From 9d362d0c535c2fbc9afc221df0391ea38c9bfea0 Mon Sep 17 00:00:00 2001 From: Dan Potter Date: Mon, 19 Dec 2022 15:03:47 -0500 Subject: [PATCH 1/2] Update to latest service library and update types --- package-lock.json | 3756 ++++++++++++++++----------------- package.json | 6 +- spec/mcode.spec.ts | 1120 +++++----- spec/trialscope.spec.ts | 56 +- src/mcode.ts | 43 +- src/profileSystemLogic.ts | 6 +- src/research-study-mapping.ts | 10 +- src/server.ts | 14 +- src/trialscope.ts | 18 +- 9 files changed, 2504 insertions(+), 2525 deletions(-) diff --git a/package-lock.json b/package-lock.json index 5f8a6e3..725a4ae 100644 --- a/package-lock.json +++ b/package-lock.json @@ -10,10 +10,9 @@ "license": "Apache-2.0", "dependencies": { "body-parser": "^1.19.0", - "clinical-trial-matching-service": "^0.0.3", + "clinical-trial-matching-service": "^0.0.7", "dotenv-flow": "^3.2.0", "express": "^4.17.1", - "fhirclient": "^2.3.11", "fhirpath": "^2.7.4", "node-fetch": "^2.6.1" }, @@ -21,8 +20,9 @@ "@istanbuljs/nyc-config-typescript": "^1.0.1", "@types/dotenv-flow": "^3.0.0", "@types/express": "^4.17.11", + "@types/fhir": "^0.0.35", "@types/jasmine": "^3.6.9", - 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"integrity": "sha1-lmRU6HZUYuN2RNNib2dCzotwll0=", + "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==", "requires": { "tr46": "~0.0.3", "webidl-conversions": "^3.0.0" @@ -8332,7 +8305,7 @@ "which-module": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/which-module/-/which-module-2.0.0.tgz", - "integrity": "sha1-2e8H3Od7mQK4o6j6SzHD4/fm6Ho=", + "integrity": "sha512-B+enWhmw6cjfVC7kS8Pj9pCrKSc5txArRyaYGe088shv/FGWH+0Rjx/xPgtsWfsUtS27FkP697E4DDhgrgoc0Q==", "dev": true }, "word-wrap": { @@ -8341,33 +8314,11 @@ "integrity": "sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ==", "dev": true }, - "wrap-ansi": { - "version": "6.2.0", - "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-6.2.0.tgz", - "integrity": "sha512-r6lPcBGxZXlIcymEu7InxDMhdW0KDxpLgoFLcguasxCaJ/SOIZwINatK9KY/tf+ZrlywOKU0UDj3ATXUBfxJXA==", - "dev": true, - "requires": { - "ansi-styles": "^4.0.0", - "string-width": "^4.1.0", - "strip-ansi": "^6.0.0" - } - }, "wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=" - }, - "write-file-atomic": { - "version": "3.0.3", - "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz", - "integrity": "sha512-AvHcyZ5JnSfq3ioSyjrBkH9yW4m7Ayk8/9My/DD9onKeu/94fwrMocemO2QAJFAlnnDN+ZDS+ZjAR5ua1/PV/Q==", - "dev": true, - "requires": { - "imurmurhash": "^0.1.4", - "is-typedarray": "^1.0.0", - "signal-exit": "^3.0.2", - "typedarray-to-buffer": "^3.1.5" - } + "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", + "dev": true }, "xml2js": { "version": "0.4.23", @@ -8376,17 +8327,19 @@ "requires": { "sax": ">=0.6.0", "xmlbuilder": "~11.0.0" + }, + "dependencies": { + "xmlbuilder": { + "version": "11.0.1", + "resolved": "https://registry.npmjs.org/xmlbuilder/-/xmlbuilder-11.0.1.tgz", + "integrity": "sha512-fDlsI/kFEx7gLvbecc0/ohLG50fugQp8ryHzMTuW9vSa1GJ0XYWKnhsUx7oie3G98+r56aTQIUB4kht42R3JvA==" + } } }, - 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"integrity": "sha1-x+sXyT4RLLEIb6bY5R+wZnt5pfk=", + "integrity": "sha512-p4a9I6X6nu6IhoGmBqAcbJy1mlC4j27vEPZX9F4L4/vZT3Lyq1VkFHw/V/PUcB9Buo+DG3iHkT0x3Qya58zc3g==", "requires": { "buffer-crc32": "~0.2.3", "fd-slicer": "~1.1.0" diff --git a/package.json b/package.json index 48c170f..d3983bb 100644 --- a/package.json +++ b/package.json @@ -23,10 +23,9 @@ "license": "Apache-2.0", "dependencies": { "body-parser": "^1.19.0", - "clinical-trial-matching-service": "^0.0.3", + "clinical-trial-matching-service": "^0.0.7", "dotenv-flow": "^3.2.0", "express": "^4.17.1", - "fhirclient": "^2.3.11", "fhirpath": "^2.7.4", "node-fetch": "^2.6.1" }, @@ -34,8 +33,9 @@ "@istanbuljs/nyc-config-typescript": "^1.0.1", "@types/dotenv-flow": "^3.0.0", "@types/express": "^4.17.11", + "@types/fhir": "^0.0.35", "@types/jasmine": "^3.6.9", - "@types/node": "^14.14.41", + "@types/node": "^18.11.17", "@types/supertest": "^2.0.11", "@typescript-eslint/eslint-plugin": "^4.22.0", "@typescript-eslint/parser": "^4.22.0", diff --git a/spec/mcode.spec.ts b/spec/mcode.spec.ts index 45cbc8c..51a40a1 100644 --- a/spec/mcode.spec.ts +++ b/spec/mcode.spec.ts @@ -1,14 +1,12 @@ -import * as mcode from '../src/mcode'; -import { Coding } from '../src/mcode'; -import { PrimaryCancerCondition } from '../src/mcode'; -import { SecondaryCancerCondition } from '../src/mcode'; - import fs from 'fs'; import path from 'path'; -import { fhir } from 'clinical-trial-matching-service'; +import { Bundle, Coding, Quantity } from 'fhir/r4'; + +import * as mcode from '../src/mcode'; +import { PrimaryCancerCondition, SecondaryCancerCondition } from '../src/mcode'; describe('ExtractedMCODE', () => { - let sampleData: fhir.Bundle; + let sampleData: Bundle; beforeAll(() => { return new Promise((resolve, reject) => { const patientDataPath = path.join(__dirname, '../../spec/data/patient_data.json'); @@ -19,7 +17,7 @@ describe('ExtractedMCODE', () => { return; } try { - sampleData = JSON.parse(data) as fhir.Bundle; + sampleData = JSON.parse(data) as Bundle; // The object we resolve to doesn't really matter resolve(sampleData); } catch (ex) { @@ -47,9 +45,9 @@ describe('ExtractedMCODE', () => { it('checkExtractedPrimaryCancerCondition', function () { const extractedData = new mcode.ExtractedMCODE(sampleData); - expect(extractedData.primaryCancerCondition[0].clinicalStatus[0].code).toBe('active'); - expect(extractedData.primaryCancerCondition[0].coding[0].code).toBe('254837009'); - expect(extractedData.primaryCancerCondition[0].histologyMorphologyBehavior[0].code).toBe('367651003'); + expect(extractedData.primaryCancerCondition[0].clinicalStatus?.[0].code).toBe('active'); + expect(extractedData.primaryCancerCondition[0].coding?.[0].code).toBe('254837009'); + expect(extractedData.primaryCancerCondition[0].histologyMorphologyBehavior?.[0].code).toBe('367651003'); }); it('checkExtractedTNMClinicalStageGroup', function () { @@ -66,9 +64,9 @@ describe('ExtractedMCODE', () => { it('checkExtractedSecondaryCancerCondition', function () { const extractedData = new mcode.ExtractedMCODE(sampleData); - expect(extractedData.secondaryCancerCondition[0].clinicalStatus[0].code).toBe('active'); - expect(extractedData.secondaryCancerCondition[0].coding[0].code).toBe('128462008'); - expect(extractedData.secondaryCancerCondition[0].bodySite[0].code).toBe('8935007'); + expect(extractedData.secondaryCancerCondition[0].clinicalStatus?.[0].code).toBe('active'); + expect(extractedData.secondaryCancerCondition[0].coding?.[0].code).toBe('128462008'); + expect(extractedData.secondaryCancerCondition[0].bodySite?.[0].code).toBe('8935007'); }); it('checkExtractedTumorMarker', function () { @@ -76,39 +74,39 @@ describe('ExtractedMCODE', () => { expect( extractedData.tumorMarker.some( (marker) => - marker.valueCodeableConcept[0].code == '10828004' && - marker.valueQuantity[0].value == 3 && - marker.valueRatio.length == 0 && - marker.code[0].code == '48676-1' && - marker.code[1].code == '85319-2' && - marker.interpretation[0].code == 'POS' + marker.valueCodeableConcept?.[0].code == '10828004' && + marker.valueQuantity?.[0].value == 3 && + marker.valueRatio?.length == 0 && + marker.code?.[0].code == '48676-1' && + marker.code?.[1].code == '85319-2' && + marker.interpretation?.[0].code == 'POS' ) ).toBeTrue(); expect( extractedData.tumorMarker.some( (marker) => - marker.valueCodeableConcept[0].code == '10828004' && - marker.valueQuantity.length == 0 && - marker.valueRatio[0].numerator.value == 1 && - marker.valueRatio[0].numerator.comparator == '>=' && - marker.valueRatio[0].denominator.value == 100 && - marker.code[0].code == '48676-1' && - marker.code[1].code == '85318-4' && - marker.interpretation.length == 0 + marker.valueCodeableConcept?.[0].code == '10828004' && + marker.valueQuantity?.length == 0 && + marker.valueRatio?.[0].numerator?.value == 1 && + marker.valueRatio?.[0].numerator.comparator == '>=' && + marker.valueRatio?.[0].denominator?.value == 100 && + marker.code?.[0].code == '48676-1' && + marker.code?.[1].code == '85318-4' && + marker.interpretation?.length == 0 ) ).toBeTrue(); expect( extractedData.tumorMarker.some( (marker) => - marker.valueCodeableConcept[0].code == '10828004' && - marker.valueQuantity.length > 0 && - marker.valueQuantity[0].value == 10 && - marker.valueQuantity[0].comparator == '>=' && - marker.valueQuantity[0].unit == '%' && - marker.valueRatio.length == 0 && - marker.code[0].code == '16112-5' && - marker.code[1].code == '85337-4' && - marker.interpretation.length == 0 + marker.valueCodeableConcept?.[0].code == '10828004' && + (marker.valueQuantity?.length ?? 0) > 0 && + marker.valueQuantity?.[0].value == 10 && + marker.valueQuantity?.[0].comparator == '>=' && + marker.valueQuantity?.[0].unit == '%' && + marker.valueRatio?.length == 0 && + marker.code?.[0].code == '16112-5' && + marker.code?.[1].code == '85337-4' && + marker.interpretation?.length == 0 ) ).toBeTrue(); }); @@ -117,15 +115,15 @@ describe('ExtractedMCODE', () => { const extractedData = new mcode.ExtractedMCODE(sampleData); expect( extractedData.cancerRelatedRadiationProcedure.some( - (procedure) => procedure.coding[0].code == '448385000' && procedure.bodySite.length == 0 + (procedure) => procedure.coding?.[0].code == '448385000' && procedure.bodySite?.length == 0 ) ).toBeTrue(); expect( extractedData.cancerRelatedRadiationProcedure.some( (procedure) => - procedure.coding[0].code == '448385000' && - procedure.bodySite.length != 0 && - procedure.bodySite[0].code == '12738006' + procedure.coding?.[0].code == '448385000' && + procedure.bodySite?.length != 0 && + procedure.bodySite?.[0].code == '12738006' ) ).toBeTrue(); }); @@ -138,46 +136,50 @@ describe('ExtractedMCODE', () => { it('checkExtractedCancerGeneticVariant', function () { const extractedData = new mcode.ExtractedMCODE(sampleData); - expect(extractedData.cancerGeneticVariant[0].code[0].system).toBe('http://loinc.org'); - expect(extractedData.cancerGeneticVariant[0].code[0].code).toBe('69548-6'); - expect(extractedData.cancerGeneticVariant[0].valueCodeableConcept[0].system).toBe('http://loinc.org'); - expect(extractedData.cancerGeneticVariant[0].valueCodeableConcept[0].code).toBe('LA9633-4'); - expect(extractedData.cancerGeneticVariant[0].interpretation[0].system).toBe( + expect(extractedData.cancerGeneticVariant[0].code?.[0].system).toBe('http://loinc.org'); + expect(extractedData.cancerGeneticVariant[0].code?.[0].code).toBe('69548-6'); + expect(extractedData.cancerGeneticVariant[0].valueCodeableConcept?.[0].system).toBe('http://loinc.org'); + expect(extractedData.cancerGeneticVariant[0].valueCodeableConcept?.[0].code).toBe('LA9633-4'); + expect(extractedData.cancerGeneticVariant[0].interpretation?.[0].system).toBe( 'http://hl7.org/fhir/ValueSet/observation-interpretation' ); - expect(extractedData.cancerGeneticVariant[0].interpretation[0].code).toBe('POS'); - expect(extractedData.cancerGeneticVariant[0].component.geneStudied[0].code.coding[0].system).toBe( + expect(extractedData.cancerGeneticVariant[0].interpretation?.[0].code).toBe('POS'); + expect(extractedData.cancerGeneticVariant[0].component?.geneStudied?.[0].code?.coding[0].system).toBe( 'http://loinc.org' ); - expect(extractedData.cancerGeneticVariant[0].component.geneStudied[0].code.coding[0].code).toBe('48018-6'); + expect(extractedData.cancerGeneticVariant[0].component?.geneStudied?.[0].code?.coding[0].code).toBe('48018-6'); expect( extractedData.normalizeCodeSystem( - extractedData.cancerGeneticVariant[0].component.geneStudied[0].valueCodeableConcept.coding[0].system + extractedData.cancerGeneticVariant[0].component?.geneStudied?.