diff --git a/backend/pkg/auth/utils.go b/backend/pkg/auth/utils.go
deleted file mode 100644
index 77709b7e..00000000
--- a/backend/pkg/auth/utils.go
+++ /dev/null
@@ -1,56 +0,0 @@
-package auth
-
-import (
- "errors"
- "github.com/golang-jwt/jwt"
- "time"
-)
-
-//TODO: this should match the ID and username for the user.
-type JWTClaim struct {
- Username string `json:"username"`
- UserId string `json:"user_id"`
- Email string `json:"email"`
- jwt.StandardClaims
-}
-
-func GenerateJWT(encryptionKey string, username string, userId string) (tokenString string, err error) {
- expirationTime := time.Now().Add(2 * time.Hour)
- claims := &JWTClaim{
- Username: username,
- Email: username,
- UserId: userId,
- StandardClaims: jwt.StandardClaims{
- ExpiresAt: expirationTime.Unix(),
- },
- }
- token := jwt.NewWithClaims(jwt.SigningMethodHS256, claims)
- tokenString, err = token.SignedString([]byte(encryptionKey))
- return
-}
-
-func ValidateToken(encryptionKey string, signedToken string) (*JWTClaim, error) {
- token, err := jwt.ParseWithClaims(
- signedToken,
- &JWTClaim{},
- func(token *jwt.Token) (interface{}, error) {
- if jwt.SigningMethodHS256 != token.Method {
- return nil, errors.New("Invalid signing algorithm")
- }
- return []byte(encryptionKey), nil
- },
- )
- if err != nil {
- return nil, err
- }
- claims, ok := token.Claims.(*JWTClaim)
- if !ok {
- err = errors.New("couldn't parse claims")
- return nil, err
- }
- if claims.ExpiresAt < time.Now().Local().Unix() {
- err = errors.New("token expired")
- return nil, err
- }
- return claims, nil
-}
diff --git a/backend/pkg/config/config.go b/backend/pkg/config/config.go
index e79fee66..189ea40b 100644
--- a/backend/pkg/config/config.go
+++ b/backend/pkg/config/config.go
@@ -27,6 +27,12 @@ func (c *configuration) Init() error {
c.SetDefault("web.src.frontend.path", "/opt/fasten/web")
c.SetDefault("web.database.location", "/opt/fasten/db/fasten.db") //TODO: should be /opt/fasten/fasten.db
+ c.SetDefault("web.couchdb.scheme", "http")
+ c.SetDefault("web.couchdb.host", "localhost")
+ c.SetDefault("web.couchdb.port", "5984")
+ c.SetDefault("web.couchdb.admin_username", "admin")
+ c.SetDefault("web.couchdb.admin_password", "mysecretpassword")
+
c.SetDefault("log.level", "INFO")
c.SetDefault("log.file", "")
diff --git a/backend/pkg/database/couchdb_repository.go b/backend/pkg/database/couchdb_repository.go
new file mode 100644
index 00000000..92ac650e
--- /dev/null
+++ b/backend/pkg/database/couchdb_repository.go
@@ -0,0 +1,88 @@
+package database
+
+import (
+ "context"
+ "fmt"
+ "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
+ "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
+ "github.com/go-kivik/couchdb/v3"
+ _ "github.com/go-kivik/couchdb/v3" // The CouchDB driver
+ "github.com/go-kivik/kivik/v3"
+ "github.com/sirupsen/logrus"
+)
+
+func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger) (DatabaseRepository, error) {
+ //backgroundContext := context.Background()
+
+ ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+ // Gorm/SQLite setup
+ ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+ globalLogger.Infof("Trying to connect to sqlite db: %s\n", appConfig.GetString("web.database.location"))
+
+ // When a transaction cannot lock the database, because it is already locked by another one,
+ // SQLite by default throws an error: database is locked. This behavior is usually not appropriate when
+ // concurrent access is needed, typically when multiple processes write to the same database.
+ // PRAGMA busy_timeout lets you set a timeout or a handler for these events. When setting a timeout,
+ // SQLite will try the transaction multiple times within this timeout.
+ // fixes #341
+ // https://rsqlite.r-dbi.org/reference/sqlitesetbusyhandler
+ // retrying for 30000 milliseconds, 30seconds - this would be unreasonable for a distributed multi-tenant application,
+ // but should be fine for local usage.
+
+ couchdbUrl := fmt.Sprintf("%s://%s:%s", appConfig.GetString("web.couchdb.scheme"), appConfig.GetString("web.couchdb.host"), appConfig.GetString("web.couchdb.port"))
+ database, err := kivik.New("couch", couchdbUrl)
+ if err != nil {
+ return nil, fmt.Errorf("Failed to connect to database! - %v", err)
+ }
+
+ err = database.Authenticate(context.Background(),
+ couchdb.BasicAuth(
+ appConfig.GetString("web.couchdb.admin_username"),
+ appConfig.GetString("web.couchdb.admin_password")),
+ )
+
+ if err != nil {
+ return nil, fmt.Errorf("Failed to authenticate to database! - %v", err)
+ }
+ globalLogger.Infof("Successfully connected to coubdb: %s\n", couchdbUrl)
+
+ deviceRepo := couchdbRepository{
+ appConfig: appConfig,
+ logger: globalLogger,
+ client: database,
+ }
+ return &deviceRepo, nil
+}
+
+type couchdbRepository struct {
+ appConfig config.Interface
+ logger logrus.FieldLogger
+
+ client *kivik.Client
+}
+
+type couchDbUser struct {
+ ID string `json:"_id"`
+ Name string `json:"name"`
+ Type string `json:"type"`
+ Roles []string `json:"roles"`
+ Password string `json:"password"`
+}
+
+func (cr *couchdbRepository) CreateUser(ctx context.Context, user *models.User) error {
+
+ newUser := &couchDbUser{
+ ID: fmt.Sprintf("%s%s", kivik.UserPrefix, user.Username),
+ Name: user.Username,
+ Type: "user",
+ Roles: []string{},
+ Password: user.Password,
+ }
+ db := cr.client.DB(ctx, "_users")
+ _, err := db.Put(ctx, newUser.ID, newUser)
+ return err
+}
+
+func (cr *couchdbRepository) Close() error {
+ return nil
+}
diff --git a/backend/pkg/database/interface.go b/backend/pkg/database/interface.go
index 7b009f1f..b5ec98ae 100644
--- a/backend/pkg/database/interface.go
+++ b/backend/pkg/database/interface.go
@@ -10,21 +10,4 @@ type DatabaseRepository interface {
Close() error
CreateUser(context.Context, *models.User) error
- GetUserByEmail(context.Context, string) (*models.User, error)
- GetCurrentUser(context.Context) *models.User
-
- GetSummary(ctx context.Context) (*models.Summary, error)
-
- UpsertResource(context.Context, *models.ResourceFhir) error
- GetResourceBySourceType(context.Context, string, string) (*models.ResourceFhir, error)
- GetResourceBySourceId(context.Context, string, string) (*models.ResourceFhir, error)
- ListResources(context.Context, models.ListResourceQueryOptions) ([]models.ResourceFhir, error)
- GetPatientForSources(ctx context.Context) ([]models.ResourceFhir, error)
- //UpsertProfile(context.Context, *models.Profile) error
- //UpsertOrganziation(context.Context, *models.Organization) error
-
- CreateSource(context.Context, *models.Source) error
- GetSource(context.Context, string) (*models.Source, error)
- GetSourceSummary(context.Context, string) (*models.SourceSummary, error)
- GetSources(context.Context) ([]models.Source, error)
}
diff --git a/backend/pkg/database/sqlite_repository.go b/backend/pkg/database/sqlite_repository.go
deleted file mode 100644
index d8354c76..00000000
--- a/backend/pkg/database/sqlite_repository.go
+++ /dev/null
@@ -1,378 +0,0 @@
-package database
-
-import (
- "context"
- "encoding/json"
- "fmt"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
- "github.com/gin-gonic/gin"
- "github.com/glebarez/sqlite"
- "github.com/google/uuid"
- "github.com/sirupsen/logrus"
- "gorm.io/gorm"
- "net/url"
-)
-
-func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger) (DatabaseRepository, error) {
- //backgroundContext := context.Background()
-
- ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- // Gorm/SQLite setup
- ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- globalLogger.Infof("Trying to connect to sqlite db: %s\n", appConfig.GetString("web.database.location"))
-
- // When a transaction cannot lock the database, because it is already locked by another one,
- // SQLite by default throws an error: database is locked. This behavior is usually not appropriate when
- // concurrent access is needed, typically when multiple processes write to the same database.
