[galaxy-commits] galaxy-dist commit 7ea4c156ae32: Add a pop-up menu for a sample if it is possible to either select datasets to transfer or transfer selected datasets for the sample. Also use better naming convention for a key variable name.

20 Nov 2010

# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Greg Von Kuster <greg@bx.psu.edu>
# Date 1289492968 18000
# Node ID 7ea4c156ae32c4757378229bfc49584df91a024a
# Parent  591c53b44ae4a6237a841adaa3abfe59829beebe
Add a pop-up menu for a sample if it is possible to either select datasets to transfer or transfer selected datasets for the sample.  Also use better naming convention for a key variable name.

--- a/lib/galaxy/web/controllers/requests_common.py
+++ b/lib/galaxy/web/controllers/requests_common.py
@@ -212,14 +212,14 @@ class RequestsCommon( BaseController, Us
         except:
             return invalid_id_redirect( trans, cntrller, request_id )
         sample_state_id = params.get( 'sample_state_id', None )
-        # Get the user entered sample information
-        current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd )
+        # 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 )
         request_widgets = self.__get_request_widgets( trans, request.id )
         return trans.fill_template( '/requests/common/view_request.mako',
                                     cntrller=cntrller, 
                                     request=request,
                                     request_widgets=request_widgets,
-                                    current_samples=current_samples,
+                                    displayable_sample_widgets=displayable_sample_widgets,
                                     status=status,
                                     message=message )
     @web.expose
@@ -415,8 +415,8 @@ class RequestsCommon( BaseController, Us
                                                                           editing_samples=editing_samples ) )
         # Get all libraries for which the current user has permission to add items.
         libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
-        # Get the user entered sample information
-        current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd )
+        # 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 )
         encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd )
         sample_operation = params.get( 'sample_operation', 'none' )
         def handle_error( **kwd ):
@@ -433,14 +433,17 @@ class RequestsCommon( BaseController, Us
             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, current_samples, libraries, **kwd )
+            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 encoded_selected_sample_ids:
-                # This gets tricky because we need the list of samples to include the same number
-                # of objects that that current_samples ( i.e., request.samples ) has.  We'll first
-                # get the set of samples corresponding to the checked 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
+                # list without problems.  We have to be careful here since the user may have
+                # used the multi-select check boxes when editing sample widgets, but didn't
+                # select all of them.  We'll first get the set of samples corresponding to the
+                # checked sample ids.
                 samples = []
                 selected_samples = []
                 for encoded_sample_id in encoded_selected_sample_ids:
@@ -453,12 +456,12 @@ class RequestsCommon( BaseController, Us
                     else:
                         samples.append( None )
                 # The __save_samples method requires sample_widgets, not sample objects
-                samples = self.__get_sample_widgets( trans, request, samples, **kwd )
+                sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd )
             else:
-                samples = current_samples
-            return self.__save_samples( trans, cntrller, request, samples, **kwd )
+                sample_widgets = displayable_sample_widgets
+            return self.__save_samples( trans, cntrller, request, sample_widgets, **kwd )
         request_widgets = self.__get_request_widgets( trans, request.id )
-        sample_copy = self.__build_copy_sample_select_field( trans, current_samples )
+        sample_copy = 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,
                                                                                                       0,
@@ -473,7 +476,7 @@ class RequestsCommon( BaseController, Us
                                     request=request,
                                     encoded_selected_sample_ids=encoded_selected_sample_ids,
                                     request_widgets=request_widgets,
-                                    current_samples=current_samples,
+                                    displayable_sample_widgets=displayable_sample_widgets,
                                     sample_copy=sample_copy, 
                                     libraries=libraries,
                                     sample_operation_select_field=sample_operation_select_field,
@@ -805,12 +808,12 @@ class RequestsCommon( BaseController, Us
         is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
         # Get the widgets for rendering the request form
         request_widgets = self.__get_request_widgets( trans, request.id )
-        current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd )
-        if not current_samples:
+        displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd )
+        if not displayable_sample_widgets:
             # Form field names are zero-based.
             sample_index = 0
         else:
-            sample_index = len( current_samples )
+            sample_index = len( displayable_sample_widgets )
         if params.get( 'add_sample_button', False ):
             # Get all libraries for which the current user has permission to add items
             libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
@@ -818,18 +821,18 @@ class RequestsCommon( BaseController, Us
             # See if the user has selected a sample to copy.
             copy_sample_index = int( params.get( 'copy_sample_index', -1 ) )
             for index in range( num_samples_to_add ):
-                id_index = len( current_samples ) + 1
+                id_index = len( displayable_sample_widgets ) + 1
                 if copy_sample_index != -1:
                     # The user has selected a sample to copy.
-                    library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True )
-                    folder_id = current_samples[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True )
-                    name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( len( current_samples ) + 1 )
-                    field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ]
+                    library_id = displayable_sample_widgets[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True )
+                    folder_id = displayable_sample_widgets[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True )
+                    name = displayable_sample_widgets[ copy_sample_index ][ 'name' ] + '_%i' % ( len( displayable_sample_widgets ) + 1 )
