[galaxy-dev] [hg] galaxy 2415: Bug fixes and new functional tests for library...

26 May 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/386e245f8076
changeset: 2415:386e245f8076
user:      Greg Von Kuster <greg@bx.psu.edu>
date:      Thu May 21 15:48:39 2009 -0400
description:
Bug fixes and new functional tests for library features that were missing them.

17 file(s) affected in this change:

lib/galaxy/model/__init__.py
lib/galaxy/web/controllers/admin.py
lib/galaxy/web/controllers/library.py
templates/admin/library/browse_library.mako
templates/admin/library/common.mako
templates/admin/library/edit_info_template.mako
templates/admin/library/folder_info.mako
templates/admin/library/ldda_edit_info.mako
templates/admin/library/new_info_template.mako
templates/library/browse_library.mako
templates/library/common.mako
templates/library/edit_info_template.mako
templates/library/ldda_edit_info.mako
templates/library/library_dataset_info.mako
templates/library/new_info_template.mako
test/base/twilltestcase.py
test/functional/test_security_and_libraries.py

diffs (2528 lines):

diff -r 1a82088aac38 -r 386e245f8076 lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py	Thu May 21 11:32:25 2009 -0400
+++ b/lib/galaxy/model/__init__.py	Thu May 21 15:48:39 2009 -0400
@@ -300,6 +300,9 @@
 
 class LibraryItemInfoPermissions( object ):
     def __init__( self, action, library_item, role ):
+        # LIBRARY_ADD -> Not Applicable
+        # LIBRARY_MODIFY -> Can modify LibraryItemInfoElement.contents
+        # LIBRARY_MANAGE -> Can change permissions on LibraryItemInfo
         self.action = action
         if isinstance( library_item, LibraryItemInfo ):
             self.library_item_info = library_item
@@ -309,6 +312,9 @@
 
 class LibraryItemInfoTemplatePermissions( object ):
     def __init__( self, action, library_item, role ):
+        # LIBRARY_ADD -> Not Applicable
+        # LIBRARY_MODIFY -> Can add or delete LibraryItemInfoTemplateElements
+        # LIBRARY_MANAGE -> Can change permissions on LibraryItemInfoTemplate
         self.action = action
         if isinstance( library_item, LibraryItemInfoTemplate ):
             self.library_item_info_template = library_item
@@ -673,7 +679,9 @@
         self.description = description
         self.root_folder = root_folder
     def get_library_item_info_templates( self, template_list=[], restrict=False ):
-        if self.library_info_template_associations:
+        # We only want the next available template in the inheritable hierarchy, so we'll only extend
+        # template_list if it is empty
+        if not template_list and self.library_info_template_associations:
             template_list.extend( [ lita.library_item_info_template for lita in self.library_info_template_associations if lita.library_item_info_template not in template_list ] )
         return template_list
 
@@ -696,11 +704,13 @@
         self.item_count += 1
     def get_library_item_info_templates( self, template_list=[], restrict=False ):
         # If restrict is True, we'll return only those templates directly associated with this Folder
-        if self.library_folder_info_template_associations:
+        # We only want the next available template in the inheritable hierarchy, so we'll only extend
+        # template_list if it is empty
+        if not template_list and self.library_folder_info_template_associations:
             template_list.extend( [ lfita.library_item_info_template for lfita in self.library_folder_info_template_associations if lfita.library_item_info_template not in template_list ] )
-        if restrict not in [ 'True', True ] and self.parent:
+        if not template_list and restrict not in [ 'True', True ] and self.parent:
             self.parent.get_library_item_info_templates( template_list )
-        elif restrict not in [ 'True', True, 'folder' ] and self.library_root:
+        elif not template_list and restrict not in [ 'True', True, 'folder' ] and self.library_root:
             for library_root in self.library_root:
                 library_root.get_library_item_info_templates( template_list )
         return template_list
@@ -759,9 +769,11 @@
     purged = property( get_purged, set_purged )
     def get_library_item_info_templates( self, template_list=[], restrict=False ):
         # If restrict is True, we'll return only those templates directly associated with this LibraryDataset
-        if self.library_dataset_info_template_associations:
+        # We only want the next available template in the inheritable hierarchy, so we'll only extend
+        # template_list if it is empty
+        if not template_list and self.library_dataset_info_template_associations:
             template_list.extend( [ ldita.library_item_info_template for ldita in self.library_dataset_info_template_associations if ldita.library_item_info_template not in template_list ] )
-        if restrict not in [ 'True', True ]:
+        if not template_list and restrict not in [ 'True', True ]:
             self.folder.get_library_item_info_templates( template_list, restrict )
         return template_list
 
@@ -828,9 +840,12 @@
         return
     def get_library_item_info_templates( self, template_list=[], restrict=False ):
         # If restrict is True, we'll return only those templates directly associated with this LibraryDatasetDatasetAssociation
-        if self.library_dataset_dataset_info_template_associations:
+        # We only want the next available template in the inheritable hierarchy, so we'll only extend
+        # template_list if it is empty
+        if not template_list and self.library_dataset_dataset_info_template_associations:
             template_list.extend( [ lddita.library_item_info_template for lddita in self.library_dataset_dataset_info_template_associations if lddita.library_item_info_template not in template_list ] )
-        self.library_dataset.get_library_item_info_templates( template_list, restrict )
+        if not template_list:
+            self.library_dataset.get_library_item_info_templates( template_list, restrict )
         return template_list
 
 class LibraryInfoTemplateAssociation( object ):
@@ -902,11 +917,22 @@
 class LibraryItemInfo( object ):
     def __init__( self, user=None ):
         self.user = user
-    def get_element_by_template_element( self, template_element ):
+    def get_element_by_template_element( self, template_element, create_element=False ):
         for element in self.elements:
             if element.library_item_info_template_element == template_element:
                 return element
-        raise 'element not found'
+        if create_element:
+            # Template elements may have been added to the template after the 
+            # library item initially inherited it, so we'll add the additional
+            # element to the library item
+            element = LibraryItemInfoElement()
+            element.library_item_info_template_element = template_element
+            element.library_item_info = self
+            element.flush()
+            self.elements.append( element )
+            return element
+        else:
+            return None
 
 class LibraryItemInfoElement( object ):
     pass
diff -r 1a82088aac38 -r 386e245f8076 lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py	Thu May 21 11:32:25 2009 -0400
+++ b/lib/galaxy/web/controllers/admin.py	Thu May 21 15:48:39 2009 -0400
@@ -848,32 +848,6 @@
                                     show_deleted=True )
     @web.expose
     @web.require_admin
-    def undelete_library( self, trans, **kwd ):
-        params = util.Params( kwd )
-        library = trans.app.model.Library.get( int( params.id ) )
-        def undelete_folder( library_folder ):
-            for folder in library_folder.folders:
-                folder.refresh()
-                undelete_folder( folder )
-            library_folder.refresh()
-            for library_dataset in library_folder.datasets:
-                library_dataset.refresh()
-                ldda = library_dataset.library_dataset_dataset_association
-                if ldda:
-                    ldda.refresh()
-                    ldda.deleted = False
-                    ldda.flush()
-                library_dataset.deleted = False
-                library_dataset.flush()
-            library_folder.deleted = False
-            library_folder.flush()
-        undelete_folder( library.root_folder )
-        library.deleted = False
-        library.flush()
-        msg = "Library '%s' and all of its contents have been marked not deleted" % library.name
-        return trans.response.send_redirect( web.url_for( action='browse_libraries', msg=util.sanitize_text( msg ), messagetype='done' ) )
-    @web.expose
-    @web.require_admin
     def purge_library( self, trans, **kwd ):
         params = util.Params( kwd )
         library = trans.app.model.Library.get( int( params.id ) )
@@ -1104,7 +1078,7 @@
             last_used_build = folder.genome_build
         replace_id = params.get( 'replace_id', None )
         if replace_id:
-            replace_dataset = trans.app.model.LibraryDataset.get( params.get( 'replace_id', None ) )
+            replace_dataset = trans.app.model.LibraryDataset.get( int( replace_id ) )
             if not last_used_build:
                 last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
         else:
@@ -1197,6 +1171,8 @@
                     permissions = {}
                     accessible = False
                     for k, v in trans.app.model.Dataset.permitted_actions.items():
+                        # TODO: need to handle case where a user has the DATASET_MANAGE_PERMISSIONS permission, but not
+                        # the DATASET_ACCESS permission, making the former useless.  Need to display a warning message.
                         in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
                         # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible
                         if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
@@ -1381,6 +1357,8 @@
                     permissions = {}
                     accessible = False
                     for k, v in trans.app.model.Dataset.permitted_actions.items():
+                        # TODO: need to handle case where a user has the DATASET_MANAGE_PERMISSIONS permission, but not
+                        # the DATASET_ACCESS permission, making the former useless.  Need to display a warning message.
                         in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
                         # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible
                         if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
@@ -1567,7 +1545,7 @@
                                             messagetype=messagetype )
     @web.expose
     @web.require_admin
-    def info_template( self, trans, library_id, id=None, num_fields=0, folder_id=None, ldda_id=None, library_dataset_id=None, **kwd ):        
+    def info_template( self, trans, library_id, id=None, num_fields=0, folder_id=None, ldda_id=None, library_dataset_id=None, **kwd ): 
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
@@ -1646,7 +1624,7 @@
                 liit.description = util.restore_text( params.get( 'description', '' ) )
                 liit.flush()
                 # Inherit the template's permissions from the library_item
-                trans.app.security_agent.copy_library_permissions( liit, library_item )
+                trans.app.security_agent.copy_library_permissions( library_item, liit )
                 # Create template association
                 if folder_id:
                     liit_assoc = trans.app.model.LibraryFolderInfoTemplateAssociation()
@@ -1694,7 +1672,13 @@
                                         msg=msg,
                                         messagetype=messagetype )
         elif action == 'edit_template':
-            if params.get( 'edit_info_template_button', False ):
+            define_or_save = 'define'
+            edit_info_template_button = params.get( 'edit_info_template_button', False )
+            if edit_info_template_button:
+                if edit_info_template_button == 'Define fields':
+                    define_or_save = 'save'
+                else:
+                    define_or_save = 'define'
                 # Save changes to existing attributes, only set name if nonempty/nonNone is passed, but always set description
                 name = params.get( 'name', None )
                 if name:
@@ -1702,7 +1686,7 @@
                 library_item.description = params.get( 'description', '' )
                 library_item.flush()
                 # Save changes to exisiting elements
-                for elem_id in params.get( 'element_ids', [] ):
+                for elem_id in util.listify( params.get( 'element_ids', [] ) ):
                     liit_element = trans.app.model.LibraryItemInfoTemplateElement.get( elem_id )
                     name = params.get( 'element_name_%s' % elem_id, None )
                     if name:
@@ -1721,7 +1705,7 @@
                     if elem_name:
                         library_item.add_element( name=elem_name, description=elem_description )
                 library_item.refresh()
-                msg = 'Information template %s has been updated' % library_item.name
+                msg = "Information template '%s' has been updated" % library_item.name
             return trans.fill_template( "/admin/library/edit_info_template.mako",
                                         liit=library_item,
                                         num_fields=num_fields,
@@ -1731,6 +1715,7 @@
                                         folder_id=folder_id,
                                         library_item_name=library_item.name,
                                         library_item_desc=library_item_desc,
+                                        define_or_save=define_or_save,
                                         msg=msg,
                                         messagetype=messagetype )
         elif action == 'permissions':
@@ -1771,6 +1756,8 @@
             library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id )
             # This response_action method requires a folder_id
             folder_id = library_item.library_dataset.folder.id
+        elif library_item_type == 'library_item_info_elememt':
+            library_item = trans.app.model.LibraryItemInfoElement.get( library_item_id )
         else:
             msg = "Invalid library item type ( %s ) specified, id ( %s )" % ( str( library_item_type ), str( library_item_id ) )
             return trans.response.send_redirect( web.url_for( controller='admin',
@@ -1869,6 +1856,7 @@
                                                                   action='library_item_info',
                                                                   library_id=library_id,
                                                                   id=id,
+                                                                  library_item_id=library_item_id,
                                                                   library_item_type=library_item_type,
                                                                   permissions=True,
                                                                   msg=util.sanitize_text( msg ),
@@ -1977,10 +1965,14 @@
             msg = 'Bad library_item_type specified: %s' % str( library_item_type )
             messagetype = 'error'
         else:
+            if library_item_type == 'library_dataset':
+                library_item_desc = 'Dataset'
+            else:
+                library_item_desc = library_item_type.capitalize()
             library_item = library_item_types[ library_item_type ].get( int( library_item_id ) )
             library_item.deleted = True
             library_item.flush()
-            msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( library_item_type, library_item.name ) )
+            msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( library_item_desc, library_item.name ) )
             messagetype = 'done'
         if library_item_type == 'library':
             return self.browse_libraries( trans, msg=msg, messagetype=messagetype )
@@ -1997,14 +1989,18 @@
             msg = 'Bad library_item_type specified: %s' % str( library_item_type )
             messagetype = 'error'
         else:
+            if library_item_type == 'library_dataset':
+                library_item_desc = 'Dataset'
+            else:
+                library_item_desc = library_item_type.capitalize()
             library_item = library_item_types[ library_item_type ].get( int( library_item_id ) )
             if library_item.purged:
-                msg = '%s %s has been purged, so it cannot be undeleted' % ( library_item_type, library_item.name )
+                msg = '%s %s has been purged, so it cannot be undeleted' % ( library_item_desc, library_item.name )
                 messagetype = 'error'
             else:
                 library_item.deleted = False
                 library_item.flush()
-                msg = util.sanitize_text( "%s '%s' has been marked undeleted" % ( library_item_type, library_item.name ) )
+                msg = util.sanitize_text( "%s '%s' has been marked undeleted" % ( library_item_desc, library_item.name ) )
                 messagetype = 'done'
         if library_item_type == 'library':
             return self.browse_libraries( trans, msg=msg, messagetype=messagetype )
diff -r 1a82088aac38 -r 386e245f8076 lib/galaxy/web/controllers/library.py
--- a/lib/galaxy/web/controllers/library.py	Thu May 21 11:32:25 2009 -0400
+++ b/lib/galaxy/web/controllers/library.py	Thu May 21 15:48:39 2009 -0400
@@ -1169,7 +1169,13 @@
                                         msg=msg,
                                         messagetype=messagetype )
         elif action == 'edit_template':
-            if params.get( 'edit_info_template_button', False ):
+            define_or_save = 'define'
+            edit_info_template_button = params.get( 'edit_info_template_button', False )
+            if edit_info_template_button:
+                if edit_info_template_button == 'Define fields':
+                    define_or_save = 'save'
+                else:
+                    define_or_save = 'define'
                 # Save changes to existing attributes, only set name if nonempty/nonNone is passed, but always set description
                 name = params.get( 'name', None )
                 if name:
@@ -1177,7 +1183,7 @@
                 library_item.description = params.get( 'description', '' )
                 library_item.flush()
                 # Save changes to exisiting elements
-                for elem_id in params.get( 'element_ids', [] ):
+                for elem_id in util.listify( params.get( 'element_ids', [] ) ):
                     liit_element = trans.app.model.LibraryItemInfoTemplateElement.get( elem_id )
                     name = params.get( 'element_name_%s' % elem_id, None )
                     if name:
@@ -1206,6 +1212,7 @@
                                         folder_id=folder_id,
                                         library_item_name=library_item.name,
                                         library_item_desc=library_item_desc,
+                                        define_or_save=define_or_save,
                                         msg=msg,
                                         messagetype=messagetype )
         elif action == 'permissions':
@@ -1246,6 +1253,8 @@
             library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id )
             # This response_action method requires a folder_id
             folder_id = library_item.library_dataset.folder.id
+        elif library_item_type == 'library_item_info_elememt':
+            library_item = trans.app.model.LibraryItemInfoElement.get( library_item_id )
         else:
             msg = "Invalid library item type ( %s ) specified, id ( %s )" % ( str( library_item_type ), str( library_item_id ) )
             return trans.response.send_redirect( web.url_for( controller='library',
@@ -1339,17 +1348,18 @@
                 trans.app.security_agent.set_all_library_permissions( library_item.library_item_info, permissions )
                 library_item.library_item_info.refresh()
