1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a4825028799b/ Changeset: a4825028799b User: greg Date: 2014-01-21 21:05:40 Summary: Improved logging for the tool shed's install and test framework. Affected #: 3 files
diff -r 8592f010fdc345910dc024ec06b68ab2cf2d6642 -r a4825028799be0f5ba846ac52ee357c53dfc4a08 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 @@ -230,46 +230,42 @@ log.debug( "Returning base_url from clean_tool_shed_url: %s" % str( base_url ) ) return base_url
-def display_repositories_by_owner( repository_dicts ): - # Group summary display by repository owner. - repository_dicts_by_owner = {} - for repository_dict in repository_dicts: - name = str( repository_dict.get( 'name', '' ) ) - owner = str( repository_dict.get('owner', '' ) ) - changeset_revision = str( repository_dict.get( 'changeset_revision', '' ) ) +def display_repositories_by_owner( repository_tups ): + """Group summary display by repository owner.""" + repository_tups_by_owner = {} + for repository_tup in repository_tups: + name, owner, changeset_revision = repository_tup if owner: - if owner in repository_dicts_by_owner: - repository_dicts_by_owner[ owner ].append( repository_dict ) + if owner in repository_tups_by_owner: + processed_repository_tups_by_owner = repository_tups_by_owner.get( owner, [] ) + if repository_tup not in processed_repository_tups_by_owner: + repository_tups_by_owner[ owner ].append( repository_tup ) else: - repository_dicts_by_owner[ owner ] = [ repository_dict ] + repository_tups_by_owner[ owner ] = [ repository_tup ] # Display grouped summary. - for owner, grouped_repository_dicts in repository_dicts_by_owner.items(): + for owner, repository_tups in repository_tups_by_owner.items(): print "# " - for repository_dict in grouped_repository_dicts: - name = str( repository_dict.get( 'name', '' ) ) - owner = str( repository_dict.get( 'owner', '' ) ) - changeset_revision = str( repository_dict.get( 'changeset_revision', '' ) ) + for repository_tup in repository_tups: + name, owner, changeset_revision = repository_tup print "# Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner )
-def display_tool_dependencies_by_name( tool_dependency_dicts ): - # Group summary display by repository owner. - tool_dependency_dicts_by_name = {} - for tool_dependency_dict in tool_dependency_dicts: - name = str( tool_dependency_dict.get( 'name', '' ) ) - type = str( tool_dependency_dict.get( 'type', '' ) ) - version = str( tool_dependency_dict.get( 'version', '' ) ) +def display_tool_dependencies_by_name( tool_dependency_tups ): + """Group summary display by repository owner.""" + tool_dependency_tups_by_name = {} + for tool_dependency_tup in tool_dependency_tups: + name, type, version = tool_dependency_tup if name: - if name in tool_dependency_dicts_by_name: - tool_dependency_dicts_by_name[ name ].append( tool_dependency_dict ) + if name in tool_dependency_tups_by_name: + processed_tool_dependency_tups_by_name = tool_dependency_tups_by_name.get( name, [] ) + if tool_dependency_tup not in processed_tool_dependency_tups_by_name: + tool_dependency_tups_by_name[ name ].append( tool_dependency_tup ) else: - tool_dependency_dicts_by_name[ name ] = [ tool_dependency_dict ] + tool_dependency_tups_by_name[ name ] = [ tool_dependency_tup ] # Display grouped summary. - for name, grouped_tool_dependency_dicts in tool_dependency_dicts_by_name.items(): + for name, tool_dependency_tups in tool_dependency_tups_by_name.items(): print "# " - for tool_dependency_dict in grouped_tool_dependency_dicts: - type = str( tool_dependency_dict.get( 'type', '' ) ) - name = str( tool_dependency_dict.get( 'name', '' ) ) - version = str( tool_dependency_dict.get( 'version', '' ) ) + for tool_dependency_tup in tool_dependency_tups: + name, type, version = tool_dependency_tup print "# %s %s version %s" % ( type, name, version )
def get_database_version( app ): @@ -546,7 +542,7 @@ global_conf.update( get_static_settings() ) return global_conf
-def initialize_install_and_test_statistics_dict( test_framework ): +def initialize_install_and_test_statistics_dict(): # Initialize a dictionary for the summary that will be printed to stdout. install_and_test_statistics_dict = {} install_and_test_statistics_dict[ 'total_repositories_processed' ] = 0 @@ -729,7 +725,7 @@ print 'The exclude file %s defines no repositories to be excluded from testing.' % xml_filename return exclude_list
