Beispiel #1
0
// WriteResponseObject writes the status code and response object to the HttpResponseWriter in
// the specified context, in the format best suited based on the request.
//
// Goweb uses the WebCodecService to decide which codec to use when responding
// see http://godoc.org/github.com/stretchr/codecs/services#WebCodecService for more information.
//
// This method should be used when the Goweb Standard Response Object does not satisfy the needs of
// the API, but other Respond* methods are recommended.
func (a *GowebAPIResponder) WriteResponseObject(ctx context.Context, status int, responseObject interface{}) error {

	service := a.GetCodecService()

	acceptHeader := ctx.HttpRequest().Header.Get("Accept")
	extension := ctx.FileExtension()
	hasCallback := len(ctx.QueryValue(CallbackParameter)) > 0

	codec, codecError := service.GetCodecForResponding(acceptHeader, extension, hasCallback)

	if codecError != nil {
		return codecError
	}

	options := ctx.CodecOptions()

	// do we need to add some options?
	if _, exists := options[constants.OptionKeyClientCallback]; hasCallback && !exists {
		options[constants.OptionKeyClientCallback] = ctx.QueryValue(CallbackParameter)
	}

	output, marshalErr := service.MarshalWithCodec(codec, responseObject, options)

	if marshalErr != nil {
		return marshalErr
	}

	// use the HTTP responder to respond
	ctx.HttpResponseWriter().Header().Set("Content-Type", codec.ContentType()) // TODO: test me
	a.httpResponder.With(ctx, status, output)

	return nil

}
Beispiel #2
0
//helper function to translate args in URL query to samtools args
//manual: http://samtools.sourceforge.net/samtools.shtml
func ParseSamtoolsArgs(ctx context.Context) (argv []string, err error) {

	query := ctx.HttpRequest().URL.Query()
	var (
		filter_options = map[string]string{
			"head":     "-h",
			"headonly": "-H",
			"count":    "-c",
		}
		valued_options = map[string]string{
			"flag":      "-f",
			"lib":       "-l",
			"mapq":      "-q",
			"readgroup": "-r",
		}
	)

	for src, des := range filter_options {
		if _, ok := query[src]; ok {
			argv = append(argv, des)
		}
	}

	for src, des := range valued_options {
		if _, ok := query[src]; ok {
			if val := query.Get(src); val != "" {
				argv = append(argv, des)
				argv = append(argv, val)
			} else {
				return nil, errors.New(fmt.Sprintf("required value not found for query arg: %s ", src))
			}
		}
	}
	return argv, nil
}
Beispiel #3
0
// DELETE: /node/{id}
func (cr *NodeController) Delete(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_DELETE {
			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_Delete: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["delete"] == false && u.Admin == false && n.Acl.Owner != u.Uuid && prights["delete"] == false {
		return responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
	}

	if err := n.Delete(); err == nil {
		return responder.RespondOK(ctx)
	} else {
		err_msg := "Err@node_Delete:Delete: " + err.Error()
		logger.Error(err_msg)
		return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
	}
}
Beispiel #4
0
// DELETE: /node/{id}
func (cr *NodeController) Delete(id string, ctx context.Context) error {
	u, err := request.Authenticate(ctx.HttpRequest())
	if err != nil && err.Error() != e.NoAuth {
		return request.AuthError(err, ctx)
	}

	if u == nil {
		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.
			err_msg := "Err@node_Read:Delete: " + err.Error()
			logger.Error(err_msg)
			return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
		}
	}

	rights := n.Acl.Check(u.Uuid)
	if !rights["delete"] {
		return responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
	}

	if err := n.Delete(); err == nil {
		return responder.RespondOK(ctx)
	} else {
		err_msg := "Err@node_Delete:Delete: " + err.Error()
		logger.Error(err_msg)
		return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
	}
}
Beispiel #5
0
// GET, POST, PUT, DELETE: /node/{nid}/acl/
// GET is the only action implemented here.
func AclRequest(ctx context.Context) {
	nid := ctx.PathValue("nid")
	rmeth := ctx.HttpRequest().Method

	u, err := request.Authenticate(ctx.HttpRequest())
	if err != nil && err.Error() != e.NoAuth {
		request.AuthError(err, ctx)
		return
	}

	// public user (no auth) can perform a GET operation with the proper node permissions
	if u == nil {
		if rmeth == "GET" && conf.ANON_READ {
			u = &user.User{Uuid: "public"}
		} else {
			responder.RespondWithError(ctx, http.StatusUnauthorized, e.NoAuth)
			return
		}
	}

