[galaxy-commits] commit/galaxy-central: smcmanus: First cut of query optimizations for browsing. At least 3 out of 5 queries were eliminated. Code is not active by default.

27 Sep 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/a995f7aca75c/
changeset:   a995f7aca75c
user:        smcmanus
date:        2012-09-27 21:42:11
summary:     First cut of query optimizations for browsing. At least 3 out of 5 queries were eliminated. Code is not active by default.
affected #:  4 files

diff -r 4f788268c76dcb77e99076dbfbc8cf65c05b00cc -r a995f7aca75c03bd180689aead6a8870928d8fdf lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1785,6 +1785,7 @@
         # we'll return the next available info_association in the inheritable hierarchy.
         # True is also returned if the info_association was inherited, and False if not.
         # This enables us to eliminate displaying any contents of the inherited template.
+        # SM: Accessing self.info_association can cause a query to be emitted
         if self.info_association:
             return self.info_association[0], inherited
         if restrict:


diff -r 4f788268c76dcb77e99076dbfbc8cf65c05b00cc -r a995f7aca75c03bd180689aead6a8870928d8fdf lib/galaxy/security/__init__.py
--- a/lib/galaxy/security/__init__.py
+++ b/lib/galaxy/security/__init__.py
@@ -225,13 +225,16 @@
             # If role.type is neither private nor sharing, it's ok to display
             return True
         return role.type != self.model.Role.types.PRIVATE and role.type != self.model.Role.types.SHARING
+
     def allow_action( self, roles, action, item ):
         """
         Method for checking a permission for the current user ( based on roles ) to perform a
         specific action on an item, which must be one of:
         Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation
         """
+        # SM: Note that calling get_item_actions will emit a query. 
         item_actions = self.get_item_actions( action, item )
+            
         if not item_actions:
             return action.model == 'restrict'
         ret_val = False
@@ -249,8 +252,152 @@
                     ret_val = True
                     break
         return ret_val
-    def can_access_dataset( self, roles, dataset ):
-        return self.dataset_is_public( dataset ) or self.allow_action( roles, self.permitted_actions.DATASET_ACCESS, dataset )
+
+
+    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.
+        # 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
+        # of queries to be generated.  
+        #
+        # Originally, get_item_actions did:
+        # return [ permission for permission in item.actions if permission.action == action.action ]
+        # The "item" can be just about anything with permissions, and referencing 
+        # item.actions causes the item's permissions to be retrieved.
+        # This method will retrieve all permissions for all "items" and only
+        # return the permissions associated with that given action.
+        # We initialize the permissions list to be empty; we will return an 
+        # empty list by default.
+        #
+        # If the dataset id has no corresponding action in its permissions,
+        # then the returned permissions will not carry an entry for the dataset.
+        ret_permissions = {} 
+        if ( len( permission_items ) > 0 ): 
+            if ( isinstance( permission_items[0], trans.model.LibraryDataset ) ):
+                ids = [ item.library_dataset_id for item in permission_items ]
+                permissions = trans.sa_session.query( trans.model.LibraryDatasetPermissions ) \
+                                   .filter( and_( trans.model.LibraryDatasetPermissions.library_dataset_id.in_( ids ),
+                                                  trans.model.LibraryDatasetPermissions.action == action ) ) \
+                                   .all()
+
+                # Massage the return data. We will return a list of permissions
+                # for each library dataset. So we initialize the return list to
+                # have an empty list for each dataset. Then each permission is 
+                # appended to the right lib dataset.
+                # TODO: Consider eliminating the initialization and just return
+                # empty values for each library dataset id.
+                for item in permission_items:
+                    ret_permissions[ item.library_dataset_id ] = [] 
+                for permission in permissions:
+                    ret_permissions[ permission.library_dataset_id ].append( permission )
+
+        # Test that we get the same response from get_item_actions each item:
+        test_code = False 
+        if test_code:
+            try:
+                log.debug( "get_actions_for_items: Test start" )
+                for item in permission_items:
+                    base_result = self.get_item_actions( action, item )
+                    new_result = ret_permissions[ item.library_dataset_id ]
+                    # For now, just test against LibraryDatasetIds; other classes
+                    # are not tested yet.
