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Re: [igraph] Namespaces and GraphML

From: Robin Müller-Bady
Subject: Re: [igraph] Namespaces and GraphML
Date: Thu, 25 Sep 2014 09:30:12 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:31.0) Gecko/20100101 Icedove/31.0

Dear Tamás,

thank you very much for that quick help!
Indeed, I use a Java tool that generates the graphml files. This tool (JAXB in Java) created the files by using the graphml-xsd file, so I assumed them to be correct. But in that case, I will try to manually look it up again, maybe something went wrong with the generation of the xml/java model.

In any case, thank you a lot for the implementation of the namespace fix!



On 09/24/2014 10:10 PM, Tamas Nepusz wrote:
Hello Robin,

I was checking the GraphML file that you sent and I was wondering whether it is indeed a 
valid GraphML file - after all, the root tag is simply <graphml> and not 
<ns3:graphml> so it is not in the GraphML namespace. The GraphML primer states that 
the root tag is also in the GraphML namespace [1]:

"The second line contains the root-element element of a GraphML document: the 
graphml element. The graphml element, like all other GraphML elements, belongs to 
the namespace http://graphml.graphdrawing.org/xmlns.”

[1] http://graphml.graphdrawing.org/primer/graphml-primer.html


On 23 September 2014 at 15:12:33, Robin Müller-Bady (address@hidden) wrote:
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:
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 _______________________________________________
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