// handleNeighbors returns the vertices and edges connected to the provided vertex
// (Should I protect this transaction like the update weight function? It is probably
// unnecessary because any update based on retrieved information will be written to a
// property which has transactional protection)
func (d *Data) handleNeighbors(ctx *datastore.VersionedCtx, db storage.GraphDB, w http.ResponseWriter, path []string) error {
labelgraph := new(LabelGraph)
temp, err := strconv.Atoi(path[0])
if err != nil {
return fmt.Errorf("Vertex number not provided")
}
id := dvid.VertexID(temp)
storedvert, err := db.GetVertex(ctx, id)
if err != nil {
return fmt.Errorf("Failed to retrieve vertix %d: %v\n", id, err)
}
labelgraph.Vertices = append(labelgraph.Vertices, labelVertex{storedvert.Id, storedvert.Weight})
for _, vert2 := range storedvert.Vertices {
vertex, err := db.GetVertex(ctx, vert2)
if err != nil {
return fmt.Errorf("Failed to retrieve vertex %d: %v\n", vertex.Id, err)
}
labelgraph.Vertices = append(labelgraph.Vertices, labelVertex{vertex.Id, vertex.Weight})
edge, err := db.GetEdge(ctx, id, vert2)
if err != nil {
return fmt.Errorf("Failed to retrieve edge %d-%d: %v\n", vertex.Id, vert2, err)
}
labelgraph.Edges = append(labelgraph.Edges, labelEdge{edge.Vertexpair.Vertex1, edge.Vertexpair.Vertex2, edge.Weight})
}
m, err := json.Marshal(labelgraph)
if err != nil {
return fmt.Errorf("Could not serialize graph")
}
w.Header().Set("Content-Type", "application/json")
fmt.Fprintf(w, string(m))
return nil
}
// handleMerge merges a list of vertices onto the final vertex in the Vertices list
func (d *Data) handleMerge(ctx *datastore.VersionedCtx, db storage.GraphDB, w http.ResponseWriter, labelgraph *LabelGraph) error {
numverts := len(labelgraph.Vertices)
if numverts < 2 {
return fmt.Errorf("Must specify at least two vertices for merging")
}
overlapweights := make(map[dvid.VertexID]float64)
vertweight := float64(0)
var keepvertex dvid.GraphVertex
allverts := make(map[dvid.VertexID]struct{})
keepverts := make(map[dvid.VertexID]struct{})
// accumulate weights, find common edges
for i, vertex := range labelgraph.Vertices {
vert, err := db.GetVertex(ctx, vertex.Id)
if err != nil {
return fmt.Errorf("Failed to retrieve vertex %d: %v\n", vertex.Id, err)
}
allverts[vert.Id] = struct{}{}
vertweight += vert.Weight
if i == (numverts - 1) {
keepvertex = vert
} else {
for _, vert2 := range vert.Vertices {
edge, err := db.GetEdge(ctx, vert.Id, vert2)
if err != nil {
return fmt.Errorf("Failed to retrieve edge %d-%d: %v\n", vertex.Id, vert2, err)
}
overlapweights[vert2] += edge.Weight
}
}
}
// examine keep vertex (save edges so only the weights are updated)
for _, vert2 := range keepvertex.Vertices {
edge, err := db.GetEdge(ctx, keepvertex.Id, vert2)
if err != nil {
return fmt.Errorf("Failed to retrieve edge %d-%d: %v\n", keepvertex.Id, vert2, err)
}
overlapweights[vert2] += edge.Weight
keepverts[vert2] = struct{}{}
}
// use specified weights even if marked as 0
for _, edge := range labelgraph.Edges {
id := edge.Id1
baseid := edge.Id2
if keepvertex.Id == edge.Id1 {
id = edge.Id2
baseid = edge.Id1
}
if baseid == keepvertex.Id {
if _, ok := overlapweights[id]; ok {
overlapweights[id] = edge.Weight
}
}
}
// if user specifies an edge weight other than 0 (?! -- somehow allow in future)
// use that weight
if labelgraph.Vertices[numverts-1].Weight != 0 {
vertweight = labelgraph.Vertices[numverts-1].Weight
}
for id2, newweight := range overlapweights {
