test/small_run_test.py

   1 '''small run test cases'''
   2
   3
   4 from __future__ import with_statement
   5
   6 import contextlib
   7 import filecmp
   8 import inspect
   9 import subprocess
  10
  11 from nose.tools import *
  12
  13 from greylag import *
  14
  15 # program and initial args required to run from test directory
  16 GREYLAG_PROGRAM = 'python2.5 ../greylag.py'
  17
  18 # temporary output file
  19 GREYLAG_OUTPUT = 'tmp-greylag-out.xml'
  20
  21 # cd to the test directory, but restore when we're done
  22 SAVE_CWD = os.getcwd()
  23 def setup(self):
  24     if os.path.exists(GREYLAG_OUTPUT):
  25         os.remove(GREYLAG_OUTPUT)
  26     os.chdir('test')
  27 def teardown(self):
  28     if os.path.exists(GREYLAG_OUTPUT):
  29         os.remove(GREYLAG_OUTPUT)
  30     os.chdir(SAVE_CWD)
  31
  32
  33 def run_gl(args):
  34     "Run greylag in a subprocess, checking for error return."
  35     subprocess.check_call(("%s -q -o %s %s"
  36                            % (GREYLAG_PROGRAM, GREYLAG_OUTPUT, args)).split())
  37
  38 def run_combination(combination=None):
  39     """Run a greylag test, as specified by combination.
  40
  41     If combination is not given, it defaults to the name of the calling
  42     function.
  43
  44     For a combination 'greylag_params_0__test_2_test', greylag will be run
  45     with a parameter file 'greylag-params-0.xml' and spectrum file
  46     'test-2.ms2'.  (Additional spectrum files can be specified, separated by
  47     '__'.)  The results will be compared to 'greylag-params-0--test-2-ok.xml'.
  48     If this baseline file is not present and the environment variable
  49     NOSEUPDATE is set, a new baseline will be created.
  50     """
  51     if combination == None:
  52         # name of caller
  53         combination = inspect.getouterframes(inspect.currentframe())[1][3]
  54     assert combination.endswith('_test')
  55     combination = combination.rpartition('_test')[0]
  56     parts = combination.split('__')
  57     params, spectra = parts[0], parts[1:]
  58     assert len(spectra) >= 1
  59     params = params.replace('_', '-') + '.xml'
  60     spectra = [ sp.replace('_', '-') + '.ms2' for sp in spectra ]
  61     correct_fn = combination.replace('_', '-') + '-ok.xml'
  62     assert os.path.exists(correct_fn) or 'NOSEUPDATE' in os.environ, 'no baseline'
  63     run_gl(params + ' ' + ' '.join(spectra))
  64     if os.path.exists(correct_fn):
  65         assert filecmp.cmp(GREYLAG_OUTPUT, correct_fn), 'output differs'
  66     else:
  67         os.rename(GREYLAG_OUTPUT, correct_fn)
  68     # FIX: now do it in parts, and compare that result
  69     # also do it for --quirks?
  70
  71 # Could do xtandem and rough compare to quirks?  Is this worth doing, since we
  72 # can expect at least small differences?  Probably we should have a separate
  73 # framework for comparing and contrasting output from any two of { greylag,
  74 # xtandem, sequest }
  75
  76
  77
  78 class modless_run_tests:
  79     def greylag_params_0__test_2_test(self):
  80         run_combination()
  81     def greylag_params_0__6323840_test(self):
  82         run_combination()