ClusterCockpit/cc-backend
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make database schema mysql compatible; use prepared statements

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This commit is contained in:
Lou Knauer 2022-01-20 10:00:55 +01:00
parent a64944f3c3
commit 9034cb90aa
10 changed files with 163 additions and 86 deletions
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2
api/rest.go
View File

@ -215,7 +215,7 @@ func (api *RestApi) startJob(rw http.ResponseWriter, r *http.Request) {
}
res, err := api.DB.NamedExec(`INSERT INTO job (
job_id, user, project, cluster, partition, array_job_id, num_nodes, num_hwthreads, num_acc,
job_id, user, project, cluster, `+"`partition`"+`, array_job_id, num_nodes, num_hwthreads, num_acc,
exclusive, monitoring_status, smt, job_state, start_time, duration, resources, meta_data
) VALUES (
:job_id, :user, :project, :cluster, :partition, :array_job_id, :num_nodes, :num_hwthreads, :num_acc,

87
config/config.go
View File

@ -4,7 +4,6 @@ import (
"context"
"encoding/json"
"fmt"
"log"
"net/http"
"os"
"path/filepath"
@ -13,13 +12,15 @@ import (
"github.com/ClusterCockpit/cc-jobarchive/auth"
"github.com/ClusterCockpit/cc-jobarchive/graph/model"
"github.com/iamlouk/lrucache"
"github.com/jmoiron/sqlx"
)
var db *sqlx.DB
var lookupConfigStmt *sqlx.Stmt
var lock sync.RWMutex
var uiDefaults map[string]interface{}
var cache lrucache.Cache = *lrucache.New(1024)
var Clusters []*model.Cluster
func Init(usersdb *sqlx.DB, authEnabled bool, uiConfig map[string]interface{}, jobArchive string) error {
@ -57,13 +58,18 @@ func Init(usersdb *sqlx.DB, authEnabled bool, uiConfig map[string]interface{}, j
_, err := db.Exec(`
CREATE TABLE IF NOT EXISTS configuration (
username varchar(255),
key varchar(255),
confkey varchar(255),
value varchar(255),
PRIMARY KEY (username, key),
PRIMARY KEY (username, confkey),
FOREIGN KEY (username) REFERENCES user (username) ON DELETE CASCADE ON UPDATE NO ACTION);`)
if err != nil {
return err
}
lookupConfigStmt, err = db.Preparex(`SELECT confkey, value FROM configuration WHERE configuration.username = ?`)
if err != nil {
return err
}
}
return nil
@ -72,38 +78,52 @@ func Init(usersdb *sqlx.DB, authEnabled bool, uiConfig map[string]interface{}, j
// Return the personalised UI config for the currently authenticated
// user or return the plain default config.
func GetUIConfig(r *http.Request) (map[string]interface{}, error) {
lock.RLock()
config := make(map[string]interface{}, len(uiDefaults))
for k, v := range uiDefaults {
config[k] = v
}
lock.RUnlock()
user := auth.GetUser(r.Context())
if user == nil {
return config, nil
lock.RLock()
copy := make(map[string]interface{}, len(uiDefaults))
for k, v := range uiDefaults {
copy[k] = v
}
lock.RUnlock()
return copy, nil
}
rows, err := db.Query(`SELECT key, value FROM configuration WHERE configuration.username = ?`, user.Username)
if err != nil {
data := cache.Get(user.Username, func() (interface{}, time.Duration, int) {
config := make(map[string]interface{}, len(uiDefaults))
for k, v := range uiDefaults {
config[k] = v
}
rows, err := lookupConfigStmt.Query(user.Username)
if err != nil {
return err, 0, 0
}
size := 0
for rows.Next() {
var key, rawval string
if err := rows.Scan(&key, &rawval); err != nil {
return err, 0, 0
}
var val interface{}
if err := json.Unmarshal([]byte(rawval), &val); err != nil {
return err, 0, 0
}
size += len(key)
size += len(rawval)
config[key] = val
}
return config, 24 * time.Hour, size
})
if err, ok := data.(error); ok {
return nil, err
}
for rows.Next() {
var key, rawval string
if err := rows.Scan(&key, &rawval); err != nil {
return nil, err
}
var val interface{}
if err := json.Unmarshal([]byte(rawval), &val); err != nil {
return nil, err
}
config[key] = val
}
return config, nil
return data.(map[string]interface{}), nil
}
// If the context does not have a user, update the global ui configuration without persisting it!
@ -111,21 +131,20 @@ func GetUIConfig(r *http.Request) (map[string]interface{}, error) {
func UpdateConfig(key, value string, ctx context.Context) error {
user := auth.GetUser(ctx)
if user == nil {
lock.RLock()
defer lock.RUnlock()
var val interface{}
if err := json.Unmarshal([]byte(value), &val); err != nil {
return err
}
lock.Lock()
defer lock.Unlock()
uiDefaults[key] = val
return nil
}
if _, err := db.Exec(`REPLACE INTO configuration (username, key, value) VALUES (?, ?, ?)`,
cache.Del(user.Username)
if _, err := db.Exec(`REPLACE INTO configuration (username, confkey, value) VALUES (?, ?, ?)`,
user.Username, key, value); err != nil {
log.Printf("db.Exec: %s\n", err.Error())
return err
}

