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[hg] galaxy 2954: History ordering bug with SQLAlchemy 0.5 (deve...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/46791b5a653b changeset: 2954:46791b5a653b user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 17:16:40 2009 -0500 description: History ordering bug with SQLAlchemy 0.5 (developers - queries are no longer ordered by primary key by default, so order explicitly if it matters) and a <model_object>.c that slipped through. diffstat: lib/galaxy/jobs/__init__.py | 2 +- lib/galaxy/web/controllers/root.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diffs (25 lines): diff -r 14e178f656ba -r 46791b5a653b lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Nov 03 16:53:14 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Tue Nov 03 17:16:40 2009 -0500 @@ -174,7 +174,7 @@ if self.track_jobs_in_database: for j in self.sa_session.query( model.Job ) \ .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \ - .filter( model.Job.c.state == model.Job.states.NEW ): + .filter( model.Job.state == model.Job.states.NEW ): job = JobWrapper( j, self.app.toolbox.tools_by_id[ j.tool_id ], self ) new_jobs.append( job ) else: diff -r 14e178f656ba -r 46791b5a653b lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Nov 03 16:53:14 2009 -0500 +++ b/lib/galaxy/web/controllers/root.py Tue Nov 03 17:16:40 2009 -0500 @@ -72,7 +72,8 @@ .filter( model.HistoryDatasetAssociation.history == history ) \ .options( eagerload( "children" ) ) \ .join( "dataset" ).filter( model.Dataset.purged == False ) \ - .options( eagerload_all( "dataset.actions" ) ) + .options( eagerload_all( "dataset.actions" ) ) \ + .order_by( model.HistoryDatasetAssociation.hid ) if not show_deleted: query = query.filter( model.HistoryDatasetAssociation.deleted == False ) return trans.stream_template_mako( "root/history.mako",

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[hg] galaxy 2953: Added 'History' column to HDA grid.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/14e178f656ba changeset: 2953:14e178f656ba user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 16:53:14 2009 -0500 description: Added 'History' column to HDA grid. diffstat: lib/galaxy/web/controllers/dataset.py | 26 +++++++++++++++++++------- templates/dataset/grid.mako | 11 ++++++++--- templates/root/history_common.mako | 2 +- 3 files changed, 28 insertions(+), 11 deletions(-) diffs (116 lines): diff -r 6491acd0bef2 -r 14e178f656ba lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Nov 03 15:39:51 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Nov 03 16:53:14 2009 -0500 @@ -45,6 +45,11 @@ """ class HistoryDatasetAssociationListGrid( grids.Grid ): + # Custom columns for grid. + class HistoryColumn( grids.GridColumn ): + def get_value( self, trans, grid, hda): + return hda.history.name + class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, hda ): if hda.deleted: @@ -52,6 +57,7 @@ return "" def get_link( self, trans, grid, hda ): return None + class TagsColumn( grids.GridColumn ): def __init__(self, col_name, key, filterable): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) @@ -107,14 +113,16 @@ return accepted_filters # Grid definition - title = "Stored Datasets" + title = "Saved Datasets" model_class = model.HistoryDatasetAssociation template='/dataset/grid.mako' default_sort_key = "-create_time" columns = [ - grids.GridColumn( "Name", key="name", - # Link name to dataset's history. + grids.GridColumn( "Name", key="name", + # Link name to dataset's history. link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ) ), + HistoryColumn( "History", key="history", + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), TagsColumn( "Tags", key="tags", filterable=True ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), @@ -285,8 +293,9 @@ log.warn( "Invalid history_dataset_association id '%r' passed to list", hda_id ) if hdas: - - if operation == "switch": + if operation == "switch" or operation == "switch_history": + # Switch to a history that the HDA resides in. + # Convert hda to histories. histories = [] for hda in hdas: @@ -295,8 +304,11 @@ # Use history controller to switch the history. TODO: is this reasonable? status, message = trans.webapp.controllers['history']._list_switch( trans, histories ) - # Current history changed, refresh history frame - trans.template_context['refresh_frames'] = ['history'] + # Current history changed, refresh history frame; if switching to a dataset, set hda seek. + trans.template_context['refresh_frames'] = ['history'] + if operation == "switch": + hda_ids = [ trans.security.encode_id( hda.id ) for hda in hdas ] + trans.template_context[ 'seek_hda_ids' ] = hda_ids # Render the list view return self.stored_list_grid( trans, status=status, message=message, **kwargs ) diff -r 6491acd0bef2 -r 14e178f656ba templates/dataset/grid.mako --- a/templates/dataset/grid.mako Tue Nov 03 15:39:51 2009 -0500 +++ b/templates/dataset/grid.mako Tue Nov 03 16:53:14 2009 -0500 @@ -92,8 +92,6 @@ t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='HistoryDatasetAssociation' )}", autocomplete_options); - //t.addClass("tag-input"); - return t; }); ## Can this be moved into base.mako? @@ -110,7 +108,14 @@ %endif %if 'history' in refresh_frames: if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=str(ids) )}"; + ## If available, include HDA ids to seek to in history request. + <% + hda_id = None + if seek_hda_ids: + hda_id = str( seek_hda_ids[0] ) # Use only the first id. + print hda_id + %> + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=hda_id )}"; if ( parent.force_right_panel ) { parent.force_right_panel( 'show' ); } diff -r 6491acd0bef2 -r 14e178f656ba templates/root/history_common.mako --- a/templates/root/history_common.mako Tue Nov 03 15:39:51 2009 -0500 +++ b/templates/root/history_common.mako Tue Nov 03 16:53:14 2009 -0500 @@ -1,6 +1,7 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id <%def name="render_dataset( data, hid, show_deleted_on_refresh = False, user_owns_dataset = True )"> + <a name="${trans.security.encode_id( data.id )}"></a> <% if data.state in ['no state','',None]: data_state = "queued" @@ -21,7 +22,6 @@ %endif ## Header row for history items (name, state, action buttons) - <a name="${trans.security.encode_id(data.id)}"></a> <div style="overflow: hidden;" class="historyItemTitleBar"> <div class="historyItemButtons"> %if data_state == "upload":

