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db_job.go
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db_job.go
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package core
import (
"errors"
"fmt"
"time"
"github.com/MG-RAST/AWE/lib/acl"
"github.com/MG-RAST/AWE/lib/conf"
"github.com/MG-RAST/AWE/lib/db"
"github.com/MG-RAST/AWE/lib/logger"
mgo "gopkg.in/mgo.v2"
"gopkg.in/mgo.v2/bson"
)
// JobInfoIndexes _
var JobInfoIndexes = []string{"name", "submittime", "completedtime", "pipeline", "clientgroups", "project", "service", "user", "priority", "userattr.submission"}
// HasInfoField _
func HasInfoField(a string) bool {
for _, b := range JobInfoIndexes {
if b == a {
return true
}
}
return false
}
// InitJobDB _
func InitJobDB() {
session := db.Connection.Session.Copy()
defer session.Close()
cj := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
cj.EnsureIndex(mgo.Index{Key: []string{"acl.owner"}, Background: true})
cj.EnsureIndex(mgo.Index{Key: []string{"acl.read"}, Background: true})
cj.EnsureIndex(mgo.Index{Key: []string{"acl.write"}, Background: true})
cj.EnsureIndex(mgo.Index{Key: []string{"acl.delete"}, Background: true})
cj.EnsureIndex(mgo.Index{Key: []string{"id"}, Unique: true})
cj.EnsureIndex(mgo.Index{Key: []string{"state"}, Background: true})
cj.EnsureIndex(mgo.Index{Key: []string{"expiration"}, Background: true})
cj.EnsureIndex(mgo.Index{Key: []string{"updatetime"}, Background: true})
for _, v := range JobInfoIndexes {
cj.EnsureIndex(mgo.Index{Key: []string{"info." + v}, Background: true})
}
cp := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_PERF)
cp.EnsureIndex(mgo.Index{Key: []string{"id"}, Unique: true})
cw := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_SUBWORKFLOWS)
//cw.EnsureIndex(mgo.Index{Key: []string{"id"}, Unique: true}) not needed, already got _id
cw.EnsureIndex(mgo.Index{Key: []string{"job_id"}, Unique: false})
}
func dbCount(q bson.M) (count int, err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
if count, err = c.Find(q).Count(); err != nil {
return 0, err
}
return count, nil
}
// get a minimal subset of the job documents required for an admin overview
// for all completed jobs younger than a month and all running jobs
func dbAdminData(special string) (data []interface{}, err error) {
// get a DB connection
session := db.Connection.Session.Copy()
// close the connection when the function completes
defer session.Close()
// set the database and collection
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
// get the completed jobs that have a completed time not older than one month
var completedjobs = bson.M{"state": "completed", "info.completedtime": bson.M{"$gt": time.Now().AddDate(0, -1, 0)}}
// get all runnning jobs (those not deleted and not completed)
var runningjobs = bson.M{"state": bson.M{"$nin": []string{"completed", "deleted"}}}
// select only those fields required for the output
var resultfields = bson.M{"_id": 0, "state": 1, "info.name": 1, "info.submittime": 1, "info.startedtime": 1, "info.completedtime": 1, "info.pipeline": 1, "tasks.createdDate": 1, "tasks.startedDate": 1, "tasks.completedDate": 1, "tasks.state": 1, "tasks.inputs.size": 1, "tasks.outputs.size": 1, special: 1}
// return all data without iterating
err = c.Find(bson.M{"$or": []bson.M{completedjobs, runningjobs}}).Select(resultfields).All(&data)
return
}
func dbFindSort(filterQuery bson.M, results *Jobs, options map[string]int, sortby string, doInit bool) (count int, err error) {
if sortby == "" {
return 0, errors.New("sortby must be an nonempty string")
}
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
query := c.Find(filterQuery)
if count, err = query.Count(); err != nil {
return 0, err
}
if limit, has := options["limit"]; has {
if offset, has := options["offset"]; has {
err = query.Sort(sortby).Limit(limit).Skip(offset).All(results)
if results != nil {
if doInit {
_, err = results.Init()
if err != nil {
return
}
}
}
return
}
}
err = query.Sort(sortby).All(results)
if err != nil {
err = fmt.Errorf("query.Sort(sortby).All(results) failed: %s", err.Error())
return
}
if results == nil {
err = fmt.Errorf("(dbFindSort) results == nil")
return
}
var countChanged int
if doInit {
countChanged, err = results.Init()
