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galaxy-dist commit af3ee1e9f9e3: Removing accidentally leftover test line from Tophat wrapper
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1282832971 14400 # Node ID af3ee1e9f9e3c0e51b7b18a323b3fa80460aa864 # Parent e95e14f5e7a0db167a276570495e38f044b17092 Removing accidentally leftover test line from Tophat wrapper --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -180,7 +180,6 @@ def __main__(): # Copy SAM File. shutil.copyfile( tmp_output_dir + "/accepted_hits.sam", options.accepted_hits_output_file ) - shutil.copyfile(tmp_output_dir + "/accepted_hits.sam", '/afs/bx.psu.edu/user/kpvincent/galaxy-commit/tophat_out.sam') except Exception, e: stop_err( 'Error in tophat:\n' + str( e ) ) finally:

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galaxy-dist commit 5d3e57e28fb7: Enhance grid framework to enable custom column sorting. Sort criteria are now mapped to a column, and the column defines the sorting to be done on the grid query. Default sorting behavior has not changed. In addition, column's model_class attribute now defaults to the grid's model_class; this should make column definitions more intuitive and shorter.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1282595659 14400 # Node ID 5d3e57e28fb7fa524a47d3a9b7e99f73ebca6676 # Parent 60448575467fef8f6a42d83906ee2a622511c541 Enhance grid framework to enable custom column sorting. Sort criteria are now mapped to a column, and the column defines the sorting to be done on the grid query. Default sorting behavior has not changed. In addition, column's model_class attribute now defaults to the grid's model_class; this should make column definitions more intuitive and shorter. Used custom sorting functionality to enable (a) case-insensitive sorting of text fields and (b) case-insensitive sorting of published item by username. --- a/templates/history/list_published.mako +++ b/templates/history/list_published.mako @@ -28,7 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${unicode( grid, 'utf-8' )} + ${h.to_unicode( grid )} </div></div> --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -107,14 +107,14 @@ class HistoryDatasetAssociationListGrid( title = "Saved Datasets" model_class = model.HistoryDatasetAssociation template='/dataset/grid.mako' - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ - grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, + grids.TextColumn( "Name", key="name", # Link name to dataset's history. - link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -38,16 +38,15 @@ class HistoryListGrid( grids.Grid ): title = "Saved Histories" model_class = model.History template='/history/grid.mako' - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ - NameColumn( "Name", key="name", model_class=model.History, + NameColumn( "Name", key="name", link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, \ - model_tag_association_class=model.HistoryTagAssociation, \ + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, \ filterable="advanced", grid_name="HistoryListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. @@ -130,10 +129,10 @@ class HistoryAllPublishedGrid( grids.Gri default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.History, model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), + NameURLColumn( "Name", key="name", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -37,8 +37,8 @@ class StoredWorkflowListGrid( grids.Grid default_filter = { "name" : "All", "tags": "All" } default_sort_key = "-update_time" columns = [ - grids.TextColumn( "Name", key="name", model_class=model.StoredWorkflow, attach_popup=True, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ), + grids.TextColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", "tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ), StepsColumn( "Steps" ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -67,10 +67,10 @@ class StoredWorkflowAllPublishedGrid( gr default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.StoredWorkflow, model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), + grids.PublicURLColumn( "Name", key="name", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/templates/visualization/list_published.mako +++ b/templates/visualization/list_published.mako @@ -28,7 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${unicode( grid, 'utf-8' )} + ${h.to_unicode( grid )} </div></div> --- a/templates/workflow/list_published.mako +++ b/templates/workflow/list_published.mako @@ -28,7 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${unicode( grid, 'utf-8' )} + ${h.to_unicode( grid )} </div></div> --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -12,11 +12,11 @@ class VisualizationListGrid( grids.Grid default_sort_key = "-update_time" default_filter = dict( title="All", deleted="False", tags="All", sharing="All" ) columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Visualization, attach_popup=True, + grids.TextColumn( "Title", key="title", attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), - grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), + grids.TextColumn( "Dbkey", key="dbkey" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -47,10 +47,10 @@ class