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Move the sequencer interface ( RequestType ) components from the requests_admin controller to a new sequencer controller.
This commit is contained in:
Greg Von Kuster
@@ -29,64 +29,6 @@ class AdminRequestsGrid( RequestsGrid ):
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cntrller='requests_admin' ) )
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]
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class RequestTypeGrid( grids.Grid ):
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# Custom column types
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class NameColumn( grids.TextColumn ):
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def get_value(self, trans, grid, request_type):
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return request_type.name
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class DescriptionColumn( grids.TextColumn ):
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def get_value(self, trans, grid, request_type):
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return request_type.desc
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class RequestFormColumn( grids.TextColumn ):
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def get_value(self, trans, grid, request_type):
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return request_type.request_form.name
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class SampleFormColumn( grids.TextColumn ):
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def get_value(self, trans, grid, request_type):
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return request_type.sample_form.name
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# Grid definition
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webapp = "galaxy"
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title = "Sequencer Configurations"
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template = "admin/requests/grid.mako"
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model_class = model.RequestType
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default_sort_key = "-create_time"
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num_rows_per_page = 50
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preserve_state = True
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use_paging = True
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default_filter = dict( deleted="False" )
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columns = [
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NameColumn( "Name",
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key="name",
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link=( lambda item: iff( item.deleted, None, dict( operation="view_request_type", id=item.id ) ) ),
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attach_popup=True,
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filterable="advanced" ),
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DescriptionColumn( "Description",
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key='desc',
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filterable="advanced" ),
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RequestFormColumn( "Request Form",
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link=( lambda item: iff( item.deleted, None, dict( operation="view_form_definition", id=item.request_form.id ) ) ) ),
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SampleFormColumn( "Sample Form",
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link=( lambda item: iff( item.deleted, None, dict( operation="view_form_definition", id=item.sample_form.id ) ) ) ),
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grids.DeletedColumn( "Deleted",
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key="deleted",
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visible=False,
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filterable="advanced" )
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]
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columns.append( grids.MulticolFilterColumn( "Search",
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cols_to_filter=[ columns[0], columns[1] ],
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key="free-text-search",
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visible=False,
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filterable="standard" ) )
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operations = [
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grids.GridOperation( "Edit configuration", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
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grids.GridOperation( "Edit permissions", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
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grids.GridOperation( "Delete configuration", allow_multiple=True, condition=( lambda item: not item.deleted ) ),
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grids.GridOperation( "Undelete configuration", condition=( lambda item: item.deleted ) ),
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]
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global_actions = [
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grids.GridAction( "Create new configuration", dict( controller='requests_admin', action='create_request_type' ) )
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]
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class DataTransferGrid( grids.Grid ):
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# Custom column types
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class NameColumn( grids.TextColumn ):
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@@ -145,7 +87,6 @@ class DataTransferGrid( grids.Grid ):
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class RequestsAdmin( BaseController, UsesFormDefinitionWidgets ):
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request_grid = AdminRequestsGrid()
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requesttype_grid = RequestTypeGrid()
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datatx_grid = DataTransferGrid()
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@web.expose
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@@ -181,7 +122,9 @@ class RequestsAdmin( BaseController, UsesFormDefinitionWidgets ):
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if operation == "reject":
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return self.reject_request( trans, **kwd )
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if operation == "view_type":
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return self.view_request_type( trans, **kwd )
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return trans.response.send_redirect( web.url_for( controller='sequencer',
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action='view_request_type',
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**kwd ) )
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if operation == "delete":
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='delete_request',
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@@ -521,11 +464,6 @@ class RequestsAdmin( BaseController, UsesFormDefinitionWidgets ):
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request_id=trans.security.encode_id( request.id ),
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status=status,
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message=message ) )
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def __check_path( self, a_path ):
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# Return a valid folder_path
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if a_path and not a_path.endswith( os.sep ):
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a_path += os.sep
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return a_path
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def __save_sample_datasets( self, trans, sample, selected_datasets_to_transfer ):
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sample_dataset_file_names = []
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if selected_datasets_to_transfer:
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@@ -734,253 +672,6 @@ class RequestsAdmin( BaseController, UsesFormDefinitionWidgets ):
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trans.sa_session.add( sample_dataset )
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trans.sa_session.flush()
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return 200, 'Done'
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# Request Type Stuff
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@web.expose
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@web.require_admin
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def browse_request_types( self, trans, **kwd ):
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if 'operation' in kwd:
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operation = kwd['operation'].lower()
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obj_id = kwd.get( 'id', None )
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if operation == "view_form_definition":
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return self.view_form_definition( trans, **kwd )
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elif operation == "view_request_type":
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return self.view_request_type( trans, **kwd )
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elif operation == "edit configuration":
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return self.edit_request_type( trans, **kwd )
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elif operation == "delete configuration":
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return self.delete_request_type( trans, **kwd )
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elif operation == "undelete configuration":
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return self.undelete_request_type( trans, **kwd )
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elif operation == "edit permissions":
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return self.request_type_permissions( trans, **kwd )
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# Render the grid view
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return self.requesttype_grid( trans, **kwd )
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@web.expose
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@web.require_admin
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def create_request_type( self, trans, **kwd ):
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params = util.Params( kwd )
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message = util.restore_text( params.get( 'message', '' ) )
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status = params.get( 'status', 'done' )
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rt_info_widgets, rt_states_widgets = self.__get_populated_request_type_widgets( trans, **kwd )
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rename_dataset_select_field = self.__build_rename_dataset_select_field( trans )
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if params.get( 'add_state_button', False ):
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# Append a new tuple to the set of states which will result in
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# empty state name and description TextFields being displayed on
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# the form.
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rt_states_widgets.append( ( "", "" ) )
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elif params.get( 'remove_state_button', False ):
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index = int( params.get( 'remove_state_button', '' ).split(" ")[2] )
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del rt_states_widgets[ index-1 ]
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elif params.get( 'create_request_type_button', False ):
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self.__save_request_type( trans, **kwd )
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message = 'The sequencer configuration has been created.'
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='browse_request_types',
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message=message,
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status=status ) )
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return trans.fill_template( '/admin/request_type/create_request_type.mako',
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rt_info_widgets=rt_info_widgets,
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rt_states_widgets=rt_states_widgets,
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rename_dataset_select_field=rename_dataset_select_field,
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message=message,
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status=status )
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@web.expose
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@web.require_admin
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def view_request_type( self, trans, **kwd ):
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request_type_id = kwd.get( 'id', None )
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try:
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request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
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except:
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return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='browse_request_types' )
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rename_dataset_select_field = self.__build_rename_dataset_select_field( trans, request_type )
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return trans.fill_template( '/admin/request_type/view_request_type.mako',
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request_type=request_type,
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rename_dataset_select_field=rename_dataset_select_field )
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@web.expose
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@web.require_admin
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def edit_request_type( self, trans, **kwd ):
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## TODO: RC: add the ability to edit the name and description of exisitng states
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params = util.Params( kwd )
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message = util.restore_text( params.get( 'message', '' ) )
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status = params.get( 'status', 'done' )
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request_type_id = params.get( 'id', None )
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try:
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request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
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except:
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return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='browse_request_types' )
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rename_dataset_select_field = self.__build_rename_dataset_select_field( trans )
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if params.get( 'add_state_button', False ):
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# Append a new tuple to the set of states which will result in
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# empty state name and description TextFields being displayed on
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# the form.
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rt_states_widgets.append( ( "", "" ) )
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elif params.get( 'remove_state_button', False ):
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index = int( params.get( 'remove_state_button', '' ).split(" ")[2] )
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del rt_states_widgets[ index-1 ]
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if params.get( 'edit_request_type_button', False ):
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self.__save_request_type( trans, **kwd )
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message = 'Changes made to sequencer configuration (%s) have been saved' % request_type.name
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return trans.fill_template( '/admin/request_type/edit_request_type.mako',
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request_type=request_type,
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rename_dataset_select_field=rename_dataset_select_field,
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message=message,
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status=status )
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def __save_request_type( self, trans, **kwd ):
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# Here we save a newly created request_type or save changed
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# attributes of an existing request_type.
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params = util.Params( kwd )
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request_type_id = params.get( 'id', None )
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name = util.restore_text( params.get( 'name', '' ) )
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desc = util.restore_text( params.get( 'desc', '' ) )
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request_form_id = params.get( 'request_form_id', None )
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request_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( request_form_id ) )
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sample_form_id = params.get( 'sample_form_id', None )
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sample_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( sample_form_id ) )
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data_dir = util.restore_text( params.get( 'data_dir', '' ) )
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data_dir = self.__check_path( data_dir )
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# Data transfer info - Make sure password is retrieved from kwd rather than Params
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# since Params may have munged the characters.
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datatx_info = dict( host=util.restore_text( params.get( 'host', '' ) ),
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username=util.restore_text( params.get( 'username', '' ) ),
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password=kwd.get( 'password', '' ),
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data_dir=data_dir,
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rename_dataset=util.restore_text( params.get( 'rename_dataset', '' ) ) )
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if request_type_id:
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# We're saving changed attributes of an existing request_type.
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request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
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request_type.name = name
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request_type.desc = desc
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request_type.request_form = request_form
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request_type.sample_form = sample_form
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request_type.datatx_info = datatx_info
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else:
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# We're saving a newly created request_type
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request_type = trans.model.RequestType( name=name,
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desc=desc,
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request_form=request_form,
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sample_form=sample_form,
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datatx_info=datatx_info )
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trans.sa_session.add( request_type )
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trans.sa_session.flush()
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i = 0
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while True:
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if kwd.has_key( 'state_name_%i' % i ):
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name = util.restore_text( params.get( 'state_name_%i' % i, None ) )
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desc = util.restore_text( params.get( 'state_desc_%i' % i, None ) )
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ss = trans.model.SampleState( name, desc, request_type )
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trans.sa_session.add( ss )
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trans.sa_session.flush()
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i += 1
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else:
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break
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def __get_populated_request_type_widgets( self, trans, **kwd ):
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request_form_definitions = self.get_all_forms( trans,
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filter=dict( deleted=False ),
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form_type=trans.model.FormDefinition.types.REQUEST )
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sample_form_definitions = self.get_all_forms( trans,
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filter=dict( deleted=False ),
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form_type=trans.model.FormDefinition.types.SAMPLE )
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if not request_form_definitions or not sample_form_definitions:
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return [],[]
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params = util.Params( kwd )
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request_form_id = params.get( 'request_form_id', 'none' )
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sample_form_id = params.get( 'sample_form_id', 'none' )
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request_form_id_select_field = build_select_field( trans,
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objs=request_form_definitions,
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label_attr='name',
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select_field_name='request_form_id',
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selected_value=request_form_id,
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refresh_on_change=False )
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sample_form_id_select_field = build_select_field( trans,
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objs=sample_form_definitions,
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label_attr='name',
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select_field_name='sample_form_id',
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selected_value=sample_form_id,
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refresh_on_change=False )
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rt_info_widgets = [ dict( label='Name',
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widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ),
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dict( label='Description',
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widget=TextField( 'desc', 40, util.restore_text( params.get( 'desc', '' ) ) ) ),
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dict( label='Request form',
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widget=request_form_id_select_field ),
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dict( label='Sample form',
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widget=sample_form_id_select_field ) ]
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# Sample states defined for this sequencer configuration
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rt_states = []
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i=0
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while True:
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if kwd.has_key( 'state_name_%i' % i ):
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rt_states.append( ( params.get( 'state_name_%i' % i, '' ),
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params.get( 'state_desc_%i' % i, '' ) ) )
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i += 1
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else:
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break
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return rt_info_widgets, rt_states
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@web.expose
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@web.require_admin
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def delete_request_type( self, trans, **kwd ):
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rt_id = kwd.get( 'id', '' )
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rt_id_list = util.listify( rt_id )
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for rt_id in rt_id_list:
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try:
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request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( rt_id ) )
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except:
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return invalid_id_redirect( trans, 'requests_admin', rt_id, action='browse_request_types' )
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request_type.deleted = True
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trans.sa_session.add( request_type )
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trans.sa_session.flush()
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status = 'done'
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message = '%i sequencer configurations has been deleted' % len( rt_id_list )
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='browse_request_types',
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message=message,
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status='done' ) )
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@web.expose
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@web.require_admin
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def undelete_request_type( self, trans, **kwd ):
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rt_id = kwd.get( 'id', '' )
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rt_id_list = util.listify( rt_id )
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for rt_id in rt_id_list:
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try:
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request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( rt_id ) )
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except:
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return invalid_id_redirect( trans, 'requests_admin', rt_id, action='browse_request_types' )
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request_type.deleted = False
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trans.sa_session.add( request_type )
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trans.sa_session.flush()
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status = 'done'
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message = '%i sequencer configurations have been undeleted' % len( rt_id_list )
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='browse_request_types',
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message=message,
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status=status ) )
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@web.expose
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@web.require_admin
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def request_type_permissions( self, trans, **kwd ):
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params = util.Params( kwd )
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message = util.restore_text( params.get( 'message', '' ) )
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status = params.get( 'status', 'done' )
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request_type_id = kwd.get( 'id', '' )
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try:
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request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
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except:
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return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='browse_request_types' )
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roles = trans.sa_session.query( trans.model.Role ) \
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.filter( trans.model.Role.table.c.deleted==False ) \
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.order_by( trans.model.Role.table.c.name )
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if params.get( 'update_roles_button', False ):
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permissions = {}
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for k, v in trans.model.RequestType.permitted_actions.items():
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in_roles = [ trans.sa_session.query( trans.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
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permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
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trans.app.security_agent.set_request_type_permissions( request_type, permissions )
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trans.sa_session.refresh( request_type )
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message = "Permissions updated for sequencer configuration '%s'" % request_type.name
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return trans.fill_template( '/admin/request_type/request_type_permissions.mako',
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request_type=request_type,
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roles=roles,
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status=status,
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message=message )
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@web.expose
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@web.require_admin
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def view_form_definition( self, trans, **kwd ):
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@@ -994,17 +685,7 @@ class RequestsAdmin( BaseController, UsesFormDefinitionWidgets ):
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# ===== Methods for building SelectFields used on various admin_requests forms
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def __build_sample_id_select_field( self, trans, request, selected_value ):
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return build_select_field( trans, request.samples, 'name', 'sample_id', selected_value=selected_value, refresh_on_change=False )
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def __build_rename_dataset_select_field( self, trans, request_type=None ):
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if request_type:
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selected_value = request_type.datatx_info.get( 'rename_dataset', trans.model.RequestType.rename_dataset_options.NO )
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else:
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selected_value = trans.model.RequestType.rename_dataset_options.NO
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return build_select_field( trans,
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objs=[ v for k, v in trans.model.RequestType.rename_dataset_options.items() ],
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label_attr='self',
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select_field_name='rename_dataset',
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selected_value=selected_value,
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refresh_on_change=False )
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# ===== Methods for building SelectFields used on various admin_requests forms - used outside this controller =====
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def build_rename_datasets_for_sample_select_field( trans, sample_dataset, selected_value='none' ):
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options = []
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@@ -0,0 +1,327 @@
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from galaxy.web.base.controller import *
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from galaxy.web.framework.helpers import time_ago, iff, grids
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from galaxy.model.orm import *
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from galaxy import model, util
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from galaxy.web.form_builder import *
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from galaxy.web.controllers.requests_common import invalid_id_redirect
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import logging, os
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|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
class SequencerGrid( grids.Grid ):
|
||||
# Custom column types
|
||||
class NameColumn( grids.TextColumn ):
|
||||
def get_value(self, trans, grid, request_type):
|
||||
return request_type.name
|
||||
class DescriptionColumn( grids.TextColumn ):
|
||||
def get_value(self, trans, grid, request_type):
|
||||
return request_type.desc
|
||||
class RequestFormColumn( grids.TextColumn ):
|
||||
def get_value(self, trans, grid, request_type):
|
||||
return request_type.request_form.name
|
||||
class SampleFormColumn( grids.TextColumn ):
|
||||
def get_value(self, trans, grid, request_type):
|
||||
return request_type.sample_form.name
|
||||
|
||||
# Grid definition
|
||||
webapp = "galaxy"
|
||||
title = "Sequencer Configurations"
|
||||
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 ) ) ) ),
|
||||
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 configuration", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
|
||||
grids.GridOperation( "Edit permissions", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
|
||||
grids.GridOperation( "Delete configuration", allow_multiple=True, condition=( lambda item: not item.deleted ) ),
|
||||
grids.GridOperation( "Undelete configuration", condition=( lambda item: item.deleted ) ),
|
||||
]
|
||||
global_actions = [
|
||||
grids.GridAction( "Create new configuration", dict( controller='sequencer', action='create_request_type' ) )
|
||||
]
|
||||
|
||||
class Sequencer( BaseController, UsesFormDefinitionWidgets ):
|
||||
sequencer_grid = SequencerGrid()
|
||||
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def browse_request_types( self, trans, **kwd ):
|
||||
if 'operation' in kwd:
|
||||
operation = kwd['operation'].lower()
|
||||
obj_id = kwd.get( 'id', None )
|
||||
if operation == "view_form_definition":
|
||||
return self.view_form_definition( trans, **kwd )
|
||||
elif operation == "view_request_type":
|
||||
return self.view_request_type( trans, **kwd )
|
||||
elif operation == "edit configuration":
|
||||
return self.edit_request_type( trans, **kwd )
|
||||
elif operation == "delete configuration":
|
||||
return self.delete_request_type( trans, **kwd )
|
||||
elif operation == "undelete configuration":
|
||||
return self.undelete_request_type( trans, **kwd )
|
||||
elif operation == "edit permissions":
|
||||
return self.request_type_permissions( trans, **kwd )
|
||||
# Render the grid view
|
||||
return self.sequencer_grid( trans, **kwd )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def create_request_type( self, trans, **kwd ):
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
rt_info_widgets, rt_states_widgets = self.__get_populated_request_type_widgets( trans, **kwd )
|
||||
rename_dataset_select_field = self.__build_rename_dataset_select_field( trans )
|
||||
if params.get( 'add_state_button', False ):
|
||||
# Append a new tuple to the set of states which will result in
|
||||
# empty state name and description TextFields being displayed on
|
||||
# the form.
|
||||
rt_states_widgets.append( ( "", "" ) )
|
||||
elif params.get( 'remove_state_button', False ):
|
||||
index = int( params.get( 'remove_state_button', '' ).split( " " )[2] )
|
||||
del rt_states_widgets[ index-1 ]
|
||||
elif params.get( 'create_request_type_button', False ):
|
||||
self.__save_request_type( trans, **kwd )
|
||||
message = 'The sequencer configuration has been created.'
|
||||
return trans.response.send_redirect( web.url_for( controller='sequencer',
|
||||
action='browse_request_types',
|
||||
message=message,
|
||||
status=status ) )
|
||||
return trans.fill_template( '/admin/request_type/create_request_type.mako',
|
||||
rt_info_widgets=rt_info_widgets,
|
||||
rt_states_widgets=rt_states_widgets,
|
||||
rename_dataset_select_field=rename_dataset_select_field,
|
||||
message=message,
|
||||
status=status )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def view_request_type( self, trans, **kwd ):
|
||||
request_type_id = kwd.get( 'id', None )
|
||||
try:
|
||||
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
|
||||
except:
|
||||
return invalid_id_redirect( trans, 'sequencer', request_type_id, action='browse_request_types' )
|
||||
rename_dataset_select_field = self.__build_rename_dataset_select_field( trans, request_type )
|
||||
return trans.fill_template( '/admin/request_type/view_request_type.mako',
|
||||
request_type=request_type,
|
||||
rename_dataset_select_field=rename_dataset_select_field )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def edit_request_type( self, trans, **kwd ):
|
||||
## TODO: RC: add the ability to edit the name and description of exisitng states
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
request_type_id = params.get( 'id', None )
|
||||
try:
|
||||
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
|
||||
except:
|
||||
return invalid_id_redirect( trans, 'sequencer', request_type_id, action='browse_request_types' )
|
||||
rename_dataset_select_field = self.__build_rename_dataset_select_field( trans )
|
||||
if params.get( 'edit_request_type_button', False ):
|
||||
self.__save_request_type( trans, **kwd )
|
||||
message = 'Changes made to sequencer configuration (%s) have been saved' % request_type.name
|
||||
return trans.fill_template( '/admin/request_type/edit_request_type.mako',
|
||||
request_type=request_type,
|
||||
rename_dataset_select_field=rename_dataset_select_field,
|
||||
message=message,
|
||||
status=status )
|
||||
def __save_request_type( self, trans, **kwd ):
|
||||
# Here we save a newly created request_type or save changed
|
||||
# attributes of an existing request_type.
|
||||
params = util.Params( kwd )
|
||||
request_type_id = params.get( 'id', None )
|
||||
name = util.restore_text( params.get( 'name', '' ) )
|
||||
desc = util.restore_text( params.get( 'desc', '' ) )
|
||||
request_form_id = params.get( 'request_form_id', None )
|
||||
request_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( request_form_id ) )
|
||||
sample_form_id = params.get( 'sample_form_id', None )
|
||||
sample_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( sample_form_id ) )
|
||||
data_dir = util.restore_text( params.get( 'data_dir', '' ) )
|
||||
data_dir = self.__check_path( data_dir )
|
||||
# Data transfer info - Make sure password is retrieved from kwd rather than Params
|
||||
# since Params may have munged the characters.
|
||||
datatx_info = dict( host=util.restore_text( params.get( 'host', '' ) ),
|
||||
username=util.restore_text( params.get( 'username', '' ) ),
|
||||
password=kwd.get( 'password', '' ),
|
||||
data_dir=data_dir,
|
||||
rename_dataset=util.restore_text( params.get( 'rename_dataset', '' ) ) )
|
||||
if request_type_id:
|
||||
# We're saving changed attributes of an existing request_type.
|
||||
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
|
||||
request_type.name = name
|
||||
request_type.desc = desc
|
||||
request_type.request_form = request_form
|
||||
request_type.sample_form = sample_form
|
||||
request_type.datatx_info = datatx_info
|
||||
else:
|
||||
# We're saving a newly created request_type
|
||||
request_type = trans.model.RequestType( name=name,
|
||||
desc=desc,
|
||||
request_form=request_form,
|
||||
sample_form=sample_form,
|
||||
datatx_info=datatx_info )
|
||||
trans.sa_session.add( request_type )
|
||||
trans.sa_session.flush()
|
||||
i = 0
|
||||
while True:
|
||||
if kwd.has_key( 'state_name_%i' % i ):
|
||||
name = util.restore_text( params.get( 'state_name_%i' % i, None ) )
|
||||
desc = util.restore_text( params.get( 'state_desc_%i' % i, None ) )
|
||||
ss = trans.model.SampleState( name, desc, request_type )
|
||||
trans.sa_session.add( ss )
|
||||
trans.sa_session.flush()
|
||||
i += 1
|
||||
else:
|
||||
break
|
||||
def __check_path( self, a_path ):
|
||||
# Return a valid folder_path
|
||||
if a_path and not a_path.endswith( os.sep ):
|
||||
a_path += os.sep
|
||||
return a_path
|
||||
def __get_populated_request_type_widgets( self, trans, **kwd ):
|
||||
request_form_definitions = self.get_all_forms( trans,
|
||||
filter=dict( deleted=False ),
|
||||
form_type=trans.model.FormDefinition.types.REQUEST )
|
||||
sample_form_definitions = self.get_all_forms( trans,
|
||||
filter=dict( deleted=False ),
|
||||
form_type=trans.model.FormDefinition.types.SAMPLE )
|
||||
if not request_form_definitions or not sample_form_definitions:
|
||||
return [],[]
|
||||
params = util.Params( kwd )
|
||||
request_form_id = params.get( 'request_form_id', 'none' )
|
||||
sample_form_id = params.get( 'sample_form_id', 'none' )
|
||||
request_form_id_select_field = build_select_field( trans,
|
||||
objs=request_form_definitions,
|
||||
label_attr='name',
|
||||
select_field_name='request_form_id',
|
||||
selected_value=request_form_id,
|
||||
refresh_on_change=False )
|
||||
sample_form_id_select_field = build_select_field( trans,
|
||||
objs=sample_form_definitions,
|
||||
label_attr='name',
|
||||
select_field_name='sample_form_id',
|
||||
selected_value=sample_form_id,
|
||||
refresh_on_change=False )
|
||||
rt_info_widgets = [ dict( label='Name',
|
||||
widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ),
|
||||
dict( label='Description',
|
||||
widget=TextField( 'desc', 40, util.restore_text( params.get( 'desc', '' ) ) ) ),
|
||||
dict( label='Request form',
|
||||
widget=request_form_id_select_field ),
|
||||
dict( label='Sample form',
|
||||
widget=sample_form_id_select_field ) ]
|
||||
# Unsaved sample states being defined for this sequencer configuration
|
||||
rt_states = []
|
||||
i=0
|
||||
while True:
|
||||
if kwd.has_key( 'state_name_%i' % i ):
|
||||
rt_states.append( ( util.restore_text( params.get( 'state_name_%i' % i, '' ) ),
|
||||
util.restore_text( params.get( 'state_desc_%i' % i, '' ) ) ) )
|
||||
i += 1
|
||||
else:
|
||||
break
|
||||
return rt_info_widgets, rt_states
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def delete_request_type( self, trans, **kwd ):
|
||||
rt_id = kwd.get( 'id', '' )
|
||||
rt_id_list = util.listify( rt_id )
|
||||
for rt_id in rt_id_list:
|
||||
try:
|
||||
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( rt_id ) )
|
||||
except:
|
||||
return invalid_id_redirect( trans, 'sequencer', rt_id, action='browse_request_types' )
|
||||
request_type.deleted = True
|
||||
trans.sa_session.add( request_type )
|
||||
trans.sa_session.flush()
|
||||
status = 'done'
|
||||
message = '%i sequencer configurations has been deleted' % len( rt_id_list )
|
||||
return trans.response.send_redirect( web.url_for( controller='sequencer',
|
||||
action='browse_request_types',
|
||||
message=message,
|
||||
status='done' ) )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def undelete_request_type( self, trans, **kwd ):
|
||||
rt_id = kwd.get( 'id', '' )
|
||||
rt_id_list = util.listify( rt_id )
|
||||
for rt_id in rt_id_list:
|
||||
try:
|
||||
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( rt_id ) )
|
||||
except:
|
||||
return invalid_id_redirect( trans, 'sequencer', rt_id, action='browse_request_types' )
|
||||
request_type.deleted = False
|
||||
trans.sa_session.add( request_type )
|
||||
trans.sa_session.flush()
|
||||
status = 'done'
|
||||
message = '%i sequencer configurations have been undeleted' % len( rt_id_list )
|
||||
return trans.response.send_redirect( web.url_for( controller='sequencer',
|
||||
action='browse_request_types',
|
||||
message=message,
|
||||
status=status ) )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def request_type_permissions( self, trans, **kwd ):
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
request_type_id = kwd.get( 'id', '' )
|
||||
try:
|
||||
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
|
||||
except:
|
||||
return invalid_id_redirect( trans, 'sequencer', request_type_id, action='browse_request_types' )
|
||||
roles = trans.sa_session.query( trans.model.Role ) \
|
||||
.filter( trans.model.Role.table.c.deleted==False ) \
|
||||
.order_by( trans.model.Role.table.c.name )
|
||||
if params.get( 'update_roles_button', False ):
