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Introduce db migration support

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This commit is contained in:
Jan Eitzinger 2023-02-21 10:57:22 +01:00
parent 643bd3fb21
commit 8ffb562d6b
14 changed files with 1435 additions and 97 deletions
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8
cmd/cc-backend/main.go
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@ -61,7 +61,7 @@ var (
)
func main() {
var flagReinitDB, flagServer, flagSyncLDAP, flagGops, flagDev, flagVersion, flagLogDateTime bool
var flagReinitDB, flagServer, flagSyncLDAP, flagGops, flagMigrateDB, flagDev, flagVersion, flagLogDateTime bool
var flagNewUser, flagDelUser, flagGenJWT, flagConfigFile, flagImportJob, flagLogLevel string
flag.BoolVar(&flagReinitDB, "init-db", false, "Go through job-archive and re-initialize the 'job', 'tag', and 'jobtag' tables (all running jobs will be lost!)")
flag.BoolVar(&flagSyncLDAP, "sync-ldap", false, "Sync the 'user' table with ldap")
@ -69,6 +69,7 @@ func main() {
flag.BoolVar(&flagGops, "gops", false, "Listen via github.com/google/gops/agent (for debugging)")
flag.BoolVar(&flagDev, "dev", false, "Enable development components: GraphQL Playground and Swagger UI")
flag.BoolVar(&flagVersion, "version", false, "Show version information and exit")
flag.BoolVar(&flagMigrateDB, "migrate-db", false, "Migrate database to supported version and exit")
flag.BoolVar(&flagLogDateTime, "logdate", false, "Set this flag to add date and time to log messages")
flag.StringVar(&flagConfigFile, "config", "./config.json", "Specify alternative path to `config.json`")
flag.StringVar(&flagNewUser, "add-user", "", "Add a new user. Argument format: `<username>:[admin,support,api,user]:<password>`")
@ -112,6 +113,11 @@ func main() {
config.Keys.DB = os.Getenv(envvar)
}
if flagMigrateDB {
repository.MigrateDB(config.Keys.DB)
os.Exit(0)
}
repository.Connect(config.Keys.DBDriver, config.Keys.DB)
db := repository.GetConnection()

8
go.mod
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@ -37,10 +37,13 @@ require (
github.com/go-openapi/jsonreference v0.20.0 // indirect
github.com/go-openapi/spec v0.20.7 // indirect
github.com/go-openapi/swag v0.22.3 // indirect
github.com/golang-migrate/migrate/v4 v4.15.2 // indirect
github.com/golang/protobuf v1.5.2 // indirect
github.com/google/uuid v1.3.0 // indirect
github.com/gorilla/securecookie v1.1.1 // indirect
github.com/gorilla/websocket v1.5.0 // indirect
github.com/hashicorp/errwrap v1.1.0 // indirect
github.com/hashicorp/go-multierror v1.1.1 // indirect
github.com/hashicorp/golang-lru v0.5.4 // indirect
github.com/influxdata/line-protocol v0.0.0-20210922203350-b1ad95c89adf // indirect
github.com/josharian/intern v1.0.0 // indirect
@ -49,7 +52,7 @@ require (
github.com/lann/builder v0.0.0-20180802200727-47ae307949d0 // indirect
github.com/lann/ps v0.0.0-20150810152359-62de8c46ede0 // indirect
github.com/mailru/easyjson v0.7.7 // indirect
github.com/matttproud/golang_protobuf_extensions v1.0.1 // indirect
github.com/matttproud/golang_protobuf_extensions v1.0.2-0.20181231171920-c182affec369 // indirect
github.com/mitchellh/mapstructure v1.5.0 // indirect
github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
github.com/modern-go/reflect2 v1.0.2 // indirect
@ -64,6 +67,7 @@ require (
github.com/swaggo/files v0.0.0-20220728132757-551d4a08d97a // indirect
github.com/urfave/cli/v2 v2.8.1 // indirect
github.com/xrash/smetrics v0.0.0-20201216005158-039620a65673 // indirect
go.uber.org/atomic v1.7.0 // indirect
golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4 // indirect
golang.org/x/net v0.0.0-20220909164309-bea034e7d591 // indirect
golang.org/x/oauth2 v0.0.0-20220223155221-ee480838109b // indirect
@ -71,7 +75,7 @@ require (
golang.org/x/text v0.3.7 // indirect
golang.org/x/tools v0.1.12 // indirect
golang.org/x/xerrors v0.0.0-20220411194840-2f41105eb62f // indirect
google.golang.org/appengine v1.6.6 // indirect
google.golang.org/appengine v1.6.7 // indirect
google.golang.org/protobuf v1.28.1 // indirect
gopkg.in/yaml.v2 v2.4.0 // indirect
gopkg.in/yaml.v3 v3.0.1 // indirect