if _, ok := allverts[id2]; !ok {
// only examine edges where the node is not internal
if _, ok := keepverts[id2]; !ok {
// if not in keepverts create new edge
err := db.AddEdge(ctx, keepvertex.Id, id2, newweight)
if err != nil {
return fmt.Errorf("Failed to create edge %d-%d: %v\n", keepvertex.Id, id2, err)
}
} else {
// else just update weight
err := db.SetEdgeWeight(ctx, keepvertex.Id, id2, newweight)
if err != nil {
return fmt.Errorf("Failed to update weight on edge %d-%d: %v\n", keepvertex.Id, id2, err)
}
}
}
}
// update vertex weight
err := db.SetVertexWeight(ctx, labelgraph.Vertices[numverts-1].Id, vertweight)
if err != nil {
return fmt.Errorf("Failed to update weight on vertex %d: %v\n", keepvertex.Id, err)
}
// remove old vertices which will remove the old edges
for i, vertex := range labelgraph.Vertices {
if i == (numverts - 1) {
break
}
err := db.RemoveVertex(ctx, vertex.Id)
if err != nil {
return fmt.Errorf("Failed to remove vertex %d: %v\n", vertex.Id, err)
}
}
return nil
}
// handleWeightUpdate POST vertex/edge weight increment/decrement. POSTing to an uncreated
// node or edge will create the node or edge (default 0 weight). Limit of 1000 vertices and 1000 edges.
func (d *Data) handleWeightUpdate(ctx *datastore.VersionedCtx, db storage.GraphDB, w http.ResponseWriter, labelgraph *LabelGraph) error {
// collect all vertices that need to be locked and wrap in transaction ("read only")
open_vertices := d.extractOpenVertices(labelgraph)
transaction_group, err := d.transaction_log.createTransactionGroup(open_vertices, true)
if err != nil {
transaction_group.closeTransaction()
return fmt.Errorf("Could not create transaction group")
}
leftover := true
// iterate until leftovers are empty
for leftover {
if len(transaction_group.lockedold_ids) == 0 {
leftover = false
}
for i, vertex := range labelgraph.Vertices {
// if it was already examined, continue
if vertex.Id == 0 {
continue
}
// if it the vertex was not locked, continue
if _, ok := transaction_group.locked_ids[vertex.Id]; !ok {
continue
}
// retrieve vertex, update or create depending on error status
storedvert, err := db.GetVertex(ctx, vertex.Id)
if err != nil {
err = db.AddVertex(ctx, vertex.Id, vertex.Weight)
if err != nil {
transaction_group.closeTransaction()
return fmt.Errorf("Failed to add vertex: %v\n", err)
}
} else {
// increment/decrement weight
err = db.SetVertexWeight(ctx, vertex.Id, storedvert.Weight+vertex.Weight)
if err != nil {
transaction_group.closeTransaction()
return fmt.Errorf("Failed to add vertex: %v\n", err)
}
}
// do not revisit
labelgraph.Vertices[i].Id = 0
}
for i, edge := range labelgraph.Edges {
// if it was already examined, continue
if edge.Id1 == 0 {
continue
}
// if it the edge was not locked, continue
if _, ok := transaction_group.locked_ids[edge.Id1]; !ok {
continue
}
if _, ok := transaction_group.locked_ids[edge.Id2]; !ok {
continue
}
// retrieve edge, update or create depending on error status
storededge, err := db.GetEdge(ctx, edge.Id1, edge.Id2)
if err != nil {
err = db.AddEdge(ctx, edge.Id1, edge.Id2, edge.Weight)
if err != nil {
transaction_group.closeTransaction()
return fmt.Errorf("Failed to add edge: %v\n", err)
}
} else {
// increment/decrement weight
err = db.SetEdgeWeight(ctx, edge.Id1, edge.Id2, storededge.Weight+edge.Weight)
if err != nil {
transaction_group.closeTransaction()
return fmt.Errorf("Failed to update edge: %v\n", err)
}
}
// do not revisit
labelgraph.Edges[i].Id1 = 0
