lxml: add namespace to input file

Question

I am parsing an xml file generated by an external program. I would then like to add custom annotations to this file, using my own namespace. My input looks as below:

Answer 1

You could replace the root element to add 'kjw' to its nsmap. Then xmlns declaration would be only in the root element.

Answer 2

Modifying the namespace mapping of a node is not possible in lxml. See this open ticket that has this feature as a wishlist item.

It originated from this thread on the lxml mailing list, where a workaround replacing the root node is given as an alternative. There are some issues with replacing the root node though: see the ticket above.

I'll put the suggested root replacement workaround code here for completeness:

>>> DOC = """<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
...   <model metaid="untitled" id="untitled">
...     <annotation>...</annotation>
...     <listOfUnitDefinitions>...</listOfUnitDefinitions>
...     <listOfCompartments>...</listOfCompartments>
...     <listOfSpecies>
...       <species metaid="s1" id="s1" name="GenA" compartment="default" initialAmount="0">
...         <annotation>
...           <celldesigner:extension>...</celldesigner:extension>
...         </annotation>
...       </species>
...       <species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
...         <annotation>
...            <celldesigner:extension>...</celldesigner:extension>
...         </annotation>
...       </species>
...     </listOfSpecies>
...     <listOfReactions>...</listOfReactions>
...   </model>
... </sbml>"""
>>> 
>>> from lxml import etree
>>> from StringIO import StringIO
>>> NS = "http://this.is.some/custom_namespace"
>>> tree = etree.ElementTree(element=None, file=StringIO(DOC))
>>> root = tree.getroot()
>>> nsmap = root.nsmap
>>> nsmap['kjw'] = NS
>>> new_root = etree.Element(root.tag, nsmap=nsmap)
>>> new_root[:] = root[:]
>>> new_root.append(etree.Element('{%s}%s' % (NS, 'test')))
>>> new_root.append(etree.Element('{%s}%s' % (NS, 'test')))

>>> print etree.tostring(new_root, pretty_print=True)
<sbml xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" xmlns:kjw="http://this.is.some/custom_namespace" xmlns="http://www.sbml.org/sbml/level2/version4"><model metaid="untitled" id="untitled">
    <annotation>...</annotation>
    <listOfUnitDefinitions>...</listOfUnitDefinitions>
    <listOfCompartments>...</listOfCompartments>
    <listOfSpecies>
      <species metaid="s1" id="s1" name="GenA" compartment="default" initialAmount="0">
        <annotation>
          <celldesigner:extension>...</celldesigner:extension>
        </annotation>
      </species>
      <species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
        <annotation>
           <celldesigner:extension>...</celldesigner:extension>
        </annotation>
      </species>
    </listOfSpecies>
    <listOfReactions>...</listOfReactions>
  </model>
<kjw:test/><kjw:test/></sbml>

Answer 3

I know this is old question, but it still valid and as of lxml 3.5.0, there is probably better solution to this problem:

cleanup_namespaces() accepts a new argument top_nsmap that moves definitions of the provided prefix-namespace mapping to the top of the tree.

So now the namespace map can be moved up with simple call to this:

nsmap = {'kjw': 'http://this.is.some/custom_namespace'}
etree.cleanup_namespaces(root, top_nsmap=nsmap)

Answer 4

Rather than dealing directly with the raw XML you could also look toward LibSBML, a library for manipulating SBML documents with language bindings for, among others, python. There you would use it like this:

>>> from libsbml import *
>>> doc = readSBML('Dropbox/SBML Models/BorisEJB.xml')
>>> species = doc.getModel().getSpecies('MAPK')
>>> species.appendAnnotation('<kjw:test xmlns:kjw="http://this.is.some/custom_namespace"/>')
0
>>> species.toSBML()
'<species id="MAPK" compartment="compartment" initialConcentration="280" boundaryCondition="false">\n  <annotation>\n
 <kjw:test xmlns:kjw="http://this.is.some/custom_namespace"/>\n  </annotation>\n</species>'
>>>

Answer 5

If you temporarily add a namespaced attribute to the root node, that does the trick.

ns = '{http://this.is.some/custom_namespace}'

# add 'kjw:foobar' attribute to root node
root.set(ns+'foobar', 'foobar')

# add kjw namespace elements (or attributes) elsewhere
... get child element species ...
species.append(etree.Element(ns + 'test'))

# remove temporary namespaced attribute from root node
del root.attrib[ns+'foobar']

Answer 6

I wrote this function to add a namespace to the root element:

def addns(tree, alias, uri):                
    root = tree.getroot()
    nsmap = root.nsmap
    nsmap[alias] = uri
    new_root = etree.Element(root.tag, attrib=root.attrib, nsmap=nsmap)
    new_root[:] = root[:]
    return new_root.getroottree()

After applying this function, you get a new tree, but you can probably change the tree instance from the single objet from which you access the tree _{... as you have a strong OO design!}.