Esempio n. 1
0
// GET: /node/{id}
func (cr *NodeController) Read(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 {
		if conf.Bool(conf.Conf["anon-read"]) {
			u = &user.User{Uuid: ""}
		} else {
			return responder.RespondWithError(ctx, http.StatusUnauthorized, e.NoAuth)
		}
	}

	// Load node and handle user unauthorized
	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.
			logger.Error("Err@node_Read:LoadNode:" + id + ":" + err.Error())

			n, err = node.LoadFromDisk(id)
			if err.Error() == "Node does not exist" {
				logger.Error(err.Error())
				return responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
			} else if err != nil {
				err_msg := "Err@node_Read:LoadNodeFromDisk:" + id + ":" + err.Error()
				logger.Error(err_msg)
				return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			}
		}
	}

	// Gather query params
	query := ctx.HttpRequest().URL.Query()

	var fFunc filter.FilterFunc = nil
	if _, ok := query["filter"]; ok {
		if filter.Has(query.Get("filter")) {
			fFunc = filter.Filter(query.Get("filter"))
		}
	}

	// Switch though param flags
	// ?download=1 or ?download_raw=1

	_, download_raw := query["download_raw"]
	if _, ok := query["download"]; ok || download_raw {
		if !n.HasFile() {
			return responder.RespondWithError(ctx, http.StatusBadRequest, "Node has no file")
		}
		filename := n.Id
		if _, ok := query["filename"]; ok {
			filename = query.Get("filename")
		}

		_, seek_ok := query["seek"]
		if _, length_ok := query["length"]; seek_ok || length_ok {
			if n.Type == "subset" {
				return responder.RespondWithError(ctx, http.StatusBadRequest, "subset nodes do not currently support seek/length offset retrieval")
			}

			var seek int64
			var length int64
			if !seek_ok {
				seek = 0
				length_str := query.Get("length")
				length, err = strconv.ParseInt(length_str, 10, 0)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "length must be an integer value")
				}
			} else if !length_ok {
				seek_str := query.Get("seek")
				seek, err = strconv.ParseInt(seek_str, 10, 0)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "seek must be an integer value")
				}
				length = n.File.Size - seek
			} else {
				seek_str := query.Get("seek")
				seek, err = strconv.ParseInt(seek_str, 10, 0)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "seek must be an integer value")
				}
				length_str := query.Get("length")
				length, err = strconv.ParseInt(length_str, 10, 0)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "length must be an integer value")
				}
			}
			r, err := n.FileReader()
			defer r.Close()
			if err != nil {
				err_msg := "Err@node_Read:Open: " + err.Error()
				logger.Error(err_msg)
				return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			}
			s := &request.Streamer{R: []file.SectionReader{}, W: ctx.HttpResponseWriter(), ContentType: "application/octet-stream", Filename: filename, Size: length, Filter: fFunc}
			s.R = append(s.R, io.NewSectionReader(r, seek, length))
			if download_raw {
				err = s.StreamRaw()
				if err != nil {
					// causes "multiple response.WriteHeader calls" error but better than no response
					err_msg := "err:@node_Read s.StreamRaw: " + err.Error()
					logger.Error(err_msg)
					return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
				}
			} else {
				err = s.Stream()
				if err != nil {
					// causes "multiple response.WriteHeader calls" error but better than no response
					err_msg := "err:@node_Read s.Stream: " + err.Error()
					logger.Error(err_msg)
					return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
				}
			}
		} else if _, ok := query["index"]; ok {
			//handling bam file
			if query.Get("index") == "bai" {
				if n.Type == "subset" {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "subset nodes do not support bam indices")
				}

				s := &request.Streamer{R: []file.SectionReader{}, W: ctx.HttpResponseWriter(), ContentType: "application/octet-stream", Filename: filename, Size: n.File.Size, Filter: fFunc}

				var region string
				if _, ok := query["region"]; ok {
					//retrieve alingments overlapped with specified region
					region = query.Get("region")
				}
				argv, err := request.ParseSamtoolsArgs(ctx)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "Invaid args in query url")
				}
				err = s.StreamSamtools(n.FilePath(), region, argv...)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "error while invoking samtools")
				}
				return nil
			}

