Merge pull request #66 from mcode/extract-surgical-procedure

WIP: mCODE Surgical Procedure Extractor

Author: Dtphelan1

src/extractors/MCODESurgicalProcedureExtractor.js

@@ -0,0 +1,57 @@
+const path = require('path');
+const { Extractor } = require('./Extractor');
+const { FHIRProcedureExtractor } = require('./FHIRProcedureExtractor');
+const { getBundleEntriesByResourceType } = require('../helpers/fhirUtils');
+const { checkCodeInVs } = require('../helpers/valueSetUtils');
+const logger = require('../helpers/logger');
+
+function getMCODESurgicalProcedures(fhirProcedures) {
+  const surgicalProcedureVSFilepath = path.resolve(__dirname, '..', 'helpers', 'valueSets', 'ValueSet-mcode-cancer-related-surgical-procedure-vs.json');
+  return fhirProcedures.filter((procedure) => {
+    const coding = procedure.resource.code ? procedure.resource.code.coding : [];
+    // NOTE: Update when checkCodeInVS checks code and system (might be able to pass in the full Coding)
+    return coding.some((c) => checkCodeInVs(c.code, surgicalProcedureVSFilepath));
+  });
+}
+
+class MCODESurgicalProcedureExtractor extends Extractor {
+  constructor({ baseFhirUrl, requestHeaders }) {
+    super({ baseFhirUrl, requestHeaders });
+    this.fhirProcedureExtractor = new FHIRProcedureExtractor({ baseFhirUrl, requestHeaders });
+  }
+
+  updateRequestHeaders(newHeaders) {
+    this.fhirProcedureExtractor.updateRequestHeaders(newHeaders);
+  }
+
+  async getFHIRProcedures(mrn, context) {
+    const proceduresInContext = getBundleEntriesByResourceType(context, 'Procedure', {});
+    if (proceduresInContext.length !== 0) {
+      logger.debug('Procedure resources found in context.');
+      return proceduresInContext;
+    }
+
+    logger.debug('Getting procedures available for patient');
+    const procedureBundle = await this.fhirProcedureExtractor.get({ mrn, context });
+
+    logger.debug(`Found ${procedureBundle.entry.length} result(s) in Procedure search`);
+    return procedureBundle.entry;
+  }
+
+  async get({ mrn, context }) {
+    const fhirProcedures = await this.getFHIRProcedures(mrn, context);
+
+    // Filter to only include procedures that are from MCODE surgical procedure VS
+    const surgicalProcedures = getMCODESurgicalProcedures(fhirProcedures);
+
+    return {
+      resourceType: 'Bundle',
+      type: 'collection',
+      entry: surgicalProcedures,
+    };
+  }
+}
+
+module.exports = {
+  MCODESurgicalProcedureExtractor,
+};

src/extractors/index.js

@@ -18,6 +18,7 @@ const { FHIRMedicationStatementExtractor } = require('./FHIRMedicationStatementE
 const { FHIRObservationExtractor } = require('./FHIRObservationExtractor');
 const { FHIRPatientExtractor } = require('./FHIRPatientExtractor');
 const { FHIRProcedureExtractor } = require('./FHIRProcedureExtractor');
+const { MCODESurgicalProcedureExtractor } = require('./MCODESurgicalProcedureExtractor');
 
 module.exports = {
   BaseFHIRExtractor,
@@ -40,4 +41,5 @@ module.exports = {
   FHIRObservationExtractor,
   FHIRPatientExtractor,
   FHIRProcedureExtractor,
+  MCODESurgicalProcedureExtractor,
 };