-def populate_dependency_install_containers( app, repository, repository_identifier_dict, install_and_test_statistics_dict, +def populate_dependency_install_containers( app, repository, repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ): """ Populate the installation containers (successful or errors) for the received repository's (which @@ -739,7 +735,10 @@ repository_name = str( repository.name ) repository_owner = str( repository.owner ) repository_changeset_revision = str( repository.changeset_revision ) - install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) + processed_successful_repository_installations = install_and_test_statistics_dict.get( 'successful_repository_installations', [] ) + if repository_identifier_tup not in processed_successful_repository_installations: + install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_tup ) + repository_identifier_dict = dict( name=repository_name, owner=repository_owner, changeset_revision=repository_changeset_revision ) tool_test_results_dict[ 'successful_installations' ][ 'current_repository' ].append( repository_identifier_dict ) params = dict( test_install_error=False, do_not_test=False ) @@ -760,7 +759,10 @@ owner=owner, changeset_revision=changeset_revision, error_message=error_message ) - install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( missing_repository_dependency_info_dict ) + processed_repositories_with_installation_error = \ + install_and_test_statistics_dict.get( 'repositories_with_installation_error', [] ) + if missing_repository_dependency_info_dict not in processed_repositories_with_installation_error: + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( missing_repository_dependency_info_dict ) tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( missing_repository_dependency_info_dict ) if repository.missing_tool_dependencies: print 'The following tool dependencies for revision %s of repository %s owned by %s have installation errors:' % \ @@ -777,7 +779,10 @@ name=name, version=version, error_message=error_message ) - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) + processed_tool_dependencies_with_installation_error = \ + install_and_test_statistics_dict.get( 'tool_dependencies_with_installation_error', [] ) + if missing_tool_dependency_info_dict not in processed_tool_dependencies_with_installation_error: + 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: print 'The following repository dependencies for revision %s of repository %s owned by %s are installed:' % \ @@ -789,11 +794,14 @@ owner = str( repository_dependency.owner ) changeset_revision = str( repository_dependency.changeset_revision ) print 'Revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + identifier_tup = ( name, owner, changeset_revision ) + processed_successful_repository_installations = install_and_test_statistics_dict.get( 'successful_repository_installations', [] ) + if identifier_tup not in processed_successful_repository_installations: + install_and_test_statistics_dict[ 'successful_repository_installations' ].append( identifier_tup ) 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: print 'The following tool dependencies for revision %s of repository %s owned by %s are installed:' % \ @@ -805,11 +813,15 @@ version = str( tool_dependency.version ) installation_directory = tool_dependency.installation_directory( app ) print 'Version %s of tool dependency %s %s is installed in: %s' % ( version, type, name, installation_directory ) + identity_tup = ( name, type, version ) + processed_successful_tool_dependency_installations = \ + install_and_test_statistics_dict.get( 'successful_tool_dependency_installations', [] ) + if identity_tup not in processed_successful_tool_dependency_installations: + install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ].append( identity_tup ) 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
@@ -901,14 +913,14 @@ owner, changeset_revision ) if required_repository is not None: - repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + repository_identifier_tup = ( name, owner, changeset_revision ) if required_repository.is_installed: # The required_repository was successfully installed, so populate the installation # containers (success and error) for the repository's immediate dependencies. params, install_and_test_statistics_dict, tool_test_results_dict = \ populate_dependency_install_containers( app, required_repository, - repository_identifier_dict, + repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ) response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, @@ -943,6 +955,7 @@ ( cleaned_tool_shed_url, name, owner, changeset_revision )
