// GET: /client/{id}
func (cr *ClientController) Read(id string, cx *goweb.Context) {
LogRequest(cx.Request)
// Gather query params
query := &Query{list: cx.Request.URL.Query()}
if query.Has("heartbeat") {
client, err := queueMgr.ClientHeartBeat(id)
if err != nil {
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
} else {
cx.RespondWithData(client.Id)
}
return
}
client, err := queueMgr.GetClient(id)
if err != nil {
if err.Error() == e.ClientNotFound {
cx.RespondWithErrorMessage(e.ClientNotFound, http.StatusBadRequest)
} else {
Log.Error("Error in GET client:" + err.Error())
cx.RespondWithError(http.StatusBadRequest)
}
return
}
cx.RespondWithData(client)
}
// POST: /client
func (cr *ClientController) Create(cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
// Parse uploaded form
_, files, err := ParseMultipartForm(cx.Request)
if err != nil {
if err.Error() != "request Content-Type isn't multipart/form-data" {
Log.Error("Error parsing form: " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
}
client, err := queueMgr.RegisterNewClient(files)
if err != nil {
msg := "Error in registering new client:" + err.Error()
Log.Error(msg)
cx.RespondWithErrorMessage(msg, http.StatusBadRequest)
return
}
//log event about client registration (CR)
Log.Event(EVENT_CLIENT_REGISTRATION, "clientid="+client.Id+";name="+client.Name)
cx.RespondWithData(client)
return
}
// POST: /job
func (cr *JobController) Create(cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
// Parse uploaded form
params, files, err := ParseMultipartForm(cx.Request)
if err != nil {
if err.Error() == "request Content-Type isn't multipart/form-data" {
cx.RespondWithErrorMessage("No job file is submitted", http.StatusBadRequest)
} else {
// Some error other than request encoding. Theoretically
// could be a lost db connection between user lookup and parsing.
// Blame the user, Its probaby their fault anyway.
Log.Error("Error parsing form: " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
}
return
}
_, has_upload := files["upload"]
_, has_awf := files["awf"]
if !has_upload && !has_awf {
cx.RespondWithErrorMessage("No job script or awf is submitted", http.StatusBadRequest)
return
}
//send job submission request and get back an assigned job number (jid)
var jid string
jid, err = queueMgr.JobRegister()
if err != nil {
Log.Error("Err@job_Create:GetNextJobNum: " + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
var job *core.Job
job, err = core.CreateJobUpload(params, files, jid)
if err != nil {
Log.Error("Err@job_Create:CreateJobUpload: " + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
queueMgr.EnqueueTasksByJobId(job.Id, job.TaskList())
//log event about job submission (JB)
Log.Event(EVENT_JOB_SUBMISSION, "jobid="+job.Id+";jid="+job.Jid+";name="+job.Info.Name+";project="+job.Info.Project)
cx.RespondWithData(job)
return
}
// DELETE: /job?suspend
func (cr *JobController) DeleteMany(cx *goweb.Context) {
LogRequest(cx.Request)
// Gather query params
query := &Query{list: cx.Request.URL.Query()}
if query.Has("suspend") {
num := queueMgr.DeleteSuspendedJobs()
cx.RespondWithData(fmt.Sprintf("deleted %d suspended jobs", num))
} else {
cx.RespondWithError(http.StatusNotImplemented)
}
return
}
func handleAuthError(err error, cx *goweb.Context) {
switch err.Error() {
case e.MongoDocNotFound:
cx.RespondWithErrorMessage("Invalid username or password", http.StatusBadRequest)
return
case e.InvalidAuth:
cx.RespondWithErrorMessage("Invalid Authorization header", http.StatusBadRequest)
return
}
log.Error("Error at Auth: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
// PUT: /client/{id} -> status update
func (cr *ClientController) Update(id string, cx *goweb.Context) {
LogRequest(cx.Request)
client, err := queueMgr.ClientHeartBeat(id)
if err != nil {
if err.Error() == e.ClientNotFound {
cx.RespondWithErrorMessage(e.ClientNotFound, http.StatusBadRequest)
} else {
Log.Error("Error in handle client heartbeat:" + err.Error())
cx.RespondWithError(http.StatusBadRequest)
}
return
}
cx.RespondWithData(client)
}
// POST: /user
// To create a new user make a empty POST to /user with user:password
// Basic Auth encoded in the header. Return new user object.
