers/elm/RetrievesHelper.ts @@ -67,6 +67,7 @@ export function findRetrieves( expressionStack: ExpressionStackEntry[] = [], withErrors: GracefulError[] = [] ): { results: DataTypeQuery[]; withErrors: GracefulError[] } { + // add mustSupport to DataTypeQuery type // Smart defaults for recursive call to avoid passing in a bunch of values that don't usually change const defaultRecursiveOpts: RecursiveCallOptions = { elm, diff --git a/src/types/Calculator.ts b/src/types/Calculator.ts index f2456e83..3612d524 100644 --- a/src/types/Calculator.ts +++ b/src/types/Calculator.ts @@ -293,6 +293,8 @@ export interface DataTypeQuery { queryInfo?: QueryInfo; /** specifies an optional template/profile for the objects that the retrieve returns to conform to */ templateId?: string; + /** mustSupport */ + mustSupport?: string[]; } export interface GapsDataTypeQuery extends DataTypeQuery { From c54df09c7c2f9ba029aadd558514f8414620e0c0 Mon Sep 17 00:00:00 2001 From: Elsa Date: Wed, 6 Mar 2024 11:10:55 -0500 Subject: [PATCH 02/16] Data requirements comparison script --- data-requirements/README.md | 54 + data-requirements/compare-output.ts | 71 - data-requirements/compare.sh | 40 +- data-requirements/compare.ts | 72 - .../elm-parser-dr/BCSEHEDISMY2022.xml.json | 703 ------- .../BreastCancerScreeningsFHIR.xml.json | 1152 ----------- .../CervicalCancerScreeningFHIR.xml.json | 552 ----- .../ColorectalCancerScreeningsFHIR.xml.json | 1133 ----------- ...WithPhysicianManagingDiabetesFHIR.xml.json | 373 ---- ...emoglobinA1cHbA1cPoorControl9FHIR.xml.json | 892 --------- ...hargedonAntithromboticTherapyFHIR.xml.json | 225 --- .../elm-parser-dr/Exam125FHIR.xml.json | 1152 ----------- .../elm-parser-dr/Exam130FHIR.xml.json | 1133 ----------- .../elm-parser-dr/FHIR347.xml.json | 1277 ------------ ...lycemiainHospitalizedPatientsFHIR.xml.json | 182 -- ...ospitalHarmSevereHypoglycemiaFHIR.xml.json | 142 -- .../elm-parser-dr/HybridHWMFHIR.xml.json | 623 ------ .../elm-parser-dr/HybridHWRFHIR.xml.json | 768 ------- ...ousThromboembolismProphylaxisFHIR.xml.json | 998 ---------- ...fferedbyPCPsincludingDentistsFHIR.xml.json | 399 ---- ...fOpioidsConcurrentPrescribingFHIR.xml.json | 198 -- .../elm-parser-input/fhir_all.csv | 806 -------- .../elm-parser-input/library/.gitignore | 4 - data-requirements/fqm-e-dr.ts | 58 + .../fqm-e-dr/BCSEHEDISMY2022-dr.json | 739 ------- .../BreastCancerScreeningsFHIR-dr.json | 1428 ------------- .../CervicalCancerScreeningFHIR-dr.json | 834 -------- .../ColorectalCancerScreeningsFHIR-dr.json | 1774 ----------------- ...nWithPhysicianManagingDiabetesFHIR-dr.json | 595 ------ ...HemoglobinA1cHbA1cPoorControl9FHIR-dr.json | 1128 ----------- ...chargedonAntithromboticTherapyFHIR-dr.json | 443 ---- data-requirements/fqm-e-dr/FHIR347-dr.json | 1189 ----------- ...glycemiainHospitalizedPatientsFHIR-dr.json | 397 ---- ...HospitalHarmSevereHypoglycemiaFHIR-dr.json | 288 --- .../fqm-e-dr/HybridHWMFHIR-dr.json | 303 --- .../fqm-e-dr/HybridHWRFHIR-dr.json | 313 --- ...nousThromboembolismProphylaxisFHIR-dr.json | 1382 ------------- ...OfferedbyPCPsincludingDentistsFHIR-dr.json | 517 ----- ...ofOpioidsConcurrentPrescribingFHIR-dr.json | 346 ---- data-requirements/parse-dr.ts | 102 - data-requirements/parse-fhir-all.ts | 76 - data-requirements/summary-compare.sh | 59 + data-requirements/summary-compare.ts | 207 ++ 43 files changed, 402 insertions(+), 24725 deletions(-) create mode 100644 data-requirements/README.md delete mode 100644 data-requirements/compare-output.ts delete mode 100644 data-requirements/compare.ts delete mode 100644 data-requirements/elm-parser-dr/BCSEHEDISMY2022.xml.json delete mode 100644 data-requirements/elm-parser-dr/BreastCancerScreeningsFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/CervicalCancerScreeningFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/ColorectalCancerScreeningsFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/DRCommunicationWithPhysicianManagingDiabetesFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/DiabetesHemoglobinA1cHbA1cPoorControl9FHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/DischargedonAntithromboticTherapyFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/Exam125FHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/Exam130FHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/FHIR347.xml.json delete mode 100644 data-requirements/elm-parser-dr/HospitalHarmHyperglycemiainHospitalizedPatientsFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/HospitalHarmSevereHypoglycemiaFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/HybridHWMFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/HybridHWRFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/IntensiveCareUnitVenousThromboembolismProphylaxisFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/PrimaryCariesPreventionasOfferedbyPCPsincludingDentistsFHIR.xml.json delete mode 100644 data-requirements/elm-parser-dr/SafeUseofOpioidsConcurrentPrescribingFHIR.xml.json delete mode 100644 data-requirements/elm-parser-input/fhir_all.csv delete mode 100644 data-requirements/elm-parser-input/library/.gitignore create mode 100644 data-requirements/fqm-e-dr.ts delete mode 100644 data-requirements/fqm-e-dr/BCSEHEDISMY2022-dr.json delete mode 100644 data-requirements/fqm-e-dr/BreastCancerScreeningsFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/CervicalCancerScreeningFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/ColorectalCancerScreeningsFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/DRCommunicationWithPhysicianManagingDiabetesFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/DiabetesHemoglobinA1cHbA1cPoorControl9FHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/DischargedonAntithromboticTherapyFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/FHIR347-dr.json delete mode 100644 data-requirements/fqm-e-dr/HospitalHarmHyperglycemiainHospitalizedPatientsFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/HospitalHarmSevereHypoglycemiaFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/HybridHWMFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/HybridHWRFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/IntensiveCareUnitVenousThromboembolismProphylaxisFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/PrimaryCariesPreventionasOfferedbyPCPsincludingDentistsFHIR-dr.json delete mode 100644 data-requirements/fqm-e-dr/SafeUseofOpioidsConcurrentPrescribingFHIR-dr.json delete mode 100644 data-requirements/parse-dr.ts delete mode 100644 data-requirements/parse-fhir-all.ts create mode 100755 data-requirements/summary-compare.sh create mode 100644 data-requirements/summary-compare.ts diff --git a/data-requirements/README.md b/data-requirements/README.md new file mode 100644 index 00000000..9a944318 --- /dev/null +++ b/data-requirements/README.md @@ -0,0 +1,54 @@ +# fqm-execution Data Requirements Output Testing/Comparison + +This directory includes scripts for comparing the data-requirements output of [fqm-execution](https://github.com/projecttacoma/fqm-execution) to the data-requirements output of the fhir_review branch of the [elm-parser-for-ecqms](https://github.com/projecttacoma/elm-parser-for-ecqms/tree/fhir_review). + +## Getting Data Requirements from the elm-parser-for-ecqms + +The scripts in this directory will get the data requirements output from the elm-parser-for-ecqms fhir_review branch for the January 2024 Connectathon bundles. On the fhir_review branch of elm-parser-for-ecqms, data-requirements are calculated for the measures in [elm-parser-for-ecqms/measures/qicore/measures](https://github.com/projecttacoma/elm-parser-for-ecqms/tree/fhir_review/measures/qicore/measures) by running the command `ruby parse-elm.rb --bundle qicore`. The results are outputted to JSON files per measure to `elm-parser-for-ecqms/data_requirements/library`. This is all done by the script and the results are moved to the `elm-parser-dr` directory. + +## Getting Data Requirements from fqm-execution + +The scripts in this directory will get the data requirements output from fqm-execution for the January 2024 Connectathon bundles. The data requirements are calculated with fqm-execution on every run for ease of testing changes to fqm-execution. Since the January 2024 Connectathon bundles are not in a GitHub repository, they will have to be manually dropped into the `jan-2024-connectathon` directory that is empty. The data requirements JSON output files will be moved to the `fqm-e-dr` directory after calculation. + +## Comparing Data Requirements + +Right now there are two ways to compare data-requirements. `compare.sh` takes a similar approach to the regression tests: data-requirements are calculated using fqm-execution and then using elm-parser-for-ecqms and their outputs are compared. This will likely not be useful with the current state of fqm-execution's data-requirements calculation as it is very different from the elm-parser-for-ecqms, but it may be in the future. + +`summary-compare.sh` also compares the data-requirements outputs from fqm-execution and elm-parser-for-ecqms, but in a way that parses through each of the data-requirements in the data-requirements array. This script may be more useful to look at how many data-requirements of each type are being outputted by either repository and if they match up. By default, this script compares the data requirements outputs of all of the measures, however using the -m|--measure flag, one can specify a single measure to compare. + +## Running the Scripts + +Before running any of the scripts, be sure to populate the `jan-2024-connectathon` directory with the corresponding measure bundles. + +To run `compare.sh`: + +``` +./compare.sh +``` + +To run `summary-compare.sh` for all measures: + +``` +./summary-compare.sh +``` + +To run `summary-compare.sh` for one measure (example: CMS996): + +``` +./summary-compare.sh -m CMS996 +``` + +## Summary Compare Output + +Right now, the `summary-compare.sh` script compares three things: the types of data requirements in either output, the data requirements of each type in either output, and the mustSupports of each data requirement in either output. + +The summary output is currently structured in the following format: + +``` +-----Data Requirements Comparison for ----- +[PASS/DIFF]: Whether or not either of the outputs has data requirements of a type that the other does not + +[PASS/FAIL (Data Requirement Type)]: Whether or not the data requirements of each output match my codeFilter.valueSet and provides details if they do not +MUST SUPPORTS +[MUST SUPPORTS PASS/FAIL(Data Requirement Type-ValueSet)]: Whether or not the mustSupports of the data requirements of each output match +``` diff --git a/data-requirements/compare-output.ts