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workflowInstance.go
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workflowInstance.go
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package core
import (
"fmt"
"path"
"reflect"
"github.com/MG-RAST/AWE/lib/acl"
"github.com/MG-RAST/AWE/lib/core/cwl"
"github.com/MG-RAST/AWE/lib/logger"
"github.com/MG-RAST/AWE/lib/rwmutex"
"github.com/davecgh/go-spew/spew"
"github.com/mitchellh/mapstructure"
)
// WI_STAT_INIT
// state on creation of object
// add to job -> WI_STAT_PENDING
// WI_STAT_PENDING
// Unevaluated workflow_instance has steps, but not tasks or subworkflows yet
// is officially part of job
// Once workflow_instance is deemed ready -> WI_STAT_READY
// it is ready when it has input
// WI_STAT_READY
// has inputs !
// WI_STAT_QUEUED
// tasks have been created and added to TaskMap
// WI_STAT_COMPLETED
// completed.
const (
WI_STAT_INIT = "init" // initial state on creation
WI_STAT_PENDING = "pending" // wants to be enqueued but may have unresolved dependencies
WI_STAT_READY = "ready" // a task ready to be enqueued/evaluated (tasks can be enqueued)
//TASK_STAT_PENDING = "pending" // a task that wants to be enqueued
//TASK_STAT_READY = "ready" // a task ready to be enqueued
WI_STAT_QUEUED = "queued" // tasks have been created
//WI_STAT_INPROGRESS = "in-progress" // a first workunit has been checkout (this does not guarantee a workunit is running right now)
//WI_STAT_SUSPEND = "suspend"
//TASK_STAT_FAILED = "failed"
//TASK_STAT_FAILED_PERMANENT = "failed-permanent" // on exit code 42
WI_STAT_COMPLETED = "completed"
)
// Object for each subworkflow
type WorkflowInstance struct {
rwmutex.RWMutex `bson:"-" json:"-" mapstructure:"-"`
LocalId string `bson:"local_id" json:"id" mapstructure:"local_id"`
//_Id string `bson:"_id" json:"_id" mapstructure:"_id"` // unique identifier for mongo, includes jobid !
JobId string `bson:"job_id" json:"job_id" mapstructure:"job_id"`
ParentId string `bson:"parent_id" json:"parent_id" mapstructure:"parent_id"` // point to workflow_parent parent, this is not trivial duer to embedded workflows
Acl *acl.Acl `bson:"acl" json:"-"`
State string `bson:"state" json:"state" mapstructure:"state"` // this is unique identifier for the workflow instance
Workflow_Definition string `bson:"workflow_definition" json:"workflow_definition" mapstructure:"workflow_definition"` // name of the workflow this instance is derived from
Workflow *cwl.Workflow `bson:"-" json:"-" mapstructure:"-"` // just a cache for the Workflow pointer
Inputs cwl.Job_document `bson:"inputs" json:"inputs" mapstructure:"inputs"`
Outputs cwl.Job_document `bson:"outputs" json:"outputs" mapstructure:"outputs"`
Tasks []*Task `bson:"tasks" json:"tasks" mapstructure:"tasks"`
RemainSteps int `bson:"remainsteps" json:"remainsteps" mapstructure:"remainsteps"`
TotalTasks int `bson:"totaltasks" json:"totaltasks" mapstructure:"totaltasks"`
Subworkflows []string `bson:"subworkflows" json:"subworkflows" mapstructure:"subworkflows"`
ParentStep *cwl.WorkflowStep `bson:"-" json:"-" mapstructure:"-"`
//Created_by string `bson:"created_by" json:"created_by" mapstructure:"created_by"`
}
func NewWorkflowInstance(local_id string, jobid string, workflow_definition string, job *Job, parent_workflow_instance_id string) (wi *WorkflowInstance, err error) {
if jobid == "" {
err = fmt.Errorf("(NewWorkflowInstance) jobid == \"\"")
return
}
logger.Debug(3, "(NewWorkflowInstance) _local_id=%s%s, workflow_definition=%s", jobid, local_id, workflow_definition)
if job == nil {
err = fmt.Errorf("(NewWorkflowInstance) job==nil ")
