mirror of
https://github.com/galaxyproject/galaxy.git
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Eliminate the use of the 'editing_samples' flag by adding the code needed to add new samples without calling the edit_samples method or mako template. Decoupling the different features makes them much cleaner and easier to maintain.
This commit is contained in:
Greg Von Kuster
@@ -36,8 +36,12 @@ class Requests( BaseController ):
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action='edit_basic_request_info',
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cntrller='requests',
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**kwd ) )
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if operation == "add_samples":
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='add_samples',
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cntrller='requests',
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**kwd ) )
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if operation == "edit_samples":
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kwd[ 'editing_samples' ] = True
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='edit_samples',
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cntrller='requests',
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@@ -104,8 +104,12 @@ class RequestsAdmin( BaseController, UsesFormDefinitions ):
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action='edit_basic_request_info',
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cntrller='requests_admin',
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**kwd ) )
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if operation == "add_samples":
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='add_samples',
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cntrller='requests_admin',
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**kwd ) )
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if operation == "edit_samples":
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kwd[ 'editing_samples' ] = True
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='edit_samples',
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cntrller='requests_admin',
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@@ -379,7 +383,6 @@ class RequestsAdmin( BaseController, UsesFormDefinitions ):
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action='edit_samples',
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cntrller='requests_admin',
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id=trans.security.encode_id( request.id ),
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editing_samples=True,
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status=status,
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message=message ) )
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# Save the sample datasets
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@@ -415,7 +415,7 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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status=status,
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message=message ) )
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@web.expose
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@web.require_login( "manage samples" )
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@web.require_login( "edit samples" )
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def edit_samples( self, trans, cntrller, **kwd ):
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params = util.Params( kwd )
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is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
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@@ -426,20 +426,11 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) )
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except:
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return invalid_id_redirect( trans, cntrller, request_id )
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# This method is called when the user is adding new samples as well as
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# editing existing samples, so we use the editing_samples flag to keep
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# track of what's occurring.
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# TODO: CRITICAL: We need another round of code fixes to abstract out
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# adding samples vs editing samples. We need to eliminate the need for
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# this editing_samples flag since it is not maintainable. Greg will do
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# this work as soon as possible.
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editing_samples = util.string_as_bool( params.get( 'editing_samples', False ) )
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if params.get( 'cancel_changes_button', False ):
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='edit_samples',
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cntrller=cntrller,
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id=request_id,
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editing_samples=editing_samples ) )
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id=request_id ) )
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libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user )
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# Build a list of sample widgets (based on the attributes of each sample) for display.
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displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd )
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@@ -457,12 +448,7 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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message = 'Select at least one sample before selecting an operation.'
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kwd[ 'message' ] = message
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handle_error( **kwd )
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if params.get( 'import_samples_button', False ):
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# Import sample field values from a csv file
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return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd )
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elif params.get( 'add_sample_button', False ):
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return self.add_sample( trans, cntrller, request_id, **kwd )
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elif params.get( 'save_samples_button', False ):
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if params.get( 'save_samples_button', False ):
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if encoded_selected_sample_ids:
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# We need the list of displayable_sample_widgets to include the same number
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# of objects that that request.samples has so that we can enumerate over each
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@@ -485,9 +471,9 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd )
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else:
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sample_widgets = displayable_sample_widgets
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return self.__save_samples( trans, cntrller, request, sample_widgets, **kwd )
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return self.__save_samples( trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd )
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request_widgets = self.__get_request_widgets( trans, request.id )
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sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets )
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sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets )
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libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans,
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request.user,
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'sample_operation',
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@@ -503,13 +489,12 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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encoded_selected_sample_ids=encoded_selected_sample_ids,
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request_widgets=request_widgets,
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displayable_sample_widgets=displayable_sample_widgets,
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sample_copy=sample_copy,
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sample_copy_select_field=sample_copy_select_field,
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libraries=libraries,
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sample_operation_select_field=sample_operation_select_field,
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libraries_select_field=libraries_select_field,
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folders_select_field=folders_select_field,
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sample_state_id_select_field=sample_state_id_select_field,
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editing_samples=editing_samples,
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status=status,
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message=message )
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@web.expose
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@@ -697,40 +682,33 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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trans.sa_session.flush()
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if cntrller == 'api':
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return 200, message
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='edit_samples',
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cntrller=cntrller,
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id=request_id,
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editing_samples=True,
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status=status,
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message=message ) )
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final_state = False
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request_type_state = request.type.final_sample_state
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if common_state.id == request_type_state.id:
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# since all the samples are in the final state, change the request state to 'Complete'
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comment = "All samples of this sequencing request are in the final sample state (%s). " % request_type_state.name
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state = request.states.COMPLETE
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final_state = True
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else:
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comment = "All samples of this sequencing request are in the (%s) sample state. " % common_state.name
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state = request.states.SUBMITTED
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event = trans.model.RequestEvent( request, state, comment )
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trans.sa_session.add( event )
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trans.sa_session.flush()
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# See if an email notification is configured to be sent when the samples
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# are in this state.
