// 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
}
}
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
}
// GET: /job/{id}
func (cr *JobController) Read(id string, cx *goweb.Context) {
LogRequest(cx.Request)
// Load job by id
job, err := core.LoadJob(id)
if err != nil {
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@job_Read:LoadJob: " + id + ":" + err.Error())
cx.RespondWithErrorMessage("job not found:"+id, http.StatusBadRequest)
return
}
}
// Base case respond with job in json
cx.RespondWithData(job)
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
}
// 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: /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)
}
}
// 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
}