VisualizationAllPublishedGrid( gri default_sort_key = "-update_time" default_filter = dict( title="All", username="All" ) columns = [ - grids.PublicURLColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Visualization, model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), + grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/templates/page/index.mako +++ b/templates/page/index.mako @@ -15,7 +15,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${grid} + ${h.to_unicode( grid )} <br><br><h2>Pages shared with you by others</h2> --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -25,11 +25,11 @@ class PageListGrid( grids.Grid ): default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" } default_sort_key = "-create_time" columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), + grids.TextColumn( "Title", key="title", attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -61,10 +61,10 @@ class PageAllPublishedGrid( grids.Grid ) default_sort_key = "-update_time" default_filter = dict( title="All", username="All" ) columns = [ - grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), + grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( @@ -107,12 +107,12 @@ class HistorySelectionGrid( ItemSelectio title = "Saved Histories" model_class = model.History columns = [ - ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), + ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -130,12 +130,12 @@ class HistoryDatasetAssociationSelection title = "Saved Datasets" model_class = model.HistoryDatasetAssociation columns = [ - ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), + ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.HistoryDatasetAssociation, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -155,12 +155,12 @@ class WorkflowSelectionGrid( ItemSelecti title = "Saved Workflows" model_class = model.StoredWorkflow columns = [ - ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), + ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.StoredWorkflow, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -175,12 +175,12 @@ class PageSelectionGrid( ItemSelectionGr title = "Saved Pages" model_class = model.Page columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced"), + grids.TextColumn( "Title", key="title", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -195,10 +195,10 @@ class VisualizationSelectionGrid( ItemSe title = "Saved Visualizations" model_class = model.Visualization columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), - grids.TextColumn( "Type", key="type", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), + grids.TextColumn( "Title", key="title", filterable="advanced" ), + grids.TextColumn( "Type", key="type" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] columns.append( @@ -299,8 +299,8 @@ class PageController( BaseController, Sh return self.sharing( trans, **kwargs ) session.flush() - # Build grid HTML and make sure to encode in utf-8 to support unicode characters. - grid = unicode( self._page_list( trans, *args, **kwargs ), 'utf-8' ) + # Build grid HTML. + grid = self._page_list( trans, *args, **kwargs ) # Build list of pages shared with user. shared_by_others = trans.sa_session \ @@ -316,7 +316,7 @@ class PageController( BaseController, Sh @web.expose def list_published( self, trans, *args, **kwargs ): - grid = unicode( self._all_published_list( trans, *args, **kwargs ), 'utf-8' ) + grid = self._all_published_list( trans, *args, **kwargs ) if 'async' in kwargs: return grid else: --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -4,6 +4,7 @@ from galaxy.web.framework.helpers import from galaxy.web import url_for from galaxy.util.json import from_json_string, to_json_string from galaxy.util.odict import odict +from galaxy.web.framework.helpers import to_unicode import sys, logging, math @@ -41,12 +42,25 @@ class Grid( object ): if operation.allow_multiple: self.has_multiple_item_operations = True break + + # If a column does not have a model class, set the column's model class + # to be the grid's model class. + for column in self.columns: + if not column.model_class: + column.model_class = self.model_class + def __call__( self, trans, **kwargs ): + # + # Get basics. + # webapp = kwargs.get( 'webapp', 'galaxy' ) status = kwargs.get( 'status', None ) message = kwargs.get( 'message', None ) + + # # Build a base filter and sort key that is the combination of the saved state and defaults. # Saved state takes preference over defaults. + # base_filter = {} if self.default_filter: # default_filter is a dictionary that provides a default set of filters based on the grid's columns. @@ -70,8 +84,11 @@ class Grid( object ): use_default_filter = False if use_default_filter_str: use_default_filter = ( use_default_filter_str.lower() == 'true' ) + + # # Process filtering arguments to (a) build a query that represents the filter and (b) builds a - # dictionary that denotes the current filter. + # dictionary that denotes the current filter. + # cur_filter_dict = {} for column in self.columns: if column.key: @@ -134,23 +151,39 @@ class Grid( object ): if not isinstance( column_filter, basestring ): column_filter = unicode(column_filter) extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") + + # # Process