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retval = request.send_email_notification( trans, common_state, final_state )
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if retval:
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message = comment + retval
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else:
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message = comment
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if cntrller == 'api':
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return 200, message
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final_state = False
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request_type_state = request.type.final_sample_state
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if common_state.id == request_type_state.id:
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# since all the samples are in the final state, change the request state to 'Complete'
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comment = "All samples of this sequencing request are in the final sample state (%s). " % request_type_state.name
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state = request.states.COMPLETE
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final_state = True
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else:
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comment = "All samples of this sequencing request are in the (%s) sample state. " % common_state.name
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state = request.states.SUBMITTED
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event = trans.model.RequestEvent( request, state, comment )
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trans.sa_session.add( event )
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trans.sa_session.flush()
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# See if an email notification is configured to be sent when the samples
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# are in this state.
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retval = request.send_email_notification( trans, common_state, final_state )
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if retval:
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message = comment + retval
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else:
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message = comment
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if cntrller == 'api':
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return 200, message
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='edit_samples',
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cntrller=cntrller,
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id=request_id,
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editing_samples=True,
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status=status,
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message=message ) )
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@web.expose
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@@ -811,6 +789,47 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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cntrller=cntrller,
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sample=sample )
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@web.expose
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@web.require_login( "add samples" )
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def add_samples( self, trans, cntrller, **kwd ):
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params = util.Params( kwd )
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is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
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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_id = params.get( 'id', None )
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try:
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request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) )
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except:
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return invalid_id_redirect( trans, cntrller, request_id )
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libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user )
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# Build a list of sample widgets (based on the attributes of each sample) for display.
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displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd )
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if params.get( 'import_samples_button', False ):
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# Import sample field values from a csv file
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return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd )
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elif params.get( 'add_sample_button', False ):
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return self.add_sample( trans, cntrller, request_id, **kwd )
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elif params.get( 'save_samples_button', False ):
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return self.__save_samples( trans, cntrller, request, displayable_sample_widgets, saving_new_samples=True, **kwd )
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request_widgets = self.__get_request_widgets( trans, request.id )
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sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets )
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libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans,
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request.user,
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'sample_operation',
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libraries,
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None,
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**kwd )
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return trans.fill_template( '/requests/common/add_samples.mako',
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cntrller=cntrller,
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request=request,
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request_widgets=request_widgets,
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displayable_sample_widgets=displayable_sample_widgets,
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sample_copy_select_field=sample_copy_select_field,
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libraries=libraries,
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libraries_select_field=libraries_select_field,
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folders_select_field=folders_select_field,
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status=status,
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message=message )
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@web.expose
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@web.require_login( "add sample" )
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def add_sample( self, trans, cntrller, request_id, **kwd ):
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params = util.Params( kwd )
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@@ -870,19 +889,13 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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field_values=field_values,
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library_select_field=library_select_field,
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folder_select_field=folder_select_field ) )
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encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd )
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sample_operation = params.get( 'sample_operation', 'none' )
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sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, sample_operation )
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sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets )
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return trans.fill_template( '/requests/common/edit_samples.mako',
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sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets )
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return trans.fill_template( '/requests/common/add_samples.mako',
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cntrller=cntrller,
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request=request,
