diff --git a/templates/library/common/browse_library.mako b/templates/library/common/browse_library.mako
index 1d87c09f19e..9bc3037177b 100644
--- a/templates/library/common/browse_library.mako
+++ b/templates/library/common/browse_library.mako
@@ -48,7 +48,6 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("libs/json2")}
     ${h.js("libs/jquery/jstorage")}
     ${common_javascripts()}
     ${self.grid_javascripts()}
@@ -207,7 +206,7 @@
     </script>
 </%def>
 
-<%def name="render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )">
+<%def name="render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )">
     <%
         ## The received ldda must always be a LibraryDatasetDatasetAssociation object.  The object id passed to methods
         ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying
@@ -215,14 +214,22 @@
         ## library_dataset, so we display the attributes from the ldda.
         
         from galaxy.webapps.galaxy.controllers.library_common import branch_deleted
-
+        
         is_admin = trans.user_is_admin() and cntrller == 'library_admin'
-        current_version = ( ldda == library_dataset.library_dataset_dataset_association )
+        
+        if ldda == library_dataset.library_dataset_dataset_association:
+            current_version = True
+            if is_admin:
+                can_modify = can_manage = True
+            elif cntrller in [ 'library', 'requests' ]:
+                can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset )
+                can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library_dataset )
+            else:
+                can_modify = can_manage = False
+        else:
+            current_version = False
         if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ):
             tracked_datasets[ldda.id] = ldda.state
-        # SM: This causes a query to be emitted, but it quickly goes down a
-        # rabbit hole of many possible inheritable cases. It may not be 
-        # possible to easily eliminate the extra query from this call.
         info_association, inherited = ldda.get_info_association( restrict=True )
         form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
     %>
@@ -303,21 +310,9 @@
     %endif
 </%def>
 
-<%def name="format_delta( tdelta )">
-    <%
-        from datetime import datetime
-        return "%d.%.6d" % ( tdelta.seconds, tdelta.microseconds )
-     %>
-</%def>
-
 <%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )">
     <%
-        from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas 
-
-        # SM: DELETEME
-        from datetime import datetime, timedelta
-        import logging
-        log = logging.getLogger( __name__ )
+        from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted
         
         is_admin = trans.user_is_admin() and cntrller == 'library_admin'
         has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False )
@@ -330,9 +325,6 @@
             pad = folder_pad + 20
             expander = h.url_for("/static/images/silk/resultset_next.png")
             folder_img = h.url_for("/static/images/silk/folder.png")
-        # SM: If this is a comma-delimited list of LDDAs, then split them up
-        # into a list. For anything else, turn created_ldda_ids into a single
-        # item list.
         if created_ldda_ids:
             created_ldda_ids = util.listify( created_ldda_ids )
         if str( folder.id ) in hidden_folder_ids:
@@ -434,39 +426,47 @@
         %>
     %endif
     <%
-        # TODO: If show_deleted is set to True, then nothing is displayed. Why? This wasn't the case
-        # in the past.
         if show_deleted:
             sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder )
         else:
             sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder )
-        # Render all the subfolders: 
-        # TODO: Check permissions first. 
-        for sub_folder in sub_folders:
-            render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )
-
-        # Map LibraryDatasets to LDDAs, then map LDDAs to Datasets.
-        # Then determine which Datasets are accessible and which are not.
-        # For every LibraryDataset, if there's an LDDA for it and it's 
-        # accessible then display it.
-        if ( len( library_datasets ) > 0 ):
-            lib_dataset_ldda_map = map_library_datasets_to_lddas( trans, library_datasets )
-            dataset_list = datasets_for_lddas( trans, lib_dataset_ldda_map.values() )
-            #can_access_datasets = trans.app.security_agent.dataset_access_mapping( trans, current_user_roles, dataset_list )
-            can_access_datasets = trans.app.security_agent.dataset_permission_map_for_access( trans, current_user_roles, dataset_list )
-            can_modify_datasets = trans.app.security_agent.item_permission_map_for_modify( trans, current_user_roles, dataset_list )
-            can_manage_datasets = trans.app.security_agent.item_permission_map_for_manage( trans, current_user_roles, dataset_list )
-            for library_dataset in library_datasets:
-                ldda = lib_dataset_ldda_map[ library_dataset.id ]
-                if ldda: 
-                    # SMTODO: Fix awkard modify/manage permission checks.
