commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8fbff1243ec6/
Changeset: 8fbff1243ec6
User: dannon
Date: 2014-08-20 18:55:32
Summary: Swap remote user logout to actually follow galaxy internal logout procedure and then redirect. Also fix logic for user dropdown -- it was preventing users from seeing stuff that was actually available before.
Affected #: 3 files
diff -r 30c4d8730943a40646341e6adf3659cf9fd36985 -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -616,11 +616,14 @@
if biostar_url:
# TODO: It would be better if we automatically logged this user out of biostar
message += '<br>To logout of Biostar, please click <a href="%s" target="_blank">here</a>.' % ( biostar_url )
- return trans.fill_template( '/user/logout.mako',
- refresh_frames=refresh_frames,
- message=message,
- status='done',
- active_view="user" )
+ if trans.app.config.use_remote_user and trans.app.config.remote_user_logout_href:
+ trans.response.send_redirect(trans.app.config.remote_user_logout_href)
+ else:
+ return trans.fill_template('/user/logout.mako',
+ refresh_frames=refresh_frames,
+ message=message,
+ status='done',
+ active_view="user" )
@web.expose
def create( self, trans, cntrller='user', redirect_url='', refresh_frames=[], **kwd ):
diff -r 30c4d8730943a40646341e6adf3659cf9fd36985 -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 static/scripts/galaxy.menu.js
--- a/static/scripts/galaxy.menu.js
+++ b/static/scripts/galaxy.menu.js
@@ -289,34 +289,24 @@
title : "Logged in as " + this.options.user.email
});
- // remote user
- if (this.options.use_remote_user && this.options.remote_user_logout_href)
- {
- tab_user.add({
- title : "Logout",
- content : this.options.remote_user_logout_href,
- target : "_top"
- });
- } else {
- tab_user.add({
- title : "Preferences",
- content : "user?cntrller=user",
- target : "galaxy_main"
- });
+ tab_user.add({
+ title : "Preferences",
+ content : "user?cntrller=user",
+ target : "galaxy_main"
+ });
- tab_user.add({
- title : "Custom Builds",
- content : "user/dbkeys",
- target : "galaxy_main"
- });
-
- tab_user.add({
- title : "Logout",
- content : "user/logout",
- target : "_top",
- divider : true
- });
- }
+ tab_user.add({
+ title : "Custom Builds",
+ content : "user/dbkeys",
+ target : "galaxy_main"
+ });
+
+ tab_user.add({
+ title : "Logout",
+ content : "user/logout",
+ target : "_top",
+ divider : true
+ });
// default tabs
tab_user.add({
diff -r 30c4d8730943a40646341e6adf3659cf9fd36985 -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 templates/user/index.mako
--- a/templates/user/index.mako
+++ b/templates/user/index.mako
@@ -19,13 +19,7 @@
%if trans.app.config.enable_openid and not trans.app.config.use_remote_user:
<li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller )}">${_('Manage OpenIDs')}</a> linked to your account</li>
%endif
- %if trans.app.config.use_remote_user:
- %if trans.app.config.remote_user_logout_href:
- <li><a href="${trans.app.config.remote_user_logout_href}" target="_top">${_('Logout')}</a></li>
- %endif
- %else:
- <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li>
- %endif
+ <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li>
%else:
<li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller )}">${_('Manage your information')}</a></li><li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('Manage your API keys')}</a></li>
https://bitbucket.org/galaxy/galaxy-central/commits/871a781a0507/
Changeset: 871a781a0507
User: dannon
Date: 2014-08-20 18:56:01
Summary: Strip trailing whitespace from galaxy.menu.js
Affected #: 1 file
diff -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 -r 871a781a05070d5a227469c55c4249dbe6945e2d static/scripts/galaxy.menu.js
--- a/static/scripts/galaxy.menu.js
+++ b/static/scripts/galaxy.menu.js
@@ -10,10 +10,10 @@
{
// options
options: null,
-
+
// link masthead class
masthead: null,
-
+
// initialize
initialize: function(options)
{
@@ -21,7 +21,7 @@
this.masthead = options.masthead;
this.create();
},
-
+
// default menu
create: function()
{
@@ -149,7 +149,7 @@
content : "visualization/list",
target : "_frame"
});
- }
+ }
this.masthead.append(tab_visualization);
//
@@ -300,14 +300,14 @@
content : "user/dbkeys",
target : "galaxy_main"
});
-
+
tab_user.add({
title : "Logout",
content : "user/logout",
target : "_top",
divider : true
});
-
+
// default tabs
tab_user.add({
title : "Saved Histories",
@@ -343,7 +343,7 @@
// add to masthead
this.masthead.append(tab_user);
}
-
+
// identify active tab
if (this.options.active_view)
this.masthead.highlight(this.options.active_view);
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Fix formatting in cloudlaunch.