if err != nil {
err = fmt.Errorf("(dbFindSort) results.Init() failed: %s", err.Error())
return
}
logger.Debug(1, "%d jobs haven been updated by Init function", countChanged)
}
return
}
// DbFindDistinct _
func DbFindDistinct(q bson.M, d string) (results interface{}, err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
err = c.Find(q).Distinct("info."+d, &results)
return
}
func dbUpdateJobState(jobID string, newState string, notes string) (err error) {
logger.Debug(3, "(dbUpdateJobState) jobID: %s", jobID)
var updateValue bson.M
if newState == JOB_STAT_COMPLETED {
updateValue = bson.M{"state": newState, "notes": notes, "info.completedtime": time.Now()}
} else {
updateValue = bson.M{"state": newState, "notes": notes}
}
return dbUpdateJobFields(jobID, updateValue)
}
func dbGetJobTasks(jobID string) (tasks []*Task, err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": jobID}
fieldname := "tasks"
err = c.Find(selector).Select(bson.M{fieldname: 1}).All(&tasks)
if err != nil {
err = fmt.Errorf("(dbGetJobTasks) Error getting tasks from jobID %s: %s", jobID, err.Error())
return
}
return
}
func dbGetJobTaskString(jobID string, taskID string, fieldname string) (result string, err error) {
var cont StructContainer
err = dbGetJobTaskField(jobID, taskID, fieldname, &cont)
if err != nil {
return
}
result = cont.Data.(string)
return
}
func dbGetJobTaskTime(jobID string, taskID string, fieldname string) (result time.Time, err error) {
var cont StructContainer
err = dbGetJobTaskField(jobID, taskID, fieldname, &cont)
if err != nil {
return
}
result = cont.Data.(time.Time)
return
}
func dbGetJobTaskInt(jobID string, taskID string, fieldname string) (result int, err error) {
var cont StructContainer
err = dbGetJobTaskField(jobID, taskID, fieldname, &cont)
if err != nil {
return
}
result = cont.Data.(int)
return
}
func dbFind(q bson.M, results *Jobs, options map[string]int) (count int, err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
query := c.Find(q)
if count, err = query.Count(); err != nil {
return 0, err
}
if limit, has := options["limit"]; has {
if offset, has := options["offset"]; has {
err = query.Limit(limit).Skip(offset).All(results)
if results != nil {
_, err = results.Init()
if err != nil {
return
}
}
return
}
return 0, errors.New("store.db.Find options limit and offset must be used together")
}
err = query.All(results)
if results != nil {
_, err = results.Init()
if err != nil {
return
}
}
return
}
func dbUpdateJobFields(jobID string, updateValue bson.M) (err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": jobID}
err = c.Update(selector, bson.M{"$set": updateValue})
if err != nil {
err = fmt.Errorf("Error updating job fields: " + err.Error())
return
}
return
}
func dbUpdateJobFieldBoolean(jobID string, fieldname string, value bool) (err error) {
updateValue := bson.M{fieldname: value}
return dbUpdateJobFields(jobID, updateValue)
}
func dbUpdateJobFieldString(jobID string, fieldname string, value string) (err error) {
updateValue := bson.M{fieldname: value}
return dbUpdateJobFields(jobID, updateValue)
}
func dbUpdateJobFieldInt(jobID string, fieldname string, value int) (err error) {
updateValue := bson.M{fieldname: value}
return dbUpdateJobFields(jobID, updateValue)
}
func dbUpdateJobFieldTime(jobID string, fieldname string, value time.Time) (err error) {
updateValue := bson.M{fieldname: value}
return dbUpdateJobFields(jobID, updateValue)
}
func dbUpdateJobFieldNull(jobID string, fieldname string) (err error) {
updateValue := bson.M{fieldname: nil}
return dbUpdateJobFields(jobID, updateValue)
}
func dbUpdateJobTaskFields(jobID string, workflowInstanceID string, taskID string, updateValue bson.M) (err error) {
session := db.Connection.Session.Copy()
defer session.Close()
database := conf.DB_COLL_JOBS
if workflowInstanceID != "" {
database = conf.DB_COLL_SUBWORKFLOWS
}
c := session.DB(conf.MONGODB_DATABASE).C(database)
var selector bson.M
var updateOp bson.M
if workflowInstanceID == "" {
selector = bson.M{"id": jobID, "tasks.taskid": taskID}
updateOp = bson.M{"$set": updateValue}
} else {
err = fmt.Errorf("not supported")
return
//unique_id := jobID + workflowInstance_id
//selector = bson.M{"_id": unique_id, "tasks.taskid": taskID}
//updateOp = bson.M{"$set": updateValue}
