October 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jmchilton: Revert old test polling behavior with respect to 'new' state.
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/42cd5d55755a/ Changeset: 42cd5d55755a User: jmchilton Date: 2014-10-14 17:21:12+00:00 Summary: Revert old test polling behavior with respect to 'new' state. So that upload failures don't cause test to hang indefinitely. Affected #: 1 file diff -r c465fdbdbdb2db64e08c31e8eb0084c20e9e50ff -r 42cd5d55755a729dd2f19ccd1ed20649ed29f6ac test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1296,7 +1296,7 @@ history_id = loads( self.last_page() )[0][ 'id' ] self.visit_url( '/api/histories/%s' % history_id ) jsondata = loads( self.last_page() ) - return jsondata[ 'state' ] in [ 'new', 'queued', 'running' ] + return jsondata[ 'state' ] in [ 'queued', 'running' ] def get_tags( self, item_id, item_class ): self.visit_url( "%s/tag/get_tagging_elt_async?item_id=%s&item_class=%s" % \ 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.

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commit/galaxy-central: jmchilton: Optimization of API polling during tool testing.
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c465fdbdbdb2/ Changeset: c465fdbdbdb2 User: jmchilton Date: 2014-10-14 16:56:50+00:00 Summary: Optimization of API polling during tool testing. Not the kind of optimization where you take something reasonable and brilliantly streamline it - but the kind of optimization where you take something ridiculus and make it less so. Oh past @jmchilton there is just no hope for you... Affected #: 1 file diff -r dbee027f74101741533851ce2634b60adca4c454 -r c465fdbdbdb2db64e08c31e8eb0084c20e9e50ff test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1294,14 +1294,9 @@ def get_running_datasets( self ): self.visit_url( '/api/histories' ) history_id = loads( self.last_page() )[0][ 'id' ] - self.visit_url( '/api/histories/%s/contents' % history_id ) + self.visit_url( '/api/histories/%s' % history_id ) jsondata = loads( self.last_page() ) - for history_item in jsondata: - self.visit_url( history_item[ 'url' ] ) - item_json = loads( self.last_page() ) - if item_json[ 'state' ] in [ 'queued', 'running', 'paused' ]: - return True - return False + return jsondata[ 'state' ] in [ 'new', 'queued', 'running' ] def get_tags( self, item_id, item_class ): self.visit_url( "%s/tag/get_tagging_elt_async?item_id=%s&item_class=%s" % \ 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.

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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset 1744b7d8e9ab
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cdd3a8a9cd7d/ Changeset: cdd3a8a9cd7d Branch: stable User: natefoo Date: 2014-10-14 13:00:24+00:00 Summary: Update tag latest_2014.10.06 for changeset 1744b7d8e9ab Affected #: 1 file diff -r 1744b7d8e9ab619d78c0516f9ccb093b0a814163 -r cdd3a8a9cd7d5d71705843d2fa448462c7ed0675 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -cb0c2ea402e4c82c7872177e874ce59de29c9c13 latest_2014.10.06 +1744b7d8e9ab619d78c0516f9ccb093b0a814163 latest_2014.10.06 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.

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[galaxyproject/usegalaxy-playbook] 3088f2: Job conf updates for Rodeo.
by GitHub 13 Oct '14

13 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3088f2a4163a7c00ea95a2b79fddb13140514c53 https://github.com/galaxyproject/usegalaxy-playbook/commit/3088f2a4163a7c00… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M files/galaxy/usegalaxy.org/dynamic_rules/reserved.py M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Job conf updates for Rodeo. Commit: 1425812883a708f6b5db52424877131d778057c6 https://github.com/galaxyproject/usegalaxy-playbook/commit/1425812883a708f6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test. Commit: 288841a0899cd5840877343c2236658352a61160 https://github.com/galaxyproject/usegalaxy-playbook/commit/288841a0899cd584… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Fix job conf (there were some unfinished changes in there). Commit: bf815e533408071a72c328b777d823f3eb9e0b67 https://github.com/galaxyproject/usegalaxy-playbook/commit/bf815e533408071a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Fix concurrency. Commit: 563afb451eb64a90d303867434159534b16b88fb https://github.com/galaxyproject/usegalaxy-playbook/commit/563afb451eb64a90… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6f878bbac19e...…

