Coverage for /pythoncovmergedfiles/medio/medio/usr/local/lib/python3.11/site-packages/networkx/readwrite/json_graph/cytoscape.py: 8%

1import networkx as nx 

2 

3__all__ = ["cytoscape_data", "cytoscape_graph"] 

4 

5 

6def cytoscape_data(G, name="name", ident="id"): 

7 """Returns data in Cytoscape JSON format (cyjs). 

8 

9 Parameters 

10 ---------- 

11 G : NetworkX Graph 

12 The graph to convert to cytoscape format 

13 name : string 

14 A string which is mapped to the 'name' node element in cyjs format. 

15 Must not have the same value as `ident`. 

16 ident : string 

17 A string which is mapped to the 'id' node element in cyjs format. 

18 Must not have the same value as `name`. 

19 

20 Returns 

21 ------- 

22 data: dict 

23 A dictionary with cyjs formatted data. 

24 

25 Raises 

26 ------ 

27 NetworkXError 

28 If the values for `name` and `ident` are identical. 

29 

30 See Also 

31 -------- 

32 cytoscape_graph: convert a dictionary in cyjs format to a graph 

33 

34 References 

35 ---------- 

36 .. [1] Cytoscape user's manual: 

37 http://manual.cytoscape.org/en/stable/index.html 

38 

39 Examples 

40 -------- 

41 >>> from pprint import pprint 

42 >>> G = nx.path_graph(2) 

43 >>> cyto_data = nx.cytoscape_data(G) 

44 >>> pprint(cyto_data, sort_dicts=False) 

45 {'data': [], 

46 'directed': False, 

47 'multigraph': False, 

48 'elements': {'nodes': [{'data': {'id': '0', 'value': 0, 'name': '0'}}, 

49 {'data': {'id': '1', 'value': 1, 'name': '1'}}], 

50 'edges': [{'data': {'source': 0, 'target': 1}}]}} 

51 

52 The :mod:`json` package can be used to serialize the resulting data 

53 

54 >>> import io, json 

55 >>> with io.StringIO() as fh: # replace io with `open(...)` to write to disk 

56 ... json.dump(cyto_data, fh) 

57 ... fh.seek(0) # doctest: +SKIP 

58 ... print(fh.getvalue()[:64]) # View the first 64 characters 

59 {"data": [], "directed": false, "multigraph": false, "elements": 

60 

61 """ 

62 if name == ident: 

63 raise nx.NetworkXError("name and ident must be different.") 

64 

65 jsondata = {"data": list(G.graph.items())} 

66 jsondata["directed"] = G.is_directed() 

67 jsondata["multigraph"] = G.is_multigraph() 

68 jsondata["elements"] = {"nodes": [], "edges": []} 

69 nodes = jsondata["elements"]["nodes"] 

70 edges = jsondata["elements"]["edges"] 

71 

72 for i, j in G.nodes.items(): 

73 n = {"data": j.copy()} 

74 n["data"]["id"] = j.get(ident) or str(i) 

75 n["data"]["value"] = i 

76 n["data"]["name"] = j.get(name) or str(i) 

77 nodes.append(n) 

78 

79 if G.is_multigraph(): 

80 for e in G.edges(keys=True): 

81 n = {"data": G.adj[e[0]][e[1]][e[2]].copy()} 

82 n["data"]["source"] = e[0] 

83 n["data"]["target"] = e[1] 

84 n["data"]["key"] = e[2] 

85 edges.append(n) 

86 else: 

87 for e in G.edges(): 

88 n = {"data": G.adj[e[0]][e[1]].copy()} 

89 n["data"]["source"] = e[0] 

90 n["data"]["target"] = e[1] 

91 edges.append(n) 

92 return jsondata 

93 

94 

95@nx._dispatchable(graphs=None, returns_graph=True) 

96def cytoscape_graph(data, name="name", ident="id"): 

97 """ 

98 Create a NetworkX graph from a dictionary in cytoscape JSON format. 

99 

100 Parameters 

101 ---------- 

102 data : dict 

103 A dictionary of data conforming to cytoscape JSON format. 

104 name : string 

105 A string which is mapped to the 'name' node element in cyjs format. 

106 Must not have the same value as `ident`. 

107 ident : string 

108 A string which is mapped to the 'id' node element in cyjs format. 

109 Must not have the same value as `name`. 

110 

111 Returns 

112 ------- 

113 graph : a NetworkX graph instance 

114 The `graph` can be an instance of `Graph`, `DiGraph`, `MultiGraph`, or 

115 `MultiDiGraph` depending on the input data. 

116 

117 Raises 

118 ------ 

119 NetworkXError 

120 If the `name` and `ident` attributes are identical. 

121 

122 See Also 

123 -------- 

124 cytoscape_data: convert a NetworkX graph to a dict in cyjs format 

125 

126 References 

127 ---------- 

128 .. [1] Cytoscape user's manual: 

129 http://manual.cytoscape.org/en/stable/index.html 

130 

131 Examples 

132 -------- 

133 >>> data_dict = { 

134 ... "data": [], 

135 ... "directed": False, 

136 ... "multigraph": False, 

137 ... "elements": { 

138 ... "nodes": [ 

139 ... {"data": {"id": "0", "value": 0, "name": "0"}}, 

140 ... {"data": {"id": "1", "value": 1, "name": "1"}}, 

141 ... ], 

142 ... "edges": [{"data": {"source": 0, "target": 1}}], 

143 ... }, 

144 ... } 

145 >>> G = nx.cytoscape_graph(data_dict) 

146 >>> G.name 

147 '' 

148 >>> G.nodes() 

149 NodeView((0, 1)) 

150 >>> G.nodes(data=True)[0] 

151 {'id': '0', 'value': 0, 'name': '0'} 

152 >>> G.edges(data=True) 

153 EdgeDataView([(0, 1, {'source': 0, 'target': 1})]) 

154 """ 

155 if name == ident: 

156 raise nx.NetworkXError("name and ident must be different.") 

157 

158 multigraph = data.get("multigraph") 

159 directed = data.get("directed") 

160 if multigraph: 

161 graph = nx.MultiGraph() 

162 else: 

163 graph = nx.Graph() 

164 if directed: 

165 graph = graph.to_directed() 

166 graph.graph = dict(data.get("data")) 

167 for d in data["elements"]["nodes"]: 

168 node_data = d["data"].copy() 

169 node = d["data"]["value"] 

170 

171 if d["data"].get(name): 

172 node_data[name] = d["data"].get(name) 

173 if d["data"].get(ident): 

174 node_data[ident] = d["data"].get(ident) 

175 

176 graph.add_node(node) 

177 graph.nodes[node].update(node_data) 

178 

179 for d in data["elements"]["edges"]: 

180 edge_data = d["data"].copy() 

181 sour = d["data"]["source"] 

182 targ = d["data"]["target"] 

183 if multigraph: 

184 key = d["data"].get("key", 0) 

185 graph.add_edge(sour, targ, key=key) 

186 graph.edges[sour, targ, key].update(edge_data) 

187 else: 

188 graph.add_edge(sour, targ) 

189 graph.edges[sour, targ].update(edge_data) 

190 return graph