Merge pull request #8 from standardhealth/ignoreFn

Add ignoreFn to syntheaToV09 and rework utils
standardhealth · Sep 4, 2019 · 1a17187 · 1a17187
2 parents 33049e2 + 1485c7b
commit 1a17187
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Showing 9 changed files with 54 additions and 16 deletions.
diff --git a/dist/app.bundle.js b/dist/app.bundle.js
diff --git a/dist/app.bundle.js.map b/dist/app.bundle.js.map
diff --git a/dist/app.node.bundle.js b/dist/app.node.bundle.js
diff --git a/dist/app.node.bundle.js.map b/dist/app.node.bundle.js.map
diff --git a/src/mapping/mappers/cerner.js b/src/mapping/mappers/cerner.js
@@ -1,9 +1,9 @@
 const {
   buildMappers
 } = require('../mapper');
-const utils = require('../../utils/common');
-const mcodeUtils09 = require('../../utils/mcodeUtils09');
+const utils = require('../../utils');
 const syntheaToV09 = require('./syntheaToV09');
+const mcodeUtils09 = utils.mcodeUtils09;
 
 let vars = {
   pStageCodes: [ 'AJCCV8 MAG-PRO P Stage', 'AJCCV8 BRE-INV P Stage'],

diff --git a/src/mapping/mappers/syntheaToV05.js b/src/mapping/mappers/syntheaToV05.js
@@ -1,5 +1,5 @@
 const { buildMappers } = require('../mapper');
-const {applyProfile} = require('../../utils/common');
+const {applyProfile} = require('../../utils');
 
 const DEFAULT_PROFILE = {
     'Patient': 'http://hl7.org/fhir/us/fhirURL/StructureDefinition/shr-entity-Patient',

diff --git a/src/mapping/mappers/syntheaToV09.js b/src/mapping/mappers/syntheaToV09.js
@@ -1,7 +1,5 @@
 const { buildMappers } = require('../mapper');
-const { applyProfile, applyProfileFunction } = require('../../utils/common');
-const mcodeUtils09 = require('../../utils/mcodeUtils09');
-
+const { applyProfile, applyProfileFunction, hasProfileFromList, mcodeUtils09 } = require('../../utils');
 
 const defaultProfile = (resourceType) => {
     switch (resourceType) {
@@ -28,6 +26,36 @@ const defaultProfile = (resourceType) => {
     }
 };
 
+const allRelevantProfiles = [
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-AllergyIntolerance',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-Condition',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-DiagnosticReport',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-Encounter',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-MedicationAdministration',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-MedicationRequest',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-Observation',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-Organization',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-Patient',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-Practitioner',
+    'http://hl7.org/fhir/us/shr/DSTU2/StructureDefinition/shr-core-Procedure',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-BloodPressure',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-BodyHeight',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-BodyWeight',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-CancerDiseaseStatus',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-CancerRelatedRadiationProcedure',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-CancerRelatedSurgicalProcedure',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-PrimaryCancerCondition',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-SecondaryCancerCondition',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMClinicalDistantMetastasesCategory',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMClinicalPrimaryTumorCategory',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMClinicalRegionalNodesCategory',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMClinicalStageGroup',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMPathologicDistantMetastasesCategory',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMPathologicPrimaryTumorCategory',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMPathologicRegionalNodesCategory',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMPathologicStageGroup',
+    'http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TumorMarkerTest'
+];
 
 const nthWord = (string, index) => {
     return string.split(' ')[index];
@@ -46,6 +74,7 @@ const stripParens = (string) => {
 
 const resourceMapping = {
     filter: () => true,
+    ignore: (resource) => hasProfileFromList(resource, allRelevantProfiles),
     default: (resource, _context) => applyProfile(resource, defaultProfile(resource.resourceType)),
     mappers: [
         {

diff --git a/src/utils/common.js b/src/utils/common.js
@@ -15,6 +15,15 @@ const addExtension = (resource, newExtension) => {
   resource.extension.push(newExtension);
 };
 
+const hasProfileFromList = (resource, profiles) => {
+  // ignore resources that already have mCODE profiles. we will assume they are profiled correctly
+  if (!resource || !resource.meta || !resource.meta.profile) {
+      return false; // i.e., do not ignore this since it has no profiles
+  }
+  // check if any of the profiles are mcode. returns null (falsy) if none found or the profile itself (truthy)
+  return resource.meta.profile.find(p => profiles.includes(p));
+}
+
 const applyProfileFunction = (profile) => {
     // return an anonymous function wrapper to apply this specific profile to given resources
     return (resource, _context) => applyProfile(resource, profile);
@@ -65,4 +74,4 @@ const find = (context, path, options = {}) => {
    return results[0];
  };
 
-module.exports = {find, applyProfile, addExtension, applyProfileFunction, isTrue, addRelated};
+module.exports = {find, applyProfile, addExtension, hasProfileFromList, applyProfileFunction, isTrue, addRelated};
diff --git a/src/utils/index.js b/src/utils/index.js
@@ -1,3 +1,3 @@
 const common = require('./common');
 const mcodeUtils09 = require('./mcodeUtils09');
-module.exports = {common, mcodeUtils09};
+module.exports = {...common, mcodeUtils09};