1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/eb4206636dd9/
changeset: eb4206636dd9
user: dannon
date: 2012-07-30 21:54:34
summary: Fix tabular display to serve raw when preview == False, which should resolve external display issues.
affected #: 1 file
diff -r cdf84aee000b28bd73bbae56b31480e9ce5a6a86 -r eb4206636dd9b385cc84f20b81d61f9ea11727c5 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -264,7 +264,7 @@
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None):
#TODO Prevent failure when displaying extremely long > 50kb lines.
- if to_ext:
+ if to_ext or not preview:
return self._serve_raw(trans, dataset, to_ext)
if chunk:
return self.get_chunk(trans, dataset, chunk)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/cdf84aee000b/
changeset: cdf84aee000b
user: natefoo
date: 2012-07-27 18:39:24
summary: Handle the varying sample ID param name ('id' or 'sample_id') in /requests_admin/manage_datasets
affected #: 1 file
diff -r aedb20d3dd7e9a1e0638c7ffb85d0993c501c30f -r cdf84aee000b28bd73bbae56b31480e9ce5a6a86 lib/galaxy/web/controllers/requests_admin.py
--- a/lib/galaxy/web/controllers/requests_admin.py
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -198,7 +198,13 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
+ # When this method is called due to a grid operation, the sample ID
+ # will be in the param 'id'. But when this method is called via a
+ # redirect from another method, the ID will be in 'sample_id'. So,
+ # check for 'id' if 'sample_id' is not provided.
sample_id = params.get( 'sample_id', None )
+ if sample_id is None:
+ sample_id = params.get( 'id', None )
try:
sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) )
except:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/aedb20d3dd7e/
changeset: aedb20d3dd7e
user: natefoo
date: 2012-07-27 16:57:29
summary: Document user_job_limit
affected #: 1 file
diff -r 099692958fcaaf9ade3c1fb430aca6860f114fe9 -r aedb20d3dd7e9a1e0638c7ffb85d0993c501c30f universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -640,6 +640,12 @@
# bytes). 0 for no limit.
#output_size_limit = 0
+# Jobs can be held back from submission to a runner if a user already has more
+# jobs queued or running than the number specified below. This prevents a
+# single user from stuffing the queue and preventing other users from being
+# able to run jobs.
+#user_job_limit = None
+
# Clustering Galaxy is not a straightforward process and requires some
# pre-configuration. See the the wiki before attempting to set any of these
# options:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/5be1bf4605c3/
changeset: 5be1bf4605c3
user: takadonet
date: 2012-06-26 21:16:25
summary: Check for 'run_as' argument in dictionary 'payload' instead of kwargs
affected #: 1 file
diff -r 40ff9b0e1549c1b083a3822b25b8337808ad8995 -r 5be1bf4605c34a96f19c1a49352ad6769e7fb020 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -134,15 +134,15 @@
return error
trans.response.set_content_type( "application/json" )
# Perform api_run_as processing, possibly changing identity
- if 'run_as' in kwargs:
+ if 'payload' in kwargs and 'run_as' in kwargs['payload']:
if not trans.user_can_do_run_as():
error_message = 'User does not have permissions to run jobs as another user'
return error
try:
- decoded_user_id = trans.security.decode_id( kwargs['run_as'] )
+ decoded_user_id = trans.security.decode_id( kwargs['payload']['run_as'] )
except TypeError:
trans.response.status = 400
- return "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['run_as'] )
+ return "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['payload']['run_as'] )
try:
user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
trans.api_inherit_admin = trans.user_is_admin()
https://bitbucket.org/galaxy/galaxy-central/changeset/e3a62476b0cd/
changeset: e3a62476b0cd
user: natefoo
date: 2012-07-27 08:14:52
summary: Merged in takadonet/galaxy-central (pull request #50)
affected #: 1 file
diff -r 594b69416e8ce8bac101cedc662240d46ac90031 -r e3a62476b0cd6eacdff24311860507311fb03808 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -134,15 +134,15 @@
return error
trans.response.set_content_type( "application/json" )
# Perform api_run_as processing, possibly changing identity
- if 'run_as' in kwargs:
+ if 'payload' in kwargs and 'run_as' in kwargs['payload']:
if not trans.user_can_do_run_as():
error_message = 'User does not have permissions to run jobs as another user'
return error
try:
- decoded_user_id = trans.security.decode_id( kwargs['run_as'] )
+ decoded_user_id = trans.security.decode_id( kwargs['payload']['run_as'] )
except TypeError:
trans.response.status = 400
- return "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['run_as'] )
+ return "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['payload']['run_as'] )
try:
user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
trans.api_inherit_admin = trans.user_is_admin()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/cb9272041d95/
changeset: cb9272041d95
user: rmarenco
date: 2012-07-23 20:17:23
summary: Added eXpress sam format support + 5 parameters (-B, -O, --calc-covar, -m, -s) with their associated tests
affected #: 15 files
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Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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