			// open file
			r, err := n.FileReader()
			defer r.Close()
			if err != nil {
				err_msg := "Err@node_Read:Open: " + err.Error()
				logger.Error(err_msg)
				return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			}

			// load index obj and info
			idxName := query.Get("index")
			idxInfo, ok := n.Indexes[idxName]
			if !ok {
				return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid index")
			}
			idx, err := n.DynamicIndex(idxName)
			if err != nil {
				return responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
			}

			if idx.Type() == "virtual" {
				if n.Type == "subset" {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "subset nodes do not currently support virtual indices")
				}

				csize := conf.CHUNK_SIZE
				if _, ok := query["chunk_size"]; ok {
					csize, err = strconv.ParseInt(query.Get("chunk_size"), 10, 64)
					if err != nil {
						return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid chunk_size")
					}
				}
				idx.Set(map[string]interface{}{"ChunkSize": csize})
			}

			var size int64 = 0
			s := &request.Streamer{R: []file.SectionReader{}, W: ctx.HttpResponseWriter(), ContentType: "application/octet-stream", Filename: filename, Filter: fFunc}

			_, hasPart := query["part"]
			if n.Type == "subset" && idxName == "chunkrecord" {
				recordIdxName := "record"
				recordIdxInfo, ok := n.Indexes[recordIdxName]
				if !ok {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid request, record index must exist to retrieve chunkrecord index on a subset node.")
				}
				recordIdx, err := n.DynamicIndex(recordIdxName)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
				}

				if !hasPart {
					// download full subset file
					fullRange := "1-" + strconv.FormatInt(recordIdxInfo.TotalUnits, 10)
					recSlice, err := recordIdx.Range(fullRange, n.IndexPath()+"/"+recordIdxName+".idx", recordIdxInfo.TotalUnits)
					if err != nil {
						return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid index subset")
					}
					for _, rec := range recSlice {
						size += rec[1]
						s.R = append(s.R, io.NewSectionReader(r, rec[0], rec[1]))
					}
				} else if hasPart {
					// download parts
					for _, p := range query["part"] {
						chunkRecSlice, err := idx.Range(p, n.IndexPath()+"/"+idxName+".idx", idxInfo.TotalUnits)
						if err != nil {
							return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid index part")
						}
						// This gets us the parts of the chunkrecord index, but we still need to convert these to record indices.
						for _, chunkRec := range chunkRecSlice {
							start := (chunkRec[0] / 16) + 1
							stop := (start - 1) + (chunkRec[1] / 16)
							recSlice, err := recordIdx.Range(strconv.FormatInt(start, 10)+"-"+strconv.FormatInt(stop, 10), n.IndexPath()+"/"+recordIdxName+".idx", recordIdxInfo.TotalUnits)
							if err != nil {
								return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid index subset")
							}
							for _, rec := range recSlice {
								size += rec[1]
								s.R = append(s.R, io.NewSectionReader(r, rec[0], rec[1]))
							}
						}
					}
				} else {
					// bad request
					return responder.RespondWithError(ctx, http.StatusBadRequest, "Index parameter requires part parameter")
				}
			} else {
				if (!hasPart) && (idxInfo.Type == "subset") {
					// download full subset file
					fullRange := "1-" + strconv.FormatInt(idxInfo.TotalUnits, 10)
					recSlice, err := idx.Range(fullRange, n.IndexPath()+"/"+idxName+".idx", idxInfo.TotalUnits)
					if err != nil {
						return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid index subset")
					}
					for _, rec := range recSlice {
						size += rec[1]
						s.R = append(s.R, io.NewSectionReader(r, rec[0], rec[1]))
					}
				} else if hasPart {
					// download parts
					for _, p := range query["part"] {
						// special case for subset ranges
						if idxInfo.Type == "subset" {
							recSlice, err := idx.Range(p, n.IndexPath()+"/"+idxName+".idx", idxInfo.TotalUnits)
							if err != nil {
								return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid index part")
							}
							for _, rec := range recSlice {
								size += rec[1]
								s.R = append(s.R, io.NewSectionReader(r, rec[0], rec[1]))
							}
						} else {
							pos, length, err := idx.Part(p, n.IndexPath()+"/"+idxName+".idx", idxInfo.TotalUnits)
							if err != nil {
								return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid index part")
							}
							size += length
							s.R = append(s.R, io.NewSectionReader(r, pos, length))
						}
					}
				} else {
					// bad request
					return responder.RespondWithError(ctx, http.StatusBadRequest, "Index parameter requires part parameter")
				}
			}
			s.Size = size
			if download_raw {
				err = s.StreamRaw()
				if err != nil {
					// causes "multiple response.WriteHeader calls" error but better than no response
					err_msg := "err:@node_Read s.StreamRaw: " + err.Error()
					logger.Error(err_msg)
					return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
				}
			} else {
				err = s.Stream()
				if err != nil {
					// causes "multiple response.WriteHeader calls" error but better than no response
					err_msg := "err:@node_Read s.Stream: " + err.Error()
					logger.Error(err_msg)
					return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
				}
			}
			// download full file
		} else {
			if n.Type == "subset" {
				// open file
				r, err := n.FileReader()
				defer r.Close()
				if err != nil {
					err_msg := "Err@node_Read:Open: " + err.Error()
					logger.Error(err_msg)
					return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
				}