                 library_item.refresh()
-                msg = "Permissions updated for field '%s'" % library_item.name
+                msg = "Permissions updated for field '%s'" % library_item.library_item_info_template_element.name
                 return trans.response.send_redirect( web.url_for( controller='library',
                                                                   action='library_item_info',
                                                                   library_id=library_id,
                                                                   id=id,
+                                                                  library_item_id=library_item_id,
                                                                   library_item_type=library_item_type,
                                                                   permissions=True,
                                                                   msg=util.sanitize_text( msg ),
                                                                   messagetype='done' ) )
             return trans.fill_template( '/library/info_permissions.mako',
-                                        library_item_info_element=library_item_info_element,
+                                        library_item_info_element=library_item,
                                         library_id=library_id,
                                         msg=msg,
                                         messagetype=messagetype )
diff -r 1a82088aac38 -r 386e245f8076 templates/admin/library/browse_library.mako
--- a/templates/admin/library/browse_library.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/admin/library/browse_library.mako	Thu May 21 15:48:39 2009 -0400
@@ -115,7 +115,8 @@
                     %if folder.library_folder_info_template_associations:
                         <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %>
                         <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, id=template.id, edit_template=True )}">Edit this folder's information template</a>
-                    %else:
+                    %elif not folder.library_folder_info_associations:
+                        ## Only allow adding a new template to the folder if a previously inherited template has not already been used
                         <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a>
                     %endif
                     <a class="action-button" href="${h.url_for( controller='admin', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a>
diff -r 1a82088aac38 -r 386e245f8076 templates/admin/library/common.mako
--- a/templates/admin/library/common.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/admin/library/common.mako	Thu May 21 15:48:39 2009 -0400
@@ -84,11 +84,10 @@
         elif isinstance( library_item, trans.app.model.LibraryDatasetDatasetAssociation ):
             library_item_type = 'library_dataset_dataset_association'
             library_item_desc = 'library dataset'
-            library_item_info_associations = library_item.library_dataset_dataset_info_associations
-        elif isinstance( library_item, trans.app.model.LibraryItemInfoElement ):
-            library_item_type = 'library_item_info'
-            library_item_desc = 'information'
-            library_item_info_associations = None
+            if library_item.library_dataset_dataset_info_associations:
+                library_item_info_associations = library_item.library_dataset_dataset_info_associations
+            elif library_item.library_dataset_dataset_info_template_associations:
+                library_item_info_associations = library_item.library_dataset_dataset_info_template_associations
     %>
     %if library_item_info_associations:
         <p/>
@@ -100,17 +99,18 @@
                     <input type="hidden" name="library_item_type" value="${library_item_type}"/>
                     %for library_item_info_association in library_item_info_associations:
                         %for template_element in library_item_info_association.library_item_info.library_item_info_template.elements:
-                            <% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element ) %>
+                            <% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element, create_element=True ) %>
                             <input type="hidden" name="id" value="${element.id}"/>
                             <div class="form-row">
-                                <label>
-                                    ${template_element.name}:
-                                    <a id="element-${element.id}-popup" class="popup-arrow" style="display: none;">▼</a>
-                                    <div popupmenu="element-${element.id}-popup">
-                                        <a class="action-button" href="${h.url_for( controller='admin', action='library_item_info', library_id=library_id, id=element.id, library_item_type='library_item_info_elememt', permissions=True )}">Edit this information's permissions</a>
-                                    </div>
-                                </label>
-                                <textarea name="info_element_${element.id}" rows="3" cols="35">${element.contents}</textarea>
+                                <label>${template_element.name}:</label>
+                                %if element.contents:
+                                    <textarea name="info_element_${element.id}" rows="3" cols="35">${element.contents}</textarea>
+                                %else:
+                                    <textarea name="info_element_${element.id}" rows="3" cols="35"></textarea>
+                                %endif
+                                <div class="toolParamHelp" style="clear: both;">
+                                    ${template_element.description}
+                                </div>
                                 <div style="clear: both"></div>
                             </div>
                         %endfor
@@ -145,11 +145,10 @@
         elif isinstance( library_item, trans.app.model.LibraryDatasetDatasetAssociation ):
             library_item_type = 'library_dataset_dataset_association'
             library_item_desc = 'library dataset'
-            library_item_info_associations = library_item.library_dataset_dataset_info_associations
-        elif isinstance( library_item, trans.app.model.LibraryItemInfoElement ):
-            library_item_type = 'library_item_info'
-            library_item_desc = 'information'
-            library_item_info_associations = None
+            if library_item.library_dataset_dataset_info_associations:
+                library_item_info_associations = library_item.library_dataset_dataset_info_associations
+            elif library_item.library_dataset_dataset_info_template_associations:
+                library_item_info_associations = library_item.library_dataset_dataset_info_template_associations
     %>
     %if library_item_info_associations:
         <p/>
@@ -158,11 +157,16 @@
             <div class="toolFormBody">
                 %for library_item_info_association in library_item_info_associations:
                     %for template_element in library_item_info_association.library_item_info.library_item_info_template.elements:
-                        <% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element ) %>
+                        <% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element, create_element=True ) %>
                         <div class="form-row">
                             <label>${template_element.name}:</label>
-                            <div style="float: left; width: 250px; margin-right: 10px;">
-                                ${element.contents}
+                            %if element.contents:
+                                <div style="float: left; width: 250px; margin-right: 10px;">
+                                    ${element.contents}
+                                </div>
+                            %endif
+                            <div class="toolParamHelp" style="clear: both;">
+                                ${template_element.description}
                             </div>
                             <div style="clear: both"></div>
                         </div>
diff -r 1a82088aac38 -r 386e245f8076 templates/admin/library/edit_info_template.mako
--- a/templates/admin/library/edit_info_template.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/admin/library/edit_info_template.mako	Thu May 21 15:48:39 2009 -0400
@@ -24,12 +24,12 @@
             <input type="hidden" name="id" value="${liit.id}"/>
             <input type="hidden" name="set_num_fields" value="${num_fields}"/>
             <div class="form-row">
-                <b>Template name:</b>
+                <label>Template name:</label>
                 <input type="text" name="name" value="${liit.name}" size="40"/>
                 <div style="clear: both"></div>
             </div>
             <div class="form-row">
-                <b>Template description (optional):</b>
+                <label>Template description (optional):</label>
                 <input type="text" name="description" value="${liit.description}" size="40"/>
                 <div style="clear: both"></div>
             </div>
@@ -39,9 +39,9 @@
             %for template_element in liit.elements:
                 <input type="hidden" name="element_ids" value="${template_element.id}"/>
                 <div class="form-row">
-                    <b>Field label:</b>
+                    <label>Field label:</label>
                     <input type="text" name="element_name_${template_element.id}" value="${template_element.name}" size="40"/>
-                    <b>Field help text (optional):</b>
+                    <label>Field help text (optional):</label>
                     <input type="text" name="element_description_${template_element.id}" value="${template_element.description}" size="40"/>
                     <div style="clear: both"></div>
                 </div>
@@ -50,22 +50,26 @@
                 <div class="form-row">
                     <div class="toolFormTitle">Additional field ${1+element_count}</div>
                     <div class="form-row">
-                        <b>Field label:</b>
+                        <label>Field label:</label>
                         <input type="text" name="new_element_name_${element_count}" value="" size="40"/>
-                        <b>Field help text (optional):</b>
+                        <label>Field help text (optional):</label>
                         <input type="text" name="new_element_description_${element_count}" value="" size="40"/>
                         <div style="clear: both"></div>
                     </div>
                 </div>
             %endfor
-            <div class="form-row">
-                <label>Add additional fields:</label>
-                <div style="float: left; width: 250px; margin-right: 10px;">
-                    <input type="text" name="num_fields" value="0" size="3"/>
+            %if define_or_save == 'define':
+                <div class="form-row">
+                    <label>Add additional fields:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <input type="text" name="num_fields" value="0" size="3"/>
+                    </div>
+                    <div style="clear: both"></div>
                 </div>
-                <div style="clear: both"></div>
-            </div>
-            <input type="submit" name="edit_info_template_button" value="Save"/>
+                <input type="submit" name="edit_info_template_button" value="Define fields"/>
+            %else:
+                <input type="submit" name="edit_info_template_button" value="Save"/>
+            %endif
         </div>
     </form>
 </div>
diff -r 1a82088aac38 -r 386e245f8076 templates/admin/library/folder_info.mako
--- a/templates/admin/library/folder_info.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/admin/library/folder_info.mako	Thu May 21 15:48:39 2009 -0400
@@ -43,5 +43,6 @@
 %elif folder.library_folder_info_template_associations:
     ${render_available_templates( folder, library_id, restrict=True )}
 %else:
+    ## Look for any inheritable templates
     ${render_available_templates( folder, library_id, restrict=False )}
 %endif
diff -r 1a82088aac38 -r 386e245f8076 templates/admin/library/ldda_edit_info.mako
--- a/templates/admin/library/ldda_edit_info.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/admin/library/ldda_edit_info.mako	Thu May 21 15:48:39 2009 -0400
@@ -56,7 +56,11 @@
             <div class="form-row">
                 <label>Message:</label>
                 <div style="float: left; width: 250px; margin-right: 10px;">
-                    <textarea name="message" rows="3" cols="35">${ldda.message}</textarea>
+                    %if ldda.message:
+                        <textarea name="message" rows="3" cols="35">${ldda.message}</textarea>
+                    %else:
+                        <textarea name="message" rows="3" cols="35"></textarea>
+                    %endif
                 </div>
                 <div class="toolParamHelp" style="clear: both;">
                     This information will be displayed in the library browser
diff -r 1a82088aac38 -r 386e245f8076 templates/admin/library/new_info_template.mako
--- a/templates/admin/library/new_info_template.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/admin/library/new_info_template.mako	Thu May 21 15:48:39 2009 -0400
@@ -54,13 +54,8 @@
         </div>
         <div class="toolFormBody">
             <div class="form-row">
-                <label>Add additional template fields:</label>
-                <div style="float: left; width: 250px; margin-right: 10px;">
-                    <input type="text" name="num_fields" value="0" size="3"/>
-                </div>
-                <div style="clear: both"></div>
+                <input type="submit" name="new_info_template_button" value="Save"/>
             </div>
-            <input type="submit" name="new_info_template_button" value="Save"/>
         </div>
     </form>
 </div>
diff -r 1a82088aac38 -r 386e245f8076 templates/library/browse_library.mako
--- a/templates/library/browse_library.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/library/browse_library.mako	Thu May 21 15:48:39 2009 -0400
@@ -105,26 +105,26 @@
 </script>
 <![endif]>
 
-<%def name="render_folder( parent, parent_pad, created_ldda_ids, library_id )">
+<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id )">
     <%
         def show_folder():
-            if trans.app.security_agent.check_folder_contents( trans.user, parent ) or trans.app.security_agent.show_library_item( trans.user, parent ):
+            if trans.app.security_agent.check_folder_contents( trans.user, folder ) or trans.app.security_agent.show_library_item( trans.user, folder ):
                 return True
             return False
         if not show_folder:
             return ""
-        root_folder = not parent.parent
+        root_folder = not folder.parent
         if root_folder:
-            pad = parent_pad
+            pad = folder_pad
         else:
-            pad = parent_pad + 20
-        if parent_pad == 0:
+            pad = folder_pad + 20
+        if folder_pad == 0:
             expander = "/static/images/silk/resultset_bottom.png"
-            folder = "/static/images/silk/folder_page.png"
+            folder_img = "/static/images/silk/folder_page.png"
             subfolder = False
         else:
             expander = "/static/images/silk/resultset_next.png"
-            folder = "/static/images/silk/folder.png"
+            folder_img = "/static/images/silk/folder.png"
             subfolder = True
         created_ldda_id_list = util.listify( created_ldda_ids )
         if created_ldda_id_list:
@@ -134,34 +134,35 @@
         <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;">
             <input type="checkbox" class="folderCheckbox" style="float: left;"/>
             <div class="rowTitle">
-                <span class="expandLink"><img src="${h.url_for( expander )}" class="expanderIcon"/><img src="${h.url_for( folder )}" class="rowIcon"/>
-                ${parent.name}
-                %if parent.description:
-                    <i>- ${parent.description}</i>
+                <span class="expandLink"><img src="${h.url_for( expander )}" class="expanderIcon"/><img src="${h.url_for( folder_img )}" class="rowIcon"/>
+                ${folder.name}
+                %if folder.description:
+                    <i>- ${folder.description}</i>
                 %endif
-                <a id="folder-${parent.id}-popup" class="popup-arrow" style="display: none;">▼</a>
-                <div popupmenu="folder-${parent.id}-popup">
-                    %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=parent ):
-                        <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=parent.id )}">Add datasets to this folder</a>
-                        <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=parent.id, library_id=library_id )}">Create a new sub-folder in this folder</a>
+                <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a>
+                <div popupmenu="folder_img-${folder.id}-popup">
+                    %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ):
+                        <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a>
+                        <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a>
                     %endif
-                    %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=parent ):
-                        <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=parent.id, library_id=library_id )}">Edit this folder's information</a>
+                    %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ):
+                        <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a>
                     %else:
-                        <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=parent.id, library_id=library_id )}">View this folder's information</a>
+                        <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">View this folder's information</a>
                     %endif
-                    %if parent.library_folder_info_template_associations:
-                        %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=parent ):
-                            <% template = parent.get_library_item_info_templates( template_list=[], restrict=True )[0] %>
+                    %if folder.library_folder_info_template_associations:
+                        %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ):
+                            <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %>
                             <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this folder's information template</a>
                         %endif
-                    %else:
-                        %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=parent ):
-                            <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, folder_id=parent.id, new_template=True )}">Add an information template to this folder</a>
+                    %elif not folder.library_folder_info_associations:
+                        ## Only allow adding a new template to the folder if a previously inherited template has not already been used
+                        %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ):
+                            <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a>
                         %endif
                     %endif
-                    %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=parent ):
-                        <a class="action-button" href="${h.url_for( controller='library', action='folder', permissions=True, id=parent.id, library_id=library_id )}">Edit this folder's permissions</a>
+                    %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=folder ):
+                        <a class="action-button" href="${h.url_for( controller='library', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a>
                     %endif
                 </div>
             </div>
@@ -172,10 +173,10 @@
     %else:
         <ul>
