2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/aefe5cf99f92/
Changeset: aefe5cf99f92
Branch: next-stable
User: abretaud
Date: 2014-02-07 11:51:41
Summary: Fix crash when recovering jobs of a removed tool
Affected #: 1 file
diff -r deea87095946ea32d28491b44a120bbc94683150 -r aefe5cf99f92eaa3a401f3f7a9edf9dce4027ed1 lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -107,7 +107,7 @@
if job.tool_id not in self.app.toolbox.tools_by_id:
log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) )
JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' )
- if job.job_runner_name is not None and job.job_runner_external_id is None:
+ elif job.job_runner_name is not None and job.job_runner_external_id is None:
# This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner.
log.debug( "(%s) Job runner assigned but no external ID recorded, adding to the job handler queue" % job.id )
job.job_runner_name = None
https://bitbucket.org/galaxy/galaxy-central/commits/5e2a4255cf09/
Changeset: 5e2a4255cf09
User: natefoo
Date: 2014-02-07 15:27:14
Summary: merge.
Affected #: 0 files
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f6f6529b8ca1/
Changeset: f6f6529b8ca1
User: abretaud
Date: 2014-02-07 11:51:41
Summary: Fix crash when recovering jobs of a removed tool
Affected #: 1 file
diff -r 086e594d372cc58a823f061c3a008a60c0c33472 -r f6f6529b8ca14267bdd3c4ab1fcd2343dffc08dd lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -107,7 +107,7 @@
if job.tool_id not in self.app.toolbox.tools_by_id:
log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) )
JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' )
- if job.job_runner_name is not None and job.job_runner_external_id is None:
+ elif job.job_runner_name is not None and job.job_runner_external_id is None:
# This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner.
log.debug( "(%s) Job runner assigned but no external ID recorded, adding to the job handler queue" % job.id )
job.job_runner_name = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/086e594d372c/
Changeset: 086e594d372c
User: guerler
Date: 2014-02-07 06:06:55
Summary: Merge
Affected #: 1 file
diff -r dc69ee2333c21cdc24d6b5855355fd5a08a8ab53 -r 086e594d372cc58a823f061c3a008a60c0c33472 lib/galaxy/web/framework/helpers/grids.py
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -777,7 +777,7 @@
return dict( operation=self.label, id=item.id )
def allowed( self, item ):
if self.condition:
- return self.condition( item )
+ return bool(self.condition( item ))
else:
return True
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/deea87095946/
Changeset: deea87095946
Branch: next-stable
User: guerler
Date: 2014-02-07 06:05:02
Summary: Grids: Convert ill defined conditions to boolean
Affected #: 1 file
diff -r d5ce503c01b7e5520133014d0927b3d062eb9705 -r deea87095946ea32d28491b44a120bbc94683150 lib/galaxy/web/framework/helpers/grids.py
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -768,7 +768,7 @@
return dict( operation=self.label, id=item.id )
def allowed( self, item ):
if self.condition:
- return self.condition( item )
+ return bool(self.condition( item ))
else:
return True
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4ede9ee8278e/
Changeset: 4ede9ee8278e
User: guerler
Date: 2014-02-07 04:34:44
Summary: Fix undelete action in quota grid
Affected #: 1 file
diff -r a2739727943039f4c8f74194491396ffa1299267 -r 4ede9ee8278e18df75a3d79b7a6b133274b058b6 lib/galaxy/actions/admin.py
--- a/lib/galaxy/actions/admin.py
+++ b/lib/galaxy/actions/admin.py
@@ -150,7 +150,7 @@
message += ', '.join( names )
return message
- def _undelete_quota( self, quota ):
+ def _undelete_quota( self, quota, params ):
quotas = util.listify( quota )
names = []
for q in quotas:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d5ce503c01b7/
Changeset: d5ce503c01b7
Branch: next-stable
User: jeremy goecks
Date: 2014-02-07 03:41:32
Summary: Prioritize gene id over transcript id for interval name in GFF data provider.
Affected #: 1 file
diff -r 54508df431ac564f4ddaf37e3c647f5b18576cbf -r d5ce503c01b7e5520133014d0927b3d062eb9705 lib/galaxy/datatypes/util/gff_util.py
--- a/lib/galaxy/datatypes/util/gff_util.py
+++ b/lib/galaxy/datatypes/util/gff_util.py
@@ -75,7 +75,7 @@
# Preference for name: GTF, GFF3, GFF.
for attr_name in [
# GTF:
- 'transcript_id', 'gene_id',
+ 'gene_id', 'transcript_id',
# GFF3:
'ID', 'id',
# GFF (TODO):
https://bitbucket.org/galaxy/galaxy-central/commits/a27397279430/
Changeset: a27397279430
User: jeremy goecks
Date: 2014-02-07 03:42:29
Summary: Merge next-stable to default
Affected #: 1 file
diff -r d92f65506e1cdc46b29aa0049d04bf2fb4179742 -r a2739727943039f4c8f74194491396ffa1299267 lib/galaxy/datatypes/util/gff_util.py
--- a/lib/galaxy/datatypes/util/gff_util.py
+++ b/lib/galaxy/datatypes/util/gff_util.py
@@ -75,7 +75,7 @@
# Preference for name: GTF, GFF3, GFF.
for attr_name in [
# GTF:
- 'transcript_id', 'gene_id',
+ 'gene_id', 'transcript_id',
# GFF3:
'ID', 'id',
# GFF (TODO):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/54508df431ac/
Changeset: 54508df431ac
Branch: next-stable
User: jmchilton
Date: 2014-02-07 00:08:36
Summary: Fix documentation on normalize remote user e-mail.
Listed values should be unmodified defaults.
Affected #: 1 file
diff -r 0a9053d624bb0bf253b51b99f07cb600b3fb3490 -r 54508df431ac564f4ddaf37e3c647f5b18576cbf universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -602,9 +602,9 @@
#remote_user_logout_href = None
# If your proxy and/or authentication source does not normalize e-mail
-# addresses or user names being passed to Galaxy - enable the following option
-# to force these to lower case.
-#normalize_remote_user_email = True
+# addresses or user names being passed to Galaxy - set the following option
+# to True to force these to lower case.
+#normalize_remote_user_email = False
# Administrative users - set this to a comma-separated list of valid Galaxy
# users (email addresses). These users will have access to the Admin section
https://bitbucket.org/galaxy/galaxy-central/commits/d92f65506e1c/
Changeset: d92f65506e1c
User: jmchilton
Date: 2014-02-07 00:08:58
Summary: Merge next-stable.
Affected #: 1 file
diff -r d282cb8daecb0748350a6ea69164071854fdaf60 -r d92f65506e1cdc46b29aa0049d04bf2fb4179742 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -602,9 +602,9 @@
#remote_user_logout_href = None
# If your proxy and/or authentication source does not normalize e-mail
-# addresses or user names being passed to Galaxy - enable the following option
-# to force these to lower case.
-#normalize_remote_user_email = True
+# addresses or user names being passed to Galaxy - set the following option
+# to True to force these to lower case.
+#normalize_remote_user_email = False
# Administrative users - set this to a comma-separated list of valid Galaxy
# users (email addresses). These users will have access to the Admin section
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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