Fetching additional referenced resources after processing.

fixing hospitalization key.
Tweaking the cerner client to use USCore resources, and then adding additional cerner specific resources.

frontend/src/lib/conduit/fhir/base/fhir401_r4_client.spec.ts

@@ -9,6 +9,8 @@ import { v4 as uuidv4 } from 'uuid';
 
 // @ts-ignore
 import * as FHIR401Client_ProcessBundle from './fixtures/FHIR401Client_ProcessBundle.json';
+// @ts-ignore
+import * as FHIR401Client_ExtractResourceReference from './fixtures/FHIR401Client_ExtractResourceReference.json';
 import {IDatabaseRepository} from '../../../database/interface';
 import {PouchdbCrypto} from '../../../database/plugins/crypto';
 import {ClientConfig} from '../../../models/client/client-config';
@@ -101,4 +103,17 @@ describe('FHIR401Client', () => {
     }, 10000);
   })
 
+  describe('ExtractResourceReference', () => {
+    it('should correctly extract resource identifier from raw resources', async () => {
+
+      //setup
+
+      //test
+      const resp = await client.ExtractResourceReference("CarePlan", FHIR401Client_ExtractResourceReference)
+      //expect
+      expect(resp.length).toEqual(2);
+      expect(resp).toEqual(['Encounter/97961321', 'Practitioner/12763770']);
+    });
+  })
+
 })

frontend/src/lib/conduit/fhir/base/fhir401_r4_client.ts

@@ -1,4 +1,4 @@
-import {IClient, IResourceBundleRaw, IResourceRaw} from '../../interface';
+import {IClient, IResourceBundleEntryRaw, IResourceBundleRaw, IResourceRaw} from '../../interface';
 import {BaseClient} from './base_client';
 import {Source} from '../../../models/database/source';
 import {IDatabaseRepository} from '../../../database/interface';
@@ -88,8 +88,29 @@ export class FHIR401Client extends BaseClient implements IClient {
         let bundle = await this.GetResourceBundlePaginated(`${resourceType}?patient=${this.source.patient}`)
         let wrappedResourceModels = await this.ProcessBundle(bundle)
         let resourceUpsertSummary = await db.UpsertResources(wrappedResourceModels)
+
         upsertSummary.updatedResources = upsertSummary.updatedResources.concat(resourceUpsertSummary.updatedResources)
         upsertSummary.totalResources += resourceUpsertSummary.totalResources
+
+
+        // check if theres any "extracted" resource references that we should sync as well
+        let extractedResourceReferences = []
+        extractedResourceReferences = wrappedResourceModels.reduce((previousVal, wrappedResource) => {
+          return previousVal.concat(this.ExtractResourceReference(wrappedResource.source_resource_type, wrappedResource.resource_raw))
+        }, extractedResourceReferences)
+
+
+        if(extractedResourceReferences.length > 0 ){
+          console.log("Extracted Resource References", extractedResourceReferences)
+
+          let extractedResourceBundle = await this.GenerateResourceBundleFromResourceIds(extractedResourceReferences)
+          let wrappedExtractedResourceBundle = await this.ProcessBundle(extractedResourceBundle)
+          let extractedResourceUpsertSummary = await db.UpsertResources(wrappedExtractedResourceBundle)
+
+          upsertSummary.updatedResources = upsertSummary.updatedResources.concat(extractedResourceUpsertSummary.updatedResources)
+          upsertSummary.totalResources += extractedResourceUpsertSummary.totalResources
+        }
+
       }
       catch (e) {
         console.error(`An error occurred while processing ${resourceType} bundle ${this.source.patient}`)
@@ -109,7 +130,7 @@ export class FHIR401Client extends BaseClient implements IClient {
    * @param resourceRaw
    * @constructor
    */
-  public async ExtractResourceReference(sourceResourceType: string, resourceRaw): Promise<string[]> {
+  public ExtractResourceReference(sourceResourceType: string, resourceRaw): string[] {
     let resourceRefs = []
 
     switch (sourceResourceType) {
@@ -258,16 +279,15 @@ export class FHIR401Client extends BaseClient implements IClient {
           resourceRefs.push(reasonReference.reference)
         })
 
-        //hospitalization[x].origin can contain
+        //hospitalization.origin can contain
         //- Location
         //- Organization
-        //hospitalization[x].destination can contain
+        resourceRefs.push(resourceRaw.hospitalization?.origin?.reference)
+
+        //hospitalization.destination can contain
         //- Location
         //- Organization
-        resourceRaw.hospitalization?.map((hospitalization) => {
-          resourceRefs.push(hospitalization.origin?.reference)
-          resourceRefs.push(hospitalization.destination?.reference)
-        })
+        resourceRefs.push(resourceRaw.hospitalization?.destination?.reference)
 
