Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/tests/test_gml.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 from ast import literal_eval |
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2 import codecs |
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3 from contextlib import contextmanager |
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4 import io |
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5 import pytest |
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6 import networkx as nx |
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7 from networkx.readwrite.gml import literal_stringizer, literal_destringizer |
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8 import os |
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9 import tempfile |
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10 from textwrap import dedent |
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11 |
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12 |
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13 class TestGraph: |
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14 @classmethod |
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15 def setup_class(cls): |
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16 cls.simple_data = """Creator "me" |
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17 Version "xx" |
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18 graph [ |
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19 comment "This is a sample graph" |
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20 directed 1 |
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21 IsPlanar 1 |
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25 label "Node 1" |
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31 label "Node 2" |
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39 source 1 |
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40 target 2 |
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41 label "Edge from node 1 to node 2" |
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42 color [line "blue" thickness 3] |
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48 label "Edge from node 2 to node 3" |
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51 source 3 |
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53 label "Edge from node 3 to node 1" |
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56 """ |
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57 |
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58 def test_parse_gml_cytoscape_bug(self): |
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59 # example from issue #321, originally #324 in trac |
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60 cytoscape_example = """ |
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61 Creator "Cytoscape" |
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62 Version 1.0 |
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63 graph [ |
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65 root_index -3 |
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66 id -3 |
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67 graphics [ |
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72 fill "#ff9999" |
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73 type "ellipse" |
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74 outline "#666666" |
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104 outline "#666666" |
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107 label "node0" |
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112 source -1 |
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113 graphics [ |
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116 type "line" |
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117 Line [ |
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118 ] |
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119 source_arrow 0 |
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120 target_arrow 3 |
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121 ] |
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122 label "DirectedEdge" |
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123 ] |
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124 edge [ |
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125 root_index -1 |
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126 target -1 |
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127 source -3 |
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128 graphics [ |
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129 width 1.5 |
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130 fill "#0000ff" |
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131 type "line" |
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132 Line [ |
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133 ] |
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134 source_arrow 0 |
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135 target_arrow 3 |
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136 ] |
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137 label "DirectedEdge" |
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138 ] |
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139 ] |
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140 """ |
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141 nx.parse_gml(cytoscape_example) |
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142 |
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143 def test_parse_gml(self): |
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144 G = nx.parse_gml(self.simple_data, label="label") |
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145 assert sorted(G.nodes()) == ["Node 1", "Node 2", "Node 3"] |
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146 assert [e for e in sorted(G.edges())] == [ |
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147 ("Node 1", "Node 2"), |
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148 ("Node 2", "Node 3"), |
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149 ("Node 3", "Node 1"), |
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150 ] |
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151 |
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152 assert [e for e in sorted(G.edges(data=True))] == [ |
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153 ( |
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154 "Node 1", |
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155 "Node 2", |
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156 { |
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157 "color": {"line": "blue", "thickness": 3}, |
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158 "label": "Edge from node 1 to node 2", |
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159 }, |
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160 ), |
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161 ("Node 2", "Node 3", {"label": "Edge from node 2 to node 3"}), |
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162 ("Node 3", "Node 1", {"label": "Edge from node 3 to node 1"}), |
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163 ] |
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164 |
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165 def test_read_gml(self): |
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166 (fd, fname) = tempfile.mkstemp() |
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167 fh = open(fname, "w") |
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168 fh.write(self.simple_data) |
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169 fh.close() |
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170 Gin = nx.read_gml(fname, label="label") |
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171 G = nx.parse_gml(self.simple_data, label="label") |
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172 assert sorted(G.nodes(data=True)) == sorted(Gin.nodes(data=True)) |
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173 assert sorted(G.edges(data=True)) == sorted(Gin.edges(data=True)) |
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174 os.close(fd) |
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175 os.unlink(fname) |
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176 |
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177 def test_labels_are_strings(self): |
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178 # GML requires labels to be strings (i.e., in quotes) |
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179 answer = """graph [ |
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180 node [ |
