1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/ebb1014b237d/ changeset: ebb1014b237d user: dannon date: 2011-07-21 16:43:16 summary: Fix bitbucket issue #612 regarding administrative job lock toggling inappropriately. Split logical forms into actual forms. affected #: 2 files (459 bytes)

--- a/lib/galaxy/web/base/controller.py Thu Jul 21 10:26:41 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Thu Jul 21 10:43:16 2011 -0400 @@ -21,7 +21,7 @@

# RE that tests for valid slug. VALID_SLUG_RE = re.compile( "^[a-z0-9-]+$" ) - + class BaseController( object ): """ Base class for Galaxy web application controllers. @@ -51,7 +51,7 @@ else: item_class = None return item_class - + Root = BaseController

class SharableItemSecurity: @@ -72,7 +72,7 @@

# # TODO: need to move UsesHistory, etc. mixins to better location - perhaps lib/galaxy/model/XXX ? -# +#

class UsesHistoryDatasetAssociation: """ Mixin for controllers that use HistoryDatasetAssociation objects. """ @@ -119,15 +119,15 @@ dataset_data = open( dataset.file_name ).read(max_peek_size) truncated = False return truncated, dataset_data - + class UsesVisualization( SharableItemSecurity ): """ Mixin for controllers that use Visualization objects. """

len_files = None - + def _get_dbkeys( self, trans ): """ Returns all valid dbkeys that a user can use in a visualization. """ - + # Read len files. if not self.len_files: len_files = glob.glob( os.path.join(trans.app.config.len_file_path, "*.len") ) @@ -137,10 +137,10 @@ user = trans.get_user() if 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) - + dbkeys = [ (v, k) for k, v in trans.db_builds if k in self.len_files or k in user_keys ] return dbkeys - + def get_visualization( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a Visualization from the database by id, verifying ownership. """ # Load workflow from database @@ -152,7 +152,7 @@ error( "Visualization not found" ) else: return self.security_check( trans.get_user(), visualization, check_ownership, check_accessible ) - + def get_visualization_config( self, trans, visualization ): """ Returns a visualization's configuration. Only works for trackster visualizations right now. """

@@ -172,16 +172,16 @@ dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(dataset_id) ) - + try: prefs = t['prefs'] except KeyError: prefs = {} - + track_type, _ = dataset.datatype.get_track_type() track_data_provider_class = get_data_provider( original_dataset=dataset ) track_data_provider = track_data_provider_class( original_dataset=dataset ) - + tracks.append( { "track_type": track_type, "name": t['name'], @@ -192,15 +192,15 @@ "tool": get_tool_def( trans, dataset ), "is_child": t.get('is_child', False) } ) - - config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ), + + config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ), "tracks": tracks, "bookmarks": bookmarks, "chrom": "", "dbkey": visualization.dbkey }

