Warning

This document is for an in-development version 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_0080_advanced_circular_dependencies

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'


[docs]class TestRepositoryCircularDependencies(ShedTwillTestCase): '''Verify that the code correctly handles circular 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)
[docs] def test_0005_create_column_repository(self): """Create and populate the column_maker repository.""" 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=[]) 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_0005_create_convert_repository(self): """Create and populate the convert_chars repository.""" 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=[]) 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_0020_create_repository_dependencies(self): '''Upload a repository_dependencies.xml file that specifies the current revision of convert_chars_0080 to the column_maker_0080 repository.''' 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_0080', 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)
[docs] def test_0025_create_dependency_on_filtering(self): '''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.''' 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_0080', additional_paths=['convert']) 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_0030_verify_repository_dependencies(self): '''Verify that each repository can depend on the other without causing an infinite loop.''' 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) self.check_repository_dependency(convert_repository, column_repository, self.get_repository_tip(column_repository)) self.check_repository_dependency(column_repository, convert_repository, self.get_repository_tip(convert_repository))
[docs] def test_0035_verify_repository_metadata(self): '''Verify that resetting the metadata does not change it.''' column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name) convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name) for repository in [column_repository, convert_repository]: self.verify_unchanged_repository_metadata(repository)