Re: [igraph] igraph crashes when loading graphml file

[Tamas Nepusz]

Dear Stefan,

I checked the attached GraphML file and it seems that the problem is caused by yEd's own tags that are used inside <data> tags to store layout-related properties. I'm not sure whether the GraphML specification actually allows that or not, but igraph only expects character data inside <data> tags. I will check the GraphML specification and adapt the parser accordingly in the upcoming igraph version if it is in fact allowed by GraphML (but I'm not sure what should be done by yEd's tags in this case - should it just be stored as is in igraph or should they be ignored with/without a warning?).

In the meanwhile, I suggest you to remove yEd-specific tags from the XML file if you don't need them in igraph (maybe pipe the file through xmllint and use grep to get rid of the unnecessary stuff - I think you should grep for "<y:", "</y:" and "yfiles.type") and try reading it again into igraph. I used the following:

xmllint your-file.graphml | grep -v -E "</?y:" | grep -v "yfiles.type" >filtered.graphml

igraph was able to read the resulting GraphML file after a warning (which refers to the three attribute specifications I filtered out with the second grep).

By the way, igraph was also able to load the GML file you sent to me and it kept the "label" attributes, as this attribute contained only plain textual data. The "graphics" and "LabelGraphics" attributes are not handled at the moment as the GML parser we use only allows string and numeric attributes.

-- 

Tamas

I have attached my graph as graphml and gml formatted files and the two python files loading the respective graphs.

 

Is there any way I can make igraph work with this graphml file?

Any help would be much appreciated.

 

 

 

Mit freundlichen Grüßen / Kind regards

Stefan Reitz 

Test Engineer

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<test_app_4.py><MenueStrukturUHV_nur_CallStacks_0_2.gml><MenueStrukturUHV_nur_CallStacks_0_2.graphml><test_app_3.py>

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