sort arguments. + # sort_key = None if 'sort' in kwargs: sort_key = kwargs['sort'] elif base_sort_key: sort_key = base_sort_key - if sort_key: + + if sort_key: if sort_key.startswith( "-" ): - # Can't use lower() on timestamp or integer objects, so func.lower() is not used here... - query = query.order_by( self.model_class.table.c.get( sort_key[1:] ).desc() ) + ascending = False + column_key = sort_key[1:] else: - # See reason for not using lower() to do case-insensitive sorting. - query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) - extra_url_args['sort'] = sort_key + ascending = True + column_key = sort_key + + # Sort key is a column key. + for column in self.columns: + if column.key == column_key: + query = column.sort( query, ascending ) + break + extra_url_args['sort'] = sort_key + + # # There might be a current row + # current_item = self.get_current_item( trans, **kwargs ) + + # # Process page number. + # if self.use_paging: if 'page' in kwargs: if kwargs['page'] == 'all': @@ -175,7 +208,10 @@ class Grid( object ): # Defaults. page_num = 1 num_pages = 1 + + # # Preserve grid state: save current filter and sort key. + # if self.preserve_state: pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name ) trans.get_user().preferences[pref_name] = unicode( to_json_string( cur_filter_dict ) ) @@ -191,7 +227,10 @@ class Grid( object ): params['async'] = ( 'async' in kwargs ) params['webapp'] = webapp trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) + + # # Render grid. + # def url( *args, **kwargs ): # Only include sort/filter arguments if not linking to another # page. This is a bit of a hack. @@ -211,9 +250,14 @@ class Grid( object ): else: new_kwargs[ 'id' ] = trans.security.encode_id( id ) return url_for( **new_kwargs ) - use_panels = ( 'use_panels' in kwargs ) and ( kwargs['use_panels'] in [ True, 'True', 'true' ] ) - async_request = ( ( self.use_async ) and ( 'async' in kwargs ) and ( kwargs['async'] in [ True, 'True', 'true'] ) ) - return trans.fill_template( iff( async_request, self.async_template, self.template), + use_panels = ( kwargs.get( 'use_panels', False ) in [ True, 'True', 'true' ] ) + async_request = ( ( self.use_async ) and ( kwargs.get( 'async', False ) in [ True, 'True', 'true'] ) ) + # Currently, filling the template returns a str object; this requires decoding the string into a + # unicode object within mako templates. What probably should be done is to return the template as + # utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid + # results via a controller method, which is require substantial changes. Hence, for now, return grid + # as str. + return trans.fill_template( iff( async_request, self.async_template, self.template ), grid=self, query=query, cur_page_num = page_num, @@ -258,11 +302,14 @@ class Grid( object ): return query class GridColumn( object ): - def __init__( self, label, grid=None, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, - # Valid values for filterable are ['standard', 'advanced', None] - filterable=None, sortable=True ): + def __init__( self, label, key=None, model_class=None, method=None, format=None, \ + link=None, attach_popup=False, visible=True, ncells=1, \ + # Valid values for filterable are ['standard', 'advanced', None] + filterable=None, sortable=True ): + """ + Create a grid column. + """ self.label = label - self.grid = grid self.key = key self.model_class = model_class self.method = method @@ -272,12 +319,9 @@ class GridColumn( object ): self.visible = visible self.ncells = ncells self.filterable = filterable - # Currently can only sort of columns that have a database - # representation, not purely derived. - if self.key and sortable: - self.sortable = True - else: - self.sortable = False + # Column must have a key to be sortable. + self.sortable = ( self.key is not None and sortable ) + def get_value( self, trans, grid, item ): if self.method: value = getattr( grid, self.method )( trans, item ) @@ -288,10 +332,12 @@ class GridColumn( object ): if self.format: value = self.format( value ) return value + def get_link( self, trans, grid, item ): if self.link and self.link( item ): return self.link( item ) return None + def filter( self, trans, user, query, column_filter ): """ Modify query to reflect the column filter. """ if column_filter == "All": @@ -301,6 +347,7 @@ class GridColumn( object ): elif column_filter == "False": query = query.filter_by( **{ self.key: False } ) return query + def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ accepted_filters_vals = [ "False", "True", "All" ] @@ -309,6 +356,15 @@ class GridColumn( object ): args = { self.key: val } accepted_filters.append( GridColumnFilter( val, args) ) return accepted_filters + + def sort( self, query, ascending ): + """ Sort query using this column. """ + if ascending: + query = query.order_by( self.model_class.table.c.get( self.key ).asc() ) + else: + query = query.order_by( self.model_class.table.c.get( self.key ).desc() ) + return query + class TextColumn( GridColumn ): """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """ @@ -332,6 +388,14 @@ class TextColumn( GridColumn ): """ Returns a SQLAlchemy criterion derived for a single filter. Single filter is the most basic filter--usually a string--and