     %endif
-        %for folder in name_sorted( parent.active_folders ):
-            ${render_folder( folder, pad, created_ldda_ids, library_id )}
+        %for child_folder in name_sorted( folder.active_folders ):
+            ${render_folder( child_folder, pad, created_ldda_ids, library_id )}
         %endfor
-        %for library_dataset in name_sorted( parent.active_datasets ):
+        %for library_dataset in name_sorted( folder.active_datasets ):
             <%
                 selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids
             %>
diff -r 1a82088aac38 -r 386e245f8076 templates/library/common.mako
--- a/templates/library/common.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/library/common.mako	Thu May 21 15:48:39 2009 -0400
@@ -80,11 +80,10 @@
         elif isinstance( library_item, trans.app.model.LibraryDatasetDatasetAssociation ):
             library_item_type = 'library_dataset_dataset_association'
             library_item_desc = 'library dataset'
-            library_item_info_associations = library_item.library_dataset_dataset_info_associations
-        elif isinstance( library_item, trans.app.model.LibraryItemInfoElement ):
-            library_item_type = 'library_item_info'
-            library_item_desc = 'information'
-            library_item_info_associations = None
+            if library_item.library_dataset_dataset_info_associations:
+                library_item_info_associations = library_item.library_dataset_dataset_info_associations
+            elif library_item.library_dataset_dataset_info_template_associations:
+                library_item_info_associations = library_item.library_dataset_dataset_info_template_associations
     %>
     %if library_item_info_associations:
         <p/>
@@ -94,44 +93,28 @@
                 <form name="edit_info" action="${h.url_for( controller='library', action='library_item_info', library_id=library_id, edit_info=True )}" method="post">
                     <input type="hidden" name="library_item_id" value="${library_item.id}"/>
                     <input type="hidden" name="library_item_type" value="${library_item_type}"/>
-                    <% render_submit_button = False %>
                     %for library_item_info_association in library_item_info_associations:
                         %for template_element in library_item_info_association.library_item_info.library_item_info_template.elements:
-                            <% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element ) %>
+                            <% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element, create_element=True ) %>
                             <input type="hidden" name="id" value="${element.id}"/>
-                            <%
-                                can_add = trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=element.library_item_info )
-                                can_modify = trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=element.library_item_info )
-                                can_manage = trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=element.library_item_info )
-                            %>
                             <div class="form-row">
-                                %if can_manage:
-                                    <label>
-                                        ${template_element.name}:
-                                        <a id="element-${element.id}-popup" class="popup-arrow" style="display: none;">▼</a>
-                                        <div popupmenu="element-${element.id}-popup">
-                                            <a class="action-button" href="${h.url_for( controller='admin', action='library_item_info', library_id=library_id, id=element.id, library_item_type='library_item_info_elememt', permissions=True )}">Edit this information's permissions</a>
-                                        </div>
-                                    </label>
+                                <label>${template_element.name}:</label>
+                                %if element.contents:
+                                    <textarea name="info_element_${element.id}" rows="3" cols="35">${element.contents}</textarea>
                                 %else:
-                                    <label>${template_element.name}:</label>
+                                    <textarea name="info_element_${element.id}" rows="3" cols="35"></textarea>
                                 %endif
-                                %if can_modify:
-                                    <textarea name="info_element_${element.id}" rows="3" cols="35">${element.contents}</textarea>
-                                    <% render_submit_button = True %>
-                                %else:
-                                    ${element.contents}
-                                %endif
+                                <div class="toolParamHelp" style="clear: both;">
+                                    ${template_element.description}
+                                </div>
                                 <div style="clear: both"></div>
                             </div>
                         %endfor
                         <div style="clear: both"></div>
                     %endfor
-                    %if render_submit_button:
-                        <div class="form-row">
-                            <input type="submit" name="edit_info_button" value="Save"/>
-                        </div>
-                    %endif
+                    <div class="form-row">
+                        <input type="submit" name="edit_info_button" value="Save"/>
+                    </div>
                 </form>
             </div>
         </div>
@@ -158,11 +141,10 @@
         elif isinstance( library_item, trans.app.model.LibraryDatasetDatasetAssociation ):
             library_item_type = 'library_dataset_dataset_association'
             library_item_desc = 'library dataset'
-            library_item_info_associations = library_item.library_dataset_dataset_info_associations
-        elif isinstance( library_item, trans.app.model.LibraryItemInfoElement ):
-            library_item_type = 'library_item_info'
-            library_item_desc = 'information'
-            library_item_info_associations = None
+            if library_item.library_dataset_dataset_info_associations:
+                library_item_info_associations = library_item.library_dataset_dataset_info_associations
+            elif library_item.library_dataset_dataset_info_template_associations:
+                library_item_info_associations = library_item.library_dataset_dataset_info_template_associations
     %>
     %if library_item_info_associations:
         <p/>
@@ -171,11 +153,14 @@
             <div class="toolFormBody">
                 %for library_item_info_association in library_item_info_associations:
                     %for template_element in library_item_info_association.library_item_info.library_item_info_template.elements:
-                        <% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element ) %>
+                        <% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element, create_element=True ) %>
                         <div class="form-row">
                             <label>${template_element.name}:</label>
                             <div style="float: left; width: 250px; margin-right: 10px;">
                                 ${element.contents}
+                            </div>
+                            <div class="toolParamHelp" style="clear: both;">
+                                ${template_element.description}
                             </div>
                             <div style="clear: both"></div>
                         </div>
diff -r 1a82088aac38 -r 386e245f8076 templates/library/edit_info_template.mako
--- a/templates/library/edit_info_template.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/library/edit_info_template.mako	Thu May 21 15:48:39 2009 -0400
@@ -27,12 +27,12 @@
                 <input type="hidden" name="id" value="${liit.id}"/>
                 <input type="hidden" name="set_num_fields" value="${num_fields}"/>
                 <div class="form-row">
-                    <b>Template name:</b>
+                    <label>Template name:</label>
                     <input type="text" name="name" value="${liit.name}" size="40"/>
                     <div style="clear: both"></div>
                 </div>
                 <div class="form-row">
-                    <b>Template description (optional):</b>
+                    <label>Template description (optional):</label>
                     <input type="text" name="description" value="${liit.description}" size="40"/>
                     <div style="clear: both"></div>
                 </div>
@@ -42,9 +42,9 @@
                 %for template_element in liit.elements:
                     <input type="hidden" name="element_ids" value="${template_element.id}"/>
                     <div class="form-row">
-                        <b>Field label:</b>
+                        <label>Field label:</label>
                         <input type="text" name="element_name_${template_element.id}" value="${template_element.name}" size="40"/>
-                        <b>Field help text (optional):</b>
+                        <label>Field help text (optional):</label>
                         <input type="text" name="element_description_${template_element.id}" value="${template_element.description}" size="40"/>
                         <div style="clear: both"></div>
                     </div>
@@ -53,22 +53,26 @@
                     <div class="form-row">
                         <div class="toolFormTitle">Additional field ${1+element_count}</div>
                         <div class="form-row">
-                            <b>Field label:</b>
+                            <label>Field label:</label>
                             <input type="text" name="new_element_name_${element_count}" value="" size="40"/>
-                            <b>Field help text (optional):</b>
+                            <label>Field help text (optional):</label>
                             <input type="text" name="new_element_description_${element_count}" value="" size="40"/>
                             <div style="clear: both"></div>
                         </div>
                     </div>
                 %endfor
-                <div class="form-row">
-                    <label>Add additional fields:</label>
-                    <div style="float: left; width: 250px; margin-right: 10px;">
-                        <input type="text" name="num_fields" value="0" size="3"/>
+                %if define_or_save == 'define':
+                    <div class="form-row">
+                        <label>Add additional fields:</label>
+                        <div style="float: left; width: 250px; margin-right: 10px;">
+                            <input type="text" name="num_fields" value="0" size="3"/>
+                        </div>
+                        <div style="clear: both"></div>
                     </div>
-                    <div style="clear: both"></div>
-                </div>
-                <input type="submit" name="edit_info_template_button" value="Save"/>
+                    <input type="submit" name="edit_info_template_button" value="Define fields"/>
+                %else:
+                    <input type="submit" name="edit_info_template_button" value="Save"/>
+                %endif
             </div>
         </form>
     %else:
diff -r 1a82088aac38 -r 386e245f8076 templates/library/ldda_edit_info.mako
--- a/templates/library/ldda_edit_info.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/library/ldda_edit_info.mako	Thu May 21 15:48:39 2009 -0400
@@ -56,7 +56,11 @@
                 <div class="form-row">
                     <label>Message:</label>
                     <div style="float: left; width: 250px; margin-right: 10px;">
-                        <textarea name="message" rows="3" cols="35">${ldda.message}</textarea>
+                        %if ldda.message:
+                            <textarea name="message" rows="3" cols="35">${ldda.message}</textarea>
+                        %else:
+                            <textarea name="message" rows="3" cols="35"></textarea>
+                        %endif
                     </div>
                     <div class="toolParamHelp" style="clear: both;">
                         This information will be displayed in the library browser
@@ -116,7 +120,7 @@
     <p/>
 %else:
     <div class="toolForm">
-        <div class="toolFormTitle">View attributes of ${ldda.name}</div>
+        <div class="toolFormTitle">View information about ${ldda.name}</div>
         <div class="toolFormBody">
             <div class="form-row">
                 <b>Name:</b> ${ldda.name}
diff -r 1a82088aac38 -r 386e245f8076 templates/library/library_dataset_info.mako
--- a/templates/library/library_dataset_info.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/library/library_dataset_info.mako	Thu May 21 15:48:39 2009 -0400
@@ -47,7 +47,7 @@
     </div>
 %else:
     <div class="toolForm">
-        <div class="toolFormTitle">View attributes of ${library_dataset.name}</div>
+        <div class="toolFormTitle">View information about ${library_dataset.name}</div>
         <div class="toolFormBody">
             <div class="form-row">
                 <b>Name:</b> ${library_dataset.name}
diff -r 1a82088aac38 -r 386e245f8076 templates/library/new_info_template.mako
--- a/templates/library/new_info_template.mako	Thu May 21 11:32:25 2009 -0400
+++ b/templates/library/new_info_template.mako	Thu May 21 15:48:39 2009 -0400
@@ -55,13 +55,8 @@
             </div>
             <div class="toolFormBody">
                 <div class="form-row">
-                    <label>Add additional template fields:</label>
-                    <div style="float: left; width: 250px; margin-right: 10px;">
-                        <input type="text" name="num_fields" value="0" size="3"/>
-                    </div>
-                    <div style="clear: both"></div>
+                    <input type="submit" name="new_info_template_button" value="Save"/>
                 </div>
-                <input type="submit" name="new_info_template_button" value="Save"/>
             </div>
         </form>
     %else:
diff -r 1a82088aac38 -r 386e245f8076 test/base/twilltestcase.py
--- a/test/base/twilltestcase.py	Thu May 21 11:32:25 2009 -0400
+++ b/test/base/twilltestcase.py	Thu May 21 15:48:39 2009 -0400
@@ -816,6 +816,19 @@
         tc.fv( "1", "2", description ) # form field 1 is the field named name...
         tc.submit( "create_library_button" )
         self.home()
+    def set_library_permissions( self, library_id, library_name, role_id, permissions_in, permissions_out ):
+        url = "admin/library?id=%s&permissions=True&update_roles_button=Save" % ( library_id )
+        for po in permissions_out:
+            key = '%s_out' % po
+            url ="%s&%s=%s" % ( url, key, str( role_id ) )
+        for pi in permissions_in:
+            key = '%s_in' % pi
+            url ="%s&%s=%s" % ( url, key, str( role_id ) )
+        self.home()
+        self.visit_url( "%s/%s" % ( self.url, url ) )
+        check_str = "Permissions updated for library '%s'" % library_name
+        self.check_page_for_string( check_str )
+        self.home()
     def rename_library( self, library_id, old_name, name='Library One Renamed', description='This is Library One Re-described' ):
         """Rename a library"""
         self.home()
@@ -829,16 +842,71 @@
         check_str = "Library '%s' has been renamed to '%s'" % ( old_name, name )
         self.check_page_for_string( check_str )
         self.home()
-    def add_library_info_template( self, library_id, library_name ):
+    def add_library_info_template( self, library_id, library_name, num_fields='2', name='Library Template 1', ele_name_0='Foo', ele_name_1='Doh' ):
         """Add a new info template to a library"""
         self.home()
         url = "%s/admin/info_template?library_id=%s&new_template=True&num_fields=2&create_info_template_button=Go" % ( self.url, library_id )
-        self.home()
         self.visit_url( url )
         check_str = "Create a new information template for library '%s'" % library_name
         self.check_page_for_string ( check_str )
-        # TODO: finish this...
-    def add_folder_info_template( self, library_id, library_name, folder_id, folder_name ):
+        tc.fv( '1', 'library_id', library_id )
+        tc.fv( '1', 'set_num_fields', num_fields )
+        tc.fv( '1', 'name', name )
+        tc.fv( '1', 'new_element_name_0', ele_name_0 )
+        tc.fv( '1', 'new_element_name_1', ele_name_1 )
+        tc.submit( 'new_info_template_button' )
+        self.home()
+    def add_library_info_template_element( self, library_id, template_id, template_name, ele_name_1, ele_desc_1, 
+                                           ele_name_2, ele_desc_2, new_ele_name='Fubar', new_ele_desc='This is the Fubar compnent' ):
+        """Add a new element to an existing library info template"""
+        self.home()
+        url = "%s/admin/info_template?library_id=%s&id=%s&edit_template=True&num_fields=1&edit_info_template_button=Save" % \
+            ( self.url, library_id, template_id )
+        self.visit_url( url )
+        check_str = "Edit template '%s'" % template_name
+        self.check_page_for_string ( check_str )
+        tc.fv( '1', 'id', template_id )
+        tc.fv( '1', 'set_num_fields', '0' )
+        tc.fv( '1', 'name', template_name )
+        tc.fv( '1', 'element_name_1', ele_name_1 )
+        tc.fv( '1', 'element_description_1', ele_desc_1 )
+        tc.fv( '1', 'element_name_2', ele_name_2 )
+        tc.fv( '1', 'element_description_2', ele_desc_2 )
+        tc.fv( '1', 'new_element_name_0', new_ele_name )
+        tc.fv( '1', 'new_element_description_0', new_ele_desc )
+        tc.submit( 'edit_info_template_button' )
+        check_str = "Information template '%s' has been updated" % template_name
+        self.check_page_for_string( check_str )
+        self.home()
+    def edit_library_info( self, library_id, library_name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents ):
+        """Add information to a library using an existing template with 2 elements"""
+        self.home()
+        self.visit_url( "%s/admin/library?information=True&id=%s" % ( self.url, library_id ) )
+        check_str = 'Other information about library %s' % library_name
+        self.check_page_for_string( check_str )
+        tc.fv( '2', ele_1_field_name, ele_1_contents )
+        tc.fv( '2', ele_2_field_name, ele_2_contents )
+        tc.submit( 'create_new_info_button' )
+        self.home()
+    def edit_library_info_template( self, library_id, id, name, name_1, desc_1, name_2, desc_2 ):
+        """Edit an existing library info template"""
+        self.home()
+        url = "%s/admin/info_template?library_id=%s&id=%s&edit_template=True" % ( self.url, library_id, id )
+        self.visit_url( url )
+        self.check_page_for_string ( 'Edit template' )
+        tc.fv( '1', 'id', id )
+        tc.fv( '1', 'set_num_fields', '0' )
+        tc.fv( '1', 'name', name )
+        tc.fv( '1', 'element_name_1', name_1 )
+        tc.fv( '1', 'element_description_1', desc_1 )
+        tc.fv( '1', 'element_name_2', name_2 )
+        tc.fv( '1', 'element_description_2', desc_2 )
+        tc.submit( 'edit_info_template_button' )
+        check_str = "Information template '%s' has been updated" % name
+        self.check_page_for_string( check_str )
+        self.home()
+    def add_folder_info_template( self, library_id, library_name, folder_id, folder_name, num_fields='2',
+                                  name='Folder Template 1', ele_name_0='Fu', ele_help_0='', ele_name_1='Bar', ele_help_1='' ):
         """Add a new info template to a folder"""
         self.home()
         url = "%s/admin/info_template?library_id=%s&folder_id=%s&new_template=True&num_fields=2&create_info_template_button=Go" % \
@@ -847,7 +915,16 @@
         self.visit_url( url )
         check_str = "Create a new information template for folder '%s'" % folder_name
         self.check_page_for_string ( check_str ) 
-        # TODO: finish this...