func (cr *UserController) Create(cx *goweb.Context) {
// Log Request
LogRequest(cx.Request)
if _, ok := cx.Request.Header["Authorization"]; !ok {
cx.RespondWithError(http.StatusUnauthorized)
return
}
header := cx.Request.Header.Get("Authorization")
tmpAuthArray := strings.Split(header, " ")
authValues, err := base64.URLEncoding.DecodeString(tmpAuthArray[1])
if err != nil {
err = errors.New("Failed to decode encoded auth settings in http request.")
cx.RespondWithError(http.StatusBadRequest)
return
}
authValuesArray := strings.Split(string(authValues), ":")
if conf.ANON_CREATEUSER == false && len(authValuesArray) != 4 {
if len(authValuesArray) == 2 {
cx.RespondWithErrorMessage(e.UnAuth, http.StatusUnauthorized)
return
} else {
cx.RespondWithError(http.StatusBadRequest)
return
}
}
name := authValuesArray[0]
passwd := authValuesArray[1]
admin := false
if len(authValuesArray) == 4 {
if authValuesArray[2] != fmt.Sprint(conf.SECRET_KEY) {
cx.RespondWithErrorMessage(e.UnAuth, http.StatusUnauthorized)
return
} else if authValuesArray[3] == "true" {
admin = true
}
}
u, err := user.New(name, passwd, admin)
if err != nil {
// Duplicate key check
if e.MongoDupKeyRegex.MatchString(err.Error()) {
log.Error("Err@user_Create: duplicate key error")
cx.RespondWithErrorMessage("Username not available", http.StatusBadRequest)
return
} else {
log.Error("Err@user_Create: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
cx.RespondWithData(u)
return
}
func streamDownload(cx *goweb.Context, node *store.Node, filename string) {
query := &Query{list: cx.Request.URL.Query()}
nf, err := node.FileReader()
if err != nil {
// File not found or some sort of file read error.
// Probably deserves more checking
log.Error("err:@preAuth node.FileReader: " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
if query.Has("filename") {
filename = query.Value("filename")
}
s := &streamer{rs: []store.SectionReader{nf}, ws: cx.ResponseWriter, contentType: "application/octet-stream", filename: filename, size: node.File.Size, filter: nil}
err = s.stream()
if err != nil {
// causes "multiple response.WriteHeader calls" error but better than no response
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
log.Error("err:@preAuth: s.stream: " + err.Error())
}
}
func PreAuthRequest(cx *goweb.Context) {
LogRequest(cx.Request)
id := cx.PathParams["id"]
if p, err := store.LoadPreAuth(id); err != nil {
if err.Error() == e.MongoDocNotFound {
cx.RespondWithNotFound()
} else {
cx.RespondWithError(http.StatusInternalServerError)
log.Error("err:@preAuth load: " + err.Error())
}
return
} else {
if node, err := store.LoadNodeUnauth(p.NodeId); err == nil {
switch p.Type {
case "download":
filename := node.Id
if fn, has := p.Options["filename"]; has {
filename = fn
}
streamDownload(cx, node, filename)
store.DeletePreAuth(id)
return
default:
cx.RespondWithError(http.StatusInternalServerError)
}
} else {
cx.RespondWithError(http.StatusInternalServerError)
log.Error("err:@preAuth loadnode: " + err.Error())
}
}
return
}
// POST: /node
func (cr *NodeController) Create(cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
u, err := AuthenticateRequest(cx.Request)
if err != nil && err.Error() != e.NoAuth {
handleAuthError(err, cx)
return
}
// Fake public user
if u == nil {
if conf.ANON_WRITE {
u = &user.User{Uuid: ""}
} else {
cx.RespondWithErrorMessage(e.NoAuth, http.StatusUnauthorized)
return
}
}
// Parse uploaded form
params, files, err := ParseMultipartForm(cx.Request)
if err != nil {
// If not multipart/form-data it will create an empty node.