1279
go.sum
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File diff suppressed because it is too large Load Diff

12
internal/auth/auth.go
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@ -85,18 +85,6 @@ func Init(db *sqlx.DB,
configs map[string]interface{}) (*Authentication, error) {
auth := &Authentication{}
auth.db = db
_, err := db.Exec(`
CREATE TABLE IF NOT EXISTS user (
username varchar(255) PRIMARY KEY NOT NULL,
password varchar(255) DEFAULT NULL,
ldap tinyint NOT NULL DEFAULT 0, /* col called "ldap" for historic reasons, fills the "AuthSource" */
name varchar(255) DEFAULT NULL,
roles varchar(255) NOT NULL DEFAULT "[]",
email varchar(255) DEFAULT NULL);`)
if err != nil {
log.Error("Error while initializing authentication -> create user table failed")
return nil, err
}
sessKey := os.Getenv("SESSION_KEY")
if sessKey == "" {

1
internal/repository/dbConnection.go
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@ -55,6 +55,7 @@ func Connect(driver string, db string) {
}
dbConnInstance = &DBConnection{DB: dbHandle}
checkDBVersion(dbHandle.DB)
})
}

61
internal/repository/init.go
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@ -19,60 +19,6 @@ import (
"github.com/ClusterCockpit/cc-backend/pkg/schema"
)
// `AUTO_INCREMENT` is in a comment because of this hack:
// https://stackoverflow.com/a/41028314 (sqlite creates unique ids automatically)
const JobsDBSchema string = `
DROP TABLE IF EXISTS jobtag;
DROP TABLE IF EXISTS job;
DROP TABLE IF EXISTS tag;
CREATE TABLE job (
id INTEGER PRIMARY KEY /*!40101 AUTO_INCREMENT */,
job_id BIGINT NOT NULL,
cluster VARCHAR(255) NOT NULL,
subcluster VARCHAR(255) NOT NULL,
start_time BIGINT NOT NULL, -- Unix timestamp
user VARCHAR(255) NOT NULL,
project VARCHAR(255) NOT NULL,
` + "`partition`" + ` VARCHAR(255) NOT NULL, -- partition is a keyword in mysql -.-
array_job_id BIGINT NOT NULL,
duration INT NOT NULL DEFAULT 0,
walltime INT NOT NULL DEFAULT 0,
job_state VARCHAR(255) NOT NULL CHECK(job_state IN ('running', 'completed', 'failed', 'cancelled', 'stopped', 'timeout', 'preempted', 'out_of_memory')),
meta_data TEXT, -- JSON
resources TEXT NOT NULL, -- JSON
num_nodes INT NOT NULL,
num_hwthreads INT NOT NULL,
num_acc INT NOT NULL,
smt TINYINT NOT NULL DEFAULT 1 CHECK(smt IN (0, 1 )),
exclusive TINYINT NOT NULL DEFAULT 1 CHECK(exclusive IN (0, 1, 2)),
monitoring_status TINYINT NOT NULL DEFAULT 1 CHECK(monitoring_status IN (0, 1, 2, 3)),
mem_used_max REAL NOT NULL DEFAULT 0.0,
flops_any_avg REAL NOT NULL DEFAULT 0.0,
mem_bw_avg REAL NOT NULL DEFAULT 0.0,
load_avg REAL NOT NULL DEFAULT 0.0,
net_bw_avg REAL NOT NULL DEFAULT 0.0,
net_data_vol_total REAL NOT NULL DEFAULT 0.0,
file_bw_avg REAL NOT NULL DEFAULT 0.0,
file_data_vol_total REAL NOT NULL DEFAULT 0.0);
CREATE TABLE tag (
id INTEGER PRIMARY KEY,
tag_type VARCHAR(255) NOT NULL,
tag_name VARCHAR(255) NOT NULL,
CONSTRAINT be_unique UNIQUE (tag_type, tag_name));
CREATE TABLE jobtag (
job_id INTEGER,
tag_id INTEGER,
PRIMARY KEY (job_id, tag_id),
FOREIGN KEY (job_id) REFERENCES job (id) ON DELETE CASCADE,
FOREIGN KEY (tag_id) REFERENCES tag (id) ON DELETE CASCADE);
`
// Indexes are created after the job-archive is traversed for faster inserts.
const JobsDbIndexes string = `
CREATE INDEX job_stats ON job (cluster,subcluster,user);
@ -211,13 +157,6 @@ func InitDB() error {
starttime := time.Now()
log.Print("Building job table...")
// Basic database structure:
_, err := db.DB.Exec(JobsDBSchema)
if err != nil {
log.Error("Error while initializing basic DB structure")
return err
}
// Inserts are bundled into transactions because in sqlite,
// that speeds up inserts A LOT.
tx, err := db.DB.Beginx()