b/data-requirements/compare-output.ts deleted file mode 100644 index b12f5b22..00000000 --- a/data-requirements/compare-output.ts +++ /dev/null @@ -1,71 +0,0 @@ -import fs from 'fs'; -import * as _ from 'lodash'; - -/** - * The purpose of this script is to comparison the output of the current fqm-execution (1.3.3) data-requirements JSON output - * to the current data-requirements JSON output of the elm-parser-for-ecqms fhir_review branch - */ - -// Get the JSON data-requirements output for a single measure from fqm-execution (put JSON file into fqm-e-input directory) -const fqmEDataRequirementsLibrary = JSON.parse( - fs.readFileSync('./fqm-e-input/ColorectalCancerScreeningsDR.json', 'utf8') -) as fhir4.Library; -const fqmEDataRequirements = fqmEDataRequirementsLibrary?.dataRequirement as fhir4.DataRequirement[]; - -// Get the JSON data-requirements output for a single measure from elm-parser-for-ecqms (put JSON file into elm-parser-input directory) -const elmParserDataRequirementsLibrary = JSON.parse( - fs.readFileSync('./elm-parser-input/library/ColorectalCancerScreeningsFHIR.xml.json', 'utf8') -) as fhir4.Library; -const elmPaserDataRequirements = elmParserDataRequirementsLibrary?.dataRequirement as fhir4.DataRequirement[]; - -// Group data requirements in each file by type in Record -let fqmEData: Record = {}; -fqmEDataRequirements.forEach(dr => { - if (fqmEData[dr.type]) { - fqmEData[dr.type].push(dr); - } else { - fqmEData[dr.type] = [dr]; - } -}); - -// Sort the data requirements by type alphabetically -let sortedFqmEData: Record = {}; - -Object.keys(fqmEData) - .sort() - .forEach(key => { - sortedFqmEData[key] = fqmEData[key]; - }); - -// Print the fqm-execution results to the console -console.log('------FQM-EXECUTION------'); - -_.forEach(sortedFqmEData, function (value, key) { - console.log(key, value.length); -}); - -// Group data requirements in each file by type in Record -let elmParserData: Record = {}; -elmPaserDataRequirements.forEach(dr => { - if (elmParserData[dr.type]) { - elmParserData[dr.type].push(dr); - } else { - elmParserData[dr.type] = [dr]; - } -}); - -// Sort the data requirements by type alphabetically -let sortedElmParserData: Record = {}; - -Object.keys(elmParserData) - .sort() - .forEach(key => { - sortedElmParserData[key] = elmParserData[key]; - }); - -// Print the fqm-execution results to the console -console.log('------ELM-PARSER------'); - -_.forEach(sortedElmParserData, function (value, key) { - console.log(key, value.length); -}); diff --git a/data-requirements/compare.sh b/data-requirements/compare.sh index 46dfe09d..e707e017 100755 --- a/data-requirements/compare.sh +++ b/data-requirements/compare.sh @@ -6,44 +6,51 @@ NC='\033[0m' VERBOSE=false -# Potentailly add data-requirement type option to just look at one type ? -# Also maybe include a verbose option ? function usage() { cat <] [-v|--verbose] + Usage: $0 [-v|--verbose] Options: - -dr/--data-requirement: Data requirement type to specifically compare - -v/--verbose: Use verbose comparison. + -v/--verbose: Use verbose comparison. Will print out diffs of failing JSON files with spacing (default: false) USAGE exit 1 } -# Clone the elm-parser-for-ecqms in the data-requirements directory if it hasn't been +while test $# != 0 +do + case "$1" in + -v | --verbose) VERBOSE=true;; + esac + shift +done + +echo "Gathering data-requirements output from the fhir_review branch of elm-parser-for-ecqms" + +# Clone the elm-parser-for-ecqms in the data-requirements directory if it hasn't been, swtich to the fhir_review branch, +# run parse_elm.rb with --bundle qicore to get data-requirements for measure bundles from the January 2024 Connectathon if [ ! -d "elm-parser-for-ecqms" ]; then git clone https://github.com/projecttacoma/elm-parser-for-ecqms.git git fetch --all cd elm-parser-for-ecqms git checkout "fhir_review" - ruby parse_elm.rb --bundle fhir + ruby parse_elm.rb --bundle qicore cd .. + if [-d "elm-parser-dr"]; then + rm -rf elm-parser-dr + fi mkdir elm-parser-dr SOURCE_DIR="elm-parser-for-ecqms/data_requirements/library" TARGET_DIR="elm-parser-dr" # Move all files from source to target directory mv "$SOURCE_DIR"/* "$TARGET_DIR" - echo "Files moved successfully" fi -echo "Gathering data-requirements output from fqm-execution using the measure bundle from ecqm-content-r4-2021" +echo "Gathering data-requirements output from fqm-execution using the measure bundles from the January 2024 Connectathon" -npx ts-node compare.ts +npx ts-node fqm-e-dr.ts -# The following code directly compares the Library data requirements outputs of both fqm-execution and elm-parser-for-ecqms -# The problem with this is that the JSON is structured slightly differently so it may not even be helpful -FAILURES=() for file in "fqm-e-dr"/*; do BASE_PATH="$(basename "$file")" BASE_NAME=${BASE_PATH%"-dr.json"*} @@ -53,19 +60,20 @@ for file in "fqm-e-dr"/*; do if ! test -f "$FQM_E_DR"; then echo -e "${RED}FAIL${NC}: $FQM_E_DR does not exist" - FAILURES+=("$FQM_E_DR") fi if ! test -f "$ELM_PARSER_DR"; then echo -e "${RED}FAIL${NC}: $ELM_PARSER_DR does not exist" - FAILURES+=("$ELM_PARSER_DR") fi if cmp --silent $FQM_E_DR $ELM_PARSER_DR; then echo -e "${GREEN}PASS${NC}: $BASE_NAME" else echo -e "${RED}FAIL${NC}: $FQM_E_DR and $ELM_PARSER_DR are different" - FAILURES+=("$BASE_NAME") + + if [ $VERBOSE = "true" ]; then + diff $FQM_E_DR $ELM_PARSER_DR + fi fi done diff --git a/data-requirements/compare.ts b/data-requirements/compare.ts deleted file mode 100644 index 25b522fa..00000000 --- a/data-requirements/compare.ts +++ /dev/null @@ -1,72 +0,0 @@ -import fs from 'fs'; -import path from 'path'; -import { Calculator } from '../src'; - -const RESET = '\x1b[0m'; -const FG_YELLOW = '\x1b[33m'; -const FG_GREEN = '\x1b[32m'; - -const ECQM_CONTENT_BASE_PATH = path.join(__dirname, '../regression/ecqm-content-r4-2021/bundles/measure'); - -async function main() { - if (fs.existsSync('./fqm-e-dr')) { - fs.rmSync('./fqm-e-dr', { recursive: true }); - } - - fs.mkdirSync('./fqm-e-dr'); - - const allDirs = fs.readdirSync(ECQM_CONTENT_BASE_PATH).map(f => ({ - shortName: f, - fullPath: path.join(ECQM_CONTENT_BASE_PATH, f) - })); - - for (const dir of allDirs) { - const basePath = dir.fullPath; - - // It is assumed that the bundle lives under the base directory with `-bundle.json added to the extension - const measureBundle = JSON.parse( - fs.readFileSync(path.join(basePath, `${dir.shortName}-bundle.json`), 'utf8') - ) as fhir4.Bundle; - - // try to calculate the data requirements for the measure bundle - try { - const { results } = await Calculator.calculateDataRequirements(measureBundle, {}); - - fs.writeFileSync(`./fqm-e-dr/${dir.shortName}-dr.json`, JSON.stringify(results, undefined, 2), 'utf8'); - console.log(`${FG_GREEN}%s${RESET}: Results written to ./fqm-e-dr/${dir.shortName}-dr.json`, 'SUCCESS'); - } catch (e) { - if (e instanceof Error) { - fs.writeFileSync( - `./fqm-e-dr/${dir.shortName}-dr.json`, - JSON.stringify({ error: e.message }, undefined, 2), - 'utf8' - ); - console.log( - `${FG_YELLOW}%s${RESET}: Results written to ./fqm-e-dr/${dir.shortName}-dr.json`, - 'EXECUTION ERROR' - ); - } - } - - // In the following code, I would like to go through the data-requirements library outputs, take just the data-requirements - // array, sort them and put them in their own files - // const fqmEDataReqs = ( - // JSON.parse(fs.readFileSync(`./fqm-e-dr/${dir.shortName}-drLib.json`, 'utf8')) as fhir4.Library - // ).dataRequirement; - - // if (!fs.existsSync(`./elm-parser-dr/${dir.shortName}.xml.json`)) continue; - - // const elmParserDataReqs = ( - // JSON.parse(fs.readFileSync(`./elm-parser-dr/${dir.shortName}.xml.json`, 'utf8')) as fhir4.Library - // ).dataRequirement; - - // fs.writeFileSync(`./fqm-e-dr/${dir.shortName}-dr.json`, JSON.stringify(fqmEDataReqs, undefined, 2), 'utf8'); - // fs.writeFileSync( - // `./elm-parser-dr/${dir.shortName}-dr.json`, - // JSON.stringify(elmParserDataReqs, undefined, 2), - // 'utf8' - // ); - } -} - -main().then(() => console.log('done')); diff --git a/data-requirements/elm-parser-dr/BCSEHEDISMY2022.xml.json b/data-requirements/elm-parser-dr/BCSEHEDISMY2022.xml.json deleted file mode 100644 index b9ccb8ff..00000000 --- a/data-requirements/elm-parser-dr/BCSEHEDISMY2022.xml.json +++ /dev/null @@ -1,703 +0,0 @@ -{ - "name": "BCSEHEDISMY2022.xml", - "status": "draft", - "type": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/library-type", - "code": "module-definition" - } - ] - }, - "dataRequirement": [ - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1329" - } - ], - "type": "Condition", - "mustSupport": [ - "code", - "clinicalStatus", - "onset", - "abatement" - ], - "codeFilter": [ - { - "path": "code", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1329" - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1330" - } - ], - "type": "Condition", - "mustSupport": [ - "code", - "clinicalStatus", - "onset", - "abatement" - ], - "codeFilter": [ - { - "path": "code", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1330" - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1465" - } - ], - "type": "Condition", - "mustSupport": [ - "code" - ], - "codeFilter": [ - { - "path": "code", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1465" - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Condition?code=Z51.5" - } - ], - "type": "Condition", - "mustSupport": [ - "clinicalStatus", - "code", - "onset", - "abatement" - ], - "codeFilter": [ - { - "path": "code", - "code": [ - { - "system": "ICD-10", - "code": "Z51.5" - } - ] - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1531" - } - ], - "type": "Condition", - "mustSupport": [ - "clinicalStatus", - "code", - "onset", - "abatement" - ], - "codeFilter": [ - { - "path": "code", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1531" - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Condition?code:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1331" - } - ], - "type": "Condition", - "mustSupport": [ - "code", - "clinicalStatus", - "onset", - "abatement" - ], - "codeFilter": [ - { - "path": "code", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1331" - } - ] - }, - { - "type": "Coverage", - "mustSupport": [ - "period" - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1810&period=ge2019-01-01T00:00:00.000Z&period=le2019-12-31T00:00:00.000Z" - } - ], - "type": "Encounter", - "mustSupport": [ - "status", - "type", - "period", - "diagnosis", - "diagnosis.condition" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1810" - } - ], - "dateFilter": [ - { - "path": "period", - "valuePeriod": { - "start": "2019-01-01T00:00:00.000Z", - "end": "2019-12-31T00:00:00.000Z" - } - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1086&period=ge2019-01-01T00:00:00.000Z&period=le2019-12-31T00:00:00.000Z" - } - ], - "type": "Encounter", - "mustSupport": [ - "status", - "type", - "diagnosis", - "diagnosis.condition", - "period" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1086" - } - ], - "dateFilter": [ - { - "path": "period", - "valuePeriod": { - "start": "2019-01-01T00:00:00.000Z", - "end": "2019-12-31T00:00:00.000Z" - } - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1532" - } - ], - "type": "Encounter", - "mustSupport": [ - "status", - "type", - "period" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1532" - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1761" - } - ], - "type": "Encounter", - "mustSupport": [ - "type", - "period", - "status" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1761" - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1189&period=ge2019-01-01T00:00:00.000Z&period=le2019-12-31T00:00:00.000Z" - } - ], - "type": "Encounter", - "mustSupport": [ - "status", - "type", - "diagnosis", - "diagnosis.condition", - "period" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1189" - } - ], - "dateFilter": [ - { - "path": "period", - "valuePeriod": { - "start": "2019-01-01T00:00:00.000Z", - "end": "2019-12-31T00:00:00.000Z" - } - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1191&period=ge2019-01-01T00:00:00.000Z&period=le2019-12-31T00:00:00.000Z" - } - ], - "type": "Encounter", - "mustSupport": [ - "status", - "type", - "diagnosis", - "diagnosis.condition", - "period" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1191" - } - ], - "dateFilter": [ - { - "path": "period", - "valuePeriod": { - "start": "2019-01-01T00:00:00.000Z", - "end": "2019-12-31T00:00:00.000Z" - } - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1446&period=ge2019-01-01T00:00:00.000Z&period=le2019-12-31T00:00:00.000Z" - } - ], - "type": "Encounter", - "mustSupport": [ - "status", - "type", - "diagnosis", - "diagnosis.condition", - "period" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1446" - } - ], - "dateFilter": [ - { - "path": "period", - "valuePeriod": { - "start": "2019-01-01T00:00:00.000Z", - "end": "2019-12-31T00:00:00.000Z" - } - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=outpatient:MedicationRequestCategory&period=ge2019-01-01T00:00:00.000Z&period=le2019-12-31T00:00:00.000Z" - } - ], - "type": "Encounter", - "mustSupport": [ - "status", - "type", - "diagnosis", - "diagnosis.condition", - "period" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "outpatient:MedicationRequestCategory" - } - ], - "dateFilter": [ - { - "path": "period", - "valuePeriod": { - "start": "2019-01-01T00:00:00.000Z", - "end": "2019-12-31T00:00:00.000Z" - } - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1450" - } - ], - "type": "Encounter", - "mustSupport": [ - "type", - "period", - "status" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1450" - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Encounter?type:in=https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1246&period=ge2019-01-01T00:00:00.000Z&period=le2019-12-31T00:00:00.000Z" - } - ], - "type": "Encounter", - "mustSupport": [ - "status", - "type", - "diagnosis", - "diagnosis.condition", - "period" - ], - "codeFilter": [ - { - "path": "type", - "valueSet": "https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1246" - } - ], - "dateFilter": [ - { - "path": "period", - "valuePeriod": { - "start": "2019-01-01T00:00:00.000Z", - "end": "2019-12-31T00:00:00.000Z" - } - } - ] - }, - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": 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newline at end of file diff --git a/data-requirements/elm-parser-dr/SafeUseofOpioidsConcurrentPrescribingFHIR.xml.json b/data-requirements/elm-parser-dr/SafeUseofOpioidsConcurrentPrescribingFHIR.xml.json deleted file mode 100644 index 3647dce5..00000000 --- a/data-requirements/elm-parser-dr/SafeUseofOpioidsConcurrentPrescribingFHIR.xml.json +++ /dev/null @@ -1,198 +0,0 @@ -{ - "name": "SafeUseofOpioidsConcurrentPrescribingFHIR.xml", - "status": "draft", - "type": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/library-type", - "code": "module-definition" - } - ] - }, - "dataRequirement": [ - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-fhirQueryPattern", - "valueString": "Condition?code:in=http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.161&clinicalStatus=active,recurrence,relapse" - } - ], - "type": "Condition", - "mustSupport": [ - "code", - "clinicalStatus", - "onset", - "abatement", - 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Neoplasm of Colon|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1001|code -ColorectalCancerScreeningsFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|active|active:ConditionClinicalStatusCodes|clinicalStatus -ColorectalCancerScreeningsFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|recurrence|recurrence:ConditionClinicalStatusCodes|clinicalStatus -ColorectalCancerScreeningsFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|relapse|relapse:ConditionClinicalStatusCodes|clinicalStatus -ColorectalCancerScreeningsFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|||onset -ColorectalCancerScreeningsFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|||abatement -ColorectalCancerScreeningsFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|||recordedDate -ColorectalCancerScreeningsFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|Total Colectomy|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1019|code -ColorectalCancerScreeningsFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|||status -ColorectalCancerScreeningsFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|||performed -ColorectalCancerScreeningsFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|Total Colectomy ICD9|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.11.1136|code -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|Fecal Occult Blood Test (FOBT)|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1011|code -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|||effective -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|||value -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|||category -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|final||status -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|amended||status -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|corrected||status -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|||category.coding -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|FIT DNA|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1039|code -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|CT Colonography|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1038|code -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|appended||status -ColorectalCancerScreeningsFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|Flexible Sigmoidoscopy|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1010|code -ColorectalCancerScreeningsFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|Colonoscopy|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1020|code -ColorectalCancerScreeningsFHIR.xml|Coverage|http://hl7.org/fhir/StructureDefinition/Coverage|Payer|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.3591|type -ColorectalCancerScreeningsFHIR.xml|Coverage|http://hl7.org/fhir/StructureDefinition/Coverage|||period -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Office Visit|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1001|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Annual Wellness Visit|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.526.3.1240|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Preventive Care Services - Established Office Visit, 18 and Up|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1025|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Preventive Care Services-Initial Office Visit, 18 and Up|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1023|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Home Healthcare Services|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1016|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Encounter Inpatient|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.666.5.307|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Discharge to home for hospice care (procedure)|428361000124107:SNOMEDCT:2017-09|hospitalization -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Discharge to healthcare facility for hospice care (procedure)|428371000124100:SNOMEDCT:2017-09|hospitalization -ColorectalCancerScreeningsFHIR.xml|ServiceRequest|http://hl7.org/fhir/StructureDefinition/ServiceRequest|Hospice care ambulatory|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1108.15|code -ColorectalCancerScreeningsFHIR.xml|ServiceRequest|http://hl7.org/fhir/StructureDefinition/ServiceRequest|active||status -ColorectalCancerScreeningsFHIR.xml|ServiceRequest|http://hl7.org/fhir/StructureDefinition/ServiceRequest|completed||status -ColorectalCancerScreeningsFHIR.xml|ServiceRequest|http://hl7.org/fhir/StructureDefinition/ServiceRequest|||intent -ColorectalCancerScreeningsFHIR.xml|ServiceRequest|http://hl7.org/fhir/StructureDefinition/ServiceRequest|||authoredOn -ColorectalCancerScreeningsFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|Hospice care ambulatory|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1108.15|code -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|Functional Assessment of Chronic Illness Therapy - Palliative Care Questionnaire (FACIT-Pal)|71007-9:LOINC|code -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Palliative Care Encounter|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1450|type -ColorectalCancerScreeningsFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|Palliative Care Intervention|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.2224|code -ColorectalCancerScreeningsFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|completed||status -ColorectalCancerScreeningsFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|in-progress||status -ColorectalCancerScreeningsFHIR.xml|DeviceRequest|http://hl7.org/fhir/StructureDefinition/DeviceRequest|Frailty Device|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1530|code -ColorectalCancerScreeningsFHIR.xml|DeviceRequest|http://hl7.org/fhir/StructureDefinition/DeviceRequest|active||status -ColorectalCancerScreeningsFHIR.xml|DeviceRequest|http://hl7.org/fhir/StructureDefinition/DeviceRequest|on-hold||status -ColorectalCancerScreeningsFHIR.xml|DeviceRequest|http://hl7.org/fhir/StructureDefinition/DeviceRequest|completed||status -ColorectalCancerScreeningsFHIR.xml|DeviceRequest|http://hl7.org/fhir/StructureDefinition/DeviceRequest|||intent -ColorectalCancerScreeningsFHIR.xml|DeviceRequest|http://hl7.org/fhir/StructureDefinition/DeviceRequest|||authoredOn -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|Frailty Device|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1530|code -ColorectalCancerScreeningsFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|Frailty Diagnosis|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1531|code -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Frailty Encounter|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1532|type -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|Frailty Symptom|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1533|code -ColorectalCancerScreeningsFHIR.xml|Observation|http://hl7.org/fhir/StructureDefinition/Observation|preliminary||status -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Acute Inpatient|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1810|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|||diagnosis -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|||diagnosis.condition -ColorectalCancerScreeningsFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|Advanced Illness|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1465|code -ColorectalCancerScreeningsFHIR.xml|MedicationRequest|http://hl7.org/fhir/StructureDefinition/MedicationRequest|Dementia Medications|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1729|medication -ColorectalCancerScreeningsFHIR.xml|MedicationRequest|http://hl7.org/fhir/StructureDefinition/MedicationRequest|||status -ColorectalCancerScreeningsFHIR.xml|MedicationRequest|http://hl7.org/fhir/StructureDefinition/MedicationRequest|||intent -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Outpatient|outpatient:MedicationRequestCategory|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Observation|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1191|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Emergency Department Visit|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.292|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Nonacute Inpatient|https://www.ncqa.org/fhir/valueset/2.16.840.1.113883.3.464.1004.1189|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Care Services in Long-Term Residential Facility|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1014|type -ColorectalCancerScreeningsFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Nursing Facility Visit|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1012|type -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|MedicationRequest|http://hl7.org/fhir/StructureDefinition/MedicationRequest|Schedule II & III Opioid Medications|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.165|medication -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|MedicationRequest|http://hl7.org/fhir/StructureDefinition/MedicationRequest|||authoredOn -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|MedicationRequest|http://hl7.org/fhir/StructureDefinition/MedicationRequest|||status -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|MedicationRequest|http://hl7.org/fhir/StructureDefinition/MedicationRequest|||intent -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|MedicationRequest|http://hl7.org/fhir/StructureDefinition/MedicationRequest|Schedule IV Benzodiazepines|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1125.1|medication -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|MedicationRequest|http://hl7.org/fhir/StructureDefinition/MedicationRequest|Discharge|discharge:MedicationRequestCategory|category -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|All Primary and Secondary Cancer|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.161|code -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|active|active:ConditionClinicalStatusCodes|clinicalStatus -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|recurrence|recurrence:ConditionClinicalStatusCodes|clinicalStatus -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|relapse|relapse:ConditionClinicalStatusCodes|clinicalStatus -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|||onset -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|||abatement -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Condition|http://hl7.org/fhir/StructureDefinition/Condition|||recordedDate -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|ServiceRequest|http://hl7.org/fhir/StructureDefinition/ServiceRequest|Palliative or Hospice Care|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.600.1.1579|code -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|ServiceRequest|http://hl7.org/fhir/StructureDefinition/ServiceRequest|||authoredOn -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|ServiceRequest|http://hl7.org/fhir/StructureDefinition/ServiceRequest|||intent -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|Palliative or Hospice Care|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.600.1.1579|code -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Procedure|http://hl7.org/fhir/StructureDefinition/Procedure|||performed -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Encounter Inpatient|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.666.5.307|type -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|||period -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|||status -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Discharge To Acute Care Facility|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.87|hospitalization -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Hospice Care Referral or Admission|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1116.365|hospitalization -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Encounter|http://hl7.org/fhir/StructureDefinition/Encounter|Patient Expired|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.309|hospitalization -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Coverage|http://hl7.org/fhir/StructureDefinition/Coverage|Payer|http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.3591|type -SafeUseofOpioidsConcurrentPrescribingFHIR.xml|Coverage|http://hl7.org/fhir/StructureDefinition/Coverage|||period diff --git a/data-requirements/elm-parser-input/library/.gitignore b/data-requirements/elm-parser-input/library/.gitignore deleted file mode 100644 index 86d0cb27..00000000 --- a/data-requirements/elm-parser-input/library/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore \ No newline at end of file diff --git a/data-requirements/fqm-e-dr.ts b/data-requirements/fqm-e-dr.ts new file mode 100644 index 00000000..dd65d579 --- /dev/null +++ b/data-requirements/fqm-e-dr.ts @@ -0,0 +1,58 @@ +import fs from 'fs'; +import path from 'path'; +import { Calculator } from '../src'; + +const RESET = '\x1b[0m'; +const FG_YELLOW = '\x1b[33m'; +const FG_GREEN = '\x1b[32m'; + +const JAN_2024_CONNECTATHON_BASE_PATH = path.join(__dirname, './jan-2024-connectathon'); + +/** + * The purpose of this function is to go through all of the measure bundles in the jan-2024-connectathon + * directory, calculate their data-requirements, and output their data-requirements to a JSON file + * corresponding to the name of the measure in the fqm-e-dr directory + */ +async function main() { + // if the fqm-e-dr directory already exists, remove it and its contents + if (fs.existsSync('./fqm-e-dr')) { + fs.rmSync('./fqm-e-dr', { recursive: true }); + } + + // create new fqm-e-dr directory within the data-requirements directory + fs.mkdirSync('./fqm-e-dr'); + + // get all of the file names (short and fullPath) from the jan-2024-connectathon directory + const allBundles = fs.readdirSync(JAN_2024_CONNECTATHON_BASE_PATH).map(f => ({ + shortName: f.split('v')[0], + fullPath: path.join(JAN_2024_CONNECTATHON_BASE_PATH, f) + })); + + for (const bundle of allBundles) { + const measureBundle = JSON.parse(fs.readFileSync(bundle.fullPath, 'utf8')) as fhir4.Bundle; + + // try to calculate the data requirements for the measure bundle + try { + const { results } = await Calculator.calculateDataRequirements(measureBundle, {}); + + // write the data-requirements results to the measure's shortName-dr.json file in the fqm-e-dr directory + fs.writeFileSync(`./fqm-e-dr/${bundle.shortName}-dr.json`, JSON.stringify(results, undefined, 2), 'utf8'); + + console.log(`${FG_GREEN}%s${RESET}: Results written to ./fqm-e-dr/${bundle.shortName}-dr.json`, 'SUCCESS'); + } catch (e) { + if (e instanceof Error) { + fs.writeFileSync( + `./fqm-e-dr/${bundle.shortName}-dr.json`, + JSON.stringify({ error: e.message }, undefined, 2), + 'utf8' + ); + console.log( + `${FG_YELLOW}%s${RESET}: Results written to ./fqm-e-dr/${bundle.shortName}-dr.json`, + 'EXECUTION ERROR' + ); + } + } + } +} + +main().then(() => console.log('fqm-execution data-requirement calculation finished')); diff --git a/data-requirements/fqm-e-dr/BCSEHEDISMY2022-dr.json b/data-requirements/fqm-e-dr/BCSEHEDISMY2022-dr.json deleted file mode 100644 index b2ab9950..00000000 --- a/data-requirements/fqm-e-dr/BCSEHEDISMY2022-dr.json +++ /dev/null @@ -1,739 +0,0 @@ -{ - "resourceType": "Library", - "type": { - "coding": [ - { - "code": "module-definition", - "system": "http://terminology.hl7.org/CodeSystem/library-type" - } - ] - }, - "status": "unknown", - "dataRequirement": [ - { - "type": "Condition", - "profile": [ - 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"depends-on", - "display": "Library FHIRHelpers", - "resource": "http://ecqi.healthit.gov/ecqms/Library/FHIRHelpers|4.0.001" - }, - { - "type": "depends-on", - "display": "Code system ConditionClinicalStatusCodes", - "resource": "http://terminology.hl7.org/CodeSystem/condition-clinical" - }, - { - "type": "depends-on", - "display": "Code system AllergyIntoleranceClinicalStatusCodes", - "resource": "http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical" - }, - { - "type": "depends-on", - "display": "Code system AllergyIntoleranceVerificationStatusCodes", - "resource": "http://terminology.hl7.org/CodeSystem/allergyintolerance-verification" - }, - { - "type": "depends-on", - "display": "Code system Diagnosis Role", - "resource": "http://terminology.hl7.org/CodeSystem/diagnosis-role" - }, - { - "type": "depends-on", - "display": "Code system LOINC", - "resource": "http://loinc.org" - }, - { - "type": "depends-on", - "display": "Code system MedicationRequestCategory", - "resource": "http://terminology.hl7.org/CodeSystem/medicationrequest-category" - }, - { - "type": "depends-on", - "display": "Code system ConditionVerificationStatusCodes", - "resource": "http://terminology.hl7.org/CodeSystem/condition-ver-status" - }, - { - "type": "depends-on", - "display": "Code system