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/

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