[0].valueCodeableConcept?.coding[0].system ?? '' ) ).toBe('HGNC'); - expect(extractedData.cancerGeneticVariant[0].component.geneStudied[0].valueCodeableConcept.coding[0].code).toBe( + expect(extractedData.cancerGeneticVariant[0].component?.geneStudied?.[0].valueCodeableConcept?.coding[0].code).toBe( 'HGNC:11389' ); - expect(extractedData.cancerGeneticVariant[0].component.geneStudied[0].interpretation.coding[0].system).toBe( + expect(extractedData.cancerGeneticVariant[0].component?.geneStudied?.[0].interpretation?.coding[0].system).toBe( 'http://hl7.org/fhir/ValueSet/observation-interpretation' ); - expect(extractedData.cancerGeneticVariant[0].component.geneStudied[0].interpretation.coding[0].code).toBe('CAR'); - expect(extractedData.cancerGeneticVariant[0].component.genomicsSourceClass[0].code.coding[0].system).toBe( + expect(extractedData.cancerGeneticVariant[0].component?.geneStudied?.[0].interpretation?.coding[0].code).toBe( + 'CAR' + ); + expect(extractedData.cancerGeneticVariant[0].component?.genomicsSourceClass?.[0].code?.coding[0].system).toBe( 'http://loinc.org' ); - expect(extractedData.cancerGeneticVariant[0].component.genomicsSourceClass[0].code.coding[0].code).toBe('48002-0'); + expect(extractedData.cancerGeneticVariant[0].component?.genomicsSourceClass?.[0].code?.coding[0].code).toBe( + '48002-0' + ); expect( - extractedData.cancerGeneticVariant[0].component.genomicsSourceClass[0].valueCodeableConcept.coding[0].system + extractedData.cancerGeneticVariant[0].component?.genomicsSourceClass?.[0].valueCodeableConcept?.coding[0].system ).toBe('http://loinc.org'); expect( - extractedData.cancerGeneticVariant[0].component.genomicsSourceClass[0].valueCodeableConcept.coding[0].code + extractedData.cancerGeneticVariant[0].component?.genomicsSourceClass?.[0].valueCodeableConcept?.coding[0].code ).toBe('LA6684-0'); - expect(extractedData.cancerGeneticVariant[0].component.genomicsSourceClass[0].interpretation.coding[0].system).toBe( - 'http://hl7.org/fhir/ValueSet/observation-interpretation' - ); - expect(extractedData.cancerGeneticVariant[0].component.genomicsSourceClass[0].interpretation.coding[0].code).toBe( - 'A' - ); + expect( + extractedData.cancerGeneticVariant[0].component?.genomicsSourceClass?.[0].interpretation?.coding[0].system + ).toBe('http://hl7.org/fhir/ValueSet/observation-interpretation'); + expect( + extractedData.cancerGeneticVariant[0].component?.genomicsSourceClass?.[0].interpretation?.coding[0].code + ).toBe('A'); }); it('checkExtractedCancerRelatedMedicationStatement', function () { @@ -193,14 +195,14 @@ describe('checkPrimaryCancerFilterLogic-BreastCancer', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Breast Cancer Filter Attributes - pcc.clinicalStatus.push({ system: 'N/A', code: 'N/A', display: 'N/A' } as Coding); - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); - pcc.histologyMorphologyBehavior.push({ system: 'N/A', code: 'N/A', display: 'N/A' } as Coding); + pcc.clinicalStatus.push({ system: 'N/A', code: 'N/A', display: 'N/A' }); + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); + pcc.histologyMorphologyBehavior.push({ system: 'N/A', code: 'N/A', display: 'N/A' }); extractedMCODE.primaryCancerCondition.push(pcc); @@ -214,17 +216,17 @@ describe('checkPrimaryCancerFilterLogic-ConcomitantInvasiveMalignancies', () => const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; - const tnmClinical: Coding[] = [] as Coding[]; - const tnmPathological: Coding[] = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; + const tnmClinical: Coding[] = []; + const tnmPathological: Coding[] = []; // Concomitant invasive malignancies Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '67097003', display: 'N/A' } as Coding); // Any code not in 'Cancer-Breast' - pcc.histologyMorphologyBehavior.push({ system: 'N/A', code: 'N/A', display: 'N/A' } as Coding); - pcc.clinicalStatus.push({ system: 'N/A', code: 'active', display: 'N/A' } as Coding); - tnmClinical.push({ system: 'AJCC', code: 'II', display: 'N/A' } as Coding); // Any code in 'Stage-2' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '67097003', display: 'N/A' }); // Any code not in 'Cancer-Breast' + pcc.histologyMorphologyBehavior.push({ system: 'N/A', code: 'N/A', display: 'N/A' }); + pcc.clinicalStatus.push({ system: 'N/A', code: 'active', display: 'N/A' }); + tnmClinical.push({ system: 'AJCC', code: 'II', display: 'N/A' }); // Any code in 'Stage-2' extractedMCODE.primaryCancerCondition.push(pcc); extractedMCODE.TNMClinicalStageGroup = tnmClinical; @@ -240,18 +242,18 @@ describe('checkPrimaryCancerFilterLogic-InvasiveBreastCancerandRecurrent', () => const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Invasive Breast Cancer and Recurrent Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Breast' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); // Any Code in 'Cancer-Breast' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '734075007', display: 'N/A' - } as Coding); // Any code in 'Morphology-Invasive' - pcc.clinicalStatus.push({ system: 'N/A', code: 'recurrence', display: 'N/A' } as Coding); + }); // Any code in 'Morphology-Invasive' + pcc.clinicalStatus.push({ system: 'N/A', code: 'recurrence', display: 'N/A' }); extractedMCODE.primaryCancerCondition.push(pcc); @@ -265,13 +267,13 @@ describe('checkPrimaryCancerFilterLogic-LocallyRecurrent', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Locally Recurrent Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); - pcc.clinicalStatus.push({ system: 'N/A', code: 'recurrence', display: 'N/A' } as Coding); + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); + pcc.clinicalStatus.push({ system: 'N/A', code: 'recurrence', display: 'N/A' }); extractedMCODE.primaryCancerCondition.push(pcc); @@ -285,13 +287,13 @@ describe('checkPrimaryCancerFilterLogic-OtherMalignancyExceptSkinOrCervical ', ( const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Other malignancy - except skin or cervical Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '67097003', display: 'N/A' } as Coding); // Any code not in 'Cancer-Breast' - pcc.clinicalStatus.push({ system: 'N/A', code: 'active', display: 'N/A' } as Coding); + pcc.coding.push({ system: 'http://snomed.info/sct', code: '67097003', display: 'N/A' }); // Any code not in 'Cancer-Breast' + pcc.clinicalStatus.push({ system: 'N/A', code: 'active', display: 'N/A' }); extractedMCODE.primaryCancerCondition.push(pcc); @@ -307,13 +309,13 @@ describe('checkSecondaryCancerFilterLogic-BrainMetastasis', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const scc: SecondaryCancerCondition = {}; - scc.clinicalStatus = [] as Coding[]; - scc.coding = [] as Coding[]; - scc.bodySite = [] as Coding[]; + scc.clinicalStatus = []; + scc.coding = []; + scc.bodySite = []; // Brain Metastasis Filter Attributes - scc.coding.push({ system: 'http://snomed.info/sct', code: '285641009', display: 'N/A' } as Coding); // Any code in 'Metastasis-Brain' - scc.clinicalStatus.push({ system: 'N/A', code: 'active', display: 'N/A' } as Coding); + scc.coding.push({ system: 'http://snomed.info/sct', code: '285641009', display: 'N/A' }); // Any code in 'Metastasis-Brain' + scc.clinicalStatus.push({ system: 'N/A', code: 'active', display: 'N/A' }); extractedMCODE.secondaryCancerCondition.push(scc); @@ -327,22 +329,22 @@ describe('checkSecondaryCancerFilterLogic-InvasiveBreastCancerAndMetastatic', () const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const scc: SecondaryCancerCondition = {}; - scc.clinicalStatus = [] as Coding[]; - scc.coding = [] as Coding[]; - scc.bodySite = [] as Coding[]; + scc.clinicalStatus = []; + scc.coding = []; + scc.bodySite = []; const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Invasive Breast Cancer and Metastatic Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Breast' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); // Any Code in 'Cancer-Breast' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '734075007', display: 'N/A' - } as Coding); // Any code in 'Morphology-Invasive' - scc.coding.push({ system: 'http://snomed.info/sct', code: '285641009', display: 'N/A' } as Coding); // Any code + }); // Any code in 'Morphology-Invasive' + scc.coding.push({ system: 'http://snomed.info/sct', code: '285641009', display: 'N/A' }); // Any code extractedMCODE.primaryCancerCondition.push(pcc); extractedMCODE.secondaryCancerCondition.push(scc); @@ -357,12 +359,12 @@ describe('checkSecondaryCancerFilterLogic-LeptomeningealMetastaticDisease', () = const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const scc: SecondaryCancerCondition = {}; - scc.clinicalStatus = [] as Coding[]; - scc.coding = [] as Coding[]; - scc.bodySite = [] as Coding[]; + scc.clinicalStatus = []; + scc.coding = []; + scc.bodySite = []; // Leptomeningeal metastatic disease Filter Attributes - scc.bodySite.push({ system: 'http://snomed.info/sct', code: '8935007', display: 'N/A' } as Coding); + scc.bodySite.push({ system: 'http://snomed.info/sct', code: '8935007', display: 'N/A' }); extractedMCODE.secondaryCancerCondition.push(scc); @@ -376,14 +378,14 @@ describe('checkSecondaryCancerFilterLogic-Metastatic', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const scc: SecondaryCancerCondition = {}; - scc.clinicalStatus = [] as Coding[]; - scc.coding = [] as Coding[]; - scc.bodySite = [] as Coding[]; - const tnmPathological: Coding[] = [] as Coding[]; + scc.clinicalStatus = []; + scc.coding = []; + scc.bodySite = []; + const tnmPathological: Coding[] = []; // Metastatic Filter Attributes - tnmPathological.push({ system: 'snomed', code: '313046007', display: 'N/A' } as Coding); // Any code in 'Stage-4' - scc.coding.push({ system: 'http://snomed.info/sct', code: '285641009', display: 'N/A' } as Coding); // Any code + tnmPathological.push({ system: 'snomed', code: '313046007', display: 'N/A' }); // Any code in 'Stage-4' + scc.coding.push({ system: 'http://snomed.info/sct', code: '285641009', display: 'N/A' }); // Any code extractedMCODE.secondaryCancerCondition.push(scc); extractedMCODE.TNMPathologicalStageGroup = tnmPathological; @@ -400,17 +402,17 @@ describe('checkHistologyMorphologyFilterLogic-InvasiveCarcinoma', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Invasive Carcinoma Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Breast' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); // Any Code in 'Cancer-Breast' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '734075007', display: 'N/A' - } as Coding); // Any code in 'Morphology-Invasive_Carcinoma' + }); // Any code in 'Morphology-Invasive_Carcinoma' extractedMCODE.primaryCancerCondition.push(pcc); @@ -424,17 +426,17 @@ describe('checkHistologyMorphologyFilterLogic-InvasiveBreastCancer', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Invasive Breast Cancer Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Breast' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); // Any Code in 'Cancer-Breast' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '446688004', display: 'N/A' - } as Coding); // Any code in 'Morphology-Invasive' + }); // Any code in 'Morphology-Invasive' extractedMCODE.primaryCancerCondition.push(pcc); @@ -450,17 +452,17 @@ describe('checkHistologyMorphologyFilterLogic-InvasiveMammoryCarcinoma-One', () const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Invasive Mammory Carcinoma Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Breast' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); // Any Code in 'Cancer-Breast' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '128701002', display: 'N/A' - } as Coding); // Any code in 'Morphology-Invas_Carc_Mix' + }); // Any code in 'Morphology-Invas_Carc_Mix' extractedMCODE.primaryCancerCondition.push(pcc); @@ -474,12 +476,12 @@ describe('checkHistologyMorphologyFilterLogic-InvasiveMammoryCarcinoma-Two', () const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; - extractedMCODE.TNMClinicalStageGroup = [] as Coding[]; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; + extractedMCODE.TNMClinicalStageGroup = []; // Invasive Mammory Carcinoma Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '444604002', display: 'N/A' } as Coding); // SNOMED#444604002 + pcc.coding.push({ system: 'http://snomed.info/sct', code: '444604002', display: 'N/A' }); // SNOMED#444604002 const tnmC = { system: 'http://snomed.info/sct', code: '444604002', display: 'N/A' }; // Any Code not in 'Stage-0' extractedMCODE.primaryCancerCondition.push(pcc); @@ -495,12 +497,12 @@ describe('checkHistologyMorphologyFilterLogic-InvasiveMammoryCarcinoma-Three', ( const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; - extractedMCODE.TNMPathologicalStageGroup = [] as Coding[]; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; + extractedMCODE.TNMPathologicalStageGroup = []; // Invasive Mammory Carcinoma Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '444604002', display: 'N/A' } as Coding); // SNOMED#444604002 + pcc.coding.push({ system: 'http://snomed.info/sct', code: '444604002', display: 'N/A' }); // SNOMED#444604002 const tnmP = { system: 'http://snomed.info/sct', code: '444604002', display: 'N/A' }; // Any Code not in 'Stage-0' extractedMCODE.primaryCancerCondition.push(pcc); @@ -516,17 +518,17 @@ describe('checkHistologyMorphologyFilterLogic-InvasiveDuctalCarcinoma', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Invasive Ductal Carcinoma Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Breast' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); // Any Code in 'Cancer-Breast' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '444134008', display: 'N/A' - } as Coding); // Any code in 'Morphology-Invas_Duct_Carc' + }); // Any code in 'Morphology-Invas_Duct_Carc' extractedMCODE.primaryCancerCondition.push(pcc); @@ -540,12 +542,12 @@ describe('checkHistologyMorphologyFilterLogic-InvasiveLobularCarcinoma', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Invasive Lobular Carcinoma Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '1080261000119100', display: 'N/A' } as Coding); // Any Code in 'Cancer-Invas Lob Carc' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '1080261000119100', display: 'N/A' }); // Any Code in 'Cancer-Invas Lob Carc' extractedMCODE.primaryCancerCondition.push(pcc); @@ -559,17 +561,17 @@ describe('checkHistologyMorphologyFilterLogic-DuctalCarcinomaInSitu', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Ductal Carcinoma In Situ Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Breast' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); // Any Code in 'Cancer-Breast' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '18680006', display: 'N/A' - } as Coding); // Any code in 'Morphology-Duct_Car_In_Situ' + }); // Any code in 'Morphology-Duct_Car_In_Situ' extractedMCODE.primaryCancerCondition.push(pcc); @@ -583,24 +585,24 @@ describe('checkHistologyMorphologyFilterLogic-Inflammatory', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; describe('checkHistologyMorphologyFilterLogic-NonInflammatoryInvasive', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Non-Inflammatory Invasive Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '254840009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Invasive-Breast' AND 'Cancer-Inflammatory' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '254840009', display: 'N/A' }); // Any Code in 'Cancer-Invasive-Breast' AND 'Cancer-Inflammatory' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '734075007', display: 'N/A' - } as Coding); // Any code in 'Morphology-Invasive' + }); // Any code in 'Morphology-Invasive' extractedMCODE.primaryCancerCondition.push(pcc); @@ -608,15 +610,15 @@ describe('checkHistologyMorphologyFilterLogic-Inflammatory', () => { expect(extractedMCODE.getHistologyMorphologyValue()).toBe('NON-INFLAMMATORY_INVASIVE'); }); }); - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.histologyMorphologyBehavior = []; // Inflammatory Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Breast' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '783541009', display: 'N/A' }); // Any Code in 'Cancer-Breast' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '32968003', display: 'N/A' - } as Coding); // Code: SNOMED 32968003' + }); // Code: SNOMED 32968003' extractedMCODE.primaryCancerCondition.push(pcc); @@ -630,17 +632,17 @@ describe('checkHistologyMorphologyFilterLogic-NonInflammatoryInvasive', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; // Non-Inflammatory Invasive Filter Attributes - pcc.coding.push({ system: 'http://snomed.info/sct', code: '254840009', display: 'N/A' } as Coding); // Any Code in 'Cancer-Invasive-Breast' AND 'Cancer-Inflammatory' + pcc.coding.push({ system: 'http://snomed.info/sct', code: '254840009', display: 'N/A' }); // Any Code in 'Cancer-Invasive-Breast' AND 'Cancer-Inflammatory' pcc.histologyMorphologyBehavior.push({ system: 'http://snomed.info/sct', code: '734075007', display: 'N/A' - } as Coding); // Any code in 'Morphology-Invasive' + }); // Any code in 'Morphology-Invasive' extractedMCODE.primaryCancerCondition.push(pcc); @@ -656,16 +658,16 @@ describe('checkStageFilterLogic-Invasive Breast Cancer and Locally Advanced', () const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const pcc: PrimaryCancerCondition = {}; - pcc.clinicalStatus = [] as Coding[]; - pcc.coding = [] as Coding[]; - pcc.histologyMorphologyBehavior = [] as Coding[]; - const tnmPathological: Coding[] = [] as Coding[]; + pcc.clinicalStatus = []; + pcc.coding = []; + pcc.histologyMorphologyBehavior = []; + const tnmPathological: Coding[] = []; // Invasive Breast Cancer and Locally Advanced Filter Attributes - pcc.clinicalStatus.push({ system: 'N/A', code: 'N/A', display: 'N/A' } as Coding); - pcc.coding.push({ system: 'http://snomed.info/sct', code: '722524005', display: 'N/A' } as Coding); // Any Code in 'Cancer-Invasive-Breast' - pcc.histologyMorphologyBehavior.push({ system: 'N/A', code: 'N/A', display: 'N/A' } as Coding); - tnmPathological.push({ system: 'snomed', code: '261640009', display: 'N/A' } as Coding); // Any code in 'Stage-3' + pcc.clinicalStatus.push({ system: 'N/A', code: 'N/A', display: 'N/A' }); + pcc.coding.push({ system: 'http://snomed.info/sct', code: '722524005', display: 'N/A' }); // Any Code in 'Cancer-Invasive-Breast' + pcc.histologyMorphologyBehavior.push({ system: 'N/A', code: 'N/A', display: 'N/A' }); + tnmPathological.push({ system: 'snomed', code: '261640009', display: 'N/A' }); // Any code in 'Stage-3' extractedMCODE.primaryCancerCondition.push(pcc); extractedMCODE.TNMPathologicalStageGroup = tnmPathological; @@ -682,10 +684,10 @@ describe('checkStageFilterLogic-Stage 0', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const tnmPathological: Coding[] = [] as Coding[]; + const tnmPathological: Coding[] = []; // Stage 0 Filter Attributes - tnmPathological.push({ system: 'snomed', code: '261645004', display: 'N/A' } as Coding); // Any code in 'Stage-0' + tnmPathological.push({ system: 'snomed', code: '261645004', display: 'N/A' }); // Any code in 'Stage-0' extractedMCODE.TNMPathologicalStageGroup = tnmPathological; @@ -701,10 +703,10 @@ describe('checkStageFilterLogic-Stage 1', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const tnmPathological: Coding[] = [] as Coding[]; + const tnmPathological: Coding[] = []; // Stage 1 Filter Attributes - tnmPathological.push({ system: 'snomed', code: '313112008', display: 'N/A' } as Coding); // Any code in 'Stage-1' + tnmPathological.push({ system: 'snomed', code: '313112008', display: 'N/A' }); // Any code in 'Stage-1' extractedMCODE.TNMPathologicalStageGroup = tnmPathological; @@ -720,10 +722,10 @@ describe('checkStageFilterLogic-Stage 2', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const tnmPathological: Coding[] = [] as Coding[]; + const tnmPathological: Coding[] = []; // Stage 2 Filter Attributes - tnmPathological.push({ system: 'snomed', code: 'Stage 2B (qualifier value)', display: 'N/A' } as Coding); // Any code in 'Stage-2 + tnmPathological.push({ system: 'snomed', code: 'Stage 2B (qualifier value)', display: 'N/A' }); // Any code in 'Stage-2 extractedMCODE.TNMPathologicalStageGroup = tnmPathological; @@ -739,10 +741,10 @@ describe('checkStageFilterLogic-Stage 3', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const tnmPathological: Coding[] = [] as Coding[]; + const tnmPathological: Coding[] = []; // Stage 3 Filter Attributes - tnmPathological.push({ system: 'snomed', code: '261640009', display: 'N/A' } as Coding); // Any code in 'Stage-3' + tnmPathological.push({ system: 'snomed', code: '261640009', display: 'N/A' }); // Any code in 'Stage-3' extractedMCODE.TNMPathologicalStageGroup = tnmPathological; @@ -758,10 +760,10 @@ describe('checkStageFilterLogic-Stage 4', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const tnmPathological: Coding[] = [] as Coding[]; + const tnmPathological: Coding[] = []; // Stage 4 Filter Attributes - tnmPathological.push({ system: 'snomed', code: '261643006', display: 'N/A' } as Coding); // Any code in 'Stage-4' + tnmPathological.push({ system: 'snomed', code: '261643006', display: 'N/A' }); // Any code in 'Stage-4' extractedMCODE.TNMPathologicalStageGroup = tnmPathological; @@ -780,11 +782,11 @@ describe('checkRadiationProcedureFilterLogic-SRS', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const crrp: mcode.CancerRelatedRadiationProcedure = {}; - crrp.bodySite = [] as Coding[]; - crrp.coding = [] as Coding[]; + crrp.bodySite = []; + crrp.coding = []; // SRS Filter Attributes - crrp.coding.push({ system: 'http://snomed.info/sct', code: '473237008', display: 'N/A' } as Coding); // Any code in 'Treatment-SRS-Brain' + crrp.coding.push({ system: 'http://snomed.info/sct', code: '473237008', display: 'N/A' }); // Any code in 'Treatment-SRS-Brain' extractedMCODE.cancerRelatedRadiationProcedure.push(crrp); @@ -798,12 +800,12 @@ describe('checkRadiationProcedureFilterLogic-WBRT', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const crrp: mcode.CancerRelatedRadiationProcedure = {}; - crrp.bodySite = [] as Coding[]; - crrp.coding = [] as Coding[]; + crrp.bodySite = []; + crrp.coding = []; // WBRT Filter Attributes - crrp.coding.push({ system: 'http://snomed.info/sct', code: '108290001', display: 'N/A' } as Coding); - crrp.bodySite.push({ system: 'http://snomed.info/sct', code: '12738006', display: 'N/A' } as Coding); + crrp.coding.push({ system: 'http://snomed.info/sct', code: '108290001', display: 'N/A' }); + crrp.bodySite.push({ system: 'http://snomed.info/sct', code: '12738006', display: 'N/A' }); extractedMCODE.cancerRelatedRadiationProcedure.push(crrp); @@ -817,11 +819,11 @@ describe('checkRadiationProcedureFilterLogic-Radiation Therapy', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const crrp: mcode.CancerRelatedRadiationProcedure = {}; - crrp.bodySite = [] as Coding[]; - crrp.coding = [] as Coding[]; + crrp.bodySite = []; + crrp.coding = []; // Radiation Therapy Filter Attributes - crrp.coding.push({ system: 'http://snomed.info/sct', code: '108290001', display: 'N/A' } as Coding); // Any code + crrp.coding.push({ system: 'http://snomed.info/sct', code: '108290001', display: 'N/A' }); // Any code extractedMCODE.cancerRelatedRadiationProcedure.push(crrp); @@ -836,10 +838,10 @@ describe('checkSurgicalProcedureFilterLogic-Resection', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const sp: Coding[] = [] as Coding[]; + const