func findFeatureArray(dec *json.Decoder) error {
for {
t, err := dec.Token()
if err == io.EOF {
break
}
if err != nil {
return err
}
if s, ok := t.(string); ok && s == "features" && dec.More() {
// we found the features element
d, err := dec.Token()
if err != nil {
return err
}
if delim, ok := d.(json.Delim); ok {
if delim.String() == "[" {
// we have our start of the array
break
} else {
// A different kind of delimiter
return fmt.Errorf("Expected features to be an array.")
}
}
}
}
if !dec.More() {
return fmt.Errorf("Cannot find any features.")
}
return nil
}
func toList(cxDecoder *json.Decoder, w io.Writer) {
// Node ID to node name map
nodeMap := make(map[string]int64)
for {
_, err := cxDecoder.Token()
if err == io.EOF {
break
} else if err != nil {
fmt.Println("Error: ", err)
return
}
for cxDecoder.More() {
token, err := cxDecoder.Token()
if err != nil {
fmt.Println(err)
}
if token == "nodes" {
processNode(cxDecoder, nodeMap)
}
}
}
err := json.NewEncoder(w).Encode(nodeMap)
if err != nil {
panic("parse err")
}
}
func decodeArray(dec *json.Decoder) (Array, error) {
arr := make(Array, 0)
for {
tok, err := dec.Token()
if err != nil {
return arr, err
}
switch token := tok.(type) {
case json.Delim:
switch rune(token) {
case ']':
return arr, nil
case '{':
obj, err := decodeObject(dec)
if err != nil {
return arr, err
}
arr = append(arr, obj)
case '[':
return decodeArray(dec)
default:
return nil, Errorf("Unexpected token %s", token)
}
}
}
}
func decodeObject(dec *json.Decoder) (Object, error) {
obj := make(Object)
for {
key, err := dec.Token()
if err != nil {
return nil, err
}
if delim, is := key.(json.Delim); is {
switch delim {
case '}':
return obj, nil
default:
return obj, Errorf("Unexpected delim: %s", delim)
}
}
// key is a Value
value, err := decode(dec)
obj[key] = value
if err != nil {
return obj, err
}
}
}
func parseSif(cxDecoder *json.Decoder, w *csv.Writer) {
// Edge slice used for later mapping
var edges []cx.Edge
// Node ID to node name map
nodeMap := make(map[int64]string)
for {
_, err := cxDecoder.Token()
if err == io.EOF {
break
} else if err != nil {
fmt.Println("Error: ", err)
return
}
for cxDecoder.More() {
token, err := cxDecoder.Token()
if err != nil {
fmt.Println(err)
}
if token == "nodes" {
processNode(cxDecoder, nodeMap)
} else if token == "edges" {
processEdge(cxDecoder, &edges)
}
}
}
writeSif(nodeMap, edges, *w)
}
func getVal(dec *json.Decoder) (any, error) {
t, err := dec.Token()
if err != nil {
return nil, err
}
switch tok := t.(type) {
case json.Delim:
switch tok {
case '[':
return decToSlice(dec)
case '{':
om := New()
err := om.(*omap).unmarshalJSON(dec)
if err != nil {
return nil, err
}
_, err = dec.Token() // }
return om, err
case ']':
return nil, endOfSlice
case '}':
return nil, fmt.Errorf("unexpected '}'")
default:
panic("unreachable code")
}
default:
return tok, nil
}
}
func consumeExpectedToken(decoder *json.Decoder, expected json.Token) error {
if actual, err := decoder.Token(); err != nil {
return err
} else if actual != expected {
return fmt.Errorf("Expected %v, not %v", expected, actual)
} else {
return nil
}
}
func processEdge(decoder *json.Decoder, edges *[]cx.Edge) {
token, err := decoder.Token()
if err != nil || token != arrayStart {
return
}
var entry cx.Edge
for decoder.More() {
err := decoder.Decode(&entry)
if err != nil {
return
}
*edges = append(*edges, entry)
}
}
func (m *omap) unmarshalJSON(dec *json.Decoder) error {
for dec.More() {
t, err := dec.Token()
if err != nil {
return err
}
key, isKey := t.(string)
if !isKey {
return fmt.Errorf("%t %s is not string(expected key)", t, t)
}
val, err := getVal(dec)
if err != nil {
return err
}
m.Set(key, val)
}
return nil
}
func (store Store) sliceFromJSONDecoder(dec *json.Decoder) ([]interface{}, error) {
var slice []interface{}
for {
t, err := dec.Token()
if err != nil {
return slice, err
}
if delim, ok := t.(json.Delim); ok && delim.String() == "]" {
return slice, nil
} else if ok && delim.String() == "{" {
item, err := store.treeBranchFromJSONDecoder(dec)
if err != nil {
return slice, err
}
slice = append(slice, item)
} else {
slice = append(slice, t)
}
}
}
func ProcJsonString(dec *json.Decoder) int {
count := 0.0
for {
t, err := dec.Token()
if err == io.EOF {
break
}
if v, ok := t.(float64); ok {
count += v
}
if t == nil {
break
}
}
return int(count)
}
func processNode(decoder *json.Decoder, nodes map[string]int64) {
_, err := decoder.Token()
if err != nil {
return
}
var entry cx.Node
for decoder.More() {
err := decoder.Decode(&entry)
if err != nil {
return
}
if entry.N == "" {
nodes[strconv.FormatInt(entry.ID, 10)] = entry.ID
} else {
nodes[entry.N] = entry.ID
}
}
}
func processNode(decoder *json.Decoder, nodes map[int64]string) {
