added database migration framework.

backend/pkg/database/gorm_common.go

@@ -32,20 +32,6 @@ type GormRepository struct {
 	EventBus event_bus.Interface
 }
 
-func (gr *GormRepository) Migrate() error {
-	err := gr.GormClient.AutoMigrate(
-		&models.User{},
-		&models.SourceCredential{},
-		&models.BackgroundJob{},
-		&models.Glossary{},
-		&models.UserSettingEntry{},
-	)
-	if err != nil {
-		return fmt.Errorf("Failed to automigrate! - %v", err)
-	}
-	return nil
-}
-
 func (gr *GormRepository) Close() error {
 	return nil
 }

backend/pkg/database/gorm_repository_migrations.go

@@ -0,0 +1,48 @@
+package database
+
+import (
+	"github.com/fastenhealth/fasten-onprem/backend/pkg/models"
+	databaseModel "github.com/fastenhealth/fasten-onprem/backend/pkg/models/database"
+	"github.com/go-gormigrate/gormigrate/v2"
+	"gorm.io/gorm"
+)
+
+func (gr *GormRepository) Migrate() error {
+
+	gr.Logger.Infoln("Database migration starting. Please wait, this process may take a long time....")
+
+	gormMigrateOptions := gormigrate.DefaultOptions
+	gormMigrateOptions.UseTransaction = true
+
+	//use echo $(date '+%Y%m%d%H%M%S') to generate new ID's
+	m := gormigrate.New(gr.GormClient, gormMigrateOptions, []*gormigrate.Migration{
+		{
+			ID: "20231017112246", // base database models //TODO: figure out how to version these correctly (SourceCredential is complicated)
+			Migrate: func(tx *gorm.DB) error {
+
+				return tx.AutoMigrate(
+					&models.BackgroundJob{},
+					&models.Glossary{},
+					&models.SourceCredential{},
+					&models.UserSettingEntry{},
+					&models.User{},
+				)
+			},
+		},
+		{
+			ID: "20231017113858", // FHIR Resource Database models.
+			Migrate: func(tx *gorm.DB) error {
+
+				//automigrate Fhir Resource Tables
+				return databaseModel.Migrate(tx)
+			},
+		},
+	})
+
+	if err := m.Migrate(); err != nil {
+		gr.Logger.Errorf("Database migration failed with error. \n Please open a github issue at https://github.com/fastenhealth/fasten-onprem and attach a copy of your fasten.db file. \n %v", err)
+		return err
+	}
+	gr.Logger.Infoln("Database migration completed successfully")
+	return nil
+}

backend/pkg/database/postgres_repository.go

@@ -7,7 +7,6 @@ import (
 	"github.com/fastenhealth/fasten-onprem/backend/pkg/config"
 	"github.com/fastenhealth/fasten-onprem/backend/pkg/event_bus"
 	"github.com/fastenhealth/fasten-onprem/backend/pkg/models"
-	databaseModel "github.com/fastenhealth/fasten-onprem/backend/pkg/models/database"
 	"github.com/sirupsen/logrus"
 	"gorm.io/driver/postgres"
 	"gorm.io/gorm"
@@ -50,12 +49,6 @@ func newPostgresRepository(appConfig config.Interface, globalLogger logrus.Field
 		return nil, err
 	}
 
-	//automigrate Fhir Resource Tables
-	err = databaseModel.Migrate(fastenRepo.GormClient)
-	if err != nil {
-		return nil, err
-	}
-
 	// create/update admin user
 	//TODO: determine if this admin user is ncessary
 	//SECURITY: validate this user is necessary

backend/pkg/database/sqlite_repository.go

@@ -7,7 +7,6 @@ import (
 	"github.com/fastenhealth/fasten-onprem/backend/pkg/config"
 	"github.com/fastenhealth/fasten-onprem/backend/pkg/event_bus"
 	"github.com/fastenhealth/fasten-onprem/backend/pkg/models"
-	databaseModel "github.com/fastenhealth/fasten-onprem/backend/pkg/models/database"
 	"github.com/glebarez/sqlite"
 	"github.com/sirupsen/logrus"
 	"gorm.io/gorm"
@@ -75,18 +74,11 @@ func newSqliteRepository(appConfig config.Interface, globalLogger logrus.FieldLo
 		EventBus:   eventBus,
 	}
 
-	//TODO: automigrate for now, this should be replaced with a migration tool once the DB has stabilized.
 	err = fastenRepo.Migrate()
 	if err != nil {
 		return nil, err
 	}
 
