class LibraryDatasetsSelectionGrid(grids.Grid):
available_tracks = None
title = "Add Datasets"
model_class = model.LibraryDatasetDatasetAssociation
default_filter = {"deleted": "False"}
default_sort_key = "-id"
columns = [
grids.GridColumn("Id", key="id"),
grids.TextColumn("Name",
key="name",
model_class=model.LibraryDatasetDatasetAssociation),
grids.TextColumn("Type",
key="extension",
model_class=model.LibraryDatasetDatasetAssociation),
]
columns.append(
grids.MulticolFilterColumn("Search name and filetype",
cols_to_filter=[columns[1], columns[2]],
key="free-text-search",
visible=False,
filterable="standard"))
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class).join(
model.Dataset.table)
def apply_query_filter(self, trans, query, **kwargs):
if self.available_tracks is None:
self.available_tracks = trans.app.datatypes_registry.get_available_tracks(
)
return query.filter(model.LibraryDatasetDatasetAssociation.user == trans.user) \
.filter(model.LibraryDatasetDatasetAssociation.extension.in_(self.available_tracks)) \
.filter(model.Dataset.state == model.Dataset.states.OK) \
.filter(model.LibraryDatasetDatasetAssociation.deleted == false()) \
.filter(model.LibraryDatasetDatasetAssociation.visible == true())
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 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 UserOpenIDGrid(grids.Grid):
use_panels = False
title = "OpenIDs linked to your account"
model_class = model.UserOpenID
template = '/user/openid_manage.mako'
default_filter = {"openid": "All"}
default_sort_key = "-create_time"
columns = [
grids.TextColumn("OpenID URL",
key="openid",
link=(lambda x: dict(action='openid_auth',
login_button="Login",
openid_url=x.openid
if not x.provider else '',
openid_provider=x.provider,
auto_associate=True))),
grids.GridColumn("Created", key="create_time", format=time_ago),
]
operations = [
grids.GridOperation("Delete", async_compatible=True),
]
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query(
self.model_class).filter(self.model_class.user_id == trans.user.id)
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 StoredWorkflowListGrid(grids.Grid):
class StepsColumn(grids.GridColumn):
def get_value(self, trans, grid, workflow):
return len(workflow.latest_workflow.steps)
# Grid definition
use_panels = True
title = "Saved Workflows"
model_class = model.StoredWorkflow
default_filter = {"name": "All", "tags": "All"}
default_sort_key = "-update_time"
columns = [
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),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search", visible=False, filterable="standard"
)
)
operations = [
grids.GridOperation("Edit", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False),
grids.GridOperation("Run", condition=(lambda item: not item.deleted), async_compatible=False),
grids.GridOperation("Copy", condition=(lambda item: not item.deleted), async_compatible=False),
grids.GridOperation("Rename", condition=(lambda item: not item.deleted), async_compatible=False),
grids.GridOperation("Sharing", condition=(lambda item: not item.deleted), async_compatible=False),
grids.GridOperation("Delete", condition=(lambda item: item.deleted), async_compatible=True),
]
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 SharedHistoryListGrid(grids.Grid):
# Custom column types
class DatasetsByStateColumn(grids.GridColumn):
def get_value(self, trans, grid, history):
rval = ''
for state in ('ok', 'running', 'queued', 'error'):
total = sum(1 for d in history.active_datasets if d.state == state)
if total:
rval += f'<div class="count-box state-color-{state}">{total}</div>'
return rval
class SharedByColumn(grids.GridColumn):
def get_value(self, trans, grid, history):
return escape(history.user.email)
# Grid definition
title = "Histories shared with you by others"
model_class = model.History
default_sort_key = "-update_time"
columns = [
grids.GridColumn("Name", key="name", attach_popup=True),
DatasetsByStateColumn("Datasets", sortable=False),
grids.GridColumn("Created", key="create_time", format=time_ago),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
SharedByColumn("Shared by", key="user_id")
]
operations = [
grids.GridOperation("View", allow_multiple=False, url_args=dict(controller="", action="histories/view")),
grids.GridOperation("Copy", allow_multiple=False),
grids.GridOperation("Unshare", allow_multiple=False)
]
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class).join('users_shared_with')
def apply_query_filter(self, trans, query, **kwargs):
return query.filter(model.HistoryUserShareAssociation.user == trans.user)
class HistoryDatasetsSelectionGrid(grids.Grid):
class DbKeyColumn(grids.GridColumn):
def filter(self, trans, user, query, dbkey):
""" Filter by dbkey through a raw SQL b/c metadata is a BLOB. """
dbkey_user, dbkey = decode_dbkey(dbkey)
dbkey = dbkey.replace("'", "\\'")
return query.filter(or_(text("metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey,
"metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey)))
class HistoryColumn(grids.GridColumn):
def get_value(self, trans, grid, hda):
return escape(hda.history.name)
def sort(self, trans, query, ascending, column_name=None):
"""Sort query using this column."""