2
frontend

@ -1 +1 @@
Subproject commit 68543017064707625d788d1e7f987434d0bb0714
Subproject commit 80650220a3d481b6fc82c305791073ed92fc9261

1
go.mod
View File

@ -6,6 +6,7 @@ require (
github.com/99designs/gqlgen v0.13.0
github.com/Masterminds/squirrel v1.5.1
github.com/go-ldap/ldap/v3 v3.4.1
github.com/go-sql-driver/mysql v1.5.0
github.com/golang-jwt/jwt/v4 v4.1.0
github.com/gorilla/handlers v1.5.1
github.com/gorilla/mux v1.8.0

37
graph/resolver.go
View File

@ -4,6 +4,7 @@ import (
"context"
"errors"
"fmt"
"log"
"regexp"
"strings"
@ -20,6 +21,31 @@ import (
type Resolver struct {
DB *sqlx.DB
findJobByIdStmt *sqlx.Stmt
findJobByIdWithUserStmt *sqlx.Stmt
}
func (r *Resolver) Init() {
findJobById, _, err := sq.Select(schema.JobColumns...).From("job").Where("job.id = ?", nil).ToSql()
if err != nil {
log.Fatal(err)
}
r.findJobByIdStmt, err = r.DB.Preparex(findJobById)
if err != nil {
log.Fatal(err)
}
findJobByIdWithUser, _, err := sq.Select(schema.JobColumns...).From("job").Where("job.id = ?", nil).Where("job.user = ?").ToSql()
if err != nil {
log.Fatal(err)
}
r.findJobByIdWithUserStmt, err = r.DB.Preparex(findJobByIdWithUser)
if err != nil {
log.Fatal(err)
}
}
// Helper function for the `jobs` GraphQL-Query. Is also used elsewhere when a list of jobs is needed.
@ -82,17 +108,12 @@ func (r *Resolver) queryJobs(ctx context.Context, filters []*model.JobFilter, pa
}
func securityCheck(ctx context.Context, query sq.SelectBuilder) sq.SelectBuilder {
val := ctx.Value(auth.ContextUserKey)
if val == nil {
user := auth.GetUser(ctx)
if user == nil || user.IsAdmin {
return query
}
user := val.(*auth.User)
if user.IsAdmin {
return query
}
return query.Where("job.user_id = ?", user.Username)
return query.Where("job.user = ?", user.Username)
}
// Build a sq.SelectBuilder out of a schema.JobFilter.

12
graph/schema.resolvers.go
View File

@ -148,14 +148,14 @@ func (r *queryResolver) Tags(ctx context.Context) ([]*schema.Tag, error) {
}
func (r *queryResolver) Job(ctx context.Context, id string) (*schema.Job, error) {
query := sq.Select(schema.JobColumns...).From("job").Where("job.id = ?", id)
query = securityCheck(ctx, query)
sql, args, err := query.ToSql()
if err != nil {
return nil, err
// This query is very common (mostly called through other resolvers such as JobMetrics),
// so we use prepared statements here.
user := auth.GetUser(ctx)
if user == nil || user.IsAdmin {
return schema.ScanJob(r.findJobByIdStmt.QueryRowx(id))
}
return schema.ScanJob(r.DB.QueryRowx(sql, args...))
return schema.ScanJob(r.findJobByIdWithUserStmt.QueryRowx(id, user.Username))
}
func (r *queryResolver) JobMetrics(ctx context.Context, id string, metrics []string, scopes []schema.MetricScope) ([]*model.JobMetricWithName, error) {

