case "POST", "PUT":
if !n.HasFile() {
cx.RespondWithErrorMessage("Node has no file", http.StatusBadRequest)
return
} else if !hasType {
cx.RespondWithErrorMessage("Index create requires type", http.StatusBadRequest)
return
}
if !contains(filteredIndexes(n.Indexes), idxType) {
cx.RespondWithErrorMessage(fmt.Sprintf("Index type %s unavailable", idxType), http.StatusBadRequest)
return
}
if conf.Bool(conf.Conf["perf-log"]) {
logger.Perf("START indexing: " + id)
}
if query.Value("index") == "bai" {
//bam index is created by the command-line tool samtools
if ext := n.FileExt(); ext == ".bam" {
if err := index.CreateBamIndex(n.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
}
}
// GET, PUT, DELETE: /node/{nid}/index/{idxType}
func IndexTypedRequest(ctx context.Context) {
nid := ctx.PathValue("nid")
idxType := ctx.PathValue("idxType")
u, err := request.Authenticate(ctx.HttpRequest())
if err != nil && err.Error() != e.NoAuth {
request.AuthError(err, ctx)
return
}
// Fake public user
if u == nil {
u = &user.User{Uuid: ""}
}
// Load node and handle user unauthorized
n, err := node.Load(nid, u.Uuid)
if err != nil {
if err.Error() == e.UnAuth {
responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
return
} else if err.Error() == e.MongoDocNotFound {
responder.RespondWithError(ctx, http.StatusNotFound, "Node not found.")
return
} else {
// In theory the db connection could be lost between
// checking user and load but seems unlikely.
err_msg := "Err@index:LoadNode: " + err.Error()
logger.Error(err_msg)
responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
return
}
}
switch ctx.HttpRequest().Method {
case "DELETE":
rights := n.Acl.Check(u.Uuid)
if !rights["write"] {
responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
return
}
if _, has := n.Indexes[idxType]; has {
if err := n.DeleteIndex(idxType); err != nil {
err_msg := err.Error()
logger.Error(err_msg)
responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
}
responder.RespondOK(ctx)
} else {
responder.RespondWithError(ctx, http.StatusBadRequest, fmt.Sprintf("Node %s does not have index of type %s.", n.Id, idxType))
}
case "GET":
if v, has := n.Indexes[idxType]; has {
responder.RespondWithData(ctx, map[string]interface{}{idxType: v})
} else {
responder.RespondWithError(ctx, http.StatusBadRequest, fmt.Sprintf("Node %s does not have index of type %s.", n.Id, idxType))
}
case "PUT":
rights := n.Acl.Check(u.Uuid)
if !rights["write"] {
responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
return
}
// Gather query params
query := ctx.HttpRequest().URL.Query()
_, forceRebuild := query["force_rebuild"]
if _, has := n.Indexes[idxType]; has {
if idxType == "size" {
responder.RespondOK(ctx)
return
} else if !forceRebuild {
responder.RespondWithError(ctx, http.StatusBadRequest, "This index already exists, please add the parameter 'force_rebuild=1' to force a rebuild of the existing index.")
return
}
}
if !n.HasFile() {
responder.RespondWithError(ctx, http.StatusBadRequest, "Node has no file.")
return
} else if idxType == "" {
responder.RespondWithError(ctx, http.StatusBadRequest, "Index create requires type.")
return
}
if _, ok := index.Indexers[idxType]; !ok && idxType != "bai" && idxType != "subset" && idxType != "column" {
responder.RespondWithError(ctx, http.StatusBadRequest, fmt.Sprintf("Index type %s unavailable.", idxType))
return
}
if idxType == "size" {
responder.RespondWithError(ctx, http.StatusBadRequest, fmt.Sprintf("Index type size is a virtual index and does not require index building."))
return
}
if conf.Bool(conf.Conf["perf-log"]) {
logger.Perf("START indexing: " + nid)
}
if idxType == "bai" {
//bam index is created by the command-line tool samtools
if n.Type == "subset" {
responder.RespondWithError(ctx, http.StatusBadRequest, "Shock does not support bam index creation on subset nodes.")