	// Load node by id
	n, err := node.Load(nid)
	if err != nil {
		if err == mgo.ErrNotFound {
			responder.RespondWithError(ctx, http.StatusNotFound, e.NodeNotFound)
			return
		} else {
			// In theory the db connection could be lost between
			// checking user and load but seems unlikely.
			err_msg := "Err@node_Acl:LoadNode: " + nid + err.Error()
			logger.Error(err_msg)
			responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			return
		}
	}

	// Only the owner, an admin, or someone with read access can view acl's.
	//
	// NOTE: If the node is publicly owned, then anyone can view all acl's. The owner can only
	//       be "public" when anonymous node creation (ANON_WRITE) is enabled in Shock config.

	rights := n.Acl.Check(u.Uuid)
	if n.Acl.Owner != u.Uuid && u.Admin == false && n.Acl.Owner != "public" && rights["read"] == false {
		responder.RespondWithError(ctx, http.StatusUnauthorized, e.UnAuth)
		return
	}

	if rmeth == "GET" {
		query := ctx.HttpRequest().URL.Query()
		verbosity := ""
		if _, ok := query["verbosity"]; ok {
			verbosity = query.Get("verbosity")
		}
		responder.RespondWithData(ctx, n.Acl.FormatDisplayAcl(verbosity))
	} else {
		responder.RespondWithError(ctx, http.StatusNotImplemented, "This request type is not implemented.")
	}
	return
}
Beispiel #6
0
func parseAclRequestTyped(ctx context.Context) (ids []string, err error) {
	var users []string
	query := ctx.HttpRequest().URL.Query()
	params, _, err := request.ParseMultipartForm(ctx.HttpRequest())
	if _, ok := query["users"]; ok && err != nil && err.Error() == "request Content-Type isn't multipart/form-data" {
		users = strings.Split(query.Get("users"), ",")
	} else if params["users"] != "" {
		users = strings.Split(params["users"], ",")
	} else {
		return nil, errors.New("Action requires list of comma separated usernames in 'users' parameter")
	}
	for _, v := range users {
		if uuid.Parse(v) != nil {
			ids = append(ids, v)
		} else {
			u := user.User{Username: v}
			if err := u.SetMongoInfo(); err != nil {
				return nil, err
			}
			ids = append(ids, u.Uuid)
		}
	}
	return ids, nil
}
Beispiel #7
0
// POST: /node
func (cr *NodeController) Create(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-write"]) {
			u = &user.User{Uuid: ""}
		} else {
			return responder.RespondWithError(ctx, http.StatusUnauthorized, e.NoAuth)
		}
	}

	// Parse uploaded form
	params, files, err := request.ParseMultipartForm(ctx.HttpRequest())
	if err != nil {
		if err.Error() == "request Content-Type isn't multipart/form-data" {
			// If not multipart/form-data it will try to read the Body of the
			// request. If the Body is not empty it will create a file from
			// the Body contents. If the Body is empty it will create an empty
			// node.
			if ctx.HttpRequest().ContentLength != 0 {
				params, files, err = request.DataUpload(ctx.HttpRequest())
				if err != nil {
					err_msg := "Error uploading data from request body:" + err.Error()
					logger.Error(err_msg)
					return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
				}
			}

			n, cn_err := node.CreateNodeUpload(u, params, files)

			if cn_err != nil {
				err_msg := "Error at create empty node: " + cn_err.Error()
				logger.Error(err_msg)
				return responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			}
			if n == nil {
				// Not sure how you could get an empty node with no error
				// Assume it's the user's fault
				return responder.RespondWithError(ctx, http.StatusBadRequest, "Error, could not create node.")
			} else {
				return responder.RespondWithData(ctx, n)
			}
		} else {
			// Some error other than request encoding. Theoretically
			// could be a lost db connection between user lookup and parsing.
			// Blame the user, Its probaby their fault anyway.
			err_msg := "Error parsing form: " + err.Error()
			logger.Error(err_msg)
			return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
		}
	}

	// Create node
	n, err := node.CreateNodeUpload(u, params, files)
	if err != nil {
		err_msg := "err@node_CreateNodeUpload: " + err.Error()
		logger.Error(err_msg)
		return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
	}
	return responder.RespondWithData(ctx, n)
}
Beispiel #8
0
// GET: /node
// To do:
// - Iterate node queries
func (cr *NodeController) ReadMany(ctx context.Context) error {
	u, err := request.Authenticate(ctx.HttpRequest())
	if err != nil && err.Error() != e.NoAuth {
		return request.AuthError(err, ctx)
	}

