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Re: [galaxy-dev] Database locked errors
by Nate Coraor 20 Aug '09

20 Aug '09

SHAUN WEBB wrote: > Yes we are using SQLite. I will look in to switching to MySQL. I know a > few people have been discussing this lately, is there a wiki page > devoted to this? There are a few pages that contain most of the information, but I'm trying to consolidate all of this right now. > I found a few errors in the log from todays activity. I've attached a > few examples in a text file. The final error relates to the job that I > stopped in the admin section. As described, some of these "queued" > datasets are not associated with job ids. > > I am concerned that if I transfer all the information as is to a mySQL > database that I will still have the same problem. The locking issues will go away with a real database server, and thus these uncaught exceptions will go away. The ultimate result is that Galaxy won't lose track of jobs because of this. --nate

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Database locked errors
by SHAUN WEBB 20 Aug '09

20 Aug '09

Hi, I'm having the following problems with our Galaxy server: This morning one of our users complained that Galaxy was crashing a lot, either: -The main page was coming up as an operational error page: Database Locked -The output history item returned an error "database is locked" -The output history item would appear to be waiting to run (grey box) but never complete This error is intermittent. I took a look at the manage jobs section on the admin page and found that all the jobs had a "new" status except one which had not been updated for over an hour and had a status of queued. I stopped this job from the admin page and after this the remaining jobs completed. However this doesn't seem to have solved the problem. I've taken a look at the database and as of today only, there are 11 datasets in the dataset table with a "queued" status. Some of these are associated with histories (and marked as deleted in hda table) and jobs (with an error status). The remaining 6 are associated with a history but not marked as deleted and there is no entry in the job_to_output_dataset table to associate these datasets with a job. I wonder if these datasets are causing the problem and galaxy is continually trying to resolve their queued status resulting in the "locked database" error. I'd be grateful if anyone can help with this or even shed some light on how the problem might have occurred and the processes galaxy uses to initiate jobs. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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SGE Cluster suggestion
by Assaf Gordon 17 Aug '09

17 Aug '09

Hello, I'm trying to move our Galaxy to the our SGE cluster, and I need couple of fine-tuning tweaks. 1. set a project name (in addition to the queue) - globally, and per tool. 2. set extra QSUB options per tool 3. Specify the actual user who submitted the job - in the "email" field and as the job name. Details: The project name is needed for accounting (requested by our SGE admins). To specify a project name, add a fourth slash to the sge URL in universe_wsgi.ini, as so: --- ## Global SGE project name , for all tools default_cluster_job_runner = sge:////GalaxyProject/ ## Tool specific project name Cut1 = sge:////OtherGalaxyProject/ ---- The extra QSUB options per tool allow requesting nodes with more memory or request more cores (=threads) per job. To specify extra options, add a fifth slash to the sge tool runner URL in univer_wsge.ini, as so: ---- ## Tool specific parameters - ## run 'cut' on a node with at least 7GB of ram Cut1 = sge:////GalaxyProject/-l virtual_free=7G/ ## run 'select first lines' on a node with 4 cores, and reserve all the cores for the tool ## allowing multi-threaded 'select lines' operation ;) Show beginning1 = sge:////GalaxyProject/-R y -pe threads 4/ ---- Note: specifying extra parameters ALWAYS overrides the project name (but the project name can be an empty string). The actual user is needed to quickly see (with qstat) who runs what (currently, the job names are "galaxy_NNNN.sh"). Comments are welcomed, -gordon.

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Re: [galaxy-dev] galaxy-dev Digest, Vol 44, Issue 22
by Ross 14 Aug '09