+                    if len( base_result ) == len( new_result ): 
+                        common_result = set(base_result).intersection( new_result )
+                        if len( common_result ) == len( base_result ):
+                            log.debug( "Match on permissions for id %d" % 
+                                       item.library_dataset_id )
+                        # TODO: Fix this failure message:
+                        else:
+                            log.debug( "Error: dataset %d; originally: %s; now: %s"
+                                     % ( item.library_dataset_id, 
+                                         base_result, new_result ) )
+                    else:
+                        log.debug( "Error: dataset %d: had %d entries, now %d entries"
+                                 % ( item.library_dataset_id, len( base_result ), 
+                                     len( new_result ) ) )
+                log.debug( "get_actions_for_items: Test end" )
+            except Exception as e:
+                log.debug( "Exception in test code: %s" % e )
+
+        return ret_permissions
+
+
+    def allow_action_on_items( self, trans, user_roles, action, items ):
+        """
+        This should be the equivalent of allow_action defined on multiple items.
+        It is meant to specifically replace allow_action for multiple 
+        LibraryDatasets, but it could be reproduced or modified for 
+        allow_action's permitted classes - Dataset, Library, LibraryFolder, and
+        LDDAs.
+        """
+        all_items_actions = self.get_actions_for_items( trans, action, items )
+
+        ret_allow_action = {}
+        # Change item to lib_dataset or vice-versa.
+        for item in items:
+            if all_items_actions.has_key( item.id ):
+                item_actions = all_items_actions[ item.id ] 
+
+                # For access, all of the dataset's 
+                if self.permitted_actions.DATASET_ACCESS == action: 
+                    ret_allow_action[ item.id ] = True
+                    for item_action in item_actions: 
+                        if item_action.role not in user_roles:
+                            ret_allow_action[ item.id ] = False
+                            break
+
+                # Else look for just one dataset role to be in the list of
+                # acceptable user roles:
+                else:
+                    ret_allow_action[ item.id ] = False
+                    for item_action in item_actions:
+                        if item_action.role in user_roles:
+                            ret_allow_action[ item.id ] = True
+                            break
+
+            else:
+                if 'restrict' == action.model:
+                    ret_allow_action[ item.id ] = True
+                else:
+                    ret_allow_action[ item.id ] = False
+
+        # Test it: the result for each dataset should match the result for
+        # allow_action:
+        test_code = False 
+        if test_code:
+            log.debug( "allow_action_for_items: test start" )
+            for item in items:
+                orig_value = self.allow_action( user_roles, action, item )
+                if orig_value == ret_allow_action[ item.id ]:
+                    log.debug( "Item %d: success" % item.id )
+                else:
+                    log.debug( "Item %d: fail: original: %s; new: %s"
+                             % ( item.id, orig_value, ret_allow_action[ item.id ] ) )
+            log.debug( "allow_action_for_items: test end" )
+        return ret_allow_action
+
+
+    def get_dataset_access_mapping( self, trans, user_roles, datasets ):
+        '''
+        For the given list of datasets, return a mapping of the datasets' ids
+        to whether they can be accessed by the user or not. The datasets input
+        is expected to be a simple list of Dataset objects. 
+        '''
+        datasets_public_map = self.datasets_are_public( trans, datasets )
+        datasets_allow_action_map = self.allow_action_on_items( trans, user_roles, self.permitted_actions.DATASET_ACCESS, datasets )
+        can_access = {}
+        for dataset in datasets:
+            can_access[ dataset.id ] = datasets_public_map[ dataset.id ] or datasets_allow_action_map[ dataset.id ]
+        return can_access
+
+    def can_access_dataset( self, user_roles, dataset ):
+        # SM: dataset_is_public will access dataset.actions, which is a 
+        # backref that causes a query to be made to DatasetPermissions 
+        retval = self.dataset_is_public( dataset ) or self.allow_action( user_roles, self.permitted_actions.DATASET_ACCESS, dataset )
+        return retval
+
     def can_manage_dataset( self, roles, dataset ):
         return self.allow_action( roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset )
     def can_access_library( self, roles, library ):
@@ -317,9 +464,14 @@
         return self.allow_action( roles, self.permitted_actions.LIBRARY_MODIFY, item )
     def can_manage_library_item( self, roles, item ):
         return self.allow_action( roles, self.permitted_actions.LIBRARY_MANAGE, item )
+
     def get_item_actions( self, action, item ):
         # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation
+        # SM: Accessing item.actions emits a query to Library_Dataset_Permissions
+        # if the item is a LibraryDataset:
+        # TODO: Pass in the item's actions - the item isn't needed
         return [ permission for permission in item.actions if permission.action == action.action ]
+
     def guess_derived_permissions_for_datasets( self, datasets=[] ):
         """Returns a dict of { action : [ role, role, ... ] } for the output dataset based upon provided datasets"""
         perms = {}
@@ -667,10 +819,55 @@
             dataset = library_dataset.library_dataset_dataset_association.dataset
             if not dataset.purged and not self.dataset_is_public( dataset ):
                 self.make_dataset_public( dataset )
+
     def dataset_is_public( self, dataset ):
         # A dataset is considered public if there are no "access" actions associated with it.  Any
         # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant.
