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Source code for tool_shed.test.functional.test_1080_advanced_circular_dependency_installation
import logging
from ..base.twilltestcase import common, ShedTwillTestCase
column_repository_name = 'column_maker_0080'
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"
convert_repository_name = 'convert_chars_0080'
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"
category_name = 'Test 0080 Advanced Circular Dependencies'
category_description = 'Test circular dependency features'
log = logging.getLogger(__name__)
running_standalone = False
[docs]class TestRepositoryDependencies(ShedTwillTestCase):
'''Testing uninstalling and reinstalling repository dependencies, and setting tool panel sections.'''
[docs] def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an 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)
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_and_populate_column_repository(self):
"""Create the category for this test suite, then create and populate column_maker."""
category = self.create_category(name=category_name, description=category_description)
global running_standalone
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=column_repository_name,
description=column_repository_description,
long_description=column_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):
self.upload_file(repository,
filename='column_maker/column_maker.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded column_maker tarball.',
strings_displayed=[],
strings_not_displayed=[])
running_standalone = True
[docs] def test_0010_create_and_populate_convert_repository(self):
'''Create and populate the convert_chars repository.'''
global running_standalone
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=convert_repository_name,
description=convert_repository_description,
long_description=convert_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):
self.upload_file(repository,
filename='convert_chars/convert_chars.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded convert_chars tarball.',
strings_displayed=[],
strings_not_displayed=[])
running_standalone = True
[docs] def test_0015_upload_dependency_xml_if_needed(self):
'''If this test is being run by itself, it will not have repository dependencies configured yet.'''
global running_standalone
if running_standalone:
convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path('test_1080', additional_paths=['convert'])
repository_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
self.create_repository_dependency(repository=column_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
repository_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
self.create_repository_dependency(repository=convert_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
[docs] def test_0020_install_convert_repository(self):
'''Install convert_chars without repository dependencies into convert_chars tool panel section.'''
self.galaxy_login(email=common.admin_email, username=common.admin_username)
self.install_repository(convert_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=False,
new_tool_panel_section_label='convert_chars')
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
browse_strings_displayed = ['convert_chars_0080',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision]
strings_displayed = ['convert_chars_0080',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Missing repository dependencies']
self.display_galaxy_browse_repositories_page(strings_displayed=browse_strings_displayed)
self.display_installed_repository_manage_page(installed_convert_repository,
strings_displayed=strings_displayed)
[docs] def test_0025_install_column_repository(self):
'''Install column maker with repository dependencies into column_maker tool panel section.'''
self.install_repository(column_repository_name,
common.test_user_1_name,
category_name,
install_repository_dependencies=True,
new_tool_panel_section_label='column_maker',
strings_displayed=['install_repository_dependencies'])
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
browse_strings_displayed = ['convert_chars_0080',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
'Add column',
installed_column_repository.installed_changeset_revision]
strings_displayed = ['column_maker_0080',
'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies']
self.display_galaxy_browse_repositories_page(strings_displayed=browse_strings_displayed)
self.display_installed_repository_manage_page(installed_column_repository,
strings_displayed=strings_displayed)
[docs] def test_0030_deactivate_convert_repository(self):
'''Deactivate convert_chars, verify that column_maker is installed and missing repository dependencies.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.deactivate_repository(installed_convert_repository)
strings_displayed = ['column_maker_0080',
'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Missing repository dependencies',
'Deactivated']
self.display_installed_repository_manage_page(installed_column_repository,
strings_displayed=strings_displayed)
[docs] def test_0035_reactivate_convert_repository(self):
'''Reactivate convert_chars, both convert_chars and column_maker should now show as installed.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.reactivate_repository(installed_convert_repository)
strings_displayed = ['convert_chars_0080',
'Compute',
'an expression on every row',
'1.1.0',
'column_maker_0080',
'Installed repository dependencies',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
installed_convert_repository.installed_changeset_revision]