cannot be a list. """ model_class_key_field = getattr( self.model_class, self.key ) return func.lower( model_class_key_field ).like( "%" + a_filter.lower() + "%" ) + + def sort( self, query, ascending ): + """ Sort column using case-insensitive alphabetical sorting. """ + if ascending: + query = query.order_by( func.lower ( self.model_class.table.c.get( self.key ) ).asc() ) + else: + query = query.order_by( func.lower( self.model_class.table.c.get( self.key ) ).desc() ) + return query class IntegerColumn( TextColumn ): """ @@ -357,7 +421,7 @@ class IntegerColumn( TextColumn ): class OwnerAnnotationColumn( TextColumn, UsesAnnotations ): """ Column that displays and filters item owner's annotations. """ - def __init__( self, col_name, key, model_class, model_annotation_association_class, filterable ): + def __init__( self, col_name, key, model_class=None, model_annotation_association_class=None, filterable=None ): GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable ) self.sortable = False self.model_annotation_association_class = model_annotation_association_class @@ -375,11 +439,9 @@ class OwnerAnnotationColumn( TextColumn, class CommunityTagsColumn( TextColumn ): """ Column that supports community tags. """ - def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): - GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable ) + def __init__( self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None ): + GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable, sortable=False ) self.model_tag_association_class = model_tag_association_class - # Tags cannot be sorted. - self.sortable = False # Column-specific attributes. self.grid_name = grid_name def get_value( self, trans, grid, item ): @@ -464,6 +526,15 @@ class OwnerColumn( TextColumn ): """ Column that lists item's owner. """ def get_value( self, trans, grid, item ): return item.user.username + + def sort( self, query, ascending ): + """ Sort column using case-insensitive alphabetical sorting on item's username. """ + if ascending: + query = query.order_by( func.lower ( self.model_class.username ).asc() ) + else: + query = query.order_by( func.lower( self.model_class.username ).desc() ) + return query + class PublicURLColumn( TextColumn ): """ Column displays item's public URL based on username and slug. """ @@ -474,7 +545,7 @@ class PublicURLColumn( TextColumn ): # TODO: provide link to set username. return None elif not item.user.slug: - # TODO: provide link to set slg + # TODO: provide link to set slug. return None class DeletedColumn( GridColumn ): --- a/templates/page/list_published.mako +++ b/templates/page/list_published.mako @@ -28,6 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${grid} - + ${h.to_unicode( grid )} + </div> + </div></%def> --- a/templates/visualization/list.mako +++ b/templates/visualization/list.mako @@ -13,7 +13,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${grid} + ${h.to_unicode( grid )} <br><br><h2>Visualizations shared with you by others</h2>

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galaxy-dist commit 7fa394981ef6: Bug fixes and basic zoom feature for mutation viz tool
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282769259 14400 # Node ID 7fa394981ef6f8d079cd8dd776cba349baca958f # Parent 95915784818931029539fd058c328e45470d34c2 Bug fixes and basic zoom feature for mutation viz tool --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -85,8 +85,6 @@ def mainsvg(opts): total = int(row[start_col+4]) diff = int(row[start_col+5]) imp = int(row[start_col+6]) - - #print 'sample_index', sample_index, total if total: x = 16+(sample_index*(WIDTH+GAP)) y = 30+(count*(HEIGHT+GAP))

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galaxy-dist commit b1a970038273: added svg datatype
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282753644 14400 # Node ID b1a9700382738ba805c20047f40541b06d33b04b # Parent d36d759bce05d7cd6db99b115ae8ebb549e09ce7 added svg datatype --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -105,6 +105,7 @@ <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/><datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/><datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>

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galaxy-dist commit 959157848189: (no commit message)
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282769169 14400 # Node ID 95915784818931029539fd058c328e45470d34c2 # Parent b1a9700382738ba805c20047f40541b06d33b04b (no commit message) --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -1,9 +1,16 @@ <tool id="mutation_visualize" name="Mutation Visualization" version="1.0.0"><description></description> - <command interpreter="python">visualize.py --input-file=$input --output-file=$out_file1 $header_row</command> + <command interpreter="python">visualize.py --input-file=$input --output-file=$out_file1 --zoom=$zoom_value $header_row</command><inputs><param format="tabular" name="input" type="data" label="Compare sequences in"></param><param name="header_row" type="boolean" label="Header in dataset?" checked="yes" truevalue="" falsevalue="--noheaders"/> + <param name="zoom_value" type="select" label="Zoom"> + <option value="1">1x</option> + <option value="2">2x</option> + <option