if 'viewport' in latest_revision.config: config['viewport'] = latest_revision.config['viewport'] - + return config - + class UsesStoredWorkflow( SharableItemSecurity ): """ Mixin for controllers that use StoredWorkflow objects. """ def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): @@ -225,7 +225,7 @@ step.upgrade_messages = module.check_and_update_state() # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) - module.add_dummy_datasets( connections=step.input_connections ) + module.add_dummy_datasets( connections=step.input_connections ) # Store state with the step step.module = module step.state = module.state @@ -270,7 +270,7 @@ """Mixin for controllers that use Galaxy form objects.""" def get_all_forms( self, trans, all_versions=False, filter=None, form_type='All' ): """ - Return all the latest forms from the form_definition_current table + Return all the latest forms from the form_definition_current table if all_versions is set to True. Otherwise return all the versions of all the forms from the form_definition table. """ @@ -684,7 +684,7 @@ trans.sa_session.flush() info_association = sra.run else: - info_association = assoc.run + info_association = assoc.run else: info_association = None if info_association: @@ -912,7 +912,7 @@ else: field_value = int( input_text_value ) elif field_type == CheckboxField.__name__: - field_value = CheckboxField.is_checked( input_value ) + field_value = CheckboxField.is_checked( input_value ) elif field_type == PasswordField.__name__: field_value = kwd.get( field_name, '' ) else: @@ -1043,7 +1043,7 @@ @web.require_login( "modify Galaxy items" ) def set_slug_async( self, trans, id, new_slug ): """ Set item slug asynchronously. """ - pass + pass @web.expose @web.require_login( "share Galaxy items" ) def sharing( self, trans, id, **kwargs ): @@ -1099,7 +1099,7 @@ item.slug = slug return True return False - + """ Deprecated: `BaseController` used to be available under the name `Root` """ @@ -1111,7 +1111,7 @@ user_list_grid = None role_list_grid = None group_list_grid = None - + @web.expose @web.require_admin def index( self, trans, **kwd ): @@ -1158,7 +1158,7 @@ toolbox=self.app.toolbox, message=message, status='done' ) - + # Galaxy Role Stuff @web.expose @web.require_admin @@ -1342,7 +1342,7 @@ action='roles', webapp=webapp, message=util.sanitize_text( message ), - status=status ) ) + status=status ) ) in_users = [] out_users = [] in_groups = [] @@ -1934,7 +1934,7 @@ def purge_user( self, trans, **kwd ): # This method should only be called for a User that has previously been deleted. # We keep the User in the database ( marked as purged ), and stuff associated - # with the user's private role in case we want the ability to unpurge the user + # with the user's private role in case we want the ability to unpurge the user # some time in the future. # Purging a deleted User deletes all of the following: # - History where user_id = User.id @@ -2158,7 +2158,7 @@

@web.expose @web.require_admin - def jobs( self, trans, stop = [], stop_msg = None, cutoff = 180, job_lock = None, **kwd ): + def jobs( self, trans, stop = [], stop_msg = None, cutoff = 180, job_lock = None, ajl_submit = None, **kwd ): deleted = [] msg = None status = None @@ -2181,10 +2181,11 @@ msg += ' for deletion: ' msg += ', '.join( deleted ) status = 'done' - if job_lock == 'lock': - trans.app.job_manager.job_queue.job_lock = True - elif job_lock == 'unlock': - trans.app.job_manager.job_queue.job_lock = False + if ajl_submit: + if job_lock == 'on': + trans.app.job_manager.job_queue.job_lock = True + else: + trans.app.job_manager.job_queue.job_lock = False 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, @@ -2209,7 +2210,7 @@ job_lock = trans.app.job_manager.job_queue.job_lock )

## ---- Utility methods ------------------------------------------------------- - + def get_user( trans, id ): """Get a User from the database by id.""" # Load user from database

--- a/templates/admin/jobs.mako Thu Jul 21 10:26:41 2011 -0400 +++ b/templates/admin/jobs.mako Thu Jul 21 10:43:16 2011 -0400 @@ -21,11 +21,11 @@ report this error". </p>

-<form name="jobs" action="${h.url_for()}" method="POST"><p/>

%if jobs: +<form name="jobs" action="${h.url_for()}" method="POST"><table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"><tr class="header"><td>&nbsp;</td> @@ -84,10 +84,12 @@ </div></div><p/> +</form> %else: <div class="infomessage">There are no unfinished jobs to show with current cutoff time.</div><p/> %endif +<form name="jobs" action="${h.url_for()}" method="POST"><div class="toolForm"><div class="toolFormTitle"> Update Jobs @@ -110,30 +112,33 @@ </div></div></div> - <p/> +</form> +<form name="jobs" action="${h.url_for()}" method="POST"> + <p/><div class="toolForm"><div class="toolFormTitle"> Administrative Job Lock </div><div class="toolFormBody"> - %if job_lock==True: <div class="form-row"> - <p>All job execution is currently locked. Click here to unlock.</p> - <input type='hidden' name='job_lock' value='unlock'/> + <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="Unlock"> + <input type="submit" class="primary-button" name="submit" value="Update"></div> - %else: - <div class="form-row"> - <p>To prevent new jobs from dispatching, you can lock the job queue here.</p> - <input type='hidden' name='job_lock' value='lock'/> - </div> - <div class="form-row"> - <input type="submit" class="primary-button" name="submit" value="Lock"> - </div> - %endif </div></div> - </form>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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