[galaxy-commits] galaxy-dist commit c1172bae7b0f: lims: requests/request_admin controller refactor

16 Jul 2010

# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User rc
# Date 1277909210 14400
# Node ID c1172bae7b0fc41e4bd52bfe73c130309c2387fe
# Parent  9289b4d7fa4d1d1b630c044dfbc102cf870f62e3
lims: requests/request_admin controller refactor
A new controller called requests_common now handles all common tasks like create/edit/delete requests & samples. The requests controller has only the grid definition and requests_admin controller has the request_type code and the sequencer data transfer code.
Also fixed a form importer bug in forms.py

--- /dev/null
+++ b/templates/requests/common/sample_events.mako
@@ -0,0 +1,65 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Events for Sample ${sample.name}</%def>
+
+<h2>Events for Sample "${sample.name}"</h2>
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(sample.request.id) )}">
+        <span>Browse this request</span></a>
+    </li>
+</ul>
+<h3>User: ${sample.request.user.email}</h3>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <table class="grid">
+        <thead>
+            <tr>
+                <th>State</th>
+                <th>Description</th>
+                <th>Last Update</th>
+                <th>Comments</th>
+            </tr>
+        </thead>
+        <tbody>
+            %for state, desc, updated, comments in events_list:    
+                <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
+                    <td><b><a>${state}</a></b></td>
+                    <td><a>${desc}</a></td>
+                    <td><a>${updated}</a></td>
+                    <td><a>${comments}</a></td>
+                </tr>             
+            %endfor
+        </tbody>
+    </table>
+</div>
+%if cntrller == 'requests_admin' and trans.user_is_admin():
+    <div class="toolForm">
+        <div class="toolFormTitle">Change current state</div>
+        <div class="toolFormBody">
+            <form name="event" action="${h.url_for( controller='requests_admin', action='save_state', new=True, sample_id=sample.id)}" method="post" >
+                    %for w in widgets:
+                        <div class="form-row">
+                            <label>
+                                ${w[0]}
+                            </label>
+                            ${w[1].get_html()}
+                            %if w[0] == 'Comments':
+                                <div class="toolParamHelp" style="clear: both;">
+                                    Optional
+                                </div>
+                            %endif
+                        </div>
+                    %endfor
+                <div class="form-row">
+                    <input type="submit" name="add_event_button" value="Save"/>
+                </div>
+            </form>
+        </div>
+    </div>
+%endif

--- a/test/functional/test_forms_and_requests.py
+++ b/test/functional/test_forms_and_requests.py
@@ -189,7 +189,7 @@ class TestFormsAndRequests( TwillTestCas
         # Make sure the request_type is not accessible by regular_user2 since regular_user2 does not have Role1.
         self.logout()
         self.login( email=regular_user2.email )
-        self.visit_url( '%s/requests/new?create=True&select_request_type=%i' % (self.url, request_type.id) )
+        self.visit_url( '%s/requests_common/new?cntrller=requests&select_request_type=True' % self.url )
         try:
             self.check_page_for_string( 'There are no request types created for a new request.' )
             raise AssertionError, 'The request_type %s is accessible by %s when it should be restricted' % ( request_type.name, regular_user2.email )
@@ -304,12 +304,12 @@ class TestFormsAndRequests( TwillTestCas
         self.logout()
         self.login( email='test@bx.psu.edu' )
         self.check_request_admin_grid(state=request_one.states.SUBMITTED, request_name=request_one.name)
-        self.visit_url( "%s/requests_admin/list?sort=-create_time&operation=show_request&id=%s" \
+        self.visit_url( "%s/requests_admin/list?operation=show&id=%s" \
                         % ( self.url, self.security.encode_id( request_one.id ) ))
         self.check_page_for_string( 'Sequencing Request "%s"' % request_one.name )
         # set bar codes for the samples
         bar_codes = [ '1234567890', '0987654321' ]
-        self.add_bar_codes( request_one.id, request_one.name, bar_codes )
+        self.add_bar_codes( request_one.id, request_one.name, bar_codes, request_one.samples )
         # change the states of all the samples of this request
         for sample in request_one.samples:
             self.change_sample_state( sample.name, sample.id, request_type.states[1].id, request_type.states[1].name )
@@ -328,11 +328,12 @@ class TestFormsAndRequests( TwillTestCas
         self.login( email='test@bx.psu.edu' )
         request_name = "RequestTwo"
         # simulate request creation
-        url_str = '%s/requests_admin/new?create=True&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&library_id=%i&folder_id=%i&refresh=True&field_2=%s&field_0=%s&field_1=%i' \
-                  % ( self.url, request_type.id, regular_user.id, request_name, library_one.id, library_one.root_folder.id, "field_2_value", 'option1', user_address.id )
+        url_str = '%s/requests_common/new?cntrller=requests_admin&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&refresh=True&field_2=%s&field_0=%s&field_1=%i' \
+                  % ( self.url, request_type.id, regular_user.id, request_name, "field_2_value", 'option1', user_address.id )
+        print url_str
         self.home()
         self.visit_url( url_str )
-        self.check_page_for_string( "The new request named %s has been created" % request_name )
+        self.check_page_for_string( "The new request named <b>%s</b> has been created" % request_name )
         global request_two
         request_two = sa_session.query( galaxy.model.Request ) \
                                 .filter( and_( galaxy.model.Request.table.c.name==request_name,
@@ -370,44 +371,44 @@ class TestFormsAndRequests( TwillTestCas
         # check if the request's state is now set to 'submitted'
         assert request_two.state is not request_two.states.REJECTED, "The state of the request '%s' should be set to '%s'" \
             % ( 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
-        # remove the request_type permissions
-        rt_actions = sa_session.query( galaxy.model.RequestTypePermissions ) \
-                               .filter(and_(galaxy.model.RequestTypePermissions.table.c.request_type_id==request_type.id) ) \
-                               .order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) ) \
-                               .all()
-        for a in rt_actions:
-            sa_session.delete( a )
-        sa_session.flush()
-        ##################
-        # Purge all libraries
-        ##################
-        for library in [ library_one ]:
-            self.delete_library_item( 'library_admin',
-                                      self.security.encode_id( library.id ),
-                                      self.security.encode_id( library.id ),
-                                      library.name,
-                                      item_type='library' )
-            self.purge_library( self.security.encode_id( library.id ), library.name )
-        ##################
-        # Eliminate all non-private roles
-        ##################
-        for role in [ role_one, role_two ]:
-            self.mark_role_deleted( self.security.encode_id( role.id ), role.name )
-            self.purge_role( self.security.encode_id( role.id ), role.name )
-            # Manually delete the role from the database
-            sa_session.refresh( role )
-            sa_session.delete( role )
-            sa_session.flush()
-        ##################
-        # Eliminate all groups
-        ##################
-        for group in [ group_one ]:
-            self.mark_group_deleted( self.security.encode_id( group.id ), group.name )
-            self.purge_group( self.security.encode_id( group.id ), group.name )
-            # Manually delete the group from the database
-            refresh( group )
-            sa_session.delete( group )
-            sa_session.flush()
+#    def test_055_reset_data_for_later_test_runs( self ):
+#        """Reseting data to enable later test runs to pass"""
+#        # Logged in as admin_user
+#        # remove the request_type permissions
+#        rt_actions = sa_session.query( galaxy.model.RequestTypePermissions ) \
+#                               .filter(and_(galaxy.model.RequestTypePermissions.table.c.request_type_id==request_type.id) ) \
+#                               .order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) ) \
+#                               .all()
+#        for a in rt_actions:
+#            sa_session.delete( a )
+#        sa_session.flush()
+#        ##################
+#        # Purge all libraries
+#        ##################
+#        for library in [ library_one ]:
+#            self.delete_library_item( 'library_admin',
+#                                      self.security.encode_id( library.id ),
+#                                      self.security.encode_id( library.id ),
+#                                      library.name,
+#                                      item_type='library' )
+#            self.purge_library( self.security.encode_id( library.id ), library.name )
+#        ##################
+#        # Eliminate all non-private roles
+#        ##################
+#        for role in [ role_one, role_two ]:
+#            self.mark_role_deleted( self.security.encode_id( role.id ), role.name )
+#            self.purge_role( self.security.encode_id( role.id ), role.name )
+#            # Manually delete the role from the database
+#            sa_session.refresh( role )
+#            sa_session.delete( role )
+#            sa_session.flush()
+#        ##################
+#        # Eliminate all groups
+#        ##################
+#        for group in [ group_one ]:
+#            self.mark_group_deleted( self.security.encode_id( group.id ), group.name )
+#            self.purge_group( self.security.encode_id( group.id ), group.name )
+#            # Manually delete the group from the database
+#            refresh( group )
+#            sa_session.delete( group )
+#            sa_session.flush()

--- a/templates/admin/requests/show_request.mako
+++ /dev/null
@@ -1,528 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/requests/sample_state.mako" import="render_sample_state" />
-<%namespace file="/requests/sample_datasets.mako" import="render_sample_datasets" />
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
-    $( "select[refresh_on_change='true']").change( function() {
-        var refresh = false;
-        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
-        if ( refresh_on_change_values ) {
-            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
-            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
-            for( i= 0; i < refresh_on_change_values.length; i++ ) {
-                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
-                    refresh = true;
-                    break;
-                }
-            }
-        }
-        else {
-            refresh = true;
-        }
-        if ( refresh ){
-            $( "#show_request" ).submit();
-        }
-    });
-});
-</script>
-
-
-<script type="text/javascript">
-$(document).ready(function(){
-    //hide the all of the element with class msg_body
-    $(".msg_body").hide();
-    //toggle the componenet with class msg_body
-    $(".msg_head").click(function(){
-        $(this).next(".msg_body").slideToggle(450);
-    });
-});
-</script>
-
-<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_admin', 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>
-
-<style type="text/css">
-.msg_head {
-    padding: 0px 0px;
-    cursor: pointer;
-}
-</style>
-
-<script type="text/javascript">
-    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> 
-
-%if request.submitted():
-    <% samples_not_ready = request.sequence_run_ready() %>
-    %if samples_not_ready:
-        ${render_msg( "Select a target library and folder for all the samples before starting the sequence run", "warning" )}
-    %endif
-%endif
-
-%if request.rejected():
-    ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )}
-%endif
-
-<div class="grid-header">
-    <h2>Sequencing Request "${request.name}"</h2>
-</div>
-
-<ul class="manage-table-actions">
-
-    %if request.unsubmitted() and request.samples:
-        <li>
-            <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_admin', action='list', operation='Submit', id=trans.security.encode_id(request.id) )}">
-            <span>Submit request</span></a>
-        </li>
-    %endif
-    %if request.submitted():
-        <li>
-            <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='Reject', id=trans.security.encode_id(request.id))}">
-            <span>Reject request</span></a>
-        </li>
-    %endif
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">
-        <span>History</span></a>
-    </li>
-
-
-</ul>
-
-<%def name="show_basic_info_form( sample_index, sample, info )">
-    <td>
-        <input type="text" name=sample_${sample_index}_name value="${info['name']}" size="10"/>
-        <div class="toolParamHelp" style="clear: both;">
-            <i>${' (required)' }</i>
-        </div>
-    </td>
-    %if sample:
-        %if sample.request.unsubmitted():
-            <td></td>
-        %else:
-            <td><input type="text" name=sample_${sample_index}_barcode value="${info['barcode']}" size="10"/></td>
-        %endif
-    %else:
-        <td></td>
-    %endif
-    %if sample:
-        %if sample.request.unsubmitted():
-            <td>Unsubmitted</td>
-        %else:
-            <td><a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a></td>
-        %endif    
-    %else:
-        <td></td>
-    %endif
-    <td>${info['lib_widget'].get_html()}</td>
-    <td>${info['folder_widget'].get_html()}</td>
-    %if request.submitted() or request.complete(): 
-        %if sample:
-            <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a></td> 
-        %else:
-            <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">Add</a></td>
-        %endif 
-    %endif 
-</%def>
-
-## This function displays the "Basic Information" grid
-<%def name="render_basic_info_grid()">
-    <h4>Sample Information</h4>
-    <table class="grid">
-        <thead>
-            <tr>
-                <th>Name</th>
-                <th>Barcode</th>
-                <th>State</th>
-                <th>Data Library</th>
-                <th>Folder</th>
-                %if request.submitted() or request.complete(): 
-                    <th>Dataset(s) 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 edit_mode == 'True':
-                    <tr>
-                        ${show_basic_info_form( sample_index, sample, info )}
-                    </tr>      
-                %else:
-                    <tr>
-                        %if sample_index in range(len(request.samples)):
-                            <td>${info['name']}</td>
-                            <td>${info['barcode']}</td>
-                            %if sample.request.unsubmitted():
-                                <td>Unsubmitted</td>
-                            %else:
-                                <td id="sampleState-${sample.id}">${render_sample_state( sample )}</td>
-                            %endif
-                                
-##                            <td>
-##                                %if sample:
-##                                    %if sample.request.unsubmitted():
-##                                        Unsubmitted
-##                                    %else:
-##                                        <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
-##                                    %endif
-##                                %endif
-##                            </td>
-                            %if info['library']:
-                                <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
-                            %else:
-                                <td></td>
-                            %endif
-                            %if info['folder']:
-                                <td>${info['folder'].name}</td>
-                            %else:
-                                <td></td>
-                            %endif
-                            %if request.submitted() or request.complete(): 
-                                <td id="sampleDatasets-${sample.id}">
-                                    ${render_sample_datasets( sample )}
-##                                    <a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a>
-                                </td>
-                            %endif
-                            
-                            
-                        %else:                                                            
-                            ${show_basic_info_form( sample_index, sample, info )}
-                        %endif
-                        %if request.unsubmitted() or request.rejected(): 
-                            <td>
-                                %if sample:
-                                    %if sample.request.unsubmitted():
-                                        <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index )}">
-                                        <img src="${h.url_for('/static/images/delete_icon.png')}" />
-                                        <span></span></a>
-                                    %endif
-                                %endif
-                            </td>
-                        %endif
-                    </tr>  
-                %endif
-            %endfor
-        </tbody>
-    </table>
-</%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>
-
-<%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:
-                    ${sample_values[field_index]}
-                %endif
-            %else:
-                <i>None</i>
-            %endif
-        </td>
-    %endfor   
-</%def>
-
-<div class="toolForm">
-    <div class="form-row">
-        <div class="msg_list">
-            <h4 class="msg_head"><u>Request Information</u></h4>
-            <div class="msg_body">
-                %for index, rd in enumerate(request_details):
-                    <div class="form-row">
-                        <label>${rd['label']}</label>
-                        %if not rd['value']:
-                            <i>None</i>
-                        %else:                      
-                            %if rd['label'] == 'State':
-                                <a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
-                            %else:
-                                ${rd['value']}     
-                            %endif
-                        %endif
-                    </div>
-                    <div style="clear: both"></div>
-                %endfor
-                <div class="form-row">
-                <ul class="manage-table-actions">
-                    <li>
-                        <a class="action-button"  href="${h.url_for( controller='requests_admin', action='list', operation='Edit', id=trans.security.encode_id(request.id))}">
-                        <span>Edit request details</span></a>
-                    </li>
-                </ul>
-                </div>
-            </div>
-        </div>
-    </div>
-</div>
-
-<br/>
-
-
-<%def name="render_grid( grid_index, grid_name, fields_dict )">
-    <br/>
-    <div class="msg_list">
-    %if grid_name:
-        <h4 class="msg_head"><u>${grid_name}</u></h4>
-    %else:
-        <h4>Grid ${grid_index}</h4>
-    %endif
-    %if edit_mode == 'False' or len(current_samples) <= len(request.samples):
-        <div class="msg_body">
-    %else:
-        <div class="msg_body2">
-    %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 edit_mode == 'True':
-                    <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:                                                            
-                            ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
-                        %endif
-                    </tr>  
-                %endif
-            %endfor
-        </tbody>
-    </table>
-    </div>
-    </div>
-</%def>
-
-<div class="toolForm">
-    ##<div class="toolFormTitle">Samples (${len(request.samples)})</div>
-    <form id="show_request" name="show_request" action="${h.url_for( controller='requests_admin', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
-        <div class="form-row">
-            %if current_samples:
-                ## first render the basic info grid 
-                ${render_basic_info_grid()}
-                ## then render the other grid(s)
-                <% trans.sa_session.refresh( request.type.sample_form ) %>
-                %for grid_index, grid_name in enumerate(request.type.sample_form.layout):
-                    ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )}
-                    <br/>
-                %endfor
-            %else:
-                <label>There are no samples.</label>
-            %endif
-        </div>      
-        %if request.samples and request.submitted():
-            <script type="text/javascript">
-                // Updater
-                updater({${ ",".join( [ '"%s" : "%s"' % ( s.id, s.current_state().name ) for s in request.samples ] ) }});
-            </script>
-        %endif
-        
-        %if edit_mode == 'False':
-            <table class="grid">
-                <tbody>
-                    <tr>
-                        <div class="form-row">
-
-                            %if request.unsubmitted():
-                                <td>
-                                    %if current_samples:
-                                        <label>Copy </label>
-                                        <input type="integer" name="num_sample_to_copy" value="1" size="3"/>
-                                        <label>sample(s) from sample</label>
-                                        ${sample_copy.get_html()}
-                                    %endif
-                                    <input type="submit" name="add_sample_button" value="Add New"/>
-                                </td>
-                            %endif
-                            <td>
-                                %if len(current_samples) and len(current_samples) <= len(request.samples):                     
-                                    <input type="submit" name="edit_samples_button" value="Edit samples"/>
-                                %endif
-                            </td>
-                        </div>
-                    </tr> 
-                </tbody>
-            </table>
-        %endif
-        %if request.samples or current_samples: 
-            <div class="form-row">
-                <div style="float: left; width: 250px; margin-right: 10px;">
-                    <input type="hidden" name="refresh" value="true" size="40"/>
-                </div>
-              <div style="clear: both"></div>
-            </div>            
-            %if edit_mode == 'True':   
-                <div class="form-row">
-                    <input type="submit" name="save_samples_button" value="Save"/>
-                    <input type="submit" name="cancel_changes_button" value="Cancel"/>
-                </div>
-            %elif request.unsubmitted():
-                <div class="form-row">
-                    <input type="submit" name="save_samples_button" value="Save"/>
-                </div>
-            %endif
-            
-        %endif
-        <input type="hidden" name="request_id" value="${request.id}" />
-    </form>
-</div>
-
-<br/>
-
-%if request.unsubmitted():
-<div class="toolForm">
-    <form id="show_request" name="show_request" action="${h.url_for( controller='requests_admin', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
-        <div class="form-row">
-            <div class="msg_list">
-                <h4 class="msg_head"><u>Import samples from csv file</u></h4>
-                <div class="msg_body">
-                    <input type="file" name="file_data" />
-                    <input type="submit" name="import_samples_button" value="Import samples"/>
-                    <br/>
-                    <div class="toolParamHelp" style="clear: both;">
-                        The csv file must be in the following format:<br/>
-                        SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
-                    </div>
-                </div>
-            </div>
-        </div>
-        <input type="hidden" name="request_id" value="${request.id}" />
-    </form>
-</div>
-%endif
-

--- a/templates/admin/samples/events.mako
+++ /dev/null
@@ -1,63 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<%def name="title()">Events for Sample ${sample.name}</%def>
-
-<h2>Events for Sample "${sample.name}"</h2>
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
-        <span>Browse this request</span></a>
-    </li>
-</ul>
-<h3>User: ${sample.request.user.email}</h3>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
-    <table class="grid">
-        <thead>
-            <tr>
-                <th>State</th>
-                <th>Description</th>
-                <th>Last Update</th>
-                <th>Comments</th>
-            </tr>
-        </thead>
-        <tbody>
-            %for state, desc, updated, comments in events_list:    
-                <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
-                    <td><b><a>${state}</a></b></td>
-                    <td><a>${desc}</a></td>
-                    <td><a>${updated}</a></td>
-                    <td><a>${comments}</a></td>
-                </tr>             
-            %endfor
-        </tbody>
-    </table>
-</div>
-<div class="toolForm">
-    <div class="toolFormTitle">Change current state</div>
-    <div class="toolFormBody">
-        <form name="event" action="${h.url_for( controller='requests_admin', action='save_state', new=True, sample_id=sample.id)}" method="post" >
-                %for w in widgets:
-                    <div class="form-row">
-                        <label>
-                            ${w[0]}
-                        </label>
-                        ${w[1].get_html()}
-                        %if w[0] == 'Comments':
-                            <div class="toolParamHelp" style="clear: both;">
-                                Optional
-                            </div>
-                        %endif
-                    </div>
-                %endfor
-            <div class="form-row">
-                <input type="submit" name="add_event_button" value="Save"/>
-            </div>
-        </form>
-    </div>
-</div>

--- a/scripts/galaxy_messaging/server/data_transfer.py
+++ b/scripts/galaxy_messaging/server/data_transfer.py
@@ -194,7 +194,7 @@ class DataTransfer(object):
         Update the data transfer status for this dataset in the database
         '''
         try:
-            log.debug('Setting status "%s" for dataset "%s"' % ( status, str(dataset_index) ) )
+            log.debug('Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str(dataset_index), str(self.sample_id) ) )
             df = from_json_string(self.galaxydb.get_sample_dataset_files(self.sample_id))
             if dataset_index == 'All':
                 for dataset in self.dataset_files:

--- a/scripts/galaxy_messaging/server/galaxydb_interface.py
+++ b/scripts/galaxy_messaging/server/galaxydb_interface.py
@@ -28,7 +28,7 @@ class GalaxyDbInterface(object):
     def __init__(self, dbstr):
         self.dbstr = dbstr
         self.db_engine = create_engine(self.dbstr)    
-#        self.db_engine.echo = True  
+        self.db_engine.echo = True  
         self.metadata = MetaData(self.db_engine)
         self.session = sessionmaker(bind=self.db_engine)
         self.event_table = Table('sample_event', self.metadata, autoload=True )

--- a/templates/requests/sample_state.mako
+++ /dev/null
@@ -1,5 +0,0 @@
-<%def name="render_sample_state( sample )">
-    <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
-</%def>
-
-${render_sample_state( sample )}

--- a/templates/admin/requests/dataset.mako
+++ b/templates/admin/requests/dataset.mako
@@ -11,7 +11,7 @@
 
 <ul class="manage-table-actions"><li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
+        <a class="action-button" href="${h.url_for( controller='requests_common', action='show_datatx_page', cntrller='requests_admin', sample_id=trans.security.encode_id(sample.id) )}"><span>Dataset transfer page</span></a></li></ul>

--- a/templates/admin/samples/bar_codes.mako
+++ /dev/null
@@ -1,46 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-
-<h2>Bar codes for Samples of Request "${request.name}"</h2>
-<h3>User: ${user.email}</h3>
-
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
-        <span>Browse this request</span></a>
-    </li>
-</ul>
-
-<div class="toolForm">
-    <form name="bar_codes" action="${h.url_for( controller='requests_admin', action='save_bar_codes', request_id=request.id)}" method="post" >
-        <table class="grid">
-            <thead>
-                <tr>
-                    <th>Name</th>
-                    <th>Description</th>
-                    <th>Bar code</th>
-                </tr>
-            </thead>
-            <tbody>
-                %for index, sample in enumerate(samples_list):    
-                    <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
-                        <td><b><a>${sample.name}</a></b></td>
-                        <td><a>${sample.desc}</a></td>
-                        <td>
-                            ${widgets[index].get_html()}
-                        </td>
-                    </tr>             
-                %endfor
-            </tbody>
-        </table>
-        <div class="form-row">
-            <input type="submit" name="save_bar_codes" value="Save"/>
-        </div>
-    </form>
-</div>

--- a/templates/requests/edit_request.mako
+++ /dev/null
@@ -1,84 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
-    $( "select[refresh_on_change='true']").change( function() {
-        var refresh = false;
-        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
-        if ( refresh_on_change_values ) {
-            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
-            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
-            for( i= 0; i < refresh_on_change_values.length; i++ ) {
-                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
-                    refresh = true;
-                    break;
-                }
-            }
-        }
-        else {
-            refresh = true;
-        }
-        if ( refresh ){
-            $( "#edit_request" ).submit();
-        }
-    });
-});
-</script>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button"  href="${h.url_for( controller='requests', action='list')}">
-        <span>Browse requests</span></a>
-    </li>
-</ul>
-
-<div class="toolForm">
-    <div class="toolFormTitle">Edit request "${request.name}"</div>
-    %if len(select_request_type.options) == 1:
-        There are no request types created for a new request.
-    %else:
-        <div class="toolFormBody">
-            <form name="edit_request" id="edit_request" action="${h.url_for( controller='requests', action='edit', request_id=request.id)}" method="post" >
-                <div class="form-row">
-                    <label>
-                        Select Request Type:
-                    </label>
-                    ${select_request_type.get_html()}
-                </div>
-
-               %if select_request_type.get_selected() != ('Select one', 'none'):
-                   %for i, field in enumerate(widgets):
-                        <div class="form-row">
-                            <label>${field['label']}</label>
-                            ${field['widget'].get_html()}
-                            %if field['label'] == 'Data library' and new_library:
-                                ${new_library.get_html()}
-                            %endif
-                            <div class="toolParamHelp" style="clear: both;">
-                                ${field['helptext']}
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                    %endfor                    
-                    <div class="form-row">
-                        <div style="float: left; width: 250px; margin-right: 10px;">
-                            <input type="hidden" name="refresh" value="true" size="40"/>
-                        </div>
-                      <div style="clear: both"></div>
-                    </div>
-                    <div class="form-row">
-                        <input type="submit" name="save_changes_request_button" value="Save changes"/> 
-                        ##<input type="submit" name="edit_samples_button" value="Edit samples"/>
-                    </div>
-               %endif
-        </form>
-    </div>
-</div>
-%endif