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encoded_selected_sample_ids=encoded_selected_sample_ids,
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request_widgets=request_widgets,
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displayable_sample_widgets=displayable_sample_widgets,
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sample_operation_select_field=sample_operation_select_field,
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sample_copy=sample_copy,
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editing_samples=False,
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sample_copy_select_field=sample_copy_select_field,
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message=message,
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status=status )
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@web.expose
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@@ -931,7 +944,6 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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action='edit_samples',
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cntrller=cntrller,
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id=trans.security.encode_id( request.id ),
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editing_samples=True,
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status=status,
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message=message ) )
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@web.expose
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@@ -957,7 +969,6 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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action='edit_samples',
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cntrller=cntrller,
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id=trans.security.encode_id( sample.request.id ),
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editing_samples=True,
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status=status,
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message=message ) )
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transfer_status = params.get( 'transfer_status', None )
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@@ -1042,15 +1053,14 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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status='error',
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message=message ) )
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request_widgets = self.__get_request_widgets( trans, request.id )
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sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets )
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return trans.fill_template( '/requests/common/edit_samples.mako',
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sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets )
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return trans.fill_template( '/requests/common/add_samples.mako',
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cntrller=cntrller,
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request=request,
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request_widgets=request_widgets,
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displayable_sample_widgets=displayable_sample_widgets,
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sample_copy=sample_copy,
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editing_samples=False )
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def __save_samples( self, trans, cntrller, request, samples, **kwd ):
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sample_copy_select_field=sample_copy_select_field )
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def __save_samples( self, trans, cntrller, request, samples, saving_new_samples=False, **kwd ):
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# Here we handle saving all new samples added by the user as well as saving
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# changes to any subset of the request's samples. A sample will not have an
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# associated SampleState until the request is submitted, at which time the
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@@ -1059,18 +1069,21 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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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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editing_samples = util.string_as_bool( params.get( 'editing_samples', False ) )
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is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
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sample_operation = params.get( 'sample_operation', 'none' )
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if saving_new_samples:
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redirect_action = 'add_samples'
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else:
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redirect_action = 'edit_samples'
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# Check for duplicate sample names within the request
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self.__validate_sample_names( trans, cntrller, request, samples, **kwd )
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if editing_samples:
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if not saving_new_samples:
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library = None
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folder = None
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def handle_error( **kwd ):
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kwd[ 'status' ] = 'error'
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='edit_samples',
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action=redirect_action,
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cntrller=cntrller,
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**kwd ) )
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# Here we handle saving changes to single samples as well as saving changes to
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@@ -1156,10 +1169,9 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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trans.sa_session.add( s )
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trans.sa_session.flush()
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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action='edit_samples',
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action=redirect_action,
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cntrller=cntrller,
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id=trans.security.encode_id( request.id ),
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editing_samples=editing_samples,
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status=status,
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message=message ) )
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def __update_samples( self, trans, cntrller, request, sample_widgets, **kwd ):
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@@ -1275,10 +1287,6 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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"""
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params = util.Params( kwd )
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sample_operation = params.get( 'sample_operation', 'none' )
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# This method is called when the user is adding new samples as well as
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# editing existing samples, so we use the editing_samples flag to keep
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# track of what's occurring.
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editing_samples = util.string_as_bool( params.get( 'editing_samples', False ) )
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sample_widgets = []
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if sample_operation != 'none':
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# The sample_operatin param has a value other than 'none', and a specified
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@@ -1488,7 +1496,6 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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return None
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def __validate_sample_names( self, trans, cntrller, request, displayable_sample_widgets, **kwd ):
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# Check for duplicate sample names for all samples of the request.