+        tc.fv( '1', 'library_id', library_id )
+        tc.fv( '1', 'folder_id', folder_id )
+        tc.fv( '1', 'set_num_fields', num_fields )
+        tc.fv( '1', 'name', name )
+        tc.fv( '1', 'new_element_name_0', ele_name_0 )
+        tc.fv( '1', 'new_element_description_0', ele_help_0.replace( '+', ' ' ) )
+        tc.fv( '1', 'new_element_name_1', ele_name_1 )
+        tc.fv( '1', 'new_element_description_1', ele_help_1.replace( '+', ' ' ) )
+        tc.submit( 'new_info_template_button' )
+        self.home()
     def add_folder( self, library_id, folder_id, name='Folder One', description='NThis is Folder One' ):
         """Create a new folder"""
         self.home()
@@ -870,16 +947,27 @@
         check_str = "Folder '%s' has been renamed to '%s'" % ( old_name, name )
         self.check_page_for_string( check_str )
         self.home()
-    def add_library_dataset( self, filename, library_id, folder_id, folder_name, file_format='auto', dbkey='hg18', roles=[], message='', root=False ):
+    def add_library_dataset( self, filename, library_id, folder_id, folder_name, file_format='auto',
+                             dbkey='hg18', roles=[], message='', root=False, check_template_str1='', check_template_str2='',
+                             check_template_str3='' ):
         """Add a dataset to a folder"""
         filename = self.get_filename( filename )
         self.home()
-        self.visit_url( "%s/admin/library_dataset_dataset_association?upload_option=upload_file&library_id=%s&folder_id=%s&message=%s" % ( self.url, library_id, folder_id, message ) )
+        self.visit_url( "%s/admin/library_dataset_dataset_association?upload_option=upload_file&library_id=%s&folder_id=%s&message=%s" % \
+                        ( self.url, library_id, folder_id, message ) )
         self.check_page_for_string( 'Upload files' )
+        # If we've been sent some template labels, make sure they are included in the upload form
+        if check_template_str1:
+            self.check_page_for_string( check_template_str1 )
+        if check_template_str2:
+            self.check_page_for_string( check_template_str2 )
+        if check_template_str3:
+            self.check_page_for_string( check_template_str3 )
         tc.fv( "1", "folder_id", folder_id )
         tc.formfile( "1", "file_data", filename )
         tc.fv( "1", "file_format", file_format )
         tc.fv( "1", "dbkey", dbkey )
+        tc.fv( "1", "message", message.replace( '+', ' ' ) )
         for role_id in roles:
             tc.fv( "1", "roles", role_id ) # form field 7 is the select list named out_groups, note the buttons...
         tc.submit( "new_dataset_button" )
@@ -887,6 +975,125 @@
             check_str = "Added 1 datasets to the library '%s' ( each is selected )." % folder_name
         else:
             check_str = "Added 1 datasets to the folder '%s' ( each is selected )." % folder_name
+        self.check_page_for_string( check_str )
+        self.home()
+    def set_library_dataset_permissions( self, library_id, folder_id, ldda_id, ldda_name, role_id, permissions_in, permissions_out ):
+        url = "admin/library_dataset_dataset_association?library_id=%s&folder_id=%s&&id=%s&permissions=True&update_roles_button=Save" % \
+            ( library_id, folder_id, ldda_id )
+        #role_ids = util.listify( role_ids )
+        #for role_id in role_ids:
+        for po in permissions_out:
+            key = '%s_out' % po
+            url ="%s&%s=%s" % ( url, key, str( role_id ) )
+        for pi in permissions_in:
+            key = '%s_in' % pi
+            url ="%s&%s=%s" % ( url, key, str( role_id ) )
+        print url
+        self.home()
+        self.visit_url( "%s/%s" % ( self.url, url ) )
+        check_str = "Permissions updated for dataset '%s'" % ldda_name
+        self.check_page_for_string( check_str )
+        self.home()
+    def edit_ldda_template_element_info( self, library_id, folder_id, ldda_id, ldda_name, ele_1_field_name, 
+                        ele_1_contents, ele_2_field_name, ele_2_contents, ele_1_help='', ele_2_help='',
+                        ele_3_field_name='', ele_3_contents='', ele_3_help='' ):
+        """Edit library_dataset_dataset_association template element information"""
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, library_id, folder_id, ldda_id ) )        
+        check_str = 'Edit attributes of %s' % ldda_name
+        self.check_page_for_string( check_str )
+        ele_1_contents = ele_1_contents.replace( '+', ' ' )
+        ele_2_contents = ele_2_contents.replace( '+', ' ' )
+        tc.fv( '4', ele_1_field_name, ele_1_contents )
+        tc.fv( '4', ele_2_field_name, ele_2_contents.replace( '+', ' ' ) )
+        if ele_3_field_name and ele_3_contents:
+            ele_3_contents = ele_3_contents.replace( '+', ' ' )
+            tc.fv( '4', ele_3_field_name, ele_3_contents )
+        tc.submit( 'edit_info_button' )
+        self.check_page_for_string( 'This is the latest version of this library dataset' )
+        self.check_page_for_string( 'The information has been updated.' )
+        self.check_page_for_string( ele_1_contents )
+        self.check_page_for_string( ele_2_contents )
+        if ele_3_field_name and ele_3_contents:
+            self.check_page_for_string( ele_3_contents )
+        if ele_1_help:
+            check_str = ele_1_help.replace( '+', ' ' )
+            self.check_page_for_string( check_str )
+        self.check_page_for_string( ele_2_contents )
+        if ele_2_help:
+            check_str = ele_2_help.replace( '+', ' ' )
+            self.check_page_for_string( check_str )
+        if ele_2_help:
+            check_str = ele_3_help.replace( '+', ' ' )
+            self.check_page_for_string( check_str )
+        self.home()
+    def edit_ldda_attribute_info( self, library_id, folder_id, ldda_id, ldda_name, new_ldda_name ):
+        """Edit library_dataset_dataset_association attribute information"""
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, library_id, folder_id, ldda_id ) )
+        check_str = 'Edit attributes of %s' % ldda_name
+        self.check_page_for_string( check_str )
+        tc.fv( '1', 'name', new_ldda_name )
+        tc.submit( 'save' )
+        check_str = 'Attributes updated for library dataset %s' % new_ldda_name
+        self.check_page_for_string( check_str )
+        check_str = 'Edit attributes of %s' % new_ldda_name
+        self.check_page_for_string( check_str )
+        self.home()
+    def upload_new_dataset_version( self, filename, library_id, folder_id, folder_name, library_dataset_id, ldda_name, file_format='auto',
+                                    dbkey='hg18', message='', check_template_str1='', check_template_str2='', check_template_str3='' ):
+        """Upload new version(s) of a dataset"""
+        self.home()
+        filename = self.get_filename( filename )
+        
+        url = "%s/admin/library_dataset_dataset_association?upload_option=upload_file&library_id=%s&folder_id=%s&replace_id=%s&message=%s" % \
+                        ( self.url, library_id, folder_id, library_dataset_id, message )
+        print "####url: ", url
+        
+        self.visit_url( "%s/admin/library_dataset_dataset_association?upload_option=upload_file&library_id=%s&folder_id=%s&replace_id=%s&message=%s" % \
+                        ( self.url, library_id, folder_id, library_dataset_id, message ) )
+        self.check_page_for_string( 'Upload files' )
+        self.check_page_for_string( 'You are currently selecting a new file to replace' )
+        self.check_page_for_string( ldda_name )
+        # If we've been sent some template labels, make sure they are included in the upload form
+        if check_template_str1:
+            self.check_page_for_string( check_template_str1 )
+        if check_template_str2:
+            self.check_page_for_string( check_template_str2 )
+        if check_template_str3:
+            self.check_page_for_string( check_template_str3 )
+        tc.formfile( "1", "file_data", filename )
+        tc.fv( "1", "file_format", file_format )
+        tc.fv( "1", "dbkey", dbkey )
+        tc.fv( "1", "message", message.replace( '+', ' ' ) )
+        tc.submit( "new_dataset_button" )
+        check_str = "Added 1 dataset versions to the library dataset '%s' in the folder '%s'." % ( ldda_name, folder_name )
+        self.check_page_for_string( check_str )
+        self.home()
+    def upload_new_dataset_versions( self, library_id, folder_id, folder_name, library_dataset_id, ldda_name, file_format='auto',
+                                    dbkey='hg18', message='', check_template_str1='', check_template_str2='', check_template_str3='' ):
+        """Upload new version(s) of a dataset using a directory of files"""
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?upload_option=upload_directory&library_id=%s&folder_id=%s&replace_id=%s" \
+                        % ( self.url, library_id, folder_id, library_dataset_id ) )
+        self.check_page_for_string( 'Upload a directory of files' )
+        self.check_page_for_string( 'You are currently selecting a new file to replace' )
+        # If we've been sent some template labels, make sure they are included in the upload form
+        if check_template_str1:
+            self.check_page_for_string( check_template_str1 )
+        if check_template_str2:
+            self.check_page_for_string( check_template_str2 )
+        if check_template_str3:
+            self.check_page_for_string( check_template_str3 )
+        tc.fv( "1", "file_format", file_format )
+        tc.fv( "1", "dbkey", dbkey )
+        tc.fv( "1", "message", message.replace( '+', ' ' ) )
+        library_dir = "%s" % self.file_dir
+        tc.fv( "1", "server_dir", "library" )
+        tc.submit( "new_dataset_button" )
+        check_str = "Added 3 dataset versions to the library dataset '%s' in the folder '%s'." % ( ldda_name, folder_name )
         self.check_page_for_string( check_str )
         self.home()
     def add_history_datasets_to_library( self, library_id, folder_id, folder_name, hda_id, root=False ):
@@ -900,15 +1107,24 @@
             check_str = "Added 1 datasets to the folder '%s' ( each is selected )." % folder_name
         self.check_page_for_string( check_str )
         self.home()
-    def add_datasets_from_library_dir( self, library_id, folder_id, folder_name, file_format='auto', dbkey='hg18', roles_tuple=[], root=False ):
+    def add_datasets_from_library_dir( self, library_id, folder_id, folder_name, file_format='auto', dbkey='hg18', roles_tuple=[],
+                                       message='', root=False, check_template_str1='', check_template_str2='', check_template_str3='' ):
         """Add a directory of datasets to a folder"""
         # roles is a list of tuples: [ ( role_id, role_description ) ]
         self.home()
         self.visit_url( "%s/admin/library_dataset_dataset_association?upload_option=upload_directory&library_id=%s&folder_id=%s" % ( self.url, library_id, folder_id ) )
         self.check_page_for_string( 'Upload a directory of files' )
+        # If we've been sent some template labels, make sure they are included in the upload form
+        if check_template_str1:
+            self.check_page_for_string( check_template_str1 )
+        if check_template_str2:
+            self.check_page_for_string( check_template_str2 )
+        if check_template_str3:
+            self.check_page_for_string( check_template_str3 )
         tc.fv( "1", "folder_id", folder_id )
         tc.fv( "1", "file_format", file_format )
         tc.fv( "1", "dbkey", dbkey )
+        tc.fv( "1", "message", message.replace( '+', ' ' ) )
         library_dir = "%s" % self.file_dir
         tc.fv( "1", "server_dir", "library" )
         for role_tuple in roles_tuple:
@@ -920,18 +1136,28 @@
             check_str = "Added 3 datasets to the folder '%s' ( each is selected )." % folder_name
         self.check_page_for_string( check_str )
         self.home()
-    def mark_library_deleted( self, library_id, library_name ):
-        """Mark a library as deleted"""
+    def delete_library_item( self, library_id, library_item_id, library_item_name, library_item_type='library_dataset' ):
+        """Mark a library item as deleted"""
         self.home()
-        self.visit_url( "%s/admin/library?id=%s&delete=True" % ( self.url, library_id ) )
-        check_str = "Library '%s' and all of its contents have been marked deleted" % library_name
+        self.visit_url( "%s/admin/delete_library_item?library_id=%s&library_item_id=%s&library_item_type=%s" \
+                        % ( self.url, library_id, library_item_id, library_item_type ) )
+        if library_item_type == 'library_dataset':
+            library_item_desc = 'Dataset'
+        else:
+            library_item_desc = library_item_type.capitalize()
+        check_str = "%s '%s' has been marked deleted" % ( library_item_desc, library_item_name )
         self.check_page_for_string( check_str )
         self.home()
-    def undelete_library( self, library_id, library_name ):
-        """Mark a library as not deleted"""
+    def undelete_library_item( self, library_id, library_item_id, library_item_name, library_item_type='library_dataset' ):
+        """Mark a library item as deleted"""
         self.home()
-        self.visit_url( "%s/admin/undelete_library?id=%s" % ( self.url, library_id ) )
-        check_str = "Library '%s' and all of its contents have been marked not deleted" % library_name
+        self.visit_url( "%s/admin/undelete_library_item?library_id=%s&library_item_id=%s&library_item_type=%s" \
+                        % ( self.url, library_id, library_item_id, library_item_type ) )
+        if library_item_type == 'library_dataset':
+            library_item_desc = 'Dataset'
+        else:
+            library_item_desc = library_item_type.capitalize()
+        check_str = "%s '%s' has been marked undeleted" % ( library_item_desc, library_item_name )
         self.check_page_for_string( check_str )
         self.home()
     def purge_library( self, library_id, library_name ):
diff -r 1a82088aac38 -r 386e245f8076 test/functional/test_security_and_libraries.py
--- a/test/functional/test_security_and_libraries.py	Thu May 21 11:32:25 2009 -0400
+++ b/test/functional/test_security_and_libraries.py	Thu May 21 15:48:39 2009 -0400
@@ -40,6 +40,15 @@
         global admin_user
         admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test@bx.psu.edu' ).first()
         assert admin_user is not None, 'Problem retrieving user with email "test@bx.psu.edu" from the database'
+        # Get the admin user's privat role for later use
+        global admin_user_private_role
+        admin_user_private_role = None
+        for role in admin_user.all_roles():
+            if role.name == admin_user.email and role.description == 'Private Role for %s' % admin_user.email:
+                admin_user_private_role = role
+                break
+        if not admin_user_private_role:
+            raise AssertionError( "Private role not found for user '%s'" % admin_user.email )
         # Make sure DefaultUserPermissions are correct
         if len( admin_user.default_permissions ) > 1:
             raise AssertionError( '%d DefaultUserPermissions were created for %s when their account was created ( should have been 1 )' \
@@ -168,14 +177,14 @@
         actions_in = [ 'manage permissions' ]
         permissions_out = [ 'DATASET_ACCESS' ]
         actions_out = [ 'access' ]
-        private_role = None
+        regular_user2_private_role = None
         for role in regular_user2.all_roles():
             if role.name == regular_user2.email and role.description == 'Private Role for %s' % regular_user2.email:
-                private_role = role
+                regular_user2_private_role = role
                 break
-        if not private_role:
+        if not regular_user2_private_role:
             raise AssertionError( "Private role not found for user '%s'" % regular_user2.email )
-        role_id = str( private_role.id )
+        role_id = str( regular_user2_private_role.id )
         # Change DefaultHistoryPermissions for the current history
         self.history_set_default_permissions( permissions_out=permissions_out, permissions_in=permissions_in, role_id=role_id )
         if len( latest_history.default_permissions ) != len( actions_in ):
@@ -283,11 +292,12 @@
         """Testing undeleting a user account"""
         self.undelete_user( user_id=regular_user3.id, email=regular_user3.email )
     def test_045_create_role( self ):
-        """Testing creating new role with 3 members, then renaming it"""
+        """Testing creating new role with 3 members ( and a new group named the same ), then renaming the role"""
         name = 'Role One'
         description = "This is Role Ones description"
         user_ids=[ str( admin_user.id ), str( regular_user1.id ), str( regular_user3.id ) ]
-        self.create_role( name=name, description=description, in_user_ids=user_ids, in_group_ids=[], private_role=admin_user.email )
+        self.create_role( name=name, description=description, in_user_ids=user_ids, in_group_ids=[],
+                          create_group_for_role='yes', private_role=admin_user.email )
         # Get the role object for later tests
         global role_one
         role_one = galaxy.model.Role.filter( galaxy.model.Role.table.c.name==name ).first()
@@ -308,6 +318,12 @@
             if len( user.roles ) != 2:
                 raise AssertionError( '%d UserRoleAssociations are associated with user %s ( should be 2 )' \
                                       % ( len( user.roles ), user.email ) )
+        # Make sure the group was created
+        self.home()
+        self.visit_page( 'admin/groups' )
+        self.check_page_for_string( name )
+        global group_zero
+        group_zero = galaxy.model.Group.filter( galaxy.model.Group.table.c.name==name ).first()
         # Rename the role
         rename = "Role One's been Renamed"
         redescription="This is Role One's Re-described"
@@ -430,7 +446,7 @@
         if len( admin_user.roles ) != 5:
             raise AssertionError( '%d UserRoleAssociations are associated with %s ( should be 5 )' % ( len( admin_user.roles ), admin_user.email ) )
     def test_070_create_library( self ):
-        """Testing creating a new library, then renaming it and renaming the root folder"""
+        """Testing creating a new library, then renaming it"""
         name = "Library One's Name"
         description = "This is Library One's description"
         self.create_library( name=name, description=description )
@@ -443,6 +459,12 @@
                                                          galaxy.model.Library.table.c.description==description,
                                                          galaxy.model.Library.table.c.deleted==False ) ).first()
         assert library_one is not None, 'Problem retrieving library named "%s" from the database' % name
+        # Set permissions on the library, sort for later testing
+        permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ]
+        permissions_out = []
+        # Role one members are: admin_user, regular_user1, regular_user3.  Each of these users will be permitted to
+        # LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE for library items.
