1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1802e93a4f18/
Changeset: 1802e93a4f18
User: natefoo
Date: 2014-06-26 02:07:58
Summary: Fix Ctrl+C (make the UpdateRepositoryManager's updater thread a daemon).
Affected #: 1 file
diff -r 6b672fb120994f308ce7914993418e67770aae14 -r 1802e93a4f1823f307de534d9b6ce73d911f6538 lib/tool_shed/galaxy_install/update_repository_manager.py
--- a/lib/tool_shed/galaxy_install/update_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/update_repository_manager.py
@@ -19,6 +19,7 @@
self.running = True
self.sleeper = Sleeper()
self.restarter = threading.Thread( target=self.__restarter )
+ self.restarter.daemon = True
self.restarter.start()
self.seconds_to_sleep = int( app.config.hours_between_check * 3600 )
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/6b672fb12099/
Changeset: 6b672fb12099
User: davebgx
Date: 2014-06-25 21:07:43
Summary: Enhance the tool shed repository API controller to allow filtering by owner's username or repository name.
Affected #: 1 file
diff -r 8a161a3990b5e19dd2b324323ba934f8a5f37c8b -r 6b672fb120994f308ce7914993418e67770aae14 lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -7,6 +7,7 @@
from galaxy import eggs
from galaxy import util
from galaxy import web
+from galaxy.model.orm import and_
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import HTTPBadRequest
from galaxy.web.framework.helpers import time_ago
@@ -297,16 +298,28 @@
return return_dict
@web.expose_api_anonymous
- def index( self, trans, deleted=False, **kwd ):
+ def index( self, trans, deleted=False, owner=None, name=None, **kwd ):
"""
GET /api/repositories
+
+ :param deleted: True/False, displays repositories that are or are not set to deleted.
+ :param owner: the owner's public username.
+ :param name: the repository name.
+
Displays a collection (list) of repositories.
"""
# Example URL: http://localhost:9009/api/repositories
repository_dicts = []
deleted = util.asbool( deleted )
+ clause_list = [ and_( trans.app.model.Repository.table.c.deprecated == False,
+ trans.app.model.Repository.table.c.deleted == deleted ) ]
+ if owner is not None:
+ clause_list.append( and_( trans.app.model.User.table.c.username == owner,
+ trans.app.model.Repository.table.c.user_id == trans.app.model.User.table.c.id ) )
+ if name is not None:
+ clause_list.append( trans.app.model.Repository.table.c.name == name )
for repository in trans.sa_session.query( trans.app.model.Repository ) \
- .filter( trans.app.model.Repository.table.c.deleted == deleted ) \
+ .filter( *clause_list ) \
.order_by( trans.app.model.Repository.table.c.name ):
repository_dict = repository.to_dict( view='collection',
value_mapper=self.__get_value_mapper( trans ) )
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/8a161a3990b5/
Changeset: 8a161a3990b5
User: jmchilton
Date: 2014-06-25 16:11:26
Summary: Another docfix for recent local job runner changes.
Affected #: 1 file
diff -r 1c40abf8bc5b7555dd276e540f487f8c288da4b2 -r 8a161a3990b5e19dd2b324323ba934f8a5f37c8b universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -804,7 +804,7 @@
# the cluster that should be sourced by the user to set up the environment
# prior to running tools. This can be especially useful for running jobs as
# the actual user, to remove the need to configure each user's environment
-# individually. This only affects cluster jobs, not local jobs.
+# individually.
#environment_setup_file = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/75c63b579ccd/
Changeset: 75c63b579ccd
User: jmchilton
Date: 2014-06-25 15:01:52
Summary: Add documentation about local runner destination option embed_metadata_in_job.
Affected #: 1 file
diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r 75c63b579ccdd63e0558dd9aefce7786677dbacd job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -102,6 +102,12 @@
<!-- Warning: Local slot count doesn't tie up additional worker threads, to prevent over
allocating machine define a second local runner with different name and fewer workers
to run this destination. -->
+ <param id="embed_metadata_in_job">True</param>
+ <!-- Above parameter will be default (with no option to set
+ to False) in an upcoming release of Galaxy, but you can
+ try it early - it will slightly speed up local jobs by
+ embedding metadata calculation in job script itself.
+ --><job_metrics /><!-- Above element demonstrates embedded job metrics definition - see
job_metrics_conf.xml.sample for full documentation on possible nested
https://bitbucket.org/galaxy/galaxy-central/commits/1c40abf8bc5b/
Changeset: 1c40abf8bc5b
User: jmchilton
Date: 2014-06-25 15:05:40
Summary: Merge.
Affected #: 1 file
diff -r 1fc71cb18c421f49be3c6629c0e53cca6b0caadb -r 1c40abf8bc5b7555dd276e540f487f8c288da4b2 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -102,6 +102,12 @@
<!-- Warning: Local slot count doesn't tie up additional worker threads, to prevent over
allocating machine define a second local runner with different name and fewer workers
to run this destination. -->
+ <param id="embed_metadata_in_job">True</param>
+ <!-- Above parameter will be default (with no option to set
+ to False) in an upcoming release of Galaxy, but you can
+ try it early - it will slightly speed up local jobs by
+ embedding metadata calculation in job script itself.
+ --><job_metrics /><!-- Above element demonstrates embedded job metrics definition - see
job_metrics_conf.xml.sample for full documentation on possible nested
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/aff21e09778e/
Changeset: aff21e09778e
User: carlfeberhard
Date: 2014-06-24 23:02:23
Summary: Fix: phantomjs apparently lacks the bind fn on the Function prototype - correct failures in history-panel (line 252) by using underscore bind instead; up the standard upload timeout interval for api tests
Affected #: 2 files
diff -r ae31e175f1cd836e89324a57d2c4276c5091f95f -r aff21e09778ece1bdbe987a4dad2adb6a26e5447 static/scripts/mvc/history/history-panel.js
--- a/static/scripts/mvc/history/history-panel.js
+++ b/static/scripts/mvc/history/history-panel.js
@@ -249,7 +249,7 @@
actions.push( {
// TODO: Only show quick pair if two things selected.
html: _l( 'Build List of Dataset Pairs (Experimental)' ),
- func: panel._showPairedCollectionModal.bind( panel )
+ func: _.bind( panel._showPairedCollectionModal, panel )
});
return new PopupMenu( $where.find( '.history-dataset-action-popup-btn' ), actions );
},
diff -r ae31e175f1cd836e89324a57d2c4276c5091f95f -r aff21e09778ece1bdbe987a4dad2adb6a26e5447 test/casperjs/modules/api.js
--- a/test/casperjs/modules/api.js
+++ b/test/casperjs/modules/api.js
@@ -555,7 +555,7 @@
};
/** amount of time allowed to upload a file (before erroring) */
-ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 12000;
+ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 30 * 1000;
/** add two casperjs steps - upload a file, wait for the job to complete, and run 'then' when they are */
ToolsAPI.prototype.thenUpload = function thenUpload( historyId, options, then ){
@@ -569,6 +569,9 @@
this.debug( 'uploadedId: ' + uploadedId );
});
+ spaceghost.debug( '---------------------------------------------------------- timeout: ' + ( options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ) );
+ spaceghost.debug( 'timeout: ' + options.timeout );
+ spaceghost.debug( 'timeout: ' + spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT );
spaceghost.then( function(){
this.waitFor(
function testHdaState(){
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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