build(deps): maintain Go dependencies and migrate mapstructure v2

backend/core/runner/db.go

@@ -145,13 +145,13 @@ func MakeDbConnection(dbUrl string, conf *gorm.Config) (*gorm.DB, error) {
 			if err != nil {
 				return nil, err
 			}
-			gormDB, err := gorm.Open(mysql.New(mysql.Config{
+			gormDB, err := gorm.Open(wrapMysqlDialector(mysql.New(mysql.Config{
 				Conn: db,
-			}), &gorm.Config{})
+			})), &gorm.Config{})
 
 			return gormDB, err
 		}
-		return gorm.Open(mysql.Open(dbUrl), conf)
+		return gorm.Open(wrapMysqlDialector(mysql.Open(dbUrl)), conf)
 	case "postgresql", "postgres", "pg":
 		return gorm.Open(postgres.Open(dbUrl), conf)
 	default:

backend/core/runner/mysql_dialector.go

@@ -0,0 +1,111 @@
+/*
+Licensed to the Apache Software Foundation (ASF) under one or more
+contributor license agreements.  See the NOTICE file distributed with
+this work for additional information regarding copyright ownership.
+The ASF licenses this file to You under the Apache License, Version 2.0
+(the "License"); you may not use this file except in compliance with
+the License.  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package runner
+
+import (
+	"fmt"
+	"strings"
+
+	"gorm.io/driver/mysql"
+	"gorm.io/gorm"
+	"gorm.io/gorm/clause"
+	gormmigrator "gorm.io/gorm/migrator"
+	"gorm.io/gorm/schema"
+)
+
+// primaryKeyIndexName is the fixed name MySQL gives to the primary key index
+const primaryKeyIndexName = "PRIMARY"
+
+// wrapMysqlDialector decorates the GORM MySQL dialector so that AutoMigrate keeps
+// working for DevLake's migration scripts.
+//
+// Since gorm.io/driver/mysql v1.6.0, `AddColumn` appends `ADD PRIMARY KEY (<col>)`
+// whenever the added field carries the `primaryKey` tag. DevLake migration scripts
+// regularly add such a column to a table that already owns a primary key, which
+// makes MySQL fail with `Error 1068: Multiple primary key defined`. Primary key
+// changes are always performed explicitly by the migration scripts (see
+// migrationhelper.ChangePrimaryKeyColumnsType), so the column is added without the
+// implicit clause, matching the behaviour of the previous driver release. The only
+// exception is an `AUTO_INCREMENT` column, which MySQL requires to be a key.
+func wrapMysqlDialector(dialector gorm.Dialector) gorm.Dialector {
+	if mysqlDialector, ok := dialector.(*mysql.Dialector); ok {
+		return safeMysqlDialector{Dialector: *mysqlDialector}
+	}
+	return dialector
+}
+
+type safeMysqlDialector struct {
+	mysql.Dialector
+}
+
+// Migrator returns the MySQL migrator with the AddColumn workaround applied
+func (d safeMysqlDialector) Migrator(db *gorm.DB) gorm.Migrator {
+	return safeMysqlMigrator{Migrator: d.Dialector.Migrator(db), db: db}
+}
+
+type safeMysqlMigrator struct {
+	gorm.Migrator
+	db *gorm.DB
+}
+
+// mysqlMigratorInternals exposes the helpers of the embedded GORM migrator that
+// are needed to rebuild the `ALTER TABLE ... ADD ...` statement
+type mysqlMigratorInternals interface {
+	RunWithValue(value interface{}, fc func(*gorm.Statement) error) error
+	FullDataTypeOf(field *schema.Field) clause.Expr
+	CurrentTable(stmt *gorm.Statement) interface{}
+}
+
+// AddColumn adds a column without implicitly promoting it to the primary key of
+// the table, see wrapMysqlDialector for the rationale
+func (m safeMysqlMigrator) AddColumn(value interface{}, name string) error {
+	base, ok := m.Migrator.(mysqlMigratorInternals)
+	if !ok {
+		return m.Migrator.AddColumn(value, name)
+	}
+	return base.RunWithValue(value, func(stmt *gorm.Statement) error {
+		field := stmt.Schema.LookUpField(name)
+		if field == nil {
+			return fmt.Errorf("failed to look up field with name: %s", name)
+		}
+		if field.IgnoreMigration {
+			return nil
+		}
+		fieldType := base.FullDataTypeOf(field)
+		columnName := clause.Column{Name: field.DBName}
+		values := []interface{}{base.CurrentTable(stmt), columnName, fieldType}
+		alterSql := "ALTER TABLE ? ADD ? ?"
+		// MySQL requires an AUTO_INCREMENT column to be a key, every other primary
+		// key is managed explicitly by the migration scripts
+		if strings.Contains(strings.ToLower(fieldType.SQL), "auto_increment") &&
+			!m.Migrator.HasIndex(value, primaryKeyIndexName) {
+			alterSql += ", ADD PRIMARY KEY (?)"
+			values = append(values, columnName)
+		}
+		return m.db.Exec(alterSql, values...).Error
+	})
+}
+
+// BuildIndexOptions forwards to the embedded migrator, GORM requires every
+// migrator to implement migrator.BuildIndexOptionsInterface while creating tables
+func (m safeMysqlMigrator) BuildIndexOptions(opts []schema.IndexOption, stmt *gorm.Statement) []interface{} {
+	if builder, ok := m.Migrator.(gormmigrator.BuildIndexOptionsInterface); ok {
+		return builder.BuildIndexOptions(opts, stmt)
+	}
+	return nil
+}

