+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: Apache-2.0
+
package main
import (
- "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
- "git.curoverse.com/arvados.git/sdk/go/keepclient"
+ "encoding/json"
+ "fmt"
+ "io"
+ "io/ioutil"
"log"
"os"
"os/exec"
"os/signal"
+ "strings"
"syscall"
+
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/keepclient"
)
type TaskDef struct {
- commands []string `json:"commands"`
- env map[string]string `json:"env"`
- stdin string `json:"stdin"`
- stdout string `json:"stdout"`
- vwd map[string]string `json:"vwd"`
- successCodes []int `json:"successCodes"`
- permanentFailCodes []int `json:"permanentFailCodes"`
- temporaryFailCodes []int `json:"temporaryFailCodes"`
+ Command []string `json:"command"`
+ Env map[string]string `json:"task.env"`
+ Stdin string `json:"task.stdin"`
+ Stdout string `json:"task.stdout"`
+ Stderr string `json:"task.stderr"`
+ Vwd map[string]string `json:"task.vwd"`
+ SuccessCodes []int `json:"task.successCodes"`
+ PermanentFailCodes []int `json:"task.permanentFailCodes"`
+ TemporaryFailCodes []int `json:"task.temporaryFailCodes"`
+ KeepTmpOutput bool `json:"task.keepTmpOutput"`
}
type Tasks struct {
- tasks []TaskDef `json:"script_parameters"`
+ Tasks []TaskDef `json:"tasks"`
}
type Job struct {
- script_parameters Tasks `json:"script_parameters"`
+ ScriptParameters Tasks `json:"script_parameters"`
}
type Task struct {
- job_uuid string `json:"job_uuid"`
- created_by_job_task_uuid string `json:"created_by_job_task_uuid"`
- parameters TaskDef `json:"parameters"`
- sequence int `json:"sequence"`
- output string `json:"output"`
- success bool `json:"success"`
- progress float32 `json:"sequence"`
+ JobUUID string `json:"job_uuid"`
+ CreatedByJobTaskUUID string `json:"created_by_job_task_uuid"`
+ Parameters TaskDef `json:"parameters"`
+ Sequence int `json:"sequence"`
+ Output string `json:"output"`
+ Success bool `json:"success"`
+ Progress float32 `json:"sequence"`
}
-func setupDirectories(tmpdir, taskUuid string) (outdir string, err error) {
- err = os.Chdir(tmpdir)
+type IArvadosClient interface {
+ Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
+ Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error)
+}
+
+func setupDirectories(crunchtmpdir, taskUUID string, keepTmp bool) (tmpdir, outdir string, err error) {
+ tmpdir = crunchtmpdir + "/tmpdir"
+ err = os.Mkdir(tmpdir, 0700)
if err != nil {
- return "", err
+ return "", "", err
}
- err = os.Mkdir("tmpdir", 0700)
- if err != nil {
- return "", err
+ if keepTmp {
+ outdir = os.Getenv("TASK_KEEPMOUNT_TMP")
+ } else {
+ outdir = crunchtmpdir + "/outdir"
+ err = os.Mkdir(outdir, 0700)
+ if err != nil {
+ return "", "", err
+ }
}
- err = os.Mkdir(taskUuid, 0700)
- if err != nil {
- return "", err
+ return tmpdir, outdir, nil
+}
+
+func checkOutputFilename(outdir, fn string) error {
+ if strings.HasPrefix(fn, "/") || strings.HasSuffix(fn, "/") {
+ return fmt.Errorf("Path must not start or end with '/'")
}
+ if strings.Index("../", fn) != -1 {
+ return fmt.Errorf("Path must not contain '../'")
+ }
+
+ sl := strings.LastIndex(fn, "/")
+ if sl != -1 {
+ os.MkdirAll(outdir+"/"+fn[0:sl], 0777)
+ }
+ return nil
+}
- os.Chdir(taskUuid)
+func copyFile(dst, src string) error {
+ in, err := os.Open(src)
if err != nil {
- return "", err
+ return err
}
+ defer in.Close()
- outdir, err = os.Getwd()
+ out, err := os.Create(dst)
if err != nil {
- return "", err
+ return err
}
+ defer out.Close()
- return outdir, nil
+ _, err = io.Copy(out, in)
+ return err
}
-func setupCommand(cmd *exec.Cmd, taskp TaskDef, keepmount, outdir string) error {
- var err error
-
