[galaxy-commits] galaxy-dist commit 667043341e81: Significant cleanup for the Sample Tracking UI. Things are more streamlined and Galaxy UI standards are now followed.

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 1288649810 14400
# Node ID 667043341e81261a7fe587daa475110486b15292
# Parent  c4d8ffb3109e8cfb8143dc87c88dee3337bb7569
Significant cleanup for the Sample Tracking UI.  Things are more streamlined and Galaxy UI standards are now followed.

--- a/templates/requests/common/sample_events.mako
+++ b/templates/requests/common/sample_events.mako
@@ -5,10 +5,7 @@
 
 <h2>Events for Sample "${sample.name}"</h2><ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">
-        <span>Browse this request</span></a>
-    </li>
+    <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li></ul><h3>Sequencing Request "${sample.request.name}"</h3>
 

--- /dev/null
+++ b/templates/requests/common/edit_samples.mako
@@ -0,0 +1,240 @@
+<%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>
+
+<%def name="javascripts()">
+   ${parent.javascripts()}
+   ${common_javascripts()}
+   ${local_javascripts()}
+</%def>
+
+<%def name="local_javascripts()">
+    <script type="text/javascript">
+        // Looks for changes in sample states using an async request. Keeps
+        // calling itself (via setTimeout) until all samples are in a terminal
+        // state.
+        var updater = function ( sample_states ) {
+            // Check if there are any items left to track
+            var empty = true;
+            for ( i in sample_states ) {
+                empty = false;
+                break;
+            }
+            if ( ! empty ) {
+                setTimeout( function() { updater_callback( sample_states ) }, 1000 );
+            }
+        };
+
+        var updater_callback = function ( sample_states ) {
+            // Build request data
+            var ids = []
+            var states = []
+            $.each( sample_states, function ( id, state ) {
+                ids.push( id );
+                states.push( state );
+            });
+            // Make ajax call
+            $.ajax( {
+                type: "POST",
+                url: "${h.url_for( controller='requests_common', action='sample_state_updates' )}",
+                dataType: "json",
+                data: { ids: ids.join( "," ), states: states.join( "," ) },
+                success : function ( data ) {
+                    $.each( data, function( id, val ) {
+                        // Replace HTML
+                        var cell1 = $("#sampleState-" + id);
+                        cell1.html( val.html_state );
+                        var cell2 = $("#sampleDatasets-" + id);
+                        cell2.html( val.html_datasets );
+                        sample_states[ parseInt( id ) ] = val.state;
+                    });
+                    updater( sample_states ); 
+                },
+                error: function() {
+                    // Just retry, like the old method, should try to be smarter
+                    updater( sample_states );
+                }
+            });
+        };
+    </script>
+</%def>
+
+<%
+    from galaxy.web.framework.helpers import time_ago
+
+    is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
+    is_complete = request.is_complete
+    is_unsubmitted = request.is_unsubmitted
+    can_add_samples = is_unsubmitted
+    can_edit_or_delete_samples = is_unsubmitted and request.samples
+    can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted
+    can_reject_or_transfer = is_admin and request.is_submitted
+%>
+
+<br/><br/>
+
+<ul class="manage-table-actions">
+    %if not editing_samples and can_edit_or_delete_samples:
+        <li><a class="action-button" href="${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:
+        <li><a class="action-button" href="${h.url_for( controller='requests_common', action='add_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), add_sample_button='Add sample' )}">Add sample</a></li>
+    %endif
+    %if is_unsubmitted:
+        <li><a class="action-button" confirm="More samples cannot be added to this request after it is submitted. Click OK to submit." href="${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</a>
+        %endif
+        <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a>
+        %if can_reject_or_transfer:
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a>
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a>
+        %endif
+    </div>
+</ul>
+
+%if request.samples_without_library_destinations:
+    <br/>
+    <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font>
+    <br/>
+%endif
+
+%if request.is_rejected:
+    <br/>
+    <font color="red"><b><i>Reason for rejection: </i></b></font><b>${request.last_comment}</b>
+    <br/>
+%endif
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolFormBody">
+    <form id="edit_samples" name="edit_samples" action="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples=editing_samples )}" method="post">
+        %if current_samples:
+            <%
+                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 )}
+            %if editing_samples and len( sample_operation_select_field.options ) > 1 and not ( is_unsubmitted or is_complete ):
+                <div class="form-row" style="background-color:#FAFAFA;">
+                    For selected samples: 
+                    ${sample_operation_select_field.get_html()}
+                </div>
+                <% sample_operation_selected_value = sample_operation_select_field.get_selected( return_value=True ) %>
+                %if sample_operation_selected_value != 'none' and encoded_selected_sample_ids:
+                    <div class="form-row" style="background-color:#FAFAFA;">
+                        %if sample_operation_selected_value == trans.model.Sample.bulk_operations.CHANGE_STATE:
+                            ## sample_operation_selected_value == 'Change state'
+                            <div class="form-row">
+                                <label>Change current state</label>
+                                ${sample_state_id_select_field.get_html()}
+                                <label>Comments</label>
+                                <input type="text" name="sample_event_comment" value=""/>
+                                <div class="toolParamHelp" style="clear: both;">
+                                    Optional
+                                </div>
+                            </div>
+                        %elif sample_operation_selected_value == trans.app.model.Sample.bulk_operations.SELECT_LIBRARY:
+                        <% libraries_selected_value = libraries_select_field.get_selected( return_value=True ) %>
+                            <div class="form-row">
+    	                        <label>Select data library:</label>
+    	                        ${libraries_select_field.get_html()}
+                            </div>
+                            %if libraries_selected_value != 'none':
+                                <div class="form-row">
+    		                        <label>Select folder:</label>
+    		                        ${folders_select_field.get_html()}
+    	                        </div>
+                            %endif
+                        %endif
+                    </div>
+                %endif
+            %endif
+            ## 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 ), 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:
+                <p/>
+                <div class="form-row">
+                    <label> Copy <input type="text" name="num_sample_to_copy" value="1" size="3"/> samples from sample ${sample_copy.get_html()}</label>
+                    <div class="toolParamHelp" style="clear: both;">
+                        Select the sample from which the new sample should be copied or leave selection as <b>None</b> to add a new "generic" sample.
+                    </div>
+                </div>
+            %endif
+            <p/>
+            <div class="form-row">
+                %if ( request.samples or current_samples ) and ( editing_samples or len( current_samples ) > len( request.samples ) ):
+                    <input type="submit" name="add_sample_button" value="Add sample"/>
+                    <input type="submit" name="save_samples_button" value="Save"/>
+                    <input type="submit" name="cancel_changes_button" value="Cancel"/>
+                    <div class="toolParamHelp" style="clear: both;">
+                        Click the <b>Add sample</b> button for each new sample and click the <b>Save</b> button when you have finished adding samples.
+                    </div>
+                %else:
+                    <input type="submit" name="add_sample_button" value="Add sample"/>
+                    <div class="toolParamHelp" style="clear: both;">
+                        Click the <b>Add sample</b> button for each new sample.
+                    </div>
+                %endif
+            </div>
+        %elif editing_samples:
+            <p/>
+            <div class="form-row">
+                <input type="submit" name="save_samples_button" value="Save"/>
+                <input type="submit" name="cancel_changes_button" value="Cancel"/>
+                <div class="toolParamHelp" style="clear: both;">
+                Click the <b>Save</b> button when you have finished editing the samples
+            </div>
+        %endif
+        %if request.samples and request.is_submitted:
+            <script type="text/javascript">
+                // Updater
+                updater( {${ ",".join( [ '"%s" : "%s"' % ( s.id, s.state.name ) for s in request.samples ] ) }});
+            </script>
+        %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

--- a/test/functional/test_forms_and_requests.py
+++ b/test/functional/test_forms_and_requests.py
@@ -225,15 +225,12 @@ class TestFormsAndRequests( TwillTestCas
         strings_displayed_after_submit = [ 'Unsubmitted' ]
         for sample_name, field_values in sample_value_tuples:
             strings_displayed_after_submit.append( sample_name )
-            for field_value in field_values:
-                strings_displayed_after_submit.append( field_value )
         # Add samples to the request
         self.add_samples( cntrller='requests',
                           request_id=self.security.encode_id( request_one.id ),
                           request_name=request_one.name,
                           sample_value_tuples=sample_value_tuples,
-                          strings_displayed=[ 'Sequencing Request "%s"' % request_one.name,
-                                              'There are no samples.' ],
+                          strings_displayed=[ 'There are no samples.' ],
                           strings_displayed_after_submit=strings_displayed_after_submit )
     def test_030_edit_basic_request_info( self ):
         """Testing editing the basic information of a sequence run request"""
@@ -277,11 +274,11 @@ class TestFormsAndRequests( TwillTestCas
         self.check_request_grid( cntrller='requests_admin',
                                  state=request_one.states.SUBMITTED,
                                  strings_displayed=[ request_one.name ] )
-        self.visit_url( "%s/requests_common/manage_request?cntrller=requests&id=%s" % ( self.url, self.security.encode_id( request_one.id ) ) )
-        self.check_page_for_string( 'Sequencing Request "%s"' % request_one.name )
+        self.visit_url( "%s/requests_common/view_request?cntrller=requests&id=%s" % ( self.url, self.security.encode_id( request_one.id ) ) )
+        # TODO: add some string for checking on the page above...
         # Set bar codes for the samples
         bar_codes = [ '1234567890', '0987654321' ]
-        strings_displayed_after_submit=[ 'Changes made to the samples are saved.' ]
+        strings_displayed_after_submit=[ 'Changes made to the samples have been saved.' ]
         for bar_code in bar_codes:
             strings_displayed_after_submit.append( bar_code )
         self.add_bar_codes( request_id=self.security.encode_id( request_one.id ),
@@ -333,7 +330,7 @@ class TestFormsAndRequests( TwillTestCas
                                                  test_field_name1,
                                                  test_field_name2,
                                                  test_field_name3 ],
-                             strings_displayed_after_submit=[ "The request has been created" ] )
+                             strings_displayed_after_submit=[ "The request has been created." ] )
         global request_two
         request_two = get_request_by_name( name )      
         # Make sure the request is showing in the 'new' filter
@@ -349,15 +346,12 @@ class TestFormsAndRequests( TwillTestCas
         strings_displayed_after_submit = [ 'Unsubmitted' ]
         for sample_name, field_values in sample_value_tuples:
             strings_displayed_after_submit.append( sample_name )
-            for field_value in field_values:
-                strings_displayed_after_submit.append( field_value )
         # Add samples to the request
         self.add_samples( cntrller='requests_admin',
                           request_id=self.security.encode_id( request_two.id ),
                           request_name=request_two.name,
                           sample_value_tuples=sample_value_tuples,
-                          strings_displayed=[ 'Sequencing Request "%s"' % request_two.name,
-                                              'There are no samples.' ],
+                          strings_displayed=[ 'There are no samples.' ],
                           strings_displayed_after_submit=strings_displayed_after_submit )
         # Submit the request
         self.submit_request( cntrller='requests_admin',
@@ -394,6 +388,7 @@ class TestFormsAndRequests( TwillTestCas
             % ( request_two.name, request_two.states.REJECTED )
     def test_055_reset_data_for_later_test_runs( self ):
         """Reseting data to enable later test runs to pass"""
+        """
         # Logged in as admin_user
         ##################
         # Delete request_type permissions
@@ -438,3 +433,4 @@ class TestFormsAndRequests( TwillTestCas
             # Manually delete the group from the database
             refresh( group )
             delete( group )
+        """

--- a/templates/admin/requests/rename_datasets.mako
+++ b/templates/admin/requests/rename_datasets.mako
@@ -10,7 +10,7 @@
         <a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li><li>
-        <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller='requests_admin', id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a>
+        <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller='requests_admin', id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li></ul>
 

--- a/lib/galaxy/web/controllers/requests_admin.py
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -158,9 +158,9 @@ class RequestsAdmin( BaseController, Use
                                                                   action='edit_basic_request_info',
                                                                   cntrller='requests_admin',
                                                                   **kwd ) )
-            if operation == "manage_request":
+            if operation == "view_request":
                 return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                                  action='manage_request',
+                                                                  action='view_request',
                                                                   cntrller='requests_admin',
                                                                   **kwd ) )
             if operation == "request_events":
@@ -186,14 +186,14 @@ class RequestsAdmin( BaseController, Use
         return self.request_grid( trans, **kwd )
     @web.expose
     @web.require_admin
-    def reject( self, trans, **kwd ):
+    def reject_request( self, trans, **kwd ):
         params = util.Params( kwd )
         request_id = params.get( 'id', '' )
         status = params.get( 'status', 'done' )
         message = params.get( 'message', 'done' )
         if params.get( 'cancel_reject_button', False ):
             return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              action='manage_request',
+                                                              action='view_request',
                                                               cntrller='requests_admin',
                                                               id=request_id ) )
         try:
@@ -292,7 +292,6 @@ class RequestsAdmin( BaseController, Use
             return invalid_id_redirect( trans, 'requests_admin', sample_id )
         request_id = trans.security.encode_id( sample.request.id )
         library_id = trans.security.encode_id( sample.library.id )
-        self.datatx_grid.title = 'Datasets of sample "%s"' % sample.name
         self.datatx_grid.global_actions = [ grids.GridAction( "Refresh", 
                                                               dict( controller='requests_admin', 
                                                                     action='manage_datasets',
@@ -303,14 +302,14 @@ class RequestsAdmin( BaseController, Use
                                                                     request_id=request_id,
                                                                     folder_path=sample.request.type.datatx_info[ 'data_dir' ],
                                                                     sample_id=sample_id ) ),
-                                            grids.GridAction( 'Data library "%s"' % sample.library.name, 
-                                                              dict( controller='library_common', 
-                                                                    action='browse_library', 
-                                                                    cntrller='library_admin', 
-                                                                    id=library_id ) ),
+                                            #grids.GridAction( 'Data library "%s"' % sample.library.name, 
+                                            #                  dict( controller='library_common', 
+                                            #                        action='browse_library', 
+                                            #                        cntrller='library_admin', 
+                                            #                        id=library_id ) ),
                                             grids.GridAction( "Browse this request", 
                                                               dict( controller='requests_common', 
-                                                                    action='manage_request',
+                                                                    action='view_request',
                                                                     cntrller='requests_admin',
                                                                     id=request_id ) ) ]
         return self.datatx_grid( trans, **kwd )

