Avoid segmentation fault from xml.parsers.expat http://bugs.python.or…

…g/issue4877
biopython · Oct 28, 2011 · 59f9cbd · 59f9cbd
1 parent 0bdb1f2
commit 59f9cbd
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diff --git a/Bio/Entrez/Parser.py b/Bio/Entrez/Parser.py
@@ -161,6 +161,10 @@ def __init__(self, validate):
 
     def read(self, handle):
         """Set up the parser and let it parse the XML results"""
+        if handle.closed:
+            #Should avoid a possible Segmentation Fault, see:
+            #http://bugs.python.org/issue4877
+            raise IOError("Can't parse a closed handle")
         try:
             self.parser.ParseFile(handle)
         except expat.ExpatError, e:

diff --git a/Tests/test_Entrez.py b/Tests/test_Entrez.py
@@ -20,6 +20,15 @@
 
 from Bio import Entrez
 
+class GeneralTests(unittest.TestCase):
+    '''General tests for Bio.Entrez'''
+    def test_closed_handle(self):
+        '''Test parsing closed handle fails gracefully
+        '''
+        handle = open('Entrez/einfo1.xml', "rb")
+        handle.close()
+        self.assertRaises(IOError, Entrez.read, handle)
+
 
 class EInfoTest(unittest.TestCase):
     '''Tests for parsing XML output returned by EInfo