1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/0b1fa1746a4c/
changeset: r5065:0b1fa1746a4c
user: natefoo
date: 2011-02-15 22:52:16
summary: lazy load jobs for job recovery and a bugfix for administrative job stops when tracking jobs in the database.
affected #: 1 file (98 bytes)
--- a/lib/galaxy/jobs/__init__.py Tue Feb 15 15:15:54 2011 -0500
+++ b/lib/galaxy/jobs/__init__.py Tue Feb 15 16:52:16 2011 -0500
@@ -112,7 +112,7 @@
else:
log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id )
self.queue.put( ( job.id, job.tool_id ) )
- for job in self.sa_session.query( model.Job ).filter( ( model.Job.state == model.Job.states.RUNNING ) | ( model.Job.state == model.Job.states.QUEUED ) ):
+ for job in self.sa_session.query( model.Job ).options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ).filter( ( model.Job.state == model.Job.states.RUNNING ) | ( model.Job.state == model.Job.states.QUEUED ) ):
if job.tool_id not in self.app.toolbox.tools_by_id:
log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) )
JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator, or' )
@@ -1129,18 +1129,18 @@
.filter( model.Job.state == model.Job.states.DELETED_NEW ).all()
for job in newly_deleted_jobs:
jobs_to_check.append( ( job, None ) )
- else:
- try:
- while 1:
- message = self.queue.get_nowait()
- if message is self.STOP_SIGNAL:
- return
- # Unpack the message
- job_id, error_msg = message
- # Get the job object and append to watch queue
- jobs_to_check.append( ( self.sa_session.query( model.Job ).get( job_id ), error_msg ) )
- except Empty:
- pass
+ # Also pull from the queue (in the case of Administrative stopped jobs)
+ try:
+ while 1:
+ message = self.queue.get_nowait()
+ if message is self.STOP_SIGNAL:
+ return
+ # Unpack the message
+ job_id, error_msg = message
+ # Get the job object and append to watch queue
+ jobs_to_check.append( ( self.sa_session.query( model.Job ).get( job_id ), error_msg ) )
+ except Empty:
+ pass
for job, error_msg in jobs_to_check:
if error_msg is not None:
job.state = job.states.ERROR
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/cbc9182db377/
changeset: r5061:cbc9182db377
user: rc
date: 2011-02-15 19:38:22
summary: Bug fix: when no library is associated with the sample link to display datasets is disabled.
affected #: 1 file (38 bytes)
--- a/templates/requests/common/common.mako Mon Feb 14 19:40:40 2011 -0500
+++ b/templates/requests/common/common.mako Tue Feb 15 13:38:22 2011 -0500
@@ -479,10 +479,10 @@
%if is_submitted or is_complete:
<td>
## An admin can select the datasets to transfer, while a non-admin can only view what has been selected
- %if is_admin:
+ %if sample.library and is_admin:
## This link will direct the admin to a page allowing them to manage datasets.
<a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a>
- %elif sample.datasets:
+ %elif sample.library and sample.datasets:
## Since this is a regular user, only display a link if there is at least 1
## selected dataset for the sample.
<a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/9f417fd7a908/
changeset: r5059:9f417fd7a908
user: jgoecks
date: 2011-02-14 23:25:09
summary: Fix attribute bug in cuffcompare wrapper.
affected #: 1 file (6 bytes)
--- a/tools/ngs_rna/cuffcompare_wrapper.xml Mon Feb 14 15:53:39 2011 -0500
+++ b/tools/ngs_rna/cuffcompare_wrapper.xml Mon Feb 14 17:25:09 2011 -0500
@@ -22,7 +22,7 @@
#else:
--ref_file="None"
#end if
- --dbkey=${first_input.input.metadata.dbkey}
+ --dbkey=${first_input.metadata.dbkey}
--index_dir=${GALAXY_DATA_INDEX_DIR}
#end if
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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