adding Base64 methods

Adding tests for BaseClient
Adding Fhir401Client
Adding fixtures for BaseClient and Fhir401Client

README.md

@@ -6,3 +6,6 @@ Find & replace the following
 - `fastenhealth` - find and replace this with your binary name
     - make sure you rename the folder as well.  
 
+# Running tests
+
+- ng test --include='**/base_client.spec.ts'       

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

@@ -1,6 +1,8 @@
-
 import {BaseClient} from './base_client';
 import {Source} from '../../../models/database/source';
+import * as BaseClient_GetRequest from './fixtures/BaseClient_GetRequest.json';
+import * as BaseClient_GetFhirVersion from './fixtures/BaseClient_GetFhirVersion.json';
+
 
 class TestClient extends BaseClient {
   constructor(source: Source) {
@@ -13,25 +15,19 @@ describe('BaseClient', () => {
 
   beforeEach(async () => {
     client = new TestClient(new Source({
-      "authorization_endpoint": "https://auth.logicahealth.org/authorize",
+      "authorization_endpoint": "https://fhirsandbox.healthit.gov/open/r4/authorize",
-      "token_endpoint": "https://auth.logicahealth.org/token",
+      "token_endpoint": "https://fhirsandbox.healthit.gov/open/r4/token",
-      "introspection_endpoint": "https://auth.logicahealth.org/introspect",
+      "introspection_endpoint": "",
-      "userinfo_endpoint": "",
+      "issuer": "https://fhirsandbox.healthit.go",
-      "scopes_supported": ["openid", "fhirUser", "patient/*.read", "offline_access"],
+      "api_endpoint_base_url": "https://fhirsandbox.healthit.gov/secure/r4/fhir",
-      "issuer": "https://auth.logicahealth.org",
+      "client_id": "9ad3ML0upIMiawLVdM5-DiPinGcv7M",
-      "grant_types_supported": ["authorization_code"],
+      "redirect_uri": "https://lighthouse.fastenhealth.com/sandbox/callback/healthit",
-      "response_types_supported": ["code"],
-      "aud": "",
-      "code_challenge_methods_supported": ["S256"],
-      "api_endpoint_base_url": "https://api.logicahealth.org/fastenhealth/data",
-      "client_id": "12b14c49-a4da-42f7-9e6f-2f19db622962",
-      "redirect_uri": "https://lighthouse.fastenhealth.com/sandbox/callback/logica",
       "confidential": false,
-      "source_type": "logica",
+      "source_type": "healthit",
-      "patient": "smart-1288992",
+      "patient": "placeholder",
-      "access_token": "xxx.xxx.xxx",
+      "access_token": "2e1be8c72d4d5225aae264a1fb7e1d3e",
-      "refresh_token": "xxx.xxx.",
+      "refresh_token": "",
-      "expires_at": 1664949030,
+      "expires_at": 16649837100, //aug 11, 2497 (for testing)
     }));
   });
 
@@ -41,14 +37,35 @@ describe('BaseClient', () => {
 
   describe('GetRequest', () => {
     it('should make an authorized request', async () => {
-      const resp = await client.GetRequest("Patient/smart-1288992")
 
-      expect(resp).toEqual({
+      //setup
-        resourceType: "Patient",
+      let response = new Response(JSON.stringify(BaseClient_GetRequest));
-        id: "source:aetna:patient"
+      Object.defineProperty(response, "url", { value: `${client.source.api_endpoint_base_url}/Patient/${client.source.patient}`});
-      });
+      spyOn(window, "fetch").and.returnValue(Promise.resolve(response));
+
+      //test
+      const resp = await client.GetRequest(`Patient/${client.source.patient}`)
+
+      //expect
+      expect(resp.resourceType).toEqual("Patient");
+      expect(resp.id).toEqual("123d41e1-0f71-4e9f-8eb2-d1b1330201a6");
     });
   })
 
+  describe('GetFhirVersion', () => {
+    it('should make an authorized request', async () => {
+      //setup
+      let response = new Response(JSON.stringify(BaseClient_GetFhirVersion));
+      Object.defineProperty(response, "url", { value: `${client.source.api_endpoint_base_url}/metadata`});
+      spyOn(window, "fetch").and.returnValue(Promise.resolve(response));
+
+      //test
+      const resp = await client.GetFhirVersion()
+
+      //expect
+      expect(resp).toEqual("4.0.1");
+    });
+  });
+
 
 })

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

@@ -1,6 +1,6 @@
 import {Source} from '../../../models/database/source';
 import * as Oauth from '@panva/oauth4webapi';
-import {IResourceInterface} from '../../interface';
+import {IResourceRaw} from '../../interface';
 
