galaxy-commits December 2013

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commit/galaxy-central: greg: 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.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

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(a)bx.psu.edu', username='test' ) - admin_user = test_db_util.get_user( 'test(a)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(a)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(a)bx.psu.edu', username='test' ) - admin_user = test_db_util.get_user( 'test(a)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/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/882d74715634/ Changeset: 882d74715634 Branch: ccat3 User: BjoernGruening Date: 2013-11-11 10:09:54 Summary: add dependency of type package to the ccat wrapper Affected #: 1 file diff -r ea6ff3d7224db5d218eefa91af1b08626229eae1 -r 882d7471563422315959211baf12e89ae0e94a29 tools/peak_calling/ccat_wrapper.xml --- a/tools/peak_calling/ccat_wrapper.xml +++ b/tools/peak_calling/ccat_wrapper.xml @@ -10,6 +10,7 @@ '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command><requirements><requirement type="binary" version="3.0">CCAT</requirement> + <requirement type="package" version="3.0">CCAT</requirement></requirements><inputs><param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > https://bitbucket.org/galaxy/galaxy-central/commits/446d410097fd/ Changeset: 446d410097fd Branch: ccat3 User: BjoernGruening Date: 2013-11-11 10:10:41 Summary: remove ccat_2_wrapper.xml, afaik it is not used anymore Affected #: 1 file diff -r 882d7471563422315959211baf12e89ae0e94a29 -r 446d410097fd99711d3ef3160f8fd4e74f9d1a94 tools/peak_calling/ccat_2_wrapper.xml --- a/tools/peak_calling/ccat_2_wrapper.xml +++ /dev/null @@ -1,130 +0,0 @@ -<tool id="peakcalling_ccat2" name="CCAT" version="0.0.1"> - <description>Control-based ChIP-seq Analysis Tool</description> - <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' - #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': - '$input_advanced_config_file' - #else: - '${ options_type.input_config_file.fields.path }' - #end if - 'CCAT in Galaxy' - '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> - <requirements> - <requirement type="binary">CCAT</requirement> - </requirements> - <inputs> - <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > - <validator type="unspecified_build" /> - </param> - <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" > - <validator type="unspecified_build" /> - </param> - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"> - <param name="input_config_file" type="select" label="Select a pre-defined configuration file"> - <options from_data_table="ccat_configurations"> - <validator type="no_options" message="No configurations are available"/> - </options> - </param> - </when> - <when value="advanced"> - <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> - <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> - <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> - <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > - <option value="1">Transition from sense strand to anti-sense strand</option> - <option value="0" selected="True">Local maximum of read-enrichment profile</option> - </param> - <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> - <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> - <param name="random_seed" type="integer" label="Random Seed" value="123456"/> - <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> - <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> - </outputs> - <configfiles> - <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': -fragmentSize ${options_type[ 'fragment_size' ]} -slidingWinSize ${options_type[ 'sliding_window_size' ]} -movingStep ${options_type[ 'moving_step' ]} -isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} -minCount ${options_type[ 'min_count' ]} -outputNum ${options_type[ 'output_num' ]} -randomSeed ${options_type[ 'random_seed' ]} -minScore ${options_type[ 'min_score' ]} -bootstrapPass ${options_type[ 'bootstrap_pass' ]} -#end if</configfile> - </configfiles> - <tests> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="basic" /> - <param name="input_config_file" value="ccat_2.0_histone_config" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="advanced" /> - <param name="fragment_size" value="200" /> - <param name="sliding_window_size" value="500" /> - <param name="moving_step" value="50" /> - <param name="is_strand_sensitive_mode" value="0" /> - <param name="min_count" value="4" /> - <param name="output_num" value="100000" /> - <param name="random_seed" value="123456" /> - <param name="min_score" value="3.0" /> - <param name="bootstrap_pass" value="50" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - </tests> - <help> -**What it does** - -This tool allows ChIP-seq peak/region calling using CCAT. - -View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. - ------- - -**Citation** - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - - </help> -</tool> https://bitbucket.org/galaxy/galaxy-central/commits/936b96845324/ Changeset: 936b96845324 Branch: ccat3 User: BjoernGruening Date: 2013-11-11 15:35:45 Summary: remove binary dependency Affected #: 1 file diff -r 446d410097fd99711d3ef3160f8fd4e74f9d1a94 -r 936b96845324311668e5ee82761ed18a551a9fa1 tools/peak_calling/ccat_wrapper.xml --- a/tools/peak_calling/ccat_wrapper.xml +++ b/tools/peak_calling/ccat_wrapper.xml @@ -9,7 +9,6 @@ 'CCAT in Galaxy' '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command><requirements> - <requirement type="binary" version="3.0">CCAT</requirement><requirement type="package" version="3.0">CCAT</requirement></requirements><inputs> https://bitbucket.org/galaxy/galaxy-central/commits/0fb6c5d7312a/ Changeset: 0fb6c5d7312a User: natefoo Date: 2013-12-20 16:23:16 Summary: Merged in BjoernGruening/galaxy-central-bgruening/ccat3 (pull request #257) Adding requirement tag to the ccat wrapper and remove old ccat2 wrapper. Affected #: 1 file diff -r 2fcb2c12183df5ee7ec96d0f1a253c23448e4410 -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 tools/peak_calling/ccat_2_wrapper.xml --- a/tools/peak_calling/ccat_2_wrapper.xml +++ /dev/null @@ -1,130 +0,0 @@ -<tool id="peakcalling_ccat2" name="CCAT" version="0.0.1"> - <description>Control-based ChIP-seq Analysis Tool</description> - <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' - #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': - '$input_advanced_config_file' - #else: - '${ options_type.input_config_file.fields.path }' - #end if - 'CCAT in Galaxy' - '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> - <requirements> - <requirement