// TODO: create another request parser for non-multipart request
// to handle this cleaner.
if err.Error() == "request Content-Type isn't multipart/form-data" {
node, err := store.CreateNodeUpload(u, params, files)
if err != nil {
log.Error("Error at create empty: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
if node == nil {
// Not sure how you could get an empty node with no error
// Assume it's the user's fault
cx.RespondWithError(http.StatusBadRequest)
return
} else {
cx.RespondWithData(node)
return
}
} else {
// Some error other than request encoding. Theoretically
// could be a lost db connection between user lookup and parsing.
// Blame the user, Its probaby their fault anyway.
log.Error("Error parsing form: " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
}
// Create node
node, err := store.CreateNodeUpload(u, params, files)
if err != nil {
log.Error("err " + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
cx.RespondWithData(node)
return
}
// GET: /user
func (cr *UserController) ReadMany(cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
u, err := AuthenticateRequest(cx.Request)
if err != nil {
if err.Error() == e.NoAuth || err.Error() == e.UnAuth {
cx.RespondWithError(http.StatusUnauthorized)
return
} else {
log.Error("Err@user_Read: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
if u.Admin {
users := user.Users{}
user.AdminGet(&users)
if len(users) > 0 {
cx.RespondWithData(users)
return
} else {
cx.RespondWithNotFound()
return
}
} else {
cx.RespondWithError(http.StatusUnauthorized)
return
}
}
// GET: /user/{id}
func (cr *UserController) Read(id string, cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
u, err := AuthenticateRequest(cx.Request)
if err != nil {
if err.Error() == e.NoAuth || err.Error() == e.UnAuth {
cx.RespondWithError(http.StatusUnauthorized)
return
} else {
log.Error("Err@user_Read: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
// Any user can access their own user info. Only admins can
// access other's info
if u.Uuid == id {
cx.RespondWithData(u)
return
} else if u.Admin {
nu, err := user.FindByUuid(id)
if err != nil {
if err.Error() == e.MongoDocNotFound {
cx.RespondWithNotFound()
return
} else {
log.Error("Err@user_Read:Admin: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
cx.RespondWithData(nu)
return
} else {
// Not sure how we could end up here but its probably the
// user's fault
cx.RespondWithError(http.StatusBadRequest)
return
}
}
// DELETE: /node/{id}
func (cr *NodeController) Delete(id string, cx *goweb.Context) {
LogRequest(cx.Request)
u, err := AuthenticateRequest(cx.Request)
if err != nil && err.Error() != e.NoAuth {
handleAuthError(err, cx)
return
}
if u == nil {
cx.RespondWithErrorMessage(e.NoAuth, http.StatusUnauthorized)
return
}
// Load node and handle user unauthorized
node, err := store.LoadNode(id, u.Uuid)
if err != nil {
if err.Error() == e.UnAuth {
cx.RespondWithError(http.StatusUnauthorized)
return
} else if err.Error() == e.MongoDocNotFound {
cx.RespondWithNotFound()
return
} else {
// In theory the db connection could be lost between
// checking user and load but seems unlikely.