 // BaseClient is an abstract/partial class, its intended to be used by FHIR clients, and generically handle OAuth requests.
 export abstract class BaseClient {
@@ -26,8 +26,14 @@ export abstract class BaseClient {
     }
   }
 
+  public async GetFhirVersion(): Promise<any> {
+    return this.GetRequest("metadata")
+      .then((resp) => {
+        return resp.fhirVersion
+      })
+  }
 
-  public async GetRequest(resourceSubpathOrNext: string): Promise<IResourceInterface> {
+  public async GetRequest(resourceSubpathOrNext: string): Promise<any> {
 
     //check if the url is absolute
     let resourceUrl: string
@@ -53,6 +59,22 @@ export abstract class BaseClient {
     // return err
   }
 
+  /////////////////////////////////////////////////////////////////////////////
+  // Protected methods
+  /////////////////////////////////////////////////////////////////////////////
+
+  protected GetPatientBundle(patientId: string): Promise<any> {
+    return this.GetRequest(`Patient/${patientId}/$everything`)
+  }
+
+  protected GetPatient(patientId: string): Promise<IResourceRaw> {
+    return this.GetRequest(`Patient/${patientId}`)
+  }
+
+  /////////////////////////////////////////////////////////////////////////////
+  // Private methods
+  /////////////////////////////////////////////////////////////////////////////
+
   private async refreshExpiredTokenIfRequired(source: Source): Promise<Source> {
     //check if token has expired, and a refreshtoken is available
     // Note: source.expires_at is in seconds, Date.now() is in milliseconds.

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

@@ -0,0 +1,80 @@
+import {FHIR401Client} from './fhir401_r4_client';
+import {Source} from '../../../models/database/source';
+import * as FHIR401Client_ProcessBundle from './fixtures/FHIR401Client_ProcessBundle.json';
+import {IResourceBundleRaw} from '../../interface';
+import {ResourceFhir} from '../../../models/database/resource_fhir';
+import {NewRepositiory} from '../../../database/pouchdb_repository';
+import {Base64} from '../../../utils/base64';
+
+class TestClient extends FHIR401Client {
+  constructor(source: Source) {
+    super(source);
+  }
+
+  public async ProcessBundle(bundle: IResourceBundleRaw): Promise<ResourceFhir[]> {
+    return super.ProcessBundle(bundle);
+  }
+}
+
+describe('FHIR401Client', () => {
+  let client: TestClient;
+
+  beforeEach(async () => {
+    client = new TestClient(new Source({
+      "_id": "source:aetna:12345",
+      "authorization_endpoint": "https://fhirsandbox.healthit.gov/open/r4/authorize",
+      "token_endpoint": "https://fhirsandbox.healthit.gov/open/r4/token",
+      "introspection_endpoint": "",
+      "issuer": "https://fhirsandbox.healthit.go",
+      "api_endpoint_base_url": "https://fhirsandbox.healthit.gov/secure/r4/fhir",
+      "client_id": "9ad3ML0upIMiawLVdM5-DiPinGcv7M",
+      "redirect_uri": "https://lighthouse.fastenhealth.com/sandbox/callback/healthit",
+      "confidential": false,
+      "source_type": "healthit",
+      "patient": "placeholder",
+      "access_token": "2e1be8c72d4d5225aae264a1fb7e1d3e",
+      "refresh_token": "",
+      "expires_at": 16649837100, //aug 11, 2497 (for testing)
+    }));
+  });
+
+  it('should be created', () => {
+    expect(client).toBeTruthy();
+  });
+
+  describe('ProcessBundle', () => {
+    it('should correctly wrap each BundleEntry with ResourceFhir', async () => {
+
+      //setup
+
+      //test
+      const resp = await client.ProcessBundle(FHIR401Client_ProcessBundle)
+      //expect
+      expect(resp.length).toEqual(206);
+      expect(resp[0].source_resource_id).toEqual("c088b7af-fc41-43cc-ab80-4a9ab8d47cd9");
+      expect(resp[0].source_resource_type).toEqual("Patient");
+    });
+  })
+
+  describe('SyncAll', () => {
+    it('should correctly add resources to the database', async () => {
+      //setup
+      let response = new Response(JSON.stringify(FHIR401Client_ProcessBundle));
+      Object.defineProperty(response, "url", { value: `${client.source.api_endpoint_base_url}/Patient/${client.source.patient}/$everything`});
+      spyOn(window, "fetch").and.returnValue(Promise.resolve(response));
+      const db = NewRepositiory("fastentest")
+
+      //test
+      const resp = await client.SyncAll(db)
+      const firstResourceFhir = resp[0]
+      const resourceIdParts = firstResourceFhir.split(":")
+
+      //expect
+      expect(resp.length).toEqual(206);
+      expect(firstResourceFhir).toEqual('resource_fhir:c291cmNlOmFldG5hOjEyMzQ1:Patient:c088b7af-fc41-43cc-ab80-4a9ab8d47cd9');
+      expect(Base64.Decode(resourceIdParts[1])).toEqual("source:aetna:12345");
+
+    });
+  })
+
+})

