def test_run_single_chm_job_no_image_singularity_abort(self):
temp_dir = tempfile.mkdtemp()
try:
scratch = os.path.join(temp_dir, 'tmp')
os.makedirs(scratch, mode=0o755)
chmrundir = os.path.join(temp_dir,
CHMJobCreator.RUN_DIR)
os.makedirs(chmrundir, mode=0o755)
con = configparser.ConfigParser()
con.set('', CHMJobCreator.CONFIG_DISABLE_HISTEQ_IMAGES,
'True')
con.set('', CHMJobCreator.CONFIG_MODEL, '/model')
con.set('', CHMJobCreator.CONFIG_IMAGES, temp_dir)
con.set('', CHMJobCreator.CONFIG_TILE_SIZE, '3x3')
con.set('', CHMJobCreator.CONFIG_OVERLAP_SIZE, '2x2')
con.add_section('1')
con.set('1', CHMJobCreator.CONFIG_INPUT_IMAGE, 'input.1.png')
con.set('1', CHMJobCreator.CONFIG_OUTPUT_IMAGE, 'output.1.png')
con.set('1', CHMJobCreator.CONFIG_ARGS, '-t 1,1 -t 1,2')
fakecmd = os.path.join(temp_dir, 'fake.py')
write_fake_cmd(fakecmd, '"stdout"',
'"ABORT: Could not create temporary '
'directory /tmp"',
0, write_image=False)
con.set('', CHMJobCreator.CONFIG_CHM_BIN,
fakecmd)
try:
chmrunner._run_single_chm_job(temp_dir,
scratch, '1', con)
self.fail('Expected SingularityAbortError')
except SingularityAbortError as e:
self.assertEqual(str(e),
'ABORT: Could not create temporary directory '
'/tmp')
o_image = os.path.join(chmrundir, 'output.1.png')
self.assertFalse(os.path.isfile(o_image))
self.assertEqual(len(os.listdir(scratch)), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_single_chm_job_success_full_path_to_out_image(self):
temp_dir = tempfile.mkdtemp()
try:
scratch = os.path.join(temp_dir, 'tmp')
os.makedirs(scratch, mode=0o755)
chmrundir = os.path.join(temp_dir,
CHMJobCreator.RUN_DIR)
os.makedirs(chmrundir, mode=0o755)
con = configparser.ConfigParser()
con.set('', CHMJobCreator.CONFIG_DISABLE_HISTEQ_IMAGES,
'False')
con.set('', CHMJobCreator.CONFIG_MODEL, '/model')
con.set('', CHMJobCreator.CONFIG_IMAGES, temp_dir)
con.set('', CHMJobCreator.CONFIG_TILE_SIZE, '3x3')
con.set('', CHMJobCreator.CONFIG_OVERLAP_SIZE, '2x2')
con.add_section('1')
con.set('1', CHMJobCreator.CONFIG_INPUT_IMAGE, 'input.1.png')
o_image = os.path.join(temp_dir, 'output.1.png')
con.set('1', CHMJobCreator.CONFIG_OUTPUT_IMAGE, o_image)
con.set('1', CHMJobCreator.CONFIG_ARGS, '-t 1,1 -t 1,2')
fakecmd = os.path.join(temp_dir, 'fake.py')
write_fake_cmd(fakecmd, '"stdout"', '"stderr"', 0)
con.set('', CHMJobCreator.CONFIG_CHM_BIN,
fakecmd)
ecode = chmrunner._run_single_chm_job(temp_dir,
scratch, '1', con)
self.assertTrue(os.path.isfile(o_image))
self.assertEqual(ecode, 0)
f = open(os.path.join(temp_dir, 'out.txt'), 'r')
out_data = f.read()
self.assertTrue('-m /model -b 3x3 -o 2x2 -t '
'1,1 -t 1,2' in out_data)
self.assertTrue(fakecmd + ' test ' +
os.path.join(temp_dir, 'input.1.png') +
' ' in out_data)
self.assertEqual(len(os.listdir(scratch)), 0)
finally:
shutil.rmtree(temp_dir)