-                    can_access = is_admin or can_access_datasets[ ldda.dataset_id ]
-                    can_modify = is_admin or ( cntrller in ['library', 'requests'] and can_modify_datasets[ ldda.dataset_id ])
-                    can_manage = is_admin or ( cntrller in ['library', 'requests'] and can_manage_datasets[ ldda.dataset_id ])
-                    selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
-                    if can_access:
-                        render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )
     %>
+    %if is_admin:
+        %for sub_folder in sub_folders:
+            ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )}
+        %endfor 
+        %for library_dataset in library_datasets:
+            <%
+                ldda = library_dataset.library_dataset_dataset_association
+                if ldda:
+                    # There should always be an ldda, but some users running their own instances have reported that
+                    # some of their LibraryDatasets have no associated lddas
+                    selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
+            %>
+            %if ldda:
+                ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )}
+            %endif
+        %endfor
+    %else:
+        %for sub_folder in sub_folders:
+            ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False, simple=simple )}
+        %endfor
+        %for library_dataset in library_datasets:
+            <%
+                ldda = library_dataset.library_dataset_dataset_association
+                if ldda:
+                    # There should always be an ldda, but some users running their own instances have reported that
+                    # some of their LibraryDatasets have no associated lddas
+                    can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset )
+                    selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
+                else:
+                    can_access = False
+            %>
+            %if can_access:
+                ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted, simple=simple )}
+            %endif
+        %endfor
+    %endif
 </%def>
 
 <%def name="render_content(simple=False)">
@@ -474,8 +474,6 @@
         from galaxy import util
         from galaxy.webapps.galaxy.controllers.library_common import branch_deleted
         from time import strftime
-        import logging
-        log = logging.getLogger( __name__ )
         
         is_admin = trans.user_is_admin() and cntrller == 'library_admin'
         
@@ -491,8 +489,6 @@
         info_association, inherited = library.get_info_association()
         form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
         
-        # SM: These are mostly display-specific; ignore them for now. 
-        # The has_accessible_folders determines if anything can be shown - use it.
         self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles )
         root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False )
         has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles )
@@ -585,16 +581,13 @@
                 </tr>
             </thead>
             <% row_counter = RowCounter() %>
-            ## SM: Here is where we render the libraries based on admin/non-admin privileges:
             %if cntrller in [ 'library', 'requests' ]:
                 ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True, simple=simple )}
-                ## SM: TODO: WTF?
                 %if not library.deleted and self.has_accessible_datasets and not simple:
                     ${render_actions_on_multiple_items()}
                 %endif
             %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ):
                 ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )}
-                ## SM: TODO: WTF?
                 %if not library.deleted and not show_deleted and self.has_accessible_datasets:
                     ${render_actions_on_multiple_items()}
                 %endif
diff --git a/templates/library/common/browse_library_opt.mako b/templates/library/common/browse_library_opt.mako
new file mode 100644
index 00000000000..1d87c09f19e
--- /dev/null
+++ b/templates/library/common/browse_library_opt.mako
@@ -0,0 +1,622 @@
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/library/common/library_item_info.mako" import="render_library_item_info" />
+<%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" />
+<%namespace file="/library/common/common.mako" import="render_compression_types_help" />
+<%namespace file="/library/common/common.mako" import="common_javascripts" />
+
+<%!
+    def inherit(context):
+        if context.get('use_panels'):
+            return '/webapps/galaxy/base_panels.mako'
+        else:
+            return '/base.mako'
+%>
+<%inherit file="${inherit(context)}"/>
+
+<%def name="init()">
+<%
+    self.has_left_panel=False
+    self.has_right_panel=False
+    self.message_box_visible=False
+    self.active_view="user"
+    self.overlay_visible=False
+    self.has_accessible_datasets = False
+%>
+</%def>
+
+##
+## Override methods from base.mako and base_panels.mako
+##
+<%def name="center_panel()">
+   <div style="overflow: auto; height: 100%;">
+       <div class="page-container" style="padding: 10px;">
+           ${render_content()}
+       </div>
+   </div>
+</%def>
+
+## Render the grid's basic elements. Each of these elements can be subclassed.
