from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os 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_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga' workflow_name = 'Workflow for 0060_filter_workflow_repository' emboss_datatypes_repository_name = 'emboss_datatypes_0050' emboss_datatypes_repository_description = "Datatypes for emboss" emboss_repository_name = 'emboss_0050' emboss_5_repository_name = 'emboss_5_0050' emboss_6_repository_name = 'emboss_6_0050' 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_0050_name = 'Test 0050 Circular Dependencies 5 Levels' category_0050_description = 'Test circular dependency features' running_standalone = False class TestResetAllRepositoryMetadata( ShedTwillTestCase ): '''Verify that the "Reset selected metadata" feature works.''' 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_filtering_repository( self ): '''Create and populate the filtering_0000 repository.''' global running_standalone self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0000 = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' ) category_0001 = self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name='filtering_0000', description="Galaxy's filtering tool", long_description="Long description of Galaxy's filtering tool", owner=common.test_user_1_name, category_id=self.security.encode_id( category_0000.id ) ) if self.repository_is_new( repository ): running_standalone = True 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=[] ) self.upload_file( repository, filename='filtering/filtering_2.2.0.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded filtering 2.2.0 tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0010_create_freebayes_repository( self ): '''Create and populate the freebayes_0010 repository.''' global running_standalone self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0010 = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name='freebayes_0010', description="Galaxy's freebayes tool", long_description="Long description of Galaxy's freebayes tool", owner=common.test_user_1_name, category_id=self.security.encode_id( category_0010.id ), strings_displayed=[] ) if running_standalone: self.upload_file( repository, filename='freebayes/freebayes.xml', filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded freebayes.xml.', strings_displayed=[], strings_not_displayed=[] ) self.upload_file( repository, filename='freebayes/tool_data_table_conf.xml.sample', filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool_data_table_conf.xml.sample', strings_displayed=[], strings_not_displayed=[] ) self.upload_file( repository, filename='freebayes/sam_fa_indices.loc.sample', filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded sam_fa_indices.loc.sample', strings_displayed=[], strings_not_displayed=[] ) self.upload_file( repository, filename='freebayes/tool_dependencies.xml', filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool_dependencies.xml', strings_displayed=[], strings_not_displayed=[] ) def test_0015_create_datatypes_0020_repository( self ): '''Create and populate the emboss_datatypes_0020 repository.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0020 = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name='emboss_datatypes_0020', description=datatypes_repository_description, long_description=datatypes_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category_0020.id ), strings_displayed=[] ) self.upload_file( repository, filename='emboss/datatypes/datatypes_conf.xml', filepath=None, valid_tools_only=False, 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_0020_repository( self ): '''Create and populate the emboss_0020 repository.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0020 = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name='emboss_0020', description=emboss_repository_long_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category_0020.id ), strings_displayed=[] ) 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.tar', strings_displayed=[], strings_not_displayed=[] ) def test_0025_create_emboss_datatypes_0030_repository( self ): '''Create and populate the emboss_0030 repository.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0030', description=datatypes_repository_description, long_description=datatypes_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category_0030.id ), strings_displayed=[] ) self.upload_file( datatypes_repository, filename='emboss/datatypes/datatypes_conf.xml', filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded datatypes_conf.xml.', strings_displayed=[], strings_not_displayed=[] ) def test_0030_create_emboss_5_repository( self ): '''Create and populate the emboss_5_0030 repository.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) emboss_5_repository = self.get_or_create_repository( name='emboss_5_0030', description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category_0030.id ), strings_displayed=[] ) self.upload_file( emboss_5_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=[] ) def test_0035_create_emboss_6_repository( self ): '''Create and populate the emboss_6_0030 repository.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) emboss_6_repository = self.get_or_create_repository( name='emboss_6_0030', description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category_0030.id ), strings_displayed=[] ) self.upload_file( emboss_6_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=[] ) def test_0040_create_emboss_0030_repository( self ): '''Create and populate the emboss_0030 repository.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) emboss_repository = self.get_or_create_repository( name='emboss_0030', description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category_0030.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=[] ) def test_0045_create_repository_dependencies_for_0030( self ): '''Create the dependency structure for test 0030.''' global running_standalone if running_standalone: datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0030', common.test_user_1_name ) emboss_repository = self.test_db_util.get_repository_by_name_and_owner( 'emboss_0030', common.test_user_1_name ) emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner( 'emboss_5_0030', common.test_user_1_name ) emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner( 'emboss_6_0030', common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss' ] ) datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) emboss_5_tuple = ( self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip( emboss_5_repository ) ) emboss_6_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_5_repository, repository_tuples=[ datatypes_tuple ], filepath=repository_dependencies_path ) self.create_repository_dependency( repository=emboss_6_repository, repository_tuples=[ datatypes_tuple ], filepath=repository_dependencies_path ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ emboss_5_tuple ], filepath=repository_dependencies_path ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ emboss_6_tuple ], filepath=repository_dependencies_path ) def test_0050_create_freebayes_repository( self ): '''Create and populate the freebayes_0040 repository.''' global running_standalone self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0040 = self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name='freebayes_0040', description="Galaxy's freebayes tool", long_description="Long description of Galaxy's freebayes tool", owner=common.test_user_1_name, category_id=self.security.encode_id( category_0040.id ), strings_displayed=[] ) if running_standalone: 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_0055_create_filtering_repository( self ): '''Create and populate the filtering_0040 repository.