1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/0de3c7e7d632/ Changeset: 0de3c7e7d632 User: greg Date: 2013-12-20 17:13:20 Summary: Eliminate the need for deactivating or uninstalling repositories in order to manage the tools loaded into app.toolbox within the tool shed's install and test framework. Affected #: 5 files

diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -128,17 +128,6 @@ del( kwd[ field_name ] ) return kwd

- def uninstall_repository( self, repository ): - """Uninstall a repository.""" - # A repository can be uninstalled only if no dependent repositories are installed. - url = '/admin_toolshed/deactivate_or_uninstall_repository?id=%s' % self.security.encode_id( repository.id ) - self.visit_url( url ) - tc.fv ( 1, "remove_from_disk", 'true' ) - tc.submit( 'deactivate_or_uninstall_repository_button' ) - strings_displayed = [ 'The repository named' ] - strings_displayed.append( 'has been uninstalled' ) - self.check_for_strings( strings_displayed, strings_not_displayed=[] ) - def visit_url( self, url, allowed_codes=[ 200 ] ): new_url = tc.go( url ) return_code = tc.browser.get_code()

diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -518,8 +518,6 @@ repository_dict, params, can_update_tool_shed ) - # Uninstall this repository since it is missing dependencies. - uninstall_repository_and_repository_dependencies( app, repository_dict )

def initialize_install_and_test_statistics_dict( test_framework ): # Initialize a dictionary for the summary that will be printed to stdout. @@ -591,7 +589,7 @@ log.exception( error_message ) return repository, error_message

-def is_excluded( exclude_list_dicts, name, owner, changeset_revision ): +def is_excluded( exclude_list_dicts, name, owner, changeset_revision, encoded_repository_metadata_id ): """ Return True if the repository defined by the received name, owner, changeset_revision should be excluded from testing for any reason. @@ -606,7 +604,7 @@ return True, reason # Skip this repository if it has a repository dependency that is in the exclude list. repository_dependency_dicts, error_message = \ - get_repository_dependencies_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + get_repository_dependencies_for_changeset_revision( galaxy_tool_shed_url, encoded_repository_metadata_id ) if error_message: log.debug( 'Error getting repository dependencies for revision %s of repository %s owned by %s:' % \ @@ -800,96 +798,3 @@ test_runner = plug_runner result = test_runner.run( tests ) return result, test_config.plugins._plugins - -def uninstall_repository_and_repository_dependencies( app, repository_dict ): - """Uninstall a repository and all of its repository dependencies.""" - # This method assumes that the repositor defined by the received repository_dict is not a repository - # dependency of another repository. - sa_session = app.install_model.context - # The dict contains the only repository the app should have installed at this point. - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - # Since this install and test framework uninstalls repositories immediately after installing and testing - # them, the values of repository.installed_changeset_revision and repository.changeset_revision should be - # the same. - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - if repository.can_uninstall( app ): - # A repository can be uninstalled only if no dependent repositories are installed. So uninstallation order - # id critical. A repository is always uninstalled first, and the each of its dependencies is checked to see - # if it can be uninstalled. - uninstall_repository_dict = dict( name=name, - owner=owner, - changeset_revision=changeset_revision ) - log.debug( 'Revision %s of repository %s owned by %s selected for uninstallation.' % ( changeset_revision, name, owner ) ) - try: - test_install_repositories.generate_uninstall_method( uninstall_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 ) - # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed - # repository and all of its repository dependencies, deleting each of them from disk. - result, _ = run_tests( test_config ) - repository_uninstall_successful = result.wasSuccessful() - except Exception, e: - repository_uninstall_successful = False - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - if repository_uninstall_successful: - # Now that the repository is uninstalled we can attempt to uninstall each of its repository dependencies. - # We have to do this through Twill in order to maintain app.toolbox and shed_tool_conf.xml in a state that - # is valid for future tests. Since some of the repository's repository dependencies may require other of - # the repository's repository dependencies, we'll keep track of the repositories we've been able to unistall. - processed_repository_dependency_ids = [] - while len( processed_repository_dependency_ids ) < len( repository.repository_dependencies ): - for repository_dependency in repository.repository_dependencies: - if repository_dependency.id not in processed_repository_dependency_ids and repository_dependency.can_uninstall( app ): - processed_repository_dependency_ids.append( repository_dependency.id ) - rd_name = str( repository_dependency.name ) - rd_owner = str( repository_dependency.owner ) - rd_changeset_revision = str( repository_dependency.changeset_revision ) - uninstall_repository_dict = dict( name=rd_name, - owner=rd_owner, - changeset_revision=rd_changeset_revision ) - log.debug( 'Revision %s of repository dependency %s owned by %s selected for uninstallation.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - # Generate a test method to uninstall the repository dependency through the embedded Galaxy application's - # web interface. - try: - test_install_repositories.generate_uninstall_method( uninstall_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 ) - # Run the uninstall method. - result, _ = run_tests( test_config ) - if not result.wasSuccessful(): - # We won't set ok here because we'll continue to uninstall whatever we can. - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - except Exception, e: - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - else: - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) - else: - log_reason_repository_cannot_be_uninstalled( app, repository ) - -def uninstall_tool_dependency( app, tool_dependency ): - """Attempt to uninstall a tool dependency.""" - sa_session = app.install_model.context - # Clean out any generated tests. This is necessary for Twill. - tool_dependency_install_path = tool_dependency.installation_directory( app ) - uninstalled, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) - if error_message: - log.debug( 'Error attempting to remove directory: %s' % str( tool_dependency_install_path ) ) - log.debug( error_message ) - else: - log.debug( 'Successfully removed tool dependency installation directory: %s' % str( tool_dependency_install_path ) ) - if not uninstalled or tool_dependency.status != app.model.ToolDependency.installation_status.UNINSTALLED: - tool_dependency.status = app.model.ToolDependency.installation_status.UNINSTALLED - sa_session.add( tool_dependency ) - sa_session.flush() - if os.path.exists( tool_dependency_install_path ): - log.debug( 'Uninstallation of tool dependency succeeded, but the installation path still exists on the filesystem. It is now being explicitly deleted.') - suc.remove_dir( tool_dependency_install_path ) -

diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af 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 @@ -9,21 +9,6 @@ class InstallTestRepositories( InstallTestRepository ): """Abstract test case that installs and uninstalls a predefined list of repositories."""

- def do_deactivate( self, repository_dict ): - self.logout() - self.login( email='test@bx.psu.edu', username='test' ) - admin_user = test_db_util.get_user( 'test@bx.psu.edu' ) - assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email - # Get the repository defined by the received repository_dict along with all of its repository dependencies - # from the database. - name = repository_dict[ 'name' ] - owner = repository_dict[ 'owner' ] - changeset_revision = repository_dict[ 'changeset_revision' ] - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - admin_user_private_role = test_db_util.get_private_role( admin_user ) - # Uninstall the repository through the web interface using twill. - self.deactivate_repository( repository ) - def do_install( self, repository_dict ): self.logout() self.login( email='test@bx.psu.edu', username='test' ) @@ -34,50 +19,6 @@ # actually install more than this singe repository because repository dependencies can be installed. self.install_repository( repository_dict )

- def do_uninstall( self, repository_dict ): - self.logout() - self.login( email='test@bx.psu.edu', username='test' ) - admin_user = test_db_util.get_user( 'test@bx.psu.edu' ) - assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email - # Get the repository defined by the received repository_dict along with all of its repository dependencies - # from the database. - name = repository_dict[ 'name' ] - owner = repository_dict[ 'owner' ] - changeset_revision = repository_dict[ 'changeset_revision' ] - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - admin_user_private_role = test_db_util.get_private_role( admin_user ) - # Uninstall the repository and all of its repository dependencies through the Galaxy web interface using twill. - self.uninstall_repository( repository ) - -def generate_deactivate_method( repository_dict=None ): - """Generate abstract test cases for the received repository_dict.""" - if repository_dict is None: - return - # Push all the toolbox tests to module level - G = globals() - # Eliminate all previous tests from G. - for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestForTool_' ): - del G[ key ] - # Create a new subclass with a method named install_repository_XXX that deactivates the - # repository specified by the received repository_dict. - name = "TestDeactivateRepository_%s_%s" % \ - ( str( repository_dict[ 'name' ] ), str( repository_dict[ 'changeset_revision' ] ) ) - baseclasses = ( InstallTestRepositories, ) - namespace = dict() - def make_deactivate_method( repository_dict ): - def test_deactivate_repository( self ): - self.do_deactivate( repository_dict ) - return test_deactivate_repository - test_method = make_deactivate_method( repository_dict ) - test_method.__doc__ = "Deactivate the repository %s." % str( repository_dict[ 'name' ] ) - namespace[ 'uninstall_repository_%s_%s' % ( str( repository_dict[ 'name' ] ), - str( repository_dict[ 'changeset_revision' ] ) ) ] = 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( str( name ), baseclasses, namespace ) - G[ name ] = new_class_obj - def generate_install_method( repository_dict=None ): """Generate abstract test cases for the defined list of repositories.""" if repository_dict is None: @@ -104,32 +45,3 @@ # from baseclasses (which should be a tuple of classes) and with namespace dict. new_class_obj = new.classobj( str( name ), baseclasses, namespace ) G[ name ] = new_class_obj - -def generate_uninstall_method( repository_dict=None ): - """Generate abstract test cases for the received repository_dict.""" - if repository_dict is None: - return - # Push all the toolbox tests to module level - G = globals() - # Eliminate all previous tests from G. - for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestForTool_' ): - del G[ key ] - # Create a new subclass with a method named install_repository_XXX that installs the repository - # specified by the received repository_dict. - name = "TestUninstallRepository_%s_%s" % \ - ( str( repository_dict[ 'name' ] ), str( repository_dict[ 'changeset_revision' ] ) ) - baseclasses = ( InstallTestRepositories, ) - namespace = dict() - def make_uninstall_method( repository_dict ): - def test_uninstall_repository( self ): - self.do_uninstall( repository_dict ) - return test_uninstall_repository - test_method = make_uninstall_method( repository_dict ) - test_method.__doc__ = "Uninstall the repository %s." % repository_dict[ 'name' ] - namespace[ 'uninstall_repository_%s_%s' % ( str( repository_dict[ 'name' ] ), - str( repository_dict[ 'changeset_revision' ] ) ) ] = 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( str( name ), baseclasses, namespace ) - G[ name ] = new_class_obj

diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -76,7 +76,7 @@ can_update_tool_shed = True

