def test_help(self):
fake_pack_path = self.create_fake_package('fake_model', license=False)
pack = package.Package(fake_pack_path)
receive_help = pack.help()
self.assertEqual(receive_help, "# This a README\n")
os.unlink(os.path.join(fake_pack_path, 'README'))
pack = package.Package(fake_pack_path)
receive_help = pack.help()
self.assertEqual(receive_help, "No help available for package 'fake_model'.")
def test_check_structure_no_metadata(self):
fake_pack_path = self.create_fake_package('fake_model', metadata=False)
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_structure()
self.assertListEqual(errors, ["The package 'fake_model' have no 'metadata.yml'."])
self.assertListEqual(warnings, [])
def test_check_structure_no_readme(self):
fake_pack_path = self.create_fake_package('fake_model', readme=False)
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_structure()
self.assertEqual(errors, [])
self.assertEqual(warnings, ["The package 'fake_model' have not any README file."])
def test_init(self):
fake_pack_path = self.create_fake_package('fake_model')
pack = package.Package(fake_pack_path)
self.assertEqual(pack.path, fake_pack_path)
self.assertEqual(pack.readme, os.path.join(fake_pack_path, 'README'))
self.assertEqual(pack.name, 'fake_model')
self.assertEqual(pack.metadata_path, os.path.join(fake_pack_path, 'metadata.yml'))
def test_check_structure_no_license(self):
fake_pack_path = self.create_fake_package('fake_model', license=False)
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_structure()
self.assertEqual(errors, [])
self.assertEqual(warnings, ["The package 'fake_model' have not any LICENSE file. "
"May be you have not right to use it."])
def test_check_model_consistency_bad_definitions(self):
fake_pack_path = self.create_fake_package('fake_model', bad_definitions=True)
pack = package.Package(fake_pack_path)
with self.catch_log(log_name='macsypy'):
errors, warnings = pack._check_model_consistency()
self.assertEqual(warnings, [])
self.assertEqual(errors, ["fake_model/model_3: min_genes_required '1' must be greater or equal than "
"min_mandatory_genes_required '2'"])
def test_check_model_consistency(self):
fake_pack_path = self.create_fake_package('fake_model')
pack = package.Package(fake_pack_path)
with self.catch_log(log_name='macsypy'):
errors, warnings = pack._check_model_consistency()
self.assertEqual(warnings, [])
self.assertEqual(errors, [])
def test_check_model_conf_bad_conf(self):
fake_pack_path = self.create_fake_package('fake_model', conf=False, bad_conf=True)
pack = package.Package(fake_pack_path)
with self.catch_log(log_name='macsypy'):
errors, warnings = pack._check_model_conf()
self.maxDiff =None
self.assertListEqual(errors, [f"The model configuration file '{fake_pack_path}/model_conf.xml' "
f"cannot be parsed: could not convert string to float: 'FOO'"])
self.assertListEqual(warnings, [])
def test_check_model_consistency_extra_profile(self):
fake_pack_path = self.create_fake_package('fake_model')
pack = package.Package(fake_pack_path)
open(os.path.join(fake_pack_path, 'profiles', 'extra_profile.hmm'), 'w').close()
with self.catch_log(log_name='macsypy'):
errors, warnings = pack._check_model_consistency()
self.assertEqual(warnings, ['The extra_profile profiles are not referenced in any definitions.'])
self.assertEqual(errors, [])
def test_check_structure_bad_path(self):
foobar = os.path.join(self.tmpdir, "foobar")
pack = package.Package(foobar)
errors, warnings = pack._check_structure()
self.assertListEqual(errors, ["The package 'foobar' does not exists."])
self.assertListEqual(warnings, [])
open(foobar, 'w').close()
errors, warnings = pack._check_structure()
self.assertListEqual(errors, ["'foobar' is not a directory "])
self.assertListEqual(warnings, [])
def test_check_model_consistency_lack_one_profile(self):
fake_pack_path = self.create_fake_package('fake_model', skip_hmm=['flgB', 'fliE'])
pack = package.Package(fake_pack_path)
with self.catch_log(log_name='macsypy'):
errors, warnings = pack._check_model_consistency()
self.assertEqual(warnings, [])
self.assertSetEqual(set(errors),
set(["'fake_model/flgB': No such profile",
"'fake_model/fliE': No such profile"])
)
def test_find_readme(self):
fake_pack_path = self.create_fake_package('fake_model')
pack = package.Package(fake_pack_path)
for ext in ('', '.rst', '.md'):
readme_path = os.path.join(pack.path, 'README' + ext)
os.rename(pack.readme, readme_path)
pack.readme = readme_path
self.assertEqual(pack._find_readme(), readme_path)
readme_path = os.path.join(pack.path, 'README.foo')
os.rename(pack.readme, readme_path)
self.assertIsNone(pack._find_readme())
def test_check_structure_no_profiles(self):
fake_pack_path = self.create_fake_package('fake_model', profiles=False)
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_structure()
self.assertListEqual(errors, ["The package 'fake_model' have no 'profiles' directory."])