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editing_samples = util.string_as_bool( kwd.get( 'editing_samples', False ) )
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message = ''
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for index in range( len( displayable_sample_widgets ) - len( request.samples ) ):
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sample_index = index + len( request.samples )
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@@ -0,0 +1,138 @@
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<%inherit file="/base.mako"/>
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<%namespace file="/message.mako" import="render_msg" />
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<%namespace file="/requests/common/common.mako" import="common_javascripts" />
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<%namespace file="/requests/common/common.mako" import="render_samples_grid" />
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<%namespace file="/requests/common/common.mako" import="render_request_type_sample_form_grids" />
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<%def name="stylesheets()">
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${parent.stylesheets()}
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${h.css( "library" )}
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</%def>
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<%def name="javascripts()">
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${parent.javascripts()}
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${common_javascripts()}
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</%def>
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<%
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from galaxy.web.framework.helpers import time_ago
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is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
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is_complete = request.is_complete
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is_submitted = request.is_submitted
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is_unsubmitted = request.is_unsubmitted
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can_add_samples = is_unsubmitted
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can_delete_samples = request.samples and not is_complete
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can_edit_samples = request.samples and ( is_admin or not is_complete )
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can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted
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can_reject = is_admin and is_submitted
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can_submit = request.samples and is_unsubmitted
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%>
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<br/><br/>
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<ul class="manage-table-actions">
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%if can_edit_samples:
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<li><a class="action-button" href="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit samples</a></li>
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%endif
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%if can_submit:
|
||||
<li><a class="action-button" confirm="More samples cannot be added to this request after it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit request</a></li>
|
||||
%endif
|
||||
<li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li>
|
||||
<div popupmenu="request-${request.id}-popup">
|
||||
<a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a>
|
||||
%if can_edit_request:
|
||||
<a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a>
|
||||
%endif
|
||||
<a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a>
|
||||
%if can_reject:
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a>
|
||||
%endif
|
||||
</div>
|
||||
</ul>
|
||||
|
||||
%if request.is_rejected:
|
||||
<p>
|
||||
<font color="red"><b>${request.last_comment}</b></font>
|
||||
</p>
|
||||
%endif
|
||||
|
||||
%if is_admin and is_submitted and request.samples_without_library_destinations:
|
||||
<p>
|
||||
<font color="red"><b><i>Select a target data library and folder for a sample before selecting it's datasets to transfer from the sequencer</i></b></font>
|
||||
</p>
|
||||
%endif
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<div class="toolFormBody">
|
||||
<form id="add_samples" name="add_samples" action="${h.url_for( controller='requests_common', action='add_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post">
|
||||
%if displayable_sample_widgets:
|
||||
<%
|
||||
grid_header = '<h3>Add Samples to Sequencing Request "%s"</h3>' % request.name
|
||||
%>
|
||||
${render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', adding_new_samples=True, encoded_selected_sample_ids=[], render_buttons=False, grid_header=grid_header )}
|
||||
## Render the other grids
|
||||
<% trans.sa_session.refresh( request.type.sample_form ) %>
|
||||
%for grid_index, grid_name in enumerate( request.type.sample_form.layout ):
|
||||
${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, adding_new_samples=True )}
|
||||
%endfor
|
||||
%else:
|
||||
<label>There are no samples.</label>
|
||||
%endif
|
||||
%if is_unsubmitted:
|
||||
## The user is adding a new sample
|
||||
%if displayable_sample_widgets:
|
||||
<p/>
|
||||
<div class="form-row">
|
||||
<label> Copy <input type="text" name="num_sample_to_copy" value="1" size="3"/> samples from sample ${sample_copy_select_field.get_html()}</label>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Select the sample from which the new sample should be copied or leave selection as <b>None</b> to add a new "generic" sample.
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
<p/>
|
||||
<div class="form-row">
|
||||
## hidden element to make twill work.
|
||||
## Greg will fix this
|
||||
<input type="hidden" name="twill" value=""/>
|
||||
%if ( request.samples or displayable_sample_widgets ) and len( displayable_sample_widgets ) > len( request.samples ):
|
||||
<input type="submit" name="add_sample_button" value="Add sample" />
|
||||
<input type="submit" name="save_samples_button" value="Save"/>
|
||||
<input type="submit" name="cancel_changes_button" value="Cancel"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Click the <b>Add sample</b> button for each new sample and click the <b>Save</b> button when you have finished adding samples.
|
||||
</div>
|
||||
%else:
|
||||
<input type="submit" name="add_sample_button" value="Add sample"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Click the <b>Add sample</b> button for each new sample.
