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Merge pull request #168 from ClusterCockpit/hotfix

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Hotfix
This commit is contained in:
Jan Eitzinger 2023-06-29 14:59:08 +02:00 committed by GitHub
commit affcba441b
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14 changed files with 196 additions and 60 deletions
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6
api/schema.graphqls
View File

@ -237,10 +237,7 @@ input JobFilter {
memUsedMax: FloatRange
exclusive: Int
sharedNode: StringInput
selfJobId: StringInput
selfStartTime: Time
selfDuration: Int
node: StringInput
}
input OrderByInput {
@ -274,6 +271,7 @@ type JobResultList {
}
type JobLinkResultList {
listQuery: String
items: [JobLink!]!
count: Int
}

80
cmd/cc-backend/main.go
View File

@ -35,6 +35,7 @@ import (
"github.com/ClusterCockpit/cc-backend/internal/repository"
"github.com/ClusterCockpit/cc-backend/internal/routerConfig"
"github.com/ClusterCockpit/cc-backend/internal/runtimeEnv"
"github.com/ClusterCockpit/cc-backend/internal/util"
"github.com/ClusterCockpit/cc-backend/pkg/archive"
"github.com/ClusterCockpit/cc-backend/pkg/log"
"github.com/ClusterCockpit/cc-backend/pkg/schema"
@ -58,15 +59,84 @@ const logoString = `
|_|
`
const envString = `
# Base64 encoded Ed25519 keys (DO NOT USE THESE TWO IN PRODUCTION!)
# You can generate your own keypair using the gen-keypair tool
JWT_PUBLIC_KEY="kzfYrYy+TzpanWZHJ5qSdMj5uKUWgq74BWhQG6copP0="
JWT_PRIVATE_KEY="dtPC/6dWJFKZK7KZ78CvWuynylOmjBFyMsUWArwmodOTN9itjL5POlqdZkcnmpJ0yPm4pRaCrvgFaFAbpyik/Q=="
# Some random bytes used as secret for cookie-based sessions (DO NOT USE THIS ONE IN PRODUCTION)
SESSION_KEY="67d829bf61dc5f87a73fd814e2c9f629"
`
const configString = `
{
"addr": "127.0.0.1:8080",
"archive": {
"kind": "file",
"path": "./var/job-archive"
},
"clusters": [
{
"name": "name",
"metricDataRepository": {
"kind": "cc-metric-store",
"url": "http://localhost:8082",
"token": ""
},
"filterRanges": {
"numNodes": {
"from": 1,
"to": 64
},
"duration": {
"from": 0,
"to": 86400
},
"startTime": {
"from": "2023-01-01T00:00:00Z",
"to": null
}
}
}
]
}
`
var (
date string
commit string
version string
)
func initEnv() {
if util.CheckFileExists("var") {
fmt.Print("Directory ./var already exists. Exiting!\n")
os.Exit(0)
}
if err := os.WriteFile("config.json", []byte(configString), 0666); err != nil {
log.Fatalf("Writing config.json failed: %s", err.Error())
}
if err := os.WriteFile(".env", []byte(envString), 0666); err != nil {
log.Fatalf("Writing .env failed: %s", err.Error())
}
if err := os.Mkdir("var", 0777); err != nil {
log.Fatalf("Mkdir var failed: %s", err.Error())
}
err := repository.MigrateDB("sqlite3", "./var/job.db")
if err != nil {
log.Fatalf("Initialize job.db failed: %s", err.Error())
}
}
func main() {
var flagReinitDB, flagServer, flagSyncLDAP, flagGops, flagMigrateDB, flagDev, flagVersion, flagLogDateTime bool
var flagReinitDB, flagInit, flagServer, flagSyncLDAP, flagGops, flagMigrateDB, flagDev, flagVersion, flagLogDateTime bool
var flagNewUser, flagDelUser, flagGenJWT, flagConfigFile, flagImportJob, flagLogLevel string
flag.BoolVar(&flagInit, "init", false, "Setup var directory, initialize swlite database file, config.json and .env")
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")
flag.BoolVar(&flagServer, "server", false, "Start a server, continues listening on port after initialization and argument handling")
@ -96,6 +166,14 @@ func main() {
// Apply config flags for pkg/log
log.Init(flagLogLevel, flagLogDateTime)
if flagInit {
initEnv()
fmt.Print("Succesfully setup environment!\n")
fmt.Print("Please review config.json and .env and adjust it to your needs.\n")
fmt.Print("Add your job-archive at ./var/job-archive.\n")
os.Exit(0)
}
// See https://github.com/google/gops (Runtime overhead is almost zero)
if flagGops {
if err := agent.Listen(agent.Options{}); err != nil {

