from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os datatypes_repository_name = 'emboss_datatypes_0030' 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_0030' emboss_5_repository_name = 'emboss_5_0030' emboss_6_repository_name = 'emboss_6_0030' emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030' emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030' class TestRepositoryDependencyRevisions( ShedTwillTestCase ): '''Test dependencies on different revisions of a repository.''' def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() 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' % test_user_1_email test_user_1_private_role = self.test_db_util.get_private_role( test_user_1 ) self.logout() 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' % admin_email admin_user_private_role = self.test_db_util.get_private_role( admin_user ) def test_0005_create_category( self ): """Create a category for this test suite""" self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' ) def test_0010_create_emboss_5_repository( self ): '''Create and populate the emboss_5_0030 repository.''' self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) category = self.test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' ) repository = self.get_or_create_repository( name=emboss_5_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 ) ) self.upload_file( repository, filename='emboss/emboss.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0015_create_emboss_6_repository( self ): '''Create and populate the emboss_6_0030 repository.''' self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) category = self.test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' ) repository = self.get_or_create_repository( name=emboss_6_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 ) ) self.upload_file( repository, filename='emboss/emboss.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0020_create_emboss_datatypes_repository( self ): '''Create and populate the emboss_datatypes_0030 repository.''' self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) category = self.test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' ) repository = self.get_or_create_repository( name=datatypes_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 ) ) self.upload_file( 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=[] ) def test_0025_create_emboss_repository( self ): '''Create and populate the emboss_0030 repository.''' self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) category = self.test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' ) 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 ) ) self.upload_file( repository, filename='emboss/emboss.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded the tool tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0030_generate_repository_dependencies_for_emboss_5( self ): '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.''' datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss5' ] ) datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) self.create_repository_dependency( repository=emboss_5_repository, repository_tuples=[ datatypes_tuple ], filepath=repository_dependencies_path ) def test_0035_generate_repository_dependencies_for_emboss_6( self ): '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.''' emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss6' ] ) datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) self.create_repository_dependency( repository=emboss_6_repository, repository_tuples=[ datatypes_tuple ], filepath=repository_dependencies_path ) def test_0040_generate_repository_dependency_on_emboss_5( self ): '''Create and upload repository_dependencies.xml for the emboss_5_0030 repository.''' emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '5' ] ) emboss_tuple = ( self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip( emboss_5_repository ) ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ emboss_tuple ], filepath=repository_dependencies_path ) def test_0045_generate_repository_dependency_on_emboss_6( self ): '''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.''' emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '5' ] ) emboss_tuple = ( self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip( emboss_6_repository ) ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ emboss_tuple ], filepath=repository_dependencies_path ) def test_0050_verify_repository_dependency_revisions( self ): '''Verify that different metadata revisions of the emboss repository have different repository dependencies.''' repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) repository_metadata = [ ( metadata.metadata, metadata.changeset_revision ) for metadata in self.get_repository_metadata( repository ) ] datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) datatypes_tip = self.get_repository_tip( datatypes_repository ) strings_displayed = [] # Iterate through all metadata revisions and check for repository dependencies. for metadata, changeset_revision in repository_metadata: # Add the dependency description and datatypes repository details to the strings to check. strings_displayed = [ 'emboss_datatypes_0030', 'user1', datatypes_tip ] strings_displayed.extend( [ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] ) self.display_manage_repository_page( repository, changeset_revision=changeset_revision, strings_displayed=strings_displayed ) def test_0055_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) for repository in [ emboss_repository, emboss_5_repository, emboss_6_repository, datatypes_repository ]: self.verify_unchanged_repository_metadata( repository )