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/30c4d8730943/
Changeset: 30c4d8730943
User: dannon
Date: 2014-08-20 18:33:11
Summary: Fix formatting in cloudlaunch.
Affected #: 1 file
diff -r fb28ce36133ffcb6a167ba95003f4608b7574942 -r 30c4d8730943a40646341e6adf3659cf9fd36985 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -40,6 +40,7 @@
("r3.8xlarge", "Memory optimized 8xLarge (32 vCPU/244GB RAM)"),
]
+
class CloudController(BaseUIController):
"""Galaxy Cloud Functions"""
@@ -56,7 +57,7 @@
share_string=share_string,
ami=ami,
bucket_default=bucket_default,
- instance_types = DEFAULT_INSTANCE_TYPES)
+ instance_types=DEFAULT_INSTANCE_TYPES)
@web.expose
def get_account_info(self, trans, key_id, secret):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Update instance types, slim down the options to recommended types. This will (eventually) make it to a single shared resource in bioblend that's used in cloudman + galaxy, but this change gets us in sync for now.
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fb28ce36133f/
Changeset: fb28ce36133f
User: dannon
Date: 2014-08-20 18:22:38
Summary: Update instance types, slim down the options to recommended types. This will (eventually) make it to a single shared resource in bioblend that's used in cloudman + galaxy, but this change gets us in sync for now.
Affected #: 2 files
diff -r cb7713c693e73d90731489e267ca52a7b585d580 -r fb28ce36133ffcb6a167ba95003f4608b7574942 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -31,6 +31,14 @@
DEFAULT_KEYPAIR = 'cloudman_keypair'
CLOUDMAN_TAG_KEY = 'galaxy:cloudman'
+DEFAULT_INSTANCE_TYPES = [
+ ("c3.large", "Compute optimized Large (2 vCPU/4GB RAM)"),
+ ("c3.2xlarge", "Compute optimized 2xLarge (8 vCPU/15GB RAM)"),
+ ("c3.8xlarge", "Compute optimized 8xLarge (32 vCPU/60GB RAM)"),
+ ("r3.large", "Memory optimized Large (2 vCPU/15GB RAM)"),
+ ("r3.2xlarge", "Memory optimized 2xLarge (8 vCPU/61GB RAM)"),
+ ("r3.8xlarge", "Memory optimized 8xLarge (32 vCPU/244GB RAM)"),
+]
class CloudController(BaseUIController):
"""Galaxy Cloud Functions"""
@@ -47,7 +55,8 @@
default_keypair=DEFAULT_KEYPAIR,
share_string=share_string,
ami=ami,
- bucket_default=bucket_default)
+ bucket_default=bucket_default,
+ instance_types = DEFAULT_INSTANCE_TYPES)
@web.expose
def get_account_info(self, trans, key_id, secret):
diff -r cb7713c693e73d90731489e267ca52a7b585d580 -r fb28ce36133ffcb6a167ba95003f4608b7574942 templates/webapps/galaxy/cloud/index.mako
--- a/templates/webapps/galaxy/cloud/index.mako
+++ b/templates/webapps/galaxy/cloud/index.mako
@@ -238,10 +238,9 @@
<div class="form-row"><label for="id_instance_type">Instance Type</label><select name="instance_type" id="id_instance_type">
- <option value="m1.large">Large</option>
- <option value="m1.xlarge">Extra Large</option>
- <option value="c3.2xlarge">Compute Optimized Double Extra Large</option>
- <option value="m2.4xlarge">High-Memory Quadruple Extra Large</option>
+ %for (itype, description) in instance_types:
+ <option value="${itype}">${description}</option>
+ %endfor
</select></div><div class="form-row">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Merged in dan/galaxy-central-prs/stable (pull request #470)
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6445c0fe7612/
Changeset: 6445c0fe7612
Branch: stable
User: dannon
Date: 2014-08-20 17:03:06
Summary: Merged in dan/galaxy-central-prs/stable (pull request #470)
Fix for resetting installed toolshed repository metadata inside of Galaxy.
