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fasten-onprem
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updating database interface. 

Using public database fields.
This commit is contained in:
Jason Kulatunga 2022-12-03 12:48:35 -08:00
parent 492d2a7efb
commit 0d57a75890
4 changed files with 60 additions and 43 deletions
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3
backend/pkg/database/interface.go
View File

@ -9,10 +9,11 @@ import (
//go:generate mockgen -source=interface.go -destination=mock/mock_database.go
type DatabaseRepository interface {
Close() error
Migrate() error
CreateUser(context.Context, *models.User) error
GetUserByEmail(context.Context, string) (*models.User, error)
GetUserByUsername(context.Context, string) (*models.User, error)
GetCurrentUser(context.Context) *models.User
GetSummary(ctx context.Context) (*models.Summary, error)

89
backend/pkg/database/sqlite_repository.go
View File

@ -40,7 +40,7 @@ func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger)
})
database, err := gorm.Open(sqlite.Open(appConfig.GetString("database.location")+pragmaStr), &gorm.Config{
//TODO: figure out how to log database queries again.
//Logger: logger
//Logger: Logger
DisableForeignKeyConstraintWhenMigrating: true,
})
@ -53,14 +53,16 @@ func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger)
}
globalLogger.Infof("Successfully connected to fasten sqlite db: %s\n", appConfig.GetString("database.location"))
deviceRepo := SqliteRepository{
AppConfig: appConfig,
Logger: globalLogger,
GormClient: database,
}
//TODO: automigrate for now
err = database.AutoMigrate(
&models.User{},
&models.SourceCredential{},
&models.ResourceFhir{},
)
err = deviceRepo.Migrate()
if err != nil {
return nil, fmt.Errorf("Failed to automigrate! - %v", err)
return nil, err
}
// create/update admin user
@ -70,19 +72,26 @@ func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger)
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
AppConfig config.Interface
Logger logrus.FieldLogger
gormClient *gorm.DB
GormClient *gorm.DB
}
func (sr *SqliteRepository) Migrate() error {
err := sr.GormClient.AutoMigrate(
&models.User{},
&models.SourceCredential{},
&models.ResourceFhir{},
)
if err != nil {
return fmt.Errorf("Failed to automigrate! - %v", err)
}
return nil
}
func (sr *SqliteRepository) Close() error {
@ -97,22 +106,22 @@ 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
}
return nil
}
func (sr *SqliteRepository) GetUserByEmail(ctx context.Context, username string) (*models.User, error) {
func (sr *SqliteRepository) GetUserByUsername(ctx context.Context, username string) (*models.User, error) {
var foundUser models.User
result := sr.gormClient.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 {
ginCtx := ctx.(*gin.Context)
var currentUser models.User
sr.gormClient.First(&currentUser, models.User{Username: ginCtx.MustGet("AUTH_USERNAME").(string)})
sr.GormClient.First(&currentUser, models.User{Username: ginCtx.MustGet("AUTH_USERNAME").(string)})
return &currentUser
}
@ -128,7 +137,7 @@ func (sr *SqliteRepository) GetSummary(ctx context.Context) (*models.Summary, er
//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).
result := sr.GormClient.WithContext(ctx).
Model(models.ResourceFhir{}).
Select("source_id, source_resource_type as resource_type, count(*) as count").
Group("source_resource_type").
@ -183,9 +192,9 @@ func (sr *SqliteRepository) UpsertRawResource(ctx context.Context, sourceCredent
ResourceRaw: datatypes.JSON(rawResource.ResourceRaw),
}
sr.logger.Infof("insert/update (%v) %v", rawResource.SourceResourceType, rawResource.SourceResourceID)
sr.Logger.Infof("insert/update (%v) %v", rawResource.SourceResourceType, rawResource.SourceResourceID)
createResult := sr.gormClient.WithContext(ctx).Where(models.OriginBase{
createResult := sr.GormClient.WithContext(ctx).Where(models.OriginBase{
SourceID: wrappedResourceModel.GetSourceID(),
SourceResourceID: wrappedResourceModel.GetSourceResourceID(),
SourceResourceType: wrappedResourceModel.GetSourceResourceType(), //TODO: and UpdatedAt > old UpdatedAt
@ -210,29 +219,29 @@ func (sr *SqliteRepository) UpsertRawResource(ctx context.Context, sourceCredent
//return results.RowsAffected > 0, results.Error
//if sr.gormClient.Debug().WithContext(ctx).
//if sr.GormClient.Debug().WithContext(ctx).
// Where(models.OriginBase{
// SourceID: wrappedResourceModel.GetSourceID(),
// SourceResourceID: wrappedResourceModel.GetSourceResourceID(),
// SourceResourceType: wrappedResourceModel.GetSourceResourceType(), //TODO: and UpdatedAt > old UpdatedAt
// }).Updates(wrappedResourceModel).RowsAffected == 0 {
// sr.logger.Infof("resource does not exist, creating: %s %s %s", wrappedResourceModel.GetSourceID(), wrappedResourceModel.GetSourceResourceID(), wrappedResourceModel.GetSourceResourceType())
// return sr.gormClient.Debug().Create(wrappedResourceModel).Error
// sr.Logger.Infof("resource does not exist, creating: %s %s %s", wrappedResourceModel.GetSourceID(), wrappedResourceModel.GetSourceResourceID(), wrappedResourceModel.GetSourceResourceType())
// return sr.GormClient.Debug().Create(wrappedResourceModel).Error
//}
//return nil
