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task.go
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task.go
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package core
import (
"errors"
"fmt"
"path"
"reflect"
"os"
"path/filepath"
"regexp"
"strings"
"time"
"github.com/MG-RAST/AWE/lib/conf"
"github.com/MG-RAST/AWE/lib/core/cwl"
"github.com/MG-RAST/AWE/lib/logger"
"github.com/MG-RAST/AWE/lib/rwmutex"
shock "github.com/MG-RAST/go-shock-client"
"github.com/davecgh/go-spew/spew"
"github.com/mitchellh/mapstructure"
)
// hierachy (in ideal case without errors):
// 1. TASK_STAT_INIT
// 2. TASK_STAT_PENDING
// 3. TASK_STAT_READY
// 4. TASK_STAT_QUEUED
// 5. TASK_STAT_INPROGRESS
// 6. TASK_STAT_COMPLETED
const (
TASK_STAT_INIT = "init" // initial state on creation of a task
TASK_STAT_PENDING = "pending" // a task that wants to be enqueued (but dependent tasks are not complete)
TASK_STAT_READY = "ready" // a task ready to be enqueued (all dependent tasks are complete , but workunits habe not yet been created)
TASK_STAT_QUEUED = "queued" // a task for which workunits have been created/queued
TASK_STAT_INPROGRESS = "in-progress" // a first workunit has been checkout (this does not guarantee a workunit is running right now)
TASK_STAT_SUSPEND = "suspend"
TASK_STAT_FAILED = "failed" // deprecated ?
TASK_STAT_FAILED_PERMANENT = "failed-permanent" // on exit code 42
TASK_STAT_COMPLETED = "completed"
TASK_STAT_SKIPPED = "user_skipped" // deprecated
TASK_STAT_FAIL_SKIP = "skipped" // deprecated
TASK_STAT_PASSED = "passed" // deprecated ?
)
var TASK_STATS_RESET = []string{TASK_STAT_QUEUED, TASK_STAT_INPROGRESS, TASK_STAT_SUSPEND}
const (
TASK_TYPE_UNKNOWN = ""
TASK_TYPE_SCATTER = "scatter"
//TASK_TYPE_WORKFLOW = "workflow"
TASK_TYPE_NORMAL = "normal"
)
// Scatter
// A task of type "scatter" generates multiple scatter children.
// List of children for a scatter task are stored in field "ScatterChildren"
// Each Scatter child points to its Scatter parent
// Scatter child outputs do not go into context object, they only go to scatter parent output array !
type TaskRaw struct {
rwmutex.RWMutex `bson:"-" json:"-" mapstructure:"-"`
Task_Unique_Identifier `bson:",inline" mapstructure:",squash"`
Id string `bson:"taskid" json:"taskid" mapstructure:"taskid"` // old-style
TaskType string `bson:"task_type" json:"task_type" mapstructure:"task_type"`
Info *Info `bson:"-" json:"-" mapstructure:"-"` // this is just a pointer to the job.Info
Cmd *Command `bson:"cmd" json:"cmd" mapstructure:"cmd"`
Partition *PartInfo `bson:"partinfo" json:"-" mapstructure:"partinfo"`
DependsOn []string `bson:"dependsOn" json:"dependsOn" mapstructure:"dependsOn"` // only needed if dependency cannot be inferred from Input.Origin
TotalWork int `bson:"totalwork" json:"totalwork" mapstructure:"totalwork"`
MaxWorkSize int `bson:"maxworksize" json:"maxworksize" mapstructure:"maxworksize"`
RemainWork int `bson:"remainwork" json:"remainwork" mapstructure:"remainwork"`
ResetTask bool `bson:"resettask" json:"-" mapstructure:"resettask"` // trigged by function - resume, recompute, resubmit
State string `bson:"state" json:"state" mapstructure:"state"`
CreatedDate time.Time `bson:"createdDate" json:"createddate" mapstructure:"createdDate"`
StartedDate time.Time `bson:"startedDate" json:"starteddate" mapstructure:"startedDate"`
CompletedDate time.Time `bson:"completedDate" json:"completeddate" mapstructure:"completedDate"`
ComputeTime int `bson:"computetime" json:"computetime" mapstructure:"computetime"`
UserAttr map[string]interface{} `bson:"userattr" json:"userattr" mapstructure:"userattr"`
ClientGroups string `bson:"clientgroups" json:"clientgroups" mapstructure:"clientgroups"`
WorkflowStep *cwl.WorkflowStep `bson:"workflowStep" json:"workflowStep" mapstructure:"workflowStep"` // CWL-only
StepOutputInterface interface{} `bson:"stepOutput" json:"stepOutput" mapstructure:"stepOutput"` // CWL-only
StepInput *cwl.Job_document `bson:"-" json:"-" mapstructure:"-"` // CWL-only
StepOutput *cwl.Job_document `bson:"-" json:"-" mapstructure:"-"` // CWL-only
//Scatter_task bool `bson:"scatter_task" json:"scatter_task" mapstructure:"scatter_task"` // CWL-only, indicates if this is a scatter_task TODO: compare with TaskType ?
