Merge branch 'master' of github.com:biopython/biopython

Bio/Entrez/Parser.py

@@ -172,6 +172,10 @@ def __init__(self, validate):
 
     def read(self, handle):
         """Set up the parser and let it parse the XML results"""
+        # HACK: remove Bio._py3k handle conversion, since the Entrez XML parser
+        # expects binary data
+        if handle.__class__.__name__ == 'EvilHandleHack':
+            handle = handle._handle
         if hasattr(handle, "closed") and handle.closed:
             #Should avoid a possible Segmentation Fault, see:
             #http://bugs.python.org/issue4877

Tests/test_Entrez_online.py

@@ -0,0 +1,70 @@
+# Copyright 2012 by Wibowo Arindrarto.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Tests for online Entrez access.
+
+This file include tests for accessing the online Entrez service and parsing the
+returned results. Note that we are merely testing the access and whether the
+results are parseable. Detailed tests on each Entrez service are not within the
+scope of this file as they are already covered in test_Entrez.py.
+
+"""
+import unittest
+
+import requires_internet
+requires_internet.check()
+
+from Bio import Entrez
+from Bio import Medline
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+
+
+Entrez.email = 'test@biopython.org'
+
+
+class EntrezOnlineCase(unittest.TestCase):
+
+    def test_read_from_url(self):
+        """Test Entrez.read from URL"""
+        einfo = Entrez.einfo()
+        rec = Entrez.read(einfo)
+        self.assertTrue(isinstance(rec, dict))
+        self.assertTrue('DbList' in rec)
+        # arbitrary number, just to make sure that DbList has contents
+        self.assertTrue(len(rec['DbList']) > 5)
+
+    def test_parse_from_url(self):
+        """Test Entrez.parse from URL"""
+        efetch = Entrez.efetch(db='protein', id='15718680,157427902,119703751',
+                retmode='xml')
+        recs = Entrez.parse(efetch)
+        recs = list(recs)
+        self.assertEqual(3, len(recs))
+        # arbitrary number, just to make sure the parser works
+        self.assertTrue(all(len(rec).keys > 5) for rec in recs)
+
+    def test_seqio_from_url(self):
+        """Test Entrez into SeqIO.read from URL"""
+        efetch = Entrez.efetch(db='nucleotide', id='186972394', rettype='gb',
+                retmode='text')
+        record = SeqIO.read(efetch, 'genbank')
+        self.assertTrue(isinstance(record, SeqRecord))
+        self.assertEqual('EU490707.1', record.id)
+        self.assertEqual(1302, len(record))
+
+    def test_medline_from_url(self):
+        """Test Entrez into Medline.read from URL"""
+        efetch = Entrez.efetch(db="pubmed", id='19304878', rettype="medline",
+                retmode="text")
+        record = Medline.read(efetch)
+        self.assertTrue(isinstance(record, dict))
+        self.assertEqual('19304878', record['PMID'])
+        self.assertEqual('10.1093/bioinformatics/btp163 [doi]', record['LID'])
+
+
+if __name__ == "__main__":
+    runner = unittest.TextTestRunner(verbosity = 2)
+    unittest.main(testRunner=runner)