type="binary">CCAT</requirement> - </requirements> - <inputs> - <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > - <validator type="unspecified_build" /> - </param> - <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" > - <validator type="unspecified_build" /> - </param> - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"> - <param name="input_config_file" type="select" label="Select a pre-defined configuration file"> - <options from_data_table="ccat_configurations"> - <validator type="no_options" message="No configurations are available"/> - </options> - </param> - </when> - <when value="advanced"> - <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> - <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> - <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> - <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > - <option value="1">Transition from sense strand to anti-sense strand</option> - <option value="0" selected="True">Local maximum of read-enrichment profile</option> - </param> - <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> - <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> - <param name="random_seed" type="integer" label="Random Seed" value="123456"/> - <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> - <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> - </outputs> - <configfiles> - <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': -fragmentSize ${options_type[ 'fragment_size' ]} -slidingWinSize ${options_type[ 'sliding_window_size' ]} -movingStep ${options_type[ 'moving_step' ]} -isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} -minCount ${options_type[ 'min_count' ]} -outputNum ${options_type[ 'output_num' ]} -randomSeed ${options_type[ 'random_seed' ]} -minScore ${options_type[ 'min_score' ]} -bootstrapPass ${options_type[ 'bootstrap_pass' ]} -#end if</configfile> - </configfiles> - <tests> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="basic" /> - <param name="input_config_file" value="ccat_2.0_histone_config" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="advanced" /> - <param name="fragment_size" value="200" /> - <param name="sliding_window_size" value="500" /> - <param name="moving_step" value="50" /> - <param name="is_strand_sensitive_mode" value="0" /> - <param name="min_count" value="4" /> - <param name="output_num" value="100000" /> - <param name="random_seed" value="123456" /> - <param name="min_score" value="3.0" /> - <param name="bootstrap_pass" value="50" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - </tests> - <help> -**What it does** - -This tool allows ChIP-seq peak/region calling using CCAT. - -View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. - ------- - -**Citation** - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - - </help> -</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Refactor method to determine excluded repositories in the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2fcb2c12183d/ Changeset: 2fcb2c12183d User: greg Date: 2013-12-20 16:05:57 Summary: Refactor method to determine excluded repositories in the tool shed's install and test framework. Affected #: 3 files diff -r bedb1e48e5c724d817f1a695ed068e0745f066cd -r 2fcb2c12183df5ee7ec96d0f1a253c23448e4410 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 @@ -591,6 +591,41 @@ log.exception( error_message ) return repository, error_message +def is_excluded( exclude_list_dicts, name, owner, changeset_revision ): + """ + Return True if the repository defined by the received name, owner, changeset_revision should + be excluded from testing for any reason. + """ + for exclude_dict in exclude_list_dicts: + reason = exclude_dict[ 'reason' ] + exclude_repositories = exclude_dict[ 'repositories' ] + # 'repositories': + # [( name, owner, changeset_revision if changeset_revision else None ), + # ( name, owner, changeset_revision if changeset_revision else None )] + if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: + 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, + encoded_repository_metadata_id ) + if error_message: + log.debug( 'Error getting repository dependencies for revision %s of repository %s owned by %s:' % \ + ( changeset_revision, name, owner ) ) + log.debug( error_message ) + else: + for repository_dependency_dict in repository_dependency_dicts: + rd_name = repository_dependency_dict[ 'name' ] + rd_owner = repository_dependency_dict[ 'owner' ] + rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] + if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ + ( rd_name, rd_owner, None ) in exclude_repositories: + reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) + return True, reason + break + return False, None + + def is_latest_downloadable_revision( url, repository_dict ): name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) diff -r bedb1e48e5c724d817f1a695ed068e0745f066cd -r 2fcb2c12183df5ee7ec96d0f1a253c23448e4410 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 @@ -151,33 +151,15 @@ # [{ 'reason': The default reason or the reason specified in this section, # 'repositories': [( name, owner, changeset_revision if changeset_revision else None ), # ( name, owner, changeset_revision if changeset_revision else None )]}] - exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file ) + exclude_list_dicts = install_and_test_base_util.parse_exclude_list( exclude_list_file ) else: - exclude_list = [] + exclude_list_dicts = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was # started up, installing repository and tool dependencies. Upon successful installation, generate a test case for each # functional test defined for each tool in the repository and execute the test cases. Record the result of the tests. # The traceback and captured output of the tool that was run will be recored for test failures. After all tests have # completed, the repository is uninstalled, so test cases don't interfere with the next repository's functional tests. for repository_dict in repositories_to_install: - # Each repository_dict looks something like: - # { "changeset_revision": "13fa22a258b5", - # "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", - # "deleted": false, - # "deprecated": false, - # "description": "Convert column case.", - # "downloadable": true, - # "id": "529fd61ab1c6cc36", - # "long_description": "This tool takes the specified columns and converts them to uppercase or lowercase.", - # "malicious": false, - # "name": "change_case", - # "owner": "test", - # "private": false, - # "repository_id": "529fd61ab1c6cc36", - # "times_downloaded": 0, - # "tool_shed_url": "http://toolshed.local:10001", - # "url": "/api/repository_revisions/529fd61ab1c6cc36", - # "user_id": "529fd61ab1c6cc36" } encoded_repository_metadata_id = repository_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_dict[ 'tool_shed_url' ] = install_and_test_base_util.galaxy_tool_shed_url @@ -195,43 +177,10 @@ log.debug( error_message ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) - # See if this repository should be skipped for any reason. - this_repository_is_in_the_exclude_list = False - requires_excluded = False - skip_reason = None - for exclude_dict in exclude_list: - reason = exclude_dict[ 'reason' ] - exclude_repositories = exclude_dict[ 'repositories' ] - # 'repositories': - # [( name, owner, changeset_revision if changeset_revision else None ), - # ( name, owner, changeset_revision if changeset_revision else None )] - if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: - this_repository_is_in_the_exclude_list = True - skip_reason = reason - break - if not this_repository_is_in_the_exclude_list: - # Skip this repository if it has a repository dependency that is in the exclude list. - repository_dependency_dicts, error_message = \ - install_and_test_base_util.get_repository_dependencies_for_changeset_revision( install_and_test_base_util.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:' % \ - ( changeset_revision, name, owner ) ) - log.debug( error_message ) - else: - for repository_dependency_dict in repository_dependency_dicts: - rd_name = repository_dependency_dict[ 'name' ] - rd_owner = repository_dependency_dict[ 'owner' ] - rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] - if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ - ( rd_name, rd_owner, None ) in exclude_repositories: - skip_reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) - requires_excluded = True - break - if this_repository_is_in_the_exclude_list or requires_excluded: + is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, name, owner, changeset_revision ) + if is_excluded: # If this repository is being skipped, register the reason. - tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) + tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) # 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, diff -r bedb1e48e5c724d817f1a695ed068e0745f066cd -r 2fcb2c12183df5ee7ec96d0f1a253c23448e4410 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 @@ -98,24 +98,6 @@ # The traceback and captured output of the tool that was run will be recored for test failures. After all tests have # completed, the repository is uninstalled, so test cases don't interfere with the next repository's functional tests. for repository_dict in repositories_to_install: - # Each repository_dict looks something like: - # { "changeset_revision": "13fa22a258b5", - # "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", - # "deleted": false, - # "deprecated": false, - # "description": "Convert column case.", - # "downloadable": true, - # "id": "529fd61ab1c6cc36", - # "long_description": "This tool takes the specified columns and converts them to uppercase or lowercase.", - # "malicious": false, - # "name": "change_case", - # "owner": "test", - # "private": false, - # "repository_id": "529fd61ab1c6cc36", - # "times_downloaded": 0, - # "tool_shed_url": "http://toolshed.local:10001", - # "url": "/api/repository_revisions/529fd61ab1c6cc36", - # "user_id": "529fd61ab1c6cc36" } encoded_repository_metadata_id = repository_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_dict[ 'tool_shed_url' ] = install_and_test_base_util.galaxy_tool_shed_url @@ -133,43 +115,10 @@ log.debug( error_message ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) - # See if this repository should be skipped for any reason. - this_repository_is_in_the_exclude_list = False - requires_excluded = False - skip_reason = None - for exclude_dict in exclude_list_dicts: - reason = exclude_dict[ 'reason' ] - exclude_repositories = exclude_dict[ 'repositories' ] - # 'repositories': - # [( name, owner, changeset_revision if changeset_revision else None ), - # ( name, owner, changeset_revision if changeset_revision else None )] - if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: - this_repository_is_in_the_exclude_list = True - skip_reason = reason - break - if not this_repository_is_in_the_exclude_list: - # Skip this repository if it has a repository dependency that is in the exclude list. - repository_dependency_dicts, error_message = \ - install_and_test_base_util.get_repository_dependencies_for_changeset_revision( install_and_test_base_util.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:' % \ - ( changeset_revision, name, owner ) ) - log.debug( error_message ) - else: - for repository_dependency_dict in repository_dependency_dicts: - rd_name = repository_dependency_dict[ 'name' ] - rd_owner = repository_dependency_dict[ 'owner' ] - rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] - if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ - ( rd_name, rd_owner, None ) in exclude_repositories: - skip_reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) - requires_excluded = True - break + is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, name, owner, changeset_revision ) 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=skip_reason ) + tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) # 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, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Fix for install_and_test_statistics_dict being set to None when a repository's tool dependencies were determined to be unsuccessfully installed.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bedb1e48e5c7/ Changeset: bedb1e48e5c7 User: inithello Date: 2013-12-20 15:55:14 Summary: Fix for install_and_test_statistics_dict being set to None when a repository's tool dependencies were determined to be unsuccessfully installed. Affected #: 1 file diff -r c77a66edf25294e1743cc0a3886f8062db5c1fff -r bedb1e48e5c724d817f1a695ed068e0745f066cd 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 @@ -300,15 +300,14 @@ tool_test_results_dict[ 'missing_test_components' ] = [] missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) if missing_tool_dependencies or repository.missing_repository_dependencies: - install_and_test_statistics_dict = \ - install_and_test_base_util.handle_missing_dependencies( app=app, - repository=repository, - missing_tool_dependencies=missing_tool_dependencies, - repository_dict=repository_dict, - tool_test_results_dicts=tool_test_results_dicts, - tool_test_results_dict=tool_test_results_dict, - params=params, - can_update_tool_shed=can_update_tool_shed ) + install_and_test_base_util.handle_missing_dependencies( app=app, + repository=repository, + missing_tool_dependencies=missing_tool_dependencies, + repository_dict=repository_dict, + tool_test_results_dicts=tool_test_results_dicts, + 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: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Make the tool shed's install and test exclude list locally accessible rather than stored in cfengine.