Merge pull request #94 from fastenhealth/elasticsearch-pagination

CONTRIBUTING.md

@@ -47,11 +47,10 @@ make backend-test
 
 # Start Development Environment
 
-To run Fasten from source, you'll need to create 3 separate processes:
+To run Fasten from source, you'll need to create 2 separate processes:
 
 - Angular Frontend
 - Go Backend
-- CouchDB Database
 
 First we'll create a development config file (`config.dev.yaml`)
 

docker-compose.yml

@@ -1,16 +1,17 @@
 version: "3.9"
 services:
-  couchdb:
+  fasten:
+    # NOTE: only developers need to build Fasten from source
+    # For production, use the pre-built image from GitHub Packages
+    # ghcr.io/fastenhealth/fasten-onprem:main
     build:
       context: .
       dockerfile: Dockerfile
-#    environment:
-#      - COUCHDB_USER=admin
-#      - COUCHDB_PASSWORD=password
+      args:
+        - FASTEN_ENV=prod
+#        - FASTEN_ENV=sandbox
     ports:
       - "9090:8080"
-      - "5984:5984"
     volumes:
-      - ./.couchdb/data:/opt/couchdb/data
-      - ./.couchdb/config:/opt/couchdb/etc/local.d
+      - ./db:/opt/fasten/db
 #      - ./config.example.yaml:/opt/fasten/config/config.yaml

frontend/package.json

@@ -36,7 +36,6 @@
     "bootstrap": "^4.4.1",
     "chart.js": "2.9.4",
     "fhirpath": "^3.3.0",
-    "fuse.js": "^6.6.2",
     "humanize-duration": "^3.27.3",
     "idb": "^7.1.0",
     "jose": "^4.10.4",
@@ -44,6 +43,7 @@
     "ng2-charts": "^2.3.0",
     "ngx-dropzone": "^3.1.0",
     "ngx-highlightjs": "^7.0.1",
+    "ngx-infinite-scroll": "^14.0.0",
     "ngx-moment": "^6.0.2",
     "rxjs": "~6.5.4",
     "tslib": "^2.0.0",

frontend/src/app/app.module.ts

@@ -30,7 +30,7 @@ import { MedicalHistoryComponent } from './pages/medical-history/medical-history
 import { ReportLabsComponent } from './pages/report-labs/report-labs.component';
 import {PipesModule} from './pipes/pipes.module';
 import { ResourceCreatorComponent } from './pages/resource-creator/resource-creator.component';
-
+import { InfiniteScrollModule } from 'ngx-infinite-scroll';
 
 @NgModule({
   declarations: [
@@ -62,6 +62,7 @@ import { ResourceCreatorComponent } from './pages/resource-creator/resource-crea
     HighlightModule,
     MomentModule,
     PipesModule,
+    InfiniteScrollModule
   ],
   providers: [
     {

frontend/src/app/models/fasten/metadata-source.ts

@@ -1,4 +1,6 @@
 export class MetadataSource {
+  platform_type: string
+  brand_logo?: string
   source_type: string
   display: string
   category: string[]

frontend/src/app/models/lighthouse/lighthouse-source-metadata.ts

@@ -1,4 +1,7 @@
-export class LighthouseSourceMetadata {
+import {MetadataSource} from '../fasten/metadata-source';
+
+export class LighthouseSourceMetadata extends MetadataSource {
+
   authorization_endpoint: string
   token_endpoint: string
   introspection_endpoint: string

frontend/src/app/models/lighthouse/lighthouse-source-search.ts

@@ -0,0 +1,21 @@
+import {MetadataSource} from '../fasten/metadata-source';
+
+export class LighthouseSourceSearch {
+  _scroll_id: string;
+  took: number;
+  timed_out: boolean;
+  hits: {
+    total: {
+      value: number;
+      relation: string;
+    };
+    max_score: number;
+    hits: {
+      _index: string;
+      _type: string;
+      _id: string;
+      _score: number;
+      _source: MetadataSource;
+    }[];
+  };
+}

frontend/src/app/pages/dashboard/dashboard.component.ts

@@ -43,6 +43,7 @@ export class DashboardComponent implements OnInit {
       this.metadataSource = metadataSource
       this.metadataSource["manual"] = {
         "source_type": "manual",
+        "platform_type": "manual",
         "display": "Manual",
         "category": ["Manual"],
         "hidden": false,

frontend/src/app/pages/medical-sources/medical-sources.component.html

@@ -32,7 +32,7 @@
             <div (click)="openModal(contentModalRef, sourceInfo)" class="card-body">
 
