1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef2b705c7de3/ Changeset: ef2b705c7de3 User: Dave Bouvier Date: 2013-05-13 19:08:39 Summary: Skip functional tests and log error message if a repository's tool dependencies fail to install correctly. Clean up uninstall method. Affected #: 1 file diff -r 604693b3ebe0283804225eac10adab2f858ec380 -r ef2b705c7de344c2c052a36ff3592e78ae5115af test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -39,6 +39,7 @@ eggs.require( "pysqlite" ) import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories +import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util import functional.test_toolbox as test_toolbox import atexit, logging, os, os.path, sys, tempfile, simplejson @@ -185,7 +186,7 @@ sa_session = app.model.context.current repositories_to_uninstall = sa_session.query( app.model.ToolShedRepository ).all() for repository in repositories_to_uninstall: - if repository.status == app.model.ToolShedRepository.states.UNINSTALLED: + if repository.status == app.model.ToolShedRepository.installation_status.UNINSTALLED: continue if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, app.model.ToolShedRepository.installation_status.ERROR, @@ -196,7 +197,7 @@ name = str( repository.name ) owner = str( repository.owner ) changeset_revision = str( repository.installed_changeset_revision ) - log.debug( 'Changeset revision %s of repository %s queued for uninstallation.' % ( changeset_revision, name ) ) + log.debug( 'Changeset revision %s of repository %s queued for uninstallation.', changeset_revision, name ) repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. test_install_repositories.generate_uninstall_method( repository_dict ) @@ -326,7 +327,7 @@ global test_toolbox for key in test_toolbox.__dict__: if key.startswith( 'TestForTool_' ): - log.info( 'Tool test found in test_toolbox, deleting: %s' % key ) + log.info( 'Tool test found in test_toolbox, deleting: %s', 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_', '' ) @@ -493,7 +494,7 @@ for i in range( 0, 9 ): try: galaxy_test_port = str( random.randint( default_galaxy_test_port_min, default_galaxy_test_port_max ) ) - log.debug( "Attempting to serve app on randomly chosen port: %s" % galaxy_test_port ) + log.debug( "Attempting to serve app on randomly chosen port: %s", galaxy_test_port ) server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) break except socket.error, e: @@ -522,10 +523,10 @@ raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) log.info( "Embedded galaxy web server started" ) if galaxy_test_proxy_port: - log.info( "The embedded Galaxy application is running on %s:%s" % ( galaxy_test_host, galaxy_test_proxy_port ) ) + log.info( "The embedded Galaxy application is running on %s:%s", galaxy_test_host, galaxy_test_proxy_port ) else: - log.info( "The embedded Galaxy application is running on %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) - log.info( "Repositories will be installed from the tool shed at %s" % galaxy_tool_shed_url ) + log.info( "The embedded Galaxy application is running on %s:%s", galaxy_test_host, galaxy_test_port ) + log.info( "Repositories will be installed from the tool shed at %s", galaxy_tool_shed_url ) success = False # If a tool_data_table_conf.test.xml file was found, add the entries from it into the app's tool data tables. if additional_tool_data_tables: @@ -541,9 +542,9 @@ try: detailed_repository_list = [] # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable. - log.info( "Retrieving repositories to install from the URL:\n%s\n" % str( galaxy_tool_shed_url ) ) + log.info( "Retrieving repositories to install from the URL:\n%s\n", str( galaxy_tool_shed_url ) ) repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, source='url' ) - log.info( "Retrieved %d repositories from the API." % len( repositories_to_install ) ) + log.info( "Retrieved %d repositories from the API.", len( repositories_to_install ) ) for repository_to_install_dict in repositories_to_install: # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the # module that will generate the install methods. @@ -552,22 +553,23 @@ # and functionally correct tools that someone has previously installed. Deleted repositories have never been installed, # and therefore do not need to be checked. If they are undeleted, this script will then test them the next time it runs. if repository_info_dict[ 'deleted' ]: - log.info( "Skipping revision %s of repository id %s (%s/%s) since the repository is deleted..." % \ - ( repository_to_install_dict[ 'changeset_revision' ], - repository_to_install_dict[ 'repository_id' ], - repository_info_dict[ 