Scatter_parent *Task_Unique_Identifier `bson:"scatter_parent" json:"scatter_parent" mapstructure:"scatter_parent"` // CWL-only, points to scatter parent
ScatterChildren []string `bson:"scatterChildren" json:"scatterChildren" mapstructure:"scatterChildren"` // use simple TaskName , CWL-only, list of all children in a subworkflow task
ScatterChildren_ptr []*Task `bson:"-" json:"-" mapstructure:"-"` // caching only, CWL-only
Finalizing bool `bson:"-" json:"-" mapstructure:"-"` // CWL-only, a lock mechanism for subworkflows and scatter tasks
CwlVersion cwl.CWLVersion `bson:"cwlVersion,omitempty" mapstructure:"cwlVersion,omitempty" mapstructure:"cwlVersion,omitempty"` // CWL-only
WorkflowInstanceId string `bson:"workflow_instance_id" json:"workflow_instance_id" mapstructure:"workflow_instance_id"` // CWL-only
job *Job `bson:"-" mapstructure:"-"` // caching only
NotReadyReason string `bson:"-" json:"notReadyReason" mapstructure:"-"`
//WorkflowParent *Task_Unique_Identifier `bson:"workflow_parent" json:"workflow_parent" mapstructure:"workflow_parent"` // CWL-only parent that created subworkflow
}
type Task struct {
TaskRaw `bson:",inline" mapstructure:",squash"`
Inputs []*IO `bson:"inputs" json:"inputs" mapstructure:"inputs"`
Outputs []*IO `bson:"outputs" json:"outputs" mapstructure:"outputs"`
Predata []*IO `bson:"predata" json:"predata" mapstructure:"predata"`
Comment string
}
// Deprecated JobDep struct uses deprecated TaskDep struct which uses the deprecated IOmap. Maintained for backwards compatibility.
// Jobs that cannot be parsed into the Job struct, but can be parsed into the JobDep struct will be translated to the new Job struct.
// (=deprecated=)
type TaskDep struct {
TaskRaw `bson:",inline"`
Inputs IOmap `bson:"inputs" json:"inputs"`
Outputs IOmap `bson:"outputs" json:"outputs"`
Predata IOmap `bson:"predata" json:"predata"`
}
type TaskLog struct {
Id string `bson:"taskid" json:"taskid"`
State string `bson:"state" json:"state"`
TotalWork int `bson:"totalwork" json:"totalwork"`
CompletedDate time.Time `bson:"completedDate" json:"completeddate"`
Workunits []*WorkLog `bson:"workunits" json:"workunits"`
}
func NewTaskRaw(task_id Task_Unique_Identifier, info *Info) (tr *TaskRaw, err error) {
logger.Debug(3, "task_id: %s", task_id)
logger.Debug(3, "task_id.JobId: %s", task_id.JobId)
logger.Debug(3, "task_id.TaskName: %s", task_id.TaskName)
var task_str string
task_str, err = task_id.String()
if err != nil {
err = fmt.Errorf("() task.String returned: %s", err.Error())
return
}
tr = &TaskRaw{
Task_Unique_Identifier: task_id,
Id: task_str,
Info: info,
Cmd: &Command{},
Partition: nil,
DependsOn: []string{},
}
return
}
func (task *TaskRaw) InitRaw(job *Job, job_id string) (changed bool, err error) {
changed = false
if len(task.Id) == 0 {
err = errors.New("(InitRaw) empty taskid")
return
}
//job_id := job.ID
if job_id == "" {
err = fmt.Errorf("(InitRaw) job_id empty")
return
}
if task.JobId == "" {
task.JobId = job_id
changed = true
}
//logger.Debug(3, "task.TaskName A: %s", task.TaskName)
job_prefix := job_id + "_"
if len(task.Id) > 0 && (!strings.HasPrefix(task.Id, job_prefix)) {
task.TaskName = task.Id
changed = true
err = fmt.Errorf("(InitRaw) A) broken task? %s", job_id)
return
}
//logger.Debug(3, "task.TaskName B: %s", task.TaskName)
