using caching mechanism for retrieving codes from MedlinePlus safely.

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/web/handler/glossary.go

@@ -5,6 +5,7 @@ import (
  "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"
@@ -47,7 +48,7 @@ func FindCodeSystem(codeSystem string) (string, error) {
 // 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)
+ databaseRepo := c.MustGet(pkg.ContextKeyTypeDatabase).(database.DatabaseRepository)
 
  codeSystemId, err := FindCodeSystem(c.Query("code_system"))
  if err != nil {
@@ -58,6 +59,31 @@ func GlossarySearchByCode(c *gin.Context) {
  })
  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"
@@ -98,15 +124,6 @@ func GlossarySearchByCode(c *gin.Context) {
  return
  }
 
- //store in DB cache
-
- //sourceCred, err := databaseRepo.GetSource(c, c.Param("sourceId"))
- //if err != nil {
- // logger.Errorln("An error occurred while retrieving source credential", err)
- // c.JSON(http.StatusInternalServerError, gin.H{"success": false})
- // return
- //}
-
  if len(response.Feed.Entry) == 0 {
  c.JSON(http.StatusOK, gin.H{"success": false, "error": "No results found"})
  return
@@ -122,6 +139,20 @@ func GlossarySearchByCode(c *gin.Context) {
  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)
  }
 }