1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d45b4b6ff827/
Changeset: d45b4b6ff827
User: davebgx
Date: 2014-09-02 22:05:45
Summary: Remove call to send_control_task that should not have been added to admin.package_tool in the first place.
Affected #: 1 file
diff -r e8ab30c9e3471de1b874e580663560f6a4a7f143 -r d45b4b6ff827386ff3de59bc155e95f2cf2f5656 lib/galaxy/web/base/controllers/admin.py
--- a/lib/galaxy/web/base/controllers/admin.py
+++ b/lib/galaxy/web/base/controllers/admin.py
@@ -67,7 +67,6 @@
tool_id = None
if params.get( 'package_tool_button', False ):
tool_id = params.get('tool_id', None)
- galaxy.queue_worker.send_control_task(trans, 'package_tool', noop_self=True, kwargs={'tool_id': tool_id} )
tool_tarball, success, message = trans.app.toolbox.package_tool( trans, tool_id )
if success:
trans.response.set_content_type( 'application/x-gzip' )
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/36327228fe4f/
Changeset: 36327228fe4f
User: martenson
Date: 2014-09-02 21:46:24
Summary: missing import
Affected #: 1 file
diff -r ec989f77c079f7036c7cb8bb303d1e6bae4a4e4d -r 36327228fe4f1f648e4fabe783d446c8dd6c1f73 lib/galaxy/managers/libraries.py
--- a/lib/galaxy/managers/libraries.py
+++ b/lib/galaxy/managers/libraries.py
@@ -6,6 +6,7 @@
from galaxy import exceptions
from galaxy.model import orm
from galaxy.managers import base as manager_base
+from galaxy.model.orm import and_, not_, or_
from sqlalchemy.orm.exc import MultipleResultsFound
from sqlalchemy.orm.exc import NoResultFound
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/9f63d9632d9d/
Changeset: 9f63d9632d9d
User: natefoo
Date: 2014-09-02 21:30:57
Summary: Make it possible to load dynamic job runner rules from somewhere other than galaxy.jobs.rules.
Affected #: 3 files
diff -r 5ce55f9f2923dcdf27150cce3addd6e1ff3782d7 -r 9f63d9632d9d690c2d5e353feac3f83f12db3f78 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -22,6 +22,17 @@
<plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /><plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" />
+ <plugin id="dynamic" type="runner">
+ <!-- The dynamic runner is not a real job running plugin and is
+ always loaded, so it does not need to be explicitly stated in
+ <plugins>. However, if you wish to change the base module
+ containing your dynamic rules, you can do so.
+
+ The `load` attribute is not required (and ignored if
+ included).
+ -->
+ <param id="rules_module">galaxy.jobs.rules</param>
+ </plugin><!-- Pulsar runners (see more at https://pulsar.readthedocs.org) --><plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"><!-- Allow optimized HTTP calls with libcurl (defaults to urllib) -->
diff -r 5ce55f9f2923dcdf27150cce3addd6e1ff3782d7 -r 9f63d9632d9d690c2d5e353feac3f83f12db3f78 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -103,6 +103,7 @@
"""
self.app = app
self.runner_plugins = []
+ self.dynamic_params = None
self.handlers = {}
self.handler_runner_plugins = {}
self.default_handler_id = None
@@ -147,6 +148,10 @@
self.runner_plugins.append(runner_info)
else:
log.error('Unknown plugin type: %s' % plugin.get('type'))
+ for plugin in self.__findall_with_required(plugins, 'plugin', ('id', 'type')):
+ if plugin.get('id') == 'dynamic' and plugin.get('type') == 'runner':
+ self.dynamic_params = self.__get_params(plugin)
+
# Load tasks if configured
if self.app.config.use_tasked_jobs:
self.runner_plugins.append(dict(id='tasks', load='tasks', workers=self.app.config.local_task_queue_workers))
diff -r 5ce55f9f2923dcdf27150cce3addd6e1ff3782d7 -r 9f63d9632d9d690c2d5e353feac3f83f12db3f78 lib/galaxy/jobs/mapper.py
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -1,6 +1,7 @@
import logging
import inspect
import os
+import sys
log = logging.getLogger( __name__ )
@@ -49,6 +50,11 @@
self.rules_module = galaxy.jobs.rules
+ if job_config.dynamic_params is not None:
+ rules_module_name = job_config.dynamic_params['rules_module']
+ __import__(rules_module_name)
+ self.rules_module = sys.modules[rules_module_name]
+
def __get_rule_modules( self ):
unsorted_module_names = self.__get_rule_module_names( )
## Load modules in reverse order to allow hierarchical overrides
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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