def test_config_file_2_dict(self):
cfg = Config(self.defaults, self.parsed_args)
res = cfg._config_file_2_dict(self.defaults, ['nimportnaoik'])
self.assertDictEqual({}, res)
cfg_file = self.find_data(
os.path.join('conf_files', 'macsy_test_conf.conf'))
res = cfg._config_file_2_dict(self.defaults, [cfg_file])
expected = {
'db_type': 'gembase',
'inter_gene_max_space': 'set_1/T2SS 2 set_1/Flagellum 4',
'min_mandatory_genes_required': 'set_1/T2SS 5 set_1/Flagellum 9',
'replicon_topology': 'circular',
'sequence_db': '/path/to/sequence/bank/fasta_file',
'topology_file': '/the/path/to/the/topology/to/use'
}
self.assertDictEqual(expected, res)
bad_cfg_file = self.find_data(
os.path.join('conf_files', 'macsy_test_bad_conf.conf'))
with self.assertRaises(ParsingError):
cfg._config_file_2_dict(self.defaults, [bad_cfg_file])
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)
