lxml: add namespace to input file

[ManiKinG]

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:<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>The issue being that lxml only declares namespaces when they are used, which means the declaration is repeated many times, like so (simplified):<sbml xmlns="namespace" xmlns:celldesigner="morenamespace" level="2" version="4"> <listOfSpecies> <species> <kjw:test xmlns:kjw="http://this.is.some/custom_namespace"/> <celldesigner:data>Some important data which must be kept</celldesigner:data> </species> <species> <kjw:test xmlns:kjw="http://this.is.some/custom_namespace"/> </species> .... </listOfSpecies></sbml>Is it possible to force lxml to write this declaration only once in a parent element, such as sbml or listOfSpecies? Or is there a good reason not to do so? The result I want would be:<sbml xmlns="namespace" xmlns:celldesigner="morenamespace" level="2" version="4" xmlns:kjw="http://this.is.some/custom_namespace"> <listOfSpecies> <species> <kjw:test/> <celldesigner:data>Some important data which must be kept</celldesigner:data> </species> <species> <kjw:test/> </species> .... </listOfSpecies></sbml>The important problem is that the existing data which is read from a file must be kept, so I cannot just make a new root element (I think?).EDIT: Code attached below.def annotateSbml(sbml_input): from lxml import etree checkSbml(sbml_input) # Makes sure the input is valid sbml/xml. ns = "http://this.is.some/custom_namespace" etree.register_namespace('kjw', ns) sbml_doc = etree.ElementTree() root = sbml_doc.parse(sbml_input, etree.XMLParser(remove_blank_text=True)) nsmap = root.nsmap nsmap['sbml'] = nsmap[None] # Makes code more readable, but seems ugly. Any alternatives to this? nsmap['kjw'] = ns ns = '{' + ns + '}' sbmlns = '{' + nsmap['sbml'] + '}' for species in root.findall('sbml:model/sbml:listOfSpecies/sbml:species', nsmap): species.append(etree.Element(ns + 'test')) sbml_doc.write("test.sbml.xml", pretty_print=True, xml_declaration=True) return