adding a glossary endpoint which attempts to get patient-friendly des…

…criptions from code. (fastenhealth#120)

backend/pkg/database/interface.go

@@ -34,6 +34,9 @@ type DatabaseRepository interface {
  GetSourceSummary(context.Context, string) (*models.SourceSummary, error)
  GetSources(context.Context) ([]models.SourceCredential, error)
 
- //used by Client
+ CreateGlossaryEntry(ctx context.Context, glossaryEntry *models.Glossary) error
+ GetGlossaryEntry(ctx context.Context, code string, codeSystem string) (*models.Glossary, error)
+
+ //used by fasten-sources Clients
  UpsertRawResource(ctx context.Context, sourceCredentials sourcePkg.SourceCredential, rawResource sourcePkg.RawResourceFhir) (bool, error)
 }

backend/pkg/database/sqlite_repository.go

@@ -57,14 +57,14 @@ func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger)
  }
  globalLogger.Infof("Successfully connected to fasten sqlite db: %s\n", appConfig.GetString("database.location"))
 
- deviceRepo := SqliteRepository{
+ fastenRepo := SqliteRepository{
  AppConfig: appConfig,
  Logger: globalLogger,
  GormClient: database,
  }
 
  //TODO: automigrate for now
- err = deviceRepo.Migrate()
+ err = fastenRepo.Migrate()
  if err != nil {
  return nil, err
  }
@@ -76,7 +76,7 @@ func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger)
  return nil, fmt.Errorf("Failed to create admin user! - %v", err)
  }
 
- return &deviceRepo, nil
+ return &fastenRepo, nil
 }
 
 type SqliteRepository struct {
@@ -91,6 +91,7 @@ func (sr *SqliteRepository) Migrate() error {
  &models.User{},
  &models.SourceCredential{},
  &models.ResourceFhir{},
+ &models.Glossary{},
  )
  if err != nil {
  return fmt.Errorf("Failed to automigrate! - %v", err)
@@ -140,6 +141,24 @@ func (sr *SqliteRepository) GetCurrentUser(ctx context.Context) (*models.User, e
  return &currentUser, nil
 }
 
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// Glossary
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+func (sr *SqliteRepository) CreateGlossaryEntry(ctx context.Context, glossaryEntry *models.Glossary) error {
+ record := sr.GormClient.Create(glossaryEntry)
+ if record.Error != nil {
+ return record.Error
+ }
+ return nil
+}
+
+func (sr *SqliteRepository) GetGlossaryEntry(ctx context.Context, code string, codeSystem string) (*models.Glossary, error) {
+ var foundGlossaryEntry models.Glossary
+ result := sr.GormClient.Where(models.Glossary{Code: code, CodeSystem: codeSystem}).First(&foundGlossaryEntry)
+ return &foundGlossaryEntry, result.Error
+}
+
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // Summary
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

backend/pkg/models/glossary.go

@@ -0,0 +1,14 @@
+package models
+
+// Glossary contains patient friendly terms for medical concepts
+// Can be retrieved by Code and CodeSystem
+// Structured similar to ValueSet https://hl7.org/fhir/valueset.html
+type Glossary struct {
+ ModelBase
+ Code string `json:"code" gorm:"uniqueIndex:idx_glossary_term"`
+ CodeSystem string `json:"code_system" gorm:"uniqueIndex:idx_glossary_term"`
+ Publisher string `json:"publisher"`
+ Title string `json:"title"`
+ Url string `json:"url"`
+ Description string `json:"description"`
+}