+                    field_values = [ val for val in displayable_sample_widgets[ copy_sample_index ][ 'field_values' ] ]
                 else:
                     # The user has not selected a sample to copy, just adding a new generic sample.
                     library_id = None
                     folder_id = None
-                    name = 'Sample_%i' % ( len( current_samples ) + 1 )
+                    name = 'Sample_%i' % ( len( displayable_sample_widgets ) + 1 )
                     field_values = [ '' for field in request.type.sample_form.fields ]
                 # Build the library_select_field and folder_select_field for the new sample being added.
                 library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans,
@@ -841,25 +844,26 @@ class RequestsCommon( BaseController, Us
                                                                                                            folder_id=folder_id,
                                                                                                            **kwd )
                 # Append the new sample to the current list of samples for the request
-                current_samples.append( dict( name=name,
-                                              barcode='',
-                                              library=None,
-                                              library_id=library_id,
-                                              folder=None,
-                                              folder_id=folder_id,
-                                              field_values=field_values,
-                                              library_select_field=library_select_field,
-                                              folder_select_field=folder_select_field ) )
+                displayable_sample_widgets.append( dict( id=None,
+                                                         name=name,
+                                                         barcode='',
+                                                         library=None,
+                                                         library_id=library_id,
+                                                         folder=None,
+                                                         folder_id=folder_id,
+                                                         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, current_samples )
+        sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets )
         return trans.fill_template( '/requests/common/edit_samples.mako',
                                     cntrller=cntrller,
                                     request=request,
                                     encoded_selected_sample_ids=encoded_selected_sample_ids,
                                     request_widgets=request_widgets,
-                                    current_samples=current_samples,
+                                    displayable_sample_widgets=displayable_sample_widgets,
                                     sample_operation_select_field=sample_operation_select_field,
                                     sample_copy=sample_copy, 
                                     editing_samples=False,
@@ -876,9 +880,9 @@ class RequestsCommon( BaseController, Us
             request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) )
         except:
             return invalid_id_redirect( trans, cntrller, request_id )
-        current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd )
+        displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd )
         sample_index = int( params.get( 'sample_id', 0 ) )
-        sample_name = current_samples[sample_index]['name']
+        sample_name = displayable_sample_widgets[sample_index]['name']
         sample = request.has_sample( sample_name )
         if sample:
             trans.sa_session.delete( sample.values )
@@ -960,7 +964,7 @@ class RequestsCommon( BaseController, Us
                                     status=status,
                                     files=[],
                                     folder_path=folder_path )
-    def __import_samples( self, trans, cntrller, request, current_samples, libraries, **kwd ):
+    def __import_samples( self, trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ):
         """
         Reads the samples csv file and imports all the samples.  The format of the csv file is:
         SampleName,DataLibrary,DataLibraryFolder,Field1,Field2....
@@ -987,19 +991,20 @@ class RequestsCommon( BaseController, Us
                         folder_id = folder.id
                 library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans,
                                                                                                            request.user,
-                                                                                                           len( current_samples ), 
+                                                                                                           len( displayable_sample_widgets ), 
                                                                                                            libraries,
                                                                                                            None,
                                                                                                            library_id,
                                                                                                            folder_id,
                                                                                                            **kwd )
-                current_samples.append( dict( name=row[0], 
-                                              barcode='',
-                                              library=None,
-                                              folder=None,
-                                              library_select_field=library_select_field,
-                                              folder_select_field=folder_select_field,
-                                              field_values=row[3:] ) )
+                displayable_sample_widgets.append( dict( id=None,
+                                                         name=row[0], 
+                                                         barcode='',
+                                                         library=None,
+                                                         folder=None,
+                                                         library_select_field=library_select_field,
+                                                         folder_select_field=folder_select_field,
+                                                         field_values=row[3:] ) )
         except Exception, e:
             if str( e ) == "'unicode' object has no attribute 'file'":
                 message = "Select a file"
@@ -1014,12 +1019,12 @@ class RequestsCommon( BaseController, Us
                                                               status='error',
                                                               message=message ) )
         request_widgets = self.__get_request_widgets( trans, request.id )
-        sample_copy = self.__build_copy_sample_select_field( trans, current_samples )
+        sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets )
         return trans.fill_template( '/requests/common/edit_samples.mako',
                                     cntrller=cntrller,
                                     request=request,
                                     request_widgets=request_widgets,
-                                    current_samples=current_samples,
+                                    displayable_sample_widgets=displayable_sample_widgets,
                                     sample_copy=sample_copy,
                                     editing_samples=False )
     def __save_samples( self, trans, cntrller, request, samples, **kwd ):
@@ -1110,17 +1115,17 @@ class RequestsCommon( BaseController, Us
             # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ).
             for index in range( len( samples ) - len( request.samples ) ):
                 sample_index = len( request.samples )
-                current_sample = samples[ sample_index ]
-                form_values = trans.model.FormValues( request.type.sample_form, current_sample[ 'field_values' ] )
+                sample_widget = samples[ sample_index ]
+                form_values = trans.model.FormValues( request.type.sample_form, sample_widget[ 'field_values' ] )
                 trans.sa_session.add( form_values )
                 trans.sa_session.flush()                    
-                s = trans.model.Sample( name=current_sample[ 'name' ],
+                s = trans.model.Sample( name=sample_widget[ 'name' ],
                                         desc='', 
                                         request=request,
                                         form_values=form_values, 
                                         bar_code='',
-                                        library=current_sample[ 'library' ],
-                                        folder=current_sample[ 'folder' ] )
+                                        library=sample_widget[ 'library' ],
+                                        folder=sample_widget[ 'folder' ] )
                 trans.sa_session.add( s )
                 trans.sa_session.flush()
         return trans.response.send_redirect( web.url_for( controller='requests_common',
@@ -1264,9 +1269,9 @@ class RequestsCommon( BaseController, Us
         for index, sample in enumerate( samples ):
             id_index = index + 1
             if sample is None:
-                # Id sample is None, then we'll use the sample from the request object since it will
-                # not have updated =values from kwd.
+                # Use the sample from the request object since it will not have updated values from kwd.
                 sample = request.samples[ index ]
+                sample_id = sample.id
                 name = sample.name
                 bar_code = sample.bar_code
                 library = sample.library
@@ -1274,6 +1279,7 @@ class RequestsCommon( BaseController, Us
                 field_values = sample.values.content
             else:
                 # Update the sample attributes from kwd
+                sample_id = None
                 name = util.restore_text( params.get( 'sample_%i_name' % index, sample.name ) )
                 bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, sample.bar_code ) )
                 library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) )
@@ -1295,7 +1301,8 @@ class RequestsCommon( BaseController, Us
                                                                                                        library_id=library_id,
                                                                                                        folder_id=folder_id,
                                                                                                        **kwd )
-            sample_widgets.append( dict( name=name,
+            sample_widgets.append( dict( id=sample_id,
+                                         name=name,
                                          barcode=bar_code,
                                          library=library,
                                          folder=folder,
@@ -1325,7 +1332,8 @@ class RequestsCommon( BaseController, Us
                                                                                                        library_id=library_id,
                                                                                                        folder_id=folder_id,
                                                                                                        **kwd )
-            sample_widgets.append( dict( name=name,
+            sample_widgets.append( dict( id=None,
+                                         name=name,
                                          barcode=bar_code,
                                          library=library,
                                          folder=folder,
@@ -1335,10 +1343,10 @@ class RequestsCommon( BaseController, Us
             index += 1
         return sample_widgets   
     # ===== Methods for building SelectFields used on various request forms =====
-    def __build_copy_sample_select_field( self, trans, current_samples ):
+    def __build_copy_sample_select_field( self, trans, displayable_sample_widgets ):
         copy_sample_index_select_field = SelectField( 'copy_sample_index' )
         copy_sample_index_select_field.add_option( 'None', -1, selected=True )  
-        for index, sample_dict in enumerate( current_samples ):
+        for index, sample_dict in enumerate( displayable_sample_widgets ):
             copy_sample_index_select_field.add_option( sample_dict[ 'name' ], index )
         return copy_sample_index_select_field  
     def __build_request_type_id_select_field( self, trans, selected_value='none' ):
@@ -1458,20 +1466,20 @@ class RequestsCommon( BaseController, Us
                 message += '<b>' + ef + '</b> '
             return message
         return None
-    def __validate_sample_names( self, trans, cntrller, request, current_samples, **kwd ):
+    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( current_samples ) - len( request.samples ) ):
+        for index in range( len( displayable_sample_widgets ) - len( request.samples ) ):
             sample_index = index + len( request.samples )
-            current_sample = current_samples[ sample_index ]
-            sample_name = current_sample[ 'name' ]
+            sample_widget = displayable_sample_widgets[ sample_index ]
+            sample_name = sample_widget[ 'name' ]
             if not sample_name.strip():
                 message = 'Enter the name of sample number %i' % sample_index
                 break
             count = 0
-            for i in range( len( current_samples ) ):
-                if sample_name == current_samples[ i ][ 'name' ]:
+            for i in range( len( displayable_sample_widgets ) ):
+                if sample_name == displayable_sample_widgets[ i ][ 'name' ]:
                     count += 1
             if count > 1: 
                 message = "You tried to add %i samples with the name (%s).  Samples belonging to a request must have unique names." % ( count, sample_name )

--- a/templates/requests/common/common.mako
+++ b/templates/requests/common/common.mako
@@ -113,7 +113,7 @@
     </script></%def>
 
-<%def name="render_editable_sample_row( cntrller, sample, current_sample_index, current_sample, encoded_selected_sample_ids )">
+<%def name="render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )"><%
         is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
         if sample:
@@ -145,7 +145,7 @@
         <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td>
     %endif
     <td valign="top">
-        <input type="text" name="sample_${current_sample_index}_name" value="${current_sample['name']}" size="10"/>
+        <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/><div class="toolParamHelp" style="clear: both;"><i>${' (required)' }</i></div>
@@ -153,10 +153,10 @@
     %if display_bar_code:
         <td valign="top">
             %if is_admin:
-                <input type="text" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}" size="10"/>
+                <input type="text" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}" size="10"/>
             %else:
-                ${current_sample['barcode']}
-                <input type="hidden" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}"/>
+                ${sample_widget['barcode']}
+                <input type="hidden" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}"/>
             %endif
         </td>
     %endif 
@@ -169,8 +169,8 @@
     %else:
         <td></td>
     %endif
-    <td valign="top">${current_sample['library_select_field'].get_html()}</td>
-    <td valign="top">${current_sample['folder_select_field'].get_html()}</td>
+    <td valign="top">${sample_widget['library_select_field'].get_html()}</td>
+    <td valign="top">${sample_widget['folder_select_field'].get_html()}</td>
     %if display_datasets:
         <td valign="top">
             ## An admin can select the datasets to transfer, while a non-admin can only view what has been selected
@@ -220,11 +220,11 @@
     %endif
     %if can_delete_samples:
         ## Delete button
-        <td valign="top"><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=current_sample_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td>
+        <td valign="top"><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=sample_widget_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td>
     %endif
 </%def>
 
