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Source code for tool_shed.test.functional.test_0040_repository_circular_dependencies
from ..base.twilltestcase import common, ShedTwillTestCase
freebayes_repository_name = 'freebayes_0040'
freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0040"
filtering_repository_name = 'filtering_0040'
filtering_repository_description = "Galaxy's filtering tool for test 0040"
filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040"
[docs]class TestRepositoryCircularDependencies(ShedTwillTestCase):
'''Verify that the code correctly displays repositories with circular repository dependencies.'''
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email
self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
admin_user = self.test_db_util.get_user(common.admin_email)
assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
self.test_db_util.get_private_role(admin_user)
[docs] def test_0005_create_category(self):
"""Create a category for this test suite"""
self.create_category(name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.')
[docs] def test_0010_create_freebayes_repository(self):
'''Create and populate freebayes_0040.'''
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=freebayes_repository_name,
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
categories=['test_0040_repository_circular_dependencies'],
strings_displayed=[])
self.upload_file(repository,
filename='freebayes/freebayes.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded the tool tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0015_create_filtering_repository(self):
'''Create and populate filtering_0040.'''
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=filtering_repository_name,
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
categories=['test_0040_repository_circular_dependencies'],
strings_displayed=[])
self.upload_file(repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded the tool tarball for filtering 1.1.0.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0020_create_dependency_on_freebayes(self):
'''Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository.'''
# The dependency structure should look like:
# Filtering revision 0 -> freebayes revision 0.
# Freebayes revision 0 -> filtering revision 1.
# Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path('test_0040', additional_paths=['filtering'])
repository_tuple = (self.url, repository.name, repository.user.username, self.get_repository_tip(repository))
self.create_repository_dependency(repository=filtering_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
[docs] def test_0025_create_dependency_on_filtering(self):
'''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.'''
# The dependency structure should look like:
# Filtering revision 0 -> freebayes revision 0.
# Freebayes revision 0 -> filtering revision 1.
# Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path('test_0040', additional_paths=['freebayes'])
repository_tuple = (self.url, repository.name, repository.user.username, self.get_repository_tip(repository))
self.create_repository_dependency(repository=freebayes_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
[docs] def test_0030_verify_repository_dependencies(self):
'''Verify that each repository can depend on the other without causing an infinite loop.'''
filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
# The dependency structure should look like:
# Filtering revision 0 -> freebayes revision 0.
# Freebayes revision 0 -> filtering revision 1.
# Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
# In this case, the displayed dependency will specify the tip revision, but this will not always be the case.
self.check_repository_dependency(filtering_repository, freebayes_repository, self.get_repository_tip(freebayes_repository))
self.check_repository_dependency(freebayes_repository, filtering_repository, self.get_repository_tip(filtering_repository))
[docs] def test_0035_verify_repository_metadata(self):
'''Verify that resetting the metadata does not change it.'''
freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
for repository in [freebayes_repository, filtering_repository]:
self.verify_unchanged_repository_metadata(repository)
[docs] def test_0040_verify_tool_dependencies(self):
'''Verify that freebayes displays tool dependencies.'''
repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
self.display_manage_repository_page(repository,
strings_displayed=['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools', 'package'],
strings_not_displayed=['Invalid tools'])