- // PRAGMA busy_timeout lets you set a timeout or a handler for these events. When setting a timeout,
- // SQLite will try the transaction multiple times within this timeout.
- // fixes #341
- // https://rsqlite.r-dbi.org/reference/sqlitesetbusyhandler
- // retrying for 30000 milliseconds, 30seconds - this would be unreasonable for a distributed multi-tenant application,
- // but should be fine for local usage.
- pragmaStr := sqlitePragmaString(map[string]string{
- "busy_timeout": "30000",
- "foreign_keys": "ON",
- })
- database, err := gorm.Open(sqlite.Open(appConfig.GetString("web.database.location")+pragmaStr), &gorm.Config{
- //TODO: figure out how to log database queries again.
- //Logger: logger
- DisableForeignKeyConstraintWhenMigrating: true,
- })
- if err != nil {
- return nil, fmt.Errorf("Failed to connect to database! - %v", err)
- }
- globalLogger.Infof("Successfully connected to scrutiny sqlite db: %s\n", appConfig.GetString("web.database.location"))
-
- //TODO: automigrate for now
- err = database.AutoMigrate(
- &models.User{},
- &models.Source{},
- &models.ResourceFhir{},
- )
- if err != nil {
- return nil, fmt.Errorf("Failed to automigrate! - %v", err)
- }
-
- // create/update admin user
- adminUser := models.User{}
- err = database.FirstOrCreate(&adminUser, models.User{Username: "admin"}).Error
- if err != nil {
- return nil, fmt.Errorf("Failed to create admin user! - %v", err)
- }
-
- deviceRepo := sqliteRepository{
- appConfig: appConfig,
- logger: globalLogger,
- gormClient: database,
- }
- return &deviceRepo, nil
-}
-
-type sqliteRepository struct {
- appConfig config.Interface
- logger logrus.FieldLogger
-
- gormClient *gorm.DB
-}
-
-func (sr *sqliteRepository) Close() error {
- return nil
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// User
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-func (sr *sqliteRepository) CreateUser(ctx context.Context, user *models.User) error {
- if err := user.HashPassword(user.Password); err != nil {
- return err
- }
- record := sr.gormClient.Create(user)
- if record.Error != nil {
- return record.Error
- }
- return nil
-}
-func (sr *sqliteRepository) GetUserByEmail(ctx context.Context, username string) (*models.User, error) {
- var foundUser models.User
- result := sr.gormClient.Where(models.User{Username: username}).First(&foundUser)
- return &foundUser, result.Error
-}
-
-func (sr *sqliteRepository) GetCurrentUser(ctx context.Context) *models.User {
- ginCtx := ctx.(*gin.Context)
- var currentUser models.User
- sr.gormClient.First(¤tUser, models.User{Username: ginCtx.MustGet("AUTH_USERNAME").(string)})
-
- return ¤tUser
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// User
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-func (sr *sqliteRepository) GetSummary(ctx context.Context) (*models.Summary, error) {
-
- // we want a count of all resources for this user by type
- var resourceCountResults []map[string]interface{}
-
- //group by resource type and return counts
- // SELECT source_resource_type as resource_type, COUNT(*) as count FROM resource_fhirs WHERE source_id = "53c1e930-63af-46c9-b760-8e83cbc1abd9" GROUP BY source_resource_type;
- result := sr.gormClient.WithContext(ctx).
- Model(models.ResourceFhir{}).
- Select("source_id, source_resource_type as resource_type, count(*) as count").
- Group("source_resource_type").
- Where(models.OriginBase{
- UserID: sr.GetCurrentUser(ctx).ID,
- }).
- Scan(&resourceCountResults)
- if result.Error != nil {
- return nil, result.Error
- }
-
- // we want a list of all sources (when they were last updated)
- sources, err := sr.GetSources(ctx)
- if err != nil {
- return nil, err
- }
-
- // we want the main Patient for each source
- patients, err := sr.GetPatientForSources(ctx)
- if err != nil {
- return nil, err
- }
-
- summary := &models.Summary{
- Sources: sources,
- ResourceTypeCounts: resourceCountResults,
- Patients: patients,
- }
-
- return summary, nil
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// Resource
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-func (sr *sqliteRepository) UpsertResource(ctx context.Context, resourceModel *models.ResourceFhir) error {
- sr.logger.Infof("insert/update (%T) %v", resourceModel, resourceModel)
-
- if sr.gormClient.Debug().WithContext(ctx).
- Where(models.OriginBase{
- SourceID: resourceModel.GetSourceID(),
- SourceResourceID: resourceModel.GetSourceResourceID(),
- SourceResourceType: resourceModel.GetSourceResourceType(), //TODO: and UpdatedAt > old UpdatedAt
- }).Updates(resourceModel).RowsAffected == 0 {
- sr.logger.Infof("resource does not exist, creating: %s %s %s", resourceModel.GetSourceID(), resourceModel.GetSourceResourceID(), resourceModel.GetSourceResourceType())
- return sr.gormClient.Debug().Create(resourceModel).Error
- }
- return nil
-}
-
-func (sr *sqliteRepository) ListResources(ctx context.Context, queryOptions models.ListResourceQueryOptions) ([]models.ResourceFhir, error) {
-
- queryParam := models.ResourceFhir{
- OriginBase: models.OriginBase{
- UserID: sr.GetCurrentUser(ctx).ID,
- },
- }
-
- if len(queryOptions.SourceResourceType) > 0 {
- queryParam.OriginBase.SourceResourceType = queryOptions.SourceResourceType
- }
-
- if len(queryOptions.SourceID) > 0 {
- sourceUUID, err := uuid.Parse(queryOptions.SourceID)
- if err != nil {
- return nil, err
- }
-
- queryParam.OriginBase.SourceID = sourceUUID
- }
-
- manifestJson, _ := json.MarshalIndent(queryParam, "", " ")
- sr.logger.Infof("THE QUERY OBJECT===========> %v", string(manifestJson))
-
- var wrappedResourceModels []models.ResourceFhir
- results := sr.gormClient.WithContext(ctx).