//if strings.HasSuffix(task.TaskName, "ERROR") {
// err = fmt.Errorf("(InitRaw) taskname is error")
// return
//}
if task.TaskName == "" && strings.HasPrefix(task.Id, job_prefix) {
var tid Task_Unique_Identifier
tid, err = New_Task_Unique_Identifier_FromString(task.Id)
if err != nil {
err = fmt.Errorf("(InitRaw) New_Task_Unique_Identifier_FromString returned: %s", err.Error())
return
}
task.Task_Unique_Identifier = tid
err = fmt.Errorf("(InitRaw) B) broken task? %s", job_id)
return
}
var task_str string
task_str, err = task.String()
if err != nil {
err = fmt.Errorf("(InitRaw) task.String returned: %s", err.Error())
return
}
task.RWMutex.Init("task_" + task_str)
// job_id is missing and task_id is only a number (e.g. on submission of old-style AWE)
if task.TaskName == "" {
err = fmt.Errorf("(InitRaw) task.TaskName empty")
return
}
if task.Id != task_str {
task.Id = task_str
changed = true
}
if task.State == "" {
task.State = TASK_STAT_INIT
changed = true
}
if job != nil {
if job.Info == nil {
err = fmt.Errorf("(InitRaw) job.Info empty")
return
}
task.Info = job.Info
}
if task.State != TASK_STAT_COMPLETED {
if task.RemainWork != task.TotalWork {
task.RemainWork = task.TotalWork
changed = true
}
}
if len(task.Cmd.Environ.Private) > 0 {
task.Cmd.HasPrivateEnv = true
}
//if strings.HasPrefix(task.Id, task.JobId+"_") {
// task.Id = strings.TrimPrefix(task.Id, task.JobId+"_")
// changed = true
//}
//if strings.HasPrefix(task.Id, "_") {
// task.Id = strings.TrimPrefix(task.Id, "_")
// changed = true
//}
if job == nil {
err = fmt.Errorf("(InitRaw) job is nil")
return
}
var context *cwl.WorkflowContext
if task.StepOutputInterface != nil {
context = job.WorkflowContext
task.StepOutput, err = cwl.NewJob_documentFromNamedTypes(task.StepOutputInterface, context)
if err != nil {
err = fmt.Errorf("(InitRaw) cwl.NewJob_documentFromNamedTypes returned: %s", err.Error())
return
}
}
// if CwlVersion != "" {
// CwlVersion := context.CwlVersion
// if task.CwlVersion != CwlVersion {
// task.CwlVersion = CwlVersion
// }
// }
if task.WorkflowStep != nil {
if job != nil {
if job.WorkflowContext == nil {
err = fmt.Errorf("(InitRaw) job.WorkflowContext == nil")
return
}
err = task.WorkflowStep.Init(job.WorkflowContext)
if err != nil {
err = fmt.Errorf("(InitRaw) task.WorkflowStep.Init returned: %s", err.Error())
return
}
}
}
return
}
// this function prevents a dead-lock when a sub-workflow task finalizes
func (task *TaskRaw) Finalize() (ok bool, err error) {
err = task.LockNamed("Finalize")
if err != nil {
return
}
defer task.Unlock()
if task.Finalizing {
// somebody else already flipped the bit
ok = false
return
}
task.Finalizing = true
ok = true
return
}
func IsValidUUID(uuid string) bool {
if len(uuid) != 36 {
return false
}
r := regexp.MustCompile("^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-4[a-fA-F0-9]{3}-[8|9|aA|bB][a-fA-F0-9]{3}-[a-fA-F0-9]{12}$")
return r.MatchString(uuid)
}
// populate DependsOn
func (task *Task) CollectDependencies() (changed bool, err error) {
deps := make(map[Task_Unique_Identifier]bool)
deps_changed := false
jobid, err := task.GetJobId()
if err != nil {
return
}
if jobid == "" {
err = fmt.Errorf("(CollectDependencies) jobid is empty")
return
}
job_prefix := jobid + "_"
// collect explicit dependencies
