1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/9d87d7c61912/ changeset: 9d87d7c61912 user: inithello date: 2013-02-27 20:28:12 summary: Enhance twill automated repository installation framework to get a list of repositories from the tool shed API, install, run functional tests defined in the tools' XML, and report success or failure back to the tool shed. affected #: 3 files

diff -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 -r 9d87d7c6191284aaf48ade4462256131c0345c8d 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 @@ -55,7 +55,7 @@ name = repository_info_dict[ 'name' ] owner = repository_info_dict[ 'owner' ] changeset_revision = repository_info_dict[ 'changeset_revision' ] - encoded_repository_id = repository_info_dict[ 'encoded_repository_id' ] + encoded_repository_id = repository_info_dict[ 'repository_id' ] tool_shed_url = repository_info_dict[ 'tool_shed_url' ] preview_params = urllib.urlencode( dict( repository_id=encoded_repository_id, changeset_revision=changeset_revision ) ) self.visit_url( '%s/repository/preview_tools_in_changeset?%s' % ( tool_shed_url, preview_params ) )

diff -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 -r 9d87d7c6191284aaf48ade4462256131c0345c8d test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py --- a/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py +++ b/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py @@ -3,7 +3,7 @@ from install_and_test_tool_shed_repositories.base.twilltestcase import InstallTestRepository log = logging.getLogger(__name__)

-class TestInstallRepositories( InstallTestRepository ): +class InstallTestRepositories( InstallTestRepository ): """Abstract test case that installs and uninstalls a predefined list of repositories.""" def do_installation( self, repository_info_dict ): self.logout() @@ -35,11 +35,11 @@ G = globals() # Eliminate all previous tests from G. for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ): + if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ) or key.startswith( 'TestForTool_' ): del G[ key ] # Create a new subclass with a method named install_repository_XXX that installs the repository specified by the provided dict. name = "TestInstallRepository_" + repository_dict[ 'name' ] - baseclasses = ( TestInstallRepositories, ) + baseclasses = ( InstallTestRepositories, ) namespace = dict() def make_install_method( repository_dict ): def test_install_repository( self ): @@ -61,11 +61,11 @@ G = globals() # Eliminate all previous tests from G. for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ): + if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ) or key.startswith( 'TestForTool_' ): del G[ key ] # Create a new subclass with a method named install_repository_XXX that installs the repository specified by the provided dict. name = "TestUninstallRepository_" + repository_dict[ 'name' ] - baseclasses = ( TestInstallRepositories, ) + baseclasses = ( InstallTestRepositories, ) namespace = dict() def make_uninstall_method( repository_dict ): def test_install_repository( self ):

diff -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 -r 9d87d7c6191284aaf48ade4462256131c0345c8d 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 @@ -4,7 +4,7 @@ # order to run functional tests on repository tools after installation. The install_and_test_tool_shed_repositories.sh # will execute this script with the appropriate parameters.

-import os, sys, shutil, tempfile, re, string +import os, sys, shutil, tempfile, re, string, urllib

# Assume we are run from the galaxy root directory, add lib to the python path cwd = os.getcwd() @@ -19,7 +19,7 @@ default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, 'test' ) ] +new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, 'test' ), os.path.join( cwd, 'scripts', 'api' ) ] new_path.extend( sys.path ) sys.path = new_path

@@ -48,6 +48,7 @@ from galaxy.app import UniverseApplication from galaxy.web import buildapp from galaxy.util import parse_xml +from galaxy.util.json import from_json_string, to_json_string

import nose.core import nose.config @@ -56,6 +57,8 @@

from base.util import parse_tool_panel_config

+from common import update + log = logging.getLogger( 'install_and_test_repositories' )

default_galaxy_test_port_min = 10000 @@ -95,7 +98,10 @@ '''

# Define a default location to find the list of repositories to check. -galaxy_repository_list = os.environ.get( 'GALAXY_INSTALL_TEST_REPOSITORY_FILE', 'repository_list.json' ) +galaxy_repository_list = os.environ.get( 'GALAXY_INSTALL_TEST_REPOSITORY_LIST_LOCATIOM', 'repository_list.json' ) +galaxy_tool_shed_url = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_URL', 'http://toolshed.local:10001' ) +tool_shed_api_key = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY', None ) +assert tool_shed_api_key is not None, 'Unable to proceed without API key.'

if 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: galaxy_encode_secret = 'changethisinproductiontoo' @@ -103,7 +109,28 @@ else: galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ]

-def get_repositories_to_install( format='json' ): +def get_api_url( base, parts=[], params=None, key=None ): + if 'api' in parts and parts.index( 'api' ) != 0: + parts.pop( parts.index( 'api' ) ) + parts.insert( 0, 'api' ) + elif 'api' not in parts: + parts.insert( 0, 'api' ) + url = '%s/%s' % ( base, '/'.join( parts ) ) + if key: + url += '?%s' % urllib.urlencode( dict( key=key ) ) + else: + url += '?%s' % urllib.urlencode( dict( key=tool_shed_api_key ) ) + if params: + url += '&%s' % params + return url + +def get_repository_info_from_api( url, repository_info_dict ): + parts = [ 'api', 'repositories', repository_info_dict[ 'repository_id' ] ] + api_url = get_api_url( base=url, parts=parts ) + extended_dict = json_from_url( api_url ) + return extended_dict + +def get_repositories_to_install( location, source='file', format='json' ): ''' Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: [ @@ -118,11 +145,34 @@ ] NOTE: If the tool shed URL specified in any dict is not present in the tool_sheds_conf.xml, the installation will fail. ''' + if source == 'file': + listing = file( location, 'r' ).read() + elif source == 'url': + assert tool_shed_api_key is not None, 'Cannot proceed without tool shed API key.' + params = urllib.urlencode( dict( downloadable='true' ) ) + api_url = get_api_url( base=location, parts=[ 'repository_revisions' ], params=params ) + if format == 'json': + return json_from_url( api_url ) + else: + raise AssertionError( 'Do not know how to handle source type %s.' % source ) if format == 'json': - return simplejson.loads( file( galaxy_repository_list, 'r' ).read() ) + return from_json_string( listing ) else: raise AssertonError( 'Unknown format %s.' % format )