return grids.GridColumn.sort(self, trans, query, ascending, column_name="history_id")
available_tracks = None
title = "Add Datasets"
model_class = model.HistoryDatasetAssociation
default_filter = {"deleted": "False", "shared": "All"}
default_sort_key = "-hid"
columns = [
grids.GridColumn("Id", key="hid"),
grids.TextColumn("Name", key="name", model_class=model.HistoryDatasetAssociation),
grids.TextColumn("Type", key="extension", model_class=model.HistoryDatasetAssociation),
grids.TextColumn("history_id", key="history_id", model_class=model.HistoryDatasetAssociation, visible=False),
HistoryColumn("History", key="history", visible=True),
DbKeyColumn("Build", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False)
]
columns.append(
grids.MulticolFilterColumn("Search name and filetype", cols_to_filter=[columns[1], columns[2]],
key="free-text-search", visible=False, filterable="standard")
)
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class).join(model.History.table).join(model.Dataset.table)
def apply_query_filter(self, trans, query, **kwargs):
if self.available_tracks is None:
self.available_tracks = trans.app.datatypes_registry.get_available_tracks()
return query.filter(model.History.user == trans.user) \
.filter(model.HistoryDatasetAssociation.extension.in_(self.available_tracks)) \
.filter(model.Dataset.state == model.Dataset.states.OK) \
.filter(model.HistoryDatasetAssociation.deleted == false()) \
.filter(model.HistoryDatasetAssociation.visible == true())
class TracksterSelectionGrid( grids.Grid ):
# Grid definition.
title = "Insert into visualization"
template = "/tracks/add_to_viz.mako"
async_template = "/page/select_items_grid_async.mako"
model_class = model.Visualization
default_sort_key = "-update_time"
use_async = True
use_paging = False
columns = [
grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="standard" ),
grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago )
]
def build_initial_query( self, trans, **kwargs ):
return trans.sa_session.query( self.model_class ).filter( self.model_class.deleted == False )
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter( self.model_class.user_id == trans.user.id )
class TracksterSelectionGrid(grids.Grid):
title = "Insert into visualization"
model_class = model.Visualization
default_sort_key = "-update_time"
use_paging = False
show_item_checkboxes = True
columns = [
grids.TextColumn("Title", key="title", model_class=model.Visualization, filterable="standard"),
grids.TextColumn("Build", key="dbkey", model_class=model.Visualization),
grids.GridColumn("Last Updated", key="update_time", format=time_ago)
]
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class)
def apply_query_filter(self, trans, query, **kwargs):
return query.filter(self.model_class.user_id == trans.user.id) \
.filter(self.model_class.deleted == false()) \
.filter(self.model_class.type == "trackster")
class HistorySelectionGrid( grids.Grid ):
"""
Grid enables user to select a history, which is then used to display
datasets from the history.