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c77a66edf252/ Changeset: c77a66edf252 User: greg Date: 2013-12-20 15:50:03 Summary: Make the tool shed's install and test exclude list locally accessible rather than stored in cfengine. Affected #: 4 files diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r c77a66edf25294e1743cc0a3886f8062db5c1fff lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py --- a/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py +++ b/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py @@ -197,7 +197,16 @@ test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) tool_test_results_dict[ 'test_environment' ] = test_environment_dict - repository_metadata.tool_test_results = tool_test_results_dict + # Store only the configured number of test runs. + num_tool_test_results_saved = int( app.config.num_tool_test_results_saved ) + if len( tool_test_results_dicts ) >= num_tool_test_results_saved: + test_results_index = num_tool_test_results_saved - 1 + new_tool_test_results_dicts = tool_test_results_dicts[ :test_results_index ] + else: + new_tool_test_results_dicts = [ d for d in tool_test_results_dicts ] + # Insert the new element into the first position in the list. + new_tool_test_results_dicts.insert( 0, tool_test_results_dict ) + repository_metadata.tool_test_results = new_tool_test_results_dicts app.sa_session.add( repository_metadata ) app.sa_session.flush() stop = time.time() diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r c77a66edf25294e1743cc0a3886f8062db5c1fff 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 @@ -41,16 +41,6 @@ self.shed_tools_dict = {} self.home() - def deactivate_repository( self, repository ): - """Deactivate a repository.""" - 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", 'false' ) - tc.submit( 'deactivate_or_uninstall_repository_button' ) - strings_displayed = [ 'The repository named' ] - strings_displayed.append( 'has been deactivated' ) - self.check_for_strings( strings_displayed, strings_not_displayed=[] ) - def initiate_installation_process( self, install_tool_dependencies=False, install_repository_dependencies=True, diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r c77a66edf25294e1743cc0a3886f8062db5c1fff 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 @@ -63,12 +63,11 @@ # Here's the directory where everything happens. Temporary directories are created within this directory to contain # the database, new repositories, etc. galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' ) +# File containing information about problematic repositories to exclude from test runs. +exclude_list_file = os.path.join( test_home_directory, 'exclude.xml' ) default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -# This file is copied to the Galaxy root directory by buildbot. -# It is managed by cfengine and is not locally available. -exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'repositories_with_tools_exclude.xml' ) # This script can be run in such a way that no Tool Shed database records should be changed. if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: @@ -138,25 +137,20 @@ return tool_id, tool_version def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): + # Initialize a dictionary for the summary that will be printed to stdout. install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict( test_framework ) error_message = '' - # Initialize a dictionary for the summary that will be printed to stdout. - total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] repositories_to_install, error_message = \ install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework ) if error_message: return None, error_message # Handle repositories not to be tested. if os.path.exists( exclude_list_file ): - # Entries in the exclude_list look something like this. - # { 'reason': The default reason or the reason specified in this section, - # 'repositories': - # [( name, owner, changeset revision if changeset revision else None ), - # ( name, owner, changeset revision if changeset revision else None )] } - # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified - # revision should be skipped. - log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ - str( exclude_list_file ) ) + log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % str( exclude_list_file ) ) + # The following exclude_list will look something like this: + # [{ 'reason': The default reason or the reason specified in this section, + # 'repositories': [( name, owner, changeset_revision if changeset_revision else None ), + # ( name, owner, changeset_revision if changeset_revision else None )]}] exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file ) else: exclude_list = [] diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r c77a66edf25294e1743cc0a3886f8062db5c1fff 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 @@ -61,12 +61,11 @@ # Here's the directory where everything happens. Temporary directories are created within this directory to contain # the database, new repositories, etc. galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' ) +# File containing information about problematic repositories to exclude from test runs. +exclude_list_file = os.path.join( test_home_directory, 'exclude.xml' ) default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -# This file is copied to the Galaxy root directory by buildbot. -# It is managed by cfengine and is not locally available. -exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'tool_dependency_definition_exclude.xml' ) # This script can be run in such a way that no Tool Shed database records should be changed. if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: @@ -77,29 +76,15 @@ test_framework = install_and_test_base_util.TOOL_DEPENDENCY_DEFINITIONS def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): + # Initialize a dictionary for the summary that will be printed to stdout. install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict( test_framework ) error_message = '' - # Initialize a dictionary for the summary that will be printed to stdout. - total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] repositories_to_install, error_message = \ install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework ) if error_message: return None, error_message - # Handle repositories not to be tested. if