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[hg] galaxy 2950: imported patch alchemy05_fixes_02
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d872c1e16afb changeset: 2950:d872c1e16afb user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 12:52:01 2009 -0500 description: imported patch alchemy05_fixes_02 diffstat: lib/galaxy/jobs/__init__.py | 6 +++--- lib/galaxy/model/mapping.py | 4 ++-- lib/galaxy/model/mapping_tests.py | 15 ++++++++------- lib/galaxy/model/migrate/versions/0025_user_info.py | 4 ++-- lib/galaxy/tools/actions/__init__.py | 7 ++++--- lib/galaxy/tools/actions/metadata.py | 5 +++-- lib/galaxy/tools/actions/upload_common.py | 4 +++- lib/galaxy/web/controllers/async.py | 6 +++--- lib/galaxy/web/controllers/dataset.py | 4 ++-- lib/galaxy/web/controllers/library.py | 6 +++--- lib/galaxy/web/controllers/library_admin.py | 12 ++++++++---- lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/root.py | 10 +++++----- lib/galaxy/web/controllers/tool_runner.py | 2 -- lib/galaxy/web/framework/__init__.py | 23 ++++++++++++++--------- test/functional/test_forms_and_requests.py | 1 + test/functional/test_security_and_libraries.py | 2 +- test/functional/test_user_info.py | 3 ++- tools/data_source/microbial_import_code.py | 6 +++--- tools/filters/lav_to_bed_code.py | 1 - tools/maf/maf_to_bed_code.py | 4 +--- 21 files changed, 69 insertions(+), 58 deletions(-) diffs (567 lines): diff -r 133252175425 -r d872c1e16afb lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -199,7 +199,7 @@ try: # Clear the session for each job so we get fresh states for # job and all datasets - self.sa_session.clear() + self.sa_session.expunge_all() # Get the real job entity corresponding to the wrapper (if we # are tracking in the database this is probably cached in # the session from the origianl query above) @@ -346,7 +346,7 @@ Prepare the job to run by creating the working directory and the config files. """ - self.sa_session.clear() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner + self.sa_session.expunge_all() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner if not os.path.exists( self.working_directory ): os.mkdir( self.working_directory ) # Restore parameters from the database @@ -477,7 +477,7 @@ the contents of the output files. """ # default post job setup - self.sa_session.clear() + self.sa_session.expunge_all() job = self.sa_session.query( model.Job ).get( self.job_id ) # if the job was deleted, don't finish it if job.state == job.states.DELETED: diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/mapping.py Tue Nov 03 12:52:01 2009 -0500 @@ -817,7 +817,7 @@ user=relation( User, backref="roles" ), non_private_roles=relation( User, backref="non_private_roles", - primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email & Role.table.c.type == 'private' ) ) ), + primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email ) ) ), role=relation( Role ) ) ) @@ -1134,7 +1134,7 @@ # Pack everything into a bunch result = Bunch( **globals() ) result.engine = engine - result.flush = lambda *args, **kwargs: Session.flush( *args, **kwargs ) + # model.flush() has been removed. result.session = Session # For backward compatibility with "model.context.current" result.context = Session diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/mapping_tests.py --- a/lib/galaxy/model/mapping_tests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/mapping_tests.py Tue Nov 03 12:52:01 2009 -0500 @@ -19,16 +19,17 @@ d1 = model.HistoryDatasetAssociation( extension="interval", metadata=dict(chromCol=1,startCol=2,endCol=3 ), history=h2, create_dataset=True ) #h2.queries.append( q1 ) #h2.queries.append( model.Query( "h2->q2" ) ) - model.context.current.flush() - model.context.current.clear() + model.session.add_all( ( u, h1, h2, d1 ) ) + model.session.flush() + model.session.expunge_all() # Check - users = model.context.current.query( model.User ).all() + users = model.session.query( model.User ).all() assert len( users ) == 1 assert users[0].email == "james(a)foo.bar.baz" assert users[0].password == "password" assert len( users[0].histories ) == 1 assert users[0].histories[0].name == "History 1" - hists = model.context.current.query( model.History ).all() + hists = model.session.query( model.History ).all() assert hists[0].name == "History 1" assert hists[1].name == ( "H" * 255 ) assert hists[0].user == users[0] @@ -38,9 +39,9 @@ assert hists[1].datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id ) # Do an update and check hists[1].name = "History 2b" - model.context.current.flush() - model.context.current.clear() - hists = model.context.current.query( model.History ).all() + model.session.flush() + model.session.expunge_all() + hists = model.session.query( model.History ).all() assert hists[0].name == "History 1" assert hists[1].name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/migrate/versions/0025_user_info.py --- a/lib/galaxy/model/migrate/versions/0025_user_info.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0025_user_info.py Tue Nov 03 12:52:01 2009 -0500 @@ -21,7 +21,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" @@ -59,4 +59,4 @@ except Exception, e: log.debug( "Adding foreign key constraint 'user_form_values_id_fk' to table 'galaxy_user' failed: %s" % ( str( e ) ) ) def downgrade(): - pass \ No newline at end of file + pass diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -235,7 +235,7 @@ # Store output out_data[ name ] = data # Store all changes to database - trans.app.model.flush() + trans.sa_session.flush() # Add all the top-level (non-child) datasets to the history for name in out_data.keys(): if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created @@ -248,7 +248,7 @@ child_dataset = out_data[ child_name ] parent_dataset.children.append( child_dataset ) # Store data after custom code runs - trans.app.model.flush() + trans.sa_session.flush() # Create the job object job = trans.app.model.Job() job.session_id = trans.get_galaxy_session().id @@ -274,7 +274,8 @@ job.add_input_dataset( name, None ) for name, dataset in out_data.iteritems(): job.add_output_dataset( name, dataset ) - trans.app.model.flush() + trans.sa_session.add( job ) + trans.sa_session.flush() # Some tools are not really executable, but jobs are still created for them ( for record keeping ). # Examples include tools that redirect to other applications ( epigraph ). These special tools must # include something that can be retrieved from the params ( e.g., REDIRECT_URL ) to keep the job diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/metadata.py Tue Nov 03 12:52:01 2009 -0500 @@ -26,7 +26,8 @@ job.tool_version = tool.version except: job.tool_version = "1.0.0" - job.flush() #ensure job.id is available + trans.sa_session.add( job ) + trans.sa_session.flush() #ensure job.id is available #add parameters to job_parameter table # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)? @@ -49,7 +50,7 @@ #Need a special state here to show that metadata is being set and also allow the job to run # i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state dataset.state = dataset.states.SETTING_METADATA - trans.app.model.flush() + trans.sa_session.flush() # Queue the job for execution trans.app.job_queue.put( job.id, tool ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Tue Nov 03 12:52:01 2009 -0500 @@ -121,6 +121,7 @@ trans.history.add_dataset( hda, genome_build = uploaded_dataset.dbkey ) permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) + trans.sa_session.flush() return hda def new_library_upload( trans, uploaded_dataset, library_bunch, state=None ): @@ -291,7 +292,8 @@ for i, dataset in enumerate( data_list ): job.add_output_dataset( 'output%i' % i, dataset ) job.state = job.states.NEW - trans.app.model.flush() + trans.sa_session.add( job ) + trans.sa_session.flush() # Queue the job for execution trans.app.job_queue.put( job.id, tool ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/async.py Tue Nov 03 12:52:01 2009 -0500 @@ -77,7 +77,7 @@ data.state = data.blurb = jobs.JOB_ERROR data.info = "Error -> %s" % STATUS - trans.model.flush() + trans.sa_session.flush() return "Data %s with status %s received. OK" % (data_id, STATUS) @@ -112,7 +112,7 @@ data.flush() open( data.file_name, 'wb' ).close() #create the file trans.history.add_dataset( data, genome_build=GALAXY_BUILD ) - trans.model.flush() + trans.sa_session.flush() trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id ) try: @@ -132,6 +132,6 @@ data.info = str(e) data.state = data.blurb = data.states.ERROR - trans.model.flush() + trans.sa_session.flush() return trans.fill_template('tool_executed.tmpl', out_data={}, tool=tool, config=self.app.config ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Nov 03 12:52:01 2009 -0500 @@ -335,7 +335,7 @@ assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark undeleted data.mark_undeleted() - self.app.model.flush() + trans.sa_session.flush() trans.log_event( "Dataset id %s has been undeleted" % str(id) ) return True return False @@ -407,7 +407,7 @@ hist.add_dataset( data.copy( copy_children = True ) ) if history in target_histories: refresh_frames = ['history'] - trans.app.model.flush() + trans.sa_session.flush() done_msg = "%i datasets copied to %i histories." % ( len( source_dataset_ids ) - invalid_datasets, len( target_histories ) ) trans.sa_session.refresh( history ) elif create_new_history: diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/library.py Tue Nov 03 12:52:01 2009 -0500 @@ -421,7 +421,7 @@ if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() msg = "Data type changed for library dataset '%s'" % ldda.name messagetype = 'done' else: @@ -463,7 +463,7 @@ setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) ldda.metadata.dbkey = dbkey ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' else: @@ -486,7 +486,7 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) ldda.datatype.set_meta( ldda ) ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' else: diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Tue Nov 03 12:52:01 2009 -0500 @@ -432,7 +432,7 @@ # The user clicked the Save button on the 'Change data type' form if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() msg = "Data type changed for library dataset '%s'" % ldda.name return trans.fill_template( "/admin/library/ldda_edit_info.mako", ldda=ldda, @@ -469,7 +469,7 @@ setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) ldda.metadata.dbkey = dbkey ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' return trans.fill_template( "/admin/library/ldda_edit_info.mako", @@ -488,7 +488,7 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) ldda.datatype.set_meta( ldda ) ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name return trans.fill_template( "/admin/library/ldda_edit_info.mako", ldda=ldda, @@ -674,6 +674,10 @@ replace_id = params.get( 'replace_id', None ) if replace_id not in [ None, 'None' ]: replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( int( replace_id ) ) + # The name is separately - by the time the new ldda is created, + # replace_dataset.name will point to the new ldda, not the one it's + # replacing. + replace_dataset_name = replace_dataset.name if not last_used_build: last_used_build = replace_dataset.library_dataset_dataset_association.dbkey # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version @@ -701,7 +705,7 @@ if created_outputs: total_added = len( created_outputs.values() ) if replace_dataset: - msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name ) + msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) else: if not folder.parent: # Libraries have the same name as their root_folder diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Tue Nov 03 12:52:01 2009 -0500 @@ -294,7 +294,7 @@ # save all the new/unsaved samples entered by the user if edit_mode == 'False': for index in range(len(current_samples)-len(request.samples)): - sample_index = index + len(request.samples) + sample_index = len(request.samples) sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] for field_index in range(len(request.type.sample_form.fields)): diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/root.py Tue Nov 03 12:52:01 2009 -0500 @@ -277,7 +277,7 @@ if not __ok_to_edit_metadata( data.id ): return trans.show_error_message( "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." ) trans.app.datatypes_registry.change_datatype( data, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() else: return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype ) ) elif params.save: @@ -303,7 +303,7 @@ data.datatype.after_edit( data ) else: msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)' - trans.app.model.flush() + trans.sa_session.flush() return trans.show_ok_message( "Attributes updated%s" % msg, refresh_frames=['history'] ) elif params.detect: # The user clicked the Auto-detect button on the 'Edit Attributes' form @@ -322,7 +322,7 @@ msg = 'Attributes updated' data.set_meta() data.datatype.after_edit( data ) - trans.app.model.flush() + trans.sa_session.flush() return trans.show_ok_message( msg, refresh_frames=['history'] ) elif params.convert_data: target_type = kwd.get("target_type", None) @@ -383,7 +383,7 @@ if job.check_if_output_datasets_deleted(): job.mark_deleted() self.app.job_manager.job_stop_queue.put( job.id ) - self.app.model.flush() + trans.sa_session.flush() @web.expose def delete( self, trans, id = None, show_deleted_on_refresh = False, **kwd): @@ -432,7 +432,7 @@ for dataset in history.datasets: dataset.deleted = True dataset.clear_associated_files() - self.app.model.flush() + trans.sa_session.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) @web.expose diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/tool_runner.py Tue Nov 03 12:52:01 2009 -0500 @@ -198,8 +198,6 @@ # pasted data datasets.append( create_dataset( 'Pasted Entry' ) ) break - if datasets: - trans.model.flush() return [ d.id for d in datasets ] @web.expose diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -139,7 +139,7 @@ self.__galaxy_session = NOT_SET base.DefaultWebTransaction.__init__( self, environ ) self.setup_i18n() - self.sa_session.clear() + self.sa_session.expunge_all() self.debug = asbool( self.app.config.get( 'debug', False ) ) # Flag indicating whether we are in workflow building mode (means # that the current history should not be used for parameter values @@ -302,12 +302,12 @@ self.galaxy_session = galaxy_session # Do we need to flush the session? if galaxy_session_requires_flush: - objects_to_flush = [ galaxy_session ] + sa_session.add( galaxy_session ) # FIXME: If prev_session is a proper relation this would not # be needed. if prev_galaxy_session: - objects_to_flush.append( prev_galaxy_session ) - sa_session.flush( objects_to_flush ) + sa_session.add( prev_galaxy_session ) + sa_session.flush() # If the old session was invalid, get a new history with our new session if invalidate_existing_session: self.new_history() @@ -427,7 +427,8 @@ if not last_accessed: # Only set default history permissions if current history is not from a previous session self.app.security_agent.history_set_default_permissions( history, dataset=True, bypass_manage_permission=True ) - self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session, history ] ) + self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session, history ) ) + self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name='galaxysession' ) def handle_user_logout( self ): @@ -439,7 +440,8 @@ prev_galaxy_session = self.galaxy_session prev_galaxy_session.is_valid = False self.galaxy_session = self.__create_new_session( prev_galaxy_session ) - self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session ] ) + self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session ) ) + self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name='galaxysession' ) @@ -466,7 +468,8 @@ def set_history( self, history ): if history and not history.deleted: self.galaxy_session.current_history = history - self.sa_session.flush( [ self.galaxy_session ] ) + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() history = property( get_history, set_history ) def new_history( self, name=None ): """ @@ -489,7 +492,8 @@ # Set the user's default history permissions self.app.security_agent.history_set_default_permissions( history ) # Save - self.sa_session.flush( [ self.galaxy_session, history ] ) + self.sa_session.add_all( ( self.galaxy_session, history ) ) + self.sa_session.flush() return history def get_user( self ): @@ -498,7 +502,8 @@ def set_user( self, user ): """Set the current user.""" self.galaxy_session.user = user - self.sa_session.flush( [ self.galaxy_session ] ) + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() user = property( get_user, set_user ) def get_user_and_roles( self ): diff -r 133252175425 -r d872c1e16afb test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_forms_and_requests.py Tue Nov 03 12:52:01 2009 -0500 @@ -29,6 +29,7 @@ .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) for fdc in fdc_list: + sa_session.refresh( fdc.latest_form ) if form_name == fdc.latest_form.name: return fdc.latest_form return None diff -r 133252175425 -r d872c1e16afb test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_security_and_libraries.py Tue Nov 03 12:52:01 2009 -0500 @@ -156,7 +156,7 @@ raise AssertionError( '%s not in history id %d default_permissions after they were changed' % ( value.action, latest_history.id ) ) # Add a dataset to the history self.upload_file( '1.bed' ) - latest_dataset = galaxy.model.Dataset.query().order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() + latest_dataset = sa_session.query( galaxy.model.Dataset ).order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() # Make sure DatasetPermissionss are correct if len( latest_dataset.actions ) != len( latest_history.default_permissions ): raise AssertionError( '%d DatasetPermissionss were created for dataset id %d when it was created ( should have been %d )' % \ diff -r 133252175425 -r d872c1e16afb test/functional/test_user_info.py --- a/test/functional/test_user_info.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_user_info.py Tue Nov 03 12:52:01 2009 -0500 @@ -14,6 +14,7 @@ .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) for fdc in fdc_list: + sa_session.refresh( fdc.latest_form ) if form_name == fdc.latest_form.name: return fdc.latest_form return None @@ -146,4 +147,4 @@ self.visit_page('forms/manage?show_filter=Deleted') self.check_page_for_string(form_one_latest.name) self.logout() - \ No newline at end of file + diff -r 133252175425 -r d872c1e16afb tools/data_source/microbial_import_code.py --- a/tools/data_source/microbial_import_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/data_source/microbial_import_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -123,7 +123,7 @@ data = app.datatypes_registry.change_datatype( data, file_type ) data.init_meta() data.set_peek() - app.model.flush() + data.flush() elif fields[0] == "#NewFile": description = fields[1] chr = fields[2] @@ -137,7 +137,7 @@ newdata.flush() app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) history.add_dataset( newdata ) - app.model.flush() + history.flush() try: copyfile(filepath,newdata.file_name) newdata.info = newdata.name @@ -148,4 +148,4 @@ newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() - app.model.flush() + newdata.flush() diff -r 133252175425 -r d872c1e16afb tools/filters/lav_to_bed_code.py --- a/tools/filters/lav_to_bed_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/filters/lav_to_bed_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -16,4 +16,3 @@ data.flush() except: continue - app.model.flush() \ No newline at end of file diff -r 133252175425 -r d872c1e16afb tools/maf/maf_to_bed_code.py --- a/tools/maf/maf_to_bed_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/maf/maf_to_bed_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -21,7 +21,6 @@ output_data.dbkey = dbkey output_data.name = basic_name + " (" + dbkey + ")" output_data.flush() - app.model.flush() output_data_list.append(output_data) elif line.startswith("#FILE"): fields = line.split("\t") @@ -36,7 +35,6 @@ app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset ) newdata.flush() history.flush() - app.model.flush() try: move(filepath,newdata.file_name) newdata.info = newdata.name @@ -47,7 +45,7 @@ newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() - app.model.flush() + newdata.flush() output_data_list.append(newdata) else: new_stdout = new_stdout + line