+<%def name="body()">
+    ${render_content()}
+</%def>
+
+<%def name="title()">Browse data library</%def>
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    ${h.css( "library" )}
+</%def>
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    ${h.js("libs/json2")}
+    ${h.js("libs/jquery/jstorage")}
+    ${common_javascripts()}
+    ${self.grid_javascripts()}
+</%def>
+
+<%def name="grid_javascripts()">
+    <script type="text/javascript">
+        var init_libraries = function() {
+            var storage_id = "library-expand-state-${trans.security.encode_id(library.id)}";
+            
+            var restore_folder_state = function() {
+                var state = $.jStorage.get(storage_id);
+                if (state) {
+                    for (var id in state) {
+                        if (state[id] === true) {
+                            var row = $("#" + id),
+                                index = row.parent().children().index(row);
+                            row.addClass("expanded").show();
+                            row.siblings().filter("tr[parent='" + index + "']").show();
+                        }
+                    }
+                }
+            };
+            
+            var save_folder_state = function() {
+                var state = {};
+                $("tr.folderRow").each( function() {
+                    var folder = $(this);
+                    state[folder.attr("id")] = folder.hasClass("expanded");
+                });
+                $.jStorage.set(storage_id, state);
+            };
+            
+            $("#library-grid").each(function() {
+                var child_of_parent_cache = {};
+                // Recursively fill in children and descendents of each row
+                var process_row = function(q, parents) {
+                    // Find my index
+                    var parent = q.parent(),
+                        this_level = child_of_parent_cache[parent] || (child_of_parent_cache[parent] = parent.children());
+                        
+                    var index = this_level.index(q);
+                    // Find my immediate children
+                    var children = $(par_child_dict[index]);
+                    // Recursively handle them
+                    var descendents = children;
+                    children.each( function() {
+                        child_descendents = process_row( $(this), parents.add(q) );
+                        descendents = descendents.add(child_descendents);
+                    });
+                    // Set up expand / hide link
+                    var expand_fn = function() {
+                        if ( q.hasClass("expanded") ) {
+                            descendents.hide();
+                            descendents.removeClass("expanded");
+                            q.removeClass("expanded");
+                        } else {
+                            children.show();
+                            q.addClass("expanded");
+                        }
+                        save_folder_state();
+                    };
+                    $("." + q.attr("id") + "-click").click(expand_fn);
+                    // Check/uncheck boxes in subfolders.
+                    q.children("td").children("input[type=checkbox]").click( function() {
+                        if ( $(this).is(":checked") ) {
+                            descendents.find("input[type=checkbox]").attr("checked", true);
+                        } else {
+                            descendents.find("input[type=checkbox]").attr("checked", false);
+                            // If you uncheck a lower level checkbox, uncheck the boxes above it
+                            // (since deselecting a child means the parent is not fully selected any more).
+                            parents.children("td").children("input[type=checkbox]").attr("checked", false);
+                        }
+                    });
+                    // return descendents for use by parent
+                    return descendents;
+                }
+                
+                // Initialize dict[parent_id] = rows_which_have_that_parent_id_as_parent_attr
+                var par_child_dict = {},
+                    no_parent = [];
+                
+                $(this).find("tbody tr").each( function() {
+                    if ( $(this).attr("parent")) {
+                        var parent = $(this).attr("parent");
+                        if (par_child_dict[parent] !== undefined) {
+                            par_child_dict[parent].push(this);
+                        } else {
+                            par_child_dict[parent] = [this];
+                        }
+                    } else {
+                        no_parent.push(this);
+                    }                        
+                });
+                
+                $(no_parent).each( function() {
+                    descendents = process_row( $(this), $([]) );
+                    descendents.hide();
+               });
+            });
+            
+            restore_folder_state();
+        };
+        $(function() {
+            init_libraries();
+        });
+        
+        // Looks for changes in dataset state using an async request. Keeps
+        // calling itself (via setTimeout) until all datasets are in a terminal
+        // state.
