class VisualizationSelectionGrid(ItemSelectionGrid):
""" Grid for selecting visualizations. """
# Grid definition.
title = "Saved Visualizations"
model_class = model.Visualization
columns = [
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(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[2]],
key="free-text-search",
visible=False,
filterable="standard"))
class HistorySelectionGrid(ItemSelectionGrid):
""" Grid for selecting histories. """
# Grid definition.
title = "Saved Histories"
model_class = model.History
columns = [
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",
filterable="advanced",
sortable=False,
visible=False),
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
def apply_query_filter(self, trans, query, **kwargs):
return query.filter_by(user=trans.user, purged=False)
class PageSelectionGrid(ItemSelectionGrid):
""" Grid for selecting pages. """
# Grid definition.
title = "Saved Pages"
model_class = model.Page
columns = [
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",
filterable="advanced",
sortable=False,
visible=False),
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
class VisualizationListGrid( grids.Grid ):
def get_url_args( item ):
"""
Returns dictionary used to create item link.
"""
url_kwargs = dict( controller='visualization', id=item.id )
#TODO: hack to build link to saved visualization - need trans in this function instead in order to do
#link_data = trans.app.visualizations_registry.get_visualizations( trans, item )
if item.type in registry.VisualizationsRegistry.BUILT_IN_VISUALIZATIONS:
url_kwargs[ 'action' ] = item.type
else:
url_kwargs[ 'action' ] = 'saved'
return url_kwargs
def get_display_name( self, trans, item ):
if trans.app.visualizations_registry and item.type in trans.app.visualizations_registry.plugins:
plugin = trans.app.visualizations_registry.plugins[ item.type ]
return plugin.config.get( 'name', item.type )
return item.type
# Grid definition
title = "Saved Visualizations"
model_class = model.Visualization
default_sort_key = "-update_time"
default_filter = dict( title="All", deleted="False", tags="All", sharing="All" )
columns = [
grids.TextColumn( "Title", key="title", attach_popup=True, link=get_url_args ),
grids.TextColumn( "Type", method='get_display_name' ),
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 ),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[ columns[0], columns[2] ],
key="free-text-search", visible=False, filterable="standard" )
)
global_actions = [
grids.GridAction( "Create new visualization", dict( action='create' ), inbound=True )
]
operations = [
grids.GridOperation( "Open", allow_multiple=False, url_args=get_url_args ),
grids.GridOperation( "Open in Circster", allow_multiple=False, condition=( lambda item: item.type == 'trackster' ), url_args=dict( action='circster' ) ),
grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit'), inbound=True),
grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted )),
grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), confirm="Are you sure you want to delete this visualization?" ),
]
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter_by( user=trans.user, deleted=False )
class VisualizationListGrid( grids.Grid ):
def get_url_args( item ):
"""
Returns dictionary used to create item link.
"""
controller = "visualization"
action = item.type
if item.type == "phyloviz":
controller = "phyloviz"
action = "visualization"
return dict( controller=controller, action=action, id=item.id )
# Grid definition
title = "Saved Visualizations"
model_class = model.Visualization
default_sort_key = "-update_time"
default_filter = dict( title="All", deleted="False", tags="All", sharing="All" )
columns = [
grids.TextColumn( "Title", key="title", attach_popup=True, link=get_url_args ),
grids.TextColumn( "Type", key="type" ),
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 ),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[ columns[0], columns[2] ],
key="free-text-search", visible=False, filterable="standard" )
)
global_actions = [
grids.GridAction( "Create new visualization", dict( action='create' ) )
]
operations = [
grids.GridOperation( "Open", allow_multiple=False, url_args=get_url_args ),
grids.GridOperation( "Open in Circster", allow_multiple=False, condition=( lambda item: item.type == 'trackster' ), url_args=dict( action='circster' ) ),
grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit') ),
grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='copy') ),
grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True, confirm="Are you sure you want to delete this visualization?" ),
]
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter_by( user=trans.user, deleted=False )
class PageListGrid( grids.Grid ):