1 0

[hg] galaxy 2951: merge heads
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2300a80d80e5 changeset: 2951:2300a80d80e5 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 13:04:35 2009 -0500 description: merge heads diffstat: lib/galaxy/tags/tag_handler.py | 8 +- lib/galaxy/web/controllers/history.py | 145 +++++++++++++++--- lib/galaxy/web/framework/helpers/grids.py | 1 + static/scripts/autocomplete_tagging.js | 2 +- static/scripts/packed/autocomplete_tagging.js | 2 +- static/scripts/packed/trackster.js | 2 +- templates/history/grid.mako | 250 +++++++++++++++++------------- test/base/twilltestcase.py | 18 +- test/functional/test_history_functions.py | 2 +- 9 files changed, 280 insertions(+), 150 deletions(-) diffs (665 lines): diff -r d872c1e16afb -r 2300a80d80e5 lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Tue Nov 03 12:52:01 2009 -0500 +++ b/lib/galaxy/tags/tag_handler.py Tue Nov 03 13:04:35 2009 -0500 @@ -3,6 +3,12 @@ class TagHandler( object ): + # Minimum tag length. + min_tag_len = 2 + + # Maximum tag length. + max_tag_len = 255 + # Tag separator. tag_separators = ',;' @@ -215,7 +221,7 @@ scrubbed_name = scrubbed_name[1:] # If name is too short or too long, return None. - if len(scrubbed_name) < 3 or len(scrubbed_name) > 255: + if len(scrubbed_name) < self.min_tag_len or len(scrubbed_name) > self.max_tag_len: return None return scrubbed_name diff -r d872c1e16afb -r 2300a80d80e5 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Nov 03 12:52:01 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Nov 03 13:04:35 2009 -0500 @@ -5,6 +5,7 @@ from galaxy.model import History from galaxy.model.orm import * from galaxy.util.json import * +from galaxy.util.odict import odict from galaxy.tags.tag_handler import TagHandler from sqlalchemy.sql.expression import ClauseElement import webhelpers, logging, operator @@ -19,12 +20,29 @@ class HistoryListGrid( grids.Grid ): # Custom column types class NameColumn( grids.GridColumn ): - def __init( self, key, link, attach_popup ): + def __init( self, key, link, attach_popup, filterable ): grids.GridColumn.__init__(self, key, link, attach_popup) def get_value( self, trans, grid, history ): return history.get_display_name() + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by name. """ + if column_filter == "All": + pass + elif column_filter: + query = query.filter( func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): rval = [] @@ -48,6 +66,7 @@ if item.users_shared_with or item.importable: return dict( operation="sharing" ) return None + class TagsColumn( grids.GridColumn ): def __init__( self, col_name, key, filterable ): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) @@ -61,7 +80,7 @@ return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=history, elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) def filter( self, db_session, query, column_filter ): - """ Modify query to include only histories with tags in column_filter. """ + """ Modify query to filter histories by tag. """ if column_filter == "All": pass elif column_filter: @@ -69,52 +88,115 @@ tag_handler = TagHandler() raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) for name, value in raw_tags.items(): - tag = tag_handler.get_tag_by_name( db_session, name ) - if tag: - query = query.filter( History.tags.any( tag_id=tag.id ) ) + if name: + # Search for tag names. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) ) if value: - query = query.filter( History.tags.any( value=value.lower() ) ) - else: - # Tag doesn't exist; unclear what to do here, but the literal thing to do is add the criterion, which - # will then yield a query that returns no results. - query = query.filter( History.tags.any( user_tname=name ) ) + # Search for tag values. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) return query def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "All": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters - - + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DeletedColumn( grids.GridColumn ): def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "Active" : "False", "Deleted" : "True", "All": "All" } + accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } accepted_filters = [] for label, val in accepted_filter_labels_and_vals.items(): args = { self.key: val } accepted_filters.append( grids.GridColumnFilter( label, args) ) return accepted_filters + + class SharingColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by sharing status. """ + if column_filter == "All": + pass + elif column_filter: + if column_filter == "private": + query = query.filter( History.users_shared_with == None ) + query = query.filter( History.importable == False ) + elif column_filter == "shared": + query = query.filter( History.users_shared_with != None ) + elif column_filter == "importable": + query = query.filter( History.importable == True ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["private"] = "private" + accepted_filter_labels_and_vals["shared"] = "shared" + accepted_filter_labels_and_vals["importable"] = "importable" + accepted_filter_labels_and_vals["all"] = "All" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + + class FreeTextSearchColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to search tags and history names. """ + if column_filter == "All": + pass + elif column_filter: + # Build tags filter. + tag_handler = TagHandler() + raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + tags_filter = None + for name, value in raw_tags.items(): + if name: + # Search for tag names. + tags_filter = History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) + if value: + # Search for tag values. + tags_filter = and_( tags_filter, func.lower( History.tags.any( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) + + # Build history name filter. + history_name_filter = func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) + + # Apply filters to query. + if tags_filter: + query = query.filter( or_( tags_filter, history_name_filter ) ) + else: + query = query.filter( history_name_filter ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters # Grid definition - title = "Stored histories" + title = "Saved Histories" model_class = model.History template='/history/grid.mako' default_sort_key = "-create_time" columns = [ NameColumn( "Name", key="name", link=( lambda history: iff( history.deleted, None, dict( operation="switch", id=history.id ) ) ), - attach_popup=True ), + attach_popup=True, filterable=True ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), TagsColumn( "Tags", key="tags", filterable=True), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - # Valid for filtering but invisible - DeletedColumn( "Status", key="deleted", visible=False, filterable=True ) + # Columns that are valid for filtering but are not visible. + DeletedColumn( "Deleted", key="deleted", visible=False, filterable=True ), + SharingColumn( "Shared", key="shared", visible=False, filterable=True ), + FreeTextSearchColumn( "Search", key="free-text-search", visible=False ) # Not filterable because it's the default search. ] operations = [ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), @@ -131,7 +213,7 @@ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ), ] - default_filter = dict( deleted="False", tags="All" ) + default_filter = dict( name="All", deleted="False", tags="All", shared="All" ) num_rows_per_page = 50 preserve_state = False use_paging = True @@ -160,6 +242,7 @@ template='/history/grid.mako' model_class = model.History default_sort_key = "-update_time" + default_filter = {} columns = [ grids.GridColumn( "Name", key="name" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), @@ -374,6 +457,18 @@ trans.sa_session.flush() @web.expose + def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): + """Return autocomplete data for history names""" + user = trans.get_user() + if not user: + return + + ac_data = "" + for history in trans.sa_session.query( History ).filter_by( user=user ).filter( func.lower( History.name ) .like(q.lower() + "%") ): + ac_data = ac_data + history.name + "\n" + return ac_data + + @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): """Import another user's history via a shared URL""" msg = "" diff -r d872c1e16afb -r 2300a80d80e5 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 12:52:01 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 13:04:35 2009 -0500 @@ -183,6 +183,7 @@ query=query, cur_page_num = page_num, num_pages = num_pages, + default_filter_dict=self.default_filter, cur_filter_dict=cur_filter_dict, sort_key=sort_key, encoded_sort_key=encoded_sort_key, diff -r d872c1e16afb -r 2300a80d80e5 static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Tue Nov 03 12:52:01 2009 -0500 +++ b/static/scripts/autocomplete_tagging.js Tue Nov 03 13:04:35 2009 -0500 @@ -309,7 +309,7 @@ new_value = new_value.replace(/^\s+|\s+$/g,""); // Too short? - if (new_value.length < 3) + if (new_value.length < 2) return false; // diff -r d872c1e16afb -r 2300a80d80e5 static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 12:52:01 2009 -0500 +++ b/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 13:04:35 2009 -0500 @@ -1,1 +1,1 @@ -var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u,v){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>").text(u).addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};v ar s=b();if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var a=function(v,u){return v+((u!=""&&u)?":"+u:"")};var h=function(u){return u.split(":")};var i=function(u){var v=$("<img src='"+p.add_tag_img+"' rollover='"+p.add_tag_img_rollover+"'/>").addClass("add-tag-button");v.click(function(){$(this).hide();m.click();return false});return v};var j=function(u){var v=$("<img src='"+p.delete_tag_img+"'/>").addClass("delete-tag-img");v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)});v.click(function(){var D=$(this).parent();var C=D.find(".tag-name").eq(0);var B=C.text();var z=h(B);var F=z[0];var y=z[1];var E=D.prev();D.remove();delete p.tags[F];var A=p.get_toggle_link_text_fn(p.tags);s.text(A);$.ajax({url:p.ajax_delete_tag_url,data:{tag_name:F},error:function(){p.tags[F]=y;if(E.hasClass("tag-button")){E .after(D)}else{m.prepend(D)}var G=p.get_toggle_link_text_fn(p.tags);alert("Remove tag failed");s.text(G);v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)})},success:function(){}});return true});var w=$("<span>").text(u).addClass("tag-name");w.click(function(){tag_name_and_value=u.split(":");p.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);if(p.editable){x.append(v)}return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+escape(v)+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+escape(v)+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true) {return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<3){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,fo rmatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});if(p.editable){m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false})}if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file +var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u,v){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>").text(u).addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};v ar s=b();if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var 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failed");s.text(G);v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)})},success:function(){}});return true});var w=$("<span>").text(u).addClass("tag-name");w.click(function(){tag_name_and_value=u.split(":");p.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);if(p.editable){x.append(v)}return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+escape(v)+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+escape(v)+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true) {return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<2){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,fo rmatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});if(p.editable){m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false})}if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file diff -r d872c1e16afb -r 2300a80d80e5 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Tue Nov 03 12:52:01 2009 -0500 +++ b/static/scripts/packed/trackster.js Tue Nov 03 13:04:35 2009 -0500 @@ -1,1 +1,1 @@ -var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=5,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(l eft_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var 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200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){thi s.