sp: Coding[] = []; // Resection Filter Attributes - sp.push({ system: 'http://snomed.info/sct', code: '446103006', display: 'N/A' } as Coding); // Any code in 'Treatment-Resection-Brain' + sp.push({ system: 'http://snomed.info/sct', code: '446103006', display: 'N/A' }); // Any code in 'Treatment-Resection-Brain' extractedMCODE.cancerRelatedSurgicalProcedure = sp; it('Test Resection Filter', () => { @@ -851,10 +853,10 @@ describe('checkSurgicalProcedureFilterLogic-Splenectomy', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const sp: Coding[] = [] as Coding[]; + const sp: Coding[] = []; // Splenectomy Filter Attributes - sp.push({ system: 'http://snomed.info/sct', code: '67097003', display: 'N/A' } as Coding); // Any code in 'Treatment-Splenectomy' + sp.push({ system: 'http://snomed.info/sct', code: '67097003', display: 'N/A' }); // Any code in 'Treatment-Splenectomy' extractedMCODE.cancerRelatedSurgicalProcedure = sp; it('Test Splenectomy Filter', () => { @@ -868,10 +870,10 @@ describe('checkSurgicalProcedureFilterLogic-BoneMarrowTransplant', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const sp: Coding[] = [] as Coding[]; + const sp: Coding[] = []; // Bone Marrow Transplant Filter Attributes - sp.push({ system: 'http://snomed.info/sct', code: '58390007', display: 'N/A' } as Coding); // One specific Code for Bone Marrow Transplant + sp.push({ system: 'http://snomed.info/sct', code: '58390007', display: 'N/A' }); // One specific Code for Bone Marrow Transplant extractedMCODE.cancerRelatedSurgicalProcedure = sp; it('Test Bone Marrow Transplant Filter', () => { @@ -883,10 +885,10 @@ describe('checkSurgicalProcedureFilterLogic-Splenectomy', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const sp: Coding[] = [] as Coding[]; + const sp: Coding[] = []; // Splenectomy Filter Attributes - sp.push({ system: 'http://snomed.info/sct', code: '782655004', display: 'N/A' } as Coding); // Any code in 'Treatment-Organ_Transplant' + sp.push({ system: 'http://snomed.info/sct', code: '782655004', display: 'N/A' }); // Any code in 'Treatment-Organ_Transplant' extractedMCODE.cancerRelatedSurgicalProcedure = sp; it('Test Splenectomy Filter', () => { @@ -900,10 +902,10 @@ describe('checkMedicationStatementFilterLogic-T-DM1', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // T-DM1 Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1371046', display: 'N/A' } as Coding); // Any code in 'Treatment-T-DM1' + ms.push({ system: 'http://rxnorm.info/sct', code: '1371046', display: 'N/A' }); // Any code in 'Treatment-T-DM1' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -919,10 +921,10 @@ describe('checkMedicationStatementFilterLogic-CDK4/6 inhibitor', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // CDK4/6 inhibitor Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1873984', display: 'N/A' } as Coding); // Any code in 'Treatment-CDK4_6_Inhibtor' + ms.push({ system: 'http://rxnorm.info/sct', code: '1873984', display: 'N/A' }); // Any code in 'Treatment-CDK4_6_Inhibtor' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -938,10 +940,10 @@ describe('checkMedicationStatementFilterLogic-Poly ICLC ', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // Poly ICLC Filter Attributes - ms.push({ system: 'NIH', code: '#C1198', display: 'N/A' } as Coding); + ms.push({ system: 'NIH', code: '#C1198', display: 'N/A' }); extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -957,11 +959,11 @@ describe('checkMedicationStatementFilterLogic-DrugCombo-1', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // DrugCombo-1 Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1371046', display: 'N/A' } as Coding); // Any code in 'Treatment-Trastuzamab' and 'Treatment-T-DM1' - ms.push({ system: 'http://rxnorm.info/sct', code: '1298949', display: 'N/A' } as Coding); // Any code in 'Treatment-Pertuzumab' + ms.push({ system: 'http://rxnorm.info/sct', code: '1371046', display: 'N/A' }); // Any code in 'Treatment-Trastuzamab' and 'Treatment-T-DM1' + ms.push({ system: 'http://rxnorm.info/sct', code: '1298949', display: 'N/A' }); // Any code in 'Treatment-Pertuzumab' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -977,10 +979,10 @@ describe('checkMedicationStatementFilterLogic-Pembrolizumab', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // Pembrolizumab Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1547545', display: 'N/A' } as Coding); // Any code in 'Treatment-Pembrolizumab' + ms.push({ system: 'http://rxnorm.info/sct', code: '1547545', display: 'N/A' }); // Any code in 'Treatment-Pembrolizumab' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -996,10 +998,10 @@ describe('checkMedicationStatementFilterLogic-mTOR inhibitor', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // mTOR inhibitor Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '845509', display: 'N/A' } as Coding); // Any code in 'Treatment-mTOR_Inhibtor' + ms.push({ system: 'http://rxnorm.info/sct', code: '845509', display: 'N/A' }); // Any code in 'Treatment-mTOR_Inhibtor' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1015,10 +1017,10 @@ describe('checkMedicationStatementFilterLogic-Concurrent Endocrine Therapy ', () // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // Concurrent Endocrine Therapy Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '262485', display: 'N/A' } as Coding); // Any code in 'Treatment-Endocrine_Therapy' + ms.push({ system: 'http://rxnorm.info/sct', code: '262485', display: 'N/A' }); // Any code in 'Treatment-Endocrine_Therapy' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1034,10 +1036,10 @@ describe('checkMedicationStatementFilterLogic-Anti-androgen', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // Anti-androgen Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '151495', display: 'N/A' } as Coding); // Any code in 'Treatment-anti-Androgen' + ms.push({ system: 'http://rxnorm.info/sct', code: '151495', display: 'N/A' }); // Any code in 'Treatment-anti-Androgen' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1053,10 +1055,10 @@ describe('checkMedicationStatementFilterLogic-anti-HER2', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // anti-HER2 Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '101306', display: 'N/A' } as Coding); // Any code in 'Treatment-anti-HER2' + ms.push({ system: 'http://rxnorm.info/sct', code: '101306', display: 'N/A' }); // Any code in 'Treatment-anti-HER2' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1072,10 +1074,10 @@ describe('checkMedicationStatementFilterLogic-Tyrosine Kinase Inhibitor', () => // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // Tyrosine Kinase Inhibitor Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1430449', display: 'N/A' } as Coding); // Any code in 'Treatment-Tyrosine_Kinase_Inhib' + ms.push({ system: 'http://rxnorm.info/sct', code: '1430449', display: 'N/A' }); // Any code in 'Treatment-Tyrosine_Kinase_Inhib' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1091,10 +1093,10 @@ describe('checkMedicationStatementFilterLogic-P13K inhibitor ', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // P13K inhibitor Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '2169302', display: 'N/A' } as Coding); // Any code in 'Treatment-P13K_Inhibitor' + ms.push({ system: 'http://rxnorm.info/sct', code: '2169302', display: 'N/A' }); // Any code in 'Treatment-P13K_Inhibitor' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1110,10 +1112,10 @@ describe('checkMedicationStatementFilterLogic-anti-PD', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // anti-PD Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1792780', display: 'N/A' } as Coding); // Any code in 'Treatment-anti-PD1,PDL1,PDL2' + ms.push({ system: 'http://rxnorm.info/sct', code: '1792780', display: 'N/A' }); // Any code in 'Treatment-anti-PD1,PDL1,PDL2' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1129,11 +1131,11 @@ describe('checkMedicationStatementFilterLogic-CDK4/6-mTOR and Endocrine', () => // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // CDK4/6-mTOR and Endocrine Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1873984', display: 'N/A' } as Coding); // Any code in 'Treatment-CDK4_6_Inhibtor' - ms.push({ system: 'http://rxnorm.info/sct', code: '262485', display: 'N/A' } as Coding); // Any code in 'Treatment-Endocrine_Therapy' + ms.push({ system: 'http://rxnorm.info/sct', code: '1873984', display: 'N/A' }); // Any code in 'Treatment-CDK4_6_Inhibtor' + ms.push({ system: 'http://rxnorm.info/sct', code: '262485', display: 'N/A' }); // Any code in 'Treatment-Endocrine_Therapy' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1151,10 +1153,10 @@ describe('checkMedicationStatementFilterLogic-antiPARP', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // anti PARP Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1918231', display: 'N/A' } as Coding); // Any code in 'Treatment-anti-PARP' + ms.push({ system: 'http://rxnorm.info/sct', code: '1918231', display: 'N/A' }); // Any code in 'Treatment-anti-PARP' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1170,10 +1172,10 @@ describe('checkMedicationStatementFilterLogic-SG', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // SG Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '2360231', display: 'N/A' } as Coding); // Any code in 'Treatment-SG' + ms.push({ system: 'http://rxnorm.info/sct', code: '2360231', display: 'N/A' }); // Any code in 'Treatment-SG' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1189,10 +1191,10 @@ describe('checkMedicationStatementFilterLogic-Treatment-anti-topoisomerase-1', ( // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // Treatment-anti-topoisomerase-1 Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1719773', display: 'N/A' } as Coding); // Any code in 'Treatment-anti-topoisomerase-1' + ms.push({ system: 'http://rxnorm.info/sct', code: '1719773', display: 'N/A' }); // Any code in 'Treatment-anti-topoisomerase-1' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1208,10 +1210,10 @@ describe('checkMedicationStatementFilterLogic-Treatment-Anti-CTLA4', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // Treatment-Anti-CTLA4 Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '1657013', display: 'N/A' } as Coding); // Any code in 'Treatment-anti-CTLA4' + ms.push({ system: 'http://rxnorm.info/sct', code: '1657013', display: 'N/A' }); // Any code in 'Treatment-anti-CTLA4' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1227,10 +1229,10 @@ describe('checkMedicationStatementFilterLogic-Treatment-Anti-CD40', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // Treatment-Anti-CD40 Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '226754', display: 'N/A' } as Coding); // Any code in 'Treatment-anti-CD40' + ms.push({ system: 'http://rxnorm.info/sct', code: '226754', display: 'N/A' }); // Any code in 'Treatment-anti-CD40' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1246,10 +1248,10 @@ describe('checkMedicationStatementFilterLogic-Treatment-Trastuz-And-Pertuz', () // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const ms: Coding[] = [] as Coding[]; + const ms: Coding[] = []; // Treatment-Trastuz-And-Pertuz Filter Attributes - ms.push({ system: 'http://rxnorm.info/sct', code: '2382609', display: 'N/A' } as Coding); // Any code in 'Treatment-Trastuz_and_Pertuz' + ms.push({ system: 'http://rxnorm.info/sct', code: '2382609', display: 'N/A' }); // Any code in 'Treatment-Trastuz_and_Pertuz' extractedMCODE.cancerRelatedMedicationStatement = ms; const medications: string[] = extractedMCODE.getMedicationStatementValues(); @@ -1268,15 +1270,15 @@ describe('checkTumorMarkerFilterLogic-HER2+', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm: mcode.TumorMarker = {}; - tm.code = [] as Coding[]; - tm.interpretation = [] as Coding[]; - tm.valueCodeableConcept = [] as Coding[]; - tm.valueQuantity = [] as mcode.Quantity[]; - tm.valueRatio = [] as mcode.Ratio[]; + tm.code = []; + tm.interpretation = []; + tm.valueCodeableConcept = []; + tm.valueQuantity = []; + tm.valueRatio = []; // HER2+ Filter Attributes - tm.