14 Aug '09

On Fri, Aug 14, 2009 at 1:14 PM, <galaxy-dev-request(a)bx.psu.edu> wrote: This is excellent - it seems very natural - another extremely compelling feature. Congratulations everyone! > Message: 4 > Date: Fri, 14 Aug 2009 13:14:02 -0400 > From: Greg Von Kuster <greg(a)bx.psu.edu> > Subject: [galaxy-dev] [hg] galaxy 2558: Integrate 'rerun' support from > Assaf Gordan. N... > To: galaxy-dev(a)bx.psu.edu > Message-ID: > <hg.52ad5635f01a.1250270042.-331200333(a)scofield.bx.psu.edu> > > details: http://www.bx.psu.edu/hg/galaxy/rev/52ad5635f01a > changeset: 2558:52ad5635f01a > user: James Taylor <james(a)jamestaylor.org> > date: Thu Aug 13 11:27:45 2009 -0400 > description: > Integrate 'rerun' support from Assaf Gordan. Not supported for all tools, but checking whether the link should be displayed is expensive currently, this can be improved ghopefully. > > 2 file(s) affected in this change: > > lib/galaxy/web/controllers/tool_runner.py > templates/root/history_common.mako > > diffs (118 lines): > > diff -r ad5232a4dbc5 -r 52ad5635f01a lib/galaxy/web/controllers/tool_runner.py > --- a/lib/galaxy/web/controllers/tool_runner.py Thu Aug 13 11:00:00 2009 -0400 > +++ b/lib/galaxy/web/controllers/tool_runner.py Thu Aug 13 11:27:45 2009 -0400 > @@ -5,6 +5,7 @@ > from galaxy.web.base.controller import * > from galaxy.util.bunch import Bunch > from galaxy.tools import DefaultToolState > +from galaxy.tools.parameters.basic import UnvalidatedValue > > import logging > log = logging.getLogger( __name__ ) > @@ -52,6 +53,80 @@ > add_frame.wiki_url = trans.app.config.wiki_url > add_frame.from_noframe = True > return trans.fill_template( template, history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) > + > + @web.expose > + def rerun( self, trans, id=None, from_noframe=None, **kwd ): > + """ > + Given a HistoryDatasetAssociation id, find the job and that created > + the dataset, extract the parameters, and display the appropriate tool > + form with parameters already filled in. > + """ > + if not id: > + error( "'id' parameter is required" ); > + try: > + id = int( id ) > + except: > + error( "Invalid value for 'id' parameter" ) > + # Get the dataset object > + data = trans.app.model.HistoryDatasetAssociation.get( id ) > + # Get the associated job, if any. If this hda was copied from another, > + # we need to find the job that created the origial hda > + job_hda = data > + while job_hda.copied_from_history_dataset_association: > + job_hda = job_hda.copied_from_history_dataset_association > + if not job_hda.creating_job_associations: > + error( "Could not find the job for this dataset" ) > + # Get the job object > + job = None > + for assoc in job_hda.creating_job_associations: > + job = assoc.job > + break > + if not job: > + raise Exception("Failed to get job information for dataset hid %d" % hid) > + # Get the tool object > + tool_id = job.tool_id > + try: > + # Load the tool > + toolbox = self.get_toolbox() > + tool = toolbox.tools_by_id.get( tool_id, None ) > + except: > + #this is expected, so not an exception > + error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id ) > + # Can't rerun upload, external data sources, et cetera. Workflow > + # compatible will proxy this for now > + if not tool.is_workflow_compatible: > + error( "The '%s' tool does not currently support rerunning." % tool.name ) > + # Get the job's parameters > + try: > + params_objects = job.get_param_values( trans.app ) > + except: > + raise Exception( "Failed to get paramemeters for dataset id %d " % hid ) > + # Unpack unvalidated values to strings, they'll be validated when the > + # form is submitted (this happens when re-running a job that was > + # initially run by a workflow) > + validated_params = {} > + for name, value in params_objects.items(): > + if isinstance( value, UnvalidatedValue ): > + validated_params [ str(name) ] = str(value) > + else: > + validated_params [ str(name) ] = value > + params_objects = validated_params > + # Create a fake tool_state for the tool, with the parameters values > + state = tool.new_state( trans ) > + state.inputs = params_objects > + tool_state_string = util.object_to_string(state.encode(tool, trans.app)) > + # Setup context for template > + history = trans.get_history() > + template = "tool_form.mako" > + vars = dict( tool_state=state, errors = {} ) > + # Is the "add frame" stuff neccesary here? > + add_frame = AddFrameData() > + add_frame.debug = trans.debug > + if from_noframe is not None: > + add_frame.wiki_url = trans.app.config.wiki_url > + add_frame.from_noframe = True > + return trans.fill_template( template, history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) > + > > @web.expose > def redirect( self, trans, redirect_url=None, **kwd ): > diff -r ad5232a4dbc5 -r 52ad5635f01a templates/root/history_common.mako > --- a/templates/root/history_common.mako Thu Aug 13 11:00:00 2009 -0400 > +++ b/templates/root/history_common.mako Thu Aug 13 11:27:45 2009 -0400 > @@ -51,9 +51,12 @@ > <div>${_('Job is currently running')}</div> > %elif data_state == "error": > <div> > - An error occurred running this job: <i>${data.display_info().strip()}</i>, > - <a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main">report this error</a> > + An error occurred running this job: <i>${data.display_info().strip()}</i> > </div> > + <div> > + <a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main">report this error</a> > + | <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main">rerun</a> > + </div> > %elif data_state == "discarded": > <div> > The job creating this dataset was cancelled before completion. > @@ -77,6 +80,7 @@ > <div> > %if data.has_data: > <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> > + | <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main">rerun</a> > %for display_app in data.datatype.get_display_types(): > <% display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> > %if len( display_links ) > 0: > > > ------------------------------ > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev > > > End of galaxy-dev Digest, Vol 44, Issue 22 > ****************************************** > -- Ross Lazarus, Associate Professor, Department of Population Medicine, Harvard Medical School; Director of Bioinformatics, Channing Laboratory, BWH 181 Longwood Ave., Boston MA 02115, USA.

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Possible Bug in SGE Runner when recovering jobs
by Assaf Gordon 14 Aug '09

14 Aug '09

Hi, Not sure if this is a bug or my configuration problem, but: 1. universe_wsgi.ini has: track_jobs_in_database = True enable_job_recovery = True 2. A tool (which uses the SGE runner) is in 'queued' state: psql# select id,tool_id,state from job where state = 'queued'; id | tool_id | state ----+-----------------+-------- 39 | Show beginning1 | queued (1 row) 3. Starting galaxy with "sh run.sh" gives: Traceback (most recent call last): File "/bh/data/hannon/gordon/galaxy/galaxy_bh_dev/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/bh/data/hannon/gordon/galaxy/galaxy_bh_dev/lib/galaxy/app.py", line 64, in __init__ self.job_manager = jobs.JobManager( self ) File "/bh/data/hannon/gordon/galaxy/galaxy_bh_dev/lib/galaxy/jobs/__init__.py", line 35, in __init__ self.job_queue = JobQueue( app, self.dispatcher ) File "/bh/data/hannon/gordon/galaxy/galaxy_bh_dev/lib/galaxy/jobs/__init__.py", line 112, in __init__ self.__check_jobs_at_startup() File "/bh/data/hannon/gordon/galaxy/galaxy_bh_dev/lib/galaxy/jobs/__init__.py", line 137, in __check_jobs_at_startup self.dispatcher.recover( job, job_wrapper ) File "/bh/data/hannon/gordon/galaxy/galaxy_bh_dev/lib/galaxy/jobs/__init__.py", line 661, in recover self.job_runners[runner_name].recover( job, job_wrapper ) File "/data/hannon/gordon/galaxy/galaxy_bh_dev/lib/galaxy/jobs/runners/sge.py", line 358, in recover sge_job_state.old_state = DRMAA.Session.QUEUED AttributeError: type object 'Session' has no attribute 'QUEUED' ------------- The immediate cause is that the DRMAA Session class does not have a "QUEUED" state. The closest thing is "QUEUED_ACTIVE" state, as evident from both sge.py lines 18-28, and from DRMAA.py line 363. On a related note, I'm not quite sure how job recovery works with SGE: Let's say a job is queued with QSUB, then galaxy is stopped. The database still says "queued", but in the meantime, the SGE cluster might run the job, and even complete it - So the job can in fact be 'running' or 'ok' or 'error', but Galaxy thinks it is queued. What will happen when Galaxy is restarted ? Is the job automatically restarted, or is the new state queried from the SGE ? Thanks, Gordon.

