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##########################################################################
# MacSyFinder - Detection of macromolecular systems in protein dataset #
# using systems modelling and similarity search. #
# Authors: Sophie Abby, Bertrand Neron #
# Copyright (c) 2014-2024 Institut Pasteur (Paris) and CNRS. #
# See the COPYRIGHT file for details #
# #
# This file is part of MacSyFinder package. #
# #
# MacSyFinder 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. #
# #
# MacSyFinder 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 MacSyFinder (COPYING). #
# If not, see <https://www.gnu.org/licenses/>. #
##########################################################################
import os
import shutil
import tempfile
import yaml
from macsypy.metadata import Metadata, Maintainer
from tests import MacsyTest
class TestMetadata(MacsyTest):
def setUp(self) -> None:
self.tmpdir = os.path.join(tempfile.gettempdir(), 'macsy_test_metadata')
if os.path.exists(self.tmpdir) and os.path.isdir(self.tmpdir):
shutil.rmtree(self.tmpdir)
os.makedirs(self.tmpdir)
def tearDown(self) -> None:
try:
shutil.rmtree(self.tmpdir)
except Exception:
pass
def test_init(self):
maintainer = Maintainer(name='joe', email='joe@bar.org')
short_desc = 'this is a short description'
meta = Metadata(maintainer, short_desc)
self.assertEqual(meta.maintainer, maintainer)
self.assertEqual(meta.short_desc, short_desc)
self.assertIsNone(meta.vers)
self.assertEqual(meta.license, '')
def test_load(self):
meta_path = self.find_data('pack_metadata', 'good_metadata.yml')
meta = Metadata.load(meta_path)
self.assertEqual(meta.maintainer, Maintainer(name='auth_name', email='auth_name@mondomain.fr'))
self.assertEqual(meta.short_desc, 'this is a short description of the repos')
self.assertEqual(meta.vers, '0.0b2')
self.assertEqual(meta.license, 'CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)')
self.assertEqual(meta.doc, 'http://link/to/the/documentation')
self.assertEqual(meta.cite, ['bla bla',
'link to publication',
'ligne 1\nligne 2\nligne 3 et bbbbb\n'])
meta_path = self.find_data('pack_metadata', 'bad_metadata.yml')
with self.assertRaises(ValueError) as ctx:
Metadata.load(meta_path)
self.assertEqual(str(ctx.exception),
f"""
- The metadata file '{meta_path}' is not valid: the element 'short_desc' is required.
- The metadata file '{meta_path}' is not valid: the element 'maintainer' is required.""")
def test_maintainer(self):
meta_path = self.find_data('pack_metadata', 'good_metadata.yml')
meta = Metadata.load(meta_path)
self.assertEqual(meta.maintainer, Maintainer(name='auth_name', email='auth_name@mondomain.fr'))
new_auth = 'joe bar'
new_email = 'joe@domain.org'
meta.maintainer = Maintainer(new_auth, new_email)
self.assertEqual(meta.maintainer, Maintainer(name=new_auth, email=new_email))
def test_short_desc(self):
meta_path = self.find_data('pack_metadata', 'good_metadata.yml')
meta = Metadata.load(meta_path)
self.assertEqual(meta.short_desc, 'this is a short description of the repos')
new_short_desc = "This is a new short desc"
meta.short_desc = new_short_desc
self.assertEqual(meta.short_desc, new_short_desc)
with self.assertRaises(ValueError) as ctx:
meta.short_desc = ''
self.assertEqual(str(ctx.exception),
"The field 'short_desc' is mandatory.")
def test_vers(self):
meta_path = self.find_data('pack_metadata', 'good_metadata.yml')
meta = Metadata.load(meta_path)
self.assertEqual(meta.vers, '0.0b2')
meta.vers = '0.0b3'
self.assertEqual(meta.vers, '0.0b3')
def test_cite(self):
meta_path = self.find_data('pack_metadata', 'good_metadata.yml')
meta = Metadata.load(meta_path)
self.assertEqual(meta.cite, ['bla bla', 'link to publication', 'ligne 1\nligne 2\nligne 3 et bbbbb\n'])
new_cite = ["citation_1", "citation_2"]
meta.cite = new_cite
self.assertEqual(meta.cite, new_cite)
def test_license(self):
meta_path = self.find_data('pack_metadata', 'good_metadata.yml')
meta = Metadata.load(meta_path)
self.assertEqual(meta.license, 'CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)')
new_license = "GPLv3"
meta.license = new_license
self.assertEqual(meta.license, new_license)
def test_copyright(self):
meta_path = self.find_data('pack_metadata', 'good_metadata.yml')
meta = Metadata.load(meta_path)
self.assertEqual(meta.copyright, '2019, Institut Pasteur, CNRS')
self.assertEqual(meta.copyright_date, '2019')
self.assertEqual(meta.copyright_holder, 'Institut Pasteur, CNRS')
meta.copyright_date = '2020-2024'
meta.copyright_holder = 'My institution'
self.assertEqual(meta.copyright, '2020-2024, My institution')
def test_doc(self):
meta_path = self.find_data('pack_metadata', 'good_metadata.yml')
meta = Metadata.load(meta_path)
self.assertEqual(meta.doc, 'http://link/to/the/documentation')
meta.doc = 'new link'
self.assertEqual(meta.doc, 'new link')
def test_save(self):
for yml_name in ('good_metadata.yml', 'metadata_no_vers.yml', 'metadata_no_license.yml',
'metadata_no_doc.yml', 'metadata_no_copyright.yml'):
with self.subTest(yml_name=yml_name):
meta_path = self.find_data('pack_metadata', yml_name)
meta = Metadata.load(meta_path)
saved_path = os.path.join(self.tmpdir, 'metadata.yml')
meta.save(saved_path)
with open(saved_path) as saved_file:
saved_yaml = yaml.safe_load(saved_file)
with open(meta_path) as ref_file:
ref_yaml = yaml.safe_load(ref_file)
self.assertDictEqual(ref_yaml, saved_yaml)
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