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Merge pull request #55 from mcode/staging-extractor
CSV Staging Extractor
2 parents 7fc4fbb + 7543251 commit 615832c

22 files changed

+1212
-16
lines changed

‎docs/staging.csv

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mrn,conditionId,stageGroup,t,n,m,type,effectiveDate
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mrn-1,example-condition-id,3C,cT3,cN3,cM0,Clinical,2020-01-01

‎src/extractors/CSVStagingExtractor.js

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const path = require('path');
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const { Extractor } = require('./Extractor');
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const { CSVModule } = require('../modules');
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const { firstEntryInBundle } = require('../helpers/fhirUtils');
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const { generateMcodeResources } = require('../templates');
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const logger = require('../helpers/logger');
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const { formatDateTime } = require('../helpers/dateUtils');
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function formatTNMCategoryData(stagingData) {
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logger.debug('Reformatting TNM Category data into template format');
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const formattedData = [];
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const {
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mrn, conditionId, t, n, m, type, effectiveDate,
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} = stagingData;
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if (!mrn || !conditionId || !effectiveDate) {
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throw new Error('Staging data is missing an expected property: mrn, conditionId, effectiveDate are required.');
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}
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// data needed for each TNM category
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const necessaryData = {
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conditionId,
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effectiveDateTime: formatDateTime(effectiveDate),
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stageType: type,
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subjectId: mrn,
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};
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if (t) formattedData.push({ ...necessaryData, valueCode: t, categoryType: 'Tumor' });
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if (m) formattedData.push({ ...necessaryData, valueCode: m, categoryType: 'Metastases' });
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if (n) formattedData.push({ ...necessaryData, valueCode: n, categoryType: 'Nodes' });
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return formattedData;
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}
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function formatStagingData(stagingData, categoryIds) {
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const {
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mrn, conditionId, type, stageGroup, effectiveDate,
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} = stagingData;
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return {
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subjectId: mrn,
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conditionId,
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type,
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stageGroup,
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effectiveDateTime: formatDateTime(effectiveDate),
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categoryIds,
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};
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}
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class CSVStagingExtractor extends Extractor {
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constructor({ filePath }) {
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super();
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this.csvModule = new CSVModule(path.resolve(filePath));
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}
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async getStagingData(mrn) {
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logger.debug('Getting Staging data');
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return this.csvModule.get('mrn', mrn);
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}
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async get({ mrn }) {
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const stagingData = await this.getStagingData(mrn);
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const entryResources = [];
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stagingData.forEach((data) => {
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const formattedCategoryData = formatTNMCategoryData(data);
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// Generate observation for each TNM category
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const mcodeCategoryResources = formattedCategoryData.map((d) => firstEntryInBundle(generateMcodeResources('TNMCategory', d)));
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// Pass category resource ids to formatStagingData
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const formattedStagingData = formatStagingData(data, mcodeCategoryResources.map((r) => r.resource.id));
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const stagingResource = firstEntryInBundle(generateMcodeResources('Staging', formattedStagingData));
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// Push all resources into entryResources
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mcodeCategoryResources.forEach((r) => entryResources.push(r));
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entryResources.push(stagingResource);
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});
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return {
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resourceType: 'Bundle',
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type: 'collection',
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entry: entryResources,
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};
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}
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}
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module.exports = {
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CSVStagingExtractor,
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};

