diff env/lib/python3.9/site-packages/networkx/readwrite/json_graph/cytoscape.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/networkx/readwrite/json_graph/cytoscape.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,110 @@
+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