def test_previous_run(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'previous_run' : 'foo',
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
try:
cfg_base = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertIsNone(cfg_base.previous_run)
cfg_base.save( cfg_base.working_dir )
#wait
time.sleep(1)
new_cfg = Config(previous_run = cfg_base.working_dir)
self.assertEqual(new_cfg.previous_run, cfg_base.working_dir)
finally:
# close loggers filehandles, so they don't block file deletion
# in shutil.rmtree calls in Windows
logging.shutdown()
try:
shutil.rmtree(new_cfg.working_dir)
except:
pass
def test_save(self):
self.parsed_args.max_nb_genes = [['Set_1/T2SS', 5],
['set_1/Flagelum', 12]]
self.parsed_args.multi_loci = 'Set_1/T2SS,set_1/Flagelum'
self.parsed_args.models = ['Set_1', 'T9SS', 'T3SS', 'T4SS_typeI']
cfg = Config(self.defaults, self.parsed_args)
expected = {k: v for k, v in cfg._options.items() if v is not None}
expected['max_nb_genes'] = 'Set_1/T2SS 5 set_1/Flagelum 12'
expected['models'] = 'Set_1 T9SS T3SS T4SS_typeI'
# save in file 'macsyfinder.conf'
with tempfile.TemporaryDirectory() as tmpdirname:
cfg_path = os.path.join(tmpdirname, 'macsyfinder.conf')
cfg.save(path_or_buf=cfg_path)
cfg.save(path_or_buf='/tmp/macsyfinder.conf')
new_args = Namespace()
new_args.cfg_file = cfg_path
restored_cfg = Config(self.defaults, new_args)
self.maxDiff = None
# the option cfg-file differ from the 2 configs
# None in cfg
# cfg_path in restored_cfg
self.assertEqual(restored_cfg._options['cfg_file'], cfg_path)
del (cfg._options['cfg_file'])
del (restored_cfg._options['cfg_file'])
self.assertDictEqual(cfg._options, restored_cfg._options)
def test_previous_run(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'previous_run' : 'foo',
'res_search_dir' : '/tmp',
}
self.assertRaises(ValueError, Config, **kwargs)
try:
cfg_base = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertIsNone(cfg_base.previous_run)
cfg_base.save( cfg_base.working_dir )
#wait
time.sleep(1)
new_cfg = Config(previous_run = cfg_base.working_dir)
self.assertEqual(new_cfg.previous_run, cfg_base.working_dir)
finally:
try:
shutil.rmtree(cfg_base.working_dir)
except:
pass
try:
shutil.rmtree(new_cfg.working_dir)
except:
pass
def test_previous_run(self):
out_dir = os.path.join(self.tmp_dir, 'macsy_test_config')
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'previous_run': 'foo',
'res_search_dir': out_dir
}
self.assertRaises(ValueError, Config, **kwargs)
try:
shutil.rmtree(out_dir)
except:
pass
self.tearDown()
try:
cfg_base = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir,
'profiles'),
res_search_dir=self.tmp_dir)
self.assertIsNone(cfg_base.previous_run)
cfg_base.save(cfg_base.working_dir)
#wait
time.sleep(1)
new_cfg = Config(previous_run=cfg_base.working_dir)
self.assertEqual(new_cfg.previous_run, cfg_base.working_dir)
finally:
# close loggers filehandles, so they don't block file deletion
# in shutil.rmtree calls in Windows
logging.shutdown()
try:
shutil.rmtree(new_cfg.working_dir)
except:
pass
try:
shutil.rmtree(cfg_base.working_dir)
except:
pass
def test_save(self):
self.parsed_args.max_nb_genes = [['Set_1/T2SS', 5],
['set_1/Flagelum', 12]]
self.parsed_args.multi_loci = 'Set_1/T2SS,set_1/Flagelum'
self.parsed_args.models = [['Set_1', 'T9SS', 'T3SS', 'T4SS_typeI']]
cfg = Config(self.defaults, self.parsed_args)
expected = {k: v for k, v in cfg._options.items() if v is not None}
expected['max_nb_genes'] = 'Set_1/T2SS 5 set_1/Flagelum 12'
expected['models'] = [('models_1', 'Set_1 T9SS T3SS T4SS_typeI')]
with tempfile.TemporaryDirectory() as tmpdirname:
cfg_path = os.path.join(tmpdirname, 'macsyfinder.conf')
cfg.save(path_or_buf=cfg_path)
saved_opt = cfg._config_file_2_dict(self.defaults, [cfg_path])
saved_opt['multi_loci'] = {
v
for v in
[v.strip() for v in saved_opt['multi_loci'].split(',')] if v
}
self.maxDiff = None
self.assertDictEqual(saved_opt, expected)