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k)}if(g){this.tile_cache.set(i,g)}a+=1}}});var LabelTrack=function(a){Track.ca ll(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dat aset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[e]=g;$(document).trigger("redra w")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(FeatureTrack.prototype,TiledTrack.pro totype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.container_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k=Math.floor(Math.max(e,(n.star t-e)*g));k-=m.measureText(n.name).width;l=Math.ceil(Math.min(a,(n.end-e)*g))}else{k=Math.floor(Math.max(e,(n.start-e)*b));l=Math.ceil(Math.min(a,(n.end-e)*b))}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospac e";v.textAlign="right";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}els e{if(f.strand=="-"){v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file +var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=10,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern( left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){ e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){th is.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k);if(g){this.tile_cache.set(i,g)}}a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low: null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[ e]=g;$(document).trigger("redraw")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(Featur eTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k= Math.floor((n.start-e)*g);k-=m.measureText(n.name).width;l=Math.ceil((n.end-e)*g)}else{k=Math.floor((n.start-e)*b);l=Math.ceil((n.end-e)*b)}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospace";v.textAlign="rig ht";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}else{if(f.strand=="-") {v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file diff -r d872c1e16afb -r 2300a80d80e5 templates/history/grid.mako --- a/templates/history/grid.mako Tue Nov 03 12:52:01 2009 -0500 +++ b/templates/history/grid.mako Tue Nov 03 13:04:35 2009 -0500 @@ -29,71 +29,20 @@ }); // Set up autocomplete for tag filter input. - var t = $("#input-tag-filter"); - t.keyup( function( e ) - { - if ( e.keyCode == 27 ) - { - // Escape key - $(this).trigger( "blur" ); - } else if ( - ( e.keyCode == 13 ) || // Return Key - ( e.keyCode == 188 ) || // Comma - ( e.keyCode == 32 ) // Space - ) - { - // - // Check input. - // - - new_value = this.value; - - // Do nothing if return key was used to autocomplete. - if (return_key_pressed_for_autocomplete == true) - { - return_key_pressed_for_autocomplete = false; - return false; - } - - // Suppress space after a ":" - if ( new_value.indexOf(": ", new_value.length - 2) != -1) - { - this.value = new_value.substring(0, new_value.length-1); - return false; - } - - // Remove trigger keys from input. - if ( (e.keyCode == 188) || (e.keyCode == 32) ) - new_value = new_value.substring( 0 , new_value.length - 1 ); - - // Trim whitespace. - new_value = new_value.replace(/^\s+|\s+$/g,""); - - // Too short? - if (new_value.length < 3) - return false; - - // - // New tag OK. - // - } - }); + var t = $("#input-tags-filter"); - // Add autocomplete to input. - var format_item_func = function(key, row_position, num_rows, value, search_term) - { - tag_name_and_value = value.split(":"); - return (tag_name_and_value.length == 1 ? tag_name_and_value[0] :tag_name_and_value[1]); - //var array = new Array(key, value, row_position, num_rows, - //search_term ); return "\"" + array.join("*") + "\""; - } var autocomplete_options = - { selectFirst: false, formatItem : format_item_func, autoFill: false, highlight: false, mustMatch: true }; + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", autocomplete_options); - - $("#page-select").change(navigate_to_page); + // Set up autocomplete for name filter input. + var t2 = $("#input-name-filter"); + + var autocomplete_options = + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; + + t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); }); ## Can this be moved into base.mako? %if refresh_frames: @@ -125,21 +74,52 @@ %endif %endif + // Filter and sort args for grid. + var filter_args = ${h.to_json_string(cur_filter_dict)}; + var sort_key = "${sort_key}"; + // - // Add a tag to the current grid filter; this adds the tag to the filter and then issues a request to refresh the grid. + // Add tag to grid filter. // function add_tag_to_grid_filter(tag_name, tag_value) { - // Use tag as a filter: replace TAGNAME with tag_name and issue query. - <% - url_args = {} - if "tags" in cur_filter_dict and cur_filter_dict["tags"] != "All": - url_args["f-tags"] = cur_filter_dict["tags"].encode("utf-8") + ", TAGNAME" - else: - url_args["f-tags"] = "TAGNAME" - %> - var url_base = "${url( url_args )}"; - var url = url_base.replace("TAGNAME", tag_name); + // Put tag name and value together. + var tag = tag_name + (tag_value != null && tag_value != "" ? ":" + tag_value : ""); + add_condition_to_grid_filter("tags", tag, true); + } + + // + // Add a filter to the current grid filter; this adds the filter and then issues a request to refresh the grid. + // + function add_condition_to_grid_filter(name, value, append) + { + // Update filter arg with new condition. + if (append) + { + // Append value. + var cur_val = filter_args[name]; + if (cur_val != "All") + cur_val = cur_val + ", " + value; + else + cur_val = value; + filter_args[name] = cur_val; + } + else + { + // Replace value. + filter_args[name] = value; + } + + // Build URL with filter args, sort key. + var filter_arg_value_strs = new Array(); + var i = 0; + for (arg in filter_args) + { + filter_arg_value_strs[i++] = "f-" + arg + "=" + filter_args[arg]; + } + var filter_str = filter_arg_value_strs.join("&"); + var url_base = "${h.url_for( controller='history', action='list')}"; + var url = url_base + "?" + filter_str + "&sort=" + sort_key; self.location = url; } @@ -154,7 +134,7 @@ var url = url_base.replace("PAGE", page_num); self.location = url; } - + </script> </%def> @@ -175,47 +155,95 @@ <div class="grid-header"> <h2>${grid.title}</h2> - - ## Print grid filter. - <form name="history_actions" action="javascript:add_tag_to_grid_filter($('#input-tag-filter').attr('value'))" method="get" > - <strong>Filter:   </strong> - %for column in grid.columns: - %if column.filterable: - <span> by ${column.label.lower()}:</span> - ## For now, include special case to handle tags. - %if column.key == "tags": - %if cur_filter_dict[column.key] != "All": - <span class="filter" "style='font-style: italic'"> - ${cur_filter_dict[column.key]} - </span> - <span>|</span> + + ## Search box and more options filter at top of grid. + <div> + ## Grid search. TODO: use more elegant way to get free text search column. + <% column = grid.columns[-1] %> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if column.key in cur_filter_dict and cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" "style='font-style: italic'">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" + action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),false)" + method="get" > + ${column.label}: + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | %endif - <input id="input-tag-filter" name="f-tags" type="text" value="" size="15"/> - <span>|</span> - %endif - - ## Handle other columns. - %for i, filter in enumerate( column.get_accepted_filters() ): - %if i > 0: - <span>|</span> - %endif - %if cur_filter_dict[column.key] == filter.args[column.key]: - <span class="filter" "style='font-style: italic'">${filter.label}</span> - %else: - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endif - %endfor - <span>     </span> + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> %endif %endfor - - ## Link to clear all filters. TODO: this should be the default filter or an empty filter. - <% - args = { "deleted" : "False", "tags" : "All" } - no_filter = GridColumnFilter("Clear Filter", args) - %> - <span><a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a></span> - </form> + | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> + %if use_form: + </form> + %endif + </div> + + ## Advanced Search + <div id="more-search-options" style="display: none; padding-top: 5px"> + <table style="border: 1px solid gray;"> + <tr><td style="text-align: left" colspan="100"> + Advanced Search | + <a href=""# onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Close</a> | + ## Link to clear all filters. + <% + no_filter = GridColumnFilter("Clear All", default_filter_dict) + %> + <a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> + </td></tr> + %for column in grid.columns: + %if column.filterable: + <tr> + ## Show div if current filter has value that is different from the default filter. + %if cur_filter_dict[column.key] != default_filter_dict[column.key]: + <script type="text/javascript"> + $('#more-search-options').css("display", "block"); + </script> + %endif + <td style="padding-left: 10px">${column.label.lower()}:</td> + <td> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" style="font-style: italic">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),true)" + method="get" > + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | + %endif + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + %endif + %endfor + %if use_form: + </form> + %endif + </td> + </tr> + %endif + %endfor + </table> + </div> </div> <form name="history_actions" action="${url()}" method="post" > <input type="hidden" name="page" value="${cur_page_num}"> @@ -291,7 +319,7 @@ extra = "" %> %if href: - <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}${extra}</a> </td> + <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}</a>${extra}</td> %else: <td >${v}${extra}</td> %endif diff -r d872c1e16afb -r 2300a80d80e5 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Nov 03 12:52:01 2009 -0500 +++ b/test/base/twilltestcase.py Tue Nov 03 13:04:35 2009 -0500 @@ -1,7 +1,7 @@ import pkg_resources pkg_resources.require( "twill==0.9" ) -import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile, re from itertools import * import twill @@ -311,20 +311,20 @@ def view_stored_active_histories( self, check_str='' ): self.home() self.visit_page( "history/list" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Rename&id' ) - self.check_page_for_string( 'operation=Switch&id' ) - self.check_page_for_string( 'operation=Delete&id' ) + self.check_page_for_string( 'operation=Rename' ) + self.check_page_for_string( 'operation=Switch' ) + self.check_page_for_string( 'operation=Delete' ) if check_str: self.check_page_for_string( check_str ) self.home() def view_stored_deleted_histories( self, check_str='' ): self.home() self.visit_page( "history/list?f-deleted=True" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Undelete&id' ) + self.check_page_for_string( 'operation=Undelete' ) if check_str: self.check_page_for_string( check_str ) self.home() @@ -723,14 +723,14 @@ # Functions associated with browsers, cookies, HTML forms and page visits def check_page_for_string( self, patt ): - """Looks for 'patt' in the current browser page""" + """Looks for 'patt' in the current browser page""" page = self.last_page() for subpatt in patt.split(): if page.find( patt ) == -1: fname = self.write_temp_file( page ) errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) raise AssertionError( errmsg ) - + def write_temp_file( self, content ): fd, fname = tempfile.mkstemp( suffix='.html', prefix='twilltestcase-' ) f = os.fdopen( fd, "w" ) diff -r d872c1e16afb -r 2300a80d80e5 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Tue Nov 03 12:52:01 2009 -0500 +++ b/test/functional/test_history_functions.py Tue Nov 03 13:04:35 2009 -0500 @@ -179,7 +179,7 @@ self.share_current_history( regular_user1.email, check_str=history3.name ) # Check out list of histories to make sure history3 was shared - self.view_stored_active_histories( check_str='operation=sharing">shared' ) + self.view_stored_active_histories( check_str='operation=sharing' ) # Enable importing history3 via a URL self.enable_import_via_link( self.security.encode_id( history3.id ), check_str='Unshare',

