class ComponentGrid(grids.Grid):
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, component):
return component.name
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, component):
return component.description
title = "Repository review components"
model_class = model.Component
template = '/webapps/community/repository_review/grid.mako'
default_sort_key = "name"
columns = [
NameColumn("Name",
key="Component.name",
link=(lambda item: dict(operation="edit", id=item.id)),
attach_popup=False),
DescriptionColumn("Description",
key="Component.description",
attach_popup=False)
]
default_filter = {}
global_actions = [
grids.GridAction(
"Add new component",
dict(controller='repository_review',
action='manage_components',
operation='create'))
]
operations = []
standard_filters = []
num_rows_per_page = 50
preserve_state = False
use_paging = True
class PageListGrid( grids.Grid ):
# Grid definition
use_panels = True
title = "Pages"
model_class = model.Page
default_filter = { "published" : "All"}
default_sort_key = "-create_time"
columns = [
grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="standard" ),
PublicURLColumn( "Public URL" ),
grids.GridColumn( "Published", key="published", format=format_bool, filterable="standard" ),
grids.GridColumn( "Created", key="create_time", format=time_ago ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
]
global_actions = [
grids.GridAction( "Add new page", dict( action='create' ) )
]
operations = [
grids.GridOperation( "View", allow_multiple=False, url_args=dict( action='display') ),
grids.GridOperation( "Edit name/id", allow_multiple=False, url_args=dict( action='edit') ),
grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ),
grids.GridOperation( "Delete" ),
grids.GridOperation( "Publish", condition=( lambda item: not item.published ) ),
grids.GridOperation( "Unpublish", condition=( lambda item: item.published ) ),
]
def apply_default_filter( self, trans, query, **kwargs ):
return query.filter_by( user=trans.user, deleted=False )
class FormsGrid( grids.Grid ):
# Custom column types
class NameColumn( grids.TextColumn ):
def get_value(self, trans, grid, form):
return form.latest_form.name
class DescriptionColumn( grids.TextColumn ):
def get_value(self, trans, grid, form):
return form.latest_form.desc
class TypeColumn( grids.TextColumn ):
def get_value(self, trans, grid, form):
return form.latest_form.type
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
# Grid definition
title = "Forms"
template = "admin/forms/grid.mako"
model_class = model.FormDefinitionCurrent
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",
model_class=model.FormDefinition,
link=( lambda item: iff( item.deleted, None, dict( operation="view", id=item.id ) ) ),
attach_popup=True,
filterable="advanced" ),
DescriptionColumn( "Description",
key='desc',
model_class=model.FormDefinition,
filterable="advanced" ),
TypeColumn( "Type" ),
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( "Create new form", dict( controller='forms',
action='new' ) )
]
class AdminRequestsGrid(RequestsGrid):
class UserColumn(grids.TextColumn):
def get_value(self, trans, grid, request):
return escape(request.user.email)
# Grid definition
columns = [col for col in RequestsGrid.columns]
columns.append(UserColumn("User", model_class=model.User, key='username'))
operations = [operation for operation in RequestsGrid.operations]
operations.append(
grids.GridOperation("Edit",
allow_multiple=False,
condition=(lambda item: not item.deleted)))
operations.append(
grids.GridOperation(
"Reject",
allow_multiple=False,
condition=(lambda item: not item.deleted and item.is_submitted)))
operations.append(
grids.GridOperation("Delete",
allow_multiple=True,
condition=(lambda item: not item.deleted)))
operations.append(
grids.GridOperation("Undelete", condition=(lambda item: item.deleted)))
global_actions = [
grids.GridAction(
"Create new request",
dict(controller='requests_common',
action='create_request',
cntrller='requests_admin'))
]
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
# Grid definition
title = "Forms"
template = "admin/forms/grid.mako"
model_class = model.FormDefinitionCurrent
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",
model_class=model.FormDefinition,
link=(lambda item: iff(item.deleted, None, dict(operation="view_latest_form_definition",
id=item.id))),
attach_popup=True,
filterable="advanced"),
DescriptionColumn("Description",
key='desc',
model_class=model.FormDefinition,
filterable="advanced"),
TypeColumn("Type"),
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("Create new form", dict(controller='forms', action='create_form_definition'))
]
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 library.name
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, library ):
if library.description:
return 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 = 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 ManageCategoryGrid( CategoryGrid ):
columns = [ col for col in CategoryGrid.columns ]
# Override the NameColumn to include an Edit link
columns[ 0 ] = CategoryGrid.NameColumn( "Name",
key="Category.name",