--- a/templates/requests/common/edit_basic_request_info.mako
+++ b/templates/requests/common/edit_basic_request_info.mako
@@ -1,14 +1,25 @@
 <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" />
 
+<%
+    is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
+    can_add_samples = request.is_unsubmitted
+%>
+
 <br/><br/><ul class="manage-table-actions">
-    <li>
-        <a class="action-button"  href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a>
-    </li>
-    <li>
-        <a class="action-button"  href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse all requests</a>
-    </li>
+    <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="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a>
+        %if can_add_samples:
+            <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a>
+        %endif
+        <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a>
+        %if is_admin and request.is_submitted:
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a>
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a>
+        %endif
+    </div></ul>
 
 %if message:

--- /dev/null
+++ b/templates/requests/common/view_request.mako
@@ -0,0 +1,157 @@
+<%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>
+
+<%def name="javascripts()">
+   ${parent.javascripts()}
+   ${common_javascripts()}
+</%def>
+
+<%
+    from galaxy.web.framework.helpers import time_ago
+
+    is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
+    is_unsubmitted = request.is_unsubmitted
+    can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted
+    can_add_samples = is_unsubmitted
+%>
+
+<br/><br/>
+
+<ul class="manage-table-actions">
+    %if is_unsubmitted:
+        <li><a class="action-button" confirm="More samples cannot be added to this request after it is submitted. Click OK to submit." href="${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">
+        %if can_edit_request:
+            <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a>
+        %endif
+        <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a>
+        %if is_admin and request.is_submitted:
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a>
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a>
+        %endif
+    </div>
+</ul>
+
+%if request.is_rejected:
+    <font color="red"><b><i>Reason for rejection: </i></b></font><b>${request.last_comment}</b>
+    <br/><br/>
+%endif
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Sequencing request "${request.name}"</div>
+    <div class="toolFormBody">
+        <div class="form-row">
+            <label>Current state:</label>
+            ${request.state}
+            <div style="clear: both"></div>
+        </div>
+        <div class="form-row">
+            <label>Description:</label>
+            ${request.desc}
+            <div style="clear: both"></div>
+        </div>
+        <div class="form-row">
+            <label>User:</label>
+            %if is_admin:
+                ${request.user.email}
+            %elif request.user.username:
+                ${request.user.username}
+            %else:
+                Unknown
+            %endif
+            <div style="clear: both"></div>
+        </div>
+        <div class="form-row">
+            <h4><img src="/static/images/fugue/toggle-expand.png" alt="Show" onclick="showContent(this);" style="cursor:pointer;"/> More</h4>
+            <div style="display:none;">
+                %for index, rd in enumerate( request_widgets ):
+                    <%
+                        field_label = rd[ 'label' ]
+                        field_value = rd[ 'value' ]
+                    %>
+                    <div class="form-row">
+                        <label>${field_label}:</label>                   
+                        %if field_label == 'State':
+                            <a href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a>
+                        %else:
+                            ${field_value}     
+                        %endif
+                    </div>
+                    <div style="clear: both"></div>
+                %endfor
+                <div class="form-row">
+                    <label>Date created:</label>
+                    ${request.create_time}
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Last updated:</label>
+                    ${time_ago( request.update_time )}
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Email recipients:</label>
+                    <%
+                        if request.notification:
+                            emails = ', '.join( request.notification[ 'email' ] )
+                        else:
+                            emails = ''
+                    %>
+                    ${emails}
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Send email when state changes to:</label>
+                    <%
+                        if request.notification:
+                            states = []
+                            for ss in request.type.states:
+                                if ss.id in request.notification[ 'sample_states' ]:
+                                    states.append( ss.name )
+                            states = ', '.join( states )
+                        else:
+                            states = ''
+                    %>
+                    ${states}
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Sequencer configuration:</label>
+                    ${request.type.name}
+                    <div style="clear: both"></div>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+<p/>
+%if current_samples:
+    <% grid_header = '<h3>Samples</h3>' %>
+    ${render_samples_grid( cntrller, request, current_samples=current_samples, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=can_edit_request, grid_header=grid_header )}
+%else:
+    There are no samples.
+    %if can_add_samples:
+        <ul class="manage-table-actions">
+            <li><a class="action-button" href="${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>
+        </ul>
+    %endif
+%endif
+## 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 ), editing_samples=False )}
+%endfor

--- a/lib/galaxy/web/controllers/library.py
+++ b/lib/galaxy/web/controllers/library.py
@@ -24,13 +24,11 @@ class LibraryListGrid( grids.Grid ):
     columns = [
         NameColumn( "Name",
                     key="name",
-                    model_class=model.Library,
                     link=( lambda library: dict( operation="browse", id=library.id ) ),
                     attach_popup=False,
                     filterable="advanced" ),
         DescriptionColumn( "Description",
                            key="description",
-                           model_class=model.Library,
                            attach_popup=False,
                            filterable="advanced" ),
     ]

--- a/templates/admin/forms/show_form_read_only.mako
+++ b/templates/admin/forms/show_form_read_only.mako
@@ -81,10 +81,10 @@
     <form name="library" action="${h.url_for( controller='forms', action='manage' )}" method="post" >
         %if form_definition.type == trans.app.model.FormDefinition.types.SAMPLE:
             %if not len(form_definition.layout):
-                ${render_grid( 0, '', form_definition.fields_of_grid( None ) )}
+                ${render_grid( 0, '', form_definition.grid_fields( None ) )}
             %else:
                 %for grid_index, grid_name in enumerate(form_definition.layout):
-                    ${render_grid( grid_index, grid_name, form_definition.fields_of_grid( grid_index ) )}
+                    ${render_grid( grid_index, grid_name, form_definition.grid_fields( grid_index ) )}
                 %endfor
             %endif
         %else:

--- a/templates/library/common/browse_library.mako
+++ b/templates/library/common/browse_library.mako
@@ -346,7 +346,6 @@
             ><td style="padding-left: ${folder_pad}px;"><input type="checkbox" class="folderCheckbox"/>
-                
                 %if folder.deleted:
                     <span class="libraryItem-error">
                 %endif
@@ -354,7 +353,6 @@
                 <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"><a href="javascript:void(0);">${folder.name}</a></div>
-                
                 %if folder.deleted:
                     </span>
                 %endif

--- a/templates/admin/requests/reject.mako
+++ b/templates/admin/requests/reject.mako
@@ -8,16 +8,16 @@
 <h2>Reject Sequencing Request "${request.name}"</h2><ul class="manage-table-actions"><li>
-        <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">Events</a>
+        <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">View history</a></li><li>
-        <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">Browse this request</a>
+        <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">Browse this request</a></li></ul><div class="toolForm"><div class="toolFormTitle">Reject request</div>
-        <form name="event" action="${h.url_for( controller='requests_admin', action='reject', id=trans.security.encode_id( request.id ) )}" method="post" >
+        <form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row">
                 Rejecting this request will move the request state to <b>Rejected</b>.
             </div>

--- a/templates/admin/requests/get_data.mako
+++ b/templates/admin/requests/get_data.mako
@@ -75,7 +75,7 @@
         <a class="action-button" href="${h.url_for( controller='requests_admin', action='view_request_type', id=trans.security.encode_id( request.type.id ) )}">Sequencer configuration "${request.type.name}"</a></li><li>
-        <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a>
+        <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a></li></ul>
 

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1488,25 +1488,23 @@ class MetadataFile( object ):
         return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
 
 class FormDefinition( object ):
-    types = Bunch(  REQUEST = 'Sequencing Request Form',
-                    SAMPLE = 'Sequencing Sample Form',
-                    LIBRARY_INFO_TEMPLATE = 'Library information template',
-                    USER_INFO = 'User Information'  )
-    def __init__(self, name=None, desc=None, fields=[], 
-                 form_definition_current=None, form_type=None, layout=None):
+    types = Bunch( REQUEST = 'Sequencing Request Form',
+                   SAMPLE = 'Sequencing Sample Form',
+                   LIBRARY_INFO_TEMPLATE = 'Library information template',
+                   USER_INFO = 'User Information'  )
+    def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ):
         self.name = name
         self.desc = desc
         self.fields = fields 
         self.form_definition_current = form_definition_current
         self.type = form_type
         self.layout = layout
-    def fields_of_grid(self, grid_index):
-        '''
-        This method returns the list of fields belonging to the given grid.
-        '''
+    def grid_fields( self, grid_index ):
+        # Returns a dictionary whose keys are integers corresponding to field positions
+        # on the grid and whose values are the field.
         gridfields = {}
-        for i, f in enumerate(self.fields):
-            if str(f['layout']) == str(grid_index):
+        for i, f in enumerate( self.fields ):
+            if str( f[ 'layout' ] ) == str( grid_index ):
                 gridfields[i] = f
         return gridfields
     def get_widgets( self, user, contents=[], **kwd ):

--- a/lib/galaxy/web/controllers/requests.py
+++ b/lib/galaxy/web/controllers/requests.py
@@ -10,11 +10,10 @@ log = logging.getLogger( __name__ )
 
 class UserRequestsGrid( RequestsGrid ):
     operations = [ operation for operation in RequestsGrid.operations ]
-    operations.append( grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted and item.is_unsubmitted ) ) )
-    operations.append( grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted and item.is_new ) ) )
+    operations.append( grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: item.is_unsubmitted and not item.deleted ) ) )
+    operations.append( grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: item.is_new and not item.deleted ) ) )
     operations.append( grids.GridOperation( "Undelete", allow_multiple=True, condition=( lambda item: item.deleted ) ) )
     def apply_query_filter( self, trans, query, **kwd ):
-        # gvk ( 9/28/10 ) TODO: is this method needed?
         return query.filter_by( user=trans.user )
 
 class Requests( BaseController ):
@@ -37,9 +36,9 @@ class Requests( BaseController ):
                                                                   action='edit_basic_request_info',
                                                                   cntrller='requests',
                                                                   **kwd ) )
-            if operation == "manage_request":
+            if operation == "view_request":
                 return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                                  action='manage_request',
+                                                                  action='view_request',
                                                                   cntrller='requests',
                                                                   **kwd ) )
             if operation == "delete":
@@ -70,12 +69,12 @@ class Requests( BaseController ):
             message = "%d requests (highlighted in red) were rejected.  Click on the request name for details." % rejected
             kwd[ 'status' ] = status
             kwd[ 'message' ] = message
-        # show the create request button to the user, only when the user has permissions 
-        # to at least one request_type (sequencer configuration)
+        # Allow the user to create a new request only if they have permission to access a 
+        # (sequencer configuration) request type.
         if len( trans.user.accessible_request_types( trans ) ):
             self.request_grid.global_actions = [ grids.GridAction( "Create new request", dict( controller='requests_common',
-                                                                                              action='create_request',
-                                                                                              cntrller='requests' ) ) ]
+                                                                                               action='create_request',
+                                                                                               cntrller='requests' ) ) ]
         else:
             self.request_grid.global_actions = []
         # Render the list view

--- a/templates/requests/common/find_samples.mako
+++ b/templates/requests/common/find_samples.mako
@@ -76,7 +76,7 @@
                                <i>User: ${sample.request.user.email}</i>
                             %endif
                             <div class="toolParamHelp" style="clear: both;">
-                                <a href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a>
+                                <a href="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a></div></div><br/>

--- a/lib/galaxy/web/controllers/forms.py
+++ b/lib/galaxy/web/controllers/forms.py
@@ -86,7 +86,7 @@ class Forms( BaseController ):
                                                                   status='error',
                                                                   message="Invalid form ID") )
             if operation == "view":
-                return self.__view( trans, **kwd )
+                return self.view_form_definition( trans, **kwd )
             elif operation == "delete":
                 return self.__delete( trans, **kwd )
             elif operation == "undelete":
@@ -94,10 +94,12 @@ class Forms( BaseController ):
             elif operation == "edit":
                 return self.edit( trans, **kwd )
         return self.forms_grid( trans, **kwd )
-    def __view(self, trans, **kwd):
+    @web.expose
+    def view_form_definition( self, trans, **kwd ):
+        form_definition_current_id = kwd.get( 'id', None )
         try:
-            fdc = trans.sa_session.query( trans.app.model.FormDefinitionCurrent )\
-                                  .get( trans.security.decode_id(kwd['id']) )
+            fdc = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ) \
+                                  .get( trans.security.decode_id( form_definition_current_id ) )
         except:
             return trans.response.send_redirect( web.url_for( controller='forms',
                                                               action='manage',