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0040 = self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name='filtering_0040', description="Galaxy's filtering tool", long_description="Long description of Galaxy's filtering tool", owner=common.test_user_1_name, category_id=self.security.encode_id( category_0040.id ), strings_displayed=[] ) 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_0060_create_dependency_structure( self ): '''Create the dependency structure for test 0040.''' global running_standalone if running_standalone: freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name ) filtering_repository = self.test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0340', additional_paths=[ 'dependencies' ] ) freebayes_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) ) filtering_tuple = ( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) ) self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ freebayes_tuple ], filepath=repository_dependencies_path ) self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ filtering_tuple ], filepath=repository_dependencies_path ) def test_0065_create_convert_repository( self ): '''Create and populate convert_chars_0050.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category = self.create_category( name=category_0050_name, description=category_0050_description ) 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=[] ) 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_0070_create_column_repository( self ): '''Create and populate convert_chars_0050.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category = self.create_category( name=category_0050_name, description=category_0050_description ) self.logout() 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=[] ) def test_0075_create_emboss_datatypes_repository( self ): '''Create and populate emboss_datatypes_0050.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category = self.create_category( name=category_0050_name, description=category_0050_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name=emboss_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=[] ) 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_0080_create_emboss_repository( self ): '''Create and populate emboss_0050.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category = self.create_category( name=category_0050_name, description=category_0050_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) 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( 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_0085_create_filtering_repository( self ): '''Create and populate filtering_0050.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category = self.create_category( name=category_0050_name, description=category_0050_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) filtering_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=[] ) self.upload_file( filtering_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_0090_create_freebayes_repository( self ): '''Create and populate freebayes_0050.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category = self.create_category( name=category_0050_name, description=category_0050_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) 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=[] ) 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_0095_create_bismark_repository( self ): '''Create and populate bismark_0050.''' global running_standalone if running_standalone: self.logout() self.login( email=common.admin_email, username=common.admin_username ) category = self.create_category( name=category_0050_name, description=category_0050_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) 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=[] ) 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_0100_create_and_upload_dependency_definitions( self ): '''Create the dependency structure for test 0050.''' global running_standalone if running_standalone: self.logout() self.login( email=common.test_user_1_email, username=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 ) 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_0050', additional_paths=[ 'freebayes' ] ) # 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_0105_create_filtering_repository( self ): '''Create and populate the filtering_0060 repository.''' self.logout() self.login( email=common.admin_email, username=common.admin_username ) category_0060 = self.create_category( name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) workflow_repository = self.get_or_create_repository( name='filtering_0060', description="Galaxy's filtering tool", long_description="Long description of Galaxy's filtering tool", owner=common.test_user_1_name, category_id=self.security.encode_id( category_0060.id ), strings_displayed=[] ) if self.repository_is_new( workflow_repository ): workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read() workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) ) workflow_filepath = self.generate_temp_path( 'test_0360', additional_paths=[ 'filtering_workflow' ] ) if not os.path.exists( workflow_filepath ): os.makedirs( workflow_filepath ) file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow ) self.upload_file( workflow_repository, filename=workflow_filename, filepath=workflow_filepath, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded filtering workflow.', strings_displayed=[], strings_not_displayed=[] ) self.upload_file( workflow_repository, filename='filtering/filtering_2.2.0.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded filtering 2.2.0 tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0110_reset_metadata_on_all_repositories( self ): '''Reset metadata on all repositories, then verify that it has not changed.''' self.logout() self.login( email=common.admin_email, username=common.admin_username ) old_metadata = dict() new_metadata = dict() repositories = self.test_db_util.get_all_repositories() for repository in repositories: old_metadata[ self.security.encode_id( repository.id ) ] = dict() for metadata in self.get_repository_metadata( repository ): old_metadata[ self.security.encode_id( repository.id ) ][ metadata.changeset_revision ] = metadata.metadata self.reset_metadata_on_selected_repositories( old_metadata.keys() ) for repository in repositories: new_metadata[ self.security.encode_id( repository.id ) ] = dict() for metadata in self.get_repository_metadata( repository ): new_metadata[ self.security.encode_id( repository.id ) ][ metadata.changeset_revision ] = metadata.metadata if old_metadata[ self.security.encode_id( repository.id ) ] != new_metadata[ self.security.encode_id( repository.id ) ]: raise AssertionError( 'Metadata changed after reset for repository %s.' % repository.name )