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181 id 0 |
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182 label "1203" |
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183 ] |
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184 ]""" |
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185 G = nx.Graph() |
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186 G.add_node(1203) |
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187 data = "\n".join(nx.generate_gml(G, stringizer=literal_stringizer)) |
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188 assert data == answer |
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189 |
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190 def test_relabel_duplicate(self): |
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191 data = """ |
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192 graph |
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193 [ |
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194 label "" |
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195 directed 1 |
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196 node |
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197 [ |
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198 id 0 |
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199 label "same" |
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200 ] |
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201 node |
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202 [ |
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203 id 1 |
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204 label "same" |
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205 ] |
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206 ] |
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207 """ |
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208 fh = io.BytesIO(data.encode("UTF-8")) |
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209 fh.seek(0) |
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210 pytest.raises(nx.NetworkXError, nx.read_gml, fh, label="label") |
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211 |
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212 def test_tuplelabels(self): |
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213 # https://github.com/networkx/networkx/pull/1048 |
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214 # Writing tuple labels to GML failed. |
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215 G = nx.OrderedGraph() |
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216 G.add_edge((0, 1), (1, 0)) |
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217 data = "\n".join(nx.generate_gml(G, stringizer=literal_stringizer)) |
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218 answer = """graph [ |
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219 node [ |
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220 id 0 |
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221 label "(0,1)" |
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222 ] |
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223 node [ |
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224 id 1 |
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225 label "(1,0)" |
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226 ] |
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227 edge [ |
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228 source 0 |
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229 target 1 |
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230 ] |
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231 ]""" |
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232 assert data == answer |
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233 |
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234 def test_quotes(self): |
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235 # https://github.com/networkx/networkx/issues/1061 |
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236 # Encoding quotes as HTML entities. |
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237 G = nx.path_graph(1) |
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238 G.name = "path_graph(1)" |
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239 attr = 'This is "quoted" and this is a copyright: ' + chr(169) |
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240 G.nodes[0]["demo"] = attr |
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241 fobj = tempfile.NamedTemporaryFile() |
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242 nx.write_gml(G, fobj) |
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243 fobj.seek(0) |
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244 # Should be bytes in 2.x and 3.x |
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245 data = fobj.read().strip().decode("ascii") |
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246 answer = """graph [ |
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247 name "path_graph(1)" |
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248 node [ |
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249 id 0 |
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250 label "0" |
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251 demo "This is "quoted" and this is a copyright: ©" |
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252 ] |
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253 ]""" |
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254 assert data == answer |
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255 |
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256 def test_unicode_node(self): |
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257 node = "node" + chr(169) |
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258 G = nx.Graph() |
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259 G.add_node(node) |
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260 fobj = tempfile.NamedTemporaryFile() |
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261 nx.write_gml(G, fobj) |
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262 fobj.seek(0) |
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263 # Should be bytes in 2.x and 3.x |
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264 data = fobj.read().strip().decode("ascii") |
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265 answer = """graph [ |
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266 node [ |
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267 id 0 |
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268 label "node©" |
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269 ] |
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270 ]""" |
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271 assert data == answer |
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272 |
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273 def test_float_label(self): |
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274 node = 1.0 |
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275 G = nx.Graph() |
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276 G.add_node(node) |
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277 fobj = tempfile.NamedTemporaryFile() |
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278 nx.write_gml(G, fobj) |
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279 fobj.seek(0) |
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280 # Should be bytes in 2.x and 3.x |
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281 data = fobj.read().strip().decode("ascii") |
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282 answer = """graph [ |
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283 node [ |
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284 id 0 |
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285 label "1.0" |
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286 ] |
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287 ]""" |
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288 assert data == answer |
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289 |
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290 def test_name(self): |
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291 G = nx.parse_gml('graph [ name "x" node [ id 0 label "x" ] ]') |
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292 assert "x" == G.graph["name"] |
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293 G = nx.parse_gml('graph [ node [ id 0 label "x" ] ]') |
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294 assert "" == G.name |
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295 assert "name" not in G.graph |