link=( lambda item: dict( operation="Edit", id=item.id ) ),
model_class=model.Category,
attach_popup=False )
global_actions = [
grids.GridAction( "Add new category",
dict( controller='admin', action='manage_categories', operation='create' ) )
]
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 )
def browse_requests( self, trans, **kwd ):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "edit":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='edit_basic_request_info',
cntrller='requests',
**kwd ) )
if operation == "add_samples":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='add_samples',
cntrller='requests',
**kwd ) )
if operation == "edit_samples":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='edit_samples',
cntrller='requests',
**kwd ) )
if operation == "view_request":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='view_request',
cntrller='requests',
**kwd ) )
if operation == "delete":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='delete_request',
cntrller='requests',
**kwd ) )
if operation == "undelete":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='undelete_request',
cntrller='requests',
**kwd ) )
if operation == "view_request_history":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='view_request_history',
cntrller='requests',
**kwd ) )
# If there are requests that have been rejected, show a message as a reminder to the user
rejected = 0
for request in trans.sa_session.query( trans.app.model.Request ) \
.filter( trans.app.model.Request.table.c.deleted==False ) \
.filter( trans.app.model.Request.table.c.user_id==trans.user.id ):
if request.is_rejected:
rejected = rejected + 1
if rejected:
status = 'warning'
message = "%d requests (highlighted in red) were rejected. Click on the request name for details." % rejected
kwd[ 'status' ] = status
kwd[ 'message' ] = message
# Allow the user to create a new request only if they have permission to access a request type.
accessible_request_types = trans.app.security_agent.get_accessible_request_types( trans, trans.user )
if accessible_request_types:
self.request_grid.global_actions = [ grids.GridAction( "Create new request", dict( controller='requests_common',
action='create_request',
cntrller='requests' ) ) ]
else:
self.request_grid.global_actions = []
# Render the list view
return self.request_grid( trans, **kwd )
def manage_datasets(self, trans, **kwd):
def handle_error(**kwd):
kwd['status'] = 'error'
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
**kwd))
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
# When this method is called due to a grid operation, the sample ID
# will be in the param 'id'. But when this method is called via a
# redirect from another method, the ID will be in 'sample_id'. So,
# check for 'id' if 'sample_id' is not provided.
sample_id = params.get('sample_id', None)
if sample_id is None:
sample_id = params.get('id', None)
try:
sample = trans.sa_session.query(trans.model.Sample).get(
trans.security.decode_id(sample_id))
except:
return invalid_id_redirect(trans, 'requests_admin', sample_id,
'sample')
if 'operation' in kwd:
operation = kwd['operation'].lower()
sample_dataset_id = params.get('id', None)
if not sample_dataset_id:
message = 'Select at least 1 dataset to %s.' % operation
kwd['message'] = message
del kwd['operation']
handle_error(**kwd)
id_list = util.listify(sample_dataset_id)
selected_sample_datasets = []
for sample_dataset_id in id_list:
try:
sample_dataset = trans.sa_session.query(
trans.model.SampleDataset).get(
trans.security.decode_id(sample_dataset_id))
except:
return invalid_id_redirect(trans, 'requests_admin',
sample_dataset_id,
'sample dataset')
selected_sample_datasets.append(sample_dataset)
if operation == "view":
return trans.fill_template(
'/admin/requests/view_sample_dataset.mako',
cntrller='requests_admin',
sample_dataset=selected_sample_datasets[0])
elif operation == "delete":
not_deleted = []
for sample_dataset in selected_sample_datasets:
# Make sure the dataset has been transferred before deleting it.
if sample_dataset in sample_dataset.sample.untransferred_dataset_files:
# Save the sample dataset
sample = sample_dataset.sample
trans.sa_session.delete(sample_dataset)
trans.sa_session.flush()
else:
not_deleted.append(sample_dataset.name)
message = '%i datasets have been deleted.' % (len(id_list) -
len(not_deleted))
if not_deleted:
status = 'warning'
message = message + ' %s could not be deleted because their transfer status is not "Not Started". ' % str(
not_deleted)
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id(sample.id),
status=status,
message=message))
elif operation == "rename":
# If one of the selected sample datasets is in the NOT_STARTED state,
# then display an error message. A NOT_STARTED state implies the dataset
# has not yet been transferred.
no_datasets_transferred = True
for selected_sample_dataset in selected_sample_datasets:
if selected_sample_dataset in selected_sample_dataset.sample.untransferred_dataset_files:
no_datasets_transferred = False
break
if no_datasets_transferred:
status = 'error'
message = 'A dataset can be renamed only if it has been transferred.'