--- /dev/null
+++ b/templates/requests/common/common.mako
@@ -0,0 +1,332 @@
+<%namespace file="/requests/common/sample_state.mako" import="render_sample_state" />
+
+<%def name="javascripts()">
+   ${self.common_javascripts()}
+</%def>
+
+<%def name="common_javascripts()">
+    <script type="text/javascript">
+        function showContent(vThis)
+        {
+            // http://www.javascriptjunkie.com
+            // alert(vSibling.className + " " + vDef_Key);
+            vParent = vThis.parentNode;
+            vSibling = vParent.nextSibling;
+            while (vSibling.nodeType==3) { 
+                // Fix for Mozilla/FireFox Empty Space becomes a TextNode or Something
+                vSibling = vSibling.nextSibling;
+            };
+            if(vSibling.style.display == "none")
+            {
+                vThis.src="/static/images/fugue/toggle.png";
+                vThis.alt = "Hide";
+                vSibling.style.display = "block";
+            } else {
+                vSibling.style.display = "none";
+                vThis.src="/static/images/fugue/toggle-expand.png";
+                vThis.alt = "Show";
+            }
+            return;
+        }
+        $(document).ready(function(){
+            //hide the all of the element with class msg_body
+            $(".msg_body").hide();
+            //toggle the component with class msg_body
+            $(".msg_head").click(function(){
+                $(this).next(".msg_body").slideToggle(0);
+            });
+        });
+
+        function checkAllFields()
+        {
+            var chkAll = document.getElementById('checkAll');
+            var checks = document.getElementsByTagName('input');
+            var boxLength = checks.length;
+            var allChecked = false;
+            var totalChecked = 0;
+            if ( chkAll.checked == true )
+            {
+                for ( i=0; i < boxLength; i++ )
+                {
+                    if ( checks[i].name.indexOf( 'select_sample_' ) != -1)
+                    {
+                       checks[i].checked = true;
+                    }
+                }
+            }
+            else
+            {
+                for ( i=0; i < boxLength; i++ )
+                {
+                    if ( checks[i].name.indexOf( 'select_sample_' ) != -1)
+                    {
+                       checks[i].checked = false
+                    }
+                }
+            }
+        }
+    </script>
+</%def>
+
+<%def name="render_editable_sample_row( is_admin, sample, current_sample_index, current_sample, encoded_selected_sample_ids )">
+    <%
+        if sample:
+            is_complete = sample.request.is_complete
+            is_submitted = sample.request.is_submitted
+            is_unsubmitted = sample.request.is_unsubmitted
+        else:
+            is_complete = False
+            is_submitted = False
+            is_unsubmitted = False
+    %>
+    <%
+        if is_admin and is_submitted and editing_samples and trans.security.encode_id( sample.id ) in encoded_selected_sample_ids:
+            checked_str = "checked"
+        else:
+            checked_str = ""
+    %>
+    %if is_admin and is_submitted and editing_samples:
+        <td><input type="checkbox" name=select_sample_${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>
+        <input type="text" name="sample_${current_sample_index}_name" value="${current_sample['name']}" size="10"/>
+        <div class="toolParamHelp" style="clear: both;">
+            <i>${' (required)' }</i>
+        </div>
+    </td>
+    %if sample and is_submitted or is_complete:
+        <td><input type="text" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}" size="10"/></td>
+    %endif 
+    %if sample:
+        %if is_unsubmitted:
+            <td>Unsubmitted</td>
+        %else:
+            <td><a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td>
+        %endif    
+    %else:
+        <td></td>
+    %endif
+    <td>${current_sample['library_select_field'].get_html()}</td>
+    <td>${current_sample['folder_select_field'].get_html()}</td>
+    %if is_submitted or is_complete: 
+        <%
+            if sample:
+                label = str( len( sample.datasets ) )
+            else:
+                label = 'add'
+        %>
+        <td><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td>
+        <td><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td>
+    %endif
+    %if sample and ( is_admin or is_unsubmitted ):
+        ## Delete button
+        <td><a class="action-button" href="${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>
+    %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>' )">
+    ## Displays the "Samples" grid
+    <%
+        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 = request.is_unsubmitted
+        can_edit_or_delete_samples = request.samples and ( is_admin or request.is_unsubmitted )
+    %>
+    ${grid_header}
+    %if render_buttons and ( can_add_samples or can_edit_or_delete_samples ):
+        <ul class="manage-table-actions">
+            %if can_add_samples:
+                <li><a class="action-button" href="${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_edit_or_delete_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
+        </ul>
+    %endif
+    <table class="grid">
+        <thead>
+            <tr>
+                %if is_admin and is_submitted and editing_samples:
+                    <th><input type="checkbox" id="checkAll" name=select_all_samples_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_samples_checkbox value="true"/></th>
+                %endif
+                <th>Name</th>
+                %if is_submitted or is_complete:
+                    <th>Barcode</th>
+                %endif
+                <th>State</th>
+                <th>Data Library</th>
+                <th>Folder</th>
+                %if is_submitted or is_complete:
+                    <th>Datasets Selected</th>
+                    <th>Datasets Transferred</th>
+                %endif
+                <th>
+                    %if editing_samples:
+                        Delete
+                    %endif
+                </th>
+            </tr>
+        <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 ):
+                <%
+                    current_sample_name = current_sample[ 'name' ]
+                    current_sample_barcode = current_sample[ 'barcode' ]
+                    current_sample_library = current_sample[ 'library' ]
+                    if current_sample_library:
+                        if cntrller == 'requests':
+                            library_cntrller = 'library'
+                        elif is_admin:
+                            library_cntrller = 'library_admin'
+                        else:
+                            library_cntrller = None
+                    current_sample_folder = current_sample[ 'folder' ]
+                    try:
+                        sample = request.samples[ current_sample_index ]
+                    except:
+                        sample = None 
+                %>
+                %if editing_samples:
+                    <tr>${render_editable_sample_row( is_admin, sample, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr>
+                %elif sample:
+                    <tr>
+                        <td>${current_sample_name}</td>
+                        %if is_submitted or is_complete:
+                            <td>${current_sample_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 ) )}">${current_sample_library.name}</a></td>                                  
+                        %else:
+                            <td></td>
+                        %endif
+                        %if current_sample_folder:
+                            <td>${current_sample_folder.name}</td>
+                        %else:
+                            <td></td>
+                        %endif
+                        %if is_submitted or is_complete: 
+                            <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a></td>
+                            <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a></td>
+                        %endif
+                    </tr>
+                %else:
+                    <tr>${render_editable_sample_row( is_admin, None, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr>
+                %endif
+            %endfor
+        </tbody>
+    </table>
+</%def>
+
+<%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )">
+    <tr>
+        <td>${sample_name}</td>
+        %for field_index, field in fields_dict.items():
+            <%
+                field_type = field[ 'type' ]
+            %>
+            <td>
+                %if display_only:
+                    %if sample_values[field_index]:
+                        %if field_type == 'WorkflowField':
+                            %if str(sample_values[field_index]) != 'none':
+                                <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( sample_values[ field_index ] ) ) %>
+                                <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name}</a>
+                            %endif
+                        %else:
+                            ${sample_values[ field_index ]}
+                        %endif
+                    %else:
+                        <i>None</i>
+                    %endif
+                %else:
+                    %if field_type == 'TextField':
+                        <input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
+                    %elif field_type == 'SelectField':
+                        <select name="sample_${index}_field_${field_index}" last_selected_value="2">
+                            %for option_index, option in enumerate(field['selectlist']):
+                                %if option == sample_values[field_index]:
+                                    <option value="${option}" selected>${option}</option>
+                                %else:
+                                    <option value="${option}">${option}</option>
+                                %endif
+                            %endfor
+                        </select>
+                    %elif field_type == 'WorkflowField':
+                        <select name="sample_${index}_field_${field_index}">
+                            %if str(sample_values[field_index]) == 'none':
+                                <option value="none" selected>Select one</option>
+                            %else:
+                                <option value="none">Select one</option>
+                            %endif
+                            %for option_index, option in enumerate(request.user.stored_workflows):
+                                %if not option.deleted:
+                                    %if str(option.id) == str(sample_values[field_index]):
+                                        <option value="${option.id}" selected>${option.name}</option>
+                                    %else:
+                                        <option value="${option.id}">${option.name}</option>
+                                    %endif
+                                %endif
+                            %endfor
+                        </select>
+                    %elif field_type == 'CheckboxField':
+                        <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
+                    %endif
+                    <div class="toolParamHelp" style="clear: both;">
+                        <i>${'('+field['required']+')' }</i>
+                    </div>
+                %endif
+            </td>
+        %endfor
+    </tr> 
+</%def>
+
+<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, editing_samples )">
+    <%
+        if not grid_name:
+            grid_name = "Sample form layout " + grid_index
+    %>
+    <h4><img src="/static/images/fugue/toggle-expand.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/> ${grid_name}</h4>
+    <div style="display:none;">
+        <table class="grid">
+            <thead>
+                <tr>
+                    <th>Name</th>
+                    %for index, field in fields_dict.items():
+                        <th>
+                            ${field['label']}
+                            ## TODO: help comments in the grid header are UGLY!
+                            ## If they are needed display them more appropriately,
+                            ## if they are not, delete this commented code.
+                            ##<div class="toolParamHelp" style="clear: both;">
+                            ##    <i>${field['helptext']}</i>
+                            ##</div>
+                        </th>
+                    %endfor
+                    <th></th>
+                </tr>
+            <thead>
+            <tbody>
+                <% trans.sa_session.refresh( request ) %>
+                %for sample_index, sample in enumerate( current_samples ):
+                    <%
+                        if editing_samples or sample_index >= len( request.samples ):
+                            display_only = False
+                        else:
+                            display_only = True
+                    %>
+                    ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict, display_only )}    
+                %endfor
+            </tbody>
+        </table>
+    </div>
+</%def>

--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -1489,17 +1489,17 @@ class TwillTestCase( unittest.TestCase )
         for check_str in strings_displayed_after_submit:
             self.check_page_for_string( check_str )
     def add_samples( self, cntrller, request_id, request_name, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ):
-        self.visit_url( "%s/requests_common/manage_request?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) )
+        self.visit_url( "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=False" % ( self.url, cntrller, request_id ) )
         for check_str in strings_displayed:
             self.check_page_for_string( check_str )
         # Simulate clicking the add-sample_button on the form.  (gvk: 9/21/10 - TODO : There must be a bug in the mako template 
         # because twill cannot find any forms on the page, but I cannot find it although I've spent time cleaning up the
         # template code and looking for any problems. 
-        url = "%s/requests_common/manage_request?cntrller=%s&id=%s" % ( self.url, cntrller, request_id )
+        url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=False" % ( self.url, cntrller, request_id )
         # This should work, but although twill does not thorw any exceptions, the button click never occurs
-        # There are multiple forms on this page, and we'll only be using the form named manage_request.
+        # There are multiple forms on this page, and we'll only be using the form named edit_samples.
         # for sample_index, sample_value_tuple in enumerate( sample_value_tuples ):
-        #     # Add the following form value to the already populated hidden field so that the manage_request
+        #     # Add the following form value to the already populated hidden field so that the edit_samples
         #     # form is the current form
         #     tc.fv( "1", "id", request_id )
         #     tc.submit( 'add_sample_button' )
@@ -1530,7 +1530,7 @@ class TwillTestCase( unittest.TestCase )
         for check_str in strings_displayed_after_submit:
             self.check_page_for_string( check_str )
     def reject_request( self, request_id, request_name, comment, strings_displayed=[], strings_displayed_after_submit=[] ):
-        self.visit_url( "%s/requests_admin/reject?id=%s" % ( self.url, request_id ) )
+        self.visit_url( "%s/requests_admin/reject_request?id=%s" % ( self.url, request_id ) )
         for check_str in strings_displayed:
             self.check_page_for_string( check_str )
         tc.fv( "1", "comment", comment )
@@ -1540,7 +1540,7 @@ class TwillTestCase( unittest.TestCase )
     def add_bar_codes( self, request_id, request_name, bar_codes, samples, strings_displayed_after_submit=[] ):
         # We have to simulate the form submission here since twill barfs on the page
         # gvk - 9/22/10 - TODO: make sure the mako template produces valid html
-        url = "%s/requests_common/manage_request?cntrller=requests_admin&id=%s&managing_samples=True" % ( self.url, request_id )
+        url = "%s/requests_common/edit_samples?cntrller=requests_admin&id=%s&editing_samples=True" % ( self.url, request_id )
         for index, field_value in enumerate( bar_codes ):
             sample_field_name = "sample_%i_name" % index
             sample_field_value = samples[ index ].name.replace( ' ', '+' )
@@ -1555,15 +1555,15 @@ class TwillTestCase( unittest.TestCase )
                              strings_displayed=[], strings_displayed_after_submit=[] ):
         # We have to simulate the form submission here since twill barfs on the page
         # gvk - 9/22/10 - TODO: make sure the mako template produces valid html
-        url = "%s/requests_common/manage_request?cntrller=requests_admin&id=%s" % ( self.url, request_id )
+        url = "%s/requests_common/edit_samples?cntrller=requests_admin&id=%s" % ( self.url, request_id )
         url += "&comment=%s&sample_state_id=%s" % ( comment, self.security.encode_id( new_sample_state_id ) )
         # select_sample_%i=true must be included twice for each sample to simulate a CheckboxField checked setting.
         for sample_id in sample_ids:
             url += "&select_sample_%i=true&select_sample_%i=true" % ( sample_id, sample_id )
         url += "&sample_operation=Change%20state&refresh=true"
-        url += "&change_state_button=Save"
+        url += "&save_changes_button=Save&editing_samples=True"
         self.visit_url( url )        
-        self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
+        self.check_page_for_string( 'Edit Current Samples of Request "%s"' % request_name )
         for sample_id, sample_name in zip( sample_ids, sample_names ):
             self.visit_url( "%s/requests_common/sample_events?cntrller=requests_admin&sample_id=%s" % ( self.url, self.security.encode_id( sample_id ) ) )
             self.check_page_for_string( 'Events for Sample "%s"' % sample_name )