+        var updater = function ( tracked_datasets ) {
+            // Check if there are any items left to track
+            var empty = true;
+            for ( i in tracked_datasets ) {
+                empty = false;
+                break;
+            }
+            if ( ! empty ) {
+                setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 );
+            }
+        };
+        var updater_callback = function ( tracked_datasets ) {
+            // Build request data
+            var ids = []
+            var states = []
+            $.each( tracked_datasets, function ( id, state ) {
+                ids.push( id );
+                states.push( state );
+            });
+            // Make ajax call
+            $.ajax( {
+                type: "POST",
+                url: "${h.url_for( controller='library_common', action='library_item_updates' )}",
+                dataType: "json",
+                data: { ids: ids.join( "," ), states: states.join( "," ) },
+                success : function ( data ) {
+                    $.each( data, function( id, val ) {
+                        // Replace HTML
+                        var cell = $("#libraryItem-" + id).find("#libraryItemInfo");
+                        cell.html( val.html );
+                        // If new state was terminal, stop tracking
+                        if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) {
+                            delete tracked_datasets[ parseInt(id) ];
+                        } else {
+                            tracked_datasets[ parseInt(id) ] = val.state;
+                        }
+                    });
+                    updater( tracked_datasets ); 
+                },
+                error: function() {
+                    // Just retry, like the old method, should try to be smarter
+                    updater( tracked_datasets );
+                }
+            });
+        };
+    </script>
+</%def>
+
+<%def name="render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )">
+    <%
+        ## The received ldda must always be a LibraryDatasetDatasetAssociation object.  The object id passed to methods
+        ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying
+        ## children, which are always lddas ).  We also need to make sure we're displaying the latest version of this
+        ## library_dataset, so we display the attributes from the ldda.
+        
+        from galaxy.webapps.galaxy.controllers.library_common import branch_deleted
+
+        is_admin = trans.user_is_admin() and cntrller == 'library_admin'
+        current_version = ( ldda == library_dataset.library_dataset_dataset_association )
+        if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ):
+            tracked_datasets[ldda.id] = ldda.state
+        # SM: This causes a query to be emitted, but it quickly goes down a
+        # rabbit hole of many possible inheritable cases. It may not be 
+        # possible to easily eliminate the extra query from this call.
+        info_association, inherited = ldda.get_info_association( restrict=True )
+        form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
+    %>
+    %if current_version and ( not ldda.library_dataset.deleted or show_deleted ):
+        <tr class="datasetRow"
+            %if parent is not None:
+                parent="${parent}"
+            %endif
+            id="libraryItem-${ldda.id}">
+            <td style="padding-left: ${pad+20}px;">
+                <input style="float: left;" type="checkbox" name="ldda_ids" id="${trans.security.encode_id( ldda.id )}" value="${trans.security.encode_id( ldda.id )}"
+                %if selected:
+                    checked="checked"
+                %endif
+                />
+                %if simple:
+                    <label for="${trans.security.encode_id( ldda.id )}">${ util.unicodify( ldda.name )}</label>
+                %else:
+                    <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${ldda.id}-popup">
+                        <a class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">
+                            %if ldda.library_dataset.deleted:
+                                <div class="libraryItem-error">${util.unicodify( ldda.name )}</div>
+                            %else:
+                                ${util.unicodify( ldda.name )}
+                            %endif     
+                        </a>
+                    </div>
+                    %if not library.deleted:
+                        <div popupmenu="dataset-${ldda.id}-popup">
+                            %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify:
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a>
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='ldda', item_id=trans.security.encode_id( ldda.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this dataset</a>
+                            %else:
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a>
+                            %endif
+                            %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and not info_association:
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a>
+                            %endif
+                            %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and info_association:
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a>
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a>
+                            %endif
+                            %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_manage:
+                                %if not trans.app.security_agent.dataset_is_public( ldda.dataset ):
+                                    <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='ldda', id=trans.security.encode_id( ldda.dataset.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a>
+                                %endif