}
//fmt.Println("(dbUpdateJobTaskFields) updateValue:")
//spew.Dump(updateValue)
err = c.Update(selector, updateOp)
if err != nil {
err = fmt.Errorf("(dbUpdateJobTaskFields) (db: %s) Error updating task %s: %s", database, taskID, err.Error())
return
}
return
}
func dbUpdateJobTaskField(jobID string, workflowInstance string, taskID string, fieldname string, value interface{}) (err error) {
updateValue := bson.M{"tasks.$." + fieldname: value}
err = dbUpdateJobTaskFields(jobID, workflowInstance, taskID, updateValue)
if err != nil {
err = fmt.Errorf("(dbUpdateJobTaskField) dbUpdateJobTaskFields returned: %s", err.Error())
}
return
}
func dbUpdateJobTaskInt(jobID string, workflowInstance string, taskID string, fieldname string, value int) (err error) {
updateValue := bson.M{"tasks.$." + fieldname: value}
err = dbUpdateJobTaskFields(jobID, workflowInstance, taskID, updateValue)
if err != nil {
err = fmt.Errorf("(dbUpdateJobTaskInt) dbUpdateJobTaskFields returned: %s", err.Error())
}
return
}
func dbUpdateJobTaskBoolean(jobID string, workflowInstance string, taskID string, fieldname string, value bool) (err error) {
updateValue := bson.M{"tasks.$." + fieldname: value}
err = dbUpdateJobTaskFields(jobID, workflowInstance, taskID, updateValue)
if err != nil {
err = fmt.Errorf("(dbUpdateJobTaskBoolean) dbUpdateJobTaskFields returned: %s", err.Error())
}
return
}
func dbUpdateJobTaskString(jobID string, workflowInstance string, taskID string, fieldname string, value string) (err error) {
updateValue := bson.M{"tasks.$." + fieldname: value}
err = dbUpdateJobTaskFields(jobID, workflowInstance, taskID, updateValue)
if err != nil {
err = fmt.Errorf("(dbUpdateJobTaskString) jobID=%s, taskID=%s, fieldname=%s, value=%s dbUpdateJobTaskFields returned: %s", jobID, taskID, fieldname, value, err.Error())
}
return
}
func dbUpdateJobTaskTime(jobID string, workflowInstance string, taskID string, fieldname string, value time.Time) (err error) {
updateValue := bson.M{"tasks.$." + fieldname: value}
err = dbUpdateJobTaskFields(jobID, workflowInstance, taskID, updateValue)
if err != nil {
err = fmt.Errorf("(dbUpdateJobTaskTime) (fieldname %s) dbUpdateJobTaskFields returned: %s", fieldname, err.Error())
}
return
}
func dbUpdateJobTaskPartition(jobID string, workflowInstance string, taskID string, partition *PartInfo) (err error) {
updateValue := bson.M{"tasks.$.partinfo": partition}
err = dbUpdateJobTaskFields(jobID, workflowInstance, taskID, updateValue)
if err != nil {
err = fmt.Errorf("(dbUpdateJobTaskPartition) dbUpdateJobTaskFields returned: %s", err.Error())
}
return
}
func dbUpdateJobTaskIO(jobID string, workflowInstance string, taskID string, fieldname string, value []*IO) (err error) {
updateValue := bson.M{"tasks.$." + fieldname: value}
err = dbUpdateJobTaskFields(jobID, workflowInstance, taskID, updateValue)
if err != nil {
err = fmt.Errorf("(dbUpdateJobTaskIO) dbUpdateJobTaskFields returned: %s", err.Error())
}
return
}
func dbIncrementJobTaskField(jobID string, taskID string, fieldname string, incrementValue int) (err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": jobID, "tasks.taskid": taskID}
updateValue := bson.M{"tasks.$." + fieldname: incrementValue}
err = c.Update(selector, bson.M{"$inc": updateValue})
if err != nil {
err = fmt.Errorf("Error incrementing jobID=%s fieldname=%s by %d: %s", jobID, fieldname, incrementValue, err.Error())
return
}
return
}
// DbUpdateJobField _
func DbUpdateJobField(jobID string, key string, value interface{}) (err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
query := bson.M{"id": jobID}
updateValue := bson.M{key: value}
update := bson.M{"$set": updateValue}
err = c.Update(query, update)
if err != nil {
err = fmt.Errorf("Error updating job %s and key %s in job: %s", jobID, key, err.Error())
return
}
return
}
// LoadJob _
func LoadJob(id string) (job *Job, err error) {
job = NewJob()
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
// A) get job document
err = c.Find(bson.M{"id": id}).One(&job)
if err != nil {
job = nil
err = fmt.Errorf("(LoadJob) c.Find failed: %s", err.Error())
return
}
// continue A, initialize
var jobChanged bool
jobChanged, err = job.Init() // values have already been set at this point...