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1744b7d8e9ab/ Changeset: 1744b7d8e9ab Branch: stable User: natefoo Date: 2014-10-14 00:48:30+00:00 Summary: Merge closed duplicate stable head with current stable. Affected #: 2 files diff -r 4a550ab8a4b2c0a45b48732edde703010a7c7509 -r 1744b7d8e9ab619d78c0516f9ccb093b0a814163 lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py +++ b/lib/galaxy/webapps/reports/buildapp.py @@ -3,22 +3,19 @@ """ import logging, atexit -import os, os.path, sys +import os, os.path from inspect import isclass -from paste.request import parse_formvars -from paste.util import import_string from paste import httpexceptions import pkg_resources from galaxy.util import asbool -import config import galaxy.model import galaxy.model.mapping -import galaxy.web.framework +import galaxy.web.framework.webapp log = logging.getLogger( __name__ ) @@ -31,7 +28,6 @@ them to the webapp. """ from galaxy.web.base.controller import BaseUIController - from galaxy.web.base.controller import ControllerUnavailable import galaxy.webapps.reports.controllers controller_dir = galaxy.webapps.reports.controllers.__path__[0] for fname in os.listdir( controller_dir ): https://bitbucket.org/galaxy/galaxy-central/commits/dbee027f7410/ Changeset: dbee027f7410 User: natefoo Date: 2014-10-14 00:49:02+00:00 Summary: Merge stable. Affected #: 2 files diff -r 3f42dfab2cee4706551c9ca0211e7cd08e35058b -r dbee027f74101741533851ce2634b60adca4c454 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac latest_2014.10.06 +cb0c2ea402e4c82c7872177e874ce59de29c9c13 latest_2014.10.06 diff -r 3f42dfab2cee4706551c9ca0211e7cd08e35058b -r dbee027f74101741533851ce2634b60adca4c454 lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py +++ b/lib/galaxy/webapps/reports/buildapp.py @@ -3,22 +3,19 @@ """ import logging, atexit -import os, os.path, sys +import os, os.path from inspect import isclass -from paste.request import parse_formvars -from paste.util import import_string from paste import httpexceptions import pkg_resources from galaxy.util import asbool -import config import galaxy.model import galaxy.model.mapping -import galaxy.web.framework +import galaxy.web.framework.webapp log = logging.getLogger( __name__ ) @@ -31,7 +28,6 @@ them to the webapp. """ from galaxy.web.base.controller import BaseUIController - from galaxy.web.base.controller import ControllerUnavailable import galaxy.webapps.reports.controllers controller_dir = galaxy.webapps.reports.controllers.__path__[0] for fname in os.listdir( controller_dir ): 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.

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commit/galaxy-central: davebgx: Additional fixes for install and test framework.
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3f42dfab2cee/ Changeset: 3f42dfab2cee User: davebgx Date: 2014-10-13 20:07:29+00:00 Summary: Additional fixes for install and test framework. Affected #: 2 files diff -r 67050bf7b3cff0e482bd6ed15b286864ffc77ae5 -r 3f42dfab2cee4706551c9ca0211e7cd08e35058b test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -118,7 +118,8 @@ tool_data_table_conf = None # Set up default tool data tables. If a non-sample version is in config/, use that. Otherwise iterate through lower # priority versions. -for conf in [ 'config/tool_data_table_conf.xml', +for conf in [ 'tool_data_table_conf.test.xml', + 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample', 'tool_data_table_conf.xml', 'tool_data_table_conf.xml.sample' ]: diff -r 67050bf7b3cff0e482bd6ed15b286864ffc77ae5 -r 3f42dfab2cee4706551c9ca0211e7cd08e35058b test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -332,13 +332,14 @@ template_path = "templates", tool_config_file = ','.join( [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] ), tool_data_path = tool_data_path, - tool_data_table_config_path = galaxy_tool_data_table_conf_file, tool_dependency_dir = tool_dependency_dir, tool_path = tool_path, tool_parse_help = False, tool_sheds_config_file = galaxy_tool_sheds_conf_file, update_integrated_tool_panel = False, use_heartbeat = False ) + if os.path.exists( galaxy_tool_data_table_conf_file ): + kwargs[ 'tool_data_table_config_path' ] = galaxy_tool_data_table_conf_file galaxy_config_file = os.environ.get( 'GALAXY_INSTALL_TEST_INI_FILE', None ) # If the user has passed in a path for the .ini file, do not overwrite it. if not galaxy_config_file: 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.

