1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/45963b149ddb/
Changeset: 45963b149ddb
User: jmchilton
Date: 2014-06-18 00:22:55
Summary: Fix typo in b267ce103960.
Affected #: 1 file
diff -r b267ce1039608f0c8fbbd42f148a372871668c22 -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
--- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
+++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
@@ -6,7 +6,7 @@
GALAXY_SLOTS="$SLURM_NTASKS"
elif [ -n "$NSLOTS" ]; then
GALAXY_SLOTS="$NSLOTS"
-elif [ -n "$PBS_NCPUS" ] then
+elif [ -n "$PBS_NCPUS" ]; then
GALAXY_SLOTS="$PBS_NCPUS"
elif [ -f "$PBS_NODEFILE" ]; then
GALAXY_SLOTS=`wc -l < $PBS_NODEFILE`
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b267ce103960/
Changeset: b267ce103960
User: jmchilton
Date: 2014-06-17 22:10:58
Summary: Fix PBS GALAXY_SLOTS configuration for torque environments explicitly defining num slots.
Affected #: 1 file
diff -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 -r b267ce1039608f0c8fbbd42f148a372871668c22 lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
--- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
+++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
@@ -6,6 +6,8 @@
GALAXY_SLOTS="$SLURM_NTASKS"
elif [ -n "$NSLOTS" ]; then
GALAXY_SLOTS="$NSLOTS"
+elif [ -n "$PBS_NCPUS" ] then
+ GALAXY_SLOTS="$PBS_NCPUS"
elif [ -f "$PBS_NODEFILE" ]; then
GALAXY_SLOTS=`wc -l < $PBS_NODEFILE`
elif [ -n "$LSB_DJOB_NUMPROC" ]; then
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/95937a7e51f2/
Changeset: 95937a7e51f2
User: greg
Date: 2014-06-17 17:24:33
Summary: For standardization and clarity, rename Galaxy's UpdateManager to be UpdateRepositoryManager.
Affected #: 4 files
diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -82,10 +82,10 @@
self.data_managers = DataManagers( self )
# If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories.
if self.config.get_bool( 'enable_tool_shed_check', False ):
- from tool_shed.galaxy_install import update_manager
- self.update_manager = update_manager.UpdateManager( self )
+ from tool_shed.galaxy_install import update_repository_manager
+ self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self )
else:
- self.update_manager = None
+ self.update_repository_manager = None
# Load proprietary datatype converters and display applications.
self.installed_repository_manager.load_proprietary_converters_and_display_applications()
# Load datatype display applications defined in local datatypes_conf.xml
@@ -159,8 +159,8 @@
self.object_store.shutdown()
if self.heartbeat:
self.heartbeat.shutdown()
- if self.update_manager:
- self.update_manager.shutdown()
+ if self.update_repository_manager is not None:
+ self.update_repository_manager.shutdown()
if self.control_worker:
self.control_worker.shutdown()
try:
diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -887,7 +887,7 @@
"""Handle a request from a local Galaxy instance."""
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- # If the request originated with the UpdateManager, it will not include a galaxy_url.
+ # If the request originated with the UpdateRepositoryManager, it will not include a galaxy_url.
galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/tool_shed/galaxy_install/update_manager.py
--- a/lib/tool_shed/galaxy_install/update_manager.py
+++ /dev/null
@@ -1,67 +0,0 @@
-"""
-Determine if installed tool shed repositories have updates available in their respective tool sheds.
-"""
-import logging
-import threading
-from galaxy.util import string_as_bool
-import tool_shed.util.shed_util_common as suc
-from tool_shed.util import common_util
-from galaxy.model.orm import and_
-
-log = logging.getLogger( __name__ )
-
-
-class UpdateManager( object ):
-
- def __init__( self, app ):
- self.app = app
- self.context = self.app.install_model.context
- # Ideally only one Galaxy server process should be able to check for repository updates.