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id(
selected_sample_datasets[0].sample.id),
status=status,
message=message))
return trans.fill_template(
'/admin/requests/rename_datasets.mako',
sample=selected_sample_datasets[0].sample,
id_list=id_list)
elif operation == "transfer":
self.initiate_data_transfer(
trans,
trans.security.encode_id(
selected_sample_datasets[0].sample.id),
sample_datasets=selected_sample_datasets)
elif operation == "view_external_service":
return trans.response.send_redirect(
web.url_for(controller='external_service',
action='view_external_service',
**kwd))
# Render the grid view
request_id = trans.security.encode_id(sample.request.id)
library_id = trans.security.encode_id(sample.library.id)
self.datatx_grid.title = 'Manage "%s" datasets' % sample.name
self.datatx_grid.global_actions = [
grids.GridAction(
"Browse target data library",
dict(controller='library_common',
action='browse_library',
cntrller='library_admin',
id=library_id)),
grids.GridAction(
"Browse this request",
dict(controller='requests_common',
action='view_request',
cntrller='requests_admin',
id=request_id))
]
return self.datatx_grid(trans, **kwd)
class InstalledRepositoryGrid(grids.Grid):
class ToolShedStatusColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
if tool_shed_repository.tool_shed_status:
tool_shed_status_str = ''
if tool_shed_repository.is_deprecated_in_tool_shed:
tool_shed_status_str += generate_deprecated_repository_img_str(
include_mouse_over=True)
if tool_shed_repository.is_latest_installable_revision:
tool_shed_status_str += generate_latest_revision_img_str(
include_mouse_over=True)
if tool_shed_repository.revision_update_available:
tool_shed_status_str += generate_revision_updates_img_str(
include_mouse_over=True)
if tool_shed_repository.upgrade_available:
tool_shed_status_str += generate_revision_upgrades_img_str(
include_mouse_over=True)
if tool_shed_repository.includes_workflows:
tool_shed_status_str += generate_includes_workflows_img_str(
include_mouse_over=True)
else:
tool_shed_status_str = generate_unknown_img_str(
include_mouse_over=True)
return tool_shed_status_str
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.name)
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return util.unicodify(tool_shed_repository.description)
class OwnerColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.owner)
class RevisionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.changeset_revision)
class StatusColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return suc.get_tool_shed_repository_status_label(
trans.app, tool_shed_repository)
class ToolShedColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.tool_shed
class DeletedColumn(grids.DeletedColumn):
def get_accepted_filters(self):
""" Returns a list of accepted filters for this column. """
accepted_filter_labels_and_vals = {
"Active": "False",
"Deactivated or uninstalled": "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 = "Installed tool shed repositories"
model_class = tool_shed_install.ToolShedRepository
template = '/admin/tool_shed_repository/grid.mako'
default_sort_key = "name"
columns = [
ToolShedStatusColumn(label=""),
NameColumn(
label="Name",
key="name",
link=(lambda item: iff(
item.status in [
tool_shed_install.ToolShedRepository.installation_status.