-<%def name="render_samples_grid( cntrller, request, current_samples, 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, editing_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='<h3>Samples</h3>' )">
     ## Displays the "Samples" grid
     <%
         trans.sa_session.refresh( request )
@@ -236,7 +236,8 @@
         can_add_samples = request.is_unsubmitted
         can_delete_samples = editing_samples and request.samples and not is_complete
         can_edit_samples = request.samples and ( is_admin or not is_complete )
-        can_select_datasets = is_admin and current_samples and ( is_submitted or 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_bar_code = request.samples and ( is_complete or is_rejected or is_submitted )
         display_datasets = request.samples and ( is_complete or is_submitted )
@@ -278,46 +279,67 @@
         <thead><tbody><% trans.sa_session.refresh( request ) %>
-            ## current_samples is a dictionary whose keys are:
-            ## name, barcode, library, folder, field_values, library_select_field, folder_select_field
-            %for current_sample_index, current_sample in enumerate( current_samples ):
+            ## displayable_sample_widgets is a dictionary whose keys are:
+            ## id, name, barcode, library, folder, field_values, library_select_field, folder_select_field
+            ## A displayable_sample_widget will have an id == None if the widget's associated sample has not
+            ## yet been saved (i.e., the use clicked the "Add sample" button but has not yet clicked the
+            ## "Save" button.
+            %for sample_widget_index, sample_widget in enumerate( displayable_sample_widgets ):
                 <%
-                    current_sample_name = current_sample[ 'name' ]
-                    current_sample_barcode = current_sample[ 'barcode' ]
-                    current_sample_library = current_sample[ 'library' ]
-                    if current_sample_library:
+                    sample_widget_name = sample_widget[ 'name' ]
+                    sample_widget_barcode = sample_widget[ 'barcode' ]
+                    sample_widget_library = sample_widget[ 'library' ]
+                    if sample_widget_library:
                         if cntrller == 'requests':
                             library_cntrller = 'library'
                         elif is_admin:
                             library_cntrller = 'library_admin'
                         else:
                             library_cntrller = None
-                    current_sample_folder = current_sample[ 'folder' ]
+                    sample_widget_folder = sample_widget[ 'folder' ]
                     try:
-                        sample = request.samples[ current_sample_index ]
+                        sample = request.samples[ sample_widget_index ]
                     except:
                         sample = None 
                 %>
                 %if editing_samples:
-                    <tr>${render_editable_sample_row( cntrller, sample, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr>
+                    <tr>${render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr>
                 %elif sample:
                     <tr>
-                        <td>${current_sample_name}</td>
+                        <td>
+                            %if sample.state and ( can_select_datasets or can_transfer_datasets ):
+                                ## A sample will have a state only after the request has been submitted.
+                                <% encoded_id = trans.security.encode_id( sample.id ) %>
+                                <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup">
+                                    ${sample.name}
+                                </div>
+                                <div popupmenu="sample-${sample.id}-popup">
+                                    %if can_select_datasets:
+                                        <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select datasets to transfer</a></li>
+                                    %endif
+                                    %if sample.untransferred_dataset_files:
+                                        <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li>
+                                    %endif
+                                </div>
+                            %else:
+                                ${sample_widget_name}
+                            %endif
+                        </td>
                         %if display_bar_code:
-                            <td>${current_sample_barcode}</td>
+                            <td>${sample_widget_barcode}</td>
                         %endif
                         %if is_unsubmitted:
                             <td>Unsubmitted</td>
                         %else:
                             <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td>
                         %endif
-                        %if current_sample_library and library_cntrller is not None:
-                            <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( current_sample_library.id ) )}">${current_sample_library.name}</a></td>                                  
+                        %if sample_widget_library and library_cntrller is not None:
+                            <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td>                                  
                         %else:
                             <td></td>
                         %endif
-                        %if current_sample_folder:
-                            <td>${current_sample_folder.name}</td>
+                        %if sample_widget_folder:
+                            <td>${sample_widget_folder.name}</td>
                         %else:
                             <td></td>
                         %endif
@@ -371,7 +393,7 @@
                     </tr>
                 %else:
                     ## The Add sample button was clicked for this sample_widget
-                    <tr>${render_editable_sample_row( cntrller, None, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr>
+                    <tr>${render_editable_sample_row( cntrller, None, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr>
                 %endif
             %endfor
         </tbody>
@@ -439,7 +461,7 @@
     </tr></%def>
 