--- a/templates/requests/new_request.mako
+++ /dev/null
@@ -1,94 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
-    $( "select[refresh_on_change='true']").change( function() {
-        var refresh = false;
-        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
-        if ( refresh_on_change_values ) {
-            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
-            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
-            for( i= 0; i < refresh_on_change_values.length; i++ ) {
-                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
-                    refresh = true;
-                    break;
-                }
-            }
-        }
-        else {
-            refresh = true;
-        }
-        if ( refresh ){
-            $( "#new_request" ).submit();
-        }
-    });
-});
-</script>
-
-<%def name="javascripts()">
-   ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
-</%def>
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "autocomplete_tagging" )}
-</%def>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button"  href="${h.url_for( controller='requests', action='list')}">
-        <span>Browse requests</span></a>
-    </li>
-</ul>
-
-<div class="toolForm">
-    <div class="toolFormTitle">Add a new request</div>
-    %if len(select_request_type.options) == 1:
-        There are no request types created for a new request.
-    %else:
-        <div class="toolFormBody">
-            <form name="new_request" id="new_request" action="${h.url_for( controller='requests', action='new', create=True )}" method="post" >
-                <div class="form-row">
-                    <label>
-                        Select Request Type:
-                    </label>
-                    ${select_request_type.get_html()}
-                </div>
-
-               %if select_request_type.get_selected() != ('Select one', 'none'):
-                   %for i, field in enumerate(widgets):
-                        <div class="form-row">
-                            <label>${field['label']}</label>
-                            ${field['widget'].get_html()}
-                            ##%if field['label'] == 'Data library' and new_library:
-                            ##    ${new_library.get_html()}
-                            ##%endif
-                            <div class="toolParamHelp" style="clear: both;">
-                                ${field['helptext']}
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                    %endfor                    
-                    <div class="form-row">
-                        <div style="float: left; width: 250px; margin-right: 10px;">
-                            <input type="hidden" name="refresh" value="true" size="40"/>
-                        </div>
-                      <div style="clear: both"></div>
-                    </div>
-                    <div class="form-row">
-                        <input type="submit" name="create_request_button" value="Save"/> 
-                        <input type="submit" name="create_request_samples_button" value="Add samples"/>
-                    </div>
-               %endif
-        </form>
-    </div>
-</div>
-%endif

--- /dev/null
+++ b/templates/requests/common/index.mako
@@ -0,0 +1,16 @@
+<%inherit file="/webapps/galaxy/base_panels.mako"/>
+
+<%def name="init()">
+<%
+    self.has_left_panel=False
+    self.has_right_panel=False
+    self.active_view="requests"
+    self.message_box_visible=False
+%>
+</%def>
+
+<%def name="center_panel()">
+
+    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="requests", action="list" )}"></iframe>
+
+</%def>

--- a/templates/sample/index.mako
+++ /dev/null
@@ -1,16 +0,0 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=False
-    self.active_view="requests"
-
-%>
-</%def>
-
-<%def name="center_panel()">
-
-    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="sample", action="list", request_id=request_id )}"></iframe>
-
-</%def>

--- a/templates/requests/show_request.mako
+++ /dev/null
@@ -1,430 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
-    $( "select[refresh_on_change='true']").change( function() {
-        var refresh = false;
-        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
-        if ( refresh_on_change_values ) {
-            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
-            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
-            for( i= 0; i < refresh_on_change_values.length; i++ ) {
-                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
-                    refresh = true;
-                    break;
-                }
-            }
-        }
-        else {
-            refresh = true;
-        }
-        if ( refresh ){
-            $( "#show_request" ).submit();
-        }
-    });
-});
-</script>
-
-
-<script type="text/javascript">
-$(document).ready(function(){
-    //hide the all of the element with class msg_body
-    $(".msg_body").hide();
-    //toggle the componenet with class msg_body
-    $(".msg_head").click(function(){
-        $(this).next(".msg_body").slideToggle(450);
-    });
-});
-</script>
-<style type="text/css">
-.msg_head {
-    padding: 0px 0px;
-    cursor: pointer;
-}
-
-}
-</style>
-
-%if request.rejected():
-    ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )}
-%endif
-
-<div class="grid-header">
-    <h2>Sequencing Request "${request.name}"</h2>
-</div>
-
-<ul class="manage-table-actions">
-    %if request.unsubmitted() and request.samples:
-        <li>
-            <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests', action='list', operation='Submit', id=trans.security.encode_id(request.id) )}">
-            <span>Submit request</span></a>
-        </li>
-    %endif
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='events', id=trans.security.encode_id(request.id) )}">
-        <span>History</span></a>
-    </li>
-    <li>
-        <a class="action-button"  href="${h.url_for( controller='requests', action='list')}">
-        <span>Browse requests</span></a>
-    </li>
-</ul>
-
-<%def name="show_basic_info_form( sample_index, sample, info )">
-    <td>
-        <input type="text" name=sample_${sample_index}_name value="${info['name']}" size="10"/>
-        <div class="toolParamHelp" style="clear: both;">
-            <i>${' (required)' }</i>
-        </div>
-    </td>
-    %if sample:
-        %if sample.request.unsubmitted():
-            <td></td>
-        %else:
-            <td><input type="text" name=sample_${sample_index}_barcode value="${info['barcode']}" size="10"/></td>
-        %endif
-    %else:
-        <td></td>
-    %endif
-    %if sample:
-        %if not sample.current_state():
-            <td>Unsubmitted</td>
-        %else:
-            <td><a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a></td>
-        %endif    
-    %else:
-        <td></td>
-    %endif
-    <td>${info['lib_widget'].get_html()}</td>
-    <td>${info['folder_widget'].get_html()}</td>
-    %if request.submitted() or request.complete(): 
-        %if sample:
-            <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a></td> 
-        %else:
-            <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">Add</a></td>
-        %endif 
-    %endif 
-</%def>
-
-## This function displays the "Basic Information" grid
-<%def name="render_basic_info_grid()">
-    <h4>Sample Information</h4>
-    <table class="grid">
-        <thead>
-            <tr>
-                <th>Name</th>
-                <th>Barcode</th>
-                <th>State</th>
-                <th>Data Library</th>
-                <th>Folder</th>
-                %if request.submitted() or request.complete(): 
-                    <th>Dataset(s) 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 edit_mode == 'True':
-                    <tr>
-                        ${show_basic_info_form( sample_index, sample, info )}
-                    </tr>      
-                %else:
-                    <tr>
-                        %if sample_index in range(len(request.samples)):
-                            <td>${info['name']}</td>
-                            <td>${info['barcode']}</td>
-                            <td>
-                                %if sample.current_state():
-                                    <a href="${h.url_for( controller='requests', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
-                                %else:
-                                    Unsubmitted
-                                %endif
-                            </td>
-                            %if info['library']:
-                                <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
-                            %else:
-                                <td></td>
-                            %endif
-                            %if info['folder']:
-                                <td>${info['folder'].name}</td>
-                            %else:
-                                <td></td>
-                            %endif
-                            %if request.submitted() or request.complete(): 
-                                <td>
-                                    <a href="${h.url_for( controller='requests', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a>
-                                </td>
-                            %endif
-                            
-                            
-                        %else:                                                            
-                            ${show_basic_info_form( sample_index, sample, info )}
-                        %endif
-                        %if request.unsubmitted() or request.rejected(): 
-                            <td>
-                                %if sample:
-                                    %if sample.request.unsubmitted():
-                                        <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index )}">
-                                        <img src="${h.url_for('/static/images/delete_icon.png')}" />
-                                        <span></span></a>
-                                    %endif
-                                %endif
-                            </td>
-                        %endif
-                    </tr>  
-                %endif
-            %endfor
-        </tbody>
-    </table>
-</%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>
-
-<%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:
-                    ${sample_values[field_index]}
-                %endif
-            %else:
-                <i>None</i>
-            %endif
-
-        </td>
-    %endfor   
-</%def>
-
-<%def name="render_grid( grid_index, grid_name, fields_dict )">
-    <br/>
-    <div class="msg_list">
-    %if grid_name:
-        <h4 class="msg_head"><u>${grid_name}</u></h4>
-    %else:
-        <h4>Grid ${grid_index}</h4>
-    %endif
-    %if edit_mode == 'False' or len(current_samples) <= len(request.samples):
-        <div class="msg_body">
-    %else:
-        <div class="msg_body2">
-    %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 edit_mode == 'True':
-                    <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:                                                            
-                            ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
-                        %endif
-                    </tr>  
-                %endif
-            %endfor
-        </tbody>
-    </table>
-    </div>
-    </div>
-</%def>
-
-<div class="toolForm">
-    <form id="request_details" name="request_details" >
-        <div class="form-row">
-            <div class="msg_list">
-                <h4 class="msg_head"><u>Request Information</u></h4>
-                <div class="msg_body">
-                    %for index, rd in enumerate(request_details):
-                        <div class="form-row">
-                            <label>${rd['label']}</label>
-                            %if not rd['value']:
-                                <i>None</i>
-                            %else:                      
-                                %if rd['label'] == 'State':
-                                    <a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
-                                %else:
-                                    ${rd['value']}     
-                                %endif
-                            %endif
-                        </div>
-                        <div style="clear: both"></div>
-                    %endfor
-                    <div class="form-row">
-                    <ul class="manage-table-actions">
-                        <li>
-                            <a class="action-button"  href="${h.url_for( controller='requests_admin', action='list', operation='Edit', id=trans.security.encode_id(request.id))}">
-                            <span>Edit request details</span></a>
-                        </li>
-                    </ul>
-                    </div>
-                </div>
-            </div>
-        </div>
-    </form>
-    <form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
-        <div class="form-row">
-            %if current_samples:
-                ## first render the basic info grid 
-                ${render_basic_info_grid()}
-                ## then render the other grid(s)
-                <% 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 ) )}
-                    <br/>
-                %endfor
-            %else:
-                <label>There are no samples.</label>
-            %endif
-        </div>
-        %if request.unsubmitted() and edit_mode == 'False':
-            <table class="grid">
-                <tbody>
-                    <tr>
-                        <div class="form-row">
-                            <td>
-                                %if current_samples:
-                                    <label>Copy </label>
-                                    <input type="integer" name="num_sample_to_copy" value="1" size="3"/>
-                                    <label>sample(s) from sample</label>
-                                    ${sample_copy.get_html()}
-                                %endif
-                                <input type="submit" name="add_sample_button" value="Add New"/>
-                            </td>
-                            <td>
-                                %if len(current_samples) and len(current_samples) <= len(request.samples):                        
-                                    <input type="submit" name="edit_samples_button" value="Edit samples"/>
-                                %endif
-                            </td>
-                        </div>
-                    </tr> 
-                </tbody>
-            </table>
-        %endif
-        %if request.unsubmitted() and (request.samples or current_samples): 
-            <div class="form-row">
-                <div style="float: left; width: 250px; margin-right: 10px;">
-                    <input type="hidden" name="refresh" value="true" size="40"/>
-                </div>
-              <div style="clear: both"></div>
-            </div>
-            <div class="form-row">
-                <input type="submit" name="save_samples_button" value="Save"/>
-                %if edit_mode == 'True':
-                    <input type="submit" name="cancel_changes_button" value="Cancel"/>
-                %endif
-            </div>
-        %endif
-        <input type="hidden" name="request_id" value="${request.id}" />
-    </form>
-</div>
-
-
-<br/>
-%if request.unsubmitted():
-<div class="toolForm">
-    <form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
-        <div class="form-row">
-            <div class="msg_list">
-                <h4 class="msg_head"><u>Import samples from csv file</u></h4>
-                <div class="msg_body">
-                    <input type="file" name="file_data" />
-                    <input type="submit" name="import_samples_button" value="Import samples"/>
-                    <br/>
-                    <div class="toolParamHelp" style="clear: both;">
-                        The csv file must be in the following format:<br/>
-                        SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
-                    </div>
-                </div>
-            </div>
-        </div>
-        <input type="hidden" name="request_id" value="${request.id}" />
-    </form>
-</div>
-%endif

--- /dev/null
+++ b/templates/requests/common/new_request.mako
@@ -0,0 +1,91 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<script type="text/javascript">
+$( function() {
+    $( "select[refresh_on_change='true']").change( function() {
+        var refresh = false;
+        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+        if ( refresh_on_change_values ) {
+            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+            for( i= 0; i < refresh_on_change_values.length; i++ ) {
+                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+                    refresh = true;
+                    break;
+                }
+            }
+        }
+        else {
+            refresh = true;
+        }
+        if ( refresh ){
+            $( "#new_request" ).submit();
+        }
+    });
+});
+</script>
+
+<%def name="javascripts()">
+   ${parent.javascripts()}
+   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+</%def>
+
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    ${h.css( "autocomplete_tagging" )}
+</%def>
+
+<br/>
+<br/>
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button"  href="${h.url_for( controller=cntrller, cntrller=cntrller, action='list')}">
+        <span>Browse requests</span></a>
+    </li>
+</ul>
+
+<div class="toolForm">
+    <div class="toolFormTitle">Add a new request</div>
+    %if len(select_request_type.options) == 1:
+        There are no request types created for a new request.
+    %else:
+        <div class="toolFormBody">
+            <form name="new_request" id="new_request" action="${h.url_for( controller='requests_common', action='new', cntrller=cntrller)}" method="post" >
+                <div class="form-row">
+                    <label>
+                        Select request type
+                    </label>
+                    ${select_request_type.get_html()}
+                </div>
+
+               %if select_request_type.get_selected() != ('Select one', 'none'):
+                   %for i, field in enumerate(widgets):
+                        <div class="form-row">
+                            <label>${field['label']}</label>
+                            ${field['widget'].get_html()}
+                            <div class="toolParamHelp" style="clear: both;">
+                                ${field['helptext']}
+                            </div>
+                            <div style="clear: both"></div>
+                        </div>
+                    %endfor                    
+                    <div class="form-row">
+                        <input type="submit" name="create_request_button" value="Save"/> 
+                        <input type="submit" name="create_request_samples_button" value="Add samples"/>
+                    </div>
+               %endif
+                <div class="form-row">
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <input type="hidden" name="refresh" value="true" size="40"/>
+                    </div>
+                  <div style="clear: both"></div>
+                </div>
+        </form>
+    </div>
+</div>
+%endif

--- a/templates/admin/requests/get_data.mako
+++ /dev/null
@@ -1,227 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$(document).ready(function(){
-    //hide the all of the element with class msg_body
-    $(".msg_body").hide();
-    //toggle the componenet with class msg_body
-    $(".msg_head").click(function(){
-        $(this).next(".msg_body").slideToggle(450);
-    });
-});
-
-
-
-
-</script>
-
-<script type="text/javascript">
-   function display_file_details(sample_id, folder_path)
-   {
-       var w = document.get_data.files_list.selectedIndex;
-       var selected_value = document.get_data.files_list.options[w].value;
-       var cell = $("#file_details");
-       if(selected_value.charAt(selected_value.length-1) != '/')
-       {
-            // Make ajax call
-            $.ajax( {
-                type: "POST",
-                url: "${h.url_for( controller='requests_admin', action='get_file_details' )}",
-                dataType: "json",
-                data: { id: sample_id, folder_path: document.get_data.folder_path.value+selected_value },
-                success : function ( data ) {
-                    cell.html( '<label>'+data+'</label>' )
-                }
-            });
-        }
-        else 
-        {
-            cell.html( '' )
-        }
-        
-       
-   }
-</script>
-
-<script type="text/javascript">
-   function open_folder1(sample_id, folder_path)
-   {
-       var w = document.get_data.files_list.selectedIndex;
-       var selected_value = document.get_data.files_list.options[w].value;
-       var cell = $("#file_details");
-       if(selected_value.charAt(selected_value.length-1) == '/')
-       {
-           document.get_data.folder_path.value = document.get_data.folder_path.value+selected_value
-            // Make ajax call
-            $.ajax( {
-                type: "POST",
-                url: "${h.url_for( controller='requests_admin', action='open_folder' )}",
-                dataType: "json",
-                data: { id: sample_id, folder_path: document.get_data.folder_path.value },
-                success : function ( data ) {
-                    document.get_data.files_list.options.length = 0
-                    for(i=0; i<data.length; i++) 
-                    {
-                        var newOpt = new Option(data[i], data[i]);
-                        document.get_data.files_list.options[i] = newOpt;
-                    }
-                    //cell.html( '<label>'+data+'</label>' )
-                    
-                }
-            });
-       }
-        else 
-        {
-            cell.html( '' )
-        }
-   }
-</script>
-
-
-<style type="text/css">
-.msg_head {
-    padding: 0px 0px;
-    cursor: pointer;
-}
-
-}
-</style>
-
-
-<h2>Data transfer from Sequencer</h2>
-<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
-<br/>
-<br/>
-
-<ul class="manage-table-actions">
-    %if sample.request.submitted() and sample.inprogress_dataset_files():
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
-        <span>Refresh this page</span></a>
-    </li>
-    %endif
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_request_types', operation='view', id=trans.security.encode_id(sample.request.type.id) )}">
-        <span>Sequencer information</span></a>
-    </li>
-    <li>
-        <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( sample.library.id ) )}">
-        <span>${sample.library.name} Data Library</span></a>
-    </li>
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
-        <span>Browse this request</span></a>
-    </li>
-</ul>
-
-<div class="toolForm">
-    %if len(dataset_files):
-##    <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
-        <div class="form-row">
-        <h4>Sample Dataset(s)</h4>
-        %if sample.untransferred_dataset_files():
-            <div class="form-row">
-                <ul class="manage-table-actions">
-                    <li>
-                        <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', start_transfer_button=True, sample_id=sample.id )}">
-                        <span>Start transfer</span></a>
-                    </li>
-                </ul>
-             </div>
-         %endif
-        <div class="form-row">
-            <table class="grid">
-            <thead>
-                <tr>
-                    <th>Dataset File</th>
-                    <th>Transfer Status</th>
-                    <th></th>
-                </tr>
-            <thead>
-                <tbody>
-                    %for dataset_index, dataset_file in enumerate(dataset_files):
-                        ${sample_dataset_files( dataset_index, dataset_file['name'], dataset_file['status'] )}
-                    %endfor
-                </tbody>
-            </table>
-        </div>
-        </div>
-
-##    </form>
-##</div>
-
-
-<br/>
-<br/>
-%endif
-
-##<div class="toolForm">
-    <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
-        <div class="form-row">
-            ##<div class="toolFormTitle">Select files for transfer</div>
-            <h4>Select files for transfer</h4>
-            <div style="width: 60%;">
-                <div class="form-row">
-                    <label>Folder path on the sequencer:</label>
-                    <input type="text" name="folder_path" value="${folder_path}" size="100"/>
-                    <input type="submit" name="browse_button" value="List contents"/>
-                    ##<input type="submit" name="open_folder" value="Open folder"/>
-                    <input type="submit" name="folder_up" value="Up"/>
-                </div>
-                <div class="form-row">
-                    <select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" ondblclick="open_folder1(${sample.id}, '${folder_path}')" onChange="display_file_details(${sample.id}, '${folder_path}')" multiple>
-                        %for index, f in enumerate(files):
-                            <option value="${f}">${f}</option>
-                        %endfor
-                    </select> 
-                    <br/>
-                    <div id="file_details" class="toolParamHelp" style="clear: both;">
-                        
-                    </div>
-                </div>
-                <div class="form-row">
-                    <div class="toolParamHelp" style="clear: both;">
-                        After selecting dataset(s), be sure to click on the <b>Start transfer</b> button. 
-                        Once the transfer is complete the dataset(s) will show up on this page.
-                    </div>
-                    <input type="submit" name="select_files_button" value="Select"/>
-                </div>
-            </div>
-        </div>
-    </form>
-</div>
-
-<%def name="sample_dataset_files( dataset_index, dataset_name, status )">
-    <tr>
-        <td>
-            <label class="msg_head"><a href="${h.url_for( controller='requests_admin', action='dataset_details', sample_id=trans.security.encode_id(sample.id), dataset_index=dataset_index )}">${dataset_name}</a></label>
-##            <div class="msg_head"><u>${dataset_file.split('/')[-1]}</u></div>
-##            <div class="msg_body">
-##                ${dataset_file}
-##            </div>
-        </td>
-        <td>
-            %if status not in [sample.transfer_status.NOT_STARTED, sample.transfer_status.COMPLETE]: 
-                <i>${status}</i>
-            %else:
-                ${status}
-            %endif
-        </td>
-        ##<td></td>
-        %if status == sample.transfer_status.NOT_STARTED: 
-        <td>
-            <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id, remove_dataset_button=True, dataset_index=dataset_index )}">
-            <img src="${h.url_for('/static/images/delete_icon.png')}" />
-            <span></span></a>
-        </td>
-        %else:
-            <td></td>
-        %endif
-    </tr>
-</%def>

--- a/templates/admin/requests/add_states.mako
+++ /dev/null
@@ -1,26 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
-    <div class="toolFormTitle">Create ${num_states} states for the '${request_type_name}' request type</div>
-    <form name="new_form_fields" action="${h.url_for( controller='requests_admin', action='request_type', name=request_type_name, description=desc, num_states=num_states, request_form_id=request_form_id, sample_form_id=sample_form_id)}" method="post" >
-        <div class="toolFormBody">
-            %for element_count in range( num_states ):
-                <div class="form-row">
-                    <label>${1+element_count}) State name:</label>
-                    <input type="text" name="state_name_${element_count}" value="" size="40"/>
-                    <label>State help text (optional):</label>
-                    <input type="text" name="state_desc_${element_count}" value="" size="40"/>
-                </div>
-                <div style="clear: both"></div>
-            %endfor
-        </div>
-        <div class="form-row">
-            <input type="submit" name="save_request_type" value="Save"/>
-        </div>
-    </form>
-</div>

--- /dev/null
+++ b/templates/requests/common/edit_request.mako
@@ -0,0 +1,84 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<script type="text/javascript">
+$( function() {
+    $( "select[refresh_on_change='true']").change( function() {
+        var refresh = false;
+        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+        if ( refresh_on_change_values ) {
+            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+            for( i= 0; i < refresh_on_change_values.length; i++ ) {
+                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+                    refresh = true;
+                    break;
+                }
+            }
+        }
+        else {
+            refresh = true;
+        }
+        if ( refresh ){
+            $( "#edit_request" ).submit();
+        }
+    });
+});
+</script>
+
+<br/>
+<br/>
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button"  href="${h.url_for( controller=cntrller, cntrller=cntrller, action='list')}">
+        <span>Browse requests</span></a>
+    </li>
+</ul>
+
+<div class="toolForm">
+    <div class="toolFormTitle">Edit request "${request.name}"</div>
+    %if len(select_request_type.options) == 1:
+        There are no request types created for a new request.
+    %else:
+        <div class="toolFormBody">
+            <form name="edit_request" id="edit_request" action="${h.url_for( controller='requests_common', cntrller=cntrller, action='edit', id=trans.security.encode_id(request.id))}" method="post" >
+                <div class="form-row">
+                    <label>
+                        Select Request Type:
+                    </label>
+                    ${select_request_type.get_html()}
+                </div>
+
+               %if select_request_type.get_selected() != ('Select one', 'none'):
+                   %for i, field in enumerate(widgets):
+                        <div class="form-row">
+                            <label>${field['label']}</label>
+                            ${field['widget'].get_html()}
+                            %if field['label'] == 'Data library' and new_library:
+                                ${new_library.get_html()}
+                            %endif
+                            <div class="toolParamHelp" style="clear: both;">
+                                ${field['helptext']}
+                            </div>
+                            <div style="clear: both"></div>
+                        </div>
+                    %endfor                    
+                    <div class="form-row">
+                        <div style="float: left; width: 250px; margin-right: 10px;">
+                            <input type="hidden" name="refresh" value="true" size="40"/>
+                        </div>
+                      <div style="clear: both"></div>
+                    </div>
+                    <div class="form-row">
+                        <input type="submit" name="save_changes_request_button" value="Save changes"/> 
+                        ##<input type="submit" name="edit_samples_button" value="Edit samples"/>
+                    </div>
+               %endif
+        </form>
+    </div>
+</div>
+%endif