1 0

[hg] galaxy 2955: trackster: much greater resolution for line tr...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d7c66019de13 changeset: 2955:d7c66019de13 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Nov 03 19:16:01 2009 -0500 description: trackster: much greater resolution for line tracks (might still need to tweak BLOCK_SIZE), fixed stacking issue in feature tracks for features sharing same name) diffstat: lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py | 4 +- lib/galaxy/visualization/tracks/data/array_tree.py | 45 ++++++----- lib/galaxy/visualization/tracks/data/interval_index.py | 6 +- lib/galaxy/web/controllers/tracks.py | 6 +- static/scripts/trackster.js | 46 +++++++---- static/trackster.css | 1 + templates/tracks/browser.mako | 1 + 7 files changed, 65 insertions(+), 44 deletions(-) diffs (293 lines): diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py --- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Tue Nov 03 19:16:01 2009 -0500 @@ -8,6 +8,8 @@ from bx.arrays.array_tree import * from bx.arrays.wiggle import IntervalReader +BLOCK_SIZE = 1000 + def main(): input_fname = sys.argv[1] @@ -16,7 +18,7 @@ reader = IntervalReader( open( input_fname ) ) # Fill array from wiggle - d = array_tree_dict_from_wiggle_reader( reader, {} ) + d = array_tree_dict_from_wiggle_reader( reader, {}, block_size = BLOCK_SIZE ) for value in d.itervalues(): value.root.build_summary() diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/visualization/tracks/data/array_tree.py --- a/lib/galaxy/visualization/tracks/data/array_tree.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Tue Nov 03 19:16:01 2009 -0500 @@ -31,11 +31,16 @@ f.close() return { 'max': float( max(root_summary.maxs) ), 'min': float( min(root_summary.mins) ) } - def get_data( self, chrom, start, end ): + def get_data( self, chrom, start, end, **kwargs ): start = int( start ) end = int( end ) - level = int( ceil( log( end - start, BLOCK_SIZE ) ) ) - 1 - + resolution = max(1, ceil(float(kwargs['resolution']))) + + level = int( floor( log( resolution, BLOCK_SIZE ) ) ) + level = max( level, 0 ) + stepsize = BLOCK_SIZE ** level + step1 = stepsize * BLOCK_SIZE + # Open the file f = open( self.dataset.file_name ) d = FileArrayTreeDict( f ) @@ -47,22 +52,20 @@ # Is the requested level valid? assert 0 <= level <= chrom_array_tree.levels # Calculate the actual start/range/step of the block we're getting - size = BLOCK_SIZE ** (level+1) - block_start = ( start // BLOCK_SIZE ) * BLOCK_SIZE - block_step = size // BLOCK_SIZE - indexes = range( block_start, block_start + size, block_step ) - # Return either data point or a summary depending on the level - if level > 0: - s = chrom_array_tree.get_summary( start, level ) - f.close() - if s is not None: - return zip( indexes, map( float, s.sums / s.counts ) ) + + results = [] + for block_start in range( start, end, stepsize * BLOCK_SIZE ): + # print block_start + # Return either data point or a summary depending on the level + indexes = range( block_start, block_start + stepsize * BLOCK_SIZE, stepsize ) + if level > 0: + s = chrom_array_tree.get_summary( block_start, level ) + if s is not None: + results.extend( zip( indexes, map( float, s.sums / s.counts ) ) ) else: - return None - else: - v = chrom_array_tree.get_leaf( start ) - f.close() - if v is not None: - return zip( indexes, map( float, v ) ) - else: - return None \ No newline at end of file + v = chrom_array_tree.get_leaf( block_start ) + if v is not None: + results.extend( zip( indexes, map( float, v ) ) ) + + f.close() + return results diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Tue Nov 03 19:16:01 2009 -0500 @@ -11,17 +11,18 @@ self.original_dataset = original_dataset self.converted_dataset = converted_dataset - def get_data( self, chrom, start, end ): + def get_data( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) chrom = str(chrom) source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) results = [] + uid = 0 for start, end, offset in index.find(chrom, start, end): source.seek(offset) feature = source.readline().split() - payload = { 'start': start, 'end': end, 'name': feature[3] } + payload = { 'uid': uid, 'start': start, 'end': end, 'name': feature[3] } try: payload['strand'] = feature[5] except IndexError: @@ -41,5 +42,6 @@ pass results.append(payload) + uid += 1 return results diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Tue Nov 03 19:16:01 2009 -0500 @@ -184,7 +184,7 @@ return manifest @web.json - def data( self, trans, dataset_id, track_type, chrom, low, high, stats=False ): + def data( self, trans, dataset_id, track_type, chrom, low, high, **kwargs ): """ Called by the browser to request a block of data """ @@ -216,10 +216,10 @@ data_provider = dataset_type_to_data_provider[ converted_dataset_type ]( converted_dataset, dataset ) # Return stats if we need them - if stats: return data_provider.get_stats( chrom ) + if 'stats' in kwargs: return data_provider.get_stats( chrom ) # Get the requested chunk of data - return data_provider.get_data( chrom, low, high ) + return data_provider.get_data( chrom, low, high, **kwargs ) def __dataset_as_type( self, trans, dataset, type ): """ diff -r 46791b5a653b -r d7c66019de13 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Nov 03 17:16:40 2009 -0500 +++ b/static/scripts/trackster.js Tue Nov 03 19:16:01 2009 -0500 @@ -1,13 +1,15 @@ /* Trackster 2009, James Taylor, Kanwei Li */ +var DEBUG = false; var DENSITY = 1000, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", DATA_LOADING = "Loading data...", - CACHED_TILES = 10, + CACHED_TILES_FEATURE = 10, + CACHED_TILES_LINE = 30, CACHED_DATA = 20, CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), RIGHT_STRAND, LEFT_STRAND; @@ -104,6 +106,9 @@ this.high = Math.ceil(high); this.center = Math.round( this.low + (this.high - this.low) / 2 ); + // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width + this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); + // Overview $("#overview-box").css( { left: ( this.low / this.span ) * $("#overview-viewport").width(), @@ -157,18 +162,16 @@ }); var TiledTrack = function() { - this.tile_cache = new Cache(CACHED_TILES); - // this.tile_cache = {}; }; $.extend( TiledTrack.prototype, Track.prototype, { draw: function() { var low = this.view.low, high = this.view.high, - range = high - low; - - var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); - resolution = Math.max( resolution, 0.1 ); - resolution = Math.min( resolution, 1000000 ); + range = high - low, + resolution = this.view.resolution; + + + if (DEBUG) { $("#debug").text(resolution); } var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); @@ -187,7 +190,7 @@ // console.log("cached tile " + tile_index); var tile_low = tile_index * DENSITY * resolution; cached.css( { - left: ( tile_low - this.view.low ) * w_scale + left: ( tile_low - low ) * w_scale }); // Our responsibility to move the element to the new parent parent_element.append( cached ); @@ -229,6 +232,7 @@ }); var LineTrack = function ( name, dataset_id, height ) { + this.tile_cache = new Cache(CACHED_TILES_LINE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -236,6 +240,7 @@ this.height_px = (height ? height : 100); this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; + this.data_queue = {}; this.cache = new Cache(CACHED_DATA); // We need to cache some data because of // asynchronous calls }; @@ -282,11 +287,17 @@ low = position * DENSITY * resolution, high = ( position + 1 ) * DENSITY * resolution, key = resolution + "_" + position; - - $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id }, function ( data ) { - track.cache[key] = data; - $(document).trigger( "redraw" ); - }); + + if (!track.data_queue[key]) { + track.data_queue[key] = true; + $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, + low: low, high: high, dataset_id: this.dataset_id, + resolution: this.view.resolution }, function ( data ) { + track.cache[key] = data; + delete track.data_queue[key]; + track.draw(); + }); + } }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { if (!this.vertical_range) { // We don't have the necessary information yet @@ -340,6 +351,7 @@ }); var FeatureTrack = function ( name, dataset_id, height ) { + this.tile_cache = new Cache(CACHED_TILES_FEATURE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -409,9 +421,9 @@ if (end_ary[j] === undefined || end_ary[j] < f_start) { end_ary[j] = f_end; if (include_labels) { - this.zi_slots[feature.name] = j; + this.zi_slots[feature.uid] = j; } else { - this.zo_slots[feature.name] = j; + this.zo_slots[feature.uid] = j; } break; } @@ -466,7 +478,7 @@ if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), - y_center = this.slots[feature.name] * this.vertical_gap; + y_center = this.slots[feature.uid] * this.vertical_gap; var thickness, y_start, thick_start = null, thick_end = null; if (feature.thick_start && feature.thick_end) { diff -r 46791b5a653b -r d7c66019de13 static/trackster.css --- a/static/trackster.css Tue Nov 03 17:16:40 2009 -0500 +++ b/static/trackster.css Tue Nov 03 19:16:01 2009 -0500 @@ -25,6 +25,7 @@ font-size: 100%; } +/*canvas{ border-right: 1px solid red; } /* debugging */ #nav { padding: 0.5em 0; background:#cccccc; diff -r 46791b5a653b -r d7c66019de13 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Nov 03 17:16:40 2009 -0500 +++ b/templates/tracks/browser.mako Tue Nov 03 19:16:01 2009 -0500 @@ -122,6 +122,7 @@ <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> </form> + <div id="debug" style="float: right"></div> </div> </div> </div>

1 0

[hg] galaxy 2948: Pack recently modified scripts.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/de764999c5af changeset: 2948:de764999c5af user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 13:00:36 2009 -0500 description: Pack recently modified scripts. diffstat: static/scripts/packed/autocomplete_tagging.js | 2 +- static/scripts/packed/trackster.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diffs (16 lines): diff -r f776fa6045ba -r de764999c5af static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 12:58:13 2009 -0500 +++ b/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 13:00:36 2009 -0500 @@ -1,1 +1,1 @@ -var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u,v){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>").text(u).addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};v ar s=b();if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var a=function(v,u){return v+((u!=""&&u)?":"+u:"")};var h=function(u){return u.split(":")};var i=function(u){var v=$("<img src='"+p.add_tag_img+"' rollover='"+p.add_tag_img_rollover+"'/>").addClass("add-tag-button");v.click(function(){$(this).hide();m.click();return false});return v};var j=function(u){var v=$("<img src='"+p.delete_tag_img+"'/>").addClass("delete-tag-img");v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)});v.click(function(){var D=$(this).parent();var C=D.find(".tag-name").eq(0);var B=C.text();var z=h(B);var F=z[0];var y=z[1];var E=D.prev();D.remove();delete p.tags[F];var A=p.get_toggle_link_text_fn(p.tags);s.text(A);$.ajax({url:p.ajax_delete_tag_url,data:{tag_name:F},error:function(){p.tags[F]=y;if(E.hasClass("tag-button")){E .after(D)}else{m.prepend(D)}var G=p.get_toggle_link_text_fn(p.tags);alert("Remove tag failed");s.text(G);v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)})},success:function(){}});return true});var w=$("<span>").text(u).addClass("tag-name");w.click(function(){tag_name_and_value=u.split(":");p.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);if(p.editable){x.append(v)}return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+escape(v)+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+escape(v)+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true) {return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<3){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,fo rmatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});if(p.editable){m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false})}if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file +var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u,v){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>").text(u).addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};v ar s=b();if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var a=function(v,u){return v+((u!=""&&u)?":"+u:"")};var h=function(u){return u.split(":")};var i=function(u){var v=$("<img src='"+p.add_tag_img+"' rollover='"+p.add_tag_img_rollover+"'/>").addClass("add-tag-button");v.click(function(){$(this).hide();m.click();return false});return v};var j=function(u){var v=$("<img src='"+p.delete_tag_img+"'/>").addClass("delete-tag-img");v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)});v.click(function(){var D=$(this).parent();var C=D.find(".tag-name").eq(0);var B=C.text();var z=h(B);var F=z[0];var y=z[1];var E=D.prev();D.remove();delete p.tags[F];var A=p.get_toggle_link_text_fn(p.tags);s.text(A);$.ajax({url:p.ajax_delete_tag_url,data:{tag_name:F},error:function(){p.tags[F]=y;if(E.hasClass("tag-button")){E .after(D)}else{m.prepend(D)}var G=p.get_toggle_link_text_fn(p.tags);alert("Remove tag failed");s.text(G);v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)})},success:function(){}});return true});var w=$("<span>").text(u).addClass("tag-name");w.click(function(){tag_name_and_value=u.split(":");p.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);if(p.editable){x.append(v)}return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+escape(v)+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+escape(v)+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true) {return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<2){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,fo rmatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});if(p.editable){m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false})}if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file diff -r f776fa6045ba -r de764999c5af static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Tue Nov 03 12:58:13 2009 -0500 +++ b/static/scripts/packed/trackster.js Tue Nov 03 13:00:36 2009 -0500 @@ -1,1 +1,1 @@ -var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=5,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(l eft_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e =this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){thi s.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k)}if(g){this.tile_cache.set(i,g)}a+=1}}});var LabelTrack=function(a){Track.ca ll(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dat aset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[e]=g;$(document).trigger("redra w")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(FeatureTrack.prototype,TiledTrack.pro totype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.container_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k=Math.floor(Math.max(e,(n.star t-e)*g));k-=m.measureText(n.name).width;l=Math.ceil(Math.min(a,(n.end-e)*g))}else{k=Math.floor(Math.max(e,(n.start-e)*b));l=Math.ceil(Math.min(a,(n.end-e)*b))}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospac e";v.textAlign="right";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}els e{if(f.strand=="-"){v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file +var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=10,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern( left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){ e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){th is.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k);if(g){this.tile_cache.set(i,g)}}a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low: null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[ e]=g;$(document).trigger("redraw")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(Featur eTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k= Math.floor((n.start-e)*g);k-=m.measureText(n.name).width;l=Math.ceil((n.end-e)*g)}else{k=Math.floor((n.start-e)*b);l=Math.ceil((n.end-e)*b)}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospace";v.textAlign="rig ht";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}else{if(f.strand=="-") {v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file