for _, deptask := range task.DependsOn {
if deptask == "" {
deps_changed = true
continue
}
if !strings.HasPrefix(deptask, job_prefix) {
deptask = job_prefix + deptask
deps_changed = true
} else {
deptask_suffix := strings.TrimPrefix(deptask, job_prefix)
if deptask_suffix == "" {
deps_changed = true
continue
}
}
t, yerr := New_Task_Unique_Identifier_FromString(deptask)
if yerr != nil {
err = fmt.Errorf("(CollectDependencies) Cannot parse entry in DependsOn: %s", yerr.Error())
return
}
if t.TaskName == "" {
// this is to fix a bug
deps_changed = true
continue
}
deps[t] = true
}
for _, input := range task.Inputs {
deptask := input.Origin
if deptask == "" {
deps_changed = true
continue
}
if !strings.HasPrefix(deptask, job_prefix) {
deptask = job_prefix + deptask
deps_changed = true
}
t, yerr := New_Task_Unique_Identifier_FromString(deptask)
if yerr != nil {
err = fmt.Errorf("(CollectDependencies) Cannot parse Origin entry in Input: %s", yerr.Error())
return
}
_, ok := deps[t]
if !ok {
// this was not yet in deps
deps[t] = true
deps_changed = true
}
}
// write all dependencies if different from before
if deps_changed {
task.DependsOn = []string{}
for deptask, _ := range deps {
var dep_task_str string
dep_task_str, err = deptask.String()
if err != nil {
err = fmt.Errorf("(CollectDependencies) dep_task.String returned: %s", err.Error())
return
}
task.DependsOn = append(task.DependsOn, dep_task_str)
}
changed = true
}
return
}
// argument job is optional, but recommended
func (task *Task) Init(job *Job, job_id string) (changed bool, err error) {
changed, err = task.InitRaw(job, job_id)
if err != nil {
return
}
dep_changes, err := task.CollectDependencies()
if err != nil {
return
}
if dep_changes {
changed = true
}
// set node / host / url for files
for _, io := range task.Inputs {
if io.Node == "" {
io.Node = "-"
}
_, err = io.DataUrl()
if err != nil {
return
}
logger.Debug(2, "inittask input: host="+io.Host+", node="+io.Node+", url="+io.Url)
}
for _, io := range task.Outputs {
if io.Node == "" {
io.Node = "-"
}
_, err = io.DataUrl()
if err != nil {
return
}
logger.Debug(2, "inittask output: host="+io.Host+", node="+io.Node+", url="+io.Url)
}
for _, io := range task.Predata {
if io.Node == "" {
io.Node = "-"
}
_, err = io.DataUrl()
if err != nil {
return
}
// predata IO can not be empty
if (io.Url == "") && (io.Node == "-") {
err = errors.New("Invalid IO, required fields url or host / node missing")
return
}
logger.Debug(2, "inittask predata: host="+io.Host+", node="+io.Node+", url="+io.Url)
}
err = task.setTokenForIO(false)
if err != nil {
return
}
return
}
// task_id_str is without prefix yet
func NewTask(job *Job, workflow_instance_id string, task_id_str string) (t *Task, err error) {
fmt.Printf("(NewTask) new task: %s %s/%s\n", job.ID, workflow_instance_id, task_id_str)
if task_id_str == "" {
err = fmt.Errorf("(NewTask) task_id is empty")
return
}
if strings.HasPrefix(task_id_str, "#main") {
err = fmt.Errorf("(NewTask) task_id_str prefix wrong: %s", task_id_str)
return
}
if job.IsCWL {
if task_id_str != "#main" {
if !strings.HasPrefix(workflow_instance_id, "#main") {
err = fmt.Errorf("(NewTask) workflow_instance_id has not #main prefix: %s", workflow_instance_id)
return
}
}
}
if job.ID == "" {
err = fmt.Errorf("(NewTask) jobid is empty!")