+        self.set_library_permissions( str( library_one.id ), library_one.name, str( role_one.id ), permissions_in, permissions_out )                                            
         # Rename the library
         rename = "Library One's been Renamed"
         redescription = "This is Library One's Re-described"
@@ -455,9 +477,149 @@
         library_one.refresh()
         self.rename_library( str( library_one.id ), library_one.name, name=name, description=description )
         library_one.refresh()
-    def test_075_add_new_folder_to_root_folder( self ):
+    def test_075_library_template_features( self ):
+        """Testing adding a template to a library, along with template features on the admin side"""
+        actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ]
+        actions.sort()
+        # Add a new information template to the library
+        template_name = 'Library Template 1'
+        ele_name_0 = 'Foo'
+        ele_name_1 = 'Doh'
+        self.add_library_info_template( library_one.id, library_one.name, name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_name_1=ele_name_1 )
+        self.home()
+        self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( ele_name_0 )
+        self.check_page_for_string( ele_name_1 )
+        self.home()
+        # Get the template for later testing
+        global library_one_template
+        library_one_template = galaxy.model.LibraryItemInfoTemplate.query().order_by( desc( galaxy.model.LibraryItemInfoTemplate.table.c.id ) ).first()
+        assert library_one_template is not None, 'Problem retrieving LibraryItemInfoTemplate for library named "%s" from the database' % str( library_one.name )
+        # Make sure the library permissions were inherited by the template
+        template_permissions = galaxy.model.LibraryItemInfoTemplatePermissions \
+            .query() \
+            .filter( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.library_item_info_template_id == library_one_template.id ) \
+            .order_by( desc( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.id ) ) \
+            .limit( 3 ) \
+            .all()
+        template_permissions = [ litp_obj.action for litp_obj in template_permissions ]
+        template_permissions.sort()
+        assert actions == template_permissions, "Template permissions for template %s not correctly inherited from library %s" \
+                                                % ( library_one_template.name, library_one.name )
+        # Make sure that the library permissions were inherited by each of the template elements
+        for library_item_info in library_one_template.library_item_infos:
+            info_permissions = galaxy.model.LibraryItemInfoPermissions \
+                .filter( galaxy.model.LibraryItemInfoPermissions.table.c.library_item_info_id == library_item_info.id ) \
+                .all()
+            info_permissions = [ liip_obj.action for liip_obj in info_permissions ]
+            info_permissions.sort()
+            assert actions == info_permissions, "Permissions for library_item_info id %s not correctly inherited from library %s" \
+                                % ( library_item_info.id, library_one.name )
+        # Need the current library_item_info_element.id
+        last_library_item_info_element_id = galaxy.model.LibraryItemInfoElement.query() \
+            .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first()
+        if last_library_item_info_element_id is None:
+            last_library_item_info_element_id = 0
+        # Add information to the library using the template
+        ele_1_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( last_library_item_info_element_id + 1 ) )
+        ele_1_contents = 'hello'
+        ele_2_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( last_library_item_info_element_id + 2 ) )
+        ele_2_contents = 'world'
+        self.edit_library_info( str( library_one.id ), library_one.name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents )
+        self.home()
+        self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( ele_1_contents )
+        self.check_page_for_string( ele_2_contents )
+        self.home()
+        self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( ele_1_contents )
+        self.check_page_for_string( ele_2_contents )
+        # Edit the template
+        new_name = 'Library Template 1 renamed'
+        new_ele_name_1 = 'wind'
+        ele_desc_1 = 'This is the wind component'
+        new_ele_name_2 = 'bag'
+        ele_desc_2 = 'This is the bag component'
+        self.edit_library_info_template( str( library_one.id ), library_one_template.id, new_name, new_ele_name_1, ele_desc_1, new_ele_name_2, ele_desc_2 )
+        self.home()
+        self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( new_ele_name_1 )
+        self.check_page_for_string( ele_desc_1 )
+        self.check_page_for_string( ele_1_contents )
+        self.check_page_for_string( new_ele_name_2 )
+        self.check_page_for_string( ele_desc_2 )
+        self.check_page_for_string( ele_2_contents )
+    def test_080_add_public_dataset_to_root_folder( self ):
+        """Testing adding a public dataset to the root folder"""
+        actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ]
+        actions.sort()
+        message = 'Testing adding a public dataset to the root folder'
+        self.add_library_dataset( '1.bed',
+                                  str( library_one.id ),
+                                  str( library_one.root_folder.id ),
+                                  library_one.root_folder.name,
+                                  file_format='bed',
+                                  dbkey='hg18',
+                                  message=message.replace( ' ', '+' ),
+                                  root=True )
+        global ldda_one
+        ldda_one = galaxy.model.LibraryDatasetDatasetAssociation.query() \
+            .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
+        assert ldda_one is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_one from the database'
+        self.home()
+        self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( "1.bed" )
+        self.check_page_for_string( message )
+        self.check_page_for_string( admin_user.email )
+        # Make sure the library permissions were inherited to the library_dataset_dataset_association
+        ldda_permissions = galaxy.model.LibraryDatasetDatasetAssociationPermissions \
+            .filter( galaxy.model.LibraryDatasetDatasetAssociationPermissions.table.c.library_dataset_dataset_association_id == ldda_one.id ) \
+            .all()
+        ldda_permissions = [ lddap_obj.action for lddap_obj in ldda_permissions ]
+        ldda_permissions.sort()
+        assert actions == ldda_permissions, "Permissions for ldda id %s not correctly inherited from library %s" \
+                            % ( ldda_one.id, library_one.name )
+        # Make sure DatasetPermissions are correct - default is 'manage permissions'
+        if len( ldda_one.dataset.actions ) > 1:
+            raise AssertionError( '%d DatasetPermissionss were created for dataset id %d when it was created ( should have been 1 )' \
+                                  % ( len( ldda_one.dataset.actions ), ldda_one.dataset.id ) )
+        dp = galaxy.model.DatasetPermissions.filter( galaxy.model.DatasetPermissions.table.c.dataset_id==ldda_one.dataset.id ).first()
+        if not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action:
+            raise AssertionError( 'The DatasetPermissions.action for dataset id %d is "%s", but it should be "manage permissions"' \
+                                  % ( ldda_one.dataset.id, dp.action ) )
+        # Make sure the library template was inherited by the ldda
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) )
+        self.check_page_for_string( 'wind' )
+        self.check_page_for_string( 'This is the wind component' )
+        self.check_page_for_string( 'bag' )
+        self.check_page_for_string( 'This is the bag component' )
+        # Make sure other users can access the dataset from the Libraries view
+        self.logout()
+        self.login( email=regular_user2.email )
+        self.home()
+        self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( "1.bed" )
+        self.logout()
+        self.login( email=admin_user.email )
+        self.home()
+    def test_085_editing_dataset_information( self ):
+        """Testing editing dataset template element information"""
+        # Need the current library_item_info_element.id
+        last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \
+            .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first()
+        global ldda_one_ele_2_field_name
+        ldda_one_ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id )
+        ele_2_contents = 'pipe'
+        global ldda_one_ele_1_field_name
+        ldda_one_ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) )
+        ele_1_contents = 'blown'
+        self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ),
+            ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents )
+        self.home()
+    def test_090_add_new_folder_to_root_folder( self ):
         """Testing adding a folder to a library root folder"""
-        self.login( email = 'test@bx.psu.edu' )
         root_folder = library_one.root_folder
         name = "Root Folder's Folder One"
         description = "This is the root folder's Folder One"
@@ -466,23 +628,238 @@
         folder_one = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==root_folder.id,
                                                               galaxy.model.LibraryFolder.table.c.name==name,
                                                               galaxy.model.LibraryFolder.table.c.description==description ) ).first()
-        assert folder_one is not None, 'Problem retrieving library folder named "Folder One" from the database'
+        assert folder_one is not None, 'Problem retrieving library folder named "%s" from the database' % name
         self.home()
         self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
         self.check_page_for_string( name )
         self.check_page_for_string( description )
-    def test_080_add_dataset_with_private_role_restriction_to_folder( self ):
-        """Testing adding a dataset with a private role restriction to a folder"""
-        # Add a dataset restricted by regular_user1 private role
-        message ='This+is+a+test'
-        self.add_library_dataset( '1.bed',
+        # Make sure the library template is inherited
+        self.home()
+        self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) )
+        self.check_page_for_string( 'wind' )
+        self.check_page_for_string( 'This is the wind component' )
+        self.check_page_for_string( 'bag' )
+        self.check_page_for_string( 'This is the bag component' )
+        self.home()
+    def test_095_add_folder_template( self ):
+        """Testing adding a new folder template to a folder"""
+        # Add a new information template to the folder
+        template_name = 'Folder Template 1'
+        ele_name_0 = 'Fu'
+        ele_help_0 = 'This is the Fu component'.replace( ' ', '+' )
+        ele_name_1 = 'Bar'
+        ele_help_1 = 'This is the Bar component'.replace( ' ', '+' )
+        self.home()
+        self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_one.id ), folder_one.name,
+                                       name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0,
+                                       ele_name_1=ele_name_1, ele_help_1=ele_help_1 )
+        self.home()
+        self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) )
+        self.check_page_for_string( ele_name_0 )
+        check_str = ele_help_0.replace( '+', ' ' )
+        self.check_page_for_string( check_str )
+        self.check_page_for_string( ele_name_1 )
+        check_str = ele_help_1.replace( '+', ' ' )
+        self.check_page_for_string( check_str )
+        self.home()
+    def test_100_add_subfolder_to_folder( self ):
+        """Testing adding a folder to a library folder"""
+        name = "Folder One's Subfolder"
+        description = "This is the Folder One's subfolder"
+        self.add_folder( str( library_one.id ), str( folder_one.id ), name=name, description=description )
+        global subfolder_one
+        subfolder_one = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==folder_one.id,
+                                                                 galaxy.model.LibraryFolder.table.c.name==name,
+                                                                 galaxy.model.LibraryFolder.table.c.description==description ) ).first()
+        assert subfolder_one is not None, 'Problem retrieving library folder named "Folder Ones Subfolder" from the database'
+        self.home()
+        self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( name )
+        self.check_page_for_string( description )
+        # Make sure the parent folder's template is inherited
+        self.home()
+        self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) )
+        self.check_page_for_string( 'Fu' )
+        self.check_page_for_string( 'This is the Fu component' )
+        self.check_page_for_string( 'Bar' )
+        self.check_page_for_string( 'This is the Bar component' )
+        # Make sure the library template is not inherited
+        try:
+            self.check_page_for_string( 'wind' )
+            raise AssertionError( 'Library template inherited by folder when it should not have been.' )
+        except:
+            pass
+        self.home()
+    def test_105_add_template_element( self ):
+        """Testing adding a new element to an existing library template"""
+        name = 'Library Template 1 renamed'
+        ele_name_1 = 'wind'
+        ele_desc_1 = 'This is the wind component'
+        ele_name_2 = 'bag'
+        ele_desc_2 = 'This is the bag component'
+        new_ele_name = 'Fubar'
+        new_ele_desc = 'This is the Fubar component'
+        library_one_template.refresh()
+        self.add_library_info_template_element( str( library_one.id ),
+                                                str( library_one_template.id ),
+                                                library_one_template.name,
+                                                ele_name_1,
+                                                ele_desc_1,
+                                                ele_name_2,
+                                                ele_desc_2,
+                                                new_ele_name=new_ele_name,
+                                                new_ele_desc=new_ele_desc )
+        # Make sure the new template element shows up on the existing library info page
+        self.home()
+        self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( library_one.name )
+        self.check_page_for_string( library_one.description )
+        self.check_page_for_string( 'wind' )
+        self.check_page_for_string( 'hello' )
+        self.check_page_for_string( 'This is the wind component' )
+        self.check_page_for_string( 'bag' )
+        self.check_page_for_string( 'world' )
+        self.check_page_for_string( 'This is the bag component' )
+        self.check_page_for_string( 'Fubar' )
+        self.check_page_for_string( 'This is the Fubar component' )
+        # Make sure the new template element does not show up on existing info pages for folder_one since it has its own template
+        self.home()
+        self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) )
+        self.check_page_for_string( 'Fu' )
+        self.check_page_for_string( 'This is the Fu component' )
+        self.check_page_for_string( 'Bar' )
+        self.check_page_for_string( 'This is the Bar component' )
+        try:
+            self.check_page_for_string( 'Fubar' )
+            raise AssertionError( 'Changed library template inherited by folder "%s" when folder had an associated template of its own' )
+        except:
+            pass
+        # Make sure the new template element shows up on existing info pages for ldda_one since it is contained in the root folder
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_one.id ) ) )
+        # Visiting the above page will have resulted in the creation of a new LibraryItemInfoElement, so we'll retrieve it
+        # for later use
+        last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \
+            .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first()
+        global ldda_one_ele_3_field_name
+        ldda_one_ele_3_field_name = "info_element_%s" % str( last_library_item_info_element.id )
+        self.check_page_for_string( 'wind' )
+        self.check_page_for_string( 'This is the wind component' )
+        self.check_page_for_string( 'bag' )
+        self.check_page_for_string( 'This is the bag component' )
+        self.check_page_for_string( 'Fubar' )
+        self.check_page_for_string( 'This is the Fubar component' )
+        self.home()
+    def test_110_add_2nd_new_folder_to_root_folder( self ):
+        """Testing adding a 2nd folder to a library root folder"""
+        root_folder = library_one.root_folder
+        name = "Folder Two"
+        description = "This is the root folder's Folder Two"
+        self.add_folder( str( library_one.id ), str( root_folder.id ), name=name, description=description )
+        global folder_two
+        folder_two = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==root_folder.id,
+                                                              galaxy.model.LibraryFolder.table.c.name==name,
+                                                              galaxy.model.LibraryFolder.table.c.description==description ) ).first()
+        assert folder_two is not None, 'Problem retrieving library folder named "%s" from the database' % name
+        self.home()
+        self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( name )
+        self.check_page_for_string( description )
+        # Make sure the changed library template is inherited to the new folder
+        self.home()
+        self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) )
