[galaxy-commits] commit/galaxy-central: inithello: Refactor summary output. Improve handling of empty tool_test_errors dict. Refactor repository information retrieval.

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/0a6b63eca3ff/ changeset: 0a6b63eca3ff user: inithello date: 2013-03-11 05:47:47 summary: Refactor summary output. Improve handling of empty tool_test_errors dict. Refactor repository information retrieval. affected #: 2 files

diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 0a6b63eca3ff6a72cd874bf36f73a2b5905aff65 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -1,7 +1,6 @@ #!/bin/sh

# A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/ -#rm -f ./test/tool_shed/run_functional_tests.log

-python test/install_and_test_tool_shed_repositories/functional_tests.py -v --with-nosehtml --html-report-file ./test/install_and_test_tool_shed_repositories/run_functional_tests.html test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py test/functional/test_toolbox.py +python test/install_and_test_tool_shed_repositories/functional_tests.py $* -v --with-nosehtml --html-report-file ./test/install_and_test_tool_shed_repositories/run_functional_tests.html test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py test/functional/test_toolbox.py

diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 0a6b63eca3ff6a72cd874bf36f73a2b5905aff65 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 @@ -242,6 +242,8 @@ api_path = metadata_dict[ 'url' ].split( '/' ) api_url = get_api_url( base=tool_shed_url, parts=api_path ) repository_metadata = json_from_url( api_url ) + if repository_metadata[ 'tool_test_errors' ] is None: + return {} return repository_metadata[ 'tool_test_errors' ]

def json_from_url( url ): @@ -276,16 +278,22 @@ result = test_runner.run( tests ) return result, test_config.plugins._plugins

+def show_summary_output( repository_info_dicts ): + repositories_by_owner = dict() + for repository in repository_info_dicts: + if repository[ 'owner' ] not in repositories_by_owner: + repositories_by_owner[ repository[ 'owner' ] ] = [] + repositories_by_owner[ repository[ 'owner' ] ].append( repository ) + for owner in repositories_by_owner: + print "# " + for repository in repositories_by_owner[ owner ]: + print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) + def main(): # ---- Configuration ------------------------------------------------------ galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', default_galaxy_test_host ) galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( default_galaxy_test_port_max ) )