"""
title = "Add Track: Select History"
model_class = model.History
template='/tracks/history_select_grid.mako'
default_sort_key = "-update_time"
datasets_action = 'list_history_datasets'
datasets_param = "f-history"
columns = [
NameColumn( "History Name", key="name", filterable="standard" ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago, visible=False ),
DbKeyPlaceholderColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False )
]
num_rows_per_page = 10
use_async = True
use_paging = True
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter_by( user=trans.user, purged=False, deleted=False, importing=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 HistoryDatasetsSelectionGrid( grids.Grid ):
# Grid definition.
available_tracks = None
title = "Add Datasets"
template = "tracks/history_datasets_select_grid.mako"
model_class = model.HistoryDatasetAssociation
default_filter = { "deleted" : "False" , "shared" : "All" }
default_sort_key = "-hid"
use_async = True
use_paging = False
columns = [
grids.GridColumn( "Id", key="hid" ),
grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ),
grids.TextColumn( "Filetype", key="extension", model_class=model.HistoryDatasetAssociation ),
HistoryColumn( "History", key="history", visible=False ),
DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False )
]
columns.append(
grids.MulticolFilterColumn( "Search name and filetype", cols_to_filter=[ columns[1], columns[2] ],
key="free-text-search", visible=False, filterable="standard" )
)
def get_current_item( self, trans, **kwargs ):
"""
Current item for grid is the history being queried. This is a bit
of hack since current_item typically means the current item in the grid.
"""
return model.History.get( trans.security.decode_id( kwargs[ 'f-history' ] ) )
def build_initial_query( self, trans, **kwargs ):
return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table )
def apply_query_filter( self, trans, query, **kwargs ):
if self.available_tracks is None:
self.available_tracks = trans.app.datatypes_registry.get_available_tracks()
return query.filter( model.HistoryDatasetAssociation.extension.in_(self.available_tracks) ) \
.filter( model.Dataset.state == model.Dataset.states.OK ) \
.filter( model.HistoryDatasetAssociation.deleted == False ) \
.filter( model.HistoryDatasetAssociation.visible == True )
class DataTransferGrid(grids.Grid):
# Custom column types
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, sample_dataset):
return escape(sample_dataset.name)
class SizeColumn(grids.TextColumn):
def get_value(self, trans, grid, sample_dataset):
return sample_dataset.size
class StatusColumn(grids.TextColumn):
def get_value(self, trans, grid, sample_dataset):
return sample_dataset.status
class ExternalServiceColumn(grids.TextColumn):
def get_value(self, trans, grid, sample_dataset):
try:
return escape(sample_dataset.external_service.name)
except:
return 'None'
# Grid definition
title = "Sample Datasets"
template = "admin/requests/sample_datasets_grid.mako"
model_class = model.SampleDataset
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = False
columns = [
NameColumn("Name",
link=(lambda item: dict(operation="view", id=item.id)),
attach_popup=True,
filterable="advanced"),
SizeColumn("Size", filterable="advanced"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
ExternalServiceColumn(
'External service',
link=(lambda item: dict(operation="view_external_service",
id=item.external_service.id)),
),
StatusColumn("Transfer Status",
filterable="advanced",
label_id_prefix='datasetTransferStatus-'),
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation(
"Transfer",
allow_multiple=True,
condition=(lambda item: item.status in
[model.SampleDataset.transfer_status.NOT_STARTED])),
grids.GridOperation(
"Rename",
allow_multiple=True,
allow_popup=False,
condition=(lambda item: item.status in
[model.SampleDataset.transfer_status.NOT_STARTED])),
grids.GridOperation(
"Delete",
allow_multiple=True,
condition=(lambda item: item.status in
[model.SampleDataset.transfer_status.NOT_STARTED]))
]
def apply_query_filter(self, trans, query, **kwd):
sample_id = kwd.get('sample_id', None)
if not sample_id:
return query
return query.filter_by(sample_id=trans.security.decode_id(sample_id))
class FormsGrid(grids.Grid):
# Custom column types
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, form):
return escape(form.latest_form.name)
