Reputation: 9792
If I have the following xml:
<uima.cas.FSArray _id="7429" size="2">
<i>7409</i>
<i>7419</i>
</uima.cas.FSArray>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7342" codingScheme="SNOMEDCT" code="269435009" oid="269435009#SNOMEDCT" score="0.0" disambiguated="false" cui="C0879626" tui="T046" preferredText="Adverse effects"/>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7322" codingScheme="SNOMEDCT" code="157754004" oid="157754004#SNOMEDCT" score="0.0" disambiguated="false" cui="C0879626" tui="T046" preferredText="Adverse effects"/>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7352" codingScheme="SNOMEDCT" code="269432007" oid="269432007#SNOMEDCT" score="0.0" disambiguated="false" cui="C0879626" tui="T046" preferredText="Adverse effects"/>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7332" codingScheme="SNOMEDCT" code="213029005" oid="213029005#SNOMEDCT" score="0.0" disambiguated="false" cui="C0879626" tui="T046" preferredText="Adverse effects"/>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7362" codingScheme="SNOMEDCT" code="157762007" oid="157762007#SNOMEDCT" score="0.0" disambiguated="false" cui="C0879626" tui="T046" preferredText="Adverse effects"/>
<uima.cas.FSArray _id="7372" size="5">
<i>7362</i>
<i>7332</i>
<i>7352</i>
<i>7322</i>
<i>7342</i>
</uima.cas.FSArray>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7235" codingScheme="SNOMEDCT" code="274241003" oid="274241003#SNOMEDCT" score="0.0" disambiguated="false" cui="C0004134" tui="T184" preferredText="Ataxia"/>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7265" codingScheme="SNOMEDCT" code="39384006" oid="39384006#SNOMEDCT" score="0.0" disambiguated="false" cui="C0004134" tui="T184" preferredText="Ataxia"/>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7255" codingScheme="SNOMEDCT" code="206825002" oid="206825002#SNOMEDCT" score="0.0" disambiguated="false" cui="C0004134" tui="T184" preferredText="Ataxia"/>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7275" codingScheme="SNOMEDCT" code="20262006" oid="20262006#SNOMEDCT" score="0.0" disambiguated="false" cui="C0004134" tui="T184" preferredText="Ataxia"/>
<org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="7245" codingScheme="SNOMEDCT" code="158202006" oid="158202006#SNOMEDCT" score="0.0" disambiguated="false" cui="C0004134" tui="T184" preferredText="Ataxia"/>
<uima.cas.FSArray _id="7285" size="5">
<i>7245</i>
<i>7275</i>
<i>7255</i>
<i>7265</i>
<i>7235</i>
I want to get the _id
and the <i>
subelements from nodes uima.cas.FSArray
i.e. looking at the first node (first three lines) I would like to retrieve something like
_id i
7429 7409
7429 7419
and similar for following uima.cas.FSArray
nodes.
I realize that the same node (without attributes appears) so I am only interested in nodes with the _id
element.
Here is my attempt:
#!/usr/bin/env python
import sys
import os
import xml.etree.cElementTree as ET
tree = ET.ElementTree(file=sys.argv[-1])
UMLSarr = {}
for x in tree.iterfind('uima.cas.FSArray'):
UMLSarr[x] = x.attrib
subArr[x] = SubElement(UMLSarr[x],"subArr",attrib='i')
but I get:
Traceback (most recent call last):
File "<stdin>", line 3, in <module>
NameError: name 'SubElement' is not defined
I've tried various other iterations of this code but I'm running into more and more errors and hoped someone could give me a hand.
Thanks.
Upvotes: 1
Views: 93
Reputation: 12168
from lxml import etree
et = etree.fromstring(xml)
for array in et.xpath('//uima.cas.FSArray[@_id]'):
print(array.xpath('@_id'), array.xpath('./i/text()'))
out:
['7429'] ['7409', '7419']
['7372'] ['7362', '7332', '7352', '7322', '7342']
['7285'] ['7245', '7275', '7255', '7265', '7235']
Upvotes: 1