diff get_data/kegg_glycan/test_getkcfKEGG.py @ 0:89592faa2875 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data/kegg_glycan/test_getkcfKEGG.py	Wed Mar 23 14:35:56 2016 -0400
@@ -0,0 +1,74 @@
+__license__ = "MIT"
+
+import unittest
+import getkcfKEGG as gk
+
+
+class SimpleUnitTest(unittest.TestCase):
+    def setUp(self):
+        import os
+
+        os.environ["http_proxy"] = ""  # work around for IOError: [Errno url error] invalid proxy for http:
+        pass
+
+    def tearDown(self):
+        pass
+
+    def test_empty_stream(self):
+        """ if empty stream then should return None"""
+        with self.assertRaises(IOError):
+            m = gk.get_kcf_from_kegg(None)
+        with self.assertRaises(IOError):
+            m = gk.get_kcf_from_kegg([])
+
+    def test_no_matching_entry(self):
+        """
+        if non G* entry  then return empty lists
+        """
+        import StringIO
+        import urllib2
+
+        glycanindex = "X00092"
+        handle = StringIO.StringIO(''.join(glycanindex))
+        m, n = gk.get_kcf_from_kegg(handle)
+        self.assertEqual(m, [])
+        self.assertEqual(n, [])
+
+    def test_malformed_entry(self):
+        """
+        if malformed entry that looks like "G*" then return HTTPError
+        """
+        import StringIO
+        import urllib2
+
+        glycanindex = "GL00092"
+        handle = StringIO.StringIO(''.join(glycanindex))
+        with self.assertRaises(urllib2.HTTPError):
+            m, n = gk.get_kcf_from_kegg(handle)
+
+    def test_glycan(self):
+        """
+        """
+        import StringIO
+
+        glycanindex = "G00092"
+        handle = StringIO.StringIO(''.join(glycanindex))
+        m, n = gk.get_kcf_from_kegg(handle)
+        self.assertIsNotNone(m)
+        self.assertIsNotNone(n)
+        self.assertEqual(1, len(m))
+        self.assertEqual(1, len(n))
+
+    def test_several_glycans(self):
+        """
+        """
+        import StringIO
+
+        glycanindex = "G00092\nG00091\nG00093"
+        handle = StringIO.StringIO(''.join(glycanindex))
+        m, n = gk.get_kcf_from_kegg(handle)
+        self.assertIsNotNone(m)
+        self.assertIsNotNone(n)
+        self.assertEqual(3, len(m))
+        self.assertEqual(3, len(n))
+