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db.go
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db.go
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package core
import (
"errors"
"fmt"
"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"
"time"
)
// mongodb has hard limit of 16 MB docuemnt size
var DocumentMaxByte = 16777216
// indexed info fields for search
var JobInfoIndexes = []string{"name", "submittime", "completedtime", "pipeline", "clientgroups", "project", "service", "user", "priority", "userattr.submission"}
type StructContainer struct {
Data interface{} `json:"data"`
}
func HasInfoField(a string) bool {
for _, b := range JobInfoIndexes {
if b == a {
return true
}
}
return false
}
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})
}
func InitClientGroupDB() {
session := db.Connection.Session.Copy()
defer session.Close()
cc := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_CGS)
cc.EnsureIndex(mgo.Index{Key: []string{"id"}, Unique: true})
cc.EnsureIndex(mgo.Index{Key: []string{"name"}, Unique: true})
cc.EnsureIndex(mgo.Index{Key: []string{"token"}, Unique: true})
}
func dbDelete(q bson.M, coll string) (err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(coll)
_, err = c.RemoveAll(q)
return
}
func dbUpsert(t interface{}) (err error) {
// test that document not to large
if nbson, err := bson.Marshal(t); err == nil {
if len(nbson) >= DocumentMaxByte {
return errors.New(fmt.Sprintf("bson document size is greater than limit of %d bytes", DocumentMaxByte))
}
}
session := db.Connection.Session.Copy()
defer session.Close()
switch t := t.(type) {
case *Job:
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
_, err = c.Upsert(bson.M{"id": t.Id}, &t)
case *JobPerf:
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_PERF)
_, err = c.Upsert(bson.M{"id": t.Id}, &t)
case *ClientGroup:
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_CGS)
_, err = c.Upsert(bson.M{"id": t.Id}, &t)
default:
fmt.Printf("invalid database entry type\n")
}
return
}
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
} else {
return count, nil
}
}
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
} else {
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 dbFindSort(q bson.M, results *Jobs, options map[string]int, sortby string) (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(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.Sort(sortby).Limit(limit).Skip(offset).All(results)
if results != nil {
err = results.Init()
if err != nil {
return
}
}
return
}
}
err = query.Sort(sortby).All(results)
if results != nil {
err = results.Init()
if err != nil {
return
}
}
return
}
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 dbFindClientGroups(q bson.M, results *ClientGroups) (count int, err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_CGS)
query := c.Find(q)
if count, err = query.Count(); err != nil {
return 0, err
}
err = query.All(results)
return
}
func dbFindSortClientGroups(q bson.M, results *ClientGroups, options map[string]int, sortby string) (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_CGS)
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.Sort(sortby).Limit(limit).Skip(offset).All(results)
return
}
}
err = query.Sort(sortby).All(results)
return
}
func dbUpdateJobState(job_id string, newState string, notes string) (err error) {
logger.Debug(3, "(dbUpdateJobState) job_id: %s", job_id)
var update_value bson.M
if newState == JOB_STAT_COMPLETED {
update_value = bson.M{"state": newState, "notes": notes, "info.completedtime": time.Now()}
} else {
update_value = bson.M{"state": newState, "notes": notes}
}
return dbUpdateJobFields(job_id, update_value)
}
func dbGetJobTasks(job_id 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": job_id}
fieldname := "tasks"
err = c.Find(selector).Select(bson.M{fieldname: 1}).All(&tasks)
if err != nil {
err = fmt.Errorf("(dbGetJobTasks) Error getting tasks from job_id %s: %s", job_id, err.Error())
return
}
return
}
func dbGetJobTaskString(job_id string, task_id string, fieldname string) (result string, err error) {
var cont StructContainer
err = dbGetJobTaskField(job_id, task_id, fieldname, &cont)
if err != nil {
return
}
result = cont.Data.(string)
return
}
func dbGetJobTaskTime(job_id string, task_id string, fieldname string) (result time.Time, err error) {