4
configs/env-template.txt
View File

@ -1,10 +1,10 @@
# Base64 encoded Ed25519 keys (DO NOT USE THESE TWO IN PRODUCTION!)
# You can generate your own keypair using `go run utils/gen-keypair.go`
# You can generate your own keypair using `go run tools/gen-keypair/main.go`
JWT_PUBLIC_KEY="kzfYrYy+TzpanWZHJ5qSdMj5uKUWgq74BWhQG6copP0="
JWT_PRIVATE_KEY="dtPC/6dWJFKZK7KZ78CvWuynylOmjBFyMsUWArwmodOTN9itjL5POlqdZkcnmpJ0yPm4pRaCrvgFaFAbpyik/Q=="
# Base64 encoded Ed25519 public key for accepting externally generated JWTs
# Keys in PEM format can be converted, see `tools/convert-pem-pubkey-for-cc/Readme.md`
# Keys in PEM format can be converted, see `tools/convert-pem-pubkey/Readme.md`
CROSS_LOGIN_JWT_PUBLIC_KEY=""
# Some random bytes used as secret for cookie-based sessions (DO NOT USE THIS ONE IN PRODUCTION)

97
internal/graph/generated/generated.go
View File

@ -114,8 +114,9 @@ type ComplexityRoot struct {
}
JobLinkResultList struct {
Count func(childComplexity int) int
Items func(childComplexity int) int
Count func(childComplexity int) int
Items func(childComplexity int) int
ListQuery func(childComplexity int) int
}
JobMetric struct {
@ -629,6 +630,13 @@ func (e *executableSchema) Complexity(typeName, field string, childComplexity in
return e.complexity.JobLinkResultList.Items(childComplexity), true
case "JobLinkResultList.listQuery":
if e.complexity.JobLinkResultList.ListQuery == nil {
break
}
return e.complexity.JobLinkResultList.ListQuery(childComplexity), true
case "JobMetric.series":
if e.complexity.JobMetric.Series == nil {
break
@ -1739,10 +1747,7 @@ input JobFilter {
memUsedMax: FloatRange
exclusive: Int
sharedNode: StringInput
selfJobId: StringInput
selfStartTime: Time
selfDuration: Int
node: StringInput
}
input OrderByInput {
@ -1776,6 +1781,7 @@ type JobResultList {
}
type JobLinkResultList {
listQuery: String
items: [JobLink!]!
count: Int
}
@ -3951,6 +3957,8 @@ func (ec *executionContext) fieldContext_Job_concurrentJobs(ctx context.Context,
IsResolver: true,
Child: func(ctx context.Context, field graphql.CollectedField) (*graphql.FieldContext, error) {
switch field.Name {
case "listQuery":
return ec.fieldContext_JobLinkResultList_listQuery(ctx, field)
case "items":
return ec.fieldContext_JobLinkResultList_items(ctx, field)
case "count":
@ -4140,6 +4148,47 @@ func (ec *executionContext) fieldContext_JobLink_jobId(ctx context.Context, fiel
return fc, nil
}
func (ec *executionContext) _JobLinkResultList_listQuery(ctx context.Context, field graphql.CollectedField, obj *model.JobLinkResultList) (ret graphql.Marshaler) {
fc, err := ec.fieldContext_JobLinkResultList_listQuery(ctx, field)
if err != nil {
return graphql.Null
}
ctx = graphql.WithFieldContext(ctx, fc)
defer func() {
if r := recover(); r != nil {
ec.Error(ctx, ec.Recover(ctx, r))
ret = graphql.Null
}
}()
resTmp, err := ec.ResolverMiddleware(ctx, func(rctx context.Context) (interface{}, error) {
ctx = rctx // use context from middleware stack in children
return obj.ListQuery, nil
})
if err != nil {
ec.Error(ctx, err)
return graphql.Null
}
if resTmp == nil {
return graphql.Null
}
res := resTmp.(*string)
fc.Result = res
return ec.marshalOString2ᚖstring(ctx, field.Selections, res)