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

	// Setup query and nodes objects
	q := bson.M{}
	nodes := node.Nodes{}

	if u != nil {
		// Admin sees all
		if !u.Admin {
			q["$or"] = []bson.M{bson.M{"acl.read": []string{}}, bson.M{"acl.read": u.Uuid}, bson.M{"acl.owner": u.Uuid}}
		}
	} else {
		if conf.Bool(conf.Conf["anon-read"]) {
			// select on only nodes with no read rights set
			q["acl.read"] = []string{}
		} else {
			return responder.RespondWithError(ctx, http.StatusUnauthorized, e.NoAuth)
		}
	}

	// Gather params to make db query. Do not include the
	// following list.
	paramlist := map[string]int{"limit": 1, "offset": 1, "query": 1, "querynode": 1, "owner": 1, "read": 1, "write": 1, "delete": 1, "public_owner": 1, "public_read": 1, "public_write": 1, "public_delete": 1}
	if _, ok := query["query"]; ok {
		for key := range query {
			if _, found := paramlist[key]; !found {
				keyStr := fmt.Sprintf("attributes.%s", key)
				value := query.Get(key)
				if value != "" {
					if numValue, err := strconv.Atoi(value); err == nil {
						q["$or"] = ListOfMaps{{keyStr: value}, {keyStr: numValue}}
					} else if value == "null" {
						q["$or"] = ListOfMaps{{keyStr: value}, {keyStr: nil}}
					} else {
						q[keyStr] = value
					}
				} else {
					existsMap := map[string]bool{
						"$exists": true,
					}
					q[keyStr] = existsMap
				}
			}
		}
	} else if _, ok := query["querynode"]; ok {
		for key := range query {
			if _, found := paramlist[key]; !found {
				value := query.Get(key)
				if value != "" {
					if numValue, err := strconv.Atoi(value); err == nil {
						q["$or"] = ListOfMaps{{key: value}, {key: numValue}}
					} else if value == "null" {
						q["$or"] = ListOfMaps{{key: value}, {key: nil}}
					} else {
						q[key] = value
					}
				} else {
					existsMap := map[string]bool{
						"$exists": true,
					}
					q[key] = existsMap
				}
			}
		}
	}

	// defaults
	limit := 25
	offset := 0
	if _, ok := query["limit"]; ok {
		limit = util.ToInt(query.Get("limit"))
	}
	if _, ok := query["offset"]; ok {
		offset = util.ToInt(query.Get("offset"))
	}

	// Allowing user to query based on ACL's with a comma-separated list of users.
	// Users can be written as a username or a UUID.
	for _, atype := range []string{"owner", "read", "write", "delete"} {
		if _, ok := query[atype]; ok {
			users := strings.Split(query.Get(atype), ",")
			for _, v := range users {
				if uuid.Parse(v) != nil {
					q["acl."+atype] = v
				} else {
					u := user.User{Username: v}
					if err := u.SetMongoInfo(); err != nil {
						err_msg := "err " + err.Error()
						logger.Error(err_msg)
						return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
					}
					q["acl."+atype] = u.Uuid
				}
			}
		}
	}

	if _, ok := query["public_owner"]; ok {
		// If search is for public_owner AND owner = non-empty string then return zero nodes, no nodes can match this query.
		if _, exists := q["acl.owner"]; exists {
			return responder.RespondWithPaginatedData(ctx, nodes, limit, offset, 0)
		}
		q["acl.owner"] = ""
	}

	// Allowing users to query based on whether ACL is public
	for _, atype := range []string{"read", "write", "delete"} {
		if _, ok := query["public_"+atype]; ok {
			sizeMap := map[string]int{
				"$size": 0,
			}
			// Currently a node cannot be public and have an ACL at the same time, so this returns zero nodes.
			if _, exists := q["acl."+atype]; exists {
				return responder.RespondWithPaginatedData(ctx, nodes, limit, offset, 0)
			} else {
				q["acl."+atype] = sizeMap
			}
		}
	}

