pyquery (lxml) not finding a tag in a well-structured XML document?

Question

I have an XML file that looks like this. The relevant bit is this:

<reference>
  <citation>Vander Wal JS, Gang CH, Griffing GT, Gadde KM. Escitalopram for treatment of night eating syndrome: a 12-week, randomized, placebo-controlled trial. J Clin Psychopharmacol. 2012 Jun;32(3):341-5. doi: 10.1097/JCP.0b013e318254239b.</citation>
  <PMID>22544016</PMID>
</reference>

I am trying to find the value of the PMID field, using PyQuery to parse the XML:

    from pyquery import PyQuery as pq

    text = open(f, 'r').read()
    d = pq(text)
    data = {}       
    data['nct_id'] = d('nct_id').text()

    print d('reference')
    reference = d('reference')
    print reference('PMID')
    data['pmid'] = reference('PMID').text()

    print data['PMID']

Why isn't this working? In the console I see the full content of reference from the first print statement, followed by two empty values:

<reference>
    <citation>Vander Wal JS, Gang CH, Griffing GT, Gadde KM. Escitalopram for treatment of night eating syndrome: a 12-week, randomized, placebo-controlled trial. J Clin Psychopharmacol. 2012 Jun;32(3):341-5. doi: 10.1097/JCP.0b013e318254239b.</citation>
    <PMID>22544016</PMID>
  </reference>

I can find other leaf nodes in the document (like nct_id) just fine using .find(), as the example code shows.

Is it that PyQuery doesn't like upper-case tags?

Answer 1

You can specifiy the parser to use and it will work:

d = pq(text, parser='xml')