log.Error("Err@node_Read:Delete: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
if err := node.Delete(); err == nil {
cx.RespondWithOK()
return
} else {
log.Error("Err@node_Delet:Delete: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
}
return
}
// DELETE: /node
func (cr *Controller) DeleteMany(cx *goweb.Context) {
request.Log(cx.Request)
cx.RespondWithError(http.StatusNotImplemented)
}
// POST: /queue
func (cr *QueueController) Create(cx *goweb.Context) {
LogRequest(cx.Request)
cx.RespondWithError(http.StatusNotImplemented)
}
// PUT: /node
func (cr *NodeController) UpdateMany(cx *goweb.Context) {
LogRequest(cx.Request)
cx.RespondWithError(http.StatusNotImplemented)
}
// GET: /node
// To do:
// - Iterate node queries
func (cr *NodeController) ReadMany(cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
u, err := AuthenticateRequest(cx.Request)
if err != nil && err.Error() != e.NoAuth {
handleAuthError(err, cx)
return
}
// Gather query params
query := &Query{list: cx.Request.URL.Query()}
// Setup query and nodes objects
q := bson.M{}
nodes := store.Nodes{}
if u != nil {
// Admin sees all
if !u.Admin {
q["$or"] = []bson.M{bson.M{"acl.read": []string{}}, bson.M{"acl.read": u.Uuid}}
}
} else {
if conf.ANON_READ {
// select on only nodes with no read rights set
q["acl.read"] = []string{}
} else {
cx.RespondWithErrorMessage(e.NoAuth, http.StatusUnauthorized)
return
}
}
// Gather params to make db query. Do not include the
// following list.
skip := map[string]int{"limit": 1, "skip": 1, "query": 1}
if query.Has("query") {
for key, val := range query.All() {
_, s := skip[key]
if !s {
q[fmt.Sprintf("attributes.%s", key)] = val[0]
}
}
}
// Limit and skip. Set default if both are not specified
if query.Has("limit") || query.Has("skip") {
var lim, off int
if query.Has("limit") {
lim, _ = strconv.Atoi(query.Value("limit"))
} else {
lim = 100
}
if query.Has("skip") {
off, _ = strconv.Atoi(query.Value("skip"))
} else {
off = 0
}
// Get nodes from db
err := nodes.GetAllLimitOffset(q, lim, off)
if err != nil {
log.Error("err " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
} else {
// Get nodes from db
err := nodes.GetAll(q)
if err != nil {
log.Error("err " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
}
cx.RespondWithData(nodes)
return
}
// PUT: /node/{id} -> multipart-form
func (cr *NodeController) Update(id string, cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
u, err := AuthenticateRequest(cx.Request)
if err != nil && err.Error() != e.NoAuth {
handleAuthError(err, cx)
return
}
// Gather query params
query := &Query{list: cx.Request.URL.Query()}
// Fake public user
if u == nil {
u = &user.User{Uuid: ""}
}
node, err := store.LoadNode(id, u.Uuid)
if err != nil {
if err.Error() == e.UnAuth {
cx.RespondWithError(http.StatusUnauthorized)
return
} else if err.Error() == e.MongoDocNotFound {
cx.RespondWithNotFound()
return
} else {
// In theory the db connection could be lost between
// checking user and load but seems unlikely.
log.Error("Err@node_Update:LoadNode: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
if query.Has("index") {
if !node.HasFile() {
cx.RespondWithErrorMessage("node file empty", http.StatusBadRequest)
return
}
if query.Value("index") == "bai" {
//bam index is created by the command-line tool samtools
if ext := node.FileExt(); ext == ".bam" {
if err := CreateBamIndex(node.FilePath()); err != nil {
cx.RespondWithErrorMessage("Error while creating bam index", http.StatusBadRequest)
return
}
return
} else {
cx.RespondWithErrorMessage("Index type bai requires .bam file", http.StatusBadRequest)
return
}
}
newIndexer := indexer.Indexer(query.Value("index"))
f, _ := os.Open(node.FilePath())
defer f.Close()
idxer := newIndexer(f)
err := idxer.Create()
if err != nil {
log.Error("err " + err.Error())
}
err = idxer.Dump(node.IndexPath() + "/record")
if err != nil {
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
} else {
cx.RespondWithOK()
return
}
} else {
params, files, err := ParseMultipartForm(cx.Request)
if err != nil {
log.Error("err " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
err = node.Update(params, files)
if err != nil {
errors := []string{e.FileImut, e.AttrImut, "parts cannot be less than 1"}
for e := range errors {
if err.Error() == errors[e] {
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
}
log.Error("err " + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
cx.RespondWithData(node)
}
return
}
// GET: /job
// To do:
// - Iterate job queries
func (cr *JobController) ReadMany(cx *goweb.Context) {
LogRequest(cx.Request)
// Gather query params
query := &Query{list: cx.Request.URL.Query()}
// Setup query and jobs objects
q := bson.M{}
jobs := new(core.Jobs)
// Gather params to make db query. Do not include the
// following list.