return
}
if strings.HasSuffix(task_id_str, "/") {
err = fmt.Errorf("(NewTask) Suffix in task_id not ok %s", task_id_str)
return
}
task_id_str = strings.TrimSuffix(task_id_str, "/")
//workflow = strings.TrimSuffix(workflow, "/")
var job_global_task_id_str string
if job.IsCWL {
job_global_task_id_str = workflow_instance_id + "/" + task_id_str
} else {
job_global_task_id_str = task_id_str
}
var tui Task_Unique_Identifier
tui, err = New_Task_Unique_Identifier(job.ID, job_global_task_id_str)
if err != nil {
err = fmt.Errorf("(NewTask) New_Task_Unique_Identifier returns: %s", err.Error())
return
}
var tr *TaskRaw
tr, err = NewTaskRaw(tui, job.Info)
if err != nil {
err = fmt.Errorf("(NewTask) NewTaskRaw returns: %s", err.Error())
return
}
t = &Task{
TaskRaw: *tr,
Inputs: []*IO{},
Outputs: []*IO{},
Predata: []*IO{},
}
t.TaskRaw.WorkflowInstanceId = workflow_instance_id
//if workflow_instance_id == "" {
// err = fmt.Errorf("(NewTask) workflow_instance_id empty")
// return
//}
return
}
func (task *Task) GetOutputs() (outputs []*IO, err error) {
outputs = []*IO{}
lock, err := task.RLockNamed("GetOutputs")
if err != nil {
return
}
defer task.RUnlockNamed(lock)
for _, output := range task.Outputs {
outputs = append(outputs, output)
}
return
}
func (task *Task) GetOutput(filename string) (output *IO, err error) {
lock, err := task.RLockNamed("GetOutput")
if err != nil {
return
}
defer task.RUnlockNamed(lock)
for _, io := range task.Outputs {
if io.FileName == filename {
output = io
return
}
}
err = fmt.Errorf("Output %s not found", filename)
return
}
func (task *TaskRaw) SetScatterChildren(qm *ServerMgr, scatterChildren []string, writelock bool) (err error) {
if writelock {
err = task.LockNamed("SetScatterChildren")
if err != nil {
return
}
defer task.Unlock()
}
if task.WorkflowInstanceId == "" {
err = dbUpdateJobTaskField(task.JobId, task.WorkflowInstanceId, task.Id, "scatterChildren", scatterChildren)
if err != nil {
err = fmt.Errorf("(SetScatterChildren) dbUpdateJobTaskField returned: %s", err.Error())
return
}
} else {
err = dbUpdateTaskField(task.JobId, task.WorkflowInstanceId, task.Id, "scatterChildren", scatterChildren)
if err != nil {
err = fmt.Errorf("(SetScatterChildren) dbUpdateTaskField returned: %s", err.Error())
return
}
}
task.ScatterChildren = scatterChildren
return
}
func (task *TaskRaw) GetScatterChildren(wi *WorkflowInstance, qm *ServerMgr) (children []*Task, err error) {
lock, err := task.RLockNamed("GetScatterChildren")
if err != nil {
return
}
defer task.RUnlockNamed(lock)
if task.ScatterChildren_ptr != nil {
children = task.ScatterChildren_ptr // should make a copy....
return
}
children = []*Task{}
for _, task_id_str := range task.ScatterChildren {
var child *Task
var ok bool
child, ok, err = wi.GetTaskByName(task_id_str, true)
if err != nil {
err = fmt.Errorf("(GetScatterChildren) wi.GetTaskByName returned: %s", err.Error())
return
}
if !ok {
err = fmt.Errorf("(GetScatterChildren) child task %s not found in TaskMap", task_id_str)
return
}
children = append(children, child)
}
task.ScatterChildren_ptr = children
return
}
func (task *TaskRaw) GetWorkflowInstance() (wi *WorkflowInstance, ok bool, err error) {
var job *Job
job, err = task.GetJob()
if err != nil {
err = fmt.Errorf("(GetWorkflowInstance) task.GetJob returned: %s", err.Error())
return
}
wi_id := task.WorkflowInstanceId
wi, ok, err = job.GetWorkflowInstance(wi_id, true)
if err != nil {
err = fmt.Errorf("(GetWorkflowInstance) job.GetWorkflowInstance returned: %s", err.Error())
return
}
if !ok {
err = fmt.Errorf("(GetWorkflowInstance) job.GetWorkflowInstance did not find: %s", wi_id)
return
}
return
}
// returns name of Parent (without jobid)
// func (task *TaskRaw) GetWorkflowParent() (p Task_Unique_Identifier, ok bool, err error) {
