Merge pull request #741 from FluxNotes/external_fhir_mapping

External fhir mapping

config-overrides.js

@@ -1,9 +1,19 @@
+const CopyWebpackPlugin = require('copy-webpack-plugin');
 const {
     override,
     useEslintRc,
+    addWebpackExternals,
+    addWebpackPlugin
 } = require("customize-cra");
 
 
 module.exports = override( 
     useEslintRc(),
+    addWebpackExternals({
+        'fhir-mapper': "Mapper",
+        'babel-polyfill': "_babelPolyfill"
+      }),
+      addWebpackPlugin(new CopyWebpackPlugin([
+        { context:'node_modules/fhir-mapper/dist/', from: 'app.bundle.js*', to: 'static/js/fhir-mapper' }
+    ]))
 );

package.json

@@ -14,7 +14,7 @@
     "downshift": "^1.31.16",
     "elasticlunr": "https://github.com/mgramigna/elasticlunr.js",
     "es6-shim": "0.35.3",
-    "fhir-mapper": "^1.0.6",
+    "fhir-mapper": "^2.0.1",
     "fhirclient": "^0.1.12",
     "flat": "^4.1.0",
     "flux_notes_treatment_options_rest_client": "^1.1.2",
@@ -95,7 +95,8 @@
     "react-scripts": "2.1.8",
     "react-test-renderer": "15.6.2",
     "redux-mock-store": "1.5.3",
-    "testcafe": "0.17.1"
+    "testcafe": "0.17.1",
+    "copy-webpack-plugin" : "5.0.4"
   },
   "resolutions": {
     "moment": "2.22.0",

public/config.js

@@ -13,8 +13,8 @@ CONFIG = {
         isExact: true,
         launchContext: {
             client: {
-                client_id: '6c12dff4-24e7-4475-a742-b08972c4ea27',
-                scope: 'patient/*.read user/*.* openid profile',
+                client_id: '5a14eeb1-973b-4362-9289-59ff27fcc29a',
+                scope:  'patient/AllergyIntolerance.read patient/Appointment.read patient/Binary.read patient/CarePlan.read patient/Condition.read patient/Contract.read patient/Device.read patient/DiagnosticReport.read patient/DocumentReference.read patient/Encounter.read patient/Goal.read patient/Immunization.read patient/MedicationAdministration.read patient/MedicationOrder.read patient/MedicationStatement.read patient/Observation.read patient/Patient.read patient/Person.read patient/Procedure.read patient/ProcedureRequest.read patient/RelatedPerson.read patient/Schedule.read patient/Slot.read user/AllergyIntolerance.read user/Appointment.read user/Binary.read user/CarePlan.read user/Condition.read user/Contract.read user/Device.read user/DiagnosticReport.read user/DocumentReference.read user/Encounter.read user/Goal.read user/Immunization.read user/MedicationAdministration.read user/MedicationOrder.read user/MedicationStatement.read user/Observation.read user/Patient.read user/Person.read user/Practitioner.read user/Procedure.read user/ProcedureRequest.read user/RelatedPerson.read user/Schedule.read user/Slot.read openid profile',
                 // note: the redirect_uri below may need to change in different environments.
                 // a relative URL (ex. /smart or ../smart) won't work in IE
                 redirect_uri: 'http://localhost:3000/smartcompass'
@@ -30,9 +30,10 @@ CONFIG = {
         display: 'Compass™',
         app: "SmartCompassApp",
         isExact: true,
-        dataSource: 'McodeV05SmartOnFhirDataSource',
+        dataSource: 'GenericSmartOnFhirDstu2DataSource',
         dataSourceProps: {
-            resourceTypes: ['Patient', 'Condition', 'Encounter', 'MedicationOrder', 'Observation', 'Organization', 'Practitioner', 'Procedure']
+            mapper: 'cernerSandbox',
+            resourceTypes: ['Patient', 'Condition', 'Encounter', 'MedicationOrder', 'Observation', 'Procedure']
         },
         logoObject: {
             path: './compass-logo.png',
@@ -60,7 +61,7 @@ CONFIG = {
             // (aka, the server listed here can be used as a 'shim')
             // server: "http://localhost:3001/1_0_2"
         }
-    },
+    }, 
     {
         path: '/smart',
         display: 'Flux Notes™',
@@ -96,7 +97,7 @@ CONFIG = {
         dataSource: 'GenericSmartOnFhirDstu2DataSource',
         shortcuts: [],
         dataSourceProps: {
-            mapper: 'syntheaToV05'
+            mapper: 'cernerSandbox'
         }
     },
     {

