Send the web freamework ( trans ) to the grid's build_initial_query() method rather than the web framework's db session so that the method can take advantage of all of the web freamwork's attributes. Change the library controller to use grids for the data libraries display.

2026-09-24 16:30:27 +08:00 · 2010-05-24 11:22:12 -04:00
parent e30171727f
commit 033bcecd0d
15 changed files with 121 additions and 98 deletions
@@ -103,8 +103,8 @@ class UserListGrid( grids.Grid ):
    use_paging = True
    def get_current_item( self, trans ):
        return trans.user
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )

 class RoleListGrid( grids.Grid ):
    class NameColumn( grids.TextColumn ):
@@ -197,8 +197,8 @@ class RoleListGrid( grids.Grid ):
    use_paging = True
    def get_current_item( self, trans ):
        return None
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )
    def apply_default_filter( self, trans, query, **kwargs ):
        return query.filter( model.Role.type != model.Role.types.PRIVATE )

@@ -275,8 +275,8 @@ class GroupListGrid( grids.Grid ):
    use_paging = True
    def get_current_item( self, trans ):
        return None
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )

 class AdminGalaxy( BaseController, Admin ):
    
@@ -110,8 +110,8 @@ class SharedHistoryListGrid( grids.Grid ):
        grids.GridOperation( "Unshare" )
    ]
    standard_filters = []
-    def build_initial_query( self, session ):
-        return session.query( self.model_class ).join( 'users_shared_with' )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class ).join( 'users_shared_with' )
    def apply_default_filter( self, trans, query, **kwargs ):
        return query.filter( model.HistoryUserShareAssociation.user == trans.user )
        
@@ -138,9 +138,9 @@ class HistoryAllPublishedGrid( grids.Grid ):
        key="free-text-search", visible=False, filterable="standard" )
                )
    operations = []
-    def build_initial_query( self, session ):
+    def build_initial_query( self, trans ):
        # Join so that searching history.user makes sense.
-        return session.query( self.model_class ).join( model.User.table )
+        return trans.sa_session.query( self.model_class ).join( model.User.table )
    def apply_default_filter( self, trans, query, **kwargs ):
        # A public history is published, has a slug, and is not deleted.
        return query.filter( self.model_class.published == True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False )
@@ -1,12 +1,73 @@
 from galaxy.web.base.controller import *
+from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.model.orm import *
 from galaxy.datatypes import sniff
-from galaxy import util
+from galaxy import model, util
 from galaxy.util.odict import odict

 log = logging.getLogger( __name__ )

+class LibraryListGrid( grids.Grid ):
+    class NameColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, library ):
+            return library.name
+    class DescriptionColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, library ):
+            if library.description:
+                return library.description
+            return ''
+    # Grid definition
+    title = "Data Libraries"
+    model_class = model.Library
+    template='/library/grid.mako'
+    default_sort_key = "name"
+    columns = [
+        NameColumn( "Name",
+                    key="name",
+                    model_class=model.Library,
+                    link=( lambda library: dict( operation="browse", id=library.id ) ),
+                    attach_popup=False,
+                    filterable="advanced" ),
+        DescriptionColumn( "Description",
+                           key="description",
+                           model_class=model.Library,
+                           attach_popup=False,
+                           filterable="advanced" ),
+    ]
+    columns.append( grids.MulticolFilterColumn( "Search", 
+                                                cols_to_filter=[ columns[0], columns[1] ], 
+                                                key="free-text-search",
+                                                visible=False,
+                                                filterable="standard" ) )
+    standard_filters = []
+    default_filter = dict( name="All", description="All", deleted="False", purged="False" )
+    num_rows_per_page = 50
+    preserve_state = False
+    use_paging = True
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class ).filter( self.model_class.table.c.deleted == False )
+    def apply_default_filter( self, trans, query, **kwd ):
+        current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ]
+        library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action
+        restricted_library_ids = [ lp.library_id for lp in trans.sa_session.query( trans.model.LibraryPermissions ) \
+                                                                           .filter( trans.model.LibraryPermissions.table.c.action == library_access_action ) \
+                                                                           .distinct() ]
+        accessible_restricted_library_ids = [ lp.library_id for lp in trans.sa_session.query( trans.model.LibraryPermissions ) \
+                                                                                      .filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action,
+                                                                                                     trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ]
+        if not trans.user:
+            # Filter to get only public libraries, a library whose id 
+            # is not in restricted_library_ids is a public library
+            return query.filter( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ) )
+        else:
+            # Filter to get libraries accessible by the current user, get both 
+            # public libraries and restricted libraries accessible by the current user.
+            return query.filter( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ),
+                                      trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) )
 class Library( BaseController ):
+    
+    library_list_grid = LibraryListGrid()
+
    @web.expose
    def index( self, trans, **kwd ):
        params = util.Params( kwd )
@@ -18,19 +79,12 @@ class Library( BaseController ):
                                    status=status )
    @web.expose
    def browse_libraries( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        current_user_roles = trans.get_current_user_roles()
-        all_libraries = trans.sa_session.query( trans.app.model.Library ) \
-                                        .filter( trans.app.model.Library.table.c.deleted==False ) \
-                                        .order_by( trans.app.model.Library.name )
-        authorized_libraries = []
-        for library in all_libraries:
-            if trans.app.security_agent.can_access_library( current_user_roles, library ):
-                authorized_libraries.append( library )
-        return trans.fill_template( '/library/browse_libraries.mako', 
-                                    libraries=authorized_libraries,
-                                    default_action=params.get( 'default_action', None ),
-                                    message=message,
-                                    status=status )
+        if 'operation' in kwd:
+            operation = kwd['operation'].lower()
+            if operation == "browse":
+                return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                                  action='browse_library',
+                                                                  cntrller='library',
+                                                                  **kwd ) )
+        # Render the list view
+        return self.library_list_grid( trans, **kwd )
@@ -69,8 +69,8 @@ class LibraryListGrid( grids.Grid ):
    num_rows_per_page = 50
    preserve_state = False
    use_paging = True
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )

 class LibraryAdmin( BaseController ):

@@ -78,16 +78,16 @@ class LibraryAdmin( BaseController ):

    @web.expose
    @web.require_admin
-    def browse_libraries( self, trans, **kwargs ):
-        if 'operation' in kwargs:
-            operation = kwargs['operation'].lower()
+    def browse_libraries( self, trans, **kwd ):
+        if 'operation' in kwd:
+            operation = kwd['operation'].lower()
            if operation == "browse":
                return trans.response.send_redirect( web.url_for( controller='library_common',
                                                                  action='browse_library',
                                                                  cntrller='library_admin',
-                                                                  **kwargs ) )
+                                                                  **kwd ) )
        # Render the list view
-        return self.library_list_grid( trans, **kwargs )
+        return self.library_list_grid( trans, **kwd )
    @web.expose
    @web.require_admin
    def create_library( self, trans, **kwd ):
@@ -71,9 +71,9 @@ class PageAllPublishedGrid( grids.Grid ):
        cols_to_filter=[ columns[0], columns[1], columns[2], columns[3] ], 
        key="free-text-search", visible=False, filterable="standard" )
                )
-    def build_initial_query( self, session ):
+    def build_initial_query( self, trans ):
        # Join so that searching history.user makes sense.
-        return session.query( self.model_class ).join( model.User.table )
+        return trans.sa_session.query( self.model_class ).join( model.User.table )
    def apply_default_filter( self, trans, query, **kwargs ):
        return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True )
                
@@ -126,8 +126,8 @@ class RequestsGrid( grids.Grid ):
    ]
    def apply_default_filter( self, trans, query, **kwd ):
        return query.filter_by( user=trans.user )
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )

 class Requests( BaseController ):
    request_grid = RequestsGrid()
@@ -71,8 +71,8 @@ class DatasetSelectionGrid( grids.Grid ):
        DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False )
    ]
    
-    def build_initial_query( self, session ):
-        return session.query( self.model_class ).join( model.History.table).join( model.Dataset.table )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class ).join( model.History.table).join( model.Dataset.table )
    def apply_default_filter( self, trans, query, **kwargs ):
        if self.available_tracks is None:
             self.available_tracks = trans.app.datatypes_registry.get_available_tracks()
@@ -55,9 +55,9 @@ class VisualizationAllPublishedGrid( grids.Grid ):
        cols_to_filter=[ columns[0], columns[1], columns[2], columns[3] ], 
        key="free-text-search", visible=False, filterable="standard" )
                )
-    def build_initial_query( self, session ):
+    def build_initial_query( self, trans ):
        # Join so that searching history.user makes sense.
-        return session.query( self.model_class ).join( model.User.table )
+        return trans.sa_session.query( self.model_class ).join( model.User.table )
    def apply_default_filter( self, trans, query, **kwargs ):
        return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True )

