Merge pull request #181 from mcode/develop

v2.0.1

Author: julianxcarter

.github/CODEOWNERS

@@ -1 +1 @@
-*   @jafeltra @mgramigna @julianxcarter @dmendelowitz @dtphelan1
+*   @julianxcarter @dmendelowitz @dtphelan1

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "mcode-extraction-framework",
-  "version": "2.0.0",
+  "version": "2.0.1",
   "description": "",
   "contributors": [
     "Julia Afeltra <jafeltra@mitre.org>",
@@ -29,7 +29,7 @@
     "fhir-crud-client": "^1.2.2",
     "fhirpath": "2.1.5",
     "lodash": "^4.17.21",
-    "moment": "^2.26.0",
+    "moment": "^2.29.3",
     "nodemailer": "^6.7.2",
     "winston": "^3.2.1"
   },

package.json

@@ -18,8 +18,12 @@ class FHIRAdverseEventExtractor extends BaseFHIRExtractor {
     try {
       allResearchStudyResources = getResearchStudiesFromContext(context);
     } catch (e) {
-      logger.error(e.message);
+      logger.debug(e.message);
       logger.debug(e.stack);
+      if (!this.study) {
+        logger.error('There is no ResearchStudy id to complete a request for Adverse Event resources; please include a ClinicalTrialInformationExtractor,'
+        + ' ResearchStudyExtractor, or "study" constructorArg in your extraction configuration.');
+      }
     }
 
     // The patient is referenced in the 'subject' field of an AdverseEvent

src/extractors/FHIRAdverseEventExtractor.js

@@ -47,6 +47,36 @@ function getConditionsFromContext(context) {
   return conditionsResourcesInContext;
 }
 
+/**
+* Parses context for AdverseEvent resources
+* @param {Object} context - Context object consisting of a FHIR Bundle
+* @return {Array} All the AdverseEvent resources found in context
+*/
+function getAdverseEventsFromContext(context) {
+  logger.debug('Getting adverse event resources from context');
+  const adverseEventResourcesInContext = getBundleResourcesByType(context, 'AdverseEvent', {}, false);
+  if (_.isEmpty(adverseEventResourcesInContext)) {
+    throw Error('Could not find any adverse events in context; ensure that an AdverseEventExtractor is used earlier in your extraction configuration');
+  }
+  logger.debug(`AdverseEvent resources found in context. Found ${adverseEventResourcesInContext.length} adverse event resources.`);
+  return adverseEventResourcesInContext;
+}
+
+/**
+* Parses context for AdverseEvent entries, which themselves contain resources
+* @param {Object} context - Context object consisting of a FHIR Bundle
+* @return {Array} All the AdverseEvents entries found in context
+*/
+function getAdverseEventEntriesFromContext(context) {
+  logger.debug('Getting adverse event entries from context');
+  const adverseEventEntriesInContext = getBundleEntriesByResourceType(context, 'AdverseEvent', {}, false);
+  if (adverseEventEntriesInContext.length === 0) {
+    throw Error('Could not find any adverse events in context; ensure that an AdverseEventExtractor is used earlier in your extraction configuration');
+  }
+  logger.debug(`AdverseEvent entries found in context. Found ${adverseEventEntriesInContext.length} adverse event resources.`);
+  return adverseEventEntriesInContext;
+}
+
 /**
 * Parses context for Encounter resources
 * @param {Object} context - Context object consisting of a FHIR Bundle
@@ -78,4 +108,6 @@ module.exports = {
   getEncountersFromContext,
   getPatientFromContext,
   getResearchStudiesFromContext,
+  getAdverseEventEntriesFromContext,
+  getAdverseEventsFromContext,
 };

src/helpers/contextUtils.js

@@ -65,10 +65,18 @@ const {
 const { getDiseaseStatusCode, getDiseaseStatusEvidenceCode, mEpochToDate } = require('./helpers/diseaseStatusUtils');
 const { formatDate, formatDateTime } = require('./helpers/dateUtils');
 const { lowercaseLookupQuery, createLowercaseLookup, createInvertedLookup } = require('./helpers/lookupUtils');
-const { getConditionEntriesFromContext, getConditionsFromContext, getEncountersFromContext, getPatientFromContext } = require('./helpers/contextUtils');
+const {
+  getConditionEntriesFromContext,
+  getConditionsFromContext,
+  getEncountersFromContext,
+  getPatientFromContext,
+  getAdverseEventsFromContext,
+  getAdverseEventEntriesFromContext,
+} = require('./helpers/contextUtils');
 const { parsePatientIds } = require('./helpers/appUtils');
 const { getConfig, validateConfig } = require('./helpers/configUtils');
 const configSchema = require('./helpers/schemas/config.schema.json');
+const { sortExtractors } = require('./helpers/dependencyUtils');
 
 module.exports = {
   // CLI Related utilities
@@ -143,11 +151,14 @@ module.exports = {
   logOperationOutcomeInfo,
   lowercaseLookupQuery,
   mEpochToDate,
+  sortExtractors,
   // Context operations
   getConditionEntriesFromContext,
   getConditionsFromContext,
   getEncountersFromContext,
   getPatientFromContext,
+  getAdverseEventEntriesFromContext,
+  getAdverseEventsFromContext,
   // Configuration file schema
   configSchema,
 };