[galaxy-commits] commit/galaxy-central: smcmanus: Removed experimental code for improving library browsing performance

17 Oct 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/91512b8e1a6c/
changeset:   91512b8e1a6c
user:        smcmanus
date:        2012-10-17 23:40:25
summary:     Removed experimental code for improving library browsing performance
affected #:  5 files

diff -r ba9a8b52e8539693606b07811a6b2bf48b071ae2 -r 91512b8e1a6ce1c91bd05482afe9a6a774a2ab93 lib/galaxy/config.py

--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -235,8 +235,10 @@
         self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) )
         # Experimental: This will not be enabled by default and will hide 
         # nonproduction code.
-        # The api_folders refers to whether the API exposes 
+        # The api_folders refers to whether the API exposes the /folders section.
         self.api_folders = string_as_bool( kwargs.get( 'api_folders', False ) )
+        # This is for testing new library browsing capabilities.
+        self.new_lib_browse = string_as_bool( kwargs.get( 'new_lib_browse', False ) )
 
     def __read_tool_job_config( self, global_conf_parser, section, key ):
         try:


diff -r ba9a8b52e8539693606b07811a6b2bf48b071ae2 -r 91512b8e1a6ce1c91bd05482afe9a6a774a2ab93 lib/galaxy/security/__init__.py
--- a/lib/galaxy/security/__init__.py
+++ b/lib/galaxy/security/__init__.py
@@ -256,7 +256,7 @@
 
     def get_actions_for_items( self, trans, action, permission_items ):
         # TODO: Rename this; it's a replacement for get_item_actions, but it
-        # doesn't represent what it's really confusing.
+        # doesn't represent what it's really doing, which is confusing.
         # TODO: Make this work for other classes besides lib_datasets.
         # That should be as easy as checking the type and writing a query for each;
         # we're avoiding using the SQLAlchemy backrefs because they can cause lots
@@ -1179,19 +1179,12 @@
             return True, ''
         action = self.permitted_actions.DATASET_ACCESS
 
-        # SM: TODO: This is for timing debug. Delete it later.
-        from datetime import datetime, timedelta
-        query_start = datetime.now()
         lddas = self.sa_session.query( self.model.LibraryDatasetDatasetAssociation ) \
                                .join( "library_dataset" ) \
                                .filter( self.model.LibraryDataset.folder == folder ) \
                                .join( "dataset" ) \
                                .options( eagerload_all( "dataset.actions" ) ) \
                                .all()
-        query_end = datetime.now()
-        query_delta = query_end - query_start
-        #log.debug( "Check folder contents: join query time: %d.%.6d sec" % 
-        #         ( query_delta.seconds, query_delta.microseconds ) )
 
         for ldda in lddas:
             ldda_access_permissions = self.get_item_actions( action, ldda.dataset )


diff -r ba9a8b52e8539693606b07811a6b2bf48b071ae2 -r 91512b8e1a6ce1c91bd05482afe9a6a774a2ab93 lib/galaxy/webapps/galaxy/api/folder_contents.py
--- a/lib/galaxy/webapps/galaxy/api/folder_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py
@@ -25,6 +25,7 @@
         log.debug( "FolderContentsController.index: enter" )
         rval = []
         current_user_roles = trans.get_current_user_roles()
+
         def traverse( folder ):
             admin = trans.user_is_admin()
             rval = []
@@ -54,6 +55,8 @@
 
         try:
             folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id )
+            parent_library = folder.parent_library
+            log.debug( "parent library type: %s" % type(parent_library) )
         except:
             folder = None
             log.error( "FolderContentsController.index: Unable to retrieve folder %s" 


diff -r ba9a8b52e8539693606b07811a6b2bf48b071ae2 -r 91512b8e1a6ce1c91bd05482afe9a6a774a2ab93 lib/galaxy/webapps/galaxy/controllers/library_common.py
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -131,17 +131,20 @@
             comptypes = get_comptypes( trans )
             try:
                 # SM: TODO: Add configuration variable asap. 
-                return trans.fill_template( 'library/common/browse_library.mako',
-                                            cntrller=cntrller,
-                                            use_panels=use_panels,
-                                            library=library,
-                                            created_ldda_ids=created_ldda_ids,
-                                            hidden_folder_ids=hidden_folder_ids,
-                                            show_deleted=show_deleted,
-                                            comptypes=comptypes,
-                                            current_user_roles=current_user_roles,
-                                            message=message,
-                                            status=status )
+                if self.app.config.new_lib_browse:
+                    pass
+                else:
+                    return trans.fill_template( 'library/common/browse_library.mako',
+                                                cntrller=cntrller,
+                                                use_panels=use_panels,
+                                                library=library,
+                                                created_ldda_ids=created_ldda_ids,
+                                                hidden_folder_ids=hidden_folder_ids,
+                                                show_deleted=show_deleted,
+                                                comptypes=comptypes,
+                                                current_user_roles=current_user_roles,
+                                                message=message,
+                                                status=status )
             except Exception, e:
                 message = 'Error attempting to display contents of library (%s): %s.' % ( str( library.name ), str( e ) )
                 status = 'error'


diff -r ba9a8b52e8539693606b07811a6b2bf48b071ae2 -r 91512b8e1a6ce1c91bd05482afe9a6a774a2ab93 templates/library/common/browse_library_opt.mako
--- a/templates/library/common/browse_library_opt.mako
+++ /dev/null
@@ -1,622 +0,0 @@
-<%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 “${library.name}”</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>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: smcmanus: Removed experimental code for improving library browsing performance

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