				idx := index.New()

				s := &request.Streamer{R: []file.SectionReader{}, W: ctx.HttpResponseWriter(), ContentType: "application/octet-stream", Filename: filename, Size: n.File.Size, Filter: fFunc}

				fullRange := "1-" + strconv.FormatInt(n.Subset.Index.TotalUnits, 10)
				recSlice, err := idx.Range(fullRange, n.Path()+"/"+n.Id+".subset.idx", n.Subset.Index.TotalUnits)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusInternalServerError, "Invalid data index for subset node.")
				}
				for _, rec := range recSlice {
					s.R = append(s.R, io.NewSectionReader(r, rec[0], rec[1]))
				}

				if download_raw {
					err = s.StreamRaw()
					if err != nil {
						// causes "multiple response.WriteHeader calls" error but better than no response
						err_msg := "err:@node_Read s.StreamRaw: " + err.Error()
						logger.Error(err_msg)
						return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
					}
				} else {
					err = s.Stream()
					if err != nil {
						// causes "multiple response.WriteHeader calls" error but better than no response
						err_msg := "err:@node_Read s.Stream: " + err.Error()
						logger.Error(err_msg)
						return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
					}
				}
			} else {
				nf, err := n.FileReader()
				defer nf.Close()
				if err != nil {
					// File not found or some sort of file read error.
					// Probably deserves more checking
					err_msg := "err:@node_Read node.FileReader: " + err.Error()
					logger.Error(err_msg)
					return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
				}
				s := &request.Streamer{R: []file.SectionReader{nf}, W: ctx.HttpResponseWriter(), ContentType: "application/octet-stream", Filename: filename, Size: n.File.Size, Filter: fFunc}
				if download_raw {
					err = s.StreamRaw()
					if err != nil {
						// causes "multiple response.WriteHeader calls" error but better than no response
						err_msg := "err:@node_Read s.StreamRaw: " + err.Error()
						logger.Error(err_msg)
						return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
					}
				} else {
					err = s.Stream()
					if err != nil {
						// causes "multiple response.WriteHeader calls" error but better than no response
						err_msg := "err:@node_Read s.Stream: " + err.Error()
						logger.Error(err_msg)
						return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
					}
				}
			}
		}
	} else if _, ok := query["download_url"]; ok {
		if n.Type == "subset" {
			return responder.RespondWithError(ctx, http.StatusBadRequest, "subset nodes do not currently support download_url operation")
		}