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, form):
return escape(form.latest_form.desc)
class TypeColumn(grids.TextColumn):
def get_value(self, trans, grid, form):
return form.latest_form.type
class StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.deleted:
return "deleted"
return "active"
# Grid definition
title = "Forms"
model_class = model.FormDefinitionCurrent
default_sort_key = "-update_time"
num_rows_per_page = 50
use_paging = True
default_filter = dict(deleted="False")
columns = [
NameColumn("Name",
key="name",
model_class=model.FormDefinition,
link=(lambda item: iff(item.deleted, None, dict(controller="admin", action="form/edit_form", id=item.id))),
attach_popup=True,
filterable="advanced"),
DescriptionColumn("Description",
key="desc",
model_class=model.FormDefinition,
filterable="advanced"),
TypeColumn("Type"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
StatusColumn("Status"),
grids.DeletedColumn("Deleted",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Delete", allow_multiple=True, condition=(lambda item: not item.deleted)),
grids.GridOperation("Undelete", condition=(lambda item: item.deleted)),
]
global_actions = [
grids.GridAction("Create new form", dict(controller="admin", action="form/create_form"))
]
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class).join(model.FormDefinition, self.model_class.latest_form_id == model.FormDefinition.id)
class LibraryListGrid(grids.Grid):
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, library):
return escape(library.name)
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, library):
if library.description:
return escape(library.description)
return ''
class StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, library):
if library.purged:
return "purged"
elif library.deleted:
return "deleted"
return ""
# Grid definition
title = "Data Libraries"
model_class = galaxy.model.Library
template = '/admin/library/grid.mako'
default_sort_key = "name"
columns = [
NameColumn(
"Data library name",
key="name",
link=(lambda library: dict(operation="browse", id=library.id)),
attach_popup=False,
filterable="advanced"),
DescriptionColumn("Data library description",
key="description",
attach_popup=False,
filterable="advanced"),
grids.GridColumn("Created", key="create_time", format=time_ago),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
StatusColumn("Status", attach_popup=False),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn("Deleted",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(
grids.MulticolFilterColumn("search dataset name, info, message, dbkey",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction(
"Create new data library",
dict(controller='library_admin', action='create_library'))
]
standard_filters = [
grids.GridColumnFilter("Active", args=dict(deleted=False)),
grids.GridColumnFilter("Deleted",
args=dict(deleted=True, purged=False)),
grids.GridColumnFilter("Purged", args=dict(purged=True)),
grids.GridColumnFilter("All", args=dict(deleted='All'))
]
default_filter = dict(name="All",
description="All",
deleted="False",
purged="False")
num_rows_per_page = 50
preserve_state = False
use_paging = True
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:
return "deleted"
return ""
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_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
# Grid definition
title = "Saved Datasets"
model_class = model.HistoryDatasetAssociation
template = '/dataset/grid.mako'
default_sort_key = "-create_time"
columns = [
grids.TextColumn(
"Name",
key="name",
model_class=model.HistoryDatasetAssociation,
# Link name to dataset's history.
link=(lambda item: iff(item.history.deleted, None,
dict(operation="switch", id=item.id))),
filterable="advanced"),
HistoryColumn("History",
key="history",
link=(lambda item: iff(
item.history.deleted, None,
dict(operation="switch_history", id=item.id)))),
grids.TagsColumn("Tags",
"tags",
model.HistoryDatasetAssociation,
model.HistoryDatasetAssociationTagAssociation,
filterable="advanced",
grid_name="HistoryDatasetAssocationListGrid"),
StatusColumn("Status", key="deleted", attach_popup=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"))
operations = []
standard_filters = []
default_filter = dict(name="All", deleted="False", tags="All")
preserve_state = False
use_paging = True
num_rows_per_page = 50
def apply_default_filter(self, trans, query, **kwargs):