-	//automigrate Fhir Resource Tables
-	err = databaseModel.Migrate(fastenRepo.GormClient)
-	if err != nil {
-		return nil, err
-	}
-
 	// create/update admin user
 	//TODO: determine if this admin user is ncessary
 	//SECURITY: validate this user is necessary

go.mod

@@ -11,6 +11,7 @@ require (
 	github.com/fastenhealth/gofhir-models v0.0.6
 	github.com/gin-gonic/gin v1.9.0
 	github.com/glebarez/sqlite v1.5.0
+	github.com/go-gormigrate/gormigrate/v2 v2.1.1
 	github.com/golang-jwt/jwt/v4 v4.4.2
 	github.com/golang/mock v1.6.0
 	github.com/google/go-github/v54 v54.0.0
@@ -27,7 +28,7 @@ require (
 	golang.org/x/exp v0.0.0-20220303212507-bbda1eaf7a17
 	golang.org/x/net v0.14.0
 	gorm.io/datatypes v1.0.7
-	gorm.io/gorm v1.25.2-0.20230530020048-26663ab9bf55
+	gorm.io/gorm v1.25.4
 )
 
 require (

go.sum

@@ -224,6 +224,8 @@ github.com/globalsign/mgo v0.0.0-20181015135952-eeefdecb41b8/go.mod h1:xkRDCp4j0
 github.com/go-gl/glfw v0.0.0-20190409004039-e6da0acd62b1/go.mod h1:vR7hzQXu2zJy9AVAgeJqvqgH9Q5CA+iKCZ2gyEVpxRU=
 github.com/go-gl/glfw/v3.3/glfw v0.0.0-20191125211704-12ad95a8df72/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8=
 github.com/go-gl/glfw/v3.3/glfw v0.0.0-20200222043503-6f7a984d4dc4/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8=
+github.com/go-gormigrate/gormigrate/v2 v2.1.1 h1:eGS0WTFRV30r103lU8JNXY27KbviRnqqIDobW3EV3iY=
+github.com/go-gormigrate/gormigrate/v2 v2.1.1/go.mod h1:L7nJ620PFDKei9QOhJzqA8kRCk+E3UbV2f5gv+1ndLc=
 github.com/go-kit/kit v0.8.0/go.mod h1:xBxKIO96dXMWWy0MnWVtmwkA9/13aqxPnvrjFYMA2as=
 github.com/go-kit/kit v0.9.0/go.mod h1:xBxKIO96dXMWWy0MnWVtmwkA9/13aqxPnvrjFYMA2as=
 github.com/go-kit/log v0.1.0/go.mod h1:zbhenjAZHb184qTLMA9ZjW7ThYL0H2mk7Q6pNt4vbaY=
@@ -1289,8 +1291,8 @@ gorm.io/driver/sqlserver v1.3.1/go.mod h1:w25Vrx2BG+CJNUu/xKbFhaKlGxT/nzRkhWCCop
 gorm.io/gorm v1.23.1/go.mod h1:l2lP/RyAtc1ynaTjFksBde/O8v9oOGIApu2/xRitmZk=
 gorm.io/gorm v1.23.6/go.mod h1:l2lP/RyAtc1ynaTjFksBde/O8v9oOGIApu2/xRitmZk=
 gorm.io/gorm v1.24.0/go.mod h1:DVrVomtaYTbqs7gB/x2uVvqnXzv0nqjB396B8cG4dBA=
-gorm.io/gorm v1.25.2-0.20230530020048-26663ab9bf55 h1:sC1Xj4TYrLqg1n3AN10w871An7wJM0gzgcm8jkIkECQ=
+gorm.io/gorm v1.25.4 h1:iyNd8fNAe8W9dvtlgeRI5zSVZPsq3OpcTu37cYcpCmw=
-gorm.io/gorm v1.25.2-0.20230530020048-26663ab9bf55/go.mod h1:L4uxeKpfBml98NYqVqwAdmV1a2nBtAec/cf3fpucW/k=
+gorm.io/gorm v1.25.4/go.mod h1:L4uxeKpfBml98NYqVqwAdmV1a2nBtAec/cf3fpucW/k=
 gotest.tools v2.2.0+incompatible/go.mod h1:DsYFclhRJ6vuDpmuTbkuFWG+y2sxOXAzmJt81HFBacw=
 honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
 honnef.co/go/tools v0.0.0-20190106161140-3f1c8253044a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=