from xml.dom import minidom
 
document = """\
<?xml version="1.0" ?>
<root>
<graphml>
    <a />
    <b />
</graphml><graphml>
    <c />
    <d />
</graphml>
</root>
"""
 
xmldoc = minidom.parseString(document)
 
newdoc = minidom.getDOMImplementation().createDocument(None, "graphml", None)
 
## ここから
root_node = newdoc.documentElement
root_node.setAttribute('xmlns', 'graphml.graphdrawing.org/xmlns')
root_node.setAttribute('xmlns:java', 'yworks.com/xml/yfiles-com...')
# みたいな感じで色々ついか
 
## ここまで
 
graphmls = xmldoc.getElementsByTagName('graphml')
for graphml in graphmls:
    for child in graphml.childNodes:
        newdoc.documentElement.appendChild(child.cloneNode(True))
 
print newdoc.toxml()

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