110 lines
3 KiB
Python
110 lines
3 KiB
Python
import networkx as nx
|
|
|
|
__all__ = ["cytoscape_data", "cytoscape_graph"]
|
|
|
|
_attrs = dict(name="name", ident="id")
|
|
|
|
|
|
def cytoscape_data(G, attrs=None):
|
|
"""Returns data in Cytoscape JSON format (cyjs).
|
|
|
|
Parameters
|
|
----------
|
|
G : NetworkX Graph
|
|
|
|
|
|
Returns
|
|
-------
|
|
data: dict
|
|
A dictionary with cyjs formatted data.
|
|
Raises
|
|
------
|
|
NetworkXError
|
|
If values in attrs are not unique.
|
|
"""
|
|
if not attrs:
|
|
attrs = _attrs
|
|
else:
|
|
attrs.update({k: v for (k, v) in _attrs.items() if k not in attrs})
|
|
|
|
name = attrs["name"]
|
|
ident = attrs["ident"]
|
|
|
|
if len({name, ident}) < 2:
|
|
raise nx.NetworkXError("Attribute names are not unique.")
|
|
|
|
jsondata = {"data": list(G.graph.items())}
|
|
jsondata["directed"] = G.is_directed()
|
|
jsondata["multigraph"] = G.is_multigraph()
|
|
jsondata["elements"] = {"nodes": [], "edges": []}
|
|
nodes = jsondata["elements"]["nodes"]
|
|
edges = jsondata["elements"]["edges"]
|
|
|
|
for i, j in G.nodes.items():
|
|
n = {"data": j.copy()}
|
|
n["data"]["id"] = j.get(ident) or str(i)
|
|
n["data"]["value"] = i
|
|
n["data"]["name"] = j.get(name) or str(i)
|
|
nodes.append(n)
|
|
|
|
if G.is_multigraph():
|
|
for e in G.edges(keys=True):
|
|
n = {"data": G.adj[e[0]][e[1]][e[2]].copy()}
|
|
n["data"]["source"] = e[0]
|
|
n["data"]["target"] = e[1]
|
|
n["data"]["key"] = e[2]
|
|
edges.append(n)
|
|
else:
|
|
for e in G.edges():
|
|
n = {"data": G.adj[e[0]][e[1]].copy()}
|
|
n["data"]["source"] = e[0]
|
|
n["data"]["target"] = e[1]
|
|
edges.append(n)
|
|
return jsondata
|
|
|
|
|
|
def cytoscape_graph(data, attrs=None):
|
|
if not attrs:
|
|
attrs = _attrs
|
|
else:
|
|
attrs.update({k: v for (k, v) in _attrs.items() if k not in attrs})
|
|
|
|
name = attrs["name"]
|
|
ident = attrs["ident"]
|
|
|
|
if len({ident, name}) < 2:
|
|
raise nx.NetworkXError("Attribute names are not unique.")
|
|
|
|
multigraph = data.get("multigraph")
|
|
directed = data.get("directed")
|
|
if multigraph:
|
|
graph = nx.MultiGraph()
|
|
else:
|
|
graph = nx.Graph()
|
|
if directed:
|
|
graph = graph.to_directed()
|
|
graph.graph = dict(data.get("data"))
|
|
for d in data["elements"]["nodes"]:
|
|
node_data = d["data"].copy()
|
|
node = d["data"]["value"]
|
|
|
|
if d["data"].get(name):
|
|
node_data[name] = d["data"].get(name)
|
|
if d["data"].get(ident):
|
|
node_data[ident] = d["data"].get(ident)
|
|
|
|
graph.add_node(node)
|
|
graph.nodes[node].update(node_data)
|
|
|
|
for d in data["elements"]["edges"]:
|
|
edge_data = d["data"].copy()
|
|
sour = d["data"].pop("source")
|
|
targ = d["data"].pop("target")
|
|
if multigraph:
|
|
key = d["data"].get("key", 0)
|
|
graph.add_edge(sour, targ, key=key)
|
|
graph.edges[sour, targ, key].update(edge_data)
|
|
else:
|
|
graph.add_edge(sour, targ)
|
|
graph.edges[sour, targ].update(edge_data)
|
|
return graph
|