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[hg] galaxy 2564: Fix for library expand buttons in IE (even tho...
by Greg Von Kuster 14 Aug '09

14 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/eb1244477b90 changeset: 2564:eb1244477b90 user: James Taylor <james(a)jamestaylor.org> date: Fri Aug 14 12:17:45 2009 -0400 description: Fix for library expand buttons in IE (even though the old way used to work, should work, and was tested). 1 file(s) affected in this change: templates/library/browse_library.mako diffs (26 lines): diff -r bfd2ee7bff9d -r eb1244477b90 templates/library/browse_library.mako --- a/templates/library/browse_library.mako Fri Aug 14 10:03:15 2009 -0400 +++ b/templates/library/browse_library.mako Fri Aug 14 12:17:45 2009 -0400 @@ -38,14 +38,21 @@ descendents = descendents.add( child_descendents ); }); // Set up expand / hide link + // HACK: assume descendents are invisible. The caller actually + // ensures this for the root node. However, if we start + // remembering folder states, we'll need something + // more sophisticated here. + var visible = false; $(q).find( "span.expandLink").click( function() { - if ( children.is( ":visible" ) ) { + if ( visible ) { descendents.hide(); descendents.removeClass( "expanded" ); q.removeClass( "expanded" ); + visible = false; } else { children.show(); q.addClass( "expanded" ); + visible = true; } }); // Check/uncheck boxes in subfolders.

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[hg] galaxy 2563: Functional test fixes for my last commit.
by Greg Von Kuster 14 Aug '09

14 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/bfd2ee7bff9d changeset: 2563:bfd2ee7bff9d user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Aug 14 10:03:15 2009 -0400 description: Functional test fixes for my last commit. 2 file(s) affected in this change: templates/admin/library/browse_libraries.mako test/base/twilltestcase.py diffs (24 lines): diff -r d2ad22e73b81 -r bfd2ee7bff9d templates/admin/library/browse_libraries.mako --- a/templates/admin/library/browse_libraries.mako Fri Aug 14 09:22:31 2009 -0400 +++ b/templates/admin/library/browse_libraries.mako Fri Aug 14 10:03:15 2009 -0400 @@ -13,7 +13,7 @@ <ul class="manage-table-actions"> %if not deleted: <li> - <a class="action-button" href="${h.url_for( controller='admin', action='library', new=True )}"><span>Create a new library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='library', new=True )}"><span>Create a new data library</span></a> </li> <li> <a class="action-button" href="${h.url_for( controller='admin', action='deleted_libraries' )}"><span>Manage deleted libraries</span></a> diff -r d2ad22e73b81 -r bfd2ee7bff9d test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Aug 14 09:22:31 2009 -0400 +++ b/test/base/twilltestcase.py Fri Aug 14 10:03:15 2009 -0400 @@ -1003,7 +1003,7 @@ """Create a new library""" self.home() self.visit_url( "%s/admin/library?new=True" % self.url ) - self.check_page_for_string( 'Create a new library' ) + self.check_page_for_string( 'Create a new data library' ) tc.fv( "1", "1", name ) # form field 1 is the field named name... tc.fv( "1", "2", description ) # form field 1 is the field named name... tc.submit( "create_library_button" )

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[hg] galaxy 2559: Fixing masthead centering again
by Greg Von Kuster 14 Aug '09

14 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/50a38a294296 changeset: 2559:50a38a294296 user: James Taylor <james(a)jamestaylor.org> date: Thu Aug 13 11:43:46 2009 -0400 description: Fixing masthead centering again 1 file(s) affected in this change: templates/base_panels.mako diffs (51 lines): diff -r 52ad5635f01a -r 50a38a294296 templates/base_panels.mako --- a/templates/base_panels.mako Thu Aug 13 11:27:45 2009 -0400 +++ b/templates/base_panels.mako Thu Aug 13 11:43:46 2009 -0400 @@ -115,18 +115,9 @@ ## Masthead <%def name="masthead()"> - <div style="position: absolute; left: 0px; width: 100%; text-align: center"> + ## Tab area, fills entire width + <div style="position: absolute; top: 0; left: 0; width: 100%; text-align: center"> - <div class="title" style="float: left;"> - <a href="/"> - <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> - Galaxy - %if app.config.brand: - <span class='brand'>/${app.config.brand}</span> - %endif - </a> - </div> - <table class="tab-group" border="0" cellspacing="0" style="margin: auto;"> <tr> @@ -231,6 +222,17 @@ </div> + ## Logo, layered over tabs to be clickable + <div class="title" style="position: absolute; top: 0; left: 0;"> + <a href="/"> + <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> + Galaxy + %if app.config.brand: + <span class='brand'>/${app.config.brand}</span> + %endif + </a> + </div> + </%def> <%def name="overlay( title='', content='' )"> @@ -283,7 +285,7 @@ </head> <body scroll="no" class="${self.body_class}"> - <div id="everything" style="position: absolute; width: 100%; height: 100%; min-width: 960px; min-height: 400px;"> + <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 960px;"> ## Background displays first <div id="background"></div> ## Layer iframes over backgrounds

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[hg] galaxy 2562: Change GUI references to Library to now be Dat...
by Greg Von Kuster 14 Aug '09