# This is a somewhat obtuse way to join the History and HDA tables. However, it's necessary
# because the initial query in build_initial_query is specificied on the HDA table (this is reasonable)
# and there's no simple property in the HDA to do the join.
return query.select_from(
model.HistoryDatasetAssociation.table.join(
model.History.table)).filter(model.History.user == trans.user)
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['__route_name__'] = 'saved_visualization'
url_kwargs['visualization_name'] = item.type
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("Build", 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"))
operations = [
grids.GridOperation("Open",
allow_multiple=False,
url_args=get_url_args),
grids.GridOperation("Edit Attributes",
allow_multiple=False,
url_args=dict(controller="",
action='visualizations/edit')),
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),
url_args=dict(controller="",
action="visualizations/sharing")),
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 HistorySelectionGrid( grids.Grid ):
# Custom columns.
class NameColumn( grids.TextColumn ):
def get_value(self, trans, grid, history):
return history.get_display_name()
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_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( model.History.users_shared_with == None )
query = query.filter( model.History.importable == False )
elif column_filter == "shared":
query = query.filter( model.History.users_shared_with != None )
elif column_filter == "importable":
query = query.filter( model.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
# Grid definition.
title = "Saved Histories"
template = "/page/select_histories_grid.mako"
model_class = model.History
default_filter = { "deleted" : "False" , "shared" : "All" }
default_sort_key = "-update_time"
use_async = True
use_paging = True
num_rows_per_page = 10
columns = [
NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ),
grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
# Columns that are valid for filtering but are not visible.
DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ),
SharingColumn( "Shared", key="shared", visible=False, filterable="advanced" ),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[ columns[0], columns[1] ],
key="free-text-search", visible=False, filterable="standard" )
)
def apply_default_filter( self, trans, query, **kwargs ):
return query.filter_by( user=trans.user, purged=False )
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict( deleted="False" )
columns = [
NameColumn( "Name",
key="name",
link=( lambda item: iff( item.deleted, None, dict( operation="view", id=item.id ) ) ),
attach_popup=True,
filterable="advanced" ),
grids.TextColumn( "Description",
key='description',
filterable="advanced" ),
ExternalServiceTypeColumn( "External Service Type" ),
grids.GridColumn( "Last Updated",
key="update_time",
format=time_ago ),
grids.DeletedColumn( "Deleted",
key="deleted",
visible=False,
filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "Search",
cols_to_filter=[ columns[0], columns[1] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
operations = [
grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted ) ),
grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),
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)
class ExternalServiceGrid(grids.Grid):
# Custom column types
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, external_service):
return external_service.name
class ExternalServiceTypeColumn(grids.TextColumn):
def get_value(self, trans, grid, external_service):
try:
return trans.app.external_service_types.all_external_service_types[
external_service.external_service_type_id].name
except KeyError:
return 'Error in loading external_service type: %s' % external_service.external_service_type_id
# Grid definition
title = "External Services"
template = "admin/external_service/grid.mako"
model_class = model.ExternalService
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict(deleted="False")
columns = [
NameColumn("Name",
key="name",
link=(lambda item: iff(item.deleted, None,
dict(operation="view", id=item.id))),
attach_popup=True,
filterable="advanced"),
grids.TextColumn("Description",
key='description',
filterable="advanced"),
ExternalServiceTypeColumn("External Service Type"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
grids.DeletedColumn("Deleted",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Edit",
allow_multiple=False,
condition=(lambda item: not item.deleted)),
grids.GridOperation("Delete",
allow_multiple=True,
condition=(lambda item: not item.deleted)),
grids.GridOperation("Undelete", condition=(lambda item: item.deleted)),
]
global_actions = [
grids.GridAction(
"Reload external service types",
dict(controller='external_service',
action='reload_external_service_types')),
grids.GridAction(
"Create new external service",
dict(controller='external_service',
action='create_external_service'))
]