- Where(queryParam).
- Find(&wrappedResourceModels)
-
- return wrappedResourceModels, results.Error
-}
-
-func (sr *sqliteRepository) GetResourceBySourceType(ctx context.Context, sourceResourceType string, sourceResourceId string) (*models.ResourceFhir, error) {
- queryParam := models.ResourceFhir{
- OriginBase: models.OriginBase{
- UserID: sr.GetCurrentUser(ctx).ID,
- SourceResourceType: sourceResourceType,
- SourceResourceID: sourceResourceId,
- },
- }
-
- var wrappedResourceModel models.ResourceFhir
- results := sr.gormClient.WithContext(ctx).
- Where(queryParam).
- First(&wrappedResourceModel)
-
- return &wrappedResourceModel, results.Error
-}
-
-func (sr *sqliteRepository) GetResourceBySourceId(ctx context.Context, sourceId string, sourceResourceId string) (*models.ResourceFhir, error) {
- sourceIdUUID, err := uuid.Parse(sourceId)
- if err != nil {
- return nil, err
- }
-
- queryParam := models.ResourceFhir{
- OriginBase: models.OriginBase{
- UserID: sr.GetCurrentUser(ctx).ID,
- SourceID: sourceIdUUID,
- SourceResourceID: sourceResourceId,
- },
- }
-
- var wrappedResourceModel models.ResourceFhir
- results := sr.gormClient.WithContext(ctx).
- Where(queryParam).
- First(&wrappedResourceModel)
-
- return &wrappedResourceModel, results.Error
-}
-
-// Get the patient for each source (for the current user)
-func (sr *sqliteRepository) GetPatientForSources(ctx context.Context) ([]models.ResourceFhir, error) {
-
- //SELECT * FROM resource_fhirs WHERE user_id = "" and source_resource_type = "Patient" GROUP BY source_id
-
- //var sourceCred models.Source
- //results := sr.gormClient.WithContext(ctx).
- // Where(models.Source{UserID: sr.GetCurrentUser(ctx).ID, ModelBase: models.ModelBase{ID: sourceUUID}}).
- // First(&sourceCred)
-
- var wrappedResourceModels []models.ResourceFhir
- results := sr.gormClient.WithContext(ctx).
- Model(models.ResourceFhir{}).
- Group("source_id").
- Where(models.OriginBase{
- UserID: sr.GetCurrentUser(ctx).ID,
- SourceResourceType: "Patient",
- }).
- Find(&wrappedResourceModels)
-
- return wrappedResourceModels, results.Error
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// Source
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-func (sr *sqliteRepository) CreateSource(ctx context.Context, sourceCreds *models.Source) error {
- sourceCreds.UserID = sr.GetCurrentUser(ctx).ID
-
- if sr.gormClient.WithContext(ctx).
- Where(models.Source{
- UserID: sourceCreds.UserID,
- SourceType: sourceCreds.SourceType,
- PatientId: sourceCreds.PatientId}).Updates(sourceCreds).RowsAffected == 0 {
- return sr.gormClient.WithContext(ctx).Create(sourceCreds).Error
- }
- return nil
-}
-
-func (sr *sqliteRepository) GetSource(ctx context.Context, sourceId string) (*models.Source, error) {
- sourceUUID, err := uuid.Parse(sourceId)
- if err != nil {
- return nil, err
- }
-
- var sourceCred models.Source
- results := sr.gormClient.WithContext(ctx).
- Where(models.Source{UserID: sr.GetCurrentUser(ctx).ID, ModelBase: models.ModelBase{ID: sourceUUID}}).
- First(&sourceCred)
-
- return &sourceCred, results.Error
-}
-
-func (sr *sqliteRepository) GetSourceSummary(ctx context.Context, sourceId string) (*models.SourceSummary, error) {
- sourceUUID, err := uuid.Parse(sourceId)
- if err != nil {
- return nil, err
- }
-
- sourceSummary := &models.SourceSummary{}
-
- source, err := sr.GetSource(ctx, sourceId)
- if err != nil {
- return nil, err
- }
- sourceSummary.Source = source
-
- //group by resource type and return counts
- // SELECT source_resource_type as resource_type, COUNT(*) as count FROM resource_fhirs WHERE source_id = "53c1e930-63af-46c9-b760-8e83cbc1abd9" GROUP BY source_resource_type;
-
- var resourceTypeCounts []map[string]interface{}
-
- result := sr.gormClient.WithContext(ctx).
- Model(models.ResourceFhir{}).
- Select("source_id, source_resource_type as resource_type, count(*) as count").
- Group("source_resource_type").
- Where(models.OriginBase{
- UserID: sr.GetCurrentUser(ctx).ID,
- SourceID: sourceUUID,
- }).
- Scan(&resourceTypeCounts)
-
- if result.Error != nil {
- return nil, result.Error
- }
-
- sourceSummary.ResourceTypeCounts = resourceTypeCounts
-
- //set patient
- var wrappedPatientResourceModel models.ResourceFhir
- results := sr.gormClient.WithContext(ctx).
- Where(models.OriginBase{
- UserID: sr.GetCurrentUser(ctx).ID,
- SourceResourceType: "Patient",
- SourceID: sourceUUID,
- }).
- First(&wrappedPatientResourceModel)
-
- if results.Error != nil {
- return nil, result.Error
- }
- sourceSummary.Patient = &wrappedPatientResourceModel
-
- return sourceSummary, nil
-}
-
-func (sr *sqliteRepository) GetSources(ctx context.Context) ([]models.Source, error) {
-
- var sourceCreds []models.Source
- results := sr.gormClient.WithContext(ctx).
- Where(models.Source{UserID: sr.GetCurrentUser(ctx).ID}).
- Find(&sourceCreds)
-
- return sourceCreds, results.Error
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// Utilities
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-func sqlitePragmaString(pragmas map[string]string) string {
- q := url.Values{}
- for key, val := range pragmas {
- q.Add("_pragma", key+"="+val)
- }
-
- queryStr := q.Encode()
- if len(queryStr) > 0 {
- return "?" + queryStr
- }
- return ""
-}
diff --git a/backend/pkg/hub/README.md b/backend/pkg/hub/README.md
deleted file mode 100644
index 773704d4..00000000
--- a/backend/pkg/hub/README.md
+++ /dev/null
@@ -1,12 +0,0 @@
-# Hub
-
-The Fasten Hub is a semi stand-alone application that can retrieve data from various Medical Providers, transform it, and
-store it in the database. This code will eventually be moved into its own repository.