		if !n.HasFile() {
			return responder.RespondWithError(ctx, http.StatusBadRequest, "Node has no file")
		} else {
			options := map[string]string{}
			if _, ok := query["filename"]; ok {
				options["filename"] = query.Get("filename")
			}
			if p, err := preauth.New(util.RandString(20), "download", n.Id, options); err != nil {
				err_msg := "err:@node_Read download_url: " + err.Error()
				logger.Error(err_msg)
				return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			} else {
				return responder.RespondWithData(ctx, util.UrlResponse{Url: util.ApiUrl(ctx) + "/preauth/" + p.Id, ValidTill: p.ValidTill.Format(time.ANSIC)})
			}
		}
	} else if _, ok := query["download_post"]; ok {
		// This is a request to post the node to another Shock server. The 'post_url' parameter is required.
		// By default the post operation will include the data file and attributes (these options can be set
		// with post_data=0/1 and post_attr=0/1).
		if n.Type == "subset" {
			return responder.RespondWithError(ctx, http.StatusBadRequest, "subset nodes do not currently support download_post operation")
		}

		post_url := ""
		if _, ok := query["post_url"]; ok {
			post_url = query.Get("post_url")
		} else {
			return responder.RespondWithError(ctx, http.StatusBadRequest, "Request type requires post_url parameter of where to post new Shock node")
		}

		post_opts := map[string]int{
			"post_data": 1,
			"post_attr": 1,
		}

		for k, _ := range post_opts {
			if _, ok := query[k]; ok {
				if query.Get(k) == "0" {
					post_opts[k] = 0
				} else if query.Get(k) == "1" {
					post_opts[k] = 1
				} else {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "Parameter "+k+" must be either 0 or 1")
				}
			}
		}

		form := client.NewForm()
		form.AddParam("file_name", n.File.Name)

		if post_opts["post_data"] == 1 {
			form.AddFile("upload", n.FilePath())
		}

		if post_opts["post_attr"] == 1 && n.Attributes != nil {
			attr, _ := json.Marshal(n.Attributes)
			form.AddParam("attributes_str", string(attr[:]))
		}

		err = form.Create()
		if err != nil {
			err_msg := "could not create multipart form for posting to Shock server: " + err.Error()
			logger.Error(err_msg)
			return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
		}

		headers := client.Header{
			"Content-Type":   form.ContentType,
			"Content-Length": strconv.FormatInt(form.Length, 10),
		}

		if _, hasAuth := ctx.HttpRequest().Header["Authorization"]; hasAuth {
			headers["Authorization"] = ctx.HttpRequest().Header.Get("Authorization")
		}

		if res, err := client.Do("POST", post_url, headers, form.Reader); err == nil {
			if res.StatusCode == 200 {
				r := responseWrapper{}
				body, _ := ioutil.ReadAll(res.Body)
				if err = json.Unmarshal(body, &r); err != nil {
					err_msg := "err:@node_Read POST: " + err.Error()
					logger.Error(err_msg)
					return responder.WriteResponseObject(ctx, http.StatusInternalServerError, err_msg)
				} else {
					return responder.WriteResponseObject(ctx, http.StatusOK, r)
				}
			} else {
				r := responseWrapper{}
				body, _ := ioutil.ReadAll(res.Body)
				if err = json.Unmarshal(body, &r); err == nil {
					err_msg := res.Status + ": " + (*r.Error)[0]
					logger.Error(err_msg)
					return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
				} else {
					err_msg := "request error: " + res.Status
					logger.Error(err_msg)
					return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
				}
			}
		} else {
			return err
		}
	} else {
		// Base case respond with node in json
		return responder.RespondWithData(ctx, n)
	}

