GraphML import

[Peter Clarke]

I have exported a GrapML which contains node attributes from the python NetworkX library. Not all nodes contain all attributes. When I try to import this into Cytoscape it fails because of this. 

Is there any way I can either specify a null value in the GraphML file that will not cause the type checking to default to the wrong data type (NaN or null for example) or have some other way around this?

Thanks! 

-Peter

[Samad Lotia]

Hi Peter,

I also tried the NetworkX's GraphML exporter and had problems, e.g. Unicode serialization and no support for list attributes. I wrote my own Python function which takes a NetworkX graph and exports it to an XGMML file, which Cytoscape accepts. Here's the Github Gist: https://gist.github.com/samadlotia/8c987acb4de07ed86fba

It should support node attributes without values. It only serializes node attributes of type int, string, and lists. Hopefully this meets your needs.

Samad

[Keiichiro Ono]

If you are working with NetworkX, an alternative is export networks &
attributes as Cytoscape.js style JSON.

http://nbviewer.ipython.org/github/keiono/cytoscape-ipy/blob/master/CytoscapeREST_Basics.ipynb

This example is used for my ongoing project (REST API module for
Cytoscape 3), but file-based import is already available for Cytoscape
3.1.1. And building JSON object is very straightforward:

https://github.com/keiono/cytoscape-ipy/blob/master/cytoscape/viewer.py#L63

Kei

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Keiichiro Ono
http://keiono.github.io/

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