	// Get nodes from db
	count, err := nodes.GetPaginated(q, limit, offset)
	if err != nil {
		err_msg := "err " + err.Error()
		logger.Error(err_msg)
		return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
	}
	return responder.RespondWithPaginatedData(ctx, nodes, limit, offset, count)
}
Beispiel #9
0
// GET: /node
// To do:
// - Iterate node queries
func (cr *NodeController) ReadMany(ctx context.Context) error {
	u, err := request.Authenticate(ctx.HttpRequest())
	if err != nil && err.Error() != e.NoAuth {
		return request.AuthError(err, ctx)
	}

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

	// Setup query and nodes objects
	// Note: query is composed of 3 sub-query objects:
	// 1) qPerm - user permissions (system-defined)
	// 2) qOpts - query options (user-defined)
	// 3) qAcls - ACL queries (user-defined)
	q := bson.M{}
	qPerm := bson.M{}
	qOpts := bson.M{}
	qAcls := bson.M{}
	nodes := node.Nodes{}

	if u != nil {
		// Skip this part if user is an admin
		if !u.Admin {
			qPerm["$or"] = []bson.M{bson.M{"acl.read": "public"}, bson.M{"acl.read": u.Uuid}, bson.M{"acl.owner": u.Uuid}}
		}
	} else {
		// User is anonymous
		if conf.ANON_READ {
			// select on only nodes that are publicly readable
			qPerm["acl.read"] = "public"
		} else {
			return responder.RespondWithError(ctx, http.StatusUnauthorized, e.NoAuth)
		}
	}

	// bson.M is a convenient alias for a map[string]interface{} map, useful for dealing with BSON in a native way.
	var OptsMArray []bson.M

	// Gather params to make db query. Do not include the following list.
	if _, ok := query["query"]; ok {
		paramlist := map[string]int{"query": 1, "limit": 1, "offset": 1, "order": 1, "direction": 1, "distinct": 1}
		for key := range query {
			if _, found := paramlist[key]; !found {
				keyStr := fmt.Sprintf("attributes.%s", key)
				for _, value := range query[key] {
					if value != "" {
						OptsMArray = append(OptsMArray, parseOption(keyStr, value))
					} else {
						OptsMArray = append(OptsMArray, bson.M{keyStr: map[string]bool{"$exists": true}})
					}
				}
			}
		}
	} else if _, ok := query["querynode"]; ok {
		paramlist := map[string]int{"querynode": 1, "limit": 1, "offset": 1, "order": 1, "direction": 1, "distinct": 1, "owner": 1, "read": 1, "write": 1, "delete": 1, "public_owner": 1, "public_read": 1, "public_write": 1, "public_delete": 1}
		for key := range query {
			if _, found := paramlist[key]; !found {
				for _, value := range query[key] {
					if value != "" {
						OptsMArray = append(OptsMArray, parseOption(key, value))
					} else {
						OptsMArray = append(OptsMArray, bson.M{key: map[string]bool{"$exists": true}})
					}
				}
			}
		}
	}

	if len(OptsMArray) > 0 {
		qOpts["$and"] = OptsMArray
	}

	// bson.M is a convenient alias for a map[string]interface{} map, useful for dealing with BSON in a native way.
	var AclsMArray []bson.M

	// Allowing user to query based on ACL's with a comma-separated list of users.
	// Restricting ACL queries to just the querynode operation.
	// Users can be written as a username or a UUID.
	if _, qok := query["querynode"]; qok {
		for _, atype := range []string{"owner", "read", "write", "delete"} {
			if _, ok := query[atype]; ok {
				users := strings.Split(query.Get(atype), ",")
				for _, v := range users {
					if uuid.Parse(v) != nil {
						AclsMArray = append(AclsMArray, bson.M{"acl." + atype: v})
					} else {
						u := user.User{Username: v}
						if err := u.SetMongoInfo(); err != nil {
							err_msg := "err " + err.Error()
							logger.Error(err_msg)
							return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
						}
						AclsMArray = append(AclsMArray, bson.M{"acl." + atype: u.Uuid})
					}
				}
			}
		}
		// Allowing users to query based on whether ACL is public
		for _, atype := range []string{"owner", "read", "write", "delete"} {
			if _, ok := query["public_"+atype]; ok {
				AclsMArray = append(AclsMArray, bson.M{"acl." + atype: "public"})
			}
		}
	}

	if len(AclsMArray) > 0 {
		qAcls["$and"] = AclsMArray
	}

	// Combine permissions query with query parameters and ACL query into one AND clause
	q["$and"] = []bson.M{qPerm, qOpts, qAcls}

