1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c15/ Changeset: af5577a24c15 User: jmchilton Date: 2014-03-07 15:18:16 Summary: Prevent 'unicode' strings being sent to pbs library as hostname. Full details here: http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-un... Not sure this is the right thing to do - so I would welcome advice/comments. Affected #: 1 file diff -r 1b8b87437c7e0b8e7a9f6a51b0ec910237e514f1 -r af5577a24c155fa04aa607ff2fec283634df2fb0 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -5,6 +5,7 @@ from datetime import timedelta from galaxy import model +from galaxy import util from galaxy.util.bunch import Bunch from galaxy.util import DATABASE_MAX_STRING_SIZE, shrink_stream_by_size from galaxy.jobs import JobDestination @@ -233,7 +234,7 @@ # Explicitly set the determined PBS destination in the persisted job destination for recovery job_destination.params['destination'] = '%s@%s' % (pbs_queue_name or '', pbs_server_name) - c = pbs.pbs_connect( pbs_server_name ) + c = pbs.pbs_connect( util.smart_str( pbs_server_name ) ) if c <= 0: errno, text = pbs.error() job_wrapper.fail( "Unable to queue job for execution. Resubmitting the job may succeed." ) @@ -449,7 +450,7 @@ servers.append( pbs_server_name ) pbs_job_state.check_count += 1 for pbs_server_name in servers: - c = pbs.pbs_connect( pbs_server_name ) + c = pbs.pbs_connect( util.smart_str( pbs_server_name ) ) if c <= 0: log.debug("connection to PBS server %s for state check failed" % pbs_server_name ) failures.append( pbs_server_name ) @@ -482,7 +483,7 @@ Returns the state of a single job, used to make sure a job is really dead. """ - c = pbs.pbs_connect( pbs_server_name ) + c = pbs.pbs_connect( util.smart_str( pbs_server_name ) ) if c <= 0: log.debug("connection to PBS server %s for state check failed" % pbs_server_name ) return None @@ -584,7 +585,7 @@ log.debug("(%s) Job queued but no destination stored in job params, cannot delete" % job_tag ) return - c = pbs.pbs_connect( pbs_server_name ) + c = pbs.pbs_connect( util.smart_str( pbs_server_name ) ) if c <= 0: log.debug("(%s) Connection to PBS server for job delete failed" % job_tag ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.