value="3">3x</option> + <option value="4">4x</option> + <option value="5">5x</option> + </param></inputs><outputs><data format="svg" name="out_file1" /> --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -17,21 +17,21 @@ import svgfig as svg COLS_PER_SAMPLE = 7 HEADER_COLS = 4 -SPACE_PAIRS = 0.8 -SPACE_SAMPLES = 1 +HEIGHT = 6 +WIDTH = 12 +BAR_WIDTH = 1.5 +GAP = 2 -HEIGHT = 4 -WIDTH = 8 colors = {'A':'blue', 'C':'green', 'G':'orange', 'T':'red'} bases = ['A', 'C', 'G', 'T' ] def mainsvg(opts): - s = svg.SVG('g') + s = svg.SVG('g', transform="translate(20,0)") # display legend - for i, b in enumerate(bases): + for i, b in enumerate( bases ): bt = svg.SVG("tspan", b, style="font-family:Verdana;font-size:3") s.append(svg.SVG("text", bt, x=12+(i*10), y=8, stroke="none", fill="black")) s.append(svg.SVG("rect", x=13+(i*10), y=5, width=4, height=3, @@ -71,10 +71,10 @@ def mainsvg(opts): #print 'position', position, ref, count # display positions - bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:3") - s.append(svg.SVG("text", bt, x=9, y=33+(count*5), stroke="none", fill="black")) - s.append(svg.SVG("rect", x=4, y=30+(count*5), width=10, height=4, - stroke='none', fill=colors[ref.upper()], fill_opacity=0.3)) + bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:4") + s.append(svg.SVG("text", bt, x=7, y=34+(count*(HEIGHT+GAP)), stroke="none", fill="black")) + s.append(svg.SVG("rect", x=0, y=30+(count*(HEIGHT+GAP)), width=14, height=HEIGHT, + stroke='none', fill=colors[ref.upper()], fill_opacity=0.2)) for sample_index in range(int((len(row)-HEADER_COLS)/COLS_PER_SAMPLE)): start_col = HEADER_COLS+(COLS_PER_SAMPLE*sample_index) @@ -88,10 +88,10 @@ def mainsvg(opts): #print 'sample_index', sample_index, total if total: - x = 16+(sample_index*10) - y = 30+(count*5) + x = 16+(sample_index*(WIDTH+GAP)) + y = 30+(count*(HEIGHT+GAP)) width = WIDTH - height = 4 + height = HEIGHT if imp == 1: fill_opacity = 0.1 @@ -104,18 +104,21 @@ def mainsvg(opts): stroke='none', fill='grey', fill_opacity=fill_opacity)) for base, value in enumerate([n_a, n_c, n_g, n_t]): width = int(math.ceil(value / total * WIDTH)) - s.append(svg.SVG("rect", x=x, y=y, width=width, height=1, + s.append(svg.SVG("rect", x=x, y=y, width=width, height=BAR_WIDTH, stroke='none', fill=colors[bases[base]], fill_opacity=0.6)) - y = y + 1 + y = y + BAR_WIDTH #print base, value, total, x, y, width count=count+1 - - w = str(int(700)) + "px" - h = str(int(1000)) + "px" - canv = svg.canvas(s, width=w, height=h, viewBox="0 0 200 300") + + #print x, y + + zoom = int(opts.zoom) + w = "%ipx" % (x*(10+zoom)) + h = "%ipx" % (y*(2+zoom)) + canv = svg.canvas(s, width=w, height=h, viewBox="0 0 %i %i" %(x+100, y+100)) canv.save(opts.output_file) @@ -123,6 +126,7 @@ if __name__ == '__main__': parser = optparse.OptionParser() parser.add_option('-i', '--input-file', dest='input_file', action='store') parser.add_option('-o', '--output-file', dest='output_file', action='store') + parser.add_option('-z', '--zoom', dest='zoom', action='store', default='1') parser.add_option('-n', '--noheaders', dest='header_row', action='store_false', default=True) (opts, args) = parser.parse_args() mainsvg(opts)

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galaxy-dist commit d36d759bce05: Fix left padding issues on the edit attributes form
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1282674785 14400 # Node ID d36d759bce05d7cd6db99b115ae8ebb549e09ce7 # Parent 5d3e57e28fb7fa524a47d3a9b7e99f73ebca6676 Fix left padding issues on the edit attributes form --- a/templates/dataset/edit_attributes.mako +++ b/templates/dataset/edit_attributes.mako @@ -82,11 +82,13 @@ </form><form name="auto_detect" action="${h.url_for( controller='root', action='edit' )}" method="post"><input type="hidden" name="id" value="${data.id}"/> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="detect" value="${_('Auto-detect')}"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - This will inspect the dataset and attempt to correct the above column values if they are not accurate. + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="detect" value="${_('Auto-detect')}"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + This will inspect the dataset and attempt to correct the above column values if they are not accurate. + </div></div></form> %if data.missing_meta(): @@ -190,9 +192,9 @@ <form name="copy_hda" action="${h.url_for( controller='dataset', action='copy_datasets', source_dataset_ids=data.id, target_history_ids=data.history_id )}" method="post"><div class="form-row"><input type="submit" name="change" value="Copy history item"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - Make a copy of this history item in your current history or any of your active histories. + <div class="toolParamHelp" style="clear: both;"> + Make a copy of this history item in your current history or any of your active histories. + </div></div></form></div>

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galaxy-dist commit 60448575467f: Merge.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1282572917 14400 # Node ID 60448575467fef8f6a42d83906ee2a622511c541 # Parent 26a0b620490dd8698deb907ecaa540e7fa19a6ee # Parent 9bcd722236bd7d74784d7317bbe53fa3f050d101 Merge.

