Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/json_graph/cytoscape.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import networkx as nx |
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2 |
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3 __all__ = ["cytoscape_data", "cytoscape_graph"] |
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4 |
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5 _attrs = dict(name="name", ident="id") |
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6 |
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7 |
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8 def cytoscape_data(G, attrs=None): |
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9 """Returns data in Cytoscape JSON format (cyjs). |
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10 |
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11 Parameters |
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12 ---------- |
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13 G : NetworkX Graph |
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14 |
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15 |
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16 Returns |
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17 ------- |
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18 data: dict |
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19 A dictionary with cyjs formatted data. |
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20 Raises |
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21 ------ |
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22 NetworkXError |
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23 If values in attrs are not unique. |
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24 """ |
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25 if not attrs: |
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26 attrs = _attrs |
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27 else: |
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28 attrs.update({k: v for (k, v) in _attrs.items() if k not in attrs}) |
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29 |
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30 name = attrs["name"] |
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31 ident = attrs["ident"] |
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32 |
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33 if len({name, ident}) < 2: |
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34 raise nx.NetworkXError("Attribute names are not unique.") |
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35 |
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36 jsondata = {"data": list(G.graph.items())} |
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37 jsondata["directed"] = G.is_directed() |
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38 jsondata["multigraph"] = G.is_multigraph() |
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39 jsondata["elements"] = {"nodes": [], "edges": []} |
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40 nodes = jsondata["elements"]["nodes"] |
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41 edges = jsondata["elements"]["edges"] |
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42 |
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43 for i, j in G.nodes.items(): |
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44 n = {"data": j.copy()} |
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45 n["data"]["id"] = j.get(ident) or str(i) |
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46 n["data"]["value"] = i |
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47 n["data"]["name"] = j.get(name) or str(i) |
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48 nodes.append(n) |
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49 |
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50 if G.is_multigraph(): |
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51 for e in G.edges(keys=True): |
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52 n = {"data": G.adj[e[0]][e[1]][e[2]].copy()} |
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53 n["data"]["source"] = e[0] |
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54 n["data"]["target"] = e[1] |
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55 n["data"]["key"] = e[2] |
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56 edges.append(n) |
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57 else: |
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58 for e in G.edges(): |
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59 n = {"data": G.adj[e[0]][e[1]].copy()} |
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60 n["data"]["source"] = e[0] |
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61 n["data"]["target"] = e[1] |
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62 edges.append(n) |
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63 return jsondata |
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64 |
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65 |
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66 def cytoscape_graph(data, attrs=None): |
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67 if not attrs: |
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68 attrs = _attrs |
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69 else: |
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70 attrs.update({k: v for (k, v) in _attrs.items() if k not in attrs}) |
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71 |
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72 name = attrs["name"] |
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73 ident = attrs["ident"] |
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74 |
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75 if len({ident, name}) < 2: |
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76 raise nx.NetworkXError("Attribute names are not unique.") |
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77 |
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78 multigraph = data.get("multigraph") |
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79 directed = data.get("directed") |
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80 if multigraph: |
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81 graph = nx.MultiGraph() |
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82 else: |
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83 graph = nx.Graph() |
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84 if directed: |
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85 graph = graph.to_directed() |
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86 graph.graph = dict(data.get("data")) |
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87 for d in data["elements"]["nodes"]: |
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88 node_data = d["data"].copy() |
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89 node = d["data"]["value"] |
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90 |
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91 if d["data"].get(name): |
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92 node_data[name] = d["data"].get(name) |
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93 if d["data"].get(ident): |
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94 node_data[ident] = d["data"].get(ident) |
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95 |
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96 graph.add_node(node) |
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97 graph.nodes[node].update(node_data) |
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98 |
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99 for d in data["elements"]["edges"]: |
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100 edge_data = d["data"].copy() |
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101 sour = d["data"].pop("source") |
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102 targ = d["data"].pop("target") |
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103 if multigraph: |
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104 key = d["data"].get("key", 0) |
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105 graph.add_edge(sour, targ, key=key) |
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106 graph.edges[sour, targ, key].update(edge_data) |
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107 else: |
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108 graph.add_edge(sour, targ) |
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109 graph.edges[sour, targ].update(edge_data) |
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110 return graph |