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comparison data_stores/tester.py @ 1:5c5027485f7d draft

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author damion
date Sun, 09 Aug 2015 16:07:50 -0400
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0:d31a1bd74e63 1:5c5027485f7d
1 #!/usr/bin/python
2 # -*- coding: utf-8 -*-
3 import optparse
4 import sys
5 import difflib
6 import os
7
8
9 class MyParser(optparse.OptionParser):
10 """
11 From http://stackoverflow.com/questions/1857346/python-optparse-how-to-include-additional-info-in-usage-output
12 Provides a better class for displaying formatted help info in epilog() portion of optParse; allows for carriage returns.
13 """
14 def format_epilog(self, formatter):
15 return self.epilog
16
17 def stop_err( msg ):
18 sys.stderr.write("%s\n" % msg)
19 sys.exit(1)
20
21
22 def __main__(self):
23
24
25 """
26 (This is run only in context of command line.)
27 FUTURE: ALLOW GLOB IMPORT OF ALL FILES OF GIVEN SUFFX, each to its own version, initial date taken from file date
28 FUTURE: ALLOW dates of versions to be adjusted.
29 """
30 options, args = self.get_command_line()
31 self.options = options
32
33 if options.test_ids:
34 return self.test(options.test_ids)
35
36
37 def get_command_line(self):
38 """
39 *************************** Parse Command Line *****************************
40
41 """
42 parser = MyParser(
43 description = 'Tests a program against given input/output files.',
44 usage = 'tester.py [program] [input files] [output files] [parameters]',
45 epilog="""
46
47
48 parser.add_option('-t', '--tests', dest='test_ids', help='Enter "all" or comma-separated id(s) of tests to run.')
49
50 return parser.parse_args()
51
52
53
54 def test(self, test_ids):
55 # Future: read this spec from test-data folder itself?
56 tests = {
57 '1': {'input':'a1','outputs':'','options':''}
58 }
59 self.test_suite('keydb.py', test_ids, tests, '/tmp/')
60
61
62 def test_suite(self, program, test_ids, tests, output_dir):
63
64 if test_ids == 'all':
65 test_ids = sorted(tests.keys())
66 else:
67 test_ids = test_ids.split(',')
68
69 for test_id in test_ids:
70 if test_id in tests:
71 test = tests[test_id]
72 test['program'] = program
73 test['base_dir'] = base_dir = os.path.dirname(__file__)
74 executable = os.path.join(base_dir,program)
75 if not os.path.isfile(executable):
76 stop_err('\n\tUnable to locate ' + executable)
77 # Each output file has to be prefixed with the output (usualy /tmp/) folder
78 test['tmp_output'] = (' ' + test['outputs']).replace(' ',' ' + output_dir)
79 # Note: output_dir output files don't get cleaned up after each test. Should they?!
80 params = '%(base_dir)s/%(program)s %(base_dir)s/test-data/%(input)s%(tmp_output)s %(options)s' % test
81 print("Test " + test_id + ': ' + params)
82 print("................")
83 os.system(params)
84 print("................")
85 for file in test['outputs'].split(' '):
86 try:
87 f1 = open(test['base_dir'] + '/test-data/' + file)
88 f2 = open(output_dir + file)
89 except IOError as details:
90 stop_err('Error in test setup: ' + str(details)+'\n')
91
92 #n=[number of context lines
93 diff = difflib.context_diff(f1.readlines(), f2.readlines(), lineterm='',n=0)
94 # One Galaxy issue: it doesn't convert entities when user downloads file.
95 # BUT IT appears to when generating directly to command line?
96 print '\nCompare ' + file
97 print '\n'.join(list(diff))
98
99 else:
100 stop_err("\nExpecting one or more test ids from " + str(sorted(tests.keys())))
101
102 stop_err("\nTest finished.")
103
104
105 if __name__ == '__main__':
106
107 keydb = KeyDb()
108 keydb.__main__()
109