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galaxy-dist commit 9bcd722236bd: Refactoring of grid framework in preparation for enhancing sorting. Removed unused keyword 'encoded_sort_key' and made all GridColumn constructor keyword parameters explicit.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1282492757 14400 # Node ID 9bcd722236bd7d74784d7317bbe53fa3f050d101 # Parent 3ab68d0ba173ea4b21317c79fdea907bd91f5a81 Refactoring of grid framework in preparation for enhancing sorting. Removed unused keyword 'encoded_sort_key' and made all GridColumn constructor keyword parameters explicit. --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -114,7 +114,7 @@ class HistoryDatasetAssociationListGrid( link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), - grids.IndividualTagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -44,7 +44,9 @@ class HistoryListGrid( grids.Grid ): link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, \ + model_tag_association_class=model.HistoryTagAssociation, \ + filterable="advanced", grid_name="HistoryListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -131,7 +133,7 @@ class HistoryAllPublishedGrid( grids.Gri NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.History, model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -70,7 +70,7 @@ class StoredWorkflowAllPublishedGrid( gr grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.StoredWorkflow, model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -15,7 +15,7 @@ class VisualizationListGrid( grids.Grid grids.TextColumn( "Title", key="title", model_class=model.Visualization, attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -50,7 +50,7 @@ class VisualizationAllPublishedGrid( gri grids.PublicURLColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Visualization, model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -27,7 +27,8 @@ class PageListGrid( grids.Grid ): columns = [ grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), - grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -63,7 +64,7 @@ class PageAllPublishedGrid( grids.Grid ) grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( @@ -107,7 +108,7 @@ class HistorySelectionGrid( ItemSelectio model_class = model.History columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -130,7 +131,7 @@ class HistoryDatasetAssociationSelection model_class = model.HistoryDatasetAssociation columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -155,7 +156,7 @@ class WorkflowSelectionGrid( ItemSelecti model_class = model.StoredWorkflow columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -175,7 +176,7 @@ class PageSelectionGrid( ItemSelectionGr model_class = model.Page columns = [ grids.TextColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -196,7 +197,7 @@ class VisualizationSelectionGrid( ItemSe columns = [ grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), grids.TextColumn( "Type", key="type", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -140,15 +140,14 @@ class Grid( object ): sort_key = kwargs['sort'] elif base_sort_key: sort_key = base_sort_key - encoded_sort_key = sort_key if sort_key: if sort_key.startswith( "-" ): # Can't use lower() on timestamp or integer objects, so func.lower() is not used here... query = query.order_by( self.model_class.table.c.get( sort_key[1:] ).desc() ) else: - # See reason for not using lower() to do case-insensitive search. + # See reason for not using lower() to do case-insensitive sorting. query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) - extra_url_args['sort'] = encoded_sort_key + extra_url_args['sort'] = sort_key # There might be a current row current_item = self.get_current_item( trans, **kwargs ) # Process page number. @@ -222,7 +221,6 @@ class Grid( object ): default_filter_dict=self.default_filter, cur_filter_dict=cur_filter_dict, sort_key=sort_key, - encoded_sort_key=encoded_sort_key, current_item=current_item, ids = kwargs.get( 'id', [] ), url = url, @@ -260,10 +258,11 @@ class Grid( object ): return query class GridColumn( object ): - def __init__( self, label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, + def __init__( self, label, grid=None, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, # Valid values for filterable are ['standard', 'advanced', None] filterable=None, sortable=True ): self.label = label + self.grid = grid self.key = key self.model_class = model_class self.method = method --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -255,7 +255,7 @@ } // Add sort argument to URL args. - url_args['sort'] = "${encoded_sort_key}"; + url_args['sort'] = "${sort_key}"; // Add async keyword to URL args. url_args['async'] = true;