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
%endif
|
||||
</form>
|
||||
</div>
|
||||
%if is_unsubmitted:
|
||||
<p/>
|
||||
##<div class="toolForm">
|
||||
##<div class="toolFormTitle">Import samples from csv file</div>
|
||||
<h4><img src="/static/images/fugue/toggle-expand.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/> Import samples from csv file</h4>
|
||||
<div style="display:none;">
|
||||
<div class="toolFormBody">
|
||||
<form id="import" name="import" action="${h.url_for( controller='requests_common', action='add_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" enctype="multipart/form-data" method="post" >
|
||||
<div class="form-row">
|
||||
<input type="file" name="file_data" />
|
||||
<input type="submit" name="import_samples_button" value="Import samples"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
The csv file must be in the following format:<br/>
|
||||
SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
|
||||
</div>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
##</div>
|
||||
%endif
|
||||
@@ -181,7 +181,7 @@
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
<%def name="render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )">
|
||||
<%def name="render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids, adding_new_samples=False )">
|
||||
<%
|
||||
trans.sa_session.refresh( request )
|
||||
is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
|
||||
@@ -190,8 +190,8 @@
|
||||
is_submitted = request.is_submitted
|
||||
is_unsubmitted = request.is_unsubmitted
|
||||
if sample:
|
||||
can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted )
|
||||
display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted )
|
||||
can_delete_samples = not adding_new_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted )
|
||||
display_checkboxes = not adding_new_samples and ( is_complete or is_rejected or is_submitted )
|
||||
display_datasets = request.samples and ( is_complete or is_submitted )
|
||||
else:
|
||||
can_delete_samples = False
|
||||
@@ -288,7 +288,7 @@
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
<%def name="render_samples_grid( cntrller, request, displayable_sample_widgets, action, editing_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='<h3>Samples</h3>' )">
|
||||
<%def name="render_samples_grid( cntrller, request, displayable_sample_widgets, action, adding_new_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='<h3>Samples</h3>' )">
|
||||
## Displays the "Samples" grid
|
||||
<%
|
||||
trans.sa_session.refresh( request )
|
||||
@@ -298,11 +298,11 @@
|
||||
is_submitted = request.is_submitted
|
||||
is_unsubmitted = request.is_unsubmitted
|
||||
can_add_samples = request.is_unsubmitted
|
||||
can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted )
|
||||
can_delete_samples = not adding_new_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted )
|
||||
can_edit_samples = request.samples and ( is_admin or not is_complete )
|
||||
can_select_datasets = is_admin and displayable_sample_widgets and ( is_submitted or is_complete )
|
||||
can_transfer_datasets = is_admin and request.samples and not request.is_rejected
|
||||
display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted )
|
||||
display_checkboxes = not adding_new_samples and ( is_complete or is_rejected or is_submitted )
|
||||
display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted )
|
||||
display_datasets = request.samples and ( is_complete or is_submitted )
|
||||
%>
|
||||
@@ -313,7 +313,7 @@
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='add_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), add_sample_button='Add sample' )}">Add sample</a></li>
|
||||
%endif
|
||||
%if can_edit_samples:
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples='True' )}">Edit samples</a></li>
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit samples</a></li>
|
||||
%endif
|
||||
</ul>
|
||||
%endif
|
||||
@@ -366,8 +366,8 @@
|
||||
except:
|
||||
sample = None
|
||||
%>
|
||||
%if editing_samples:
|
||||
<tr>${render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr>
|
||||
%if not adding_new_samples:
|
||||
<tr>${render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids, adding_new_samples=False )}</tr>
|
||||
%elif sample:
|
||||
<tr>
|
||||
<td>
|
||||
@@ -463,7 +463,7 @@
|
||||
</tr>
|
||||
%else:
|
||||
## The Add sample button was clicked for this sample_widget
|
||||
<tr>${render_editable_sample_row( cntrller, request, None, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr>
|
||||
<tr>${render_editable_sample_row( cntrller, request, None, sample_widget_index, sample_widget, encoded_selected_sample_ids, adding_new_samples=True )}</tr>
|
||||
%endif
|
||||
%endfor
|
||||
</tbody>
|
||||
@@ -552,7 +552,7 @@
|
||||
</tr>
|
||||
</%def>
|
||||
|
||||
<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, displayable_sample_widgets, editing_samples )">
|
||||
<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, displayable_sample_widgets, adding_new_samples )">
|
||||
<%
|
||||
if not grid_name:
|
||||