1 0

[hg] galaxy 2949: imported patch alchemy05_fixes_01
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/133252175425 changeset: 2949:133252175425 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 12:52:00 2009 -0500 description: imported patch alchemy05_fixes_01 diffstat: eggs.ini | 10 +- lib/galaxy/model/mapping.py | 2 +- lib/galaxy/model/migrate/check.py | 2 +- lib/galaxy/model/migrate/versions/0003_security_and_libraries.py | 4 +- lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py | 2 +- lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py | 4 +- lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py | 2 +- lib/galaxy/model/migrate/versions/0008_galaxy_forms.py | 4 +- lib/galaxy/model/migrate/versions/0009_request_table.py | 2 +- lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py | 4 +- lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py | 4 +- lib/galaxy/model/migrate/versions/0012_user_address.py | 4 +- lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py | 2 +- lib/galaxy/model/migrate/versions/0017_library_item_indexes.py | 2 +- lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py | 2 +- lib/galaxy/model/migrate/versions/0019_request_library_folder.py | 4 +- lib/galaxy/model/migrate/versions/0020_library_upload_job.py | 4 +- lib/galaxy/model/orm/ext/assignmapper.py | 38 ++++++--- lib/galaxy/web/controllers/forms.py | 2 +- lib/galaxy/web/controllers/history.py | 2 +- lib/galaxy/web/controllers/page.py | 4 +- lib/galaxy/web/controllers/workflow.py | 22 ++-- lib/galaxy/web/framework/helpers/grids.py | 4 +- 23 files changed, 73 insertions(+), 57 deletions(-) diffs (502 lines): diff -r 80915982fdb2 -r 133252175425 eggs.ini --- a/eggs.ini Tue Nov 03 11:28:34 2009 -0500 +++ b/eggs.ini Tue Nov 03 12:52:00 2009 -0500 @@ -28,6 +28,7 @@ [eggs:noplatform] amqplib = 0.6.1 Beaker = 1.4 +decorator = 3.1.2 docutils = 0.4 elementtree = 1.2.6_20050316 lrucache = 0.2 @@ -41,8 +42,8 @@ PasteScript = 1.3.6 Routes = 1.6.3 simplejson = 1.5 -SQLAlchemy = 0.4.7p1 -sqlalchemy_migrate = 0.4.5 +SQLAlchemy = 0.5.6 +sqlalchemy_migrate = 0.5.4 Tempita = 0.1 twill = 0.9 WebError = 0.8a @@ -77,6 +78,7 @@ guppy = http://pypi.python.org/packages/source/g/guppy/guppy-0.1.8.tar.gz amqplib = http://py-amqplib.googlecode.com/files/amqplib-0.6.1.tgz Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-1.4.tar.gz +decorator = http://pypi.python.org/packages/source/d/decorator/decorator-3.1.2.tar.gz docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz @@ -90,8 +92,8 @@ PSI = http://pypi.python.org/packages/source/P/PSI/PSI-0.3b1.1.tar.gz Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.ta… -SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.4.7p1.tar.… -sqlalchemy_migrate = http://pypi.python.org/packages/source/s/sqlalchemy-migrate/sqlalchemy-migr… +SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.5.6.tar.gz +sqlalchemy_migrate = http://pypi.python.org/packages/source/s/sqlalchemy-migrate/sqlalchemy-migr… Tempita = http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz twill = http://darcs.idyll.org/~t/projects/twill-0.9.tar.gz WebError = http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/mapping.py Tue Nov 03 12:52:00 2009 -0500 @@ -18,7 +18,7 @@ from sqlalchemy.ext.associationproxy import association_proxy metadata = MetaData() -context = Session = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) +context = Session = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) # For backward compatibility with "context.current" context.current = Session diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/check.py Tue Nov 03 12:52:00 2009 -0500 @@ -7,7 +7,7 @@ from migrate.versioning import repository, schema from sqlalchemy import * -from sqlalchemy.exceptions import NoSuchTableError +from sqlalchemy.exc import NoSuchTableError log = logging.getLogger( __name__ ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0003_security_and_libraries.py --- a/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py Tue Nov 03 12:52:00 2009 -0500 @@ -1,6 +1,6 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -20,7 +20,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) if migrate_engine.name == 'postgres': # http://blog.pythonisito.com/2008/01/cascading-drop-table-with-sqlalchemy.ht… diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py --- a/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py Tue Nov 03 12:52:00 2009 -0500 @@ -12,7 +12,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) User_table = Table( "galaxy_user", metadata, autoload=True ) HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Tue Nov 03 12:52:00 2009 -0500 @@ -23,7 +23,7 @@ metadata = MetaData( migrate_engine ) -context = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) +context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) ## classes @@ -662,7 +662,7 @@ log.debug( "Fixing a discrepancy concerning deleted shared history items." ) affected_items = 0 start_time = time.time() - for dataset in context.query( Dataset ).filter( and_( Dataset.c.deleted == True, Dataset.c.purged == False ) ): + for dataset in context.query( Dataset ).filter( and_( Dataset.deleted == True, Dataset.purged == False ) ): for dataset_instance in dataset.history_associations + dataset.library_associations: if not dataset_instance.deleted: dataset.deleted = False diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py --- a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Tue Nov 03 12:52:00 2009 -0500 @@ -16,7 +16,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0008_galaxy_forms.py --- a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py Tue Nov 03 12:52:00 2009 -0500 @@ -11,7 +11,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -31,7 +31,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0009_request_table.py --- a/lib/galaxy/model/migrate/versions/0009_request_table.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0009_request_table.py Tue Nov 03 12:52:00 2009 -0500 @@ -9,7 +9,7 @@ from migrate.changeset import * import sys, logging from galaxy.model.custom_types import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py --- a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py Tue Nov 03 12:52:00 2009 -0500 @@ -10,7 +10,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -30,7 +30,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py --- a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Tue Nov 03 12:52:00 2009 -0500 @@ -5,7 +5,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -25,7 +25,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0012_user_address.py --- a/lib/galaxy/model/migrate/versions/0012_user_address.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0012_user_address.py Tue Nov 03 12:52:00 2009 -0500 @@ -6,7 +6,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime @@ -24,7 +24,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py --- a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py Tue Nov 03 12:52:00 2009 -0500 @@ -17,7 +17,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import sys, logging diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0017_library_item_indexes.py --- a/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py Tue Nov 03 12:52:00 2009 -0500 @@ -16,7 +16,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) LibraryFolder_table = Table( "library_folder", metadata, autoload=True ) LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) LibraryDataset_table = Table( "library_dataset", metadata, autoload=True ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py --- a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py Tue Nov 03 12:52:00 2009 -0500 @@ -5,7 +5,7 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * import migrate.changeset diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0019_request_library_folder.py --- a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py Tue Nov 03 12:52:00 2009 -0500 @@ -1,6 +1,6 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime @@ -18,7 +18,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0020_library_upload_job.py --- a/lib/galaxy/model/migrate/versions/0020_library_upload_job.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0020_library_upload_job.py Tue Nov 03 12:52:00 2009 -0500 @@ -1,6 +1,6 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime @@ -18,7 +18,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/orm/ext/assignmapper.py --- a/lib/galaxy/model/orm/ext/assignmapper.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/orm/ext/assignmapper.py Tue Nov 03 12:52:00 2009 -0500 @@ -15,22 +15,36 @@ from sqlalchemy import util, exceptions import types -from sqlalchemy.orm import mapper, Query +from sqlalchemy.orm import Query +from sqlalchemy.orm import mapper as sqla_mapper -def _monkeypatch_session_method(name, session, class_, make_list=False): - def do(self, *args, **kwargs): - if make_list: - self = [ self ] - return getattr(session, name)( self, *args, **kwargs ) +def _monkeypatch_session_method( name, session, class_ ): + # TODO: eliminate this method by fixing the session flushes + def do( self, *args, **kwargs ): + if self not in session.deleted: + session.add( self ) + return session.flush() try: do.__name__ = name except: pass - if not hasattr(class_, name): - setattr(class_, name, do) - + if not hasattr( class_, name ): + setattr( class_, name, do ) +def session_mapper( scoped_session, class_, *args, **kwargs ): + def mapper( cls, *arg, **kw ): + validate = kw.pop( 'validate', False ) + if cls.__init__ is object.__init__: + def __init__( self, **kwargs ): + for key, value in kwargs.items(): + if validate: + if not cls_mapper.has_property( key ): + raise TypeError( "Invalid __init__ argument: '%s'" % key ) + setattr( self, key, value ) + cls.__init__ = __init__ + cls.query = scoped_session.query_property() + _monkeypatch_session_method( 'flush', scoped_session, cls ) + return sqla_mapper( cls, *arg, **kw ) + return mapper( class_, *args, **kwargs ) def assign_mapper( session, class_, *args, **kwargs ): - m = class_.mapper = session.mapper( class_, *args, **kwargs ) - for name in ( 'flush', ): - _monkeypatch_session_method( name, session, class_, make_list=True ) + m = class_.mapper = session_mapper( session, class_, *args, **kwargs ) return m diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/forms.py Tue Nov 03 12:52:00 2009 -0500 @@ -450,7 +450,7 @@ # create corresponding row in the form_definition_current table fd.form_definition_current = fdc fdc.latest_form = fd - trans.sa_session.save_or_update( fdc ) + trans.sa_session.add( fdc ) trans.sa_session.flush() msg = "The new form named '%s' has been created. " % (fd.name) return fd, msg diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Nov 03 12:52:00 2009 -0500 @@ -726,7 +726,7 @@ share.history = history share.user = send_to_user session = trans.sa_session - session.save_or_update( share ) + session.add( share ) session.flush() if history not in shared_histories: shared_histories.append( history ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/page.py Tue Nov 03 12:52:00 2009 -0500 @@ -135,7 +135,7 @@ page_revision.content = "" # Persist session = trans.sa_session - session.save_or_update( page ) + session.add( page ) session.flush() # Display the management page ## trans.set_message( "Page '%s' created" % page.title ) @@ -240,4 +240,4 @@ raise web.httpexceptions.HTTPNotFound() return trans.fill_template( "page/display.mako", page=page ) - \ No newline at end of file + diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Tue Nov 03 12:52:00 2009 -0500 @@ -30,7 +30,7 @@ user = trans.get_user() workflows = trans.sa_session.query( model.StoredWorkflow ) \ .filter_by( user=user, deleted=False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ @@ -53,13 +53,13 @@ user = trans.get_user() workflows = trans.sa_session.query( model.StoredWorkflow ) \ .filter_by( user=user, deleted=False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ .filter_by( user=user ) \ - .filter( model.StoredWorkflow.c.deleted == False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .filter( model.StoredWorkflow.deleted == False ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() return trans.fill_template( "workflow/list_for_run.mako", workflows = workflows, @@ -91,7 +91,7 @@ share.stored_workflow = stored share.user = other session = trans.sa_session - session.save_or_update( share ) + session.add( share ) session.flush() trans.set_message( "Workflow '%s' shared with user '%s'" % ( stored.name, other.email ) ) return trans.response.send_redirect( url_for( controller='workflow', action='sharing', id=id ) ) @@ -142,7 +142,7 @@ share.stored_workflow = stored share.user = trans.user session = trans.sa_session - session.save_or_update( share ) + session.add( share ) session.flush() # Redirect to load galaxy frames. return trans.response.send_redirect( url_for( controller='workflow' ) ) @@ -180,7 +180,7 @@ new_stored.user = user # Persist session = trans.sa_session - session.save_or_update( new_stored ) + session.add( new_stored ) session.flush() # Display the management page trans.set_message( 'Clone created with name "%s"' % new_stored.name ) @@ -205,7 +205,7 @@ stored_workflow.latest_workflow = workflow # Persist session = trans.sa_session - session.save_or_update( stored_workflow ) + session.add( stored_workflow ) session.flush() # Display the management page trans.set_message( "Workflow '%s' created" % stored_workflow.name ) @@ -514,7 +514,7 @@ stored.name = workflow_name workflow.stored_workflow = stored stored.latest_workflow = workflow - trans.sa_session.save_or_update( stored ) + trans.sa_session.add( stored ) trans.sa_session.flush() # Index page with message return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) @@ -656,12 +656,12 @@ ids_in_menu = set( [ x.stored_workflow_id for x in user.stored_workflow_menu_entries ] ) workflows = trans.sa_session.query( model.StoredWorkflow ) \ .filter_by( user=user, deleted=False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ .filter_by( user=user ) \ - .filter( model.StoredWorkflow.c.deleted == False ) \ + .filter( model.StoredWorkflow.deleted == False ) \ .all() return trans.fill_template( "workflow/configure_menu.mako", workflows=workflows, diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 12:52:00 2009 -0500 @@ -111,10 +111,10 @@ if sort_key.startswith( "-" ): sort_key = sort_key[1:] sort_order = 'desc' - query = query.order_by( self.model_class.c.get( sort_key ).desc() ) + query = query.order_by( self.model_class.table.c.get( sort_key ).desc() ) else: sort_order = 'asc' - query = query.order_by( self.model_class.c.get( sort_key ).asc() ) + query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) extra_url_args['sort'] = encoded_sort_key # There might be a current row