SNOMEDCT", - "resource": "http://snomed.info/sct" - }, - { - "type": "depends-on", - "display": "Code system RoleCode", - "resource": "http://terminology.hl7.org/CodeSystem/v3-RoleCode" - }, - { - "type": "depends-on", - "display": "Value set Emergency Department Visit", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.292" - }, - { - "type": "depends-on", - "display": "Value set Encounter Inpatient", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.666.5.307" - }, - { - "type": "depends-on", - "display": "Value set Observation Services", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.143" - }, - { - "type": "depends-on", - "display": "Value set Present on Admission or Clinically Undetermined", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1147.197" - }, - { - "type": "depends-on", - "display": "Value set Ethnicity", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837" - }, - { - "type": "depends-on", - "display": "Value set ONC Administrative Sex", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1" - }, - { - "type": "depends-on", - "display": "Value set Payer", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.3591" - }, - { - "type": "depends-on", - "display": "Value set Race", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.836" - }, - { - "type": "depends-on", - "display": "Library SDE", - "resource": "http://ecqi.healthit.gov/ecqms/Library/SupplementalDataElementsFHIR4|2.0.000" - }, - { - "type": "depends-on", - "display": "Library Global", - "resource": "http://ecqi.healthit.gov/ecqms/Library/MATGlobalCommonFunctionsFHIR4|6.1.000" - }, - { - "type": "depends-on", - "display": "Value set All Primary and Secondary Cancer", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.161" - }, - { - "type": "depends-on", - "display": "Value set Discharge To Acute Care Facility", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.87" - }, - { - "type": "depends-on", - "display": "Value set Hospice Care Referral or Admission", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1116.365" - }, - { - "type": "depends-on", - "display": "Value set Palliative or Hospice Care", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.600.1.1579" - }, - { - "type": "depends-on", - "display": "Value set Patient Expired", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.309" - }, - { - "type": "depends-on", - "display": "Value set Schedule II & III Opioid Medications", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.165" - }, - { - "type": "depends-on", - "display": "Value set Schedule IV Benzodiazepines", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1125.1" - } - ] -} \ No newline at end of file diff --git a/data-requirements/parse-dr.ts b/data-requirements/parse-dr.ts deleted file mode 100644 index 9553b41d..00000000 --- a/data-requirements/parse-dr.ts +++ /dev/null @@ -1,102 +0,0 @@ -import { DataRequirement } from 'fhir/r4'; -import fs from 'fs'; -import * as _ from 'lodash'; - -type DataRequirementType = { - 'Data Type': string; - 'Template Id': string; - 'Data Type Value Set'?: string; - 'Data Type Value OID': string; - Attribute: string; -}; - -let sortedFqmEData: Record = {}; - -// Get Data Requirements from fqm-execution output -const fqmEDRLib = JSON.parse( - fs.readFileSync('./fqm-e-input/ColorectalCancerScreeningsDR.json', 'utf8') -) as fhir4.Library; - -// Group data requirements by type in Record -let fqmEData: Record = {}; -fqmEDRLib.dataRequirement?.forEach(dr => { - if (fqmEData[dr.type]) { - fqmEData[dr.type].push(dr); - } else { - fqmEData[dr.type] = [dr]; - } -}); - -// Sort the data requirements by type alphabetically -Object.keys(fqmEData) - .sort() - .forEach(key => { - sortedFqmEData[key] = fqmEData[key]; - }); - -// Print the fqm-execution results to the console -console.log('------FQM-EXECUTION------'); - -_.forEach(sortedFqmEData, function (value, key) { - console.log(key, value.length); -}); - -// Get Data Requirements from the elm-parser output of fhir_all.csv -const elmParserDR = JSON.parse( - fs.readFileSync('./elm-parser-json/all/ColorectalCancerScreeningsFHIR.json', 'utf8') -) as DataRequirementType[]; - -// Group data requirements by type in Record -let elmParserData: Record = {}; -elmParserDR.forEach(dr => { - if (elmParserData[dr['Data Type']]) { - elmParserData[dr['Data Type']].push(dr); - } else { - elmParserData[dr['Data Type']] = [dr]; - } -}); - -// Sort the data requirements by type alphabetically -let sortedData: Record = {}; -Object.keys(elmParserData) - .sort() - .forEach(key => { - sortedData[key] = elmParserData[key]; - }); - -// Print the elm-parser results to the console -console.log('------ELM-PARSER-FHIR-ALL------'); - -_.forEach(sortedData, function (value, key) { - console.log(key, value.length); -}); - -// Get Data Requirements from th elm-parser by_measure output -const elmParserByMeasureDR = JSON.parse( - fs.readFileSync('./elm-parser-json/by_measure/ColorectalCancerScreeningsFHIR.json', 'utf8') -) as DataRequirementType[]; - -// Group data requirements by type in Record -let elmParserByMeasureData: Record = {}; -elmParserByMeasureDR.forEach(dr => { - if (elmParserByMeasureData[dr['Data Type']]) { - elmParserByMeasureData[dr['Data Type']].push(dr); - } else { - elmParserByMeasureData[dr['Data Type']] = [dr]; - } -}); - -// Sort the data requirements by type alphabetically -let sortedByMeasureData: Record = {}; -Object.keys(elmParserByMeasureData) - .sort() - .forEach(key => { - sortedByMeasureData[key] = elmParserByMeasureData[key]; - }); - -// Print the elm-parser results to the console -console.log('------ELM-PARSER-BY-MEASURE------'); - -_.forEach(sortedByMeasureData, function (value, key) { - console.log(key, value.length); -}); diff --git a/data-requirements/parse-fhir-all.ts b/data-requirements/parse-fhir-all.ts deleted file mode 100644 index 04b42372..00000000 --- a/data-requirements/parse-fhir-all.ts +++ /dev/null @@ -1,76 +0,0 @@ -import fs from 'fs'; -import Papa from 'papaparse'; -import * as csv from 'fast-csv'; - -// create directory for by_measure outputs if it doesn't exist -if (!fs.existsSync('./elm-parser-input/by_measure_all')) { - fs.mkdirSync('./elm-parser-input/by_measure_all'); -} - -if (!fs.existsSync('./elm-parser-json')) { - fs.mkdirSync('./elm-parser-json'); -} - -if (!fs.existsSync('./elm-parser-json/all')) { - fs.mkdirSync('./elm-parser-json/all'); -} - -if (!fs.existsSync('./elm-parser-json/by_measure')) { - fs.mkdirSync('./elm-parser-json/by_measure'); -} - -// Go through fhir_all.csv and split measures into their own csv files in the by_measure directory -const fhirAllFile = fs.createReadStream('./elm-parser-input/fhir_all.csv'); -Papa.parse(fhirAllFile, { - header: true, - delimiter: '|', - complete: (results: any) => { - const groups: Record = {}; - results.data.forEach((row: any) => { - const attribute = row['Measure']; - if (!groups[attribute]) { - groups[attribute] = []; - } - groups[attribute].push(row); - }); - for (const attribute in groups) { - const ws = fs.createWriteStream(`./elm-parser-input/by_measure_all/${attribute}.csv`); - csv.write(groups[attribute], { headers: true }).pipe(ws); - } - } -}); - -// Go through each of the csv files in elm_parser_input/by_measure_all and convert them to JSON -fs.readdirSync('./elm-parser-input/by_measure_all').forEach(file => { - const fileStream = fs.createReadStream(`./elm-parser-input/by_measure_all/${file}`); - Papa.parse(fileStream, { - header: true, - delimiter: ',', - complete: (results: any) => { - const fileName = file.split('.')[0]; - fs.writeFileSync(`./elm-parser-json/all/${fileName}.json`, JSON.stringify(results.data, null, 2), 'utf8'); - } - }); -}); - -// Go through each of the csv files in elm_parser_input/by_measure and convert them to JSON -fs.readdirSync('elm-parser-input/by_measure').forEach(file => { - const fileStream = fs.createReadStream(`elm-parser-input/by_measure/${file}`); - Papa.parse(fileStream, { - header: false, - delimiter: '|', - complete: (results: any) => { - let jsonResults: any[] = []; - results.data.forEach((row: any) => { - jsonResults.push({ - 'Data Type': row[0], - 'Template Id': row[1], - 'Data Type Value OID': row[2], - Attribute: row[3] - }); - }); - const fileName = file.split('.')[0]; - fs.writeFileSync(`./elm-parser-json/by_measure/${fileName}.json`, JSON.stringify(jsonResults, null, 2), 'utf8'); - } - }); -}); diff --git a/data-requirements/summary-compare.sh b/data-requirements/summary-compare.sh new file mode 100755 index 00000000..94168da8 --- /dev/null +++ b/data-requirements/summary-compare.sh @@ -0,0 +1,59 @@ +#!/bin/bash + +RED='\033[0;31m' +GREEN='\033[0;32m' +NC='\033[0m' + +MUST_SUPPORT=false + +function usage() { + cat <] + + Options: + -m/--measure: Name of the CMS measure to compare data requirements results (default: all) +USAGE + exit 1 +} + +while test $# != 0 +do + case "$1" in + -m | --measure) + shift + MEASURE=$1 + ;; + *) usage ;; + esac + shift +done + + +echo "Gathering data-requirements output from the fhir_review branch of elm-parser-for-ecqms" + +# Clone the elm-parser-for-ecqms in the data-requirements directory if it hasn't been, swtich to the fhir_review branch, +# run parse_elm.rb with --bundle qicore to get data-requirements for measure bundles from the January 2024 Connectathon +if [ ! -d "elm-parser-for-ecqms" ]; then + git clone https://github.com/projecttacoma/elm-parser-for-ecqms.git + git fetch --all + cd elm-parser-for-ecqms + git checkout "fhir_review" + ruby parse_elm.rb --bundle fhir + cd .. + if [-d "elm-parser-dr"]; then + rm -rf elm-parser-dr + fi + mkdir elm-parser-dr + SOURCE_DIR="elm-parser-for-ecqms/data_requirements/library" + TARGET_DIR="elm-parser-dr" + + # Move all files from source to target directory + mv "$SOURCE_DIR"/* "$TARGET_DIR" +fi + +echo "Gathering data-requirements output from fqm-execution using the measure bundles from the January 2024 Connectathon" + +npx ts-node fqm-e-dr.ts + +npx ts-node summary-compare.ts $MEASURE \ No newline at end of file diff --git a/data-requirements/summary-compare.ts b/data-requirements/summary-compare.ts new file mode 100644 index 00000000..a4653377 --- /dev/null +++ b/data-requirements/summary-compare.ts @@ -0,0 +1,207 @@ +import fs from 'fs'; +import _ from 'lodash'; +import path from 'path'; + +const ELM_PARSER_DR_BASE_PATH = path.join(__dirname, './elm-parser-dr'); +const FQM_E_DR_BASE_PATH = path.join(__dirname, './fqm-e-dr'); + +const measure = process.argv[2] ?? 