diff --git a/lib/galaxy/web/controllers/requests.py b/lib/galaxy/web/controllers/requests.py index 4b1b3efa6e0..f1d1cd7045d 100644 --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -36,8 +36,12 @@ class Requests( BaseController ): action='edit_basic_request_info', cntrller='requests', **kwd ) ) + if operation == "add_samples": + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='add_samples', + cntrller='requests', + **kwd ) ) if operation == "edit_samples": - kwd[ 'editing_samples' ] = True return trans.response.send_redirect( web.url_for( controller='requests_common', action='edit_samples', cntrller='requests', diff --git a/lib/galaxy/web/controllers/requests_admin.py b/lib/galaxy/web/controllers/requests_admin.py index b4acc9082ed..64c1145b5c4 100644 --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -104,8 +104,12 @@ class RequestsAdmin( BaseController, UsesFormDefinitions ): action='edit_basic_request_info', cntrller='requests_admin', **kwd ) ) + if operation == "add_samples": + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='add_samples', + cntrller='requests_admin', + **kwd ) ) if operation == "edit_samples": - kwd[ 'editing_samples' ] = True return trans.response.send_redirect( web.url_for( controller='requests_common', action='edit_samples', cntrller='requests_admin', @@ -379,7 +383,6 @@ class RequestsAdmin( BaseController, UsesFormDefinitions ): action='edit_samples', cntrller='requests_admin', id=trans.security.encode_id( request.id ), - editing_samples=True, status=status, message=message ) ) # Save the sample datasets diff --git a/lib/galaxy/web/controllers/requests_common.py b/lib/galaxy/web/controllers/requests_common.py index 693adcd5487..5532e6f3b67 100644 --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -415,7 +415,7 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): status=status, message=message ) ) @web.expose - @web.require_login( "manage samples" ) + @web.require_login( "edit samples" ) def edit_samples( self, trans, cntrller, **kwd ): params = util.Params( kwd ) is_admin = cntrller == 'requests_admin' and trans.user_is_admin() @@ -426,20 +426,11 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, cntrller, request_id ) - # This method is called when the user is adding new samples as well as - # editing existing samples, so we use the editing_samples flag to keep - # track of what's occurring. - # TODO: CRITICAL: We need another round of code fixes to abstract out - # adding samples vs editing samples. We need to eliminate the need for - # this editing_samples flag since it is not maintainable. Greg will do - # this work as soon as possible. - editing_samples = util.string_as_bool( params.get( 'editing_samples', False ) ) if params.get( 'cancel_changes_button', False ): return trans.response.send_redirect( web.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, - id=request_id, - editing_samples=editing_samples ) ) + id=request_id ) ) libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) # Build a list of sample widgets (based on the attributes of each sample) for display. displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) @@ -457,12 +448,7 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): message = 'Select at least one sample before selecting an operation.' kwd[ 'message' ] = message handle_error( **kwd ) - if params.get( 'import_samples_button', False ): - # Import sample field values from a csv file - return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) - elif params.get( 'add_sample_button', False ): - return self.add_sample( trans, cntrller, request_id, **kwd ) - elif params.get( 'save_samples_button', False ): + if params.get( 'save_samples_button', False ): if encoded_selected_sample_ids: # We need the list of displayable_sample_widgets to include the same number # of objects that that request.samples has so that we can enumerate over each @@ -485,9 +471,9 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd ) else: sample_widgets = displayable_sample_widgets - return self.__save_samples( trans, cntrller, request, sample_widgets, **kwd ) + return self.__save_samples( trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) - sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) + sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, request.user, 'sample_operation', @@ -503,13 +489,12 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): encoded_selected_sample_ids=encoded_selected_sample_ids, request_widgets=request_widgets, displayable_sample_widgets=displayable_sample_widgets, - sample_copy=sample_copy, + sample_copy_select_field=sample_copy_select_field, libraries=libraries, sample_operation_select_field=sample_operation_select_field, libraries_select_field=libraries_select_field, folders_select_field=folders_select_field, sample_state_id_select_field=sample_state_id_select_field, - editing_samples=editing_samples, status=status, message=message ) @web.expose @@ -697,40 +682,33 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): trans.sa_session.flush() if cntrller == 'api': return 200, message - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='edit_samples', - cntrller=cntrller, - id=request_id, - editing_samples=True, - status=status, - message=message ) ) - final_state = False - request_type_state = request.type.final_sample_state - if common_state.id == request_type_state.id: - # since all the samples are in the final state, change the request state to 'Complete' - comment = "All samples of this sequencing request are in the final sample state (%s). " % request_type_state.name - state = request.states.COMPLETE - final_state = True else: - comment = "All samples of this sequencing request are in the (%s) sample state. " % common_state.name - state = request.states.SUBMITTED - event = trans.model.RequestEvent( request, state, comment ) - trans.sa_session.add( event ) - trans.sa_session.flush() - # See if an email notification is configured to be sent when the samples - # are in this state. - retval = request.send_email_notification( trans, common_state, final_state ) - if retval: - message = comment + retval - else: - message = comment - if cntrller == 'api': - return 200, message + final_state = False + request_type_state = request.type.final_sample_state + if common_state.id == request_type_state.id: + # since all the samples are in the final state, change the request state to 'Complete' + comment = "All samples of this sequencing request are in the final sample state (%s). " % request_type_state.name + state = request.states.COMPLETE + final_state = True + else: + comment = "All samples of this sequencing request are in the (%s) sample state. " % common_state.name + state = request.states.SUBMITTED + event = trans.model.RequestEvent( request, state, comment ) + trans.sa_session.add( event ) + trans.sa_session.flush() + # See if an email notification is configured to be sent when the samples + # are in this state. + retval = request.send_email_notification( trans, common_state, final_state ) + if retval: + message = comment + retval + else: + message = comment + if cntrller == 'api': + return 200, message return trans.response.send_redirect( web.