self.assertListEqual(warnings, [])
open(os.path.join(pack.path, 'profiles'), 'w').close()
errors, warnings = pack._check_structure()
self.assertListEqual(errors, ["'/tmp/macsy_test_package/fake_model/profiles' is not a directory."])
self.assertListEqual(warnings, [])
def test_check(self):
fake_pack_path = self.create_fake_package('fake_model')
load_metadata_meth = package.Package._load_metadata
bad_meta_data = {"short_desc": "this is a short description of the repos",
"doc": "http://link/to/the/documentation",
"copyright": "2019, Institut Pasteur, CNRS"
}
try:
package.Package._load_metadata = lambda x: bad_meta_data
pack = package.Package(fake_pack_path)
errors, warnings = pack.check()
finally:
package.Package._load_metadata = load_metadata_meth
self.assertListEqual(errors,
["field 'maintainer' is mandatory in metadata_path.",
"field 'vers' is mandatory in metadata_path."])
self.assertListEqual(warnings,
["It's better if the field 'cite' is setup in metadata_path file",
"It's better if the field 'license' is setup in metadata_path file"])
def test_check_metadata(self):
fake_pack_path = self.create_fake_package('fake_model')
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_metadata()
self.assertEqual(errors, [])
self.assertEqual(warnings, [])
load_metadata_meth = package.Package._load_metadata
#################
# No maintainer #
#################
no_auth_meta_data = self.metadata.copy()
del no_auth_meta_data['maintainer']
try:
package.Package._load_metadata = lambda x: no_auth_meta_data
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_metadata()
finally:
package.Package._load_metadata = load_metadata_meth
self.assertEqual(errors, ["field 'maintainer' is mandatory in metadata_path."])
self.assertEqual(warnings, [])
#################
# No short desc #
#################
no_short_desc_metadata = self.metadata.copy()
del no_short_desc_metadata['short_desc']
try:
package.Package._load_metadata = lambda x: no_short_desc_metadata
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_metadata()
finally:
package.Package._load_metadata = load_metadata_meth
self.assertEqual(errors, ["field 'short_desc' is mandatory in metadata_path."])
self.assertEqual(warnings, [])
###########
# No vers #
###########
no_vers_metadata = self.metadata.copy()
del no_vers_metadata['vers']
try:
package.Package._load_metadata = lambda x: no_vers_metadata
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_metadata()
finally:
package.Package._load_metadata = load_metadata_meth
self.assertEqual(errors, ["field 'vers' is mandatory in metadata_path."])
self.assertEqual(warnings, [])
###########
# No cite #
###########
no_cite_metadata = self.metadata.copy()
del no_cite_metadata['cite']
try:
package.Package._load_metadata = lambda x: no_cite_metadata
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_metadata()
finally:
package.Package._load_metadata = load_metadata_meth
self.assertEqual(errors, [])
self.assertEqual(warnings, ["It's better if the field 'cite' is setup in metadata_path file"])
##########
# No doc #
##########
no_doc_metadata = self.metadata.copy()
del no_doc_metadata['doc']
try:
package.Package._load_metadata = lambda x: no_doc_metadata
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_metadata()
finally:
package.Package._load_metadata = load_metadata_meth
self.assertEqual(errors, [])
self.assertEqual(warnings, ["It's better if the field 'doc' is setup in metadata_path file"])
##############
# No license #
##############
no_license_metadata = self.metadata.copy()
del no_license_metadata['license']
try:
package.Package._load_metadata = lambda x: no_license_metadata
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_metadata()
finally:
package.Package._load_metadata = load_metadata_meth
self.assertEqual(errors, [])
self.assertEqual(warnings, ["It's better if the field 'license' is setup in metadata_path file"])
################
# No copyright #
################
no_copyright_metadata = self.metadata.copy()
del no_copyright_metadata['copyright']
try:
package.Package._load_metadata = lambda x: no_copyright_metadata
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_metadata()
finally:
package.Package._load_metadata = load_metadata_meth
self.assertEqual(errors, [])
self.assertEqual(warnings, ["It's better if the field 'copyright' is setup in metadata_path file"])
##################
# No maintainer name #
##################
# this test must the last of the set
# because we remove a key in maintainer value
# the copy is a shallow copy
# so maintainer value is a reference to the good_metadata[maintainer]
# side effect
no_auth_name_meta_data = self.metadata.copy()
del no_auth_name_meta_data['maintainer']['name']
try:
package.Package._load_metadata = lambda x: no_auth_name_meta_data
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_metadata()
finally:
package.Package._load_metadata = load_metadata_meth
self.assertEqual(errors, ["field 'maintainer.name' is mandatory in metadata_path."])
