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Source code for tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies

import os

from ..base.twilltestcase import common, ShedTwillTestCase


[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) admin_user = self.test_db_util.get_galaxy_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_galaxy_private_role(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 0010 category and upload the freebayes repository to the tool shed, if necessary.''' category = self.create_category(name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.') self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository(name='freebayes_0010', description="Galaxy's freebayes tool", long_description="Long description of Galaxy's freebayes tool", owner=common.test_user_1_name, category_id=self.security.encode_id(category.id)) if self.repository_is_new(repository): self.upload_file(repository, filename='freebayes/freebayes.xml', filepath=None, valid_tools_only=False, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded the tool xml.', strings_displayed=['Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf'], strings_not_displayed=[]) self.upload_file(repository, filename='freebayes/tool_data_table_conf.xml.sample', filepath=None, valid_tools_only=False, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded the tool data table sample file.', strings_displayed=[], strings_not_displayed=[]) self.upload_file(repository, filename='freebayes/sam_fa_indices.loc.sample', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool data table .loc file.', strings_displayed=[], strings_not_displayed=[]) self.upload_file(repository, filename=os.path.join('freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml'), filepath=None, valid_tools_only=False, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded malformed tool dependency XML.', strings_displayed=['Exception attempting to parse', 'not well-formed'], strings_not_displayed=[]) self.upload_file(repository, filename=os.path.join('freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml'), filepath=None, valid_tools_only=False, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded invalid tool dependency XML.', strings_displayed=['The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration'], strings_not_displayed=[]) self.upload_file(repository, filename=os.path.join('freebayes', 'tool_dependencies.xml'), filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded valid tool dependency XML.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0010_install_freebayes_repository(self): '''Install the freebayes repository into the Galaxy instance.''' self.galaxy_login(email=common.admin_email, username=common.admin_username) strings_displayed = ['install Tool Shed managed', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18'] self.install_repository('freebayes_0010', common.test_user_1_name, 'Test 0010 Repository With Tool Dependencies', strings_displayed=strings_displayed, new_tool_panel_section_label='test_1210') installed_repository = self.test_db_util.get_installed_repository_by_name_owner('freebayes_0010', common.test_user_1_name) strings_displayed = ['freebayes_0010', "Galaxy's freebayes tool", 'user1', self.url.replace('http://', ''), installed_repository.installed_changeset_revision] self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
[docs] def test_0015_uninstall_freebayes_repository(self): '''Uninstall the freebayes repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner('freebayes_0010', 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_freebayes_repository(self): '''Reinstall the freebayes repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner('freebayes_0010', common.test_user_1_name) self.reinstall_repository(installed_repository) strings_displayed = ['freebayes_0010', "Galaxy's freebayes tool", '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', 'FreeBayes']) 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_freebayes_repository(self): '''Deactivate the freebayes repository without removing it from disk.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner('freebayes_0010', common.test_user_1_name) self.deactivate_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_0030_reactivate_freebayes_repository(self): '''Reactivate the freebayes 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('freebayes_0010', common.test_user_1_name) self.reactivate_repository(installed_repository) strings_displayed = ['freebayes_0010', "Galaxy's freebayes tool", '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', 'FreeBayes']) self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed) self.verify_tool_metadata_for_installed_repository(installed_repository)