# Custom column.
class URLColumn( grids.PublicURLColumn ):
def get_value( self, trans, grid, item ):
return url_for(controller='page', action='display_by_username_and_slug', username=item.user.username, slug=item.slug )
# Grid definition
use_panels = True
title = "Pages"
model_class = model.Page
default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" }
default_sort_key = "-update_time"
columns = [
grids.TextColumn( "Title", key="title", attach_popup=True, filterable="advanced" ),
URLColumn( "Public URL" ),
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 ),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[ columns[0], columns[2] ],
key="free-text-search", visible=False, filterable="standard" )
)
global_actions = [
grids.GridAction( "Add new page", dict( action='create' ) )
]
operations = [
grids.DisplayByUsernameAndSlugGridOperation( "View", allow_multiple=False ),
grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ),
grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit') ),
grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
grids.GridOperation( "Delete", confirm="Are you sure you want to delete this page?" ),
]
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter_by( user=trans.user, deleted=False )
class HistoryDatasetAssociationSelectionGrid(ItemSelectionGrid):
""" Grid for selecting HDAs. """
# Grid definition.
title = "Saved Datasets"
model_class = model.HistoryDatasetAssociation
columns = [
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",
filterable="advanced",
sortable=False,
visible=False),
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
def apply_query_filter(self, trans, query, **kwargs):
# To filter HDAs by user, need to join HDA and History table and then filter histories by user. This is necessary because HDAs do not have
# a user relation.
return query.select_from(
model.HistoryDatasetAssociation.table.join(
model.History.table)).filter(model.History.user == trans.user)
class HistoryListGrid(grids.Grid):
# Custom column types
class ItemCountColumn(grids.GridColumn):
def get_value(self, trans, grid, history):
return str(history.hid_counter - 1)
class HistoryListNameColumn(NameColumn):
def get_link(self, trans, grid, history):
link = None
if not history.deleted:
link = dict(operation="Switch", id=history.id, use_panels=grid.use_panels, async_compatible=True)
return link
class DeletedColumn(grids.DeletedColumn):
def get_value(self, trans, grid, history):
if history == trans.history:
return "<strong>current history</strong>"
if history.purged:
return "deleted permanently"
elif history.deleted:
return "deleted"
return ""
def sort(self, trans, query, ascending, column_name=None):
if ascending:
query = query.order_by(self.model_class.table.c.purged.asc(), self.model_class.update_time.desc())
else:
query = query.order_by(self.model_class.table.c.purged.desc(), self.model_class.update_time.desc())
return query
def build_initial_query(self, trans, **kwargs):
# Override to preload sharing information used when fetching data for grid.
query = super().build_initial_query(trans, **kwargs)
query = query.options(undefer("users_shared_with_count"))
return query
# Grid definition
title = "Saved Histories"
model_class = model.History
default_sort_key = "-update_time"
columns = [
HistoryListNameColumn("Name", key="name", attach_popup=True, filterable="advanced"),
ItemCountColumn("Items", key="item_count", sortable=False),
grids.GridColumn("Datasets", key="datasets_by_state", sortable=False, nowrap=True, delayed=True),
grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation,
filterable="advanced", grid_name="HistoryListGrid"),
grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False, use_shared_with_count=True),
grids.GridColumn("Size on Disk", key="disk_size", sortable=False, delayed=True),
grids.GridColumn("Created", key="create_time", format=time_ago),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
DeletedColumn("Status", key="deleted", filterable="advanced")
]
columns.append(
grids.MulticolFilterColumn(
"search history names and tags",
cols_to_filter=[columns[0], columns[3]],
key="free-text-search", visible=False, filterable="standard")
)
global_actions = [
grids.GridAction("Import history", dict(controller="", action="histories/import"))
]
operations = [
grids.GridOperation("Switch", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=True),
grids.GridOperation("View", allow_multiple=False, url_args=dict(controller="", action="histories/view")),
grids.GridOperation("Share or Publish", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(controller="", action="histories/sharing")),
grids.GridOperation("Change Permissions", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(controller="", action="histories/permissions")),
grids.GridOperation("Copy", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False),
grids.GridOperation("Rename", condition=(lambda item: not item.deleted), url_args=dict(controller="", action="histories/rename"), target="top"),
grids.GridOperation("Delete", condition=(lambda item: not item.deleted), async_compatible=True),
grids.GridOperation("Delete Permanently", condition=(lambda item: not item.purged), confirm="History contents will be removed from disk, this cannot be undone. Continue?", async_compatible=True),
grids.GridOperation("Undelete", condition=(lambda item: item.deleted and not item.purged), async_compatible=True),
]
standard_filters = [
grids.GridColumnFilter("Active", args=dict(deleted=False)),
grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
grids.GridColumnFilter("All", args=dict(deleted='All')),
]
default_filter = dict(name="All", deleted="False", tags="All", sharing="All")
num_rows_per_page = 15
use_paging = True
info_text = "Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted."
def get_current_item(self, trans, **kwargs):
return trans.get_history()
def apply_query_filter(self, trans, query, **kwargs):
return query.filter_by(user=trans.user, importing=False)