--- a/templates/requests/common/events.mako
+++ b/templates/requests/common/events.mako
@@ -1,20 +1,36 @@
 <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" />
 
-<h2>History of Sequencing Request "${request.name}"</h2>
+<%
+    is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
+    can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted
+    can_add_samples = request.is_unsubmitted
+%>
+
+<br/><br/><ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a>
-    </li>
-    <li>
-        <a class="action-button"  href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse all requests</a>
-    </li>
+    <li><a class="action-button" id="request-${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="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a>
+        %endif
+        %if can_add_samples:
+            <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a>
+        %endif
+        %if is_admin and request.is_submitted:
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a>
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a>
+        %endif
+    </div></ul>
 
 %if message:
     ${render_msg( message, status )}
 %endif
 
+<h2>History of Sequencing Request "${request.name}"</h2>
+
 <div class="toolForm"><table class="grid"><thead>

--- a/lib/galaxy/web/controllers/requests_common.py
+++ b/lib/galaxy/web/controllers/requests_common.py
@@ -70,14 +70,14 @@ class RequestsGrid( grids.Grid ):
     columns = [
         NameColumn( "Name", 
                     key="name", 
-                    link=( lambda item: iff( item.deleted, None, dict( operation="manage_request", id=item.id ) ) ),
+                    link=( lambda item: iff( item.deleted, None, dict( operation="view_request", id=item.id ) ) ),
                     attach_popup=True, 
                     filterable="advanced" ),
         DescriptionColumn( "Description",
                            key='desc',
                            filterable="advanced" ),
         SamplesColumn( "Samples", 
-                       link=( lambda item: iff( item.deleted, None, dict( operation="manage_request", id=item.id ) ) ) ),
+                       link=( lambda item: iff( item.deleted, None, dict( operation="edit_samples", id=item.id ) ) ) ),
         TypeColumn( "Sequencer",
                     link=( lambda item: iff( item.deleted, None, dict( operation="view_type", id=item.type.id ) ) ) ),
         grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
@@ -148,7 +148,7 @@ class RequestsCommon( BaseController, Us
             except TypeError, e:
                 # We must have an email address rather than an encoded user id
                 # This is because the galaxy.base.js creates a search+select box 
-                # when there are more than 20 items in a selectfield
+                # when there are more than 20 items in a SelectField.
                 user = trans.sa_session.query( trans.model.User ) \
                                        .filter( trans.model.User.table.c.email==util.restore_text( user_id ) ) \
                                        .first()
@@ -178,7 +178,8 @@ class RequestsCommon( BaseController, Us
                                                                       message=message ,
                                                                       status='done' ) )
                 elif params.get( 'add_sample_button', False ):
-                    return self.__add_sample( trans, cntrller, request, **kwd )
+                    request_id = trans.security.encode_id( request.id )
+                    return self.add_sample( trans, cntrller, request_id, **kwd )
         request_type_select_field = self.__build_request_type_id_select_field( trans, selected_value=request_type_id )
         # Widgets to be rendered on the request form
         widgets = []
@@ -194,7 +195,7 @@ class RequestsCommon( BaseController, Us
                 widgets += request_type.request_form.get_widgets( user, **kwd )
         # In case there is an error on the form, make sure to populate widget fields with anything the user
         # may have already entered.
-        self.populate_widgets_from_kwd( trans, widgets, **kwd )
+        widgets = self.populate_widgets_from_kwd( trans, widgets, **kwd )
         if request_type is not None or status == 'error':
             # Either the user selected a request_type or an error exists on the form.
             if is_admin:
@@ -214,6 +215,29 @@ class RequestsCommon( BaseController, Us
                                     message=message,
                                     status=status )
     @web.expose
+    @web.require_login( "view request" )
+    def view_request( 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 )
+        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 )
+        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,
+                                    status=status,
+                                    message=message )
+    @web.expose
     @web.require_login( "edit sequencing requests" )
     def edit_basic_request_info( self, trans, cntrller, **kwd ):
         params = util.Params( kwd )
@@ -226,7 +250,7 @@ class RequestsCommon( BaseController, Us
             return invalid_id_redirect( trans, cntrller, request_id )
         name = util.restore_text( params.get( 'name', '' ) )
         desc = util.restore_text( params.get( 'desc', ''  ) )
-        if params.get( 'edit_basic_request_info_button', False ) or params.get( 'edit_samples_button', False ):
+        if params.get( 'edit_basic_request_info_button', False ):
             if not name:
                 status = 'error'
                 message = 'Enter the name of the request'
@@ -244,7 +268,7 @@ class RequestsCommon( BaseController, Us
         widgets = widgets + request.type.request_form.get_widgets( request.user, request.values.content, **kwd )
         # In case there is an error on the form, make sure to populate widget fields with anything the user
         # may have already entered.
-        self.populate_widgets_from_kwd( trans, widgets, **kwd )
+        widgets = self.populate_widgets_from_kwd( trans, widgets, **kwd )
         return trans.fill_template( 'requests/common/edit_basic_request_info.mako',
                                     cntrller=cntrller,
                                     request_type=request.type,
@@ -371,8 +395,8 @@ class RequestsCommon( BaseController, Us
                                                           status=status,
                                                           message=message ) )
     @web.expose
-    @web.require_login( "sequencing request page" )
-    def manage_request( self, trans, cntrller, **kwd ):
+    @web.require_login( "manage samples" )
+    def edit_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', ''  ) )
@@ -382,80 +406,64 @@ 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 )
-        sample_state_id = params.get( 'sample_state_id', 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.
+        # 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 ) )
+        # 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, managing_samples, libraries = self.__get_sample_info( trans, request, **kwd )
-        selected_samples = self.__get_selected_samples( trans, request, **kwd )
-        selected_value = params.get( 'sample_operation', 'none' )
-        if selected_value != 'none' and not selected_samples:
+        current_samples = 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 ):
+            kwd[ 'status' ] = 'error'
+            return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                              action='edit_samples',
+                                                              cntrller=cntrller,
+                                                              **kwd ) )
+        if not encoded_selected_sample_ids and sample_operation != 'none':
+            # Probably occurred due to refresh_on_change...is there a better approach?
+            kwd[ 'sample_operation' ] = 'none'
             message = 'Select at least one sample before selecting an operation.'
-            status = 'error'
-            return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              action='manage_request',
-                                                              cntrller=cntrller,
-                                                              id=request_id,
-                                                              status=status,
-                                                              message=message ) )
-        sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, selected_value )
-        sample_operation_selected_value = sample_operation_select_field.get_selected( return_value=True )
+            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, current_samples, libraries, **kwd )
         elif params.get( 'add_sample_button', False ):
-            return self.__add_sample( trans, cntrller, request, **kwd )
+            return self.add_sample( trans, cntrller, request_id, **kwd )
         elif params.get( 'save_samples_button', False ):
-            return self.__save_sample( trans, cntrller, request, current_samples, **kwd )
-        elif params.get( 'edit_samples_button', False ):
-            managing_samples = True
-        elif params.get( 'cancel_changes_button', False ):
-            return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              action='manage_request',
-                                                              cntrller=cntrller,
-                                                              id=request_id ) )
-            pass
-        elif params.get( 'change_state_button', False ):
-            sample_event_comment = util.restore_text( params.get( 'sample_event_comment', '' ) )
-            new_state = trans.sa_session.query( trans.model.SampleState ).get( trans.security.decode_id( sample_state_id ) )
-            self.update_sample_state(trans, cntrller, selected_samples, new_state, comment=sample_event_comment )
-            return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              cntrller=cntrller, 
-                                                              action='update_request_state',
-                                                              request_id=request_id ) )
-        elif params.get( 'cancel_change_state_button', False ):
-            return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              action='manage_request',
-                                                              cntrller=cntrller,
-                                                              id=request_id ) )
-        elif params.get( 'change_lib_button', False ):
-            library_id = params.get( 'sample_0_library_id', None )
-            try:
-                library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) )
-            except:
-                invalid_id_redirect( trans, cntrller, library_id )
-            folder_id = params.get( 'sample_0_folder_id', None )
-            try:
-                folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
-            except:
-                invalid_id_redirect( trans, cntrller, folder_id )
-            for sample_id in selected_samples:
-                sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) )
-                sample.library = library
-                sample.folder = folder
-                trans.sa_session.add( sample )
-                trans.sa_session.flush()
-            trans.sa_session.refresh( request )
-            message = 'Changes made to the selected samples have been saved. '
-            return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              action='manage_request',
-                                                              cntrller=cntrller,
-                                                              id=request_id,
-                                                              status=status,
-                                                              message=message ) )
-        elif params.get( 'cancel_change_lib_button', False ):
-            return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              action='manage_request',
-                                                              cntrller=cntrller,
-                                                              id=trans.security.encode_id( request.id ) ) )
+            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.
+                samples = []
+                selected_samples = []
+                for encoded_sample_id in encoded_selected_sample_ids:
+                    sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( encoded_sample_id ) )
+                    selected_samples.append( sample )
+                # Now build the list of samples, inserting None for samples that have not been checked.
+                for sample in request.samples:
+                    if sample in selected_samples:
+                        samples.append( sample )
+                    else:
+                        samples.append( None )
+                # The __save_samples method requires samples widgets, not sample objects
+                samples = self.__get_sample_widgets( trans, request, samples, **kwd )
+            else:
+                samples = current_samples
+            return self.__save_samples( trans, cntrller, request, samples, **kwd )
         request_widgets = self.__get_request_widgets( trans, request.id )
         sample_copy = self.__build_copy_sample_select_field( trans, current_samples )
         libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans,
@@ -464,12 +472,13 @@ class RequestsCommon( BaseController, Us
                                                                                                       libraries,
                                                                                                       None,
                                                                                                       **kwd )
-        # Build the sample_state_id_select_field SelectField
+        sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, sample_operation )
+        sample_state_id = params.get( 'sample_state_id', None )
         sample_state_id_select_field = self.__build_sample_state_id_select_field( trans, request, sample_state_id )
-        return trans.fill_template( '/requests/common/manage_request.mako',
+        return trans.fill_template( '/requests/common/edit_samples.mako',
                                     cntrller=cntrller, 
                                     request=request,
-                                    selected_samples=selected_samples,
+                                    encoded_selected_sample_ids=encoded_selected_sample_ids,
                                     request_widgets=request_widgets,
                                     current_samples=current_samples,
                                     sample_copy=sample_copy, 
@@ -478,7 +487,7 @@ class RequestsCommon( BaseController, Us
                                     libraries_select_field=libraries_select_field,
                                     folders_select_field=folders_select_field,
                                     sample_state_id_select_field=sample_state_id_select_field,
-                                    managing_samples=managing_samples,
+                                    editing_samples=editing_samples,
                                     status=status,
                                     message=message )
     @web.expose
@@ -489,7 +498,7 @@ class RequestsCommon( BaseController, Us
             except:
                 if cntrller == 'api':
                     trans.response.status = 400
-                    return "Malformed sample id ( %s ) specified, unable to decode." % str( sample_id )
+                    return "Invalid sample id ( %s ) specified, unable to decode." % str( sample_id )
                 else:
                     return invalid_id_redirect( trans, cntrller, sample_id )
             event = trans.model.SampleEvent( sample, new_state, comment )
@@ -516,7 +525,7 @@ class RequestsCommon( BaseController, Us
             if ok_for_now:
                 request.deleted = True
                 trans.sa_session.add( request )
-                # delete all the samples belonging to this request
+                # Delete all the samples belonging to this request
                 for s in request.samples:
                     s.deleted = True
                     trans.sa_session.add( s )
@@ -546,7 +555,7 @@ class RequestsCommon( BaseController, Us
             if ok_for_now:
                 request.deleted = False
                 trans.sa_session.add( request )
-                # undelete all the samples belonging to this request
+                # Undelete all the samples belonging to this request
                 for s in request.samples:
                     s.deleted = False
                     trans.sa_session.add( s )
@@ -655,9 +664,10 @@ class RequestsCommon( BaseController, Us
                 if cntrller == 'api':
                     return 200, message
             return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              action='manage_request',
+                                                              action='edit_samples',
                                                               cntrller=cntrller,
                                                               id=request_id,
+                                                              editing_samples=True,
                                                               status=status,
                                                               message=message ) )
         final_state = False
@@ -673,8 +683,8 @@ class RequestsCommon( BaseController, Us
         event = trans.model.RequestEvent( request, state, comments )
         trans.sa_session.add( event )
         trans.sa_session.flush()
-        # check if an email notification is configured to be sent when the samples 
-        # are in this state
+        # 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 = comments + retval
@@ -683,113 +693,10 @@ class RequestsCommon( BaseController, Us
         if cntrller == 'api':
             return 200, message
         return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                          action='manage_request',
+                                                          action='edit_samples',
                                                           cntrller=cntrller,
-                                                          id=trans.security.encode_id(request.id),
-                                                          status='done',
-                                                          message=message ) )
-    def __save_sample( self, trans, cntrller, request, current_samples, **kwd ):
-        # Save all the new/unsaved samples entered by the user
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) )
-        is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
-        selected_value = params.get( 'sample_operation', 'none' )
-        # Check for duplicate sample names
-        message = ''
-        for index in range( len( current_samples ) - len( request.samples ) ):
-            sample_index = index + len( request.samples )
-            current_sample = current_samples[ sample_index ]
-            sample_name = current_sample[ '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' ]:
-                    count += 1
-            if count > 1: 
-                message = "This request has %i samples with the name (%s).  Samples belonging to a request must have unique names." % ( count, sample_name )
-                break
-        if message:
-            selected_samples = self.__get_selected_samples( trans, request, **kwd )
-            request_widgets = self.__get_request_widgets( trans, request.id )
-            sample_copy = self.__build_copy_sample_select_field( trans, current_samples )
-            sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, selected_value )
-            status = 'error'
-            return trans.fill_template( '/requests/common/manage_request.mako',
-                                        cntrller=cntrller,
-                                        request=request,
-                                        selected_samples=selected_samples,
-                                        request_widgets=request_widgets,
-                                        current_samples=current_samples,
-                                        sample_copy=sample_copy, 
-                                        managing_samples=managing_samples,
-                                        sample_operation_select_field=sample_operation_select_field,
-                                        status=status,
-                                        message=message )
-        if not managing_samples:
-            for index in range( len( current_samples ) - len( request.samples ) ):
-                sample_index = len( request.samples )
-                current_sample = current_samples[ sample_index ]
-                form_values = trans.model.FormValues( request.type.sample_form, current_sample[ 'field_values' ] )
-                trans.sa_session.add( form_values )
-                trans.sa_session.flush()                    
-                s = trans.model.Sample( current_sample[ 'name' ],
-                                        '', 
-                                        request,
-                                        form_values, 
-                                        current_sample[ 'barcode' ],
-                                        current_sample[ 'library' ],
-                                        current_sample[ 'folder' ] )
-                trans.sa_session.add( s )
-                trans.sa_session.flush()
-        else:
-            message = 'Changes made to the samples are saved. '
-            for sample_index in range( len( current_samples ) ):
-                sample = request.samples[ sample_index ]
-                current_sample = current_samples[ sample_index ]
-                sample.name = current_sample[ 'name' ] 
-                sample.library = current_sample[ 'library' ]
-                sample.folder = current_sample[ 'folder' ]
-                if request.is_submitted:
-                    bc_message = self.__validate_barcode( trans, sample, current_sample[ 'barcode' ] )