- if taskp.vwd != nil {
- for k, v := range taskp.vwd {
- os.Symlink(keepmount+"/"+v, outdir+"/"+k)
+func setupCommand(cmd *exec.Cmd, taskp TaskDef, outdir string, replacements map[string]string) (stdin, stdout, stderr string, err error) {
+ if taskp.Vwd != nil {
+ for k, v := range taskp.Vwd {
+ v = substitute(v, replacements)
+ err = checkOutputFilename(outdir, k)
+ if err != nil {
+ return "", "", "", err
+ }
+ if taskp.KeepTmpOutput {
+ err = copyFile(v, outdir+"/"+k)
+ } else {
+ err = os.Symlink(v, outdir+"/"+k)
+ }
+ if err != nil {
+ return "", "", "", err
+ }
}
}
- if taskp.stdin != "" {
+ if taskp.Stdin != "" {
// Set up stdin redirection
- cmd.Stdin, err = os.Open(keepmount + "/" + taskp.stdin)
+ stdin = substitute(taskp.Stdin, replacements)
+ cmd.Stdin, err = os.Open(stdin)
if err != nil {
- return err
+ return "", "", "", err
}
}
- if taskp.stdout != "" {
+ if taskp.Stdout != "" {
+ err = checkOutputFilename(outdir, taskp.Stdout)
+ if err != nil {
+ return "", "", "", err
+ }
// Set up stdout redirection
- cmd.Stdout, err = os.Create(outdir + "/" + taskp.stdout)
+ stdout = outdir + "/" + taskp.Stdout
+ cmd.Stdout, err = os.Create(stdout)
if err != nil {
- return err
+ return "", "", "", err
}
} else {
cmd.Stdout = os.Stdout
}
- if taskp.env != nil {
+ if taskp.Stderr != "" {
+ err = checkOutputFilename(outdir, taskp.Stderr)
+ if err != nil {
+ return "", "", "", err
+ }
+ // Set up stderr redirection
+ stderr = outdir + "/" + taskp.Stderr
+ cmd.Stderr, err = os.Create(stderr)
+ if err != nil {
+ return "", "", "", err
+ }
+ } else {
+ cmd.Stderr = os.Stderr
+ }
+
+ if taskp.Env != nil {
// Set up subprocess environment
cmd.Env = os.Environ()
- for k, v := range taskp.env {
+ for k, v := range taskp.Env {
+ v = substitute(v, replacements)
cmd.Env = append(cmd.Env, k+"="+v)
}
}
- return nil
+ return stdin, stdout, stderr, nil
}
-func setupSignals(cmd *exec.Cmd) {
- // Set up signal handlers
- // Forward SIGINT, SIGTERM and SIGQUIT to inner process
+// Set up signal handlers. Go sends signal notifications to a "signal
+// channel".
+func setupSignals(cmd *exec.Cmd) chan os.Signal {
sigChan := make(chan os.Signal, 1)
- go func(sig <-chan os.Signal) {
- catch := <-sig
- if cmd.Process != nil {
- cmd.Process.Signal(catch)
- }
- }(sigChan)
signal.Notify(sigChan, syscall.SIGTERM)
signal.Notify(sigChan, syscall.SIGINT)
signal.Notify(sigChan, syscall.SIGQUIT)
+ return sigChan
}
func inCodes(code int, codes []int) bool {
const TASK_TEMPFAIL = 111
-type TempFail struct{ InnerError error }
+type TempFail struct{ error }
type PermFail struct{}
-func (s TempFail) Error() string {
- return s.InnerError.Error()
-}
-
func (s PermFail) Error() string {
return "PermFail"
}
-func runner(api arvadosclient.IArvadosClient,
+func substitute(inp string, subst map[string]string) string {
+ for k, v := range subst {
+ inp = strings.Replace(inp, k, v, -1)
+ }
+ return inp
+}
+
+func getKeepTmp(outdir string) (manifest string, err error) {
+ fn, err := os.Open(outdir + "/" + ".arvados#collection")
+ if err != nil {
+ return "", err
+ }
+ defer fn.Close()
+
+ buf, err := ioutil.ReadAll(fn)
+ if err != nil {
+ return "", err
+ }
+ collection := arvados.Collection{}
+ err = json.Unmarshal(buf, &collection)
+ return collection.ManifestText, err
+}
+
+func runner(api IArvadosClient,
kc IKeepClient,
- jobUuid, taskUuid, tmpdir, keepmount string,
+ jobUUID, taskUUID, crunchtmpdir, keepmount string,
jobStruct Job, taskStruct Task) error {
var err error
- taskp := taskStruct.parameters
+ taskp := taskStruct.Parameters
// If this is task 0 and there are multiple tasks, dispatch subtasks
// and exit.
