Accessing child XML elements with XPATH in Python

Question

I'm parsing this XML file: https://www.dropbox.com/s/i6hga7nvmcd6rxx/ct.cps?dl=0

From each <Reaction> tag I want its name attribute and the name attribute of its <Constant> children.

from lxml import etree

NSMAP = {"c": "http://www.copasi.org/static/schema"}

parsed = etree.parse('ct.cps')

for a in parsed.xpath("//c:Reaction", namespaces=NSMAP):
    print a.attrib['name']

I can access each of the two elements' name attributes by using the above code. However, when I'm in one iteration of the <Reaction> elements, how could I then access subelements and list them out?

I've tried this:

for a in parsed.xpath("//c:Reaction", namespaces=NSMAP):
    for b in a.xpath('Constant'):
        print b.attrib['name']

But it doesn't work.

Here's a sample of the XML

</rdf:RDF>
        </MiriamAnnotation>
      </Metabolite>
    </ListOfMetabolites>
    <ListOfReactions>
      <Reaction key="Reaction_0" name="v1" reversible="false" fast="false">
        <MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
  <rdf:Description rdf:about="#Reaction_0">
    <dcterms:created>
      <rdf:Description>
        <dcterms:W3CDTF>2015-06-16T22:13:07Z</dcterms:W3CDTF>
      </rdf:Description>
    </dcterms:created>
  </rdf:Description>
</rdf:RDF>
        </MiriamAnnotation>
        <ListOfSubstrates>
          <Substrate metabolite="Metabolite_5" stoichiometry="1"/>
        </ListOfSubstrates>
        <ListOfModifiers>
          <Modifier metabolite="Metabolite_9" stoichiometry="1"/>
        </ListOfModifiers>
        <ListOfConstants>
          <Constant key="Parameter_4344" name="Kcat" value="433.724"/>
          <Constant key="Parameter_4343" name="km" value="479.617"/>
        </ListOfConstants>
        <KineticLaw function="Function_40">
          <ListOfCallParameters>
            <CallParameter functionParameter="FunctionParameter_264">
              <SourceParameter reference="Parameter_4344"/>
            </CallParameter>
            <CallParameter functionParameter="FunctionParameter_254">
              <SourceParameter reference="Metabolite_9"/>
            </CallParameter>
            <CallParameter functionParameter="FunctionParameter_258">
              <SourceParameter reference="Metabolite_5"/>
            </CallParameter>
            <CallParameter functionParameter="FunctionParameter_266">
              <SourceParameter reference="Parameter_4343"/>
            </CallParameter>
          </ListOfCallParameters>
        </KineticLaw>
      </Reaction>
      <Reaction key="Reaction_1" name="v2" reversible="false" fast="false">
        <MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
  <rdf:Description rdf:about="#Reaction_1">

Instead of using dropbox link please paste the relevant contents of the xml file here (not the complete xml file) — Anand S Kumar
– Anand S Kumar, Commented Jul 5, 2015 at 18:10

Anand S Kumar · Accepted Answer · 2015-07-05 18:34:55Z

2

When your parent element in an xml has a namespace, the child are also of same namespace (unless explicitely specified in the xml element), so when you are trying to search for them using XPATH , you will have to specify namespace, for children as well.

Try the following -

for a in parsed.xpath("//c:Reaction", namespaces=NSMAP):
    for b in a.xpath(".//c:Constant", namespaces=NSMAP):
        print b.attrib['name']

edited Jul 5, 2015 at 18:34

answered Jul 5, 2015 at 18:19

Anand S Kumar

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6 Comments

Charon Over a year ago

Ah yes, that works. THanks. However that gives me too many answers. Id just like each constant to appear once - how would I do that?

Anand S Kumar Over a year ago

Each constant would only appear once, there may be that many constants in the xml

Charon Over a year ago

No there's only about 20, that produces loads. Because there's two for loops, won't there be repeats?

Anand S Kumar Over a year ago

No, each of the outer for loop iterates over each different reaction element, and then the inner for loop iterates over each constant element in each reaction element. So the two for loops would not lead to duplicates, but maybe there is something else in your code leading to this?

Charon Over a year ago

There are only 26 <Constant> tags in the whole xml, so this code must be creating duplicates

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