	// process distinct query
	if _, ok := query["distinct"]; ok {
		dField := query.Get("distinct")
		if !node.HasAttributeField(dField) {
			err_msg := "err unable to run distinct query on non-indexed attributes field: " + dField
			logger.Error(err_msg)
			return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
		}
		results, err := node.DbFindDistinct(q, dField)
		if err != nil {
			err_msg := "err " + err.Error()
			logger.Error(err_msg)
			return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
		}
		return responder.RespondWithData(ctx, results)
	}

	// defaults
	order := "created_on"
	direction := "-"
	limit := 25
	offset := 0

	// get from query
	if _, ok := query["query"]; ok {
		if _, ok := query["order"]; ok {
			order = fmt.Sprintf("attributes.%s", query.Get("order"))
		}
	} else {
		if _, ok := query["order"]; ok {
			order = query.Get("order")
		}
	}
	if _, ok := query["direction"]; ok {
		if query.Get("direction") == "asc" {
			direction = ""
		}
	}
	if _, ok := query["limit"]; ok {
		limit = util.ToInt(query.Get("limit"))
	}
	if _, ok := query["offset"]; ok {
		offset = util.ToInt(query.Get("offset"))
	}

	// Get nodes from db
	order = direction + order
	count, err := nodes.GetPaginated(q, limit, offset, order)
	if err != nil {
		err_msg := "err " + err.Error()
		logger.Error(err_msg)
		return responder.RespondWithError(ctx, http.StatusBadRequest, err_msg)
	}
	return responder.RespondWithPaginatedData(ctx, nodes, limit, offset, count)
}
Beispiel #10
0
func ApiUrl(ctx context.Context) string {
	if conf.Conf["api-url"] != "" {
		return conf.Conf["api-url"]
	}
	return "http://" + ctx.HttpRequest().Host
}
Beispiel #11
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
}
Beispiel #12
0
// GET, POST, PUT, DELETE: /node/{nid}/acl/{type}
func AclTypedRequest(ctx context.Context) {
	nid := ctx.PathValue("nid")
	rtype := ctx.PathValue("type")
	rmeth := ctx.HttpRequest().Method
	query := ctx.HttpRequest().URL.Query()
	verbosity := ""
	if _, ok := query["verbosity"]; ok {
		verbosity = query.Get("verbosity")
	}

	u, err := request.Authenticate(ctx.HttpRequest())
	if err != nil && err.Error() != e.NoAuth {
		request.AuthError(err, ctx)
		return
	}

	if !validAclTypes[rtype] {
		responder.RespondWithError(ctx, http.StatusBadRequest, "Invalid acl type")
		return
	}

	// Load node by id
	n, err := node.Load(nid)
	if err != nil {
		if err == mgo.ErrNotFound {
			responder.RespondWithError(ctx, http.StatusNotFound, e.NodeNotFound)
			return
		} else {
			// In theory the db connection could be lost between
			// checking user and load but seems unlikely.
			err_msg := "Err@node_Acl:LoadNode: " + nid + err.Error()
			logger.Error(err_msg)
			responder.RespondWithError(ctx, http.StatusInternalServerError, err_msg)
			return
		}
	}

	// public user (no auth) can perform a GET operation given the proper node permissions
	if u == nil {
		rights := n.Acl.Check("public")
		if rmeth == "GET" && conf.ANON_READ && (rights["read"] || n.Acl.Owner == "public") {
			responder.RespondWithData(ctx, n.Acl.FormatDisplayAcl(verbosity))
			return
		} else {
			responder.RespondWithError(ctx, http.StatusUnauthorized, e.NoAuth)
			return
		}
	}

	// Users that are not an admin or the node owner can only delete themselves from an ACL.
	if n.Acl.Owner != u.Uuid && u.Admin == false {
		// Users that are not an admin or the node owner cannot remove public from ACL's.
		if rtype == "public_read" || rtype == "public_write" || rtype == "public_delete" || rtype == "public_all" {
			responder.RespondWithError(ctx, http.StatusBadRequest, "Users that are not node owners can only delete themselves from ACLs.")
			return
		}