var cont StructContainer
err = dbGetJobTaskField(job_id, task_id, fieldname, &cont)
if err != nil {
return
}
result = cont.Data.(time.Time)
return
}
func dbGetJobTaskInt(job_id string, task_id string, fieldname string) (result int, err error) {
var cont StructContainer
err = dbGetJobTaskField(job_id, task_id, fieldname, &cont)
if err != nil {
return
}
result = cont.Data.(int)
return
}
// TODO: warning: this does not cope with subfields such as "partinfo.index"
func dbGetJobTaskField(job_id string, task_id 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": job_id}
projection := bson.M{"tasks": bson.M{"$elemMatch": bson.M{"taskid": task_id}}, "tasks." + fieldname: 1}
temp_result := bson.M{}
err = c.Find(selector).Select(projection).One(&temp_result)
if err != nil {
err = fmt.Errorf("(dbGetJobTaskField) Error getting field from job_id %s , task_id %s and fieldname %s: %s", job_id, task_id, fieldname, err.Error())
return
}
logger.Debug(3, "GOT: %v", temp_result)
tasks_unknown := temp_result["tasks"]
tasks, ok := tasks_unknown.([]interface{})
if !ok {
err = fmt.Errorf("Array expected, but not found")
return
}
if len(tasks) == 0 {
err = fmt.Errorf("result task array empty")
return
}
first_task := tasks[0].(bson.M)
test_result, ok := first_task[fieldname]
if !ok {
err = fmt.Errorf("Field %s not in task object", fieldname)
return
}
result.Data = test_result
logger.Debug(3, "GOT2: %v", result)
logger.Debug(3, "(dbGetJobTaskField) %s got something", fieldname)
return
}
func dbGetJobTask(job_id string, task_id string) (result *Task, err error) {
dummy_job := NewJob()
dummy_job.Init()
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": job_id}
projection := bson.M{"tasks": bson.M{"$elemMatch": bson.M{"taskid": task_id}}}
err = c.Find(selector).Select(projection).One(&dummy_job)
if err != nil {
err = fmt.Errorf("(dbGetJobTask) Error getting field from job_id %s , task_id %s : %s", job_id, task_id, err.Error())
return
}
if len(dummy_job.Tasks) != 1 {
err = fmt.Errorf("(dbGetJobTask) len(dummy_job.Tasks) != 1 len(dummy_job.Tasks)=%d", len(dummy_job.Tasks))
return
}
result = dummy_job.Tasks[0]
return
}
func dbGetPrivateEnv(job_id string, task_id string) (result map[string]string, err error) {
task, err := dbGetJobTask(job_id, task_id)
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(job_id string, fieldname string) (result int, err error) {
err = dbGetJobField(job_id, fieldname, &result)
if err != nil {
return
}
return
}
func dbGetJobFieldString(job_id string, fieldname string) (result string, err error) {
err = dbGetJobField(job_id, fieldname, &result)
if err != nil {
return
}
return
}
func dbGetJobField(job_id 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": job_id}
err = c.Find(selector).Select(bson.M{fieldname: 1}).One(&result)
if err != nil {
err = fmt.Errorf("(dbGetJobField) Error getting field from job_id %s and fieldname %s: %s", job_id, fieldname, err.Error())
return
}
return
}
type Job_Acl struct {
Acl acl.Acl `bson:"acl" json:"-"`
}
func DBGetJobAcl(job_id 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": job_id}
job := Job_Acl{}
err = c.Find(selector).Select(bson.M{"acl": 1}).One(&job)
if err != nil {
err = fmt.Errorf("Error getting acl field from job_id %s: %s", job_id, err.Error())
return
}
_acl = job.Acl
return
}
func dbGetJobFieldTime(job_id 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": job_id}
err = c.Find(selector).Select(bson.M{fieldname: 1}).One(&result)
if err != nil {
err = fmt.Errorf("(dbGetJobFieldTime) Error getting field from job_id %s and fieldname %s: %s", job_id, fieldname, err.Error())
return
}
return
}
func dbUpdateJobFields(job_id string, update_value 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": job_id}
err = c.Update(selector, bson.M{"$set": update_value})
if err != nil {
err = fmt.Errorf("Error updating job fields: " + err.Error())
return
}
return
}
func dbUpdateJobFieldBoolean(job_id string, fieldname string, value bool) (err error) {
update_value := bson.M{fieldname: value}
return dbUpdateJobFields(job_id, update_value)
}
func dbUpdateJobFieldString(job_id string, fieldname string, value string) (err error) {
update_value := bson.M{fieldname: value}
return dbUpdateJobFields(job_id, update_value)
}