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' - tm.valueQuantity.push({ value: '3+', comparator: '=' } as mcode.Quantity); + tm.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' + tm.valueQuantity.push({ value: 3, comparator: '>=' }); extractedMCODE.tumorMarker.push(tm); @@ -1290,24 +1292,24 @@ describe('checkTumorMarkerFilterLogic-HER2+ and ER+', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; // HER2+ Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' - tm1.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' } as Coding); + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' + tm1.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' }); // ER+ Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' } as Coding); // Any code in 'Biomarker-ER' - tm2.valueQuantity.push({ value: '11', comparator: '>=', unit: '%', code: '%' } as mcode.Quantity); + tm2.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' }); // Any code in 'Biomarker-ER' + tm2.valueQuantity.push({ value: 11, comparator: '>=', unit: '%', code: '%' }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1323,31 +1325,31 @@ describe('checkTumorMarkerFilterLogic-HER2+ and PR+', () => { const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); extractedMCODE.tumorMarker = [] as mcode.TumorMarker[]; const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; // HER2+ Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' tm1.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'POS', display: 'N/A' - } as Coding); + }); // PR+ Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' } as Coding); // Any code in 'Biomarker-PR' + tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' }); // Any code in 'Biomarker-PR' tm2.valueRatio.push({ - numerator: { value: '30', comparator: '>=', unit: '%', code: '%' } as mcode.Quantity, - denominator: { value: '2', comparator: '>=', unit: '%', code: '%' } as mcode.Quantity - } as mcode.Ratio); + numerator: { value: 30, comparator: '>=', unit: '%', code: '%' }, + denominator: { value: 2, comparator: '>=', unit: '%', code: '%' } + }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1362,28 +1364,28 @@ describe('checkTumorMarkerFilterLogic-ER+ and HER-', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; // HER2- Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' - tm1.valueQuantity.push({ value: '2+', comparator: '=' } as mcode.Quantity); + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' + tm1.valueQuantity.push({ value: 2, comparator: '>=' }); // ER+ Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' } as Coding); // Any code in 'Biomarker-ER' + tm2.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' }); // Any code in 'Biomarker-ER' tm2.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'DET', display: 'N/A' - } as Coding); + }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1398,32 +1400,32 @@ describe('checkTumorMarkerFilterLogic-PR+ and HER-', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; // HER2- Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' tm1.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'NEG', display: 'N/A' - } as Coding); + }); // PR+ Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' } as Coding); // Any code in 'Biomarker-PR' + tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' }); // Any code in 'Biomarker-PR' tm2.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'H', display: 'N/A' - } as Coding); + }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1438,37 +1440,37 @@ describe('checkTumorMarkerFilterLogic-ER+ and HER2- and FGFR amplifications', () const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; const tm3: mcode.TumorMarker = {}; - tm3.code = [] as Coding[]; - tm3.interpretation = [] as Coding[]; - tm3.valueCodeableConcept = [] as Coding[]; - tm3.valueQuantity = [] as mcode.Quantity[]; - tm3.valueRatio = [] as mcode.Ratio[]; + tm3.code = []; + tm3.interpretation = []; + tm3.valueCodeableConcept = []; + tm3.valueQuantity = []; + tm3.valueRatio = []; // HER2- Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' tm1.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'NEG', display: 'N/A' - } as Coding); + }); // ER+ Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' } as Coding); // Any code in 'Biomarker-ER' - tm2.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' } as Coding); + tm2.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' }); // Any code in 'Biomarker-ER' + tm2.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' }); // FGFR Amplifications Attributes - tm3.code.push({ system: 'http://loinc.info/sct', code: '42785-6', display: 'N/A' } as Coding); // Any code in 'Biomarker-FGFR' - tm3.valueQuantity.push({ value: '1', comparator: '>=', unit: '%', code: '%' } as mcode.Quantity); + tm3.code.push({ system: 'http://loinc.info/sct', code: '42785-6', display: 'N/A' }); // Any code in 'Biomarker-FGFR' + tm3.valueQuantity.push({ value: 1, comparator: '>=', unit: '%', code: '%' }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1484,37 +1486,37 @@ describe('checkTumorMarkerFilterLogic-PR+ and HER- and FGFR Amplifications', () const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; const tm3: mcode.TumorMarker = {}; - tm3.code = [] as Coding[]; - tm3.interpretation = [] as Coding[]; - tm3.valueCodeableConcept = [] as Coding[]; - tm3.valueQuantity = [] as mcode.Quantity[]; - tm3.valueRatio = [] as mcode.Ratio[]; + tm3.code = []; + tm3.interpretation = []; + tm3.valueCodeableConcept = []; + tm3.valueQuantity = []; + tm3.valueRatio = []; // HER2- Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' - tm1.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '260385009', display: 'N/A' } as Coding); + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' + tm1.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '260385009', display: 'N/A' }); // PR+ Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' } as Coding); // Any code in 'Biomarker-PR' - tm2.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' } as Coding); + tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' }); // Any code in 'Biomarker-PR' + tm2.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' }); // FGFR Amplifications Attributes - tm3.code.push({ system: 'http://loinc.info/sct', code: '42785-6', display: 'N/A' } as Coding); // Any code in 'Biomarker-FGFR' + tm3.code.push({ system: 'http://loinc.info/sct', code: '42785-6', display: 'N/A' }); // Any code in 'Biomarker-FGFR' tm3.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'POS', display: 'N/A' - } as mcode.Quantity); + }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1530,40 +1532,40 @@ describe('checkTumorMarkerFilterLogic-ER+ and PR+ and HER2-', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; const tm3: mcode.TumorMarker = {}; - tm3.code = [] as Coding[]; - tm3.interpretation = [] as Coding[]; - tm3.valueCodeableConcept = [] as Coding[]; - tm3.valueQuantity = [] as mcode.Quantity[]; - tm3.valueRatio = [] as mcode.Ratio[]; + tm3.code = []; + tm3.interpretation = []; + tm3.valueCodeableConcept = []; + tm3.valueQuantity = []; + tm3.valueRatio = []; // HER2- Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' - tm1.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '260385009', display: 'N/A' } as Coding); + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' + tm1.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '260385009', display: 'N/A' }); // PR+ Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' } as Coding); // Any code in 'Biomarker-PR' + tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' }); // Any code in 'Biomarker-PR' tm2.valueRatio.push({ - numerator: { value: '100', comparator: '>=', unit: '%', code: '%' } as mcode.Quantity, - denominator: { value: '3', comparator: '>=', unit: '%', code: '%' } as mcode.Quantity - } as mcode.Ratio); + numerator: { value: 100, comparator: '>=', unit: '%', code: '%' }, + denominator: { value: 3, comparator: '>=', unit: '%', code: '%' } + }); // ER+ Filter Attributes - tm3.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' } as Coding); // Any code in 'Biomarker-ER' + tm3.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' }); // Any code in 'Biomarker-ER' tm3.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'H', display: 'N/A' - } as Coding); + }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1579,40 +1581,40 @@ describe('checkTumorMarkerFilterLogic-Triple negative', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; const tm3: mcode.TumorMarker = {}; - tm3.code = [] as Coding[]; - tm3.interpretation = [] as Coding[]; - tm3.valueCodeableConcept = [] as Coding[]; - tm3.valueQuantity = [] as mcode.Quantity[]; - tm3.valueRatio = [] as mcode.Ratio[]; + tm3.code = []; + tm3.interpretation = []; + tm3.valueCodeableConcept = []; + tm3.valueQuantity = []; + tm3.valueRatio = []; // HER2- Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' - tm1.valueQuantity.push({ value: '2+', comparator: '=' } as mcode.Quantity); + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' + tm1.valueQuantity.push({ value: 2, comparator: '>=' }); // PR- Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' } as Coding); // Any code in 'Biomarker-PR' + tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' }); // Any code in 'Biomarker-PR' tm2.valueRatio.push({ - numerator: { value: '1', comparator: '<', unit: '%', code: '%' } as mcode.Quantity, - denominator: { value: '110', comparator: '<', unit: '%', code: '%' } as mcode.Quantity - } as mcode.Ratio); + numerator: { value: 1, comparator: '<', unit: '%', code: '%' }, + denominator: { value: 110, comparator: '<', unit: '%', code: '%' } + }); // ER- Filter Attributes - tm3.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' } as Coding); // Any code in 'Biomarker-ER' + tm3.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' }); // Any code in 'Biomarker-ER' tm3.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'N', display: 'N/A' - } as Coding); + }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1628,37 +1630,37 @@ describe('checkTumorMarkerFilterLogic-Triple negative-10', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; const tm3: mcode.TumorMarker = {}; - tm3.code = [] as Coding[]; - tm3.interpretation = [] as Coding[]; - tm3.valueCodeableConcept = [] as Coding[]; - tm3.valueQuantity = [] as mcode.Quantity[]; - tm3.valueRatio = [] as mcode.Ratio[]; + tm3.code = []; + tm3.interpretation = []; + tm3.valueCodeableConcept = []; + tm3.valueQuantity = []; + tm3.valueRatio = []; // HER2- Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' - tm1.valueQuantity.push({ value: '1', comparator: '=' } as mcode.Quantity); + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' + tm1.valueQuantity.push({ value: 1 }); // PR- Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' } as Coding); // Any code in 'Biomarker-PR' - tm2.valueQuantity.push({ value: '9', comparator: '<', unit: '%', code: '%' } as mcode.Quantity); + tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' }); // Any code in 'Biomarker-PR' + tm2.valueQuantity.push({ value: 9, comparator: '<', unit: '%', code: '%' }); // ER- Filter Attributes - tm3.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' } as Coding); // Any code in 'Biomarker-ER' + tm3.