-
-# Types
-
-There are multiple protocols used by the Medical Provider industry to transfer patient data, the following mechanisms are the
-ones that Fasten supports
-
-### FHIR
-
diff --git a/backend/pkg/hub/factory.go b/backend/pkg/hub/factory.go
deleted file mode 100644
index b863bdf4..00000000
--- a/backend/pkg/hub/factory.go
+++ /dev/null
@@ -1,58 +0,0 @@
-package hub
-
-import (
- "context"
- "errors"
- "fmt"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/aetna"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/athena"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/bluebutton"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/careevolution"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/cerner"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/cigna"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/epic"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/healthit"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/logica"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/manual"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
- "github.com/sirupsen/logrus"
- "net/http"
-)
-
-func NewClient(sourceType pkg.SourceType, ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, credentials models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
-
- var sourceClient base.Client
- var updatedSource *models.Source
- var err error
- switch sourceType {
- case pkg.SourceTypeAetna:
- sourceClient, updatedSource, err = aetna.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeAthena:
- sourceClient, updatedSource, err = athena.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeAnthem:
- sourceClient, updatedSource, err = cigna.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeBlueButtonMedicare:
- sourceClient, updatedSource, err = bluebutton.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeCareEvolution:
- sourceClient, updatedSource, err = careevolution.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeCerner:
- sourceClient, updatedSource, err = cerner.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeCigna:
- sourceClient, updatedSource, err = cigna.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeEpic:
- sourceClient, updatedSource, err = epic.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeHealthIT:
- sourceClient, updatedSource, err = healthit.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeLogica:
- sourceClient, updatedSource, err = logica.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- case pkg.SourceTypeManual:
- sourceClient, updatedSource, err = manual.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
- default:
- return nil, updatedSource, errors.New(fmt.Sprintf("Unknown Source Type: %s", sourceType))
- }
-
- return sourceClient, updatedSource, err
-}
diff --git a/backend/pkg/hub/internal/fhir/aetna/client.go b/backend/pkg/hub/internal/fhir/aetna/client.go
deleted file mode 100644
index c5f6d219..00000000
--- a/backend/pkg/hub/internal/fhir/aetna/client.go
+++ /dev/null
@@ -1,49 +0,0 @@
-package aetna
-
-import (
- "context"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
- "github.com/sirupsen/logrus"
- "net/http"
-)
-
-type AetnaClient struct {
- *base.FHIR401Client
-}
-
-func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
- baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
- return AetnaClient{
- baseClient,
- }, updatedSource, err
-}
-
-//Overrides
-
-func (c AetnaClient) SyncAll(db database.DatabaseRepository) error {
-
- bundle, err := c.GetResourceBundle("Patient")
- if err != nil {
- c.Logger.Infof("An error occurred while getting patient bundle %s", c.Source.PatientId)
- return err
- }
-
- wrappedResourceModels, err := c.ProcessBundle(bundle)
- if err != nil {
- c.Logger.Infof("An error occurred while processing patient bundle %s", c.Source.PatientId)
- return err
- }
- //todo, create the resources in dependency order
-
- for _, apiModel := range wrappedResourceModels {
- err = db.UpsertResource(context.Background(), &apiModel)
- if err != nil {
- c.Logger.Info("An error occurred while upserting resource")
- return err
- }
- }
- return nil
-}
diff --git a/backend/pkg/hub/internal/fhir/athena/client.go b/backend/pkg/hub/internal/fhir/athena/client.go
deleted file mode 100644
index 33d54727..00000000
--- a/backend/pkg/hub/internal/fhir/athena/client.go
+++ /dev/null
@@ -1,49 +0,0 @@
-package athena
-
-import (
- "context"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
- "github.com/sirupsen/logrus"
- "net/http"
-)
-
-type AthenaClient struct {
- *base.FHIR401Client
-}
-
-func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
- baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
- return AthenaClient{
- baseClient,
- }, updatedSource, err
-}
-
-func (c AthenaClient) SyncAll(db database.DatabaseRepository) error {
- supportedResources := []string{
- "AllergyIntolerance",
- //"Binary",
- "CarePlan",
- "CareTeam",
- "Condition",
- "Device",
- "DiagnosticReport",
- "DocumentReference",
- "Encounter",
- "Goal",
- "Immunization",
- //"Location",
- //"Medication",
- //"MedicationRequest",
- "Observation",
- //"Organization",
- //"Patient",
- //"Practitioner",
- "Procedure",
- //"Provenance",
- }
-
- return c.SyncAllByResourceName(db, supportedResources)
-}
diff --git a/backend/pkg/hub/internal/fhir/base/base_client.go b/backend/pkg/hub/internal/fhir/base/base_client.go
deleted file mode 100644
index a2b3565c..00000000
--- a/backend/pkg/hub/internal/fhir/base/base_client.go
+++ /dev/null
@@ -1,154 +0,0 @@
-package base
-
-import (
- "context"
- "encoding/json"
- "fmt"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
- "github.com/sirupsen/logrus"
- "golang.org/x/oauth2"
- "io"
- "log"
- "net/http"
- "net/url"
- "os"
- "strings"
- "time"
-)
-
-type BaseClient struct {
- Context context.Context
- AppConfig config.Interface
- Logger logrus.FieldLogger
-
- OauthClient *http.Client
- Source models.Source
- Headers map[string]string
-}
-
-func (c *BaseClient) SyncAllBundle(db database.DatabaseRepository, bundleFile *os.File) error {
- panic("SyncAllBundle functionality is not available on this client")
-}
-
-func NewBaseClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (*BaseClient, *models.Source, error) {
- var httpClient *http.Client
- var updatedSource *models.Source
- if len(testHttpClient) == 0 {
- //check if we need to refresh the access token
- //https://github.com/golang/oauth2/issues/84#issuecomment-520099526
- // https://chromium.googlesource.com/external/github.com/golang/oauth2/+/8f816d62a2652f705144857bbbcc26f2c166af9e/oauth2.go#239
- conf := &oauth2.Config{
- ClientID: source.ClientId,
- ClientSecret: "",
- Endpoint: oauth2.Endpoint{
- AuthURL: source.OauthAuthorizationEndpoint,
- TokenURL: source.OauthTokenEndpoint,
- },
- //RedirectURL: "",
- //Scopes: nil,
- }
- token := &oauth2.Token{
- TokenType: "Bearer",
- RefreshToken: source.RefreshToken,
- AccessToken: source.AccessToken,
- Expiry: time.Unix(source.ExpiresAt, 0),
- }
- if token.Expiry.Before(time.Now()) { // expired so let's update it
- log.Println("access token expired, refreshing...")
- src := conf.TokenSource(ctx, token)
- newToken, err := src.Token() // this actually goes and renews the tokens
- if err != nil {
- return nil, nil, err
- }
- if newToken.AccessToken != token.AccessToken {
- token = newToken
-
- // update the "source" credential with new data (which will need to be sent
- updatedSource = &source
- updatedSource.AccessToken = newToken.AccessToken
- updatedSource.ExpiresAt = newToken.Expiry.Unix()
- // Don't overwrite `RefreshToken` with an empty value
- // if this was a token refreshing request.
