from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import logging log = logging.getLogger( __name__ ) bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100" bwa_package_repository_name = 'package_bwa_0_5_9_0100' bwa_package_repository_description = "BWA Tool" bwa_package_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9." category_name = 'Test 0100 Complex Repository Dependencies' category_description = 'Test 0100 Complex Repository Dependencies' class TestComplexRepositoryDependencies( ShedTwillTestCase ): '''Test features related to complex repository dependencies.''' 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_bwa_package_repository( self ): '''Create and populate package_bwa_0_5_9_0100.''' category = self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) # Create a repository named package_bwa_0_5_9_0100 owned by user1. repository = self.get_or_create_repository( name=bwa_package_repository_name, description=bwa_package_repository_description, long_description=bwa_package_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='bwa/complex/tool_dependencies.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool_dependencies.xml.', strings_displayed=[ 'This repository currently contains a single file named tool_dependencies.xml' ], strings_not_displayed=[] ) # Visit the manage repository page for package_bwa_0_5_9_0100. self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'will not be', 'to this repository' ] ) def test_0010_create_bwa_base_repository( self ): '''Create and populate bwa_base_0100.''' category = self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) # Create a repository named bwa_base_repository_0100 owned by user1. repository = self.get_or_create_repository( name=bwa_base_repository_name, description=bwa_base_repository_description, long_description=bwa_base_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) # Populate the repository named bwa_base_repository_0100 with a bwa_base tool archive. self.upload_file( repository, filename='bwa/complex/bwa_base.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.', strings_displayed=[], strings_not_displayed=[] ) def test_0015_generate_complex_repository_dependency_invalid_shed_url( self ): '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) # The repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = 'http://http://this is not an url!' name = 'package_bwa_0_5_9_0100' owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) strings_displayed = [ 'Repository dependencies are currently supported only within the same tool shed' ] # Populate the dependent repository named bwa_base_repository_0100 with an invalid tool_dependencies.xml file. repository_tuple = ( url, name, owner, changeset_revision ) self.create_repository_dependency( repository=base_repository, filepath=dependency_path, repository_tuples=[ repository_tuple ], strings_displayed=strings_displayed, complex=True, package='bwa', version='0.5.9' ) def test_0020_generate_complex_repository_dependency_invalid_repository_name( self ): '''Generate and upload a complex repository definition that specifies an invalid repository name.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = self.url name = 'invalid_repository!?' owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) strings_displayed = [ 'because the name is invalid' ] # Populate the dependent base_repository named package_bwa_0_5_9_0100 with an invalid tool_dependencies.xml file. repository_tuple = ( url, name, owner, changeset_revision ) self.create_repository_dependency( repository=base_repository, filepath=dependency_path, repository_tuples=[ repository_tuple ], strings_displayed=strings_displayed, complex=True, package='bwa', version='0.5.9' ) def test_0025_generate_complex_repository_dependency_invalid_owner_name( self ): '''Generate and upload a complex repository definition that specifies an invalid owner.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = self.url name = 'package_bwa_0_5_9_0100' owner = 'invalid_owner!?' changeset_revision = self.get_repository_tip( tool_repository ) strings_displayed = [ 'because the owner is invalid.' ] repository_tuple = ( url, name, owner, changeset_revision ) self.create_repository_dependency( repository=base_repository, filepath=dependency_path, repository_tuples=[ repository_tuple ], strings_displayed=strings_displayed, complex=True, package='bwa', version='0.5.9' ) def test_0030_generate_complex_repository_dependency_invalid_changeset_revision( self ): '''Generate and upload a complex repository definition that specifies an invalid changeset revision.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = self.url name = 'package_bwa_0_5_9_0100' owner = 'user1' changeset_revision = '1234abcd' strings_displayed = [ 'because the changeset revision is invalid.' ] repository_tuple = ( url, name, owner, changeset_revision ) self.create_repository_dependency( repository=base_repository, filepath=dependency_path, repository_tuples=[ repository_tuple ], strings_displayed=strings_displayed, complex=True, package='bwa', version='0.5.9' ) def test_0035_generate_complex_repository_dependency( self ): '''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.''' # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] ) url = self.url name = 'package_bwa_0_5_9_0100' owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) repository_tuple = ( url, name, owner, changeset_revision ) self.create_repository_dependency( repository=base_repository, filepath=dependency_path, repository_tuples=[ repository_tuple ], complex=True, package='bwa', version='0.5.9' ) self.check_repository_dependency( base_repository, depends_on_repository=tool_repository ) self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package', changeset_revision ] ) def test_0040_generate_tool_dependency( self ): '''Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.''' # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) # Generate a tool_dependencies.xml file that points to an arbitrary file in the local filesystem. file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( tool_repository, filename=xml_filename, filepath=new_tool_dependency_path, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded new tool_dependencies.xml.', strings_displayed=[], strings_not_displayed=[] ) # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. repository_tip = self.get_repository_tip( tool_repository ) strings_displayed = [ 'bwa', '0.5.9', 'package' ] strings_displayed.append( repository_tip ) strings_not_displayed=[ previous_changeset ] self.display_manage_repository_page( tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) # Visit the manage page of the package_bwa_0_5_9_0100 to confirm the valid tool dependency definition. self.display_manage_repository_page( tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) # Visit the manage page of the bwa_base_repository_0100 to confirm the valid tool dependency definition # and the updated changeset revision (updated tip) of the package_bwa_0_5_9_0100 repository is displayed # as the required repository revision. The original revision defined in the previously uploaded # tool_dependencies.xml file will be updated. self.display_manage_repository_page( base_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )