5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d8fef0600148/ Changeset: d8fef0600148 User: jmchilton Date: 2014-10-14 19:25:54+00:00 Summary: Save one extra database hit per API query. Honestly I can see the query no longer being emitted but I was unable to detect any difference in performance. Affected #: 1 file diff -r 42cd5d55755a729dd2f19ccd1ed20649ed29f6ac -r d8fef0600148c4b6f4ed7d6a95ba4681d07a67a8 lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -23,6 +23,7 @@ eggs.require( "SQLAlchemy >= 0.4" ) from sqlalchemy import and_ from sqlalchemy.orm.exc import NoResultFound +from sqlalchemy.orm import joinedload from galaxy.exceptions import MessageException @@ -337,7 +338,7 @@ # Retrieve the galaxy_session id via the unique session_key galaxy_session = self.sa_session.query( self.app.model.GalaxySession ) \ .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, #noqa - self.app.model.GalaxySession.table.c.is_valid==True ) ).first() #noqa + self.app.model.GalaxySession.table.c.is_valid==True ) ).options( joinedload( "user" ) ).first() #noqa # If remote user is in use it can invalidate the session and in some # cases won't have a cookie set above, so we need to to check some # things now. https://bitbucket.org/galaxy/galaxy-central/commits/6cd78dca65d1/ Changeset: 6cd78dca65d1 User: jmchilton Date: 2014-10-14 19:25:55+00:00 Summary: Less aggressive test polling. Affected #: 1 file diff -r d8fef0600148c4b6f4ed7d6a95ba4681d07a67a8 -r 6cd78dca65d15db75cd98a2733e2dd22db800561 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -2441,7 +2441,7 @@ return self.wait_for(lambda: self.get_running_datasets(), **kwds) def wait_for( self, func, **kwd ): - sleep_amount = 0.1 + sleep_amount = 0.2 slept = 0 walltime_exceeded = 86400 while slept <= walltime_exceeded: https://bitbucket.org/galaxy/galaxy-central/commits/b6cb3aabfba4/ Changeset: b6cb3aabfba4 User: jmchilton Date: 2014-10-14 19:25:55+00:00 Summary: Fix set_metadata.py for environmental set Galaxy properties. At least for the local job runner. This variant of property loading does correctly interpolate %(here) so there is no longer a need to catch those exceptions and object store related properties can use %(here). Affected #: 1 file diff -r 6cd78dca65d15db75cd98a2733e2dd22db800561 -r b6cb3aabfba4ec844f346fb2d363e47822a3d989 scripts/set_metadata.py --- a/scripts/set_metadata.py +++ b/scripts/set_metadata.py @@ -35,6 +35,7 @@ from galaxy.objectstore import build_object_store_from_config from galaxy import config import ConfigParser +from galaxy.util.properties import load_app_properties def set_meta_with_tool_provided( dataset_instance, file_dict, set_meta_kwds ): @@ -63,18 +64,7 @@ # Set up reference to object store # First, read in the main config file for Galaxy; this is required because # the object store configuration is stored there - conf = ConfigParser.ConfigParser() - conf.read(config_file_name) - conf_dict = {} - for section in conf.sections(): - for option in conf.options(section): - try: - conf_dict[option] = conf.get(section, option) - except ConfigParser.InterpolationMissingOptionError: - # Because this is not called from Paste Script, %(here)s variable - # is not initialized in the config file so skip those fields - - # just need not to use any such fields for the object store conf... - log.debug("Did not load option %s from %s" % (option, config_file_name)) + conf_dict = load_app_properties( ini_file=config_file_name ) # config object is required by ObjectStore class so create it now universe_config = config.Configuration(**conf_dict) universe_config.ensure_tempdir() https://bitbucket.org/galaxy/galaxy-central/commits/f94766d53345/ Changeset: f94766d53345 User: jmchilton Date: 2014-10-14 19:25:55+00:00 Summary: Switch local runner to set metadata externally by default. Affected #: 1 file diff -r b6cb3aabfba4ec844f346fb2d363e47822a3d989 -r f94766d533450d6e69f6c14000719082f40f84e6 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -23,7 +23,7 @@ DEFAULT_POOL_SLEEP_TIME = 1 # TODO: Set to false and just get rid of this option. It would simplify this # class nicely. -John -DEFAULT_EMBED_METADATA_IN_JOB = False +DEFAULT_EMBED_METADATA_IN_JOB = True class LocalJobRunner( BaseJobRunner ): https://bitbucket.org/galaxy/galaxy-central/commits/5238a1e029e9/ Changeset: 5238a1e029e9 User: jmchilton Date: 2014-10-14 19:25:55+00:00 Summary: Add ability to disable asynchronous data uploads in tool tests. Honestly - need to find a way to make this the default if sqlite is the target. Affected #: 1 file diff -r f94766d533450d6e69f6c14000719082f40f84e6 -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -21,6 +21,7 @@ # and result in sqlite errors on larger tests or larger numbers of # tests. VERBOSE_ERRORS = util.asbool( os.environ.get( "GALAXY_TEST_VERBOSE_ERRORS", False ) ) +UPLOAD_ASYNC = util.asbool( os.environ.get( "GALAXY_TEST_UPLOAD_ASYNC", True ) ) ERROR_MESSAGE_DATASET_SEP = "--------------------------------------" @@ -33,10 +34,15 @@ # Upload any needed files upload_waits = [] - for test_data in all_test_data: - upload_waits.append( galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) ) - for upload_wait in upload_waits: - upload_wait() + if UPLOAD_ASYNC: + for test_data in all_test_data: + upload_waits.append( galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) ) + for upload_wait in upload_waits: + upload_wait() + else: + for test_data in all_test_data: + upload_wait = galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) + upload_wait() class GalaxyInteractorApi( object ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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