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a>
+                            %endif
+                            %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify:
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a>
+                            %endif
+                            %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data:
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into selected histories</a>
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a>
+                            %endif
+                            %if can_modify:
+                                %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted:
+                                    <a class="action-button" confirm="Click OK to delete dataset '${util.unicodify( ldda.name )}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a>
+                                %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted:
+                                    <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a>
+                                %endif
+                            %endif
+                        </div>
+                    %endif
+                %endif
+            </td>
+            % if not simple:
+                <td id="libraryItemInfo">${render_library_item_info( ldda )}</td>
+                <td>${ldda.extension}</td>
+            % endif
+            <td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td>
+            <td>${ldda.get_size( nice_size=True )}</td>
+        </tr>
+        <%
+            my_row = row_counter.count
+            row_counter.increment()
+        %>
+    %endif
+</%def>
+
+<%def name="format_delta( tdelta )">
+    <%
+        from datetime import datetime
+        return "%d.%.6d" % ( tdelta.seconds, tdelta.microseconds )
+     %>
+</%def>
+
+<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )">
+    <%
+        from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas 
+
+        # SM: DELETEME
+        from datetime import datetime, timedelta
+        import logging
+        log = logging.getLogger( __name__ )
+        
+        is_admin = trans.user_is_admin() and cntrller == 'library_admin'
+        has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False )
+        
+        if root_folder:
+            pad = folder_pad
+            expander = h.url_for("/static/images/silk/resultset_bottom.png")
+            folder_img = h.url_for("/static/images/silk/folder_page.png")
+        else:
+            pad = folder_pad + 20
+            expander = h.url_for("/static/images/silk/resultset_next.png")
+            folder_img = h.url_for("/static/images/silk/folder.png")
+        # SM: If this is a comma-delimited list of LDDAs, then split them up
+        # into a list. For anything else, turn created_ldda_ids into a single
+        # item list.
+        if created_ldda_ids:
+            created_ldda_ids = util.listify( created_ldda_ids )
+        if str( folder.id ) in hidden_folder_ids:
+            return ""
+        my_row = None
+        if is_admin:
+            can_add = can_modify = can_manage = True
+        elif cntrller in [ 'library' ]:
+            can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, folder )
+            if not can_access:
+                can_show, folder_ids = \
+                    trans.app.security_agent.show_library_item( trans.user,
+                                                                current_user_roles,
+                                                                folder,
+                                                                [ trans.app.security_agent.permitted_actions.LIBRARY_ADD,
+                                                                  trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
+                                                                  trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] )
+                if not can_show:
+                    return ""
+            can_add = trans.app.security_agent.can_add_library_item( current_user_roles, folder )
+            can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, folder )
+            can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, folder )
+        else:
+            can_add = can_modify = can_manage = False
+            
+        form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
+        info_association, inherited = folder.get_info_association( restrict=True )
+    %>
+    %if not root_folder and ( not folder.deleted or show_deleted ):
+        <% encoded_id = trans.security.encode_id( folder.id ) %>
+        <tr id="folder-${encoded_id}" class="folderRow libraryOrFolderRow"
+            %if parent is not None:
+                parent="${parent}"
+                style="display: none;"
+            %endif
+            >
+            <td style="padding-left: ${folder_pad}px;">
+                <input type="checkbox" class="folderCheckbox"/>
+                <span class="expandLink folder-${encoded_id}-click">
+                    <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup">
+                        <a class="folder-${encoded_id}-click" href="javascript:void(0);">
+                            <span class="rowIcon"></span>
+                            %if folder.deleted:
+                                <div class="libraryItem-error">${folder.name}</div>
+                            %else:
+                                ${folder.name}
+                            %endif
+                        </a>
+                    </div>
+                </span>
+                %if not library.deleted:
+                    <div popupmenu="folder_img-${folder.id}-popup">
+                        %if not branch_deleted( folder ) and can_add:
+                            <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a>
+                            <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a>
