// 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 }
// Options: /node func (cr *Controller) Options(cx *goweb.Context) { request.Log(cx.Request) cx.RespondWithOK() 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 }
// Options: /node func (cr *NodeController) Options(cx *goweb.Context) { LogRequest(cx.Request) cx.RespondWithOK() 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 }
func RespondOk(cx *goweb.Context) { LogRequest(cx.Request) cx.RespondWithOK() return }