def print_install_and_test_results( install_stage_type, install_and_test_statistics_dict, error_message ): + "Print statistics for the current test run." if error_message: print "Error returned from install_and_test_repositories:" print error_message @@ -962,29 +975,29 @@ print "####################################################################################" print "# %s - installation script for %s completed." % ( now, install_stage_type ) print "# Repository revisions processed: %s" % str( total_repositories_processed ) - if successful_repository_installations is not None: + if successful_repository_installations: print "# ----------------------------------------------------------------------------------" - print "# The following %d revisions were successfully installed:" % len( successful_repository_installations ) + print "# The following revisions were successfully installed:" display_repositories_by_owner( successful_repository_installations ) - if repositories_with_installation_error is not None: + if repositories_with_installation_error: print "# ----------------------------------------------------------------------------------" - print "# The following %d revisions have installation errors:" % len( repositories_with_installation_error ) + print "# The following revisions have installation errors:" display_repositories_by_owner( repositories_with_installation_error ) - if successful_tool_dependency_installations is not None: + if successful_tool_dependency_installations: print "# ----------------------------------------------------------------------------------" - print "# The following %d tool dependencies were successfully installed:" % len( successful_tool_dependency_installations ) + print "# The following tool dependencies were successfully installed:" display_tool_dependencies_by_name( successful_tool_dependency_installations ) - if tool_dependencies_with_installation_error is not None: + if tool_dependencies_with_installation_error: print "# ----------------------------------------------------------------------------------" - print "# The following %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) + print "# The following tool dependencies have installation errors:" display_tool_dependencies_by_name( tool_dependencies_with_installation_error ) - if all_tests_passed is not None: + if all_tests_passed: print '# ----------------------------------------------------------------------------------' - print "# The following %d revisions successfully passed all functional tests:" % len( all_tests_passed ) + print "# The following revisions successfully passed all functional tests:" display_repositories_by_owner( all_tests_passed ) - if at_least_one_test_failed is not None: + if at_least_one_test_failed: print '# ----------------------------------------------------------------------------------' - print "# The following %d revisions failed at least 1 functional test:" % len( at_least_one_test_failed ) + print "# The following revisions failed at least 1 functional test:" display_repositories_by_owner( at_least_one_test_failed ) print "####################################################################################"
diff -r 8592f010fdc345910dc024ec06b68ab2cf2d6642 -r a4825028799be0f5ba846ac52ee357c53dfc4a08 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 @@ -142,7 +142,7 @@ global test_toolbox test_toolbox = imported_test_toolbox # 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 ) + install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict() error_message = '' 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 ) @@ -174,7 +174,7 @@ owner = str( repository_dict.get( 'owner', '' ) ) changeset_revision = str( repository_dict.get( 'changeset_revision', '' ) ) print "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) - repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + repository_identifier_tup = ( name, owner, changeset_revision ) # Retrieve the stored list of tool_test_results_dicts. tool_test_results_dicts, error_message = \ install_and_test_base_util.get_tool_test_results_dicts( install_and_test_base_util.galaxy_tool_shed_url, @@ -216,7 +216,10 @@ if error_message: # The repository installation failed. print '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 ) + processed_repositories_with_installation_error = \ + install_and_test_statistics_dict.get( 'repositories_with_installation_error', [] ) + if repository_identifier_tup not in processed_repositories_with_installation_error: + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_tup ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message params = dict( test_install_error=True, do_not_test=False ) @@ -245,7 +248,7 @@ params, install_and_test_statistics_dict, tool_test_results_dict = \ install_and_test_base_util.populate_dependency_install_containers( app, repository, - repository_identifier_dict, + repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ) # Populate the installation containers (success or error) for the repository's immediate repository @@ -289,7 +292,10 @@ 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 ) + processed_at_least_one_test_failed = \ + install_and_test_statistics_dict.get( 'at_least_one_test_failed', [] ) + if repository_identifier_tup not in processed_at_least_one_test_failed: + install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_tup ) # Record the status of this repository in the tool shed. params[ 'tools_functionally_correct' ] = False response_dict = \ @@ -522,9 +528,13 @@ install_and_test_statistics_dict, error_message = install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ) - install_and_test_base_util.print_install_and_test_results( 'repositories with tools', - install_and_test_statistics_dict, - error_message ) + try: + install_and_test_base_util.print_install_and_test_results( 'repositories with tools', + install_and_test_statistics_dict, + error_message ) + except Exception, e: + log.exception( 'Attempting to print the following dictionary...