+                        %endif
+                        %if not branch_deleted( folder ):
+                            %if has_accessible_library_datasets:
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a>
+                            %endif
+                            %if can_modify:
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a>
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='folder', item_id=trans.security.encode_id( folder.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this folder</a>
+                            %else:
+                                <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a>
+                            %endif
+                        %endif
+                        %if not branch_deleted( folder ) and can_modify and not info_association:
+                            <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a>
+                        %endif
+                        %if not branch_deleted( folder ) and can_modify and info_association:
+                            <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a>
+                            <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a>
+                        %endif
+                        %if not branch_deleted( folder ) and can_manage:
+                           %if not trans.app.security_agent.folder_is_public( folder ):
+                               <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='folder', id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a>
+                           %endif
+                            <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a>
+                        %endif
+                        %if can_modify:
+                            %if not library.deleted and not folder.deleted:
+                                <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a>
+                            %elif not library.deleted and folder.deleted and not folder.purged:
+                                <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a>
+                            %endif
+                        %endif
+                    </div>
+                %endif
+            <td>
+            %if folder.description:
+                ${folder.description}
+            %endif
+            <td colspan="3"></td>
+        </tr>
+        <%
+            my_row = row_counter.count
+            row_counter.increment()
+        %>
+    %endif
+    <%
+        # TODO: If show_deleted is set to True, then nothing is displayed. Why? This wasn't the case
+        # in the past.
+        if show_deleted:
+            sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder )
+        else:
+            sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder )
+        # Render all the subfolders: 
+        # TODO: Check permissions first. 
+        for sub_folder in sub_folders:
+            render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )
+
+        # Map LibraryDatasets to LDDAs, then map LDDAs to Datasets.
+        # Then determine which Datasets are accessible and which are not.
+        # For every LibraryDataset, if there's an LDDA for it and it's 
+        # accessible then display it.
+        if ( len( library_datasets ) > 0 ):
+            lib_dataset_ldda_map = map_library_datasets_to_lddas( trans, library_datasets )
+            dataset_list = datasets_for_lddas( trans, lib_dataset_ldda_map.values() )
+            #can_access_datasets = trans.app.security_agent.dataset_access_mapping( trans, current_user_roles, dataset_list )
+            can_access_datasets = trans.app.security_agent.dataset_permission_map_for_access( trans, current_user_roles, dataset_list )
+            can_modify_datasets = trans.app.security_agent.item_permission_map_for_modify( trans, current_user_roles, dataset_list )
+            can_manage_datasets = trans.app.security_agent.item_permission_map_for_manage( trans, current_user_roles, dataset_list )
+            for library_dataset in library_datasets:
+                ldda = lib_dataset_ldda_map[ library_dataset.id ]
+                if ldda: 
+                    # SMTODO: Fix awkard modify/manage permission checks.
+                    can_access = is_admin or can_access_datasets[ ldda.dataset_id ]
+                    can_modify = is_admin or ( cntrller in ['library', 'requests'] and can_modify_datasets[ ldda.dataset_id ])
+                    can_manage = is_admin or ( cntrller in ['library', 'requests'] and can_manage_datasets[ ldda.dataset_id ])
+                    selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
+                    if can_access:
+                        render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )
+    %>
+</%def>
+
+<%def name="render_content(simple=False)">
+    <%
+        from galaxy import util
+        from galaxy.webapps.galaxy.controllers.library_common import branch_deleted
+        from time import strftime
+        import logging
+        log = logging.getLogger( __name__ )
+        
+        is_admin = trans.user_is_admin() and cntrller == 'library_admin'
+        
+        if is_admin:
+            can_add = can_modify = can_manage = True
+        elif cntrller in [ 'library', 'requests' ]:
+            can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library )
+            can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library )
+            can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library )
+        else:
+            can_add = can_modify = can_manage = False
+            
+        info_association, inherited = library.get_info_association()
+        form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
+        
+        # SM: These are mostly display-specific; ignore them for now. 
+        # The has_accessible_folders determines if anything can be shown - use it.