return
}
wi = &WorkflowInstance{LocalId: local_id, JobId: jobid, Workflow_Definition: workflow_definition, ParentId: parent_workflow_instance_id}
wi.State = WI_STAT_INIT
_, err = wi.Init(job)
if err != nil {
err = fmt.Errorf("(NewWorkflowInstance) wi.Init returned: %s", err.Error())
return
}
if wi.Acl == nil {
err = fmt.Errorf("(NewWorkflowInstance) wi.Acl == nil , init failed ? ")
return
}
return
}
func NewWorkflowInstanceFromInterface(original interface{}, job *Job, context *cwl.WorkflowContext, do_init bool) (wi *WorkflowInstance, err error) {
original, err = cwl.MakeStringMap(original, context)
if err != nil {
return
}
switch original.(type) {
case map[string]interface{}:
original_map, ok := original.(map[string]interface{})
if !ok {
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) not a map: %s", spew.Sdump(original))
return
}
inputs_if, has_inputs := original_map["inputs"]
if has_inputs {
var inputs *cwl.Job_document
inputs, err = cwl.NewJob_documentFromNamedTypes(inputs_if, context)
if err != nil {
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) (for inputs) NewJob_document returned: %s", err.Error())
return
}
original_map["inputs"] = *inputs
}
outputs_if, has_outputs := original_map["outputs"]
if has_outputs {
var outputs *cwl.Job_document
outputs, err = cwl.NewJob_documentFromNamedTypes(outputs_if, context)
if err != nil {
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) (for outputs) NewJob_document returned: %s", err.Error())
return
}
original_map["outputs"] = *outputs
}
tasks_if, has_tasks := original_map["tasks"]
if has_tasks {
var tasks []*Task
tasks, err = NewTasksFromInterface(tasks_if, context)
if err != nil {
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) (for outputs) NewTasksFromInterface returned: %s", err.Error())
return
}
original_map["tasks"] = tasks
}
wi = &WorkflowInstance{}
err = mapstructure.Decode(original_map, wi)
if err != nil {
fmt.Println("original_map:")
spew.Dump(original_map)
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) mapstructure.Decode returned: %s", err.Error())
return
}
if do_init {
_, err = wi.Init(job)
if err != nil {
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) wi.Init returned: %s", err.Error())
return
}
}
case *WorkflowInstance:
var ok bool
wi, ok = original.(*WorkflowInstance)
if !ok {
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) type assertion problem")
return
}
if do_init {
_, err = wi.Init(job)
if err != nil {
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) wi.Init returned: %s", err.Error())
return
}
}
default:
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) type unknown, %s", reflect.TypeOf(original))
return
}
if context != nil {
for i, _ := range wi.Inputs {
inp_named := &wi.Inputs[i]
inp_id := inp_named.Id
inp_value := inp_named.Value
err = context.Add(inp_id, inp_value, "NewWorkflowInstanceFromInterface")
if err != nil {
err = fmt.Errorf("(NewWorkflowInstanceFromInterface) context.Add returned: %s", err.Error())
return
}
}
}
return
}
func NewWorkflowInstanceArrayFromInterface(original []interface{}, job *Job, context *cwl.WorkflowContext) (wis []*WorkflowInstance, err error) {
wis = []*WorkflowInstance{}
for i, _ := range original {
var wi *WorkflowInstance
wi, err = NewWorkflowInstanceFromInterface(original[i], job, context, true)
if err != nil {
err = fmt.Errorf("(NewWorkflowInstanceArrayFromInterface) NewWorkflowInstanceFromInterface returned: %s", err.Error())
return
}
wis = append(wis, wi)
}
return
}
func (wi *WorkflowInstance) AddTask(task *Task, db_sync string, write_lock bool) (err error) {