skip := map[string]int{"limit": 1, "skip": 1, "query": 1}
if query.Has("query") {
for key, val := range query.All() {
_, s := skip[key]
if !s {
q[key] = val[0]
}
}
} else if query.Has("active") {
q["state"] = core.JOB_STAT_SUBMITTED
} else if query.Has("suspend") {
q["state"] = core.JOB_STAT_SUSPEND
}
// Limit and skip. Set default if both are not specified
if query.Has("limit") || query.Has("skip") {
var lim, off int
if query.Has("limit") {
lim, _ = strconv.Atoi(query.Value("limit"))
} else {
lim = 100
}
if query.Has("skip") {
off, _ = strconv.Atoi(query.Value("skip"))
} else {
off = 0
}
// Get jobs from db
err := jobs.GetAllLimitOffset(q, lim, off)
if err != nil {
Log.Error("err " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
} else {
// Get jobs from db
err := jobs.GetAll(q)
if err != nil {
Log.Error("err " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
}
//getting real active (in-progress) job (some jobs are in "submitted" states but not in the queue,
//because they may have failed and not recovered from the mongodb).
if query.Has("active") {
filtered_jobs := []core.Job{}
act_jobs := queueMgr.GetActiveJobs()
length := jobs.Length()
for i := 0; i < length; i++ {
job := jobs.GetJobAt(i)
if _, ok := act_jobs[job.Id]; ok {
filtered_jobs = append(filtered_jobs, job)
}
}
cx.RespondWithData(filtered_jobs)
return
}
//geting suspended job in the current queue (excluding jobs in db but not in qmgr)
if query.Has("suspend") {
filtered_jobs := []core.Job{}
suspend_jobs := queueMgr.GetSuspendJobs()
length := jobs.Length()
for i := 0; i < length; i++ {
job := jobs.GetJobAt(i)
if _, ok := suspend_jobs[job.Id]; ok {
filtered_jobs = append(filtered_jobs, job)
}
}
cx.RespondWithData(filtered_jobs)
return
}
cx.RespondWithData(jobs)
return
}
// GET: /node/{id}
// ToDo: clean up this function. About to get unmanageable
func (cr *NodeController) Read(id string, cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
u, err := AuthenticateRequest(cx.Request)
if err != nil && err.Error() != e.NoAuth {
handleAuthError(err, cx)
return
}
// Fake public user
if u == nil {
if conf.ANON_READ {
u = &user.User{Uuid: ""}
} else {
cx.RespondWithErrorMessage(e.NoAuth, http.StatusUnauthorized)
return
}
}
// Gather query params
query := &Query{list: cx.Request.URL.Query()}
var fFunc filter.FilterFunc = nil
if query.Has("filter") {
if filter.Has(query.Value("filter")) {
fFunc = filter.Filter(query.Value("filter"))
}
}
// Load node and handle user unauthorized
node, err := store.LoadNode(id, u.Uuid)
if err != nil {
if err.Error() == e.UnAuth {
cx.RespondWithError(http.StatusUnauthorized)
return
} else if err.Error() == e.MongoDocNotFound {
cx.RespondWithNotFound()
return
} else {
// In theory the db connection could be lost between
// checking user and load but seems unlikely.
log.Error("Err@node_Read:LoadNode: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
// Switch though param flags
// ?download=1
if query.Has("download") {
if !node.HasFile() {
cx.RespondWithErrorMessage("File not found", http.StatusBadRequest)
return
}
//_, chunksize :=
// ?index=foo
if query.Has("index") {
//handling bam file
if query.Value("index") == "bai" {
s := &streamer{rs: []store.SectionReader{}, ws: cx.ResponseWriter, contentType: "application/octet-stream", filename: node.Id, size: node.File.Size, filter: fFunc}
var region string
if query.Has("region") {
//retrieve alingments overlapped with specified region
region = query.Value("region")
}
argv, err := ParseSamtoolsArgs(query)
if err != nil {
cx.RespondWithErrorMessage("Invaid args in query url", http.StatusBadRequest)
return
}
err = s.stream_samtools(node.FilePath(), region, argv...)
