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_grind import *
  14
  15
  16 # parallel job processes
  17 CPUS = 4
  18
  19 # program locations
  20 GREYLAG_PROGRAM = '../greylag_grind.py'
  21 GREYLAGMP_PROGRAM = '../greylag.py'
  22
  23 # temporary output file
  24 GREYLAG_OUTPUT = 'tmp-greylag-out.xml'
  25
  26 # cd to the test directory, but restore when we're done
  27 SAVE_CWD = os.getcwd()
  28 def setup(self):
  29     if os.path.exists(GREYLAG_OUTPUT):
  30         os.remove(GREYLAG_OUTPUT)
  31     os.chdir('test')
  32 def teardown(self):
  33     if os.path.exists(GREYLAG_OUTPUT):
  34         os.remove(GREYLAG_OUTPUT)
  35     os.chdir(SAVE_CWD)
  36
  37
  38 def run_gl(args):
  39     "Run greylag in a subprocess, checking for error return."
  40     subprocess.check_call(("%s -q -o %s %s"
  41                            % (GREYLAG_PROGRAM, GREYLAG_OUTPUT, args)).split())
  42
  43 def run_gl_mp(args):
  44     "Run greylag in multiple subprocesses, checking for error return."
  45     subprocess.check_call(("%s %s -q -o %s %s"
  46                            % (GREYLAGMP_PROGRAM, CPUS, GREYLAG_OUTPUT,
  47                               args)).split())
  48
  49 def run_combination(combination=None):
  50     """Run a greylag test, as specified by combination.
  51
  52     If combination is not given, it defaults to the name of the calling
  53     function.
  54
  55     For a combination 'greylag_params_0__test_2_test', greylag will be run
  56     with a parameter file 'greylag-params-0.xml' and spectrum file
  57     'test-2.ms2'.  (Additional spectrum files can be specified, separated by
  58     '__'.)  The results will be compared to 'greylag-params-0--test-2-ok.xml'.
  59     If this baseline file is not present and the environment variable
  60     NOSEUPDATE is set, a new baseline will be created.
  61
  62     Normally the test will only be done using greylag-mp.py, to speed things
  63     up.  If single_cpu is True, a single greylag.py process is used.  The
  64     results should be identical.
  65     """
  66     if combination == None:
  67         # name of caller
  68         combination = inspect.getouterframes(inspect.currentframe())[1][3]
  69     assert combination.endswith('_test')
  70     combination = combination.rpartition('_test')[0]
  71     run = run_gl
  72     if combination.endswith('_mp'):
  73         run = run_gl_mp
  74         combination = combination.rpartition('_mp')[0]
  75     parts = combination.split('__')
  76     params, spectra = parts[0], parts[1:]
  77     assert len(spectra) >= 1
  78     params = params.replace('_', '-') + '.xml'
  79     spectra = [ sp.replace('_', '-') + '.ms2' for sp in spectra ]
  80     ok_fn = combination.replace('_', '-') + '-ok.xml'
  81     assert os.path.exists(ok_fn) or 'NOSEUPDATE' in os.environ, 'no baseline'
  82
  83     run(params + ' ' + ' '.join(spectra))
  84     if os.path.exists(ok_fn):
  85         assert filecmp.cmp(GREYLAG_OUTPUT, ok_fn), 'output differs'
  86     else:
  87         os.rename(GREYLAG_OUTPUT, ok_fn)
  88     # also do it for --quirks?
  89
  90
  91 # Could do xtandem and rough compare to quirks?  Is this worth doing, since we
  92 # can expect at least small differences?  Probably we should have a separate
  93 # framework for comparing and contrasting output from any two of { greylag,
  94 # xtandem, sequest }
  95
  96
  97
  98 class modless_run_tests:
  99     def greylag_params_0__test_2_test(self):
 100         run_combination()
 101     def greylag_params_0__test_2_mp_test(self):
 102         run_combination()
 103     def greylag_params_0__6323840_test(self):
 104         run_combination()
 105     def greylag_params_0__6323840_mp_test(self):
 106         run_combination()
 107
 108     def greylag_params_yeast_0__test_2_test(self):
 109         run_combination()
 110     def greylag_params_yeast_0__test_2_mp_test(self):
 111         run_combination()