--- a/lib/galaxy/web/controllers/requests.py
+++ b/lib/galaxy/web/controllers/requests.py
@@ -84,7 +84,7 @@ class RequestsGrid( grids.Grid ):
         NameColumn( "Name", 
                     key="name", 
                     model_class=model.Request,
-                    link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ),
+                    link=( lambda item: iff( item.deleted, None, dict( operation="show", id=item.id ) ) ),
                     attach_popup=True, 
                     filterable="advanced" ),
         DescriptionColumn( "Description",
@@ -92,7 +92,7 @@ class RequestsGrid( grids.Grid ):
                            model_class=model.Request,
                            filterable="advanced" ),
         SamplesColumn( "Sample(s)", 
-                       link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ),
+                       link=( lambda item: iff( item.deleted, None, dict( operation="show", id=item.id ) ) ), ),
         TypeColumn( "Type" ),
         grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
         grids.DeletedColumn( "Deleted", 
@@ -120,7 +120,8 @@ class RequestsGrid( grids.Grid ):
 
     ]
     global_actions = [
-        grids.GridAction( "Create new request", dict( controller='requests', 
+        grids.GridAction( "Create new request", dict( controller='requests_common',
+                                                      cntrller='requests', 
                                                       action='new', 
                                                       select_request_type='True' ) )
     ]
@@ -149,18 +150,36 @@ class Requests( BaseController ):
                                                                   action='list',
                                                                   status='error',
                                                                   message="Invalid request ID") )
-            if operation == "show_request":
-                return self.__show_request( trans, **kwd )
+            if operation == "show":
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests',
+                                                                  action='show',
+                                                                  **kwd ) )
             elif operation == "submit":
-                return self.__submit_request( trans, **kwd )
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests',
+                                                                  action='submit',
+                                                                  **kwd ) )
             elif operation == "delete":
-                return self.__delete_request( trans, **kwd )
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests',
+                                                                  action='delete',
+                                                                  **kwd ) )
             elif operation == "undelete":
-                return self.__undelete_request( trans, **kwd )
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests',
+                                                                  action='undelete',
+                                                                  **kwd ) )
             elif operation == "edit":
-                return self.__edit_request( trans, **kwd )
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests',
+                                                                  action='edit',
+                                                                  show=True, **kwd ) )
             elif operation == "events":
-                return self.__request_events( trans, **kwd )
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests',
+                                                                  action='events',
+                                                                  **kwd ) )
         # if there are one or more requests that has been rejected by the admin
         # recently, then show a message as a reminder to the user
         rlist = trans.sa_session.query( trans.app.model.Request ) \
@@ -176,915 +195,4 @@ class Requests( BaseController ):
                              % rejected 
         # Render the list view
         return self.request_grid( trans, **kwd )
-    def __request_events(self, trans, **kwd):
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            message = "Invalid request ID"
-            log.warn( message )
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              status='error',
-                                                              message=message,
-                                                              **kwd) )
-        events_list = []
-        all_events = request.events
-        for event in all_events:         
-            events_list.append((event.state, time_ago(event.update_time), event.comment))
-        return trans.fill_template( '/requests/events.mako', 
-                                    events_list=events_list, request=request)
-    def request_details(self, trans, id):
-        '''
-        Shows the request details
-        '''
-        request = trans.sa_session.query( trans.app.model.Request ).get( id )
-        # list of widgets to be rendered on the request form
-        request_details = []
-        # main details
-        request_details.append(dict(label='Description', 
-                                    value=request.desc, 
-                                    helptext=''))
-        request_details.append(dict(label='Type', 
-                                    value=request.type.name, 
-                                    helptext=''))
-
-        request_details.append(dict(label='State', 
-                                    value=request.state(), 
-                                    helptext=''))
-        request_details.append(dict(label='Date created', 
-                                    value=request.create_time, 
-                                    helptext=''))
-        # form fields
-        for index, field in enumerate(request.type.request_form.fields):
-            if field['required']:
-                req = 'Required'
-            else:
-                req = 'Optional'
-            if field['type'] == 'AddressField':
-                if request.values.content[index]:
-                    request_details.append(dict(label=field['label'],
-                                                value=trans.sa_session.query( trans.app.model.UserAddress ).get( int( request.values.content[index] ) ).get_html(),
-                                                helptext=field['helptext']+' ('+req+')'))
-                else:
-                    request_details.append(dict(label=field['label'],
-                                                value=None,
-                                                helptext=field['helptext']+' ('+req+')'))
-
-            else: 
-                request_details.append(dict(label=field['label'],
-                                            value=request.values.content[index],
-                                            helptext=field['helptext']+' ('+req+')'))
-        if request.notify:
-            notify = 'Yes'
-        else:
-            notify = 'No'
-        request_details.append(dict(label='Send email notification once the sequencing request is complete', 
-                                    value=notify, 
-                                    helptext=''))
-        return request_details   
-    def __show_request(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        add_sample = params.get('add_sample', False)
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID") )
-        # get all data libraries accessible to this user
-        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
-        current_samples = []
-        for i, s in enumerate(request.samples):
-            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
-            current_samples.append(dict(name=s.name,
-                                        barcode=s.bar_code,
-                                        library=s.library,
-                                        folder=s.folder,
-                                        dataset_files=s.dataset_files,
-                                        field_values=s.values.content,
-                                        lib_widget=lib_widget,
-                                        folder_widget=folder_widget))
-        if add_sample:
-            lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
-                                                               len(current_samples)+1, 
-                                                               libraries, None, **kwd)
-            current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
-                                        barcode='',
-                                        library=None,
-                                        folder=None,
-                                        dataset_files=[],
-                                        field_values=['' for field in request.type.sample_form.fields],
-                                        lib_widget=lib_widget,
-                                        folder_widget=folder_widget))
-        return trans.fill_template( '/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples=current_samples,
-                                    sample_copy=self.__copy_sample(current_samples), 
-                                    details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False'  ) ),
-                                    message=message, status=status )
-    def __library_widgets(self, trans, user, sample_index, libraries, sample=None, lib_id=None, folder_id=None, **kwd):
-        '''
-        This method creates the data library & folder selectbox for creating &
-        editing samples. First we get a list of all the libraries accessible to
-        the current user and display it in a selectbox. If the user has selected an
-        existing library then display all the accessible sub folders of the selected 
-        data library. 
-        '''
-        params = util.Params( kwd )
-        # data library selectbox
-        if not lib_id:
-            lib_id = params.get( "sample_%i_library_id" % sample_index, 'none'  )
-        selected_lib = None
-        if sample and lib_id == 'none':
-            if sample.library:
-                lib_id = str(sample.library.id)
-                selected_lib = sample.library
-        # create data library selectbox with refresh on change enabled
-        lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
-        lib_widget = SelectField( "sample_%i_library_id" % sample_index, 
-                                refresh_on_change=True, 
-                                refresh_on_change_values=lib_id_list )
-        # fill up the options in the Library selectbox
-        # first option 'none' is the value for "Select one" option
-        if lib_id == 'none':
-            lib_widget.add_option('Select one', 'none', selected=True)
-        else:
-            lib_widget.add_option('Select one', 'none')
-        # all the libraries available to the selected user
-        for lib, hidden_folder_ids in libraries.items():
-            if str(lib.id) == str(lib_id):
-                lib_widget.add_option(lib.name, lib.id, selected=True)
-                selected_lib, selected_hidden_folder_ids = lib, hidden_folder_ids.split(',')
-            else:
-                lib_widget.add_option(lib.name, lib.id)
-            lib_widget.refresh_on_change_values.append(lib.id)
-        # create the folder selectbox
-        folder_widget = SelectField( "sample_%i_folder_id" % sample_index )
-        # when editing a request, either the user has already selected a subfolder or not
-        if sample:
-            if sample.folder:
-                current_fid = sample.folder.id
-            else: 
-                # when a folder not yet associated with the request then the 
-                # the current folder is set to the root_folder of the 
-                # parent data library if present. 
-                if sample.library:
-                    current_fid = sample.library.root_folder.id
-                else:
-                    current_fid = params.get( "sample_%i_folder_id" % sample_index, 'none'  )
-        else:
-            if folder_id:
-                current_fid = folder_id
-            else:
-                current_fid = 'none'
-        # first option
-        if lib_id == 'none':
-            folder_widget.add_option('Select one', 'none', selected=True)
-        else:
-            folder_widget.add_option('Select one', 'none')
-        if selected_lib:
-            # get all show-able folders for the selected library
-            showable_folders = trans.app.security_agent.get_showable_folders( user, user.all_roles(), 
-                                                                              selected_lib, 
-                                                                              [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], 
-                                                                              selected_hidden_folder_ids )
-            for f in showable_folders:
-                if str(f.id) == str(current_fid):
-                    folder_widget.add_option(f.name, f.id, selected=True)
-                else:
-                    folder_widget.add_option(f.name, f.id)
-        return lib_widget, folder_widget
-    def __update_samples(self, trans, request, **kwd):
-        '''
-        This method retrieves all the user entered sample information and
-        returns an list of all the samples and their field values
-        '''
-        params = util.Params( kwd )
-        details = params.get( 'details', 'hide' )
-        edit_mode = params.get( 'edit_mode', 'False' )
-        # get all data libraries accessible to this user
-        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
-        
-        current_samples = []
-        for i, s in enumerate(request.samples):
-            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
-            current_samples.append(dict(name=s.name,
-                                        barcode=s.bar_code,
-                                        library=s.library,
-                                        folder=s.folder,
-                                        field_values=s.values.content,
-                                        lib_widget=lib_widget,
-                                        folder_widget=folder_widget))
-        if edit_mode == 'False':
-            sample_index = len(request.samples) 
-        else:
-            sample_index = 0
-        while True:
-            lib_id = None
-            folder_id = None
-            if params.get( 'sample_%i_name' % sample_index, ''  ):
-                # data library
-                try:
-                    library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'sample_%i_library_id' % sample_index, None ) ) )
-                    lib_id = library.id
-                except:
-                    library = None
-                # folder
-                try:
-                    folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'sample_%i_folder_id' % sample_index, None ) ) )
-                    folder_id = folder.id
-                except:
-                    if library:
-                        folder = library.root_folder
-                    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 edit_mode == 'False':
-                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, 
-                                                                                                     request.user, 
-                                                                                                     sample_index, 
-                                                                                                     libraries, 
-                                                                                                     None, lib_id, folder_id, **kwd)
-                    current_samples.append(sample_info)
-                else:
-                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, 
-                                                                                                     request.user, 
-                                                                                                     sample_index, 
-                                                                                                     libraries, 
-                                                                                                     request.samples[sample_index], 
-                                                                                                     **kwd)
-                    current_samples[sample_index] =  sample_info
-                sample_index = sample_index + 1
-            else:
-                break
-        return current_samples, details, edit_mode, libraries
-    def __copy_sample(self, current_samples):
-        copy_list = SelectField('copy_sample')
-        copy_list.add_option('None', -1, selected=True)  
-        for i, s in enumerate(current_samples):
-            copy_list.add_option(s['name'], i)
-        return copy_list
-    def __import_samples(self, trans, request, current_samples, details, libraries, **kwd):
-        '''
-        This method reads the samples csv file and imports all the samples
-        The format of the csv file is:
-        SampleName,DataLibrary,DataLibraryFolder,Field1,Field2....
-        ''' 
-        try:
-            params = util.Params( kwd )
-            edit_mode = params.get( 'edit_mode', 'False' )
-            file_obj = params.get('file_data', '')
-            reader = csv.reader(file_obj.file)
-            for row in reader:
-                lib_id = None
-                folder_id = None
-                lib = trans.sa_session.query( trans.app.model.Library ) \
-                                      .filter( and_( trans.app.model.Library.table.c.name==row[1], \
-                                                     trans.app.model.Library.table.c.deleted==False ) )\
-                                      .first()
-                if lib:
-                    folder = trans.sa_session.query( trans.app.model.LibraryFolder ) \
-                                             .filter( and_( trans.app.model.LibraryFolder.table.c.name==row[2], \
-                                                            trans.app.model.LibraryFolder.table.c.deleted==False ) )\
-                                             .first()
-                    if folder:
-                        lib_id = lib.id
-                        folder_id = folder.id
-                lib_widget, folder_widget = self.__library_widgets(trans, request.user, len(current_samples), 
-                                                                   libraries, None, lib_id, folder_id, **kwd)
-                current_samples.append(dict(name=row[0], 
-                                            barcode='',
-                                            library=None,
-                                            folder=None,
-                                            lib_widget=lib_widget,
-                                            folder_widget=folder_widget,
-                                            field_values=row[3:]))  
-            return trans.fill_template( '/admin/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=current_samples,
-                                        sample_copy=self.__copy_sample(current_samples), 
-                                        details=details,
-                                        edit_mode=edit_mode)
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                          action='list',
-                                                          operation='show_request',
-                                                          id=trans.security.encode_id(request.id),
-                                                          status='error',
-                                                          message='Error in importing samples file' ))
-
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def show_request(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID",
-                                                              **kwd) )
-        # get the user entered sample details
-        current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
-        if params.get('import_samples_button', False) == 'Import samples':
-            return self.__import_samples(trans, request, current_samples, details, libraries, **kwd)
-        elif params.get('add_sample_button', False) == 'Add New':
-            # add an empty or filled sample
-            # if the user has selected a sample no. to copy then copy the contents 
-            # of the src sample to the new sample else an empty sample
-            src_sample_index = int(params.get( 'copy_sample', -1  ))
-            # get the number of new copies of the src sample
-            num_sample_to_copy = int(params.get( 'num_sample_to_copy', 1  ))
-            if src_sample_index == -1:
-                for ns in range(num_sample_to_copy):
-                    # empty sample
-                    lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
-                                                                       len(current_samples), 
-                                                                       libraries, None, **kwd)
-                    current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
-                                                barcode='',
-                                                library=None,
-                                                folder=None,
-                                                field_values=['' for field in request.type.sample_form.fields],
-                                                lib_widget=lib_widget,
-                                                folder_widget=folder_widget))
-            else:
-                src_library_id = current_samples[src_sample_index]['lib_widget'].get_selected()[1]
-                src_folder_id = current_samples[src_sample_index]['folder_widget'].get_selected()[1]
-                for ns in range(num_sample_to_copy):
-                    lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
-                                                                       len(current_samples), 
-                                                                       libraries, sample=None, 
-                                                                       lib_id=src_library_id,
-                                                                       folder_id=src_folder_id,
-                                                                       **kwd)
-                    current_samples.append(dict(name=current_samples[src_sample_index]['name']+'_%i' % (len(current_samples)+1),
-                                                barcode='',
-                                                library_id='none',
-                                                folder_id='none',
-                                                field_values=[val for val in current_samples[src_sample_index]['field_values']],
-                                                lib_widget=lib_widget,
-                                                folder_widget=folder_widget))
-            return trans.fill_template( '/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=current_samples,
-                                        sample_copy=self.__copy_sample(current_samples), 
-                                        details=details,
-                                        edit_mode=edit_mode)
-        elif params.get('save_samples_button', False) == 'Save':
-            # check for duplicate sample names
-            message = ''
-            for index in range(len(current_samples)-len(request.samples)):
-                sample_index = index + len(request.samples)
-                sample_name = current_samples[sample_index]['name']
-                if not sample_name.strip():
-                    message = 'Please 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 = count + 1
-                if count > 1: 
-                    message = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
-                    break
-            if message:
-                return trans.fill_template( '/requests/show_request.mako',
-                                            request=request,
-                                            request_details=self.request_details(trans, request.id),
-                                            current_samples = current_samples,
-                                            sample_copy=self.__copy_sample(current_samples), 
-                                            details=details, edit_mode=edit_mode,
-                                            status='error', message=message)
-            # save all the new/unsaved samples entered by the user
-            if edit_mode == 'False':
-                for index in range(len(current_samples)-len(request.samples)):
-                    sample_index = len(request.samples)
-                    form_values = trans.app.model.FormValues(request.type.sample_form, 
-                                                             current_samples[sample_index]['field_values'])
-                    trans.sa_session.add( form_values )
-                    trans.sa_session.flush()                    
-                    s = trans.app.model.Sample(current_samples[sample_index]['name'], '', 
-                                               request, form_values, 
-                                               current_samples[sample_index]['barcode'],
-                                               current_samples[sample_index]['library'],
-                                               current_samples[sample_index]['folder'], 
-                                               dataset_files=[])
-                    trans.sa_session.add( s )
-                    trans.sa_session.flush()
-            else:
-                status = 'done'
-                message = 'Changes made to the sample(s) are saved. '
-                for sample_index in range(len(current_samples)):
-                    sample = request.samples[sample_index]
-                    sample.name = current_samples[sample_index]['name'] 
-                    sample.library = current_samples[sample_index]['library']
-                    sample.folder = current_samples[sample_index]['folder']
-                    if request.submitted():
-                        bc_message = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode'])
-                        if bc_message:
-                            status = 'error'
-                            message += bc_message
-                        else:
-                            sample.bar_code = current_samples[sample_index]['barcode']
-                    trans.sa_session.add( sample )
-                    trans.sa_session.flush()
-                    form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
-                    form_values.content = current_samples[sample_index]['field_values']
-                    trans.sa_session.add( form_values )
-                    trans.sa_session.flush()
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                          action='list',
-                                                          operation='show_request',
-                                                          id=trans.security.encode_id(request.id),
-                                                          status=status,
-                                                          message=message ))
-        elif params.get('edit_samples_button', False) == 'Edit samples':
-            edit_mode = 'True'
-            return trans.fill_template( '/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=current_samples,
-                                        sample_copy=self.__copy_sample(current_samples), 
-                                        details=details, libraries=libraries,
-                                        edit_mode=edit_mode)
-        elif params.get('cancel_changes_button', False) == 'Cancel':
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                          action='list',
-                                                          operation='show_request',
-                                                          id=trans.security.encode_id(request.id)) )
-        else:
-            return trans.fill_template( '/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=current_samples,
-                                        sample_copy=self.__copy_sample(current_samples), 
-                                        details=details, libraries=libraries,
-                                        edit_mode=edit_mode, status=status, message=message)
-
-            
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def delete_sample(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
-        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
-        sample_index = int(params.get('sample_id', 0))
-        sample_name = current_samples[sample_index]['name']
-        s = request.has_sample(sample_name)
-        if s:
-            trans.sa_session.delete( s.values )
-            trans.sa_session.delete( s )
-            trans.sa_session.flush()
-        del current_samples[sample_index]  
-        return trans.fill_template( '/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples = current_samples,
-                                    sample_copy=self.__copy_sample(current_samples), 
-                                    details=details,
-                                    edit_mode=edit_mode)
-    def __select_request_type(self, trans, rtid):
-        requesttype_list = trans.user.accessible_request_types(trans)
-        rt_ids = ['none']
-        for rt in requesttype_list:
-            if not rt.deleted:
-                rt_ids.append(str(rt.id))
-        select_reqtype = SelectField('select_request_type', 
-                                     refresh_on_change=True, 
-                                     refresh_on_change_values=rt_ids[1:])
-        if rtid == 'none':
-            select_reqtype.add_option('Select one', 'none', selected=True)
-        else:
-            select_reqtype.add_option('Select one', 'none')
-        for rt in requesttype_list:
-            if not rt.deleted:
-                if rtid == rt.id:
-                    select_reqtype.add_option(rt.name, rt.id, selected=True)
-                else:
-                    select_reqtype.add_option(rt.name, rt.id)
-        return select_reqtype
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def new(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        if params.get('select_request_type', False) == 'True':
-            return trans.fill_template( '/requests/new_request.mako',
-                                        select_request_type=self.__select_request_type(trans, 'none'),                                 
-                                        widgets=[],                                   
-                                        message=message,
-                                        status=status)
-        elif params.get('create', False) == 'True':
-            if params.get('create_request_button', False) == 'Save' \
-               or params.get('create_request_samples_button', False) == 'Add samples':
-                request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
-                if not util.restore_text(params.get('name', '')):
-                    message = 'Please enter the <b>Name</b> of the request'
-                    kwd['create'] = 'True'
-                    kwd['status'] = 'error'
-                    kwd['message'] = message
-                    kwd['create_request_button'] = None
-                    kwd['create_request_samples_button'] = None
-                    return trans.response.send_redirect( web.url_for( controller='requests',
-                                                                      action='new',
-                                                                      **kwd) )
-                request = self.__save_request(trans, None, **kwd)
-                message = 'The new request named <b>%s</b> has been created' % request.name
-                if params.get('create_request_button', False) == 'Save':
-                    return trans.response.send_redirect( web.url_for( controller='requests',
-                                                                      action='list',
-                                                                      message=message ,
-                                                                      status='done') )
-                elif params.get('create_request_samples_button', False) == 'Add samples':
-                    new_kwd = {}
-                    new_kwd['id'] = trans.security.encode_id(request.id)
-                    new_kwd['operation'] = 'show_request'
-                    new_kwd['add_sample'] = True
-                    return trans.response.send_redirect( web.url_for( controller='requests',
-                                                                      action='list',
-                                                                      message=message ,
-                                                                      status='done',
-                                                                      **new_kwd) )
-            else:
-                return self.__show_request_form(trans, **kwd)
-        elif params.get('refresh', False) == 'true':
-            return self.__show_request_form(trans, **kwd)
-    def __show_request_form(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        try:
-            request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
-        except:
-            return trans.fill_template( '/requests/new_request.mako',
-                                        select_request_type=self.__select_request_type(trans, 'none'),                                 
-                                        widgets=[],                                   
-                                        message=message,
-                                        status=status)
-        form_values = None
-        select_request_type = self.__select_request_type(trans, request_type.id)
-        # list of widgets to be rendered on the request form
-        widgets = []
-        widgets.append(dict(label='Name of the Experiment', 
-                            widget=TextField('name', 40, 
-                                             util.restore_text( params.get( 'name', ''  ) )), 
-                            helptext='(Required)'))
-        widgets.append(dict(label='Description', 
-                            widget=TextField('desc', 40,
-                                             util.restore_text( params.get( 'desc', ''  ) )), 
-                            helptext='(Optional)'))
-        widgets = widgets + request_type.request_form.get_widgets( trans.user, **kwd )
-        widgets.append(dict(label='Send email notification once the sequencing request is complete', 
-                            widget=CheckboxField('email_notify', False), 
-                            helptext=''))
-        return trans.fill_template( '/requests/new_request.mako',
-                                    select_request_type=select_request_type,
-                                    request_type=request_type,
-                                    widgets=widgets,
-                                    message=message,
-                                    status=status)
-    def __validate(self, trans, request):
-        '''
-        Validates the request entered by the user 
-        '''
-        empty_fields = []
-        # check rest of the fields of the form
-        for index, field in enumerate(request.type.request_form.fields):
-            if field['required'] == 'required' and request.values.content[index] in ['', None]:
-                empty_fields.append(field['label'])
-        if empty_fields:
-            message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name
-            for ef in empty_fields:
-                message = message + '<b>' +ef + '</b><br/>'
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              operation='edit',
-                                                              status = 'error',
-                                                              message=message,
-                                                              id=trans.security.encode_id(request.id) ))
-        # now check the required fields of all the samples of this request
-        for s in request.samples:
-            for index, field in enumerate(request.type.sample_form.fields):
-                if field['required'] == 'required' and s.values.content[index] in ['', None]:
-                    empty_fields.append((s.name, field['label']))
-        if empty_fields:
-            message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name
-            for sname, ef in empty_fields:
-                message = message + '<b>%s</b> field of sample <b>%s</b><br/>' % (ef, sname)
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              operation='show_request',
-                                                              status = 'error',
-                                                              message=message,
-                                                              id=trans.security.encode_id(request.id) ))
-    def __save_request(self, trans, request=None, **kwd):
-        '''
-        This method saves a new request if request_id is None. 
-        '''
-        params = util.Params( kwd )
-        request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
-        name = util.restore_text(params.get('name', ''))
-        desc = util.restore_text(params.get('desc', ''))
-        notify = CheckboxField.is_checked( params.get('email_notify', '') )
-        # library
-        try:
-            library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'library_id', None ) ) )
-        except:
-            library = None
-        try:
-            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'folder_id', None ) ) )
-        except:
-            if library:
-                folder = library.root_folder
-            else:
-                folder = None
-        # fields
-        values = []
-        for index, field in enumerate(request_type.request_form.fields):
-            if field['type'] == 'AddressField':
-                value = util.restore_text(params.get('field_%i' % index, ''))
-                if value == 'new':
-                    # save this new address in the list of this user's addresses
-                    user_address = trans.app.model.UserAddress( user=trans.user )
-                    user_address.desc = util.restore_text(params.get('field_%i_short_desc' % index, ''))
-                    user_address.name = util.restore_text(params.get('field_%i_name' % index, ''))
-                    user_address.institution = util.restore_text(params.get('field_%i_institution' % index, ''))
-                    user_address.address = util.restore_text(params.get('field_%i_address1' % index, ''))+' '+util.restore_text(params.get('field_%i_address2' % index, ''))
-                    user_address.city = util.restore_text(params.get('field_%i_city' % index, ''))
-                    user_address.state = util.restore_text(params.get('field_%i_state' % index, ''))
-                    user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, ''))
-                    user_address.country = util.restore_text(params.get('field_%i_country' % index, ''))
-                    user_address.phone = util.restore_text(params.get('field_%i_phone' % index, ''))
-                    trans.sa_session.add( user_address )
-                    trans.sa_session.flush()
-                    trans.sa_session.refresh( trans.user )
-                    values.append(int(user_address.id))
-                elif value == unicode('none'):
-                    values.append('')
-                else:
-                    values.append(int(value))
-            elif field['type'] == 'CheckboxField':
-                values.append(CheckboxField.is_checked( params.get('field_%i' % index, '') )) 
-            else:
-                values.append(util.restore_text(params.get('field_%i' % index, '')))
-        form_values = trans.app.model.FormValues(request_type.request_form, values)
-        trans.sa_session.add( form_values )
-        trans.sa_session.flush()
-        if not request:
-            request = trans.app.model.Request(name, desc, request_type, 
-                                              trans.user, form_values, notify)
-            trans.sa_session.add( request )
-            trans.sa_session.flush()
-            trans.sa_session.refresh( request )
-            # create an event with state 'New' for this new request
-            comments = "Request created."
-            event = trans.app.model.RequestEvent(request, request.states.NEW, comments)
-            trans.sa_session.add( event )
-            trans.sa_session.flush()
-        else:
-            request.name = name
-            request.desc = desc
-            request.type = request_type
-            request.user = trans.user
-            request.values = form_values
-            request.notify = notify
-            trans.sa_session.add( request )
-            trans.sa_session.flush()
-        return request
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def edit(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID",
-                                                              **kwd) )
-        if params.get('show', False) == 'True':
-            return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd)
-        elif params.get('save_changes_request_button', False) == 'Save changes' \
-             or params.get('edit_samples_button', False) == 'Edit samples':
-                request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
-                if not util.restore_text(params.get('name', '')):
-                    message = 'Please enter the <b>Name</b> of the request'
-                    kwd['status'] = 'error'
-                    kwd['message'] = message
-                    kwd['show'] = 'True'
-                    return trans.response.send_redirect( web.url_for( controller='requests',
-                                                                      action='edit',
-                                                                      **kwd) )
-                request = self.__save_request(trans, request, **kwd)
-                message = 'The changes made to the request named %s has been saved' % request.name
-                if params.get('save_changes_request_button', False) == 'Save changes':
-                    return trans.response.send_redirect( web.url_for( controller='requests',
-                                                                      action='list',
-                                                                      message=message ,
-                                                                      status='done') )
-                elif params.get('edit_samples_button', False) == 'Edit samples':
-                    new_kwd = {}
-                    new_kwd['request_id'] = request.id
-                    new_kwd['edit_samples_button'] = 'Edit samples'
-                    return trans.response.send_redirect( web.url_for( controller='requests',
-                                                                      action='show_request',
-                                                                      message=message ,
-                                                                      status='done',
-                                                                      **new_kwd) )
-        elif params.get('refresh', False) == 'true':
-            return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd)
-            
-    def __edit_request(self, trans, **kwd):
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            message = "Invalid request ID"
-            log.warn( message )
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              status='error',
-                                                              message=message) )
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        select_request_type = self.__select_request_type(trans, request.type.id)
-        # list of widgets to be rendered on the request form
-        widgets = []
-        if util.restore_text( params.get( 'name', ''  ) ):
-            name = util.restore_text( params.get( 'name', ''  ) )
-        else:
-            name = request.name
-        widgets.append(dict(label='Name', 
-                            widget=TextField('name', 40, name), 
-                            helptext='(Required)'))
-        if util.restore_text( params.get( 'desc', ''  ) ):
-            desc = util.restore_text( params.get( 'desc', ''  ) )
-        else:
-            desc = request.desc
-        widgets.append(dict(label='Description', 
-                            widget=TextField('desc', 40, desc), 
-                            helptext='(Optional)'))
-        widgets = widgets + request.type.request_form.get_widgets( trans.user, request.values.content, **kwd )
-        widgets.append(dict(label='Send email notification once the sequencing request is complete', 
-                            widget=CheckboxField('email_notify', request.notify), 
-                            helptext=''))
-        return trans.fill_template( '/requests/edit_request.mako',
-                                    select_request_type=select_request_type,
-                                    request_type=request.type,
-                                    request=request,
-                                    widgets=widgets,
-                                    message=message,
-                                    status=status)
-        return self.__show_request_form(trans)
-    def __delete_request(self, trans, **kwd):
-        id_list = util.listify( kwd['id'] )
-        delete_failed = []
-        for id in id_list:
-            try:
-                request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) )
-            except:
-                message = "Invalid request ID"
-                log.warn( message )
-                return trans.response.send_redirect( web.url_for( controller='requests',
-                                                                  action='list',
-                                                                  status='error',
-                                                                  message=message,
-                                                                  **kwd) )
-            # a request cannot be deleted once its submitted
-            if not request.new():
-                delete_failed.append(request.name)
-            else:
-                request.deleted = True
-                trans.sa_session.add( request )
-                # delete all the samples belonging to this request
-                for s in request.samples:
-                    s.deleted = True
-                    trans.sa_session.add( s )
-                trans.sa_session.flush()
-        if not len(delete_failed):
-            message = '%i request(s) has been deleted.' % len(id_list)
-            status = 'done'
-        else:
-            message = '%i request(s) has been deleted. %i request %s could not be deleted as they have been submitted.' % (len(id_list)-len(delete_failed), 
-                                                                                                               len(delete_failed), str(delete_failed))
-            status = 'warning'
-        return trans.response.send_redirect( web.url_for( controller='requests',
-                                                          action='list',
-                                                          status=status,
-                                                          message=message) )
-    def __undelete_request(self, trans, **kwd):
-        id_list = util.listify( kwd['id'] )
-        for id in id_list:
-            try:
-                request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) )
-            except:
-                message = "Invalid request ID"
-                log.warn( message )
-                return trans.response.send_redirect( web.url_for( controller='requests',
-                                                                  action='list',
-                                                                  status='error',
-                                                                  message=message,
-                                                                  **kwd) )
-            request.deleted = False
-            trans.sa_session.add( request )
-            # undelete all the samples belonging to this request
-            for s in request.samples:
-                s.deleted = False
-                trans.sa_session.add( s )
-            trans.sa_session.flush()
-        return trans.response.send_redirect( web.url_for( controller='requests',
-                                                          action='list',
-                                                          status='done',
-                                                          message='%i request(s) has been undeleted.' % len(id_list) ) )
-    def __submit_request(self, trans, **kwd):
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            message = "Invalid request ID"
-            log.warn( message )
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              status='error',
-                                                              message=message,
-                                                              **kwd) )
-        # check if all the required request and its sample fields have been filled 
-        self.__validate(trans, request)
-        # change the request state to 'Submitted'
-        comments = "Sequencing request is in progress."
-        event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, comments)
-        trans.sa_session.add( event )
-        trans.sa_session.flush()
-        # get the new state
-        new_state = request.type.states[0]
-        for s in request.samples:
-            event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system')
-            trans.sa_session.add( event )
-            trans.sa_session.flush()
-        return trans.response.send_redirect( web.url_for( controller='requests',
-                                                          action='list',
-                                                          id=trans.security.encode_id(request.id),
-                                                          status='done',
-                                                          message='The request <b>%s</b> has been submitted.' % request.name
-                                                          ) )
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def show_events(self, trans, **kwd):
-        params = util.Params( kwd )
-        try:
-            sample_id = int(params.get('sample_id', False))
-            sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id )
-        except:
-            message = "Invalid sample ID"
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              status='error',
-                                                              message=message,
-                                                              **kwd) )
-        events_list = []
-        all_events = sample.events
-        for event in all_events:
-            events_list.append((event.state.name, event.state.desc, time_ago(event.update_time), event.comment))
-        return trans.fill_template( '/sample/sample_events.mako', 
-                                    events_list=events_list,
-                                    sample_name=sample.name,
-                                    request=sample.request)
-    #
-    # Data transfer from sequencer
-    #
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def show_datatx_page( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' ) 
-        try:
-            sample = trans.sa_session.query( trans.app.model.Sample ).get( trans.security.decode_id( kwd['sample_id'] ) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid sample ID",
-                                                              **kwd) )
-        return trans.fill_template( '/requests/show_data.mako', 
-                                    sample=sample, dataset_files=sample.dataset_files )
+    