69
internal/repository/migration.go Normal file
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@ -0,0 +1,69 @@
// Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
// All rights reserved.
// Use of this source code is governed by a MIT-style
// license that can be found in the LICENSE file.
package repository
import (
"database/sql"
"embed"
"fmt"
"os"
"github.com/ClusterCockpit/cc-backend/pkg/log"
"github.com/golang-migrate/migrate/v4"
"github.com/golang-migrate/migrate/v4/database/sqlite3"
"github.com/golang-migrate/migrate/v4/source/iofs"
)
const supportedVersion uint = 2
//go:embed migrations/*.sql
var migrationFiles embed.FS
func checkDBVersion(db *sql.DB) {
driver, err := sqlite3.WithInstance(db, &sqlite3.Config{})
if err != nil {
log.Fatal(err)
}
d, err := iofs.New(migrationFiles, "migrations")
if err != nil {
log.Fatal(err)
}
m, err := migrate.NewWithInstance("iofs", d, "sqlite3", driver)
if err != nil {
log.Fatal(err)
}
v, _, err := m.Version()
if err != nil {
if err == migrate.ErrNilVersion {
log.Warn("Legacy database without version or missing database file!")
} else {
log.Fatal(err)
}
}
if v < supportedVersion {
log.Warnf("Unsupported database version %d, need %d.\nPlease backup your database file and run cc-backend --migrate-db", v, supportedVersion)
os.Exit(0)
}
}
func MigrateDB(db string) {
d, err := iofs.New(migrationFiles, "migrations")
if err != nil {
log.Fatal(err)
}
m, err := migrate.NewWithSourceInstance("iofs", d, fmt.Sprintf("sqlite3://%s?_foreign_keys=on", db))
if err != nil {
log.Fatal(err)
}
if err := m.Up(); err != nil {
log.Fatal(err)
}
m.Close()
}

5
internal/repository/migrations/01_init-schema.down.sql Normal file
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@ -0,0 +1,5 @@
DROP TABLE IF EXISTS job;
DROP TABLE IF EXISTS tags;
DROP TABLE IF EXISTS jobtag;
DROP TABLE IF EXISTS configuration;
DROP TABLE IF EXISTS user;