‎src/extractors/index.js

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@@ -1,4 +1,14 @@
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const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
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const { CSVCancerDiseaseStatusExtractor } = require('./CSVCancerDiseaseStatusExtractor');
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const { CSVCancerRelatedMedicationExtractor } = require('./CSVCancerRelatedMedicationExtractor');
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const { CSVClinicalTrialInformationExtractor } = require('./CSVClinicalTrialInformationExtractor');
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const { CSVConditionExtractor } = require('./CSVConditionExtractor');
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const { CSVObservationExtractor } = require('./CSVObservationExtractor');
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const { CSVPatientExtractor } = require('./CSVPatientExtractor');
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const { CSVProcedureExtractor } = require('./CSVProcedureExtractor');
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const { CSVStagingExtractor } = require('./CSVStagingExtractor');
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const { CSVTreatmentPlanChangeExtractor } = require('./CSVTreatmentPlanChangeExtractor');
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const { Extractor } = require('./Extractor');
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const { FHIRAllergyIntoleranceExtractor } = require('./FHIRAllergyIntoleranceExtractor');
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const { FHIRConditionExtractor } = require('./FHIRConditionExtractor');
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const { FHIRDocumentReferenceExtractor } = require('./FHIRDocumentReferenceExtractor');
@@ -8,26 +18,18 @@ const { FHIRMedicationStatementExtractor } = require('./FHIRMedicationStatementE
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const { FHIRObservationExtractor } = require('./FHIRObservationExtractor');
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const { FHIRPatientExtractor } = require('./FHIRPatientExtractor');
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const { FHIRProcedureExtractor } = require('./FHIRProcedureExtractor');
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const { CSVCancerDiseaseStatusExtractor } = require('./CSVCancerDiseaseStatusExtractor');
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const { CSVClinicalTrialInformationExtractor } = require('./CSVClinicalTrialInformationExtractor');
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const { CSVCancerRelatedMedicationExtractor } = require('./CSVCancerRelatedMedicationExtractor');
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const { CSVConditionExtractor } = require('./CSVConditionExtractor');
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const { CSVPatientExtractor } = require('./CSVPatientExtractor');
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const { CSVTreatmentPlanChangeExtractor } = require('./CSVTreatmentPlanChangeExtractor');
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const { CSVObservationExtractor } = require('./CSVObservationExtractor');
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const { CSVProcedureExtractor } = require('./CSVProcedureExtractor');
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const { Extractor } = require('./Extractor');
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module.exports = {
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BaseFHIRExtractor,
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CSVCancerDiseaseStatusExtractor,
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CSVCancerRelatedMedicationExtractor,
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CSVClinicalTrialInformationExtractor,
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CSVConditionExtractor,
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CSVObservationExtractor,
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CSVPatientExtractor,
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CSVProcedureExtractor,
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CSVObservationExtractor,
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CSVStagingExtractor,
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CSVTreatmentPlanChangeExtractor,
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CSVCancerRelatedMedicationExtractor,
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Extractor,
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FHIRAllergyIntoleranceExtractor,
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FHIRConditionExtractor,

‎src/index.js

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@@ -3,13 +3,14 @@ const { BaseClient } = require('./client/BaseClient');
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const {
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BaseFHIRExtractor,
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CSVCancerDiseaseStatusExtractor,
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CSVCancerRelatedMedicationExtractor,
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CSVClinicalTrialInformationExtractor,
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CSVConditionExtractor,
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CSVObservationExtractor,
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CSVPatientExtractor,
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CSVProcedureExtractor,
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CSVStagingExtractor,
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CSVTreatmentPlanChangeExtractor,
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CSVObservationExtractor,
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CSVCancerRelatedMedicationExtractor,
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Extractor,
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FHIRAllergyIntoleranceExtractor,
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FHIRConditionExtractor,
@@ -54,14 +55,15 @@ module.exports = {
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BaseFHIRExtractor,
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BaseFHIRModule,
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CSVCancerDiseaseStatusExtractor,
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CSVCancerRelatedMedicationExtractor,
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CSVClinicalTrialInformationExtractor,
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CSVConditionExtractor,
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CSVModule,
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CSVPatientExtractor,
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CSVObservationExtractor,
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CSVProcedureExtractor,
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CSVStagingExtractor,
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CSVTreatmentPlanChangeExtractor,
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CSVCancerRelatedMedicationExtractor,
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CSVObservationExtractor,
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Extractor,
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FHIRAllergyIntoleranceExtractor,
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FHIRConditionExtractor,

‎src/templates/ResourceGenerator.js

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@@ -11,6 +11,8 @@ const { patientTemplate } = require('./PatientTemplate');
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const { procedureTemplate } = require('./ProcedureTemplate');
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const { researchStudyTemplate } = require('./ResearchStudyTemplate');
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const { researchSubjectTemplate } = require('./ResearchSubjectTemplate');
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const { stagingTemplate } = require('./StagingTemplate');
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const { tnmCategoryTemplate } = require('./TNMCategoryTemplate');
1416

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const fhirTemplateLookup = {
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CancerDiseaseStatus: cancerDiseaseStatusTemplate,
@@ -22,6 +24,8 @@ const fhirTemplateLookup = {
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Procedure: procedureTemplate,
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ResearchStudy: researchStudyTemplate,
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ResearchSubject: researchSubjectTemplate,
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Staging: stagingTemplate,
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TNMCategory: tnmCategoryTemplate,
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};
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function loadFhirTemplate(mcodeProfileID) {