grid_name = "Sample form layout " + grid_index
|
||||
@@ -575,7 +575,7 @@
|
||||
<% trans.sa_session.refresh( request ) %>
|
||||
%for sample_index, sample in enumerate( displayable_sample_widgets ):
|
||||
<%
|
||||
if editing_samples or sample_index >= len( request.samples ):
|
||||
if not adding_new_samples or sample_index >= len( request.samples ):
|
||||
display_only = False
|
||||
else:
|
||||
display_only = True
|
||||
|
||||
@@ -38,7 +38,6 @@
|
||||
is_unsubmitted = request.is_unsubmitted
|
||||
can_add_samples = is_unsubmitted
|
||||
can_delete_samples = request.samples and not is_complete
|
||||
can_edit_samples = request.samples and ( is_admin or not is_complete )
|
||||
can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted
|
||||
can_reject = is_admin and is_submitted
|
||||
can_submit = request.samples and is_unsubmitted
|
||||
@@ -47,10 +46,7 @@
|
||||
<br/><br/>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
%if not editing_samples and can_edit_samples:
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples='True' )}">Edit samples</a></li>
|
||||
%endif
|
||||
%if editing_samples and can_add_samples:
|
||||
%if can_add_samples:
|
||||
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='add_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), add_sample_button='Add sample' )}">Add sample</a></li>
|
||||
%endif
|
||||
%if can_submit:
|
||||
@@ -86,16 +82,13 @@
|
||||
%endif
|
||||
|
||||
<div class="toolFormBody">
|
||||
<form id="edit_samples" name="edit_samples" action="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples=editing_samples )}" method="post">
|
||||
<form id="edit_samples" name="edit_samples" action="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post">
|
||||
%if displayable_sample_widgets:
|
||||
<%
|
||||
if editing_samples:
|
||||
grid_header = '<h3>Edit Current Samples of Sequencing Request "%s"</h3>' % request.name
|
||||
else:
|
||||
grid_header = '<h3>Add Samples to Sequencing Request "%s"</h3>' % request.name
|
||||
grid_header = '<h3>Edit Current Samples of Sequencing Request "%s"</h3>' % request.name
|
||||
%>
|
||||
${render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', editing_samples=editing_samples, encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )}
|
||||
%if editing_samples and len( sample_operation_select_field.options ) > 1 and not is_unsubmitted:
|
||||
${render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )}
|
||||
%if len( sample_operation_select_field.options ) > 1 and not is_unsubmitted:
|
||||
<div class="form-row" style="background-color:#FAFAFA;">
|
||||
For selected samples:
|
||||
${sample_operation_select_field.get_html()}
|
||||
@@ -133,53 +126,21 @@
|
||||
## Render the other grids
|
||||
<% trans.sa_session.refresh( request.type.sample_form ) %>
|
||||
%for grid_index, grid_name in enumerate( request.type.sample_form.layout ):
|
||||
${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=editing_samples )}
|
||||
${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, adding_new_samples=False )}
|
||||
%endfor
|
||||
%else:
|
||||
<label>There are no samples.</label>
|
||||
%endif
|
||||
%if not editing_samples and is_unsubmitted:
|
||||
## The user is adding a new sample
|
||||
%if displayable_sample_widgets:
|
||||
<p/>
|
||||
<div class="form-row">
|
||||
<label> Copy <input type="text" name="num_sample_to_copy" value="1" size="3"/> samples from sample ${sample_copy.get_html()}</label>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Select the sample from which the new sample should be copied or leave selection as <b>None</b> to add a new "generic" sample.
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
<p/>
|
||||
<div class="form-row">
|
||||
## hidden element to make twill work.
|
||||
## Greg will fix this
|
||||
<input type="hidden" name="twill" value=""/>
|
||||
%if ( request.samples or displayable_sample_widgets ) and ( editing_samples or len( displayable_sample_widgets ) > len( request.samples ) ):
|
||||
<input type="submit" name="add_sample_button" value="Add sample" />
|
||||
<input type="submit" name="save_samples_button" value="Save"/>
|
||||
<input type="submit" name="cancel_changes_button" value="Cancel"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Click the <b>Add sample</b> button for each new sample and click the <b>Save</b> button when you have finished adding samples.
|
||||
</div>
|
||||
%else:
|
||||
<input type="submit" name="add_sample_button" value="Add sample"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Click the <b>Add sample</b> button for each new sample.
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
%elif editing_samples:
|
||||
<p/>
|
||||
<div class="form-row">
|
||||
## hidden element to make twill work.
|
||||
## Greg will fix this
|
||||
<input type="hidden" name="twill" value=""/>
|
||||
<input type="submit" name="save_samples_button" value="Save"/>
|
||||
<input type="submit" name="cancel_changes_button" value="Cancel"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Click the <b>Save</b> button when you have finished editing the samples
