Coverage for /pythoncovmergedfiles/medio/medio/usr/local/lib/python3.9/dist-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 >>> G = nx.path_graph(2) 

42 >>> nx.cytoscape_data(G) # doctest: +SKIP 

43 {'data': [], 

44 'directed': False, 

45 'multigraph': False, 

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

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

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

49 """ 

50 if name == ident: 

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

52 

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

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

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

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

57 nodes = jsondata["elements"]["nodes"] 

58 edges = jsondata["elements"]["edges"] 

59 

60 for i, j in G.nodes.items(): 

61 n = {"data": j.copy()} 

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

63 n["data"]["value"] = i 

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

65 nodes.append(n) 

66 

67 if G.is_multigraph(): 

68 for e in G.edges(keys=True): 

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

70 n["data"]["source"] = e[0] 

71 n["data"]["target"] = e[1] 

72 n["data"]["key"] = e[2] 

73 edges.append(n) 

74 else: 

75 for e in G.edges(): 

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

77 n["data"]["source"] = e[0] 

78 n["data"]["target"] = e[1] 

79 edges.append(n) 

80 return jsondata 

81 

82 

83@nx._dispatch(graphs=None) 

84def cytoscape_graph(data, name="name", ident="id"): 

85 """ 

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

87 

88 Parameters 

89 ---------- 

90 data : dict 

91 A dictionary of data conforming to cytoscape JSON format. 

92 name : string 

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

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

95 ident : string 

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

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

98 

99 Returns 

100 ------- 

101 graph : a NetworkX graph instance 

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

103 `MultiDiGraph` depending on the input data. 

104 

105 Raises 

106 ------ 

107 NetworkXError 

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

109 

110 See Also 

111 -------- 

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

113 

114 References 

115 ---------- 

116 .. [1] Cytoscape user's manual: 

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

118 

119 Examples 

120 -------- 

121 >>> data_dict = { 

122 ... 'data': [], 

123 ... 'directed': False, 

124 ... 'multigraph': False, 

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

126 ... {'data': {'id': '1', 'value': 1, 'name': '1'}}], 

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

128 ... } 

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

130 >>> G.name 

131 '' 

132 >>> G.nodes() 

133 NodeView((0, 1)) 

134 >>> G.nodes(data=True)[0] 

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

136 >>> G.edges(data=True) 

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

138 """ 

139 if name == ident: 

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

141 

142 multigraph = data.get("multigraph") 

143 directed = data.get("directed") 

144 if multigraph: 

145 graph = nx.MultiGraph() 

146 else: 

147 graph = nx.Graph() 

148 if directed: 

149 graph = graph.to_directed() 

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

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

152 node_data = d["data"].copy() 

153 node = d["data"]["value"] 

154 

155 if d["data"].get(name): 

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

157 if d["data"].get(ident): 

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

159 

160 graph.add_node(node) 

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

162 

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

164 edge_data = d["data"].copy() 

165 sour = d["data"]["source"] 

166 targ = d["data"]["target"] 

167 if multigraph: 

168 key = d["data"].get("key", 0) 

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

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

171 else: 

172 graph.add_edge(sour, targ) 

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

174 return graph