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@jmchilton
Created March 4, 2014 19:21
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Fix for passing unicode values to pbs library in Galaxy pbs runner.
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index 6fd577a..22f12a5 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -5,6 +5,7 @@ import traceback
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 @@ class PBSJobRunner( AsynchronousJobRunner ):
# 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 @@ class PBSJobRunner( AsynchronousJobRunner ):
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 @@ class PBSJobRunner( AsynchronousJobRunner ):
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 @@ class PBSJobRunner( AsynchronousJobRunner ):
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 )
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