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Source code for networkx.readwrite.json_graph.cytoscape

#    BSD license.

import networkx as nx

__all__ = ['cytoscape_data', 'cytoscape_graph']

_attrs = dict(name='name', ident='id')


[docs]def cytoscape_data(G, attrs=None): """Return 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(set([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
[docs]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(set([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