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