	return nil
}
Esempio n. 2
0
func mapRoutes() {
	goweb.MapBefore(func(ctx context.Context) error {
		req := ctx.HttpRequest()
		host, _, _ := net.SplitHostPort(req.RemoteAddr)
		if host == "::1" {
			host = "localhost"
		}
		suffix := ""
		if _, ok := req.Header["Authorization"]; ok {
			suffix += " AUTH"
		}
		if l, has := req.Header["Content-Length"]; has {
			suffix += " Content-Length: " + l[0]
		}
		logger.Info("access", fmt.Sprintf("%s REQ RECEIVED \"%s %s%s\"", host, ctx.MethodString(), req.RequestURI, suffix))
		return nil
	})

	goweb.MapAfter(func(ctx context.Context) error {
		req := ctx.HttpRequest()
		host, _, _ := net.SplitHostPort(req.RemoteAddr)
		if host == "::1" {
			host = "localhost"
		}
		suffix := ""
		if _, ok := req.Header["Authorization"]; ok {
			suffix += " AUTH"
		}
		if l, has := req.Header["Content-Length"]; has {
			suffix += " Content-Length: " + l[0]
		}
		logger.Info("access", fmt.Sprintf("RESPONDED TO %s \"%s %s%s\"", host, ctx.MethodString(), req.RequestURI, suffix))
		return nil
	})

	goweb.Map("/preauth/{id}", func(ctx context.Context) error {
		if ctx.HttpRequest().Method == "OPTIONS" {
			return responder.RespondOK(ctx)
		}
		pcon.PreAuthRequest(ctx)
		return nil
	})

	goweb.Map("/node/{nid}/acl/{type}", func(ctx context.Context) error {
		if ctx.HttpRequest().Method == "OPTIONS" {
			return responder.RespondOK(ctx)
		}
		acon.AclTypedRequest(ctx)
		return nil
	})

	goweb.Map("/node/{nid}/acl/", func(ctx context.Context) error {
		if ctx.HttpRequest().Method == "OPTIONS" {
			return responder.RespondOK(ctx)
		}
		acon.AclRequest(ctx)
		return nil
	})

	goweb.Map("/node/{nid}/index/{idxType}", func(ctx context.Context) error {
		if ctx.HttpRequest().Method == "OPTIONS" {
			return responder.RespondOK(ctx)
		}
		icon.IndexTypedRequest(ctx)
		return nil
	})

	goweb.Map("/openparts", func(ctx context.Context) error {
		ids := node.LockMgr.GetNodes()
		return responder.RespondWithData(ctx, ids)
	})

	goweb.Map("/", func(ctx context.Context) error {
		host := util.ApiUrl(ctx)

		attrs := strings.Split(conf.MONGODB_ATTRIBUTE_INDEXES, ",")
		for k, v := range attrs {
			attrs[k] = strings.TrimSpace(v)
		}

		anonPerms := new(anonymous)
		anonPerms.Read = conf.ANON_READ
		anonPerms.Write = conf.ANON_WRITE
		anonPerms.Delete = conf.ANON_DELETE

		var auth []string
		if conf.AUTH_GLOBUS_TOKEN_URL != "" && conf.AUTH_GLOBUS_PROFILE_URL != "" {
			auth = append(auth, "globus")
		}
		if conf.AUTH_MGRAST_OAUTH_URL != "" {
			auth = append(auth, "mgrast")
		}

		r := resource{
			A: attrs,
			C: conf.ADMIN_EMAIL,
			D: host + "/wiki/",
			I: "Shock",
			O: auth,
			P: *anonPerms,
			R: []string{"node"},
			S: time.Now().Format(longDateForm),
			T: "Shock",
			U: host + "/",
			V: "[% VERSION %]",
		}
		return responder.WriteResponseObject(ctx, http.StatusOK, r)
	})

	nodeController := new(ncon.NodeController)
	goweb.MapController(nodeController)

	goweb.MapStatic("/wiki", conf.PATH_SITE)

