1

I am trying to read a gexf file using nx and get the above error:

import networkx as nx
nx.read_gexf('KwNet-Journals/KwNet-Journals.gexf')

The gexf file can be found here.

keramat
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3 Answers3

3

NetworkX doesn't support GEXF 1.3 that this file is in.

In [5]: pdb
Automatic pdb calling has been turned ON

In [6]: nx.read_gexf(r"<...>\KwNet-Journals.gexf")
<...>
NetworkXError: No <graph> element in GEXF file.
<...>

ipdb> l
    688         for version in self.versions:
    689             self.set_version(version)
    690             g = self.xml.find(f"{{{self.NS_GEXF}}}graph")
    691             if g is not None:
    692                 return self.make_graph(g)
--> 693         raise nx.NetworkXError("No <graph> element in GEXF file.")
    694
<...>

ipdb> self.NS_GEXF
'http://www.gexf.net/1.2draft'

ipdb> q

In [7]: ! head "<...>\KwNet-Journals.gexf"
<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.3" version="1.3" xmlns:viz="http://www.gexf.net/1.3/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd">
  <meta lastmodifieddate="2020-02-07">
    <creator>Gephi 0.9</creator>
    <description></description>
  </meta>
  <graph defaultedgetype="undirected" timeformat="double" timerepresentation="timestamp" mode="dynamic">
<...>


In [10]: nx.read_gexf(r"<...>\KwNet-Journals.gexf", version='1.3')

NetworkXError: Unknown GEXF version 1.3.
> c:\python38\lib\site-packages\networkx\readwrite\gexf.py(253)set_version()
    251         d = self.versions.get(version)
    252         if d is None:
--> 253             raise nx.NetworkXError(f"Unknown GEXF version {version}.")
    254         self.NS_GEXF = d["NS_GEXF"]
    255         self.NS_VIZ = d["NS_VIZ"]

ipdb> version
'1.3'

ipdb> self.versions.keys()
dict_keys(['1.1draft', '1.2draft'])
ivan_pozdeev
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  • Thanks for your answer, any ideas for reading or converting this file to use that in python? – keramat Jan 30 '21 at 10:08
  • @keramat Add support of that version to NetworkX? If you need the graph specifically in NetworkX, I see no other way. – ivan_pozdeev Jan 30 '21 at 10:11
  • @keramat You can forge the version inside the file to deceive the version checker but since it's another version of the format, it'll probably break somewhere else down the line. – ivan_pozdeev Jan 30 '21 at 10:12
  • Did you find any solution to your problem? I need to import a gexf file into Networkx and I've having the same issue... – gccallie Dec 07 '21 at 11:22
1

You might be able to get away by replacing the header of the GEXF file with namespace descriptions related to GEXF version 1.2. That is, remove

<gexf xmlns="http://www.gexf.net/1.3" version="1.3" 
xmlns:viz="http://www.gexf.net/1.3/viz" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd">

and insert

<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft" 
xmlns:viz="http://www.gexf.net/1.2/viz" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
xsi:schemaLocation="http://www.gexf.net/1.2draft 
http://www.gexf.net/1.2draft/gexf.xsd">

Ideally, NetworkX is to be revised for support for GEXF that Gephi, for example, uses by default.

Jukka Huhtamäki
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1

I do not take any pride in this answer as it circumvents XML syntax. However, as it gets the job done, I will share it anyway.

f = io.open("demo.gexf", mode="r", encoding="utf-8")
gexf = f.read()
gexf = gexf.replace('xmlns="http://www.gexf.net/1.3"', 'xmlns="http://www.gexf.net/1.2draft"')\
.replace('version="1.3"',  'version="1.2"')\
.replace('http://www.gexf.net/1.3', 'http://www.gexf.net/1.2')
out = io.open("demo-fixed.gexf", mode='w', encoding="utf-8")
out.write(gexf)
Jukka Huhtamäki
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