backend/pkg/models/medlineplus_connect_results.go

@@ -0,0 +1,59 @@
+package models
+
+import "time"
+
+type MedlinePlusConnectResults struct {
+ Feed struct {
+ Base string `json:"base"`
+ Lang string `json:"lang"`
+ Xsi string `json:"xsi"`
+ Title struct {
+ Type string `json:"type"`
+ Value string `json:"_value"`
+ } `json:"title"`
+ Updated struct {
+ Value time.Time `json:"_value"`
+ } `json:"updated"`
+ ID struct {
+ Value string `json:"_value"`
+ } `json:"id"`
+ Author struct {
+ Name struct {
+ Value string `json:"_value"`
+ } `json:"name"`
+ URI struct {
+ Value string `json:"_value"`
+ } `json:"uri"`
+ } `json:"author"`
+ Subtitle struct {
+ Type string `json:"type"`
+ Value string `json:"_value"`
+ } `json:"subtitle"`
+ Category []struct {
+ Scheme string `json:"scheme"`
+ Term string `json:"term"`
+ } `json:"category"`
+ Entry []MedlinePlusConnectResultEntry `json:"entry"`
+ } `json:"feed"`
+}
+
+type MedlinePlusConnectResultEntry struct {
+ Title struct {
+ Value string `json:"_value"`
+ Type string `json:"type"`
+ } `json:"title"`
+ Link []struct {
+ Href string `json:"href"`
+ Rel string `json:"rel"`
+ } `json:"link"`
+ ID struct {
+ Value string `json:"_value"`
+ } `json:"id"`
+ Summary struct {
+ Type string `json:"type"`
+ Value string `json:"_value"`
+ } `json:"summary"`
+ Updated struct {
+ Value time.Time `json:"_value"`
+ } `json:"updated"`
+}