- if taskStruct.sequence == 0 {
- if len(jobStruct.script_parameters.tasks) == 1 {
- taskp = jobStruct.script_parameters.tasks[0]
+ if taskStruct.Sequence == 0 {
+ if len(jobStruct.ScriptParameters.Tasks) == 1 {
+ taskp = jobStruct.ScriptParameters.Tasks[0]
} else {
- for _, task := range jobStruct.script_parameters.tasks {
+ for _, task := range jobStruct.ScriptParameters.Tasks {
err := api.Create("job_tasks",
map[string]interface{}{
- "job_task": Task{job_uuid: jobUuid,
- created_by_job_task_uuid: taskUuid,
- sequence: 1,
- parameters: task}},
+ "job_task": Task{
+ JobUUID: jobUUID,
+ CreatedByJobTaskUUID: taskUUID,
+ Sequence: 1,
+ Parameters: task}},
nil)
if err != nil {
return TempFail{err}
}
}
- err = api.Update("job_tasks", taskUuid,
+ err = api.Update("job_tasks", taskUUID,
map[string]interface{}{
- "job_task": Task{
- output: "",
- success: true,
- progress: 1.0}},
+ "job_task": map[string]interface{}{
+ "output": "",
+ "success": true,
+ "progress": 1.0}},
nil)
return nil
}
}
- // Set up subprocess
- cmd := exec.Command(taskp.commands[0], taskp.commands[1:]...)
-
- var outdir string
- outdir, err = setupDirectories(tmpdir, taskUuid)
+ var tmpdir, outdir string
+ tmpdir, outdir, err = setupDirectories(crunchtmpdir, taskUUID, taskp.KeepTmpOutput)
if err != nil {
return TempFail{err}
}
+ replacements := map[string]string{
+ "$(task.tmpdir)": tmpdir,
+ "$(task.outdir)": outdir,
+ "$(task.keep)": keepmount}
+
+ log.Printf("crunchrunner: $(task.tmpdir)=%v", tmpdir)
+ log.Printf("crunchrunner: $(task.outdir)=%v", outdir)
+ log.Printf("crunchrunner: $(task.keep)=%v", keepmount)
+
+ // Set up subprocess
+ for k, v := range taskp.Command {
+ taskp.Command[k] = substitute(v, replacements)
+ }
+
+ cmd := exec.Command(taskp.Command[0], taskp.Command[1:]...)