\n\n%s\n\n...threw the following exception...\n\n%s\n\n' % \ + ( str( install_and_test_statistics_dict ), str( e ) ) ) log.debug( "Shutting down..." ) # Gracefully shut down the embedded web server and UniverseApplication. if server: @@ -586,7 +596,7 @@ name = str( repository.name ) owner = str( repository.owner ) changeset_revision = str( repository.changeset_revision ) - repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + repository_identifier_tup = ( name, owner, changeset_revision ) # Generate the test methods for this installed repository. We need to pass testing_shed_tools=True here # or twill will look in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test # files. @@ -615,8 +625,9 @@ test_result = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version ) 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 - install_and_test_statistics_dict[ 'all_tests_passed' ].append( passed_repository_dict ) + processed_all_tests_passed = install_and_test_statistics_dict.get( 'all_tests_passed', [] ) + if repository_identifier_tup not in processed_all_tests_passed: + install_and_test_statistics_dict[ 'all_tests_passed' ].append( repository_identifier_tup ) params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) @@ -639,8 +650,9 @@ ( changeset_revision, name, owner ) failed_test_dicts = get_failed_test_dicts( result, from_tool_test=True ) 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 ) + processed_at_least_one_test_failed = install_and_test_statistics_dict.get( 'at_least_one_test_failed', [] ) + if repository_identifier_tup not in processed_at_least_one_test_failed: + install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_tup ) is_latest_downloadable_revision, error_message = \ install_and_test_base_util.is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, repository_dict )
diff -r 8592f010fdc345910dc024ec06b68ab2cf2d6642 -r a4825028799be0f5ba846ac52ee357c53dfc4a08 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 @@ -77,7 +77,7 @@
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 ) + install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict() error_message = '' 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 ) @@ -108,7 +108,7 @@ owner = str( repository_dict.get( 'owner', '' ) ) changeset_revision = str( repository_dict.get( 'changeset_revision', '' ) ) print "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) - repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + repository_identifier_tup = ( name, owner, changeset_revision ) # Retrieve the stored list of tool_test_results_dicts. tool_test_results_dicts, error_message = \ install_and_test_base_util.get_tool_test_results_dicts( install_and_test_base_util.galaxy_tool_shed_url, @@ -150,7 +150,10 @@ if error_message: # The repository installation failed. print '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 ) + processed_repositories_with_installation_error = \ + install_and_test_statistics_dict.get( 'repositories_with_installation_error', [] ) + if repository_identifier_tup not in processed_repositories_with_installation_error: + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_tup ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message params = dict( test_install_error=True, do_not_test=False ) @@ -173,7 +176,7 @@ params, install_and_test_statistics_dict, tool_test_results_dict = \ install_and_test_base_util.populate_dependency_install_containers( app, repository, - repository_identifier_dict, + repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ) response_dict = \ @@ -412,9 +415,13 @@ install_and_test_statistics_dict, error_message = install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ) - install_and_test_base_util.print_install_and_test_results( 'tool dependency definitions', - install_and_test_statistics_dict, - error_message ) + try: + install_and_test_base_util.print_install_and_test_results( 'tool dependency definitions', + install_and_test_statistics_dict, + error_message ) + except Exception, e: + log.exception( 'Attempting to print the following dictionary...\n\n%s\n\n...threw the following exception...\n\n%s\n\n' % \ + ( str( install_and_test_statistics_dict ), str( e ) ) ) log.debug( "Shutting down..." ) # Gracefully shut down the embedded web server and UniverseApplication. if server:
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.