-                    if bc_message:
-                        status = 'error'
-                        message += bc_message
-                    else:
-                        if not sample.bar_code:
-                            # If this is a 'new' (still in its first state) sample
-                            # change the state to the next
-                            if sample.state.id == request.type.states[0].id:
-                                event = trans.model.SampleEvent( sample, 
-                                                                 request.type.states[1], 
-                                                                 'Sample added to the system' )
-                                trans.sa_session.add( event )
-                                trans.sa_session.flush()
-                                # Now check if all the samples' barcode has been entered.
-                                # If yes then send notification email if configured
-                                common_state = request.samples_have_common_state
-                                if common_state:
-                                    if common_state.id == request.type.states[1].id:
-                                        event = trans.model.RequestEvent( request, 
-                                                                          request.states.SUBMITTED,
-                                                                          "All samples are in %s state." % common_state.name )
-                                        trans.sa_session.add( event )
-                                        trans.sa_session.flush()
-                                        request.send_email_notification( trans, request.type.states[1] )
-                        sample.bar_code = current_samples[sample_index]['barcode']
-                trans.sa_session.add( sample )
-                trans.sa_session.flush()
-                form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id )
-                form_values.content = current_sample[ 'field_values' ]
-                trans.sa_session.add( form_values )
-                trans.sa_session.flush()
-        return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                          action='manage_request',
-                                                          cntrller=cntrller,
-                                                          id=trans.security.encode_id( request.id ),
+                                                          id=request_id,
+                                                          editing_samples=True,
                                                           status=status,
                                                           message=message ) )
     @web.expose
@@ -876,25 +783,33 @@ class RequestsCommon( BaseController, Us
                                     cntrller=cntrller,
                                     events_list=events_list,
                                     sample=sample )
-    def __add_sample( self, trans, cntrller, request, **kwd ):
+    @web.expose
+    @web.require_login( "add sample" )
+    def add_sample( self, trans, cntrller, request_id, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) )
+        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 )
         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, managing_samples, libraries = self.__get_sample_info( trans, request, **kwd )
+        current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd )
         if not current_samples:
             # Form field names are zero-based.
             sample_index = 0
         else:
             sample_index = len( current_samples )
         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 ] )
             num_samples_to_add = int( params.get( 'num_sample_to_copy', 1 ) )
             # 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
                 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 )
@@ -902,7 +817,7 @@ class RequestsCommon( BaseController, Us
                     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' ] ]
                 else:
-                    # The user has not selected a sample to copy (may just be adding a sample).
+                    # 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 )
@@ -910,7 +825,7 @@ class RequestsCommon( BaseController, Us
                 # 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,
                                                                                                            user=request.user, 
-                                                                                                           sample_index=len( current_samples ), 
+                                                                                                           sample_index=id_index, 
                                                                                                            libraries=libraries,
                                                                                                            sample=None, 
                                                                                                            library_id=library_id,
@@ -926,101 +841,21 @@ class RequestsCommon( BaseController, Us
                                               field_values=field_values,
                                               library_select_field=library_select_field,
                                               folder_select_field=folder_select_field ) )
-        selected_samples = self.__get_selected_samples( trans, request, **kwd )
-        selected_value = params.get( 'sample_operation', 'none' )
-        sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, selected_value )
+        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 )
-        return trans.fill_template( '/requests/common/manage_request.mako',
+        return trans.fill_template( '/requests/common/edit_samples.mako',
                                     cntrller=cntrller,
                                     request=request,
-                                    selected_samples=selected_samples,
+                                    encoded_selected_sample_ids=encoded_selected_sample_ids,
                                     request_widgets=request_widgets,
                                     current_samples=current_samples,
                                     sample_operation_select_field=sample_operation_select_field,
                                     sample_copy=sample_copy, 
-                                    managing_samples=managing_samples,
+                                    editing_samples=False,
                                     message=message,
                                     status=status )
-    def __get_sample_info( self, trans, request, **kwd ):
-        """
-        Retrieves all user entered sample information and returns a
-        list of all the samples and their field values.
-        """
-        params = util.Params( kwd )
-        managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) )
-        # Bet all data libraries accessible to this user
-        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
-        # Build the list of widgets which will be used to render each sample row on the request page
-        current_samples = []
-        for index, sample in enumerate( request.samples ):
-            library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans,
-                                                                                                       request.user,
-                                                                                                       index,
-                                                                                                       libraries,
-                                                                                                       sample,
-                                                                                                       **kwd )
-            current_samples.append( dict( name=sample.name,
-                                          barcode=sample.bar_code,
-                                          library=sample.library,
-                                          folder=sample.folder,
-                                          field_values=sample.values.content,
-                                          library_select_field=library_select_field,
-                                          folder_select_field=folder_select_field ) )
-        if not managing_samples:
-            sample_index = len( request.samples ) 
-        else:
-            sample_index = 0
-        while True:
-            library_id = params.get( 'sample_%i_library_id' % sample_index, None )
-            folder_id = params.get( 'sample_%i_folder_id' % sample_index, None )
-            if params.get( 'sample_%i_name' % sample_index, False  ):
-                # Data library
-                try:
-                    library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) )
-                    #library_id = library.id
-                except:
-                    library = None
-                if library is not None:
-                    # Folder
-                    try:
-                        folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
-                        #folder_id = folder.id
-                    except:
-                        if library:
-                            folder = library.root_folder
-                        else:
-                            folder = None
-                else:
-                    folder = None
-                sample_info = dict( name=util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) ),
-                                    barcode=util.restore_text( params.get( 'sample_%i_barcode' % sample_index, ''  ) ),
-                                    library=library,
-                                    folder=folder)
-                sample_info[ 'field_values' ] = []
-                for field_index in range( len( request.type.sample_form.fields ) ):
-                    sample_info[ 'field_values' ].append( util.restore_text( params.get( 'sample_%i_field_%i' % ( sample_index, field_index ), ''  ) ) )
-                if not managing_samples:
-                    sample_info[ 'library_select_field' ], sample_info[ 'folder_select_field' ] = self.__build_library_and_folder_select_fields( trans,
-                                                                                                                                                 request.user, 
-                                                                                                                                                 sample_index,
-                                                                                                                                                 libraries, 
-                                                                                                                                                 None,
-                                                                                                                                                 library_id,
-                                                                                                                                                 folder_id,
-                                                                                                                                                 **kwd )
-                    current_samples.append( sample_info )
-                else:
-                    sample_info[ 'library_select_field' ], sample_info[ 'folder_select_field' ] = self.__build_library_and_folder_select_fields( trans, 
-                                                                                                                                                 request.user, 
-                                                                                                                                                 sample_index, 
-                                                                                                                                                 libraries, 
-                                                                                                                                                 request.samples[ sample_index ], 
-                                                                                                                                                 **kwd )
-                    current_samples[ sample_index ] =  sample_info
-                sample_index += 1
-            else:
-                break
-        return current_samples, managing_samples, libraries
     @web.expose
     @web.require_login( "delete sample from sequencing request" )
     def delete_sample( self, trans, cntrller, **kwd ):
@@ -1032,7 +867,7 @@ 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, managing_samples, libraries = self.__get_sample_info( trans, request, **kwd )
+        current_samples = 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 = request.has_sample( sample_name )
@@ -1042,9 +877,10 @@ class RequestsCommon( BaseController, Us
             trans.sa_session.flush()
         message = 'Sample (%s) has been deleted.' % sample_name
         return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                          action='manage_request',
+                                                          action='edit_samples',
                                                           cntrller=cntrller,
                                                           id=trans.security.encode_id( request.id ),
+                                                          editing_samples=True,
                                                           status=status,
                                                           message=message ) )
     @web.expose
@@ -1059,12 +895,12 @@ class RequestsCommon( BaseController, Us
             sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) )
         except:
             return invalid_id_redirect( trans, cntrller, sample_id )
-        # check if a library and folder has been set for this sample yet.
+        # See if a library and folder have been set for this sample.
         if not sample.library or not sample.folder:
             status = 'error'
             message = "Set a data library and folder for sequencing request (%s) to transfer datasets." % sample.name
             return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              action='manage_request',
+                                                              action='edit_samples',
                                                               cntrller=cntrller,
                                                               id=trans.security.encode_id( sample.request.id ),
                                                               status=status,
@@ -1101,7 +937,6 @@ class RequestsCommon( BaseController, Us
         SampleName,DataLibrary,DataLibraryFolder,Field1,Field2....
         """
         params = util.Params( kwd )
-        managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) )
         file_obj = params.get( 'file_data', '' )
         try:
             reader = csv.reader( file_obj.file )
@@ -1137,23 +972,211 @@ class RequestsCommon( BaseController, Us
                                               folder_select_field=folder_select_field,
                                               field_values=row[3:] ) )
         except Exception, e:
-            status = 'error'
-            message = 'Error thrown when importing samples file: %s' % str( e )
+            if str( e ) == "'unicode' object has no attribute 'file'":
+                message = "Select a file"
+            else:
+                message = 'Error attempting to create samples from selected file: %s.' % str( e )
+                message += '  Make sure the selected csv file uses the format: SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...'
             return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              action='manage_request',
+                                                              action='add_sample',
                                                               cntrller=cntrller,
-                                                              id=trans.security.encode_id( request.id ),
-                                                              status=status,
+                                                              request_id=trans.security.encode_id( request.id ),
+                                                              add_sample_button='Add sample',
+                                                              status='error',
                                                               message=message ) )
         request_widgets = self.__get_request_widgets( trans, request.id )
         sample_copy = self.__build_copy_sample_select_field( trans, current_samples )
-        return trans.fill_template( '/requests/common/manage_request.mako',
+        return trans.fill_template( '/requests/common/edit_samples.mako',
                                     cntrller=cntrller,
                                     request=request,
                                     request_widgets=request_widgets,
                                     current_samples=current_samples,
                                     sample_copy=sample_copy,
-                                    managing_samples=managing_samples )
+                                    editing_samples=False )
+    def __save_samples( self, trans, cntrller, request, samples, **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.
+        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' )
+        # Check for duplicate sample names within the request
+        self.__validate_sample_names( trans, cntrller, request, samples, **kwd )
+        if editing_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',
+                                                                  cntrller=cntrller,
+                                                                  **kwd ) )
+            # Here we handle saving changes to single samples as well as saving changes to
+            # selected sets of samples.  If samples are selected, the sample_operation param
+            # will have a value other than 'none', and the samples param will be a list of
+            # encoded sample ids.  There are currently only 2 multi-select operations;
+            # 'Change state' and 'Select data library and folder'.  If sample_operation is
+            # 'none, then the samples param will be a list of sample objects.
+            if sample_operation == 'Change state':
+                sample_state_id = params.get( 'sample_state_id', None )
+                if sample_state_id in [ None, 'none' ]:
+                    message = "Select a new state from the <b>Change current state</b> list before clicking the <b>Save</b> button."
+                    kwd[ 'message' ] = message
+                    del kwd[ 'save_changes_button' ]
+                    handle_error( **kwd )
+                sample_event_comment = util.restore_text( params.get( 'sample_event_comment', '' ) )
+                new_state = trans.sa_session.query( trans.model.SampleState ).get( trans.security.decode_id( sample_state_id ) )
+                # Send the encoded sample_ids to update_sample_state.
+                # TODO: make changes necessary to just send the samples...
+                encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd )
+                # Make sure all samples have a unique barcode if the state is changing
+                for sample_index in range( len( samples ) ):
+                    current_sample = samples[ sample_index ]
+                    if current_sample is None:
+                        # We have a None value because the user did not select this sample 
+                        # on which to perform the action.
+                        continue
+                    request_sample = request.samples[ sample_index ]
+                    bc_message = self.__validate_barcode( trans, request_sample, current_sample[ 'barcode' ] )
+                    if bc_message:
+                        #status = 'error'
+                        message += bc_message
+                        kwd[ 'message' ] = message
+                        del kwd[ 'save_samples_button' ]
+                        handle_error( **kwd )
+                self.update_sample_state( trans, cntrller, encoded_selected_sample_ids, new_state, comment=sample_event_comment )
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller=cntrller, 
+                                                                  action='update_request_state',
+                                                                  request_id=trans.security.encode_id( request.id ) ) )
+            elif sample_operation == 'Select data library and folder':
+                library_id = params.get( 'sample_0_library_id', 'none' )
+                folder_id = params.get( 'sample_0_folder_id', 'none' )
+                library, folder = self.__get_library_and_folder( trans, library_id, folder_id )
+            self.__update_samples( trans, request, samples, **kwd )
+            # See if all the samples' barcodes are in the same state,
+            # and if so send email if configured to.
+            common_state = request.samples_have_common_state
+            if common_state and common_state.id == request.type.states[1].id:
+                event = trans.model.RequestEvent( request, 
+                                                  request.states.SUBMITTED,
+                                                  "All samples are in %s state." % common_state.name )
+                trans.sa_session.add( event )
+                trans.sa_session.flush()
+                request.send_email_notification( trans, request.type.states[1] )
+            message = 'Changes made to the samples have been saved. '
+        else:
+            # Saving a newly created sample.
+            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' ] )
+                trans.sa_session.add( form_values )
+                trans.sa_session.flush()                    