6
graph/stats.go
View File

@ -30,13 +30,13 @@ func (r *queryResolver) jobsStatistics(ctx context.Context, filter []*model.JobF
// `socketsPerNode` and `coresPerSocket` can differ from cluster to cluster, so we need to explicitly loop over those.
for _, cluster := range config.Clusters {
for _, partition := range cluster.Partitions {
corehoursCol := fmt.Sprintf("SUM(job.duration * job.num_nodes * %d * %d) / 3600", partition.SocketsPerNode, partition.CoresPerSocket)
corehoursCol := fmt.Sprintf("ROUND(SUM(job.duration * job.num_nodes * %d * %d) / 3600)", partition.SocketsPerNode, partition.CoresPerSocket)
var query sq.SelectBuilder
if groupBy == nil {
query = sq.Select(
"''",
"COUNT(job.id)",
"SUM(job.duration) / 3600",
"ROUND(SUM(job.duration) / 3600)",
corehoursCol,
).From("job")
} else {
@ -44,7 +44,7 @@ func (r *queryResolver) jobsStatistics(ctx context.Context, filter []*model.JobF
query = sq.Select(
col,
"COUNT(job.id)",
"SUM(job.duration) / 3600",
"ROUND(SUM(job.duration) / 3600)",
corehoursCol,
).From("job").GroupBy(col)
}

29
init-db.go
View File

@ -13,32 +13,34 @@ import (
"github.com/jmoiron/sqlx"
)
// `AUTO_INCREMENT` is in a comment because of this hack:
// https://stackoverflow.com/a/41028314 (sqlite creates unique ids automatically)
const JOBS_DB_SCHEMA string = `
DROP TABLE IF EXISTS jobtag;
DROP TABLE IF EXISTS job;
DROP TABLE IF EXISTS tag;
DROP TABLE IF EXISTS jobtag;
CREATE TABLE job (
id INTEGER PRIMARY KEY AUTOINCREMENT, -- Not needed in sqlite
id INTEGER PRIMARY KEY /*!40101 AUTO_INCREMENT */,
job_id BIGINT NOT NULL,
cluster VARCHAR(255) NOT NULL,
start_time TIMESTAMP 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`" + ` VARCHAR(255) NOT NULL, -- partition is a keyword in mysql -.-
array_job_id BIGINT NOT NULL,
duration INT,
job_state VARCHAR(255) CHECK(job_state IN ('running', 'completed', 'failed', 'canceled', 'stopped', 'timeout')) NOT NULL,
meta_data TEXT, -- json, but sqlite has no json type
resources TEXT NOT NULL, -- json, but sqlite has no json type
job_state VARCHAR(255) NOT NULL CHECK(job_state IN ('running', 'completed', 'failed', 'canceled', 'stopped', 'timeout')),
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 CHECK(smt IN (0, 1 )) NOT NULL DEFAULT 1,
exclusive TINYINT CHECK(exclusive IN (0, 1, 2)) NOT NULL DEFAULT 1,
monitoring_status TINYINT CHECK(monitoring_status IN (0, 1 )) NOT NULL DEFAULT 1,
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 )),
mem_used_max REAL NOT NULL DEFAULT 0.0,
flops_any_avg REAL NOT NULL DEFAULT 0.0,
@ -89,7 +91,7 @@ func initDB(db *sqlx.DB, archive string) error {
}
stmt, err := tx.PrepareNamed(`INSERT INTO job (
job_id, user, project, cluster, partition, array_job_id, num_nodes, num_hwthreads, num_acc,
job_id, user, project, cluster, ` + "`partition`" + `, array_job_id, num_nodes, num_hwthreads, num_acc,
exclusive, monitoring_status, smt, job_state, start_time, duration, resources, meta_data,
mem_used_max, flops_any_avg, mem_bw_avg, load_avg, net_bw_avg, net_data_vol_total, file_bw_avg, file_data_vol_total
) VALUES (
@ -199,8 +201,9 @@ func loadJob(tx *sqlx.Tx, stmt *sqlx.NamedStmt, tags map[string]int64, path stri
}
job := schema.Job{
BaseJob: jobMeta.BaseJob,
StartTime: time.Unix(jobMeta.StartTime, 0),
BaseJob: jobMeta.BaseJob,
StartTime: time.Unix(jobMeta.StartTime, 0),
StartTimeUnix: jobMeta.StartTime,
}
// TODO: Other metrics...

