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#########################################################################
# MacSyLib - Python library to detect macromolecular systems #
# in prokaryotes protein dataset using systems modelling #
# and similarity search. #
# #
# Authors: Sophie Abby, Bertrand Neron #
# Copyright (c) 2014-2025 Institut Pasteur (Paris) and CNRS. #
# See the COPYRIGHT file for details #
# #
# This file is part of MacSyLib package. #
# #
# MacSyLib is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# MacSyLib is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details . #
# #
# You should have received a copy of the GNU General Public License #
# along with MacSyLib (COPYING). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
import logging
import colorlog
import xml.etree.ElementTree as Et
import macsylib
from macsylib.error import MacsylibError
from macsylib.model_conf_parser import ModelConfParser
import macsylib.model_conf_parser
from tests import MacsyTest
class TestModelConfParser(MacsyTest):
def setUp(self) -> None:
macsylib.init_logger(name='macsylib')
macsylib.logger_set_level(name='macsylib', level=logging.INFO)
logger = colorlog.getLogger('macsylib')
macsylib.model_conf_parser._log = logger
def test_parse(self):
expected_conf = {'itself_weight': 11.0,
'exchangeable_weight': 12.0,
'mandatory_weight': 13.0,
'accessory_weight': 14.0,
'neutral_weight': 0.0,
'out_of_cluster_weight': 10.0,
'redundancy_penalty': 20.0,
'e_value_search': 0.12,
'i_evalue_sel': 0.012,
'coverage_profile': 0.55,
'cut_ga': False}
conf_file = self.find_data('conf_files', 'model_conf.xml')
mcp = ModelConfParser(conf_file)
test_conf = mcp.parse()
self.assertDictEqual(expected_conf, test_conf)
def test_parse_wo_filtering(self):
expected_conf = {'itself_weight': 11.0,
'exchangeable_weight': 12.0,
'mandatory_weight': 13.0,
'accessory_weight': 14.0,
'neutral_weight': 0.0,
'redundancy_penalty': 20.0,
'out_of_cluster_weight': 10.0}
conf_file = self.find_data('conf_files', 'model_conf_wo_filtering.xml')
mcp = ModelConfParser(conf_file)
test_conf = mcp.parse()
self.assertDictEqual(expected_conf, test_conf)
def test_parse_wo_weights(self):
expected_conf = {'e_value_search': 0.12,
'i_evalue_sel': 0.012,
'coverage_profile': 0.55,
'cut_ga': False}
conf_file = self.find_data('conf_files', 'model_conf_wo_weights.xml')
mcp = ModelConfParser(conf_file)
test_conf = mcp.parse()
self.assertDictEqual(expected_conf, test_conf)
def test_parse_bad_file(self):
conf_file = self.find_data('conf_files', 'project.conf')
mcp = ModelConfParser(conf_file)
with self.catch_log(log_name='macsylib'):
with self.assertRaises(MacsylibError) as ctx:
mcp.parse()
self.assertEqual(str(ctx.exception),
f"unable to parse model configuration '{conf_file}' : syntax error: line 2, column 0"
)
def test_parse_weights(self):
expected_weights = {'itself_weight': 11.0,
'exchangeable_weight': 12.0,
'mandatory_weight': 13.0,
'accessory_weight': 14.0,
'neutral_weight': 0.0,
'redundancy_penalty': 20.0,
'out_of_cluster_weight': 10.0,
}
conf_file = self.find_data('conf_files', 'model_conf.xml')
tree = Et.parse(conf_file)
model_node = tree.getroot()
mcp = ModelConfParser(conf_file)
recieved_weights = mcp.parse_weights(model_node.find("./weights"))
self.assertDictEqual(expected_weights, recieved_weights)
def test_parse_filtering(self):
expected_filters = {'e_value_search': 0.12,
'i_evalue_sel': 0.012,
'coverage_profile': 0.55,
'cut_ga': False
}
conf_file = self.find_data('conf_files', 'model_conf.xml')
tree = Et.parse(conf_file)
model_node = tree.getroot()
mcp = ModelConfParser(conf_file)
filtering_node = model_node.find("./filtering")
recieved_filters = mcp.parse_filtering(filtering_node)
self.assertDictEqual(recieved_filters, expected_filters)
# test cut_ga True
cut_ga_node = filtering_node.find('cut_ga')
cut_ga_node.text = 'True'
recieved_filters = mcp.parse_filtering(filtering_node)
self.assertTrue('cut_ga' in recieved_filters)
# test bad value for cut_ga
cut_ga_node.text = 'FOO'
with self.catch_log(log_name='macsylib'):
with self.assertRaises(MacsylibError) as ctx:
mcp.parse_filtering(filtering_node)
self.assertEqual(str(ctx.exception),
f"cannot parse 'cut_ga' element in '{conf_file}' expect True, 1, False, 0 got : 'FOO'"
)
# test no cut_ga element
filtering_node.remove(cut_ga_node)
recieved_filters = mcp.parse_filtering(filtering_node)
del(expected_filters['cut_ga'])
self.assertDictEqual(expected_filters, recieved_filters)
def test_parse_w_unkown_tag(self):
expected_filters = {'e_value_search': 0.12,
'i_evalue_sel': 0.012,
'coverage_profile': 0.55,
'cut_ga': False
}
conf_file = self.find_data('conf_files', 'model_conf.xml')
tree = Et.parse(conf_file)
model_node = tree.getroot()
mcp = ModelConfParser(conf_file)
filter_node = model_node.find("./filtering")
extra_elt = Et.SubElement(filter_node, 'nimportnaoik')
extra_elt.text = 'Foo'
with self.catch_log(log_name='macsylib') as log:
recieved_filters = mcp.parse_filtering(model_node.find("./filtering"))
log_msg = log.get_value().strip()
self.assertEqual(log_msg,
f"unknown element 'nimportnaoik' in '{conf_file}' ignore it."
)
self.assertDictEqual(recieved_filters, expected_filters)
def test_parse_w_bad_value_lxml(self):
conf_file = self.find_data('conf_files', 'model_conf.xml')
tree = Et.parse(conf_file)
model_node = tree.getroot()
mcp = ModelConfParser(conf_file)
filter_node = model_node.find("./filtering")
coverage_node = filter_node.find('coverage_profile')
coverage_node.text = "FOO"
with self.catch_log(log_name='macsylib'):
with self.assertRaises(MacsylibError) as ctx:
mcp.parse_filtering(model_node.find("./filtering"))
self.assertEqual(str(ctx.exception),
f"The model configuration file '{conf_file}' is not valid: could not convert string to float: 'FOO'"
)
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