// lock, err := task.RLockNamed("GetParent")
// if err != nil {
// return
// }
// defer task.RUnlockNamed(lock)
// if task.WorkflowParent == nil {
// ok = false
// return
// }
// p = *task.WorkflowParent
// return
// }
// func (task *TaskRaw) GetWorkflowParentStr() (parent_id_str string, err error) {
// lock, err := task.RLockNamed("GetWorkflowParentStr")
// if err != nil {
// return
// }
// defer task.RUnlockNamed(lock)
// parent_id_str = ""
// if task.WorkflowParent != nil {
// parent_id_str, _ = task.WorkflowParent.String()
// }
// return
// }
func (task *TaskRaw) GetState() (state string, err error) {
lock, err := task.RLockNamed("GetState")
if err != nil {
return
}
defer task.RUnlockNamed(lock)
state = task.State
return
}
func (task *TaskRaw) GetTaskType() (type_str string, err error) {
lock, err := task.RLockNamed("GetTaskType")
if err != nil {
return
}
defer task.RUnlockNamed(lock)
type_str = task.TaskType
return
}
func (task *Task) SetTaskType(type_str string, writelock bool) (err error) {
if writelock {
err = task.LockNamed("SetTaskType")
if err != nil {
return
}
defer task.Unlock()
}
if task.WorkflowInstanceId == "" {
err = dbUpdateJobTaskString(task.JobId, task.WorkflowInstanceId, task.Id, "task_type", type_str)
if err != nil {
err = fmt.Errorf("(task/SetTaskType) dbUpdateJobTaskString returned: %s", err.Error())
return
}
} else {
err = dbUpdateTaskString(task.JobId, task.WorkflowInstanceId, task.Id, "task_type", type_str)
if err != nil {
err = fmt.Errorf("(task/SetTaskType) dbUpdateTaskString returned: %s", err.Error())
return
}
}
task.TaskType = type_str
return
}
func (task *TaskRaw) SetCreatedDate(t time.Time) (err error) {
err = task.LockNamed("SetCreatedDate")
if err != nil {
return
}
defer task.Unlock()
if task.WorkflowInstanceId == "" {
err = dbUpdateJobTaskTime(task.JobId, task.WorkflowInstanceId, task.Id, "createdDate", t)
if err != nil {
err = fmt.Errorf("(task/SetCreatedDate) dbUpdateJobTaskTime returned: %s", err.Error())
return
}
} else {
err = dbUpdateTaskTime(task.JobId, task.WorkflowInstanceId, task.Id, "createdDate", t)
if err != nil {
err = fmt.Errorf("(task/SetCreatedDate) dbUpdateTaskTime returned: %s", err.Error())
return
}
}
task.CreatedDate = t
return
}
func (task *TaskRaw) SetStartedDate(t time.Time) (err error) {
err = task.LockNamed("SetStartedDate")
if err != nil {
return
}
defer task.Unlock()
if task.WorkflowInstanceId == "" {
err = dbUpdateJobTaskTime(task.JobId, task.WorkflowInstanceId, task.Id, "startedDate", t)
if err != nil {
err = fmt.Errorf("(task/SetStartedDate) dbUpdateJobTaskTime returned: %s", err.Error())
return
}
} else {
err = dbUpdateTaskTime(task.JobId, task.WorkflowInstanceId, task.Id, "startedDate", t)
if err != nil {
err = fmt.Errorf("(task/SetStartedDate) dbUpdateTaskTime returned: %s", err.Error())
return
}
}
task.StartedDate = t
return
}
func (task *TaskRaw) SetCompletedDate(t time.Time, lock bool) (err error) {
if lock {
err = task.LockNamed("SetCompletedDate")
if err != nil {
return
}
defer task.Unlock()
}
if task.WorkflowInstanceId == "" {
err = dbUpdateJobTaskTime(task.JobId, task.WorkflowInstanceId, task.Id, "completedDate", t)
if err != nil {
err = fmt.Errorf("(task/SetCompletedDate) dbUpdateJobTaskTime returned: %s", err.Error())
return
}
} else {
err = dbUpdateTaskTime(task.JobId, task.WorkflowInstanceId, task.Id, "completedDate", t)
if err != nil {
err = fmt.Errorf("(task/SetCompletedDate) dbUpdateTaskTime returned: %s", err.Error())
return
}
}
task.CompletedDate = t
return
}
func (task *TaskRaw) SetStepOutput(jd *cwl.Job_document, lock bool) (err error) {
if lock {
err = task.LockNamed("SetStepOutput")
if err != nil {
return
}
defer task.Unlock()
}
if task.WorkflowInstanceId == "" {