62
internal/repository/migrations/01_init-schema.up.sql Normal file
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@ -0,0 +1,62 @@
CREATE TABLE IF NOT EXISTS job (
id INTEGER PRIMARY KEY,
job_id BIGINT NOT NULL,
cluster VARCHAR(255) NOT NULL,
subcluster VARCHAR(255) NOT NULL,
start_time BIGINT NOT NULL, -- Unix timestamp
user VARCHAR(255) NOT NULL,
project VARCHAR(255) NOT NULL,
partition VARCHAR(255) NOT NULL,
array_job_id BIGINT NOT NULL,
duration INT NOT NULL DEFAULT 0,
walltime INT NOT NULL DEFAULT 0,
job_state VARCHAR(255) NOT NULL
CHECK(job_state IN ('running', 'completed', 'failed', 'cancelled',
'stopped', 'timeout', 'preempted', 'out_of_memory')),
meta_data TEXT, -- JSON
resources TEXT NOT NULL, -- JSON
num_nodes INT NOT NULL,
num_hwthreads INT NOT NULL,
num_acc INT NOT NULL,
smt TINYINT NOT NULL DEFAULT 1 CHECK(smt IN (0, 1 )),
exclusive TINYINT NOT NULL DEFAULT 1 CHECK(exclusive IN (0, 1, 2)),
monitoring_status TINYINT NOT NULL DEFAULT 1 CHECK(monitoring_status IN (0, 1, 2, 3)),
mem_used_max REAL NOT NULL DEFAULT 0.0,
flops_any_avg REAL NOT NULL DEFAULT 0.0,
mem_bw_avg REAL NOT NULL DEFAULT 0.0,
load_avg REAL NOT NULL DEFAULT 0.0,
net_bw_avg REAL NOT NULL DEFAULT 0.0,
net_data_vol_total REAL NOT NULL DEFAULT 0.0,
file_bw_avg REAL NOT NULL DEFAULT 0.0,
file_data_vol_total REAL NOT NULL DEFAULT 0.0);
CREATE TABLE IF NOT EXISTS tag (
id INTEGER PRIMARY KEY,
tag_type VARCHAR(255) NOT NULL,
tag_name VARCHAR(255) NOT NULL,
CONSTRAINT be_unique UNIQUE (tag_type, tag_name));
CREATE TABLE IF NOT EXISTS jobtag (
job_id INTEGER,
tag_id INTEGER,
PRIMARY KEY (job_id, tag_id),
FOREIGN KEY (job_id) REFERENCES job (id) ON DELETE CASCADE,
FOREIGN KEY (tag_id) REFERENCES tag (id) ON DELETE CASCADE);
CREATE TABLE IF NOT EXISTS configuration (
username varchar(255),
confkey varchar(255),
value varchar(255),
PRIMARY KEY (username, confkey),
FOREIGN KEY (username) REFERENCES user (username) ON DELETE CASCADE ON UPDATE NO ACTION);
CREATE TABLE IF NOT EXISTS user (
username varchar(255) PRIMARY KEY NOT NULL,
password varchar(255) DEFAULT NULL,
ldap tinyint NOT NULL DEFAULT 0, /* col called "ldap" for historic reasons, fills the "AuthSource" */
name varchar(255) DEFAULT NULL,
roles varchar(255) NOT NULL DEFAULT "[]",
email varchar(255) DEFAULT NULL);

0
internal/repository/migrations/02_add-index.down.sql Normal file
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5
internal/repository/migrations/02_add-index.up.sql Normal file
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@ -0,0 +1,5 @@
CREATE INDEX IF NOT EXISTS job_stats ON job (cluster,subcluster,user);
CREATE INDEX IF NOT EXISTS job_by_user ON job (user);
CREATE INDEX IF NOT EXISTS job_by_starttime ON job (start_time);
CREATE INDEX IF NOT EXISTS job_by_job_id ON job (job_id);
CREATE INDEX IF NOT EXISTS job_by_state ON job (job_state);

12
internal/repository/user.go
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@ -33,18 +33,6 @@ func GetUserCfgRepo() *UserCfgRepo {
userCfgRepoOnce.Do(func() {
db := GetConnection()
_, err := db.DB.Exec(`
CREATE TABLE IF NOT EXISTS configuration (
username varchar(255),
confkey varchar(255),
value varchar(255),
PRIMARY KEY (username, confkey),
FOREIGN KEY (username) REFERENCES user (username) ON DELETE CASCADE ON UPDATE NO ACTION);`)
if err != nil {
log.Fatalf("db.DB.exec() error: %v", err)
}
lookupConfigStmt, err := db.DB.Preparex(`SELECT confkey, value FROM configuration WHERE configuration.username = ?`)
if err != nil {
log.Fatalf("db.DB.Preparex() error: %v", err)

10
test/integration_test.go
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@ -269,11 +269,7 @@ func setup(t *testing.T) *api.RestApi {
t.Fatal(err)
}
dbfilepath := filepath.Join(tmpdir, "test.db")
f, err := os.Create(dbfilepath)
if err != nil {
t.Fatal(err)
}
f.Close()
repository.MigrateDB(dbfilepath)
cfgFilePath := filepath.Join(tmpdir, "config.json")
if err := os.WriteFile(cfgFilePath, []byte(testconfig), 0666); err != nil {
@ -294,10 +290,6 @@ func setup(t *testing.T) *api.RestApi {
t.Fatal(err)
}
if _, err := db.DB.Exec(repository.JobsDBSchema); err != nil {
t.Fatal(err)
}
jobRepo := repository.GetJobRepository()
resolver := &graph.Resolver{DB: db.DB, Repo: jobRepo}

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test/test.db
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