[Tutor] how to extract text by specifying an element using ElementTree

ps python ps_python3 at yahoo.co.in
Tue Dec 20 18:26:39 CET 2005

Dear Drs. Johnson and Yoo , 
 for the last 1 week I have been working on parsing
the elements from a bunch of XML files following your

until now I have been unsuccessul.  I have no clue why
i am failing. 

I have ~16K XML files. this data obtained from johns
hopkins university (of course these are public data
and is allowed to use for teaching and non-commercial

from elementtree.ElementTree import ElementTree
>>> mydata = ElementTree(file='00004.xml')
>>> for process in
	print process.text

>>> for proc in mydata.findall('functions'):
	print proc


I do not understand why I am unable to parse this
file. I questioned if this file is not well structures
(well formedness). I feel it is properly structured
and yet it us unparsable.  

Would you please help me /guide me what the problem
is.  Apologies if i am completely ignoring somethings.

PS: Attached is the XML file that I am using. 

--- Kent Johnson <kent37 at tds.net> wrote:

> ps python wrote:
> >  Kent and Dany, 
> > Thanks for your replies.  
> > 
> > Here fromstring() assuming that the input is in a
> kind
> > of text format. 
> Right, that is for the sake of a simple example.
> > 
> > what should be the case when I am reading files
> > directly. 
> > 
> > I am using the following :
> > 
> > from elementtree.ElementTree import ElementTree
> > mydata = ElementTree(file='00001.xml')
> > iter = root.getiterator()
> > 
> > Here the whole XML document is loaded as element
> tree
> > and how should this iter into a format where I can
> > apply findall() method. 
> Call findall() directly on mydata, e.g.
> for process in
> mydata.findall('//biological_process'):
>    print process.text
> The path //biological_process means find any
> biological_process element 
> at any depth from the root element.
> Kent
> _______________________________________________
> Tutor maillist  -  Tutor at python.org
> http://mail.python.org/mailman/listinfo/tutor

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