'owner' ], - repository_info_dict[ 'name' ] ) ) + log.info( "Skipping revision %s of repository id %s (%s/%s) since the repository is deleted...", + repository_to_install_dict[ 'changeset_revision' ], + repository_to_install_dict[ 'repository_id' ], + repository_info_dict[ 'owner' ], + repository_info_dict[ 'name' ] ) continue # Now merge the dict returned from /api/repository_revisions with the detailed dict we just retrieved. detailed_repository_list.append( dict( repository_info_dict.items() + repository_to_install_dict.items() ) ) repositories_tested = len( detailed_repository_list ) - log.info( 'After removing deleted repositories from the list, %d remain to be tested.' % repositories_tested ) + log.info( 'After removing deleted repositories from the list, %d remain to be tested.', repositories_tested ) if '-list_repositories' in sys.argv: log.info( "The API returned the following repositories, not counting deleted:" ) for repository_info_dict in detailed_repository_list: - log.info( "%s owned by %s changeset revision %s" % ( repository_info_dict.get( 'name', None ), - repository_info_dict.get( 'owner', None ), - repository_info_dict.get( 'changeset_revision', None ) ) ) + log.info( "%s owned by %s changeset revision %s", + repository_info_dict.get( 'name', None ), + repository_info_dict.get( 'owner', None ), + repository_info_dict.get( 'changeset_revision', None ) ) # This loop will iterate through the list of repositories generated by the above code, having already filtered out any # that were marked as deleted. For each repository, it will generate a test method that will use Twill to install that # repository into the embedded Galaxy application that was started up, selecting to install repository and tool @@ -608,8 +610,8 @@ # Get the name and owner out of the repository info dict. name = str( repository_info_dict[ 'name' ] ) owner = str( repository_info_dict[ 'owner' ] ) - log.info( "Installing and testing revision %s of repository id %s (%s/%s)..." % \ - ( str( changeset_revision ), str( repository_id ), owner, name ) ) + log.info( "Installing and testing revision %s of repository id %s (%s/%s)...", + str( changeset_revision ), str( repository_id ), owner, name ) # Explicitly clear tests from twill's test environment. remove_generated_tests( app ) # Use the repository information dict to generate an install method that will install the repository into the embedded @@ -626,7 +628,7 @@ # If the installation succeeds, configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed if success: - log.debug( 'Installation of %s succeeded, running all defined functional tests.' % name ) + log.debug( 'Installation of %s succeeded, running all defined functional tests.', 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. @@ -663,6 +665,15 @@ # "traceback": "The captured traceback." # }, # ] + # "installation_errors": + # [ + # { + # "name": "The name of the repository.", + # "owner": "The owner of the repository.", + # "changeset_revision": "The changeset revision of the repository.", + # "error_message": "The message stored in tool_dependency.error_message." + # }, + # ] # "missing_test_components": # [ # { @@ -682,14 +693,42 @@ repository_status[ 'test_environment' ] = test_environment repository_status[ 'passed_tests' ] = [] repository_status[ 'failed_tests' ] = [] + repository_status[ 'installation_errors' ] = [] + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + missing_tool_dependencies = repository.includes_tool_dependencies and repository.missing_tool_dependencies if 'missing_test_components' not in repository_status: repository_status[ 'missing_test_components' ] = [] if not has_test_data: + # If the repository does not have a test-data directory, any functional tests in the tool configuration will + # fail. Mark the repository as failed and skip installation. log.error( 'Test data is missing for this repository. Updating repository and skipping functional tests.' ) # Record the lack of test data. - failed_tests = dict( tool_id=None, tool_version=None, tool_guid=None, - missing_components="Repository %s is missing a test-data directory." % name ) - repository_status[ 'missing_test_components' ].append( failed_tests ) + for tool in repository.metadata[ 'tools' ]: + tool_id = tool[ 'id' ] + tool_version = tool[ 'version' ] + tool_guid = tool[ 'guid' ] + # In keeping with the standard display layout, add the error message to the dict for each tool individually. + failed_tests = dict( tool_id=tool_id, tool_version=tool_version, tool_guid=tool_guid, + missing_components="Repository %s is missing a test-data directory." % name ) + repository_status[ 