From 5f840e3fee7929cbc85e2fd0bfe962f6bd460ed5 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 16 Feb 2012 13:07:49 +0000
Subject: [PATCH] Entrez dbSNP api suddenly returns other XML structure
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@478 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/Retriever.py | 33 +++++++++------------------------
1 file changed, 9 insertions(+), 24 deletions(-)
diff --git a/mutalyzer/Retriever.py b/mutalyzer/Retriever.py
index 8ce25d43..3124c8f3 100644
--- a/mutalyzer/Retriever.py
+++ b/mutalyzer/Retriever.py
@@ -278,11 +278,17 @@ class Retriever(object) :
response_text = response.read()
+ if response_text == '\n':
+ # This is apparently what dbSNP returns for non-existing dbSNP id
+ self._output.addMessage(__file__, 4, 'EENTREZ',
+ 'ID rs%s could not be found in dbSNP.' \
+ % id)
+ return []
+
try:
# Parse the output.
doc = minidom.parseString(response_text)
- exchange_set = doc.getElementsByTagName('ExchangeSet')
- rs = exchange_set[0].getElementsByTagName('Rs')
+ rs = doc.getElementsByTagName('Rs')[0]
except expat.ExpatError as e:
# Could not parse XML.
self._output.addMessage(__file__, 4, 'EENTREZ', 'Unknown dbSNP ' \
@@ -300,29 +306,8 @@ class Retriever(object) :
'Result from dbSNP: %s' % response_text)
return []
- if len(rs) < 1:
- # No Rs result element.
- text = []
- for node in exchange_set[0].childNodes:
- if node.nodeType == node.TEXT_NODE:
- text.append(node.data)
- message = ''.join(text)
- if message.find('cannot get document summary') != -1:
- # Entrez does not have this rs ID.
- self._output.addMessage(__file__, 4, 'EENTREZ',
- 'ID rs%s could not be found in dbSNP.' \
- % id)
- else:
- # Something else was wrong (print {message} to see more).
- self._output.addMessage(__file__, 4, 'EENTREZ',
- 'Unkown dbSNP error. Got no result ' \
- 'from dbSNP.')
- self._output.addMessage(__file__, -1, 'INFO',
- 'Message from dbSNP: %s' % message)
- return []
-
snps = []
- for i in rs[0].getElementsByTagName('hgvs'):
+ for i in rs.getElementsByTagName('hgvs'):
snps.append(i.lastChild.data.encode('utf8'))
return snps
--
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