test_framework = install_and_test_base_util.REPOSITORIES_WITH_TOOLS - + def get_failed_test_dicts( test_result, from_tool_test=True ): """Extract any useful data from the test_result.failures and test_result.errors attributes.""" failed_test_dicts = [] @@ -177,7 +177,11 @@ log.debug( error_message ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) - is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, name, owner, changeset_revision ) + is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, + name, + owner, + changeset_revision, + encoded_repository_metadata_id ) if is_excluded: # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) @@ -193,28 +197,15 @@ ( changeset_revision, name, owner ) ) else: tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) - # Explicitly clear tests from twill's test environment. - remove_generated_tests( app ) # Proceed with installing repositories and testing contained tools. repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1 if error_message: # The repository installation failed. - log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \ - ( changeset_revision, name, owner ) ) + log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message - # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. - log.debug( 'Attempting to uninstall revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) - try: - repository = \ - test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - except Exception, e: - error_message = 'Unable to find revision %s of repository %s owned by %s: %s.' % \ - ( changeset_revision, name, owner, str( e ) ) - log.exception( error_message ) - params = dict( test_install_error=True, - do_not_test=False ) + params = dict( test_install_error=True ) # TODO: do something useful with response_dict response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, tool_test_results_dicts, @@ -222,19 +213,10 @@ repository_dict, params, can_update_tool_shed ) - try: - # We are uninstalling this repository and all of its repository dependencies. - install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict ) - except Exception, e: - log.exception( 'Error attempting to uninstall revision %s of repository %s owned by %s: %s' % \ - ( changeset_revision, name, owner, str( e ) ) ) - # Clean out any generated tests. This is necessary for Twill. - remove_generated_tests( app ) - install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) + else: + # The repository was successfully installed. log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ ( changeset_revision, name, owner ) ) - else: - # The repository was successfully installed. params, install_and_test_statistics_dict, tool_test_results_dict = \ install_and_test_base_util.register_installed_and_missing_dependencies( app, repository, @@ -257,26 +239,23 @@ tool_test_results_dict=tool_test_results_dict, params=params, can_update_tool_shed=can_update_tool_shed ) - # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. - test_toolbox.toolbox = app.toolbox else: - # This repository and all of its dependencies were successfully installed. - # Configure and run functional tests for this repository. This is equivalent to + log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) + # Generate the shed_tools_dict that specifies the location of test data contained within this repository. + # and configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed - remove_install_tests() - log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) - # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository - # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, - # and the tools_functionally_correct flag to False, as well as updating tool_test_results. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + # Find the path to the test-data directory within the installed repository. has_test_data, shed_tools_dict = \ parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) - # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional - # test framework can find it. + # If the repository has a test-data directory we write the generated shed_tools_dict to a temporary + # file so the functional test framework can find it. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) + # Remove twills' old generated test before building the new tests for the current tools. + remove_tests( app ) try: install_and_test_statistics_dict = test_repository_tools( app, repository, @@ -441,6 +420,8 @@ config_items.append( config_tuple ) # Write a temporary file, based on universe_wsgi.ini.sample, using the configuration options defined above. generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) + # kwargs must be a list when passed to the Galaxy webapp (i.e., UniverseApplication). + # The following is used to set metadata externally. kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] # Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh. kwargs[ 'global_conf' ] = install_and_test_base_util.get_webapp_global_conf() @@ -581,46 +562,45 @@ # Return a "successful" response to buildbot. return 0

