NetworkX读取Cytoscape json bug？

Question

我正在尝试将Cytoscape Json (*cyjs)读取到NetworkX图中。到目前为止还没有成功，我也尝试了其他格式。以下是一个输入示例：

{
  "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,
        "selected" : false
      },
      "position" : {
        "x" : -236.0,
        "y" : -66.0
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "183",
        "shared_name" : "Node 1",
        "name" : "Node 1",
        "SUID" : 183,
        "selected" : false
      },
      "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,
        "selected" : false
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "191",
        "source" : "183",
        "target" : "185",
        "shared_name" : "Node 1 (interacts with) Node 2",
        "shared_interaction" : "interacts with",
        "name" : "Node 1 (interacts with) Node 2",
        "interaction" : "interacts with",
        "SUID" : 191,
        "selected" : false
      },
      "selected" : false
    } ]
  }
}

这是一个简单的有向图：

​

​

当我尝试使用Netorkx阅读它时

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

我得到了以下信息：

...
    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'

有没有人有一个从Cytoscape成功输入NetworkX的工作示例？

任何帮助或见解都将不胜感激。

Answer 1

使用json编写自己的解析器，提取边列表，从边列表中构建图形。类似于(确保名称在这里是唯一的)

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