func dbUpdateJobFieldInt(job_id string, fieldname string, value int) (err error) {
update_value := bson.M{fieldname: value}
return dbUpdateJobFields(job_id, update_value)
}
func dbUpdateJobFieldTime(job_id string, fieldname string, value time.Time) (err error) {
update_value := bson.M{fieldname: value}
return dbUpdateJobFields(job_id, update_value)
}
func dbUpdateJobFieldNull(job_id string, fieldname string) (err error) {
update_value := bson.M{fieldname: nil}
return dbUpdateJobFields(job_id, update_value)
}
func dbUpdateJobTaskFields(job_id string, task_id string, update_value bson.M) (err error) {
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_JOBS)
selector := bson.M{"id": job_id, "tasks.taskid": task_id}
err = c.Update(selector, bson.M{"$set": update_value})
if err != nil {
err = fmt.Errorf("(dbUpdateJobTaskFields) Error updating task: " + err.Error())
return
}
return
}
func dbUpdateJobTaskField(job_id string, task_id string, fieldname string, value interface{}) (err error) {
update_value := bson.M{"tasks.$." + fieldname: value}
return dbUpdateJobTaskFields(job_id, task_id, update_value)
}
func dbUpdateJobTaskInt(job_id string, task_id string, fieldname string, value int) (err error) {
update_value := bson.M{"tasks.$." + fieldname: value}
return dbUpdateJobTaskFields(job_id, task_id, update_value)
}
func dbUpdateJobTaskString(job_id string, task_id string, fieldname string, value string) (err error) {
update_value := bson.M{"tasks.$." + fieldname: value}
return dbUpdateJobTaskFields(job_id, task_id, update_value)
}
func dbUpdateJobTaskTime(job_id string, task_id string, fieldname string, value time.Time) (err error) {
update_value := bson.M{"tasks.$." + fieldname: value}
return dbUpdateJobTaskFields(job_id, task_id, update_value)
}
func dbUpdateJobTaskPartition(job_id string, task_id string, partition *PartInfo) (err error) {
update_value := bson.M{"tasks.$.partinfo": partition}
return dbUpdateJobTaskFields(job_id, task_id, update_value)
}
func dbUpdateJobTaskIO(job_id string, task_id string, fieldname string, value []*IO) (err error) {
update_value := bson.M{"tasks.$." + fieldname: value}
return dbUpdateJobTaskFields(job_id, task_id, update_value)
}
func dbIncrementJobTaskField(job_id string, task_id string, fieldname string, increment_value 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": job_id, "tasks.taskid": task_id}
update_value := bson.M{"tasks.$." + fieldname: increment_value}
err = c.Update(selector, bson.M{"$inc": update_value})
if err != nil {
err = fmt.Errorf("Error incrementing job_id=%s fieldname=%s by %d: %s", job_id, fieldname, increment_value, err.Error())
return
}
return
}
func DbUpdateJobField(job_id 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": job_id}
update_value := bson.M{key: value}
update := bson.M{"$set": update_value}
err = c.Update(query, update)
if err != nil {
err = fmt.Errorf("Error updating job %s and key %s in job: %s", job_id, key, err.Error())
return
}
return
}
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)
err = c.Find(bson.M{"id": id}).One(&job)
if err != nil {
job = nil
return
}
changed, xerr := job.Init()
if xerr != nil {
err = xerr
return
}
// To fix incomplete or inconsistent database entries
if changed {
job.Save()
}
return
}
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 LoadClientGroup(id string) (clientgroup *ClientGroup, err error) {
clientgroup = new(ClientGroup)
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_CGS)
if err = c.Find(bson.M{"id": id}).One(&clientgroup); err == nil {
return clientgroup, nil
}
return nil, err
}
func LoadClientGroupByName(name string) (clientgroup *ClientGroup, err error) {
clientgroup = new(ClientGroup)
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_CGS)
if err = c.Find(bson.M{"name": name}).One(&clientgroup); err == nil {
return clientgroup, nil
}
return nil, err
}
func LoadClientGroupByToken(token string) (clientgroup *ClientGroup, err error) {
clientgroup = new(ClientGroup)
session := db.Connection.Session.Copy()
defer session.Close()
c := session.DB(conf.MONGODB_DATABASE).C(conf.DB_COLL_CGS)
if err = c.Find(bson.M{"token": token}).One(&clientgroup); err == nil {
return clientgroup, nil
}
return nil, err
}
func DeleteClientGroup(id string) (err error) {
err = dbDelete(bson.M{"id": id}, conf.DB_COLL_CGS)
return
}