-def remove_generated_tests( app ): +def remove_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 = [] - tools_to_delete = [] + tools_to_delete_by_id = [] global test_toolbox + # Find all tests previously generated by twill. for key in test_toolbox.__dict__: if key.startswith( 'TestForTool_' ): - log.debug( 'Tool test found in test_toolbox, deleting: %s' % str( key ) ) + log.debug( 'Tool test %s discovered in test_toolbox.' % str( 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_', '' ) - for tool in app.toolbox.tools_by_id: - if tool.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ): - tools_to_delete.append( tool ) + for app_tool_id in app.toolbox.tools_by_id: + if app_tool_id.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ): + tools_to_delete_by_id.append( tool_id ) + # Delete the discovered twill-generated tests. for key in tests_to_delete: - # Now delete the tests found in the previous loop. - del test_toolbox.__dict__[ key ] - for tool in tools_to_delete: - del app.toolbox.tools_by_id[ tool ] - -def remove_install_tests(): - """ - Delete any configured repository installation tests from the test_toolbox.__dict__, otherwise nose will find them - and try to install the repository again while running tool functional tests. - """ - tests_to_delete = [] - global test_toolbox + if key in test_toolbox.__dict__: + log.debug( 'Deleting test %s from test_toolbox.' % str( key ) ) + del test_toolbox.__dict__[ key ] + for tool_id in tools_to_delete_by_id: + if tool_id in app.toolbox.tools_by_id: + log.debug( 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) ) + del app.toolbox.tools_by_id[ tool_id ] # Push all the toolbox tests to module level for key in test_install_repositories.__dict__: if key.startswith( 'TestInstallRepository_' ): - log.debug( 'Repository installation process found, deleting: %s' % str( key ) ) + log.debug( 'Repository installation process test %s discovered.' % str( key ) ) # We can't delete this test just yet, we're still iterating over __dict__. tests_to_delete.append( key ) + # Delete the discovered twill-generated tests. for key in tests_to_delete: - # Now delete the tests found in the previous loop. - del test_install_repositories.__dict__[ key ] + if key in test_install_repositories.__dict__: + log.debug( 'Deleting test %s from test_toolbox.' % str( key ) ) + del test_install_repositories.__dict__[ key ]

def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, install_and_test_statistics_dict ): @@ -629,7 +609,9 @@ owner = str( repository.owner ) changeset_revision = str( repository.changeset_revision ) repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) - # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. + # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the + # appropriate test methods. At this point, app.toolbox contains the upload tool and all tools contained + # in the repository. test_toolbox.toolbox = app.toolbox # Generate the test methods for this installed repository. We need to pass in True here, or it will look # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. @@ -692,15 +674,6 @@ can_update_tool_shed ) log.debug( 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ ( changeset_revision, name, owner ) ) - # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the - # repository using Twill. - log.debug( 'Uninstalling changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) - # We are uninstalling this repository and all of its repository dependencies. - install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict ) - # Clean out any generated tests. This is necessary for Twill. - remove_generated_tests( app ) - # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. - test_toolbox.toolbox = app.toolbox return install_and_test_statistics_dict

if __name__ == "__main__":

diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -115,7 +115,11 @@ log.debug( error_message ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) - is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, name, owner, changeset_revision ) + is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, + name, + owner, + changeset_revision, + encoded_repository_metadata_id ) if this_repository_is_in_the_exclude_list or requires_excluded: # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=reason )

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

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