               <div class="h-100 d-flex align-items-center">
-                <img [src]="'assets/sources/'+sourceInfo?.metadata['source_type']+'.png'" [alt]="sourceInfo?.metadata.display" class="img-fluid">
+                <img [src]="'assets/sources/'+(sourceInfo.metadata.brand_logo ? sourceInfo.metadata.brand_logo : sourceInfo.metadata.source_type+'.png')" [alt]="sourceInfo?.metadata.display" class="img-fluid">
               </div>
               <div *ngIf="status[sourceInfo.metadata?.source_type]" class="progress">
                 <div [style.width]="status[sourceInfo?.metadata?.source_type] == 'authorize' ? '33%' : '66%'" class="bg-indigo progress-bar progress-bar-striped progress-bar-animated" role="progressbar"></div>
@@ -71,34 +71,38 @@
 
       <!-- Search -->
       <div class="row row-sm sticky-top pt-2" style="position:sticky;">
-        <div class="col-lg-4">
+        <div class="col-lg-8">
           <div class="input-group mb-3">
             <div class="input-group-prepend">
               <span class="input-group-text" id="search-prefix">Search</span>
             </div>
-            <input (keyup)="searchTermChanged($event)" type="text" class="form-control" placeholder="Search Term">
+            <input (keyup)="searchTermUpdate.next($event.target.value)" type="text" class="form-control" placeholder="Search Term">
+            <div class="input-group-append">
+              <span class="input-group-text">{{this.availableSourceList.length}} of {{this.totalAvailableSourceList}} results</span>
+            </div>
+
           </div><!-- input-group -->
         </div><!-- col -->
-<!--        <div class="col-lg-4">-->
-<!--          <div class="d-flex text-center">-->
-<!--            <small>{{this.availableSourceList.length}} of {{this.totalAvailableSourceList}} sources</small>-->
-<!--          </div>-->
-<!--        </div>-->
       </div>
 
 
-      <div *ngIf="!loading else isLoadingTemplate" class="row row-sm">
+      <div *ngIf="!loading else isLoadingTemplate" class="row row-sm"
+           infiniteScroll
+           [infiniteScrollDistance]="2"
+           [infiniteScrollThrottle]="50"
+           (scrolled)="onScroll()"
+      >
         <div *ngFor="let sourceData of availableSourceList" (click)="connectHandler($event, sourceData.metadata.source_type)" class="col-sm-3 mg-b-20 px-3">
           <div class="card h-100 d-flex align-items-center justify-content-center mt-3 mt-3 rounded-0 cursor-pointer" [ngClass]="{'card-disable': sourceData.metadata.hidden}">
             <div class="card-body d-flex align-items-center">
-              <img style="max-height: 130px;" [src]="'assets/sources/'+sourceData.metadata.source_type+'.png'" [alt]="metadataSources[sourceData.metadata.source_type].display" class="img-fluid">
+              <img style="max-height: 130px;" [src]="'assets/sources/'+(sourceData.metadata.brand_logo ? sourceData.metadata.brand_logo : sourceData.metadata.source_type+'.png')" [alt]="sourceData.metadata.display" class="img-fluid">
               <div *ngIf="status[sourceData.metadata.source_type]" class="progress">
                 <div [style.width]="status[sourceData.metadata.source_type] == 'authorize' ? '33%' : '66%'" class="bg-indigo progress-bar progress-bar-striped progress-bar-animated" role="progressbar"></div>
               </div>
             </div>
             <div class="card-footer text-center p-1" style="width:100%">
               <small class="tx-gray-700">
-                {{metadataSources[sourceData.metadata.source_type].display}}
+                {{sourceData.metadata.display}}
               </small>
             </div>
           </div>

frontend/src/app/pages/medical-sources/medical-sources.component.ts

@@ -10,8 +10,9 @@ import {Location} from '@angular/common';
 import {ToastService} from '../../services/toast.service';
 import {ToastNotification, ToastType} from '../../models/fasten/toast';
 import {environment} from '../../../environments/environment';
-import {forkJoin} from 'rxjs';
-import Fuse from 'fuse.js'
+import {BehaviorSubject, forkJoin, Subject} from 'rxjs';
+import {LighthouseSourceSearch} from '../../models/lighthouse/lighthouse-source-search';
+import {debounceTime, distinctUntilChanged} from 'rxjs/operators';
 // If you dont import this angular will import the wrong "Location"
 
 export const sourceConnectWindowTimeout = 24*5000 //wait 2 minutes (5 * 24 = 120)
@@ -32,8 +33,6 @@ export class MedicalSourcesComponent implements OnInit {
   environment_name = environment.environment_name
   status: { [name: string]: string } = {}
 