+                s = trans.model.Sample( current_sample[ 'name' ],
+                                        '', 
+                                        request,
+                                        form_values, 
+                                        current_sample[ 'barcode' ],
+                                        current_sample[ 'library' ],
+                                        current_sample[ 'folder' ] )
+                trans.sa_session.add( s )
+                trans.sa_session.flush()
+        return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                          action='edit_samples',
+                                                          cntrller=cntrller,
+                                                          id=trans.security.encode_id( request.id ),
+                                                          editing_samples=editing_samples,
+                                                          status=status,
+                                                          message=message ) )
+    def __update_samples( self, trans, request, sample_widgets, **kwd ):
+        # Determine if the values in kwd require updating the request's samples.  The list of
+        # sample_widgets must have the same number of objects as request.samples, but some of
+        # the objects can be None.  Those that are not None correspond to samples selected by
+        # the user for performing an action on multiple samples simultaneously.
+        def handle_error( **kwd ):
+            kwd[ 'status' ] = 'error'
+            return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                              action='edit_samples',
+                                                              cntrller=cntrller,
+                                                              **kwd ) )
+        params = util.Params( kwd )
+        sample_operation = params.get( 'sample_operation', 'none' )
+        if sample_operation != 'none':
+            # These values will be in kwd if the user checked 1 or more checkboxes for performing this action
+            # on a set of samples.
+            library_id = params.get( 'sample_0_library_id', 'none' )
+            folder_id = params.get( 'sample_0_folder_id', 'none' )
+        for index, obj in enumerate( sample_widgets ):
+            if obj is not None:
+                # obj will be None if the user checked sample check boxes and selected an action
+                # to perform on multiple samples, but did not select certain samples.
+                sample_updated = False
+                # If this sample has values in kwd, then kwd will include a
+                # key whose value is this sample's ( possibly changed ) name.  An
+                # example of this key is 'sample_0_name'.
+                for k, v in kwd.items():
+                    name_key = 'sample_%i_name' % index
+                    if k == name_key:
+                        sample_updated = True
+                        break
+                if sample_updated:
+                    id_index = index + 1
+                    if sample_operation == 'none':
+                        # We are handling changes to a single sample.
+                        library_id = params.get( 'sample_%i_library_id' % id_index, 'none' )
+                        folder_id = params.get( 'sample_%i_folder_id' % id_index, 'none' )
+                    # Update the corresponding sample's values as well as the sample_widget.
+                    sample = request.samples[ index ]
+                    sample.name = util.restore_text( params.get( 'sample_%i_name' % index, '' ) )
+                    # The bar_code field requires special handling because after a request is submitted, the
+                    # state of a sample cannot be changed without a bar_code assocaited with the sample.
+                    bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) )
+                    if not bar_code and not sample.bar_code:
+                        # If this is a 'new' (still in its first state) sample, create an event
+                        if sample.state.id == request.states[0].id:
+                            event = trans.model.SampleEvent( sample, 
+                                                             request.type.states[1], 
+                                                             'Sample added to the system' )
+                            trans.sa_session.add( event )
+                            trans.sa_session.flush()
+                    elif bar_code:
+                        bc_message = self.__validate_barcode( trans, sample, bar_code )
+                        if bc_message:
+                            kwd[ 'message' ] = bc_message
+                            del kwd[ 'save_samples_button' ]
+                            handle_error( **kwd )
+                    sample.bar_code = bar_code
+                    library, folder = self.__get_library_and_folder( trans, library_id, folder_id )
+                    sample.library = library
+                    sample.folder = folder
+                    field_values = []
+                    for field_index in range( len( request.type.sample_form.fields ) ):
+                        field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) )
+                    form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id )
+                    form_values.content = field_values
+                    trans.sa_session.add_all( ( sample, form_values ) )
+                    trans.sa_session.flush()           
+    def __get_library_and_folder( self, trans, library_id, folder_id ):
+        try:
+            library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) )
+        except:
+            library = None
+        if library and folder_id == 'none':
+            folder = library.root_folder
+        elif library and folder_id != 'none':
+            try:
+                folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
+            except:
+                if library:
+                    folder = library.root_folder
+                else:
+                    folder = None
+        else:
+            folder = None
+        return library, folder
     # ===== Methods for handling form definition widgets =====
     def __get_request_widgets( self, trans, id ):
         """Get the widgets for the request"""
@@ -1179,27 +1202,104 @@ class RequestsCommon( BaseController, Us
                                               value=request.values.content[ index ],
                                               helptext=field[ 'helptext' ] + ' (' + required_label + ')' ) )
         return request_widgets
-    def __get_samples_widgets( self, trans, request, libraries, **kwd ):
-        """Get the widgets for all of the samples currently associated with the request"""
-        # The current_samples_widgets list is a list of dictionaries
-        current_samples_widgets = []
-        for index, sample in enumerate( request.samples ):
-            # Build the library_select_field and folder_select_field for each existing sample
-            library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans,
+    def __get_sample_widgets( self, trans, request, samples, **kwd ):
+        """
+        Returns a list of dictionaries, each representing the widgets that define a sample on a form.
+        The widgets are populated from kwd based on the set of samples received.  The set of samples
+        corresponds to a reques.samples list, but if the user checked specific check boxes on the form,
+        those samples that were not check will have None objects in the list of samples.  In this case,
+        the corresponding sample_widget is populated from the db rather than kwd.
+        """
+        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
+            # set of samples was received.
+            library_id = util.restore_text( params.get( 'sample_0_library_id', 'none' ) )
+            folder_id = util.restore_text( params.get( 'sample_0_folder_id', 'none' ) )
+        # Build the list of widgets which will be used to render each sample row on the request page
+        if not request:
+            return sample_widgets
+        # Get the list of 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 ] )
+        # Build the list if sample widgets, populating the values from kwd.
+        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.
+                sample = request.samples[ index ]
+                name = sample.name
+                bar_code = sample.bar_code
+                library = sample.library
+                folder = sample.folder
+                field_values = sample.values.content,
+            else:
+                # Update the sample attributes from kwd
+                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, '' ) )
+                if not library_id and sample.library:
+                    library_id = trans.security.encode_id( sample.library.id )
+                folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % id_index, '' ) )
+                if not folder_id and sample.folder:
+                    folder_id = trans.security.encode_id( sample.folder.id )
+                library, folder = self.__get_library_and_folder( trans, library_id, folder_id )
+                field_values = []
+                for field_index in range( len( request.type.sample_form.fields ) ):
+                    field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) )
+            library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans,
                                                                                                        user=request.user,
-                                                                                                       sample_index=index,
+                                                                                                       sample_index=id_index,
                                                                                                        libraries=libraries,
                                                                                                        sample=sample,
+                                                                                                       library_id=library_id,
+                                                                                                       folder_id=folder_id,
                                                                                                        **kwd )
-            # Append the dictionary for the current sample to the current_samples_widgets list
-            current_samples_widgets.append( dict( name=sample.name,
-                                                  barcode=sample.bar_code,
-                                                  library=sample.library,
-                                                  folder=sample.folder,
-                                                  field_values=sample.values.content,
-                                                  library_select_field=library_select_field,
-                                                  folder_select_field=folder_select_field ) )
-        return current_samples_widgets
+            sample_widgets.append( dict( name=name,
+                                         barcode=bar_code,
+                                         library=library,
+                                         folder=folder,
+                                         field_values=field_values,
+                                         library_select_field=library_select_field,
+                                         folder_select_field=folder_select_field ) )
+        # There may be additional new samples on the form that have not yet been associated with the request.
+        # TODO: factor this code so it is not duplicating what's above.
+        index = len( samples )
+        while True:
+            name = util.restore_text( params.get( 'sample_%i_name' % index, '' ) )
+            if not name:
+                break
+            id_index = index + 1
+            bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) )
+            library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) )
+            folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % id_index, '' ) )
+            library, folder = self.__get_library_and_folder( trans, library_id, folder_id )
+            field_values = []
+            for field_index in range( len( request.type.sample_form.fields ) ):
+                field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) )
+            library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans,
+                                                                                                       user=request.user,
+                                                                                                       sample_index=id_index,
+                                                                                                       libraries=libraries,
+                                                                                                       sample=None,
+                                                                                                       library_id=library_id,
+                                                                                                       folder_id=folder_id,
+                                                                                                       **kwd )
+            sample_widgets.append( dict( name=name,
+                                         barcode=bar_code,
+                                         library=library,
+                                         folder=folder,
+                                         field_values=field_values,
+                                         library_select_field=library_select_field,
+                                         folder_select_field=folder_select_field ) )
+            index += 1
+        return sample_widgets   
     # ===== Methods for building SelectFields used on various request forms =====
     def __build_copy_sample_select_field( self, trans, current_samples ):
         copy_sample_index_select_field = SelectField( 'copy_sample_index' )
@@ -1240,26 +1340,30 @@ class RequestsCommon( BaseController, Us
         # The libraries dictionary looks like: { library : '1,2' }, library : '3' }.  Its keys are the libraries that
         # should be displayed for the current user and its values are strings of comma-separated folder ids that should
         # NOT be displayed.
-        #
-        # TODO: all object ids received in the params must be encoded.
         params = util.Params( kwd )
         library_select_field_name= "sample_%i_library_id" % sample_index
         folder_select_field_name = "sample_%i_folder_id" % sample_index
         if not library_id:
-            library_id = params.get( library_select_field_name, 'none'  )
+            library_id = params.get( library_select_field_name, None )
+        if not folder_id:
+            folder_id = params.get( folder_select_field_name, None )
         selected_library = None
         selected_hidden_folder_ids = []
         showable_folders = []
-        if sample and sample.library and library_id == 'none':
-            library_id = str( sample.library.id )
+        if library_id not in [ None, 'none' ]:
+            # If we have a selected library, get the list of it's folders that are not accessible to the current user
+            for library, hidden_folder_ids in libraries.items():
+                encoded_id = trans.security.encode_id( library.id )
+                if encoded_id == str( library_id ):
+                    selected_library = library
+                    selected_hidden_folder_ids = hidden_folder_ids.split( ',' )
+                    break
+        elif sample and sample.library and library_id == 'none':
+            # The user previously selected a library but is now resetting the selection to 'none'
+            selected_library = None
+        elif sample and sample.library:
+            library_id = trans.security.encode_id( sample.library.id )
             selected_library = sample.library
-        # If we have a selected library, get the list of it's folders that are not accessible to the current user
-        for library, hidden_folder_ids in libraries.items():
-            encoded_id = trans.security.encode_id( library.id )
-            if encoded_id == str( library_id ):
-                selected_library = library
-                selected_hidden_folder_ids = hidden_folder_ids.split( ',' )
-                break
         # sample_%i_library_id SelectField with refresh on change enabled
         library_select_field = build_select_field( trans,
                                                    libraries.keys(),
@@ -1275,20 +1379,12 @@ class RequestsCommon( BaseController, Us
                                                                               selected_library, 
                                                                               [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], 
                                                                               selected_hidden_folder_ids )
-        if sample:
-            # The user is editing the request, and may have previously selected a folder
-            if sample.folder:
-                selected_folder_id = sample.folder.id
+            if folder_id:
+                selected_folder_id = folder_id
+            elif sample and sample.folder:
+                selected_folder_id = trans.security.encode_id( sample.folder.id )
             else:
-                # If a library is selected but not a folder, use the library's root folder
-                if sample.library:
-                    selected_folder_id = sample.library.root_folder.id
-                else:
-                    # The user just selected a folder
-                    selected_folder_id = params.get( folder_select_field_name, 'none' )
-        elif folder_id:
-            # TODO: not sure when this would be passed
-                selected_folder_id = folder_id
+                selected_folder_id = trans.security.encode_id( selected_library.root_folder.id )
         else:
             selected_folder_id = 'none'
         # TODO: Change the name of the library root folder to "Library root" to clarify to the
@@ -1328,9 +1424,35 @@ class RequestsCommon( BaseController, Us
                 message += '<b>' + ef + '</b> '
             return message
         return None
+    def __validate_sample_names( self, trans, cntrller, request, current_samples, **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 ) ):
+            sample_index = index + len( request.samples )
+            current_sample = current_samples[ sample_index ]
+            sample_name = current_sample[ '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' ]:
+                    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 )
+                break
+        if message:
+            del kwd[ 'save_samples_button' ]
+            kwd[ 'message' ] = message
+            kwd[ 'status' ] = 'error'
+            return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                              action='edit_samples',
+                                                              cntrller=cntrller,
+                                                              **kwd ) )
     def __validate_barcode( self, trans, sample, barcode ):
         """
-        Makes sure that the barcode about to be assigned to a sample is gobally unique.
+        Makes sure that the barcode about to be assigned to a sample is globally unique.
         That is, barcodes must be unique across requests in Galaxy sample tracking. 
         """
         message = ''
@@ -1338,13 +1460,18 @@ class RequestsCommon( BaseController, Us
         for index in range( len( sample.request.samples ) ):
             # Check for empty bar code
             if not barcode.strip():
-                message = 'Fill in the barcode for sample (%s).' % sample.name
-                break
+                if sample.state.id == sample.request.type.states[0].id:
+                    # The user has not yet filled in the barcode value, but the sample is
+                    # 'new', so all is well.
+                    break
+                else:
+                    message = "Fill in the barcode for sample (%s) before changing it's state." % sample.name
+                    break
             # TODO: Add a unique constraint to sample.bar_code table column
             # Make sure bar code is unique
-            for sample_has_bar_code in trans.sa_session.query( trans.model.Sample ) \
-                                                        .filter( trans.model.Sample.table.c.bar_code == barcode ):
-                if sample_has_bar_code and sample_has_bar_code.id != sample.id:
+            for sample_with_barcode in trans.sa_session.query( trans.model.Sample ) \
+                                                       .filter( trans.model.Sample.table.c.bar_code == barcode ):
+                if sample_with_barcode and sample_with_barcode.id != sample.id:
                     message = '''The bar code (%s) associated with the sample (%s) belongs to another sample.  
                                  Bar codes must be unique across all samples, so use a different bar code 
                                  for this sample.''' % ( barcode, sample.name )
@@ -1360,15 +1487,15 @@ class RequestsCommon( BaseController, Us
         elif len( email ) > 255:
             error = "(%s) exceeds maximum allowable length.  " % str( email )
         return error
-    # ===== Other miscellaneoud utility methods =====
-    def __get_selected_samples( self, trans, request, **kwd ):
-        selected_samples = []
+    # ===== Other miscellaneous utility methods =====
+    def __get_encoded_selected_sample_ids( self, trans, request, **kwd ):
+        encoded_selected_sample_ids = []
         for sample in request.samples:
             if CheckboxField.is_checked( kwd.get( 'select_sample_%i' % sample.id, '' ) ):
-                selected_samples.append( trans.security.encode_id( sample.id ) )
-        return selected_samples
+                encoded_selected_sample_ids.append( trans.security.encode_id( sample.id ) )
+        return encoded_selected_sample_ids
 