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galaxy-dist commit 3ab68d0ba173: Fixes for performance problems with display link generation.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User James Taylor <james(a)jamestaylor.org> # Date 1282421852 14400 # Node ID 3ab68d0ba173ea4b21317c79fdea907bd91f5a81 # Parent 7242f2dffed302ad6d0d727e43ede1ed65c39463 Fixes for performance problems with display link generation. 1) In "ucsc_links", "generate_display_viewport" was being called before the check for configured UCSC browsers matching the dataset's build. Thus, Galaxy would scan the start of the file for every dataset, regardless of whether UCSC links were displayed in the UI 2) When generating the viewport, if an exception was thrown parsing the chrom/start/end columns (for example, if the metadata was set wrong causing a non-numeric string to be found in the start column) the loop would continue WITHOUT executing the scan to end of line and update of the number of lines processed. Thus, on any file with incorrect metadata, every line of the file would be read and split. --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -1,7 +1,7 @@ """ Interval datatypes +""" -""" import pkg_resources pkg_resources.require( "bx-python" ) @@ -20,10 +20,8 @@ import math log = logging.getLogger(__name__) -# -# contain the meta columns and the words that map to it -# list aliases on the right side of the : in decreasing order of priority -# +# Contains the meta columns and the words that map to it; list aliases on the +# right side of the : in decreasing order of priority alias_spec = { 'chromCol' : [ 'chrom' , 'CHROMOSOME' , 'CHROM', 'Chromosome Name' ], 'startCol' : [ 'start' , 'START', 'chromStart', 'txStart', 'Start Position (bp)' ], @@ -38,9 +36,11 @@ for key, value in alias_spec.items(): for elem in value: alias_helper[elem] = key -#Constants for configuring viewport generation -VIEWPORT_READLINE_BUFFER_SIZE = 1048576 #1MB -VIEWPORT_MAX_READS_PER_LINE = 10 # If a line is greater than VIEWPORT_MAX_READS_PER_LINE * VIEWPORT_READLINE_BUFFER_SIZE bytes in size, then we will not generate a viewport for that dataset +# Constants for configuring viewport generation: If a line is greater than +# VIEWPORT_MAX_READS_PER_LINE * VIEWPORT_READLINE_BUFFER_SIZE bytes in size, +# then we will not generate a viewport for that dataset +VIEWPORT_READLINE_BUFFER_SIZE = 1048576 # 1MB +VIEWPORT_MAX_READS_PER_LINE = 10 class Interval( Tabular ): """Tab delimited data containing interval information""" @@ -150,55 +150,66 @@ class Interval( Tabular ): and dataset.metadata.endCol except: return False + def get_estimated_display_viewport( self, dataset, chrom_col = None, start_col = None, end_col = None ): """Return a chrom, start, stop tuple for viewing a file.""" viewport_feature_count = 100 # viewport should check at least 100 features; excludes comment lines max_line_count = max( viewport_feature_count, 500 ) # maximum number of lines to check; includes comment lines - if self.displayable( dataset ): - try: - chrom = None - start = sys.maxint - end = 0 - if chrom_col is None: - chrom_col = int( dataset.metadata.chromCol ) - 1 - if start_col is None: - start_col = int( dataset.metadata.startCol ) - 1 - if end_col is None: - end_col = int( dataset.metadata.endCol ) - 1 - max_col = max( chrom_col, start_col, end_col ) - fh = open( dataset.file_name ) - while True: + if not self.displayable( dataset ): + return ( None, None, None ) + try: + # If column indexes were not passwed, determine from metadata + if chrom_col is None: + chrom_col = int( dataset.metadata.chromCol ) - 1 + if start_col is None: + start_col = int( dataset.metadata.startCol ) - 1 + if end_col is None: + end_col = int( dataset.metadata.endCol ) - 1 + # Scan lines of file to find a reasonable chromosome and range + chrom = None + start = sys.maxint + end = 0 + max_col = max( chrom_col, start_col, end_col ) + fh = open( dataset.file_name ) + while True: + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + # Stop if at end of file + if not line: + break + # Skip comment lines + if not line.startswith( '#' ): + try: + fields = line.rstrip().split( '\t' ) + if len( fields ) > max_col: + if chrom is None or chrom == fields[ chrom_col ]: + start = min( start, int( fields[ start_col ] ) ) + end = max( end, int( fields[ end_col ] ) ) + # Set chrom last, in case start and end are not integers + chrom = fields[ chrom_col ] + viewport_feature_count -= 1 + except Exception, e: + # Most likely a non-integer field has been encountered + # for start / stop. Just ignore and make sure we finish + # reading the line and decrementing the counters. + pass + # Make sure we are at the next new line + readline_count = VIEWPORT_MAX_READS_PER_LINE + while line.rstrip( '\n\r' ) == line: + assert readline_count > 0, Exception( 'Viewport readline count exceeded for dataset %s.' % dataset.id ) line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) if not line: break #EOF - if not line.startswith( '#' ): - try: - fields = line.rstrip().split( '\t' ) - if len( fields ) > max_col: - if chrom is None or chrom == fields[ chrom_col ]: - start = min( start, int( fields[ start_col ] ) ) - end = max( end, int( fields[ end_col ] ) ) - chrom = fields[ chrom_col ] #set chrom last, in case start and end are not integers - viewport_feature_count -= 1 - except Exception: - #most likely a non-integer field has been encountered for start / stop - continue - #make sure we are at the next new line - readline_count = VIEWPORT_MAX_READS_PER_LINE - while line.rstrip( '\n\r' ) == line: - assert readline_count > 0, Exception( 'Viewport readline count exceeded for dataset %s.' % dataset.id ) - line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) - if not line: break #EOF - readline_count -= 1 - max_line_count -= 1 - if not viewport_feature_count or not max_line_count: - #exceeded viewport or total line count to check - break - if chrom is not None: - return ( chrom, str( start ), str( end ) ) #Necessary to return strings? - except Exception, e: - #unexpected error, possibly missing metadata - log.exception( str( e ) ) - return ( None, None, None ) #could not determine viewport + readline_count -= 1 + max_line_count -= 1 + if not viewport_feature_count or not max_line_count: + #exceeded viewport or total line count to check + break + if chrom is not None: + return ( chrom, str( start ), str( end ) ) # Necessary to return strings? + except Exception, e: + # Unexpected error, possibly missing metadata + log.exception( "Exception caught attempting to generate viewport for dataset '%d'", dataset.id ) + return ( None, None, None ) + def as_ucsc_display_file( self, dataset, **kwd ): """Returns file contents with only the bed data""" fd, temp_name = tempfile.mkstemp() @@ -252,22 +263,39 @@ class Interval( Tabular ): out = "Can't create peek %s" % str( exc ) return out def ucsc_links( self, dataset, type, app, base_url ): + """ + Generate links to UCSC genome browser sites based on the dbkey + and content of dataset. + """ + # Filter UCSC sites to only those that are supported by this build and + # enabled. + valid_sites = [ ( name, url ) + for name, url in util.get_ucsc_by_build( dataset.dbkey ) + if name in app.config.ucsc_display_sites ] + if not valid_sites: + return [] + # If there are any valid sites, we need to generate the estimated + # viewport + chrom, start, stop = self.get_estimated_display_viewport( dataset ) + if chrom is None: + return [] + # Accumulate links for valid sites ret_val = [] - chrom, start, stop = self.get_estimated_display_viewport( dataset ) - if chrom is not None: - for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): - if site_name in app.config.ucsc_display_sites: - # HACK: UCSC doesn't support https, so force http even - # if our URL scheme is https. Making this work - # requires additional hackery in your upstream proxy. - # If UCSC ever supports https, remove this hack. - internal_url = "%s" % url_for( controller='/dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - if base_url.startswith( 'https://' ): - base_url = base_url.replace( 'https', 'http', 1 ) - display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) - redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) - ret_val.append( (site_name, link) ) + for site_name, site_url in valid_sites: + internal_url = url_for( controller='/dataset', dataset_id=dataset.id, + action='display_at', filename='ucsc_' + site_name ) + # HACK: UCSC doesn't support https, so force http even if our URL + # scheme is https. Making this work requires additional + # hackery in your upstream proxy. If UCSC ever supports + # https, remove this hack. + if base_url.startswith( 'https://' ): + base_url = base_url.replace( 'https', 'http', 1 ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" + % (base_url, url_for( controller='root' ), dataset.id, type) ) + redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" + % (site_url, dataset.dbkey, chrom, start, stop ) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + ret_val.append( ( site_name, link ) ) return ret_val def validate( self, dataset ): """Validate an interval file using the bx GenomicIntervalReader"""

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galaxy-dist commit 7242f2dffed3: Fixed another bug in column join so it will handle filling empty columns properly
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1282338256 14400 # Node ID 7242f2dffed302ad6d0d727e43ede1ed65c39463 # Parent 8a3d3fba037061a818b4417978542ae7b71f2e1a Fixed another bug in column join so it will handle filling empty columns properly --- a/tools/new_operations/column_join.py +++ b/tools/new_operations/column_join.py @@ -241,10 +241,14 @@ def __main__(): new_split_line = split_line[:] split_line = [] for i, item in enumerate( new_split_line ): - if item: + col = i + 1 + if not item: + try: + split_line.append( fill_empty[ i + 1 ] ) + except KeyError: + split_line.append( item ) + else: split_line.append( item ) - else: - split_line.append( fill_empty[ i + 1 ] ) # add actual data to be output below if ''.join( split_line ): for col in cols: @@ -265,9 +269,11 @@ def __main__(): fout.write( '%s%s' % ( delimiter, delimiter.join( current_data ) ) ) elif current_data: fout.write( '%s%s%s' % ( current, delimiter, delimiter.join( current_data ) ) ) + last_lines = ''.join( current_lines ) + else: + last_lines = None last_loc = loc old_current = current - last_lines = ''.join( current_lines ) first_line = False # fill trailing empty columns for final line if last_loc < len( inputs ) - 1:

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