import networkx as nx
__all__ = ["cytoscape_data", "cytoscape_graph"]
[docs]def cytoscape_data(G, attrs=None, name="name", ident="id"):
"""Returns data in Cytoscape JSON format (cyjs).
Parameters
----------
G : NetworkX Graph
The graph to convert to cytoscape format
attrs : dict or None (default=None)
A dictionary containing the keys 'name' and 'ident' which are mapped to
the 'name' and 'id' node elements in cyjs format. All other keys are
ignored. Default is `None` which results in the default mapping
``dict(name="name", ident="id")``.
.. deprecated:: 2.6
The `attrs` keyword argument will be replaced with `name` and
`ident` in networkx 3.0
name : string
A string which is mapped to the 'name' node element in cyjs format.
Must not have the same value as `ident`.
ident : string
A string which is mapped to the 'id' node element in cyjs format.
Must not have the same value as `name`.
Returns
-------
data: dict
A dictionary with cyjs formatted data.
Raises
------
NetworkXError
If the values for `name` and `ident` are identical.
See Also
--------
cytoscape_graph: convert a dictionary in cyjs format to a graph
References
----------
.. [1] Cytoscape user's manual:
http://manual.cytoscape.org/en/stable/index.html
Examples
--------
>>> G = nx.path_graph(2)
>>> nx.cytoscape_data(G) # doctest: +SKIP
{'data': [],
'directed': False,
'multigraph': False,
'elements': {'nodes': [{'data': {'id': '0', 'value': 0, 'name': '0'}},
{'data': {'id': '1', 'value': 1, 'name': '1'}}],
'edges': [{'data': {'source': 0, 'target': 1}}]}}
"""
# ------ TODO: Remove between the lines in 3.0 ----- #
if attrs is not None:
import warnings
msg = (
"\nThe `attrs` keyword argument of cytoscape_data is deprecated\n"
"and will be removed in networkx 3.0.\n"
"It is replaced with explicit `name` and `ident` keyword\n"
"arguments.\n"
"To make this warning go away and ensure usage is forward\n"
"compatible, replace `attrs` with `name` and `ident`,\n"
"for example:\n\n"
" >>> cytoscape_data(G, attrs={'name': 'foo', 'ident': 'bar'})\n\n"
"should instead be written as\n\n"
" >>> cytoscape_data(G, name='foo', ident='bar')\n\n"
"in networkx 3.0.\n"
"The default values of 'name' and 'id' will not change."
)
warnings.warn(msg, DeprecationWarning, stacklevel=2)
name = attrs["name"]
ident = attrs["ident"]
# -------------------------------------------------- #
if name == ident:
raise nx.NetworkXError("name and ident must be different.")
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, name="name", ident="id"):
"""
Create a NetworkX graph from a dictionary in cytoscape JSON format.
Parameters
----------
data : dict
A dictionary of data conforming to cytoscape JSON format.
attrs : dict or None (default=None)
A dictionary containing the keys 'name' and 'ident' which are mapped to
the 'name' and 'id' node elements in cyjs format. All other keys are
ignored. Default is `None` which results in the default mapping
``dict(name="name", ident="id")``.
.. deprecated:: 2.6
The `attrs` keyword argument will be replaced with `name` and
`ident` in networkx 3.0
name : string
A string which is mapped to the 'name' node element in cyjs format.
Must not have the same value as `ident`.
ident : string
A string which is mapped to the 'id' node element in cyjs format.
Must not have the same value as `name`.
Returns
-------
graph : a NetworkX graph instance
The `graph` can be an instance of `Graph`, `DiGraph`, `MultiGraph`, or
`MultiDiGraph` depending on the input data.
Raises
------
NetworkXError
If the `name` and `ident` attributes are identical.
See Also
--------
cytoscape_data: convert a NetworkX graph to a dict in cyjs format
References
----------
.. [1] Cytoscape user's manual:
http://manual.cytoscape.org/en/stable/index.html
Examples
--------
>>> data_dict = {
... 'data': [],
... 'directed': False,
... 'multigraph': False,
... 'elements': {'nodes': [{'data': {'id': '0', 'value': 0, 'name': '0'}},
... {'data': {'id': '1', 'value': 1, 'name': '1'}}],
... 'edges': [{'data': {'source': 0, 'target': 1}}]}
... }
>>> G = nx.cytoscape_graph(data_dict)
>>> G.name
''
>>> G.nodes()
NodeView((0, 1))
>>> G.nodes(data=True)[0]
{'id': '0', 'value': 0, 'name': '0'}
>>> G.edges(data=True)
EdgeDataView([(0, 1, {'source': 0, 'target': 1})])
"""
# ------ TODO: Remove between the lines in 3.0 ----- #
if attrs is not None:
import warnings
msg = (
"\nThe `attrs` keyword argument of cytoscape_data is deprecated\n"
"and will be removed in networkx 3.0.\n"
"It is replaced with explicit `name` and `ident` keyword\n"
"arguments.\n"
"To make this warning go away and ensure usage is forward\n"
"compatible, replace `attrs` with `name` and `ident`,\n"
"for example:\n\n"
" >>> cytoscape_data(G, attrs={'name': 'foo', 'ident': 'bar'})\n\n"
"should instead be written as\n\n"
" >>> cytoscape_data(G, name='foo', ident='bar')\n\n"
"The default values of 'name' and 'id' will not change."
)
warnings.warn(msg, DeprecationWarning, stacklevel=2)
name = attrs["name"]
ident = attrs["ident"]
# -------------------------------------------------- #
if name == ident:
raise nx.NetworkXError("name and ident must be different.")
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"]["source"]
targ = d["data"]["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