#!/usr/bin/env python # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. from corebio.utils import * import unittest from StringIO import StringIO import re class test_utils(unittest.TestCase) : assertTrue = unittest.TestCase.failUnless assertFalse = unittest.TestCase.failIf def test_isfloat(self) : self.failUnless( isfloat('0.5')) self.failUnless( isfloat( ' 0') ) self.failUnless( isfloat( '+1000000000 ') ) self.failUnless( isfloat( '2') ) self.failUnless( isfloat( '0000.2323') ) self.failUnless( isfloat( '0.1e-23') ) self.failUnless( isfloat( ' -0.5e+23') ) self.assertFalse( isfloat( None) ) self.assertFalse( isfloat( '') ) self.assertFalse( isfloat( 'asdad') ) self.assertFalse( isfloat( 'q34sd') ) self.assertFalse( isfloat( '92384.kjdfghiksw')) self.assertFalse( isfloat( 'adf!@#nn') ) def test_isint(self) : self.failUnless( isint('0')) self.failUnless( isint('-1')) self.failUnless( isint('10')) self.failUnless( isint('100101012234')) self.failUnless( isint('000')) self.assertFalse( isint( None) ) self.assertFalse( isint( '') ) self.assertFalse( isint( 'asdad') ) self.assertFalse( isint( 'q34sd') ) self.assertFalse( isint( '0.23')) self.assertFalse( isint( 'adf!@#nn') ) def test_remove_whitespace(self) : self.assertEquals( remove_whitespace(" kjashd askjdh askjdh\tasdf"), "kjashdaskjdhaskjdhasdf"), def test_isblank(self) : blank = ('', ' ', '\n', '\t \n\n') not_blank = (' a',) for s in blank : self.assertTrue( isblank(s)) for s in not_blank: self.assertFalse( isblank(s)) def test_group_count(self): test = 'aaabbbbcccddea' out = group_count(test) self.assertTrue( tuple(out) == (('a',3),('b',4),('c',3),('d',2),('e',1),('a',1)) ) def test_reiterate(self) : i = Reiterate( iter("123456") ) for item in i : pass self.assertRaises(StopIteration, i.next ) self.assertFalse( i.has_item() ) self.assertTrue( i.peek() is None ) # pushback i = Reiterate( iter("123456") ) i.next() i.push("0") self.assertEquals( "0", i.next()) p = i.peek() n = i.next() self.assertEquals(p,n) self.assertEquals( i.index() ,2) self.assertTrue( i.has_item() ) # Repeated application of Reiterate should return same iterator. assert i is iter(i) assert i is Reiterate(i) def test_token(self) : t = Token( 'kind', 'some data', 4, 3) s = str(t) r = repr(t) t2 = eval(r) assert t2.typeof == 'kind' def test_struct(self) : s = Struct(a=3,b=4) s2 = eval(repr(s)) assert s2.a == 3 def test_invert_dict(self) : d = dict( a=3, b=4) invd =invert_dict(d) assert 3 in invd assert invd[3] == 'a' def test_crc64(self) : assert crc64("IHATEMATH") == "E3DCADD69B01ADD1" def test_crc32(self) : assert crc32("Test the CRC-32 of this string.") == "%08X"%1571220330 def test_find_command(self) : p = find_command('more') p = find_command('python') self.assertRaises( EnvironmentError, find_command, 'NOSUCH') #print p def test_ArgumentValueError(self): message = "Some message" component = "whatsit" try: raise ArgumentError(message, component) except ArgumentError, err: assert err.msg == message assert err.key == component try: raise ArgumentError(message, component, 10) except ValueError, err: assert err.msg == message assert err.key == component assert err.value ==10 def test_frozendict(self) : d = frozendict( a='b', c='c') assert d['a'] == 'b' self.assertRaises(AttributeError, lambda D: D.pop(), d) def test_file_index(self): stream = StringIO(tfile) idx = FileIndex(stream) assert idx[0].startswith('line 0') assert idx[4].startswith('line 4') def parser(f) : return int(f.readline().split()[1]) idx = FileIndex(stream, parser=parser) assert len(idx) == 5 assert idx[0] == 0 assert idx[4] == 4 key = re.compile(r"(line \d)") def linekey(line) : k = key.search(line) if k is None: return None return k.group(1) idx = FileIndex(stream, linekey=linekey, parser=parser) self.assertEquals(len(idx), 4) assert idx[0] == 0 assert idx[3] == 4 self.assertRaises(IndexError, idx.__getitem__, 5) #print idx._key_dict assert idx['line 1'] == 1 assert idx['line 4'] == 4 assert 'line 1' in idx assert not ('Blah' in idx) assert not (20 in idx) # Test iteration over values t = 0 for v in idx : t+=v assert t == 8 def test_resource(self) : fn = resource_filename(__name__, 'data/cap.fa', __file__) assert fn.endswith('test_corebio/data/cap.fa') f = resource_stream(__name__, 'data/cap.fa', __file__) s = resource_string(__name__, 'data/cap.fa', __file__) assert s.startswith('>aldB') tfile = """line 0 line 1 Blah line 3 line 4 """ if __name__ == '__main__': unittest.main()