- self.running = True
- self.sleeper = Sleeper()
- self.restarter = threading.Thread( target=self.__restarter )
- self.restarter.start()
- self.seconds_to_sleep = int( app.config.hours_between_check * 3600 )
-
- def __restarter( self ):
- log.info( 'Update manager restarter starting up...' )
- while self.running:
- # Make a call to the tool shed for each installed repository to get the latest status information in the tool shed for the
- # repository. This information includes items like newer installable repository revisions, current revision updates, whether
- # the repository revision is the latest installable revision, and whether the repository has been deprecated in the tool shed.
- for repository in self.context.query( self.app.install_model.ToolShedRepository ) \
- .filter( self.app.install_model.ToolShedRepository.table.c.deleted == False ):
- tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository )
- if tool_shed_status_dict:
- if tool_shed_status_dict != repository.tool_shed_status:
- repository.tool_shed_status = tool_shed_status_dict
- self.context.flush()
- else:
- # The received tool_shed_status_dict is an empty dictionary, so coerce to None.
- tool_shed_status_dict = None
- if tool_shed_status_dict != repository.tool_shed_status:
- repository.tool_shed_status = tool_shed_status_dict
- self.context.flush()
- self.sleeper.sleep( self.seconds_to_sleep )
- log.info( 'Update manager restarter shutting down...' )
-
- def shutdown( self ):
- self.running = False
- self.sleeper.wake()
-
-
-class Sleeper( object ):
- """Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method is called (from a different thread)."""
-
- def __init__( self ):
- self.condition = threading.Condition()
-
- def sleep( self, seconds ):
- self.condition.acquire()
- self.condition.wait( seconds )
- self.condition.release()
-
- def wake( self ):
- self.condition.acquire()
- self.condition.notify()
- self.condition.release()
diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/tool_shed/galaxy_install/update_repository_manager.py
--- /dev/null
+++ b/lib/tool_shed/galaxy_install/update_repository_manager.py
@@ -0,0 +1,69 @@
+"""
+Determine if installed tool shed repositories have updates available in their respective tool sheds.
+"""
+import logging
+import threading
+import tool_shed.util.shed_util_common as suc
+
+log = logging.getLogger( __name__ )
+
+
+class UpdateRepositoryManager( object ):
+
+ def __init__( self, app ):
+ self.app = app
+ self.context = self.app.install_model.context
+ # Ideally only one Galaxy server process should be able to check for repository updates.
+ self.running = True
+ self.sleeper = Sleeper()
+ self.restarter = threading.Thread( target=self.__restarter )
+ self.restarter.start()
+ self.seconds_to_sleep = int( app.config.hours_between_check * 3600 )
+
+ def __restarter( self ):
+ log.info( 'Update repository manager restarter starting up...' )
+ while self.running:
+ # Make a call to the Tool Shed for each installed repository to get the latest
+ # status information in the Tool Shed for the repository. This information includes
+ # items like newer installable repository revisions, current revision updates, whether
+ # the repository revision is the latest installable revision, and whether the repository
+ # has been deprecated in the Tool Shed.
+ for repository in self.context.query( self.app.install_model.ToolShedRepository ) \
+ .filter( self.app.install_model.ToolShedRepository.table.c.deleted == False ):
+ tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository )
+ if tool_shed_status_dict:
+ if tool_shed_status_dict != repository.tool_shed_status:
+ repository.tool_shed_status = tool_shed_status_dict
+ self.context.flush()
+ else:
+ # The received tool_shed_status_dict is an empty dictionary, so coerce to None.
+ tool_shed_status_dict = None
+ if tool_shed_status_dict != repository.tool_shed_status:
+ repository.tool_shed_status = tool_shed_status_dict
+ self.context.flush()
+ self.sleeper.sleep( self.seconds_to_sleep )
+ log.info( 'Update repository manager restarter shutting down...' )
+
+ def shutdown( self ):
+ self.running = False
+ self.sleeper.wake()
+
+
+class Sleeper( object ):
+ """
+ Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method
+ is called (from a different thread).
+ """
+
+ def __init__( self ):
+ self.condition = threading.Condition()
+
+ def sleep( self, seconds ):
+ self.condition.acquire()
+ self.condition.wait( seconds )
+ self.condition.release()
+
+ def wake( self ):
+ self.condition.acquire()
+ self.condition.notify()
+ self.condition.release()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.