‎src/templates/StagingTemplate.js

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const { coding, reference, valueX } = require('./snippets');
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3+
// Returns staging specific data based whether it is clinical or pathologic
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function getTypeSpecificData(type) {
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if (type === 'Clinical') {
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return {
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categoryCode: 'survey',
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code: '21908-9',
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profileUrl: 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-stage-group',
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};
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}
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if (type === 'Pathologic') {
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return {
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categoryCode: 'laboratory',
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code: '21902-2',
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profileUrl: 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-pathological-stage-group',
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};
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}
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throw new Error('Provided staging type must be "Clinical" or "Pathologic"');
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}
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function hasMemberTemplate(categoryIds) {
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if (!categoryIds || categoryIds.length === 0) return {};
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return {
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hasMember: categoryIds.map((id) => reference({ id })),
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};
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}
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function stagingTemplate({
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id,
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subjectId,
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conditionId,
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type,
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stageGroup,
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effectiveDateTime,
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categoryIds,
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}) {
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if (!(id && subjectId && conditionId && effectiveDateTime && stageGroup && type)) {
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throw Error('Trying to render a StagingTemplate, but a required argument is missing;'
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+ ' ensure that id, subjectId, conditionId, effectiveDateTime, stageGroup, type, are all present');
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}
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const typeSpecificData = getTypeSpecificData(type);
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const { categoryCode, code, profileUrl } = typeSpecificData;
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return {
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resourceType: 'Observation',
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id,
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meta: {
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profile: [profileUrl],
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},
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status: 'final',
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category: [
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{
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coding: [
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coding({
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system:
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'http://terminology.hl7.org/CodeSystem/observation-category',
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code: categoryCode,
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}),
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],
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},
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],
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code: {
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coding: [
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coding({
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system: 'http://loinc.org',
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code,
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}),
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],
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},
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subject: reference({ id: subjectId }),
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effectiveDateTime,
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...valueX({ code: stageGroup, system: 'http://cancerstaging.org' }, 'valueCodeableConcept'),
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focus: [reference({ id: conditionId })],
79+
...hasMemberTemplate(categoryIds),
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};
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}
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module.exports = {
84+
stagingTemplate,
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};

‎src/templates/TNMCategoryTemplate.js

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const { coding, reference, valueX } = require('./snippets');
2+
3+
// Returns category specific data based on stage and category type
4+
function getCategorySpecificData(stageType, categoryType) {
5+
if (stageType === 'Clinical') {
6+
const categoryCode = 'survey';
7+
if (categoryType === 'Tumor') {
8+
return {
9+
categoryCode,
10+
profileUrl: 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-primary-tumor-category',
11+
code: '21905-5',
12+
};
13+
}
14+
if (categoryType === 'Metastases') {
15+
return {
16+
categoryCode,
17+
profileUrl: 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-distant-metastases-category',
18+
code: '21907-1',
19+
};
20+
}
21+
if (categoryType === 'Nodes') {
22+
return {
23+
categoryCode,
24+
profileUrl: 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-regional-nodes-category',
25+
code: '21906-3',
26+
};
27+
}
28+
} else if (stageType === 'Pathologic') {
29+
const categoryCode = 'laboratory';
30+
if (categoryType === 'Tumor') {
31+
return {
32+
categoryCode,
33+
profileUrl: 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-pathological-primary-tumor-category',
34+
code: '21899-0',
35+
};
36+
}
37+
if (categoryType === 'Metastases') {
38+
return {
39+
categoryCode,
40+
profileUrl: 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-pathological-distant-metastases-category',
41+
code: '21901-4',
42+
};
43+
}
44+
if (categoryType === 'Nodes') {
45+
return {
46+
categoryCode,
47+
profileUrl: 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-pathological-regional-nodes-category',
48+
code: '21900-6',
49+
};
50+
}
51+
}
52+
53+
throw new Error('Provided stage and category types are not valid.');
54+
}
55+
56+
function tnmCategoryTemplate({
57+
id, subjectId, conditionId, valueCode, effectiveDateTime, categoryType, stageType,
58+
}) {
59+
if (!(id && subjectId && conditionId && valueCode && effectiveDateTime && categoryType && stageType)) {
60+
throw Error('Trying to render a TNMCategoryTemplate, but a required argument is missing;'
61+
+ ' ensure that id, subjectId, conditionId, valueCode, effectiveDateTime, categoryType, and stageType, are all present');
62+
}
63+
64+
const categorySpecificData = getCategorySpecificData(stageType, categoryType);
65+
const { categoryCode, code, profileUrl } = categorySpecificData;
66+
67+
return {
68+
resourceType: 'Observation',
69+
id,
70+
meta: {
71+
profile: [profileUrl],
72+
},
73+
status: 'final',
74+
category: [
75+
{
76+
coding: [
77+
coding({
78+
system:
79+
'http://terminology.hl7.org/CodeSystem/observation-category',
80+
code: categoryCode,
81+
}),
82+
],
83+
},
84+
],
85+
code: {
86+
coding: [
87+
coding({
88+
system: 'http://loinc.org',
89+
code,
90+
}),
91+
],
92+
},
93+
subject: reference({ id: subjectId }),
94+
effectiveDateTime,
95+
...valueX({ code: valueCode, system: 'http://cancerstaging.org' }, 'valueCodeableConcept'),
96+
focus: [reference({ id: conditionId })],
97+
};
98+
}
99+
100+
module.exports = {
101+
tnmCategoryTemplate,
102+
};

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