Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for tool_shed.test.functional.test_1090_repository_dependency_handling
import logging
from ..base.twilltestcase import common, ShedTwillTestCase
column_repository_name = 'column_maker_1085'
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"
convert_repository_name = 'convert_chars_1085'
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"
category_name = 'Test 1085 Advanced Circular Dependencies'
category_description = 'Test circular dependency features'
log = logging.getLogger(__name__)
[docs]class TestRepositoryDependencies(ShedTwillTestCase):
'''Testing the behavior of repository dependencies with 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 a category for this test suite and add repositories to it."""
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=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=[])
[docs] def test_0010_create_and_populate_convert_repository(self):
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=[])
[docs] def test_0015_create_and_upload_dependency_files(self):
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_1085', additional_paths=['column'])
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_repositories(self):
'''Install column_maker into column_maker tool panel section and install repository dependencies.'''
self.galaxy_login(email=common.admin_email, username=common.admin_username)
self.install_repository(column_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
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_1085',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_1085',
'Add column',
installed_column_repository.installed_changeset_revision]
strings_displayed = ['convert_chars_1085',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_1085',
installed_column_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_convert_repository,
strings_displayed=strings_displayed)
[docs] def test_0025_uninstall_column_repository(self):
'''uninstall column_maker, verify same section'''
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)
self.test_db_util.ga_refresh(installed_column_repository)
self.check_galaxy_repository_tool_panel_section(installed_column_repository, 'column_maker')
[docs] def test_0030_uninstall_convert_repository(self):
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
self.uninstall_repository(installed_convert_repository)
self.test_db_util.ga_refresh(installed_convert_repository)
self.check_galaxy_repository_tool_panel_section(installed_convert_repository, 'column_maker')
[docs] def test_0035_reinstall_column_repository(self):
'''reinstall column_maker into new section 'new_column_maker' (no_changes = false), no dependencies'''
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_tool_dependencies=False,
install_repository_dependencies=False,
new_tool_panel_section_label='new_column_maker',
no_changes=False)
strings_displayed = ['column_maker_1085',
'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision]
self.display_installed_repository_manage_page(installed_column_repository,
strings_displayed=strings_displayed)
[docs] def test_0040_reinstall_convert_repository(self):
'''reinstall convert_chars into new section 'new_convert_chars' (no_changes = false), no dependencies'''
installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
common.test_user_1_name)
self.reinstall_repository(installed_convert_repository,
install_tool_dependencies=False,
install_repository_dependencies=False,
new_tool_panel_section_label='new_convert_chars',
no_changes=False)
strings_displayed = ['convert_chars_1085',
'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision]
self.display_installed_repository_manage_page(installed_convert_repository,
strings_displayed=strings_displayed)
# The following check fails somewhere around 5% of the time maybe on Jenkins.
# https://jenkins.galaxyproject.org/job/docker-toolshed/5578/
# https://jenkins.galaxyproject.org/job/docker-toolshed/5198/
# def test_0045_uninstall_and_verify_tool_panel_sections( self ):
# '''uninstall both and verify tool panel sections'''
# 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_convert_repository )
# self.uninstall_repository( installed_column_repository )
# self.test_db_util.ga_refresh( installed_convert_repository )
# self.test_db_util.ga_refresh( installed_column_repository )
# self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'new_column_maker' )
# self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'new_convert_chars' )