+        self.check_page_for_string( 'wind' )
+        self.check_page_for_string( 'This is the wind component' )
+        self.check_page_for_string( 'bag' )
+        self.check_page_for_string( 'This is the bag component' )
+        self.check_page_for_string( 'Fubar' )
+        self.check_page_for_string( 'This is the Fubar component' )
+        self.home()
+    def test_115_add_public_dataset_to_root_folders_2nd_subfolder( self ):
+        """Testing adding a public dataset to the root folder's 2nd sub-folder"""
+        actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ]
+        actions.sort()
+        message = "Testing adding a public dataset to the folder named %s" % folder_two.name
+        self.add_library_dataset( '2.bed',
                                   str( library_one.id ),
-                                  str( folder_one.id ),
-                                  folder_one.name,
+                                  str( folder_two.id ),
+                                  folder_two.name,
                                   file_format='bed',
                                   dbkey='hg18',
-                                  roles=[ str( regular_user1_private_role.id ) ],
-                                  message=message,
+                                  message=message.replace( ' ', '+' ),
+                                  root=False )
+        global ldda_two
+        ldda_two = galaxy.model.LibraryDatasetDatasetAssociation.query() \
+            .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
+        assert ldda_two is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_two from the database'
+        self.home()
+        self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( "2.bed" )
+        self.check_page_for_string( message )
+        self.check_page_for_string( admin_user.email )
+    def test_120_add_template_to_root_folders_2nd_subfolder( self ):
+        """Testing adding a template to the root folder's 2nd sub-folder"""
+        # Before adding the folder template, the inherited library template should be displayed
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) )
+        self.check_page_for_string( 'wind' )
+        self.check_page_for_string( 'This is the wind component' )
+        self.check_page_for_string( 'bag' )
+        self.check_page_for_string( 'This is the bag component' )
+        self.check_page_for_string( 'Fubar' )
+        self.check_page_for_string( 'This is the Fubar component' )
+        self.home()
+        # Add a new folde template
+        template_name = 'Folder 2 Template'
+        ele_name_0 = 'kill'
+        ele_help_0 = 'This is the kill component'.replace( ' ', '+' )
+        ele_name_1 = 'bill'
+        ele_help_1 = 'This is the bill component'.replace( ' ', '+' )
+        self.home()
+        self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_two.id ), folder_two.name,
+                                       name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0,
+                                       ele_name_1=ele_name_1, ele_help_1=ele_help_1 )
+        # Make sure the new template id displayed on the folder information page
+        self.home()
+        self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) )
+        self.check_page_for_string( ele_name_0 )
+        check_str = ele_help_0.replace( '+', ' ' )
+        self.check_page_for_string( check_str )
+        self.check_page_for_string( ele_name_1 )
+        check_str = ele_help_1.replace( '+', ' ' )
+        self.check_page_for_string( check_str )
+        # The library dataset ldda_two had previously inherited the library template prior to the new folder template
+        # being introduced, so the library template should still be displayed on the ldda information page
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) )
+        self.check_page_for_string( 'wind' )
+        self.check_page_for_string( 'This is the wind component' )
+        self.check_page_for_string( 'bag' )
+        self.check_page_for_string( 'This is the bag component' )
+        self.check_page_for_string( 'Fubar' )
+        self.check_page_for_string( 'This is the Fubar component' )
+        # Make sure the new folder template is not displayed
+        try:
+            self.check_page_for_string( 'kill' )
+            raise AssertionError( 'New folder template elements incorrectly included in information page for ldda "%s"' % ldda_two.name )
+        except:
+            pass
+        self.home()
+    def test_125_add_2nd_public_dataset_to_root_folders_2nd_subfolder( self ):
+        """Testing adding a 2nd public dataset to the root folder's 2nd sub-folder"""
+        actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ]
+        actions.sort()
+        message = "Testing adding a 2nd public dataset to the folder named %s" % folder_two.name
+        self.add_library_dataset( '3.bed',
+                                  str( library_one.id ),
+                                  str( folder_two.id ),
+                                  folder_two.name,
+                                  file_format='bed',
+                                  dbkey='hg18',
+                                  message=message.replace( ' ', '+' ),
                                   root=False )
         global ldda_three
         ldda_three = galaxy.model.LibraryDatasetDatasetAssociation.query() \
@@ -490,11 +867,67 @@
         assert ldda_three is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_three from the database'
         self.home()
         self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
-        self.check_page_for_string( "1.bed" )
+        self.check_page_for_string( "3.bed" )
+        self.check_page_for_string( message )
         self.check_page_for_string( admin_user.email )
-    def test_085_accessing_dataset_with_private_role_restriction( self ):
+    def test_130_editing_dataset_information_with_new_folder_template( self ):
+        """Testing editing dataset template element information with new inherited folder template"""
+        # Need the current library_item_info_element.id
+        last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \
+            .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first()
+        # Make sure the changed inherited template is included in the ldda information
+        ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id )
+        ele_2_contents = 'II'
+        ele_2_help = 'This is the bill component'
+        ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) )
+        ele_1_contents = 'Volume'
+        ele_1_help = 'This is the kill component'
+        self.edit_ldda_template_element_info( str( library_one.id ), str( folder_two.id ), str( ldda_three.id ),
+            ldda_three.name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents,
+            ele_1_help=ele_1_help, ele_2_help=ele_2_help )
+        self.home()
+    def test_135_add_dataset_with_private_role_restriction_to_folder( self ):
+        """Testing adding a dataset with a private role restriction to a folder"""
+        # Add a dataset restricted by the following:
+        # DATASET_MANAGE_PERMISSIONS = "test@bx.psu.edu" via DefaultUserPermissions
+        # DATASET_ACCESS = "regular_user1" private role via this test method
+        # LIBRARY_ADD = "Role One" via inheritance from parent folder
+        # LIBRARY_MODIFY = "Role One" via inheritance from parent folder
+        # LIBRARY_MANAGE = "Role One" via inheritance from parent folder
+        # "Role One" members are: test@bx.psu.edu, test1@bx.psu.edu, test3@bx.psu.edu
+        # This means that only user test1@bx.psu.edu can see the dataset from the Libraries view
+        #
+        # TODO: this demonstrates a weakness in our logic:  If test@bx.psu.edu cannot
+        # access the dataset from the Libraries view, then the DATASET_MANAGE_PERMISSIONS
+        # setting is useless if test@bx.psu.edu is not an admin.  This should be corrected,
+        # by displaying a warning message on the permissions form.
+        message ='This is a test of the fourth dataset uploaded'
+        ele_name_0 = 'Fu'
+        ele_name_1 = 'Bar'
+        self.add_library_dataset( '4.bed',
+                                  str( library_one.id ),
+                                  str( folder_one.id ),
+                                  folder_one.name,
+                                  file_format='bed',
+                                  dbkey='hg18',
+                                  roles=[ str( regular_user1_private_role.id ) ],
+                                  message=message.replace( ' ', '+' ),
+                                  root=False,
+                                  check_template_str1=ele_name_0,
+                                  check_template_str2=ele_name_1 )
+        global ldda_four
+        ldda_four = galaxy.model.LibraryDatasetDatasetAssociation.query() \
+            .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
+        assert ldda_four is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_four from the database'
+        self.home()
+        self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( "4.bed" )
+        self.check_page_for_string( message )
+        self.check_page_for_string( admin_user.email )
+        self.home()
+    def test_140_accessing_dataset_with_private_role_restriction( self ):
         """Testing accessing a dataset with a private role restriction"""
-        # admin_user should not be able to see 1.bed from the analysis view's access librarys
+        # admin_user should not be able to see 2.bed from the analysis view's access libraries
         self.home()
         self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
         try:
@@ -502,21 +935,21 @@
             raise AssertionError( '%s can see library folder %s when it contains only datasets restricted by role %s' \
                                   % ( admin_user.email, folder_one.name, regular_user1_private_role.description ) )
         except:
-            pass # This is the behavior we want
+            pass
         try:
-            self.check_page_for_string( '1.bed' )
-            raise AssertionError( '%s can see dataset 1.bed in library folder %s when it was restricted by role %s' \
+            self.check_page_for_string( '4.bed' )
+            raise AssertionError( '%s can see dataset 4.bed in library folder %s when it was restricted by role %s' \
                                   % ( admin_user.email, folder_one.name, regular_user1_private_role.description ) )
         except:
-            pass # This is the behavior we want
+            pass
         self.logout()
-        # regular_user1 should be able to see 1.bed from the analysis view's access librarys
+        # regular_user1 should be able to see 4.bed from the analysis view's access librarys
         # since it was associated with regular_user1's private role
         self.login( email='test1@bx.psu.edu' )
         self.home()
         self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
         self.check_page_for_string( folder_one.name )
-        self.check_page_for_string( '1.bed' )
+        self.check_page_for_string( '4.bed' )
         self.logout()
         # regular_user2 should not be able to see 1.bed from the analysis view's access librarys
         self.login( email='test2@bx.psu.edu' )
@@ -525,82 +958,139 @@
             raise AssertionError( '%s can see library folder %s when it contains only datasets restricted by role %s' \
                                   % ( regular_user2.email, folder_one.name, regular_user1_private_role.description ) )
         except:
-            pass # This is the behavior we want
+            pass
         try:
-            self.check_page_for_string( '1.bed' )
-            raise AssertionError( '%s can see dataset 1.bed in library folder %s when it was restricted by role %s' \
+            self.check_page_for_string( '4.bed' )
+            raise AssertionError( '%s can see dataset 4.bed in library folder %s when it was restricted by role %s' \
                                   % ( regular_user2.email, folder_one.name, regular_user1_private_role.description ) )
         except:
-            pass # This is the behavior we want
+            pass
         self.logout()
-        # regular_user3 should not be able to see 1.bed from the analysis view's access librarys
+        # regular_user3 should not be able to see 2.bed from the analysis view's access librarys
         self.login( email='test3@bx.psu.edu' )
         try:
             self.check_page_for_string( folder_one.name )
             raise AssertionError( '%s can see library folder %s when it contains only datasets restricted by role %s' \
                                   % ( regular_user3.email, folder_one.name, regular_user1_private_role.description ) )
         except:
-            pass # This is the behavior we want
+            pass
         try:
-            self.check_page_for_string( '1.bed' )
-            raise AssertionError( '%s can see dataset 1.bed in library folder %s when it was restricted by role %s' \
+            self.check_page_for_string( '4.bed' )
+            raise AssertionError( '%s can see dataset 4.bed in library folder %s when it was restricted by role %s' \
                                   % ( regular_user3.email, folder_one.name, regular_user1_private_role.description ) )
         except:
             pass # This is the behavior we want
         self.logout()
-    def test_090_add_dataset_with_role_restriction_to_folder( self ):
-        """Testing adding a dataset with a role restriction to a folder"""
+        self.login( email=admin_user.email )
+        self.home()
+    def test_145_change_dataset_access_permission( self ):
+        """Testing changing the access permission on a dataset with a private role restriction"""
+        # We need admin_user to be able to access 2.bed
+        permissions_in = [ k for k, v in galaxy.model.Dataset.permitted_actions.items() ] + \
+                         [ k for k, v in galaxy.model.Library.permitted_actions.items() ]
+        permissions_out = []
+        role_ids = "%s,%s" % ( str( role_one.id ), str( admin_user_private_role.id ) )
+        self.set_library_dataset_permissions( str( library_one.id ), str( folder_one.id ), str( ldda_four.id ), ldda_four.name,
+                                              role_ids, permissions_in, permissions_out )
+        # admin_user should now be able to see 4.bed from the analysis view's access libraries
+        self.home()
+        self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( ldda_four.name )
+        self.home()
+    def test_150_editing_restricted_datasets_information( self ):
+        """Testing editing a restricted library dataset's template element information"""
+        ele_1_contents = ''
+        ele_2_contents = ''
+        ele_3_contents = 'Adding Fubar text'
+        self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ),
+            ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents,
+            ele_1_help='This is the wind component'.replace( ' ', '+' ),
+            ele_2_help='This is the bag component'.replace( ' ', '+' ),
+            ele_3_field_name=ldda_one_ele_3_field_name, ele_3_contents=ele_3_contents.replace( ' ', '+'  ) )
+        # Check the updated information from the libraries view
+        self.home()
+        self.visit_url( '%s/library/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s' \
+                        % ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) )
+        self.check_page_for_string( ele_3_contents )
+        try:
+            self.check_page_for_string( 'blown' )
+            raise AssertionError( 'Element contents were not correctly eliminated when the information was edited for ldda %s' % ldda_one.name)
+        except:
+            pass
+        self.home()
+    def test_155_add_dataset_with_role_associated_with_group_and_users( self ):
+        """Testing adding a dataset with a role that is associated with a group and users"""
         self.login( email='test@bx.psu.edu' )
         # Add a dataset restricted by role_two, which is currently associated as follows:
         # groups: group_two
         # users: test@bx.psu.edu, test1@bx.psu.edu via group_two
-        message ='This+is+a+test'
-        self.add_library_dataset( '2.bed',
+        message = 'Testing adding a dataset with a role that is associated with a group and users'
+        ele_name_0 = 'Fu'
+        ele_name_1 = 'Bar'
+        self.add_library_dataset( '5.bed',
                                   str( library_one.id ),
                                   str( folder_one.id ),
                                   folder_one.name,
                                   file_format='bed',
                                   dbkey='hg17',
                                   roles=[ str( role_two.id ) ],
-                                  message=message,
-                                  root=False )
-        global ldda_two
-        ldda_two = galaxy.model.LibraryDatasetDatasetAssociation.query() \
+                                  message=message.replace( ' ', '+' ),
+                                  root=False,
+                                  check_template_str1=ele_name_0,
+                                  check_template_str2=ele_name_1 )
+        global ldda_five
+        ldda_five = galaxy.model.LibraryDatasetDatasetAssociation.query() \
             .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
-        assert ldda_two is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_two from the database'
+        assert ldda_five is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_five from the database'
         self.home()
         self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
-        self.check_page_for_string( "2.bed" )
+        self.check_page_for_string( "5.bed" )
+        self.check_page_for_string( message )
         self.check_page_for_string( admin_user.email )
-    def test_095_accessing_datasets_with_role_restriction( self ):
-        """Testing accessing a dataset with a role restriction"""
-        # admin_user should be able to see 2.bed since she is associated with role_two
+        self.home()
+    def test_160_accessing_dataset_with_role_associated_with_group_and_users( self ):