os.path.exists( exclude_list_file ): - # Entries in the exclude_list look something like this. - # { 'reason': The default reason or the reason specified in this section, - # 'repositories': - # [( name, owner, changeset revision if changeset revision else None ), - # ( name, owner, changeset revision if changeset revision else None )] } - # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified - # revision should be skipped. - # We are testing deprecated repositories because it is possible that a deprecated repository contains valid tools that - # someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are - # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted - # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. - log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ - str( exclude_list_file ) ) + log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % str( exclude_list_file ) ) # The following exclude_list will look something like this: # [{ 'reason': The default reason or the reason specified in this section, # 'repositories': [( name, owner, changeset_revision if changeset_revision else None ), @@ -201,19 +186,9 @@ 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 ) # TODO: do something useful with response_dict @@ -223,14 +198,6 @@ 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 ) ) ) - log.debug( 'Installation failed 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 = \ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for testing repositories with tools using the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3e2b61de5a23/ Changeset: 3e2b61de5a23 User: greg Date: 2013-12-20 03:20:57 Summary: Fix for testing repositories with tools using the tool shed's install and test framework. Affected #: 1 file diff -r 9e9746198fd8c49380d42a2b4657ef241dda8f6a -r 3e2b61de5a2322563c1ffa49e03c118144f5068c 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 @@ -155,10 +155,6 @@ # ( name, owner, changeset revision if changeset revision else None )] } # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified # revision should be skipped. - # We are testing deprecated repositories because it is possible that a deprecated repository contains valid tools that - # someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are - # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted - # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ str( exclude_list_file ) ) exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file ) @@ -739,7 +735,9 @@ tool_test_results_dict[ 'failed_tests' ] = failed_test_dicts failed_repository_dict = repository_identifier_dict install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( failed_repository_dict ) - set_do_not_test = not is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, repository_dict ) + set_do_not_test = \ + not install_and_test_base_util.is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, + repository_dict ) params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Re-add changeset_revision to the information returned from the tool shed's repository_dependencies api method.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9e9746198fd8/ Changeset: 9e9746198fd8 User: greg Date: 2013-12-19 23:30:29 Summary: Re-add changeset_revision to the information returned from the tool shed's repository_dependencies api method. Affected #: 1 file diff -r 7701d6b5e1b62f501e827a3cc6ee880e8955f036 -r 9e9746198fd8c49380d42a2b4657ef241dda8f6a lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -91,6 +91,8 @@ tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] repository_dependency = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_dependency_dict = repository_dependency.to_dict( view='element', value_mapper=value_mapper ) + # We have to add the changeset_revision of of the repository dependency. + repository_dependency_dict[ 'changeset_revision' ] = changeset_revision repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', action='show', id=trans.security.encode_id( repository_dependency.id ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Code cleanup for the tool shed's new repository_revisions' repository_dependencies method.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7701d6b5e1b6/ Changeset: 7701d6b5e1b6 User: greg Date: 2013-12-19 23:22:32 Summary: Code cleanup for the tool shed's new repository_revisions' repository_dependencies method. Affected #: 1 file diff -r f8e9f9f0f64d853fe6db058b6c4ffaa9e497c781 -r 7701d6b5e1b62f501e827a3cc6ee880e8955f036 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -79,6 +79,8 @@ :param id: the encoded id of the `RepositoryMetadata` object """ # Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb12… + value_mapper = { 'id' : trans.security.encode_id, + 'user_id' : trans.security.encode_id } repository_dependencies_dicts = [] try: repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) @@ -87,22 +89,12 @@ rd_tups = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] for rd_tup in rd_tups: tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] - repository_dependencies_dict = dict( tool_shed=str( tool_shed ), - name=str( name ), - owner=str( owner ), - changeset_revision=str( changeset_revision ) ) - rd = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - encoded_rd_id = trans.security.encode_id( rd.id ) - rd_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, - encoded_rd_id, - changeset_revision ) - if rd_repository_metadata is None: - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - rd_repository_metadata = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) - repository_dependencies_dict[ 'url' ] = web.url_for( controller='repository_revisions', - action='show', - id=trans.security.encode_id( rd_repository_metadata.id ) ) - repository_dependencies_dicts.append( repository_dependencies_dict ) + repository_dependency = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + repository_dependency_dict = repository_dependency.to_dict( view='element', value_mapper=value_mapper ) + repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', + action='show', + id=trans.security.encode_id( repository_dependency.id ) ) + repository_dependencies_dicts.append( repository_dependency_dict ) return repository_dependencies_dicts except Exception, e: message = "Error in the Tool Shed repository_revisions API in repository_dependencies: %s" % str( e ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Grids: Add history refresh