backend/go.mod

@@ -10,12 +10,12 @@ require (
 	github.com/go-errors/errors v1.4.2 // indirect
 	github.com/go-git/go-git/v5 v5.19.2
 	github.com/go-playground/validator/v10 v10.19.0
+	github.com/go-viper/mapstructure/v2 v2.5.0
 	github.com/gocarina/gocsv v0.0.0-20220707092902-b9da1f06c77e
 	github.com/google/uuid v1.3.0
 	github.com/jackc/pgx/v5 v5.10.0
 	github.com/libgit2/git2go/v34 v34.0.0
 	github.com/magiconair/properties v1.8.5
-	github.com/mitchellh/mapstructure v1.5.0
 	github.com/panjf2000/ants/v2 v2.4.6
 	github.com/robfig/cron/v3 v3.0.0
 	github.com/sirupsen/logrus v1.10.0
@@ -34,23 +34,24 @@ require (
 	golang.org/x/oauth2 v0.36.0
 	golang.org/x/sync v0.22.0
 	gorm.io/datatypes v1.0.1
-	gorm.io/driver/mysql v1.5.1
-	gorm.io/driver/postgres v1.5.2
-	gorm.io/gorm v1.25.5
+	gorm.io/driver/mysql v1.6.0
+	gorm.io/driver/postgres v1.6.2
+	gorm.io/gorm v1.31.2
 )
 
 require (
 	github.com/chainguard-dev/git-urls v1.0.2
-	github.com/coreos/go-oidc/v3 v3.9.0
-	github.com/go-sql-driver/mysql v1.7.1
+	github.com/coreos/go-oidc/v3 v3.20.0
+	github.com/go-sql-driver/mysql v1.8.1
 	github.com/golang-jwt/jwt/v5 v5.3.1
 	github.com/merico-ai/graphql v0.0.0-20260206020408-b7fd267bcfac
 	github.com/rogpeppe/go-internal v1.14.1
-	golang.org/x/mod v0.38.0
+	golang.org/x/mod v0.40.0
 )
 
 require (
 	dario.cat/mergo v1.0.0 // indirect
+	filippo.io/edwards25519 v1.1.0 // indirect
 	github.com/KyleBanks/depth v1.2.1 // indirect
 	github.com/Microsoft/go-winio v0.6.2 // indirect
 	github.com/ProtonMail/go-crypto v1.1.6 // indirect
@@ -70,7 +71,7 @@ require (
 	github.com/gin-contrib/sse v0.1.0 // indirect
 	github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376 // indirect
 	github.com/go-git/go-billy/v5 v5.9.0 // indirect
-	github.com/go-jose/go-jose/v3 v3.0.1 // indirect
+	github.com/go-jose/go-jose/v4 v4.1.4 // indirect
 	github.com/go-openapi/jsonpointer v0.19.5 // indirect
 	github.com/go-openapi/jsonreference v0.19.6 // indirect
 	github.com/go-openapi/spec v0.20.4 // indirect
@@ -98,6 +99,7 @@ require (
 	github.com/leodido/go-urn v1.4.0 // indirect
 	github.com/mailru/easyjson v0.7.7 // indirect
 	github.com/mattn/go-isatty v0.0.19 // indirect
+	github.com/mitchellh/mapstructure v1.4.1 // indirect
 	github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
 	github.com/modern-go/reflect2 v1.0.2 // indirect
 	github.com/pelletier/go-toml v1.9.3 // indirect
@@ -120,7 +122,7 @@ require (
 	golang.org/x/net v0.58.0 // indirect
 	golang.org/x/sys v0.47.0 // indirect
 	golang.org/x/text v0.41.0 // indirect
-	golang.org/x/tools v0.48.0 // indirect
+	golang.org/x/tools v0.49.0 // indirect
 	google.golang.org/protobuf v1.36.12 // indirect
 	gopkg.in/ini.v1 v1.67.0 // indirect
 	gopkg.in/warnings.v0 v0.1.2 // indirect