+        """Testing accessing a dataset with a role that is associated with a group and users"""
+        # admin_user should be able to see 5.bed since she is associated with role_two
         self.home()
         self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
-        self.check_page_for_string( "2.bed" )
+        self.check_page_for_string( "5.bed" )
         self.check_page_for_string( admin_user.email )
         self.logout()
-        # regular_user1 should be able to see 2.bed since she is associated with group_two
+        # regular_user1 should be able to see 5.bed since she is associated with group_two
         self.login( email = 'test1@bx.psu.edu' )
         self.home()
         self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
         self.check_page_for_string( folder_one.name )
-        self.check_page_for_string( '2.bed' )
+        self.check_page_for_string( '5.bed' )
         self.check_page_for_string( admin_user.email )
-        # Check the permissions on the dataset - should be 'access', which only allows viewing the information
+        # Check the permissions on the dataset 5.bed - they are as folows:
+        # DATASET_MANAGE_PERMISSIONS = test@bx.psu.edu
+        # DATASET_ACCESS = Role Two
+        #                  Role Two associations: test@bx.psu.edu and Group Two
+        #                  Group Two members: Role One, Role Two, test1@bx.psu.edu
+        #                  Role One associations: test@bx.psu.edu, test1@bx.psu.edu, test3@bx.psu.edu
+        # LIBRARY_ADD = Role One
+        #               Role One aassociations: test@bx.psu.edu, test1@bx.psu.edu, test3@bx.psu.edu
+        # LIBRARY_MODIFY = Role One
+        #                  Role One aassociations: test@bx.psu.edu, test1@bx.psu.edu, test3@bx.psu.edu
+        # LIBRARY_MANAGE = Role One
+        #                  Role One aassociations: test@bx.psu.edu, test1@bx.psu.edu, test3@bx.psu.edu
         self.home()
-        self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' % ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_two.id ) ) )
-        self.check_page_for_string( '2.bed' )
+        self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' \
+                        % ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_five.id ) ) )
+        self.check_page_for_string( '5.bed' )
         self.check_page_for_string( 'This is the latest version of this library dataset' )
-        self.check_page_for_string( 'View attributes of 2.bed' )
+        # Current user test1@bx.psu.edu has Role One, which has the LIBRARY_MODIFY permission
+        self.check_page_for_string( 'Edit attributes of 5.bed' )
         self.home()
         # Test importing the restricted dataset into a history, can't use the 
         # ~/admin/libraries form as twill barfs on it so we'll simulate the form submission
         # by going directly to the form action
-        self.visit_url( '%s/library/datasets?do_action=add&ldda_ids=%d&library_id=%s' % ( self.url, ldda_two.id, str( library_one.id ) ) )
+        self.visit_url( '%s/library/datasets?do_action=add&ldda_ids=%d&library_id=%s' \
+                        % ( self.url, ldda_five.id, str( library_one.id ) ) )
         self.check_page_for_string( '1 dataset(s) have been imported into your history' )
         self.logout()
-        # regular_user2 should not be able to see 2.bed
+        # regular_user2 should not be able to see 5.bed
         self.login( email = 'test2@bx.psu.edu' )
         self.home()
         self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
@@ -609,96 +1099,35 @@
             raise AssertionError( '%s can see library folder %s when it contains only datasets restricted by role %s' \
                                   % ( regular_user2.email, folder_one.name, regular_user1_private_role.description ) )
         except:
-            pass # This is the behavior we want
+            pass
         try:
-            self.check_page_for_string( '2.bed' )
-            raise AssertionError( '%s can see dataset 2.bed in library folder %s when it was restricted by role %s' \
+            self.check_page_for_string( '5.bed' )
+            raise AssertionError( '%s can see dataset 5.bed in library folder %s when it was restricted by role %s' \
                                   % ( regular_user2.email, folder_one.name, regular_user1_private_role.description ) )
         except:
-            pass # This is the behavior we want
-        # regular_user3 should not be able to see 2.bed
+            pass
+        # regular_user3 should not be able to see folder_one ( even though it does not contain any datasets that she
+        # can access ) since she has Role One, and Role One has all library permissions ( see above ).
         self.login( email = 'test3@bx.psu.edu' )
         self.home()
         self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( folder_one.name )
+        # regular_user3 should not be able to see 5.bed since users must have every role associated
+        # with the dataset in order to access it, and regular_user3 isnot associated with Role Two
         try:
-            self.check_page_for_string( folder_one.name )
-            raise AssertionError( '%s can see library folder %s when it contains only datasets restricted by role %s' \
+            self.check_page_for_string( '5.bed' )
+            raise AssertionError( '%s can see dataset 5.bed in library folder %s when it was restricted by role %s' \
                                   % ( regular_user3.email, folder_one.name, regular_user1_private_role.description ) )
         except:
-            pass # This is the behavior we want
-        try:
-            self.check_page_for_string( '2.bed' )
-            raise AssertionError( '%s can see dataset 2.bed in library folder %s when it was restricted by role %s' \
-                                  % ( regular_user3.email, folder_one.name, regular_user1_private_role.description ) )
-        except:
-            pass # This is the behavior we want
+            pass
         self.logout()
-    def test_100_add_public_dataset_to_root_folder( self ):
-        """Testing adding a public dataset to a library root folder"""
         self.login( email='test@bx.psu.edu' )
-        folder = library_one.root_folder
-        message ='This+is+a+test'
-        self.add_library_dataset( '3.bed',
-                                  str( library_one.id ),
-                                  str( folder.id ),
-                                  folder.name,
-                                  file_format='bed',
-                                  dbkey='hg16',
-                                  roles=[],
-                                  message=message,
-                                  root=True )
-        global ldda_three
-        ldda_three = galaxy.model.LibraryDatasetDatasetAssociation.query() \
-            .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
-        assert ldda_three is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_three from the database'
-        self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) )
-        self.check_page_for_string( "3.bed" )
-        self.check_page_for_string( admin_user.email )
-        self.logout()
-    def test_105_access_public_library_dataset( self ):
-        """Testing accessing a public library dataset"""
-        # regular_user1 should not be able to see 3.bed
-        self.login( email = 'test1@bx.psu.edu' )
-        self.home()
-        self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
-        self.check_page_for_string( library_one.name )
-        self.check_page_for_string( '3.bed' )
-        self.check_page_for_string( admin_user.email )
-        self.logout()
-        # regular_user2 should not be able to see 3.bed
-        self.login( email = 'test2@bx.psu.edu' )
-        self.home()
-        self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
-        self.check_page_for_string( library_one.name )
-        self.check_page_for_string( '3.bed' )
-        self.check_page_for_string( admin_user.email )
-        self.logout()
-        # regular_user3 should not be able to see 3.bed
-        self.login( email = 'test3@bx.psu.edu' )
-        self.home()
-        self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
-        self.check_page_for_string( library_one.name )
-        self.check_page_for_string( '3.bed' )
-        self.check_page_for_string( admin_user.email )
-        # Test selecting "View this dataset's information"
-        self.home()
-        self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' % ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_three.id ) ) )
-        self.check_page_for_string( '3.bed' )
-        self.check_page_for_string( 'This is the latest version of this library dataset' )
-        self.check_page_for_string( 'View attributes of 3.bed' )
-        # Test importing a library dataset into a history
-        self.home()
-        self.visit_url( '%s/library/datasets?library_id=%s&do_action=add&ldda_ids=%d' % ( self.url, str( library_one.id ), ldda_three.id ) )
-        self.check_page_for_string( '1 dataset(s) have been imported into your history' )
-        self.logout()
-    def test_110_copy_dataset_from_history_to_root_folder( self ):
-        """Testing copying a dataset from the current history to a library root folder"""
-        folder = library_one.root_folder
-        self.login( email='test@bx.psu.edu' )
+    def test_165_copy_dataset_from_history_to_subfolder( self ):
+        """Testing copying a dataset from the current history to a subfolder"""
         self.new_history()
-        self.upload_file( "1.bed" )
+        self.upload_file( "6.bed" )
         latest_hda = galaxy.model.HistoryDatasetAssociation.query().order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first()
-        self.add_history_datasets_to_library( str( library_one.id ), str( folder.id ), folder.name, str( latest_hda.id ), root=True )
+        self.add_history_datasets_to_library( str( library_one.id ), str( subfolder_one.id ), subfolder_one.name, str( latest_hda.id ), root=False )
         # Test for DatasetPermissionss, the default setting is "manage permissions"
         last_dataset_created = galaxy.model.Dataset.query().order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first()
         dps = galaxy.model.DatasetPermissions.filter( galaxy.model.DatasetPermissions.table.c.dataset_id==last_dataset_created.id ).all()
@@ -708,14 +1137,145 @@
             raise AssertionError( 'More than 1 DatasetPermissionss created for dataset id: %d' % last_dataset_created.id )
         for dp in dps:
             if not dp.action == 'manage permissions':
-                raise AssertionError( 'DatasetPermissions.action "%s" is not the DefaultHistoryPermission setting of "manage permissions"' % \
-                                      str( dp.action ) )
-    def test_115_add_datasets_from_library_dir( self ):
-        """Testing adding 3 datasets from a library directory to a folder"""
+                raise AssertionError( 'DatasetPermissions.action "%s" is not the DefaultHistoryPermission setting of "manage permissions"' \
+                                      % str( dp.action ) )
+        global ldda_six
+        ldda_six = galaxy.model.LibraryDatasetDatasetAssociation.query() \
+            .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
+        assert ldda_six is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six from the database'
+        # Make sure the correct template was inherited
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) )
+        self.check_page_for_string( 'Fu' )
+        self.check_page_for_string( 'This is the Fu component' )
+        self.check_page_for_string( 'Bar' )
+        self.check_page_for_string( 'This is the Bar component' )
+    def test_170_editing_dataset_attribute_info( self ):
+        """Testing editing a datasets attribute information"""
+        new_ldda_name = '6.bed ( version 1 )'
+        self.edit_ldda_attribute_info( str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ), ldda_six.name, new_ldda_name )
+        self.home()
+        ldda_six.refresh()
+        self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( ldda_six.name )
+        self.home()
+    def test_175_uploading_new_dataset_version( self ):
+        """Testing uploading a new version of a dataset"""
+        message = 'Testing uploading a new version of a dataset'
+        self.upload_new_dataset_version( '6.bed',
+                                         str( library_one.id ),
+                                         str( subfolder_one.id ),
+                                         str( subfolder_one.name ),
+                                         str( ldda_six.library_dataset.id ),
+                                         ldda_six.name,
+                                         file_format='auto',
+                                         dbkey='hg18',
+                                         message=message.replace( ' ', '+' ),
+                                         check_template_str1='Fu',
+                                         check_template_str2='Bar' )
+        global ldda_six_version_two
+        ldda_six_version_two = galaxy.model.LibraryDatasetDatasetAssociation.query() \
+            .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
+        assert ldda_six_version_two is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six_version_two from the database'
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_two.id ) ) )
+        self.check_page_for_string( 'This is the latest version of this library dataset' )
+        # Make sure the correct template was inherited
+        self.check_page_for_string( 'Fu' )
+        self.check_page_for_string( 'This is the Fu component' )
+        self.check_page_for_string( 'Bar' )
+        self.check_page_for_string( 'This is the Bar component' )
+        check_str = 'Expired versions of %s' % ldda_six_version_two.name
+        self.check_page_for_string( check_str )
+        self.check_page_for_string( ldda_six.name )
+        self.home()
+        # Make sure th permissions are the same
+        ldda_six.refresh()
+        if len( ldda_six.actions ) != len( ldda_six_version_two.actions ):
+            raise AssertionError( 'ldda "%s" actions "%s" != ldda "%s" actions "%s"' \
+                % ( ldda_six.name, str( ldda_six.actions ),
+                    ldda_six_version_two.name, str( ldda_six_version_two.actions ) ) )
+        if len( ldda_six.library_dataset.actions ) != len( ldda_six_version_two.library_dataset.actions ):
+            raise AssertionError( 'ldda.library_dataset "%s" actions "%s" != ldda.library_dataset "%s" actions "%s"' \
+                % ( ldda_six.name, str( ldda_six.library_dataset.actions ), ldda_six_version_two.name, str( ldda_six_version_two.library_dataset.actions ) ) )
+        if len( ldda_six.dataset.actions ) != len( ldda_six_version_two.dataset.actions ):
+            raise AssertionError( 'ldda.dataset "%s" actions "%s" != ldda.dataset "%s" actions "%s"' \
+                % ( ldda_six.name, str( ldda_six.dataset.actions ), ldda_six_version_two.name, str( ldda_six_version_two.dataset.actions ) ) )
+        # Check the previous version
+        self.visit_url( "%s/admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) )
+        self.check_page_for_string( 'This is an expired version of this library dataset' )
+        self.home()
+    def test_180_uploading_new_dataset_versions( self ):
+        """Testing uploading new versions of a dataset using a directory of files"""
+        message = 'Testing uploading new versions of a dataset using a directory of files'
+        ldda_six_version_two.refresh()
+        self.upload_new_dataset_versions( str( library_one.id ),
+                                          str( subfolder_one.id ),
+                                          str( subfolder_one.name ),
+                                          str( ldda_six_version_two.library_dataset.id ),
+                                          ldda_six_version_two.name,
+                                          file_format='auto',
+                                          dbkey='hg18',
+                                          message=message.replace( ' ', '+' ),
+                                          check_template_str1='Fu',
+                                          check_template_str2='Bar' )
+        global ldda_six_version_five
+        ldda_six_version_five = galaxy.model.LibraryDatasetDatasetAssociation.query() \
+            .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
+        assert ldda_six_version_five is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six_version_five from the database'
+        self.home()
+        self.visit_url( "%s/admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_five.id ) ) )
+        self.check_page_for_string( 'This is the latest version of this library dataset' )
+        # Make sure the correct template was inherited
+        self.check_page_for_string( 'Fu' )
+        self.check_page_for_string( 'This is the Fu component' )
+        self.check_page_for_string( 'Bar' )
+        self.check_page_for_string( 'This is the Bar component' )
+        check_str = 'Expired versions of %s' % ldda_six_version_five.name
+        self.check_page_for_string( check_str )
+        self.check_page_for_string( ldda_six.name )
+        self.home()
+        # Make sure th permissions are the same
+        ldda_six.refresh()
+        if len( ldda_six.actions ) != len( ldda_six_version_five.actions ):
+            raise AssertionError( 'ldda "%s" actions "%s" != ldda "%s" actions "%s"' \
+                % ( ldda_six.name, str( ldda_six.actions ),
+                    ldda_six_version_five.name, str( ldda_six_version_five.actions ) ) )
+        if len( ldda_six.library_dataset.actions ) != len( ldda_six_version_five.library_dataset.actions ):
+            raise AssertionError( 'ldda.library_dataset "%s" actions "%s" != ldda.library_dataset "%s" actions "%s"' \
+                % ( ldda_six.name, str( ldda_six.library_dataset.actions ), ldda_six_version_five.name, str( ldda_six_version_five.library_dataset.actions ) ) )
+        if len( ldda_six.dataset.actions ) != len( ldda_six_version_five.dataset.actions ):