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8e9f9f0f64d/ Changeset: f8e9f9f0f64d User: guerler Date: 2013-12-19 22:30:23 Summary: Grids: Add history refresh Affected #: 3 files diff -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c -r f8e9f9f0f64d853fe6db058b6c4ffaa9e497c781 static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -158,7 +158,18 @@ .keyup(function () { $(this).css("font-style", "normal"); }); }); }, - + + // refresh frames + handle_refresh: function (refresh_frames) { + if (refresh_frames) { + if ($.inArray('history', refresh_frames) > -1) { + if( top.Galaxy && top.Galaxy.currHistoryPanel ){ + top.Galaxy.currHistoryPanel.loadCurrentHistory(); + } + } + } + }, + // Initialize init_grid: function(grid_config) { @@ -167,7 +178,10 @@ // get options var options = this.grid.attributes; - + + // handle refresh requests + this.handle_refresh(options.refresh_frames); + // strip protocol and domain var url = this.grid.get('url_base'); url = url.replace(/^.*\/\/[^\/]+/, ''); diff -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c -r f8e9f9f0f64d853fe6db058b6c4ffaa9e497c781 static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh 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value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in t.columns){var f=t.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var s=r.column_config[f.label];var l=s.link;var n=s.value;var q=s.inbound;if(jQuery.type(n)==="string"){n=n.replace(/\/\//g,"/")}var d="";var p="";if(f.attach_popup){d="grid-"+h+"-popup";p="menubutton";if(l!=""){p+=" split"}p+=" popup"}m+="<td "+e+">";if(l){if(t.operations.length!=0){m+='<div id="'+d+'" class="'+p+'" style="float: left;">'}var o="";if(q){o="use-inbound"}else{o="use-outbound"}m+='<a class="label '+o+'" href="'+l+'" onclick="return false;">'+n+"</a>";if(t.operations.length!=0){m+="</div>"}}else{m+='<div id="'+d+'" class="'+p+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+n+"</label></div>"}m+="</td>"}}m+="</tr>";u++}return m},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file +jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var 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q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var 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selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file diff -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c -r f8e9f9f0f64d853fe6db058b6c4ffaa9e497c781 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -15,7 +15,6 @@ return '/base.mako' %><%inherit file="${inherit(context)}"/> -<%namespace file="/refresh_frames.mako" import="handle_refresh_frames" /><%namespace file="/display_common.mako" import="get_class_plural" /><%def name="load(embedded = False, insert = None)"> @@ -67,9 +66,14 @@ 'use_panels' : context.get('use_panels'), 'insert' : insert, 'default_filter_dict' : default_filter_dict, - 'advanced_search' : advanced_search + 'advanced_search' : advanced_search, + 'refresh_frames' : [] } + # add refresh frames + if refresh_frames: + self.grid_config['refresh_frames'] = refresh_frames + ## add current item if exists if current_item: self.grid_config['current_item_id'] = current_item.id @@ -243,7 +247,6 @@ }); </script> - ${handle_refresh_frames()} </%def><%def name="stylesheets()"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhancements and fixes for registering statistics and test results in the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ac5eb19c0bd/ Changeset: 4ac5eb19c0bd User: greg Date: 2013-12-19 21:56:50 Summary: Enhancements and fixes for registering statistics and test results in the tool shed's install and test framework. Affected #: 3 files diff -r 3bbb2f8e43b109b5adc8925a52ed23d9f31cd236 -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c 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 @@ -476,7 +476,7 @@ return global_conf def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, tool_test_results_dicts, - tool_test_results_dict, can_update_tool_shed ): + tool_test_results_dict, params, can_update_tool_shed ): """Handle missing repository or tool dependencies for an installed repository.""" # If a tool dependency fails to install correctly, this should be considered an installation error, # and functional tests should be skipped, since the tool dependency needs to be correctly installed @@ -508,11 +508,9 @@ owner=owner, changeset_revision=changeset_revision, error_message=error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( missing_repository_dependency_info_dict ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ]\ + .append( missing_repository_dependency_info_dict ) # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=True ) # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, @@ -663,6 +661,73 @@ log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) return exclude_list +def register_installed_and_missing_dependencies( app, repository, repository_identifier_dict, install_and_test_statistics_dict, + tool_test_results_dict ): + # The repository was successfully installed. + log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) ) + install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) + tool_test_results_dict[ 'successful_installations' ][ 'current_repository' ].append( repository_identifier_dict ) + params = dict( test_install_error=False, + do_not_test=False ) + if repository.missing_repository_dependencies: + params[ 'test_install_error' ] = True + # Keep statistics for this repository's repository dependencies that resulted in installation errors. + for missing_repository_dependency in repository.missing_repository_dependencies: + tool_shed = str( missing_repository_dependency.tool_shed ) + name = str( missing_repository_dependency.name ) + owner = str( missing_repository_dependency.owner ) + changset_revision = str( missing_repository_dependency.changeset_revision ) + error_message = unicodify( missing_repository_dependency.error_message ) + missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, + name=name, + owner=owner, + changset_revision=changset_revision, + error_message=error_message ) + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( missing_repository_dependency_dict ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( missing_repository_dependency_info_dict ) + if repository.missing_tool_dependencies: + params[ 'test_install_error' ] = True + # Keep statistics for this repository's tool dependencies that resulted in installation errors. + for missing_tool_dependency in repository.missing_tool_dependencies: + name = str( missing_tool_dependency.name ) + type = str( missing_tool_dependency.type ) + version = str( missing_tool_dependency.version ) + error_message = unicodify( missing_tool_dependency.error_message ) + missing_tool_dependency_info_dict = dict( type=type, + name=name, + version=version, + error_message=error_message ) + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) + tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( missing_tool_dependency_info_dict ) + if repository.installed_repository_dependencies: + # Keep statistics for this repository's tool dependencies that resulted in successful installations. + for repository_dependency in repository.installed_repository_dependencies: + tool_shed = str( repository_dependency.tool_shed ) + name = str( repository_dependency.name ) + owner = str( repository_dependency.owner ) + changeset_revision = str( repository_dependency.changeset_revision ) + repository_dependency_info_dict = dict( tool_shed=tool_shed, + name=name, + owner=owner, + changeset_revision=changeset_revision ) + install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_dependency_info_dict ) + tool_test_results_dict[ 'successful_installations' ][ 'repository_dependencies' ].append( repository_dependency_info_dict ) + if repository.installed_tool_dependencies: + # Keep statistics for this repository's tool dependencies that resulted in successful installations. + for tool_dependency in repository.installed_tool_dependencies: + name = str( tool_dependency.name ) + type = str( tool_dependency.type ) + version = str( tool_dependency.version ) + installation_directory = tool_dependency.installation_directory( app ) + tool_dependency_info_dict = dict( type=type, + name=name, + version=version, + installation_directory=installation_directory ) + install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ].append( tool_dependency_info_dict ) + tool_test_results_dict[ 'successful_installations' ][ 'tool_dependencies' ].append( tool_dependency_info_dict ) + return params, install_and_test_statistics_dict, tool_test_results_dict + def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params, can_update_tool_shed ): """ Update the repository metadata tool_test_results and appropriate flags using the Tool SHed API. This method diff -r 3bbb2f8e43b109b5adc8925a52ed23d9f31cd236 -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c 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 @@ -207,15 +207,40 @@ tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) # See if this repository should be skipped for any reason. this_repository_is_in_the_exclude_list = False + requires_excluded = False skip_reason = None for exclude_dict in exclude_list: reason = exclude_dict[ 'reason' ] exclude_repositories = exclude_dict[ 'repositories' ] + # 'repositories': + # [( name, owner, changeset_revision if changeset_revision else None ), + # ( name, owner, changeset_revision if changeset_revision else None )] if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: this_repository_is_in_the_exclude_list = True skip_reason = reason break - if this_repository_is_in_the_exclude_list: + if not this_repository_is_in_the_exclude_list: + # Skip this repository if it has a repository dependency that is in the exclude list. + repository_dependency_dicts, error_message = \ + install_and_test_base_util.get_repository_dependencies_for_changeset_revision( install_and_test_base_util.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:' % \ + ( changeset_revision, name, owner ) ) + log.debug( error_message ) + else: + for repository_dependency_dict in repository_dependency_dicts: + rd_name = repository_dependency_dict[ 'name' ] + rd_owner = repository_dependency_dict[ 'owner' ] + rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] + if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ + ( rd_name, rd_owner, None ) in exclude_repositories: + skip_reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) + requires_excluded = True + break + 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=skip_reason ) params = dict( do_not_test=False ) # TODO: do something useful with response_dict @@ -243,7 +268,8 @@ # 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 ) + 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 ) ) @@ -269,19 +295,13 @@ log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ ( changeset_revision, name, owner ) ) else: - log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ - ( changeset_revision, name, owner ) ) - # Keep statistics for this repository's tool dependencies that resulted in installation errors. - for missing_tool_dependency in repository.missing_tool_dependencies: - name = str( missing_tool_dependency.name ) - type = str( missing_tool_dependency.type ) - version = str( missing_tool_dependency.version ) - error_message = unicodify( missing_tool_dependency.error_message ) - missing_tool_dependency_info_dict = dict( type=type, - name=name, - version=version, - error_message=error_message ) - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) + # 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, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) # Add an empty 'missing_test_results' entry if it is missing from the tool_test_results_dict. The # ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered information in the # 'missing_test_components' entry of the tool_test_results_dict dictionary for repositories that are @@ -297,25 +317,28 @@ repository_dict=repository_dict, tool_test_results_dicts=tool_test_results_dicts, 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. - install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) - # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed + # 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( {} ) ) - 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() ) ) + 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. 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 ) ) ) + log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), + str( shed_tools_dict ) ) ) try: install_and_test_statistics_dict = test_repository_tools( app, repository, @@ -327,10 +350,9 @@ exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) log.exception( exception_message ) tool_test_results_dict[ 'failed_tests' ].append( exception_message ) + install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=False ) + params[ 'tools_functionally_correct' ] = False # 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, @@ -339,7 +361,6 @@ repository_dict, params, can_update_tool_shed ) - install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) return install_and_test_statistics_dict, error_message def main(): @@ -564,11 +585,12 @@ all_tests_passed = install_and_test_statistics_dict[ 'all_tests_passed' ] at_least_one_test_failed = install_and_test_statistics_dict[ 'at_least_one_test_failed' ] successful_repository_installations = install_and_test_statistics_dict[ 'successful_repository_installations' ] + successful_tool_dependency_installations = install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ] repositories_with_installation_error = install_and_test_statistics_dict[ 'repositories_with_installation_error' ] tool_dependencies_with_installation_error = install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] now = time.strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" - print "# %s - installation script for repositories containing tools completed." % now + print "# %s - installation and test script for repositories containing tools completed." % now print "# Repository revisions processed: %s" % str( total_repositories_processed ) if successful_repository_installations: print "# ----------------------------------------------------------------------------------" @@ -586,6 +608,10 @@ print '# ----------------------------------------------------------------------------------' print "# The following %d revisions have installation errors:" % len( repositories_with_installation_error ) install_and_test_base_util.display_repositories_by_owner( repositories_with_installation_error ) + if successful_tool_dependency_installations: + print "# ----------------------------------------------------------------------------------" + print "# The following %d tool dependencies were successfully installed:" % len( successful_tool_dependency_installations ) + install_and_test_base_util.display_tool_dependencies_by_name( successful_tool_dependency_installations ) if tool_dependencies_with_installation_error: print "# ----------------------------------------------------------------------------------" print "# The following %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) @@ -691,7 +717,7 @@ tool_test_results_dict[ 'passed_tests' ].append( test_result ) # Update the repository_metadata table in the tool shed's database to include the passed tests. passed_repository_dict = repository_identifier_dict - results_dict[ 'all_tests_passed' ].append( passed_repository_dict ) + install_and_test_statistics_dict[ 'all_tests_passed' ].append( passed_repository_dict ) params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) diff -r 3bbb2f8e43b109b5adc8925a52ed23d9f31cd236 -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c 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 @@ -182,8 +182,8 @@ ( rd_changeset_revision, rd_name, rd_owner ) requires_excluded = True break - # Register the reason this repository is being skipped if, in fact, it is. 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=skip_reason ) params = dict( do_not_test=False ) # TODO: do something useful with response_dict @@ -233,77 +233,12 @@ ( changeset_revision, name, owner ) ) else: # The repository was successfully installed. - log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ - ( changeset_revision, name, owner ) ) - install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) - tool_test_results_dict[ 'successful_installations' ][ 'current_repository' ]\ - .append( repository_identifier_dict ) - params = dict( test_install_error=False, - do_not_test=False ) - if repository.missing_repository_dependencies: - params[ 'test_install_error' ] = True - # Keep statistics for this repository's repository dependencies that resulted in installation errors. - for missing_repository_dependency in repository.missing_repository_dependencies: - tool_shed = str( missing_repository_dependency.tool_shed ) - name = str( missing_repository_dependency.name ) - owner = str( missing_repository_dependency.owner ) - changset_revision = str( missing_repository_dependency.changeset_revision ) - error_message = unicodify( missing_repository_dependency.error_message ) - missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, - name=name, - owner=owner, - changset_revision=changset_revision, - error_message=error_message ) - install_and_test_statistics_dict[ 'repositories_with_installation_error' ]\ - .append( missing_repository_dependency_dict ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ]\ - .append( missing_repository_dependency_info_dict ) - if repository.missing_tool_dependencies: - params[ 'test_install_error' ] = True - # Keep statistics for this repository's tool dependencies that resulted in installation errors. - for missing_tool_dependency in repository.missing_tool_dependencies: - name = str( missing_tool_dependency.name ) - type = str( missing_tool_dependency.type ) - version = str( missing_tool_dependency.version ) - error_message = unicodify( missing_tool_dependency.error_message ) - missing_tool_dependency_info_dict = dict( type=type, - name=name, - version=version, - error_message=error_message ) - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ]\ - .append( missing_tool_dependency_info_dict ) - tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ]\ - .append( missing_tool_dependency_info_dict ) - if repository.installed_repository_dependencies: - # Keep statistics for this repository's tool dependencies that resulted in successful installations. - for repository_dependency in repository.installed_repository_dependencies: - tool_shed = str( repository_dependency.tool_shed ) - name = str( repository_dependency.name ) - owner = str( repository_dependency.owner ) - changeset_revision = str( repository_dependency.changeset_revision ) - repository_dependency_info_dict = dict( tool_shed=tool_shed, - name=name, - owner=owner, - changeset_revision=changeset_revision ) - install_and_test_statistics_dict[ 'successful_repository_installations' ]\ - .append( repository_dependency_info_dict ) - tool_test_results_dict[ 'successful_installations' ][ 'repository_dependencies' ]\ - .append( repository_dependency_info_dict ) - if repository.installed_tool_dependencies: - # Keep statistics for this repository's tool dependencies that resulted in successful installations. - for tool_dependency in repository.installed_tool_dependencies: - name = str( tool_dependency.name ) - type = str( tool_dependency.type ) - version = str( tool_dependency.version ) - installation_directory = tool_dependency.installation_directory( app ) - tool_dependency_info_dict = dict( type=type, - name=name, - version=version, - installation_directory=installation_directory ) - install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ]\ - .append( tool_dependency_info_dict ) - tool_test_results_dict[ 'successful_installations' ][ 'tool_dependencies' ]\ - .append( tool_dependency_info_dict ) + params, install_and_test_statistics_dict, tool_test_results_dict = \ + install_and_test_base_util.register_installed_and_missing_dependencies( app, + repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) # 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, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits December 2013