+        # SM: Accessing dataset.actions will cause a query to be emitted.
         return self.permitted_actions.DATASET_ACCESS.action not in [ a.action for a in dataset.actions ]
+
+    def datasets_are_public( self, trans, datasets ):
+        '''
+        Given a transaction object and a list of Datasets, return
+        a mapping from Dataset ids to whether the Dataset is public 
+        or not. All Dataset ids should be returned in the mapping's keys.
+        '''
+        # We go the other way around from dataset_is_public: we start with 
+        # all datasets being marked as public. If there is an access action 
+        # associated with the dataset, then we mark it as nonpublic:
+        datasets_public = {}
+        dataset_ids = [ dataset.id for dataset in datasets ]
+        for dataset_id in dataset_ids:
+            datasets_public[ dataset_id ] = True
+
+        # Now get all datasets which have DATASET_ACCESS actions:
+        access_data_perms = trans.sa_session.query( trans.app.model.DatasetPermissions ) \
+                                 .filter( and_( trans.app.model.DatasetPermissions.dataset_id in dataset_ids,
+                                                trans.app.model.DatasetPermissions.action == self.permitted_actions.DATASET_ACCESS.action ) ) \
+                                 .all()
+
+        # Every dataset returned has "access" privileges associated with it,
+        # so it's not public.
+        for permission in access_data_perms:
+            datasets_public[ permission.dataset_id ] = False 
+
+        # Test code: Check if the results match up with the original:
+        test_code = False 
+        if test_code:
+            log.debug( "datasets_are_public test: check datasets_are_public matches dataset_is_public:" )
+            test_success = True
+            for dataset in datasets:
+                orig_is_public = self.dataset_is_public( dataset )
+                if orig_is_public == datasets_public[ dataset.id ]:
+                    log.debug( "\tMatch for dataset %d" % dataset.id )
+                else:
+                    success = False
+                    log.error( "\tERROR: Did not match: single is_public: %s; multiple is_public: %s" 
+                             % ( single_is_public, datasets_public[ dataset.id ] ) )
+            log.debug( "datasets_are_public: test succeeded? %s" % test_success )
+        return datasets_public
+
+
     def make_dataset_public( self, dataset ):
         # A dataset is considered public if there are no "access" actions associated with it.  Any
         # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant.
@@ -707,7 +904,7 @@
                     # Ensure that roles being associated with DATASET_ACCESS are a subset of the legitimate roles
                     # derived from the roles associated with the access permission on item if it's not public.  This
                     # will keep ill-legitimate roles from being associated with the DATASET_ACCESS permission on the
-                    # dataset (i.e., in the case where item is a library, if Role1 is associated with LIBRARY_ACCESS,
+                    # dataset (i.e., in the case where item is .a library, if Role1 is associated with LIBRARY_ACCESS,
                     # then only those users that have Role1 should be associated with DATASET_ACCESS.
                     legitimate_roles = self.get_legitimate_roles( trans, item, cntrller )
                     ill_legitimate_roles = []
@@ -944,12 +1141,21 @@
         if self.can_add_library_item( roles, folder ):
             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 )
             if not ldda_access_permissions:


diff -r 4f788268c76dcb77e99076dbfbc8cf65c05b00cc -r a995f7aca75c03bd180689aead6a8870928d8fdf lib/galaxy/web/controllers/library_common.py
--- a/lib/galaxy/web/controllers/library_common.py
+++ b/lib/galaxy/web/controllers/library_common.py
@@ -92,6 +92,65 @@
                         #"force_history_refresh": force_history_refresh
                     }
         return rval
+
+    def display_folder_hierarchy( self, trans_in, cntrller_in, use_panels_in, library_in, created_ldda_ids_in, hidden_folder_ids_in, show_deleted_in, comptypes_in, current_user_roles_in, message_in, status ):
+        log.debug( "display_folder_hierarchy: enter" )
+        # SM: Determine if this is an admin user (trans.user_is_admin and cntrller
+        # is library_admin). If so, then the user gets add, modify, manage permissions.