-<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, current_samples, editing_samples )">
+<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, displayable_sample_widgets, editing_samples )"><%
         if not grid_name:
             grid_name = "Sample form layout " + grid_index
@@ -466,7 +488,7 @@
             <thead><tbody><% trans.sa_session.refresh( request ) %>
-                %for sample_index, sample in enumerate( current_samples ):
+                %for sample_index, sample in enumerate( displayable_sample_widgets ):
                     <%
                         if editing_samples or sample_index >= len( request.samples ):
                             display_only = False
@@ -505,7 +527,7 @@
                     <tr><td>
                             %if is_admin:
-                                <% encoded_id = trans.security.encode_id(dataset.id) %>
+                                <% encoded_id = trans.security.encode_id( dataset.id ) %><span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"><a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a>

--- a/templates/requests/common/edit_samples.mako
+++ b/templates/requests/common/edit_samples.mako
@@ -72,14 +72,14 @@
 
 <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">
-        %if current_samples:
+        %if displayable_sample_widgets:
             <%
                 if editing_samples:
                     grid_header = '<h3>Edit Current Samples of Request "%s"</h3>' % request.name
                 else:
                     grid_header = '<h3>Add Samples to Request "%s"</h3>' % request.name
             %>
-            ${render_samples_grid( cntrller, request, current_samples, action='edit_samples', editing_samples=editing_samples, encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )}
+            ${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:
                 <div class="form-row" style="background-color:#FAFAFA;">
                     For selected samples: 
@@ -118,14 +118,14 @@
             ## 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 ), current_samples=current_samples, 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, editing_samples=editing_samples )}
             %endfor
         %else:
             <label>There are no samples.</label>
         %endif  
         %if not editing_samples and is_unsubmitted:
             ## The user is adding a new sample
-            %if current_samples:
+            %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>
@@ -138,7 +138,7 @@
             <div class="form-row">
                 ## hidden element to make twill work.
                 <input type="hidden" name="hidden_input" value=""/>
-                %if ( request.samples or current_samples ) and ( editing_samples or len( current_samples ) > len( request.samples ) ):
+                %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"/>

--- a/templates/requests/common/view_request.mako
+++ b/templates/requests/common/view_request.mako
@@ -148,12 +148,12 @@
     </div></div><p/>
-%if current_samples:
+%if displayable_sample_widgets:
     <%
         grid_header = '<h3>Samples</h3>'
         render_buttons = can_edit_samples
     %>
-    ${render_samples_grid( cntrller, request, current_samples=current_samples, 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', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )}
 %else:
     There are no samples.
     %if can_add_samples:
@@ -165,5 +165,5 @@
 ## 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 ), current_samples=current_samples, 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, editing_samples=False )}
 %endfor

    

[galaxy-commits] galaxy-dist commit 7ea4c156ae32: Add a pop-up menu for a sample if it is possible to either select datasets to transfer or transfer selected datasets for the sample. Also use better naming convention for a key variable name.

commits-noreply＠bitbucket.org