CLONING
], None, dict(operation="manage_repository", id=item.id))),
attach_popup=True),
DescriptionColumn(label="Description"),
OwnerColumn(label="Owner"),
RevisionColumn(label="Revision"),
StatusColumn(label="Installation Status", filterable="advanced"),
ToolShedColumn(label="Tool shed"),
# Columns that are valid for filtering but are not visible.
DeletedColumn(label="Status",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction(
label="Update tool shed status",
url_args=dict(
controller='admin_toolshed',
action='update_tool_shed_status_for_installed_repository',
all_installed_repositories=True),
inbound=False)
]
operations = [ grids.GridOperation( label="Update tool shed status",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='update tool shed status' ) ),
grids.GridOperation( label="Get updates",
condition=( lambda item: \
not item.deleted and \
item.revision_update_available and \
item.status not in \
[ tool_shed_install.ToolShedRepository.installation_status.ERROR,
tool_shed_install.ToolShedRepository.installation_status.NEW ] ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='get updates' ) ),
grids.GridOperation( label="Install latest revision",
condition=( lambda item: item.upgrade_available ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='install latest revision' ) ),
grids.GridOperation( label="Install",
condition=( lambda item: \
not item.deleted and \
item.status == tool_shed_install.ToolShedRepository.installation_status.NEW ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='manage_repository',
operation='install' ) ),
grids.GridOperation( label="Deactivate or uninstall",
condition=( lambda item: \
not item.deleted and \
item.status != tool_shed_install.ToolShedRepository.installation_status.NEW ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='deactivate or uninstall' ) ),
grids.GridOperation( label="Reset to install",
condition=( lambda item: \
( item.status == tool_shed_install.ToolShedRepository.installation_status.ERROR ) ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='reset to install' ) ),
grids.GridOperation( label="Activate or reinstall",
condition=( lambda item: item.deleted ),
allow_multiple=False,
target=None,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='activate or reinstall' ) ),
grids.GridOperation( label="Purge",
condition=( lambda item: item.is_new ),
allow_multiple=False,
target=None,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='purge' ) ) ]
standard_filters = []
default_filter = dict(deleted="False")
num_rows_per_page = 50
preserve_state = False
use_paging = False
def build_initial_query(self, trans, **kwd):
return trans.install_model.context.query( self.model_class ) \
.order_by( self.model_class.table.c.tool_shed,
self.model_class.table.c.name,
self.model_class.table.c.owner,
self.model_class.table.c.ctx_rev )
@property
def legend(self):
legend_str = '%s Updates are available in the Tool Shed for this revision<br/>' % generate_revision_updates_img_str(
)
legend_str += '%s A newer installable revision is available for this repository<br/>' % generate_revision_upgrades_img_str(
)
legend_str += '%s This is the latest installable revision of this repository<br/>' % generate_latest_revision_img_str(
)
legend_str += '%s This repository is deprecated in the Tool Shed<br/>' % generate_deprecated_repository_img_str(
)
legend_str += '%s This repository contains exported workflows<br/>' % generate_includes_workflows_img_str(
)
legend_str += '%s Unable to get information from the Tool Shed<br/>' % generate_unknown_img_str(
)
return legend_str
class QuotaListGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, quota ):
return escape(quota.name)
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, quota ):
if quota.description:
return escape(quota.description)
return ''
class AmountColumn( grids.TextColumn ):
def get_value( self, trans, grid, quota ):
return quota.operation + quota.display_amount
class StatusColumn( grids.GridColumn ):
def get_value( self, trans, grid, quota ):
if quota.deleted:
return "deleted"
elif quota.default:
return "<strong>default for %s users</strong>" % quota.default[0].type
return ""
class UsersColumn( grids.GridColumn ):
def get_value( self, trans, grid, quota ):
if quota.users:
return len( quota.users )
return 0
class GroupsColumn( grids.GridColumn ):
def get_value( self, trans, grid, quota ):
if quota.groups:
return len( quota.groups )
return 0
# Grid definition
title = "Quotas"
model_class = model.Quota
template = '/admin/quota/grid.mako'
default_sort_key = "name"
columns = [
NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="Change amount", id=item.id, webapp="galaxy" ) ),
model_class=model.Quota,
attach_popup=True,
filterable="advanced" ),
DescriptionColumn( "Description",
key='description',
model_class=model.Quota,
attach_popup=False,
filterable="advanced" ),
AmountColumn( "Amount",
key='amount',
model_class=model.Quota,
attach_popup=False,
filterable="advanced" ),
UsersColumn( "Users", attach_popup=False ),