-  metadataSources: {[name:string]: MetadataSource} = {}
-
   connectedSourceList: SourceListItem[] = [] //source's are populated for this list
   availableSourceList: SourceListItem[] = []
   totalAvailableSourceList: number = 0
@@ -42,8 +41,10 @@ export class MedicalSourcesComponent implements OnInit {
   closeResult = '';
   modalSelectedSourceListItem:SourceListItem = null;
 
-  searchIndex = null
-  searchTerm: string = ""
+  scrollId: string = ""
+  scrollComplete: boolean = false
+  searchTermUpdate = new BehaviorSubject<string>("");
+  showHidden: boolean = false
 
   constructor(
     private lighthouseApi: LighthouseService,
@@ -57,29 +58,20 @@ export class MedicalSourcesComponent implements OnInit {
 
   ngOnInit(): void {
     this.loading = true
-    forkJoin([this.lighthouseApi.getLighthouseSourceMetadataMap(false), this.fastenApi.getSources()]).subscribe(results => {
+    forkJoin([this.lighthouseApi.findLighthouseSources("", "", this.showHidden), this.fastenApi.getSources()]).subscribe(results => {
       this.loading = false
+
+      //handle connected sources sources
+      const connectedSources = results[1] as Source[]
+      forkJoin(connectedSources.map((source) => this.lighthouseApi.getLighthouseSource(source.source_type))).subscribe((connectedMetadata) => {
+        for(const ndx in connectedSources){
+          this.connectedSourceList.push({source: connectedSources[ndx], metadata: connectedMetadata[ndx]})
+        }
+      })
+
+
       //handle source metadata map response
-      this.metadataSources = results[0] as {[name:string]: MetadataSource}
-
-      //handle sources
-      const sourceList = results[1] as Source[]
-
-      for (const sourceType in this.metadataSources) {
-        let isConnected = false
-        for(const connectedSource of sourceList){
-          if(connectedSource.source_type == sourceType){
-            this.connectedSourceList.push({source: connectedSource, metadata: this.metadataSources[sourceType]})
-            isConnected = true
-            break
-          }
-        }
-
-        if(!isConnected){
-          //this source has not been found in the connected list, lets add it to the available list.
-          this.availableSourceList.push({metadata: this.metadataSources[sourceType]})
-        }
-      }
+      this.populateAvailableSourceList(results[0] as LighthouseSourceSearch)
 
 
       //check if we've just started connecting a "source_type"
@@ -97,55 +89,59 @@ export class MedicalSourcesComponent implements OnInit {
 
         this.callback(callbackSourceType).then(console.log)
       }
-      this.totalAvailableSourceList = this.availableSourceList.length
-
-      //setup Search
-      const options = {
-        // isCaseSensitive: false,
-        // includeScore: false,
-        // shouldSort: true,
-        // includeMatches: false,
-        findAllMatches: true,
-        // minMatchCharLength: 1,
-        // location: 0,
-        // threshold: 0.6,
-        // distance: 100,
-        // useExtendedSearch: false,
-        // ignoreLocation: false,
-        // ignoreFieldNorm: false,
-        // fieldNormWeight: 1,
-        keys: [
-          "metadata.display",
-          "metadata.category",
-          "metadata.source_type"
-        ]
-      };
-
-      this.searchIndex = new Fuse(this.availableSourceList, options);
-
 
     }, err => {
       this.loading = false
     })
+
+
+    //register a callback for when the search term changes
+    this.searchTermUpdate
+      .pipe(
+        debounceTime(200),
+        distinctUntilChanged(),
+      )
+      .subscribe(value => {
+        console.log("search term changed:", value)
+
+        //reset available sources
+        this.availableSourceList = []
+        this.scrollId = ""
+        this.scrollComplete = false
+        this.totalAvailableSourceList = 0
+
+        this.lighthouseApi.findLighthouseSources(value, this.scrollId, this.showHidden)
+          .subscribe((results) => {
+            this.populateAvailableSourceList(results)
+          })
+      });
+
   }
 
-  public searchTermChanged($event):void {
-    this.searchTerm = $event.target.value
-    console.log("search term changed:", )
+  private populateAvailableSourceList(results: LighthouseSourceSearch): void {
+    this.totalAvailableSourceList = results.hits.total.value
+    if(results.hits.hits.length == 0){
+      this.scrollComplete = true
+      console.log("scroll complete")
+      return
+    }
+    this.scrollId = results._scroll_id
+    this.availableSourceList = this.availableSourceList.concat(results.hits.hits.map((result) => {
+      return {metadata: result._source}
+    }).filter((item) => {
+      return !this.connectedSourceList.find((connectedItem) => connectedItem.metadata.source_type == item.metadata.source_type)
+    }))
+  }
 