14 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d2ad22e73b81 changeset: 2562:d2ad22e73b81 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Aug 14 09:22:31 2009 -0400 description: Change GUI references to Library to now be Data Library, and merge 2 history grid templates into 1. 43 file(s) affected in this change: lib/galaxy/web/controllers/history.py lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py templates/admin/center.mako templates/admin/dataset_security/role.mako templates/admin/index.mako templates/admin/library/browse_libraries.mako templates/admin/library/browse_library.mako templates/admin/library/folder_info.mako templates/admin/library/folder_permissions.mako templates/admin/library/ldda_edit_info.mako templates/admin/library/ldda_info.mako templates/admin/library/ldda_permissions.mako templates/admin/library/library_dataset_info.mako templates/admin/library/library_dataset_permissions.mako templates/admin/library/library_info.mako templates/admin/library/library_permissions.mako templates/admin/library/new_dataset.mako templates/admin/library/new_folder.mako templates/admin/library/new_library.mako templates/admin/library/select_info_template.mako templates/admin/requests/show_request.mako templates/base_panels.mako templates/history/shared_grid.mako templates/history/stored_grid.mako templates/library/browse_libraries.mako templates/library/browse_library.mako templates/library/folder_info.mako templates/library/folder_permissions.mako templates/library/ldda_edit_info.mako templates/library/ldda_info.mako templates/library/ldda_permissions.mako templates/library/library_dataset_info.mako templates/library/library_dataset_permissions.mako templates/library/library_info.mako templates/library/library_permissions.mako templates/library/new_dataset.mako templates/library/new_folder.mako templates/library/select_info_template.mako templates/requests/edit_request.mako templates/requests/new_request.mako templates/requests/show_request.mako test/functional/test_security_and_libraries.py diffs (1125 lines): diff -r 172548982c18 -r d2ad22e73b81 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Thu Aug 13 12:19:00 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Fri Aug 14 09:22:31 2009 -0400 @@ -161,7 +161,7 @@ status, message = self._list_undelete( trans, histories ) trans.sa_session.flush() # Render the list view - return self.stored_list_grid( trans, status=status, message=message, template='/history/stored_grid.mako', **kwargs ) + return self.stored_list_grid( trans, status=status, message=message, template='/history/grid.mako', **kwargs ) def _list_delete( self, trans, histories ): """Delete histories""" n_deleted = 0 @@ -239,14 +239,14 @@ if operation == "clone": if not id: message = "Select a history to clone" - return self.shared_list_grid( trans, status='error', message=message, template='/history/shared_grid.mako', **kwargs ) + return self.shared_list_grid( trans, status='error', message=message, template='/history/grid.mako', **kwargs ) # When cloning shared histories, only copy active datasets new_kwargs = { 'clone_choice' : 'active' } return self.clone( trans, id, **new_kwargs ) elif operation == 'unshare': if not id: message = "Select a history to unshare" - return self.shared_list_grid( trans, status='error', message=message, template='/history/shared_grid.mako', **kwargs ) + return self.shared_list_grid( trans, status='error', message=message, template='/history/grid.mako', **kwargs ) ids = util.listify( id ) histories = [] for history_id in ids: @@ -260,7 +260,7 @@ message = "Unshared %d shared histories" % len( ids ) status = 'done' # Render the list view - return self.shared_list_grid( trans, status=status, message=message, template='/history/shared_grid.mako', **kwargs ) + return self.shared_list_grid( trans, status=status, message=message, template='/history/grid.mako', **kwargs ) @web.expose def delete_current( self, trans ): """Delete just the active history -- this does not require a logged in user.""" diff -r 172548982c18 -r d2ad22e73b81 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Thu Aug 13 12:19:00 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Fri Aug 14 09:22:31 2009 -0400 @@ -152,16 +152,12 @@ helptext='')) # library associated if request.library: - request_details.append(dict(label='Library', - value=request.library.name, - helptext='Associated library where the resultant \ - dataset will be stored')) + value = request.library.name else: - request_details.append(dict(label='Library', - value=None, - helptext='Associated library where the resultant \ - dataset will be stored')) - + value = None + request_details.append( dict( label='Data library', + value=value, + helptext='Data library where the resultant dataset will be stored' ) ) # form fields for index, field in enumerate(request.type.request_form.fields): if field['required']: @@ -492,18 +488,17 @@ else: lib_list.add_option(lib.name, lib.id) if lib_id == 'new': - lib_list.add_option('Create a new library', 'new', selected=True) + lib_list.add_option('Create a new data library', 'new', selected=True) else: - lib_list.add_option('Create a new library', 'new') - widget = dict(label='Library', + lib_list.add_option('Create a new data library', 'new') + widget = dict(label='Data library', widget=lib_list, - helptext='Associated library where the resultant \ - dataset will be stored.') + helptext='Data library where the resultant dataset will be stored.') if lib_id == 'new': - new_lib = dict(label='Create a new Library', + new_lib = dict(label='Create a new data library', widget=TextField('new_library_name', 40, util.restore_text( params.get( 'new_library_name', '' ) )), - helptext='Enter a library name here to request a new library') + helptext='Enter a name here to request a new data library') return [widget, new_lib] else: return [widget] @@ -558,7 +553,7 @@ ''' empty_fields = [] if not request.library: - empty_fields.append('Library') + empty_fields.append('Data library') # check rest of the fields of the form for index, field in enumerate(request.type.request_form.fields): if field['required'] == 'required' and request.values.content[index] in ['', None]: diff -r 172548982c18 -r d2ad22e73b81 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Thu Aug 13 12:19:00 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Fri Aug 14 09:22:31 2009 -0400 @@ -144,10 +144,9 @@ value=str(request.user.email), helptext='')) # library associated - request_details.append(dict(label='Library', + request_details.append(dict(label='Data library', value=trans.app.model.Library.get(request.library_id).name, - helptext='Associated library where the resultant \ - dataset will be stored')) + helptext='Data library where the resultant dataset will be stored')) # form fields for index, field in enumerate(request.type.request_form.fields): if field['required']: diff -r 172548982c18 -r d2ad22e73b81 templates/admin/center.mako --- a/templates/admin/center.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/center.mako Fri Aug 14 09:22:31 2009 -0400 @@ -17,7 +17,7 @@ <li> <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with each group (both private and non-private roles). Non-private roles include a link to a page that allows you to manage the users - and groups that are associated with the role. The page also includes a view of the library datasets that are associated with the + and groups that are associated with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied to each dataset. </li> <p/> @@ -32,9 +32,9 @@ <p/> <ul> <li> - <strong>Manage libraries</strong> - Dataset libraries enable a Galaxy administrator to upload datasets into a library. Currently, - only administrators can create dataset libraries, but permission to perform the following functions on the library can be granted to - users (a library item is one of: a library, a library folder, a library dataset). + <strong>Manage data libraries</strong> - Data libraries enable a Galaxy administrator to upload datasets into a data library. Currently, + only administrators can create data libraries, but permission to perform the following functions on the data library can be granted to + users (a library item is one of: a data library, a library folder, a library dataset). <p/> <ul> <li><strong>add library item</strong> - Role members can add library items to this library or folder</li> @@ -42,12 +42,12 @@ <li><strong>manage library permissions</strong> - Role members can manage permissions applied to this library item</li> </ul> <p/> - The default behavior is for no permissions to be applied to a library item, but applied permissions are inherited downward, so it is - important to set desired permissions on a new library when it is created. When this is done, new folders and datasets added to the - library will automatically inherit those permissions. In the same way, permissions can be applied