|
||||
permissions = {}
|
||||
for k, v in trans.model.RequestType.permitted_actions.items():
|
||||
in_roles = [ trans.sa_session.query( trans.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
|
||||
permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
|
||||
trans.app.security_agent.set_request_type_permissions( request_type, permissions )
|
||||
trans.sa_session.refresh( request_type )
|
||||
message = "Permissions updated for sequencer configuration '%s'" % request_type.name
|
||||
return trans.fill_template( '/admin/request_type/request_type_permissions.mako',
|
||||
request_type=request_type,
|
||||
roles=roles,
|
||||
status=status,
|
||||
message=message )
|
||||
|
||||
# ===== Methods for building SelectFields used on various admin_requests forms
|
||||
def __build_rename_dataset_select_field( self, trans, request_type=None ):
|
||||
if request_type:
|
||||
selected_value = request_type.datatx_info.get( 'rename_dataset', trans.model.RequestType.rename_dataset_options.NO )
|
||||
else:
|
||||
selected_value = trans.model.RequestType.rename_dataset_options.NO
|
||||
return build_select_field( trans,
|
||||
objs=[ v for k, v in trans.model.RequestType.rename_dataset_options.items() ],
|
||||
label_attr='self',
|
||||
select_field_name='rename_dataset',
|
||||
selected_value=selected_value,
|
||||
refresh_on_change=False )
|
||||
@@ -17,7 +17,7 @@
|
||||
and a <b>Sequencing Sample Form</b>, which must be created first. Click the <b>Create new form</b>
|
||||
button to create them.
|
||||
%else:
|
||||
<form name="create_request_type" action="${h.url_for( controller='requests_admin', action='create_request_type')}" method="post" >
|
||||
<form name="create_request_type" action="${h.url_for( controller='sequencer', action='create_request_type')}" method="post" >
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Create a new sequencer configuration</div>
|
||||
%for rt_info in rt_info_widgets:
|
||||
|
||||
@@ -4,21 +4,24 @@
|
||||
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='view_request_type', id=trans.security.encode_id( request_type.id ) )}">Browse configuration</a></li>
|
||||
%if not request_type.deleted:
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}">Edit permissions</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_request_type', id=trans.security.encode_id( request_type.id ) )}">Delete configuration</a></li>
|
||||
%endif
|
||||
%if request_type.deleted:
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='undelete_request_type', id=trans.security.encode_id( request_type.id ) )}">Undelete configuration</a></li>
|
||||
%endif
|
||||
<li><a class="action-button" id="request_type-${request_type.id}-popup" class="menubutton">Configuration Actions</a></li>
|
||||
<div popupmenu="request_type-${request_type.id}-popup">
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='view_request_type', id=trans.security.encode_id( request_type.id ) )}">Browse configuration</a></li>
|
||||
%if not request_type.deleted:
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}">Edit permissions</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='delete_request_type', id=trans.security.encode_id( request_type.id ) )}">Delete configuration</a></li>
|
||||
%endif
|
||||
%if request_type.deleted:
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='undelete_request_type', id=trans.security.encode_id( request_type.id ) )}">Undelete configuration</a></li>
|
||||
%endif
|
||||
</div>
|
||||
</ul>
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<form name="edit_request_type" action="${h.url_for( controller='requests_admin', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}" method="post" >
|
||||
<form name="edit_request_type" action="${h.url_for( controller='sequencer', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}" method="post" >
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">"Edit ${request_type.name}" sequencer configuration</div>
|
||||
<div class="form-row">
|
||||
|
||||
@@ -0,0 +1 @@
|
||||
<%inherit file="/grid_base.mako"/>
|
||||
@@ -25,9 +25,12 @@
|
||||
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='view_request_type', id=trans.security.encode_id( request_type.id ) )}">Browse configuration</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}">Edit configuration</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_request_type', id=trans.security.encode_id( request_type.id ) )}">Delete configuration</a></li>
|
||||
<li><a class="action-button" id="request_type-${request_type.id}-popup" class="menubutton">Configuration Actions</a></li>
|
||||
<div popupmenu="request_type-${request_type.id}-popup">
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='view_request_type', id=trans.security.encode_id( request_type.id ) )}">Browse configuration</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}">Edit configuration</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='delete_request_type', id=trans.security.encode_id( request_type.id ) )}">Delete configuration</a></li>
|
||||
</div>
|
||||
</ul>
|
||||
|
||||
%if message:
|
||||
@@ -37,7 +40,7 @@
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Manage access permissions on sequencer interface "${request_type.name}"</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='requests_admin', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post">