token, err := decoder.Token()
if err != nil || token != arrayStart {
return
}
var entry cx.Node
for decoder.More() {
err := decoder.Decode(&entry)
if err != nil {
return
}
if entry.N == "" {
nodes[entry.ID] = strconv.FormatInt(entry.ID, 10)
} else {
nodes[entry.ID] = entry.N
}
}
}
func ProcJsonObject(dec *json.Decoder) (float64, bool) {
count := 0.0
seen_red := false
for {
t, err := dec.Token()
if err == io.EOF || t == nil {
break
}
if v, ok := t.(json.Delim); ok {
if v.String() == "{" {
ncount, seen := ProcJsonObject(dec)
if !seen {
count += ncount
}
} else if v.String() == "}" {
return count, seen_red
} else if v.String() == "[" {
ncount, _ := ProcJsonObject(dec)
count += ncount
} else if v.String() == "]" {
return count, seen_red
}
}
if v, ok := t.(string); ok {
if v == "red" {
seen_red = true
}
}
if v, ok := t.(float64); ok {
count += v
}
}
return count, seen_red
}
func decode(dec *json.Decoder) (Model, error) {
tok, err := dec.Token()
if err != nil {
return nil, err
}
switch token := tok.(type) {
case json.Delim:
switch rune(token) {
case '{':
return decodeObject(dec)
case '[':
return decodeArray(dec)
default:
return nil, Errorf("Unexpected token %s", token)
}
default:
return token, nil
}
}
func (store Store) treeItemFromJSONDecoder(dec *json.Decoder) (sops.TreeItem, error) {
var item sops.TreeItem
key, err := dec.Token()
if err != nil {
return item, err
}
if k, ok := key.(string); ok {
item.Key = k
} else if d, ok := key.(json.Delim); ok && d.String() == "}" {
return item, errEndOfObject
} else {
return item, fmt.Errorf("Expected JSON object key, got %s of type %T instead", key, key)
}
value, err := dec.Token()
if err != nil {
return item, err
}
if delim, ok := value.(json.Delim); ok {
if delim.String() == "[" {
v, err := store.sliceFromJSONDecoder(dec)
if err != nil {
return item, err
}
item.Value = v
}
if delim.String() == "{" {
v, err := store.treeBranchFromJSONDecoder(dec)
if err != nil {
return item, err
}
item.Value = v
}
} else {
item.Value = value
}
return item, nil
}
// parse one level of the json translation file, this func will also parse sublevels by calling
func readLevel(jspath string, dec *json.Decoder, tr map[string]string) {
if jspath == "" {
t, err := dec.Token()
if err != nil {
log.Fatal("translate error 1: ", err)
}
if fmt.Sprintf("%T:%v", t, t) != "json.Delim:{" {
log.Fatal("translate error 1.1: bad translaton file format")
}
//fmt.Printf("%s> %T:%v\n", jspath, t, t)
}
for dec.More() {
t1, err1 := dec.Token()
t2, err2 := dec.Token()
if err1 != nil {
log.Fatal("translate error 2: ", err1)
}
if err2 != nil {
log.Fatal("translate error 3: ", err2)
}
//fmt.Printf("%s: %T:%v => %T:%v\n", jspath, t1, t1, t2, t2)
var newpath string
if jspath == "" {
newpath = fmt.Sprintf("%v", t1)
} else {
newpath = fmt.Sprintf("%s.%v", jspath, t1)
}
if fmt.Sprintf("%T:%v", t2, t2) == "json.Delim:{" {
readLevel(newpath, dec, tr)
} else {
tr[newpath] = fmt.Sprintf("%v", t2)
//fmt.Printf("%s => %v\n", newpath, t2)
}
}
t, err := dec.Token()
if err != nil {
log.Fatal("translate error 3=4: ", err)
}
if fmt.Sprintf("%T:%v", t, t) != "json.Delim:}" {
log.Fatal("translate error 4.1: bad translaton file format")
}
//fmt.Printf("%s< %T:%v\n", jspath, t, t)
}
func run(cxDecoder *json.Decoder, w io.Writer) {
// Initialize handlers
handlers := initHandlers()
// Network Object
networkAttr := make(map[string]interface{})
// Elements
var nodes []cyjs.CyJSNode
var edges []cyjs.CyJSEdge
layout := make(map[string]interface{})
vps := make(map[string]interface{})
elements := cyjs.Elements{Nodes: nodes, Edges: edges}
// Temp storage for attributes
nodeAttrs := make(map[string]interface{})
edgeAttrs := make(map[string]interface{})
cxData := make(map[string]interface{})
// Basic Cytoscape.js object
cyjsNetwork := cyjs.CyJS{Data: networkAttr, Elements: elements,
CxData: cxData}
for {
_, err := cxDecoder.Token()
if err == io.EOF {
break
} else if err != nil {
log.Println(err)
return
}
// Decode entry one-by-one.
for cxDecoder.More() {
var entry map[string]interface{}
err := cxDecoder.Decode(&entry)
if err != nil {
log.Fatal(err)
}
parseCxEntry(handlers, entry, &cyjsNetwork, &nodeAttrs,
&edgeAttrs, &layout, &vps)
}
}
assignNodeAttr(cyjsNetwork.Elements.Nodes, nodeAttrs, layout)
assignEdgeAttr(cyjsNetwork.Elements.Edges, edgeAttrs)
// Add style to net (if style data is available...)
if vps != nil && reflect.ValueOf(vps).IsNil() == false {
if vps["style"] != nil {
cyjsNetwork.Style = vps["style"].([]cyjs.SelectorEntry)
}
}
jsonString, err := json.Marshal(cyjsNetwork)
if err != nil {
fmt.Println("ERR: ", err)
} else {
// fmt.Println(string(jsonString))
w.Write(jsonString)
}
//debug()
}