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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset cb0c2ea402e4
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4a550ab8a4b2/ Changeset: 4a550ab8a4b2 Branch: stable User: natefoo Date: 2014-10-13 19:00:25+00:00 Summary: Update tag latest_2014.10.06 for changeset cb0c2ea402e4 Affected #: 1 file diff -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 -r 4a550ab8a4b2c0a45b48732edde703010a7c7509 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac latest_2014.10.06 +cb0c2ea402e4c82c7872177e874ce59de29c9c13 latest_2014.10.06 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.

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commit/galaxy-central: dannon: Merged in dannon/galaxy-central-prmaker/stable (pull request #527)
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/67050bf7b3cf/ Changeset: 67050bf7b3cf User: dannon Date: 2014-10-13 18:01:54+00:00 Summary: Merged in dannon/galaxy-central-prmaker/stable (pull request #527) [STABLE] Relocate job_lock from the queue to the JobManager itself. This fixes NoopQueue not having a job_lock errors seen in Admin->Jobs Affected #: 0 files 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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cb0c2ea402e4/ Changeset: cb0c2ea402e4 Branch: stable User: dannon Date: 2014-10-13 14:19:32+00:00 Summary: Relocate job_lock from the queue to the JobManager itself. This fixes NoopQueue not having a job_lock errors seen in Admin->Jobs Affected #: 4 files diff -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -53,7 +53,6 @@ """Start the job manager""" self.app = app self.dispatcher = dispatcher - self.job_lock = False self.sa_session = app.model.context self.track_jobs_in_database = self.app.config.track_jobs_in_database @@ -174,7 +173,7 @@ try: # If jobs are locked, there's nothing to monitor and we skip # to the sleep. - if not self.job_lock: + if not self.app.job_manager.job_lock: self.__monitor_step() except: log.exception( "Exception in monitor_step" ) diff -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -26,6 +26,7 @@ else: self.job_handler = NoopHandler() self.job_queue = self.job_stop_queue = NoopQueue() + self.job_lock = False self.job_handler.start() def shutdown( self ): diff -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -110,7 +110,7 @@ job_lock = kwargs.get('job_lock', False) # job_queue is exposed in the root app, but this will be 'fixed' at some # point, so we're using the reference from the handler. - app.job_manager.job_handler.job_queue.job_lock = job_lock + app.job_manager.job_lock = job_lock log.info("Administrative Job Lock is now set to %s. Jobs will %s dispatch." % (job_lock, "not" if job_lock else "now")) diff -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1107,7 +1107,7 @@ kwargs={'job_lock': False } ) job_lock = False else: - job_lock = trans.app.job_manager.job_handler.job_queue.job_lock + job_lock = trans.app.job_manager.job_lock cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) ) jobs = trans.sa_session.query( trans.app.model.Job ) \ .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time, https://bitbucket.org/galaxy/galaxy-central/commits/67050bf7b3cf/ Changeset: 67050bf7b3cf User: dannon Date: 2014-10-13 18:01:54+00:00 Summary: Merged in dannon/galaxy-central-prmaker/stable (pull request #527) [STABLE] Relocate job_lock from the queue to the JobManager itself. This fixes NoopQueue not having a job_lock errors seen in Admin->Jobs Affected #: 0 files 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.

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commit/galaxy-central: dan: Close branch stable
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/85ca6ed4af00/ Changeset: 85ca6ed4af00 Branch: stable User: dan Date: 2014-10-13 17:54:05+00:00 Summary: Close branch stable Affected #: 0 files 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.

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