		// Parse user list
		ids, err := parseAclRequestTyped(ctx)
		if err != nil {
			responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
			return
		}
		if rmeth == "DELETE" {
			if len(ids) != 1 || (len(ids) == 1 && ids[0] != u.Uuid) {
				responder.RespondWithError(ctx, http.StatusBadRequest, "Users that are not node owners can delete only themselves from ACLs.")
				return
			}
			if rtype == "owner" {
				responder.RespondWithError(ctx, http.StatusBadRequest, "Deleting node ownership is not a supported request type.")
				return
			}
			if rtype == "all" {
				n.Acl.UnSet(ids[0], map[string]bool{"read": true, "write": true, "delete": true})
			} else {
				n.Acl.UnSet(ids[0], map[string]bool{rtype: true})
			}
			n.Save()
			responder.RespondWithData(ctx, n.Acl.FormatDisplayAcl(verbosity))
			return
		}
		responder.RespondWithError(ctx, http.StatusBadRequest, "Users that are not node owners can only delete themselves from ACLs.")
		return
	}

	// At this point we know we're dealing with an admin or the node owner.
	// Admins and node owners can view/edit/delete ACLs
	if rmeth == "GET" {
		responder.RespondWithData(ctx, n.Acl.FormatDisplayAcl(verbosity))
		return
	} else if rmeth == "POST" || rmeth == "PUT" {
		if rtype == "public_read" || rtype == "public_write" || rtype == "public_delete" || rtype == "public_all" {
			if rtype == "public_read" {
				n.Acl.Set("public", map[string]bool{"read": true})
			} else if rtype == "public_write" {
				n.Acl.Set("public", map[string]bool{"write": true})
			} else if rtype == "public_delete" {
				n.Acl.Set("public", map[string]bool{"delete": true})
			} else if rtype == "public_all" {
				n.Acl.Set("public", map[string]bool{"read": true, "write": true, "delete": true})
			}
			n.Save()
			responder.RespondWithData(ctx, n.Acl.FormatDisplayAcl(verbosity))
			return
		}

		// Parse user list
		ids, err := parseAclRequestTyped(ctx)
		if err != nil {
			responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
			return
		}
		if rtype == "owner" {
			if len(ids) == 1 {
				n.Acl.SetOwner(ids[0])
			} else {
				responder.RespondWithError(ctx, http.StatusBadRequest, "Too many users. Nodes may have only one owner.")
				return
			}
		} else if rtype == "all" {
			for _, i := range ids {
				n.Acl.Set(i, map[string]bool{"read": true, "write": true, "delete": true})
			}
		} else {
			for _, i := range ids {
				n.Acl.Set(i, map[string]bool{rtype: true})
			}
		}
		n.Save()
		responder.RespondWithData(ctx, n.Acl.FormatDisplayAcl(verbosity))
		return
	} else if rmeth == "DELETE" {
		if rtype == "public_read" || rtype == "public_write" || rtype == "public_delete" || rtype == "public_all" {
			if rtype == "public_read" {
				n.Acl.UnSet("public", map[string]bool{"read": true})
			} else if rtype == "public_write" {
				n.Acl.UnSet("public", map[string]bool{"write": true})
			} else if rtype == "public_delete" {
				n.Acl.UnSet("public", map[string]bool{"delete": true})
			} else if rtype == "public_all" {
				n.Acl.UnSet("public", map[string]bool{"read": true, "write": true, "delete": true})
			}
			n.Save()
			responder.RespondWithData(ctx, n.Acl.FormatDisplayAcl(verbosity))
			return
		}

		// Parse user list
		ids, err := parseAclRequestTyped(ctx)
		if err != nil {
			responder.RespondWithError(ctx, http.StatusBadRequest, err.Error())
			return
		}
		if rtype == "owner" {
			responder.RespondWithError(ctx, http.StatusBadRequest, "Deleting ownership is not a supported request type.")
			return
		} else if rtype == "all" {
			for _, i := range ids {
				n.Acl.UnSet(i, map[string]bool{"read": true, "write": true, "delete": true})
			}
		} else {
			for _, i := range ids {
				n.Acl.UnSet(i, map[string]bool{rtype: true})
			}
		}
		n.Save()
		responder.RespondWithData(ctx, n.Acl.FormatDisplayAcl(verbosity))
		return
	} else {
		responder.RespondWithError(ctx, http.StatusNotImplemented, "This request type is not implemented.")
		return
	}
}
Beispiel #13
0
func ApiUrl(ctx context.Context) string {
	if conf.API_URL != "" {
		return conf.API_URL
	}
	return "http://" + ctx.HttpRequest().Host
}
Beispiel #14
0
// 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
}
Beispiel #15
0
// 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
}
Beispiel #16
0
// 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
}