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#!/usr/bin/env python
"""Tests of the db utility functions and classes."""
from cogent.util.unit_test import TestCase, main
from cogent.db.util import UrlGetter, expand_slice, last_nondigit_index,make_lists_of_expanded_slices_of_set_size,make_lists_of_accessions_of_set_size
from os import remove
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
class db_util_tests(TestCase):
"""Tests of top-level functions."""
def test_last_nondigit_index(self):
"""last_nondigit_index should return i such that s[i:] is numeric"""
ldi = last_nondigit_index
self.assertEqual(ldi('3'), 0)
self.assertEqual(ldi('345'), 0)
self.assertEqual(ldi('a34'), 1)
self.assertEqual(ldi('abc234'), 3)
self.assertEqual(ldi('abcd'), None)
def test_expand_slice(self):
"""expand_slice should get accession range"""
self.assertEqual(expand_slice(slice('AF1001','AF1003')), \
['AF1001','AF1002','AF1003'])
#can't expand if accession prefixes
self.assertRaises(TypeError, expand_slice, slice('AF100:','AG1002'))
#should keep leading zeros
self.assertEqual(expand_slice(slice('AF0001','AF0003')), \
['AF0001','AF0002','AF0003'])
def test_make_lists_of_expanded_slices_of_set_size(self):
"""make_lists_of_expanded_slices_of_set_size: should return a
list of lists"""
expected_list = ['HM780503 HM780504 HM780505','HM780506']
observed = make_lists_of_expanded_slices_of_set_size(slice('HM780503','HM780506'),size_limit=3)
self.assertEqual(observed,expected_list)
def make_lists_of_accessions_of_set_size(self):
"""make_lists_of_expanded_slices_of_set_size: should return a
list of lists"""
expected_list = ['HM780503 HM780506 HM780660 HM780780']
observed = make_lists_of_accessions_of_set_size(['HM780503','HM780506', 'HM780660', 'HM780780'],size_limit=3)
self.assertEqual(observed,expected_list)
class UrlGetterTests(TestCase):
"""Tests of the UrlGetter class"""
def retrieval_test(self):
"""Urlgetter should init, read and retrieve"""
class Google(UrlGetter):
BaseUrl='http://www.google.com'
g = Google()
#test URL construction
self.assertEqual(str(g), 'http://www.google.com')
#test reading
text = g.read()
assert '<title>Google</title>' in text
#test file getting
fname = '/tmp/google_test'
g.retrieve(fname)
g_file = open(fname)
g_text = g_file.read()
self.assertEqual(g_text, text)
g_text.close()
remove(fname)
if __name__ == '__main__':
main()
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