- # Initialize some variables for the summary that will be printed to stdout. - repositories_tested = 0 - repositories_passed = [] - repositories_failed = [] - tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales @@ -444,38 +452,19 @@ 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 + # Initialize some variables for the summary that will be printed to stdout. + repositories_tested = 0 + repositories_passed = [] + repositories_failed = [] + repositories_failed_install = [] try: - # Iterate through a list of repository info dicts. + 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 ) ) repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, source='url' ) log.info( "Retrieved %d repositories to install..." % len( repositories_to_install ) ) repositories_tested = len( repositories_to_install ) - # This loop will iterate through the list of repositories returned by the above method, skipping any that are 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 dependencies if they are - # defined. If the installation completes successfully, it will then generate a test case for each functional test - # defined for each tool in the repository, and execute the generated test cases. When this completes, it will record - # the result of the tests, and if any failed, the traceback and captured output of the tool that was run. - # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with - # the next repository's functional tests. for repository_to_install_dict in repositories_to_install: - """ - Each repository_to_install_dict looks something like: - { - "changeset_revision": "13fa22a258b5", - "downloadable": true, - "id": "529fd61ab1c6cc36", - "malicious": false, - "repository_id": "529fd61ab1c6cc36", - "url": "/api/repository_revisions/529fd61ab1c6cc36" - } - """ - repository_status = dict() - repository_id = repository_to_install_dict.get( 'repository_id', None ) - changeset_revision = repository_to_install_dict.get( 'changeset_revision', None ) - metadata_revision_id = repository_to_install_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_to_install_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url # 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. repository_info_dict = get_repository_info_from_api( galaxy_tool_shed_url, repository_to_install_dict ) @@ -483,13 +472,31 @@ # 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 since the repository is deleted..." % ( str( changeset_revision ), str( repository_id ) ) ) + log.info( "Skipping revision %s of repository id %s (%s/%s) since the repository is deleted..." % \ + ( repository_info_dict[ 'changeset_revision' ], + repository_info_dict[ 'repository_id' ], + repository_info_dict[ 'owner' ], + repository_info_dict[ 'name' ] ) ) continue - log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) ) - # Add repository details to the basic repository dict. - repository_dict = dict( repository_info_dict.items() + repository_to_install_dict.items() ) + # 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() ) ) + 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 ) ) ) + # 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 + # dependencies if they are defined. If the installation completes successfully, it will then generate a test case for + # each functional test defined for each tool in the repository, and execute the generated test cases. When this completes, + # it will record the result of the tests, and if any failed, the traceback and captured output of the tool that was run. + # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with + # the next repository's functional tests. + for repository_info_dict in detailed_repository_list: """ - After the addition of the repository details, each repository_dict should now contain something like: + Each repository_info_dict looks something like: { "changeset_revision": "13fa22a258b5", "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", @@ -510,11 +517,19 @@ "user_id": "529fd61ab1c6cc36" } """ - name = repository_dict[ 'name' ] - owner = repository_dict[ 'owner' ] + repository_status = dict() + repository_id = repository_info_dict.get( 'repository_id', None ) + changeset_revision = repository_info_dict.get( 'changeset_revision', None ) + metadata_revision_id = repository_info_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_info_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url + log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) ) + # Get the name and owner out of the repository info dict. + name = repository_info_dict[ 'name' ] + owner = repository_info_dict[ 'owner' ] # Use the repository information dict to generate an install method that will install the repository into the embedded # Galaxy application, with tool dependencies and repository dependencies, if any. - test_install_repositories.generate_install_method( repository_dict ) + test_install_repositories.generate_install_method( repository_info_dict ) os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host # Configure nose to run the install method as a test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) @@ -526,7 +541,7 @@ # 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.' % repository_dict[ '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_errors. @@ -574,17 +589,18 @@ # }, # ] # } - repository_status = get_tool_test_errors_from_api( galaxy_tool_shed_url, repository_dict ) + repository_status = get_tool_test_errors_from_api( galaxy_tool_shed_url, repository_info_dict ) + if 'test_environment' not in repository_status: + repository_status[ 'test_environment' ] = {} test_environment = get_test_environment( repository_status[ 'test_environment' ] ) test_environment[ 'galaxy_database_version' ] = get_database_version( app ) test_environment[ 'galaxy_revision'] = get_repository_current_revision( os.getcwd() ) repository_status[ 'test_environment' ] = test_environment repository_status[ 'tests_passed' ] = [] repository_status[ 'test_errors' ] = [] + repository_status[ 'invalid_tests' ] = [] if not has_test_data: log.error( 'Test data is missing for this repository. Updating repository and skipping functional tests.' ) - repository_status[ 'test_environment' ] = get_test_environment() - test_id = 'Find functional test data for %s' % repository_dict[ 'name' ] # Record the lack of test data. test_errors = dict( tool_id=None, tool_version=None, tool_guid=None, reason_test_is_invalid="Repository %s is missing a test-data directory." % name ) @@ -593,7 +609,7 @@ register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, tests_passed=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( repository_dict ) + execute_uninstall_method( repository_info_dict ) # 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 ) ) @@ -618,9 +634,7 @@ # Run the configured tests. result, test_plugins = run_tests( test_config ) success = result.wasSuccessful() - # Record some information about the environment in which this test was run, in case a failure is specific to a certain processor - # architecture or operating system. - repository_dict[ 'test_environment' ] = test_environment + # Use the ReportResults nose plugin to get a list of tests that passed. for plugin in test_plugins: if hasattr( plugin, 'getTestStatus' ): test_identifier = '%s/%s' % ( owner, name ) @@ -637,10 +651,8 @@ # controller with the status of the test. This also sets the do_not_test and tools_functionally correct flags, and # updates the time_last_tested field to today's date. repositories_passed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - repository_status[ 'test_environment' ] = test_environment register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, tests_passed=True ) - log.debug( 'Revision %s of repository %s installed and passed functional tests.' % \ - ( repository_dict[ 'changeset_revision' ], repository_dict[ '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: @@ -686,14 +698,15 @@ repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, tests_passed=False ) log.debug( 'Revision %s of repository %s installed successfully, but did not pass functional tests.' % \ - ( repository_dict[ 'changeset_revision' ], repository_dict[ 'name' ] ) ) + ( changeset_revision, name ) ) # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - execute_uninstall_method( repository_dict ) + execute_uninstall_method( repository_info_dict ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: - log.debug( 'Repository %s failed to install correctly.' % repository_dict[ 'name' ] ) + repositories_failed_install.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + log.debug( 'Repository %s failed to install correctly.' % name ) except: log.exception( "Failure running tests" )

@@ -728,29 +741,17 @@ print "# Repository revisions tested: %d" % repositories_tested if repositories_tested > 0: if repositories_passed: - passed_repositories_by_owner = dict() - for repository in repositories_passed: - if repository[ 'owner' ] not in passed_repositories_by_owner: - passed_repositories_by_owner[ repository[ 'owner' ] ] = [] - passed_repositories_by_owner[ repository[ 'owner' ] ].append( repository ) print "# " print "# Repositories passed:" - for owner in passed_repositories_by_owner: - print "# " - for repository in passed_repositories_by_owner[ owner ]: - print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) + show_summary_output( repositories_passed ) if repositories_failed: - failed_repositories_by_owner = dict() - for repository in repositories_failed: - if repository[ 'owner' ] not in failed_repositories_by_owner: - failed_repositories_by_owner[ repository[ 'owner' ] ] = [] - failed_repositories_by_owner[ repository[ 'owner' ] ].append( repository ) print "# " print "# Repositories failed:" - for owner in failed_repositories_by_owner: - print "# " - for repository in failed_repositories_by_owner[ owner ]: - print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) + show_summary_output( repositories_failed ) + if repositories_failed_install: + print "# " + print "# Repositories not installed correctly:" + show_summary_output( repositories_failed_install ) print "####################################################################################"

if success:

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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