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