}
func (ec *executionContext) fieldContext_JobLinkResultList_listQuery(ctx context.Context, field graphql.CollectedField) (fc *graphql.FieldContext, err error) {
fc = &graphql.FieldContext{
Object: "JobLinkResultList",
Field: field,
IsMethod: false,
IsResolver: false,
Child: func(ctx context.Context, field graphql.CollectedField) (*graphql.FieldContext, error) {
return nil, errors.New("field of type String does not have child fields")
},
}
return fc, nil
}
func (ec *executionContext) _JobLinkResultList_items(ctx context.Context, field graphql.CollectedField, obj *model.JobLinkResultList) (ret graphql.Marshaler) {
fc, err := ec.fieldContext_JobLinkResultList_items(ctx, field)
if err != nil {
@ -11148,7 +11197,7 @@ func (ec *executionContext) unmarshalInputJobFilter(ctx context.Context, obj int
asMap[k] = v
}
fieldsInOrder := [...]string{"tags", "jobId", "arrayJobId", "user", "project", "jobName", "cluster", "partition", "duration", "minRunningFor", "numNodes", "numAccelerators", "numHWThreads", "startTime", "state", "flopsAnyAvg", "memBwAvg", "loadAvg", "memUsedMax", "exclusive", "sharedNode", "selfJobId", "selfStartTime", "selfDuration"}
fieldsInOrder := [...]string{"tags", "jobId", "arrayJobId", "user", "project", "jobName", "cluster", "partition", "duration", "minRunningFor", "numNodes", "numAccelerators", "numHWThreads", "startTime", "state", "flopsAnyAvg", "memBwAvg", "loadAvg", "memUsedMax", "exclusive", "node"}
for _, k := range fieldsInOrder {
v, ok := asMap[k]
if !ok {
@ -11315,35 +11364,11 @@ func (ec *executionContext) unmarshalInputJobFilter(ctx context.Context, obj int
if err != nil {
return it, err
}
case "sharedNode":
case "node":
var err error
ctx := graphql.WithPathContext(ctx, graphql.NewPathWithField("sharedNode"))
it.SharedNode, err = ec.unmarshalOStringInput2ᚖgithubᚗcomᚋClusterCockpitᚋccᚑbackendᚋinternalᚋgraphᚋmodelᚐStringInput(ctx, v)
if err != nil {
return it, err
}
case "selfJobId":
var err error
ctx := graphql.WithPathContext(ctx, graphql.NewPathWithField("selfJobId"))
it.SelfJobID, err = ec.unmarshalOStringInput2ᚖgithubᚗcomᚋClusterCockpitᚋccᚑbackendᚋinternalᚋgraphᚋmodelᚐStringInput(ctx, v)
if err != nil {
return it, err
}
case "selfStartTime":
var err error
ctx := graphql.WithPathContext(ctx, graphql.NewPathWithField("selfStartTime"))
it.SelfStartTime, err = ec.unmarshalOTime2ᚖtimeᚐTime(ctx, v)
if err != nil {
return it, err
}
case "selfDuration":
var err error
ctx := graphql.WithPathContext(ctx, graphql.NewPathWithField("selfDuration"))
it.SelfDuration, err = ec.unmarshalOInt2ᚖint(ctx, v)
ctx := graphql.WithPathContext(ctx, graphql.NewPathWithField("node"))
it.Node, err = ec.unmarshalOStringInput2ᚖgithubᚗcomᚋClusterCockpitᚋccᚑbackendᚋinternalᚋgraphᚋmodelᚐStringInput(ctx, v)
if err != nil {
return it, err
}
@ -12055,6 +12080,10 @@ func (ec *executionContext) _JobLinkResultList(ctx context.Context, sel ast.Sele
switch field.Name {
case "__typename":
out.Values[i] = graphql.MarshalString("JobLinkResultList")
case "listQuery":
out.Values[i] = ec._JobLinkResultList_listQuery(ctx, field, obj)
case "items":
out.Values[i] = ec._JobLinkResultList_items(ctx, field, obj)

