fixed error where the source ID was not populated whne source is first created, causing next SyncAll command to have invalid source_id values.

Created default SyncAll function (using $everything) and SyncAllByResourceName which can be used as a fallback.

cleaned up DB layer , dont use Model unless Gorm cannot figure out the table. Use pointers consistently.
When syncing resources, store errors in a map, so that all resources get synced before returing errors

backend/pkg/database/interface.go

@@ -11,11 +11,11 @@ type DatabaseRepository interface {
 
 	CreateUser(context.Context, *models.User) error
 	GetUserByEmail(context.Context, string) (*models.User, error)
-	GetCurrentUser(context.Context) models.User
+	GetCurrentUser(context.Context) *models.User
 
 	GetSummary(ctx context.Context) (*models.Summary, error)
 
-	UpsertResource(context.Context, models.ResourceFhir) error
+	UpsertResource(context.Context, *models.ResourceFhir) error
 	GetResource(context.Context, string) (*models.ResourceFhir, error)
 	GetResourceBySourceId(context.Context, string, string) (*models.ResourceFhir, error)
 	ListResources(context.Context, models.ListResourceQueryOptions) ([]models.ResourceFhir, error)

backend/pkg/database/sqlite_repository.go

@@ -89,7 +89,7 @@ func (sr *sqliteRepository) CreateUser(ctx context.Context, user *models.User) e
 	if err := user.HashPassword(user.Password); err != nil {
 		return err
 	}
-	record := sr.gormClient.Create(&user)
+	record := sr.gormClient.Create(user)
 	if record.Error != nil {
 		return record.Error
 	}
@@ -97,16 +97,16 @@ func (sr *sqliteRepository) CreateUser(ctx context.Context, user *models.User) e
 }
 func (sr *sqliteRepository) GetUserByEmail(ctx context.Context, username string) (*models.User, error) {
 	var foundUser models.User
-	result := sr.gormClient.Model(models.User{}).Where(models.User{Username: username}).First(&foundUser)
+	result := sr.gormClient.Where(models.User{Username: username}).First(&foundUser)
 	return &foundUser, result.Error
 }
 
-func (sr *sqliteRepository) GetCurrentUser(ctx context.Context) models.User {
+func (sr *sqliteRepository) GetCurrentUser(ctx context.Context) *models.User {
 	ginCtx := ctx.(*gin.Context)
 	var currentUser models.User
-	sr.gormClient.Model(models.User{}).First(&currentUser, models.User{Username: ginCtx.MustGet("AUTH_USERNAME").(string)})
+	sr.gormClient.First(&currentUser, models.User{Username: ginCtx.MustGet("AUTH_USERNAME").(string)})
 
-	return currentUser
+	return &currentUser
 }
 
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -157,17 +157,17 @@ func (sr *sqliteRepository) GetSummary(ctx context.Context) (*models.Summary, er
 // Resource
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
-func (sr *sqliteRepository) UpsertResource(ctx context.Context, resourceModel models.ResourceFhir) error {
+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).Model(&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 {
+		}).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().Model(&resourceModel).Create(&resourceModel).Error
+		return sr.gormClient.Debug().Create(resourceModel).Error
 	}
 	return nil
 }
@@ -274,12 +274,12 @@ func (sr *sqliteRepository) GetPatientForSources(ctx context.Context) ([]models.
 func (sr *sqliteRepository) CreateSource(ctx context.Context, sourceCreds *models.Source) error {
 	sourceCreds.UserID = sr.GetCurrentUser(ctx).ID
 
-	if sr.gormClient.WithContext(ctx).Model(&sourceCreds).
+	if sr.gormClient.WithContext(ctx).
 		Where(models.Source{
 			UserID:     sourceCreds.UserID,
 			SourceType: sourceCreds.SourceType,
-			PatientId:  sourceCreds.PatientId}).Updates(&sourceCreds).RowsAffected == 0 {
+			PatientId:  sourceCreds.PatientId}).Updates(sourceCreds).RowsAffected == 0 {
-		return sr.gormClient.WithContext(ctx).Create(&sourceCreds).Error
+		return sr.gormClient.WithContext(ctx).Create(sourceCreds).Error
 	}
 	return nil
 }

backend/pkg/hub/internal/fhir/aetna/client.go

@@ -39,7 +39,7 @@ func (c AetnaClient) SyncAll(db database.DatabaseRepository) error {
 	//todo, create the resources in dependency order
 
 	for _, apiModel := range wrappedResourceModels {
-		err = db.UpsertResource(context.Background(), apiModel)
+		err = db.UpsertResource(context.Background(), &apiModel)
 		if err != nil {
 			c.Logger.Info("An error occurred while upserting resource")
 			return err