- if newToken.RefreshToken != "" {
- updatedSource.RefreshToken = newToken.RefreshToken
- }
-
- }
- }
-
- // OLD CODE
- httpClient = oauth2.NewClient(ctx, oauth2.StaticTokenSource(token))
-
- } else {
- //Testing mode.
- httpClient = testHttpClient[0]
- }
-
- httpClient.Timeout = 10 * time.Second
-
- return &BaseClient{
- Context: ctx,
- AppConfig: appConfig,
- Logger: globalLogger,
- OauthClient: httpClient,
- Source: source,
- Headers: map[string]string{},
- }, updatedSource, nil
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// HttpClient
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-func (c *BaseClient) GetRequest(resourceSubpathOrNext string, decodeModelPtr interface{}) error {
- resourceUrl, err := url.Parse(resourceSubpathOrNext)
- if err != nil {
- return err
- }
- if !resourceUrl.IsAbs() {
- resourceUrl, err = url.Parse(fmt.Sprintf("%s/%s", strings.TrimRight(c.Source.ApiEndpointBaseUrl, "/"), strings.TrimLeft(resourceSubpathOrNext, "/")))
- }
- if err != nil {
- return err
- }
-
- req, err := http.NewRequest(http.MethodGet, resourceUrl.String(), nil)
- if err != nil {
- return err
- }
-
- for key, val := range c.Headers {
- //req.Header.Add("Accept", "application/json+fhir")
- req.Header.Add(key, val)
- }
-
- //resp, err := c.OauthClient.Get(url)
- resp, err := c.OauthClient.Do(req)
-
- if err != nil {
- return err
- }
- defer resp.Body.Close()
-
- if resp.StatusCode >= 300 || resp.StatusCode < 200 {
- b, _ := io.ReadAll(resp.Body)
- return fmt.Errorf("An error occurred during request %s - %d - %s [%s]", resourceUrl, resp.StatusCode, resp.Status, string(b))
- }
-
- err = ParseBundle(resp.Body, decodeModelPtr)
- return err
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// Helper Functions
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-func ParseBundle(r io.Reader, decodeModelPtr interface{}) error {
- decoder := json.NewDecoder(r)
- //decoder.DisallowUnknownFields() //make sure we throw an error if unknown fields are present.
- err := decoder.Decode(decodeModelPtr)
- if err != nil {
- return err
- }
- return err
-}
diff --git a/backend/pkg/hub/internal/fhir/base/fhir401_client.go b/backend/pkg/hub/internal/fhir/base/fhir401_client.go
deleted file mode 100644
index 8aaab185..00000000
--- a/backend/pkg/hub/internal/fhir/base/fhir401_client.go
+++ /dev/null
@@ -1,208 +0,0 @@
-package base
-
-import (
- "context"
- "fmt"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
- "github.com/fastenhealth/gofhir-models/fhir401"
- fhirutils "github.com/fastenhealth/gofhir-models/fhir401/utils"
- "github.com/samber/lo"
- "github.com/sirupsen/logrus"
- "gorm.io/datatypes"
- "net/http"
-)
-
-type FHIR401Client struct {
- *BaseClient
-}
-
-func NewFHIR401Client(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (*FHIR401Client, *models.Source, error) {
- baseClient, updatedSource, err := NewBaseClient(ctx, appConfig, globalLogger, source, testHttpClient...)
- return &FHIR401Client{
- baseClient,
- }, updatedSource, err
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// Sync
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-func (c *FHIR401Client) SyncAll(db database.DatabaseRepository) error {
-
- bundle, err := c.GetPatientBundle(c.Source.PatientId)
- if err != nil {
- return err
- }
-
- wrappedResourceModels, err := c.ProcessBundle(bundle)
- if err != nil {
- c.Logger.Infof("An error occurred while processing patient bundle %s", c.Source.PatientId)
- return err
- }
- //todo, create the resources in dependency order
-
- for _, apiModel := range wrappedResourceModels {
- err = db.UpsertResource(context.Background(), &apiModel)
- if err != nil {
- return err
- }
- }
- return nil
-}
-
-//TODO, find a way to sync references that cannot be searched by patient ID.
-func (c *FHIR401Client) SyncAllByResourceName(db database.DatabaseRepository, resourceNames []string) error {
-
- //Store the Patient
- patientResource, err := c.GetPatient(c.Source.PatientId)
- if err != nil {
- return err
- }
- patientJson, err := patientResource.MarshalJSON()
- if err != nil {
- return err
- }
-
- patientResourceType, patientResourceId := patientResource.ResourceRef()
- patientResourceFhir := models.ResourceFhir{
- OriginBase: models.OriginBase{
- UserID: c.Source.UserID,
- SourceID: c.Source.ID,
- SourceResourceType: patientResourceType,
- SourceResourceID: *patientResourceId,
- },
- Payload: datatypes.JSON(patientJson),
- }
- db.UpsertResource(context.Background(), &patientResourceFhir)
-
- //error map storage.
- syncErrors := map[string]error{}
-
- //Store all other resources.
- for _, resourceType := range resourceNames {
- bundle, err := c.GetResourceBundle(fmt.Sprintf("%s?patient=%s", resourceType, c.Source.PatientId))
- if err != nil {
- syncErrors[resourceType] = err
- continue
- }
- wrappedResourceModels, err := c.ProcessBundle(bundle)
- if err != nil {
- c.Logger.Infof("An error occurred while processing %s bundle %s", resourceType, c.Source.PatientId)
- syncErrors[resourceType] = err
- continue
- }
- for _, apiModel := range wrappedResourceModels {
- err = db.UpsertResource(context.Background(), &apiModel)
- if err != nil {
- syncErrors[resourceType] = err
- continue
- }
- }
- }
-
- if len(syncErrors) > 0 {
- return fmt.Errorf("%d error(s) occurred during sync: %v", len(syncErrors), syncErrors)
- }
- return nil
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// FHIR
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-func (c *FHIR401Client) GetResourceBundle(relativeResourcePath string) (fhir401.Bundle, error) {
-
- // https://www.hl7.org/fhir/patient-operation-everything.html
- bundle := fhir401.Bundle{}
- err := c.GetRequest(relativeResourcePath, &bundle)
- if err != nil {
- return bundle, err
- }
- var next string
- var prev string
- var self string
- for _, link := range 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
- }
- }
-
- for len(next) > 0 && next != self && next != prev {
- c.Logger.Debugf("Paginated request => %s", next)
- nextBundle := fhir401.Bundle{}
- err := c.GetRequest(next, &nextBundle)
- if err != nil {
- return bundle, nil //ignore failures when paginating?
- }
- bundle.Entry = append(bundle.Entry, nextBundle.Entry...)