if write_lock {
err = wi.LockNamed("WorkflowInstance/AddTask")
if err != nil {
err = fmt.Errorf("(AddTask) wi.LockNamed returned: %s", err.Error())
return
}
defer wi.Unlock()
}
if task.WorkflowInstanceId == "" {
err = fmt.Errorf("(AddTask) task.WorkflowInstanceId empty")
return
}
wi.Tasks = append(wi.Tasks, task)
//wi.RemainSteps += 1
//wi.TotalTasks = len(wi.Tasks)
if db_sync == "db_sync_yes" {
err = wi.Save(false)
if err != nil {
err = fmt.Errorf("(WorkflowInstance/AddTask) wi.Save returned: %s", err.Error())
return
}
}
return
}
func (wi *WorkflowInstance) SetState(state string, db_sync string, write_lock bool) (err error) {
if write_lock {
err = wi.LockNamed("WorkflowInstance/SetState")
if err != nil {
err = fmt.Errorf("(WorkflowInstance/SetState) wi.LockNamed returned: %s", err.Error())
return
}
defer wi.Unlock()
}
wi.State = state
if db_sync == "db_sync_yes" {
wi.Save(false)
}
return
}
func (wi *WorkflowInstance) SetSubworkflows(steps []string, write_lock bool) (err error) {
if write_lock {
err = wi.LockNamed("WorkflowInstance/SetSubworkflows")
if err != nil {
err = fmt.Errorf("(WorkflowInstance/SetSubworkflows) wi.LockNamed returned: %s", err.Error())
return
}
defer wi.Unlock()
}
wi.Subworkflows = steps
wi.Save(false)
return
}
func (wi *WorkflowInstance) GetWorkflow(context *cwl.WorkflowContext) (workflow *cwl.Workflow, err error) {
workflow_def_str := wi.Workflow_Definition
if context == nil {
err = fmt.Errorf("(WorkflowInstance/GetWorkflow) context == nil")
return
}
workflow, err = context.GetWorkflow(workflow_def_str)
if err != nil {
err = fmt.Errorf("(WorkflowInstance/GetWorkflow) context.GetWorkflow returned: %s", err.Error())
return
}
return
}
// db_sync is a string because a bool would be misunderstood as a lock indicator ("db_sync_no", db_sync_yes
// func (wi *WorkflowInstance) SetTasks(tasks []*Task, db_sync string) (err error) {
// err = wi.LockNamed("WorkflowInstance/SetTasks")
// if err != nil {
// err = fmt.Errorf("(WorkflowInstance/SetTasks) wi.LockNamed returned: %s", err.Error())
// return
// }
// defer wi.Unlock()
// wi.Tasks = tasks
// wi.RemainTasks = len(tasks)
// wi.TotalTasks = len(tasks)
// if db_sync == "db_sync_yes" {
// err = wi.Save(false)
// if err != nil {
// return
// }
// }
// return
// }
func (wi *WorkflowInstance) GetTask(task_id Task_Unique_Identifier, read_lock bool) (task *Task, ok bool, err error) {
ok = false
if read_lock {
var lock rwmutex.ReadLock
lock, err = wi.RLockNamed("WorkflowInstance/GetTask")
if err != nil {
return
}
defer wi.RUnlockNamed(lock)
}
for _, t := range wi.Tasks {
if t.Task_Unique_Identifier == task_id {
ok = true
task = t
}
}
return
}
// get tasks form from all subworkflows in the job
func (wi *WorkflowInstance) GetTasks(read_lock bool) (tasks []*Task, err error) {
tasks = []*Task{}
if read_lock {
var lock rwmutex.ReadLock
lock, err = wi.RLockNamed("WorkflowInstance/GetTasks")
if err != nil {
return
}
defer wi.RUnlockNamed(lock)
}
logger.Debug(3, "(GetTasks) is not cwl")
for _, task := range wi.Tasks {
tasks = append(tasks, task)
}
return
}
func (wi *WorkflowInstance) TaskCount() (count int) {
lock, err := wi.RLockNamed("TaskCount")
if err != nil {
return
}
defer wi.RUnlockNamed(lock)
count = 0
if wi.Tasks == nil {
return
}
count = len(wi.Tasks)
return
}
func (wi *WorkflowInstance) GetId(read_lock bool) (id string, err error) {
if read_lock {
var lock rwmutex.ReadLock
lock, err = wi.RLockNamed("GetId")
if err != nil {
err = fmt.Errorf("(WorkflowInstance/GetId) RLockNamed returned: %s", err.Error())
return
}
defer wi.RUnlockNamed(lock)
}
id = wi.JobId + "_" + wi.LocalId