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296 |
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297 def test_graph_types(self): |
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298 for directed in [None, False, True]: |
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299 for multigraph in [None, False, True]: |
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300 gml = "graph [" |
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301 if directed is not None: |
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302 gml += " directed " + str(int(directed)) |
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303 if multigraph is not None: |
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304 gml += " multigraph " + str(int(multigraph)) |
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305 gml += ' node [ id 0 label "0" ]' |
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306 gml += " edge [ source 0 target 0 ]" |
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307 gml += " ]" |
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308 G = nx.parse_gml(gml) |
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309 assert bool(directed) == G.is_directed() |
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310 assert bool(multigraph) == G.is_multigraph() |
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311 gml = "graph [\n" |
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312 if directed is True: |
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313 gml += " directed 1\n" |
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314 if multigraph is True: |
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315 gml += " multigraph 1\n" |
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316 gml += """ node [ |
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317 id 0 |
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318 label "0" |
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319 ] |
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320 edge [ |
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321 source 0 |
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322 target 0 |
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323 """ |
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324 if multigraph: |
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325 gml += " key 0\n" |
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326 gml += " ]\n]" |
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327 assert gml == "\n".join(nx.generate_gml(G)) |
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328 |
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329 def test_data_types(self): |
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330 data = [ |
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331 True, |
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332 False, |
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333 10 ** 20, |
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334 -2e33, |
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335 "'", |
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336 '"&&&""', |
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337 [{(b"\xfd",): "\x7f", chr(0x4444): (1, 2)}, (2, "3")], |
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338 ] |
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339 try: # fails under IronPython |
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340 data.append(chr(0x14444)) |
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341 except ValueError: |
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342 data.append(chr(0x1444)) |
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343 data.append(literal_eval("{2.3j, 1 - 2.3j, ()}")) |
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344 G = nx.Graph() |
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345 G.name = data |
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346 G.graph["data"] = data |
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347 G.add_node(0, int=-1, data=dict(data=data)) |
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348 G.add_edge(0, 0, float=-2.5, data=data) |
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349 gml = "\n".join(nx.generate_gml(G, stringizer=literal_stringizer)) |
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350 G = nx.parse_gml(gml, destringizer=literal_destringizer) |
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351 assert data == G.name |
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352 assert {"name": data, "data": data} == G.graph |
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353 assert list(G.nodes(data=True)) == [(0, dict(int=-1, data=dict(data=data)))] |
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354 assert list(G.edges(data=True)) == [(0, 0, dict(float=-2.5, data=data))] |
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355 G = nx.Graph() |
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356 G.graph["data"] = "frozenset([1, 2, 3])" |
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357 G = nx.parse_gml(nx.generate_gml(G), destringizer=literal_eval) |
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358 assert G.graph["data"] == "frozenset([1, 2, 3])" |
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359 |
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360 def test_escape_unescape(self): |
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361 gml = """graph [ |
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362 name "&"䑄��&unknown;" |
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363 ]""" |
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364 G = nx.parse_gml(gml) |
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365 assert ( |
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366 '&"\x0f' + chr(0x4444) + "��&unknown;" |
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367 == G.name |
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368 ) |
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369 gml = "\n".join(nx.generate_gml(G)) |
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370 alnu = "#1234567890;&#x1234567890abcdef" |
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371 answer = ( |
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372 """graph [ |
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373 name "&"䑄&""" |
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374 + alnu |
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375 + """;&unknown;" |
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376 ]""" |
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377 ) |
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378 assert answer == gml |
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379 |
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380 def test_exceptions(self): |
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381 pytest.raises(ValueError, literal_destringizer, "(") |
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382 pytest.raises(ValueError, literal_destringizer, "frozenset([1, 2, 3])") |
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383 pytest.raises(ValueError, literal_destringizer, literal_destringizer) |
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384 pytest.raises(ValueError, literal_stringizer, frozenset([1, 2, 3])) |
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385 pytest.raises(ValueError, literal_stringizer, literal_stringizer) |
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386 with tempfile.TemporaryFile() as f: |
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387 f.write(codecs.BOM_UTF8 + b"graph[]") |
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388 f.seek(0) |
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389 pytest.raises(nx.NetworkXError, nx.read_gml, f) |
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390 |
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391 def assert_parse_error(gml): |
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392 pytest.raises(nx.NetworkXError, nx.parse_gml, gml) |
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393 |
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394 assert_parse_error(["graph [\n\n", "]"]) |
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395 assert_parse_error("") |
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396 assert_parse_error('Creator ""') |
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397 assert_parse_error("0") |
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398 assert_parse_error("graph ]") |
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399 assert_parse_error("graph [ 1 ]") |
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400 assert_parse_error("graph [ 1.E+2 ]") |
