NetworkX 读取 Cytoscape json 错误？

如何解决NetworkX 读取 Cytoscape json 错误？

我正在尝试将 Cytoscape Json (*cyjs) 读入 NetworkX 图。到目前为止没有运气，我也尝试了其他格式。这是一个示例输入：

{
  "format_version" : "1.0","generated_by" : "cytoscape-3.8.2","target_cytoscapejs_version" : "~2.1","data" : {
    "shared_name" : "Network","name" : "Network","SUID" : 172,"__Annotations" : [ ],"selected" : true
  },"elements" : {
    "nodes" : [ {
      "data" : {
        "id" : "187","shared_name" : "Node 3","name" : "Node 3","SUID" : 187,"selected" : false
      },"position" : {
        "x" : -387.81580333030377,"y" : 6.552640965689666
      },"selected" : false
    },{
      "data" : {
        "id" : "185","shared_name" : "Node 2","name" : "Node 2","SUID" : 185,"position" : {
        "x" : -236.0,"y" : -66.0
      },{
      "data" : {
        "id" : "183","shared_name" : "Node 1","name" : "Node 1","SUID" : 183,"position" : {
        "x" : -392.0,"y" : -89.0
      },"selected" : false
    } ],"edges" : [ {
      "data" : {
        "id" : "189","source" : "187","target" : "185","shared_name" : "Node 3 (interacts with) Node 2","shared_interaction" : "interacts with","name" : "Node 3 (interacts with) Node 2","interaction" : "interacts with","SUID" : 189,{
      "data" : {
        "id" : "191","source" : "183","shared_name" : "Node 1 (interacts with) Node 2","name" : "Node 1 (interacts with) Node 2","SUID" : 191,"selected" : false
    } ]
  }
}

这是一个简单的有向图：

当我尝试使用 Netorkx 阅读时

import json
from networkx.readwrite.json_graph import cytoscape_data,cytoscape_graph
cyjs = json.load(open("Network.cyjs"))
graph = cytoscape_graph(cyjs)

我得到以下信息：

...
    graph = cytoscape_graph(cyjs)
  File "/$HOMEDIR/.local/lib/python3.8/site-packages/networkx/readwrite/json_graph/cytoscape.py",line 89,in cytoscape_graph
    node = d["data"]["value"]
KeyError: 'value'

有人有从 Cytoscape 成功输入 NetworkX 的工作示例吗？

任何帮助或见解将不胜感激。

解决方法

使用 json 编写自己的解析器，提取边列表，从边列表构建图。类似的东西（确保这里的名称是唯一的）

import networkx as nx
import json

def cyjs2graph(cyjs_file_name):

    cyjson = json.load(open(cyjs_file_name))

    name_from_id = {}
    for node in cyjson["elements"]["nodes"]:
        name_from_id[node['data']['id']] = node['data']['name']

    edge_list = []
    for edge in cyjson["elements"]["edges"]:
        src_id = edge['data']['source']
        src_name = name_from_id[src_id]
        tgt_id   = edge['data']['target']
        tgt_name = name_from_id[tgt_id]
        edge_list.append([src_name,tgt_name])
    graph = nx.from_edgelist(edge_list,create_using=nx.DiGraph)
    return graph