Affected #: 1 file
diff -r 354fb22316ef3d259cb81f3af40af8aeb0334187 -r 6445c0fe761258410a17b95ad2f221a9e60fc5c7 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1717,7 +1717,7 @@
else:
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- repositories_select_field = irmm.build_repository_ids_select_field( trans )
+ repositories_select_field = irmm.build_repository_ids_select_field()
return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 5 months
commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/14e588f9674c/
Changeset: 14e588f9674c
Branch: stable
User: dan
Date: 2014-08-20 16:48:48
Summary: Fix for resetting installed toolshed repository metadata inside of Galaxy.
Affected #: 1 file
diff -r d2fc633d1bcc2d02c5efccf923c4e3ce5336512a -r 14e588f9674ce69d9a8d56f188b26a4e788809be lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1717,7 +1717,7 @@
else:
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- repositories_select_field = irmm.build_repository_ids_select_field( trans )
+ repositories_select_field = irmm.build_repository_ids_select_field()
return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,
https://bitbucket.org/galaxy/galaxy-central/commits/6445c0fe7612/
Changeset: 6445c0fe7612
Branch: stable
User: dannon
Date: 2014-08-20 17:03:06
Summary: Merged in dan/galaxy-central-prs/stable (pull request #470)
Fix for resetting installed toolshed repository metadata inside of Galaxy.
Affected #: 1 file
diff -r 354fb22316ef3d259cb81f3af40af8aeb0334187 -r 6445c0fe761258410a17b95ad2f221a9e60fc5c7 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1717,7 +1717,7 @@
else:
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- repositories_select_field = irmm.build_repository_ids_select_field( trans )
+ repositories_select_field = irmm.build_repository_ids_select_field()
return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Fix for resetting installed toolshed repository metadata inside of Galaxy.
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/cb7713c693e7/
Changeset: cb7713c693e7
User: dan
Date: 2014-08-20 16:48:48
Summary: Fix for resetting installed toolshed repository metadata inside of Galaxy.
Affected #: 1 file
diff -r a49333fbaf635b37fd4b96ce89ffc50166b2326e -r cb7713c693e73d90731489e267ca52a7b585d580 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1717,7 +1717,7 @@
else:
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- repositories_select_field = irmm.build_repository_ids_select_field( trans )
+ repositories_select_field = irmm.build_repository_ids_select_field()
return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org
3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/cfbcb00008cb/
Changeset: cfbcb00008cb
User: dannon
Date: 2014-08-20 15:48:19
Summary: Re-enable administrative job lock, works with multiple handler processes using the internal message queue
Affected #: 5 files
diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -53,6 +53,7 @@
"""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
@@ -168,7 +169,10 @@
"""
while self.running:
try:
- self.__monitor_step()
+ # If jobs are locked, there's nothing to monitor and we skip
+ # to the sleep.
+ if not self.job_lock:
+ self.__monitor_step()
except:
log.exception( "Exception in monitor_step" )
# Sleep
diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 lib/galaxy/queue_worker.py
--- a/lib/galaxy/queue_worker.py
+++ b/lib/galaxy/queue_worker.py
@@ -105,5 +105,14 @@
table_names = app.tool_data_tables.reload_tables( table_names=params.get('table_name', None))
log.debug("Finished data table reload for %s" % table_names)
+
+def admin_job_lock(app, **kwargs):
+ 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
+ log.debug("Job dispatching is now set to %s" % job_lock)
+
control_message_to_task = { 'reload_tool': reload_tool,
- 'reload_tool_data_tables': reload_tool_data_tables}
+ 'reload_tool_data_tables': reload_tool_data_tables,
+ 'admin_job_lock': admin_job_lock}
diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 lib/galaxy/queues.py
--- a/lib/galaxy/queues.py
+++ b/lib/galaxy/queues.py
@@ -27,7 +27,8 @@
Refactor later to actually persist this somewhere instead of building it repeatedly.
"""
- return [Queue('control.%s' % q, galaxy_exchange, routing_key='control') for q in config.server_names]
+ return [Queue('control.%s' % q, galaxy_exchange, routing_key='control') for
+ q in config.server_names]
def control_queue_from_config(config):
diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 lib/galaxy/web/base/controllers/admin.py
--- a/lib/galaxy/web/base/controllers/admin.py
+++ b/lib/galaxy/web/base/controllers/admin.py
@@ -1037,6 +1037,7 @@
heap = heap.theone
return trans.fill_template( '/admin/memdump.mako', heap = heap, ids = ids, sorts = sorts, breadcrumb = breadcrumb, msg = msg )
+
@web.expose
@web.require_admin
def jobs( self, trans, stop = [], stop_msg = None, cutoff = 180, job_lock = None, ajl_submit = None, **kwd ):
@@ -1069,6 +1070,17 @@
msg += ', '.join( deleted )
status = 'done'
trans.sa_session.flush()
+ if ajl_submit:
+ if job_lock == 'on':
+ galaxy.queue_worker.send_control_task(trans, 'admin_job_lock',
+ kwargs={'job_lock': True } )
+ job_lock = True
+ else:
+ galaxy.queue_worker.send_control_task(trans, 'admin_job_lock',
+ kwargs={'job_lock': False } )
+ job_lock = False
+ else:
+ job_lock = trans.app.job_manager.job_handler.job_queue.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,
@@ -1089,7 +1101,8 @@
last_updated = last_updated,
cutoff = cutoff,
msg = msg,
- status = status )
+ status = status,
+ job_lock = job_lock)
## ---- Utility methods -------------------------------------------------------
diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 templates/admin/jobs.mako
--- a/templates/admin/jobs.mako
+++ b/templates/admin/jobs.mako
@@ -133,3 +133,33 @@
</div></div></form>
+
+<form name="jobs" action="${h.url_for(controller='admin', action='jobs')}" method="POST">
+ <p/>
+ <div class="toolForm">
+ <div class="toolFormTitle">
+ Administrative Job Lock
+ </div>
+ <div class="toolFormBody">
+ <div class="form-row">
+ <input type="hidden" name="ajl_submit" value="True"/>
+ %if job_lock==True:
+ <p>Job dispatching is currently <strong>locked</strong>.</p>
+ <label>
+ <input type='checkbox' name='job_lock' checked='checked' />
+ Prevent jobs from dispatching.
+ </label>
+ %else:
+ <p>Job dispatching is currently <strong>unlocked</strong>.</p>
+ <label>
+ <input type='checkbox' name='job_lock' />
+ Prevent jobs from dispatching.
+ </label>
+ %endif
+ </div>
+ <div class="form-row">
+ <input type="submit" class="primary-button" name="submit" value="Update">
+ </div>
+ </div>
+ </div>
+</form>
https://bitbucket.org/galaxy/galaxy-central/commits/b232fa5e0dc4/
Changeset: b232fa5e0dc4
User: dannon
Date: 2014-08-20 15:49:00
Summary: Merge.
Affected #: 2 files
diff -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 -r b232fa5e0dc40ca809ea826a73111e6be8645b95 README.txt
--- a/README.txt
+++ b/README.txt
@@ -1,31 +1,34 @@
-GALAXY
-======
-http://galaxyproject.org/
-
-The latest information about Galaxy is always available via the Galaxy
-website above.
-
-HOW TO START
-============
-Galaxy requires Python 2.6 or 2.7. To check your python version, run:
-
-% python -V
-Python 2.7.3
-
-Start Galaxy:
-
-% sh run.sh
-
-Once Galaxy completes startup, you should be able to view Galaxy in your
-browser at:
-
-http://localhost:8080
-
-You may wish to make changes from the default configuration. This can be done
-in the universe_wsgi.ini file. Tools are configured in tool_conf.xml. Details
-on adding tools can be found on the Galaxy website (linked above).