+        self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles )
+        root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False )
+        has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles )
+        
+        tracked_datasets = {}
+        
+        class RowCounter( object ):
+            def __init__( self ):
+                self.count = 0
+            def increment( self ):
+                self.count += 1
+            def __str__( self ):
+                return str( self.count )
+    %>
+    
+    <h2>Data Library &ldquo;${library.name}&rdquo;</h2>
+    
+     <ul class="manage-table-actions">
+         %if not library.deleted and ( is_admin or can_add ):
+             <li><a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a></li>
+             <li><a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( library.root_folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add folder</a></li>
+         %endif
+         %if ( ( not library.deleted ) and ( can_modify or can_manage ) ) or ( can_modify and not library.purged ) or ( library.purged ):
+             <li><a class="action-button" id="library-${library.id}-popup" class="menubutton">Library Actions</a></li>
+             <div popupmenu="library-${library.id}-popup">
+                 %if not library.deleted:
+                     %if can_modify:
+                         <a class="action-button" href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a>
+                         <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a>
+                         %if show_deleted:
+                             <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a>
+                         %else:
+                             <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a>
+                         %endif
+                     %endif
+                     %if can_modify and not library.info_association:
+                         <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a>
+                     %endif
+                     %if can_modify and info_association:
+                         <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a>
+                         <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a>
+                     %endif
+                     %if can_manage:
+                         %if not trans.app.security_agent.library_is_public( library, contents=True ):
+                             <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='library', id=trans.security.encode_id( library.id ), contents=True, use_panels=use_panels, show_deleted=show_deleted )}">Make public</a>
+                         %endif
+                         <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a>
+                     %endif
+                     %if root_folder_has_accessible_library_datasets:
+                        <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a>
+                     %endif
+                 %elif can_modify and not library.purged:
+                     <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a>
+                 %elif library.purged:
+                     <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">This data library has been purged</a>
+                 %endif
+             </div>
+         %endif
+    </ul>
+    
+    %if message:
+        ${render_msg( message, status )}
+    %endif
+
+    %if library.synopsis not in [ '', 'None', None ]:
+        <div class="libraryItemBody">
+            ${library.synopsis}
+        </div>
+    %endif
+    
+    %if self.has_accessible_datasets:
+        <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post">
+    %endif
+    %if has_accessible_folders:
+        <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid">
+            <thead>
+                <tr class="libraryTitle">
+                    <th>
+                        %if self.has_accessible_datasets:
+                            <input type="checkbox" id="checkAll" name=select_all_datasets_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_datasets_checkbox value="true"/>
+                        %endif
+                        Name
+                    </th>
+                    % if not simple:
+                        <th>Message</th>
+                        <th>Data type</th>
+                    % endif
+                    <th>Date uploaded</th>
+                    <th>File size</th>
+                </tr>
+            </thead>
+            <% row_counter = RowCounter() %>
+            ## SM: Here is where we render the libraries based on admin/non-admin privileges:
+            %if cntrller in [ 'library', 'requests' ]:
+                ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True, simple=simple )}
+                ## SM: TODO: WTF?
+                %if not library.deleted and self.has_accessible_datasets and not simple:
+                    ${render_actions_on_multiple_items()}
+                %endif
+            %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ):
+                ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )}
+                ## SM: TODO: WTF?
+                %if not library.deleted and not show_deleted and self.has_accessible_datasets:
+                    ${render_actions_on_multiple_items()}
+                %endif
+            %endif
+        </table>
+    %endif
+    %if self.has_accessible_datasets:
+        </form>
+    %endif
+     
+    %if tracked_datasets:
+        <script type="text/javascript">
+            // Updater
+            updater({${ ",".join( [ '"%s" : "%s"' % ( k, v ) for k, v in tracked_datasets.iteritems() ] ) }});
+        </script>
+        <!-- running: do not change this comment, used by TwillTestCase.library_wait -->
+    %endif
+    
+    %if self.has_accessible_datasets and not simple:
+        ${render_compression_types_help( comptypes )}
+    %endif
+    %if not has_accessible_folders:
+        The data library '${library.name}' does not contain any datasets that you can access.
+    %endif
+</%def>