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

[Tamás Nepusz]

Hi,

So I tried to get as close to your setup as possible; I tried it on Ubuntu 
12.10 with Python 2.7.3 and igraph 0.6.5 and it seemed to work just fine for 
me. Are you on a 64-bit platform? Have you compiled igraph yourself or did you 
use the official packages? If all else fails, I'll try to reproduce your issue 
in a virtual machine but I have to know exactly how you obtained igraph and its 
Python interface.

All the best,
Tamas


On 29 Apr 2013, at 10:35, Gábor Tóth <address@hidden> wrote:

> Hi Tamas,
> 
> My Platform is Ubuntu 12.10
> 
> My python version is : Python 2.7.3
> 
> My Igraph version is: 0.6.5
> 
> I did the same commands you did:
> 
> >>> g=load("test_for_igraph.graphml")
> >>> g.vertex_attributes()
> ['propernoun', 'noun', 'pronoun', 'adverb', 'id', 'number', 'vocid', 'label', 
> 'adjective', 'verb', 'ambiguity', 'operator', 'other']
> >>> print g.vs["adverb"][:10]
> [5e-324, 5e-324, 5e-324, 5e-324, 5e-324, 5e-324, 5e-324, 5e-324, 5e-324, 
> 5e-324]
> 
> 
> Thanks again,
> 
> Gabor
> 
> 
> 
> On Mon, Apr 29, 2013 at 9:07 AM, Tamás Nepusz <address@hidden> wrote:
> 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
> > _______________________________________________
> > igraph-help mailing list
> > address@hidden
> > https://lists.nongnu.org/mailman/listinfo/igraph-help
> >
> > <test_for_igraph.graphml.zip>_______________________________________________
> > igraph-help mailing list
> > address@hidden
> > https://lists.nongnu.org/mailman/listinfo/igraph-help
> 
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