         //location[x].location can contain
         //- Location
@@ -440,7 +460,6 @@ export class FHIR401Client extends BaseClient implements IClient {
     // remove all null values, remove all duplicates
     let cleanResourceRefs = resourceRefs.filter(i => !(typeof i === 'undefined' || i === null));
     cleanResourceRefs = [...new Set(cleanResourceRefs)]
-
     return cleanResourceRefs
   }
 
@@ -504,6 +523,24 @@ export class FHIR401Client extends BaseClient implements IClient {
       })
   }
 
+  /**
+   * Given a list of resource ids (Patient/xxx, Observation/yyyy), request these resources and generate a pseudo-bundle file
+   * @param resourceIds
+   * @constructor
+   * @protected
+   */
+  protected async GenerateResourceBundleFromResourceIds(resourceIds: string[]): Promise<IResourceBundleRaw>{
+
+    resourceIds = [...new Set(resourceIds)] //make sure they are unique references.
+    let rawResourceRefs = await Promise.all(resourceIds.map(async (extractedResourceRef) => {
+      return {
+        resource: await this.GetRequest(extractedResourceRef) as IResourceRaw
+      } as IResourceBundleEntryRaw
+    }))
+
+    return {resourceType: "Bundle", entry: rawResourceRefs}
+  }
+
   /**
    * Retrieve a resource bundle. While "next" link is present in response, continue to request urls and append BundleEntries
    * @param relativeResourcePath

frontend/src/lib/conduit/fhir/base/fixtures/FHIR401Client_ExtractResourceReference.json

@@ -0,0 +1,41 @@
+{
+  "resourceType": "CarePlan",
+  "id": "197543976",
+  "meta": {
+    "versionId": "1",
+    "lastUpdated": "2021-10-04T14:46:33.000Z"
+  },
+  "text": {
+    "status": "additional",
+    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Care Plan</b></p><p><b>Patient</b>: SMART, NANCYU NHA EEEEEE</p><p><b>Title</b>: Comorbidities found via Retrieve Dx</p><p><b>Description</b>: Malnutrition:Severe --- Inputs [Height: 165.1, Weight: 25, BMI (Calculated): 9.171615976368047]\n\nAnoxic Brain Injury\n\n</p><p><b>Status</b>: Active</p><p><b>Intent</b>: Plan</p><p><b>Category</b>: Assessment and Plan of Treatment</p><p><b>Author</b>: P., MD, Cardio</p><p><b>Effective Period</b>: Oct  4, 2021  2:46 P.M. UTC</p></div>"
+  },
+  "status": "active",
+  "intent": "plan",
+  "category": [
+    {
+      "coding": [
+        {
+          "system": "http://hl7.org/fhir/us/core/CodeSystem/careplan-category",
+          "code": "assess-plan",
+          "display": "Assessment and Plan of Treatment"
+        }
+      ],
+      "text": "Assessment and Plan of Treatment"
+    }
+  ],
+  "title": "Comorbidities found via Retrieve Dx",
+  "subject": {
+    "reference": "Patient/12724066",
+    "display": "SMART, NANCYU NHA EEEEEE"
+  },
+  "encounter": {
+    "reference": "Encounter/97961321"
+  },
+  "period": {
+    "start": "2021-10-04T14:46:33.000Z"
+  },
+  "author": {
+    "reference": "Practitioner/12763770",
+    "display": "P., MD, Cardio"
+  }
+}

frontend/src/lib/conduit/fhir/cerner_client.ts

@@ -18,23 +18,15 @@ export class CernerClient  extends FHIR401Client implements IClient {
    * @constructor
    */
   async SyncAll(db: IDatabaseRepository): Promise<UpsertSummary> {
-    const supportedResources: string[] = [
-      "AllergyIntolerance",
-      "CarePlan",
-      "CareTeam",
-      "Condition",
+    const supportedResources: string[] = this.usCoreResources.concat([
+      "Account",
+      "Appointment",
       "Consent",
-      "Device",
-      "Encounter",
       "FamilyMemberHistory",
-      "Goal",
-      "Immunization",
       "InsurancePlan",
       "MedicationRequest",
       "NutritionOrder",
-      "Observation",
       "Person",
-      "Procedure",
       "Provenance",
       "Questionnaire",
       "QuestionnaireResponse",
@@ -42,7 +34,7 @@ export class CernerClient  extends FHIR401Client implements IClient {
       "Schedule",
       "ServiceRequest",
       "Slot",
-    ]
+    ])
 
     return this.SyncAllByResourceName(db, supportedResources)
   }