-    let searchResults
-    if(this.searchTerm){
-      searchResults = this.searchIndex.search(this.searchTerm).map((result) => {
-        return result.item
+  public onScroll(): void {
+    if(this.scrollComplete){
+      return
+    }
+
+    this.lighthouseApi.findLighthouseSources(this.searchTermUpdate.getValue(), this.scrollId, this.showHidden)
+      .subscribe((results) => {
+        this.populateAvailableSourceList(results)
       })
-    }
-    else {
-      //emtpy search term, show all (original) values.
-      searchResults = this.searchIndex.getIndex().docs
-    }
-
-    this.availableSourceList = searchResults
-    console.log(this.availableSourceList)
   }
 
   /**
@@ -222,7 +218,14 @@ export class MedicalSourcesComponent implements OnInit {
           console.log("NO PATIENT ID present, decoding jwt to extract patient")
           //const introspectionResp = await Oauth.introspectionRequest(as, client, payload.access_token)
           //console.log(introspectionResp)
-          payload.patient = this.jwtDecode(payload.id_token)["profile"].replace(/^(Patient\/)/,'')
+          let decodedIdToken = this.jwtDecode(payload.id_token)
+          //nextGen uses fhirUser instead of profile.
+          payload.patient = decodedIdToken["profile"] || decodedIdToken["fhirUser"]
+
+          if(payload.patient){
+            payload.patient = payload.patient.replace(/^(Patient\/)/,'')
+          }
+
         }
 
 

frontend/src/app/services/lighthouse.service.ts

@@ -9,6 +9,7 @@ import * as Oauth from '@panva/oauth4webapi';
 import {SourceState} from '../models/fasten/source-state';
 import {MetadataSource} from '../models/fasten/metadata-source';
 import {uuidV4} from '../../lib/utils/uuid';
+import {LighthouseSourceSearch} from '../models/lighthouse/lighthouse-source-search';
 
 @Injectable({
   providedIn: 'root'
@@ -18,6 +19,27 @@ export class LighthouseService {
   constructor(private _httpClient: HttpClient) {
   }
 
+  public findLighthouseSources(searchTerm: string, scrollId= "", showHidden = false): Observable<LighthouseSourceSearch> {
+    const endpointUrl = new URL(`${environment.lighthouse_api_endpoint_base}/list/search`);
+    if(showHidden){
+      endpointUrl.searchParams.set('show_hidden', 'true');
+    }
+    if(scrollId){
+      endpointUrl.searchParams.set('scroll_id', scrollId);
+    }
+    if(searchTerm){
+      endpointUrl.searchParams.set('query', searchTerm);
+    }
+
+    return this._httpClient.get<ResponseWrapper>(endpointUrl.toString())
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("Metadata RESPONSE", response)
+          return response.data as LighthouseSourceSearch
+        })
+      );
+  }
+
   public getLighthouseSourceMetadataMap(showHidden = false): Observable<{[name: string]: MetadataSource}> {
     const endpointUrl = new URL(`${environment.lighthouse_api_endpoint_base}/list`);
     if(showHidden){

frontend/src/assets/sources/360care-of-massachusetts.svg

@@ -0,0 +1,95 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 16.0.4, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 width="408px" height="104px" viewBox="0 0 408 104" enable-background="new 0 0 408 104" xml:space="preserve">
+<g>
+	<defs>
+		<rect id="SVGID_1_" x="4" y="4" width="400" height="96"/>
+	</defs>
+	<clipPath id="SVGID_2_">
+		<use xlink:href="#SVGID_1_"  overflow="visible"/>
+	</clipPath>
+	<g clip-path="url(#SVGID_2_)">
+		<rect x="-3.115" y="-9.004" fill="#005ea6" width="430.518" height="109.004"/>
+		<rect x="-1.113" y="82.424" fill="#FFFFFF" width="430.518" height="4.291"/>
+		<rect x="-3.115" y="86.715" fill="#C41623" width="430.518" height="50.596"/>
+	</g>
+</g>
+<path fill="#FFFFFF" d="M404,4v96H4V4H404 M408,0h-4H4H0v4v96v4h4h400h4v-4V4V0L408,0z"/>
+<g>
+	<path fill="#FFFFFF" d="M76.748,65.242c0-1.219,0-42.146,0-42.146h-13.23c0,0,0,39.166,0,40.318
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+	<polygon fill="#FFFFFF" points="191.463,62.031 168.209,23.096 152.834,23.096 152.834,83.531 165.455,83.531 165.455,42.6 
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