CODEWITHSUNDEEP
pythonelementtree
hrtachetosing
hrtachetosing

Reputation: 13

Python Element Tree Handling Tags within Tags XML

I am working with the xml labels from dailymed.nlm.nih.gov. I am having a problem when reading the Contraindications associated with a drug. I want all of the content inside of the tag, but it cuts off once I hit the inner tag. I have tried iterating over all the subelements but the best I could do was get the "Warning" to display. "; anuria; hypersensitivity to ..." was lost. If anyone know of a way to get this data using the parser it would help a lot. Thank you!

 <component>
        <section ID="LINK_8e9e0719-efa5-451c-bea3-d547298ad0a1">
           <id root="8e9e0719-efa5-451c-bea3-d547298ad0a1"/>
           <code code="34070-3" codeSystem="2.16.840.1.113883.6.1" displayName="CONTRAINDICATIONS SECTION"/>
           <title>CONTRAINDICATIONS</title>
           <text>
              <paragraph>Atenolol and chlorthalidone tablets are contraindicated in patients with: sinus bradycardia; heart block greater than first degree; cardiogenic shock; overt cardiac failure (see<content styleCode="bold">
                    <linkHtml href="#LINK_0df2629f-13c7-4b14-8664-475c32377c68">WARNINGS</linkHtml>
                 </content>); anuria; hypersensitivity to this product or to sulfonamide-derived drugs.</paragraph>
           </text>
           <effectiveTime value="20101001"/>
        </section>
     </component>

Upvotes: 0

Views: 445

Answers (1)

sotapme
sotapme

Reputation: 4903

Presuming you're using something like the following you need to use ET.tostring which will get all the text of child elements.

import xml.etree.ElementTree as ET
txt = """
<component>
<section ID="LINK_8e9e0719-efa5-451c-bea3-d547298ad0a1">
    <id root="8e9e0719-efa5-451c-bea3-d547298ad0a1"/>
    <code code="34070-3" codeSystem="2.16.840.1.113883.6.1" displayName="CONTRAINDICATIONS SECTION"/
    <title>CONTRAINDICATIONS</title>
    <text>
    <paragraph>Atenolol and chlorthalidone tablets are contraindicated in patients with: sinus brady
        <linkHtml href="#LINK_0df2629f-13c7-4b14-8664-475c32377c68">WARNINGS</linkHtml>
            </content>); anuria; hypersensitivity to this product or to sulfonamide-derived drugs.</
    </text>
    <effectiveTime value="20101001"/>
</section>
</component>"""

root = ET.fromstring(txt)

for e in root.iter('text'):
    print ">>"
    print ET.tostring(e, method="text")
    print "<<"

Gives

>>

    Atenolol and chlorthalidone tablets are contraindicated in patients with: sinus bradycardia; heart block greater than first degree; cardiogenic shock; overt cardiac failure (see
        WARNINGS
            ); anuria; hypersensitivity to this product or to sulfonamide-derived drugs.


<<

Upvotes: 1

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