Merge pull request #82 from mcode/epic-staging-ext-context

Creates a getConditionsFromContext function for parsing Condition resources off Context

Author: mgramigna

src/helpers/contextUtils.js

@@ -1,24 +1,50 @@
+const _ = require('lodash');
 const logger = require('./logger');
 const { getBundleEntriesByResourceType, getBundleResourcesByType } = require('./fhirUtils');
 
+/**
+* Parses context a Patient resource
+* @param {Object} context - Context object consisting of a FHIR Bundle
+* @return {Object} The first Patient resource found in the bundle
+*/
 function getPatientFromContext(mrn, context) {
   logger.debug('Getting patient from context');
-  const patientInContext = getBundleResourcesByType(context, 'Patient', {}, true);
-  if (!patientInContext) {
+  const patientResourceInContext = getBundleResourcesByType(context, 'Patient', {}, true);
+  if (!patientResourceInContext) {
     throw Error('Could not find a patient in context; ensure that a PatientExtractor is used earlier in your extraction configuration');
   }
   logger.debug('Patient resource found in context.');
-  return patientInContext;
+  return patientResourceInContext;
 }
 
-function getConditionEntriesFromContext(mrn, context) {
-  logger.debug('Getting conditions from context');
-  const conditionsInContext = getBundleEntriesByResourceType(context, 'Condition', {}, false);
-  if (conditionsInContext.length === 0) {
+/**
+* Parses context for Condition entries, which themselves contain resources
+* @param {Object} context - Context object consisting of a FHIR Bundle
+* @return {Array} All the conditions entries found in context
+*/
+function getConditionEntriesFromContext(context) {
+  logger.debug('Getting condition entries from context');
+  const conditionEntriesInContext = getBundleEntriesByResourceType(context, 'Condition', {}, false);
+  if (conditionEntriesInContext.length === 0) {
+    throw Error('Could not find any conditions in context; ensure that a ConditionExtractor is used earlier in your extraction configuration');
+  }
+  logger.debug(`Condition entries found in context. Found ${conditionEntriesInContext.length} condition resources.`);
+  return conditionEntriesInContext;
+}
+
+/**
+* Parses context for Condition resources
+* @param {Object} context - Context object consisting of a FHIR Bundle
+* @return {Array} All the conditions resources found in context
+*/
+function getConditionsFromContext(context) {
+  logger.debug('Getting condition resources from context');
+  const conditionsResourcesInContext = getBundleResourcesByType(context, 'Condition', {}, false);
+  if (_.isEmpty(conditionsResourcesInContext)) {
     throw Error('Could not find any conditions in context; ensure that a ConditionExtractor is used earlier in your extraction configuration');
   }
-  logger.debug(`Condition resources found in context. Found ${conditionsInContext.length} condition resources.`);
-  return conditionsInContext;
+  logger.debug(`Condition resources found in context. Found ${conditionsResourcesInContext.length} condition resources.`);
+  return conditionsResourcesInContext;
 }
 
 /**
@@ -28,16 +54,17 @@ function getConditionEntriesFromContext(mrn, context) {
 */
 function getEncountersFromContext(context) {
   logger.debug('Getting encounter resources from context');
-  const encountersInContext = getBundleResourcesByType(context, 'Encounter');
-  if (encountersInContext.length === 0) {
+  const encounterResourcesInContext = getBundleResourcesByType(context, 'Encounter');
+  if (encounterResourcesInContext.length === 0) {
     throw Error('Could not find any encounter resources in context; ensure that an EncounterExtractor is used earlier in your extraction configuration');
   }
-  logger.debug(`Condition resources found in context. Found ${encountersInContext.length} condition resources.`);
-  return encountersInContext;
+  logger.debug(`Condition resources found in context. Found ${encounterResourcesInContext.length} condition resources.`);
+  return encounterResourcesInContext;
 }
 
 module.exports = {
   getConditionEntriesFromContext,
+  getConditionsFromContext,
   getEncountersFromContext,
   getPatientFromContext,
 };

src/index.js

@@ -64,7 +64,7 @@ const {
 } = require('./helpers/conditionUtils');
 const { getDiseaseStatusCode, getDiseaseStatusEvidenceCode, mEpochToDate } = require('./helpers/diseaseStatusUtils');
 const { formatDate, formatDateTime } = require('./helpers/dateUtils');
-const { getConditionEntriesFromContext, getEncountersFromContext, getPatientFromContext } = require('./helpers/contextUtils');
+const { getConditionEntriesFromContext, getConditionsFromContext, getEncountersFromContext, getPatientFromContext } = require('./helpers/contextUtils');
 
 module.exports = {
   // CLI Related utilities
@@ -134,6 +134,7 @@ module.exports = {
   mEpochToDate,
   // Context operations
   getConditionEntriesFromContext,
+  getConditionsFromContext,
   getEncountersFromContext,
   getPatientFromContext,
 };

test/helpers/contextUtils.test.js

@@ -1,4 +1,4 @@
-const { getConditionEntriesFromContext, getEncountersFromContext, getPatientFromContext } = require('../../src/helpers/contextUtils');
+const { getConditionEntriesFromContext, getConditionsFromContext, getEncountersFromContext, getPatientFromContext } = require('../../src/helpers/contextUtils');
 
 const MOCK_PATIENT_MRN = '123';
 
@@ -27,7 +27,42 @@ describe('getPatientFromContext', () => {
   });
 });
 
-describe('getConditionFromContext', () => {
+describe('getConditionsFromContext', () => {
+  const conditionResource = {
+    resourceType: 'Condition',
+    id: 'mCODEConditionExample01',
+  };
+  const conditionResource2 = {
+    resourceType: 'Condition',
+    id: 'mCODEConditionExample02',
+  };
+  const conditionContext = {
+    resourceType: 'Bundle',
+    type: 'collection',
+    entry: [
+      {
+        fullUrl: 'context-url-1',
+        resource: conditionResource,
+      },
+      {
+        fullUrl: 'context-url-2',
+        resource: conditionResource2,
+      },
+    ],
+  };
+  test('Should return Condition resource in context', () => {
+    const conditions = getConditionsFromContext(conditionContext);
+    expect(conditions).toContain(conditionResource);
+    expect(conditions).toContain(conditionResource2);
+  });
+
+  test('Should throw an error if there is no Condition resource in context', () => {
+    expect(() => getConditionsFromContext({}))
+      .toThrow('Could not find any conditions in context; ensure that a ConditionExtractor is used earlier in your extraction configuration');
+  });
+});
+
+describe('getConditionEntriesFromContext', () => {
   const conditionResource = {
     resourceType: 'Condition',
     id: 'mCODEConditionExample01',
@@ -47,8 +82,8 @@ describe('getConditionFromContext', () => {
     ],
   };
 
-  test('Should return all Condition resources in context', () => {
-    const conditions = getConditionEntriesFromContext(MOCK_PATIENT_MRN, conditionContext);
+  test('Should return all Condition entries in context', () => {
+    const conditions = getConditionEntriesFromContext(conditionContext);
     expect(conditions).toHaveLength(2);
     expect(conditions[0]).toEqual({
       fullUrl: 'context-url-1',
@@ -57,7 +92,7 @@ describe('getConditionFromContext', () => {
   });
 
   test('Should throw an error if there are no conditions in context', () => {
-    expect(() => getConditionEntriesFromContext(MOCK_PATIENT_MRN, {}))
+    expect(() => getConditionEntriesFromContext({}))
       .toThrow('Could not find any conditions in context; ensure that a ConditionExtractor is used earlier in your extraction configuration');
   });
 });