backend/go.sum

@@ -39,6 +39,8 @@ cloud.google.com/go/storage v1.10.0/go.mod h1:FLPqc6j+Ki4BU591ie1oL6qBQGu2Bl/tZ9
 dario.cat/mergo v1.0.0 h1:AGCNq9Evsj31mOgNPcLyXc+4PNABt905YmuqPYYpBWk=
 dario.cat/mergo v1.0.0/go.mod h1:uNxQE+84aUszobStD9th8a29P2fMDhsBdgRYvZOxGmk=
 dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
+filippo.io/edwards25519 v1.1.0 h1:FNf4tywRC1HmFuKW5xopWpigGjJKiJSV0Cqo0cJWDaA=
+filippo.io/edwards25519 v1.1.0/go.mod h1:BxyFTGdWcka3PhytdK4V28tE5sGfRvvvRV7EaN4VDT4=
 github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU=
 github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
 github.com/KyleBanks/depth v1.2.1 h1:5h8fQADFrWtarTdtDudMmGsC7GPbOAu6RVB3ffsVFHc=
@@ -89,8 +91,8 @@ github.com/cockroachdb/logtags v0.0.0-20230118201751-21c54148d20b h1:r6VH0faHjZe
 github.com/cockroachdb/logtags v0.0.0-20230118201751-21c54148d20b/go.mod h1:Vz9DsVWQQhf3vs21MhPMZpMGSht7O/2vFW2xusFUVOs=
 github.com/cockroachdb/redact v1.1.5 h1:u1PMllDkdFfPWaNGMyLD1+so+aq3uUItthCFqzwPJ30=
 github.com/cockroachdb/redact v1.1.5/go.mod h1:BVNblN9mBWFyMyqK1k3AAiSxhvhfK2oOZZ2lK+dpvRg=
-github.com/coreos/go-oidc/v3 v3.9.0 h1:0J/ogVOd4y8P0f0xUh8l9t07xRP/d8tccvjHl2dcsSo=
-github.com/coreos/go-oidc/v3 v3.9.0/go.mod h1:rTKz2PYwftcrtoCzV5g5kvfJoWcm0Mk8AF8y1iAQro4=
+github.com/coreos/go-oidc/v3 v3.20.0 h1:EtE0WIBHk03N+DqGkY4+UONzzZHk7amKt6IyNd7OsZE=
+github.com/coreos/go-oidc/v3 v3.20.0/go.mod h1:DYCf24+ncYi+XkIH97GY1+dqoRlbaSI26KVTCI9SrY4=
 github.com/coreos/go-semver v0.3.0/go.mod h1:nnelYz7RCh+5ahJtPPxZlU+153eP4D4r3EedlOD2RNk=
 github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e/go.mod h1:F5haX7vjVVG0kc13fIWeqUViNPyEJxv/OmvnBo0Yme4=
 github.com/coreos/go-systemd v0.0.0-20190719114852-fd7a80b32e1f/go.mod h1:F5haX7vjVVG0kc13fIWeqUViNPyEJxv/OmvnBo0Yme4=
@@ -147,8 +149,8 @@ github.com/go-git/go-git/v5 v5.19.2/go.mod h1:QqCBE1EFN5ddFmrliLQ3/ntRCUjZU3EJuw
 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-jose/go-jose/v3 v3.0.1 h1:pWmKFVtt+Jl0vBZTIpz/eAKwsm6LkIxDVVbFHKkchhA=
-github.com/go-jose/go-jose/v3 v3.0.1/go.mod h1:RNkWWRld676jZEYoV3+XK8L2ZnNSvIsxFMht0mSX+u8=
+github.com/go-jose/go-jose/v4 v4.1.4 h1:moDMcTHmvE6Groj34emNPLs/qtYXRVcd6S7NHbHz3kA=
+github.com/go-jose/go-jose/v4 v4.1.4/go.mod h1:x4oUasVrzR7071A4TnHLGSPpNOm2a21K9Kf04k1rs08=
 github.com/go-openapi/jsonpointer v0.19.3/go.mod h1:Pl9vOtqEWErmShwVjC8pYs9cog34VGT37dQOVbmoatg=
 github.com/go-openapi/jsonpointer v0.19.5 h1:gZr+CIYByUqjcgeLXnQu2gHYQC9o73G2XUeOFYEICuY=