|
||||
<form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='sequencer', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post">
|
||||
<div class="form-row">
|
||||
<%
|
||||
current_actions = request_type.actions
|
||||
|
||||
@@ -3,14 +3,17 @@
|
||||
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
%if not request_type.deleted:
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}">Edit configuration</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}">Edit permissions</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_request_type', id=trans.security.encode_id( request_type.id ) )}">Delete configuration</a></li>
|
||||
%endif
|
||||
%if request_type.deleted:
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='undelete_request_type', id=trans.security.encode_id( request_type.id ) )}">Undelete configuration</a></li>
|
||||
%endif
|
||||
<li><a class="action-button" id="request_type-${request_type.id}-popup" class="menubutton">Configuration Actions</a></li>
|
||||
<div popupmenu="request_type-${request_type.id}-popup">
|
||||
%if not request_type.deleted:
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}">Edit configuration</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}">Edit permissions</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='delete_request_type', id=trans.security.encode_id( request_type.id ) )}">Delete configuration</a></li>
|
||||
%endif
|
||||
%if request_type.deleted:
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='undelete_request_type', id=trans.security.encode_id( request_type.id ) )}">Undelete configuration</a></li>
|
||||
%endif
|
||||
</div>
|
||||
</ul>
|
||||
|
||||
%if message:
|
||||
|
||||
@@ -77,7 +77,7 @@ ${h.js( "ui.core", "jquery.cookie", "jquery.dynatree" )}
|
||||
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='view_request_type', id=trans.security.encode_id( request.type.id ) )}">Sequencer configuration</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='sequencer', action='view_request_type', id=trans.security.encode_id( request.type.id ) )}">Sequencer configuration</a></li>
|
||||
%if can_transfer_datasets:
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li>
|
||||
%endif
|
||||
|
||||
@@ -323,10 +323,6 @@
|
||||
%elif sample.datasets and len(sample.datasets ) == len( transferred_dataset_files ):
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">View transferred datasets</a></li>
|
||||
%endif
|
||||
###
|
||||
### For demo
|
||||
<li><a class="action-button" target="demolocal" href="http://localhost:9011/">Validate sample sheet</a></li>
|
||||
###
|
||||
</div>
|
||||
%else:
|
||||
${sample_widget_name}
|
||||
|
||||
@@ -114,7 +114,7 @@
|
||||
</div>
|
||||
<div class="toolSectionBody">
|
||||
<div class="toolSectionBg">
|
||||
<div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='browse_request_types' )}" target="galaxy_main">Manage sequencers</a></div>
|
||||
<div class="toolTitle"><a href="${h.url_for( controller='sequencer', action='browse_request_types' )}" target="galaxy_main">Manage sequencers</a></div>
|
||||
<div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='browse_requests' )}" target="galaxy_main">Sequencing requests</a></div>
|
||||
<div class="toolTitle"><a href="${h.url_for( controller='requests_common', action='find_samples', cntrller='requests_admin' )}" target="galaxy_main">Find samples</a></div>
|
||||
</div>
|
||||
|
||||
@@ -1463,7 +1463,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
self.check_page_for_string( check_str )
|
||||
def create_request_type( self, name, desc, request_form_id, sample_form_id, states, strings_displayed=[], strings_displayed_after_submit=[] ):
|
||||
self.home()
|
||||
self.visit_url( "%s/requests_admin/create_request_type" % self.url )
|
||||
self.visit_url( "%s/sequencer/create_request_type" % self.url )
|
||||
for check_str in strings_displayed:
|
||||
self.check_page_for_string( check_str )
|
||||
tc.fv( "1", "name", name )
|
||||
@@ -1479,7 +1479,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
self.check_page_for_string( check_str )
|
||||
def request_type_permissions( self, request_type_id, request_type_name, role_ids_str, permissions_in, permissions_out ):
|
||||
# role_ids_str must be a comma-separated string of role ids
|
||||
url = "requests_admin/request_type_permissions?id=%s&update_roles_button=Save" % ( request_type_id )
|
||||
url = "sequencer/request_type_permissions?id=%s&update_roles_button=Save" % ( request_type_id )
|
||||
for po in permissions_out:
|
||||
key = '%s_out' % po
|
||||
url ="%s&%s=%s" % ( url, key, role_ids_str )
|
||||
@@ -1494,7 +1494,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
def view_request_type( self, request_type_id, request_type_name, sample_states, strings_displayed=[] ):
|
||||
'''View request_type details'''
|
||||
self.home()
|
||||
self.visit_url( "%s/requests_admin/view_request_type?id=%s" % ( self.url, request_type_id ) )
|
||||
self.visit_url( "%s/sequencer/view_request_type?id=%s" % ( self.url, request_type_id ) )
|
||||
self.check_page_for_string( '"%s" sequencer configuration' % request_type_name )
|
||||
for name, desc in sample_states:
|
||||
self.check_page_for_string( name )
|
||||
|
||||
Reference in New Issue
Block a user