return
}
if ext := n.FileExt(); ext == ".bam" {
if err := index.CreateBamIndex(n.FilePath()); err != nil {
responder.RespondWithError(ctx, http.StatusInternalServerError, "Error while creating bam index.")
return
}
responder.RespondOK(ctx)
return
} else {
responder.RespondWithError(ctx, http.StatusBadRequest, "Index type bai requires .bam file.")
return
}
}
subsetSize := int64(0)
count := int64(0)
indexFormat := ""
subsetName := ""
if idxType == "subset" {
// Utilizing the multipart form parser since we need to upload a file.
params, files, err := request.ParseMultipartForm(ctx.HttpRequest())
if err != nil {
responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
return
}
parentIndex, hasParent := params["parent_index"]
if !hasParent {
responder.RespondWithError(ctx, http.StatusBadRequest, "Index type subset requires parent_index param.")
return
} else if _, has := n.Indexes[parentIndex]; !has {
responder.RespondWithError(ctx, http.StatusBadRequest, fmt.Sprintf("Node %s does not have index of type %s.", n.Id, parentIndex))
return
}
newIndex, hasName := params["index_name"]
if !hasName {
responder.RespondWithError(ctx, http.StatusBadRequest, "Index type subset requires index_name param.")
return
} else if _, reservedName := index.Indexers[newIndex]; reservedName || newIndex == "bai" {
responder.RespondWithError(ctx, http.StatusBadRequest, fmt.Sprintf("%s is a reserved index name and cannot be used to create a custom subset index.", newIndex))
return
}
subsetName = newIndex
subsetIndices, hasFile := files["subset_indices"]
if !hasFile {
responder.RespondWithError(ctx, http.StatusBadRequest, "Index type subset requires subset_indices file.")
return
}
f, _ := os.Open(subsetIndices.Path)
defer f.Close()
idxer := index.NewSubsetIndexer(f)
// we default to "array" index format for backwards compatibility
indexFormat = "array"
if n.Indexes[parentIndex].Format == "array" || n.Indexes[parentIndex].Format == "matrix" {
indexFormat = n.Indexes[parentIndex].Format
}
count, subsetSize, err = index.CreateSubsetIndex(&idxer, n.IndexPath()+"/"+newIndex+".idx", n.IndexPath()+"/"+parentIndex+".idx", indexFormat, n.Indexes[parentIndex].TotalUnits)
if err != nil {
logger.Error("err " + err.Error())
responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
return
}
} else if idxType == "column" {
// Gather query params
query := ctx.HttpRequest().URL.Query()
if n.Type == "subset" {
responder.RespondWithError(ctx, http.StatusBadRequest, "Shock does not support column index creation on subset nodes.")
return
}
if _, exists := query["number"]; !exists {
err_msg := "Index type column requires a number parameter in the url."
logger.Error(err_msg)
responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
return
}
num_str := query.Get("number")
idxType = idxType + num_str
num, err := strconv.Atoi(num_str)
if err != nil || num < 1 {
err_msg := "Index type column requires a number parameter in the url of an integer greater than zero."
logger.Error(err_msg)
responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
return
}
f, _ := os.Open(n.FilePath())
defer f.Close()
idxer := index.NewColumnIndexer(f)
count, indexFormat, err = index.CreateColumnIndex(&idxer, num, n.IndexPath()+"/"+idxType+".idx")
if err != nil {
logger.Error("err " + err.Error())
responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
return
}
} else {
if n.Type == "subset" && (idxType != "chunkrecord" || n.Subset.Parent.IndexName != "record") {
responder.RespondWithError(ctx, http.StatusBadRequest, "For subset nodes, Shock currently only supports subset and chunkrecord indexes. Also, for a chunkrecord index, the subset node must have been generated from a record index.")