 github.com/go-openapi/jsonpointer v0.19.5/go.mod h1:Pl9vOtqEWErmShwVjC8pYs9cog34VGT37dQOVbmoatg=
@@ -168,10 +170,11 @@ github.com/go-playground/universal-translator v0.18.1/go.mod h1:xekY+UJKNuX9WP91
 github.com/go-playground/validator/v10 v10.19.0 h1:ol+5Fu+cSq9JD7SoSqe04GMI92cbn0+wvQ3bZ8b/AU4=
 github.com/go-playground/validator/v10 v10.19.0/go.mod h1:dbuPbCMFw/DrkbEynArYaCwl3amGuJotoKCe95atGMM=
 github.com/go-sql-driver/mysql v1.5.0/go.mod h1:DCzpHaOWr8IXmIStZouvnhqoel9Qv2LBy8hT2VhHyBg=
-github.com/go-sql-driver/mysql v1.7.0/go.mod h1:OXbVy3sEdcQ2Doequ6Z5BW6fXNQTmx+9S1MCJN5yJMI=
-github.com/go-sql-driver/mysql v1.7.1 h1:lUIinVbN1DY0xBg0eMOzmmtGoHwWBbvnWubQUrtU8EI=
-github.com/go-sql-driver/mysql v1.7.1/go.mod h1:OXbVy3sEdcQ2Doequ6Z5BW6fXNQTmx+9S1MCJN5yJMI=
+github.com/go-sql-driver/mysql v1.8.1 h1:LedoTUt/eveggdHS9qUFC1EFSa8bU2+1pZjSRpvNJ1Y=
+github.com/go-sql-driver/mysql v1.8.1/go.mod h1:wEBSXgmK//2ZFJyE+qWnIsVGmvmEKlqwuVSjsCm7DZg=
 github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY=
+github.com/go-viper/mapstructure/v2 v2.5.0 h1:vM5IJoUAy3d7zRSVtIwQgBj7BiWtMPfmPEgAXnvj1Ro=
+github.com/go-viper/mapstructure/v2 v2.5.0/go.mod h1:oJDH3BJKyqBA2TXFhDsKDGDTlndYOZ6rGS0BRZIxGhM=
 github.com/gocarina/gocsv v0.0.0-20220707092902-b9da1f06c77e h1:GMIV+S6grz+vlIaUsP+fedQ6L+FovyMPMY26WO8dwQE=
 github.com/gocarina/gocsv v0.0.0-20220707092902-b9da1f06c77e/go.mod h1:5YoVOkjYAQumqlV356Hj3xeYh4BdZuLE0/nRkf2NKkI=
 github.com/goccy/go-json v0.10.2 h1:CrxCmQqYDkv1z7lO7Wbh2HN93uovUHgrECaO5ZrCXAU=
@@ -393,8 +396,9 @@ github.com/mattn/go-isatty v0.0.9/go.mod h1:YNRxwqDuOph6SZLI9vUUz6OYw3QyUt7WiY2y
 github.com/mattn/go-isatty v0.0.12/go.mod h1:cbi8OIDigv2wuxKPP5vlRcQ1OAZbq2CE4Kysco4FUpU=
 github.com/mattn/go-isatty v0.0.19 h1:JITubQf0MOLdlGRuRq+jtsDlekdYPia9ZFsB8h/APPA=
 github.com/mattn/go-isatty v0.0.19/go.mod h1:W+V8PltTTMOvKvAeJH7IuucS94S2C6jfK/D7dTCTo3Y=
-github.com/mattn/go-sqlite3 v1.14.5 h1:1IdxlwTNazvbKJQSxoJ5/9ECbEeaTTyeU7sEAZ5KKTQ=
 github.com/mattn/go-sqlite3 v1.14.5/go.mod h1:WVKg1VTActs4Qso6iwGbiFih2UIHo0ENGwNd0Lj+XmI=
+github.com/mattn/go-sqlite3 v1.14.22 h1:2gZY6PC6kBnID23Tichd1K+Z0oS6nE/XwU+Vz/5o4kU=
+github.com/mattn/go-sqlite3 v1.14.22/go.mod h1:Uh1q+B4BYcTPb+yiD3kU8Ct7aC0hY9fxUwlHK0RXw+Y=
 github.com/merico-ai/graphql v0.0.0-20260206020408-b7fd267bcfac h1:J3wm8OohrRkYf/+Zy5GxqvhzcP2qHGJRduxTUUbBMdw=
 github.com/merico-ai/graphql v0.0.0-20260206020408-b7fd267bcfac/go.mod h1:4WSOgvd/Sv6eLKJE6fvrXlmxePBDGhbwRYKEBeqJr8g=