+        # Otherwise, if this is the library/requests controller then lookup those 
+        # three permissions. Otherwise, it's all not true.
+        #
+        # Now get the library's info_assocation (?). TODO: Look into this.
+        # Determine if there are accessible folders:
+        #   1. Is the root folder accessible to this user?
+        #   2. IS the root folder accessible to this user (without looking downward)?
+        #   3. Is this guy an admin OR is the root folder accessible to this user?
+        #   Evidently roles are used each time.
+        # 
+        # Then show management buttons and links, and then call render_folders
+
+        # render_folder:
+        # Repeat determining if this is an admin user: 
+        #     is_admin = trans.user_is_admin() and cntrller == 'library_admin'
+        # Turn the list of created lddas into a list - split by comma, turn one 
+        # element into its own list, and leave lists alone. 
+        # (Christ) If this is an admin user, then all permissions are granted.
+        # O.w., if this is the library controller,
+        # determine the folder ids along with whether the folders can be 
+        # shown, and determine the other three admin permissions.
+        # O.w., no modifications are allowed - it's view-only.
+        # Get the form type and (sigh) again get the folder's info_association (?)
+        # Display information about the folder.
+        # Get the list of deleted (if shown) and non-deleted datasets and subfolders.
+        # Call render_folder for every subfolder
+        # For every library dataset, determine the ldda. If there is an ldda, then
+        # determine if the ldda's dataset can be displayed. 
+
+        # TODO: Move this to a security function/method later.
+        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_in, library )
+            can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles_in, library )
+            can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles_in, library )
+        else:
+            can_add = can_modify = can_manage = False
+
+        info_association, inherited = library_in.get_info_association()
+        log.debug( "type(info_association): %s" % type(info_association) )
+        log.debug( "type(inherited): %s" % type(inherited) )
+        
+        # SM: determine if folders are accessible underneath here:
+        has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles_in ) 
+        if has_accessible_folders and cntrller in ['library', 'requests']:
+            self.display_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted = show_deleted, parent=None, root_folder=True, simple=simple )
+        elif ( trans_in.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ):
+            # SM: TODO: Start here.
+            pass
+        pass
+
     @web.expose
     def browse_library( self, trans, cntrller, **kwd ):
         params = util.Params( kwd )
@@ -128,22 +187,36 @@
                 message += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset."
                 status = "info"
             comptypes = get_comptypes( trans )
-            try:
-                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'
+            # SM: Retrieve the entire hierarchy and pass it to the template to fill in.
+            # We'll eliminate the mako from retrieving stuff for now.
+            # SM: TODO: Add configuration item
+            # if trans.app.config.optimize_folders:
+            if False:
+                hierarchy = self.display_folder_hierarchy( trans, cntrller, use_panels, library,
+                                                      created_ldda_ids, hidden_folder_ids,
+                                                      show_deleted, comptypes,
+                                                      current_user_roles, message,
+                                                      status )
+
+            else:
+                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 )
+                except Exception, e:
+                    message = 'Error attempting to display contents of library (%s): %s.' % ( str( library.name ), str( e ) )
+                    status = 'error'
         default_action = params.get( 'default_action', None )
+
         return trans.response.send_redirect( web.url_for( use_panels=use_panels,
                                                           controller=cntrller,
                                                           action='browse_libraries',
@@ -2534,16 +2607,57 @@
                            .options( eagerload_all( "actions" ) ) \
                            .order_by( trans.app.model.LibraryFolder.table.c.name ) \
                            .all()
+
+def map_library_datasets_to_lddas( trans, lib_datasets ):
+    '''
+    Given a list of LibraryDatasets, return a map from the LibraryDatasets
+    to their LDDAs. If an LDDA does not exist for a LibraryDataset, then
+    there will be no entry in the return hash.
+    '''
+    # Get a list of the LibraryDatasets' ids so that we can pass it along to
+    # a query to retrieve the LDDAs. This eliminates querying for each 
+    # LibraryDataset.
