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Source code for tool_shed.test.functional.test_1020_install_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 for test 0020'
emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020'
base_datatypes_count = 0
repository_datatypes_count = 0
[docs]class ToolWithRepositoryDependencies(ShedTwillTestCase):
'''Test installing a repository with 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)
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)
[docs] def test_0005_ensure_repositories_and_categories_exist(self):
'''Create the 0020 category and any missing repositories.'''
global repository_datatypes_count
category = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Test 0020 Basic Repository 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):
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_browse_tool_shed(self):
"""Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
global base_datatypes_count
self.galaxy_login(email=common.admin_email, username=common.admin_username)
base_datatypes_count = int(self.get_datatypes_count())
self.browse_tool_shed(url=self.url, strings_displayed=['Test 0020 Basic Repository Dependencies'])
category = self.test_db_util.get_category_by_name('Test 0020 Basic Repository Dependencies')
self.browse_category(category, strings_displayed=['emboss_0020'])
self.preview_repository_in_tool_shed('emboss_0020', common.test_user_1_name, strings_displayed=['emboss_0020', 'Valid tools'])
[docs] def test_0015_install_emboss_repository(self):
'''Install the emboss repository without installing tool dependencies.'''
global repository_datatypes_count
global base_datatypes_count
strings_displayed = ['Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package']
self.install_repository('emboss_0020',
common.test_user_1_name,
'Test 0020 Basic Repository Dependencies',
strings_displayed=strings_displayed,
install_tool_dependencies=False,
new_tool_panel_section_label='test_1020')
installed_repository = self.test_db_util.get_installed_repository_by_name_owner('emboss_0020', common.test_user_1_name)
strings_displayed = ['emboss_0020',
'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020',
'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', 'antigenic'])
self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
strings_displayed = ['emboss', '5.0.0', 'package']
self.check_installed_repository_tool_dependencies(installed_repository, strings_displayed=strings_displayed, dependencies_installed=False)
self.verify_tool_metadata_for_installed_repository(installed_repository)
current_datatypes = int(self.get_datatypes_count())
assert current_datatypes > base_datatypes_count, 'Installing emboss did not add new datatypes. Expected: %d. Found: %d' % \
(base_datatypes_count + repository_datatypes_count, current_datatypes)
[docs] def test_0020_verify_installed_repository_metadata(self):
'''Verify that resetting the metadata on an installed repository does not change the metadata.'''
self.verify_installed_repository_metadata_unchanged('emboss_0020', common.test_user_1_name)
[docs] def test_0025_deactivate_datatypes_repository(self):
'''Deactivate the emboss_datatypes repository without removing it from disk.'''
global repository_datatypes_count
global base_datatypes_count
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(datatypes_repository_name, common.test_user_1_name)
old_datatypes_count = int(self.get_datatypes_count())
self.deactivate_repository(installed_repository)
current_datatypes = int(self.get_datatypes_count())
assert current_datatypes < old_datatypes_count, 'Uninstalling emboss did not remove datatypes.'
[docs] def test_0030_reactivate_datatypes_repository(self):
'''Reactivate the datatypes repository and verify that the datatypes are again present.'''
global repository_datatypes_count
global base_datatypes_count
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(datatypes_repository_name, common.test_user_1_name)
self.reactivate_repository(installed_repository)
current_datatypes = int(self.get_datatypes_count())
assert current_datatypes > base_datatypes_count, 'Reactivating emboss did not add new datatypes.'