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=request_id, - editing_samples=True, status=status, message=message ) ) @web.expose @@ -811,6 +789,47 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): cntrller=cntrller, sample=sample ) @web.expose + @web.require_login( "add samples" ) + def add_samples( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + request_id = params.get( 'id', None ) + try: + request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) + except: + return invalid_id_redirect( trans, cntrller, request_id ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) + # Build a list of sample widgets (based on the attributes of each sample) for display. + displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + if params.get( 'import_samples_button', False ): + # Import sample field values from a csv file + return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) + elif params.get( 'add_sample_button', False ): + return self.add_sample( trans, cntrller, request_id, **kwd ) + elif params.get( 'save_samples_button', False ): + return self.__save_samples( trans, cntrller, request, displayable_sample_widgets, saving_new_samples=True, **kwd ) + request_widgets = self.__get_request_widgets( trans, request.id ) + sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) + libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, + request.user, + 'sample_operation', + libraries, + None, + **kwd ) + return trans.fill_template( '/requests/common/add_samples.mako', + cntrller=cntrller, + request=request, + request_widgets=request_widgets, + displayable_sample_widgets=displayable_sample_widgets, + sample_copy_select_field=sample_copy_select_field, + libraries=libraries, + libraries_select_field=libraries_select_field, + folders_select_field=folders_select_field, + status=status, + message=message ) + @web.expose @web.require_login( "add sample" ) def add_sample( self, trans, cntrller, request_id, **kwd ): params = util.Params( kwd ) @@ -870,19 +889,13 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): field_values=field_values, library_select_field=library_select_field, folder_select_field=folder_select_field ) ) - encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) - sample_operation = params.get( 'sample_operation', 'none' ) - sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, sample_operation ) - sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) - return trans.fill_template( '/requests/common/edit_samples.mako', + sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) + return trans.fill_template( '/requests/common/add_samples.mako', cntrller=cntrller, request=request, - encoded_selected_sample_ids=encoded_selected_sample_ids, request_widgets=request_widgets, displayable_sample_widgets=displayable_sample_widgets, - sample_operation_select_field=sample_operation_select_field, - sample_copy=sample_copy, - editing_samples=False, + sample_copy_select_field=sample_copy_select_field, message=message, status=status ) @web.expose @@ -931,7 +944,6 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), - editing_samples=True, status=status, message=message ) ) @web.expose @@ -957,7 +969,6 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ), - editing_samples=True, status=status, message=message ) ) transfer_status = params.get( 'transfer_status', None ) @@ -1042,15 +1053,14 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): status='error', message=message ) ) request_widgets = self.__get_request_widgets( trans, request.id ) - sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) - return trans.fill_template( '/requests/common/edit_samples.mako', + sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) + return trans.fill_template( '/requests/common/add_samples.mako', cntrller=cntrller, request=request, request_widgets=request_widgets, displayable_sample_widgets=displayable_sample_widgets, - sample_copy=sample_copy, - editing_samples=False ) - def __save_samples( self, trans, cntrller, request, samples, **kwd ): + sample_copy_select_field=sample_copy_select_field ) + def __save_samples( self, trans, cntrller, request, samples, saving_new_samples=False, **kwd ): # Here we handle saving all new samples added by the user as well as saving # changes to any subset of the request's samples. A sample will not have an # associated SampleState until the request is submitted, at which time the @@ -1059,18 +1069,21 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - editing_samples = util.string_as_bool( params.get( 'editing_samples', False ) ) is_admin = cntrller == 'requests_admin' and trans.user_is_admin() sample_operation = params.get( 'sample_operation', 'none' ) + if saving_new_samples: + redirect_action = 'add_samples' + else: + redirect_action = 'edit_samples' # Check for duplicate sample names within the request self.__validate_sample_names( trans, cntrller, request, samples, **kwd ) - if editing_samples: + if not saving_new_samples: library = None folder = None def handle_error( **kwd ): kwd[ 'status' ] = 'error' return trans.response.send_redirect( web.url_for( controller='requests_common', - action='edit_samples', + action=redirect_action, cntrller=cntrller, **kwd ) ) # Here we handle saving changes to single samples as well as saving changes to @@ -1156,10 +1169,9 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): trans.sa_session.add( s ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_common', - action='edit_samples', + action=redirect_action, cntrller=cntrller, id=trans.security.encode_id( request.id ), - editing_samples=editing_samples, status=status, message=message ) ) def __update_samples( self, trans, cntrller, request, sample_widgets, **kwd ): @@ -1275,10 +1287,6 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): """ params = util.Params( kwd ) sample_operation = params.get( 'sample_operation', 'none' ) - # This method is called when the user is adding new samples as well as - # editing existing samples, so we use the editing_samples flag to keep - # track of what's occurring. - editing_samples = util.string_as_bool( params.get( 'editing_samples', False ) ) sample_widgets = [] if sample_operation != 'none': # The sample_operatin param has a value other than 'none', and a specified @@ -1488,7 +1496,6 @@ class RequestsCommon( BaseController, UsesFormDefinitions ): return None def __validate_sample_names( self, trans, cntrller, request, displayable_sample_widgets, **kwd ): # Check for duplicate sample names for all samples of the request. - editing_samples = util.string_as_bool( kwd.get( 'editing_samples', False ) ) message = '' for index in range( len( displayable_sample_widgets ) - len( request.samples ) ): sample_index = index + len( request.samples ) diff --git a/templates/requests/common/add_samples.mako b/templates/requests/common/add_samples.mako new file mode 100644 index 00000000000..a0c14b4a391 --- /dev/null +++ b/templates/requests/common/add_samples.mako @@ -0,0 +1,138 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/requests/common/common.mako" import="common_javascripts" /> +<%namespace file="/requests/common/common.mako" import="render_samples_grid" /> +<%namespace file="/requests/common/common.mako" import="render_request_type_sample_form_grids" /> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} + + +<%def name="javascripts()"> + ${parent.javascripts()} + ${common_javascripts()} + + +<% + from galaxy.web.framework.helpers import time_ago + + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = request.is_complete + is_submitted = request.is_submitted + 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 +%> + +