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

@@ -0,0 +1,62 @@
+import {IClient, IResourceBundleRaw, IResourceRaw} from '../../interface';
+import {BaseClient} from './base_client';
+import {Source} from '../../../models/database/source';
+import {IDatabaseRepository} from '../../../database/interface';
+import {ResourceFhir} from '../../../models/database/resource_fhir';
+
+export class FHIR401Client extends BaseClient implements IClient {
+
+  //clients extending this class must validate fhirVersion matches using conformance/metadata url.
+  fhirVersion = "4.0.1"
+
+  constructor(source: Source) {
+    super(source);
+  }
+
+  public async SyncAll(db: IDatabaseRepository): Promise<string[]> {
+    const bundle = await this.GetPatientBundle(this.source.patient)
+
+    const wrappedResourceModels = await this.ProcessBundle(bundle)
+    //todo, create the resources in dependency order
+
+    //TODO bulk insert
+    // for(let dbModel of wrappedResourceModels){
+    //   db.CreateResource(dbModel)
+    // }
+    console.log(wrappedResourceModels)
+    return db.CreateResources(wrappedResourceModels)
+
+  }
+
+  public async SyncAllBundle(db: IDatabaseRepository, bundleFile: any): Promise<any> {
+    return Promise.resolve(undefined);
+  }
+
+  /////////////////////////////////////////////////////////////////////////////
+  // Protected methods
+  /////////////////////////////////////////////////////////////////////////////
+  protected async ProcessBundle(bundle: IResourceBundleRaw): Promise<ResourceFhir[]> {
+    // console.log(bundle)
+    // process each entry in bundle
+    return bundle.entry
+      .filter((bundleEntry) => {
+        return bundleEntry.resource.id // keep this entry if it has an ID, skip otherwise.
+      })
+      .map((bundleEntry) => {
+        const wrappedResourceModel = new ResourceFhir()
+        wrappedResourceModel.source_id = this.source._id
+        wrappedResourceModel.source_resource_id = bundleEntry.resource.id
+        wrappedResourceModel.source_resource_type = bundleEntry.resource.resourceType
+        wrappedResourceModel.resource_raw = bundleEntry.resource
+        // TODO find a way to safely/consistently get the resource updated date (and other metadata) which shoudl be added to the model.
+        // wrappedResourceModel.updated_at = bundleEntry.resource.meta?.lastUpdated
+        return wrappedResourceModel
+      })
+
+
+  }
+
+  /////////////////////////////////////////////////////////////////////////////
+  // Private methods
+  /////////////////////////////////////////////////////////////////////////////
+}