return
}
func (wi *WorkflowInstance) GetState(read_lock bool) (state string, err error) {
if read_lock {
var lock rwmutex.ReadLock
lock, err = wi.RLockNamed("GetState")
if err != nil {
err = fmt.Errorf("(WorkflowInstance/GetState) RLockNamed returned: %s", err.Error())
return
}
defer wi.RUnlockNamed(lock)
}
state = wi.State
return
}
func (wi *WorkflowInstance) Init(job *Job) (changed bool, err error) {
changed = false
wi.RWMutex.Init("WorkflowInstance")
if wi.Acl == nil {
if job.Acl.Owner == "" {
err = fmt.Errorf("(WorkflowInstance/Init) no job.Acl.Owner")
return
}
wi.Acl = &job.Acl
changed = true
}
if wi.Acl == nil {
err = fmt.Errorf("(WorkflowInstance/Init) still wi.Acl == nil ??? ")
return
}
var t_changed bool
for i, _ := range wi.Tasks {
t_changed, err = wi.Tasks[i].Init(job, wi.JobId)
if err != nil {
err = fmt.Errorf("(WorkflowInstance/Init) task.Init returned: %s", err.Error())
return
}
if t_changed {
changed = true
}
}
return
}
func (wi *WorkflowInstance) Save(read_lock bool) (err error) {
if read_lock {
var lock rwmutex.ReadLock
lock, err = wi.RLockNamed("WorkflowInstance/Save")
if err != nil {
return
}
defer wi.RUnlockNamed(lock)
}
if wi.LocalId == "" {
err = fmt.Errorf("(WorkflowInstance/Save) job id empty")
return
}
if wi.Acl == nil {
err = fmt.Errorf("(WorkflowInstance/Save) wi.Acl == nil ")
return
}
logger.Debug(1, "(WorkflowInstance/Save) dbUpsert next: %s", wi.LocalId)
//spew.Dump(job)
err = dbUpsert(wi)
if err != nil {
spew.Dump(wi)
err = fmt.Errorf("(WorkflowInstance/Save) dbUpsert failed (id=%s) error=%s", wi.LocalId, err.Error())
return
}
logger.Debug(1, "(WorkflowInstance/Save) wi saved: %s", wi.LocalId)
return
}
func (wi *WorkflowInstance) SetOutputs(outputs cwl.Job_document, context *cwl.WorkflowContext) (err error) {
err = wi.LockNamed("WorkflowInstance/SetOutputs")
if err != nil {
err = fmt.Errorf("(WorkflowInstance/SetOutputs) wi.LockNamed returned: %s", err.Error())
return
}
defer wi.Unlock()
wi.Outputs = outputs
err = wi.Save(false)
if err != nil {
err = fmt.Errorf("(WorkflowInstance/SetOutputs) Save() returned: %s", err.Error())
return
}
return
}
func (wi *WorkflowInstance) GetOutput(name string, read_lock bool) (obj cwl.CWLType, ok bool, err error) {
if read_lock {
var lock rwmutex.ReadLock
lock, err = wi.RLockNamed("GetOutput")
if err != nil {
err = fmt.Errorf("(WorkflowInstance/GetOutput) RLockNamed returned: %s", err.Error())
return
}
defer wi.RUnlockNamed(lock)
}
ok = true
if wi.Outputs == nil {
err = fmt.Errorf("(WorkflowInstance/GetOutput) not Outputs")
return
}
for i, _ := range wi.Outputs {
named_output := wi.Outputs[i]
named_output_base := path.Base(named_output.Id)
if named_output_base == name {
obj = named_output.Value
return
}
}
ok = false
return
}
func (wi *WorkflowInstance) DecreaseRemainSteps() (remain int, err error) {
err = wi.LockNamed("WorkflowInstance/DecreaseRemainSteps")
if err != nil {
err = fmt.Errorf("(WorkflowInstance/DecreaseRemainSteps) wi.LockNamed returned: %s", err.Error())
return
}
defer wi.Unlock()
if wi.RemainSteps <= 0 {
err = fmt.Errorf("(WorkflowInstance/DecreaseRemainSteps) RemainSteps is already %d", wi.RemainSteps)
return
}
wi.RemainSteps -= 1
//err = dbUpdateJobWorkflow_instancesFieldInt(wi.JobId, wi.Id, "remainsteps", wi.RemainSteps)
err = dbIncrementJobWorkflow_instancesField(wi.JobId, wi.LocalId, "remainsteps", -1) // TODO return correct value for remain
//err = wi.Save()
if err != nil {
err = fmt.Errorf("(WorkflowInstance/DecreaseRemainSteps) dbIncrementJobWorkflow_instancesField() returned: %s", err.Error())
return
}
remain = wi.RemainSteps
return
}