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/

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