-
- next = "" //reset the pointers
- self = ""
- prev = ""
- for _, link := range 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, err
-
-}
-
-func (c *FHIR401Client) GetPatientBundle(patientId string) (fhir401.Bundle, error) {
- return c.GetResourceBundle(fmt.Sprintf("Patient/%s/$everything", patientId))
-}
-
-func (c *FHIR401Client) GetPatient(patientId string) (fhir401.Patient, error) {
-
- patient := fhir401.Patient{}
- err := c.GetRequest(fmt.Sprintf("Patient/%s", patientId), &patient)
- return patient, err
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// Process Bundles
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-func (c *FHIR401Client) ProcessBundle(bundle fhir401.Bundle) ([]models.ResourceFhir, error) {
-
- //process each entry in bundle
- wrappedResourceModels := lo.FilterMap[fhir401.BundleEntry, models.ResourceFhir](bundle.Entry, func(bundleEntry fhir401.BundleEntry, _ int) (models.ResourceFhir, bool) {
- originalResource, _ := fhirutils.MapToResource(bundleEntry.Resource, false)
-
- resourceType, resourceId := originalResource.(ResourceInterface).ResourceRef()
-
- // TODO find a way to safely/consistently get the resource updated date (and other metadata) which shoudl be added to the model.
- //if originalResource.Meta != nil && originalResource.Meta.LastUpdated != nil {
- // if parsed, err := time.Parse(time.RFC3339Nano, *originalResource.Meta.LastUpdated); err == nil {
- // patientProfile.UpdatedAt = parsed
- // }
- //}
- if resourceId == nil {
- //no resourceId present for this resource, we'll ignore it.
- return models.ResourceFhir{}, false
- }
-
- wrappedResourceModel := models.ResourceFhir{
- OriginBase: models.OriginBase{
- ModelBase: models.ModelBase{},
- UserID: c.Source.UserID,
- SourceID: c.Source.ID,
- SourceResourceID: *resourceId,
- SourceResourceType: resourceType,
- },
- Payload: datatypes.JSON(bundleEntry.Resource),
- }
-
- return wrappedResourceModel, true
- })
- return wrappedResourceModels, nil
-}
diff --git a/backend/pkg/hub/internal/fhir/base/fhir401_client_test.go b/backend/pkg/hub/internal/fhir/base/fhir401_client_test.go
deleted file mode 100644
index f306995f..00000000
--- a/backend/pkg/hub/internal/fhir/base/fhir401_client_test.go
+++ /dev/null
@@ -1,80 +0,0 @@
-package base
-
-import (
- "context"
- "encoding/json"
- mock_config "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config/mock"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
- "github.com/fastenhealth/gofhir-models/fhir401"
- "github.com/golang/mock/gomock"
- "github.com/sirupsen/logrus"
- "github.com/stretchr/testify/require"
- "io/ioutil"
- "net/http"
- "os"
- "testing"
-)
-
-// helpers
-func readTestFixture(path string) ([]byte, error) {
- jsonFile, err := os.Open(path)
- if err != nil {
- return nil, err
- }
- defer jsonFile.Close()
- return ioutil.ReadAll(jsonFile)
-}
-
-func TestNewFHIR401Client(t *testing.T) {
- t.Parallel()
- //setup
- mockCtrl := gomock.NewController(t)
- defer mockCtrl.Finish()
- fakeConfig := mock_config.NewMockInterface(mockCtrl)
-
- testLogger := logrus.WithFields(logrus.Fields{
- "type": "test",
- })
-
- //test
- client, _, err := NewFHIR401Client(context.Background(), fakeConfig, testLogger, models.Source{
- RefreshToken: "test-refresh-token",
- AccessToken: "test-access-token",
- }, &http.Client{})
-
- //assert
- require.NoError(t, err)
- require.Equal(t, client.Source.AccessToken, "test-access-token")
- require.Equal(t, client.Source.RefreshToken, "test-refresh-token")
-}
-
-func TestFHIR401Client_ProcessBundle(t *testing.T) {
- t.Parallel()
- //setup
- mockCtrl := gomock.NewController(t)
- defer mockCtrl.Finish()
- fakeConfig := mock_config.NewMockInterface(mockCtrl)
- testLogger := logrus.WithFields(logrus.Fields{
- "type": "test",
- })
- client, _, err := NewFHIR401Client(context.Background(), fakeConfig, testLogger, models.Source{
- RefreshToken: "test-refresh-token",
- AccessToken: "test-access-token",
- }, &http.Client{})
- require.NoError(t, err)
-
- jsonBytes, err := readTestFixture("testdata/fixtures/401-R4/bundle/cigna_syntheticuser05-everything.json")
- require.NoError(t, err)
- var bundle fhir401.Bundle
- err = json.Unmarshal(jsonBytes, &bundle)
- require.NoError(t, err)
-
- // test
- wrappedResourceModels, err := client.ProcessBundle(bundle)
- //log.Printf("%v", wrappedResourceModels)
-
- //assert
- require.NoError(t, err)
- require.Equal(t, 11, len(wrappedResourceModels))
- //require.Equal(t, "A00000000000005", profile.SourceResourceID)
-}
diff --git a/backend/pkg/hub/internal/fhir/base/fhir430_client.go b/backend/pkg/hub/internal/fhir/base/fhir430_client.go
deleted file mode 100644
index 2f134fc4..00000000
--- a/backend/pkg/hub/internal/fhir/base/fhir430_client.go
+++ /dev/null
@@ -1,81 +0,0 @@
-package base
-
-import (
- "context"
- "fmt"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
- "github.com/fastenhealth/gofhir-models/fhir430"
- fhirutils "github.com/fastenhealth/gofhir-models/fhir430/utils"
- "github.com/samber/lo"
- "github.com/sirupsen/logrus"
- "gorm.io/datatypes"
- "net/http"
-)
-
-type FHIR430Client struct {
- *BaseClient
-}
-
-func NewFHIR430Client(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (*FHIR430Client, *models.Source, error) {
- baseClient, updatedSource, err := NewBaseClient(ctx, appConfig, globalLogger, source, testHttpClient...)
- return &FHIR430Client{
- baseClient,
- }, updatedSource, err
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// FHIR
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-func (c *FHIR430Client) GetPatientEverything(patientId string) (*fhir430.Bundle, error) {
-
- // https://www.hl7.org/fhir/patient-operation-everything.html
- bundle := fhir430.Bundle{}
- err := c.GetRequest(fmt.Sprintf("Patient/%s/$everything", patientId), &bundle)
- return &bundle, err
-}
-
-func (c *FHIR430Client) GetPatient(patientId string) (*fhir430.Patient, error) {
-
- patient := fhir430.Patient{}
- err := c.GetRequest(fmt.Sprintf("Patient/%s", patientId), &patient)
- return &patient, err
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// Process Bundles
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-func (c *FHIR430Client) ProcessBundle(bundle fhir430.Bundle) ([]models.ResourceFhir, error) {
-
- //process each entry in bundle
- wrappedResourceModels := lo.FilterMap[fhir430.BundleEntry, models.ResourceFhir](bundle.Entry, func(bundleEntry fhir430.BundleEntry, _ int) (models.ResourceFhir, bool) {
- originalResource, _ := fhirutils.MapToResource(bundleEntry.Resource, false)
-
- resourceType, resourceId := originalResource.(ResourceInterface).ResourceRef()
-
- // TODO find a way to safely/consistently get the resource updated date (and other metadata) which shoudl be added to the model.