--- a/lib/galaxy/web/controllers/forms.py
+++ b/lib/galaxy/web/controllers/forms.py
@@ -474,8 +474,7 @@ class Forms( BaseController ):
             return trans.response.send_redirect( web.url_for( controller='forms',
                                                               action='new',
                                                               status='error',
-                                                              message='Error in importing <b>%s</b> file' % csv_file,
-                                                              **kwd))
+                                                              message='Error in importing <b>%s</b> file' % csv_file.file))
         self.__imported_from_file = True
         return fields, list(layouts)
     def __validate_form(self, **kwd):

--- a/templates/admin/requests/edit_request.mako
+++ /dev/null
@@ -1,88 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
-    $( "select[refresh_on_change='true']").change( function() {
-        var refresh = false;
-        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
-        if ( refresh_on_change_values ) {
-            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
-            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
-            for( i= 0; i < refresh_on_change_values.length; i++ ) {
-                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
-                    refresh = true;
-                    break;
-                }
-            }
-        }
-        else {
-            refresh = true;
-        }
-        if ( refresh ){
-            $( "#edit_request" ).submit();
-        }
-    });
-});
-</script>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
-        <span>Browse this request</span></a>
-    </li>
-    <li>
-        <a class="action-button"  href="${h.url_for( controller='requests_admin', action='list')}">
-        <span>Browse requests</span></a>
-    </li>
-</ul>
-
-<div class="toolForm">
-    <div class="toolFormTitle">Edit request "${request.name}" from ${request.user.email}</div>
-    %if len(select_request_type.options) == 1:
-        There are no request types created for a new request.
-    %else:
-        <div class="toolFormBody">
-            <form name="edit_request" id="edit_request" action="${h.url_for( controller='requests_admin', action='edit', request_id=request.id)}" method="post" >
-                <div class="form-row">
-                    <label>
-                        Select Request Type:
-                    </label>
-                    ${select_request_type.get_html()}
-                </div>
-
-               %if select_request_type.get_selected() != ('Select one', 'none'):
-                   %for i, field in enumerate(widgets):
-                        <div class="form-row">
-                            <label>${field['label']}</label>
-                            ${field['widget'].get_html()}
-                            %if field['label'] == 'Library' and new_library:
-                                ${new_library.get_html()}
-                            %endif
-                            <div class="toolParamHelp" style="clear: both;">
-                                ${field['helptext']}
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                    %endfor                    
-                    <div class="form-row">
-                        <div style="float: left; width: 250px; margin-right: 10px;">
-                            <input type="hidden" name="refresh" value="true" size="40"/>
-                        </div>
-                      <div style="clear: both"></div>
-                    </div>
-                    <div class="form-row">
-                        <input type="submit" name="save_changes_request_button" value="Save changes"/> 
-                        ##<input type="submit" name="edit_samples_button" value="Edit samples"/>
-                    </div>
-               %endif
-        </form>
-    </div>
-</div>
-%endif

--- a/templates/requests/sample_datasets.mako
+++ /dev/null
@@ -1,7 +0,0 @@
-<%def name="render_sample_datasets( sample )">
-    <a href="${h.url_for(controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id))}">${sample.transferred_dataset_files()}/${len(sample.dataset_files)}</a>
-</%def>
-
-
-
-${render_sample_datasets( sample )}

--- /dev/null
+++ b/templates/requests/common/events.mako
@@ -0,0 +1,39 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<h2>History of Sequencing Request "${request.name}"</h2>
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
+        <span>Browse this request</span></a>
+    </li>
+    <li>
+        <a class="action-button"  href="${h.url_for( controller=cntrller, action='list')}">
+        <span>Browse all requests</span></a>
+    </li>
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <table class="grid">
+        <thead>
+            <tr>
+                <th>State</th>
+                <th>Last Update</th>
+                <th>Comments</th>
+            </tr>
+        </thead>
+        <tbody>
+            %for state, updated, comments in events_list:    
+                <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
+                    <td><b><a>${state}</a></b></td>
+                    <td><a>${updated}</a></td>
+                    <td><a>${comments}</a></td>
+                </tr>             
+            %endfor
+        </tbody>
+    </table>
+</div>

--- /dev/null
+++ b/templates/requests/common/show_request.mako
@@ -0,0 +1,547 @@
+<%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" />
+
+
+
+<script type="text/javascript">
+$( function() {
+    $( "select[refresh_on_change='true']").change( function() {
+        var refresh = false;
+        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+        if ( refresh_on_change_values ) {
+            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+            for( i= 0; i < refresh_on_change_values.length; i++ ) {
+                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+                    refresh = true;
+                    break;
+                }
+            }
+        }
+        else {
+            refresh = true;
+        }
+        if ( refresh ){
+            $( "#show_request" ).submit();
+        }
+    });
+});
+</script>
+
+
+<script type="text/javascript">
+$(document).ready(function(){
+    //hide the all of the element with class msg_body
+    $(".msg_body").hide();
+    //toggle the componenet with class msg_body
+    $(".msg_head").click(function(){
+        $(this).next(".msg_body").slideToggle(450);
+    });
+});
+</script>
+
+<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, cntrller ) {
+                    // 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>
+
+<style type="text/css">
+.msg_head {
+    padding: 0px 0px;
+    cursor: pointer;
+}
+</style>
+
+<script type="text/javascript">
+    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> 
+
+%if request.submitted():
+    <% samples_not_ready = request.sequence_run_ready() %>
+    %if samples_not_ready:
+        ${render_msg( "Select a target library and folder for all the samples before starting the sequence run", "warning" )}
+    %endif
+%endif
+
+%if request.rejected():
+    ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )}
+%endif
+
+<div class="grid-header">
+    <h2>Sequencing Request "${request.name}"</h2>
+</div>
+
+<ul class="manage-table-actions">
+
+    %if request.unsubmitted() and request.samples:
+        <li>
+            <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller=cntrller, action='list', operation='Submit', id=trans.security.encode_id(request.id) )}">
+            <span>Submit request</span></a>
+        </li>
+    %endif
+    %if cntrller == 'requests_admin' and trans.user_is_admin():
+        %if request.submitted():
+            <li>
+                <a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='reject', id=trans.security.encode_id(request.id))}">
+                <span>Reject request</span></a>
+            </li>
+        %endif
+    %endif
+    <li>
+        <a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='events', id=trans.security.encode_id(request.id) )}">
+        <span>History</span></a>
+    </li>
+    <li>
+        <a class="action-button"  href="${h.url_for( controller=cntrller, action='list')}">
+        <span>Browse requests</span></a>
+    </li>
+
+</ul>
+
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+
+
+
+<div class="toolForm">
+    <div class="form-row">
+        <div class="msg_list">
+            <h4 class="msg_head"><u>Request Information</u></h4>
+            <div class="msg_body">
+                %for index, rd in enumerate(request_details):
+                    <div class="form-row">
+                        <label>${rd['label']}</label>
+                        %if not rd['value']:
+                            <i>None</i>
+                        %else:                      
+                            %if rd['label'] == 'State':
+                                <a href="${h.url_for( controller=cntrller, action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
+                            %else:
+                                ${rd['value']}     
+                            %endif
+                        %endif
+                    </div>
+                    <div style="clear: both"></div>
+                %endfor
+                <div class="form-row">
+                <ul class="manage-table-actions">
+                    <li>
+                        <a class="action-button"  href="${h.url_for( controller='requests_admin', action='list', operation='Edit', id=trans.security.encode_id(request.id))}">
+                        <span>Edit request details</span></a>
+                    </li>
+                </ul>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+
+<br/>
+
+<div class="toolForm">
+    <form id="show_request" name="show_request" action="${h.url_for( controller='requests_common', cntrller=cntrller, action='request_page', edit_mode=edit_mode )}"  method="post" >
+        <div class="form-row">
+            %if current_samples:
+                ## first render the basic info grid 
+                ${render_basic_info_grid()}
+                ## then render the other grid(s)
+                <% trans.sa_session.refresh( request.type.sample_form ) %>
+                %for grid_index, grid_name in enumerate(request.type.sample_form.layout):
+                    ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )}
+                    <br/>
+                %endfor
+            %else:
+                <label>There are no samples.</label>
+            %endif
+        </div>      
+        %if request.samples and request.submitted():
+            <script type="text/javascript">
+                // Updater
+                updater({${ ",".join( [ '"%s" : "%s"' % ( s.id, s.current_state().name ) for s in request.samples ] ) }});
+            </script>
+        %endif
+        
+        %if edit_mode == 'False':
+            <table class="grid">
+                <tbody>
+                    <tr>
+                        <div class="form-row">
+
+                            %if request.unsubmitted():
+                                <td>
+                                    %if current_samples:
+                                        <label>Copy </label>
+                                        <input type="integer" name="num_sample_to_copy" value="1" size="3"/>
+                                        <label>sample(s) from sample</label>
+                                        ${sample_copy.get_html()}
+                                    %endif
+                                    <input type="submit" name="add_sample_button" value="Add New"/>
+                                </td>
+                            %endif
+                            <td>
+                                %if len(current_samples) and len(current_samples) <= len(request.samples):                     
+                                    <input type="submit" name="edit_samples_button" value="Edit samples"/>
+                                %endif
+                            </td>
+                        </div>
+                    </tr> 
+                </tbody>
+            </table>
+        %endif
+        %if request.samples or current_samples: 
+            <div class="form-row">
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="hidden" name="refresh" value="true" size="40"/>
+                </div>
+              <div style="clear: both"></div>
+            </div>            
+            %if edit_mode == 'True':   
+                <div class="form-row">
+                    <input type="submit" name="save_samples_button" value="Save"/>
+                    <input type="submit" name="cancel_changes_button" value="Cancel"/>
+                </div>
+            %elif request.unsubmitted():
+                <div class="form-row">
+                    <input type="submit" name="save_samples_button" value="Save"/>
+                </div>
+            %endif
+            
+        %endif
+        <input type="hidden" name="id" value="${trans.security.encode_id(request.id)}" />
+    </form>
+</div>
+
+<br/>
+
+%if request.unsubmitted():
+<div class="toolForm">
+    <form id="import" name="import" action="${h.url_for( controller='requests_common', action='request_page', edit_mode=edit_mode, request_id=trans.security.encode_id(request.id) )}" enctype="multipart/form-data" method="post" >
+        <div class="form-row">
+            <div class="msg_list">
+                <h4 class="msg_head"><u>Import samples from csv file</u></h4>
+                <div class="msg_body">
+                    <input type="file" name="file_data" />
+                    <input type="submit" name="import_samples_button" value="Import samples"/>
+                    <br/>
+                    <div class="toolParamHelp" style="clear: both;">
+                        The csv file must be in the following format:<br/>
+                        SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
+                    </div>
+                </div>
+            </div>
+        </div>
+##        <input type="hidden" name="request_id" value="${request.id}" />
+    </form>
+</div>
+%endif
+
+<%def name="render_grid( grid_index, grid_name, fields_dict )">
+    <br/>
+    <div class="msg_list">
+    %if grid_name:
+        <h4 class="msg_head"><u>${grid_name}</u></h4>
+    %else:
+        <h4>Grid ${grid_index}</h4>
+    %endif
+    %if edit_mode == 'False' or len(current_samples) <= len(request.samples):
+        <div class="msg_body">
+    %else:
+        <div class="msg_body2">
+    %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 edit_mode == 'True':
+                    <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()">
+    <h4>Sample Information</h4>
+    <table class="grid">
+        <thead>
+            <tr>
+                <th>Name</th>
+                <th>Barcode</th>
+                <th>State</th>
+                <th>Data Library</th>
+                <th>Folder</th>
+                %if request.submitted() or request.complete(): 
+                    <th>Dataset(s) 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 edit_mode == 'True':
+                    <tr>
+                        ${show_basic_info_form( sample_index, sample, info )}
+                    </tr>      
+                %else:
+                    <tr>
+                        %if sample_index in range(len(request.samples)):
+                            <td>${info['name']}</td>
+                            <td>${info['barcode']}</td>
+                            %if sample.request.unsubmitted():
+                                <td>Unsubmitted</td>
+                            %else:
+                                <td id="sampleState-${sample.id}">${render_sample_state( cntrller, sample )}</td>
+                            %endif
+                            %if info['library']:
+                                <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
+                            %else:
+                                <td></td>
+                            %endif
+                            %if info['folder']:
+                                <td>${info['folder'].name}</td>
+                            %else:
+                                <td></td>
+                            %endif
+                            %if request.submitted() or request.complete(): 
+                                <td id="sampleDatasets-${sample.id}">
+                                    ${render_sample_datasets( cntrller, sample )}
+                                </td>
+                            %endif
+                            
+                            
+                        %else:                                                            
+                            ${show_basic_info_form( sample_index, sample, info )}
+                        %endif
+                        %if request.unsubmitted() or request.rejected(): 
+                            <td>
+                                %if sample:
+                                    %if sample.request.unsubmitted():
+                                        <a class="action-button" href="${h.url_for( controller='requests_common', cntrller=cntrller, action='delete_sample', request_id=request.id, sample_id=sample_index )}">
+                                        <img src="${h.url_for('/static/images/delete_icon.png')}" />
+                                        <span></span></a>
+                                    %endif
+                                %endif
+                            </td>
+                        %endif
+                    </tr>  
+                %endif
+            %endfor
+        </tbody>
+    </table>
+</%def>
+
+<%def name="show_basic_info_form( sample_index, sample, info )">
+    <td>
+        <input type="text" name=sample_${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.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 cntrller == 'requests_admin':
+        %if sample:
+            %if sample.request.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.unsubmitted():
+            <td>Unsubmitted</td>
+        %else:
+            <td><a href="${h.url_for( controller='requests_admin', action='sample_events', sample_id=sample.id)}">${sample.current_state().name}</a></td>
+        %endif    
+    %else:
+        <td></td>
+    %endif
+    <td>${info['lib_widget'].get_html()}</td>
+    <td>${info['folder_widget'].get_html()}</td>
+    %if request.submitted() or request.complete(): 
+        %if sample:
+            <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a></td> 
+        %else:
+            <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">Add</a></td>
+        %endif 
+    %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>
+
+
+
+
+
+
+
+
+
+

--- a/templates/admin/requests/new_request.mako
+++ /dev/null
@@ -1,94 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
-    $( "select[refresh_on_change='true']").change( function() {
-        var refresh = false;
-        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
-        if ( refresh_on_change_values ) {
-            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
-            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
-            for( i= 0; i < refresh_on_change_values.length; i++ ) {
-                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
-                    refresh = true;
-                    break;
-                }
-            }
-        }
-        else {
-            refresh = true;
-        }
-        if ( refresh ){
-            $( "#new_request" ).submit();
-        }
-    });
-});
-</script>
-
-<%def name="javascripts()">
-   ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
-</%def>
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "autocomplete_tagging" )}
-</%def>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button"  href="${h.url_for( controller='requests_admin', action='list')}">
-        <span>Browse requests</span></a>
-    </li>
-</ul>
-
-<div class="toolForm">
-    <div class="toolFormTitle">Add a new request</div>
-    %if len(select_request_type.options) == 1:
-        There are no request types created for a new request.
-    %else:
-        <div class="toolFormBody">
-            <form name="new_request" id="new_request" action="${h.url_for( controller='requests_admin', action='new', create=True )}" method="post" >
-                <div class="form-row">
-                    <label>
-                        Select Request Type
-                    </label>
-                    ${select_request_type.get_html()}
-                </div>
-
-               %if select_request_type.get_selected() != ('Select one', 'none'):
-                   %for i, field in enumerate(widgets):
-                        <div class="form-row">
-                            <label>${field['label']}</label>
-                            ${field['widget'].get_html()}
-                            %if field['label'] == 'Library' and new_library:
-                                ${new_library.get_html()}
-                            %endif
-                            <div class="toolParamHelp" style="clear: both;">
-                                ${field['helptext']}
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                    %endfor                    
-                    <div class="form-row">
-                        <div style="float: left; width: 250px; margin-right: 10px;">
-                            <input type="hidden" name="refresh" value="true" size="40"/>
-                        </div>
-                      <div style="clear: both"></div>
-                    </div>
-                    <div class="form-row">
-                        <input type="submit" name="create_request_button" value="Save"/> 
-                        <input type="submit" name="create_request_samples_button" value="Add samples"/>
-                    </div>
-               %endif
-        </form>
-    </div>
-</div>
-%endif