backend/pkg/web/handler/glossary.go

@@ -0,0 +1,158 @@
+package handler
+
+import (
+ "context"
+ "encoding/json"
+ "fmt"
+ "github.com/fastenhealth/fastenhealth-onprem/backend/pkg"
+ "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
+ "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
+ "github.com/fastenhealth/gofhir-models/fhir401"
+ "github.com/gin-gonic/gin"
+ "github.com/sirupsen/logrus"
+ "log"
+ "net"
+ "net/http"
+ "net/url"
+ "strings"
+ "time"
+)
+
+func FindCodeSystem(codeSystem string) (string, error) {
+ log.Printf("codeSystem: %s", codeSystem)
+ if strings.HasPrefix(codeSystem, "2.16.840.1.113883.6.") {
+ return codeSystem, nil
+ }
+
+ //https://terminology.hl7.org/external_terminologies.html
+ codeSystemIds := map[string]string{
+ "http:https://hl7.org/fhir/sid/icd-10-cm": "2.16.840.1.113883.6.90",
+ "http:https://hl7.org/fhir/sid/icd-10": "2.16.840.1.113883.6.90",
+ "http:https://terminology.hl7.org/CodeSystem/icd9cm": "2.16.840.1.113883.6.103",
+ "http:https://snomed.info/sct": "2.16.840.1.113883.6.96",
+ "http:https://www.nlm.nih.gov/research/umls/rxnorm": "2.16.840.1.113883.6.88",
+ "http:https://hl7.org/fhir/sid/ndc": "2.16.840.1.113883.6.69",
+ "http:https://loinc.org": "2.16.840.1.113883.6.1",
+ "http:https://www.ama-assn.org/go/cpt": "2.16.840.1.113883.6.12",
+ }
+
+ if codeSystemId, ok := codeSystemIds[codeSystem]; ok {
+ return codeSystemId, nil
+ } else {
+ return "", fmt.Errorf("Code System not found")
+ }
+
+}
+
+// https://medlineplus.gov/medlineplus-connect/web-service/
+// NOTE: max requests is 100/min
+func GlossarySearchByCode(c *gin.Context) {
+ logger := c.MustGet(pkg.ContextKeyTypeLogger).(*logrus.Entry)
+ databaseRepo := c.MustGet(pkg.ContextKeyTypeDatabase).(database.DatabaseRepository)
+
+ codeSystemId, err := FindCodeSystem(c.Query("code_system"))
+ if err != nil {
+ logger.Error(err)
+ c.JSON(http.StatusBadRequest, gin.H{
+ "success": false,
+ "error": err.Error(),
+ })
+ return
+ }
+ if c.Query("code") == "" {
+ c.JSON(http.StatusBadRequest, gin.H{
+ "success": false,
+ "error": "code is required",
+ })
+ return
+ }
+
+ //Check if the code is in the DB cache
+ foundGlossaryEntry, err := databaseRepo.GetGlossaryEntry(c, c.Query("code"), codeSystemId)
+ if err == nil {
+ //found in DB cache
+ logger.Debugf("Found code (%s %s) in DB cache", c.Query("code"), codeSystemId)
+ dateStr := foundGlossaryEntry.UpdatedAt.Format(time.RFC3339)
+ valueSet := fhir401.ValueSet{
+ Title: &foundGlossaryEntry.Title,
+ Url: &foundGlossaryEntry.Url,
+ Description: &foundGlossaryEntry.Description,
+ Date: &dateStr,
+ Publisher: &foundGlossaryEntry.Publisher,
+ }
+
+ c.JSON(http.StatusOK, valueSet)
+ return
+ }
+
+ // Define the URL for the MedlinePlus Connect Web Service API
+ medlinePlusConnectEndpoint := "https://connect.medlineplus.gov/service"
+
+ // Define the query parameters
+ params := url.Values{
+ "informationRecipient.languageCode.c": []string{"en"},
+ "knowledgeResponseType": []string{"application/json"},
+ "mainSearchCriteria.v.c": []string{c.Query("code")},
+ "mainSearchCriteria.v.cs": []string{codeSystemId},
+ }
+
+ // Send the HTTP GET request to the API and retrieve the response
+ //TODO: when using IPV6 to communicate with MedlinePlus, we're getting timeouts. Force IPV4
+ var (
+ zeroDialer net.Dialer
+ httpClient = &http.Client{
+ Timeout: 10 * time.Second,
+ }
+ )
+ transport := http.DefaultTransport.(*http.Transport).Clone()
+ transport.DialContext = func(ctx context.Context, network, addr string) (net.Conn, error) {
+ return zeroDialer.DialContext(ctx, "tcp4", addr)
+ }
+ httpClient.Transport = transport
+ resp, err := httpClient.Get(medlinePlusConnectEndpoint + "?" + params.Encode())
+ if err != nil {
+ fmt.Println("Error sending request:", err)
+ return
+ }
+ defer resp.Body.Close()
+
+ // Parse the JSON response into a struct
+ var response models.MedlinePlusConnectResults
+ err = json.NewDecoder(resp.Body).Decode(&response)
+ if err != nil {
+ fmt.Println("Error parsing response:", err)
+ return
+ }
+
+ if len(response.Feed.Entry) == 0 {
+ c.JSON(http.StatusOK, gin.H{"success": false, "error": "No results found"})
+ return
+ } else {
+ foundEntry := response.Feed.Entry[0]
+
+ dateStr := foundEntry.Updated.Value.Format(time.RFC3339)
+ valueSet := fhir401.ValueSet{
+ Title: &foundEntry.Title.Value,
+ Url: &foundEntry.Link[0].Href,
+ Description: &foundEntry.Summary.Value,
+ Date: &dateStr,
+ Publisher: &response.Feed.Author.Name.Value,
+ }
+
+ //store in DB cache (ignore errors)
+ databaseRepo.CreateGlossaryEntry(c, &models.Glossary{
+ ModelBase: models.ModelBase{
+ CreatedAt: foundEntry.Updated.Value,
+ UpdatedAt: foundEntry.Updated.Value,
+ },
+ Code: c.Query("code"),
+ CodeSystem: codeSystemId,
+ Publisher: response.Feed.Author.Name.Value,
+ Title: foundEntry.Title.Value,
+ Url: foundEntry.Link[0].Href,
+ Description: foundEntry.Summary.Value,
+ })
+
+ c.JSON(http.StatusOK, valueSet)
+ }
+}