+def json_from_url( url ): + url_handle = urllib.urlopen( url ) + url_contents = url_handle.read() + return from_json_string( url_contents ) + +def register_test_failure( url, metadata_id, test_errors ): + params = dict( tools_functionally_correct='false', do_not_test='true', tool_test_errors=test_errors ) + return update( tool_shed_api_key, '%s/api/%s' % ( galaxy_tool_shed_url, '/'.join( [ 'repository_revisions', metadata_id ] ) ), params ) + +def register_test_success( url, metadata_id ): + params = dict( tools_functionally_correct='true', do_not_test='false' ) + return update( tool_shed_api_key, '%s/api/%s' % ( galaxy_tool_shed_url, '/'.join( [ 'repository_revisions', metadata_id ] ) ), params ) + def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) plug_loader = test_config.plugins.prepareTestLoader( loader ) @@ -162,6 +212,7 @@ galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_MIGRATED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) galaxy_shed_tools_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) if 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' in os.environ: tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ) else: @@ -302,8 +353,13 @@ log.info( "Tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) success = False try: + repository_status = [] # Iterate through a list of repository info dicts. - for repository_dict in get_repositories_to_install(): + for repository_dict in get_repositories_to_install( galaxy_tool_shed_url, source='url' ): + metadata_revision_id = repository_dict[ 'id' ] + repository_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url + repository_info = get_repository_info_from_api( galaxy_tool_shed_url, repository_dict ) + repository_dict = dict( repository_info.items() + repository_dict.items() ) # Generate the method that will install this repository into the running Galaxy instance. test_install_repositories.generate_install_method( repository_dict ) os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host @@ -319,9 +375,12 @@ if success: log.debug( 'Installation of %s succeeded, running any defined functional tests.' % repository_dict[ 'name' ] ) # Parse the tool panel config to get the test-data path for this repository. - shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, {} ) + if not os.path.exists( galaxy_shed_tools_dict ): + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) + shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + log.debug( shed_tools_dict ) # Write this to a file, so the functional test framework can find it. - file( galaxy_shed_tools_dict, 'w' ).write( simplejson.dumps( shed_tools_dict ) ) + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) # Set up the environment so that test.functional.test_toolbox can find the Galaxy server we configured in this framework. os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host @@ -337,10 +396,52 @@ # Run the configured tests. result = run_tests( test_config ) success = result.wasSuccessful() + repository_dict[ 'functional_tests_passed' ] = success if success: + register_test_success( galaxy_tool_shed_url, metadata_revision_id ) log.debug( 'Repository %s installed and passed functional tests.' % repository_dict[ 'name' ] ) else: + # If the functional tests fail, log the output and submit it to the tool shed whence the repository was installed. + repository_dict[ 'tool_test_errors' ] = [] + for failure in result.failures: + label = str( failure[0] ) + log_output = failure[1].replace( '\n', '\n' ) + log_output = re.sub( r'control \d+:.+', r'', log_output ) + log_output = re.sub( r'\n+', r'\n', log_output ) + appending_to = 'output' + tmp_output = {} + output = {} + for line in log_output.split( '\n' ): + if line.startswith( 'Traceback' ): + appending_to = 'traceback' + elif 'request returned None from get_history' in line: + continue + elif '>> begin captured logging <<' in line: + appending_to = 'logging' + continue + elif '>> begin captured stdout <<' in line: + appending_to = 'stdout' + continue + elif '>> begin captured stderr <<' in line: + appending_to = 'stderr' + continue + if appending_to not in tmp_output: + tmp_output[ appending_to ] = [] + tmp_output[ appending_to ].append( line ) + for output_type in tmp_output: + output[ output_type ] = '\n'.join( tmp_output[ output_type ] ) + repository_dict[ 'tool_test_errors' ].append( dict( test=label, output=output ) ) + register_test_failure( galaxy_tool_shed_url, metadata_revision_id, repository_dict[ 'tool_test_errors' ] ) log.debug( 'Repository %s installed, but did not pass functional tests.' % repository_dict[ 'name' ] ) + repository_status.append( repository_dict ) + # Delete the completed tool functional tests from the test_toolbox.__dict__, otherwise nose will find them and try to re-run the + # tests after uninstalling the repository. + tests_to_delete = [] + for key in test_toolbox.__dict__: + if key.startswith( 'TestForTool_' ): + tests_to_delete.append( key ) + for key in tests_to_delete: + del test_toolbox.__dict__[ key ] # Generate an uninstall method for this repository, so that the next repository has a clean environment for testing. test_install_repositories.generate_uninstall_method( repository_dict ) # Set up nose to run the generated uninstall method as a functional test.

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

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