to a folder, which will be + The default behavior is for no permissions to be applied to a data library item, but applied permissions are inherited downward, so it is + important to set desired permissions on a new data library when it is created. When this is done, new folders and datasets added to the + data library will automatically inherit those permissions. In the same way, permissions can be applied to a folder, which will be automatically inherited by all contained datasets and sub-folders. <p/> - The "Libraries" menu item allows users to access the datasets in a library as long as they are not restricted from accessing them. + The "Data Libraries" menu item allows users to access the datasets in a data library as long as they are not restricted from accessing them. Importing a library dataset into a history will not make a copy of the dataset, but will be a "pointer" to the dataset on disk. This approach allows for multiple users to use a single (possibly very large) dataset file. </li> @@ -72,7 +72,7 @@ </ul> </li> </ul> -<p><strong>Data Security and Dataset Libraries</strong></p> +<p><strong>Data Security and Data Libraries</strong></p> <p/> <strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>. The data security @@ -121,8 +121,8 @@ <strong>access</strong> - users associated with the role can import this dataset into their history for analysis. <p> If no roles with the "access" permission are associated with a dataset, the dataset is "public" and may be accessed by - anyone. Public library datasets will be accessible to all users (as well as anyone not logged in during a Galaxy session) - from the list of libraries displayed when the "Libraries" menu item is selected. + anyone. Public data library datasets will be accessible to all users (as well as anyone not logged in during a Galaxy session) + from the list of data libraries displayed when the "Data Libraries" menu item is selected. </p> <p> Associating a dataset with a role that includes the "access" permission restricts the set of users that can access it. diff -r 172548982c18 -r d2ad22e73b81 templates/admin/dataset_security/role.mako --- a/templates/admin/dataset_security/role.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/dataset_security/role.mako Fri Aug 14 09:22:31 2009 -0400 @@ -84,7 +84,7 @@ <br clear="left"/> <br/> %if len( library_dataset_actions ) > 0: - <h3>Library datasets associated with role '${role.name}'</h3> + <h3>Data library datasets associated with role '${role.name}'</h3> <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> <tr> <td> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/index.mako --- a/templates/admin/index.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/index.mako Fri Aug 14 09:22:31 2009 -0400 @@ -89,7 +89,7 @@ </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_libraries' )}" target="galaxy_main">Manage libraries</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_libraries' )}" target="galaxy_main">Manage data libraries</a></div> </div> </div> <div class="toolSectionPad"></div> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/browse_libraries.mako --- a/templates/admin/library/browse_libraries.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/browse_libraries.mako Fri Aug 14 09:22:31 2009 -0400 @@ -1,13 +1,13 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<%def name="title()">Browse Libraries</%def> +<%def name="title()">Browse Data Libraries</%def> <h2> %if deleted: Deleted %endif - Libraries + Data Libraries </h2> <ul class="manage-table-actions"> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/browse_library.mako Fri Aug 14 09:22:31 2009 -0400 @@ -162,16 +162,16 @@ %if deleted: Deleted %endif - Library '${library.name}' + Data Library “${library.name}” </h2> <ul class="manage-table-actions"> %if not deleted: <li> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a> </li> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a> + <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this data library</a> </li> %endif </ul> @@ -200,24 +200,24 @@ library_item_ids = {} library_item_ids[ 'library' ] = library.id %> - <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this library's information</a> + <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this data library's information</a> ## Editing templates disabled until we determine optimal approach to re-linking library item to new version of form definition ##%if library.info_association: ## <% form_id = library.info_association[0].template.id %> - ## <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form_id, show_form=True )}">Edit this library's information template</a> + ## <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form_id, show_form=True )}">Edit this data library's information template</a> ##%else: %if not library.info_association: - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, add=True )}">Add an information template to this library</a> + <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, add=True )}">Add an information template to this data library</a> %endif - <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, permissions=True )}">Edit this library's permissions</a> - <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this library and its contents</a> + <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, permissions=True )}">Edit this data library's permissions</a> + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this data library and its contents</a> %if show_deleted: - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted library items</a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted data library items</a> %else: - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted library items</a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted data library items</a> %endif %elif not library.purged: - <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Undelete this library</a> + <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Undelete this data library</a> %endif </div> </th> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/folder_info.mako --- a/templates/admin/library/folder_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/folder_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/folder_permissions.mako --- a/templates/admin/library/folder_permissions.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/folder_permissions.mako Fri Aug 14 09:22:31 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/ldda_edit_info.mako --- a/templates/admin/library/ldda_edit_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/ldda_edit_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -12,7 +12,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/ldda_info.mako --- a/templates/admin/library/ldda_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/ldda_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -20,7 +20,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id, deleted=library.deleted, show_deleted=show_deleted )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id, deleted=library.deleted, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/ldda_permissions.mako --- a/templates/admin/library/ldda_permissions.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/ldda_permissions.mako Fri Aug 14 09:22:31 2009 -0400 @@ -15,7 +15,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/library_dataset_info.mako --- a/templates/admin/library/library_dataset_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/library_dataset_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/library_dataset_permissions.mako --- a/templates/admin/library/library_dataset_permissions.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/library_dataset_permissions.mako Fri Aug 14 09:22:31 2009 -0400 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/library_info.mako --- a/templates/admin/library/library_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/library_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/library_permissions.mako --- a/templates/admin/library/library_permissions.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/library_permissions.mako Fri Aug 14 09:22:31 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/new_dataset.mako --- a/templates/admin/library/new_dataset.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/new_dataset.mako Fri Aug 14 09:22:31 2009 -0400 @@ -4,7 +4,7 @@ <% import os, os.path %> -<b>Create new library datasets</b> +<b>Create new data library datasets</b> <a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="upload-librarydataset--popup"> <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a> @@ -16,7 +16,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -142,7 +142,7 @@ <textarea name="message" rows="3" cols="35"></textarea> </div> <div class="toolParamHelp" style="clear: both;"> - This information will be displayed in the "Information" column for this dataset in the library browser + This information will be displayed in the "Information" column for this dataset in the data library browser </div> <div style="clear: both"></div> </div> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/new_folder.mako --- a/templates/admin/library/new_folder.