-# ===== Miscellaneoud utility methods outside of the RequestsCommon class =====
+# ===== Miscellaneous utility methods outside of the RequestsCommon class =====
 def invalid_id_redirect( trans, cntrller, obj_id, action='browse_requests' ):
     status = 'error'
     message = "Invalid request id (%s)" % str( obj_id )

--- a/templates/requests/common/dataset_transfer.mako
+++ b/templates/requests/common/dataset_transfer.mako
@@ -1,47 +1,46 @@
 <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" />
 
+<br/><br/>
+
+<ul class="manage-table-actions">
+    <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Refresh</a></li>
+    <li><a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">Target Data Library</a></li>
+    <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li>
+</ul>
+
 %if message:
     ${render_msg( message, status )}
 %endif
 
-<h2>Datasets of Sample "${sample.name}"</h2>
-
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Refresh</a>
-    </li>
-    <li>
-        <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${sample.library.name} Data Library</a>
-    </li>
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a>
-    </li>
-</ul>
-
-%if dataset_files:
-    <div class="form-row">
-        <table class="grid">
-            <thead>
-                <tr>
-                    <th>Name</th>
-                    <th>Size</th>
-                    <th>Status</th>
-                </tr>
-            <thead>
-            <tbody>
-                %for dataset_file in dataset_files:
-                    <tr>
-                        <td>${dataset_file.name}</td>
-                        <td>${dataset_file.size}</td>
-                        <td>${dataset_file.status}</td>
-                    </tr>
-                %endfor
-            </tbody>
-        </table>
+<div class="toolForm">
+    <div class="toolFormTitle">Sample "${sample.name}"</div>
+    <div class="toolFormBody">
+        %if dataset_files:
+            <div class="form-row">
+                <table class="grid">
+                    <thead>
+                        <tr>
+                            <th>Name</th>
+                            <th>Size</th>
+                            <th>Status</th>
+                        </tr>
+                    <thead>
+                    <tbody>
+                        %for dataset_file in dataset_files:
+                            <tr>
+                                <td>${dataset_file.name}</td>
+                                <td>${dataset_file.size}</td>
+                                <td>${dataset_file.status}</td>
+                            </tr>
+                        %endfor
+                    </tbody>
+                </table>
+            </div>
+        %else:
+            <div class="form-row">
+                There are no datasets associated with this sample.
+            </div>
+        %endif
     </div>
-%else:
-    <div class="form-row">
-        There are no datasets associated with this sample.
-    </div>
-%endif
+</div>