@@ -75,9 +75,9 @@ class StoredWorkflowAllPublishedGrid( grids.Grid ):
        key="free-text-search", visible=False, filterable="standard" )
                )
    operations = []
-    def build_initial_query( self, session ):
+    def build_initial_query( self, trans ):
        # Join so that searching stored_workflow.user makes sense.
-        return session.query( self.model_class ).join( model.User.table )
+        return trans.sa_session.query( self.model_class ).join( model.User.table )
    def apply_default_filter( self, trans, query, **kwargs ):
        # A public workflow is published, has a slug, and is not deleted.
        return query.filter( self.model_class.published==True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False )
@@ -45,7 +45,6 @@ class Grid( object ):
        webapp = kwargs.get( 'webapp', 'galaxy' )
        status = kwargs.get( 'status', None )
        message = kwargs.get( 'message', None )
-        session = trans.sa_session
        # Build a base filter and sort key that is the combination of the saved state and defaults. Saved state takes preference over defaults.
        base_filter = {}
        if self.default_filter:
@@ -60,7 +59,7 @@ class Grid( object ):
            if pref_name in trans.get_user().preferences:
                base_sort_key = from_json_string( trans.get_user().preferences[pref_name] )
        # Build initial query
-        query = self.build_initial_query( session )
+        query = self.build_initial_query( trans )
        query = self.apply_default_filter( trans, query, **kwargs )
        # Maintain sort state in generated urls
        extra_url_args = {}
@@ -258,8 +257,8 @@ class Grid( object ):
        pass
    def get_current_item( self, trans ):
        return None
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )
    def apply_default_filter( self, trans, query, **kwargs):
        return query
    
@@ -113,8 +113,8 @@ class UserListGrid( grids.Grid ):
    use_paging = True
    def get_current_item( self, trans ):
        return trans.user
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )

 class RoleListGrid( grids.Grid ):
    class NameColumn( grids.TextColumn ):
@@ -211,8 +211,8 @@ class RoleListGrid( grids.Grid ):
    use_paging = True
    def get_current_item( self, trans ):
        return None
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )
    def apply_default_filter( self, trans, query, **kwd ):
        return query.filter( model.Role.type != model.Role.types.PRIVATE )

@@ -294,8 +294,8 @@ class GroupListGrid( grids.Grid ):
    use_paging = True
    def get_current_item( self, trans ):
        return None
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )

 class ManageCategoryListGrid( grids.Grid ):
    class NameColumn( grids.TextColumn ):
@@ -360,8 +360,8 @@ class ManageCategoryListGrid( grids.Grid ):
    use_paging = True
    def get_current_item( self, trans ):
        return None
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )

 class ToolsByCategoryListGrid( grids.Grid ):
    class NameColumn( grids.TextColumn ):
@@ -423,8 +423,8 @@ class ToolsByCategoryListGrid( grids.Grid ):
    num_rows_per_page = 50
    preserve_state = False
    use_paging = True
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )
    def apply_default_filter( self, trans, query, **kwd ):
        ids = kwd.get( 'ids', False )
        if ids:
@@ -546,8 +546,8 @@ class ToolListGrid( grids.Grid ):
    num_rows_per_page = 50
    preserve_state = False
    use_paging = True
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )
    def apply_default_filter( self, trans, query, **kwd ):
        ids = kwd.get( 'ids', False )
        if ids:
@@ -94,8 +94,8 @@ class ToolListGrid( grids.Grid ):
    num_rows_per_page = 50
    preserve_state = False
    use_paging = True
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )
    def apply_default_filter( self, trans, query, **kwd ):
        ids = kwd.get( 'ids', False )
        if not ids:
@@ -218,8 +218,8 @@ class ToolsByUserListGrid( grids.Grid ):
    num_rows_per_page = 50
    preserve_state = False
    use_paging = True
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )
    def apply_default_filter( self, trans, query, **kwd ):
        ids = kwd.get( 'ids', False )
        if not ids:
@@ -295,8 +295,8 @@ class ToolsByCategoryListGrid( grids.Grid ):
    num_rows_per_page = 50
    preserve_state = False
    use_paging = True
-    def build_initial_query( self, session ):
-        return session.query( self.model_class )
+    def build_initial_query( self, trans ):
+        return trans.sa_session.query( self.model_class )

 class ToolController( BaseController ):

@@ -1,31 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<%def name="title()">Browse Data Libraries</%def>
-
-<h2>Data Libraries</h2>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-%if not libraries:
-    You are not authorized to access any libraries
-%else:
-    <table class="grid">
-        <thead>
-            <tr>
-                <th>Name</th>
-                <th>Description</th>
-            </tr>
-        </thead>
-        <tbody>
-            %for library in libraries:    
-                <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
-                    <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( library.id ), hidden_folder_ids='' )}">${library.name}</a></td>
-                    <td>${library.description}</td>
-                </tr>             
-            %endfor
-        </tbody>
-    </table>
-%endif
@@ -0,0 +1 @@
+<%inherit file="/grid_base.mako"/>
@@ -192,7 +192,7 @@ class TestLibrarySecurity( TwillTestCase ):
        # regular_user2 should not be to see the library since they do not have 
        # Role One which is associated with the LIBRARY_ACCESS permission
        self.login( email=regular_user2.email )
-        self.browse_libraries_regular_user( check_str1="You are not authorized to access any libraries" )
+        self.browse_libraries_regular_user( check_str1="No Items" )
        self.logout()
        # regular_user3 should not be able to see 1.bed from the analysis view's access librarys
        self.login( email=regular_user3.email )