1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6cd4058d7b32/
changeset: 6cd4058d7b32
user: dan
date: 2013-01-11 21:41:29
summary: Fix for external display applications and permissions.
affected #: 1 file
diff -r 3674685eeb0d171b9f4c0b01e2c7f56cfba86ce7 -r 6cd4058d7b32f788e3c7484f0c5709e89cfbed0f lib/galaxy/webapps/galaxy/controllers/dataset.py
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -163,8 +163,11 @@
assert hda and self._can_access_dataset( trans, hda )
return hda.creating_job
- def _can_access_dataset( self, trans, dataset_association, allow_admin=True ):
- return ( allow_admin and trans.user_is_admin() ) or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset_association.dataset )
+ def _can_access_dataset( self, trans, dataset_association, allow_admin=True, additional_roles=None ):
+ roles = trans.get_current_user_roles()
+ if additional_roles:
+ roles = roles + additional_roles
+ return ( allow_admin and trans.user_is_admin() ) or trans.app.security_agent.can_access_dataset( roles, dataset_association.dataset )
@web.expose
def errors( self, trans, id ):
@@ -736,7 +739,7 @@
link_name = urllib.unquote_plus( link_name )
if None in [ app_name, link_name ]:
return trans.show_error_message( "A display application name and link name must be provided." )
- if self._can_access_dataset( trans, data ):
+ if self._can_access_dataset( trans, data, additional_roles=user_roles ):
msg = []
refresh = False
display_app = trans.app.datatypes_registry.display_applications.get( app_name )
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/be7625f376d1/
changeset: be7625f376d1
user: james_taylor
date: 2013-01-11 20:49:24
summary: ClusterJobRunner: make sure workers are daemon threads, shutdown now works again
affected #: 1 file
diff -r 71a616ffce1c85aa31d3e5311d5babfc12c49381 -r be7625f376d16cefa2fb4984fa6483f37b4b71d4 lib/galaxy/jobs/runners/__init__.py
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -152,6 +152,7 @@
nworkers = self.app.config.cluster_job_queue_workers
for i in range( nworkers ):
worker = threading.Thread( name="%s.work_thread-%d" % (self.runner_name, i), target=self.run_next )
+ worker.setDaemon( True )
worker.start()
self.work_threads.append( worker )
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/e9f81b5154bb/
changeset: e9f81b5154bb
user: inithello
date: 2013-01-11 19:31:02
summary: Fix for installing a repository with set_environment tool dependencies.
affected #: 1 file
diff -r e5ec6ed8f0337893cf4bc64e61089471b00b28b0 -r e9f81b5154bb71c6c12d4591c8f9519e52c93212 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -791,9 +791,17 @@
tool_dependencies = {}
missing_tool_dependencies = {}
for td_key, val in all_tool_dependencies.items():
- # Since we have a new install, missing tool dependencies have never been installed.
- val[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED
- missing_tool_dependencies[ td_key ] = val
+ # Set environment tool dependencies are a list, set each member to never installed.
+ if td_key == 'set_environment':
+ new_val = []
+ for requirement_dict in val:
+ requirement_dict[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED
+ new_val.append( requirement_dict )
+ missing_tool_dependencies[ td_key ] = new_val
+ else:
+ # Since we have a new install, missing tool dependencies have never been installed.
+ val[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED
+ missing_tool_dependencies[ td_key ] = val
else:
tool_dependencies = None
missing_tool_dependencies = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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