GroupsColumn( "Groups", attach_popup=False ),
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",
cols_to_filter=[ columns[0], columns[1], columns[2] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
global_actions = [
grids.GridAction( "Add new quota", dict( controller='admin', action='quotas', operation='create' ) )
]
operations = [ grids.GridOperation( "Rename",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="rename_quota" ) ),
grids.GridOperation( "Change amount",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="edit_quota" ) ),
grids.GridOperation( "Manage users and groups",
condition=( lambda item: not item.default and not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="manage_users_and_groups_for_quota" ) ),
grids.GridOperation( "Set as different type of default",
condition=( lambda item: item.default ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="set_quota_default" ) ),
grids.GridOperation( "Set as default",
condition=( lambda item: not item.default and not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="set_quota_default" ) ),
grids.GridOperation( "Unset as default",
condition=( lambda item: item.default and not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="unset_quota_default" ) ),
grids.GridOperation( "Delete",
condition=( lambda item: not item.deleted and not item.default ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="mark_quota_deleted" ) ),
grids.GridOperation( "Undelete",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="undelete_quota" ) ),
grids.GridOperation( "Purge",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="purge_quota" ) ) ]
standard_filters = [
grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
]
num_rows_per_page = 50
preserve_state = False
use_paging = True
class UserListGrid( grids.Grid ):
class EmailColumn( grids.TextColumn ):
def get_value( self, trans, grid, user ):
return escape(user.email)
class UserNameColumn( grids.TextColumn ):
def get_value( self, trans, grid, user ):
if user.username:
return escape(user.username)
return 'not set'
class StatusColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.purged:
return "purged"
elif user.deleted:
return "deleted"
return ""
class GroupsColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.groups:
return len( user.groups )
return 0
class RolesColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.roles:
return len( user.roles )
return 0
class ExternalColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.external:
return 'yes'
return 'no'
class LastLoginColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.galaxy_sessions:
return self.format( user.galaxy_sessions[ 0 ].update_time )
return 'never'
class TimeCreatedColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
return user.create_time.strftime('%x')
class ActivatedColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.active:
return 'Y'
else:
return 'N'
# Grid definition
title = "Users"
model_class = model.User
template = '/admin/user/grid.mako'
default_sort_key = "email"
columns = [
EmailColumn( "Email",
key="email",
model_class=model.User,
link=( lambda item: dict( operation="information", id=item.id, webapp="galaxy" ) ),
attach_popup=True,
filterable="advanced",
target="top" ),
UserNameColumn( "User Name",
key="username",
model_class=model.User,
attach_popup=False,
filterable="advanced" ),
GroupsColumn( "Groups", attach_popup=False ),
RolesColumn( "Roles", attach_popup=False ),
ExternalColumn( "External", attach_popup=False ),
LastLoginColumn( "Last Login", format=time_ago ),
StatusColumn( "Status", attach_popup=False ),
TimeCreatedColumn( "Created", attach_popup=False ),
ActivatedColumn( "Activated", 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",
cols_to_filter=[ columns[0], columns[1] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
global_actions = [
grids.GridAction( "Create new user", dict( controller='admin', action='users', operation='create', webapp="galaxy" ) )
]
operations = [
grids.GridOperation( "Manage Roles and Groups",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="manage_roles_and_groups_for_user" ) ),
grids.GridOperation( "Reset Password",
condition=( lambda item: not item.deleted ),
allow_multiple=True,
allow_popup=False,
url_args=dict( webapp="galaxy", action="reset_user_password" ) ),
grids.GridOperation( "Recalculate Disk Usage",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="recalculate_user_disk_usage" ) )
]
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' ) )
]
num_rows_per_page = 50
preserve_state = False
use_paging = True
def get_current_item( self, trans, **kwargs ):
return trans.user
class GroupListGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, group ):
return escape(group.name)
class StatusColumn( grids.GridColumn ):
def get_value( self, trans, grid, group ):
if group.deleted:
return "deleted"
return ""
class RolesColumn( grids.GridColumn ):
def get_value( self, trans, grid, group ):
if group.roles:
return len( group.roles )
return 0
class UsersColumn( grids.GridColumn ):
def get_value( self, trans, grid, group ):
if group.members:
return len( group.members )
return 0
# Grid definition
title = "Groups"
model_class = model.Group
template = '/admin/dataset_security/group/grid.mako'
default_sort_key = "name"
columns = [
NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="Manage users and roles", id=item.id, webapp="galaxy" ) ),
model_class=model.Group,
attach_popup=True,
filterable="advanced" ),
UsersColumn( "Users", attach_popup=False ),
RolesColumn( "Roles", attach_popup=False ),
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",
cols_to_filter=[ columns[0], columns[1], columns[2] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
global_actions = [
grids.GridAction( "Add new group", dict( controller='admin', action='groups', operation='create', webapp="galaxy" ) )
]
operations = [ grids.GridOperation( "Rename",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="rename_group" ) ),
grids.GridOperation( "Delete",
condition=( lambda item: not item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="mark_group_deleted" ) ),
grids.GridOperation( "Undelete",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="undelete_group" ) ),
grids.GridOperation( "Purge",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="purge_group" ) ) ]
standard_filters = [
grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
]
num_rows_per_page = 50
preserve_state = False
use_paging = True
class RoleListGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, role ):
return escape(role.name)
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, role ):
if role.description:
return escape(role.description)
return ''
class TypeColumn( grids.TextColumn ):
def get_value( self, trans, grid, role ):
return role.type
class StatusColumn( grids.GridColumn ):
def get_value( self, trans, grid, role ):
if role.deleted:
return "deleted"
return ""
class GroupsColumn( grids.GridColumn ):
def get_value( self, trans, grid, role ):
if role.groups:
return len( role.groups )
return 0
class UsersColumn( grids.GridColumn ):
def get_value( self, trans, grid, role ):
if role.users:
return len( role.users )
return 0
# Grid definition
title = "Roles"
model_class = model.Role
template = '/admin/dataset_security/role/grid.mako'
default_sort_key = "name"
columns = [
NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) ),
model_class=model.Role,
attach_popup=True,
filterable="advanced" ),
DescriptionColumn( "Description",
key='description',
model_class=model.Role,
attach_popup=False,
filterable="advanced" ),
TypeColumn( "Type",
key='type',
model_class=model.Role,
attach_popup=False,
filterable="advanced" ),
GroupsColumn( "Groups", attach_popup=False ),
UsersColumn( "Users", attach_popup=False ),
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",
cols_to_filter=[ columns[0], columns[1], columns[2] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
global_actions = [
grids.GridAction( "Add new role", dict( controller='admin', action='roles', operation='create' ) )
]
operations = [ grids.GridOperation( "Edit",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="rename_role" ) ),
grids.GridOperation( "Delete",
condition=( lambda item: not item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="mark_role_deleted" ) ),
grids.GridOperation( "Undelete",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="undelete_role" ) ),
grids.GridOperation( "Purge",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="purge_role" ) ) ]
standard_filters = [
grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
]
num_rows_per_page = 50
preserve_state = False
use_paging = True
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter( model.Role.type != model.Role.types.PRIVATE )
class UserGrid(grids.Grid):
class UserLoginColumn(grids.TextColumn):
def get_value(self, trans, grid, user):
return escape(user.email)
class UserNameColumn(grids.TextColumn):
def get_value(self, trans, grid, user):
if user.username:
return escape(user.username)
return 'not set'
class GroupsColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.groups:
return len(user.groups)
return 0
class RolesColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.roles:
return len(user.roles)
return 0
class ExternalColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.external:
return 'yes'
return 'no'
class LastLoginColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.galaxy_sessions:
return self.format(user.galaxy_sessions[0].update_time)
return 'never'
class StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.purged:
return "purged"
elif user.deleted:
return "deleted"
return ""
class EmailColumn(grids.GridColumn):
def filter(self, trans, user, query, column_filter):
if column_filter == 'All':
return query
return query.filter(
and_(model.Tool.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == column_filter))
title = "Users"
model_class = model.User
default_sort_key = "email"