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/new_folder.mako Fri Aug 14 09:22:31 2009 -0400 @@ -4,7 +4,7 @@ <br/<br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/new_library.mako --- a/templates/admin/library/new_library.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/new_library.mako Fri Aug 14 09:22:31 2009 -0400 @@ -6,13 +6,13 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Create a new library</div> + <div class="toolFormTitle">Create a new data library</div> <div class="toolFormBody"> <form name="library" action="${h.url_for( controller='admin', action='library' )}" method="post" > <div class="form-row"> <label>Name:</label> <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="New Library" size="40"/> + <input type="text" name="name" value="New data library" size="40"/> </div> <div style="clear: both"></div> </div> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/library/select_info_template.mako --- a/templates/admin/library/select_info_template.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/library/select_info_template.mako Fri Aug 14 09:22:31 2009 -0400 @@ -4,7 +4,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/admin/requests/show_request.mako Fri Aug 14 09:22:31 2009 -0400 @@ -48,7 +48,7 @@ %if not rd['value']: <i>None</i> %else: - %if rd['label'] == 'Library': + %if rd['label'] == 'Data library': <a href="${h.url_for( controller='admin', action='browse_library', id=request.library.id )}">${rd['value']}</a> %else: ${rd['value']} diff -r 172548982c18 -r d2ad22e73b81 templates/base_panels.mako --- a/templates/base_panels.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/base_panels.mako Fri Aug 14 09:22:31 2009 -0400 @@ -139,14 +139,14 @@ ${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))} - ${tab( "libraries", "Libraries", h.url_for( controller='library', action='index' ))} + ${tab( "libraries", "Data Libraries", h.url_for( controller='library', action='index' ))} %if trans.request_types(): <td class="tab"> <a>Lab</a> <div class="submenu"> <ul> - <li><a target="requests" href="${h.url_for( controller='requests', action='index' )}">Sequencing Requests</a></li> + <li><a href="${h.url_for( controller='requests', action='index' )}">Sequencing Requests</a></li> </ul> </div> </td> diff -r 172548982c18 -r d2ad22e73b81 templates/history/shared_grid.mako --- a/templates/history/shared_grid.mako Thu Aug 13 12:19:00 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,197 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="title()">${grid.title}</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - ## TODO: generalize and move into galaxy.base.js - $(document).ready(function() { - $(".grid").each( function() { - var grid = this; - var checkboxes = $(this).find("input.grid-row-select-checkbox"); - var update = $(this).find( "span.grid-selected-count" ); - $(checkboxes).each( function() { - $(this).change( function() { - var n = $(checkboxes).filter("[checked]").size(); - update.text( n ); - }); - }) - }); - }); - ## Can this be moved into base.mako? - %if refresh_frames: - %if 'masthead' in refresh_frames: - ## Refresh masthead == user changes (backward compatibility) - if ( parent.user_changed ) { - %if trans.user: - parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); - %else: - parent.user_changed( null, false ); - %endif - } - %endif - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - %if 'tools' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_tools ) { - parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; - if ( parent.force_left_panel ) { - parent.force_left_panel( 'show' ); - } - } - %endif - %endif - </script> -</%def> - -<%def name="stylesheets()"> - <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> - <style> - ## Not generic to all grids -- move to base? - .count-box { - min-width: 1.1em; - padding: 5px; - border-width: 1px; - border-style: solid; - text-align: center; - display: inline-block; - } - </style> -</%def> - -%if grid.standard_filters: - <div class="grid-header"> - <h2>${grid.title}</h2> - <span class="title">Filter:</span> - %for i, filter in enumerate( grid.standard_filters ): - %if i > 0: - <span>|</span> - %endif - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endfor - </div> -%endif - -%if message: - <p> - <div class="${message_type}message transient-message">${message}</div> - <div style="clear: both"></div> - </p> -%endif -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<form name="history_shared_by_others" action="${url()}" method="post" > - <table class="grid"> - <thead> - <tr> - <th></th> - %for column in grid.columns: - %if column.visible: - <% - href = "" - extra = "" - if column.sortable: - if sort_key == column.key: - if sort_order == "asc": - href = url( sort=( "-" + column.key ) ) - extra = "↓" - else: - href = url( sort=( column.key ) ) - extra = "↑" - else: - href = url( sort=column.key ) - %> - <th\ - %if column.ncells > 1: - colspan="${column.ncells}" - %endif - > - %if href: - <a href="${href}">${column.label}</a> - %else: - ${column.label} - %endif - <span>${extra}</span> - </th> - %endif - %endfor - <th></th> - </tr> - </thead> - <tbody> - %for i, history in enumerate( query ): - <tr> - ## Item selection column - <td style="width: 1.5em;"> - <input type="checkbox" name="id" value=${trans.security.encode_id( history.id )} class="grid-row-select-checkbox" /> - </td> - ## Data columns - %for column in grid.columns: - %if column.visible: - <% - # Link - link = column.get_link( trans, grid, history ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, history ) - if column.ncells == 1: - value = [ value ] - %> - %for cellnum, v in enumerate( value ): - <% - # Attach popup menu? - if column.attach_popup and cellnum == 0: - extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">▼</a>' % i - else: - extra = "" - %> - %if href: - <td><a href="${href}">${v}</a> ${extra}</td> - %else: - <td >${v}${extra}</td> - %endif - </td> - %endfor - %endif - %endfor - ## Actions column - <td> - <div popupmenu="grid-${i}-popup"> - %for operation in grid.operations: - %if operation.allowed( history ): - <a class="action-button" href="${url( operation=operation.label, id=history.id )}">${operation.label}</a> - %endif - %endfor - </div> - </td> - </tr> - %endfor - </tbody> - <tfoot> - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected histories: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - </tfoot> - </table> -</form> diff -r 172548982c18 -r d2ad22e73b81 templates/history/stored_grid.mako --- a/templates/history/stored_grid.mako Thu Aug 13 12:19:00 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,196 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">${grid.title}</%def> - -%if message: - <p> - <div class="${message_type}message transient-message">${message}</div> - <div style="clear: both"></div> - </p> -%endif - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - ## TODO: generalize and move into galaxy.base.js - $(document).ready(function() { - $(".grid").each( function() { - var grid = this; - var checkboxes = $(this).find("input.grid-row-select-checkbox"); - var update = $(this).find( "span.grid-selected-count" ); - $(checkboxes).each( function() { - $(this).change( function() { - var n = $(checkboxes).filter("[checked]").size(); - update.text( n ); - }); - }) - }); - }); - ## Can this be moved into base.mako? - %if refresh_frames: - %if 'masthead' in refresh_frames: - ## Refresh masthead == user changes (backward compatibility) - if ( parent.user_changed ) { - %if trans.user: - parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); - %else: - parent.user_changed( null, false ); - %endif - } - %endif - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - %if 'tools' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_tools ) { - parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; - if ( parent.force_left_panel ) { - parent.force_left_panel( 'show' ); - } - } - %endif - %endif - </script> -</%def> - -<%def name="stylesheets()"> - <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> - <style> - ## Not generic to all grids -- move to base? - .count-box { - min-width: 1.1em; - padding: 5px; - border-width: 1px; - border-style: solid; - text-align: center; - display: inline-block; - } - </style> -</%def> - -%if grid.standard_filters: - <div class="grid-header"> - <h2>${grid.title}</h2> - <span class="title">Filter:</span> - %for i, filter in enumerate( grid.standard_filters ): - %if i > 0: - <span>|</span> - %endif - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endfor - </div> -%endif - -<form name="history_actions" action="${url()}" method="post" > - <table class="grid"> - <thead> - <tr> - <th></th> - %for column in grid.columns: - %if column.visible: - <% - href = "" - extra = "" - if column.sortable: - if sort_key == column.key: - if sort_order == "asc": - href = url( sort=( "-" + column.key ) ) - extra = "↓" - else: - href = url( sort=( column.key ) ) - extra = "↑" - else: - href = url( sort=column.key ) - %> - <th\ - %if column.ncells > 1: - colspan="${column.ncells}" - %endif - > - %if href: - <a href="${href}">${column.label}</a> - %else: - ${column.label} - %endif - <span>${extra}</span> - </th> - %endif - %endfor - <th></th> - </tr> - </thead> - <tbody> - %for i, item in enumerate( query ): - <tr \ - %if current_item == item: - class="current" \ - %endif - > - ## Item selection column - <td style="width: 1.5em;"> - <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> - </td> - ## Data columns - %for column in grid.columns: - %if column.visible: - <% - # Link - link = column.get_link( trans, grid, item ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, item ) - if column.ncells == 1: - value = [ value ] - %> - %for cellnum, v in enumerate( value ): - <% - # Attach popup menu? - if column.attach_popup and cellnum == 0: - extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">▼</a>' % i - else: - extra = "" - %> - %if href: - <td><a href="${href}">${v}</a> ${extra}</td> - %else: - <td >${v}${extra}</td> - %endif - </td> - %endfor - %endif - %endfor - ## Actions column - <td> - <div popupmenu="grid-${i}-popup"> - %for operation in grid.operations: - %if operation.allowed( item ): - <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> - %endif - %endfor - </div> - </td> - </tr> - %endfor - </tbody> - <tfoot> - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected histories: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - </tfoot> - </table> -</form> diff -r 172548982c18 -r d2ad22e73b81 templates/library/browse_libraries.mako --- a/templates/library/browse_libraries.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/browse_libraries.mako Fri Aug 14 09:22:31 2009 -0400 @@ -1,9 +1,9 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<%def name="title()">Browse Libraries</%def> +<%def name="title()">Browse Data Libraries</%def> -<h2>Libraries</h2> +<h2>Data Libraries</h2> %if msg: ${render_msg( msg, messagetype )} diff -r 172548982c18 -r d2ad22e73b81 templates/library/browse_library.mako --- a/templates/library/browse_library.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/browse_library.mako Fri Aug 14 09:22:31 2009 -0400 @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> <% from galaxy import util %> -<%def name="title()">Browse Library</%def> +<%def name="title()">Browse data library</%def> <%def name="stylesheets()"> <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> <link href="${h.url_for('/static/style/library.css')}" rel="stylesheet" type="text/css" /> @@ -211,7 +211,7 @@ %endfor </%def> -<h2>Library “${library.name}”</h2> +<h2>Data Library “${library.name}”</h2> <ul class="manage-table-actions"> %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): diff -r 172548982c18 -r d2ad22e73b81 templates/library/folder_info.mako --- a/templates/library/folder_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/folder_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/folder_permissions.mako --- a/templates/library/folder_permissions.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/folder_permissions.mako Fri Aug 14 09:22:31 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/ldda_edit_info.mako --- a/templates/library/ldda_edit_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/ldda_edit_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -12,7 +12,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/ldda_info.mako --- a/templates/library/ldda_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/ldda_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -19,7 +19,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/ldda_permissions.mako --- a/templates/library/ldda_permissions.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/ldda_permissions.mako Fri Aug 14 09:22:31 2009 -0400 @@ -15,7 +15,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/library_dataset_info.mako --- a/templates/library/library_dataset_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/library_dataset_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/library_dataset_permissions.mako --- a/templates/library/library_dataset_permissions.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/library_dataset_permissions.mako Fri Aug 14 09:22:31 2009 -0400 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/library_info.mako --- a/templates/library/library_info.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/library_info.mako Fri Aug 14 09:22:31 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library.id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library.id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/library_permissions.mako --- a/templates/library/library_permissions.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/library_permissions.mako Fri Aug 14 09:22:31 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library.id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library.id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/new_dataset.mako --- a/templates/library/new_dataset.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/new_dataset.mako Fri Aug 14 09:22:31 2009 -0400 @@ -16,7 +16,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -68,7 +68,7 @@ %elif upload_option == 'upload_directory': <div class="form-row"> <% - # Directories of files from the Libraries view are restricted to a + # Directories of files from the Data Libraries view are restricted to a # sub-directory named the same as the current user's email address # contained within the configured setting for user_library_import_dir user_library_import_dir = os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) diff -r 172548982c18 -r d2ad22e73b81 templates/library/new_folder.mako --- a/templates/library/new_folder.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/new_folder.mako Fri Aug 14 09:22:31 2009 -0400 @@ -4,7 +4,7 @@ <br/<br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/library/select_info_template.mako --- a/templates/library/select_info_template.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/library/select_info_template.mako Fri Aug 14 09:22:31 2009 -0400 @@ -4,7 +4,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 172548982c18 -r d2ad22e73b81 templates/requests/edit_request.mako --- a/templates/requests/edit_request.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/requests/edit_request.mako Fri Aug 14 09:22:31 2009 -0400 @@ -58,7 +58,7 @@ <div class="form-row"> <label>${field['label']}</label> ${field['widget'].get_html()} - %if field['label'] == 'Library' and new_library: + %if field['label'] == 'Data library' and new_library: ${new_library.get_html()} %endif <div class="toolParamHelp" style="clear: both;"> diff -r 172548982c18 -r d2ad22e73b81 templates/requests/new_request.mako --- a/templates/requests/new_request.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/requests/new_request.mako Fri Aug 14 09:22:31 2009 -0400 @@ -58,7 +58,7 @@ <div class="form-row"> <label>${field['label']}</label> ${field['widget'].get_html()} - %if field['label'] == 'Library' and new_library: + %if field['label'] == 'Data library' and new_library: ${new_library.get_html()} %endif <div class="toolParamHelp" style="clear: both;"> diff -r 172548982c18 -r d2ad22e73b81 templates/requests/show_request.mako --- a/templates/requests/show_request.mako Thu Aug 13 12:19:00 2009 -0400 +++ b/templates/requests/show_request.mako Fri Aug 14 09:22:31 2009 -0400 @@ -79,7 +79,7 @@ %if not rd['value']: <i>None</i> %else: - %if rd['label'] == 'Library': + %if rd['label'] == 'Data library': %if rd['value']: <a href="${h.url_for( controller='library', action='browse_library', id=request.library.id )}">${rd['value']}</a> %else: diff -r 172548982c18 -r d2ad22e73b81 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Thu Aug 13 12:19:00 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Fri Aug 14 09:22:31 2009 -0400 @@ -1451,7 +1451,7 @@ check_edit_page2( latest_3_lddas ) self.home() def test_195_upload_directory_of_files_from_libraries_view( self ): - """Testing uploading a directory of files to a root folder from the Libraries view""" + """Testing uploading a directory of files to a root folder from the Data Libraries view""" # admin_user will not have the option sto upload a directory of files from the # Libraries view since a sub-directory named the same as their email is not contained # in the configured user_library_import_dir. However, since members of role_one have