backend/pkg/web/server.go

@@ -46,6 +46,7 @@ func (ae *AppEngine) Setup(logger *logrus.Entry) *gin.Engine {
  //r.Any("/database/*proxyPath", handler.CouchDBProxy)
  //r.GET("/cors/*proxyPath", handler.CORSProxy)
  //r.OPTIONS("/cors/*proxyPath", handler.CORSProxy)
+ api.GET("/glossary/code", handler.GlossarySearchByCode)
 
  secure := api.Group("/secure").Use(middleware.RequireAuth())
  {
@@ -61,6 +62,7 @@ func (ae *AppEngine) Setup(logger *logrus.Entry) *gin.Engine {
  secure.GET("/resource/graph", handler.GetResourceFhirGraph)
  secure.GET("/resource/fhir/:sourceId/:resourceId", handler.GetResourceFhir)
  secure.POST("/resource/composition", handler.CreateResourceComposition)
+
  }
 
  if ae.Config.GetBool("web.allow_unsafe_endpoints") {

frontend/src/app/components/glossary-lookup/glossary-lookup.component.html

@@ -0,0 +1,8 @@
+<div *ngIf="!loading else isLoadingTemplate">
+ <div [innerHTML]="description"></div>
+ <p>Source: <a [href]="url">{{source}}</a></p>
+</div>
+
+<ng-template #isLoadingTemplate>
+ <app-loading-spinner [loadingTitle]="'Please wait, loading glossary entry...'"></app-loading-spinner>
+</ng-template>

frontend/src/app/components/glossary-lookup/glossary-lookup.component.scss

@@ -0,0 +1,5 @@
+:host {
+ max-height:300px;
+ overflow-y:scroll;
+ display: inline-block;
+}

frontend/src/app/components/glossary-lookup/glossary-lookup.component.spec.ts

@@ -0,0 +1,23 @@
+import { ComponentFixture, TestBed } from '@angular/core/testing';
+
+import { GlossaryLookupComponent } from './glossary-lookup.component';
+
+describe('GlossaryLookupComponent', () => {
+ let component: GlossaryLookupComponent;
+ let fixture: ComponentFixture<GlossaryLookupComponent>;
+
+ beforeEach(async () => {
+ await TestBed.configureTestingModule({
+ declarations: [ GlossaryLookupComponent ]
+ })
+ .compileComponents();
+
+ fixture = TestBed.createComponent(GlossaryLookupComponent);
+ component = fixture.componentInstance;
+ fixture.detectChanges();
+ });
+
+ it('should create', () => {
+ expect(component).toBeTruthy();
+ });
+});

frontend/src/app/components/glossary-lookup/glossary-lookup.component.ts

@@ -0,0 +1,36 @@
+import {Component, Input, OnInit} from '@angular/core';
+import {FastenApiService} from '../../services/fasten-api.service';
+import {DomSanitizer, SafeHtml} from '@angular/platform-browser';
+
+@Component({
+ selector: 'app-glossary-lookup',
+ templateUrl: './glossary-lookup.component.html',
+ styleUrls: ['./glossary-lookup.component.scss']
+})
+export class GlossaryLookupComponent implements OnInit {
+
+ @Input() code: string
+ @Input() codeSystem: string
+ @Input() snippetLength: number = -1
+
+ description: SafeHtml = ""
+ url: string = ""
+ source: string = ""
+ loading: boolean = true
+
+ constructor(private fastenApi: FastenApiService, private sanitized: DomSanitizer) { }
+
+ ngOnInit(): void {
+ this.fastenApi.getGlossarySearchByCode(this.code, this.codeSystem).subscribe(result => {
+ this.loading = false
+ console.log(result)
+ this.url = result?.url
+ this.source = result?.publisher
+ this.description = this.sanitized.bypassSecurityTrustHtml(result?.description)
+ // this.description = result.description
+ }, error => {
+ this.loading = false
+ })
+ }
+
+}