Parsing XML Object Python 3.4

Question

Basically what I am doing is using urllib.request to make an API call to pubmed, receive an XML file in return, and am trying to parse it with no luck.

I have tried using Element Tree and other modules with no luck. I believe there may be an issue with XML object itself.

#Imorting URL Request Modules for API Calls
#Also importing ElemenTree as it seems to be best for XML parsing

import urllib.request 
import urllib.parse 
import re 
import xml.etree.ElementTree as ET 
from urllib import request 

#Now I can make the API call.  
id_request = urllib.request.urlopen('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=17570568')

#id_request will be an object that I'm not sure I understand?  
#id_request Returns: "<http.client.HTTPResponse object at 0x0000000003693FD0>"
#Let's now read this baby in XML format!
id_pubmed = id_request.read()

#If I look at the id_pubmed object, I not have the XML file I want to parse.

You can see what the XML file id_pubmed is calling/prints here: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=17570568

My issue is I can't get Element Tree to parse this at all. I have tried:

tree = ET.parse(id_pubmed)
root = tree.getroot()

as well as various other suggestions from https://docs.python.org/3/library/xml.etree.elementtree.html#module-xml.etree.ElementTree

Anand S Kumar · Accepted Answer · 2015-08-20 14:49:54Z

2

ET.parse() method requires either the location of the xml file (on local file system) or a file like object , but your id_pubmed seems to be a string .

In that case , you should use ET.fromstring() . Example -

root = ET.fromstring(id_pubmed)

answered Aug 20, 2015 at 14:49

Anand S Kumar

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2 Comments

Sean Over a year ago

This seems to work! Thank you, I suspected it was an issue with the method I was trying to use on my object.

Sean Over a year ago

Ahh, I tried to do this earlier and it did not work. It works now!

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