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Re: [igraph] Namespaces and GraphML

From: Tamás Nepusz
Subject: Re: [igraph] Namespaces and GraphML
Date: Wed, 24 Sep 2014 10:09:03 +0200

Hi there,

It looks like we were being sloppy when we implemented the GraphML parser and 
simply assumed that GraphML tags are in the default namespace. We cannot offer 
you an easy fix right now -- I'm working on the issue, but this will probably 
get into igraph 0.7.2 only. You can follow our progress on the issue here:


If you are willing to recompile igraph from scratch, you will probably be able 
to cherry-pick the patch (which I will post on the issue page above) and merge 
into your copy of igraph. Alternatively, you can probably use Python's 
ElementTree module to load the GraphML file, move every GraphML-related tag to 
the default namespace, write it out again, and then load it using igraph. This 
would probably be safer than manipulating the XML file via awk/sed. Also, 
command-line XML manipulation tools such as XMLStarlet might provide you with 
an easier way to move GraphML-related stuff to the default namespace, but I'm 
not familiar with those.

Thanks for the bug report!


-----Original Message-----
From: Robin Müller-Bady <address@hidden>
Reply: Help for igraph users <address@hidden>>
Date: 23 September 2014 at 15:12:33
To:address@hidden <address@hidden>>
Subject:  [igraph] Namespaces and GraphML

> Hi there,
> I am using igraph in order to read, process and write graphml files of
> graphml version 1.1 (http://graphml.graphdrawing.org/xmlns/1.1/graphml.xsd).  
> I get the graphml files from a java generator and postpress them with
> the igraph python interface.
> The problem is, that the java graphml generator creates specific
> namespaces in the files, e.g.
> "xmlns:ns2="http://www.w3.org/1999/xlink"; " such that it results in a
> file that looks like follows:
> > xmlns:ns3="http://graphml.graphdrawing.org/xmlns";>
> which is not readable by igraph anymore ("igraph._igraph.InternalError:
> Error at foreign-graphml.c:1139: Graph index was too large, Invalid value").
> I am currently using Debian Jessie with igraph 0.7.0 and Python 2.7.8.
> You have any ideas on how to fix that without processing the file
> through awk/sed?
> Regards,
> Robin
> _______________________________________________
> igraph-help mailing list
> address@hidden
> https://lists.nongnu.org/mailman/listinfo/igraph-help

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