from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os emboss_datatypes_repository_name = 'emboss_datatypes_0050' emboss_datatypes_repository_description = "Datatypes for emboss" emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes" emboss_repository_name = 'emboss_0050' emboss_repository_description = "Galaxy's emboss tool" emboss_repository_long_description = "Long description of Galaxy's emboss tool" filtering_repository_name = 'filtering_0050' filtering_repository_description = "Galaxy's filtering tool" filtering_repository_long_description = "Long description of Galaxy's filtering tool" freebayes_repository_name = 'freebayes_0050' freebayes_repository_description = "Galaxy's freebayes tool" freebayes_repository_long_description = "Long description of Galaxy's freebayes tool" column_repository_name = 'column_maker_0050' column_repository_description = "Add column" column_repository_long_description = "Compute an expression on every row" convert_repository_name = 'convert_chars_0050' convert_repository_description = "Convert delimiters" convert_repository_long_description = "Convert delimiters to tab" bismark_repository_name = 'bismark_0050' bismark_repository_description = "A flexible aligner." bismark_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications." category_name = 'Test 0050 Circular Dependencies 5 Levels' category_description = 'Test circular dependency features' running_standalone = False class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ): '''Verify that the code correctly handles circular dependencies down to n levels.''' 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_convert_repository( self ): '''Create and populate convert_chars_0050.''' category = self.create_category( name=category_name, description=category_description ) global running_standalone self.logout() 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=[] ) if self.repository_is_new( repository ): running_standalone = True 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=[] ) def test_0010_create_column_repository( self ): '''Create and populate convert_chars_0050.''' category = self.create_category( name=category_name, description=category_description ) 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=[] ) if self.repository_is_new( repository ): 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=[] ) def test_0015_create_emboss_datatypes_repository( self ): '''Create and populate emboss_datatypes_0050.''' category = self.create_category( name=category_name, description=category_description ) repository = self.get_or_create_repository( name=emboss_datatypes_repository_name, description=emboss_datatypes_repository_description, long_description=emboss_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( repository ): 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_0020_create_emboss_repository( self ): '''Create and populate emboss_0050.''' category = self.create_category( name=category_name, description=category_description ) 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=[] ) if self.repository_is_new( repository ): self.upload_file( 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 tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0025_create_filtering_repository( self ): '''Create and populate filtering_0050.''' category = self.create_category( name=category_name, description=category_description ) repository = self.get_or_create_repository( name=filtering_repository_name, description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) if self.repository_is_new( repository ): self.upload_file( repository, filename='filtering/filtering_1.1.0.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded filtering 1.1.0 tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0030_create_freebayes_repository( self ): '''Create and populate freebayes_0050.''' category = self.create_category( name=category_name, description=category_description ) repository = self.get_or_create_repository( name=freebayes_repository_name, description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) if self.repository_is_new( repository ): self.upload_file( repository, filename='freebayes/freebayes.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded freebayes tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0035_create_bismark_repository( self ): '''Create and populate bismark_0050.''' category = self.create_category( name=category_name, description=category_description ) repository = self.get_or_create_repository( name=bismark_repository_name, description=bismark_repository_description, long_description=bismark_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) if self.repository_is_new( repository ): self.upload_file( repository, filename='bismark/bismark.tar', filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded bismark tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0040_create_and_upload_dependency_definitions( self ): '''Set up the dependency structure.''' global running_standalone if running_standalone: 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 ) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) bismark_repository = self.test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) dependency_xml_path = self.generate_temp_path( 'test_1050', additional_paths=[ 'dependencies' ] ) # convert_chars depends on column_maker # column_maker depends on convert_chars # emboss depends on emboss_datatypes # emboss_datatypes depends on bismark # freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker # filtering depends on emboss column_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip( column_repository ) ) convert_tuple = ( self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip( convert_repository ) ) freebayes_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) ) emboss_tuple = ( self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip( emboss_repository ) ) datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) bismark_tuple = ( self.url, bismark_repository.name, bismark_repository.user.username, self.get_repository_tip( bismark_repository ) ) self.create_repository_dependency( repository=convert_repository, repository_tuples=[ column_tuple ], filepath=dependency_xml_path ) self.create_repository_dependency( repository=column_repository, repository_tuples=[ convert_tuple ], filepath=dependency_xml_path ) self.create_repository_dependency( repository=datatypes_repository, repository_tuples=[ bismark_tuple ], filepath=dependency_xml_path ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ datatypes_tuple ], filepath=dependency_xml_path ) self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple ], filepath=dependency_xml_path ) self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ emboss_tuple ], filepath=dependency_xml_path ) def test_0045_verify_repository_dependencies( self ): '''Verify that the generated dependency circle does not cause an infinite loop. Expected structure: id: 2 key: http://toolshed.local:10001__ESEP__filtering__ESEP__test__ESEP__871602b4276b ['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04'] id: 3 key: http://toolshed.local:10001__ESEP__emboss_datatypes__ESEP__test__ESEP__dbd4f68bf507 ['http://toolshed.local:10001', 'freebayes', 'test', 'f40028114098'] id: 4 key: http://toolshed.local:10001__ESEP__freebayes__ESEP__test__ESEP__f40028114098 ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507'] ['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04'] ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0'] id: 5 key: http://toolshed.local:10001__ESEP__column_maker__ESEP__test__ESEP__83e956bdbac0 ['http://toolshed.local:10001', 'convert_chars', 'test', 'b28134220c8a'] id: 6 key: http://toolshed.local:10001__ESEP__convert_chars__ESEP__test__ESEP__b28134220c8a ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0'] id: 7 key: http://toolshed.local:10001__ESEP__emboss_5__ESEP__test__ESEP__8de5fe0d7b04 ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507'] ''' emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_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 ) convert_repository = self.test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) bismark_repository = self.test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) self.check_repository_dependency( convert_repository, column_repository ) self.check_repository_dependency( column_repository, convert_repository ) self.check_repository_dependency( emboss_datatypes_repository, bismark_repository ) self.check_repository_dependency( emboss_repository, emboss_datatypes_repository ) self.check_repository_dependency( filtering_repository, emboss_repository ) for repository in [ emboss_datatypes_repository, emboss_repository, column_repository ]: self.check_repository_dependency( freebayes_repository, repository ) freebayes_dependencies = [ freebayes_repository, emboss_datatypes_repository, emboss_repository, column_repository ] strings_displayed = [ '%s depends on %s.' % ( freebayes_repository.name, ', '.join( repo.name for repo in freebayes_dependencies ) ) ] self.display_manage_repository_page( freebayes_repository, strings_displayed=strings_displayed ) def test_0050_verify_tool_dependencies( self ): '''Check that freebayes and emboss display tool dependencies.''' freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) self.display_manage_repository_page( freebayes_repository, strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies' ] ) self.display_manage_repository_page( emboss_repository, strings_displayed=[ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] ) def test_0055_install_column_repository( self ): '''Install column_maker with repository dependencies.''' self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) self.install_repository( column_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label='column_maker' ) # This should result in column_maker and convert_chars being installed, and the rest never installed. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ) ] strings_displayed = [ 'column_maker_0050', 'convert_chars_0050' ] strings_not_displayed = [ 'emboss_datatypes_0050', 'emboss_0050', 'filtering_0050', 'freebayes_0050', 'bismark_0050' ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) self.verify_installed_repositories( installed_repositories=installed_repositories ) def test_0060_install_emboss_repository( self ): '''Install emboss_5 with repository dependencies.''' global running_standalone original_datatypes = self.get_datatypes_count() self.install_repository( emboss_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label='emboss_5_0050' ) if running_standalone: assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.' # Now we have emboss_datatypes, emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed. installed_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), ( column_repository_name, common.test_user_1_name ), ( emboss_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), ( bismark_repository_name, common.test_user_1_name ) ] strings_displayed = [ 'emboss_datatypes_0050', 'emboss_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050' ] strings_not_displayed = [ 'filtering_0050', 'freebayes_0050' ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) self.verify_installed_repositories( installed_repositories ) def test_0065_deactivate_datatypes_repository( self ): '''Deactivate emboss_datatypes and verify that the datatypes count is reduced.''' original_datatypes = self.get_datatypes_count() repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) self.deactivate_repository( repository ) assert original_datatypes > self.get_datatypes_count(), 'Deactivating emboss_datatypes did not remove datatypes.' # Now we have emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, and emboss_datatypes deactivated. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( emboss_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), ( bismark_repository_name, common.test_user_1_name ) ] strings_displayed = [ 'emboss_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050' ] strings_not_displayed = [ 'emboss_datatypes_0050', 'filtering_0050', 'freebayes_0050' ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) self.verify_installed_repositories( installed_repositories ) def test_0070_uninstall_emboss_repository( self ): '''Uninstall the emboss_5 repository.''' repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.uninstall_repository( repository ) strings_not_displayed = [ repository.name, repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) self.test_db_util.ga_refresh( repository ) self.check_galaxy_repository_tool_panel_section( repository, 'emboss_5_0050' ) # Now we have bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, emboss_datatypes deactivated, # and emboss uninstalled. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), ( bismark_repository_name, common.test_user_1_name ) ] strings_displayed = [ 'column_maker_0050', 'convert_chars_0050', 'bismark_0050' ] strings_not_displayed = [ 'emboss_0050', 'emboss_datatypes_0050', 'filtering_0050', 'freebayes_0050' ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) self.verify_installed_repositories( installed_repositories ) def test_0075_install_freebayes_repository( self ): '''Install freebayes with repository dependencies. This should also automatically reactivate emboss_datatypes and reinstall emboss_5.''' original_datatypes = self.get_datatypes_count() strings_displayed = [ 'Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ] self.install_repository( freebayes_repository_name, common.test_user_1_name, category_name, strings_displayed=strings_displayed, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label='freebayes' ) assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.' emboss_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) strings_displayed = [ 'emboss_0050', 'emboss_datatypes_0050', emboss_repository.installed_changeset_revision, datatypes_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) # Installing freebayes should automatically reinstall emboss and reactivate emboss_datatypes. # Now column_maker, convert_chars, emboss, emboss_datatypes, freebayes, and bismark should be installed. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( emboss_datatypes_repository_name, common.test_user_1_name ), ( emboss_repository_name, common.test_user_1_name ), ( freebayes_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), ( bismark_repository_name, common.test_user_1_name ) ] strings_displayed = [ 'emboss_0050', 'emboss_datatypes_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050', 'freebayes_0050' ] strings_not_displayed = [ 'filtering_0050' ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) self.verify_installed_repositories( installed_repositories )