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401 assert_parse_error('graph [ "A" ]') |
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402 assert_parse_error("graph [ ] graph ]") |
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403 assert_parse_error("graph [ ] graph [ ]") |
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404 assert_parse_error("graph [ data [1, 2, 3] ]") |
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405 assert_parse_error("graph [ node [ ] ]") |
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406 assert_parse_error("graph [ node [ id 0 ] ]") |
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407 nx.parse_gml('graph [ node [ id "a" ] ]', label="id") |
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408 assert_parse_error("graph [ node [ id 0 label 0 ] node [ id 0 label 1 ] ]") |
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409 assert_parse_error("graph [ node [ id 0 label 0 ] node [ id 1 label 0 ] ]") |
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410 assert_parse_error("graph [ node [ id 0 label 0 ] edge [ ] ]") |
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411 assert_parse_error("graph [ node [ id 0 label 0 ] edge [ source 0 ] ]") |
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412 nx.parse_gml("graph [edge [ source 0 target 0 ] node [ id 0 label 0 ] ]") |
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413 assert_parse_error("graph [ node [ id 0 label 0 ] edge [ source 1 target 0 ] ]") |
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414 assert_parse_error("graph [ node [ id 0 label 0 ] edge [ source 0 target 1 ] ]") |
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415 assert_parse_error( |
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416 "graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] " |
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417 "edge [ source 0 target 1 ] edge [ source 1 target 0 ] ]" |
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418 ) |
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419 nx.parse_gml( |
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420 "graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] " |
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421 "edge [ source 0 target 1 ] edge [ source 1 target 0 ] " |
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422 "directed 1 ]" |
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423 ) |
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424 nx.parse_gml( |
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425 "graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] " |
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426 "edge [ source 0 target 1 ] edge [ source 0 target 1 ]" |
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427 "multigraph 1 ]" |
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428 ) |
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429 nx.parse_gml( |
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430 "graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] " |
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431 "edge [ source 0 target 1 key 0 ] edge [ source 0 target 1 ]" |
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432 "multigraph 1 ]" |
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433 ) |
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434 assert_parse_error( |
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435 "graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] " |
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436 "edge [ source 0 target 1 key 0 ] edge [ source 0 target 1 key 0 ]" |
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437 "multigraph 1 ]" |
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438 ) |
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439 nx.parse_gml( |
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440 "graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] " |
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441 "edge [ source 0 target 1 key 0 ] edge [ source 1 target 0 key 0 ]" |
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442 "directed 1 multigraph 1 ]" |
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443 ) |
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444 |
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445 # Tests for string convertable alphanumeric id and label values |
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446 nx.parse_gml("graph [edge [ source a target a ] node [ id a label b ] ]") |
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447 nx.parse_gml( |
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448 "graph [ node [ id n42 label 0 ] node [ id x43 label 1 ]" |
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449 "edge [ source n42 target x43 key 0 ]" |
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450 "edge [ source x43 target n42 key 0 ]" |
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451 "directed 1 multigraph 1 ]" |
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452 ) |
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453 assert_parse_error( |
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454 "graph [edge [ source u'u\4200' target u'u\4200' ] " |
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455 + "node [ id u'u\4200' label b ] ]" |
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456 ) |
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457 |
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458 def assert_generate_error(*args, **kwargs): |
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459 pytest.raises( |
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460 nx.NetworkXError, lambda: list(nx.generate_gml(*args, **kwargs)) |
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461 ) |
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462 |
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463 G = nx.Graph() |
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464 G.graph[3] = 3 |
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465 assert_generate_error(G) |
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466 G = nx.Graph() |
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467 G.graph["3"] = 3 |
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468 assert_generate_error(G) |
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469 G = nx.Graph() |
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470 G.graph["data"] = frozenset([1, 2, 3]) |
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471 assert_generate_error(G, stringizer=literal_stringizer) |
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472 G = nx.Graph() |
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473 G.graph["data"] = [] |
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474 assert_generate_error(G) |
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475 assert_generate_error(G, stringizer=len) |
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476 |
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477 def test_label_kwarg(self): |
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478 G = nx.parse_gml(self.simple_data, label="id") |
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479 assert sorted(G.nodes) == [1, 2, 3] |
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480 labels = [G.nodes[n]["label"] for n in sorted(G.nodes)] |
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481 assert labels == ["Node 1", "Node 2", "Node 3"] |
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482 |
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483 G = nx.parse_gml(self.simple_data, label=None) |
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484 assert sorted(G.nodes) == [1, 2, 3] |
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485 labels = [G.nodes[n]["label"] for n in sorted(G.nodes)] |
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486 assert labels == ["Node 1", "Node 2", "Node 3"] |
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487 |
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488 def test_outofrange_integers(self): |
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489 # GML restricts integers to 32 signed bits. |
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490 # Check that we honor this restriction on export |
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491 G = nx.Graph() |
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492 # Test export for numbers that barely fit or don't fit into 32 bits, |
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493 # and 3 numbers in the middle |
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494 numbers = { |