self.display_installed_repository_manage_page(installed_column_repository,
strings_displayed=strings_displayed)
[docs] def test_0040_deactivate_column_repository(self):
'''Deactivate column_maker, verify that convert_chars is installed and missing repository dependencies.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.deactivate_repository(installed_column_repository)
strings_displayed = ['convert_chars_0080',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Missing repository dependencies',
'Deactivated']
self.display_installed_repository_manage_page(installed_convert_repository,
strings_displayed=strings_displayed)
[docs] def test_0045_deactivate_convert_repository(self):
'''Deactivate convert_chars, verify that both convert_chars and column_maker are deactivated.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.deactivate_repository(installed_convert_repository)
strings_not_displayed = ['column_maker_0080',
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision]
self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
[docs] def test_0050_reactivate_column_repository(self):
'''Reactivate column_maker. This should not automatically reactivate convert_chars, so column_maker should be displayed as installed but missing repository dependencies.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.reactivate_repository(installed_column_repository)
strings_displayed = ['column_maker_0080',
'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Missing repository dependencies',
'Deactivated']
self.display_installed_repository_manage_page(installed_column_repository,
strings_displayed=strings_displayed)
[docs] def test_0055_reactivate_convert_repository(self):
'''Activate convert_chars. Both convert_chars and column_maker should now show as installed.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.reactivate_repository(installed_convert_repository)
strings_displayed = ['column_maker_0080',
'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies']
self.display_installed_repository_manage_page(installed_column_repository,
strings_displayed=strings_displayed)
strings_displayed = ['convert_chars_0080',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies']
self.display_installed_repository_manage_page(installed_convert_repository,
strings_displayed=strings_displayed)
[docs] def test_0060_uninstall_column_repository(self):
'''Uninstall column_maker. Verify that convert_chars is installed and missing repository dependencies.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.uninstall_repository(installed_column_repository)
strings_displayed = ['convert_chars_0080',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Missing repository dependencies',
'Uninstalled']
self.display_installed_repository_manage_page(installed_convert_repository,
strings_displayed=strings_displayed)
self.test_db_util.install_session.refresh(installed_column_repository)
[docs] def test_0065_reinstall_column_repository(self):
'''Reinstall column_maker without repository dependencies, verify both convert_chars and column_maker are installed.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.reinstall_repository(installed_column_repository, install_repository_dependencies=False)
strings_displayed = ['column_maker_0080',
'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies']
self.display_installed_repository_manage_page(installed_column_repository,
strings_displayed=strings_displayed)
strings_displayed = ['convert_chars_0080',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies']
self.display_installed_repository_manage_page(installed_convert_repository,
strings_displayed=strings_displayed)
[docs] def test_0070_uninstall_convert_repository(self):
'''Uninstall convert_chars, verify column_maker installed but missing repository dependencies.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.deactivate_repository(installed_convert_repository)
strings_displayed = ['column_maker_0080',
'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Missing repository dependencies',
'Deactivated']
self.display_installed_repository_manage_page(installed_column_repository,
strings_displayed=strings_displayed)
self.test_db_util.install_session.refresh(installed_convert_repository)
[docs] def test_0075_uninstall_column_repository(self):
'''Uninstall column_maker, verify that both convert_chars and column_maker are uninstalled.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.deactivate_repository(installed_column_repository)
strings_displayed = ['convert_chars_0080',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Missing repository dependencies',
'Activate or reinstall repository',
'Deactivated']
self.display_installed_repository_manage_page(installed_convert_repository,
strings_displayed=strings_displayed)
[docs] def test_0080_reinstall_convert_repository(self):
'''Reinstall convert_chars with repository dependencies, verify that this installs both convert_chars and column_maker.'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
common.test_user_1_name)
self.reinstall_repository(installed_convert_repository,
install_repository_dependencies=True,
no_changes=False)
strings_displayed = ['column_maker_0080',
'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies']
self.display_installed_repository_manage_page(installed_column_repository,
strings_displayed=strings_displayed)
strings_displayed = ['convert_chars_0080',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies']
self.display_installed_repository_manage_page(installed_convert_repository,
strings_displayed=strings_displayed)