public/index.html

@@ -13,7 +13,9 @@
                 return window.fluxnotes_app.receive_command(name,data);
             }
     </script>
+    <script src="static/js/fhir-mapper/app.bundle.js" language="javascript"></script>
     <script src="config.js" language="javascript"></script>
+    <script src="mapper.js" language="javascript"></script>
   </head>
   <body>
     <div id="root"></div>

src/dataaccess/GenericSmartOnFhirDstu2DataSource.jsx

@@ -1,11 +1,15 @@
 import McodeV05SmartOnFhirDataSource from "./McodeV05SmartOnFhirDataSource";
 import processFHIRResources from './utils/fhir-entry-processor';
-import mappers from 'fhir-mapper';
+import mappers from './mappers';
 
 class GenericSmartOnFhirDstu2DataSource extends McodeV05SmartOnFhirDataSource {
     constructor(props) {
         super(props);
-        this.mapper = props && props.mapper ? mappers[props.mapper] : null;
+        if (props && typeof props.mapper === 'string') {
+            this.mapper = mappers[props.mapper];
+        } else {
+            this.mapper = props && props.mapper ? props.mapper: null;
+        }
     }
 
     getPatient(id, callback) {

src/dataaccess/McodeV05SmartOnFhirDataSource.jsx

@@ -69,7 +69,7 @@ class McodeV05SmartOnFhirDataSource extends IDataSource {
     }
 
     _handleResponseBundle(newBundle, prevBundle=null) {
-        if (prevBundle) {
+        if (prevBundle && newBundle && newBundle.entry) {
             // merge the entries from the previous bundle into the new one
             newBundle.entry.unshift(...prevBundle.entry);
             newBundle.total = newBundle.entry.length;