return
}
newIndexer := index.Indexers[idxType]
f, _ := os.Open(n.FilePath())
defer f.Close()
var idxer index.Indexer
if n.Type == "subset" {
idxer = newIndexer(f, n.Type, n.Subset.Index.Format, n.IndexPath()+"/"+n.Subset.Parent.IndexName+".idx")
} else {
idxer = newIndexer(f, n.Type, "", "")
}
count, indexFormat, err = idxer.Create(n.IndexPath() + "/" + idxType + ".idx")
if err != nil {
logger.Error("err " + err.Error())
responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
return
}
}
if count == 0 {
responder.RespondWithError(ctx, http.StatusBadRequest, "Index empty.")
return
}
idxInfo := node.IdxInfo{
Type: idxType,
TotalUnits: count,
AvgUnitSize: n.File.Size / count,
Format: indexFormat,
}
//if idxType == "chunkrecord" {
// idxInfo.AvgUnitSize = conf.CHUNK_SIZE
//}
if idxType == "subset" {
idxType = subsetName
idxInfo.AvgUnitSize = subsetSize / count
}
if err := n.SetIndexInfo(idxType, idxInfo); err != nil {
logger.Error("[email protected]: " + err.Error())
}
if conf.Bool(conf.Conf["perf-log"]) {
logger.Perf("END indexing: " + nid)
}
responder.RespondOK(ctx)
return
default:
responder.RespondWithError(ctx, http.StatusNotImplemented, "This request type is not implemented.")
}
return
}
// PUT: /node/{id} -> multipart-form
func (cr *Controller) Update(id string, cx *goweb.Context) {
// Log Request and check for Auth
request.Log(cx.Request)
u, err := request.Authenticate(cx.Request)
if err != nil && err.Error() != e.NoAuth {
request.AuthError(err, cx)
return
}
// Gather query params
query := util.Q(cx.Request.URL.Query())
// Fake public user
if u == nil {
u = &user.User{Uuid: ""}
}
n, err := node.Load(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.
logger.Error("Err@node_Update:LoadNode: " + err.Error())
cx.RespondWithError(http.StatusInternalServerError)
return
}
}
if query.Has("index") {
if conf.Bool(conf.Conf["perf-log"]) {
logger.Perf("START indexing: " + id)
}
if !n.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 := n.FileExt(); ext == ".bam" {
if err := index.CreateBamIndex(n.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 := index.Indexers[idxtype]; !ok {
cx.RespondWithErrorMessage("invalid index type", http.StatusBadRequest)
return
}
newIndexer := index.Indexers[idxtype]
f, _ := os.Open(n.FilePath())
defer f.Close()
idxer := newIndexer(f)
count, err := idxer.Create()
if err != nil {
logger.Error("err " + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
if err := idxer.Dump(n.IndexPath() + "/" + query.Value("index") + ".idx"); err != nil {
logger.Error("err " + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
idxInfo := node.IdxInfo{
Type: query.Value("index"),
TotalUnits: count,
AvgUnitSize: n.File.Size / count,
}
if idxtype == "chunkrecord" {
idxInfo.AvgUnitSize = conf.CHUNK_SIZE
}
if err := n.SetIndexInfo(query.Value("index"), idxInfo); err != nil {
logger.Error("[email protected]: " + err.Error())
}
if conf.Bool(conf.Conf["perf-log"]) {
logger.Perf("END indexing: " + id)
}
cx.RespondWithOK()
return
} else {
if conf.Bool(conf.Conf["perf-log"]) {
logger.Perf("START PUT data: " + id)
}
params, files, err := request.ParseMultipartForm(cx.Request)
if err != nil {
logger.Error("err@node_ParseMultipartForm: " + err.Error())
cx.RespondWithError(http.StatusBadRequest)
return
}
err = n.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
}
}
logger.Error("err@node_Update: " + id + ":" + err.Error())
cx.RespondWithErrorMessage(err.Error(), http.StatusBadRequest)
return
}
cx.RespondWithData(n)
if conf.Bool(conf.Conf["perf-log"]) {
logger.Perf("END PUT data: " + id)
}
}
return
}
// PUT: /node/{id} -> multipart-form
func (cr *NodeController) Replace(id string, ctx context.Context) error {
u, err := request.Authenticate(ctx.HttpRequest())
if err != nil && err.Error() != e.NoAuth {
return request.AuthError(err, ctx)
}
// public user (no auth) can be used in some cases
if u == nil {
if conf.ANON_WRITE {
u = &user.User{Uuid: "public"}
} else {
return responder.RespondWithError(ctx, http.StatusUnauthorized, e.NoAuth)
}
}
// Load node by id
n, err := node.Load(id)
if err != nil {
if err == mgo.ErrNotFound {
return responder.RespondWithError(ctx, http.StatusNotFound, e.NodeNotFound)
} else {
// In theory the db connection could be lost between
// checking user and load but seems unlikely.
