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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.'