}
if leftover {
// wait on update to channel if there are leftovers
transaction_group.waitForChange()
// close transaction, create new transaction from leftovers in labelgraph
transaction_group.closeTransaction()
open_vertices = d.extractOpenVertices(labelgraph)
transaction_group, _ = d.transaction_log.createTransactionGroup(open_vertices, true)
}
}
transaction_group.closeTransaction()
return nil
}
// handleSubgraph loads, retrieves, or deletes a subgraph (more description in REST interface)
func (d *Data) handleSubgraphBulk(ctx *datastore.VersionedCtx, db storage.GraphDB, w http.ResponseWriter, labelgraph *LabelGraph, method string) error {
var err error
if !d.setBusy() {
return fmt.Errorf("Server busy with bulk transaction")
}
defer d.setNotBusy()
// initial new graph
labelgraph2 := new(LabelGraph)
labelgraph2.Transactions = make([]transactionItem, 0)
labelgraph2.Vertices = make([]labelVertex, 0)
labelgraph2.Edges = make([]labelEdge, 0)
// ?! do not grab edges that connect to outside vertices
if method == "get" {
var vertices []dvid.GraphVertex
var edges []dvid.GraphEdge
if len(labelgraph.Vertices) > 0 {
used_vertices := make(map[dvid.VertexID]struct{})
for _, vertex := range labelgraph.Vertices {
used_vertices[vertex.Id] = struct{}{}
storedvert, err := db.GetVertex(ctx, vertex.Id)
if err != nil {
return fmt.Errorf("Failed to retrieve vertix %d: %v\n", vertex.Id, err)
}
vertices = append(vertices, storedvert)
for _, vert2 := range storedvert.Vertices {
if _, ok := used_vertices[vert2]; !ok {
edge, err := db.GetEdge(ctx, storedvert.Id, vert2)
if err != nil {
return fmt.Errorf("Failed to retrieve edge %d-%d: %v\n", storedvert.Id, vert2, err)
}
edges = append(edges, edge)
}
}
}
} else {
// if no set of vertices are supplied, just grab the whole graph
vertices, err = db.GetVertices(ctx)
if err != nil {
return fmt.Errorf("Failed to retrieve vertices: %v\n", err)
}
edges, err = db.GetEdges(ctx)
if err != nil {
return fmt.Errorf("Failed to retrieve edges: %v\n", err)
}
}
for _, vertex := range vertices {
labelgraph2.Vertices = append(labelgraph2.Vertices, labelVertex{vertex.Id, vertex.Weight})
}
for _, edge := range edges {
labelgraph2.Edges = append(labelgraph2.Edges, labelEdge{edge.Vertexpair.Vertex1, edge.Vertexpair.Vertex2, edge.Weight})
}
m, err := json.Marshal(labelgraph2)
if err != nil {
return fmt.Errorf("Could not serialize graph")
}
w.Header().Set("Content-Type", "application/json")
fmt.Fprintf(w, string(m))
} else if method == "post" {
// add list of vertices and edges from supplied JSON -- overwrite existing values
for _, vertex := range labelgraph.Vertices {
err := db.AddVertex(ctx, vertex.Id, vertex.Weight)
if err != nil {
return fmt.Errorf("Failed to add vertex: %v\n", err)
}
}
for _, edge := range labelgraph.Edges {
err := db.AddEdge(ctx, edge.Id1, edge.Id2, edge.Weight)
if err != nil {
return fmt.Errorf("Failed to add edge: %v\n", err)
}
}
} else if method == "delete" {
// delete the vertices supplied and all of their edges or delete the whole graph
if len(labelgraph.Vertices) > 0 || len(labelgraph.Edges) > 0 {
for _, vertex := range labelgraph.Vertices {
db.RemoveVertex(ctx, vertex.Id)
}
for _, edge := range labelgraph.Edges {
db.RemoveEdge(ctx, edge.Id1, edge.Id2)
}
} else {
err = db.RemoveGraph(ctx)
if err != nil {
return fmt.Errorf("Failed to remove graph: %v\n", err)
}
}
} else {
err = fmt.Errorf("Does not support PUT")
}
return err
}
