1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a91d8ea3c9e2/ changeset: a91d8ea3c9e2 user: inithello date: 2013-01-09 22:20:07 summary: Tool shed functional tests for installing repositories with circular dependencies into separate tool panel sections. affected #: 2 files diff -r a7049f42a9d9b4bef6804dee53a2bc8bcc1a2916 -r a91d8ea3c9e2e9d6cc8cfd85c7085bf1175b4f5c test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -60,6 +60,10 @@ def check_for_valid_tools( self, repository, strings_displayed=[], strings_not_displayed=[] ): strings_displayed.append( 'Valid tools' ) self.display_manage_repository_page( repository, strings_displayed, strings_not_displayed ) + def check_galaxy_repository_db_status( self, repository_name, owner, expected_status ): + installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, owner ) + assert installed_repository.status == expected_status, 'Status in database is %s, expected %s' % \ + ( installed_repository.status, expected_status ) def check_galaxy_repository_tool_panel_section( self, repository, expected_tool_panel_section ): metadata = repository.metadata assert 'tools' in metadata, 'Tools not found in metadata: %s' % metadata diff -r a7049f42a9d9b4bef6804dee53a2bc8bcc1a2916 -r a91d8ea3c9e2e9d6cc8cfd85c7085bf1175b4f5c test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py @@ -0,0 +1,149 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +freebayes_repository_name = 'freebayes_0040' +freebayes_repository_description = "Galaxy's freebayes tool" +freebayes_repository_long_description = "Long description of Galaxy's freebayes tool" + +filtering_repository_name = 'filtering_0040' +filtering_repository_description = "Galaxy's filtering tool" +filtering_repository_long_description = "Long description of Galaxy's filtering tool" + +category_name = 'test_0040_repository_circular_dependencies' + +running_standalone = False + +class TestInstallingCircularDependencies( ShedTwillTestCase ): + '''Verify that the code correctly handles installing repositories with circular 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 = 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 = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = 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 = test_db_util.get_private_role( admin_user ) + def test_0005_create_freebayes_repository( self ): + '''Create and populate freebayes_0040.''' + global running_standalone + category = self.create_category( name=category_name, 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_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 ): + running_standalone = True + self.upload_file( repository, + 'freebayes/freebayes.tar', + strings_displayed=[], + commit_message='Uploaded freebayes.tar.' ) + def test_0015_create_filtering_repository( self ): + '''Create and populate filtering_0040.''' + global running_standalone + category = self.create_category( name=category_name, 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_repository_name, + description=filtering_repository_description, + long_description=filtering_repository_long_description, + owner=common.test_user_1_name, + categories=[ 'test_0040_repository_circular_dependencies' ], + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'filtering/filtering_1.1.0.tar', + strings_displayed=[], + commit_message='Uploaded filtering.tar.' ) + def test_0020_create_repository_dependencies( self ): + '''Set up the filtering and freebayes repository dependencies.''' + # The dependency structure should look like: + # Filtering revision 0 -> freebayes revision 0. + # Freebayes revision 0 -> filtering revision 1. + # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes. + global running_standalone + if running_standalone: + repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'filtering' ] ) + self.generate_repository_dependency_xml( [ repository ], + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), + dependency_description='Filtering 1.1.0 depends on the freebayes repository.' ) + self.upload_file( filtering_repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded dependency on freebayes' ) + repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'freebayes' ] ) + self.generate_repository_dependency_xml( [ repository ], + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), + dependency_description='Freebayes depends on the filtering repository.' ) + self.upload_file( freebayes_repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded dependency on filtering' ) + def test_0025_install_freebayes_repository( self ): + '''Install freebayes with blank tool panel section, without tool dependencies but with repository dependencies.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + 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 ) + def test_0030_uninstall_freebayes_repository( self ): + '''Uninstall freebayes, verify tool panel section and missing repository dependency.''' + installed_freebayes_repository = test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) + installed_filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) + self.uninstall_repository( installed_freebayes_repository, remove_from_disk=True ) + test_db_util.ga_refresh( installed_freebayes_repository ) + self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, '' ) + strings_displayed = [ 'Missing repository', 'freebayes' ] + self.display_installed_repository_manage_page( installed_filtering_repository, strings_displayed=strings_displayed ) + self.check_galaxy_repository_db_status( freebayes_repository_name, + common.test_user_1_name, + 'Uninstalled' ) + def test_0035_reinstall_freebayes_repository( self ): + '''Reinstall freebayes into 'freebayes' tool panel section.''' + installed_freebayes_repository = test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, + common.test_user_1_name ) + self.reinstall_repository( installed_freebayes_repository, + install_tool_dependencies=False, + install_repository_dependencies=True, + new_tool_panel_section='freebayes', + no_changes=False ) + def test_0040_uninstall_filtering_repository( self ): + '''Uninstall filtering, verify tool panel section.''' + installed_filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) + installed_freebayes_repository = test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) + self.uninstall_repository( installed_filtering_repository, remove_from_disk=True ) + test_db_util.ga_refresh( installed_filtering_repository ) + self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, '' ) + strings_displayed = [ 'Missing repository', 'filtering' ] + self.display_installed_repository_manage_page( installed_freebayes_repository, strings_displayed=strings_displayed ) + self.check_galaxy_repository_db_status( filtering_repository_name, + common.test_user_1_name, + 'Uninstalled' ) + def test_0045_uninstall_freebayes_repository( self ): + '''Uninstall freebayes, verify tool panel section and missing repository dependency.''' + installed_freebayes_repository = test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) + installed_filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) + self.uninstall_repository( installed_freebayes_repository, remove_from_disk=True ) + test_db_util.ga_refresh( installed_freebayes_repository ) + self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, 'freebayes' ) + strings_displayed = [ 'Missing repository', 'freebayes' ] + self.display_installed_repository_manage_page( installed_filtering_repository, strings_displayed=strings_displayed ) + self.check_galaxy_repository_db_status( freebayes_repository_name, + common.test_user_1_name, + 'Uninstalled' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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