--- a/templates/sample/sample_events.mako
+++ /dev/null
@@ -1,45 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<%def name="title()">Events for Sample ${sample_name}</%def>
-
-
-<h2>Events for Sample "${sample_name}"</h2>
-
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
-        <span>Browse this request</span></a>
-    </li>
-    <li>
-        <a class="action-button"  href="${h.url_for( controller='requests', action='list')}">
-        <span>Browse requests</span></a>
-    </li>
-</ul>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
-    <table class="grid">
-        <thead>
-            <tr>
-                <th>State</th>
-                <th>Description</th>
-                <th>Updated</th>
-                <th>Comments</th>
-            </tr>
-        </thead>
-        <tbody>
-            %for state, desc, updated, comments in events_list:    
-                <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
-                    <td><b><a>${state}</a></b></td>
-                    <td><a>${desc}</a></td>
-                    <td><a>${updated}</a></td>
-                    <td><a>${comments}</a></td>
-                </tr>             
-            %endfor
-        </tbody>
-    </table>
-</div>

--- /dev/null
+++ b/templates/requests/common/sample_datasets.mako
@@ -0,0 +1,7 @@
+<%def name="render_sample_datasets( cntrller, sample )">
+    <a href="${h.url_for(controller='requests_common', cntrller=cntrller, action='show_datatx_page', sample_id=trans.security.encode_id(sample.id))}">${sample.transferred_dataset_files()}/${len(sample.dataset_files)}</a>
+</%def>
+
+
+
+${render_sample_datasets( cntrller, sample )}

--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -1485,14 +1485,13 @@ class TwillTestCase( unittest.TestCase )
             url ="%s&%s=%s" % ( url, key, role_ids_str )
         self.home()
         self.visit_url( "%s/%s" % ( self.url, url ) )
-        print url
         check_str = "Permissions updated for request type '%s'" % request_type_name
         self.check_page_for_string( check_str )
         self.home()
     def create_request( self, request_type_id, name, desc, fields ):
         self.home()
-        self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % ( self.url, 
-                                                                                 request_type_id ) )
+        self.visit_url( "%s/requests_common/new?select_request_type=%i&refresh=true&cntrller=requests" % ( self.url, 
+                                                                                                           request_type_id ) )
         self.check_page_for_string( 'Add a new request' )
         tc.fv( "1", "name", name )
         tc.fv( "1", "desc", desc )
@@ -1514,21 +1513,20 @@ class TwillTestCase( unittest.TestCase )
         self.check_page_for_string( new_desc )
     def add_samples( self, request_id, request_name, samples ):
         self.home()
-        url = "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) )
+        url = "%s/requests/list?operation=show&id=%s" % ( self.url, self.security.encode_id( request_id ) )
         self.visit_url( url )
         self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
         self.check_page_for_string( 'There are no samples.' )
         # this redundant stmt below is add so that the second form in 
         # the page gets selected
-        tc.fv( "3", "request_id", request_id )
+        url = ["%s/requests_common/request_page?cntrller=requests&edit_mode=False&id=%s" % ( self.url, self.security.encode_id( request_id ) )]
         for sample_index, sample in enumerate(samples):
-            tc.submit( "add_sample_button" )
-            self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
             sample_name, fields = sample
-            tc.fv( "3", "sample_%i_name" % sample_index, sample_name )
+            url.append("sample_%i_name=%s" % (sample_index, sample_name.replace(' ', '+')))
             for field_index, field_value in enumerate(fields):
-                tc.fv( "3", "sample_%i_field_%i" % ( sample_index, field_index ), field_value )
-        tc.submit( "save_samples_button" )
+                url.append("sample_%i_field_%i=%s" % ( sample_index, field_index , field_value.replace(' ', '+') ))
+        url.append("save_samples_button=Save")
+        self.visit_url('&'.join(url))
         for sample_name, fields in samples:
             self.check_page_for_string( sample_name )
             self.check_page_for_string( 'Unsubmitted' )
@@ -1549,19 +1547,24 @@ class TwillTestCase( unittest.TestCase )
         tc.fv( "1", "comment", comment )
         tc.submit( "reject_button" )
         self.check_page_for_string( 'Request <b>%s</b> has been rejected.' % request_name )
-        self.visit_url( "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) ))
+        self.visit_url( "%s/requests/list?&operation=show&id=%s" % ( self.url, self.security.encode_id( request_id ) ))
         self.check_page_for_string( comment )
-    def add_bar_codes( self, request_id, request_name, bar_codes ):
+    def add_bar_codes( self, request_id, request_name, bar_codes, samples ):
         self.home()
-        self.visit_url( "%s/requests_admin/bar_codes?request_id=%i" % (self.url, request_id) )
-        self.check_page_for_string( 'Bar codes for Samples of Request "%s"' % request_name )
+        url = "%s/requests/list?operation=show&id=%s" % ( self.url, self.security.encode_id( request_id ) )
+        self.visit_url( url )
+        self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
+        url = ["%s/requests_common/request_page?save_samples_button=Save&cntrller=requests&edit_mode=True&id=%s" % ( self.url, self.security.encode_id( request_id ) )]
         for index, bar_code in enumerate(bar_codes):
-            tc.fv( "1", "sample_%i_bar_code" % index, bar_code )
-        tc.submit( "save_bar_codes" )
-        self.check_page_for_string( 'Bar codes have been saved for this request' )
+            url.append("sample_%i_barcode=%s" % (index, bar_code ))
+            url.append("sample_%i_name=%s" % (index, samples[index].name.replace(' ', '+') ))
+        self.visit_url('&'.join(url))
+        self.check_page_for_string( 'Changes made to the sample(s) are saved.' )
+        for index, bar_code in enumerate(bar_codes):
+            self.check_page_for_string( bar_code )
     def change_sample_state( self, sample_name, sample_id, new_state_id, new_state_name, comment='' ):
         self.home()
-        self.visit_url( "%s/requests_admin/show_events?sample_id=%i" % (self.url, sample_id) )
+        self.visit_url( "%s/requests_common/sample_events?cntrller=requests_admin&sample_id=%i" % (self.url, sample_id) )
         self.check_page_for_string( 'Events for Sample "%s"' % sample_name )
         tc.fv( "1", "select_state", str(new_state_id) )
         tc.fv( "1", "comment", comment )

--- a/templates/requests/show_data.mako
+++ /dev/null
@@ -1,86 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$(document).ready(function(){
-    //hide the all of the element with class msg_body
-    $(".msg_body").hide();
-    //toggle the componenet with class msg_body
-    $(".msg_head").click(function(){
-        $(this).next(".msg_body").slideToggle(450);
-    });
-});
-</script>
-<style type="text/css">
-.msg_head {
-    padding: 0px 0px;
-    cursor: pointer;
-}
-
-}
-</style>
-
-
-<h2>Data transfer from Sequencer</h2>
-<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
-
-<ul class="manage-table-actions">
-    %if sample.request.submitted() and sample.inprogress_dataset_files():
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
-        <span>Refresh this page</span></a>
-    </li>
-    %endif
-    %if sample.library:
-    <li>
-        <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">
-        <span>${sample.library.name} Data Library</span></a>
-    </li>
-    %endif
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
-        <span>Browse this request</span></a>
-    </li>
-</ul>
-
-<div class="toolForm">
-    <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
-        <div class="form-row">
-            %if len(dataset_files):
-                <table class="grid">
-                    <thead>
-                        <tr>
-                            <th>Dataset File</th>
-                            <th>Transfer Status</th>
-                        </tr>
-                    <thead>
-                    <tbody>
-                        %for dataset_index, dataset_file in enumerate(dataset_files):
-                            ${sample_dataset_files( dataset_index, dataset_file[0], dataset_file[1] )}
-                        %endfor
-                    </tbody>
-                </table>
-            %else:
-                There are no dataset files.
-            %endif
-        </div>
-    </form>
-</div>
-
-<%def name="sample_dataset_files( dataset_index, dataset_file, status )">
-    <tr>
-        <td>${dataset_file.split('/')[-1]}</td>
-        <td>
-            %if status == sample.transfer_status.IN_PROGRESS: 
-                <i>${status}</i>
-            %else:
-                ${status}
-            %endif
-        </td>
-    </tr>
-</%def>