if err != nil {
err = fmt.Errorf("(LoadJob) job.Init failed: %s", err.Error())
return
}
// B) get WorkflowInstances
if job.IsCWL {
c2 := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_SUBWORKFLOWS)
WIsIf := []interface{}{} // have to use interface, because mongo cannot handle interface types
err = c2.Find(bson.M{"job_id": id}).All(&WIsIf)
if err != nil {
job = nil
err = fmt.Errorf("(LoadJob) (DB_COLL_SUBWORKFLOWS) c.Find failed: %s", err.Error())
return
}
if len(WIsIf) == 0 {
err = fmt.Errorf("(LoadJob) no matching WorkflowInstances found for job %s", id)
return
}
var wis []*WorkflowInstance
wis, err = NewWorkflowInstanceArrayFromInterface(WIsIf, job, job.WorkflowContext)
if err != nil {
err = fmt.Errorf("(LoadJob) NewWorkflowInstanceArrayFromInterface returned: %s", err.Error())
return
}
if len(wis) == 0 {
err = fmt.Errorf("(LoadJob) NewWorkflowInstanceArrayFromInterface returned no WorkflowInstances for job %s", id)
return
}
for i := range wis {
var wiChanged bool
wi := wis[i]
wiChanged, err = wi.Init(job)
if err != nil {
err = fmt.Errorf("(LoadJob) wis[i].Init returned: %s", err.Error())
return
}
if wiChanged {
err = wi.Save(true)
if err != nil {
err = fmt.Errorf("(LoadJob) wi.Save() returned: %s", err.Error())
return
}
}
// add WorkflowInstance to job
fmt.Printf("(LoadJob) loading: %s\n", wi.LocalID)
err = job.AddWorkflowInstance(wi, DbSyncFalse, true) // load from database
if err != nil {
err = fmt.Errorf("(LoadJob) AddWorkflowInstance returned: %s", err.Error())
return
}
wiUniqueID, _ := wi.GetID(true)
err = GlobalWorkflowInstanceMap.Add(wiUniqueID, wi)
if err != nil {
err = fmt.Errorf("(LoadJob) GlobalWorkflowInstanceMap.Add returned: %s", err.Error())
return
}
}
}
// To fix incomplete or inconsistent database entries
if jobChanged {
err = job.Save()
if err != nil {
err = fmt.Errorf("(LoadJob) job.Save() returned: %s", err.Error())
return
}
}
return
}
// LoadJobPerf _
func LoadJobPerf(id string) (perf *JobPerf, err error) {
perf = new(JobPerf)
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_PERF)
if err = c.Find(bson.M{"id": id}).One(&perf); err == nil {
return perf, nil
}
return nil, err
}
func dbGetJobTaskField(jobID string, taskID string, fieldname string, result *StructContainer) (err error) {
arrayName := "tasks"
idField := "taskid"
return dbGetJobArrayField(jobID, taskID, arrayName, idField, fieldname, result)
}
// TODO: warning: this does not cope with subfields such as "partinfo.index"
func dbGetJobArrayField(jobID string, taskID string, array_name string, id_field string, fieldname string, result *StructContainer) (err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": jobID}
projection := bson.M{array_name: bson.M{"$elemMatch": bson.M{id_field: taskID}}, array_name + "." + fieldname: 1}
temp_result := bson.M{}
err = c.Find(selector).Select(projection).One(&temp_result)
if err != nil {
err = fmt.Errorf("(dbGetJobArrayField) Error getting field from jobID %s , %s=%s and fieldname %s: %s", jobID, id_field, taskID, fieldname, err.Error())
return
}
//logger.Debug(3, "GOT: %v", temp_result)
tasks_unknown := temp_result[array_name]
tasks, ok := tasks_unknown.([]interface{})
if !ok {
err = fmt.Errorf("(dbGetJobArrayField) Array expected, but not found")
return
}
if len(tasks) == 0 {
err = fmt.Errorf("(dbGetJobArrayField) result task array empty")
return
}
firstTask := tasks[0].(bson.M)
testResult, ok := firstTask[fieldname]
if !ok {
err = fmt.Errorf("(dbGetJobArrayField) Field %s not in task object", fieldname)
return
