read_graphml fails to open graphml file generated by Cytoscape

[manihamidi]

networkx.read_graphml fails to import a graphml file generated by Cytoscape returning the following error:

Traceback (most recent call last):

  File "<ipython-input-323-63e903596d6f>", line 1, in <module>
    G = nx.read_graphml(path_to_graphml_file)

  File "<decorator-gen-327>", line 2, in read_graphml

  File "C:\Users\Mani\Anaconda\lib\site-packages\networkx\utils\decorators.py", line 220, in _open_file
    result = func(*new_args, **kwargs)

  File "C:\Users\Mani\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 154, in read_graphml
    return glist[0]

---

• Cytoscape is a popular graph visualization tool.

[manihamidi]

Temporary way of getting around the problem:

Manually add these variables to the start-tag of the graphml file generated by cytoscape:

xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"

i.e. open the graphml file in a text editor, and replace the second line ("< graphml >") with this:

 <graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">

[progval]

Can you provide an example file?

[manihamidi]

Here is the content of the graphml file that I exported from Cytoscape 3.4.0 (used cytoscape itself to make a simple 2-node, 2-attribute network with 1 edge):

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml>
    <key attr.name="SUID" attr.type="long" for="node" id="SUID"/>
    <key attr.name="shared name" attr.type="string" for="node" id="shared name"/>
    <key attr.name="name" attr.type="string" for="node" id="name"/>
    <key attr.name="selected" attr.type="boolean" for="node" id="selected"/>
    <key attr.name="first_attr" attr.type="int" for="node" id="first_attr"/>
    <key attr.name="second_attr" attr.type="string" for="node" id="second_attr"/>
    <key attr.name="SUID" attr.type="long" for="node" id="SUID"/>
    <key attr.name="shared name" attr.type="string" for="node" id="shared name"/>
    <key attr.name="shared interaction" attr.type="string" for="node" id="shared interaction"/>
    <key attr.name="name" attr.type="string" for="node" id="name"/>
    <key attr.name="selected" attr.type="boolean" for="node" id="selected"/>
    <key attr.name="interaction" attr.type="string" for="node" id="interaction"/>
    <key attr.name="SUID" attr.type="long" for="node" id="SUID"/>
    <key attr.name="shared name" attr.type="string" for="node" id="shared name"/>
    <key attr.name="name" attr.type="string" for="node" id="name"/>
    <key attr.name="selected" attr.type="boolean" for="node" id="selected"/>
    <key attr.name="__Annotations" attr.type="string" for="node" id="__Annotations"/>
    <graph edgedefault="directed" id="Network">
        <node id="63">
            <data key="SUID">63</data>
            <data key="shared name">Node 1</data>
            <data key="name">Node 1</data>
            <data key="selected">false</data>
            <data key="second_attr">'hello'</data>
        </node>
        <node id="62">
            <data key="SUID">62</data>
            <data key="shared name">Node 2</data>
            <data key="name">Node 2</data>
            <data key="selected">false</data>
            <data key="first_attr">1</data>
        </node>
        <edge source="63" target="62">
            <data key="SUID">64</data>
            <data key="shared name">Node 1 (interacts with) Node 2</data>
            <data key="shared interaction">interacts with</data>
            <data key="name">Node 1 (interacts with) Node 2</data>
            <data key="selected">false</data>
            <data key="interaction">interacts with</data>
        </edge>
    </graph>
</graphml>

and then I tried to open it with networkx and got this:

G_t = nx.read_graphml(path_t)
Traceback (most recent call last):

  File "<ipython-input-21-4a0389e1bd47>", line 1, in <module>
    G_t = nx.read_graphml(path_t)

  File "<decorator-gen-328>", line 2, in read_graphml

  File "C:\Users\Mani\Anaconda\lib\site-packages\networkx\utils\decorators.py", line 220, in _open_file
    result = func(*new_args, **kwargs)

  File "C:\Users\Mani\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 154, in read_graphml
    return glist[0]

IndexError: list index out of range

As I explained in previous comment above, if you replace <graphml> with xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd", in the graphml file using your text editor, nx.read_graphml will function as expected.