--- /dev/null
+++ b/lib/galaxy/web/controllers/requests_common.py
@@ -0,0 +1,1099 @@
+from galaxy.web.base.controller import *
+from galaxy.web.framework.helpers import time_ago, iff, grids
+from galaxy.model.orm import *
+from galaxy.datatypes import sniff
+from galaxy import model, util
+from galaxy.util.streamball import StreamBall
+import logging, tempfile, zipfile, tarfile, os, sys, subprocess
+from galaxy.web.form_builder import * 
+from datetime import datetime, timedelta
+from galaxy.web.controllers.forms import get_all_forms
+from sqlalchemy.sql.expression import func, and_
+from sqlalchemy.sql import select
+import pexpect
+import ConfigParser, threading, time
+from amqplib import client_0_8 as amqp
+import csv
+log = logging.getLogger( __name__ )
+
+
+class RequestsCommon( BaseController ):
+    
+    @web.json
+    def sample_state_updates( self, trans, ids=None, states=None, cntrller=None ):
+        # Avoid caching
+        trans.response.headers['Pragma'] = 'no-cache'
+        trans.response.headers['Expires'] = '0'
+        # Create new HTML for any that have changed
+        rval = {}
+        if ids is not None and states is not None:
+            ids = map( int, ids.split( "," ) )
+            states = states.split( "," )
+            for id, state in zip( ids, states ):
+                sample = trans.sa_session.query( self.app.model.Sample ).get( id )
+                if sample.current_state().name != state:
+                    rval[id] = {
+                        "state": sample.current_state().name,
+                        "datasets": len(sample.dataset_files),
+                        "html_state": unicode( trans.fill_template( "requests/common/sample_state.mako", sample=sample, cntrller=cntrller ), 'utf-8' ),
+                        "html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako", trans=trans, sample=sample, cntrller=cntrller ), 'utf-8' )
+                    }
+        return rval
+
+    
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def new(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        if params.get('select_request_type', False) == 'True':
+            return trans.fill_template( '/requests/common/new_request.mako',
+                                        cntrller=cntrller,
+                                        select_request_type=self.__select_request_type(trans, 'none'),                                 
+                                        widgets=[],                                   
+                                        message=message,
+                                        status=status)
+        elif params.get('create_request_button', False) == 'Save' \
+           or params.get('create_request_samples_button', False) == 'Add samples':
+            request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
+            if not util.restore_text(params.get('name', '')) \
+                or util.restore_text(params.get('select_user', '')) == unicode('none'):
+                message = 'Please enter the <b>Name</b> of the request and the <b>user</b> on behalf of whom this request will be submitted before saving this request'
+                kwd['create'] = 'True'
+                kwd['status'] = 'error'
+                kwd['message'] = message
+                kwd['create_request_button'] = None
+                kwd['create_request_samples_button'] = None
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller=cntrller,
+                                                                  action='new',
+                                                                  **kwd) )
+            request = self.__save_request(trans, None, **kwd)
+            message = 'The new request named <b>%s</b> has been created' % request.name
+            if params.get('create_request_button', False) == 'Save':
+                return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                                  action='list',
+                                                                  message=message ,
+                                                                  status='done') )
+            elif params.get('create_request_samples_button', False) == 'Add samples':
+                new_kwd = {}
+                new_kwd['id'] = trans.security.encode_id(request.id)
+                new_kwd['operation'] = 'show'
+                new_kwd['add_sample'] = True
+                return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                                  action='list',
+                                                                  message=message ,
+                                                                  status='done',
+                                                                  **new_kwd) )
+        elif params.get('refresh', False) == 'true':
+            return self.__show_request_form(trans, **kwd)
+        
+    def __select_request_type(self, trans, rtid):
+        requesttype_list = trans.user.accessible_request_types(trans)
+        rt_ids = ['none']
+        for rt in requesttype_list:
+            if not rt.deleted:
+                rt_ids.append(str(rt.id))
+        select_reqtype = SelectField('select_request_type', 
+                                     refresh_on_change=True, 
+                                     refresh_on_change_values=rt_ids[1:])
+        if rtid == 'none':
+            select_reqtype.add_option('Select one', 'none', selected=True)
+        else:
+            select_reqtype.add_option('Select one', 'none')
+        for rt in requesttype_list:
+            if not rt.deleted:
+                if rtid == rt.id:
+                    select_reqtype.add_option(rt.name, rt.id, selected=True)
+                else:
+                    select_reqtype.add_option(rt.name, rt.id)
+        return select_reqtype
+    
+    def __show_request_form(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        try:
+            request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
+        except:
+            return trans.fill_template( '/requests/common/new_request.mako',
+                                        cntrller=cntrller, 
+                                        select_request_type=self.__select_request_type(trans, 'none'),                                 
+                                        widgets=[],                                   
+                                        message=message,
+                                        status=status)
+        form_values = None
+        select_request_type = self.__select_request_type(trans, request_type.id)
+        # user
+        if cntrller == 'requests_admin' and trans.user_is_admin():
+            user_id = params.get( 'select_user', 'none' )
+            try:
+                user = trans.sa_session.query( trans.app.model.User ).get( int( user_id ) )
+            except:
+                user = None
+        elif cntrller == 'requests':
+            user = trans.user
+        # list of widgets to be rendered on the request form
+        widgets = []
+        if cntrller == 'requests_admin' and trans.user_is_admin():
+            widgets.append(dict(label='Select user',
+                                widget=self.__select_user(trans, user_id),
+                                helptext='The request would be submitted on behalf of this user (Required)'))
+        widgets.append(dict(label='Name of the Experiment', 
+                            widget=TextField('name', 40, 
+                                             util.restore_text( params.get( 'name', ''  ) )), 
+                            helptext='(Required)'))
+        widgets.append(dict(label='Description', 
+                            widget=TextField('desc', 40,
+                                             util.restore_text( params.get( 'desc', ''  ) )), 
+                            helptext='(Optional)'))
+        widgets = widgets + request_type.request_form.get_widgets( user, **kwd )
+        widgets.append(dict(label='Send email notification when the sequencing request is complete', 
+                            widget=CheckboxField('email_notify', False), 
+                            helptext='Email would be sent to the lab admin and the user for whom this request has been created.'))
+        return trans.fill_template( '/requests/common/new_request.mako',
+                                    cntrller=cntrller,
+                                    select_request_type=select_request_type,
+                                    request_type=request_type,                                    
+                                    widgets=widgets,
+                                    message=message,
+                                    status=status)
+    def __select_user(self, trans, userid):
+        user_list = trans.sa_session.query( trans.app.model.User )\
+                                    .order_by( trans.app.model.User.email.asc() )
+        user_ids = ['none']
+        for user in user_list:
+            if not user.deleted:
+                user_ids.append(str(user.id))
+        select_user = SelectField('select_user', 
+                                  refresh_on_change=True, 
+                                  refresh_on_change_values=user_ids[1:])
+        if userid == 'none':
+            select_user.add_option('Select one', 'none', selected=True)
+        else:
+            select_user.add_option('Select one', 'none')
+        for user in user_list:
+            if not user.deleted:
+                if userid == str(user.id):
+                    select_user.add_option(user.email, user.id, selected=True)
+                else:
+                    select_user.add_option(user.email, user.id)
+        return select_user
+    def __save_request(self, trans, request, **kwd):
+        '''
+        This method saves a new request if request_id is None. 
+        '''
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
+        if request:
+            user = request.user
+        else:
+            if cntrller == 'requests_admin' and trans.user_is_admin():
+                user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'select_user', '' ) ) )
+            elif cntrller == 'requests':
+                user = trans.user
+        name = util.restore_text(params.get('name', ''))
+        desc = util.restore_text(params.get('desc', ''))
+        notify = CheckboxField.is_checked( params.get('email_notify', '') )
+        # fields
+        values = []
+        for index, field in enumerate(request_type.request_form.fields):
+            if field['type'] == 'AddressField':
+                value = util.restore_text(params.get('field_%i' % index, ''))
+                if value == 'new':
+                    # save this new address in the list of this user's addresses
+                    user_address = trans.app.model.UserAddress( user=user )
+                    user_address.desc = util.restore_text(params.get('field_%i_short_desc' % index, ''))
+                    user_address.name = util.restore_text(params.get('field_%i_name' % index, ''))
+                    user_address.institution = util.restore_text(params.get('field_%i_institution' % index, ''))
+                    user_address.address = util.restore_text(params.get('field_%i_address1' % index, ''))+' '+util.restore_text(params.get('field_%i_address2' % index, ''))
+                    user_address.city = util.restore_text(params.get('field_%i_city' % index, ''))
+                    user_address.state = util.restore_text(params.get('field_%i_state' % index, ''))
+                    user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, ''))
+                    user_address.country = util.restore_text(params.get('field_%i_country' % index, ''))
+                    user_address.phone = util.restore_text(params.get('field_%i_phone' % index, ''))
+                    trans.sa_session.add( user_address )
+                    trans.sa_session.flush()
+                    trans.sa_session.refresh( user )
+                    values.append(int(user_address.id))
+                elif value == unicode('none'):
+                    values.append('')
+                else:
+                    values.append(int(value))
+            elif field['type'] == 'CheckboxField':
+                values.append(CheckboxField.is_checked( params.get('field_%i' % index, '') )) 
+            else:
+                values.append(util.restore_text(params.get('field_%i' % index, '')))
+        form_values = trans.app.model.FormValues(request_type.request_form, values)
+        trans.sa_session.add( form_values )
+        trans.sa_session.flush()
+        if not request:
+            request = trans.app.model.Request(name, desc, request_type, 
+                                              user, form_values, notify)
+            trans.sa_session.add( request )
+            trans.sa_session.flush()
+            trans.sa_session.refresh( request )
+            # create an event with state 'New' for this new request
+            if request.user.email is not trans.user:
+                comments = "Request created by admin (%s) on behalf of %s." % (trans.user.email, request.user.email)
+            else:
+                comments = "Request created."
+            event = trans.app.model.RequestEvent(request, request.states.NEW, comments)
+            trans.sa_session.add( event )
+            trans.sa_session.flush()
+        else:
+            request.name = name
+            request.desc = desc
+            request.type = request_type
+            request.user = user
+            request.notify = notify
+            request.values = form_values
+            trans.sa_session.add( request )
+            trans.sa_session.flush()
+        return request
+    
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def edit(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id( params.get( 'id', None ) ) )
+        except:
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid request ID") )
+        if params.get('show', False) == 'True':
+            return self.__edit_request(trans, **kwd)
+        elif params.get('save_changes_request_button', False) == 'Save changes' \
+             or params.get('edit_samples_button', False) == 'Edit samples':
+                request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
+                if not util.restore_text(params.get('name', '')):
+                    message = 'Please enter the <b>Name</b> of the request'
+                    kwd['status'] = 'error'
+                    kwd['message'] = message
+                    kwd['show'] = 'True'
+                    return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                      cntrller=cntrller,
+                                                                      action='edit',
+                                                                      **kwd) )
+                request = self.__save_request(trans, request, **kwd)
+                message = 'The changes made to the request named %s has been saved' % request.name
+                if params.get('save_changes_request_button', False) == 'Save changes':
+                    return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                                      cntrller=cntrller,
+                                                                      action='list',
+                                                                      message=message ,
+                                                                      status='done') )
+                elif params.get('edit_samples_button', False) == 'Edit samples':
+                    new_kwd = {}
+                    new_kwd['id'] = request.id
+                    new_kwd['edit_samples_button'] = 'Edit samples'
+                    return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                                      cntrller=cntrller,
+                                                                      action='show',
+                                                                      message=message ,
+                                                                      status='done',
+                                                                      **new_kwd) )
+        elif params.get('refresh', False) == 'true':
+            return self.__edit_request(trans, **kwd)
+        
+    def __edit_request(self, trans, **kwd):
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
+        except:
+            message = "Invalid request ID"
+            log.warn( message )
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              cntrller=cntrller,
+                                                              action='list',
+                                                              status='error',
+                                                              message=message) )
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        select_request_type = self.__select_request_type(trans, request.type.id)
+        # list of widgets to be rendered on the request form
+        widgets = []
+        if util.restore_text( params.get( 'name', ''  ) ):
+            name = util.restore_text( params.get( 'name', ''  ) )
+        else:
+            name = request.name
+        widgets.append(dict(label='Name', 
+                            widget=TextField('name', 40, name), 
+                            helptext='(Required)'))
+        if util.restore_text( params.get( 'desc', ''  ) ):
+            desc = util.restore_text( params.get( 'desc', ''  ) )
+        else:
+            desc = request.desc
+        widgets.append(dict(label='Description', 
+                            widget=TextField('desc', 40, desc), 
+                            helptext='(Optional)'))
+        widgets = widgets + request.type.request_form.get_widgets( request.user, request.values.content, **kwd )
+        widgets.append(dict(label='Send email notification once the sequencing request is complete', 
+                            widget=CheckboxField('email_notify', request.notify), 
+                            helptext=''))
+        return trans.fill_template( 'requests/common/edit_request.mako',
+                                    cntrller=cntrller,
+                                    select_request_type=select_request_type,
+                                    request_type=request.type,
+                                    request=request,
+                                    widgets=widgets,
+                                    message=message,
+                                    status=status)
+    def __validate(self, trans, cntrller, request):
+        '''
+        Validates the request entered by the user 
+        '''
+        if not request.samples:
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              operation='show',
+                                                              message='Please add one or more samples to this request before submitting.',
+                                                              status='error',
+                                                              id=trans.security.encode_id(request.id)) )
+        empty_fields = []
+        # check rest of the fields of the form
+        for index, field in enumerate(request.type.request_form.fields):
+            if field['required'] == 'required' and request.values.content[index] in ['', None]:
+                empty_fields.append(field['label'])
+        if empty_fields:
+            message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name
+            for ef in empty_fields:
+                message = message + '<b>' +ef + '</b><br/>'
+            return message
+        return None
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def submit(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
+        except:
+            message = "Invalid request ID"
+            log.warn( message )
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              status='error',
+                                                              message=message,
+                                                              **kwd) )
+        message = self.__validate(trans, cntrller, request)
+        if message:
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              operation='edit',
+                                                              status = 'error',
+                                                              message=message,
+                                                              id=trans.security.encode_id(request.id) ) )
+        # change the request state to 'Submitted'
+        if request.user.email is not trans.user:
+            comments = "Request submitted by admin (%s) on behalf of %s." % (trans.user.email, request.user.email)
+        else:
+            comments = ""
+        event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, comments)
+        trans.sa_session.add( event )
+        trans.sa_session.flush()
+        # change the state of each of the samples of thus request
+        new_state = request.type.states[0]
+        for s in request.samples:
+            event = trans.app.model.SampleEvent(s, new_state, 'Samples created.')
+            trans.sa_session.add( event )
+        trans.sa_session.add( request )
+        trans.sa_session.flush()
+        return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                          action='list',
+                                                          id=trans.security.encode_id(request.id),
+                                                          status='done',
+                                                          message='The request <b>%s</b> has been submitted.' % request.name
+                                                          ) )
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def delete(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        id_list = util.listify( kwd['id'] )
+        for id in id_list:
+            try:
+                request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) )
+            except:
+                message = "Invalid request ID"
+                log.warn( message )
+                return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                                  action='list',
+                                                                  status='error',
+                                                                  message=message,
+                                                                  **kwd) )
+            request.deleted = True
+            trans.sa_session.add( request )
+            # delete all the samples belonging to this request
+            for s in request.samples:
+                s.deleted = True
+                trans.sa_session.add( s )
+            trans.sa_session.flush()
+        message = '%i request(s) has been deleted.' % len(id_list)
+        status = 'done'
+        return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                          action='list',
+                                                          status=status,
+                                                          message=message) )
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def undelete(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        id_list = util.listify( kwd['id'] )
+        for id in id_list:
+            try:
+                request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) )
+            except:
+                message = "Invalid request ID"
+                log.warn( message )
+                return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                                  action='list',
+                                                                  status='error',
+                                                                  message=message,
+                                                                  **kwd) )
+            request.deleted = False
+            trans.sa_session.add( request )
+            # undelete all the samples belonging to this request
+            for s in request.samples:
+                s.deleted = False
+                trans.sa_session.add( s )
+            trans.sa_session.flush()
+        return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                          action='list',
+                                                          status='done',
+                                                          message='%i request(s) has been undeleted.' % len(id_list) ) )
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def events(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
+        except:
+            message = "Invalid request ID"
+            log.warn( message )
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              status='error',
+                                                              message=message) )
+        events_list = []
+        all_events = request.events
+        for event in all_events:         
+            events_list.append((event.state, time_ago(event.update_time), event.comment))
+        return trans.fill_template( '/requests/common/events.mako', 
+                                    cntrller=cntrller,
+                                    events_list=events_list, request=request)
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def show(self, trans, **kwd):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        status = params.get( 'status', 'done' )
+        add_sample = params.get('add_sample', False)
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
+        except:
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid request ID") )
+        # get all data libraries accessible to this user
+        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
+        current_samples = []
+        for i, s in enumerate(request.samples):
+            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
+            current_samples.append(dict(name=s.name,
+                                        barcode=s.bar_code,
+                                        library=s.library,
+                                        folder=s.folder,
+                                        dataset_files=s.dataset_files,
+                                        field_values=s.values.content,
+                                        lib_widget=lib_widget,
+                                        folder_widget=folder_widget))
+        if add_sample:
+            lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
+                                                               len(current_samples)+1, 
+                                                               libraries, None, **kwd)
+            current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
+                                        barcode='',
+                                        library=None,
+                                        folder=None,
+                                        dataset_files=[],
+                                        field_values=['' for field in request.type.sample_form.fields],
+                                        lib_widget=lib_widget,
+                                        folder_widget=folder_widget))
+        return trans.fill_template( '/requests/common/show_request.mako',
+                                    cntrller=cntrller,
+                                    request=request,
+                                    request_details=self.request_details(trans, request.id),
+                                    current_samples=current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False'  ) ),
+                                    message=message, status=status )
+
+    def __update_samples(self, trans, request, **kwd):
+        '''
+        This method retrieves all the user entered sample information and
+        returns an list of all the samples and their field values
+        '''
+        params = util.Params( kwd )
+        details = params.get( 'details', 'hide' )
+        edit_mode = params.get( 'edit_mode', 'False' )
+        # get all data libraries accessible to this user
+        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
+        
+        current_samples = []
+        for i, s in enumerate(request.samples):
+            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
+            current_samples.append(dict(name=s.name,
+                                        barcode=s.bar_code,
+                                        library=s.library,
+                                        folder=s.folder,
+                                        field_values=s.values.content,
+                                        lib_widget=lib_widget,
+                                        folder_widget=folder_widget))
+        if edit_mode == 'False':
+            sample_index = len(request.samples) 
+        else:
+            sample_index = 0
+        while True:
+            lib_id = None
+            folder_id = None
+            if params.get( 'sample_%i_name' % sample_index, ''  ):
+                # data library
+                try:
+                    library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'sample_%i_library_id' % sample_index, None ) ) )
+                    lib_id = library.id
+                except:
+                    library = None
+                # folder
+                try:
+                    folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'sample_%i_folder_id' % sample_index, None ) ) )
+                    folder_id = folder.id
+                except:
+                    if library:
+                        folder = library.root_folder
+                    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 edit_mode == 'False':
+                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, request.user, 
+                                                                                                     sample_index, libraries, 
+                                                                                                     None, lib_id, folder_id, **kwd)
+                    current_samples.append(sample_info)
+                else:
+                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, 
+                                                                                                     request.user, 
+                                                                                                     sample_index, 
+                                                                                                     libraries, 
+                                                                                                     request.samples[sample_index], 
+                                                                                                     **kwd)
+                    current_samples[sample_index] =  sample_info
+                sample_index = sample_index + 1
+            else:
+                break
+        return current_samples, details, edit_mode, libraries
+
+    def __library_widgets(self, trans, user, sample_index, libraries, sample=None, lib_id=None, folder_id=None, **kwd):
+        '''
+        This method creates the data library & folder selectbox for creating &
+        editing samples. First we get a list of all the libraries accessible to
+        the current user and display it in a selectbox. If the user has selected an
+        existing library then display all the accessible sub folders of the selected 
+        data library. 
+        '''
+        params = util.Params( kwd )
+        # data library selectbox
+        if not lib_id:
+            lib_id = params.get( "sample_%i_library_id" % sample_index, 'none'  )
+        selected_lib = None
+        if sample and lib_id == 'none':
+            if sample.library:
+                lib_id = str(sample.library.id)
+                selected_lib = sample.library
+        # create data library selectbox with refresh on change enabled
+        lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
+        lib_widget = SelectField( "sample_%i_library_id" % sample_index, 
+                                refresh_on_change=True, 
+                                refresh_on_change_values=lib_id_list )
+        # fill up the options in the Library selectbox
+        # first option 'none' is the value for "Select one" option
+        if lib_id == 'none':
+            lib_widget.add_option('Select one', 'none', selected=True)
+        else:
+            lib_widget.add_option('Select one', 'none')
+        # all the libraries available to the selected user
+        for lib, hidden_folder_ids in libraries.items():
+            if str(lib.id) == str(lib_id):
+                lib_widget.add_option(lib.name, lib.id, selected=True)
+                selected_lib, selected_hidden_folder_ids = lib, hidden_folder_ids.split(',')
+            else:
+                lib_widget.add_option(lib.name, lib.id)
+            lib_widget.refresh_on_change_values.append(lib.id)
+        # create the folder selectbox
+        folder_widget = SelectField( "sample_%i_folder_id" % sample_index )
+        # when editing a request, either the user has already selected a subfolder or not
+        if sample:
+            if sample.folder:
+                current_fid = sample.folder.id
+            else: 
+                # when a folder not yet associated with the request then the 
+                # the current folder is set to the root_folder of the 
+                # parent data library if present. 
+                if sample.library:
+                    current_fid = sample.library.root_folder.id
+                else:
+                    current_fid = params.get( "sample_%i_folder_id" % sample_index, 'none'  )
+        else:
+            if folder_id:
+                current_fid = folder_id
+            else:
+                current_fid = 'none'
+        # first option
+        if lib_id == 'none':
+            folder_widget.add_option('Select one', 'none', selected=True)
+        else:
+            folder_widget.add_option('Select one', 'none')
+        if selected_lib:
+            # get all show-able folders for the selected library
+            showable_folders = trans.app.security_agent.get_showable_folders( user, user.all_roles(), 
+                                                                              selected_lib, 
+                                                                              [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], 
+                                                                              selected_hidden_folder_ids )
+            for f in showable_folders:
+                if str(f.id) == str(current_fid):
+                    folder_widget.add_option(f.name, f.id, selected=True)
+                else:
+                    folder_widget.add_option(f.name, f.id)
+        return lib_widget, folder_widget
+
+    def __copy_sample(self, current_samples):
+        copy_list = SelectField('copy_sample')
+        copy_list.add_option('None', -1, selected=True)  
+        for i, s in enumerate(current_samples):
+            copy_list.add_option(s['name'], i)
+        return copy_list  
+    
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def request_page(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id( kwd['id']) )
+        except:
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid request ID") )
+        # get the user entered sample details
+        current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
+        if params.get('import_samples_button', False) == 'Import samples':
+            return self.__import_samples(trans, cntrller, request, current_samples, details, libraries, **kwd)
+        elif params.get('add_sample_button', False) == 'Add New':
+            # add an empty or filled sample
+            # if the user has selected a sample no. to copy then copy the contents 
+            # of the src sample to the new sample else an empty sample
+            src_sample_index = int(params.get( 'copy_sample', -1  ))
+            # get the number of new copies of the src sample
+            num_sample_to_copy = int(params.get( 'num_sample_to_copy', 1  ))
+            if src_sample_index == -1:
+                for ns in range(num_sample_to_copy):
+                    # empty sample
+                    lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
+                                                                       len(current_samples), 
+                                                                       libraries, None, **kwd)
+                    current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
+                                                barcode='',
+                                                library=None,
+                                                folder=None,
+                                                field_values=['' for field in request.type.sample_form.fields],
+                                                lib_widget=lib_widget,
+                                                folder_widget=folder_widget))
+            else:
+                src_library_id = current_samples[src_sample_index]['lib_widget'].get_selected()[1]
+                src_folder_id = current_samples[src_sample_index]['folder_widget'].get_selected()[1]
+                for ns in range(num_sample_to_copy):
+                    lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
+                                                                       len(current_samples), 
+                                                                       libraries, sample=None, 
+                                                                       lib_id=src_library_id,
+                                                                       folder_id=src_folder_id,
+                                                                       **kwd)
+                    current_samples.append(dict(name=current_samples[src_sample_index]['name']+'_%i' % (len(current_samples)+1),
+                                                barcode='',
+                                                library_id='none',
+                                                folder_id='none',
+                                                field_values=[val for val in current_samples[src_sample_index]['field_values']],
+                                                lib_widget=lib_widget,
+                                                folder_widget=folder_widget))
+            return trans.fill_template( '/requests/common/show_request.mako',
+                                        cntrller=cntrller,
+                                        request=request,
+                                        request_details=self.request_details(trans, request.id),
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details,
+                                        edit_mode=edit_mode)
+        elif params.get('save_samples_button', False) == 'Save':
+            # check for duplicate sample names
+            message = ''
+            for index in range(len(current_samples)-len(request.samples)):
+                sample_index = index + len(request.samples)
+                sample_name = current_samples[sample_index]['name']
+                if not sample_name.strip():
+                    message = 'Please 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 = count + 1
+                if count > 1: 
+                    message = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
+                    break
+            if message:
+                return trans.fill_template( '/requests/common/show_request.mako',
+                                            cntrller=cntrller,
+                                            request=request,
+                                            request_details=self.request_details(trans, request.id),
+                                            current_samples = current_samples,
+                                            sample_copy=self.__copy_sample(current_samples), 
+                                            details=details, edit_mode=edit_mode,
+                                            status='error', message=message)
+            # save all the new/unsaved samples entered by the user
+            if edit_mode == 'False':
+                for index in range(len(current_samples)-len(request.samples)):
+                    sample_index = len(request.samples)
+                    form_values = trans.app.model.FormValues(request.type.sample_form, 
+                                                             current_samples[sample_index]['field_values'])
+                    trans.sa_session.add( form_values )
+                    trans.sa_session.flush()                    
+                    s = trans.app.model.Sample(current_samples[sample_index]['name'], '', 
+                                               request, form_values, 
+                                               current_samples[sample_index]['barcode'],
+                                               current_samples[sample_index]['library'],
+                                               current_samples[sample_index]['folder'], 
+                                               dataset_files=[])
+                    trans.sa_session.add( s )
+                    trans.sa_session.flush()
+
+            else:
+                status = 'done'
+                message = 'Changes made to the sample(s) are saved. '
+                for sample_index in range(len(current_samples)):
+                    sample = request.samples[sample_index]
+                    sample.name = current_samples[sample_index]['name'] 
+                    sample.library = current_samples[sample_index]['library']
+                    sample.folder = current_samples[sample_index]['folder']
+                    if request.submitted():
+                        bc_message = self.__validate_barcode(trans, sample, current_samples[sample_index]['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.current_state().id == request.type.states[0].id:
+                                    event = trans.app.model.SampleEvent(sample, 
+                                                                        request.type.states[1], 
+                                                                        'Sample added to the system')
+                                    trans.sa_session.add( event )
+                                    trans.sa_session.flush()
+                            sample.bar_code = current_samples[sample_index]['barcode']
+                    trans.sa_session.add( sample )
+                    trans.sa_session.flush()
+                    form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
+                    form_values.content = current_samples[sample_index]['field_values']
+                    trans.sa_session.add( form_values )
+                    trans.sa_session.flush()
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              operation='show',
+                                                              id=trans.security.encode_id(request.id),
+                                                              status=status,
+                                                              message=message ))
+        elif params.get('edit_samples_button', False) == 'Edit samples':
+            edit_mode = 'True'
+            return trans.fill_template( '/requests/common/show_request.mako',
+                                        cntrller=cntrller,
+                                        request=request,
+                                        request_details=self.request_details(trans, request.id),
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details, libraries=libraries,
+                                        edit_mode=edit_mode)
+        elif params.get('cancel_changes_button', False) == 'Cancel':
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              operation='show',
+                                                              id=trans.security.encode_id(request.id)) )
+        else:
+            return trans.fill_template( '/requests/common/show_request.mako',
+                                        cntrller=cntrller,
+                                        request=request,
+                                        request_details=self.request_details(trans, request.id),
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details, libraries=libraries,
+                                        edit_mode=edit_mode, status=status, message=message)
+            
+    def __import_samples(self, trans, cntrller, request, current_samples, details, libraries, **kwd):
+        '''
+        This method reads the samples csv file and imports all the samples
+        The format of the csv file is:
+        SampleName,DataLibrary,DataLibraryFolder,Field1,Field2....
+        ''' 
+        try:
+            params = util.Params( kwd )
+            edit_mode = params.get( 'edit_mode', 'False' )
+            file_obj = params.get('file_data', '')
+            reader = csv.reader(file_obj.file)
+            for row in reader:
+                lib_id = None
+                folder_id = None
+                lib = trans.sa_session.query( trans.app.model.Library ) \
+                                      .filter( and_( trans.app.model.Library.table.c.name==row[1], \
+                                                     trans.app.model.Library.table.c.deleted==False ) )\
+                                      .first()
+                if lib:
+                    folder = trans.sa_session.query( trans.app.model.LibraryFolder ) \
+                                             .filter( and_( trans.app.model.LibraryFolder.table.c.name==row[2], \
+                                                            trans.app.model.LibraryFolder.table.c.deleted==False ) )\
+                                             .first()
+                    if folder:
+                        lib_id = lib.id
+                        folder_id = folder.id
+                lib_widget, folder_widget = self.__library_widgets(trans, request.user, len(current_samples), 
+                                                                   libraries, None, lib_id, folder_id, **kwd)
+                current_samples.append(dict(name=row[0], 
+                                            barcode='',
+                                            library=None,
+                                            folder=None,
+                                            lib_widget=lib_widget,
+                                            folder_widget=folder_widget,
+                                            field_values=row[3:]))  
+            return trans.fill_template( '/requests/common/show_request.mako',
+                                        cntrller=cntrller,
+                                        request=request,
+                                        request_details=self.request_details(trans, request.id),
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details,
+                                        edit_mode=edit_mode)
+        except:
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              operation='show',
+                                                              id=trans.security.encode_id(request.id),
+                                                              status='error',
+                                                              message='Error in importing samples file' ))
+
+    def __validate_barcode(self, trans, sample, barcode):
+        '''
+        This method makes sure that the given barcode about to be assigned to 
+        the given sample is gobally unique. That is, barcodes must be unique 
+        across requests in Galaxy LIMS 
+        '''
+        message = ''
+        for index in range(len(sample.request.samples)):
+            # check for empty bar code
+            if not barcode.strip():
+                message = 'Please fill the barcode for sample <b>%s</b>.' % sample.name
+                break
+            # check all the saved bar codes
+            all_samples = trans.sa_session.query( trans.app.model.Sample )
+            for s in all_samples:
+                if barcode == s.bar_code:
+                    if sample.id == s.id:
+                        continue
+                    else:
+                        message = '''The bar code <b>%s</b> of sample <b>%s</b>  
+                                 belongs another sample. The sample bar codes must be 
+                                 unique throughout the system''' % \
+                                 (barcode, sample.name)
+                        break
+            if message:
+                break
+        return message
+
+
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def delete_sample(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
+        current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
+        sample_index = int(params.get('sample_id', 0))
+        sample_name = current_samples[sample_index]['name']
+        s = request.has_sample(sample_name)
+        if s:
+            trans.sa_session.delete( s.values )
+            trans.sa_session.delete( s )
+            trans.sa_session.flush()
+        del current_samples[sample_index]  
+        return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                          action='list',
+                                                          operation='show',
+                                                          id=trans.security.encode_id(request.id),
+                                                          status='done',
+                                                          message='Sample <b>%s</b> has been deleted.' % sample_name ))
+        return trans.fill_template( '/requests/common/show_request.mako',
+                                    controller=cntrller,
+                                    request=request,
+                                    request_details=self.request_details(trans, request.id),
+                                    current_samples = current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details=details,
+                                    edit_mode=edit_mode)
+    def request_details(self, trans, id):
+        '''
+        Shows the request details
+        '''
+        request = trans.sa_session.query( trans.app.model.Request ).get( id )
+        # list of widgets to be rendered on the request form
+        request_details = []
+        # main details
+        request_details.append(dict(label='User', 
+                                    value=str(request.user.email), 
+                                    helptext=''))
+        request_details.append(dict(label='Description', 
+                                    value=request.desc, 
+                                    helptext=''))
+        request_details.append(dict(label='Type', 
+                                    value=request.type.name, 
+                                    helptext=''))
+        request_details.append(dict(label='State', 
+                                    value=request.state(), 
+                                    helptext=''))
+        request_details.append(dict(label='Date created', 
+                                    value=request.create_time, 
+                                    helptext=''))
+        # form fields
+        for index, field in enumerate(request.type.request_form.fields):
+            if field['required']:
+                req = 'Required'
+            else:
+                req = 'Optional'
+            if field['type'] == 'AddressField':
+                if request.values.content[index]:
+                    request_details.append(dict(label=field['label'],
+                                                value=trans.sa_session.query( trans.app.model.UserAddress ).get( int( request.values.content[index] ) ).get_html(),
+                                                helptext=field['helptext']+' ('+req+')'))
+                else:
+                    request_details.append(dict(label=field['label'],
+                                                value=None,
+                                                helptext=field['helptext']+' ('+req+')'))
+            else: 
+                request_details.append(dict(label=field['label'],
+                                            value=request.values.content[index],
+                                            helptext=field['helptext']+' ('+req+')'))
+        if request.notify:
+            notify = 'Yes'
+        else:
+            notify = 'No'
+        request_details.append(dict(label='Send email notification once the sequencing request is complete', 
+                                    value=notify, 
+                                    helptext=''))
+        return request_details
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def sample_events(self, trans, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        try:
+            sample_id = int(params.get('sample_id', False))
+            sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id )
+        except:
+            message = "Invalid sample ID"
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              status='error',
+                                                              message=message) )
+        events_list = []
+        all_events = sample.events
+        for event in all_events:         
+            events_list.append((event.state.name, event.state.desc, 
+                                time_ago(event.update_time), 
+                                event.comment))
+        widgets, title = self.__change_state_widgets(trans, sample)
+        return trans.fill_template( '/requests/common/sample_events.mako', 
+                                    cntrller=cntrller,
+                                    events_list=events_list,
+                                    sample=sample, widgets=widgets, title=title)
+    def __change_state_widgets(self, trans, sample):
+        possible_states = sample.request.type.states 
+        curr_state = sample.current_state() 
+        states_input = SelectField('select_state')
+        for state in possible_states:
+            if curr_state.name == state.name:
+                states_input.add_option(state.name+' (Current)', state.id, selected=True)
+            else:
+                states_input.add_option(state.name, state.id)
+        widgets = []
+        widgets.append(('Select the new state of the sample from the list of possible state(s)',
+                      states_input))
+        widgets.append(('Comments', TextArea('comment')))
+        title = 'Change current state'
+        return widgets, title
+    @web.expose
+    @web.require_admin
+    def show_datatx_page( self, trans, **kwd ):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' ) 
+        try:
+            sample = trans.sa_session.query( trans.app.model.Sample ).get( trans.security.decode_id( kwd['sample_id'] ) )
+        except:
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid sample ID") )
+        # check if a library and folder has been set for this sample yet.
+        if not sample.library or not sample.folder:
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              operation='show',
+                                                              status='error',
+                                                              message="Set a data library and folder for <b>%s</b> to transfer dataset(s)." % sample.name,
+                                                              id=trans.security.encode_id(sample.request.id) ) )             
+        if params.get( 'folder_path', ''  ):
+            folder_path = util.restore_text( params.get( 'folder_path', ''  ) )
+        else:
+            if len(sample.dataset_files):
+                folder_path = os.path.dirname(sample.dataset_files[-1]['filepath'][:-1])
+            else:
+                folder_path = util.restore_text( sample.request.type.datatx_info.get('data_dir', '') )
+        if folder_path and folder_path[-1] != os.sep:
+            folder_path += os.sep
+        if not sample.request.type.datatx_info['host'] or not sample.request.type.datatx_info['username'] \
+           or not sample.request.type.datatx_info['password']:
+            status = 'error'
+            message = 'The sequencer login information is incomplete. Click on the <b>Sequencer information</b> to add login details.'
+        return trans.fill_template( '/requests/common/get_data.mako', 
+                                    cntrller=cntrller, sample=sample, 
+                                    dataset_files=sample.dataset_files,
+                                    message=message, status=status, files=[],
+                                    folder_path=folder_path )

--- a/templates/requests/events.mako
+++ /dev/null
@@ -1,39 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<h2>History of Sequencing Request "${request.name}"</h2>
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
-        <span>Browse this request</span></a>
-    </li>
-    <li>
-        <a class="action-button"  href="${h.url_for( controller='requests', action='list')}">
-        <span>Browse all requests</span></a>
-    </li>
-</ul>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
-    <table class="grid">
-        <thead>
-            <tr>
-                <th>State</th>
-                <th>Last Update</th>
-                <th>Comments</th>
-            </tr>
-        </thead>
-        <tbody>
-            %for state, updated, comments in events_list:    
-                <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
-                    <td><b><a>${state}</a></b></td>
-                    <td><a>${updated}</a></td>
-                    <td><a>${comments}</a></td>
-                </tr>             
-            %endfor
-        </tbody>
-    </table>
-</div>

--- /dev/null
+++ b/templates/requests/common/sample_state.mako
@@ -0,0 +1,5 @@
+<%def name="render_sample_state( cntrller, sample )">
+    <a href="${h.url_for( controller='requests_common', cntrller=cntrller, action='sample_events', sample_id=sample.id)}">${sample.current_state().name}</a>
+</%def>
+
+${render_sample_state( cntrller, sample )}