|
||||
</div>
|
||||
%endif
|
||||
<p/>
|
||||
<div class="form-row">
|
||||
## hidden element to make twill work.
|
||||
## Greg will fix this
|
||||
<input type="hidden" name="twill" value=""/>
|
||||
<input type="submit" name="save_samples_button" value="Save"/>
|
||||
<input type="submit" name="cancel_changes_button" value="Cancel"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Click the <b>Save</b> button when you have finished editing the samples
|
||||
</div>
|
||||
%if request.samples and request.is_submitted:
|
||||
<script type="text/javascript">
|
||||
// Updater
|
||||
@@ -188,24 +149,3 @@
|
||||
%endif
|
||||
</form>
|
||||
</div>
|
||||
%if is_unsubmitted and not editing_samples:
|
||||
<p/>
|
||||
##<div class="toolForm">
|
||||
##<div class="toolFormTitle">Import samples from csv file</div>
|
||||
<h4><img src="/static/images/fugue/toggle-expand.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/> Import samples from csv file</h4>
|
||||
<div style="display:none;">
|
||||
<div class="toolFormBody">
|
||||
<form id="import" name="import" action="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples=editing_samples )}" enctype="multipart/form-data" method="post" >
|
||||
<div class="form-row">
|
||||
<input type="file" name="file_data" />
|
||||
<input type="submit" name="import_samples_button" value="Import samples"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
The csv file must be in the following format:<br/>
|
||||
SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
|
||||
</div>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
##</div>
|
||||
%endif
|
||||
|
||||
@@ -160,11 +160,11 @@
|
||||
grid_header = '<h3>Samples</h3>'
|
||||
render_buttons = can_edit_samples
|
||||
%>
|
||||
${render_samples_grid( cntrller, request, displayable_sample_widgets=displayable_sample_widgets, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )}
|
||||
${render_samples_grid( cntrller, request, displayable_sample_widgets=displayable_sample_widgets, action='view_request', adding_new_samples=True, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )}
|
||||
## Render the other grids
|
||||
<% trans.sa_session.refresh( request.type.sample_form ) %>
|
||||
%for grid_index, grid_name in enumerate( request.type.sample_form.layout ):
|
||||
${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=False )}
|
||||
${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, adding_new_samples=False )}
|
||||
%endfor
|
||||
%else:
|
||||
There are no samples.
|
||||
|
||||
@@ -1605,7 +1605,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
for check_str in strings_displayed_after_submit:
|
||||
self.check_page_for_string( check_str )
|
||||
def edit_samples( self, cntrller, request_id, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ):
|
||||
url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id )
|
||||
url = "%s/requests_common/edit_samples?cntrller=%s&id=%s" % ( self.url, cntrller, request_id )
|
||||
self.visit_url( url )
|
||||
for check_str in strings_displayed:
|
||||
self.check_page_for_string( check_str )
|
||||
@@ -1620,7 +1620,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
for check_str in strings_displayed_after_submit:
|
||||
self.check_page_for_string( check_str )
|
||||
def add_bar_codes( self, cntrller, request_id, bar_codes, strings_displayed=[], strings_displayed_after_submit=[] ):
|
||||
url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id )
|
||||
url = "%s/requests_common/edit_samples?cntrller=%s&id=%s" % ( self.url, cntrller, request_id )
|
||||
self.visit_url( url )
|
||||
for check_str in strings_displayed:
|
||||
self.check_page_for_string( check_str )
|
||||
@@ -1642,7 +1642,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
for check_str in strings_displayed_after_submit:
|
||||
self.check_page_for_string( check_str )
|
||||
def change_sample_state( self, request_id, sample_ids, new_sample_state_id, comment='', strings_displayed=[], strings_displayed_after_submit=[] ):
|
||||
url = "%s/requests_common/edit_samples?cntrller=requests_admin&id=%s&editing_samples=True" % ( self.url, request_id )
|
||||
url = "%s/requests_common/edit_samples?cntrller=requests_admin&id=%s" % ( self.url, request_id )
|
||||
self.visit_url( url )
|
||||
for check_str in strings_displayed:
|
||||
self.check_page_for_string( check_str )
|
||||
@@ -1658,7 +1658,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
for check_str in strings_displayed_after_submit:
|
||||
self.check_page_for_string( check_str )
|
||||
def change_sample_target_data_library( self, cntrller, request_id, sample_ids, new_library_id, new_folder_id, folder_options=[], comment='', strings_displayed=[], strings_displayed_after_submit=[] ):
|
||||
url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id )
|
||||
url = "%s/requests_common/edit_samples?cntrller=%s&id=%s" % ( self.url, cntrller, request_id )
|
||||
self.visit_url( url )
|
||||
for check_str in strings_displayed:
|
||||
self.check_page_for_string( check_str )
|
||||
|
||||
Reference in New Issue
Block a user