if err != nil {
cx.RespondWithErrorMessage("error while involking samtools", http.StatusBadRequest)
return
}
return
}
// if forgot ?part=N
if !query.Has("part") {
cx.RespondWithErrorMessage("Index parameter requires part parameter", http.StatusBadRequest)
return
}
// open file
r, err := node.FileReader()
if err != nil {
log.Error("Err@node_Read:Open: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
// load index
idx, err := node.Index(query.Value("index"))
if err != nil {
cx.RespondWithErrorMessage("Invalid index", http.StatusBadRequest)
return
}
if idx.Type() == "virtual" {
csize := int64(1048576)
if query.Has("chunksize") {
csize, err = strconv.ParseInt(query.Value("chunksize"), 10, 64)
if err != nil {
cx.RespondWithErrorMessage("Invalid chunksize", http.StatusBadRequest)
return
}
}
idx.Set(map[string]interface{}{"ChunkSize": csize})
}
var size int64 = 0
s := &streamer{rs: []store.SectionReader{}, ws: cx.ResponseWriter, contentType: "application/octet-stream", filename: node.Id, filter: fFunc}
for _, p := range query.List("part") {
pos, length, err := idx.Part(p)
if err != nil {
cx.RespondWithErrorMessage("Invalid index part", http.StatusBadRequest)
return
}
size += length
s.rs = append(s.rs, io.NewSectionReader(r, pos, length))
}
s.size = size
err = s.stream()
if err != nil {
// causes "multiple response.WriteHeader calls" error but better than no response
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
log.Error("err: " + err.Error())
}
} else { //!query.Has("index")
nf, err := node.FileReader()
if err != nil {
// File not found or some sort of file read error.
// Probably deserves more checking
log.Error("err " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
s := &streamer{rs: []store.SectionReader{nf}, ws: cx.ResponseWriter, contentType: "application/octet-stream", filename: node.Id, size: node.File.Size, filter: fFunc}
err = s.stream()
if err != nil {
// causes "multiple response.WriteHeader calls" error but better than no response
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
log.Error("err " + err.Error())
}
}
return
} else if query.Has("pipe") {
cx.RespondWithError(http.StatusNotImplemented)
} else if query.Has("list") {
cx.RespondWithError(http.StatusNotImplemented)
} else {
// Base case respond with node in json
cx.RespondWithData(node)
}
}
// DELETE: /node/{id}
func (cr *NodeController) Delete(id string, cx *goweb.Context) {
LogRequest(cx.Request)
cx.RespondWithError(http.StatusNotImplemented)
}
// GET: /node
// To do:
// - Iterate node queries
func (cr *NodeController) ReadMany(cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
u, err := AuthenticateRequest(cx.Request)
if err != nil && err.Error() != e.NoAuth {
handleAuthError(err, cx)
return
}
// Gather query params
query := &Query{list: cx.Request.URL.Query()}
// Setup query and nodes objects
q := bson.M{}
nodes := store.Nodes{}
if u != nil {
// Admin sees all
if !u.Admin {
q["$or"] = []bson.M{bson.M{"acl.read": []string{}}, bson.M{"acl.read": u.Uuid}, bson.M{"acl.owner": u.Uuid}}
}
} else {
if conf.ANON_READ {
// select on only nodes with no read rights set
q["acl.read"] = []string{}
} else {
cx.RespondWithErrorMessage(e.NoAuth, http.StatusUnauthorized)
return
}
}
// Gather params to make db query. Do not include the
// following list.