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

@@ -0,0 +1,159 @@
+{
+  "resourceType": "Patient",
+  "id": "123d41e1-0f71-4e9f-8eb2-d1b1330201a6",
+  "meta": {
+    "versionId": "1.0"
+  },
+  "extension": [
+    {
+      "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+      "extension": [
+        {
+          "url": "ombCategory",
+          "valueCoding": {
+            "system": "urn:oid:2.16.840.1.113883.6.238",
+            "code": "2054-5",
+            "display": "Black or African American"
+          }
+        },
+        {
+          "url": "text",
+          "valueString": "Black or African American"
+        }
+      ]
+    },
+    {
+      "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+      "extension": [
+        {
+          "url": "ombCategory",
+          "valueCoding": {
+            "system": "urn:oid:2.16.840.1.113883.6.238",
+            "code": "2135-2",
+            "display": "Hispanic or Latino"
+          }
+        },
+        {
+          "url": "text",
+          "valueString": "Hispanic or Latino"
+        }
+      ]
+    },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+      "valueString": "Ramona980 Franco581"
+    },
+    {
+      "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
+      "valueCode": "M"
+    },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+      "valueCode": "masked"
+    }
+  ],
+  "identifier": [
+    {
+      "system": "https://github.com/synthetichealth/synthea",
+      "value": "123d41e1-0f71-4e9f-8eb2-d1b1330201a6"
+    },
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+            "code": "MR",
+            "display": "Medical Record Number"
+          }
+        ]
+      },
+      "system": "http://hospital.smarthealthit.org",
+      "value": "123d41e1-0f71-4e9f-8eb2-d1b1330201a6"
+    },
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+            "code": "SS",
+            "display": "Social Security Number"
+          }
+        ]
+      },
+      "system": "http://hl7.org/fhir/sid/us-ssn",
+      "value": "999-50-6731"
+    },
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+            "code": "DL",
+            "display": "Drivers License"
+          }
+        ]
+      },
+      "system": "urn:oid:2.16.840.1.113883.4.3.25",
+      "value": "S99957478"
+    }
+  ],
+  "name": [
+    {
+      "use": "official",
+      "family": "Gutiérrez115",
+      "given": [
+        "Hugo693"
+      ],
+      "prefix": [
+        "Mr."
+      ]
+    }
+  ],
+  "telecom": [
+    {
+      "system": "phone",
+      "value": "555-914-6475",
+      "use": "home"
+    }
+  ],
+  "gender": "male",
+  "birthDate": "1969-01-12",
+  "address": [
+    {
+      "line": [
+        "[\"293 Douglas Ramp\"]"
+      ],
+      "city": "Natick",
+      "state": "MA",
+      "postalCode": "01999",
+      "country": "US",
+      "period": {
+        "start": "1969-01-12T00:00:00+00:00"
+      }
+    }
+  ],
+  "maritalStatus": {
+    "coding": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus",
+        "code": "M",
+        "display": "M"
+      }
+    ],
+    "text": "M"
+  },
+  "multipleBirthBoolean": false,
+  "communication": [
+    {
+      "language": {
+        "coding": [
+          {
+            "system": "urn:ietf:bcp:47",
+            "code": "es",
+            "display": "Spanish"
+          }
+        ]
+      }
+    }
+  ]
+}

frontend/src/lib/conduit/interface.ts

@@ -1,14 +1,45 @@
 import {IDatabaseRepository} from '../database/interface';
 
 export interface IClient {
+  fhirVersion: string
   GetRequest(resourceSubpath: string): Promise<any>
+  GetFhirVersion(): Promise<any>
   SyncAll(db: IDatabaseRepository): Promise<any>
 
   //Manual client ONLY functions
   SyncAllBundle(db: IDatabaseRepository, bundleFile: any): Promise<any>
 }
 
-export interface IResourceInterface {
+//This is the "raw" Fhir resource
+export interface IResourceRaw {
   resourceType: string
   id?: string
+  meta?: IResourceMetaRaw
+}
+// This is the "raw" Fhir Bundle resource
+export interface IResourceBundleRaw {
+  resourceType: string
+  id?: string
+  entry: IResourceBundleEntryRaw[]
+  total?: number
+  link?: IResourceBundleLinkRaw[]
+  meta?: IResourceMetaRaw
+}
+
+export interface IResourceBundleLinkRaw {
+  id?: string
+  relation: string
+  url: string
+}
+
+export interface IResourceBundleEntryRaw {
+  id?: string
+  fullUrl?: string
+  resource: IResourceRaw
+}
+
+export interface IResourceMetaRaw {
+  id?: string
+  versionId?: string
+  lastUpdated: string
 }

frontend/src/lib/database/constants.ts

@@ -1,3 +1,4 @@
 export enum DocType {
-  Source= "source",
+  Source = "source",
+  ResourceFhir = "resource_fhir"
 }

frontend/src/lib/database/interface.ts

@@ -1,7 +1,11 @@
 import {Source} from '../models/database/source';
+import {ResourceFhir} from '../models/database/resource_fhir';
 // import {SourceSummary} from '../../app/models/fasten/source-summary';
 
 export interface IDatabaseDocument {
+  _id?: string
+  _rev?: string
+  doc_type: string
   populateId(): void
 }
 
@@ -31,4 +35,10 @@ export interface IDatabaseRepository {
   DeleteSource(source_id: string): Promise<boolean>
   // GetSourceSummary(source_id: string): Promise<SourceSummary>
   GetSources(): Promise<IDatabasePaginatedResponse>
+
+
+  CreateResource(resource: ResourceFhir): Promise<string>
+  CreateResources(resources: ResourceFhir[]): Promise<string[]>
+  GetResource(resource_id: string): Promise<ResourceFhir>
+  GetResources(): Promise<IDatabasePaginatedResponse>
 }

frontend/src/lib/database/pouchdb_repository.spec.ts

@@ -43,7 +43,7 @@ describe('PouchdbRepository', () => {
 
       const createdSource = await repository.GetSource(createdId)
 