- //if originalResource.Meta != nil && originalResource.Meta.LastUpdated != nil {
- // if parsed, err := time.Parse(time.RFC3339Nano, *originalResource.Meta.LastUpdated); err == nil {
- // patientProfile.UpdatedAt = parsed
- // }
- //}
- if resourceId == nil {
- //no resourceId present for this resource, we'll ignore it.
- return models.ResourceFhir{}, false
- }
-
- wrappedResourceModel := models.ResourceFhir{
- OriginBase: models.OriginBase{
- ModelBase: models.ModelBase{},
- UserID: c.Source.UserID,
- SourceID: c.Source.ID,
- SourceResourceID: *resourceId,
- SourceResourceType: resourceType,
- },
- Payload: datatypes.JSON(bundleEntry.Resource),
- }
-
- return wrappedResourceModel, true
- })
- return wrappedResourceModels, nil
-}
diff --git a/backend/pkg/hub/internal/fhir/base/interface.go b/backend/pkg/hub/internal/fhir/base/interface.go
deleted file mode 100644
index b9559811..00000000
--- a/backend/pkg/hub/internal/fhir/base/interface.go
+++ /dev/null
@@ -1,19 +0,0 @@
-package base
-
-import (
- "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
- "os"
-)
-
-//go:generate mockgen -source=interface.go -destination=mock/mock_client.go
-type Client interface {
- GetRequest(resourceSubpath string, decodeModelPtr interface{}) error
- SyncAll(db database.DatabaseRepository) error
-
- //Manual client ONLY functions
- SyncAllBundle(db database.DatabaseRepository, bundleFile *os.File) error
-}
-
-type ResourceInterface interface {
- ResourceRef() (string, *string)
-}
diff --git a/backend/pkg/hub/internal/fhir/base/mock/mock_client.go b/backend/pkg/hub/internal/fhir/base/mock/mock_client.go
deleted file mode 100644
index 3e4c3dc7..00000000
--- a/backend/pkg/hub/internal/fhir/base/mock/mock_client.go
+++ /dev/null
@@ -1,116 +0,0 @@
-// Code generated by MockGen. DO NOT EDIT.
-// Source: interface.go
-
-// Package mock_base is a generated GoMock package.
-package mock_base
-
-import (
- os "os"
- reflect "reflect"
-
- database "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
- gomock "github.com/golang/mock/gomock"
-)
-
-// MockClient is a mock of Client interface.
-type MockClient struct {
- ctrl *gomock.Controller
- recorder *MockClientMockRecorder
-}
-
-// MockClientMockRecorder is the mock recorder for MockClient.
-type MockClientMockRecorder struct {
- mock *MockClient
-}
-
-// NewMockClient creates a new mock instance.
-func NewMockClient(ctrl *gomock.Controller) *MockClient {
- mock := &MockClient{ctrl: ctrl}
- mock.recorder = &MockClientMockRecorder{mock}
- return mock
-}
-
-// EXPECT returns an object that allows the caller to indicate expected use.
-func (m *MockClient) EXPECT() *MockClientMockRecorder {
- return m.recorder
-}
-
-// GetRequest mocks base method.
-func (m *MockClient) GetRequest(resourceSubpath string, decodeModelPtr interface{}) error {
- m.ctrl.T.Helper()
- ret := m.ctrl.Call(m, "GetRequest", resourceSubpath, decodeModelPtr)
- ret0, _ := ret[0].(error)
- return ret0
-}
-
-// GetRequest indicates an expected call of GetRequest.
-func (mr *MockClientMockRecorder) GetRequest(resourceSubpath, decodeModelPtr interface{}) *gomock.Call {
- mr.mock.ctrl.T.Helper()
- return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetRequest", reflect.TypeOf((*MockClient)(nil).GetRequest), resourceSubpath, decodeModelPtr)
-}
-
-// SyncAll mocks base method.
-func (m *MockClient) SyncAll(db database.DatabaseRepository) error {
- m.ctrl.T.Helper()
- ret := m.ctrl.Call(m, "SyncAll", db)
- ret0, _ := ret[0].(error)
- return ret0
-}
-
-// SyncAll indicates an expected call of SyncAll.
-func (mr *MockClientMockRecorder) SyncAll(db interface{}) *gomock.Call {
- mr.mock.ctrl.T.Helper()
- return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "SyncAll", reflect.TypeOf((*MockClient)(nil).SyncAll), db)
-}
-
-// SyncAllBundle mocks base method.
-func (m *MockClient) SyncAllBundle(db database.DatabaseRepository, bundleFile *os.File) error {
- m.ctrl.T.Helper()
- ret := m.ctrl.Call(m, "SyncAllBundle", db, bundleFile)
- ret0, _ := ret[0].(error)
- return ret0
-}
-
-// SyncAllBundle indicates an expected call of SyncAllBundle.
-func (mr *MockClientMockRecorder) SyncAllBundle(db, bundleFile interface{}) *gomock.Call {
- mr.mock.ctrl.T.Helper()
- return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "SyncAllBundle", reflect.TypeOf((*MockClient)(nil).SyncAllBundle), db, bundleFile)
-}
-
-// MockResourceInterface is a mock of ResourceInterface interface.
-type MockResourceInterface struct {
- ctrl *gomock.Controller
- recorder *MockResourceInterfaceMockRecorder
-}
-
-// MockResourceInterfaceMockRecorder is the mock recorder for MockResourceInterface.
-type MockResourceInterfaceMockRecorder struct {
- mock *MockResourceInterface
-}
-
-// NewMockResourceInterface creates a new mock instance.
-func NewMockResourceInterface(ctrl *gomock.Controller) *MockResourceInterface {
- mock := &MockResourceInterface{ctrl: ctrl}
- mock.recorder = &MockResourceInterfaceMockRecorder{mock}
- return mock
-}
-
-// EXPECT returns an object that allows the caller to indicate expected use.
-func (m *MockResourceInterface) EXPECT() *MockResourceInterfaceMockRecorder {
- return m.recorder
-}
-
-// ResourceRef mocks base method.
-func (m *MockResourceInterface) ResourceRef() (string, *string) {
- m.ctrl.T.Helper()
- ret := m.ctrl.Call(m, "ResourceRef")
- ret0, _ := ret[0].(string)
- ret1, _ := ret[1].(*string)
- return ret0, ret1
-}
-
-// ResourceRef indicates an expected call of ResourceRef.
-func (mr *MockResourceInterfaceMockRecorder) ResourceRef() *gomock.Call {
- mr.mock.ctrl.T.Helper()
- return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "ResourceRef", reflect.TypeOf((*MockResourceInterface)(nil).ResourceRef))
-}
diff --git a/backend/pkg/hub/internal/fhir/base/test_helpers.go b/backend/pkg/hub/internal/fhir/base/test_helpers.go
deleted file mode 100644
index 3d39514d..00000000
--- a/backend/pkg/hub/internal/fhir/base/test_helpers.go
+++ /dev/null
@@ -1,51 +0,0 @@
-package base
-
-import (
- "context"
- "crypto/tls"
- "github.com/seborama/govcr"
- "golang.org/x/oauth2"
- "net/http"
- "path"
- "testing"
-)
-
-func OAuthVcrSetup(t *testing.T, enableRecording bool) *http.Client {
- accessToken := "PLACEHOLDER"
- if enableRecording {
- //this has to be disabled because CI is empty inside docker containers.
