Newer
Older
John Chilton
committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
from test_utils import TempDirectoryTestCase
from lwr.util import JobDirectory
from lwr.tools.validator import ExpressionValidator
from os.path import join
class ValidatorTest(TempDirectoryTestCase):
def test_literal(self):
xml = """
<expression>
<literal value="tophat2" />
</expression>"""
self.__assertValid(xml, "tophat2")
self.__assertInvalid(xml, "bowtie")
def test_two_literals(self):
xml = """
<expression>
<literal value="python" />
<literal value="setup.py" />
</expression>"""
self.__assertValid(xml, "python setup.py")
self.__assertInvalid(xml, "pythonsetup.py")
def test_parameter(self):
xml = """
<expression>
<literal value="tophat2" />
<parameter name="--mate-std-dev">
<literal value="4" />
</parameter>
</expression>"""
self.__assertValid(xml, "tophat2 --mate-std-dev 4")
self.__assertValid(xml, "tophat2 --mate-std-dev=4")
self.__assertInvalid(xml, "tophat2 --mate-std-dev=5")
def test_integer(self):
xml = """
<expression>
<literal value="tophat2" />
<parameter name="--mate-std-dev">
<integer />
</parameter>
</expression>"""
self.__assertValid(xml, "tophat2 --mate-std-dev 4")
self.__assertValid(xml, "tophat2 --mate-std-dev=4")
self.__assertInvalid(xml, "tophat2 --mate-std-dev=5.0")
def test_float(self):
xml = """
<expression>
<literal value="tophat2" />
<parameter name="--mate-std-dev">
<float />
</parameter>
</expression>"""
self.__assertValid(xml, "tophat2 --mate-std-dev 4")
self.__assertValid(xml, "tophat2 --mate-std-dev=4")
self.__assertValid(xml, "tophat2 --mate-std-dev=5.0")
self.__assertValid(xml, "tophat2 --mate-std-dev=4e10")
self.__assertValid(xml, "tophat2 --mate-std-dev=-1.0e10")
self.__assertValid(xml, "tophat2 --mate-std-dev=-.0e10")
self.__assertInvalid(xml, "tophat2 --mate-std-dev=cat")
def test_tool_wrapper(self):
xml = """
<expression>
<tool_wrapper name="tool1_wrapper.py" />
</expression>
"""
self.__assertValid(xml, "%s" % join(self.temp_directory, '1', 'tool_files', 'tool1_wrapper.py'))
self.__assertInvalid(xml, "tool1_wrapper.py")
def test_config_file(self):
xml = """
<expression>
<literal value="tophat2" />
<configfile name="top_opts" />
</expression>
"""
self.__assertValid(xml, "tophat2 %s" % join(self.temp_directory, '1', 'configs', 'top_opts'))
self.__assertInvalid(xml, "tophat2 ../%s" % join(self.temp_directory, '1', 'configs', 'top_opts'))
self.__assertInvalid(xml, "tophat2 %s" % join(self.temp_directory, '1', 'configs', 'top_optsX'))
def __validator(self, xml):
return ExpressionValidator(xml)
@property
def job_directory(self):
return JobDirectory(self.temp_directory, '1')
def __is_valid(self, xml, contents):
return self.__validator(xml).validate(self.job_directory, contents)
def __assertValid(self, xml, contents):
self.assertTrue(self.__is_valid(xml, contents), "%s did not validate against %s" % (contents, xml))
def __assertInvalid(self, xml, contents):
self.assertFalse(self.__is_valid(xml, contents), "%s falsely validated against %s" % (contents, xml))