'missing_test_components' ].append( failed_tests ) + # Record the status of this repository in the tool shed. + register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) + # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the + # repository using Twill. + execute_uninstall_method( app ) + # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. + test_toolbox.toolbox = app.toolbox + repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + elif missing_tool_dependencies: + # If a tool dependency fails to install correctly, this should be considered a missing test component, + # as the tools depend on the tool dependency being present in order to return coherent results. + log.error( 'One or more tool dependencies of this repository are marked as missing.' ) + log.error( 'Updating repository and skipping functional tests.' ) + # In keeping with the standard display layout, add the error message to the dict for each tool individually. + for dependency in repository.missing_tool_dependencies: + test_result = dict( name=name, owner=owner, changeset_revision=changeset_revision, + error_message=dependency.error_message ) + repository_status[ 'installation_errors' ].append( test_result ) # Record the status of this repository in the tool shed. register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the @@ -702,7 +741,7 @@ # If the repository does have 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.info( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, str( shed_tools_dict ) ) ) + log.info( 'Saved generated shed_tools_dict to %s\nContents: %s', galaxy_shed_tools_dict, str( shed_tools_dict ) ) # Set the GALAXY_TOOL_SHED_TEST_FILE environment variable to the path of the shed_tools_dict file, so that test.base.twilltestcase.setUp # will find and parse it properly. os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict @@ -727,6 +766,7 @@ break repository_status[ 'passed_tests' ] = [] for test_id in passed_tests: + # Normalize the tool ID and version display. tool_id, tool_version = get_tool_info_from_test_id( test_id ) test_result = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version ) repository_status[ 'passed_tests' ].append( test_result ) @@ -737,7 +777,7 @@ # updates the time_last_tested field to today's date. repositories_passed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=True ) - log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( changeset_revision, name ) ) + log.debug( 'Revision %s of repository %s installed and passed functional tests.', changeset_revision, name ) else: # If the functional tests fail, log the output and update the failed changeset revision's metadata record in the tool shed via the API. for failure in result.failures + result.errors: @@ -782,25 +822,26 @@ # field to today's date. repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) - log.debug( 'Revision %s of repository %s installed successfully, but did not pass functional tests.' % \ - ( changeset_revision, name ) ) + log.debug( 'Revision %s of repository %s installed successfully, but did not pass functional tests.', + changeset_revision, name ) # 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' % \ - ( repository_info_dict[ 'changeset_revision' ], repository_info_dict[ 'name' ] ) ) + log.debug( 'Uninstalling changeset revision %s of repository %s', + repository_info_dict[ 'changeset_revision' ], + repository_info_dict[ 'name' ] ) success = execute_uninstall_method( app ) if not success: - log.error( 'Repository %s failed to uninstall.' ) + log.error( 'Repository %s failed to uninstall.', repository_info_dict[ 'name' ] ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. - log.debug( 'Uninstalling repository %s' % repository_info_dict[ 'name' ] ) + log.debug( 'Uninstalling repository %s', repository_info_dict[ 'name' ] ) success = execute_uninstall_method( app ) if not success: - log.error( 'Repository %s failed to uninstall.' ) + log.error( 'Repository %s failed to uninstall.', repository_info_dict[ 'name' ] ) repositories_failed_install.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - log.debug( 'Repository %s failed to install correctly.' % repository_info_dict[ 'name' ] ) + log.debug( 'Repository %s failed to install correctly.', repository_info_dict[ 'name' ] ) except: log.exception( "Failure running tests" ) @@ -822,7 +863,7 @@ try: for dir in [ galaxy_test_tmp_dir ]: if os.path.exists( dir ): - log.info( "Cleaning up temporary files in %s" % dir ) + log.info( "Cleaning up temporary files in %s", dir ) shutil.rmtree( dir ) except: pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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