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495 "toosmall": (-(2 ** 31)) - 1, |
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496 "small": -(2 ** 31), |
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497 "med1": -4, |
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498 "med2": 0, |
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499 "med3": 17, |
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500 "big": (2 ** 31) - 1, |
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501 "toobig": 2 ** 31, |
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502 } |
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503 G.add_node("Node", **numbers) |
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504 |
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505 fd, fname = tempfile.mkstemp() |
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506 try: |
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507 nx.write_gml(G, fname) |
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508 # Check that the export wrote the nonfitting numbers as strings |
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509 G2 = nx.read_gml(fname) |
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510 for attr, value in G2.nodes["Node"].items(): |
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511 if attr == "toosmall" or attr == "toobig": |
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512 assert type(value) == str |
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513 else: |
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514 assert type(value) == int |
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515 finally: |
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516 os.close(fd) |
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517 os.unlink(fname) |
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518 |
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519 |
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520 @contextmanager |
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521 def byte_file(): |
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522 _file_handle = io.BytesIO() |
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523 yield _file_handle |
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524 _file_handle.seek(0) |
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525 |
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526 |
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527 class TestPropertyLists: |
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528 def test_writing_graph_with_multi_element_property_list(self): |
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529 g = nx.Graph() |
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530 g.add_node("n1", properties=["element", 0, 1, 2.5, True, False]) |
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531 with byte_file() as f: |
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532 nx.write_gml(g, f) |
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533 result = f.read().decode() |
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534 |
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535 assert result == dedent( |
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536 """\ |
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537 graph [ |
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538 node [ |
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539 id 0 |
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540 label "n1" |
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541 properties "element" |
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542 properties 0 |
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543 properties 1 |
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544 properties 2.5 |
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545 properties 1 |
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546 properties 0 |
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547 ] |
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548 ] |
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549 """ |
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550 ) |
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551 |
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552 def test_writing_graph_with_one_element_property_list(self): |
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553 g = nx.Graph() |
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554 g.add_node("n1", properties=["element"]) |
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555 with byte_file() as f: |
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556 nx.write_gml(g, f) |
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557 result = f.read().decode() |
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558 |
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559 assert result == dedent( |
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560 """\ |
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561 graph [ |
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562 node [ |
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563 id 0 |
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564 label "n1" |
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565 properties "_networkx_list_start" |
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566 properties "element" |
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567 ] |
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568 ] |
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569 """ |
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570 ) |
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571 |
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572 def test_reading_graph_with_list_property(self): |
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573 with byte_file() as f: |
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574 f.write( |
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575 dedent( |
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576 """ |
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577 graph [ |
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578 node [ |
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579 id 0 |
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580 label "n1" |
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581 properties "element" |
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582 properties 0 |
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583 properties 1 |
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584 properties 2.5 |
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585 ] |
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586 ] |
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587 """ |
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588 ).encode("ascii") |
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589 ) |
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590 f.seek(0) |
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591 graph = nx.read_gml(f) |
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592 assert graph.nodes(data=True)["n1"] == {"properties": ["element", 0, 1, 2.5]} |
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593 |
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594 def test_reading_graph_with_single_element_list_property(self): |
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595 with byte_file() as f: |
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596 f.write( |
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597 dedent( |
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598 """ |
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599 graph [ |
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600 node [ |
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601 id 0 |
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602 label "n1" |
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603 properties "_networkx_list_start" |
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604 properties "element" |
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605 ] |
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606 ] |
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607 """ |
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608 ).encode("ascii") |
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609 ) |
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610 f.seek(0) |
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611 graph = nx.read_gml(f) |
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612 assert graph.nodes(data=True)["n1"] == {"properties": ["element"]} |