	// Map the favicon
	//goweb.MapStaticFile("/favicon.ico", "static-files/favicon.ico")

	// Catch-all handler for everything that we don't understand
	goweb.Map(func(ctx context.Context) error {
		return responder.RespondWithError(ctx, http.StatusBadRequest, "Parameters do not match a valid Shock request type.")
	})
}
Esempio n. 3
0
// GET: /node/{id}
func (cr *NodeController) Read(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 {
		if conf.Bool(conf.Conf["anon-read"]) {
			u = &user.User{Uuid: ""}
		} else {
			return responder.RespondWithError(ctx, http.StatusUnauthorized, e.NoAuth)
		}
	}

	// Gather query params
	query := ctx.HttpRequest().URL.Query()

	var fFunc filter.FilterFunc = nil
	if _, ok := query["filter"]; ok {
		if filter.Has(query.Get("filter")) {
			fFunc = filter.Filter(query.Get("filter"))
		}
	}

	// Load node and handle user unauthorized
	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.
			logger.Error("Err@node_Read:LoadNode:" + id + ":" + err.Error())

			n, err = node.LoadFromDisk(id)
			if err != nil {
				err_msg := "Err@node_Read:LoadNodeFromDisk:" + id + ":" + err.Error()
				logger.Error(err_msg)
				return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			}
		}
	}

	// Switch though param flags
	// ?download=1
	if _, ok := query["download"]; ok {
		if !n.HasFile() {
			return responder.RespondWithError(ctx, http.StatusBadRequest, "Node has no file")
		}
		filename := n.Id
		if _, ok := query["filename"]; ok {
			filename = query.Get("filename")
		}

		if _, ok := query["index"]; ok {
			//handling bam file
			if query.Get("index") == "bai" {
				s := &request.Streamer{R: []file.SectionReader{}, W: ctx.HttpResponseWriter(), ContentType: "application/octet-stream", Filename: filename, Size: n.File.Size, Filter: fFunc}

				var region string

				if _, ok := query["region"]; ok {
					//retrieve alingments overlapped with specified region
					region = query.Get("region")
				}

				argv, err := request.ParseSamtoolsArgs(ctx)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "Invaid args in query url")
				}

				err = s.StreamSamtools(n.FilePath(), region, argv...)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "error while involking samtools")
				}

				return nil
			}

			// if forgot ?part=N
			if _, ok := query["part"]; !ok {
				return responder.RespondWithError(ctx, http.StatusBadRequest, "Index parameter requires part parameter")
			}
			// open file
			r, err := n.FileReader()
			defer r.Close()
			if err != nil {
				err_msg := "Err@node_Read:Open: " + err.Error()
				logger.Error(err_msg)
				return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			}
			// load index
			idx, err := n.Index(query.Get("index"))
			if err != nil {
				return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid index")
			}