'all'; + +const RESET = '\x1b[0m'; +const FG_YELLOW = '\x1b[33m'; +const FG_GREEN = '\x1b[32m'; +const FG_RED = '\x1b[31m'; + +export type DRFilePath = { + shortName: string; + fullPath: string; +}; + +async function main() { + let files: DRFilePath[] = []; + + // if no measure is specified, go through all the data requirements output for all of the measures + if (measure === 'all') { + // get all of the data-requirements output files from elm-parser-dr + files = fs.readdirSync(ELM_PARSER_DR_BASE_PATH).map(f => ({ + shortName: f.split('.xml')[0], + fullPath: path.join(ELM_PARSER_DR_BASE_PATH, f) + })); + } else { + const file = fs.existsSync(path.join(ELM_PARSER_DR_BASE_PATH, `${measure}.xml.json`)); + if (file) { + files = [{ shortName: measure, fullPath: path.join(ELM_PARSER_DR_BASE_PATH, `${measure}.xml.json`) }]; + } else { + console.log(`No data-requirements output found for measure ${measure}`); + } + } + + for (const elmParserDRFile of files) { + const measureName = elmParserDRFile.shortName; + const fqmEDRFilePath = path.join(FQM_E_DR_BASE_PATH, `${measureName}-dr.json`); + + // Skip measures that do not have a corresponding data-requirements output in fqm-e-dr + if (!fs.existsSync(fqmEDRFilePath)) continue; + + console.log(`\n-----Data Requirements Comparison for ${measureName}-----`); + + const fqmEDRLib = JSON.parse(fs.readFileSync(fqmEDRFilePath, 'utf8')) as fhir4.Library; + const elmParserDRLib = JSON.parse(fs.readFileSync(elmParserDRFile.fullPath, 'utf8')) as fhir4.Library; + + if (!fqmEDRLib.resourceType) { + console.log( + `${FG_RED}%s${RESET}: An error occurred in calculating data-requirements in fqm-execution for ${measureName}`, + 'EXECUTION ERROR' + ); + continue; + } + + const fqmEDR = fqmEDRLib.dataRequirement as fhir4.DataRequirement[]; + const elmParserDR = elmParserDRLib.dataRequirement as fhir4.DataRequirement[]; + + let fqmEData: Record = {}; + fqmEDR.forEach(dr => { + if (fqmEData[dr.type]) { + fqmEData[dr.type].push(dr); + } else { + fqmEData[dr.type] = [dr]; + } + }); + + // Sort the data requirements by type alphabetically + let sortedFqmEData: Record = {}; + Object.keys(fqmEData) + .sort() + .forEach(key => { + sortedFqmEData[key] = fqmEData[key]; + }); + + // Group data requirements by type in Record + let elmParserData: Record = {}; + elmParserDR.forEach(dr => { + if (elmParserData[dr.type]) { + elmParserData[dr.type].push(dr); + } else { + elmParserData[dr.type] = [dr]; + } + }); + + // Sort the data requirements by type alphabetically + let sortedElmParserData: Record = {}; + Object.keys(elmParserData) + .sort() + .forEach(key => { + sortedElmParserData[key] = elmParserData[key]; + }); + + // get the data requirements types that the output do not have in common, if any + const keyDifferences = _.difference(Object.keys(sortedElmParserData), Object.keys(sortedFqmEData)); + + if (keyDifferences.length > 0) { + const missingElmParserKeys: string[] = []; + const missingFqmEKeys: string[] = []; + + keyDifferences.forEach(key => { + if (Object.keys(sortedElmParserData).includes(key)) { + missingFqmEKeys.push(key); + } else { + missingElmParserKeys.push(key); + } + }); + console.log(`${FG_RED}%s${RESET}: Missing DR Types`, 'DIFF'); + if (missingElmParserKeys.length > 0) { + console.log( + `elm-parser: missing data-requirements of the following type(s): ${missingElmParserKeys.toString()}` + ); + } + if (missingFqmEKeys.length > 0) { + console.log(`fqm-execution: missing data-requirements of the following type(s): ${missingFqmEKeys.toString()}`); + } + } else { + console.log(`${FG_GREEN}%s${RESET}: No Missing DR Types`, 'PASS'); + } + + console.log('\n'); + + // get the keys that both outputs have in common to go through + const keys = _.intersection(Object.keys(sortedElmParserData), Object.keys(sortedFqmEData)); + + for (const key of keys) { + const elmParserDRByKey = sortedElmParserData[key]; + const fqmEDRByKey = sortedFqmEData[key]; + + // get the data requirements from the elm-parser output that do not exist in the fqm-execution output + // i.e. is there a data requirement in the fqm-execution output of the same type that has a codeFilter entry with + // a valueSet that is the same + const missingDRs = elmParserDRByKey.filter(dr => + fqmEDRByKey.every(dr2 => dr.codeFilter?.every(cf => dr2.codeFilter?.every(cf2 => cf.valueSet !== cf2.valueSet))) + ); + + // get the data requirements from the fqm-execution output that do not exist in the elm-parser output + const missingELMDRs = fqmEDRByKey.filter(dr => + elmParserDRByKey.every(dr2 => + dr.codeFilter?.every(cf => dr2.codeFilter?.every(cf2 => cf.valueSet !== cf2.valueSet)) + ) + ); + + if (missingDRs.length === 0 && missingELMDRs.length === 0 && elmParserDRByKey.length === fqmEDRByKey.length) { + console.log(`${FG_GREEN}%s${RESET}: data requirements of type ${key} match`, `PASS (${key})`); + } else if (missingDRs.length > 0 || missingELMDRs.length > 0) { + console.log(`${FG_RED}%s${RESET}: `, `FAIL (${key})`); + if (missingDRs.length > 0) { + const missingvValueSets = missingDRs.map(dr => dr.codeFilter?.find(cf => cf.valueSet)?.valueSet); + console.log( + `fqm-execution is missing the data requirement of type ${key} for the following valuesets: ${JSON.stringify( + missingvValueSets + )}` + ); + } + if (missingELMDRs.length > 0) { + const missingELMValueSets = missingELMDRs.map(dr => dr.codeFilter?.find(cf => cf.valueSet)?.valueSet); + console.log( + `elm-parser-for-ecqms is missing the data requirement(s) of type ${key} for the following valueset(s): ${JSON.stringify( + missingELMValueSets + )}` + ); + } + } else { + console.log( + `${FG_RED}%s${RESET}: something else went wrong (fqm-execution: ${fqmEDRByKey.length}, elm-parser: ${elmParserDRByKey.length})`, + `FAIL (${key})` + ); + } + + console.log(`${FG_YELLOW}%s${RESET}`, 'MUST SUPPORTS'); + + // go through all of the data requirements from the elm-parser and if any of them have a codeFilter.valueSet that match a data requirement + // from fqm-execution, then see if the mustSupports match and if they don't, print them out + // TO DO: maybe make this a flag + elmParserDRByKey.forEach(dr => { + const elmParserMustSupports = dr.mustSupport; + const elmParserValueSet = dr.codeFilter?.find(cf => cf.valueSet)?.valueSet; + + if (elmParserValueSet) { + const fqmEMatchMustSupports = fqmEDRByKey.find(dr => + dr.codeFilter?.some(cf => cf.valueSet === elmParserValueSet) + )?.mustSupport; + + const equalMustSupports = _.isEqual(elmParserMustSupports, fqmEMatchMustSupports); + + if (!equalMustSupports) { + console.log(`${FG_RED}%s${RESET}:`, `MUST SUPPORTS FAIL (${key}-${elmParserValueSet})`); + console.log(`fqm-execution has the following mustSupports: ${fqmEMatchMustSupports ?? ''}`); + console.log(`elm-parser-for-ecqms has the following mustSupports: ${elmParserMustSupports}`); + } else { + console.log( + `${FG_GREEN}%s${RESET}: matching mustSupports`, + `MUST SUPPORTS PASS (${key}-${elmParserValueSet})` + ); + } + } + }); + console.log('\n'); + } + } +} + +main().then(() => console.log('done')); From 24d92bad689ae7f2217d76195d36849bb4758a90 Mon Sep 17 00:00:00 2001 From: Elsa Date: Wed, 6 Mar 2024 11:35:45 -0500 Subject: [PATCH 03/16] Removed file, add git files, remove unnecessary dependencies --- .gitignore | 4 + .gitkeep | 1 + ColorectalCancerScreeningsDR.json | 1774 -------------------------- data-requirements/summary-compare.ts | 8 +- package-lock.json | 182 --- package.json | 3 - 6 files changed, 9 insertions(+), 1963 deletions(-) create mode 100644 .gitkeep delete mode 100644 ColorectalCancerScreeningsDR.json diff --git a/.gitignore b/.gitignore index 77afa766..223af405 100644 --- a/.gitignore +++ b/.gitignore @@ -12,3 +12,7 @@ regression/output/*-* regression/connectathon regression/ecqm-content-r4-2021 regression/ecqm-content-qicore-2022 +data-requirements/elm-parser-for-ecqms +data-requirements/fqm-e-dr +data-requirements/elm-parser-dr +data-requirements/jan-2024-connectathon diff --git a/.gitkeep b/.gitkeep new file mode 100644 index 00000000..a119fbd5 --- /dev/null +++ b/.gitkeep @@ -0,0 +1 @@ +data-requirements/jan-2024-connectathon \ No newline at end of file diff --git a/ColorectalCancerScreeningsDR.json b/ColorectalCancerScreeningsDR.json deleted file mode 100644 index bdd0852e..00000000 --- a/ColorectalCancerScreeningsDR.json +++ /dev/null @@ -1,1774 +0,0 @@ -{ - 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}, - { - "type": "depends-on", - "display": "Value set Malignant Neoplasm of Colon", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1001" - }, - { - "type": "depends-on", - "display": "Value set Office Visit", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1001" - }, - { - "type": "depends-on", - "display": "Value set Online Assessments", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1089" - }, - { - "type": "depends-on", - "display": "Value set Preventive Care Services - Established Office Visit, 18 and Up", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1025" - }, - { - "type": "depends-on", - "display": "Value set Preventive Care Services-Initial Office Visit, 18 and Up", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1023" - }, - { - "type": "depends-on", - "display": "Value set Telephone Visits", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1080" - }, - { - "type": "depends-on", - "display": "Value set Total Colectomy", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1019" - }, - { - "type": "depends-on", - "display": "Value set Total Colectomy ICD9", - "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.11.1136" - } - ] -} \ No newline at end of file diff --git a/data-requirements/summary-compare.ts b/data-requirements/summary-compare.ts index a4653377..01082d73 100644 --- a/data-requirements/summary-compare.ts +++ b/data-requirements/summary-compare.ts @@ -59,7 +59,7 @@ async function main() { const fqmEDR = fqmEDRLib.dataRequirement as fhir4.DataRequirement[]; const elmParserDR = elmParserDRLib.dataRequirement as fhir4.DataRequirement[]; - let fqmEData: Record = {}; + const fqmEData: Record = {}; fqmEDR.forEach(dr => { if (fqmEData[dr.type]) { fqmEData[dr.type].push(dr); @@ -69,7 +69,7 @@ async function main() { }); // Sort the data requirements by type alphabetically - let sortedFqmEData: Record = {}; + const sortedFqmEData: Record = {}; Object.keys(fqmEData) .sort() .forEach(key => { @@ -77,7 +77,7 @@ async function main() { }); // Group data requirements by type in Record - let elmParserData: Record = {}; + const elmParserData: Record = {}; elmParserDR.forEach(dr => { if (elmParserData[dr.type]) { elmParserData[dr.type].push(dr); @@ -87,7 +87,7 @@ async function main() { }); // Sort the data requirements by type alphabetically - let sortedElmParserData: Record = {}; + const sortedElmParserData: Record = {}; Object.keys(elmParserData) .sort() .forEach(key => { diff --git a/package-lock.json b/package-lock.json index 4e446506..27800ceb 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,11 +14,9 @@ "commander": "^6.1.0", "cql-exec-fhir": "^2.1.3", "cql-execution": "^3.0.1", - "fast-csv": "^5.0.1", "handlebars": "^4.7.7", "lodash": "^4.17.21", "moment": "^2.29.4", - "papaparse": "^5.4.1", "uuid": "^8.3.1" }, "bin": { @@ -29,7 +27,6 @@ "@types/jest": "^26.0.5", "@types/lodash": "^4.14.170", "@types/node": "^14.0.23", - 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"lodash.uniq": { - "version": "4.5.0", - "resolved": "https://registry.npmjs.org/lodash.uniq/-/lodash.uniq-4.5.0.tgz", - "integrity": "sha512-xfBaXQd9ryd9dlSDvnvI0lvxfLJlYAZzXomUYzLKtUeOQvOP5piqAWuGtrhWeqaXK9hhoM/iyJc5AV+XfsX3HQ==" - }, "log-symbols": { "version": "5.1.0", "resolved": "https://registry.npmjs.org/log-symbols/-/log-symbols-5.1.0.tgz", @@ -11274,11 +11097,6 @@ "integrity": "sha512-R4nPAVTAU0B9D35/Gk3uJf/7XYbQcyohSKdvAxIRSNghFl4e71hVoGnBNQz9cWaXxO2I10KTC+3jMdvvoKw6dQ==", "dev": true }, - "papaparse": { - "version": "5.4.1", - "resolved": "https://registry.npmjs.org/papaparse/-/papaparse-5.4.1.tgz", - "integrity": "sha512-HipMsgJkZu8br23pW15uvo6sib6wne/4woLZPlFf3rpDyMe9ywEXUsuD7+6K9PRkJlVT51j/sCOYDKGGS3ZJrw==" - }, "parent-module": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz", diff --git a/package.json b/package.json index e51da80a..e16ffa61 100644 --- a/package.json +++ b/package.json @@ -16,11 +16,9 @@ "commander": "^6.1.0", "cql-exec-fhir": "^2.1.3", "cql-execution": "^3.0.1", - "fast-csv": "^5.0.1", "handlebars": "^4.7.7", "lodash": "^4.17.21", "moment": "^2.29.4", - "papaparse": "^5.4.1", "uuid": "^8.3.1" }, "devDependencies": { @@ -28,7 +26,6 @@ "@types/jest": "^26.0.5", "@types/lodash": "^4.14.170", "@types/node": "^14.0.23", - "@types/papaparse": "^5.3.14", "@types/uuid": "^8.3.0", "@typescript-eslint/eslint-plugin": "^5.45.0", "@typescript-eslint/parser": "^5.45.0", From 9fe41364f754e62f98da6aa357e8bb53be54c8ef Mon Sep 17 00:00:00 2001 From: Elsa Date: Wed, 6 Mar 2024 12:07:36 -0500 Subject: [PATCH 04/16] Remove changes that snuck in --- src/helpers/DataRequirementHelpers.ts | 1 - src/helpers/elm/RetrievesHelper.ts | 1 - src/types/Calculator.ts | 2 -- 3 files changed, 4 deletions(-) diff --git a/src/helpers/DataRequirementHelpers.ts b/src/helpers/DataRequirementHelpers.ts index 52ce4e52..01d2c7cc 100644 --- a/src/helpers/DataRequirementHelpers.ts +++ b/src/helpers/DataRequirementHelpers.ts @@ -58,7 +58,6 @@ export async function getDataRequirements( if (retrieve.queryLocalId && retrieve.queryLibraryName && parameters['Measurement Period']) { const library = elmJSONs.find(lib => lib.library.identifier.id === retrieve.queryLibraryName); if (library) { - // use something else here, perhaps parseDRInfo retrieve.queryInfo = await parseQueryInfo( library, elmJSONs, diff --git a/src/helpers/elm/RetrievesHelper.ts b/src/helpers/elm/RetrievesHelper.ts index 547d2872..2a3f0734 100644 --- a/src/helpers/elm/RetrievesHelper.ts +++ b/src/helpers/elm/RetrievesHelper.ts @@ -67,7 +67,6 @@ export function findRetrieves( expressionStack: ExpressionStackEntry[] = [], withErrors: GracefulError[] = [] ): { results: DataTypeQuery[]; withErrors: GracefulError[] } { - // add mustSupport to DataTypeQuery type // Smart defaults for recursive call to avoid passing in a bunch of values that don't usually change const defaultRecursiveOpts: RecursiveCallOptions = { elm, diff --git a/src/types/Calculator.ts b/src/types/Calculator.ts index 3612d524..f2456e83 100644 --- a/src/types/Calculator.ts +++ b/src/types/Calculator.ts @@ -293,8 +293,6 @@ export interface DataTypeQuery { queryInfo?: QueryInfo; /** specifies an optional template/profile for the objects that the retrieve returns to conform to */ templateId?: string; - /** mustSupport */ - mustSupport?: string[]; } export interface GapsDataTypeQuery extends DataTypeQuery { From 166e86a9f0891633e969d09e8a55127f83899c9f Mon Sep 17 00:00:00 2001 From: Elsa Date: Mon, 11 Mar 2024 10:36:12 -0400 Subject: [PATCH 05/16] Change --bundle fhir to --bundle qicore --- data-requirements/summary-compare.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data-requirements/summary-compare.sh b/data-requirements/summary-compare.sh index 94168da8..5f4db159 100755 --- a/data-requirements/summary-compare.sh +++ b/data-requirements/summary-compare.sh @@ -39,7 +39,7 @@ if [ ! -d "elm-parser-for-ecqms" ]; then git fetch --all cd elm-parser-for-ecqms git checkout "fhir_review" - ruby parse_elm.rb --bundle fhir + ruby parse_elm.rb --bundle qicore cd .. if [-d "elm-parser-dr"]; then rm -rf elm-parser-dr From 1c090438e6ca5f31792421f459e6a59cb64514b2 Mon Sep 17 00:00:00 2001 From: Elsa Date: Mon, 11 Mar 2024 10:40:50 -0400 Subject: [PATCH 06/16] Readme change --- data-requirements/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data-requirements/README.md b/data-requirements/README.md index 9a944318..9354eb21 100644 --- a/data-requirements/README.md +++ b/data-requirements/README.md @@ -4,7 +4,7 @@ This directory includes scripts for comparing the data-requirements output of [f ## Getting Data Requirements from the elm-parser-for-ecqms -The scripts in this directory will get the data requirements output from the elm-parser-for-ecqms fhir_review branch for the January 2024 Connectathon bundles. On the fhir_review branch of elm-parser-for-ecqms, data-requirements are calculated for the measures in [elm-parser-for-ecqms/measures/qicore/measures](https://github.com/projecttacoma/elm-parser-for-ecqms/tree/fhir_review/measures/qicore/measures) by running the command `ruby parse-elm.rb --bundle qicore`. The results are outputted to JSON files per measure to `elm-parser-for-ecqms/data_requirements/library`. This is all done by the script and the results are moved to the `elm-parser-dr` directory. +The scripts in this directory will get the data requirements output from the elm-parser-for-ecqms fhir_review branch for the January 2024 Connectathon bundles. On the fhir_review branch of elm-parser-for-ecqms, data-requirements are calculated for the measures in [elm-parser-for-ecqms/measures/qicore/measures](https://github.com/projecttacoma/elm-parser-for-ecqms/tree/fhir_review/measures/qicore/measures) by running the command `ruby parse_elm.rb --bundle qicore`. The results are outputted to JSON files per measure to `elm-parser-for-ecqms/data_requirements/library`. This is all done by the script and the results are moved to the `elm-parser-dr` directory. ## Getting Data Requirements from fqm-execution From f236bbb56b61e939e2f26d6cf2d53932d272375a Mon Sep 17 00:00:00 2001 From: Elsa Date: Mon, 11 Mar 2024 11:53:17 -0400 Subject: [PATCH 07/16] gitignore changes --- .gitignore | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 223af405..d20f08f9 100644 --- a/.gitignore +++ b/.gitignore @@ -12,7 +12,7 @@ regression/output/*-* regression/connectathon regression/ecqm-content-r4-2021 regression/ecqm-content-qicore-2022 -data-requirements/elm-parser-for-ecqms +data-requirements/elm-parser-for-ecqms/* data-requirements/fqm-e-dr -data-requirements/elm-parser-dr +data-requirements/elm-parser-dr/* data-requirements/jan-2024-connectathon From 59d5bf319bc7c147667a48f5d73ec05621d84ed7 Mon Sep 17 00:00:00 2001 From: Elsa Date: Mon, 11 Mar 2024 12:08:03 -0400 Subject: [PATCH 08/16] gitignore changes and more gitkeeps --- .gitignore | 5 ++--- .gitkeep | 1 - data-requirements/elm-parser-for-ecqms | 1 - 3 files changed, 2 insertions(+), 5 deletions(-) delete mode 100644 .gitkeep delete mode 160000 data-requirements/elm-parser-for-ecqms diff --git a/.gitignore b/.gitignore index d20f08f9..f230e9fc 100644 --- a/.gitignore +++ b/.gitignore @@ -12,7 +12,6 @@ regression/output/*-* regression/connectathon regression/ecqm-content-r4-2021 regression/ecqm-content-qicore-2022 -data-requirements/elm-parser-for-ecqms/* -data-requirements/fqm-e-dr +data-requirements/fqm-e-dr/* +data-requirements/jan-2024-connectathon/* data-requirements/elm-parser-dr/* -data-requirements/jan-2024-connectathon diff --git a/.gitkeep b/.gitkeep deleted file mode 100644 index a119fbd5..00000000 --- a/.gitkeep +++ /dev/null @@ -1 +0,0 @@ -data-requirements/jan-2024-connectathon \ No newline at end of file diff --git a/data-requirements/elm-parser-for-ecqms b/data-requirements/elm-parser-for-ecqms deleted file mode 160000 index 06beaecd..00000000 --- a/data-requirements/elm-parser-for-ecqms +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 06beaecd1339edbbee0ffe5a7b16531d8fe7d6af From ff7cfc09f002031e06d1980e8db5d3ce7b54c67d Mon Sep 17 00:00:00 2001 From: Elsa Date: Mon, 11 Mar 2024 12:14:41 -0400 Subject: [PATCH 09/16] Add .gitkeeps to directories --- data-requirements/elm-parser-dr/.gitkeep | 0 data-requirements/fqm-e-dr/.gitkeep | 0 data-requirements/jan-2024-connectathon/.gitkeep | 0 3 files changed, 0 insertions(+), 0 deletions(-) create mode 100644 data-requirements/elm-parser-dr/.gitkeep create mode 100644 data-requirements/fqm-e-dr/.gitkeep create mode 100644 data-requirements/jan-2024-connectathon/.gitkeep diff --git a/data-requirements/elm-parser-dr/.gitkeep b/data-requirements/elm-parser-dr/.gitkeep new file mode 100644 index 00000000..e69de29b diff --git a/data-requirements/fqm-e-dr/.gitkeep b/data-requirements/fqm-e-dr/.gitkeep new file mode 100644 index 00000000..e69de29b diff --git a/data-requirements/jan-2024-connectathon/.gitkeep b/data-requirements/jan-2024-connectathon/.gitkeep new file mode 100644 index 00000000..e69de29b From b23430588e60e5d6c10a3dca471911b8e2e006af Mon Sep 17 00:00:00 2001 From: Elsa Date: Mon, 11 Mar 2024 12:55:21 -0400 Subject: [PATCH 10/16] Readme additions --- README.md | 63 +++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 43 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 02013183..b0c651d5 100644 --- a/README.md +++ b/README.md @@ -887,39 +887,41 @@ The order of these populations is determined by most inclusive to least inclusiv To disable this behavior, use the `disableHTMLOrdering` calculation option. ### Statement-level HTML -Optionally, `fqm-execution` can generate the stylized HTML markup for each individual statement. To access the statement-level HTML, specify the `buildStatementLevelHTML` in the `CalculationOptions` prior to measure calculation. From the `detailedResults` returned for a given patient, the `statementLevelHTML` will be available as an element on each `statementResult` whose relevance is *not* N/A. + +Optionally, `fqm-execution` can generate the stylized HTML markup for each individual statement. To access the statement-level HTML, specify the `buildStatementLevelHTML` in the `CalculationOptions` prior to measure calculation. From the `detailedResults` returned for a given patient, the `statementLevelHTML` will be available as an element on each `statementResult` whose relevance is _not_ N/A. ```typescript [ { - "patientId": "test-patient", - "detailedResults": [ + patientId: 'test-patient', + detailedResults: [ { - "groupId": "test-group", - "statementResults": [ + groupId: 'test-group', + statementResults: [ // no HTML returned since relevance is NA { - "libraryName": "MATGlobalCommonFunctionsFHIR4", - "statementName": "Patient", - "final": "NA", - "relevance": "NA", - "isFunction": false, - "pretty": "NA" + libraryName: 'MATGlobalCommonFunctionsFHIR4', + statementName: 'Patient', + final: 'NA', + relevance: 'NA', + isFunction: false, + pretty: 'NA' }, { - "libraryName": "CancerScreening", - "statementName": "SDE Sex", - "final": "TRUE", - "relevance": "TRUE", - "isFunction": false, - "pretty": "CODE: http://hl7.org/fhir/v3/AdministrativeGender F, Female", - "statementLevelHTML": "