+    lib_dataset_ids = [ x.library_dataset_dataset_association_id for x in lib_datasets ]
+    lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
+                            .filter( trans.app.model.LibraryDatasetDatasetAssociation.id.in_( lib_dataset_ids ) ) \
+                            .all()
+    
+    # Map the LibraryDataset to the returned LDDAs:
+    ret_lddas = {}
+    for ldda in lddas:
+        ret_lddas[ldda.library_dataset_id] = ldda
+    return ret_lddas
+
+def datasets_for_lddas( trans, lddas ):
+    '''
+    Given a list of LDDAs, return a list of Datasets for them. 
+    '''
+    dataset_ids = [ x.dataset_id for x in lddas ]
+    datasets = trans.sa_session.query( trans.app.model.Dataset ) \
+                               .filter( trans.app.model.Dataset.id.in_( dataset_ids ) ) \
+                               .all()
+    return datasets 
+
 def active_folders_and_library_datasets( trans, folder ):
+    # SM: TODO: Eliminate timing code
+    from datetime import datetime, timedelta
+    query_start = datetime.now()
     folders = active_folders( trans, folder )
     library_datasets = trans.sa_session.query( trans.model.LibraryDataset ) \
                                        .filter( and_( trans.model.LibraryDataset.table.c.deleted == False,
                                                       trans.model.LibraryDataset.table.c.folder_id == folder.id ) ) \
                                        .order_by( trans.model.LibraryDataset.table.c._name ) \
                                        .all()
+    query_end = datetime.now()
+    query_delta = query_end - query_start
+    #log.debug( "active_folders_and_library_datasets: %d.%.6d" % 
+    #           ( query_delta.seconds, query_delta.microseconds ) )
     return folders, library_datasets
+
 def activatable_folders_and_library_datasets( trans, folder ):
     folders = activatable_folders( trans, folder )
+    from datetime import datetime, timedelta
+    query_start = datetime.now()
     library_datasets = trans.sa_session.query( trans.model.LibraryDataset ) \
                                        .filter( trans.model.LibraryDataset.table.c.folder_id == folder.id ) \
                                        .join( ( trans.model.LibraryDatasetDatasetAssociation.table,
@@ -2553,6 +2667,10 @@
                                        .filter( trans.model.Dataset.table.c.deleted == False ) \
                                        .order_by( trans.model.LibraryDataset.table.c._name ) \
                                        .all()
+    query_end = datetime.now()
+    query_delta = query_end - query_start
+    log.debug( "activatable_folders_and_library_datasets: %d.%.6d" % 
+               ( query_delta.seconds, query_delta.microseconds ) )
     return folders, library_datasets
 def branch_deleted( folder ):
     # Return True if a folder belongs to a branch that has been deleted


diff -r 4f788268c76dcb77e99076dbfbc8cf65c05b00cc -r a995f7aca75c03bd180689aead6a8870928d8fdf templates/library/common/browse_library_opt.mako
--- /dev/null
+++ b/templates/library/common/browse_library_opt.mako
@@ -0,0 +1,630 @@
+<%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, 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.web.controllers.library_common import branch_deleted
+        # SM: DELETEME
+        import logging
+        log = logging.getLogger( __name__ )
+        
+        is_admin = trans.user_is_admin() and cntrller == 'library_admin'
+        
+        if ldda == library_dataset.library_dataset_dataset_association:
+            current_version = True
+            if is_admin:
+                can_modify = can_manage = True
+            elif cntrller in [ 'library', 'requests' ]:
+                #log.debug( "SM: Query 4: backref to Library_Dataset_Permissions" )
+                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
+        #log.debug( "SM: Query 5 call: LibraryDatasetDatasetInfoAssocation" )
+        info_association, inherited = ldda.get_info_association( restrict=True )
+        # SM: The form type is for displaying URLs only; ignore for now.
+        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.web.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.get_dataset_access_mapping( trans, current_user_roles, dataset_list )
+            for library_dataset in library_datasets:
+                ldda = lib_dataset_ldda_map[ library_dataset.id ]
+                if ldda: 
+                    can_access = is_admin or can_access_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, 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.web.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: First cut of query optimizations for browsing. At least 3 out of 5 queries were eliminated. Code is not active by default.

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