err = dbUpdateJobTaskField(task.JobId, task.WorkflowInstanceId, task.Id, "stepOutput", *jd)
if err != nil {
err = fmt.Errorf("(task/SetStepOutput) dbUpdateJobTaskField returned: %s", err.Error())
return
}
} else {
err = dbUpdateTaskField(task.JobId, task.WorkflowInstanceId, task.Id, "stepOutput", *jd)
if err != nil {
err = fmt.Errorf("(task/SetStepOutput) dbUpdateTaskField returned: %s", err.Error())
return
}
}
task.StepOutput = jd
task.StepOutputInterface = jd
return
}
// only for debugging purposes
func (task *TaskRaw) GetStateNamed(name string) (state string, err error) {
lock, err := task.RLockNamed("GetState/" + name)
if err != nil {
return
}
defer task.RUnlockNamed(lock)
state = task.State
return
}
func (task *TaskRaw) GetId(me string) (id Task_Unique_Identifier, err error) {
lock, err := task.RLockNamed("GetId:" + me)
if err != nil {
return
}
defer task.RUnlockNamed(lock)
id = task.Task_Unique_Identifier
return
}
func (task *TaskRaw) GetJobId() (id string, err error) {
lock, err := task.RLockNamed("GetJobId")
if err != nil {
return
}
defer task.RUnlockNamed(lock)
id = task.JobId
return
}
func (task *TaskRaw) GetJob() (job *Job, err error) {
lock, err := task.RLockNamed("GetJob")
if err != nil {
return
}
defer task.RUnlockNamed(lock)
if task.job != nil {
job = task.job
return
}
jobid := task.JobId
job, err = GetJob(jobid)
if err != nil {
err = fmt.Errorf("(TaskRaw/GetJob) global GetJob returned: %s", err.Error())
return
}
// this is writing while we just have a readlock, not so nice
task.job = job
return
}
// also updates wi.RemainTasks, task.SetCompletedDate
func (task *TaskRaw) SetState(wi *WorkflowInstance, new_state string, writeLock bool) (err error) {
if writeLock {
err = task.LockNamed("SetState")
if err != nil {
return
}
defer task.Unlock()
}
old_state := task.State
taskid := task.Id
jobid := task.JobId
if jobid == "" {
err = fmt.Errorf("task %s has no job id", taskid)
return
}
if old_state == new_state {
return
}
if task.WorkflowInstanceId == "" {
err = dbUpdateJobTaskString(jobid, task.WorkflowInstanceId, taskid, "state", new_state)
if err != nil {
err = fmt.Errorf("(TaskRaw/SetState) dbUpdateJobTaskString returned: %s", err.Error())
return
}
} else {
err = dbUpdateTaskString(jobid, task.WorkflowInstanceId, taskid, "state", new_state)
if err != nil {
err = fmt.Errorf("(TaskRaw/SetState) dbUpdateTaskString returned: %s", err.Error())
return
}
}
logger.Debug(3, "(Task/SetState) %s new state: \"%s\" (old state \"%s\")", taskid, new_state, old_state)
task.State = new_state
if new_state == TASK_STAT_COMPLETED {
if wi != nil {
_, err = wi.IncrementRemainSteps(-1, true)
if err != nil {
err = fmt.Errorf("(task/SetState) wi.DecreaseRemainSteps returned: %s", err.Error())
return
}
}
err = task.SetCompletedDate(time.Now(), false)
if err != nil {
err = fmt.Errorf("(task/SetState) task.SetCompletedDate returned: %s", err.Error())
return
}
} else if old_state == TASK_STAT_COMPLETED {
// in case a completed task is marked as something different
//var job *Job
//job, err = GetJob(jobid)
//if err != nil {
// return
//}
//_, err = job.IncrementRemainSteps(1, "task/SetState")
//if err != nil {
// err = fmt.Errorf("(task/SetState) IncrementRemainSteps returned: %s", err.Error())
// return
//}
initTime := time.Time{}
err = task.SetCompletedDate(initTime, false)
if err != nil {
err = fmt.Errorf("(task/SetState) SetCompletedDate returned: %s", err.Error())
return
}
}
return
}
func (task *TaskRaw) GetDependsOn() (dep []string, err error) {
lock, err := task.RLockNamed("GetDependsOn")
if err != nil {
return
}
defer task.RUnlockNamed(lock)
dep = task.DependsOn
return
}
// checks and creates indices on input shock nodes if needed
func (task *Task) CreateInputIndexes() (err error) {