err_msg := "Err@node_Update:LoadNode: " + id + ":" + err.Error()
logger.Error(err_msg)
return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
}
}
rights := n.Acl.Check(u.Uuid)
prights := n.Acl.Check("public")
if rights["write"] == false && u.Admin == false && n.Acl.Owner != u.Uuid && prights["write"] == false {
return responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
}
if conf.LOG_PERF {
logger.Perf("START PUT data: " + id)
}
params, files, err := request.ParseMultipartForm(ctx.HttpRequest())
// clean up temp dir !!
defer node.RemoveAllFormFiles(files)
if err != nil {
err_msg := "err@node_ParseMultipartForm: " + err.Error()
logger.Error(err_msg)
return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
}
// need delete rights to set expiration
if _, hasExpiration := params["expiration"]; hasExpiration {
if rights["delete"] == false && u.Admin == false && n.Acl.Owner != u.Uuid && prights["delete"] == false {
return responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
}
}
if _, hasCopyData := params["copy_data"]; hasCopyData {
_, err = node.Load(params["copy_data"])
if err != nil {
return request.AuthError(err, ctx)
}
}
if _, hasParentNode := params["parent_node"]; hasParentNode {
_, err = node.Load(params["parent_node"])
if err != nil {
return request.AuthError(err, ctx)
}
}
err = n.Update(params, files)
if err != nil {
err_msg := "err@node_Update: " + id + ": " + err.Error()
logger.Error(err_msg)
return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
}
responder.RespondWithData(ctx, n)
if conf.LOG_PERF {
logger.Perf("END PUT data: " + id)
}
return nil
}
// PUT: /node/{id} -> multipart-form
func (cr *NodeController) Replace(id string, ctx context.Context) error {
u, err := request.Authenticate(ctx.HttpRequest())
if err != nil && err.Error() != e.NoAuth {
return request.AuthError(err, ctx)
}
// Fake public user
if u == nil {
u = &user.User{Uuid: ""}
}
n, err := node.Load(id, u.Uuid)
if err != nil {
if err.Error() == e.UnAuth {
return responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
} else if err.Error() == e.MongoDocNotFound {
return responder.RespondWithError(ctx, http.StatusNotFound, "Node not found")
} else {
// In theory the db connection could be lost between
// checking user and load but seems unlikely.
err_msg := "Err@node_Update:LoadNode: " + err.Error()
logger.Error(err_msg)
return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
}
}
rights := n.Acl.Check(u.Uuid)
if !rights["write"] {
return responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
}
if conf.Bool(conf.Conf["perf-log"]) {
logger.Perf("START PUT data: " + id)
}
params, files, err := request.ParseMultipartForm(ctx.HttpRequest())
if err != nil {
err_msg := "err@node_ParseMultipartForm: " + err.Error()
logger.Error(err_msg)
return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
}
if _, hasCopyData := params["copy_data"]; hasCopyData {
_, err = node.Load(params["copy_data"], u.Uuid)
if err != nil {
return request.AuthError(err, ctx)
}
}
if _, hasParentNode := params["parent_node"]; hasParentNode {
_, err = node.Load(params["parent_node"], u.Uuid)
if err != nil {
return request.AuthError(err, ctx)
}
}
err = n.Update(params, files)
if err != nil {
err_msg := "err@node_Update: " + id + ": " + err.Error()
logger.Error(err_msg)
return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
}
responder.RespondWithData(ctx, n)
if conf.Bool(conf.Conf["perf-log"]) {
logger.Perf("END PUT data: " + id)
}
return nil
}