1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/324d023bbf59/ Changeset: 324d023bbf59 User: inithello Date: 2013-05-03 21:25:20 Summary: Explicitly uninstall all installed repositories after each set of tests has finished running. This prevents certain edge cases from interfering with subsequent tests. Affected #: 2 files

diff -r e5577cd833abbd0ad072d55f4b56d1458105991b -r 324d023bbf59aafb4be03cbb9842456aab0a1965 test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py --- a/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py +++ b/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py @@ -3,8 +3,10 @@ from install_and_test_tool_shed_repositories.base.twilltestcase import InstallTestRepository log = logging.getLogger(__name__)

+ class InstallTestRepositories( InstallTestRepository ): """Abstract test case that installs and uninstalls a predefined list of repositories.""" + def do_installation( self, repository_info_dict ): self.logout() self.login( email='test@bx.psu.edu', username='test' ) @@ -73,7 +75,7 @@ return test_install_repository test_method = make_uninstall_method( repository_dict ) test_method.__doc__ = "Uninstall the repository %s." % repository_dict[ 'name' ] - namespace[ 'install_repository_%s' % repository_dict[ 'name' ] ] = test_method + namespace[ 'uninstall_repository_%s' % repository_dict[ 'name' ] ] = test_method # The new.classobj function returns a new class object, with name name, derived # from baseclasses (which should be a tuple of classes) and with namespace dict. new_class_obj = new.classobj( name, baseclasses, namespace )

diff -r e5577cd833abbd0ad072d55f4b56d1458105991b -r 324d023bbf59aafb4be03cbb9842456aab0a1965 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -179,19 +179,26 @@ return passed_tests return []

-def execute_uninstall_method( repository_dict ): - # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them - # and try to re-run the tests after uninstalling the repository, which will cause false failure reports, - # since the test data has been deleted from disk by now. - tests_to_delete = [] - for key in test_toolbox.__dict__: - if key.startswith( 'TestForTool_' ): - log.info( 'Tool test found in test_toolbox, deleting: %s' % key ) - tests_to_delete.append( key ) - for key in tests_to_delete: - del test_toolbox.__dict__[ key ] - # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. - test_install_repositories.generate_uninstall_method( repository_dict ) +def execute_uninstall_method( app ): + # Clean out any generated tests. + remove_generated_tests( app ) + sa_session = app.model.context.current + repositories_to_uninstall = sa_session.query( app.model.ToolShedRepository ).all() + for repository in repositories_to_uninstall: + if repository.status == app.model.ToolShedRepository.states.UNINSTALLED: + continue + if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, + app.model.ToolShedRepository.installation_status.ERROR, + app.model.ToolShedRepository.installation_status.INSTALLED ]: + repository.status = app.model.ToolShedRepository.installation_status.ERROR + sa_session.add( repository ) + sa_session.flush() + name = str( repository.name ) + owner = str( repository.owner ) + changeset_revision = str( repository.installed_changeset_revision ) + repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. + test_install_repositories.generate_uninstall_method( repository_dict ) # Set up nose to run the generated uninstall method as a functional test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) @@ -309,6 +316,25 @@ else: return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False )

+def remove_generated_tests( app ): + # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them + # and try to re-run the tests after uninstalling the repository, which will cause false failure reports, + # since the test data has been deleted from disk by now. + tests_to_delete = [] + global test_toolbox + for key in test_toolbox.__dict__: + if key.startswith( 'TestForTool_' ): + log.info( 'Tool test found in test_toolbox, deleting: %s' % key ) + # We can't delete this test just yet, we're still iterating over __dict__. + tests_to_delete.append( key ) + tool_id = key.replace( 'TestForTool_', '' ) + if tool_id in app.toolbox.tools_by_id: + # But we can remove the relevant tool from app.toolbox.tools_by_id. + del app.toolbox.tools_by_id[ tool_id ] + for key in tests_to_delete: + # Now delete the tests found in the previous loop. + del test_toolbox.__dict__[ key ] + def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) test_config.plugins.addPlugin( ReportResults() ) @@ -417,12 +443,12 @@ global_conf = { '__file__' : 'universe_wsgi.ini.sample' } if not database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_max_overflow' ] = '20' + kwargs[ 'database_engine_option_pool_size' ] = '10' app = UniverseApplication( admin_users = 'test@bx.psu.edu', allow_user_creation = True, allow_user_deletion = True, allow_library_path_paste = True, database_connection = database_connection, - database_engine_option_pool_size = '10', datatype_converters_config_file = "datatype_converters_conf.xml.sample", file_path = galaxy_file_path, global_conf = global_conf, @@ -546,7 +572,14 @@ # it will record the result of the tests, and if any failed, the traceback and captured output of the tool that was run. # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with # the next repository's functional tests. + keep_skipping = True for repository_info_dict in detailed_repository_list: + if repository_info_dict[ 'name' ] == 'simsearch' and repository_info_dict[ 'changeset_revision' ] == '430f55978191': + keep_skipping = False + if keep_skipping: + continue + if repository_info_dict[ 'name' ] == 'sortmerna': + continue """ Each repository_info_dict looks something like: { @@ -575,10 +608,13 @@ metadata_revision_id = repository_info_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_info_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url - log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) ) # Get the name and owner out of the repository info dict. - name = repository_info_dict[ 'name' ] - owner = repository_info_dict[ 'owner' ] + name = str( repository_info_dict[ 'name' ] ) + owner = str( repository_info_dict[ 'owner' ] ) + log.info( "Installing and testing revision %s of repository id %s (%s/%s)..." % \ + ( str( changeset_revision ), str( repository_id ), owner, name ) ) + # Explicitly clear tests from twill's test environment. + remove_generated_tests( app ) # Use the repository information dict to generate an install method that will install the repository into the embedded # Galaxy application, with tool dependencies and repository dependencies, if any. test_install_repositories.generate_install_method( repository_info_dict ) @@ -661,7 +697,7 @@ register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - execute_uninstall_method( repository_info_dict ) + execute_uninstall_method( app ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) @@ -675,6 +711,8 @@ os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port + # Explicitly clear tests from twill's test environment. + remove_generated_tests( app ) # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. test_toolbox.toolbox = app.toolbox # Generate the test methods for this installed repository. We need to pass in True here, or it will look @@ -751,14 +789,23 @@ register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) log.debug( 'Revision %s of repository %s installed successfully, but did not pass functional tests.' % \ ( changeset_revision, name ) ) - # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the + # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - success = execute_uninstall_method( repository_info_dict ) + log.debug( 'Uninstalling changeset revision %s of repository %s' % \ + ( repository_info_dict[ 'changeset_revision' ], repository_info_dict[ 'name' ] ) ) + success = execute_uninstall_method( app ) + if not success: + log.error( 'Repository %s failed to uninstall.' ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: + # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. + log.debug( 'Uninstalling repository %s' % repository_info_dict[ 'name' ] ) + success = execute_uninstall_method( app ) + if not success: + log.error( 'Repository %s failed to uninstall.' ) repositories_failed_install.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - log.debug( 'Repository %s failed to install correctly.' % name ) + log.debug( 'Repository %s failed to install correctly.' % repository_info_dict[ 'name' ] ) except: log.exception( "Failure running tests" )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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