1 0

[hg] galaxy 2947: Improved search functionality for history grid...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f776fa6045ba changeset: 2947:f776fa6045ba user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 12:58:13 2009 -0500 description: Improved search functionality for history grid: (a) generic free text search box and (b) advanced search using name, tag, deleted status, and shared status. diffstat: lib/galaxy/tags/tag_handler.py | 8 +- lib/galaxy/web/controllers/history.py | 145 +++++++++++++++++--- lib/galaxy/web/framework/helpers/grids.py | 1 + static/scripts/autocomplete_tagging.js | 2 +- templates/history/grid.mako | 250 +++++++++++++++++++--------------- test/base/twilltestcase.py | 18 +- test/functional/test_history_functions.py | 2 +- 7 files changed, 278 insertions(+), 148 deletions(-) diffs (649 lines): diff -r 80915982fdb2 -r f776fa6045ba lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/tags/tag_handler.py Tue Nov 03 12:58:13 2009 -0500 @@ -3,6 +3,12 @@ class TagHandler( object ): + # Minimum tag length. + min_tag_len = 2 + + # Maximum tag length. + max_tag_len = 255 + # Tag separator. tag_separators = ',;' @@ -215,7 +221,7 @@ scrubbed_name = scrubbed_name[1:] # If name is too short or too long, return None. - if len(scrubbed_name) < 3 or len(scrubbed_name) > 255: + if len(scrubbed_name) < self.min_tag_len or len(scrubbed_name) > self.max_tag_len: return None return scrubbed_name diff -r 80915982fdb2 -r f776fa6045ba lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Nov 03 12:58:13 2009 -0500 @@ -5,6 +5,7 @@ from galaxy.model import History from galaxy.model.orm import * from galaxy.util.json import * +from galaxy.util.odict import odict from galaxy.tags.tag_handler import TagHandler from sqlalchemy.sql.expression import ClauseElement import webhelpers, logging, operator @@ -19,12 +20,29 @@ class HistoryListGrid( grids.Grid ): # Custom column types class NameColumn( grids.GridColumn ): - def __init( self, key, link, attach_popup ): + def __init( self, key, link, attach_popup, filterable ): grids.GridColumn.__init__(self, key, link, attach_popup) def get_value( self, trans, grid, history ): return history.get_display_name() + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by name. """ + if column_filter == "All": + pass + elif column_filter: + query = query.filter( func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): rval = [] @@ -48,6 +66,7 @@ if item.users_shared_with or item.importable: return dict( operation="sharing" ) return None + class TagsColumn( grids.GridColumn ): def __init__( self, col_name, key, filterable ): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) @@ -61,7 +80,7 @@ return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=history, elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) def filter( self, db_session, query, column_filter ): - """ Modify query to include only histories with tags in column_filter. """ + """ Modify query to filter histories by tag. """ if column_filter == "All": pass elif column_filter: @@ -69,52 +88,115 @@ tag_handler = TagHandler() raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) for name, value in raw_tags.items(): - tag = tag_handler.get_tag_by_name( db_session, name ) - if tag: - query = query.filter( History.tags.any( tag_id=tag.id ) ) + if name: + # Search for tag names. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) ) if value: - query = query.filter( History.tags.any( value=value.lower() ) ) - else: - # Tag doesn't exist; unclear what to do here, but the literal thing to do is add the criterion, which - # will then yield a query that returns no results. - query = query.filter( History.tags.any( user_tname=name ) ) + # Search for tag values. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) return query def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "All": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters - - + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DeletedColumn( grids.GridColumn ): def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "Active" : "False", "Deleted" : "True", "All": "All" } + accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } accepted_filters = [] for label, val in accepted_filter_labels_and_vals.items(): args = { self.key: val } accepted_filters.append( grids.GridColumnFilter( label, args) ) return accepted_filters + + class SharingColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by sharing status. """ + if column_filter == "All": + pass + elif column_filter: + if column_filter == "private": + query = query.filter( History.users_shared_with == None ) + query = query.filter( History.importable == False ) + elif column_filter == "shared": + query = query.filter( History.users_shared_with != None ) + elif column_filter == "importable": + query = query.filter( History.importable == True ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["private"] = "private" + accepted_filter_labels_and_vals["shared"] = "shared" + accepted_filter_labels_and_vals["importable"] = "importable" + accepted_filter_labels_and_vals["all"] = "All" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + + class FreeTextSearchColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to search tags and history names. """ + if column_filter == "All": + pass + elif column_filter: + # Build tags filter. + tag_handler = TagHandler() + raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + tags_filter = None + for name, value in raw_tags.items(): + if name: + # Search for tag names. + tags_filter = History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) + if value: + # Search for tag values. + tags_filter = and_( tags_filter, func.lower( History.tags.any( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) + + # Build history name filter. + history_name_filter = func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) + + # Apply filters to query. + if tags_filter: + query = query.filter( or_( tags_filter, history_name_filter ) ) + else: + query = query.filter( history_name_filter ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters # Grid definition - title = "Stored histories" + title = "Saved Histories" model_class = model.History template='/history/grid.mako' default_sort_key = "-create_time" columns = [ NameColumn( "Name", key="name", link=( lambda history: iff( history.deleted, None, dict( operation="switch", id=history.id ) ) ), - attach_popup=True ), + attach_popup=True, filterable=True ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), TagsColumn( "Tags", key="tags", filterable=True), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - # Valid for filtering but invisible - DeletedColumn( "Status", key="deleted", visible=False, filterable=True ) + # Columns that are valid for filtering but are not visible. + DeletedColumn( "Deleted", key="deleted", visible=False, filterable=True ), + SharingColumn( "Shared", key="shared", visible=False, filterable=True ), + FreeTextSearchColumn( "Search", key="free-text-search", visible=False ) # Not filterable because it's the default search. ] operations = [ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), @@ -131,7 +213,7 @@ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ), ] - default_filter = dict( deleted="False", tags="All" ) + default_filter = dict( name="All", deleted="False", tags="All", shared="All" ) num_rows_per_page = 50 preserve_state = False use_paging = True @@ -160,6 +242,7 @@ template='/history/grid.mako' model_class = model.History default_sort_key = "-update_time" + default_filter = {} columns = [ grids.GridColumn( "Name", key="name" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), @@ -374,6 +457,18 @@ trans.sa_session.flush() @web.expose + def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): + """Return autocomplete data for history names""" + user = trans.get_user() + if not user: + return + + ac_data = "" + for history in trans.sa_session.query( History ).filter_by( user=user ).filter( func.lower( History.name ) .like(q.lower() + "%") ): + ac_data = ac_data + history.name + "\n" + return ac_data + + @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): """Import another user's history via a shared URL""" msg = "" diff -r 80915982fdb2 -r f776fa6045ba lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 12:58:13 2009 -0500 @@ -183,6 +183,7 @@ query=query, cur_page_num = page_num, num_pages = num_pages, + default_filter_dict=self.default_filter, cur_filter_dict=cur_filter_dict, sort_key=sort_key, encoded_sort_key=encoded_sort_key, diff -r 80915982fdb2 -r f776fa6045ba static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Tue Nov 03 11:28:34 2009 -0500 +++ b/static/scripts/autocomplete_tagging.js Tue Nov 03 12:58:13 2009 -0500 @@ -309,7 +309,7 @@ new_value = new_value.replace(/^\s+|\s+$/g,""); // Too short? - if (new_value.length < 3) + if (new_value.length < 2) return false; // diff -r 80915982fdb2 -r f776fa6045ba templates/history/grid.mako --- a/templates/history/grid.mako Tue Nov 03 11:28:34 2009 -0500 +++ b/templates/history/grid.mako Tue Nov 03 12:58:13 2009 -0500 @@ -29,71 +29,20 @@ }); // Set up autocomplete for tag filter input. - var t = $("#input-tag-filter"); - t.keyup( function( e ) - { - if ( e.keyCode == 27 ) - { - // Escape key - $(this).trigger( "blur" ); - } else if ( - ( e.keyCode == 13 ) || // Return Key - ( e.keyCode == 188 ) || // Comma - ( e.keyCode == 32 ) // Space - ) - { - // - // Check input. - // - - new_value = this.value; - - // Do nothing if return key was used to autocomplete. - if (return_key_pressed_for_autocomplete == true) - { - return_key_pressed_for_autocomplete = false; - return false; - } - - // Suppress space after a ":" - if ( new_value.indexOf(": ", new_value.length - 2) != -1) - { - this.value = new_value.substring(0, new_value.length-1); - return false; - } - - // Remove trigger keys from input. - if ( (e.keyCode == 188) || (e.keyCode == 32) ) - new_value = new_value.substring( 0 , new_value.length - 1 ); - - // Trim whitespace. - new_value = new_value.replace(/^\s+|\s+$/g,""); - - // Too short? - if (new_value.length < 3) - return false; - - // - // New tag OK. - // - } - }); + var t = $("#input-tags-filter"); - // Add autocomplete to input. - var format_item_func = function(key, row_position, num_rows, value, search_term) - { - tag_name_and_value = value.split(":"); - return (tag_name_and_value.length == 1 ? tag_name_and_value[0] :tag_name_and_value[1]); - //var array = new Array(key, value, row_position, num_rows, - //search_term ); return "\"" + array.join("*") + "\""; - } var autocomplete_options = - { selectFirst: false, formatItem : format_item_func, autoFill: false, highlight: false, mustMatch: true }; + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", autocomplete_options); - - $("#page-select").change(navigate_to_page); + // Set up autocomplete for name filter input. + var t2 = $("#input-name-filter"); + + var autocomplete_options = + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; + + t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); }); ## Can this be moved into base.mako? %if refresh_frames: @@ -125,21 +74,52 @@ %endif %endif + // Filter and sort args for grid. + var filter_args = ${h.to_json_string(cur_filter_dict)}; + var sort_key = "${sort_key}"; + // - // Add a tag to the current grid filter; this adds the tag to the filter and then issues a request to refresh the grid. + // Add tag to grid filter. // function add_tag_to_grid_filter(tag_name, tag_value) { - // Use tag as a filter: replace TAGNAME with tag_name and issue query. - <% - url_args = {} - if "tags" in cur_filter_dict and cur_filter_dict["tags"] != "All": - url_args["f-tags"] = cur_filter_dict["tags"].encode("utf-8") + ", TAGNAME" - else: - url_args["f-tags"] = "TAGNAME" - %> - var url_base = "${url( url_args )}"; - var url = url_base.replace("TAGNAME", tag_name); + // Put tag name and value together. + var tag = tag_name + (tag_value != null && tag_value != "" ? ":" + tag_value : ""); + add_condition_to_grid_filter("tags", tag, true); + } + + // + // Add a filter to the current grid filter; this adds the filter and then issues a request to refresh the grid. + // + function add_condition_to_grid_filter(name, value, append) + { + // Update filter arg with new condition. + if (append) + { + // Append value. + var cur_val = filter_args[name]; + if (cur_val != "All") + cur_val = cur_val + ", " + value; + else + cur_val = value; + filter_args[name] = cur_val; + } + else + { + // Replace value. + filter_args[name] = value; + } + + // Build URL with filter args, sort key. + var filter_arg_value_strs = new Array(); + var i = 0; + for (arg in filter_args) + { + filter_arg_value_strs[i++] = "f-" + arg + "=" + filter_args[arg]; + } + var filter_str = filter_arg_value_strs.join("&"); + var url_base = "${h.url_for( controller='history', action='list')}"; + var url = url_base + "?" + filter_str + "&sort=" + sort_key; self.location = url; } @@ -154,7 +134,7 @@ var url = url_base.replace("PAGE", page_num); self.location = url; } - + </script> </%def> @@ -175,47 +155,95 @@ <div class="grid-header"> <h2>${grid.title}</h2> - - ## Print grid filter. - <form name="history_actions" action="javascript:add_tag_to_grid_filter($('#input-tag-filter').attr('value'))" method="get" > - <strong>Filter:   </strong> - %for column in grid.columns: - %if column.filterable: - <span> by ${column.label.lower()}:</span> - ## For now, include special case to handle tags. - %if column.key == "tags": - %if cur_filter_dict[column.key] != "All": - <span class="filter" "style='font-style: italic'"> - ${cur_filter_dict[column.key]} - </span> - <span>|</span> + + ## Search box and more options filter at top of grid. + <div> + ## Grid search. TODO: use more elegant way to get free text search column. + <% column = grid.columns[-1] %> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if column.key in cur_filter_dict and cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" "style='font-style: italic'">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" + action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),false)" + method="get" > + ${column.label}: + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | %endif - <input id="input-tag-filter" name="f-tags" type="text" value="" size="15"/> - <span>|</span> - %endif - - ## Handle other columns. - %for i, filter in enumerate( column.get_accepted_filters() ): - %if i > 0: - <span>|</span> - %endif - %if cur_filter_dict[column.key] == filter.args[column.key]: - <span class="filter" "style='font-style: italic'">${filter.label}</span> - %else: - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endif - %endfor - <span>     </span> + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> %endif %endfor - - ## Link to clear all filters. TODO: this should be the default filter or an empty filter. - <% - args = { "deleted" : "False", "tags" : "All" } - no_filter = GridColumnFilter("Clear Filter", args) - %> - <span><a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a></span> - </form> + | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> + %if use_form: + </form> + %endif + </div> + + ## Advanced Search + <div id="more-search-options" style="display: none; padding-top: 5px"> + <table style="border: 1px solid gray;"> + <tr><td style="text-align: left" colspan="100"> + Advanced Search | + <a href=""# onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Close</a> | + ## Link to clear all filters. + <% + no_filter = GridColumnFilter("Clear All", default_filter_dict) + %> + <a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> + </td></tr> + %for column in grid.columns: + %if column.filterable: + <tr> + ## Show div if current filter has value that is different from the default filter. + %if cur_filter_dict[column.key] != default_filter_dict[column.key]: + <script type="text/javascript"> + $('#more-search-options').css("display", "block"); + </script> + %endif + <td style="padding-left: 10px">${column.label.lower()}:</td> + <td> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" style="font-style: italic">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),true)" + method="get" > + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | + %endif + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + %endif + %endfor + %if use_form: + </form> + %endif + </td> + </tr> + %endif + %endfor + </table> + </div> </div> <form name="history_actions" action="${url()}" method="post" > <input type="hidden" name="page" value="${cur_page_num}"> @@ -291,7 +319,7 @@ extra = "" %> %if href: - <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}${extra}</a> </td> + <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}</a>${extra}</td> %else: <td >${v}${extra}</td> %endif diff -r 80915982fdb2 -r f776fa6045ba test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Nov 03 11:28:34 2009 -0500 +++ b/test/base/twilltestcase.py Tue Nov 03 12:58:13 2009 -0500 @@ -1,7 +1,7 @@ import pkg_resources pkg_resources.require( "twill==0.9" ) -import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile, re from itertools import * import twill @@ -311,20 +311,20 @@ def view_stored_active_histories( self, check_str='' ): self.home() self.visit_page( "history/list" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Rename&id' ) - self.check_page_for_string( 'operation=Switch&id' ) - self.check_page_for_string( 'operation=Delete&id' ) + self.check_page_for_string( 'operation=Rename' ) + self.check_page_for_string( 'operation=Switch' ) + self.check_page_for_string( 'operation=Delete' ) if check_str: self.check_page_for_string( check_str ) self.home() def view_stored_deleted_histories( self, check_str='' ): self.home() self.visit_page( "history/list?f-deleted=True" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Undelete&id' ) + self.check_page_for_string( 'operation=Undelete' ) if check_str: self.check_page_for_string( check_str ) self.home() @@ -723,14 +723,14 @@ # Functions associated with browsers, cookies, HTML forms and page visits def check_page_for_string( self, patt ): - """Looks for 'patt' in the current browser page""" + """Looks for 'patt' in the current browser page""" page = self.last_page() for subpatt in patt.split(): if page.find( patt ) == -1: fname = self.write_temp_file( page ) errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) raise AssertionError( errmsg ) - + def write_temp_file( self, content ): fd, fname = tempfile.mkstemp( suffix='.html', prefix='twilltestcase-' ) f = os.fdopen( fd, "w" ) diff -r 80915982fdb2 -r f776fa6045ba test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Tue Nov 03 11:28:34 2009 -0500 +++ b/test/functional/test_history_functions.py Tue Nov 03 12:58:13 2009 -0500 @@ -179,7 +179,7 @@ self.share_current_history( regular_user1.email, check_str=history3.name ) # Check out list of histories to make sure history3 was shared - self.view_stored_active_histories( check_str='operation=sharing">shared' ) + self.view_stored_active_histories( check_str='operation=sharing' ) # Enable importing history3 via a URL self.enable_import_via_link( self.security.encode_id( history3.id ), check_str='Unshare',

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[hg] galaxy 2946: Fix new functional tests script return code (f...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/80915982fdb2 changeset: 2946:80915982fdb2 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 11:28:34 2009 -0500 description: Fix new functional tests script return code (for buildbot) diffstat: scripts/functional_tests.py | 11 +++++++---- 1 files changed, 7 insertions(+), 4 deletions(-) diffs (34 lines): diff -r c96e886f883f -r 80915982fdb2 scripts/functional_tests.py --- a/scripts/functional_tests.py Tue Nov 03 10:26:42 2009 -0500 +++ b/scripts/functional_tests.py Tue Nov 03 11:28:34 2009 -0500 @@ -155,7 +155,7 @@ log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) - rval = False + success = False try: @@ -186,7 +186,7 @@ result = test_runner.run( tests ) - rval = result.wasSuccessful() + success = result.wasSuccessful() except: log.exception( "Failure running tests" ) @@ -206,7 +206,10 @@ app = None log.info( "Embedded Universe application stopped" ) - return rval + if success: + return 0 + else: + return 1 if __name__ == "__main__": - main() + sys.exit( main() )

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[hg] galaxy 2945: Fixed a bug in the user selectbox in new reque...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c96e886f883f changeset: 2945:c96e886f883f user: rc date: Tue Nov 03 10:26:42 2009 -0500 description: Fixed a bug in the user selectbox in new requests page diffstat: lib/galaxy/web/controllers/requests_admin.py | 9 +++------ 1 files changed, 3 insertions(+), 6 deletions(-) diffs (34 lines): diff -r 7594fc81bdfc -r c96e886f883f lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Tue Nov 03 07:58:24 2009 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Tue Nov 03 10:26:42 2009 -0500 @@ -377,8 +377,10 @@ msg=msg, messagetype=messagetype) def __select_user(self, trans, userid): + user_list = trans.sa_session.query( trans.app.model.User )\ + .order_by( trans.app.model.User.email.asc() ) user_ids = ['none'] - for user in trans.sa_session.query( trans.app.model.User ): + for user in user_list: if not user.deleted: user_ids.append(str(user.id)) select_user = SelectField('select_user', @@ -388,10 +390,6 @@ select_user.add_option('Select one', 'none', selected=True) else: select_user.add_option('Select one', 'none') - def __get_email(user): - return user.email - user_list = trans.sa_session.query( trans.app.model.User ) - #user_list.sort(key=__get_email) for user in user_list: if not user.deleted: if userid == str(user.id): @@ -399,7 +397,6 @@ else: select_user.add_option(user.email, user.id) return select_user - def __library_ui(self, trans, user, request=None, **kwd): ''' This method creates the data library & folder selectbox for new &

1 0