--- /dev/null
+++ b/templates/requests/common/get_data.mako
@@ -0,0 +1,239 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<script type="text/javascript">
+$(document).ready(function(){
+    //hide the all of the element with class msg_body
+    $(".msg_body").hide();
+    //toggle the componenet with class msg_body
+    $(".msg_head").click(function(){
+        $(this).next(".msg_body").slideToggle(450);
+    });
+});
+
+
+
+
+</script>
+
+<script type="text/javascript">
+   function display_file_details(sample_id, folder_path)
+   {
+       var w = document.get_data.files_list.selectedIndex;
+       var selected_value = document.get_data.files_list.options[w].value;
+       var cell = $("#file_details");
+       if(selected_value.charAt(selected_value.length-1) != '/')
+       {
+            // Make ajax call
+            $.ajax( {
+                type: "POST",
+                url: "${h.url_for( controller='requests_admin', action='get_file_details' )}",
+                dataType: "json",
+                data: { id: sample_id, folder_path: document.get_data.folder_path.value+selected_value },
+                success : function ( data ) {
+                    cell.html( '<label>'+data+'</label>' )
+                }
+            });
+        }
+        else 
+        {
+            cell.html( '' )
+        }
+        
+       
+   }
+</script>
+
+<script type="text/javascript">
+   function open_folder1(sample_id, folder_path)
+   {
+       var w = document.get_data.files_list.selectedIndex;
+       var selected_value = document.get_data.files_list.options[w].value;
+       var cell = $("#file_details");
+       if(selected_value.charAt(selected_value.length-1) == '/')
+       {
+           document.get_data.folder_path.value = document.get_data.folder_path.value+selected_value
+            // Make ajax call
+            $.ajax( {
+                type: "POST",
+                url: "${h.url_for( controller='requests_admin', action='open_folder' )}",
+                dataType: "json",
+                data: { id: sample_id, folder_path: document.get_data.folder_path.value },
+                success : function ( data ) {
+                    document.get_data.files_list.options.length = 0
+                    for(i=0; i<data.length; i++) 
+                    {
+                        var newOpt = new Option(data[i], data[i]);
+                        document.get_data.files_list.options[i] = newOpt;
+                    }
+                    //cell.html( '<label>'+data+'</label>' )
+                    
+                }
+            });
+       }
+        else 
+        {
+            cell.html( '' )
+        }
+   }
+</script>
+
+
+<style type="text/css">
+.msg_head {
+    padding: 0px 0px;
+    cursor: pointer;
+}
+
+}
+</style>
+
+
+<h2>Data transfer from Sequencer</h2>
+<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
+<br/>
+<br/>
+
+<ul class="manage-table-actions">
+    %if sample.request.submitted() and sample.inprogress_dataset_files():
+        <li>
+            <a class="action-button" href="${h.url_for( controller='requests_common', cntrller=cntrller, action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
+            <span>Refresh this page</span></a>
+        </li>
+    %endif
+    %if cntrller == 'requests_admin' and trans.user_is_admin():
+        <li>
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_request_types', operation='view', id=trans.security.encode_id(sample.request.type.id) )}">
+            <span>Sequencer information</span></a>
+        </li>
+    
+        <li>
+            <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( sample.library.id ) )}">
+            <span>${sample.library.name} Data Library</span></a>
+        </li>
+    %else:
+        <li>
+            <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">
+            <span>${sample.library.name} Data Library</span></a>
+        </li>
+    %endif
+    <li>
+        <a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(sample.request.id) )}">
+        <span>Browse this request</span></a>
+    </li>
+</ul>
+
+<div class="toolForm">
+    %if len(dataset_files):
+        <div class="form-row">
+            <h4>Sample Dataset(s)</h4>
+            %if sample.untransferred_dataset_files() and cntrller == 'requests_admin':
+                <div class="form-row">
+                    <ul class="manage-table-actions">
+                        <li>
+                            <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', start_transfer_button=True, sample_id=sample.id )}">
+                            <span>Start transfer</span></a>
+                        </li>
+                    </ul>
+                 </div>
+             %endif
+            <div class="form-row">
+                <table class="grid">
+                <thead>
+                    <tr>
+                        <th>Dataset File</th>
+                        <th>Transfer Status</th>
+                        <th></th>
+                    </tr>
+                <thead>
+                    <tbody>
+                        %for dataset_index, dataset_file in enumerate(dataset_files):
+                            ${sample_dataset_files( dataset_index, dataset_file['name'], dataset_file['status'] )}
+                        %endfor
+                    </tbody>
+                </table>
+            </div>
+        </div>
+    %else:
+        <div class="form-row">
+            There are no dataset files associated with this sample.
+        </div>
+    %endif
+    
+    <br/>
+    <br/>
+
+    %if cntrller == 'requests_admin' and trans.user_is_admin():
+        <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', cntrller=cntrller, action='get_data', sample_id=sample.id)}" method="post" >
+            <div class="form-row">
+                ##<div class="toolFormTitle">Select files for transfer</div>
+                <h4>Select files for transfer</h4>
+                <div style="width: 60%;">
+                    <div class="form-row">
+                        <label>Folder path on the sequencer:</label>
+                        <input type="text" name="folder_path" value="${folder_path}" size="100"/>
+                        <input type="submit" name="browse_button" value="List contents"/>
+                        ##<input type="submit" name="open_folder" value="Open folder"/>
+                        <input type="submit" name="folder_up" value="Up"/>
+                    </div>
+                    <div class="form-row">
+                        <select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" ondblclick="open_folder1(${sample.id}, '${folder_path}')" onChange="display_file_details(${sample.id}, '${folder_path}')" multiple>
+                            %for index, f in enumerate(files):
+                                <option value="${f}">${f}</option>
+                            %endfor
+                        </select> 
+                        <br/>
+                        <div id="file_details" class="toolParamHelp" style="clear: both;">
+                            
+                        </div>
+                    </div>
+                    <div class="form-row">
+                        <div class="toolParamHelp" style="clear: both;">
+                            After selecting dataset(s), be sure to click on the <b>Start transfer</b> button. 
+                            Once the transfer is complete the dataset(s) will show up on this page.
+                        </div>
+                        <input type="submit" name="select_files_button" value="Select"/>
+                    </div>
+                </div>
+            </div>
+        </form>
+    %endif
+</div>
+
+
+
+
+<%def name="sample_dataset_files( dataset_index, dataset_name, status )">
+    <tr>
+        
+        <td>
+            %if cntrller == 'requests_admin' and trans.user_is_admin():
+                <label class="msg_head"><a href="${h.url_for( controller='requests_admin', action='dataset_details', sample_id=trans.security.encode_id(sample.id), dataset_index=dataset_index )}">${dataset_name}</a></label>
+            %else:
+                ${dataset_name}
+            %endif
+        </td>
+        <td>
+            %if status not in [sample.transfer_status.NOT_STARTED, sample.transfer_status.COMPLETE]: 
+                <i>${status}</i>
+            %else:
+                ${status}
+            %endif
+        </td>
+        ##<td></td>
+        %if status == sample.transfer_status.NOT_STARTED and cntrller == 'requests_admin' and trans.user_is_admin(): 
+        <td>
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id, remove_dataset_button=True, dataset_index=dataset_index )}">
+            <img src="${h.url_for('/static/images/delete_icon.png')}" />
+            <span></span></a>
+        </td>
+        %else:
+            <td></td>
+        %endif
+    </tr>
+</%def>

--- a/templates/admin/requests/events.mako
+++ /dev/null
@@ -1,36 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<h2>History of Sequencing Request "${request.name}"</h2>
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
-        <span>Browse this request</span></a>
-    </li>
-</ul>
-<h3>User: ${request.user.email}</h3>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
-    <table class="grid">
-        <thead>
-            <tr>
-                <th>State</th>
-                <th>Last Update</th>
-                <th>Comments</th>
-            </tr>
-        </thead>
-        <tbody>
-            %for state, updated, comments in events_list:    
-                <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
-                    <td><b><a>${state}</a></b></td>
-                    <td><a>${updated}</a></td>
-                    <td><a>${comments}</a></td>
-                </tr>             
-            %endfor
-        </tbody>
-    </table>
-</div>

--- a/lib/galaxy/web/controllers/requests_admin.py
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -95,7 +95,7 @@ class RequestsGrid( grids.Grid ):
         NameColumn( "Name", 
                     key="name", 
                     model_class=model.Request,
-                    link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ),
+                    link=( lambda item: iff( item.deleted, None, dict( operation="show", id=item.id ) ) ),
                     attach_popup=True, 
                     filterable="advanced" ),
         DescriptionColumn( "Description",
@@ -103,7 +103,7 @@ class RequestsGrid( grids.Grid ):
                            model_class=model.Request,
                            filterable="advanced" ),
         SamplesColumn( "Sample(s)", 
-                       link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ),
+                       link=( lambda item: iff( item.deleted, None, dict( operation="show", id=item.id ) ) ), ),
         TypeColumn( "Type",
                     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 ),
@@ -137,7 +137,8 @@ class RequestsGrid( grids.Grid ):
         grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),    
     ]
     global_actions = [
-        grids.GridAction( "Create new request", dict( controller='requests_admin', 
+        grids.GridAction( "Create new request", dict( controller='requests_common',
+                                                      cntrller='requests_admin',
                                                       action='new', 
                                                       select_request_type='True' ) )
     ]
@@ -218,6 +219,58 @@ class RequestsAdmin( BaseController ):
     @web.require_admin
     def index( self, trans ):
         return trans.fill_template( "/admin/requests/index.mako" )
+    
+    @web.expose
+    @web.require_admin
+    def list( self, trans, **kwd ):
+        '''
+        List all request made by the current user
+        '''
+        if 'operation' in kwd:
+            operation = kwd['operation'].lower()
+            if not kwd.get( 'id', None ):
+                return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                                  action='list',
+                                                                  status='error',
+                                                                  message="Invalid request ID") )
+            if operation == "show":
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests_admin',
+                                                                  action='show',
+                                                                  **kwd ) )
+            elif operation == "submit":
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests_admin',
+                                                                  action='submit',
+                                                                  **kwd ) )
+            elif operation == "delete":
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests_admin',
+                                                                  action='delete',
+                                                                  **kwd ) )
+            elif operation == "undelete":
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests_admin',
+                                                                  action='undelete',
+                                                                  **kwd ) )
+            elif operation == "edit":
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests_admin',
+                                                                  action='edit',
+                                                                  show=True, **kwd ) )
+            elif operation == "events":
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  cntrller='requests_admin',
+                                                                  action='events',
+                                                                  **kwd ) )
+            elif operation == "reject":
+                return self.__reject_request( trans, **kwd )
+            elif operation == "view_type":
+                return self.__view_request_type( trans, **kwd )
+            elif operation == "upload_datasets":
+                return self.__upload_datasets( trans, **kwd )
+        # Render the grid view
+        return self.request_grid( trans, **kwd )
 
     @web.json
     def get_file_details( self, trans, id=None, folder_path=None ):
@@ -246,239 +299,6 @@ class RequestsAdmin( BaseController ):
         sample = trans.sa_session.query( self.app.model.Sample ).get( int(id) )
         return self.__get_files(trans, sample, folder_path)
 
-    
-    @web.json
-    def sample_state_updates( self, trans, ids=None, states=None ):
-        # Avoid caching
-        trans.response.headers['Pragma'] = 'no-cache'
-        trans.response.headers['Expires'] = '0'
-        # Create new HTML for any that have changed
-        rval = {}
-        if ids is not None and states is not None:
-            ids = map( int, ids.split( "," ) )
-            states = states.split( "," )
-            for id, state in zip( ids, states ):
-                sample = trans.sa_session.query( self.app.model.Sample ).get( id )
-                if sample.current_state().name != state:
-                    rval[id] = {
-                        "state": sample.current_state().name,
-                        "datasets": len(sample.dataset_files),
-                        "html_state": unicode( trans.fill_template( "requests/sample_state.mako", sample=sample ), 'utf-8' ),
-                        "html_datasets": unicode( trans.fill_template( "requests/sample_datasets.mako", trans=trans, sample=sample ), 'utf-8' )
-                    }
-        return rval
-    
-    @web.expose
-    @web.require_admin
-    def list( self, trans, **kwd ):
-        '''
-        List all request made by the current user
-        '''
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
-            if not kwd.get( 'id', None ):
-                return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                  action='list',
-                                                                  status='error',
-                                                                  message="Invalid request ID") )
-            if operation == "show_request":
-                return self.__show_request( trans, **kwd )
-            elif operation == "submit":
-                return self.__submit_request( trans, **kwd )
-            elif operation == "delete":
-                return self.__delete_request( trans, **kwd )
-            elif operation == "undelete":
-                return self.__undelete_request( trans, **kwd )
-            elif operation == "edit":
-                return self.__edit_request( trans, **kwd )
-            elif operation == "reject":
-                return self.__reject_request( trans, **kwd )
-            elif operation == "events":
-                return self.__request_events( trans, **kwd )
-            elif operation == "view_type":
-                return self.__view_request_type( trans, **kwd )
-            elif operation == "upload_datasets":
-                return self.__upload_datasets( trans, **kwd )
-        # Render the grid view
-        return self.request_grid( trans, **kwd )
-    @web.expose
-    @web.require_admin
-    def edit(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID",
-                                                              **kwd) )
-        if params.get('show', False) == 'True':
-            return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd)
-        elif params.get('save_changes_request_button', False) == 'Save changes' \
-             or params.get('edit_samples_button', False) == 'Edit samples':
-                request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
-                if not util.restore_text(params.get('name', '')):
-                    message = 'Please enter the <b>Name</b> of the request'
-                    kwd['status'] = 'error'
-                    kwd['message'] = message
-                    kwd['show'] = 'True'
-                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                      action='edit',
-                                                                      **kwd) )
-                request = self.__save_request(trans, request, **kwd)
-                message = 'The changes made to the request named %s has been saved' % request.name
-                if params.get('save_changes_request_button', False) == 'Save changes':
-                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                      action='list',
-                                                                      message=message ,
-                                                                      status='done') )
-                elif params.get('edit_samples_button', False) == 'Edit samples':
-                    new_kwd = {}
-                    new_kwd['request_id'] = request.id
-                    new_kwd['edit_samples_button'] = 'Edit samples'
-                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                      action='show_request',
-                                                                      message=message ,
-                                                                      status='done',
-                                                                      **new_kwd) )
-        elif params.get('refresh', False) == 'true':
-            return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd)
-        
-    def __edit_request(self, trans, **kwd):
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            message = "Invalid request ID"
-            log.warn( message )
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message=message) )
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        select_request_type = self.__select_request_type(trans, request.type.id)
-        # list of widgets to be rendered on the request form
-        widgets = []
-        if util.restore_text( params.get( 'name', ''  ) ):
-            name = util.restore_text( params.get( 'name', ''  ) )
-        else:
-            name = request.name
-        widgets.append(dict(label='Name', 
-                            widget=TextField('name', 40, name), 
-                            helptext='(Required)'))
-        if util.restore_text( params.get( 'desc', ''  ) ):
-            desc = util.restore_text( params.get( 'desc', ''  ) )
-        else:
-            desc = request.desc
-        widgets.append(dict(label='Description', 
-                            widget=TextField('desc', 40, desc), 
-                            helptext='(Optional)'))
-        widgets = widgets + request.type.request_form.get_widgets( request.user, request.values.content, **kwd )
-        widgets.append(dict(label='Send email notification once the sequencing request is complete', 
-                            widget=CheckboxField('email_notify', request.notify), 
-                            helptext=''))
-        return trans.fill_template( '/admin/requests/edit_request.mako',
-                                    select_request_type=select_request_type,
-                                    request_type=request.type,
-                                    request=request,
-                                    widgets=widgets,
-                                    message=message,
-                                    status=status)
-        return self.__show_request_form(trans)
-    def __delete_request(self, trans, **kwd):
-        id_list = util.listify( kwd['id'] )
-        for id in id_list:
-            try:
-                request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) )
-            except:
-                message = "Invalid request ID"
-                log.warn( message )
-                return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                  action='list',
-                                                                  status='error',
-                                                                  message=message,
-                                                                  **kwd) )
-            request.deleted = True
-            trans.sa_session.add( request )
-            # delete all the samples belonging to this request
-            for s in request.samples:
-                s.deleted = True
-                trans.sa_session.add( s )
-            trans.sa_session.flush()
-        message = '%i request(s) has been deleted.' % len(id_list)
-        status = 'done'
-        return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          status=status,
-                                                          message=message) )
-    def __undelete_request(self, trans, **kwd):
-        id_list = util.listify( kwd['id'] )
-        for id in id_list:
-            try:
-                request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) )
-            except:
-                message = "Invalid request ID"
-                log.warn( message )
-                return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                  action='list',
-                                                                  status='error',
-                                                                  message=message,
-                                                                  **kwd) )
-            request.deleted = False
-            trans.sa_session.add( request )
-            # undelete all the samples belonging to this request
-            for s in request.samples:
-                s.deleted = False
-                trans.sa_session.add( s )
-            trans.sa_session.flush()
-        return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          status='done',
-                                                          message='%i request(s) has been undeleted.' % len(id_list) ) )
-    def __submit_request(self, trans, **kwd):
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            message = "Invalid request ID"
-            log.warn( message )
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message=message,
-                                                              **kwd) )
-        message = self.__validate(trans, request)
-        if message:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              operation='edit',
-                                                              status = 'error',
-                                                              message=message,
-                                                              id=trans.security.encode_id(request.id) ) )
-        # change the request state to 'Submitted'
-        if request.user.email is not trans.user:
-            comments = "Request submitted by admin (%s) on behalf of %s." % (trans.user.email, request.user.email)
-        else:
-            comments = ""
-        event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, comments)
-        trans.sa_session.add( event )
-        trans.sa_session.flush()
-        # change the state of each of the samples of thus request
-        new_state = request.type.states[0]
-        for s in request.samples:
-            event = trans.app.model.SampleEvent(s, new_state, 'Samples created.')
-            trans.sa_session.add( event )
-        trans.sa_session.add( request )
-        trans.sa_session.flush()
-        return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          id=trans.security.encode_id(request.id),
-                                                          status='done',
-                                                          message='The request <b>%s</b> has been submitted.' % request.name
-                                                          ) )
     def __reject_request(self, trans, **kwd):
         try:
             request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
@@ -526,759 +346,10 @@ class RequestsAdmin( BaseController ):
                                                           status='done',
                                                           message='Request <b>%s</b> has been rejected.' % request.name) )
     