4
schema/job.go
View File

@ -35,7 +35,8 @@ type BaseJob struct {
type Job struct {
ID int64 `json:"id" db:"id"`
BaseJob
StartTime time.Time `json:"startTime" db:"start_time"`
StartTimeUnix int64 `json:"-" db:"start_time"`
StartTime time.Time `json:"startTime"`
MemUsedMax float64 `json:"-" db:"mem_used_max"`
FlopsAnyAvg float64 `json:"-" db:"flops_any_avg"`
MemBwAvg float64 `json:"-" db:"mem_bw_avg"`
@ -83,6 +84,7 @@ func ScanJob(row Scannable) (*Job, error) {
return nil, err
}
job.StartTime = time.Unix(job.StartTimeUnix, 0)
if job.Duration == 0 && job.State == JobStateRunning {
job.Duration = int32(time.Since(job.StartTime).Seconds())
}

69
server.go
View File

@ -35,6 +35,8 @@ import (
"github.com/gorilla/handlers"
"github.com/gorilla/mux"
"github.com/jmoiron/sqlx"
_ "github.com/go-sql-driver/mysql"
_ "github.com/mattn/go-sqlite3"
)
@ -55,7 +57,10 @@ type ProgramConfig struct {
// Folder where static assets can be found, will be served directly
StaticFiles string `json:"static-files"`
// Currently only SQLite3 ist supported, so this should be a filename
// 'sqlite3' or 'mysql' (mysql will work for mariadb as well)
DBDriver string `json:"db-driver"`
// For sqlite3 a filename, for mysql a DSN in this format: https://github.com/go-sql-driver/mysql#dsn-data-source-name (Without query parameters!).
DB string `json:"db"`
// Path to the job-archive
@ -87,6 +92,7 @@ var programConfig ProgramConfig = ProgramConfig{
Addr: ":8080",
DisableAuthentication: false,
StaticFiles: "./frontend/public",
DBDriver: "sqlite3",
DB: "./var/job.db",
JobArchive: "./var/job-archive",
AsyncArchiving: true,
@ -116,7 +122,6 @@ var programConfig ProgramConfig = ProgramConfig{
"plot_view_showRoofline": true,
"plot_view_showStatTable": true,
},
MachineStateDir: "./var/machine-state",
}
func main() {
@ -147,14 +152,25 @@ func main() {
}
var err error
// This might need to change for other databases:
db, err = sqlx.Open("sqlite3", fmt.Sprintf("%s?_foreign_keys=on", programConfig.DB))
if err != nil {
log.Fatal(err)
}
if programConfig.DBDriver == "sqlite3" {
db, err = sqlx.Open("sqlite3", fmt.Sprintf("%s?_foreign_keys=on", programConfig.DB))
if err != nil {
log.Fatal(err)
}
// Only for sqlite, not needed for any other database:
db.SetMaxOpenConns(1)
db.SetMaxOpenConns(1)
} else if programConfig.DBDriver == "mysql" {
db, err = sqlx.Open("mysql", fmt.Sprintf("%s?multiStatements=true", programConfig.DB))
if err != nil {
log.Fatal(err)
}
db.SetConnMaxLifetime(time.Minute * 3)
db.SetMaxOpenConns(10)
db.SetMaxIdleConns(10)
} else {
log.Fatalf("unsupported database driver: %s", programConfig.DBDriver)
}
// Initialize sub-modules...
@ -220,18 +236,20 @@ func main() {
// Build routes...
resolver := &graph.Resolver{DB: db}
resolver.Init()
graphQLEndpoint := handler.NewDefaultServer(generated.NewExecutableSchema(generated.Config{Resolvers: resolver}))
if os.Getenv("DEBUG") != "1" {
graphQLEndpoint.SetRecoverFunc(func(ctx context.Context, err interface{}) error {
switch e := err.(type) {
case string:
return fmt.Errorf("panic: %s", e)
case error:
return fmt.Errorf("panic caused by: %w", e)
}
// graphQLEndpoint.SetRecoverFunc(func(ctx context.Context, err interface{}) error {
// switch e := err.(type) {
// case string:
// return fmt.Errorf("panic: %s", e)
// case error:
// return fmt.Errorf("panic caused by: %w", e)
// }
// return errors.New("internal server error (panic)")
// })
return errors.New("internal server error (panic)")
})
}
graphQLPlayground := playground.Handler("GraphQL playground", "/query")
api := &api.RestApi{
@ -388,6 +406,19 @@ func monitoringRoutes(router *mux.Router, resolver *graph.Resolver) {
}
filterPresets["tags"] = tags
}
if query.Get("numNodes") != "" {
parts := strings.Split(query.Get("numNodes"), "-")
if len(parts) == 2 {
a, e1 := strconv.Atoi(parts[0])
b, e2 := strconv.Atoi(parts[1])
if e1 == nil && e2 == nil {
filterPresets["numNodes"] = map[string]int{"from": a, "to": b}
}
}
}
if query.Get("jobId") != "" {
filterPresets["jobId"] = query.Get("jobId")
}
return filterPresets
}