-
-Not all dependencies are included for the tools provided in the sample
-tool_conf.xml. A full list of external dependencies is available at:
-
-https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
+GALAXY
+======
+http://galaxyproject.org/
+
+The latest information about Galaxy is always available via the Galaxy
+website above.
+
+HOW TO START
+============
+Galaxy requires Python 2.6 or 2.7. To check your python version, run:
+
+% python -V
+Python 2.7.3
+
+Start Galaxy:
+
+% sh run.sh
+
+Once Galaxy completes startup, you should be able to view Galaxy in your
+browser at:
+
+http://localhost:8080
+
+You may wish to make changes from the default configuration. This can be done
+in the universe_wsgi.ini file. Tools can be either installed from the Tool Shed
+or added manually. For details please see the Galaxy wiki:
+
+https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial.
+
+
+Not all dependencies are included for the tools provided in the sample
+tool_conf.xml. A full list of external dependencies is available at:
+
+https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
\ No newline at end of file
diff -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 -r b232fa5e0dc40ca809ea826a73111e6be8645b95 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1268,6 +1268,7 @@
except:
error("That history does not exist.")
try: # use a try/finally block to restore the user's current history
+ default_target_history = trans.get_history()
if kwargs:
# If kwargs were provided, the states for each step should have
# been POSTed
@@ -1329,7 +1330,7 @@
trans.sa_session.add( new_history )
target_history = new_history
else:
- target_history = trans.get_history()
+ target_history = default_target_history
# Build replacement dict for this workflow execution.
replacement_dict = {}
https://bitbucket.org/galaxy/galaxy-central/commits/a49333fbaf63/
Changeset: a49333fbaf63
User: dannon
Date: 2014-08-20 16:31:01
Summary: Clarify job lock log statement, swap loglevel from debug to info.
Affected #: 1 file
diff -r b232fa5e0dc40ca809ea826a73111e6be8645b95 -r a49333fbaf635b37fd4b96ce89ffc50166b2326e lib/galaxy/queue_worker.py
--- a/lib/galaxy/queue_worker.py
+++ b/lib/galaxy/queue_worker.py
@@ -54,7 +54,7 @@
if body.get('noop', None) != self.app.config.server_name:
try:
f = self.task_mapping[body['task']]
- log.debug("Instance recieved '%s' task, executing now." % body['task'])
+ log.info("Instance recieved '%s' task, executing now." % body['task'])
f(self.app, **body['kwargs'])
except Exception:
# this shouldn't ever throw an exception, but...
@@ -111,7 +111,8 @@
# 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
- log.debug("Job dispatching is now set to %s" % job_lock)
+ log.info("Administrative Job Lock is now set to %s. Jobs will %s dispatch."
+ % (job_lock, "not" if job_lock else "now"))
control_message_to_task = { 'reload_tool': reload_tool,
'reload_tool_data_tables': reload_tool_data_tables,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Attempt to ensure batch workflows are all properly assigned to same history.
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/86fd99a90b81/
Changeset: 86fd99a90b81
User: jmchilton
Date: 2014-08-20 14:44:02
Summary: Attempt to ensure batch workflows are all properly assigned to same history.
... in case trans.get_history() changes during scheduling. I believe this was what was happening here (http://dev.list.galaxyproject.org/redirecting-to-unnamed-history-td466541...) though I have no proof - nonetheless this won't hurt anything.
Affected #: 1 file
diff -r 481b64dd8dff0d2c52388e906a1632370536ef67 -r 86fd99a90b81c84eb4f7489ce016c6d1ed10496a lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1268,6 +1268,7 @@
except:
error("That history does not exist.")
try: # use a try/finally block to restore the user's current history
+ default_target_history = trans.get_history()
if kwargs:
# If kwargs were provided, the states for each step should have
# been POSTed
@@ -1329,7 +1330,7 @@
trans.sa_session.add( new_history )
target_history = new_history
else:
- target_history = trans.get_history()
+ target_history = default_target_history
# Build replacement dict for this workflow execution.
replacement_dict = {}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 5 months