+
cmd.Dir = outdir
- err = setupCommand(cmd, taskp, keepmount, outdir)
+ var stdin, stdout, stderr string
+ stdin, stdout, stderr, err = setupCommand(cmd, taskp, outdir, replacements)
if err != nil {
return err
}
- setupSignals(cmd)
-
// Run subprocess and wait for it to complete
- log.Printf("Running %v", cmd.Args)
+ if stdin != "" {
+ stdin = " < " + stdin
+ }
+ if stdout != "" {
+ stdout = " > " + stdout
+ }
+ if stderr != "" {
+ stderr = " 2> " + stderr
+ }
+ log.Printf("Running %v%v%v%v", cmd.Args, stdin, stdout, stderr)
+
+ var caughtSignal os.Signal
+ sigChan := setupSignals(cmd)
+
+ err = cmd.Start()
+ if err != nil {
+ signal.Stop(sigChan)
+ return TempFail{err}
+ }
+
+ finishedSignalNotify := make(chan struct{})
+ go func(sig <-chan os.Signal) {
+ for sig := range sig {
+ caughtSignal = sig
+ cmd.Process.Signal(caughtSignal)
+ }
+ close(finishedSignalNotify)
+ }(sigChan)
- err = cmd.Run()
+ err = cmd.Wait()
+ signal.Stop(sigChan)
+
+ close(sigChan)
+ <-finishedSignalNotify
+
+ if caughtSignal != nil {
+ log.Printf("Caught signal %v", caughtSignal)
+ return PermFail{}
+ }
if err != nil {
// Run() returns ExitError on non-zero exit code, but we handle
}
}
- const success = 1
- const permfail = 2
- const tempfail = 2
- var status int
+ var success bool
exitCode := cmd.ProcessState.Sys().(syscall.WaitStatus).ExitStatus()
log.Printf("Completed with exit code %v", exitCode)
- if inCodes(exitCode, taskp.successCodes) {
- status = success
- } else if inCodes(exitCode, taskp.permanentFailCodes) {
- status = permfail
- } else if inCodes(exitCode, taskp.temporaryFailCodes) {
- return TempFail{nil}
- } else if cmd.ProcessState.Success() {
- status = success
+ if inCodes(exitCode, taskp.PermanentFailCodes) {
+ success = false
+ } else if inCodes(exitCode, taskp.TemporaryFailCodes) {
+ return TempFail{fmt.Errorf("Process tempfail with exit code %v", exitCode)}
+ } else if inCodes(exitCode, taskp.SuccessCodes) || cmd.ProcessState.Success() {
+ success = true
} else {
- status = permfail
+ success = false
}
// Upload output directory
- manifest, err := WriteTree(kc, outdir)
+ var manifest string
+ if taskp.KeepTmpOutput {
+ manifest, err = getKeepTmp(outdir)
+ } else {
+ manifest, err = WriteTree(kc, outdir)
+ }
if err != nil {
return TempFail{err}
}
// Set status
- err = api.Update("job_tasks", taskUuid,
+ err = api.Update("job_tasks", taskUUID,
map[string]interface{}{
"job_task": Task{
- output: manifest,
- success: status == success,
- progress: 1}},
+ Output: manifest,
+ Success: success,
+ Progress: 1}},
nil)
if err != nil {
return TempFail{err}
}
- if status == success {
+ if success {
return nil
} else {
return PermFail{}
}
func main() {
- syscall.Umask(0077)
-
api, err := arvadosclient.MakeArvadosClient()
if err != nil {
log.Fatal(err)
}
- jobUuid := os.Getenv("JOB_UUID")
- taskUuid := os.Getenv("TASK_UUID")
+ jobUUID := os.Getenv("JOB_UUID")
+ taskUUID := os.Getenv("TASK_UUID")
tmpdir := os.Getenv("TASK_WORK")
keepmount := os.Getenv("TASK_KEEPMOUNT")
var jobStruct Job
var taskStruct Task
- err = api.Get("jobs", jobUuid, nil, &jobStruct)
+ err = api.Get("jobs", jobUUID, nil, &jobStruct)
if err != nil {
log.Fatal(err)
}
- err = api.Get("job_tasks", taskUuid, nil, &taskStruct)
+ err = api.Get("job_tasks", taskUUID, nil, &taskStruct)
if err != nil {
log.Fatal(err)
}
var kc IKeepClient
- kc, err = keepclient.MakeKeepClient(&api)
- err = runner(api, kc, jobUuid, taskUuid, tmpdir, keepmount, jobStruct, taskStruct)
+ kc, err = keepclient.MakeKeepClient(api)
+ if err != nil {
+ log.Fatal(err)
+ }
+
+ syscall.Umask(0022)
+ err = runner(api, kc, jobUUID, taskUUID, tmpdir, keepmount, jobStruct, taskStruct)
if err == nil {
os.Exit(0)
projects / arvados.git / blobdiff