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Source code for tool_shed.test.functional.test_1040_install_repository_basic_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"
category_name = 'test_0040_repository_circular_dependencies'
running_standalone = False
[docs]class TestInstallingCircularDependencies(ShedTwillTestCase):
'''Verify that the code correctly handles installing repositories with circular 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, f'Problem retrieving user with email {common.test_user_1_email} from the database'
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, f'Problem retrieving user with email {common.admin_email} from the database'
self.test_db_util.get_private_role(admin_user)
[docs] def test_0005_create_freebayes_repository(self):
'''Create and populate freebayes_0040.'''
global running_standalone
category = self.create_category(name=category_name, description='Testing handling of circular repository dependencies.')
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,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
if self.repository_is_new(repository):
running_standalone = True
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.'''
global running_standalone
category = self.create_category(name=category_name, description='Testing handling of circular repository dependencies.')
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,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
if self.repository_is_new(repository):
running_standalone = True
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_repository_dependencies(self):
'''Set up the filtering and freebayes repository dependencies.'''
# 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.
global running_standalone
if running_standalone:
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_1040', additional_paths=['circular'])
repository_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))
self.create_repository_dependency(repository=filtering_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
repository_tuple = (self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip(filtering_repository))
self.create_repository_dependency(repository=freebayes_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
[docs] def test_0025_install_freebayes_repository(self):
'''Install freebayes with blank tool panel section, without tool dependencies but with repository dependencies.'''
self.galaxy_login(email=common.admin_email, username=common.admin_username)
strings_displayed = ['Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18']
self.install_repository(freebayes_repository_name,
common.test_user_1_name,
category_name,
strings_displayed=strings_displayed,
install_tool_dependencies=False,
install_repository_dependencies=True)
[docs] def test_0030_uninstall_filtering_repository(self):
'''Deactivate filtering, verify tool panel section and missing repository dependency.'''
installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner(freebayes_repository_name, common.test_user_1_name)
installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(filtering_repository_name, common.test_user_1_name)
self.display_installed_repository_manage_page(installed_freebayes_repository)
self.display_installed_repository_manage_page(installed_filtering_repository)
self.deactivate_repository(installed_filtering_repository)
self.test_db_util.ga_refresh(installed_filtering_repository)
self.check_galaxy_repository_tool_panel_section(installed_filtering_repository, 'Get Data')
strings_displayed = ['Missing repository', 'filtering', 'freebayes_0040', 'user1', "Galaxy's freebayes tool for test 0040"]
self.display_installed_repository_manage_page(installed_freebayes_repository, strings_displayed=strings_displayed)
self.check_galaxy_repository_db_status(filtering_repository_name,
common.test_user_1_name,
'Deactivated')
[docs] def test_0035_reactivate_filtering_repository(self):
'''Reinstall filtering into 'filtering' tool panel section.'''
installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(freebayes_repository_name,
common.test_user_1_name)
self.reinstall_repository(installed_filtering_repository,
install_tool_dependencies=False,
install_repository_dependencies=True,
new_tool_panel_section_label='filtering',
no_changes=False)
[docs] def test_0040_uninstall_freebayes_repository(self):
'''Deactivate freebayes, verify tool panel section and missing repository dependency.'''
installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner(freebayes_repository_name, common.test_user_1_name)
installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(filtering_repository_name, common.test_user_1_name)
self.display_installed_repository_manage_page(installed_freebayes_repository)
self.display_installed_repository_manage_page(installed_filtering_repository)
self.deactivate_repository(installed_freebayes_repository)
self.test_db_util.ga_refresh(installed_freebayes_repository)
self.check_galaxy_repository_tool_panel_section(installed_freebayes_repository, 'Get Data')
strings_displayed = ['Missing repository', 'freebayes', 'filtering_0040', 'user1', "Galaxy's filtering tool for test 0040"]
self.display_installed_repository_manage_page(installed_filtering_repository, strings_displayed=strings_displayed)
self.check_galaxy_repository_db_status('freebayes_0040',
'user1',
'Deactivated')
[docs] def test_0045_deactivate_filtering_repository(self):
'''Deactivate filtering, verify tool panel section.'''
installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(filtering_repository_name, common.test_user_1_name)
installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner(freebayes_repository_name, common.test_user_1_name)
self.display_installed_repository_manage_page(installed_freebayes_repository)
self.display_installed_repository_manage_page(installed_filtering_repository)
self.deactivate_repository(installed_filtering_repository)
self.test_db_util.ga_refresh(installed_filtering_repository)
strings_displayed = ['Missing repository', 'filtering', 'freebayes_0040', 'user1', "Galaxy's freebayes tool for test 0040"]
self.display_installed_repository_manage_page(installed_freebayes_repository, strings_displayed=strings_displayed)
self.check_galaxy_repository_db_status(filtering_repository_name,
common.test_user_1_name,
'Deactivated')