+            raise AssertionError( 'ldda.dataset "%s" actions "%s" != ldda.dataset "%s" actions "%s"' \
+                % ( ldda_six.name, str( ldda_six.dataset.actions ), ldda_six_version_five.name, str( ldda_six_version_five.dataset.actions ) ) )
+        # Check the previous version
+        self.visit_url( "%s/admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \
+                        ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_two.id ) ) )
+        self.check_page_for_string( 'This is an expired version of this library dataset' )
+        self.home()
+    def test_185_upload_datasets_from_library_dir( self ):
+        """Testing uploading 3 datasets from a library directory to a root folder"""
+        message = 'This is a test for uploading a directory of files'
         roles_tuple = [ ( str( role_one.id ), role_one.name ) ] 
-        self.add_datasets_from_library_dir( str( library_one.id ), str( folder_one.id ), folder_one.name, roles_tuple=roles_tuple, root=False )
-    def test_120_change_permissions_on_datasets_imported_from_library( self ):
-        """Testing changing the permissions on library datasets imported into a history"""
+        self.add_datasets_from_library_dir( str( library_one.id ),
+                                            str( library_one.root_folder.id ),
+                                            library_one.root_folder.name,
+                                            roles_tuple=roles_tuple,
+                                            message=message.replace( '+', ' ' ),
+                                            root=True,
+                                            check_template_str1='wind',
+                                            check_template_str2='bag',
+                                            check_template_str3='Fubar' )
+        self.home()
+        self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) )
+        self.check_page_for_string( admin_user.email )
+        self.check_page_for_string( message )
+        self.home()
+    def test_190_change_permissions_on_datasets_uploaded_from_library_dir( self ):
+        """Testing changing the permissions on datasets uploaded from a directory"""
         # It would be nice if twill functioned such that the above test resulted in a
         # form with the uploaded datasets selected, but it does not ( they're not checked ),
         # so we'll have to simulate this behavior ( not ideal ) for the 'edit' action.  We
@@ -807,21 +1367,22 @@
                     self.check_page_for_string( check_str )
                     raise AssertionError( '%s incorrectly has DATASET_MANAGE_PERMISSIONS on datasets imported from a library' % admin_user.email )
                 except:
-                    pass # This is the behavior we want
+                    pass
                 try:
                     # This should no longer be possible
                     self.check_page_for_string( 'Role members can manage the roles associated with this dataset' )
                     raise AssertionError( '%s incorrectly has DATASET_MANAGE_PERMISSIONS on datasets imported from a library' % admin_user.email )
                 except:
-                    pass # This is the behavior we want
+                    pass
                 try:
                     # This should no longer be possible
                     self.check_page_for_string( 'Role members can import this dataset into their history for analysis' )
                     raise AssertionError( '%s incorrectly has DATASET_MANAGE_PERMISSIONS on datasets imported from a library' % admin_user.email )
                 except:
-                    pass # This is the behavior we want
+                    pass
         check_edit_page2( latest_3_lddas )
-    def test_125_mark_group_deleted( self ):
+        self.home()
+    def test_195_mark_group_deleted( self ):
         """Testing marking a group as deleted"""
         self.home()
         self.visit_url( '%s/admin/groups' % self.url )
@@ -835,13 +1396,13 @@
             raise AssertionError( '%s incorrectly lost all members when it was marked as deleted.' % group_two.name )
         if not group_two.roles:
             raise AssertionError( '%s incorrectly lost all role associations when it was marked as deleted.' % group_two.name )
-    def test_130_undelete_group( self ):
+    def test_200_undelete_group( self ):
         """Testing undeleting a deleted group"""
         self.undelete_group( str( group_two.id ), group_two.name )
         group_two.refresh()
         if group_two.deleted:
             raise AssertionError( '%s was not correctly marked as not deleted.' % group_two.name )
-    def test_135_mark_role_deleted( self ):
+    def test_205_mark_role_deleted( self ):
         """Testing marking a role as deleted"""
         self.home()
         self.visit_url( '%s/admin/roles' % self.url )
@@ -855,83 +1416,90 @@
             raise AssertionError( '%s incorrectly lost all user associations when it was marked as deleted.' % role_two.name )
         if not role_two.groups:
             raise AssertionError( '%s incorrectly lost all group associations when it was marked as deleted.' % role_two.name )
-    def test_140_undelete_role( self ):
+    def test_210_undelete_role( self ):
         """Testing undeleting a deleted role"""
         self.undelete_role( str( role_two.id ), role_two.name )
-    def test_145_mark_library_deleted( self ):
+    def test_215_mark_dataset_deleted( self ):
+        """Testing marking a library dataset as deleted"""
+        self.home()
+        self.delete_library_item( str( library_one.id ), str( ldda_two.library_dataset.id ), ldda_two.name, library_item_type='library_dataset' )
+        self.home()
+        self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) )
+        try:
+            # 2.bed was only contained in the library in 1 place, so it should no longer display
+            self.check_page_for_string( ldda_two.name )
+            raise AssertionError( "Dataset '%s' is incorrectly displayed in the library after it has been deleted." % ldda_two.name )
+        except:
+            pass
+        self.home()
+    def test_220_display_deleted_dataset( self ):
+        """Testing displaying deleted dataset"""
+        self.home()
+        self.visit_url( "%s/admin/browse_library?id=%s&show_deleted=True" % ( self.url, str( library_one.id ) ) )
+        self.check_page_for_string( ldda_two.name )
+        self.home()
+    def test_225_hide_deleted_dataset( self ):
+        """Testing hiding deleted dataset"""
+        self.home()
+        self.visit_url( "%s/admin/browse_library?id=%s&show_deleted=False" % ( self.url, str( library_one.id ) ) )
+        try:
+            self.check_page_for_string( ldda_two.name )
+            raise AssertionError( "Dataset '%s' is incorrectly displayed in the library after it has been deleted." % ldda_two.name )
+        except:
+            pass
+        self.home()
+    def test_230_mark_folder_deleted( self ):
+        """Testing marking a library folder as deleted"""
+        self.home()
+        self.delete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
+        self.home()
+        self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) )
+        try:
+            self.check_page_for_string( folder_two.name )
+            raise AssertionError( "Folder '%s' is incorrectly displayed in the library after it has been deleted." % folder_two.name )
+        except:
+            pass
+        self.home()
+    def test_230_mark_folder_undeleted( self ):
+        """Testing marking a library folder as undeleted"""
+        self.home()
+        self.undelete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
+        self.home()
+        self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) )
+        self.check_page_for_string( folder_two.name )
+        try:
+            # 2.bed was deleted before the folder was deleted, so state should have been saved.  In order
+            # fro 2.bed to be displayed, it would itself have to be marked undeleted.
+            self.check_page_for_string( ldda_two.name )
+            raise AssertionError( "Dataset '%s' is incorrectly displayed in the library after parent folder was undeleted." % ldda_two.name )
+        except:
+            pass
+        self.home()
+    def test_235_mark_library_deleted( self ):
         """Testing marking a library as deleted"""
-        # TODO: this needs to be re-engineered...
-        self.mark_library_deleted( str( library_one.id ), library_one.name )
-        # Make sure the library was deleted
-        library_one.refresh()
-        if not library_one.deleted:
-            raise AssertionError( 'The library id %s named "%s" has not been marked as deleted.' % ( str( library_one.id ), library_one.name ) )
-        def check_folder( library_folder ):
-            for folder in library_folder.folders:
-                folder.refresh()
-                # Make sure all of the library_folders are deleted
-                if not folder.deleted:
-                    raise AssertionError( 'The library_folder named "%s" has not been marked as deleted ( library.id: %s ).' % \
-                                          ( folder.name, str( library_one.id ) ) )
-                check_folder( folder )
-            # Make sure all of the LibraryDatasets and associated objects are deleted
-            library_folder.refresh()
-            for library_dataset in library_folder.datasets:
-                library_dataset.refresh()
-                ldda = library_dataset.library_dataset_dataset_association
-                if ldda:
-                    ldda.refresh()
-                    if not ldda.deleted:
-                        raise AssertionError( 'The library_dataset_dataset_association id %s named "%s" has not been marked as deleted ( library.id: %s ).' % \
-                                              ( str( ldda.id ), ldda.name, str( library_one.id ) ) )
-                    # Make sure none of the datasets have been deleted since that should occur only when the library is purged
-                    ldda.dataset.refresh()
-                    if ldda.dataset.deleted:
-                        raise AssertionError( 'The dataset with id "%s" has been marked as deleted when it should not have been.' % ldda.dataset.id )
-                if not library_dataset.deleted:
-                    raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as deleted ( library.id: %s ).' % \
-                                          ( str( library_dataset.id ), library_dataset.name, str( library_one.id ) ) )
-        check_folder( library_one.root_folder )
-    def test_150_undelete_library( self ):
-        """Testing marking a library as not deleted"""
-        self.undelete_library( str( library_one.id ), library_one.name )
-        # Make sure the library is undeleted
-        library_one.refresh()
-        if library_one.deleted:
-            raise AssertionError( 'The library id %s named "%s" has not been marked as undeleted.' % ( str( library_one.id ), library_one.name ) )
-        def check_folder( library_folder ):
-            for folder in library_folder.folders:
-                folder.refresh()
-                # Make sure all of the library_folders are undeleted
-                if folder.deleted:
-                    raise AssertionError( 'The library_folder id %s named "%s" has not been marked as undeleted ( library.id: %s ).' % \
-                                          ( str( folder.id ), folder.name, str( library_one.id ) ) )
-                check_folder( folder )
-            # Make sure all of the LibraryDatasets and associated objects are undeleted
-            library_folder.refresh()
-            for library_dataset in library_folder.datasets:
-                library_dataset.refresh()
-                ldda = library_dataset.library_dataset_dataset_association
-                if ldda:
-                    ldda.refresh()
-                    if ldda.deleted:
-                        raise AssertionError( 'The library_dataset_dataset_association id %s named "%s" has not been marked as undeleted ( library.id: %s ).' % \
-                                              ( str( ldda.id ), ldda.name, str( library_one.id ) ) )
-                    # Make sure all of the datasets have been undeleted
-                    if ldda.dataset.deleted:
-                        raise AssertionError( 'The dataset with id "%s" has not been marked as undeleted.' % ldda.dataset.id )
-                if library_dataset.deleted:
-                    raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as undeleted ( library.id: %s ).' % \
-                                          ( str( library_dataset.id ), library_dataset.name, str( library_one.id ) ) )
-        check_folder( library_one.root_folder )
-        # Mark library as deleted again so we can test purging it
-        self.mark_library_deleted( str( library_one.id ), library_one.name )
-        # Make sure the library is deleted again
-        library_one.refresh()
-        if not library_one.deleted:
-            raise AssertionError( 'The library id %s named "%s" has not been marked as deleted after it was undeleted.' % \
-                                  ( str( library_one.id ), library_one.name ) )
-    def test_155_purge_user( self ):
+        self.home()
+        # First mark folder_two as deleted to further test state saving when we undelete the library
+        self.delete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
+        self.delete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' )
+        self.home()
+        self.visit_page( 'admin/deleted_libraries' )
+        self.check_page_for_string( library_one.name )
+        self.home()
+    def test_240_mark_library_undeleted( self ):
+        """Testing marking a library as undeleted"""
+        self.home()
+        self.undelete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' )
+        self.home()
+        self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) )
+        self.check_page_for_string( library_one.name )
+        try:
+            # folder_two was marked deleted before the library was deleted, so it should not be displayed
+            self.check_page_for_string( folder_two.name )
+            raise AssertionError( "Deleted folder '%s' is incorrectly displayed in the library after the library was undeleted." % folder_two.name )
+        except:
+            pass
+        self.home()
+    def test_245_purge_user( self ):
         """Testing purging a user account"""
         self.mark_user_deleted( user_id=regular_user3.id, email=regular_user3.email )
         self.purge_user( str( regular_user3.id ), regular_user3.email )
@@ -976,7 +1544,7 @@
             role = galaxy.model.Role.get( ura.role_id )
             if role.type != 'private':
                 raise AssertionError( 'UserRoleAssociations for user %s are not related with the private role.' % regular_user3.email )
-    def test_160_manually_unpurge_user( self ):
+    def test_250_manually_unpurge_user( self ):
         """Testing manually un-purging a user account"""
         # Reset the user for later test runs.  The user's private Role and DefaultUserPermissions for that role
         # should have been preserved, so all we need to do is reset purged and deleted.
@@ -984,7 +1552,7 @@
         regular_user3.purged = False
         regular_user3.deleted = False
         regular_user3.flush()
-    def test_165_purge_group( self ):
+    def test_255_purge_group( self ):
         """Testing purging a group"""
         group_id = str( group_two.id )
         self.mark_group_deleted( group_id, group_two.name )
@@ -999,7 +1567,7 @@
             raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_id )
         # Undelete the group for later test runs
         self.undelete_group( group_id, group_two.name )
-    def test_170_purge_role( self ):
+    def test_260_purge_role( self ):
         """Testing purging a role"""
         role_id = str( role_two.id )
         self.mark_role_deleted( role_id, role_two.name )
@@ -1024,14 +1592,14 @@
         dp = galaxy.model.DatasetPermissions.filter( galaxy.model.DatasetPermissions.table.c.role_id == role_id ).all()
         if dp:
             raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_id )
-    def test_175_manually_unpurge_role( self ):
+    def test_265_manually_unpurge_role( self ):
         """Testing manually un-purging a role"""
         # Manually unpurge, then undelete the role for later test runs
         # TODO: If we decide to implement the GUI feature for un-purging a role, replace this with a method call
         role_two.purged = False
         role_two.flush()
         self.undelete_role( str( role_two.id ), role_two.name )
-    def test_180_purge_library( self ):
+    def test_270_purge_library( self ):
         """Testing purging a library"""
         self.purge_library( str( library_one.id ), library_one.name )
         # Make sure the library was purged
@@ -1065,8 +1633,17 @@
                     raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as deleted.' % \
                                           ( str( library_dataset.id ), library_dataset.name ) )
         check_folder( library_one.root_folder )
-    def test_185_reset_data_for_later_test_runs( self ):
+    def test_275_reset_data_for_later_test_runs( self ):
         """Reseting data to enable later test runs to pass"""
+        ##################
+        # Eliminate all templates and info associations
+        ##################
+        for lia in library_one.library_info_associations:
+            lia.delete()
+            lia.flush()
+        for lita in library_one.library_info_template_associations:
+            lita.delete()
+            lita.flush()
         ##################
         # Eliminate all non-private roles
         ##################
@@ -1080,7 +1657,7 @@
         ##################
         # Eliminate all groups
         ##################
-        for group in [ group_one, group_two ]:
+        for group in [ group_zero, group_one, group_two ]:
             self.mark_group_deleted( str( group.id ), group.name )
             self.purge_group( str( group.id ), group.name )
             # Manually delete the group from the database

    