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Source code for tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies
from ..base.twilltestcase import common, ShedTwillTestCase
datatypes_repository_name = 'emboss_datatypes_0020'
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools."
emboss_repository_name = 'emboss_0020'
emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
base_datatypes_count = 0
repository_datatypes_count = 0
running_standalone = False
[docs]class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
'''Test uninstalling and reinstalling a repository with tool dependencies.'''
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
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_ensure_repositories_and_categories_exist(self):
'''Create the 0020 category and upload the emboss repository to the tool shed, if necessary.'''
global repository_datatypes_count
global running_standalone
category = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Tests for a repository with tool dependencies.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
datatypes_repository = self.get_or_create_repository(name=datatypes_repository_name,
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
if self.repository_is_new(datatypes_repository):
running_standalone = True
self.upload_file(datatypes_repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[])
emboss_repository = self.get_or_create_repository(name=emboss_repository_name,
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.upload_file(emboss_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
repository_dependencies_path = self.generate_temp_path('test_1020', additional_paths=['emboss', '5'])
repository_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
self.create_repository_dependency(repository=emboss_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))
[docs] def test_0010_install_emboss_repository(self):
'''Install the emboss repository into the Galaxy instance.'''
global repository_datatypes_count
global base_datatypes_count
self.galaxy_login(email=common.admin_email, username=common.admin_username)
base_datatypes_count = int(self.get_datatypes_count())
strings_displayed = ['Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package']
self.install_repository(emboss_repository_name,
common.test_user_1_name,
'Test 0020 Basic Repository Dependencies',
strings_displayed=strings_displayed,
new_tool_panel_section_label='test_1210')
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
strings_displayed = ['emboss_0020',
'Galaxy wrappers for Emboss version 5.0.0 tools',
'user1',
self.url.replace('http://', ''),
installed_repository.installed_changeset_revision]
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
current_datatypes = int(self.get_datatypes_count())
# If we are running this test by itself, installing the emboss repository should also install the emboss_datatypes
# repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes
# have been added, otherwise verify that the count is unchanged.
if running_standalone:
assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.'
else:
assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.'
[docs] def test_0015_uninstall_emboss_repository(self):
'''Uninstall the emboss repository.'''
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
self.uninstall_repository(installed_repository)
strings_not_displayed = [installed_repository.name, installed_repository.installed_changeset_revision]
self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
[docs] def test_0020_reinstall_emboss_repository(self):
'''Reinstall the emboss repository.'''
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
self.reinstall_repository(installed_repository)
strings_displayed = ['emboss_0020',
'Galaxy wrappers for Emboss version 5.0.0 tools',
'user1',
self.url.replace('http://', ''),
installed_repository.installed_changeset_revision]
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'emboss'])
self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
self.verify_tool_metadata_for_installed_repository(installed_repository)
[docs] def test_0025_deactivate_emboss_repository(self):
'''Deactivate the emboss repository without removing it from disk.'''
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
self.deactivate_repository(installed_repository)
strings_not_displayed = ['emboss_0020',
installed_repository.installed_changeset_revision]
self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
[docs] def test_0030_reactivate_emboss_repository(self):
'''Reactivate the emboss repository and verify that it now shows up in the list of installed repositories.'''
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
self.reactivate_repository(installed_repository)
strings_displayed = ['emboss_0020',
'Galaxy wrappers for Emboss version 5.0.0 tools',
'user1',
self.url.replace('http://', ''),
installed_repository.installed_changeset_revision]
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'emboss'])
self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
self.verify_tool_metadata_for_installed_repository(installed_repository)