10
internal/graph/model/models_gen.go
View File

@ -57,10 +57,7 @@ type JobFilter struct {
LoadAvg *FloatRange `json:"loadAvg"`
MemUsedMax *FloatRange `json:"memUsedMax"`
Exclusive *int `json:"exclusive"`
SharedNode *StringInput `json:"sharedNode"`
SelfJobID *StringInput `json:"selfJobId"`
SelfStartTime *time.Time `json:"selfStartTime"`
SelfDuration *int `json:"selfDuration"`
Node *StringInput `json:"node"`
}
type JobLink struct {
@ -69,8 +66,9 @@ type JobLink struct {
}
type JobLinkResultList struct {
Items []*JobLink `json:"items"`
Count *int `json:"count"`
ListQuery *string `json:"listQuery"`
Items []*JobLink `json:"items"`
Count *int `json:"count"`
}
type JobMetricWithName struct {

4
internal/graph/schema.resolvers.go
View File

@ -32,9 +32,7 @@ func (r *jobResolver) Tags(ctx context.Context, obj *schema.Job) ([]*schema.Tag,
}
// ConcurrentJobs is the resolver for the concurrentJobs field.
func (r *jobResolver) ConcurrentJobs(
ctx context.Context, obj *schema.Job) (*model.JobLinkResultList, error) {
func (r *jobResolver) ConcurrentJobs(ctx context.Context, obj *schema.Job) (*model.JobLinkResultList, error) {
if obj.State == schema.JobStateRunning {
obj.Duration = int32(time.Now().Unix() - obj.StartTimeUnix)
}

32
internal/repository/job.go
View File

@ -10,6 +10,7 @@ import (
"encoding/json"
"errors"
"fmt"
"math"
"strconv"
"sync"
"time"
@ -17,6 +18,7 @@ import (
"github.com/ClusterCockpit/cc-backend/internal/auth"
"github.com/ClusterCockpit/cc-backend/internal/graph/model"
"github.com/ClusterCockpit/cc-backend/internal/metricdata"
"github.com/ClusterCockpit/cc-backend/internal/util"
"github.com/ClusterCockpit/cc-backend/pkg/log"
"github.com/ClusterCockpit/cc-backend/pkg/lrucache"
"github.com/ClusterCockpit/cc-backend/pkg/schema"
@ -298,7 +300,7 @@ func (r *JobRepository) FindConcurrentJobs(
return nil, nil
}
query, qerr := SecurityCheck(ctx, sq.Select("job.id", "job.job_id").From("job"))
query, qerr := SecurityCheck(ctx, sq.Select("job.id", "job.job_id", "job.start_time").From("job"))
if qerr != nil {
return nil, qerr
}
@ -308,6 +310,7 @@ func (r *JobRepository) FindConcurrentJobs(
var stopTime int64
startTime = job.StartTimeUnix
hostname := job.Resources[0].Hostname
if job.State == schema.JobStateRunning {
stopTime = time.Now().Unix()
@ -322,11 +325,11 @@ func (r *JobRepository) FindConcurrentJobs(
queryRunning := query.Where("job.job_state = ?").Where("(job.start_time BETWEEN ? AND ? OR job.start_time < ?)",
"running", startTimeTail, stopTimeTail, startTime)
queryRunning = queryRunning.Where("job.resources LIKE ?", fmt.Sprint("%", job.Resources[0].Hostname, "%"))
queryRunning = queryRunning.Where("job.resources LIKE ?", fmt.Sprint("%", hostname, "%"))
query = query.Where("job.job_state != ?").Where("((job.start_time BETWEEN ? AND ?) OR (job.start_time + job.duration) BETWEEN ? AND ? OR (job.start_time < ?) AND (job.start_time + job.duration) > ?)",
"running", startTimeTail, stopTimeTail, startTimeFront, stopTimeTail, startTime, stopTime)
query = query.Where("job.resources LIKE ?", fmt.Sprint("%", job.Resources[0].Hostname, "%"))
query = query.Where("job.resources LIKE ?", fmt.Sprint("%", hostname, "%"))
rows, err := query.RunWith(r.stmtCache).Query()
if err != nil {
@ -335,16 +338,21 @@ func (r *JobRepository) FindConcurrentJobs(
}
items := make([]*model.JobLink, 0, 10)
minStart := int64(math.MaxInt64)
maxStart := int64(0)
for rows.Next() {
var id, jobId sql.NullInt64
var id, jobId, startTime sql.NullInt64
if err = rows.Scan(&id, &jobId); err != nil {
if err = rows.Scan(&id, &jobId, &startTime); err != nil {
log.Warn("Error while scanning rows")
return nil, err
}
if id.Valid {
minStart = util.Min(minStart, startTime.Int64)
maxStart = util.Max(maxStart, startTime.Int64)
items = append(items,
&model.JobLink{
ID: fmt.Sprint(id.Int64),
@ -360,14 +368,17 @@ func (r *JobRepository) FindConcurrentJobs(
}
for rows.Next() {
var id, jobId sql.NullInt64
var id, jobId, startTime sql.NullInt64
if err := rows.Scan(&id, &jobId); err != nil {
if err := rows.Scan(&id, &jobId, &startTime); err != nil {
log.Warn("Error while scanning rows")
return nil, err
}
if id.Valid {
minStart = util.Min(minStart, startTime.Int64)
maxStart = util.Max(maxStart, startTime.Int64)
items = append(items,
&model.JobLink{
ID: fmt.Sprint(id.Int64),
@ -377,10 +388,13 @@ func (r *JobRepository) FindConcurrentJobs(
}
cnt := len(items)
queryString := fmt.Sprintf("cluster=%s&startTime=%d-%d&node=%s",
job.Cluster, minStart, maxStart, hostname)
return &model.JobLinkResultList{
Items: items,
Count: &cnt,
ListQuery: &queryString,
Items: items,
Count: &cnt,
}, nil
}