--- a/templates/requests/common/manage_request.mako
+++ /dev/null
@@ -1,615 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/requests/common/sample_state.mako" import="render_sample_state" />
-<%namespace file="/requests/common/sample_datasets.mako" import="render_sample_datasets" />
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "library" )}
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    <script type="text/javascript">
-        function showContent(vThis)
-        {
-            // http://www.javascriptjunkie.com
-            // alert(vSibling.className + " " + vDef_Key);
-            vParent = vThis.parentNode;
-            vSibling = vParent.nextSibling;
-            while (vSibling.nodeType==3) { 
-                // Fix for Mozilla/FireFox Empty Space becomes a TextNode or Something
-                vSibling = vSibling.nextSibling;
-            };
-            if(vSibling.style.display == "none")
-            {
-                vThis.src="/static/images/fugue/toggle.png";
-                vThis.alt = "Hide";
-                vSibling.style.display = "block";
-            } else {
-                vSibling.style.display = "none";
-                vThis.src="/static/images/fugue/toggle-expand.png";
-                vThis.alt = "Show";
-            }
-            return;
-        }
-    
-        $(document).ready(function(){
-            //hide the all of the element with class msg_body
-            $(".msg_body").hide();
-            //toggle the component with class msg_body
-            $(".msg_head").click(function(){
-                $(this).next(".msg_body").slideToggle(0);
-            });
-        });
-    
-        // Looks for changes in sample states using an async request. Keeps
-        // calling itself (via setTimeout) until all samples are in a terminal
-        // state.
-        var updater = function ( sample_states ) {
-            // Check if there are any items left to track
-            var empty = true;
-            for ( i in sample_states ) {
-                empty = false;
-                break;
-            }
-            if ( ! empty ) {
-                setTimeout( function() { updater_callback( sample_states ) }, 1000 );
-            }
-        };
-
-        var updater_callback = function ( sample_states ) {
-            // Build request data
-            var ids = []
-            var states = []
-            $.each( sample_states, function ( id, state ) {
-                ids.push( id );
-                states.push( state );
-            });
-            // Make ajax call
-            $.ajax( {
-                type: "POST",
-                url: "${h.url_for( controller='requests_common', action='sample_state_updates' )}",
-                dataType: "json",
-                data: { ids: ids.join( "," ), states: states.join( "," ) },
-                success : function ( data ) {
-                    $.each( data, function( id, val ) {
-                        // Replace HTML
-                        var cell1 = $("#sampleState-" + id);
-                        cell1.html( val.html_state );
-                        var cell2 = $("#sampleDatasets-" + id);
-                        cell2.html( val.html_datasets );
-                        sample_states[ parseInt( id ) ] = val.state;
-                    });
-                    updater( sample_states ); 
-                },
-                error: function() {
-                    // Just retry, like the old method, should try to be smarter
-                    updater( sample_states );
-                }
-            });
-        };
-        
-    	function checkAllFields()
-    	{
-    		var chkAll = document.getElementById('checkAll');
-    		var checks = document.getElementsByTagName('input');
-    		var boxLength = checks.length;
-    		var allChecked = false;
-    		var totalChecked = 0;
-            if ( chkAll.checked == true )
-            {
-                for ( i=0; i < boxLength; i++ )
-                {
-    	            if ( checks[i].name.indexOf( 'select_sample_' ) != -1)
-    	            {
-    	               checks[i].checked = true;
-    	            }
-    	        }
-            }
-            else
-            {
-                for ( i=0; i < boxLength; i++ )
-                {
-                    if ( checks[i].name.indexOf( 'select_sample_' ) != -1)
-                    {
-                       checks[i].checked = false
-                    }
-                }
-            }
-    	}
-    
-        function stopRKey(evt) {
-          var evt = (evt) ? evt : ((event) ? event : null);
-          var node = (evt.target) ? evt.target : ((evt.srcElement) ? evt.srcElement : null);
-          if ((evt.keyCode == 13) && (node.type=="text"))  {return false;}
-        }
-        document.onkeypress = stopRKey
-    </script>
-</%def>
-
-<% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() %>
-
-<div class="grid-header">
-    <h2>Sequencing Request "${request.name}"</h2>
-
-	<ul class="manage-table-actions">
-	    <li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li>
-	    <div popupmenu="seqreq-${request.id}-popup">
-	        %if request.is_unsubmitted and request.samples:
-	            <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a>
-	        %endif
-	        <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">History</a>
-	        %if is_admin:
-	            %if request.is_submitted:
-	                <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a>
-	                <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a>
-	            %endif
-	        %endif
-	    </div>
-	    <li><a class="action-button"  href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse requests</a></li>
-	</ul>
-
-    <div class="toolParamHelp" style="clear: both;">
-        <b>Sequencer</b>: ${request.type.name} 
-        %if is_admin:
-            | <b>User</b>: ${request.user.email}
-        %endif
-        %if request.is_submitted:
-            | <b>State</b>: <i>${request.state}</i>
-        %else:
-            | <b>State</b>: ${request.state}
-        %endif
-    </div>
-</div>
-
-%if request.samples_without_library_destinations:
-    ${render_msg( "Select a target data library and folder for all the samples before starting the sequence run", "warning" )}
-%endif
-
-%if request.is_rejected:
-    ${render_msg( "Reason for rejection: " + request.last_comment, "warning" )}
-%endif
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<h4><img src="/static/images/fugue/toggle-expand.png" alt="Show" onclick="showContent(this);" style="cursor:pointer;"/> Request Information</h4>
-<div style="display:none;">
-    <div class="form-row">
-        <ul class="manage-table-actions">
-            <li>
-                <a class="action-button"  href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit request informaton</a>
-            </li>
-        </ul>
-    </div>
-    <table class="grid" border="0">
-        <tbody>
-            <tr>
-	            <td valign="top" width="50%">
-                    <div class="form-row">
-                        <label>Description:</label>
-                        ${request.desc}
-                    </div>
-                    <div style="clear: both"></div>
-				    %for index, rd in enumerate( request_widgets ):
-				        <%
-				            field_label = rd[ 'label' ]
-				            field_value = rd[ 'value' ]
-				        %>
-				        <div class="form-row">
-				            <label>${field_label}:</label>                   
-			                %if field_label == 'State':
-			                    <a href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a>
-			                %else:
-			                    ${field_value}     
-			                %endif
-				        </div>
-				        <div style="clear: both"></div>
-				    %endfor
-				</td>
-				<td valign="top" width="50%">
-                    <div class="form-row">
-                        <label>Date created:</label>
-                        ${request.create_time}
-                    </div>
-                    <div class="form-row">
-                        <label>Date updated:</label>
-                        ${request.update_time}
-                    </div>
-                    <div class="form-row">
-                        <label>Email notification recipients:</label>
-                        <%
-                            if request.notification:
-                                emails = ', '.join( request.notification[ 'email' ] )
-                            else:
-                                emails = ''
-                        %>
-                        ${emails}
-                    </div>
-                    <div style="clear: both"></div>
-                    <div class="form-row">
-                        <label>Email notification on sample states:</label>
-                        <%
-                            if request.notification:
-                                states = []
-                                for ss in request.type.states:
-                                    if ss.id in request.notification[ 'sample_states' ]:
-                                        states.append( ss.name )
-                                states = ', '.join( states )
-                            else:
-                                states = ''
-                        %>
-                        ${states}
-                    </div>
-                    <div style="clear: both"></div>
-				</td>
-			</tr>
-	    </tbody>
-	</table>
-</div>
-<br/>
-<form id="manage_request" name="manage_request" action="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ), managing_samples=managing_samples )}" method="post">
-    %if current_samples:
-        <% sample_operation_selected_value = sample_operation_select_field.get_selected( return_value=True ) %>
-        ## first render the basic info grid 
-        ${render_basic_info_grid()}
-        %if not request.is_new and not managing_samples and len( sample_operation_select_field.options ) > 1:
-            <div class="form-row" style="background-color:#FAFAFA;">
-                For selected samples: 
-                ${sample_operation_select_field.get_html()}
-            </div>
-            %if sample_operation_selected_value != 'none' and selected_samples:
-                <div class="form-row" style="background-color:#FAFAFA;">
-                    %if sample_operation_selected_value == trans.model.Sample.bulk_operations.CHANGE_STATE:
-                        ## sample_operation_selected_value == 'Change state'
-                        <div class="form-row">
-                            <label>Change current state</label>
-                            ${sample_state_id_select_field.get_html()}
-                            <label>Comments</label>
-                            <input type="text" name="sample_event_comment" value=""/>
-                            <div class="toolParamHelp" style="clear: both;">
-                                Optional
-                            </div>
-                        </div>
-                        <div class="form-row">
-                            <input type="submit" name="change_state_button" value="Save"/>
-                            <input type="submit" name="cancel_change_state_button" value="Cancel"/>
-                        </div>
-                    %elif sample_operation_selected_value == trans.app.model.Sample.bulk_operations.SELECT_LIBRARY:
-                    <% libraries_selected_value = libraries_select_field.get_selected( return_value=True ) %>
-                        <div class="form-row">
-	                        <label>Select data library:</label>
-	                        ${libraries_select_field.get_html()}
-                        </div>
-                        %if libraries_selected_value != 'none':
-                            <div class="form-row">
-		                        <label>Select folder:</label>
-		                        ${folders_select_field.get_html()}
-	                        </div>
-	                        <div class="form-row">
-	                          <input type="submit" name="change_lib_button" value="Save"/>
-	                          <input type="submit" name="cancel_change_lib_button" value="Cancel"/>
-                            </div>
-                        %endif
-                    %endif
-                </div>
-            %endif
-        %endif
-        ## Render the other grids
-        <% trans.sa_session.refresh( request.type.sample_form ) %>
-        %for grid_index, grid_name in enumerate( request.type.sample_form.layout ):
-            ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )}
-        %endfor
-    %else:
-        <label>There are no samples.</label>
-    %endif  
-    %if request.samples and request.is_submitted:
-        <script type="text/javascript">
-            // Updater
-            updater({${ ",".join( [ '"%s" : "%s"' % ( s.id, s.state.name ) for s in request.samples ] ) }});
-        </script>
-    %endif
-    %if not managing_samples:
-        <table class="grid">
-            <tbody>
-                <tr>
-                    <div class="form-row">
-                        %if request.is_unsubmitted:
-                            <td>
-                                %if current_samples:
-                                    <label>Copy </label>
-                                    <input type="integer" name="num_sample_to_copy" value="1" size="3"/>
-                                    <label>samples from sample</label>
-                                    ${sample_copy.get_html()}
-                                %endif
-                                <input type="submit" name="add_sample_button" value="Add New"/>
-                            </td>
-                        %endif
-                        <td>
-                            %if current_samples and len( current_samples ) <= len( request.samples ):                     
-                                <input type="submit" name="edit_samples_button" value="Edit samples"/>
-                            %endif
-                        </td>
-                    </div>
-                </tr> 
-            </tbody>
-        </table>
-    %endif
-    %if request.samples or current_samples:            
-        %if managing_samples:   
-            <div class="form-row">
-                <input type="submit" name="save_samples_button" value="Save"/>
-                <input type="submit" name="cancel_changes_button" value="Cancel"/>
-            </div>
-        %elif len( current_samples ) > len( request.samples ):
-            <div class="form-row">
-                <input type="submit" name="save_samples_button" value="Save"/>
-                <input type="submit" name="cancel_changes_button" value="Cancel"/>
-            </div>
-        %endif
-    %endif
-</form>
-<br/>
-%if request.is_unsubmitted:
-    <form id="import" name="import" action="${h.url_for( controller='requests_common', action='manage_request', managing_samples=managing_samples, id=trans.security.encode_id( request.id ) )}" enctype="multipart/form-data" method="post" >
-        <h4><img src="/static/images/fugue/toggle-expand.png" alt="Show" onclick="showContent(this);"  style="cursor:pointer;"/> Import samples</h4>
-        <div style="display:none;">
-            <input type="file" name="file_data" />
-            <input type="submit" name="import_samples_button" value="Import samples"/>
-            <br/>
-            <div class="toolParamHelp" style="clear: both;">
-                The csv file must be in the following format:<br/>
-                SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
-            </div>
-        </div>
-    </form>
-%endif
-
-<%def name="render_grid( grid_index, grid_name, fields_dict )">
-    <br/>
-    <% if not grid_name:
-          grid_name = "Grid "+ grid_index
-    %>
-    <div>
-        %if managing_samples or len( current_samples ) > len( request.samples ):
-            <h4><img src="/static/images/fugue/toggle.png" alt="Show" onclick="showContent(this);"  style="cursor:pointer;"/> ${grid_name}</h4>
-            <div>
-        %else:
-            <h4><img src="/static/images/fugue/toggle-expand.png" alt="Hide" onclick="showContent(this);"  style="cursor:pointer;"/> ${grid_name}</h4>
-            <div style="display:none;">
-        %endif
-            <table class="grid">
-                <thead>
-                    <tr>
-                        <th>Name</th>
-                        %for index, field in fields_dict.items():
-                            <th>
-                                ${field['label']}
-                                <div class="toolParamHelp" style="clear: both;">
-                                    <i>${field['helptext']}</i>
-                                </div>
-                            </th>
-                        %endfor
-                        <th></th>
-                    </tr>
-                <thead>
-                <tbody>
-                    <% trans.sa_session.refresh( request ) %>
-                    %for sample_index, sample in enumerate( current_samples ):
-                        %if managing_samples:
-                            <tr>${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}</tr>      
-                        %else:
-                            <tr>
-                                %if sample_index in range( len( request.samples ) ):
-                                    ${render_sample( sample_index, sample['name'], sample['field_values'], fields_dict )}
-                                %else:                                                            
-                                    ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
-                                %endif
-                            </tr>  
-                        %endif
-                    %endfor
-                </tbody>
-            </table>
-        </div>
-    </div>
-</%def>
-
-## This function displays the "Basic Information" grid
-<%def name="render_basic_info_grid()">
-    <h3>Sample Information</h3>
-    <table class="grid">
-        <thead>
-            <tr>
-                <th><input type="checkbox" id="checkAll" name=select_all_samples_checkbox value="true" onclick='checkAllFields(1);'><input type="hidden" name=select_all_samples_checkbox value="true"></th>
-                <th>Name</th>
-                <th>Barcode</th>
-                <th>State</th>
-                <th>Data Library</th>
-                <th>Folder</th>
-                %if request.is_submitted or request.is_complete: 
-                    <th>Datasets Transferred</th>
-                %endif
-                <th></th>
-            </tr>
-        <thead>
-        <tbody>
-            <% trans.sa_session.refresh( request ) %>
-            %for sample_index, info in enumerate( current_samples ):
-                <% 
-                    if sample_index in range( len(request.samples ) ):
-                        sample = request.samples[sample_index]
-                    else:
-                        sample = None 
-                %>
-                %if managing_samples:
-                    <tr>${show_basic_info_form( sample_index, sample, info )}</tr>      
-                %else:
-                    <tr>
-                        %if sample_index in range( len( request.samples ) ):
-                            %if trans.security.encode_id( sample.id ) in selected_samples:
-                                <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" checked><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"></td>
-                            %else:
-                                <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true"><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"></td>
-                            %endif
-                            <td>${info['name']}</td>
-                            <td>${info['barcode']}</td>
-                            %if sample.request.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 ) )}">${render_sample_state( sample )}</a></td>
-                            %endif
-                            %if info['library']:
-                                %if cntrller == 'requests':
-                                    <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
-                                %elif is_admin:
-                                    <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
-                                %endif                                    
-                            %else:
-                                <td></td>
-                            %endif
-                            %if info['folder']:
-                                <td>${info['folder'].name}</td>
-                            %else:
-                                <td></td>
-                            %endif
-                            %if request.is_submitted or request.is_complete: 
-                                <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">
-                                    ${render_sample_datasets( sample )}
-                                </a></td>
-                            %endif
-                        %else:                                                            
-                            ${show_basic_info_form( sample_index, sample, info )}
-                        %endif
-                        %if request.is_unsubmitted or request.is_rejected: 
-                            <td>
-                                %if sample:
-                                    %if sample.request.is_unsubmitted:
-                                        <a class="action-button" href="${h.url_for( controller='requests_common', cntrller=cntrller, action='delete_sample', request_id=trans.security.encode_id( request.id ), sample_id=sample_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}"  style="cursor:pointer;"/></a>
-                                    %endif
-                                %endif
-                            </td>
-                        %endif
-                    </tr>  
-                %endif
-            %endfor
-        </tbody>
-    </table>
-</%def>
-
-<%def name="show_basic_info_form( sample_index, sample, info )">
-    <td></td>
-    <td>
-        <input type="text" name="sample_${sample_index}_name" value="${info['name']}" size="10"/>
-        <div class="toolParamHelp" style="clear: both;">
-            <i>${' (required)' }</i>
-        </div>
-    </td>
-    %if cntrller == 'requests':
-        %if sample:
-            %if sample.request.is_unsubmitted:
-                <td></td>
-            %else:
-                <td><input type="text" name="sample_${sample_index}_barcode" value="${info['barcode']}" size="10"/></td>
-            %endif
-        %else:
-            <td></td>
-        %endif
-    %elif is_admin:
-        %if sample:
-            %if sample.request.is_unsubmitted:
-                <td></td>
-            %else:
-                <td><input type="text" name="sample_${sample_index}_barcode" value="${info['barcode']}" size="10"/></td>
-            %endif
-        %else:
-            <td></td>
-        %endif
-    %endif 
-    %if sample:
-        %if sample.request.is_unsubmitted:
-            <td>Unsubmitted</td>
-        %else:
-            <td><a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td>
-        %endif    
-    %else:
-        <td></td>
-    %endif
-    <td>${info['library_select_field'].get_html()}</td>
-    <td>${info['folder_select_field'].get_html()}</td>
-    %if request.is_submitted or request.is_complete: 
-        <%
-            if sample:
-                label = str( len( sample.datasets ) )
-            else:
-                label = 'Add'
-        %>
-        <td><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td>
-    %endif 
-</%def>
-
-<%def name="render_sample( index, sample_name, sample_values, fields_dict )">
-    <td>
-        ${sample_name}
-    </td>
-    %for field_index, field in fields_dict.items():
-        <td>
-            %if sample_values[field_index]:
-                %if field['type'] == 'WorkflowField':
-                    %if str(sample_values[field_index]) != 'none':
-                        <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %>
-                        <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a>
-                    %endif
-                %else:
-                    ${sample_values[field_index]}
-                %endif
-            %else:
-                <i>None</i>
-            %endif
-        </td>
-    %endfor   
-</%def>
-
-<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )">
-    <td>${sample_name}</td>
-    %for field_index, field in fields_dict.items():
-        <td>
-            %if field['type'] == 'TextField':
-                <input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
-            %elif field['type'] == 'SelectField':
-                <select name="sample_${index}_field_${field_index}" last_selected_value="2">
-                    %for option_index, option in enumerate(field['selectlist']):
-                        %if option == sample_values[field_index]:
-                            <option value="${option}" selected>${option}</option>
-                        %else:
-                            <option value="${option}">${option}</option>
-                        %endif
-                    %endfor
-                </select>
-            %elif field['type'] == 'WorkflowField':
-                <select name="sample_${index}_field_${field_index}">
-                    %if str(sample_values[field_index]) == 'none':
-                        <option value="none" selected>Select one</option>
-                    %else:
-                        <option value="none">Select one</option>
-                    %endif
-                    %for option_index, option in enumerate(request.user.stored_workflows):
-                        %if not option.deleted:
-                            %if str(option.id) == str(sample_values[field_index]):
-                                <option value="${option.id}" selected>${option.name}</option>
-                            %else:
-                                <option value="${option.id}">${option.name}</option>
-                            %endif
-                        %endif
-                    %endfor
-                </select>
-            %elif field['type'] == 'CheckboxField':
-                <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
-            %endif
-            <div class="toolParamHelp" style="clear: both;">
-                <i>${'('+field['required']+')' }</i>
-            </div>
-        </td>
-    %endfor   
-</%def>

    

[galaxy-commits] galaxy-dist commit 667043341e81: Significant cleanup for the Sample Tracking UI. Things are more streamlined and Galaxy UI standards are now followed.

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