1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bc3fd881b07f/ Changeset: bc3fd881b07f User: jmchilton Date: 2014-04-23 03:50:18 Summary: Unit tests for job conf parsing. Update advanced job sample to fix "bugs" discovered during testing limit parsing. Affected #: 2 files diff -r 68b49fdc63e2445ee2124e0185373d964bc64bc8 -r bc3fd881b07f5904ccad6d2d187e7d8e3c506652 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -159,8 +159,8 @@ <limits><!-- Certain limits can be defined. --><limit type="registered_user_concurrent_jobs">2</limit> - <limit type="unregistered_user_concurrent_jobs">1</limit> - <limit type="job_walltime">24:00:00</limit> + <limit type="anonymous_user_concurrent_jobs">1</limit> + <limit type="walltime">24:00:00</limit><limit type="concurrent_jobs" id="local">1</limit><limit type="concurrent_jobs" tag="mycluster">2</limit><limit type="concurrent_jobs" tag="longjobs">1</limit> diff -r 68b49fdc63e2445ee2124e0185373d964bc64bc8 -r bc3fd881b07f5904ccad6d2d187e7d8e3c506652 test/unit/jobs/test_job_configuration.py --- /dev/null +++ b/test/unit/jobs/test_job_configuration.py @@ -0,0 +1,128 @@ +import datetime +import os +import shutil +import tempfile +import unittest + +from galaxy.util import bunch +from galaxy.jobs import JobConfiguration + +# File would be slightly more readable if contents were embedded directly, but +# there are advantages to testing the documentation/examples. +SIMPLE_JOB_CONF = os.path.join( os.path.dirname( __file__ ), "..", "..", "..", "job_conf.xml.sample_basic" ) +ADVANCED_JOB_CONF = os.path.join( os.path.dirname( __file__ ), "..", "..", "..", "job_conf.xml.sample_advanced" ) + + +class JobConfXmlParserTestCase( unittest.TestCase ): + + def setUp( self ): + self.temp_directory = tempfile.mkdtemp() + self.config = bunch.Bunch( + job_config_file=os.path.join( self.temp_directory, "job_conf.xml" ), + use_tasked_jobs=False, + ) + self.__write_config_from( SIMPLE_JOB_CONF ) + self.app = bunch.Bunch( config=self.config ) + self.__job_configuration = None + + def tearDown( self ): + shutil.rmtree( self.temp_directory ) + + def test_load_simple_runner( self ): + runner_plugin = self.job_config.runner_plugins[ 0 ] + assert runner_plugin[ "id" ] == "local" + assert runner_plugin[ "load" ] == "galaxy.jobs.runners.local:LocalJobRunner" + assert runner_plugin[ "workers" ] == 4 + + def test_tasks_disabled( self ): + assert len( [ r for r in self.job_config.runner_plugins if r[ "id" ] == "tasks" ] ) == 0 + + def test_configuration_of_tasks( self ): + self.config.use_tasked_jobs = True + self.config.local_task_queue_workers = 5 + task_runners = [ r for r in self.job_config.runner_plugins if r[ "id" ] == "tasks" ] + assert len( task_runners ) == 1 + assert task_runners[ 0 ][ "workers" ] == 5 + + def test_load_simple_handler( self ): + main_handler = self.job_config.handlers[ "main" ] + assert main_handler[ 0 ] == "main" + + def test_if_one_handler_implicit_default( self ): + assert self.job_config.default_handler_id == "main" + + def test_explicit_handler_default( self ): + self.__with_advanced_config() + assert self.job_config.default_handler_id == "handlers" + + def test_handler_tag_parsing( self ): + self.__with_advanced_config() + assert "handler0" in self.job_config.handlers[ "handlers" ] + assert "handler1" in self.job_config.handlers[ "handlers" ] + + def test_load_simple_destination( self ): + local_dest = self.job_config.destinations[ "local" ][ 0 ] + assert local_dest.id == "local" + assert local_dest.runner == "local" + + def test_load_destination_params( self ): + self.__with_advanced_config() + pbs_dest = self.job_config.destinations[ "pbs_longjobs" ][ 0 ] + assert pbs_dest.id == "pbs_longjobs" + assert pbs_dest.runner == "pbs" + dest_params = pbs_dest.params + assert dest_params[ "Resource_List" ] == "walltime=72:00:00" + + def test_destination_tags( self ): + self.__with_advanced_config() + longjob_dests = self.job_config.destinations[ "longjobs" ] + assert len( longjob_dests ) == 2 + assert longjob_dests[ 0 ].id == "pbs_longjobs" + assert longjob_dests[ 1 ].id == "remote_cluster" + + def test_load_tool( self ): + self.__with_advanced_config() + baz_tool = self.job_config.tools[ "baz" ][ 0 ] + assert baz_tool.id == "baz" + assert baz_tool.handler == "special_handlers" + assert baz_tool.destination == "bigmem" + + def test_load_tool_params( self ): + self.__with_advanced_config() + foo_tool = self.job_config.tools[ "foo" ][ 0 ] + assert foo_tool.params[ "source" ] == "trackster" + + def test_default_limits( self ): + limits = self.job_config.limits + assert limits.registered_user_concurrent_jobs is None + assert limits.anonymous_user_concurrent_jobs is None + assert limits.walltime is None + assert limits.walltime_delta is None + assert limits.output_size is None + assert limits.concurrent_jobs == {} + + def test_limit_overrides( self ): + self.__with_advanced_config() + limits = self.job_config.limits + assert limits.registered_user_concurrent_jobs == 2 + assert limits.anonymous_user_concurrent_jobs == 1 + assert limits.concurrent_jobs[ "local" ] == 1 + assert limits.concurrent_jobs[ "mycluster" ] == 2 + assert limits.concurrent_jobs[ "longjobs" ] == 1 + assert limits.walltime_delta == datetime.timedelta( 0, 0, 0, 0, 0, 24 ) + + @property + def job_config( self ): + if not self.__job_configuration: + self.__job_configuration = JobConfiguration( self.app ) + return self.__job_configuration + + def __with_advanced_config( self ): + self.__write_config_from( ADVANCED_JOB_CONF ) + + def __write_config_from( self, path ): + self.__write_config( open( path, "r" ).read() ) + + def __write_config( self, contents ): + with open( os.path.join( self.temp_directory, "job_conf.xml" ), "w" ) as f: + f.write( contents ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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