-    def __request_events(self, trans, **kwd):
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            message = "Invalid request ID"
-            log.warn( message )
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message=message,
-                                                              **kwd) )
-        events_list = []
-        all_events = request.events
-        for event in all_events:         
-            events_list.append((event.state, time_ago(event.update_time), event.comment))
-        return trans.fill_template( '/admin/requests/events.mako', 
-                                    events_list=events_list, request=request)
-        
     def __upload_datasets(self, trans, **kwd):
         return trans.fill_template( '/admin/requests/upload_datasets.mako' )
-#
-#---- Request Creation ----------------------------------------------------------
-#    
-    def __select_request_type(self, trans, rtid):
-        requesttype_list = trans.user.accessible_request_types(trans)
-        rt_ids = ['none']
-        for rt in requesttype_list:
-            if not rt.deleted:
-                rt_ids.append(str(rt.id))
-        select_reqtype = SelectField('select_request_type', 
-                                     refresh_on_change=True, 
-                                     refresh_on_change_values=rt_ids[1:])
-        if rtid == 'none':
-            select_reqtype.add_option('Select one', 'none', selected=True)
-        else:
-            select_reqtype.add_option('Select one', 'none')
-        for rt in requesttype_list:
-            if not rt.deleted:
-                if rtid == rt.id:
-                    select_reqtype.add_option(rt.name, rt.id, selected=True)
-                else:
-                    select_reqtype.add_option(rt.name, rt.id)
-        return select_reqtype
-    @web.expose
-    @web.require_admin
-    def new(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        if params.get('select_request_type', False) == 'True':
-            return trans.fill_template( '/admin/requests/new_request.mako',
-                                        select_request_type=self.__select_request_type(trans, 'none'),                                 
-                                        widgets=[],                                   
-                                        message=message,
-                                        status=status)
-        elif params.get('create', False) == 'True':
-            if params.get('create_request_button', False) == 'Save' \
-               or params.get('create_request_samples_button', False) == 'Add samples':
-                request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
-                if not util.restore_text(params.get('name', '')) \
-                    or util.restore_text(params.get('select_user', '')) == unicode('none'):
-                    message = 'Please enter the <b>Name</b> of the request and the <b>user</b> on behalf of whom this request will be submitted before saving this request'
-                    kwd['create'] = 'True'
-                    kwd['status'] = 'error'
-                    kwd['message'] = message
-                    kwd['create_request_button'] = None
-                    kwd['create_request_samples_button'] = None
-                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                      action='new',
-                                                                      **kwd) )
-                request = self.__save_request(trans, None, **kwd)
-                message = 'The new request named %s has been created' % request.name
-                if params.get('create_request_button', False) == 'Save':
-                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                      action='list',
-                                                                      message=message ,
-                                                                      status='done') )
-                elif params.get('create_request_samples_button', False) == 'Add samples':
-                    new_kwd = {}
-                    new_kwd['id'] = trans.security.encode_id(request.id)
-                    new_kwd['operation'] = 'show_request'
-                    new_kwd['add_sample'] = True
-                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                      action='list',
-                                                                      message=message ,
-                                                                      status='done',
-                                                                      **new_kwd) )
-            else:
-                return self.__show_request_form(trans, **kwd)
-        elif params.get('refresh', False) == 'true':
-            return self.__show_request_form(trans, **kwd)
-    def __show_request_form(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        try:
-            request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
-        except:
-            return trans.fill_template( '/admin/requests/new_request.mako',
-                                        select_request_type=self.__select_request_type(trans, 'none'),                                 
-                                        widgets=[],                                   
-                                        message=message,
-                                        status=status)
-        form_values = None
-        select_request_type = self.__select_request_type(trans, request_type.id)
-        # user
-        user_id = params.get( 'select_user', 'none' )
-        try:
-            user = trans.sa_session.query( trans.app.model.User ).get( int( user_id ) )
-        except:
-            user = None
-        # list of widgets to be rendered on the request form
-        widgets = []
-        widgets.append(dict(label='Select user',
-                            widget=self.__select_user(trans, user_id),
-                            helptext='The request would be submitted on behalf of this user (Required)'))
-        widgets.append(dict(label='Name of the Experiment', 
-                            widget=TextField('name', 40, 
-                                             util.restore_text( params.get( 'name', ''  ) )), 
-                            helptext='(Required)'))
-        widgets.append(dict(label='Description', 
-                            widget=TextField('desc', 40,
-                                             util.restore_text( params.get( 'desc', ''  ) )), 
-                            helptext='(Optional)'))
-        widgets = widgets + request_type.request_form.get_widgets( user, **kwd )
-        widgets.append(dict(label='Send email notification once the sequencing request is complete', 
-                            widget=CheckboxField('email_notify', False), 
-                            helptext='Email would be sent to the lab admin and the user for whom this request has been created.'))
-        return trans.fill_template( '/admin/requests/new_request.mako',
-                                    select_request_type=select_request_type,
-                                    request_type=request_type,                                    
-                                    widgets=widgets,
-                                    message=message,
-                                    status=status)
-    def __select_user(self, trans, userid):
-        user_list = trans.sa_session.query( trans.app.model.User )\
-                                    .order_by( trans.app.model.User.email.asc() )
-        user_ids = ['none']
-        for user in user_list:
-            if not user.deleted:
-                user_ids.append(str(user.id))
-        select_user = SelectField('select_user', 
-                                  refresh_on_change=True, 
-                                  refresh_on_change_values=user_ids[1:])
-        if userid == 'none':
-            select_user.add_option('Select one', 'none', selected=True)
-        else:
-            select_user.add_option('Select one', 'none')
-        for user in user_list:
-            if not user.deleted:
-                if userid == str(user.id):
-                    select_user.add_option(user.email, user.id, selected=True)
-                else:
-                    select_user.add_option(user.email, user.id)
-        return select_user
-    def __validate(self, trans, request):
-        '''
-        Validates the request entered by the user 
-        '''
-        if not request.samples:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              operation='show_request',
-                                                              message='Please add one or more samples to this request before submitting.',
-                                                              status='error',
-                                                              id=trans.security.encode_id(request.id)) )
-        empty_fields = []
-        # check rest of the fields of the form
-        for index, field in enumerate(request.type.request_form.fields):
-            if field['required'] == 'required' and request.values.content[index] in ['', None]:
-                empty_fields.append(field['label'])
-        if empty_fields:
-            message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name
-            for ef in empty_fields:
-                message = message + '<b>' +ef + '</b><br/>'
-            return message
-        return None
-    def __save_request(self, trans, request=None, **kwd):
-        '''
-        This method saves a new request if request_id is None. 
-        '''
-        params = util.Params( kwd )
-        request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
-        if request:
-            user = request.user
-        else:
-            user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'select_user', '' ) ) )
-        name = util.restore_text(params.get('name', ''))
-        desc = util.restore_text(params.get('desc', ''))
-        notify = CheckboxField.is_checked( params.get('email_notify', '') )
-        # fields
-        values = []
-        for index, field in enumerate(request_type.request_form.fields):
-            if field['type'] == 'AddressField':
-                value = util.restore_text(params.get('field_%i' % index, ''))
-                if value == 'new':
-                    # save this new address in the list of this user's addresses
-                    user_address = trans.app.model.UserAddress( user=user )
-                    user_address.desc = util.restore_text(params.get('field_%i_short_desc' % index, ''))
-                    user_address.name = util.restore_text(params.get('field_%i_name' % index, ''))
-                    user_address.institution = util.restore_text(params.get('field_%i_institution' % index, ''))
-                    user_address.address = util.restore_text(params.get('field_%i_address1' % index, ''))+' '+util.restore_text(params.get('field_%i_address2' % index, ''))
-                    user_address.city = util.restore_text(params.get('field_%i_city' % index, ''))
-                    user_address.state = util.restore_text(params.get('field_%i_state' % index, ''))
-                    user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, ''))
-                    user_address.country = util.restore_text(params.get('field_%i_country' % index, ''))
-                    user_address.phone = util.restore_text(params.get('field_%i_phone' % index, ''))
-                    trans.sa_session.add( user_address )
-                    trans.sa_session.flush()
-                    trans.sa_session.refresh( trans.user )
-                    values.append(int(user_address.id))
-                elif value == unicode('none'):
-                    values.append('')
-                else:
-                    values.append(int(value))
-            elif field['type'] == 'CheckboxField':
-                values.append(CheckboxField.is_checked( params.get('field_%i' % index, '') )) 
-            else:
-                values.append(util.restore_text(params.get('field_%i' % index, '')))
-        form_values = trans.app.model.FormValues(request_type.request_form, values)
-        trans.sa_session.add( form_values )
-        trans.sa_session.flush()
-        if not request:
-            request = trans.app.model.Request(name, desc, request_type, 
-                                              user, form_values, notify)
-            trans.sa_session.add( request )
-            trans.sa_session.flush()
-            trans.sa_session.refresh( request )
-            # create an event with state 'New' for this new request
-            if request.user.email is not trans.user:
-                comments = "Request created by admin (%s) on behalf of %s." % (trans.user.email, request.user.email)
-            else:
-                comments = "Request created."
-            event = trans.app.model.RequestEvent(request, request.states.NEW, comments)
-            trans.sa_session.add( event )
-            trans.sa_session.flush()
-        else:
-            request.name = name
-            request.desc = desc
-            request.type = request_type
-            request.user = user
-            request.notify = notify
-            request.values = form_values
-            trans.sa_session.add( request )
-            trans.sa_session.flush()
-        return request
-#
-#---- Request Page ----------------------------------------------------------
-#    
-    def __show_request(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        add_sample = params.get('add_sample', False)
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID") )
-        # get all data libraries accessible to this user
-        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
-        current_samples = []
-        for i, s in enumerate(request.samples):
-            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
-            current_samples.append(dict(name=s.name,
-                                        barcode=s.bar_code,
-                                        library=s.library,
-                                        folder=s.folder,
-                                        dataset_files=s.dataset_files,
-                                        field_values=s.values.content,
-                                        lib_widget=lib_widget,
-                                        folder_widget=folder_widget))
-        if add_sample:
-            lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
-                                                               len(current_samples)+1, 
-                                                               libraries, None, **kwd)
-            current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
-                                        barcode='',
-                                        library=None,
-                                        folder=None,
-                                        dataset_files=[],
-                                        field_values=['' for field in request.type.sample_form.fields],
-                                        lib_widget=lib_widget,
-                                        folder_widget=folder_widget))
-        return trans.fill_template( '/admin/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples=current_samples,
-                                    sample_copy=self.__copy_sample(current_samples), 
-                                    details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False'  ) ),
-                                    message=message, status=status )
-    def __library_widgets(self, trans, user, sample_index, libraries, sample=None, lib_id=None, folder_id=None, **kwd):
-        '''
-        This method creates the data library & folder selectbox for creating &
-        editing samples. First we get a list of all the libraries accessible to
-        the current user and display it in a selectbox. If the user has selected an
-        existing library then display all the accessible sub folders of the selected 
-        data library. 
-        '''
-        params = util.Params( kwd )
-        # data library selectbox
-        if not lib_id:
-            lib_id = params.get( "sample_%i_library_id" % sample_index, 'none'  )
-        selected_lib = None
-        if sample and lib_id == 'none':
-            if sample.library:
-                lib_id = str(sample.library.id)
-                selected_lib = sample.library
-        # create data library selectbox with refresh on change enabled
-        lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
-        lib_widget = SelectField( "sample_%i_library_id" % sample_index, 
-                                refresh_on_change=True, 
-                                refresh_on_change_values=lib_id_list )
-        # fill up the options in the Library selectbox
-        # first option 'none' is the value for "Select one" option
-        if lib_id == 'none':
-            lib_widget.add_option('Select one', 'none', selected=True)
-        else:
-            lib_widget.add_option('Select one', 'none')
-        # all the libraries available to the selected user
-        for lib, hidden_folder_ids in libraries.items():
-            if str(lib.id) == str(lib_id):
-                lib_widget.add_option(lib.name, lib.id, selected=True)
-                selected_lib, selected_hidden_folder_ids = lib, hidden_folder_ids.split(',')
-            else:
-                lib_widget.add_option(lib.name, lib.id)
-            lib_widget.refresh_on_change_values.append(lib.id)
-        # create the folder selectbox
-        folder_widget = SelectField( "sample_%i_folder_id" % sample_index )
-        # when editing a request, either the user has already selected a subfolder or not
-        if sample:
-            if sample.folder:
-                current_fid = sample.folder.id
-            else: 
-                # when a folder not yet associated with the request then the 
-                # the current folder is set to the root_folder of the 
-                # parent data library if present. 
-                if sample.library:
-                    current_fid = sample.library.root_folder.id
-                else:
-                    current_fid = params.get( "sample_%i_folder_id" % sample_index, 'none'  )
-        else:
-            if folder_id:
-                current_fid = folder_id
-            else:
-                current_fid = 'none'
-        # first option
-        if lib_id == 'none':
-            folder_widget.add_option('Select one', 'none', selected=True)
-        else:
-            folder_widget.add_option('Select one', 'none')
-        if selected_lib:
-            # get all show-able folders for the selected library
-            showable_folders = trans.app.security_agent.get_showable_folders( user, user.all_roles(), 
-                                                                              selected_lib, 
-                                                                              [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], 
-                                                                              selected_hidden_folder_ids )
-            for f in showable_folders:
-                if str(f.id) == str(current_fid):
-                    folder_widget.add_option(f.name, f.id, selected=True)
-                else:
-                    folder_widget.add_option(f.name, f.id)
-        return lib_widget, folder_widget
-    def __update_samples(self, trans, request, **kwd):
-        '''
-        This method retrieves all the user entered sample information and
-        returns an list of all the samples and their field values
-        '''
-        params = util.Params( kwd )
-        details = params.get( 'details', 'hide' )
-        edit_mode = params.get( 'edit_mode', 'False' )
-        # get all data libraries accessible to this user
-        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
-        
-        current_samples = []
-        for i, s in enumerate(request.samples):
-            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
-            current_samples.append(dict(name=s.name,
-                                        barcode=s.bar_code,
-                                        library=s.library,
-                                        folder=s.folder,
-                                        field_values=s.values.content,
-                                        lib_widget=lib_widget,
-                                        folder_widget=folder_widget))
-        if edit_mode == 'False':
-            sample_index = len(request.samples) 
-        else:
-            sample_index = 0
-        while True:
-            lib_id = None
-            folder_id = None
-            if params.get( 'sample_%i_name' % sample_index, ''  ):
-                # data library
-                try:
-                    library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'sample_%i_library_id' % sample_index, None ) ) )
-                    lib_id = library.id
-                except:
-                    library = None
-                # folder
-                try:
-                    folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'sample_%i_folder_id' % sample_index, None ) ) )
-                    folder_id = folder.id
-                except:
-                    if library:
-                        folder = library.root_folder
-                    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 edit_mode == 'False':
-                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, request.user, 
-                                                                                                     sample_index, libraries, 
-                                                                                                     None, lib_id, folder_id, **kwd)
-                    current_samples.append(sample_info)
-                else:
-                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, 
-                                                                                                     request.user, 
-                                                                                                     sample_index, 
-                                                                                                     libraries, 
-                                                                                                     request.samples[sample_index], 
-                                                                                                     **kwd)
-                    current_samples[sample_index] =  sample_info
-                sample_index = sample_index + 1
-            else:
-                break
-        return current_samples, details, edit_mode, libraries
-    def __copy_sample(self, current_samples):
-        copy_list = SelectField('copy_sample')
-        copy_list.add_option('None', -1, selected=True)  
-        for i, s in enumerate(current_samples):
-            copy_list.add_option(s['name'], i)
-        return copy_list  
-    def __import_samples(self, trans, request, current_samples, details, libraries, **kwd):
-        '''
-        This method reads the samples csv file and imports all the samples
-        The format of the csv file is:
-        SampleName,DataLibrary,DataLibraryFolder,Field1,Field2....
-        ''' 
-        try:
-            params = util.Params( kwd )
-            edit_mode = params.get( 'edit_mode', 'False' )
-            file_obj = params.get('file_data', '')
-            reader = csv.reader(file_obj.file)
-            for row in reader:
-                lib_id = None
-                folder_id = None
-                lib = trans.sa_session.query( trans.app.model.Library ) \
-                                      .filter( and_( trans.app.model.Library.table.c.name==row[1], \
-                                                     trans.app.model.Library.table.c.deleted==False ) )\
-                                      .first()
-                if lib:
-                    folder = trans.sa_session.query( trans.app.model.LibraryFolder ) \
-                                             .filter( and_( trans.app.model.LibraryFolder.table.c.name==row[2], \
-                                                            trans.app.model.LibraryFolder.table.c.deleted==False ) )\
-                                             .first()
-                    if folder:
-                        lib_id = lib.id
-                        folder_id = folder.id
-                lib_widget, folder_widget = self.__library_widgets(trans, request.user, len(current_samples), 
-                                                                   libraries, None, lib_id, folder_id, **kwd)
-                current_samples.append(dict(name=row[0], 
-                                            barcode='',
-                                            library=None,
-                                            folder=None,
-                                            lib_widget=lib_widget,
-                                            folder_widget=folder_widget,
-                                            field_values=row[3:]))  
-            return trans.fill_template( '/admin/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=current_samples,
-                                        sample_copy=self.__copy_sample(current_samples), 
-                                        details=details,
-                                        edit_mode=edit_mode)
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          operation='show_request',
-                                                          id=trans.security.encode_id(request.id),
-                                                          status='error',
-                                                          message='Error in importing samples file' ))
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def show_request(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID",
-                                                              **kwd) )
-        # get the user entered sample details
-        current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
-        if params.get('import_samples_button', False) == 'Import samples':
-            return self.__import_samples(trans, request, current_samples, details, libraries, **kwd)
-        elif params.get('add_sample_button', False) == 'Add New':
-            # add an empty or filled sample
-            # if the user has selected a sample no. to copy then copy the contents 
-            # of the src sample to the new sample else an empty sample
-            src_sample_index = int(params.get( 'copy_sample', -1  ))
-            # get the number of new copies of the src sample
-            num_sample_to_copy = int(params.get( 'num_sample_to_copy', 1  ))
-            if src_sample_index == -1:
-                for ns in range(num_sample_to_copy):
-                    # empty sample
-                    lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
-                                                                       len(current_samples), 
-                                                                       libraries, None, **kwd)
-                    current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
-                                                barcode='',
-                                                library=None,
-                                                folder=None,
-                                                field_values=['' for field in request.type.sample_form.fields],
-                                                lib_widget=lib_widget,
-                                                folder_widget=folder_widget))
-            else:
-                src_library_id = current_samples[src_sample_index]['lib_widget'].get_selected()[1]
-                src_folder_id = current_samples[src_sample_index]['folder_widget'].get_selected()[1]
-                for ns in range(num_sample_to_copy):
-                    lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
-                                                                       len(current_samples), 
-                                                                       libraries, sample=None, 
-                                                                       lib_id=src_library_id,
-                                                                       folder_id=src_folder_id,
-                                                                       **kwd)
-                    current_samples.append(dict(name=current_samples[src_sample_index]['name']+'_%i' % (len(current_samples)+1),
-                                                barcode='',
-                                                library_id='none',
-                                                folder_id='none',
-                                                field_values=[val for val in current_samples[src_sample_index]['field_values']],
-                                                lib_widget=lib_widget,
-                                                folder_widget=folder_widget))
-            return trans.fill_template( '/admin/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=current_samples,
-                                        sample_copy=self.__copy_sample(current_samples), 
-                                        details=details,
-                                        edit_mode=edit_mode)
-        elif params.get('save_samples_button', False) == 'Save':
-            # check for duplicate sample names
-            message = ''
-            for index in range(len(current_samples)-len(request.samples)):
-                sample_index = index + len(request.samples)
-                sample_name = current_samples[sample_index]['name']
-                if not sample_name.strip():
-                    message = 'Please 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 = count + 1
-                if count > 1: 
-                    message = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
-                    break
-            if message:
-                return trans.fill_template( '/admin/requests/show_request.mako',
-                                            request=request,
-                                            request_details=self.request_details(trans, request.id),
-                                            current_samples = current_samples,
-                                            sample_copy=self.__copy_sample(current_samples), 
-                                            details=details, edit_mode=edit_mode,
-                                            status='error', message=message)
-            # save all the new/unsaved samples entered by the user
-            if edit_mode == 'False':
-                for index in range(len(current_samples)-len(request.samples)):
-                    sample_index = len(request.samples)
-                    form_values = trans.app.model.FormValues(request.type.sample_form, 
-                                                             current_samples[sample_index]['field_values'])
-                    trans.sa_session.add( form_values )
-                    trans.sa_session.flush()                    
-                    s = trans.app.model.Sample(current_samples[sample_index]['name'], '', 
-                                               request, form_values, 
-                                               current_samples[sample_index]['barcode'],
-                                               current_samples[sample_index]['library'],
-                                               current_samples[sample_index]['folder'], 
-                                               dataset_files=[])
-                    trans.sa_session.add( s )
-                    trans.sa_session.flush()
+            
 
-            else:
-                status = 'done'
-                message = 'Changes made to the sample(s) are saved. '
-                for sample_index in range(len(current_samples)):
-                    sample = request.samples[sample_index]
-                    sample.name = current_samples[sample_index]['name'] 
-                    sample.library = current_samples[sample_index]['library']
-                    sample.folder = current_samples[sample_index]['folder']
-                    if request.submitted():
-                        bc_message = self.__validate_barcode(trans, sample, current_samples[sample_index]['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.current_state().id == request.type.states[0].id:
-                                    event = trans.app.model.SampleEvent(sample, 
-                                                                        request.type.states[1], 
-                                                                        'Sample added to the system')
-                                    trans.sa_session.add( event )
-                                    trans.sa_session.flush()
-                            sample.bar_code = current_samples[sample_index]['barcode']
-                    trans.sa_session.add( sample )
-                    trans.sa_session.flush()
-                    form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
-                    form_values.content = current_samples[sample_index]['field_values']
-                    trans.sa_session.add( form_values )
-                    trans.sa_session.flush()
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          operation='show_request',
-                                                          id=trans.security.encode_id(request.id),
-                                                          status=status,
-                                                          message=message ))
-        elif params.get('edit_samples_button', False) == 'Edit samples':
-            edit_mode = 'True'
-            return trans.fill_template( '/admin/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=current_samples,
-                                        sample_copy=self.__copy_sample(current_samples), 
-                                        details=details, libraries=libraries,
-                                        edit_mode=edit_mode)
-        elif params.get('cancel_changes_button', False) == 'Cancel':
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          operation='show_request',
-                                                          id=trans.security.encode_id(request.id)) )
-        else:
-            return trans.fill_template( '/admin/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=current_samples,
-                                        sample_copy=self.__copy_sample(current_samples), 
-                                        details=details, libraries=libraries,
-                                        edit_mode=edit_mode, status=status, message=message)
-
-            
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def delete_sample(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
-        current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
-        sample_index = int(params.get('sample_id', 0))
-        sample_name = current_samples[sample_index]['name']
-        s = request.has_sample(sample_name)
-        if s:
-            trans.sa_session.delete( s.values )
-            trans.sa_session.delete( s )
-            trans.sa_session.flush()
-        del current_samples[sample_index]  
-        return trans.fill_template( '/admin/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples = current_samples,
-                                    sample_copy=self.__copy_sample(current_samples), 
-                                    details=details,
-                                    edit_mode=edit_mode)
-    @web.expose
-    @web.require_admin
-    def request_details(self, trans, id):
-        '''
-        Shows the request details
-        '''
-        request = trans.sa_session.query( trans.app.model.Request ).get( id )
-        # list of widgets to be rendered on the request form
-        request_details = []
-        # main details
-        request_details.append(dict(label='User', 
-                                    value=str(request.user.email), 
-                                    helptext=''))
-        request_details.append(dict(label='Description', 
-                                    value=request.desc, 
-                                    helptext=''))
-        request_details.append(dict(label='Type', 
-                                    value=request.type.name, 
-                                    helptext=''))
-        request_details.append(dict(label='State', 
-                                    value=request.state(), 
-                                    helptext=''))
-        request_details.append(dict(label='Date created', 
-                                    value=request.create_time, 
-                                    helptext=''))
-        # form fields
-        for index, field in enumerate(request.type.request_form.fields):
-            if field['required']:
-                req = 'Required'
-            else:
-                req = 'Optional'
-            if field['type'] == 'AddressField':
-                if request.values.content[index]:
-                    request_details.append(dict(label=field['label'],
-                                                value=trans.sa_session.query( trans.app.model.UserAddress ).get( int( request.values.content[index] ) ).get_html(),
-                                                helptext=field['helptext']+' ('+req+')'))
-                else:
-                    request_details.append(dict(label=field['label'],
-                                                value=None,
-                                                helptext=field['helptext']+' ('+req+')'))
-            else: 
-                request_details.append(dict(label=field['label'],
-                                            value=request.values.content[index],
-                                            helptext=field['helptext']+' ('+req+')'))
-        if request.notify:
-            notify = 'Yes'
-        else:
-            notify = 'No'
-        request_details.append(dict(label='Send email notification once the sequencing request is complete', 
-                                    value=notify, 
-                                    helptext=''))
-        return request_details
-    def __validate_barcode(self, trans, sample, barcode):
-        '''
-        This method makes sure that the given barcode about to be assigned to 
-        the given sample is gobally unique. That is, barcodes must be unique 
-        across requests in Galaxy LIMS 
-        '''
-        message = ''
-        for index in range(len(sample.request.samples)):
-            # check for empty bar code
-            if not barcode.strip():
-                message = 'Please fill the barcode for sample <b>%s</b>.' % sample.name
-                break
-            # check all the saved bar codes
-            all_samples = trans.sa_session.query( trans.app.model.Sample )
-            for s in all_samples:
-                if barcode == s.bar_code:
-                    if sample.id == s.id:
-                        continue
-                    else:
-                        message = '''The bar code <b>%s</b> of sample <b>%s</b>  
-                                 belongs another sample. The sample bar codes must be 
-                                 unique throughout the system''' % \
-                                 (barcode, sample.name)
-                        break
-            if message:
-                break
-        return message
     @web.expose
     @web.require_admin
     def bar_codes(self, trans, **kwd):
@@ -1410,21 +481,7 @@ class RequestsAdmin( BaseController ):
                 email_content = "To: %s\nFrom: no-reply@nowhere.edu\nSubject: %s\n\n%s" % (request.user.email, subject, body)
                 mail.write( email_content )
                 x = mail.close()
-    def change_state(self, trans, sample):
-        possible_states = sample.request.type.states 
-        curr_state = sample.current_state() 
-        states_input = SelectField('select_state')
-        for state in possible_states:
-            if curr_state.name == state.name:
-                states_input.add_option(state.name+' (Current)', state.id, selected=True)
-            else:
-                states_input.add_option(state.name, state.id)
-        widgets = []
-        widgets.append(('Select the new state of the sample from the list of possible state(s)',
-                      states_input))
-        widgets.append(('Comments', TextArea('comment')))
-        title = 'Change current state'
-        return widgets, title
+
     @web.expose
     @web.require_admin
     def save_state(self, trans, **kwd):
@@ -1449,71 +506,14 @@ class RequestsAdmin( BaseController ):
         trans.sa_session.add( event )
         trans.sa_session.flush()
         self.__set_request_state( trans, sample.request )
-        return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='show_events',
+        return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                          cntrller='requests_admin', 
+                                                          action='sample_events',
                                                           sample_id=sample.id))
-    @web.expose
-    @web.require_admin
-    def show_events(self, trans, **kwd):
-        params = util.Params( kwd )
-        try:
-            sample_id = int(params.get('sample_id', False))
-            sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id )
-        except:
-            message = "Invalid sample ID"
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message=message,
-                                                              **kwd) )
-        events_list = []
-        all_events = sample.events
-        for event in all_events:         
-            events_list.append((event.state.name, event.state.desc, 
-                                time_ago(event.update_time), event.comment))
-        widgets, title = self.change_state(trans, sample)
-        return trans.fill_template( '/admin/samples/events.mako', 
-                                    events_list=events_list,
-                                    sample=sample, widgets=widgets, title=title)
-
     #
     # Data transfer from sequencer
     #
-    @web.expose
-    @web.require_admin
-    def show_datatx_page( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' ) 
-        try:
-            sample = trans.sa_session.query( trans.app.model.Sample ).get( trans.security.decode_id( kwd['sample_id'] ) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid sample ID",
-                                                              **kwd) )
-        # check if a library and folder has been set for this sample yet.
-        if not sample.library or not sample.folder:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              operation='show_request',
-                                                              status='error',
-                                                              message="Set a data library and folder for <b>%s</b> to transfer dataset(s)." % sample.name,
-                                                              id=trans.security.encode_id(sample.request.id) ) )             
-        if params.get( 'folder_path', ''  ):
-            folder_path = util.restore_text( params.get( 'folder_path', ''  ) )
-        else:
-            if len(sample.dataset_files):
-                folder_path = os.path.dirname(sample.dataset_files[-1]['filepath'][:-1])
-            else:
-                folder_path = util.restore_text( sample.request.type.datatx_info.get('data_dir', '') )
-        if folder_path[-1] != os.sep:
-            folder_path += os.sep
-        return trans.fill_template( '/admin/requests/get_data.mako', 
-                                    sample=sample, dataset_files=sample.dataset_files,
-                                    message=message, status=status, files=[],
-                                    folder_path=folder_path )
+
     def __get_files(self, trans, sample, folder_path):
         '''
         This method retrieves the filenames to be transfer from the remote host.
@@ -1521,7 +521,8 @@ class RequestsAdmin( BaseController ):
         datatx_info = sample.request.type.datatx_info
         if not datatx_info['host'] or not datatx_info['username'] or not datatx_info['password']:
             message = "Error in sequencer login information." 
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+            return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                              cntrller='requests_admin' ,
                                                               action='show_datatx_page', 
                                                               sample_id=trans.security.encode_id(sample.id),
                                                               status='error',
@@ -1536,7 +537,8 @@ class RequestsAdmin( BaseController ):
                                           timeout=10)
         if 'No such file or directory' in output:
             message = "No such folder (%s) exists on the sequencer." % folder_path
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+            return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                              cntrller='requests_admin' ,
                                                               action='show_datatx_page',
                                                               sample_id=trans.security.encode_id(sample.id),
                                                               message=message, status='error',
@@ -1574,7 +576,8 @@ class RequestsAdmin( BaseController ):
         if params.get( 'start_transfer_button', False ) == 'True':
             return self.__start_datatx(trans, sample)
         if not folder_path:
-            return trans.fill_template( '/admin/requests/get_data.mako',
+            return trans.fill_template( '/requests/common/get_data.mako',
+                                        cntrller='requests_admin',
                                         sample=sample, files=[], 
                                         dataset_files=sample.dataset_files,
                                         folder_path=folder_path )
@@ -1585,7 +588,8 @@ class RequestsAdmin( BaseController ):
             files = self.__get_files(trans, sample, folder_path)
             if folder_path[-1] != os.sep:
                 folder_path += os.sep
-            return trans.fill_template( '/admin/requests/get_data.mako',
+            return trans.fill_template( '/requests/common/get_data.mako',
+                                        cntrller='requests_admin',
                                         sample=sample, files=files, 
                                         dataset_files=sample.dataset_files,
                                         folder_path=folder_path )
@@ -1596,7 +600,8 @@ class RequestsAdmin( BaseController ):
             files = self.__get_files(trans, sample, folder_path)
             if folder_path[-1] != os.sep:
                 folder_path += os.sep
-            return trans.fill_template( '/admin/requests/get_data.mako',
+            return trans.fill_template( '/requests/common/get_data.mako',
+                                        cntrller='requests_admin',
                                         sample=sample, files=files, 
                                         dataset_files=sample.dataset_files,
                                         folder_path=folder_path )
@@ -1607,7 +612,8 @@ class RequestsAdmin( BaseController ):
             files = self.__get_files(trans, sample, folder_path)
             if folder_path[-1] != os.sep:
                 folder_path += os.sep
-            return trans.fill_template( '/admin/requests/get_data.mako',
+            return trans.fill_template( '/requests/common/get_data.mako',
+                                        cntrller='requests_admin',
                                         sample=sample, files=files, 
                                         dataset_files=sample.dataset_files,
                                         folder_path=folder_path )
@@ -1618,7 +624,8 @@ class RequestsAdmin( BaseController ):
             del sample.dataset_files[dataset_index]
             trans.sa_session.add( sample )
             trans.sa_session.flush()
-            return trans.fill_template( '/admin/requests/get_data.mako', 
+            return trans.fill_template( '/requests/common/get_data.mako', 
+                                        cntrller='requests_admin',
                                         sample=sample, files=files,
                                         dataset_files=sample.dataset_files,
                                         folder_path=folder_path)
@@ -1651,7 +658,8 @@ class RequestsAdmin( BaseController ):
                                                               folder_path=folder_path,
                                                               open_folder=True))
 
-        return trans.response.send_redirect( web.url_for( controller='requests_admin',
+        return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                          cntrller='requests_admin' ,
                                                           action='show_datatx_page', 
                                                           sample_id=trans.security.encode_id(sample.id),
                                                           folder_path=folder_path))
@@ -1780,13 +788,15 @@ class RequestsAdmin( BaseController ):
            not datatx_info['username'] or \
            not datatx_info['password']:
             message = "Error in sequencer login information." 
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+            return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                              cntrller='requests_admin' ,
                                                               action='show_datatx_page', 
                                                               sample_id=trans.security.encode_id(sample.id),
                                                               status='error',
                                                               message=message))
         self.__send_message(trans, datatx_info, sample)
-        return trans.response.send_redirect( web.url_for( controller='requests_admin',
+        return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                          cntrller='requests_admin' ,
                                                           action='show_datatx_page', 
                                                           sample_id=trans.security.encode_id(sample.id),
                                                           folder_path=datatx_info['data_dir']))

    

[galaxy-commits] galaxy-dist commit c1172bae7b0f: lims: requests/request_admin controller refactor

commits-noreply＠bitbucket.org