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' }); // Any code in 'Biomarker-ER' tm3.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'N', display: 'N/A' - } as Coding); + }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1674,50 +1676,50 @@ describe('checkTumorMarkerFilterLogic-Triple negative and RB Positive', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; const tm3: mcode.TumorMarker = {}; - tm3.code = [] as Coding[]; - tm3.interpretation = [] as Coding[]; - tm3.valueCodeableConcept = [] as Coding[]; - tm3.valueQuantity = [] as mcode.Quantity[]; - tm3.valueRatio = [] as mcode.Ratio[]; + tm3.code = []; + tm3.interpretation = []; + tm3.valueCodeableConcept = []; + tm3.valueQuantity = []; + tm3.valueRatio = []; const tm4: mcode.TumorMarker = {}; - tm4.code = [] as Coding[]; - tm4.interpretation = [] as Coding[]; - tm4.valueCodeableConcept = [] as Coding[]; - tm4.valueQuantity = [] as mcode.Quantity[]; - tm4.valueRatio = [] as mcode.Ratio[]; + tm4.code = []; + tm4.interpretation = []; + tm4.valueCodeableConcept = []; + tm4.valueQuantity = []; + tm4.valueRatio = []; // HER2- Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' - tm1.valueQuantity.push({ value: '1', comparator: '=' } as mcode.Quantity); + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' + tm1.valueQuantity.push({ value: 1 }); // PR- Filter Attributes - tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' } as Coding); // Any code in 'Biomarker-PR' + tm2.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' }); // Any code in 'Biomarker-PR' tm2.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'ND', display: 'N/A' - } as Coding); + }); // ER- Filter Attributes - tm3.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' } as Coding); // Any code in 'Biomarker-ER' + tm3.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' }); // Any code in 'Biomarker-ER' tm3.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'N', display: 'N/A' - } as Coding); + }); // RB+ Attributes - tm4.code.push({ system: 'http://loinc.info/sct', code: '42795-5', display: 'N/A' } as Coding); // Any code in 'Biomarker-RB' - tm4.valueQuantity.push({ value: '51', comparator: '>', unit: '%', code: '%' } as mcode.Quantity); + tm4.code.push({ system: 'http://loinc.info/sct', code: '42795-5', display: 'N/A' }); // Any code in 'Biomarker-RB' + tm4.valueQuantity.push({ value: 51, comparator: '>', unit: '%', code: '%' }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -1734,19 +1736,19 @@ describe('Ratio and Quantity Error Tests', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; - - // Invalid Operator - tm1.valueQuantity.push({ value: '51', comparator: '!=', unit: '%', code: '%' } as mcode.Quantity); + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; + + // Intentionally insert invalid comparator + tm1.valueQuantity.push({ value: 51, comparator: '!=', unit: '%', code: '%' } as unknown as Quantity); // Invalid Operator tm1.valueRatio.push({ - numerator: { value: '1', comparator: '<', unit: '%', code: '%' } as mcode.Quantity, - denominator: { value: '110', comparator: '<', unit: '%', code: '%' } as mcode.Quantity - } as mcode.Ratio); + numerator: { value: 1, comparator: '<', unit: '%', code: '%' }, + denominator: { value: 110, comparator: '<', unit: '%', code: '%' } + }); it('Test Quantity Error', () => { expect(extractedMCODE.quantityMatch(3, '%', [10], '<')).toBe(false); @@ -1755,8 +1757,8 @@ describe('Ratio and Quantity Error Tests', () => { it('Test Ratio Error', () => { expect( extractedMCODE.ratioMatch( - { value: '1', comparator: '<', unit: '%', code: '%' } as mcode.Quantity, - { value: '1', comparator: '<', unit: '%', code: '%' } as mcode.Quantity, + { value: 1, comparator: '<', unit: '%', code: '%' }, + { value: 1, comparator: '<', unit: '%', code: '%' }, 10, '<' ) @@ -1771,8 +1773,8 @@ describe('checkTumorMarkerFilterLogic-BRCA1-Germline', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const cgv: mcode.CancerGeneticVariant = { - valueCodeableConcept: [] as Coding[], - interpretation: [] as Coding[], + valueCodeableConcept: [], + interpretation: [], component: {} as mcode.CancerGeneticVariantComponent }; const cgvComponent: mcode.CancerGeneticVariantComponent = { @@ -1780,28 +1782,28 @@ describe('checkTumorMarkerFilterLogic-BRCA1-Germline', () => { genomicsSourceClass: [] as mcode.CancerGeneticVariantComponentType[] }; const cgvGeneStudied: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; const cgvGenomicSourceClass: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; // BRCA1-Germline Filter Attributes - cgvGeneStudied.valueCodeableConcept.coding.push({ system: 'hgnc', code: '1100', display: 'BRCA1' }); - cgv.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' }); - cgv.valueCodeableConcept.push({ system: 'http://loinc.info/sct', code: 'LA9633-4', display: 'N/A' }); - cgv.interpretation.push({ system: 'N/A', code: 'CAR', display: 'CAR' }); - cgvGeneStudied.interpretation.coding.push({ system: 'N/A', code: 'CAR', display: 'CAR' }); - cgvGenomicSourceClass.valueCodeableConcept.coding.push({ + cgvGeneStudied.valueCodeableConcept?.coding.push({ system: 'hgnc', code: '1100', display: 'BRCA1' }); + cgv.valueCodeableConcept?.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' }); + cgv.valueCodeableConcept?.push({ system: 'http://loinc.info/sct', code: 'LA9633-4', display: 'N/A' }); + cgv.interpretation?.push({ system: 'N/A', code: 'CAR', display: 'CAR' }); + cgvGeneStudied.interpretation?.coding.push({ system: 'N/A', code: 'CAR', display: 'CAR' }); + cgvGenomicSourceClass.valueCodeableConcept?.coding.push({ system: ' http://loinc.info/sct', code: 'LA6683-2', display: 'N/A' }); - cgvComponent.geneStudied.push(cgvGeneStudied); - cgvComponent.genomicsSourceClass.push(cgvGenomicSourceClass); + cgvComponent.geneStudied?.push(cgvGeneStudied); + cgvComponent.genomicsSourceClass?.push(cgvGenomicSourceClass); cgv.component = cgvComponent; extractedMCODE.cancerGeneticVariant.push(cgv); @@ -1815,8 +1817,8 @@ describe('checkTumorMarkerFilterLogic-BRCA2-Germline', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const cgv: mcode.CancerGeneticVariant = { - valueCodeableConcept: [] as Coding[], - interpretation: [] as Coding[], + valueCodeableConcept: [], + interpretation: [], component: {} as mcode.CancerGeneticVariantComponent }; const cgvComponent: mcode.CancerGeneticVariantComponent = { @@ -1824,25 +1826,25 @@ describe('checkTumorMarkerFilterLogic-BRCA2-Germline', () => { genomicsSourceClass: [] as mcode.CancerGeneticVariantComponentType[] }; const cgvGeneStudied: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; const cgvGenomicSourceClass: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; // BRCA2-Germline Filter Attributes - cgvGeneStudied.valueCodeableConcept.coding.push({ system: 'hgnc', code: '1101', display: 'BRCA2' }); - cgv.valueCodeableConcept.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' }); - cgvGenomicSourceClass.valueCodeableConcept.coding.push({ + cgvGeneStudied.valueCodeableConcept?.coding.push({ system: 'hgnc', code: '1101', display: 'BRCA2' }); + cgv.valueCodeableConcept?.push({ system: 'http://snomed.info/sct', code: '10828004', display: 'N/A' }); + cgvGenomicSourceClass.valueCodeableConcept?.coding.push({ system: ' http://loinc.info/sct', code: 'LA6683-2', display: 'N/A' }); - cgvComponent.geneStudied.push(cgvGeneStudied); - cgvComponent.genomicsSourceClass.push(cgvGenomicSourceClass); + cgvComponent.geneStudied?.push(cgvGeneStudied); + cgvComponent.genomicsSourceClass?.push(cgvGenomicSourceClass); cgv.component = cgvComponent; extractedMCODE.cancerGeneticVariant.push(cgv); @@ -1856,8 +1858,8 @@ describe('checkTumorMarkerFilterLogic-BRCA1-Somatic', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const cgv: mcode.CancerGeneticVariant = { - valueCodeableConcept: [] as Coding[], - interpretation: [] as Coding[], + valueCodeableConcept: [], + interpretation: [], component: {} as mcode.CancerGeneticVariantComponent }; const cgvComponent: mcode.CancerGeneticVariantComponent = { @@ -1865,25 +1867,25 @@ describe('checkTumorMarkerFilterLogic-BRCA1-Somatic', () => { genomicsSourceClass: [] as mcode.CancerGeneticVariantComponentType[] }; const cgvGeneStudied: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; const cgvGenomicSourceClass: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; // BRCA1-Somatic Filter Attributes - cgvGeneStudied.valueCodeableConcept.coding.push({ system: 'hgnc', code: '1100', display: 'BRCA1' }); - cgv.valueCodeableConcept.push({ system: 'http://loinc.info/sct', code: 'LA9633-4', display: 'N/A' }); - cgvGenomicSourceClass.valueCodeableConcept.coding.push({ + cgvGeneStudied.valueCodeableConcept?.coding.push({ system: 'hgnc', code: '1100', display: 'BRCA1' }); + cgv.valueCodeableConcept?.push({ system: 'http://loinc.info/sct', code: 'LA9633-4', display: 'N/A' }); + cgvGenomicSourceClass.valueCodeableConcept?.coding.push({ system: ' http://loinc.info/sct', code: 'LA6684-0', display: 'N/A' }); - cgvComponent.geneStudied.push(cgvGeneStudied); - cgvComponent.genomicsSourceClass.push(cgvGenomicSourceClass); + cgvComponent.geneStudied?.push(cgvGeneStudied); + cgvComponent.genomicsSourceClass?.push(cgvGenomicSourceClass); cgv.component = cgvComponent; extractedMCODE.cancerGeneticVariant.push(cgv); @@ -1897,8 +1899,8 @@ describe('checkTumorMarkerFilterLogic-BRCA2-Somatic', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const cgv: mcode.CancerGeneticVariant = { - valueCodeableConcept: [] as Coding[], - interpretation: [] as Coding[], + valueCodeableConcept: [], + interpretation: [], component: {} as mcode.CancerGeneticVariantComponent }; const cgvComponent: mcode.CancerGeneticVariantComponent = { @@ -1906,25 +1908,25 @@ describe('checkTumorMarkerFilterLogic-BRCA2-Somatic', () => { genomicsSourceClass: [] as mcode.CancerGeneticVariantComponentType[] }; const cgvGeneStudied: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; const cgvGenomicSourceClass: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; // BRCA2-Somatic Filter Attributes - cgvGeneStudied.valueCodeableConcept.coding.push({ system: 'hgnc', code: '1101', display: 'BRCA2' }); - cgv.interpretation.push({ system: 'N/A', code: 'CAR', display: 'CAR' }); - cgvGenomicSourceClass.valueCodeableConcept.coding.push({ + cgvGeneStudied.valueCodeableConcept?.coding.push({ system: 'hgnc', code: '1101', display: 'BRCA2' }); + cgv.interpretation?.push({ system: 'N/A', code: 'CAR', display: 'CAR' }); + cgvGenomicSourceClass.valueCodeableConcept?.coding.push({ system: ' http://loinc.info/sct', code: 'LA6684-0', display: 'N/A' }); - cgvComponent.geneStudied.push(cgvGeneStudied); - cgvComponent.genomicsSourceClass.push(cgvGenomicSourceClass); + cgvComponent.geneStudied?.push(cgvGeneStudied); + cgvComponent.genomicsSourceClass?.push(cgvGenomicSourceClass); cgv.component = cgvComponent; extractedMCODE.cancerGeneticVariant.push(cgv); @@ -1938,8 +1940,8 @@ describe('checkTumorMarkerFilterLogic-BRCA1', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const cgv: mcode.CancerGeneticVariant = { - valueCodeableConcept: [] as Coding[], - interpretation: [] as Coding[], + valueCodeableConcept: [], + interpretation: [], component: {} as mcode.CancerGeneticVariantComponent }; const cgvComponent: mcode.CancerGeneticVariantComponent = { @@ -1947,15 +1949,15 @@ describe('checkTumorMarkerFilterLogic-BRCA1', () => { genomicsSourceClass: [] as mcode.CancerGeneticVariantComponentType[] }; const cgvGeneStudied: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; // BRCA1 Filter Attributes - cgvGeneStudied.valueCodeableConcept.coding.push({ system: 'hgnc', code: '1100', display: 'BRCA1' }); - cgvGeneStudied.interpretation.coding.push({ system: 'N/A', code: 'A', display: 'AWW' }); + cgvGeneStudied.valueCodeableConcept?.coding.push({ system: 'hgnc', code: '1100', display: 'BRCA1' }); + cgvGeneStudied.interpretation?.coding.push({ system: 'N/A', code: 'A', display: 'AWW' }); - cgvComponent.geneStudied.push(cgvGeneStudied); + cgvComponent.geneStudied?.push(cgvGeneStudied); cgv.component = cgvComponent; extractedMCODE.cancerGeneticVariant.push(cgv); @@ -1969,8 +1971,8 @@ describe('checkTumorMarkerFilterLogic-BRCA2', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const cgv: mcode.CancerGeneticVariant = { - valueCodeableConcept: [] as Coding[], - interpretation: [] as Coding[], + valueCodeableConcept: [], + interpretation: [], component: {} as mcode.CancerGeneticVariantComponent }; const cgvComponent: mcode.CancerGeneticVariantComponent = { @@ -1978,15 +1980,15 @@ describe('checkTumorMarkerFilterLogic-BRCA2', () => { genomicsSourceClass: [] as mcode.CancerGeneticVariantComponentType[] }; const cgvGeneStudied: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; // BRCA2 Filter Attributes - cgvGeneStudied.valueCodeableConcept.coding.push({ system: 'hgnc', code: '1101', display: 'BRCA2' }); - cgv.interpretation.push({ system: 'N/A', code: 'POS', display: 'POS' }); + cgvGeneStudied.valueCodeableConcept?.coding.push({ system: 'hgnc', code: '1101', display: 'BRCA2' }); + cgv.interpretation?.push({ system: 'N/A', code: 'POS', display: 'POS' }); - cgvComponent.geneStudied.push(cgvGeneStudied); + cgvComponent.geneStudied?.push(cgvGeneStudied); cgv.component = cgvComponent; extractedMCODE.cancerGeneticVariant.push(cgv); @@ -2001,8 +2003,8 @@ describe('checkTumorMarkerFilterLogic-empty-components-added', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const cgv: mcode.CancerGeneticVariant = { - valueCodeableConcept: [] as Coding[], - interpretation: [] as Coding[], + valueCodeableConcept: [], + interpretation: [], component: {} as mcode.CancerGeneticVariantComponent }; const cgvComponent: mcode.CancerGeneticVariantComponent = { @@ -2011,17 +2013,17 @@ describe('checkTumorMarkerFilterLogic-empty-components-added', () => { }; const cgvGenomicSourceClass: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; const cgvGeneStudied: mcode.CancerGeneticVariantComponentType = { - valueCodeableConcept: { coding: [] as Coding[] }, - interpretation: { coding: [] as Coding[] } + valueCodeableConcept: { coding: [] }, + interpretation: { coding: [] } }; - cgvComponent.geneStudied.push(cgvGeneStudied); - cgvComponent.genomicsSourceClass.push(cgvGenomicSourceClass); + cgvComponent.geneStudied?.push(cgvGeneStudied); + cgvComponent.genomicsSourceClass?.push(cgvGenomicSourceClass); cgv.component = cgvComponent; extractedMCODE.cancerGeneticVariant.push(cgv); @@ -2036,24 +2038,24 @@ describe('checkTumorMarkerFilterLogic-PR+', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; const tm2: mcode.TumorMarker = {}; - tm2.code = [] as Coding[]; - tm2.interpretation = [] as Coding[]; - tm2.valueCodeableConcept = [] as Coding[]; - tm2.valueQuantity = [] as mcode.Quantity[]; - tm2.valueRatio = [] as mcode.Ratio[]; + tm2.code = []; + tm2.interpretation = []; + tm2.valueCodeableConcept = []; + tm2.valueQuantity = []; + tm2.valueRatio = []; // PR+ Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' } as Coding); // Any code in 'Biomarker-PR' + tm1.code.push({ system: 'http://loinc.info/sct', code: '85339-0', display: 'N/A' }); // Any code in 'Biomarker-PR' tm1.valueRatio.push({ - numerator: { value: '100', comparator: '>=', unit: '%', code: '%' } as mcode.Quantity, - denominator: { value: '3', comparator: '>=', unit: '%', code: '%' } as mcode.Quantity - } as mcode.Ratio); + numerator: { value: 100, comparator: '>=', unit: '%', code: '%' }, + denominator: { value: 3, comparator: '>=', unit: '%', code: '%' } + }); extractedMCODE.tumorMarker.push(tm1); extractedMCODE.tumorMarker.push(tm2); @@ -2068,19 +2070,19 @@ describe('checkTumorMarkerFilterLogic-ER+', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; // ER+ Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' } as Coding); // Any code in 'Biomarker-ER' + tm1.code.push({ system: 'http://loinc.info/sct', code: '85337-4', display: 'N/A' }); // Any code in 'Biomarker-ER' tm1.interpretation.push({ system: 'http://hl7.org/fhir/R4/valueset-observation-interpretation.html', code: 'H', display: 'N/A' - } as Coding); + }); extractedMCODE.tumorMarker.push(tm1); @@ -2094,15 +2096,15 @@ describe('checkTumorMarkerFilterLogicHER-', () => { const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); const tm1: mcode.TumorMarker = {}; - tm1.code = [] as Coding[]; - tm1.interpretation = [] as Coding[]; - tm1.valueCodeableConcept = [] as Coding[]; - tm1.valueQuantity = [] as mcode.Quantity[]; - tm1.valueRatio = [] as mcode.Ratio[]; + tm1.code = []; + tm1.interpretation = []; + tm1.valueCodeableConcept = []; + tm1.valueQuantity = []; + tm1.valueRatio = []; // HER2- Filter Attributes - tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' } as Coding); // Any code in 'Biomarker-HER2' - tm1.valueQuantity.push({ value: '2+', comparator: '=' } as mcode.Quantity); + tm1.code.push({ system: 'http://loinc.info/sct', code: '32996-1', display: 'N/A' }); // Any code in 'Biomarker-HER2' + tm1.valueQuantity.push({ value: 2, comparator: '>=' }); extractedMCODE.tumorMarker.push(tm1); @@ -2155,7 +2157,7 @@ describe('InvalidCodeProfileTest', () => { // Initialize const patientBundle = null; const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); - const code: Coding = { system: 'http://icD-10.info/sct', code: '32996-1', display: 'N/A' } as Coding; + const code: Coding = { system: 'http://icD-10.info/sct', code: '32996-1', display: 'N/A' }; it('Test that an error throws for an invalid code profile input.', () => { expect(extractedMCODE.codeIsInSheet(code, 'INVALID_TEST_SHEET')).toBe(false); diff --git a/spec/trialscope.spec.ts b/spec/trialscope.spec.ts index 33dc16a..aff1892 100644 --- a/spec/trialscope.spec.ts +++ b/spec/trialscope.spec.ts @@ -1,3 +1,8 @@ +import { ClinicalTrialsGovService, ResearchStudy } from 'clinical-trial-matching-service'; +import { Bundle, BundleEntry, FhirResource } from 'fhir/r4'; +// For spying purposes: +import nock from 'nock'; + import { isTrialScopeResponse, isTrialScopeErrorResponse, @@ -6,9 +11,6 @@ import { TrialScopeServerError, TrialScopeTrial } from '../src/trialscope'; -import { fhir, ClinicalTrialsGovService, ResearchStudy } from 'clinical-trial-matching-service'; -// For spying purposes: -import nock from 'nock'; describe('isTrialScopeResponse', () => { it('returns false with a non-object', () => { @@ -45,12 +47,12 @@ describe('isTrialScopeErrorResponse', () => { describe('TrialScopeQuery', () => { it('ignores bad entries', () => { // This involves a bit of lying to TypeScript - const patientBundle: fhir.Bundle = { + const patientBundle: Bundle = { resourceType: 'Bundle', type: 'collection', entry: [] }; - patientBundle.entry.push(({ invalid: true } as unknown) as fhir.BundleEntry); + patientBundle.entry?.push({ invalid: true } as unknown as BundleEntry); new TrialScopeQuery(patientBundle); // Success is the object being created at all }); @@ -126,7 +128,7 @@ describe('TrialScopeQuery', () => { // TypeScript assumes extra fields are an error, although in this case the // FHIR types supplies are somewhat intentionally sparse as they're not a // full definition - const condition: fhir.Resource = { + const condition: FhirResource = { resourceType: 'Condition', meta: { profile: [ @@ -134,6 +136,7 @@ describe('TrialScopeQuery', () => { 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition' ] }, + subject: {}, clinicalStatus: { coding: [ { @@ -174,7 +177,7 @@ describe('TrialScopeQuery', () => { } } ] - } as fhir.Resource; + }; const query = new TrialScopeQuery({ resourceType: 'Bundle', type: 'collection', @@ -203,15 +206,19 @@ describe('TrialScopeQuery', () => { // currently the case let m = /mcode:\s*{(.*?)}/.exec(graphQL); expect(m).toBeTruthy(); - const mcodeFilters = m[1]; - expect(mcodeFilters).toMatch(/primaryCancer:\s*BREAST_CANCER/); + if (m) { + const mcodeFilters = m[1]; + expect(mcodeFilters).toMatch(/primaryCancer:\s*BREAST_CANCER/); + } m = /baseFilters:\s*{(.*?)}/.exec(graphQL); expect(m).toBeTruthy(); - const baseFilters = m[1]; - expect(baseFilters).toMatch(/zipCode:\s*"01234"/); - expect(baseFilters).toMatch(/travelRadius:\s*15\b/); - expect(baseFilters).toMatch(/phase:\s*PHASE_1\b/); - expect(baseFilters).toMatch(/recruitmentStatus:\s*RECRUITING\b/); + if (m) { + const baseFilters = m[1]; + expect(baseFilters).toMatch(/zipCode:\s*"01234"/); + expect(baseFilters).toMatch(/travelRadius:\s*15\b/); + expect(baseFilters).toMatch(/phase:\s*PHASE_1\b/); + expect(baseFilters).toMatch(/recruitmentStatus:\s*RECRUITING\b/); + } }); it("excludes parameters that weren't included", () => { @@ -234,11 +241,13 @@ describe('TrialScopeQuery', () => { const graphQL = query.toQuery(); const m = /baseFilters:\s*{(.*?)}/.exec(graphQL); expect(m).toBeTruthy(); - const baseFilters = m[1]; - expect(baseFilters).toMatch(/zipCode:\s*"98765"/); - expect(baseFilters).not.toMatch('travelRadius'); - expect(baseFilters).not.toMatch('phase'); - expect(baseFilters).not.toMatch('recruitmentStatus'); + if (m) { + const baseFilters = m[1]; + expect(baseFilters).toMatch(/zipCode:\s*"98765"/); + expect(baseFilters).not.toMatch('travelRadius'); + expect(baseFilters).not.toMatch('phase'); + expect(baseFilters).not.toMatch('recruitmentStatus'); + } }); }); @@ -256,8 +265,6 @@ describe('TrialScopeQueryRunner', () => { }); afterEach(() => { expect(scope.isDone()).toBeTrue(); - interceptor = null; - scope = null; }); it('handles an empty response', () => { @@ -308,7 +315,7 @@ describe('TrialScopeQueryRunner', () => { }); describe('runQuery', () => { - let patientBundle: fhir.Bundle; + let patientBundle: Bundle; beforeEach(() => { // This is basically the minimum bundle required to run a query patientBundle = { @@ -460,8 +467,9 @@ describe('TrialScopeQueryRunner', () => { expected.enrollment = [reference]; // For the sake of this test, kill the createResourceId functions // (it shouldn't be enumerable anyway) - expected.createReferenceId = null; - (actual.entry[i].resource as ResearchStudy).createReferenceId = null; + // Note this involves lying to the TypeScript compiler + (expected as unknown as { createReferenceId: null }).createReferenceId = null; + (actual.entry[i].resource as unknown as { createReferenceId: null }).createReferenceId = null; expect(actual.entry[i].resource).toEqual(expected); } expect(actual.entry[0].search.score).toEqual(1); diff --git a/src/mcode.ts b/src/mcode.ts index 22a5c78..a74ee66 100644 --- a/src/mcode.ts +++ b/src/mcode.ts @@ -1,10 +1,9 @@ -import { fhirclient } from 'fhirclient/lib/types'; +import { Bundle, Coding, Quantity, Ratio, Resource } from 'fhir/r4'; import * as fhirpath from 'fhirpath'; import { CodeProfile, ProfileSystemCodes } from './profileSystemLogic'; import profile_system_codes_json from '../data/profile-system-codes-json.json'; -import { fhir } from 'clinical-trial-matching-service'; const profile_system_codes = profile_system_codes_json as ProfileSystemCodes; @@ -12,25 +11,6 @@ export type FHIRPath = string; // fhirpath now has official TypeScript types. Unfortunately, the result they use is "any" export type PathLookupResult = Record | string | number; -export interface Coding { - system?: string; - code?: string; - display?: string; -} - -export interface Quantity { - value?: number | string; - comparator?: string; - unit?: string; - system?: string; - code?: string; -} - -export interface Ratio { - numerator?: Quantity; - denominator?: Quantity; -} - export interface PrimaryCancerCondition { clinicalStatus?: Coding[]; coding?: Coding[]; @@ -89,7 +69,7 @@ export class ExtractedMCODE { ecogPerformaceStatus: number; karnofskyPerformanceStatus: number; - constructor(patientBundle: fhir.Bundle) { + constructor(patientBundle: Bundle | null) { if (patientBundle != null) { for (const entry of patientBundle.entry) { if (!