-      expect(createdSource.docType).toEqual(DocType.Source);
+      expect(createdSource.doc_type).toEqual(DocType.Source);
       expect(createdSource.patient).toEqual('patient');
       expect(createdSource.source_type).toEqual(SourceType.Aetna);
       expect(createdSource.access_token).toEqual('hello-world');

frontend/src/lib/database/pouchdb_repository.ts

@@ -3,6 +3,7 @@ import {IDatabasePaginatedResponse, IDatabaseDocument, IDatabaseRepository} from
 import * as PouchDB from 'pouchdb/dist/pouchdb';
 // import * as PouchDB from 'pouchdb';
 import {DocType} from './constants';
+import {ResourceFhir} from '../models/database/resource_fhir';
 
 export function NewRepositiory(databaseName: string = 'fasten'): IDatabaseRepository {
   return new PouchdbRepository(databaseName)
@@ -44,6 +45,32 @@ export class PouchdbRepository implements IDatabaseRepository {
     return this.deleteDocument(source_id)
   }
 
+  public async CreateResource(resource: ResourceFhir): Promise<string> {
+    return this.createDocument(resource);
+  }
+
+  public async CreateResources(resources: ResourceFhir[]): Promise<string[]> {
+    return this.createBulk(resources);
+  }
+
+  public async GetResource(resource_id: string): Promise<ResourceFhir> {
+    return this.getDocument(resource_id)
+      .then((doc) => {
+        return new ResourceFhir(doc)
+      })
+  }
+
+  public async GetResources(): Promise<IDatabasePaginatedResponse> {
+    return this.findDocumentByDocType(DocType.ResourceFhir)
+      .then((docWrapper) => {
+
+        docWrapper.rows = docWrapper.rows.map((result) => {
+          return new ResourceFhir(result.doc)
+        })
+        return docWrapper
+      })
+  }
+
 
   ///////////////////////////////////////////////////////////////////////////////////////
   // CRUD Operators
@@ -73,6 +100,15 @@ export class PouchdbRepository implements IDatabaseRepository {
       );
   }
 
+  // create multiple documents, returns a list of generated ids
+  private createBulk(docs: IDatabaseDocument[]): Promise<string[]> {
+    return this.GetDB()
+      .bulkDocs(docs.map((doc) => { doc.populateId(); return doc }))
+      .then((results): string[] => {
+        return results.map((result) => result.id)
+      })
+  }
+
   private getDocument(id: string): Promise<any> {
     return this.GetDB()
       .get(id)

frontend/src/lib/models/database/resource_fhir.ts

@@ -0,0 +1,32 @@
+import {DocType} from '../../database/constants';
+import {IResourceRaw} from '../../conduit/interface';
+import {Base64} from '../../utils/base64';
+
+export class ResourceFhir {
+  _id?: string
+  _rev?: string
+  doc_type: string
+
+  created_at?: Date
+  updated_at?: Date
+  source_id: string
+  source_resource_type: string
+  source_resource_id: string
+
+  resource_raw: IResourceRaw
+
+  constructor(object?: any) {
+    if(object){
+      object.doc_type = DocType.ResourceFhir
+      return Object.assign(this, object)
+    } else{
+      this.doc_type = DocType.ResourceFhir
+      return this
+    }
+  }
+
+  populateId(){
+    //TODO: source_id should be base64 encoded (otherwise we get nested : chars)
+    this._id = `${this.doc_type}:${Base64.Encode(this.source_id)}:${this.source_resource_type}:${this.source_resource_id}`
+  }
+}

frontend/src/lib/models/database/source.ts

@@ -5,7 +5,7 @@ import {DocType} from '../../../lib/database/constants';
 export class Source extends LighthouseSourceMetadata{
   _id?: string
   _rev?: string
-  docType: string
+  doc_type: string
   source_type: SourceType
 
   patient: string
@@ -16,11 +16,11 @@ export class Source extends LighthouseSourceMetadata{
 
   constructor(object: any) {
     super()
-    object.docType = DocType.Source
+    object.doc_type = DocType.Source
     return Object.assign(this, object)
   }
 
   populateId(){
-    this._id = `source:${this.source_type}:${this.patient}`
+    this._id = `${this.doc_type}:${this.source_type}:${this.patient}`
   }
 }

frontend/src/lib/utils/base64.ts

@@ -0,0 +1,8 @@
+export class Base64 {
+  public static Encode(data: string): string {
+    return btoa(data)
+  }
+  public static Decode(data: string): string {
+    return atob(data)
+  }
+}

frontend/tsconfig.spec.json

@@ -1,6 +1,7 @@
 {
   "extends": "./tsconfig.json",
   "compilerOptions": {
+    "resolveJsonModule": true,
     "outDir": "./out-tsc/spec",
     "types": [
       "jasmine",