src/dataaccess/mappers/CernerSandboxMapper.js

@@ -0,0 +1,76 @@
+import {
+    buildMappers,
+    mappers,
+    utils
+} from 'fhir-mapper';
+
+const primaryCancerConditionCodes = [
+    '254837009', // Malignant neoplasm of breast (disorder) (B)
+    '93761005', // Primary malignant neoplasm of colon (C)
+    '109838007', // Overlapping malignant neoplasm of colon (C)
+    '363406005', // Malignant tumor of colon (C)
+    '94260004', // Secondary malignant neoplasm of colon (C) -- note this is a "secondary" code but is intended to be a primary cancer
+    '254637007', // Non-small cell lung cancer (disorder) (L)
+    '254632001', // Small cell carcinoma of lung (disorder) (L)
+    '424132000', // Non-small cell carcinoma of lung, TNM stage 1 (disorder) (L)
+    '425048006', // Non-small cell carcinoma of lung, TNM stage 2 (disorder) (L)
+    '422968005', // Non-small cell carcinoma of lung, TNM stage 3 (disorder) (L)
+    '423121009', // Non-small cell carcinoma of lung, TNM stage 4 (disorder) (L)
+    '67811000119102', // Primary small cell malignant neoplasm of lung, TNM stage 1 (disorder) (L)
+    '67821000119109', // Primary small cell malignant neoplasm of lung, TNM stage 2 (disorder) (L)
+    '67831000119107', // Primary small cell malignant neoplasm of lung, TNM stage 3 (disorder) (L)
+    '67841000119103', // Primary small cell malignant neoplasm of lung, TNM stage 4 (disorder) (L)
+    // note that none of the 3 prostate cancer codes are in the recommended VS
+    '126906006', // Neoplasm of prostate (P)
+    '92691004', // Carcinoma in situ of prostate (disorder) (P)
+    '314994000', // Metastasis from malignant tumor of prostate (disorder) (P) -- also a "secondary" code but intended to be a primary cancer
+];
+
+
+
+let mapper = {
+    filter: () => true,
+    default: (resource, context) => mappers['syntheaToV05'].execute(resource, context),
+    mappers: [
+        {
+            filter: "Condition.code.coding.where($this.code in %primaryCancerConditionCodes.first())",
+            exec: (resource, context) =>
+                utils.applyProfile(resource, 'http://hl7.org/fhir/us/fhirURL/StructureDefinition/oncocore-CancerDisorderPresent')
+        },
+        {filter: "Observation.code.text = 'AJCCV7 Breast Distant Metastasis (M) Pat'",
+            exec: (resource, context) => {
+                resource.code = {coding: [{code: '21901-4'  , system: 'http://loinc.org'}]};
+                resource.valueCodeableConcept.coding = [{code: resource.valueCodeableConcept.text }];
+
+                // utils.applyProfile(resource, 'http://hl7.org/fhir/us/fhirURL/StructureDefinition/');
+                return resource;
+            }
+        },
+        {filter: "Observation.code.text  = 'AJCCV7 Breast Distant Metastasis (M) Cli'",
+            exec: (resource, context) => {
+                resource.code = {coding: [{code: '21907-1'  , system: 'http://loinc.org'}]};
+                resource.valueCodeableConcept.coding = [{code: resource.valueCodeableConcept.text }];
+                utils.applyProfile(resource, 'http://hl7.org/fhir/us/fhirURL/StructureDefinition/oncocore-TNMClinicalDistantMetastasesClassification');
+                return resource;
+            }
+        },
+        {filter: "Observation.code.text  = 'AJCCV7 Breast Regional Lymph Nodes (N) P'",
+            exec: (resource, context) => {
+                resource.code = {coding: [{code: '21900-6'  , system: 'http://loinc.org'}]};
+                resource.valueCodeableConcept.coding = [{code: resource.valueCodeableConcept.text }];
+                //utils.applyProfile(resource, 'http://hl7.org/fhir/us/fhirURL/StructureDefinition/');
+                return resource;
+            }
+        },
+        {filter: "Observation.code.text  = 'AJCCV7 Breast Regional Lymph Nodes (N) C'",
+            exec: (resource, context) => {
+                resource.code = {coding: [{code: '21906-3'  , system: 'http://loinc.org'}]};
+                resource.valueCodeableConcept.coding = [{code: resource.valueCodeableConcept.text }];
+                utils.applyProfile(resource, 'http://hl7.org/fhir/us/fhirURL/StructureDefinition/oncocore-TNMClinicalRegionalNodesClassification');
+                return resource;
+            }
+        }],
+};
+export default buildMappers(mapper, {
+    primaryCancerConditionCodes
+});

src/dataaccess/mappers/index.js

@@ -0,0 +1,3 @@
+import {mappers} from 'fhir-mapper';
+import cernerSandbox from './CernerSandboxMapper';
+export default {...mappers, cernerSandbox};

src/model/base/FluxConditionPresentAssertion.js

@@ -42,22 +42,22 @@ class FluxConditionPresentAssertion extends FluxEntry {
     }
 
     get code() {
-        if (!this._condition.findingTopicCode || !this._condition.findingTopicCode.value) return null;
-        return this._condition.findingTopicCode.value.coding[0].code.value;
+        if (!this._getTopicCodeCoding()){ return null;}
+        return this._getTopicCodeCoding().code.value;
     }
 
     get codeSystem() {
-        if (!this._condition.findingTopicCode || !this._condition.findingTopicCode.value) return null;
-        return this._condition.findingTopicCode.value.coding[0].codeSystem.value;
+        if (!this._getTopicCodeCoding()) return null;
+        return this._getTopicCodeCoding().codeSystem.value;
     }
 
     get codeURL() {
         return this.codeSystem + "/" + this.code;
     }
 
     get type() {
-        if (!this._condition.findingTopicCode || !this._condition.findingTopicCode.value) return null;
-        return this._displayTextOrCode(this._condition.findingTopicCode.value.coding[0]);
+        if (!this._getTopicCodeCoding()) return null;
+        return this._displayTextOrCode(this._getTopicCodeCoding());
     }
 
     get observation() {
@@ -599,6 +599,13 @@ class FluxConditionPresentAssertion extends FluxEntry {
         return 0;
     }
 
+    _getTopicCodeCoding(){
+        if (this._condition.findingTopicCode &&
+            this._condition.findingTopicCode.value && 
+            this._condition.findingTopicCode.value.coding && 
+            this._condition.findingTopicCode.value.coding.length > 0 ) return this._condition.findingTopicCode.value.coding[0];
+        return null;
+    }
     /**
      * Extract a human-readable string from a code.
      *