}
result.Data = testResult
//logger.Debug(3, "GOT2: %v", result)
logger.Debug(3, "(dbGetJobArrayField) %s got something", fieldname)
return
}
func dbGetJobTask(jobID string, taskID string) (result *Task, err error) {
dummyJob := NewJob()
dummyJob.Init()
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": jobID}
projection := bson.M{"tasks": bson.M{"$elemMatch": bson.M{"taskid": taskID}}}
err = c.Find(selector).Select(projection).One(&dummyJob)
if err != nil {
err = fmt.Errorf("(dbGetJobTask) Error getting field from jobID %s , taskID %s : %s", jobID, taskID, err.Error())
return
}
if len(dummyJob.Tasks) != 1 {
err = fmt.Errorf("(dbGetJobTask) len(dummy_job.Tasks) != 1 len(dummy_job.Tasks)=%d", len(dummyJob.Tasks))
return
}
result = dummyJob.Tasks[0]
return
}
func dbGetPrivateEnv(jobID string, taskID string) (result map[string]string, err error) {
task, err := dbGetJobTask(jobID, taskID)
if err != nil {
return
}
result = task.Cmd.Environ.Private
for key, val := range result {
logger.Debug(3, "(dbGetPrivateEnv) got %s=%s ", key, val)
}
return
}
func dbGetJobFieldInt(jobID string, fieldname string) (result int, err error) {
err = dbGetJobField(jobID, fieldname, &result)
if err != nil {
return
}
return
}
func dbGetJobFieldString(jobID string, fieldname string) (result string, err error) {
err = dbGetJobField(jobID, fieldname, &result)
logger.Debug(3, "(dbGetJobFieldString) result: %s", result)
if err != nil {
return
}
return
}
func dbGetJobField(jobID string, fieldname string, result interface{}) (err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": jobID}
err = c.Find(selector).Select(bson.M{fieldname: 1}).One(&result)
if err != nil {
err = fmt.Errorf("(dbGetJobField) Error getting field from jobID %s and fieldname %s: %s", jobID, fieldname, err.Error())
return
}
return
}
// JobACL _
type JobACL struct {
ACL acl.Acl `bson:"acl" json:"-"`
}
// DBGetJobACL _
func DBGetJobACL(jobID string) (_acl acl.Acl, err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": jobID}
job := JobACL{}
err = c.Find(selector).Select(bson.M{"acl": 1}).One(&job)
if err != nil {
err = fmt.Errorf("Error getting acl field from jobID %s: %s", jobID, err.Error())
return
}
_acl = job.ACL
return
}
func dbGetJobFieldTime(jobID string, fieldname string) (result time.Time, err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": jobID}
err = c.Find(selector).Select(bson.M{fieldname: 1}).One(&result)
if err != nil {
err = fmt.Errorf("(dbGetJobFieldTime) Error getting field from jobID %s and fieldname %s: %s", jobID, fieldname, err.Error())
return
}
return
}
func dbPushJobTask(jobID string, task *Task) (err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": jobID}
change := bson.M{"$push": bson.M{"tasks": task}}
err = c.Update(selector, change)
if err != nil {
err = fmt.Errorf("Error adding task: " + err.Error())
return
}
//fmt.Printf("(dbPushJobTask) added task: %s\n", task.Task_Unique_Identifier.TaskName)
//test, _ := LoadJob(jobID)
//spew.Dump(test)
//panic("done")
return
}
// // CWL: task in WorkflowInstance
// func dbUpdateTaskFields(jobID string, taskID string, updateValue bson.M) (err error) {
// session := db.Connection.Session.Copy()
// defer session.Close()
// c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
// selector := bson.M{"id": jobID, "tasks.taskid": taskID}
// err = c.Update(selector, bson.M{"$set": updateValue})
// if err != nil {
// err = fmt.Errorf("(dbUpdateTaskFields) Error updating task: " + err.Error())
// return
// }
// return
// }