}
func (sr *SqliteRepository) UpsertResource(ctx context.Context, resourceModel *models.ResourceFhir) error {
sr.logger.Infof("insert/update (%T) %v", resourceModel, resourceModel)
sr.Logger.Infof("insert/update (%T) %v", resourceModel, resourceModel)
if sr.gormClient.WithContext(ctx).
if sr.GormClient.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.Create(resourceModel).Error
sr.Logger.Infof("resource does not exist, creating: %s %s %s", resourceModel.GetSourceID(), resourceModel.GetSourceResourceID(), resourceModel.GetSourceResourceType())
return sr.GormClient.Create(resourceModel).Error
}
return nil
}
@ -259,10 +268,10 @@ func (sr *SqliteRepository) ListResources(ctx context.Context, queryOptions mode
}
manifestJson, _ := json.MarshalIndent(queryParam, "", " ")
sr.logger.Infof("THE QUERY OBJECT===========> %v", string(manifestJson))
sr.Logger.Infof("THE QUERY OBJECT===========> %v", string(manifestJson))
var wrappedResourceModels []models.ResourceFhir
results := sr.gormClient.WithContext(ctx).
results := sr.GormClient.WithContext(ctx).
Where(queryParam).
Find(&wrappedResourceModels)
@ -279,7 +288,7 @@ func (sr *SqliteRepository) GetResourceBySourceType(ctx context.Context, sourceR
}
var wrappedResourceModel models.ResourceFhir
results := sr.gormClient.WithContext(ctx).
results := sr.GormClient.WithContext(ctx).
Where(queryParam).
First(&wrappedResourceModel)
@ -301,7 +310,7 @@ func (sr *SqliteRepository) GetResourceBySourceId(ctx context.Context, sourceId
}
var wrappedResourceModel models.ResourceFhir
results := sr.gormClient.WithContext(ctx).
results := sr.GormClient.WithContext(ctx).
Where(queryParam).
First(&wrappedResourceModel)
@ -314,12 +323,12 @@ func (sr *SqliteRepository) GetPatientForSources(ctx context.Context) ([]models.
//SELECT * FROM resource_fhirs WHERE user_id = "" and source_resource_type = "Patient" GROUP BY source_id
//var sourceCred models.SourceCredential
//results := sr.gormClient.WithContext(ctx).
//results := sr.GormClient.WithContext(ctx).
// Where(models.SourceCredential{UserID: sr.GetCurrentUser(ctx).ID, ModelBase: models.ModelBase{ID: sourceUUID}}).
// First(&sourceCred)
var wrappedResourceModels []models.ResourceFhir
results := sr.gormClient.WithContext(ctx).
results := sr.GormClient.WithContext(ctx).
Model(models.ResourceFhir{}).
Group("source_id").
Where(models.OriginBase{
@ -339,7 +348,7 @@ func (sr *SqliteRepository) CreateSource(ctx context.Context, sourceCreds *model
sourceCreds.UserID = sr.GetCurrentUser(ctx).ID
//Assign will **always** update the source credential in the DB with data passed into this function.
return sr.gormClient.WithContext(ctx).
return sr.GormClient.WithContext(ctx).
Where(models.SourceCredential{
UserID: sourceCreds.UserID,
SourceType: sourceCreds.SourceType,
@ -354,7 +363,7 @@ func (sr *SqliteRepository) GetSource(ctx context.Context, sourceId string) (*mo
}
var sourceCred models.SourceCredential
results := sr.gormClient.WithContext(ctx).
results := sr.GormClient.WithContext(ctx).
Where(models.SourceCredential{UserID: sr.GetCurrentUser(ctx).ID, ModelBase: models.ModelBase{ID: sourceUUID}}).
First(&sourceCred)
@ -380,7 +389,7 @@ func (sr *SqliteRepository) GetSourceSummary(ctx context.Context, sourceId strin
var resourceTypeCounts []map[string]interface{}
result := sr.gormClient.WithContext(ctx).
result := sr.GormClient.WithContext(ctx).
Model(models.ResourceFhir{}).
Select("source_id, source_resource_type as resource_type, count(*) as count").
Group("source_resource_type").
@ -398,7 +407,7 @@ func (sr *SqliteRepository) GetSourceSummary(ctx context.Context, sourceId strin
//set patient
var wrappedPatientResourceModel models.ResourceFhir
results := sr.gormClient.WithContext(ctx).
results := sr.GormClient.WithContext(ctx).
Where(models.OriginBase{
UserID: sr.GetCurrentUser(ctx).ID,
SourceResourceType: "Patient",
@ -417,7 +426,7 @@ func (sr *SqliteRepository) GetSourceSummary(ctx context.Context, sourceId strin
func (sr *SqliteRepository) GetSources(ctx context.Context) ([]models.SourceCredential, error) {
var sourceCreds []models.SourceCredential
results := sr.gormClient.WithContext(ctx).
results := sr.GormClient.WithContext(ctx).
Where(models.SourceCredential{UserID: sr.GetCurrentUser(ctx).ID}).
Find(&sourceCreds)

9
backend/pkg/models/user.go
View File

@ -1,12 +1,19 @@
package models
import "golang.org/x/crypto/bcrypt"
import (
"golang.org/x/crypto/bcrypt"
)
type User struct {
ModelBase
FullName string `json:"full_name"`
Username string `json:"username" gorm:"unique"`
Password string `json:"password"`
//additional optional metadata that Fasten stores with users
Picture string `json:"picture"`
Email string `json:"email"`
//Roles datatypes.JSON `json:"roles"`
}
func (user *User) HashPassword(password string) error {

2
backend/pkg/web/handler/auth.go
View File

@ -41,7 +41,7 @@ func AuthSignin(c *gin.Context) {
return
}
foundUser, err := databaseRepo.GetUserByEmail(c, user.Username)
foundUser, err := databaseRepo.GetUserByUsername(c, user.Username)
if err != nil || foundUser == nil {
c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": fmt.Sprintf("could not find user: %s", user.Username)})
return