adding all FHIR client methods.

Adding documentation.

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

@@ -1,6 +1,9 @@
 import {BaseClient} from './base_client';
 import {Source} from '../../../models/database/source';
+
+// @ts-ignore
 import * as BaseClient_GetRequest from './fixtures/BaseClient_GetRequest.json';
+// @ts-ignore
 import * as BaseClient_GetFhirVersion from './fixtures/BaseClient_GetFhirVersion.json';
 
 

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

@@ -26,6 +26,11 @@ export abstract class BaseClient {
     }
   }
 
+  /**
+   * This function gets the FhirVersion as specified by the api CapabilityStatement endpoint (metadata)
+   * https://build.fhir.org/capabilitystatement.html
+   * @constructor
+   */
   public async GetFhirVersion(): Promise<any> {
     return this.GetRequest("metadata")
       .then((resp) => {
@@ -33,6 +38,12 @@ export abstract class BaseClient {
       })
   }
 
+  /**
+   * This function will make an authenticated request against an OAuth protected resource. If the AccessToken used has expired, it will attempt
+   * to use a refresh token (if present) to get a new AccessToken.
+   * @param resourceSubpathOrNext
+   * @constructor
+   */
   public async GetRequest(resourceSubpathOrNext: string): Promise<any> {
 
     //check if the url is absolute
@@ -63,13 +74,6 @@ export abstract class BaseClient {
   // 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

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

@@ -1,11 +1,13 @@
 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';
 
+// @ts-ignore
+import * as FHIR401Client_ProcessBundle from './fixtures/FHIR401Client_ProcessBundle.json';
+
 class TestClient extends FHIR401Client {
   constructor(source: Source) {
     super(source);

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

@@ -13,28 +13,106 @@ export class FHIR401Client extends BaseClient implements IClient {
     super(source);
   }
 
+  /**
+   * This function attempts to retrieve a Patient Bundle and sync all resources to the database
+   * @param db
+   * @constructor
+   */
   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);
+  /**
+   * If Patient-everything api endpoint is unavailable (SyncAll) this function can be used to search for each resource associated with a Patient
+   * and sync them to the database.
+   * @param db
+   * @param resourceNames
+   * @constructor
+   */
+  public async SyncAllByResourceName(db: IDatabaseRepository, resourceNames: string[]): Promise<string[]>{
+    //Store the Patient
+    const patientResource = await this.GetPatient(this.source.patient)
+
+    const patientResourceFhir = new ResourceFhir()
+    patientResourceFhir.source_id = this.source._id
+    patientResourceFhir.source_resource_type = patientResource.resourceType
+    patientResourceFhir.source_resource_id = patientResource.id
+    patientResourceFhir.resource_raw = patientResource
+
+    await db.CreateResource(patientResourceFhir)
+
+    //error map storage.
+    let syncErrors = {}
+
+    //Store all other resources.
+    for(let resourceType of resourceNames) {
+
+      try {
+        let bundle = await this.GetResourceBundlePaginated(`${resourceType}?patient=${this.source.patient}`)
+        let wrappedResourceModels = await this.ProcessBundle(bundle)
+
+        for(let apiModel of wrappedResourceModels){
+          await db.CreateResource(apiModel)
+        }
+      }
+      catch (e) {
+        console.error(`An error occurred while processing ${resourceType} bundle ${this.source.patient}`)
+        syncErrors[resourceType] = e
+        continue
+      }
+    }
+
+    //TODO: correctly return newly inserted documents
+    return []
+  }
+
+  /**
+   * This function is used to sync all resources from a Bundle file. Not applicable to this Client
+   * @param db
+   * @param bundleFile
+   * @constructor
+   */
+  public async SyncAllFromBundleFile(db: IDatabaseRepository, bundleFile: any): Promise<any> {
+    return Promise.reject(new Error("not implemented"));
   }
 
   /////////////////////////////////////////////////////////////////////////////
   // Protected methods
   /////////////////////////////////////////////////////////////////////////////
+  /**
+   * This function attempts to retrieve the Patient Bundle using the Patient-everything api endpoint (if available)
+   * This response may be paginated
+   * https://hl7.org/fhir/operation-patient-everything.html
+   * @param patientId
+   * @constructor
+   * @protected
+   */
+  protected GetPatientBundle(patientId: string): Promise<any> {
+    return this.GetResourceBundlePaginated(`Patient/${patientId}/$everything`)
+  }
+
+  /**
+   * This function retrieves a patient resource
+   * @param patientId
+   * @constructor
+   * @protected
+   */
+  protected GetPatient(patientId: string): Promise<IResourceRaw> {
+    return this.GetRequest(`Patient/${patientId}`)
+  }
+
+  /**
+   * This function parses a FHIR Bundle and wraps each BundleEntry resource in a ResourceFhir object which can be stored in the DB.
+   * @param bundle
+   * @constructor
+   * @protected
+   */
   protected async ProcessBundle(bundle: IResourceBundleRaw): Promise<ResourceFhir[]> {
     // console.log(bundle)
     // process each entry in bundle
@@ -52,11 +130,55 @@ export class FHIR401Client extends BaseClient implements IClient {
         // wrappedResourceModel.updated_at = bundleEntry.resource.meta?.lastUpdated
         return wrappedResourceModel
       })
-
-
   }
 
   /////////////////////////////////////////////////////////////////////////////
   // Private methods
   /////////////////////////////////////////////////////////////////////////////
+
+  /**
+   * Retrieve a resource bundle. While "next" link is present in response, continue to request urls and append BundleEntries
+   * @param relativeResourcePath
+   * @constructor
+   * @private
+   */
+  private async GetResourceBundlePaginated(relativeResourcePath: string): Promise<IResourceBundleRaw> {
+    // https://www.hl7.org/fhir/patient-operation-everything.html
+
+    const bundle = await this.GetRequest(relativeResourcePath) as IResourceBundleRaw
+
+    let next: string
+    let prev: string
+    let self: string
+    for(let link of bundle.link || []){
+      if(link.relation == "next"){
+        next = link.url
+      } else if(link.relation == "self"){
+        self = link.url
+      } else if(link.relation == "previous"){
+        prev = link.url
+      }
+    }
+
+    while(next && next != self && next != prev){
+      console.debug(`Paginated request => ${next}`)
+      let nextBundle = await this.GetRequest(next) as IResourceBundleRaw
+      bundle.entry = bundle.entry.concat(nextBundle.entry)
+
+      next = "" //reset the pointers
+      self = ""
+      prev = ""
+      for(let link of nextBundle.link){
+        if(link.relation == "next"){
+          next = link.url
+        } else if(link.relation == "self"){
+          self = link.url
+        } else if(link.relation == "previous"){
+          prev = link.url
+        }
+      }
+    }
+
+    return bundle
+  }
 }

frontend/src/lib/conduit/interface.ts

@@ -4,10 +4,19 @@ export interface IClient {
   fhirVersion: string
   GetRequest(resourceSubpath: string): Promise<any>
   GetFhirVersion(): Promise<any>
+
+  /**
+   * This function attempts to retrieve a Patient Bundle and sync all resources to the database
+   * @param db
+   * @constructor
+   */
   SyncAll(db: IDatabaseRepository): Promise<any>
 
+
+  SyncAllByResourceName(db: IDatabaseRepository, resourceNames: string[]): Promise<string[]>
+
   //Manual client ONLY functions
-  SyncAllBundle(db: IDatabaseRepository, bundleFile: any): Promise<any>
+  SyncAllFromBundleFile(db: IDatabaseRepository, bundleFile: any): Promise<any>
 }
 
 //This is the "raw" Fhir resource