// 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 {
// No Auth is not damning. Other errors are probably a dead db connection
if err.Error() != e.NoAuth {
if err.Error() == e.MongoDocNotFound {
cx.RespondWithErrorMessage("Invalid username or password", http.StatusBadRequest)
return
} else {
fmt.Println("Error at Auth:", err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
}
// Fake public user
if u == nil {
u = &user.User{Uuid: ""}
}
// 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 {
fmt.Println("Unauthorized")
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.
fmt.Println("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("node file not found", http.StatusBadRequest)
return
}
//_, chunksize :=
// ?index=foo
if query.Has("index") {
// if forgot ?part=N
if !query.Has("part") {
cx.RespondWithErrorMessage("Index parameter requires part parameter", http.StatusBadRequest)
return
}
// open file
r, err := os.Open(node.DataPath())
defer r.Close()
if err != nil {
fmt.Println("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: []io.ReadCloser{}, 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, NewSectionReaderCloser(r, pos, length))
}
s.size = size
err = s.stream()
if err != nil {
// fix
fmt.Println("err", err.Error())
}
} else {
nf, err := os.Open(node.DataPath())
if err != nil {
// File not found or some sort of file read error.
// Probably deserves more checking
fmt.Println("err", err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
s := &streamer{rs: []io.ReadCloser{nf}, ws: cx.ResponseWriter, contentType: "application/octet-stream", filename: node.Id, size: node.File.Size, filter: fFunc}
err = s.stream()
if err != nil {
// fix
fmt.Println("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)
}
}
// 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 {
// No Auth is not damning. Other errors are probably a dead db connection
if err.Error() != e.NoAuth {
if err.Error() == e.MongoDocNotFound {
cx.RespondWithErrorMessage("Invalid username or password", http.StatusBadRequest)
return
} else {
fmt.Println("Error at Auth:", err.Error())
cx.RespondWithError(http.StatusInternalServerError)
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 {
fmt.Println("Unauthorized")
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.
fmt.Println("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
}
newIndexer := indexer.Indexer(query.Value("index"))
f, _ := os.Open(node.DataPath())
defer f.Close()
idxer := newIndexer(f)
err := idxer.Create()
if err != nil {
fmt.Println(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 {
fmt.Println("err", err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
err = node.Update(params, files)
if err != nil {
errors := []string{"node file already set and is immutable", "node file immutable", "node attributes immutable", "node part already exists and is immutable"}
for e := range errors {
if err.Error() == errors[e] {
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
}
fmt.Println("err", err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
cx.RespondWithData(node)
}
return
}