6
internal/repository/migration.go
View File

@ -16,7 +16,7 @@ import (
"github.com/golang-migrate/migrate/v4/source/iofs"
)
const Version uint = 5
const Version uint = 6
//go:embed migrations/*
var migrationFiles embed.FS
@ -53,6 +53,8 @@ func checkDBVersion(backend string, db *sql.DB) error {
if err != nil {
return err
}
default:
log.Fatalf("unsupported database backend: %s", backend)
}
v, _, err := m.Version()
@ -99,6 +101,8 @@ func MigrateDB(backend string, db string) error {
if err != nil {
return err
}
default:
log.Fatalf("unsupported database backend: %s", backend)
}
if err := m.Up(); err != nil {

1
internal/repository/migrations/mysql/06_change-config.down.sql Normal file
View File

@ -0,0 +1 @@
ALTER TABLE configuration MODIFY value VARCHAR(255);

1
internal/repository/migrations/mysql/06_change-config.up.sql Normal file
View File

@ -0,0 +1 @@
ALTER TABLE configuration MODIFY value TEXT;

4
internal/repository/migrations/sqlite3/06_change-config.down.sql Normal file
View File

@ -0,0 +1,4 @@
ALTER TABLE configuration ADD COLUMN value_new varchar(255);
INSERT INTO configuration (value_new) SELECT value FROM configuration;
ALTER TABLE configuration DROP COLUMN value;
ALTER TABLE configuration RENAME COLUMN value_new TO value;

4
internal/repository/migrations/sqlite3/06_change-config.up.sql Normal file
View File

@ -0,0 +1,4 @@
ALTER TABLE configuration ADD COLUMN value_new TEXT;
INSERT INTO configuration (value_new) SELECT value FROM configuration;
ALTER TABLE configuration DROP COLUMN value;
ALTER TABLE configuration RENAME COLUMN value_new TO value;

3
internal/repository/query.go
View File

@ -208,6 +208,9 @@ func BuildWhereClause(filter *model.JobFilter, query sq.SelectBuilder) sq.Select
if filter.NumHWThreads != nil {
query = buildIntCondition("job.num_hwthreads", filter.NumHWThreads, query)
}
if filter.Node != nil {
query = buildStringCondition("job.resources", filter.Node, query)
}
if filter.FlopsAnyAvg != nil {
query = buildFloatCondition("job.flops_any_avg", filter.FlopsAnyAvg, query)
}

4
internal/util/util_test.go
View File

@ -15,6 +15,10 @@ import (
func TestCheckFileExists(t *testing.T) {
tmpdir := t.TempDir()
if !util.CheckFileExists(tmpdir) {
t.Fatal("expected true, got false")
}
filePath := filepath.Join(tmpdir, "version.txt")
if err := os.WriteFile(filePath, []byte(fmt.Sprintf("%d", 1)), 0666); err != nil {