			if idx.Type() == "virtual" {
				csize := conf.CHUNK_SIZE
				if _, ok := query["chunk_size"]; ok {
					csize, err = strconv.ParseInt(query.Get("chunk_size"), 10, 64)
					if err != nil {
						return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid chunk_size")
					}
				}
				idx.Set(map[string]interface{}{"ChunkSize": csize})
			}
			var size int64 = 0
			s := &request.Streamer{R: []file.SectionReader{}, W: ctx.HttpResponseWriter(), ContentType: "application/octet-stream", Filename: filename, Filter: fFunc}
			for _, p := range query["part"] {
				pos, length, err := idx.Part(p)
				if err != nil {
					return responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid index part")
				}
				size += length
				s.R = append(s.R, 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
				err_msg := "err:@node_Read s.stream: " + err.Error()
				logger.Error(err_msg)
				responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
			}
		} else {
			nf, err := n.FileReader()
			defer nf.Close()
			if err != nil {
				// File not found or some sort of file read error.
				// Probably deserves more checking
				err_msg := "err:@node_Read node.FileReader: " + err.Error()
				logger.Error(err_msg)
				return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
			}
			s := &request.Streamer{R: []file.SectionReader{nf}, W: ctx.HttpResponseWriter(), ContentType: "application/octet-stream", Filename: filename, Size: n.File.Size, Filter: fFunc}
			err = s.Stream()
			if err != nil {
				// causes "multiple response.WriteHeader calls" error but better than no response
				err_msg := "err:@node_Read: s.stream: " + err.Error()
				logger.Error(err_msg)
				responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
			}
		}
	} else if _, ok := query["download_url"]; ok {
		if !n.HasFile() {
			return responder.RespondWithError(ctx, http.StatusBadRequest, "Node has not file")
		} else if u.Uuid == "" {
			return responder.RespondWithError(ctx, http.StatusUnauthorized, e.NoAuth)
		} else {
			options := map[string]string{}
			if _, ok := query["filename"]; ok {
				options["filename"] = query.Get("filename")
			}
			if p, err := preauth.New(util.RandString(20), "download", n.Id, options); err != nil {
				err_msg := "err:@node_Read download_url: " + err.Error()
				logger.Error(err_msg)
				responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			} else {
				responder.RespondWithData(ctx, util.UrlResponse{Url: util.ApiUrl(ctx) + "/preauth/" + p.Id, ValidTill: p.ValidTill.Format(time.ANSIC)})
			}
		}
	} else {
		// Base case respond with node in json
		responder.RespondWithData(ctx, n)
	}
	return nil
}
Esempio n. 4
0
func mapRoutes() {
	goweb.MapBefore(func(ctx context.Context) error {
		req := ctx.HttpRequest()
		host, _, _ := net.SplitHostPort(req.RemoteAddr)
		if host == "::1" {
			host = "localhost"
		}
		suffix := ""
		if _, ok := req.Header["Authorization"]; ok {
			suffix += " AUTH"
		}
		if l, has := req.Header["Content-Length"]; has {
			suffix += " Content-Length: " + l[0]
		}
		logger.Info("access", fmt.Sprintf("%s REQ RECEIVED \"%s %s%s\"", host, ctx.MethodString(), req.RequestURI, suffix))
		return nil
	})

	goweb.MapAfter(func(ctx context.Context) error {
		req := ctx.HttpRequest()
		host, _, _ := net.SplitHostPort(req.RemoteAddr)
		if host == "::1" {
			host = "localhost"
		}
		suffix := ""
		if _, ok := req.Header["Authorization"]; ok {
			suffix += " AUTH"
		}
		if l, has := req.Header["Content-Length"]; has {
			suffix += " Content-Length: " + l[0]
		}
		logger.Info("access", fmt.Sprintf("RESPONDED TO %s \"%s %s%s\"", host, ctx.MethodString(), req.RequestURI, suffix))
		return nil
	})

	goweb.Map("/preauth/{id}", func(ctx context.Context) error {
		if ctx.HttpRequest().Method == "OPTIONS" {
			return responder.RespondOK(ctx)
		}
		pcon.PreAuthRequest(ctx)
		return nil
	})

	goweb.Map("/node/{nid}/acl/{type}", func(ctx context.Context) error {
		if ctx.HttpRequest().Method == "OPTIONS" {
			return responder.RespondOK(ctx)
		}
		acon.AclTypedRequest(ctx)
		return nil
	})

	goweb.Map("/node/{nid}/acl/", func(ctx context.Context) error {
		if ctx.HttpRequest().Method == "OPTIONS" {
			return responder.RespondOK(ctx)
		}
		acon.AclRequest(ctx)
		return nil
	})

	goweb.Map("/node/{nid}/index/{idxType}", func(ctx context.Context) error {
		if ctx.HttpRequest().Method == "OPTIONS" {
			return responder.RespondOK(ctx)
		}
		icon.IndexTypedRequest(ctx)
		return nil
	})

	goweb.Map("/", func(ctx context.Context) error {
		host := util.ApiUrl(ctx)

