Re: [igraph] Graphml Import / Export, keeping boolean values and using id as index

[Tamás Nepusz]

Dear Gábor,

That's weird, I loaded the GraphML file you sent; all the boolean attributes 
came through just fine and they even survive a save-load cycle:

In [1]: g=load("test_for_igraph.graphml")
In [2]: g.vertex_attributes()
Out[2]:  
['propernoun',
 'noun',
 'pronoun',
 'adverb',
 'id',
 'number',
 'vocid',
 'label',
 'adjective',
 'verb',
 'ambiguity',
 'operator',
 'other']
In [3]: print g.vs["adverb"][:10]
[False, False, False, False, False, False, False, False, False, False]
In [4]: g.write_graphml("test.graphml")
In [5]: g2=load("test.graphml")
/Users/ntamas/virtualenvs/default/lib/python2.7/site-packages/python_igraph-0.7-py2.7-macosx-10.8-intel.egg/igraph/__init__.py:2130:
 RuntimeWarning: Could not add vertex ids, there is already an 'id' vertex 
attribute at ../../src/foreign-graphml.c:416
In [6]: print g2.vs["adverb"][:10]
[False, False, False, False, False, False, False, False, False, False]

What platform are you running igraph on, which igraph version it is, and in 
which version of Python?

-- 
T.

On 29 Apr 2013, at 09:19, Gábor Tóth <address@hidden> wrote:

> Dear Tamas,
> 
> Thanks for the prompt reply, I am attaching my graphml file in a zipped file.
> 
> FYI, this is the header of the exported version, it seems that boolean value 
> is transformed into double.
> 
> <!-- Created by igraph -->
>   <key id="v_propernoun" for="node" attr.name="propernoun" 
> attr.type="double"/>
>   <key id="v_noun" for="node" attr.name="noun" attr.type="double"/>
>   <key id="v_pronoun" for="node" attr.name="pronoun" attr.type="double"/>
>   <key id="v_adverb" for="node" attr.name="adverb" attr.type="double"/>
> 
> 
> 
> 
> Best,
> 
> Gabor
> 
> 
> On Sun, Apr 28, 2013 at 8:02 PM, Tamás Nepusz <address@hidden> wrote:
> Hi,
> 
> > By using Igraph python have imported a graphml file that I created with 
> > TinkerGraph. First, in the imported graphml file nodes have boolean values, 
> > however after the import they don't have them anymore:
> Can you post your GraphML file or any other GraphML file that reproduces the 
> issue? I tried the following on my machine and it worked:
> 
> In [1]: g=Graph(1)
> In [2]: g.vs[0]["test"] = True
> In [3]: g.write_graphml("test.graphml")
> In [4]: g2=load("test.graphml")
> In [5]: g2.vs[0]["test"]
> Out[5]:  True
> 
> > How can I import grahml files by keeping boolean values? When I created the 
> > graphm file in TinkerGraph I used the id attribute as index.
> > How could Igraph use the id attribute of the node as index after the 
> > import? As you can see, the index is 2317 in Igraph, and not 363.
> igraph vertex indices have nothing to do with the indices of the nodes in the 
> GraphML file, especially because GraphML node IDs are not guaranteed to be 
> integers, so in the vast majority of cases, igraph would have to invent its 
> own IDs anyway (since the C core of igraph always uses a range of integers 
> from 0 to |V|-1 where |V| is the number of vertices).
> 
> > <node id="n2317">
> >       <data key="v_propernoun">4.94066e-324</data>
> >       <data key="v_noun">4.94066e-324</data>
> [...snip...]
> > </node>
> >
> > Again, the question, how can I use the original id attribute (363) instead 
> > of n2317?
> You can't (for reasons mentioned above) and I don't really see why you would 
> want to keep the same ID. The IDs are just internal references within the 
> GraphML file with no semantic meaning. If your IDs *do* have some semantic 
> meaning, just duplicate them as a vertex attribute and use the attribute 
> instead.
> 
> > Is there a way not putting v before the name of attributes and n before the 
> > id?
> No, there isn't, for different reasons. The v_ prefix before the attribute 
> names are required because theoretically you could have a graph where both 
> the edges and the vertices have an attribute with the same name. To avoid 
> such conflicts, igraph prefixes the identifiers of the vertex attributes with 
> v_ and the identifiers of edge attributes with e_. Note, however, that this 
> does *not* mean that the attribute itself is renamed since "key" is also just 
> an internal reference within the GraphML file. The *name* of the attribute 
> corresponding to a specific key is given by the attr.name attribute of the 
> corresponding <key> tag in the GraphML file. E.g., in the example I listed 
> above, the "test" attribute is declared like this in the GraphML file:
> 
> <key id="v_test" for="node" attr.name="test" attr.type="boolean"/>
> 
> You can see that its internal ID within the GraphML file is "v_test" to avoid 
> conflicts with possibly existing edge attributes with the same name, but the 
> _name_ in the attr.name attribute of the <key> tag is declared as "test", and 
> not "v_test".
> 
> As for the "n" prefix before the node IDs, it is also required because IDs 
> that start with digits are not valid IDs in XML files (although of course 
> many parsers accept them). This is not immediately obvious but it follows 
> from the following W3C recommendation:
> 
> http://www.w3.org/TR/REC-xml/
> 
> See, in particular, Section 3.3.1 
> (http://www.w3.org/TR/REC-xml/#sec-attribute-types) which says that "Values 
> of type ID must match the Name production", and Section 2.3 
> (http://www.w3.org/TR/REC-xml/#NT-Name), which says that "The first character 
> of a Name must be a NameStartChar", and the BNF rule for NameStartChar is 
> also defined as:
> 
> NameStartChar ::=       ":" | [A-Z] | "_" | [a-z] | [#xC0-#xD6] | [#xD8-#xF6] 
> | [#xF8-#x2FF] | [#x370-#x37D] | [#x37F-#x1FFF] | [#x200C-#x200D] | 
> [#x2070-#x218F] | [#x2C00-#x2FEF] | [#x3001-#xD7FF] | [#xF900-#xFDCF] | 
> [#xFDF0-#xFFFD] | [#x10000-#xEFFFF]
> 
> So, in a nutshell, igraph uses the "n" prefix for node IDs because node IDs 
> cannot start with numbers.
> 
> All the best,
> Tamas
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