graphml and list types

[tcb]

Hi,

I have some graphml files which come from graph-tool and they have properties which networkx cannot read. The properties are node positions- a list of floats- and it seems list types are not supported by networkx graphml at all (reading or writing).

This is what I get when I try to write a list type to graphml

G=nx.Graph()

G.add_node(1, pos=[1,2])

nx.write_graphml(G, '/tmp/g.xml')

networkx/readwrite/graphml.py in add_data(self, name, element_type, value, scope, default)

    241         if element_type not in self.xml_type:

    242             raise nx.NetworkXError('GraphML writer does not support '

--> 243                                    '%s as data values.'%element_type)

    244         key_id = self.get_key(name, self.xml_type[element_type], scope, default)

    245         data_element = Element("data", key=key_id)

NetworkXError: GraphML writer does not support <type 'list'> as data values.

And the graphml file I would like read looks something like this:

 <!-- property keys --> 

 <key id="key0" for="node" attr.name="centrality" attr.type="int" /> 

 <key id="key1" for="node" attr.name="pos" attr.type="vector_float" /> 

 <graph id="G" edgedefault="undirected" parse.nodeids="canonical" parse.edgeids="canonical" parse.order="nodesfirst"> 

 <!-- graph properties --> 

 <!-- vertices --> 

 <node id="n0"> <data key="key0">2</data> <data key="key1">0x1.54206f8b25c6cp+3, 0x1.489af2ba23c76p+3</data> </node> 

So the 'pos' attribute is a 2d list of floats with type 'vector_double'.

and when I try to read this I get:

networkx/readwrite/graphml.py in find_graphml_keys(self, graph_element)

    512             graphml_keys[attr_id] = {

    513                 "name":attr_name,

--> 514                 "type":self.python_type[attr_type],

    515                 "for":k.get("for")}

    516             # check for "default" subelement of key element

KeyError: 'vector_float'

graph-tool (http://projects.skewed.de/graph-tool/) seems to read/write only graphml, so the easiest solution for me would be if networkx could read/write these graphml attributes properly. I'm happy to have a look at it myself, but I would appreciate some guidance on what's the best way to go about adding this support.

thanks

-

[Aric Hagberg]

I guess the attr.type "vector_float" must be an extension to the
GraphML standard? There must be some schema (listed in your file
header) that describes that. See
http://graphml.graphdrawing.org/primer/graphml-primer.html#EXT for
some info
If you want to add support for that open an issue at the github site
and we can comment there.
Aric

[tcb]

no problem:

https://github.com/networkx/networkx/issues/843

Aric

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