		attrs := strings.Split(conf.Conf["mongodb-attribute-indexes"], ",")
		for k, v := range attrs {
			attrs[k] = strings.TrimSpace(v)
		}

		r := resource{
			A: attrs,
			C: conf.Conf["admin-email"],
			D: host + "/wiki/",
			I: "Shock",
			R: []string{"node"},
			T: "Shock",
			U: host + "/",
			V: "[% VERSION %]",
		}
		return responder.WriteResponseObject(ctx, http.StatusOK, r)
	})

	nodeController := new(ncon.NodeController)
	goweb.MapController(nodeController)

	goweb.MapStatic("/wiki", conf.Conf["site-path"])

	// Map the favicon
	//goweb.MapStaticFile("/favicon.ico", "static-files/favicon.ico")

	// Catch-all handler for everything that we don't understand
	goweb.Map(func(ctx context.Context) error {
		return responder.RespondWithError(ctx, http.StatusBadRequest, "Parameters do not match a valid Shock request type.")
	})
}
Esempio n. 5
0
func mapRoutes() {
	goweb.MapBefore(func(ctx context.Context) error {
		req := ctx.HttpRequest()
		host, _, _ := net.SplitHostPort(req.RemoteAddr)
		if host == "::1" {
			host = "localhost"
		}
		suffix := ""
		if _, ok := req.Header["Authorization"]; ok {
			suffix += " AUTH"
		}
		if l, has := req.Header["Content-Length"]; has {
			suffix += " Content-Length: " + l[0]
		}
		logger.Info("access", fmt.Sprintf("%s REQ RECEIVED \"%s %s%s\"", host, ctx.MethodString(), req.RequestURI, suffix))
		return nil
	})

	goweb.MapAfter(func(ctx context.Context) error {
		req := ctx.HttpRequest()
		host, _, _ := net.SplitHostPort(req.RemoteAddr)
		if host == "::1" {
			host = "localhost"
		}
		suffix := ""
		if _, ok := req.Header["Authorization"]; ok {
			suffix += " AUTH"
		}
		if l, has := req.Header["Content-Length"]; has {
			suffix += " Content-Length: " + l[0]
		}
		logger.Info("access", fmt.Sprintf("RESPONDED TO %s \"%s %s%s\"", host, ctx.MethodString(), req.RequestURI, suffix))
		return nil
	})

	goweb.Map("/preauth/{id}", func(ctx context.Context) error {
		pcon.PreAuthRequest(ctx)
		return nil
	})

	goweb.Map("/node/{nid}/acl/{type}", func(ctx context.Context) error {
		acon.AclTypedRequest(ctx)
		return nil
	})

	goweb.Map("/node/{nid}/acl/", func(ctx context.Context) error {
		acon.AclRequest(ctx)
		return nil
	})

	goweb.Map("/node/{nid}/index/{idxType}", func(ctx context.Context) error {
		icon.IndexTypedRequest(ctx)
		return nil
	})

	goweb.Map("/", func(ctx context.Context) error {
		host := util.ApiUrl(ctx)
		r := resource{
			R: []string{"node"},
			U: host + "/",
			D: host + "/documentation.html",
			C: conf.Conf["admin-email"],
			I: "Shock",
			T: "Shock",
		}
		return responder.WriteResponseObject(ctx, http.StatusOK, r)
	})

	nodeController := new(ncon.NodeController)
	goweb.MapController(nodeController)

	goweb.MapStatic("/assets", conf.Conf["site-path"]+"/assets")
	goweb.MapStaticFile("/documentation.html", conf.Conf["site-path"]+"/pages/main.html")

	// Map the favicon
	//goweb.MapStaticFile("/favicon.ico", "static-files/favicon.ico")

	// Catch-all handler for everything that we don't understand
	goweb.Map(func(ctx context.Context) error {
		return responder.RespondWithError(ctx, http.StatusNotFound, "File not found")
	})
}