self.assertEqual(warnings, [])
def test_check_structure(self):
fake_pack_path = self.create_fake_package('fake_model')
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_structure()
self.assertListEqual(errors, [])
self.assertListEqual(warnings, [])
def test_metadata(self):
fake_pack_path = self.create_fake_package('fake_model')
pack = package.Package(fake_pack_path)
self.assertDictEqual(pack.metadata, self.metadata)
self.assertDictEqual(pack.metadata, self.metadata)
def test_info(self):
fake_pack_path = self.create_fake_package('fake_model', license=False)
pack = package.Package(fake_pack_path)
info = pack.info()
expected_info = """
fake_model (0.0b2)
maintainer: auth_name <*****@*****.**>
this is a short description of the repos
how to cite:
\t- bla bla
\t- link to publication
\t- ligne 1
\t ligne 2
\t ligne 3 et bbbbb
documentation
\thttp://link/to/the/documentation
This data are released under CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)
copyright: 2019, Institut Pasteur, CNRS
"""
self.assertEqual(info, expected_info)
load_metadata_meth = package.Package._load_metadata
###########
# No cite #
###########
no_cite_metadata = self.metadata.copy()
del no_cite_metadata['cite']
try:
package.Package._load_metadata = lambda x: no_cite_metadata
pack = package.Package(fake_pack_path)
info = pack.info()
finally:
package.Package._load_metadata = load_metadata_meth
expected_info = """
fake_model (0.0b2)
maintainer: auth_name <*****@*****.**>
this is a short description of the repos
how to cite:
\t- No citation available
documentation
\thttp://link/to/the/documentation
This data are released under CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)
copyright: 2019, Institut Pasteur, CNRS
"""
self.assertEqual(info, expected_info)
##########
# No doc #
##########
no_doc_metadata = self.metadata.copy()
del no_doc_metadata['doc']
try:
package.Package._load_metadata = lambda x: no_doc_metadata
pack = package.Package(fake_pack_path)
info = pack.info()
finally:
package.Package._load_metadata = load_metadata_meth
expected_info = """
fake_model (0.0b2)
maintainer: auth_name <*****@*****.**>
this is a short description of the repos
how to cite:
\t- bla bla
\t- link to publication
\t- ligne 1
\t ligne 2
\t ligne 3 et bbbbb
documentation
\tNo documentation available
This data are released under CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)
copyright: 2019, Institut Pasteur, CNRS
"""
self.assertEqual(info, expected_info)
##############
# No license #
##############
no_license_metadata = self.metadata.copy()
del no_license_metadata['license']
try:
package.Package._load_metadata = lambda x: no_license_metadata
pack = package.Package(fake_pack_path)
info = pack.info()
finally:
package.Package._load_metadata = load_metadata_meth
expected_info = """
fake_model (0.0b2)
maintainer: auth_name <*****@*****.**>
this is a short description of the repos
how to cite:
\t- bla bla
\t- link to publication
\t- ligne 1
\t ligne 2
\t ligne 3 et bbbbb
documentation
\thttp://link/to/the/documentation
This data are released under No license available
copyright: 2019, Institut Pasteur, CNRS
"""
self.assertEqual(info, expected_info)
def test_check_model_conf_no_conf(self):
fake_pack_path = self.create_fake_package('fake_model', conf=False)
pack = package.Package(fake_pack_path)
errors, warnings = pack._check_model_conf()
self.assertListEqual(errors, [])
self.assertListEqual(warnings, [])