+ + + +%if request.is_rejected: +

+ ${request.last_comment} +

+%endif + +%if is_admin and is_submitted and request.samples_without_library_destinations: +

+ Select a target data library and folder for a sample before selecting it's datasets to transfer from the sequencer +

+%endif + +%if message: + ${render_msg( message, status )} +%endif + +
+
+ %if displayable_sample_widgets: + <% + grid_header = '

Add Samples to Sequencing Request "%s"

' % 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: + + %endif + %if is_unsubmitted: + ## The user is adding a new sample + %if displayable_sample_widgets: +

+

+ +
+ Select the sample from which the new sample should be copied or leave selection as None to add a new "generic" sample. +
+
+ %endif +

+

+ ## hidden element to make twill work. + ## Greg will fix this + + %if ( request.samples or displayable_sample_widgets ) and len( displayable_sample_widgets ) > len( request.samples ): + + + +
+ Click the Add sample button for each new sample and click the Save button when you have finished adding samples. +
+ %else: + +
+ Click the Add sample button for each new sample. +
+ %endif +
+ %endif +
+
+%if is_unsubmitted: +

+ ##

+ ##
Import samples from csv file
+

Hide Import samples from csv file

+
+
+
+
+ + +
+ The csv file must be in the following format:
+ SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2... +
+
+
+
+
+ ##
+%endif diff --git a/templates/requests/common/common.mako b/templates/requests/common/common.mako index 889a59a0094..1abb997f88f 100644 --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -181,7 +181,7 @@ %endif -<%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 name="render_samples_grid( cntrller, request, displayable_sample_widgets, action, editing_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='

Samples

' )"> +<%def name="render_samples_grid( cntrller, request, displayable_sample_widgets, action, adding_new_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='

Samples

' )"> ## 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 @@
  • Add sample
    • %endif %if can_edit_samples: -
  • Edit samples
    • +
  • Edit samples
    • %endif %endif @@ -366,8 +366,8 @@ except: sample = None %> - %if editing_samples: - ${render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )} + %if not adding_new_samples: + ${render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids, adding_new_samples=False )} %elif sample: @@ -463,7 +463,7 @@ %else: ## The Add sample button was clicked for this sample_widget - ${render_editable_sample_row( cntrller, request, None, sample_widget_index, sample_widget, encoded_selected_sample_ids )} + ${render_editable_sample_row( cntrller, request, None, sample_widget_index, sample_widget, encoded_selected_sample_ids, adding_new_samples=True )} %endif %endfor @@ -552,7 +552,7 @@ -<%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 diff --git a/templates/requests/common/edit_samples.mako b/templates/requests/common/edit_samples.mako index f3f0ac7e6c1..dd91049d287 100644 --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -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 @@