\n...\n
" - }, + libraryName: 'CancerScreening', + statementName: 'SDE Sex', + final: 'TRUE', + relevance: 'TRUE', + isFunction: false, + pretty: 'CODE: http://hl7.org/fhir/v3/AdministrativeGender F, Female', + statementLevelHTML: + '
\n...\n
' + } ] } ] } -] +]; ``` ## Group Clause Coverage Highlighting @@ -1214,6 +1216,27 @@ const evaluateMeasure = async (args, { req }) => { }; ``` +## Special Testing + +### Regression Testing + +The `./regression` directory is organized for internal calculation testing between branches of `fqm-execution`. The idea is that if changes are made to calculation on a local branch, running regression will compare the calculation output of measures in the following three repositories (`connectathon`, `ecqm-content-qi-2022`, `ecqm-content-r4-2021`) from the local branch to the calculation output of those measures from the master branch (or another user-specified branch). The `./run-regression.sh` script takes the following options: + +``` +-b, --base-branch Base branch to compare results with (default: master) +-v, --verbose Use verbose regression. Will print out diffs of failing JSON files with spacing (default: false) +``` + +To run the regression testing script, in the `./regression` directory run: + +```bash +./run-regression +``` + +### Data Requirements Testing + +The `./data-requirements` directory is organized for internal data-requirements calculation testing between `fqm-execution` and the `fhir_review` branch of [elm-parser-for-ecqms](https://github.com/projecttacoma/elm-parser-for-ecqms/tree/fhir_review). See the [README](https://github.com/projecttacoma/fqm-execution/data-requirements/README.md) in this directory for more information. + # Contributing For suggestions or contributions, please use [GitHub Issues](https://github.com/projecttacoma/fqm-execution/issues) or open a [Pull Request](https://github.com/projecttacoma/fqm-execution/pulls). From 109afd82ebff28db7396d4f3eef70f0d51b83bd3 Mon Sep 17 00:00:00 2001 From: Elsa Date: Mon, 11 Mar 2024 13:13:21 -0400 Subject: [PATCH 11/16] Add npm install reminder to the data reqs readme --- data-requirements/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data-requirements/README.md b/data-requirements/README.md index 9354eb21..ee2b902d 100644 --- a/data-requirements/README.md +++ b/data-requirements/README.md @@ -18,7 +18,7 @@ Right now there are two ways to compare data-requirements. `compare.sh` takes a ## Running the Scripts -Before running any of the scripts, be sure to populate the `jan-2024-connectathon` directory with the corresponding measure bundles. +Before running any of the scripts, be sure to populate the `jan-2024-connectathon` directory with the corresponding measure bundles. Also confirm that additional dependencies required for these scripts are installed with `npm install`. To run `compare.sh`: From dfca89f04f4a05d53a97823bb77a7a0ea434deec Mon Sep 17 00:00:00 2001 From: Elsa Date: Mon, 11 Mar 2024 14:18:00 -0400 Subject: [PATCH 12/16] Fixed json parse and -d command errors --- data-requirements/compare.sh | 2 +- data-requirements/fqm-e-dr.ts | 11 +++++++---- data-requirements/summary-compare.sh | 4 ++-- 3 files changed, 10 insertions(+), 7 deletions(-) diff --git a/data-requirements/compare.sh b/data-requirements/compare.sh index e707e017..3b18efb9 100755 --- a/data-requirements/compare.sh +++ b/data-requirements/compare.sh @@ -36,7 +36,7 @@ if [ ! -d "elm-parser-for-ecqms" ]; then git checkout "fhir_review" ruby parse_elm.rb --bundle qicore cd .. - if [-d "elm-parser-dr"]; then + if [ -d "elm-parser-dr" ]; then rm -rf elm-parser-dr fi mkdir elm-parser-dr diff --git a/data-requirements/fqm-e-dr.ts b/data-requirements/fqm-e-dr.ts index dd65d579..e7daf328 100644 --- a/data-requirements/fqm-e-dr.ts +++ b/data-requirements/fqm-e-dr.ts @@ -23,10 +23,13 @@ async function main() { fs.mkdirSync('./fqm-e-dr'); // get all of the file names (short and fullPath) from the jan-2024-connectathon directory - const allBundles = fs.readdirSync(JAN_2024_CONNECTATHON_BASE_PATH).map(f => ({ - shortName: f.split('v')[0], - fullPath: path.join(JAN_2024_CONNECTATHON_BASE_PATH, f) - })); + const allBundles = fs + .readdirSync(JAN_2024_CONNECTATHON_BASE_PATH) + .filter(f => f !== '.gitkeep') + .map(f => ({ + shortName: f.split('v')[0], + fullPath: path.join(JAN_2024_CONNECTATHON_BASE_PATH, f) + })); for (const bundle of allBundles) { const measureBundle = JSON.parse(fs.readFileSync(bundle.fullPath, 'utf8')) as fhir4.Bundle; diff --git a/data-requirements/summary-compare.sh b/data-requirements/summary-compare.sh index 5f4db159..a101e45e 100755 --- a/data-requirements/summary-compare.sh +++ b/data-requirements/summary-compare.sh @@ -34,14 +34,14 @@ echo "Gathering data-requirements output from the fhir_review branch of elm-pars # Clone the elm-parser-for-ecqms in the data-requirements directory if it hasn't been, swtich to the fhir_review branch, # run parse_elm.rb with --bundle qicore to get data-requirements for measure bundles from the January 2024 Connectathon -if [ ! -d "elm-parser-for-ecqms" ]; then +if [ ! -d "data-requirements/elm-parser-for-ecqms" ]; then git clone https://github.com/projecttacoma/elm-parser-for-ecqms.git git fetch --all cd elm-parser-for-ecqms git checkout "fhir_review" ruby parse_elm.rb --bundle qicore cd .. - if [-d "elm-parser-dr"]; then + if [ -d "elm-parser-dr" ]; then rm -rf elm-parser-dr fi mkdir elm-parser-dr From 0aee9ac18793d38e1180d7f56cd36230cfa1917a Mon Sep 17 00:00:00 2001 From: Elsa Date: Wed, 20 Mar 2024 12:59:29 -0400 Subject: [PATCH 13/16] Ignore .ds_store --- data-requirements/fqm-e-dr.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data-requirements/fqm-e-dr.ts b/data-requirements/fqm-e-dr.ts index e7daf328..2b2e0f1d 100644 --- a/data-requirements/fqm-e-dr.ts +++ b/data-requirements/fqm-e-dr.ts @@ -25,7 +25,7 @@ async function main() { // get all of the file names (short and fullPath) from the jan-2024-connectathon directory const allBundles = fs .readdirSync(JAN_2024_CONNECTATHON_BASE_PATH) - .filter(f => f !== '.gitkeep') + .filter(f => !f.startsWith('.')) .map(f => ({ shortName: f.split('v')[0], fullPath: path.join(JAN_2024_CONNECTATHON_BASE_PATH, f) From 738e5392725fa0655f235af29341f9bd5d8632d7 Mon Sep 17 00:00:00 2001 From: Elsa Date: Wed, 20 Mar 2024 16:56:09 -0400 Subject: [PATCH 14/16] Make sure summary-compare only runs the elm-parser if the directory is not there --- data-requirements/summary-compare.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data-requirements/summary-compare.sh b/data-requirements/summary-compare.sh index a101e45e..90158106 100755 --- a/data-requirements/summary-compare.sh +++ b/data-requirements/summary-compare.sh @@ -34,7 +34,7 @@ echo "Gathering data-requirements output from the fhir_review branch of elm-pars # Clone the elm-parser-for-ecqms in the data-requirements directory if it hasn't been, swtich to the fhir_review branch, # run parse_elm.rb with --bundle qicore to get data-requirements for measure bundles from the January 2024 Connectathon -if [ ! -d "data-requirements/elm-parser-for-ecqms" ]; then +if [ ! -d "elm-parser-for-ecqms" ]; then git clone https://github.com/projecttacoma/elm-parser-for-ecqms.git git fetch --all cd elm-parser-for-ecqms From 7b8bd32426a56728709e71734f7797ec0939bb41 Mon Sep 17 00:00:00 2001 From: Elsa Date: Wed, 20 Mar 2024 16:58:41 -0400 Subject: [PATCH 15/16] Add elm parser to gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index f230e9fc..0c9b2a5e 100644 --- a/.gitignore +++ b/.gitignore @@ -15,3 +15,4 @@ regression/ecqm-content-qicore-2022 data-requirements/fqm-e-dr/* data-requirements/jan-2024-connectathon/* data-requirements/elm-parser-dr/* +data-requirements/elm-parser-for-ecqms \ No newline at end of file From 5ea2981f7b170c1c101e0421de2c4fbcc0916ca4 Mon Sep 17 00:00:00 2001 From: Elsa Date: Thu, 21 Mar 2024 08:52:51 -0400 Subject: [PATCH 16/16] Make sure .gitkeep files do not get removed --- data-requirements/compare.sh | 2 +- data-requirements/fqm-e-dr.ts | 14 +++++++++----- data-requirements/summary-compare.sh | 2 +- 3 files changed, 11 insertions(+), 7 deletions(-) diff --git a/data-requirements/compare.sh b/data-requirements/compare.sh index 3b18efb9..08338f38 100755 --- a/data-requirements/compare.sh +++ b/data-requirements/compare.sh @@ -37,7 +37,7 @@ if [ ! -d "elm-parser-for-ecqms" ]; then ruby parse_elm.rb --bundle qicore cd .. if [ -d "elm-parser-dr" ]; then - rm -rf elm-parser-dr + rm -rf elm-parser-dr/*.json fi mkdir elm-parser-dr SOURCE_DIR="elm-parser-for-ecqms/data_requirements/library" diff --git a/data-requirements/fqm-e-dr.ts b/data-requirements/fqm-e-dr.ts index 2b2e0f1d..8510d188 100644 --- a/data-requirements/fqm-e-dr.ts +++ b/data-requirements/fqm-e-dr.ts @@ -1,4 +1,4 @@ -import fs from 'fs'; +import fs, { readdirSync } from 'fs'; import path from 'path'; import { Calculator } from '../src'; @@ -16,12 +16,16 @@ const JAN_2024_CONNECTATHON_BASE_PATH = path.join(__dirname, './jan-2024-connect async function main() { // if the fqm-e-dr directory already exists, remove it and its contents if (fs.existsSync('./fqm-e-dr')) { - fs.rmSync('./fqm-e-dr', { recursive: true }); + readdirSync('./fqm-e-dr').forEach(file => { + if (file.endsWith('.json')) { + fs.rmSync(`./fqm-e-dr/${file}`); + } + }); + } else { + // create new fqm-e-dr directory within the data-requirements directory + fs.mkdirSync('./fqm-e-dr'); } - // create new fqm-e-dr directory within the data-requirements directory - fs.mkdirSync('./fqm-e-dr'); - // get all of the file names (short and fullPath) from the jan-2024-connectathon directory const allBundles = fs .readdirSync(JAN_2024_CONNECTATHON_BASE_PATH) diff --git a/data-requirements/summary-compare.sh b/data-requirements/summary-compare.sh index 90158106..56d60462 100755 --- a/data-requirements/summary-compare.sh +++ b/data-requirements/summary-compare.sh @@ -42,7 +42,7 @@ if [ ! -d "elm-parser-for-ecqms" ]; then ruby parse_elm.rb --bundle qicore cd .. if [ -d "elm-parser-dr" ]; then - rm -rf elm-parser-dr + rm -rf elm-parser-dr/*.json fi mkdir elm-parser-dr SOURCE_DIR="elm-parser-for-ecqms/data_requirements/library"