 github.com/miekg/dns v1.0.14/go.mod h1:W1PPwlIAgtquWBMBEV9nkV9Cazfe8ScdGz/Lj7v3Nrg=
@@ -405,9 +409,8 @@ github.com/mitchellh/gox v0.4.0/go.mod h1:Sd9lOJ0+aimLBi73mGofS1ycjY8lL3uZM3JPS4
 github.com/mitchellh/iochan v1.0.0/go.mod h1:JwYml1nuB7xOzsp52dPpHFffvOCDupsG0QubkSMEySY=
 github.com/mitchellh/mapstructure v0.0.0-20160808181253-ca63d7c062ee/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh9fWfEaFds41c1Y=
 github.com/mitchellh/mapstructure v1.1.2/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh9fWfEaFds41c1Y=
+github.com/mitchellh/mapstructure v1.4.1 h1:CpVNEelQCZBooIPDn+AR3NpivK/TIKU8bDxdASFVQag=
 github.com/mitchellh/mapstructure v1.4.1/go.mod h1:bFUtVrKA4DC2yAKiSyO/QUcy7e+RRV2QTWOzhPopBRo=
-github.com/mitchellh/mapstructure v1.5.0 h1:jeMsZIYE/09sWLaz43PL7Gy6RuMjD2eJVyuac5Z2hdY=
-github.com/mitchellh/mapstructure v1.5.0/go.mod h1:bFUtVrKA4DC2yAKiSyO/QUcy7e+RRV2QTWOzhPopBRo=
 github.com/modern-go/concurrent v0.0.0-20180228061459-e0a39a4cb421/go.mod h1:6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=
 github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd h1:TRLaZ9cD/w8PVh93nsPXa1VrQ6jlwL5oN8l14QlcNfg=
 github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd/go.mod h1:6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=
@@ -605,8 +608,8 @@ golang.org/x/mod v0.4.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/mod v0.4.1/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/mod v0.4.2/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4/go.mod h1:jJ57K6gSWd91VN4djpZkiMVwK6gcyfeH4XE8wZrZaV4=
-golang.org/x/mod v0.38.0 h1:MECBjubtXD7yj4HrhIUcywNaGeNVUdfVnxmPajOk4yk=
-golang.org/x/mod v0.38.0/go.mod h1:V6Xz0pq8TQ3dGqVQ1FVHuelZpAL0uNhSkk9ogYP3c40=
+golang.org/x/mod v0.40.0 h1:hUv+3cXcdRHz08UmSiOob7sadHig73uo5bkXxQ/tvUs=
+golang.org/x/mod v0.40.0/go.mod h1:0/weTWkPWGBikyTWAX3dkjVztMmBA5hM0DH6BElSupE=
 golang.org/x/net v0.0.0-20180724234803-3673e40ba225/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
 golang.org/x/net v0.0.0-20180826012351-8a410e7b638d/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
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@@ -816,8 +819,8 @@ golang.org/x/tools v0.0.0-20210106214847-113979e3529a/go.mod h1:emZCQorbCU4vsT4f
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@@ -955,23 +958,23 @@ gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
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