Mercurial > repos > chrisb > gap_all_glycan_tools

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

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author chrisb
date Wed, 23 Mar 2016 14:35:56 -0400
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-1:000000000000 0:89592faa2875
1 __license__ = "MIT"
2
3 import unittest
4 import getkcfKEGG as gk
5
6
7 class SimpleUnitTest(unittest.TestCase):
8 def setUp(self):
9 import os
10
11 os.environ["http_proxy"] = "" # work around for IOError: [Errno url error] invalid proxy for http:
12 pass
13
14 def tearDown(self):
15 pass
16
17 def test_empty_stream(self):
18 """ if empty stream then should return None"""
19 with self.assertRaises(IOError):
20 m = gk.get_kcf_from_kegg(None)
21 with self.assertRaises(IOError):
22 m = gk.get_kcf_from_kegg([])
23
24 def test_no_matching_entry(self):
25 """
26 if non G* entry then return empty lists
27 """
28 import StringIO
29 import urllib2
30
31 glycanindex = "X00092"
32 handle = StringIO.StringIO(''.join(glycanindex))
33 m, n = gk.get_kcf_from_kegg(handle)
34 self.assertEqual(m, [])
35 self.assertEqual(n, [])
36
37 def test_malformed_entry(self):
38 """
39 if malformed entry that looks like "G*" then return HTTPError
40 """
41 import StringIO
42 import urllib2
43
44 glycanindex = "GL00092"
45 handle = StringIO.StringIO(''.join(glycanindex))
46 with self.assertRaises(urllib2.HTTPError):
47 m, n = gk.get_kcf_from_kegg(handle)
48
49 def test_glycan(self):
50 """
51 """
52 import StringIO
53
54 glycanindex = "G00092"
55 handle = StringIO.StringIO(''.join(glycanindex))
56 m, n = gk.get_kcf_from_kegg(handle)
57 self.assertIsNotNone(m)
58 self.assertIsNotNone(n)
59 self.assertEqual(1, len(m))
60 self.assertEqual(1, len(n))
61
62 def test_several_glycans(self):
63 """
64 """
65 import StringIO
66
67 glycanindex = "G00092\nG00091\nG00093"
68 handle = StringIO.StringIO(''.join(glycanindex))
69 m, n = gk.get_kcf_from_kegg(handle)
70 self.assertIsNotNone(m)
71 self.assertIsNotNone(n)
72 self.assertEqual(3, len(m))
73 self.assertEqual(3, len(n))
74