// handleProperty retrieves or deletes properties that can be added to a vertex or edge -- data posted
// or retrieved uses default compression
func (d *Data) handleProperty(ctx *datastore.VersionedCtx, db storage.GraphDB, w http.ResponseWriter, r *http.Request, path []string, method string) error {
edgemode := false
var propertyname string
if len(path) == 3 {
edgemode = true
propertyname = path[2]
} else if len(path) != 2 {
return fmt.Errorf("Incorrect number of parameters specified for handling properties")
} else {
propertyname = path[1]
}
temp, err := strconv.Atoi(path[0])
if err != nil {
return fmt.Errorf("Vertex number not provided")
}
id1 := dvid.VertexID(temp)
id2 := dvid.VertexID(0)
if edgemode {
temp, err := strconv.Atoi(path[1])
if err != nil {
return fmt.Errorf("Vertex number not provided")
}
id2 = dvid.VertexID(temp)
}
// remove a property from a vertex or edge
if method == "delete" {
if edgemode {
db.RemoveEdgeProperty(ctx, id1, id2, propertyname)
if err != nil {
return fmt.Errorf("Failed to remove edge property %d-%d %s: %v\n", id1, id2, propertyname, err)
}
} else {
db.RemoveVertexProperty(ctx, id1, propertyname)
if err != nil {
return fmt.Errorf("Failed to remove vertex property %d %s: %v\n", id1, propertyname, err)
}
}
} else if method == "get" {
var data []byte
if edgemode {
data, err = db.GetEdgeProperty(ctx, id1, id2, propertyname)
} else {
data, err = db.GetVertexProperty(ctx, id1, propertyname)
}
if err != nil {
return fmt.Errorf("Failed to get property %s: %v\n", propertyname, err)
}
uncompress := true
value, _, e := dvid.DeserializeData(data, uncompress)
if e != nil {
err = fmt.Errorf("Unable to deserialize data for property '%s': %v\n", propertyname, e.Error())
return err
}
w.Header().Set("Content-Type", "application/octet-stream")
_, err = w.Write(value)
if err != nil {
return err
}
} else if method == "post" {
// read as binary and load into propertyname
data, err := ioutil.ReadAll(r.Body)
if err != nil {
return err
}
serialization, err := dvid.SerializeData(data, d.Compression(), d.Checksum())
if err != nil {
return fmt.Errorf("Unable to serialize data: %v\n", err)
}
if edgemode {
err = db.SetEdgeProperty(ctx, id1, id2, propertyname, serialization)
} else {
err = db.SetVertexProperty(ctx, id1, propertyname, serialization)
}
if err != nil {
return fmt.Errorf("Failed to add property %s: %v\n", propertyname, err)
}
}
return err
}
// handelPropertyTransaction allows gets/posts (really puts) of edge or vertex properties.
func (d *Data) handlePropertyTransaction(ctx *datastore.VersionedCtx, db storage.GraphDB, w http.ResponseWriter, r *http.Request, path []string, method string) error {
if len(path) < 2 {
return fmt.Errorf("Must specify edges or vertices in URI and property name")
}
if method == "delete" {
return fmt.Errorf("Transactional delete not supported")
}
edgemode := false
if path[0] == "edges" {
edgemode = true
} else if path[0] != "vertices" {
return fmt.Errorf("Must specify edges or vertices in URI")
}
propertyname := path[1]
readonly := false
if method == "get" {
readonly = true
}
data, err := ioutil.ReadAll(r.Body)
// only allow 1000 vertices to be locked
transactions, start, err := d.transaction_log.createTransactionGroupBinary(data, readonly)
defer transactions.closeTransaction()
if err != nil {
return fmt.Errorf("Failed to create property transaction: %v", err)
}
returned_data := transactions.exportTransactionsBinary()
if method == "post" {
// deserialize transaction (vertex or edge) -- use URI?