backend/pkg/hub/internal/fhir/athena/client.go

@@ -2,7 +2,6 @@ package athena
 
 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/hub/internal/fhir/base"
@@ -23,7 +22,6 @@ func NewClient(ctx context.Context, appConfig config.Interface, globalLogger log
 }
 
 func (c AthenaClient) SyncAll(db database.DatabaseRepository) error {
-
 	supportedResources := []string{
 		"AllergyIntolerance",
 		//"Binary",
@@ -46,25 +44,6 @@ func (c AthenaClient) SyncAll(db database.DatabaseRepository) error {
 		"Procedure",
 		//"Provenance",
 	}
-	for _, resourceType := range supportedResources {
-		bundle, err := c.GetResourceBundle(fmt.Sprintf("%s?patient=%s", resourceType, c.Source.PatientId))
-		if err != nil {
-			return err
-		}
-		wrappedResourceModels, err := c.ProcessBundle(bundle)
-		if err != nil {
-			c.Logger.Infof("An error occurred while processing %s bundle %s", resourceType, 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
 
+	return c.SyncAllByResourceName(db, supportedResources)
 }

backend/pkg/hub/internal/fhir/base/fhir401_client.go

@@ -43,7 +43,7 @@ func (c *FHIR401Client) SyncAll(db database.DatabaseRepository) error {
 	//todo, create the resources in dependency order
 
 	for _, apiModel := range wrappedResourceModels {
-		err = db.UpsertResource(context.Background(), apiModel)
+		err = db.UpsertResource(context.Background(), &apiModel)
 		if err != nil {
 			return err
 		}
@@ -51,6 +51,62 @@ func (c *FHIR401Client) SyncAll(db database.DatabaseRepository) error {
 	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
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

backend/pkg/hub/internal/fhir/bluebutton/client.go

@@ -3,6 +3,7 @@ package bluebutton
 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"
@@ -19,3 +20,12 @@ func NewClient(ctx context.Context, appConfig config.Interface, globalLogger log
 		baseClient,
 	}, updatedSource, err
 }
+
+func (c BlueButtonClient) SyncAll(db database.DatabaseRepository) error {
+
+	supportedResources := []string{
+		"ExplanationOfBenefit",
+		"Coverage",
+	}
+	return c.SyncAllByResourceName(db, supportedResources)
+}

backend/pkg/hub/internal/fhir/cerner/client.go

@@ -2,7 +2,6 @@ package cerner
 
 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/hub/internal/fhir/base"
@@ -50,25 +49,5 @@ func (c CernerClient) SyncAll(db database.DatabaseRepository) error {
 		"ServiceRequest",
 		"Slot",
 	}
-	for _, resourceType := range supportedResources {
+	return c.SyncAllByResourceName(db, supportedResources)
-		bundle, err := c.GetResourceBundle(fmt.Sprintf("%s?patient=%s", resourceType, c.Source.PatientId))
-		if err != nil {
-			continue //TODO: skippping failures in the resource retrival
-		}
-		wrappedResourceModels, err := c.ProcessBundle(bundle)
-		if err != nil {
-			c.Logger.Infof("An error occurred while processing %s bundle %s", resourceType, 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
 }

backend/pkg/hub/internal/fhir/epic/client.go

@@ -3,6 +3,7 @@ package epic
 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"
@@ -21,3 +22,33 @@ func NewClient(ctx context.Context, appConfig config.Interface, globalLogger log
 		baseClient,
 	}, updatedSource, err
 }
+
+func (c EpicClient) SyncAll(db database.DatabaseRepository) error {
+
+	supportedResources := []string{
+		"AllergyIntolerance",
+		"CarePlan",
+		"CareTeam",
+		"Condition",
+		"Consent",
+		"Device",
+		"Encounter",
+		"FamilyMemberHistory",
+		"Goal",
+		"Immunization",
+		"InsurancePlan",
+		"MedicationRequest",
+		"NutritionOrder",
+		"Observation",
+		"Person",
+		"Procedure",
+		"Provenance",
+		"Questionnaire",
+		"QuestionnaireResponse",
+		"RelatedPerson",
+		"Schedule",
+		"ServiceRequest",
+		"Slot",
+	}
+	return c.SyncAllByResourceName(db, supportedResources)
+}