('resource' in entry)) { @@ -319,12 +299,8 @@ export class ExtractedMCODE { } } - lookup( - resource: fhirclient.FHIR.Resource, - path: FHIRPath, - environment?: { [key: string]: string } - ): PathLookupResult[] { - return fhirpath.evaluate(resource, path, environment); + lookup(resource: Resource, path: FHIRPath, environment?: { [key: string]: string }): PathLookupResult[] { + return fhirpath.evaluate(resource, path, environment) as PathLookupResult[]; } resourceProfile(profiles: PathLookupResult[], key: string): boolean { for (const profile of profiles) { @@ -1299,13 +1275,10 @@ export class ExtractedMCODE { const system = this.normalizeCodeSystem(coding.system); for (const sheetName of sheetNames) { let codeProfile: CodeProfile = undefined; - try { - codeProfile = profile_system_codes[sheetName] as CodeProfile; // Pull the codes for the profile - } finally { - if (codeProfile == undefined) { - console.error('Code Profile ' + sheetName + ' is undefined.'); - continue; - } + codeProfile = profile_system_codes[sheetName]; // Pull the codes for the profile + if (codeProfile == undefined) { + console.error('Code Profile ' + sheetName + ' is undefined.'); + continue; } let codeSet: { code: string }[] = codeProfile[system] as { code: string }[]; // Pull the system codes from the codes diff --git a/src/profileSystemLogic.ts b/src/profileSystemLogic.ts index 11a3848..3bc12d3 100644 --- a/src/profileSystemLogic.ts +++ b/src/profileSystemLogic.ts @@ -1,10 +1,10 @@ -import { Coding } from './mcode'; +import { Coding } from 'fhir/r4'; export interface ProfileType { types: string[]; } export interface ProfileSystemCodes { - [key: string] : CodeProfile; + [key: string]: CodeProfile; 'Cancer-Skin'?: CodeProfile; 'Treatment-Pertuzumab'?: CodeProfile; 'Treatment-SRS-Brain'?: CodeProfile; @@ -45,7 +45,7 @@ export interface ProfileSystemCodes { 'Biomarker-ER'?: CodeProfile; } export interface CodeProfile { - [key: string] : { code: string }[]; + [key: string]: { code: string }[]; SNOMED?: { code: string }[]; RxNorm?: { code: string }[]; ICD10?: { code: string }[]; diff --git a/src/research-study-mapping.ts b/src/research-study-mapping.ts index 61bad4b..5c8180f 100644 --- a/src/research-study-mapping.ts +++ b/src/research-study-mapping.ts @@ -1,6 +1,8 @@ -import { ResearchStudy, fhir, convertStringsToCodeableConcept } from 'clinical-trial-matching-service'; +import { ResearchStudy, convertStringsToCodeableConcept } from 'clinical-trial-matching-service'; import { TrialScopeTrial } from './trialscope'; +type ResearchStudyStatus = ResearchStudy['status']; + // Mappings between trialscope value sets and FHIR value sets const phaseCodeMap = new Map([ ['Early Phase 1', 'early-phase-1'], @@ -13,7 +15,7 @@ const phaseCodeMap = new Map([ ['Phase 4', 'phase-4'] ]); -const statusMap = new Map([ +const statusMap = new Map([ ['Active, not recruiting', 'closed-to-accrual'], ['Approved for marketing', 'approved'], ['Available', 'active'], @@ -22,7 +24,7 @@ const statusMap = new Map([ ['Recruiting', 'active'] ]); -function convertStatus(tsStatus: string): fhir.ResearchStudyStatus { +function convertStatus(tsStatus: string): ResearchStudyStatus { return statusMap.get(tsStatus); } @@ -55,7 +57,7 @@ export function convertTrialScopeToResearchStudy(trial: TrialScopeTrial, id: num }; } if (trial.studyType) { - result.category = [{ text: "Study Type: " + trial.studyType }]; + result.category = [{ text: 'Study Type: ' + trial.studyType }]; } if (trial.conditions) { const conditions = convertStringsToCodeableConcept(trial.conditions); diff --git a/src/server.ts b/src/server.ts index d60af3a..a6559eb 100644 --- a/src/server.ts +++ b/src/server.ts @@ -1,20 +1,16 @@ +import { ClinicalTrialsGovService, ClinicalTrialMatchingService, configFromEnv } from 'clinical-trial-matching-service'; +import * as dotenv from 'dotenv-flow'; import express from 'express'; -import TrialScopeQueryRunner from './trialscope'; +import { Bundle } from 'fhir/r4'; -import { - fhir, - ClinicalTrialsGovService, - ClinicalTrialMatchingService, - configFromEnv -} from 'clinical-trial-matching-service'; -import * as dotenv from 'dotenv-flow'; +import TrialScopeQueryRunner from './trialscope'; export class TrialScopeService extends ClinicalTrialMatchingService { queryRunner: TrialScopeQueryRunner; backupService: ClinicalTrialsGovService; constructor(config: Record) { - super((patientBundle: fhir.Bundle) => { + super((patientBundle: Bundle) => { return this.queryRunner.runQuery(patientBundle); }, config); diff --git a/src/trialscope.ts b/src/trialscope.ts index 4d73fc3..1474692 100644 --- a/src/trialscope.ts +++ b/src/trialscope.ts @@ -1,12 +1,12 @@ /** * Module for running queries via TrialScope */ -import { ClinicalTrialsGovService, ServerError } from 'clinical-trial-matching-service'; +import { ClientError, ClinicalTrialsGovService, SearchSet, ServerError } from 'clinical-trial-matching-service'; +import { Bundle, ResearchStudy } from 'fhir/r4'; import https from 'https'; import { IncomingMessage } from 'http'; -import { convertTrialScopeToResearchStudy } from './research-study-mapping'; -import { ClientError, SearchSet, fhir } from 'clinical-trial-matching-service'; import * as mcode from './mcode'; +import { convertTrialScopeToResearchStudy } from './research-study-mapping'; /** * Maps FHIR phases to TrialScope phases. @@ -183,7 +183,7 @@ export class TrialScopeQuery { phase = 'any'; recruitmentStatus: string | null = null; after?: string = null; - first = 30; + first: number | null = 30; mcode?: { [key: string]: string; primaryCancer: string; @@ -226,11 +226,11 @@ export class TrialScopeQuery { 'maximumAge' ]; - constructor(patientBundle: fhir.Bundle) { + constructor(patientBundle: Bundle) { const extractedMCODE = new mcode.ExtractedMCODE(patientBundle); console.log(extractedMCODE); - let stageValues = extractedMCODE.getStageValues(); - let medicationStatementValues = extractedMCODE.getMedicationStatementValues(); + const stageValues = extractedMCODE.getStageValues(); + const medicationStatementValues = extractedMCODE.getMedicationStatementValues(); this.mcode = { primaryCancer: extractedMCODE.getPrimaryCancerValue(), secondaryCancer: extractedMCODE.getSecondaryCancerValue(), @@ -332,7 +332,7 @@ export class TrialScopeQuery { export class TrialScopeQueryRunner { constructor(public endpoint: string, private token: string, private backupService: ClinicalTrialsGovService) {} - runQuery(patientBundle: fhir.Bundle): Promise { + runQuery(patientBundle: Bundle): Promise { // update for advanced matches query return new Promise((resolve, reject) => { const query = new TrialScopeQuery(patientBundle); @@ -378,7 +378,7 @@ export class TrialScopeQueryRunner { */ convertToSearchSet(trialscopeResponse: TrialScopeResponse): Promise { const searchSet = new SearchSet(); - const studies: fhir.ResearchStudy[] = []; + const studies: ResearchStudy[] = []; let index = 0; for (const node of trialscopeResponse.data.advancedMatches.edges) { const trial: TrialScopeTrial = node.node; From f878d4cb6966a7b26f0fc8407fdd491052b8eb33 Mon Sep 17 00:00:00 2001 From: Dan Potter Date: Mon, 19 Dec 2022 15:07:33 -0500 Subject: [PATCH 2/2] Update to latest dependencies where possible node-fetch is left at 2.6.7 because the 3.0 version moves to ESM, which breaks our current TypeScript/Node config. --- package-lock.json | 1595 +++++++++++++++++++++++-------------------- package.json | 18 +- spec/server.spec.ts | 5 +- 3 files changed, 853 insertions(+), 765 deletions(-) diff --git a/package-lock.json b/package-lock.json index 725a4ae..f3e1b10 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13,7 +13,7 @@ "clinical-trial-matching-service": "^0.0.7", "dotenv-flow": "^3.2.0", "express": "^4.17.1", - "fhirpath": "^2.7.4", + "fhirpath": "^3.3.0", "node-fetch": "^2.6.1" }, "devDependencies": { @@ -21,21 +21,21 @@ "@types/dotenv-flow": "^3.0.0", "@types/express": "^4.17.11", "@types/fhir": "^0.0.35", - 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}, - "dependencies": { - "tslib": { - "version": "1.14.1", - "resolved": "https://registry.npmjs.org/tslib/-/tslib-1.14.1.tgz", - "integrity": "sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg==", - "dev": true - } } }, "type-check": { @@ -8268,10 +8357,10 @@ "resolved": "https://registry.npmjs.org/utils-merge/-/utils-merge-1.0.1.tgz", "integrity": "sha512-pMZTvIkT1d+TFGvDOqodOclx0QWkkgi6Tdoa8gC8ffGAAqz9pzPTZWAybbsHHoED/ztMtkv/VoYTYyShUn81hA==" }, - "v8-compile-cache": { - "version": "2.3.0", - "resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz", - "integrity": "sha512-l8lCEmLcLYZh4nbunNZvQCJc5pv7+RCwa8q/LdUx8u7lsWvPDKmpodJAJNwkAhJC//dFY48KuIEmjtd4RViDrA==", + "v8-compile-cache-lib": { + "version": "3.0.1", + "resolved": "https://registry.npmjs.org/v8-compile-cache-lib/-/v8-compile-cache-lib-3.0.1.tgz", + "integrity": "sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg==", "dev": true }, "vary": { @@ -8418,12 +8507,6 @@ "requires": { "p-limit": "^2.2.0" } - }, - "path-exists": { - "version": "4.0.0", - "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz", - "integrity": "sha512-ak9Qy5Q7jYb2Wwcey5Fpvg2KoAc/ZIhLSLOSBmRmygPsGwkVVt0fZa0qrtMz+m6tJTAHfZQ8FnmB4MG4LWy7/w==", - "dev": true } } }, @@ -8451,6 +8534,12 @@ "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", "dev": true + }, + "yocto-queue": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", + "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", + "dev": true } } } diff --git a/package.json b/package.json index d3983bb..ab2a1bc 100644 --- a/package.json +++ b/package.json @@ -26,7 +26,7 @@ "clinical-trial-matching-service": "^0.0.7", "dotenv-flow": "^3.2.0", "express": "^4.17.1", - "fhirpath": "^2.7.4", + "fhirpath": "^3.3.0", "node-fetch": "^2.6.1" }, "devDependencies": { @@ -34,21 +34,21 @@ "@types/dotenv-flow": "^3.0.0", "@types/express": "^4.17.11", "@types/fhir": "^0.0.35", - "@types/jasmine": "^3.6.9", + "@types/jasmine": "^4.3.1", "@types/node": "^18.11.17", "@types/supertest": "^2.0.11", - "@typescript-eslint/eslint-plugin": "^4.22.0", - "@typescript-eslint/parser": "^4.22.0", - "eslint": "^7.24.0", - "eslint-config-prettier": "^7.2.0", - "eslint-plugin-prettier": "^3.4.0", + "@typescript-eslint/eslint-plugin": "^5.47.0", + "@typescript-eslint/parser": "^5.47.0", + "eslint": "^8.30.0", + "eslint-config-prettier": "^8.5.0", + "eslint-plugin-prettier": "^4.2.1", "fhir": "^4.8.2", - "jasmine": "^3.7.0", + "jasmine": "^4.5.0", "nock": "^13.0.11", "nyc": "^15.1.0", "prettier": "^2.1.0", "supertest": "^6.1.3", - "ts-node": "^9.1.1", + "ts-node": "^10.9.1", "typescript": "^4.2.4" } } diff --git a/spec/server.spec.ts b/spec/server.spec.ts index e26d736..2c8ecde 100644 --- a/spec/server.spec.ts +++ b/spec/server.spec.ts @@ -21,7 +21,7 @@ describe('TrailScopeService', () => { return request(server).get('/').set('Accept', 'application/json').expect(200); }); - it('uses the query runner', (done) => { + it('uses the query runner', () => { const runQuery = spyOn(service.queryRunner, 'runQuery').and.callFake(() => { return Promise.resolve(new SearchSet([])); }); @@ -30,9 +30,8 @@ describe('TrailScopeService', () => { .send({ resourceType: 'Bundle', type: 'collection', entry: [] }) .set('Accept', 'application/json') .expect(200) - .end(() => { + .then(() => { expect(runQuery).toHaveBeenCalled(); - done(); }); }); });