paramlist := map[string]int{"limit": 1, "offset": 1, "query": 1, "querynode": 1}
if query.Has("query") {
for key, val := range query.All() {
_, s := paramlist[key]
if !s {
q[fmt.Sprintf("attributes.%s", key)] = val[0]
}
}
} else if query.Has("querynode") {
for key, val := range query.All() {
if key == "type" {
querytypes := strings.Split(query.Value("type"), ",")
q["type"] = bson.M{"$all": querytypes}
} else {
_, s := paramlist[key]
if !s {
q[key] = val[0]
}
}
}
}
// defaults
limit := 25
offset := 0
if query.Has("limit") {
limit = ToInt(query.Value("limit"))
}
if query.Has("offset") {
offset = ToInt(query.Value("offset"))
}
// Get nodes from db
count, err := nodes.GetPaginated(q, limit, offset)
if err != nil {
log.Error("err " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
cx.RespondWithPaginatedData(nodes, limit, offset, count)
return
}
// PUT: /node/{id} -> multipart-form
func (cr *NodeController) Update(id string, cx *goweb.Context) {
// Log Request and check for Auth
LogRequest(cx.Request)
u, err := AuthenticateRequest(cx.Request)
if err != nil && err.Error() != e.NoAuth {
handleAuthError(err, cx)
return
}
// Gather query params
query := &Query{list: cx.Request.URL.Query()}
// Fake public user
if u == nil {
u = &user.User{Uuid: ""}
}
node, err := store.LoadNode(id, u.Uuid)
if err != nil {
if err.Error() == e.UnAuth {
cx.RespondWithError(http.StatusUnauthorized)
return
} else if err.Error() == e.MongoDocNotFound {
cx.RespondWithNotFound()
return
} else {
// In theory the db connection could be lost between
// checking user and load but seems unlikely.
log.Error("Err@node_Update:LoadNode: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
if query.Has("index") {
if conf.PERF_LOG {
log.Perf("START indexing: " + id)
}
if !node.HasFile() {
cx.RespondWithErrorMessage("node file empty", http.StatusBadRequest)
return
}
if query.Value("index") == "bai" {
//bam index is created by the command-line tool samtools
if ext := node.FileExt(); ext == ".bam" {
if err := CreateBamIndex(node.FilePath()); err != nil {
cx.RespondWithErrorMessage("Error while creating bam index", http.StatusBadRequest)
return
}
return
} else {
cx.RespondWithErrorMessage("Index type bai requires .bam file", http.StatusBadRequest)
return
}
}
idxtype := query.Value("index")
if _, ok := indexer.Indexers[idxtype]; !ok {
cx.RespondWithErrorMessage("invalid index type", http.StatusBadRequest)
return
}
newIndexer := indexer.Indexer(idxtype)
f, _ := os.Open(node.FilePath())
defer f.Close()
idxer := newIndexer(f)
count, err := idxer.Create()
if err != nil {
log.Error("err " + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
if err := idxer.Dump(node.IndexPath() + "/" + query.Value("index") + ".idx"); err != nil {
log.Error("err " + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
idxInfo := store.IdxInfo{
Type: query.Value("index"),
TotalUnits: count,
AvgUnitSize: node.File.Size / count,
}
if idxtype == "chunkrecord" {
idxInfo.AvgUnitSize = conf.CHUNK_SIZE
}
if err := node.SetIndexInfo(query.Value("index"), idxInfo); err != nil {
log.Error("[email protected]: " + err.Error())
}
if conf.PERF_LOG {
log.Perf("END indexing: " + id)
}
cx.RespondWithOK()
return
} else {
if conf.PERF_LOG {
log.Perf("START PUT data: " + id)
}
params, files, err := ParseMultipartForm(cx.Request)
if err != nil {
log.Error("err@node_ParseMultipartForm: " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
err = node.Update(params, files)
if err != nil {
errors := []string{e.FileImut, e.AttrImut, "parts cannot be less than 1"}
for e := range errors {
if err.Error() == errors[e] {
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
}
log.Error("err@node_Update: " + id + ":" + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
cx.RespondWithData(node)
if conf.PERF_LOG {
log.Perf("END PUT data: " + id)
}
}
return
}