backend/pkg/hub/internal/fhir/healthit/client.go

@@ -3,6 +3,7 @@ package healthit
 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"
@@ -21,3 +22,33 @@ func NewClient(ctx context.Context, appConfig config.Interface, globalLogger log
 		baseClient,
 	}, updatedSource, err
 }
+
+func (c HealthItClient) SyncAll(db database.DatabaseRepository) error {
+
+	supportedResources := []string{
+		"AllergyIntolerance",
+		"CarePlan",
+		"CareTeam",
+		"Condition",
+		"Consent",
+		"Device",
+		"Encounter",
+		"FamilyMemberHistory",
+		"Goal",
+		"Immunization",
+		"InsurancePlan",
+		"MedicationRequest",
+		"NutritionOrder",
+		"Observation",
+		"Person",
+		"Procedure",
+		"Provenance",
+		"Questionnaire",
+		"QuestionnaireResponse",
+		"RelatedPerson",
+		"Schedule",
+		"ServiceRequest",
+		"Slot",
+	}
+	return c.SyncAllByResourceName(db, supportedResources)
+}

backend/pkg/hub/internal/fhir/manual/client.go

@@ -85,7 +85,7 @@ func (m ManualClient) SyncAllBundle(db database.DatabaseRepository, bundleFile *
 	}
 	// we need to upsert all resources (and make sure they are associated with new Source)
 	for _, apiModel := range resourceFhirList {
-		err = db.UpsertResource(context.Background(), apiModel)
+		err = db.UpsertResource(context.Background(), &apiModel)
 		if err != nil {
 			return fmt.Errorf("an error occurred while upserting resources: %w", err)
 		}

backend/pkg/web/handler/metadata.go

@@ -10,21 +10,21 @@ import (
 func GetMetadataSource(c *gin.Context) {
 	metadataSource := map[string]models.MetadataSource{
 
-		string(pkg.SourceTypeLogica):   {Display: "Logica (Sandbox)", SourceType: pkg.SourceTypeLogica, Category: []string{"Sandbox"}, Supported: true},
 		string(pkg.SourceTypeAthena):   {Display: "Athena (Sandbox)", SourceType: pkg.SourceTypeAthena, Category: []string{"Sandbox"}, Supported: true},
+		string(pkg.SourceTypeEpic):     {Display: "Epic (Sandbox)", SourceType: pkg.SourceTypeEpic, Category: []string{"Sandbox"}, Supported: true},
+		string(pkg.SourceTypeLogica):   {Display: "Logica (Sandbox)", SourceType: pkg.SourceTypeLogica, Category: []string{"Sandbox"}, Supported: true},
 		string(pkg.SourceTypeHealthIT): {Display: "HealthIT (Sandbox)", SourceType: pkg.SourceTypeHealthIT, Category: []string{"Sandbox"}, Supported: true},
 
 		// enabled
 		string(pkg.SourceTypeAetna):              {Display: "Aetna", SourceType: pkg.SourceTypeAetna, Category: []string{"Insurance"}, Supported: true},
 		string(pkg.SourceTypeCigna):              {Display: "Cigna", SourceType: pkg.SourceTypeCigna, Category: []string{"Insurance", "Hospital"}, Supported: true},
+		string(pkg.SourceTypeBlueButtonMedicare): {Display: "Medicare/VA Health (BlueButton)", SourceType: pkg.SourceTypeBlueButtonMedicare, Category: []string{"Hospital"}, Supported: true},
 
 		//TODO: infinite pagination for Encounters??
 		string(pkg.SourceTypeCerner): {Display: "Cerner (Sandbox)", SourceType: pkg.SourceTypeCerner, Category: []string{"Sandbox"}, Supported: true},
 
-		//TODO: does not support $everything endpoint.
+		//TODO: fails with CORS error when swapping token. Should be confidential client.
-		string(pkg.SourceTypeBlueButtonMedicare): {Display: "Medicare/VA Health (BlueButton)", SourceType: pkg.SourceTypeBlueButtonMedicare, Category: []string{"Hospital"}, Supported: true},
+		string(pkg.SourceTypeCareEvolution): {Display: "CareEvolution (Sandbox)", SourceType: pkg.SourceTypeCareEvolution, Category: []string{"Sandbox"}, Supported: false},
-		string(pkg.SourceTypeEpic):               {Display: "Epic (Sandbox)", SourceType: pkg.SourceTypeEpic, Category: []string{"Sandbox"}, Supported: true},
-		string(pkg.SourceTypeCareEvolution):      {Display: "CareEvolution (Sandbox)", SourceType: pkg.SourceTypeCareEvolution, Category: []string{"Sandbox"}, Supported: true},
 
 		// pending
 		string(pkg.SourceTypeAnthem):           {Display: "Anthem", SourceType: pkg.SourceTypeAnthem, Category: []string{"Insurance"}},