- accessToken = ""
- }
-
- ts := oauth2.StaticTokenSource(
- //setting a real access token here will allow API calls to connect successfully
- &oauth2.Token{AccessToken: accessToken},
- )
-
- tr := http.DefaultTransport.(*http.Transport)
- tr.TLSClientConfig = &tls.Config{
- InsecureSkipVerify: true, //disable certificate validation because we're playing back http requests.
- }
- insecureClient := http.Client{
- Transport: tr,
- }
-
- ctx := context.WithValue(oauth2.NoContext, oauth2.HTTPClient, insecureClient)
- tc := oauth2.NewClient(ctx, ts)
-
- vcrConfig := govcr.VCRConfig{
- Logging: true,
- CassettePath: path.Join("testdata", "govcr-fixtures"),
- Client: tc,
-
- //this line ensures that we do not attempt to create new recordings.
- //Comment this out if you would like to make recordings.
- DisableRecording: !enableRecording,
- }
-
- // HTTP headers are case-insensitive
- vcrConfig.RequestFilters.Add(govcr.RequestDeleteHeaderKeys("User-Agent", "user-agent"))
-
- vcr := govcr.NewVCR(t.Name(), &vcrConfig)
- return vcr.Client
-}
diff --git a/backend/pkg/hub/internal/fhir/base/testdata/fixtures/401-R4/bundle/cigna_syntheticuser05-everything.json b/backend/pkg/hub/internal/fhir/base/testdata/fixtures/401-R4/bundle/cigna_syntheticuser05-everything.json
deleted file mode 100644
index 7512cc65..00000000
--- a/backend/pkg/hub/internal/fhir/base/testdata/fixtures/401-R4/bundle/cigna_syntheticuser05-everything.json
+++ /dev/null
@@ -1,1542 +0,0 @@
-{
- "meta": {
- "source": "https://p-hi2.digitaledge.cigna.com"
- },
- "entry": [{
- "fullUrl": "https://p-hi2.digitaledge.cigna.com/PatientAccess/v1-devportal/Patient/ifp-A00000000000005",
- "resource": {
- "id": "ifp-A00000000000005",
- "meta": {
- "lastUpdated": "2022-06-20T15:45:22.043000+00:00",
- "profile": ["http://hl7.org/fhir/us/carin-bb/StructureDefinition/C4BB-Patient"],
- "source": "IFP#CqP06ARvJo9XS9Cl",
- "versionId": "1"
- },
- "text": {
- "div": "| Identifier | A00000000000005 |
| Date of birth | 12 January 2013 |
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: -2282623849526784568 Population seed: 0
Care Plan for Asthma self management.
Activities:
- Asthma self management
- Asthma self management
- Asthma self management
Care plan is meant to treat Childhood asthma.
Care Plan for Self care.
Activities:
Care Plan for Lifestyle education regarding hypertension.
Activities:
- Lifestyle education regarding hypertension
- Lifestyle education regarding hypertension
- Lifestyle education regarding hypertension
- Lifestyle education regarding hypertension
Care plan is meant to treat Hypertension.
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: 6854428927621892691 Population seed: 0
Care Plan for Diabetes self management plan.
Activities:
- Diabetes self management plan
- Diabetes self management plan
Care plan is meant to treat Prediabetes.
Care Plan for Respiratory therapy.
Activities:
- Respiratory therapy
- Respiratory therapy
Care plan is meant to treat Acute bronchitis (disorder).
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: 1176089665387826969 Population seed: 0
Care Plan for Diabetes self management plan.
Activities:
- Diabetes self management plan
- Diabetes self management plan
Care plan is meant to treat Prediabetes.
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: 5245364836250954000 Population seed: 0
Care Plan for Respiratory therapy.
Activities:
- Respiratory therapy
- Respiratory therapy
Care plan is meant to treat Acute bronchitis (disorder).
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: 3041628524624170284 Population seed: 0
Care Plan for Self care.
Activities:
- Self care
- Self care
- Self care
Care Plan for Care plan (record artifact).
Activities:
- Care plan (record artifact)
- Care plan (record artifact)
- Care plan (record artifact)
Care plan is meant to treat Drug overdose.
Care Plan for Routine antenatal care.
Activities:
- Routine antenatal care
- Routine antenatal care
- Routine antenatal care
Care plan is meant to treat Normal pregnancy.
Care Plan for Respiratory therapy.
Activities:
- Respiratory therapy
- Respiratory therapy
Care plan is meant to treat Acute bronchitis (disorder).
Care Plan for Routine antenatal care.
Activities:
- Routine antenatal care
- Routine antenatal care
- Routine antenatal care
Care plan is meant to treat Normal pregnancy.
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: 4482083831205177148 Population seed: 0
Care Plan for Fracture care.
Activities:
- Fracture care
- Fracture care
Care plan is meant to treat Closed fracture of hip.
Care Plan for Respiratory therapy.
Activities:
- Respiratory therapy
- Respiratory therapy
Care plan is meant to treat Acute bronchitis (disorder).
Care Plan for Respiratory therapy.
Activities:
- Respiratory therapy
- Respiratory therapy
Care plan is meant to treat Acute bronchitis (disorder).
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: 7251516320691860882 Population seed: 0
Care Plan for Diabetes self management plan.
Activities:
- Diabetes self management plan
- Diabetes self management plan
Care plan is meant to treat Prediabetes.
Care Plan for Hyperlipidemia clinical management plan.
Activities:
- Hyperlipidemia clinical management plan
- Hyperlipidemia clinical management plan
Care plan is meant to treat Hyperlipidemia.
Care Plan for Musculoskeletal care.
Activities:
- Musculoskeletal care
- Musculoskeletal care
Care plan is meant to treat Localized, primary osteoarthritis of the hand.
Care Plan for Heart failure self management plan.
Activities:
- Heart failure self management plan
- Heart failure self management plan
Care plan is meant to treat Chronic congestive heart failure (disorder).
Care Plan for Inpatient care plan (record artifact).
Activities:
- Inpatient care plan (record artifact)
- Inpatient care plan (record artifact)
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: 2978214333338970539 Population seed: 0
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: -6016242411370302863 Population seed: 0
Care Plan for Wound care.
Activities:
Care plan is meant to treat Laceration of thigh.
Care Plan for Lifestyle education regarding hypertension.
Activities:
- Lifestyle education regarding hypertension
- Lifestyle education regarding hypertension
- Lifestyle education regarding hypertension
- Lifestyle education regarding hypertension
Care plan is meant to treat Hypertension.
Generated by
Synthea.Version identifier: v2.4.0-404-ge7ce2295\n . Person seed: 186383988687977231 Population seed: 0
Care Plan for Lifestyle education regarding hypertension.
Activities:
- Lifestyle education regarding hypertension
- Lifestyle education regarding hypertension
- Lifestyle education regarding hypertension
- Lifestyle education regarding hypertension
Care plan is meant to treat Hypertension.