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

14 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 14 Oct '14

14 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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commit/galaxy-central: nsoranzo: Fix import bug for run_reports.sh . Remove unused imports.
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ea936c90b939/ Changeset: ea936c90b939 Branch: stable User: nsoranzo Date: 2014-10-13 16:27:45+00:00 Summary: Fix import bug for run_reports.sh . Remove unused imports. Import bug: File "/opt/galaxy-central/lib/galaxy/webapps/reports/buildapp.py", line 25, in <module> class ReportsWebApplication( galaxy.web.framework.webapp.WebApplication ): AttributeError: 'module' object has no attribute 'webapp' The bug was introduced by commit d57655849ac4 . Affected #: 1 file diff -r 0215d23d79717f46e7715e209048606975693dd7 -r ea936c90b93933326dc3b163aaca361b5cafb5b7 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: dannon: Fix Xslx binary (bad merge?).
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/861fd5d6c459/ Changeset: 861fd5d6c459 User: dannon Date: 2014-10-13 16:55:31+00:00 Summary: Fix Xslx binary (bad merge?). Affected #: 1 file diff -r be638dd2f087e895bb611a132999ec8309db0c03 -r 861fd5d6c459284aed91a2c92a01e5cd09064c18 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -281,22 +281,6 @@ return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) -class Xlsx(Binary): - """Class for Excel 2007 (xlsx) files""" - file_ext="xlsx" - def sniff( self, filename ): - # Xlsx is compressed in zip format and must not be uncompressed in Galaxy. - try: - if zipfile.is_zipfile( filename ): - tempzip = zipfile.ZipFile( filename ) - if "[Content_Types].xml" in tempzip.namelist() and tempzip.read("[Content_Types].xml").find(b'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml') != -1: - return True - return False - except: - return False - -Binary.register_sniffable_binary_format("xlsx", "xlsx", Xlsx) - # ------------- Dataproviders # pipe through samtools view @@ -639,3 +623,19 @@ Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) +class Xlsx(Binary): + """Class for Excel 2007 (xlsx) files""" + file_ext="xlsx" + def sniff( self, filename ): + # Xlsx is compressed in zip format and must not be uncompressed in Galaxy. + try: + if zipfile.is_zipfile( filename ): + tempzip = zipfile.ZipFile( filename ) + if "[Content_Types].xml" in tempzip.namelist() and tempzip.read("[Content_Types].xml").find(b'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml') != -1: + return True + return False + except: + return False + +Binary.register_sniffable_binary_format("xlsx", "xlsx", Xlsx) + 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: 3 new changesets
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/701c01f794e2/ Changeset: 701c01f794e2 User: dannon Date: 2014-10-13 14:44:11+00:00 Summary: Simplify to_json_string/from_json_string; without the extra logging there's no reason to wrap the functions and pass args Affected #: 1 file diff -r 738cdb119ce34e570224eb87ee7a270caa53f39b -r 701c01f794e2fc6cf5586fde68a0d7a33a161790 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -15,13 +15,8 @@ log = logging.getLogger( __name__ ) - -def to_json_string(*args, **kwargs): - return json.dumps(*args, **kwargs) - - -def from_json_string(*args, **kwargs): - return json.loads(*args, **kwargs) +to_json_string = dumps +from_json_string = loads def json_fix( val ): https://bitbucket.org/galaxy/galaxy-central/commits/cce814e5b0fe/ Changeset: cce814e5b0fe Branch: docker-work User: dannon Date: 2014-10-13 15:24:21+00:00 Summary: Branch prune. Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/be638dd2f087/ Changeset: be638dd2f087 User: dannon Date: 2014-10-13 15:24:36+00:00 Summary: Merge. Affected #: 1 file diff -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 -r be638dd2f087e895bb611a132999ec8309db0c03 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -15,13 +15,8 @@ log = logging.getLogger( __name__ ) - -def to_json_string(*args, **kwargs): - return json.dumps(*args, **kwargs) - - -def from_json_string(*args, **kwargs): - return json.loads(*args, **kwargs) +to_json_string = dumps +from_json_string = loads def json_fix( val ): 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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