1 0

[hg] galaxy 2561: Restoring history/grid.mako
by Greg Von Kuster 14 Aug '09

14 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/172548982c18 changeset: 2561:172548982c18 user: James Taylor <james(a)jamestaylor.org> date: Thu Aug 13 12:19:00 2009 -0400 description: Restoring history/grid.mako 1 file(s) affected in this change: templates/history/grid.mako diffs (200 lines): diff -r ff4b7ca79092 -r 172548982c18 templates/history/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/history/grid.mako Thu Aug 13 12:19:00 2009 -0400 @@ -0,0 +1,196 @@ +<%inherit file="/base.mako"/> +<%def name="title()">${grid.title}</%def> + +%if message: + <p> + <div class="${message_type}message transient-message">${message}</div> + <div style="clear: both"></div> + </p> +%endif + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + ## TODO: generalize and move into galaxy.base.js + $(document).ready(function() { + $(".grid").each( function() { + var grid = this; + var checkboxes = $(this).find("input.grid-row-select-checkbox"); + var update = $(this).find( "span.grid-selected-count" ); + $(checkboxes).each( function() { + $(this).change( function() { + var n = $(checkboxes).filter("[checked]").size(); + update.text( n ); + }); + }) + }); + }); + ## Can this be moved into base.mako? + %if refresh_frames: + %if 'masthead' in refresh_frames: + ## Refresh masthead == user changes (backward compatibility) + if ( parent.user_changed ) { + %if trans.user: + parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); + %else: + parent.user_changed( null, false ); + %endif + } + %endif + %if 'history' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + if ( parent.force_right_panel ) { + parent.force_right_panel( 'show' ); + } + } + %endif + %if 'tools' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_tools ) { + parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; + if ( parent.force_left_panel ) { + parent.force_left_panel( 'show' ); + } + } + %endif + %endif + </script> +</%def> + +<%def name="stylesheets()"> + <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> + <style> + ## Not generic to all grids -- move to base? + .count-box { + min-width: 1.1em; + padding: 5px; + border-width: 1px; + border-style: solid; + text-align: center; + display: inline-block; + } + </style> +</%def> + +%if grid.standard_filters: + <div class="grid-header"> + <h2>${grid.title}</h2> + <span class="title">Filter:</span> + %for i, filter in enumerate( grid.standard_filters ): + %if i > 0: + <span>|</span> + %endif + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + %endfor + </div> +%endif + +<form name="history_actions" action="${url()}" method="post" > + <table class="grid"> + <thead> + <tr> + <th></th> + %for column in grid.columns: + %if column.visible: + <% + href = "" + extra = "" + if column.sortable: + if sort_key == column.key: + if sort_order == "asc": + href = url( sort=( "-" + column.key ) ) + extra = "↓" + else: + href = url( sort=( column.key ) ) + extra = "↑" + else: + href = url( sort=column.key ) + %> + <th\ + %if column.ncells > 1: + colspan="${column.ncells}" + %endif + > + %if href: + <a href="${href}">${column.label}</a> + %else: + ${column.label} + %endif + <span>${extra}</span> + </th> + %endif + %endfor + <th></th> + </tr> + </thead> + <tbody> + %for i, item in enumerate( query ): + <tr \ + %if current_item == item: + class="current" \ + %endif + > + ## Item selection column + <td style="width: 1.5em;"> + <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> + </td> + ## Data columns + %for column in grid.columns: + %if column.visible: + <% + # Link + link = column.get_link( trans, grid, item ) + if link: + href = url( **link ) + else: + href = None + # Value (coerced to list so we can loop) + value = column.get_value( trans, grid, item ) + if column.ncells == 1: + value = [ value ] + %> + %for cellnum, v in enumerate( value ): + <% + # Attach popup menu? + if column.attach_popup and cellnum == 0: + extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">▼</a>' % i + else: + extra = "" + %> + %if href: + <td><a href="${href}">${v}</a> ${extra}</td> + %else: + <td >${v}${extra}</td> + %endif + </td> + %endfor + %endif + %endfor + ## Actions column + <td> + <div popupmenu="grid-${i}-popup"> + %for operation in grid.operations: + %if operation.allowed( item ): + <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> + %endif + %endfor + </div> + </td> + </tr> + %endfor + </tbody> + <tfoot> + <tr> + <td></td> + <td colspan="100"> + For <span class="grid-selected-count"></span> selected histories: + %for operation in grid.operations: + %if operation.allow_multiple: + <input type="submit" name="operation" value="${operation.label}" class="action-button"> + %endif + %endfor + </td> + </tr> + </tfoot> + </table> +</form>

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