num_properties := binary.LittleEndian.Uint64(data[start:])
start += 8
for i := uint64(0); i < num_properties; i++ {
temp := binary.LittleEndian.Uint64(data[start:])
id := dvid.VertexID(temp)
var id2 dvid.VertexID
start += 8
if edgemode {
temp = binary.LittleEndian.Uint64(data[start:])
id2 = dvid.VertexID(temp)
start += 8
}
data_size := binary.LittleEndian.Uint64(data[start:])
start += 8
data_begin := start
start += int(data_size)
data_end := start
if data_begin == data_end {
continue
}
// check if post is possible
if _, ok := transactions.locked_ids[id]; !ok {
continue
}
if edgemode {
if _, ok := transactions.locked_ids[id2]; !ok {
continue
}
}
// execute post
serialization, err := dvid.SerializeData(data[data_begin:data_end], d.Compression(), d.Checksum())
if err != nil {
return fmt.Errorf("Unable to serialize data: %v\n", err)
}
if edgemode {
err = db.SetEdgeProperty(ctx, id, id2, propertyname, serialization)
} else {
err = db.SetVertexProperty(ctx, id, propertyname, serialization)
}
if err != nil {
return fmt.Errorf("Failed to add property %s: %v\n", propertyname, err)
}
}
} else {
num_properties := binary.LittleEndian.Uint64(data[start:])
start += 8
num_properties_loc := len(returned_data)
longbuf := make([]byte, 8, 8)
binary.LittleEndian.PutUint64(longbuf, 0)
returned_data = append(returned_data, longbuf...)
num_executed_transactions := uint64(0)
// read the vertex or edge properties desired
for i := uint64(0); i < num_properties; i++ {
temp := binary.LittleEndian.Uint64(data[start:])
id := dvid.VertexID(temp)
var id2 dvid.VertexID
start += 8
if edgemode {
temp := binary.LittleEndian.Uint64(data[start:])
id2 = dvid.VertexID(temp)
start += 8
}
// check if post is possible
if _, ok := transactions.locked_ids[id]; !ok {
continue
}
if edgemode {
if _, ok := transactions.locked_ids[id2]; !ok {
continue
}
}
// execute get command
var dataout []byte
if edgemode {
dataout, err = db.GetEdgeProperty(ctx, id, id2, propertyname)
} else {
dataout, err = db.GetVertexProperty(ctx, id, propertyname)
}
// serialize return data only if there is return data and no error;
// otherwise return just return the id and size of 0
var data_serialized []byte
if (err == nil) && len(dataout) > 0 {
uncompress := true
data_serialized, _, err = dvid.DeserializeData(dataout, uncompress)
if err != nil {
return fmt.Errorf("Unable to deserialize data for property '%s': %v\n", propertyname, err)
}
}
// save transaction
num_executed_transactions += 1
binary.LittleEndian.PutUint64(longbuf, uint64(id))
returned_data = append(returned_data, longbuf...)
if edgemode {
binary.LittleEndian.PutUint64(longbuf, uint64(id2))
returned_data = append(returned_data, longbuf...)
}
binary.LittleEndian.PutUint64(longbuf, uint64(len(data_serialized)))
returned_data = append(returned_data, longbuf...)
returned_data = append(returned_data, data_serialized...)
}
// update the number of transactions
binary.LittleEndian.PutUint64(returned_data[num_properties_loc:], num_executed_transactions)
}
w.Header().Set("Content-Type", "application/octet-stream")
_, err = w.Write(returned_data)
return err
}