columns = [
UserLoginColumn(
"Email",
key="email",
link=(lambda item: dict(operation="information", id=item.id)),
attach_popup=True,
filterable="advanced"),
UserNameColumn("User Name",
key="username",
attach_popup=False,
filterable="advanced"),
GroupsColumn("Groups", attach_popup=False),
RolesColumn("Roles", attach_popup=False),
ExternalColumn("External", attach_popup=False),
LastLoginColumn("Last Login", format=time_ago),
StatusColumn("Status", attach_popup=False),
# Columns that are valid for filtering but are not visible.
EmailColumn("Email", key="email", visible=False)
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction(
"Create new user",
dict(controller='admin', action='users', operation='create'))
]
operations = [
grids.GridOperation(
"Manage Roles and Groups",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(action="manage_roles_and_groups_for_user")),
grids.GridOperation("Reset Password",
condition=(lambda item: not item.deleted),
allow_multiple=True,
allow_popup=False,
url_args=dict(action="reset_user_password"))
]
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'))
]
use_paging = False
def get_current_item(self, trans, **kwargs):
return trans.user
class RoleGrid(grids.Grid):
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, role):
return escape(str(role.name))
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, role):
if role.description:
return str(role.description)
return ''
class TypeColumn(grids.TextColumn):
def get_value(self, trans, grid, role):
return str(role.type)
class StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.deleted:
return "deleted"
return ""
class GroupsColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.groups:
return len(role.groups)
return 0
class RepositoriesColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.repositories:
return len(role.repositories)
return 0
class UsersColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.users:
return len(role.users)
return 0
title = "Roles"
model_class = model.Role
default_sort_key = "name"
columns = [
NameColumn("Name",
key="name",
link=(lambda item: dict(
operation="Manage role associations", id=item.id)),
attach_popup=True,
filterable="advanced"),
DescriptionColumn("Description",
key='description',
attach_popup=False,
filterable="advanced"),
GroupsColumn("Groups", attach_popup=False),
RepositoriesColumn("Repositories", attach_popup=False),
UsersColumn("Users", 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",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction(
"Add new role",
dict(controller='admin', action='roles', operation='create'))
]
# Repository admin roles currently do not have any operations since they are managed automatically based
# on other events. For example, if a repository is renamed, its associated admin role is automatically
# renamed accordingly and if a repository is deleted its associated admin role is automatically deleted.
operations = [
grids.GridOperation("Rename",
condition=(lambda item: not item.deleted and
not item.is_repository_admin_role),
allow_multiple=False,
url_args=dict(action="rename_role")),
grids.GridOperation("Delete",
condition=(lambda item: not item.deleted and
not item.is_repository_admin_role),
allow_multiple=True,
url_args=dict(action="mark_role_deleted")),
grids.GridOperation("Undelete",
condition=(lambda item: item.deleted and not item.
is_repository_admin_role),
allow_multiple=True,
url_args=dict(action="undelete_role")),
grids.GridOperation("Purge",
condition=(lambda item: item.deleted and not item.
is_repository_admin_role),
allow_multiple=True,
url_args=dict(action="purge_role"))
]
standard_filters = [
grids.GridColumnFilter("Active", args=dict(deleted=False)),
grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
grids.GridColumnFilter("All", args=dict(deleted='All'))
]
use_paging = False
def apply_query_filter(self, trans, query, **kwd):
return query.filter(model.Role.type != model.Role.types.PRIVATE)
class RequestTypeGrid(grids.Grid):
# Custom column types
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, request_type):
return escape(request_type.name)
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, request_type):
return escape(request_type.desc)
class RequestFormColumn(grids.TextColumn):
def get_value(self, trans, grid, request_type):
return escape(request_type.request_form.name)
class SampleFormColumn(grids.TextColumn):
def get_value(self, trans, grid, request_type):
return escape(request_type.sample_form.name)
class ExternalServiceColumn(grids.IntegerColumn):
def get_value(self, trans, grid, request_type):
if request_type.external_services:
return len(request_type.external_services)
return 'No external service assigned'
# Grid definition
title = "Request Types"
template = "admin/request_type/grid.mako"
model_class = model.RequestType
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_request_type", id=item.id))),
attach_popup=True,
filterable="advanced"),
DescriptionColumn("Description", key='desc', filterable="advanced"),
RequestFormColumn("Request Form",
link=(lambda item: iff(
item.deleted, None,
dict(operation="view_form_definition",
id=item.request_form.id)))),
SampleFormColumn(
"Sample Form",
link=(lambda item: iff(
item.deleted, None,
dict(operation="view_form_definition", id=item.sample_form.id))
)),
ExternalServiceColumn("External Services"),
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 request type",
allow_multiple=False,
condition=(lambda item: not item.deleted)),
grids.GridOperation("Edit permissions",
allow_multiple=False,
condition=(lambda item: not item.deleted)),
grids.GridOperation(
"Use run details template",
allow_multiple=False,
condition=(
lambda item: not item.deleted and not item.run_details)),
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 request type",
dict(controller='request_type', action='create_request_type'))
]
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'))
]
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' ) )
]
class ExternalService( BaseUIController, UsesFormDefinitionsMixin ):
external_service_grid = ExternalServiceGrid()
@web.expose
@web.require_admin
def browse_external_services( self, trans, **kwd ):
if 'operation' in kwd:
operation = kwd['operation'].lower()
obj_id = kwd.get( 'id', None )
if operation == "view":
return self.view_external_service( trans, **kwd )
elif operation == "edit":