Ted, have you considered if you can do what you need with the 'allowed'
method of GridOperation? It let's you define a callable condition that
determines if that operation is allowed on a given item. It does not have
access to trans but it would be reasonable to add that.


--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Mon, Jan 7, 2013 at 2:55 AM, Ted Goldstein <t...@soe.ucsc.edu> wrote:

> HI Greg,
> I thought of this. But there is potential bug in it which has security
> implications.  Though it is a low probability event, I have seen this sort
> of leakage happen in other environments where user data was stuck into
> globally shared objects.   The grid object is shared by all requests.  You
> are storing user specific data in the GridOperation. So if there is an
> unfortunate context switch in the middle of the setting the ids int the
> grid operation but before they are used,  the user specific data of one
> user will be visible to the other user.   Of course the solution is to make
> sure the grid is not shared (e.g. it is instantiated or  deep-copied) in
> the function or at least in the request thread that uses it.
>
> Thanks,  I will do this with on a deepcopy of the Grid to ensure that it
> doesn't et shared between threads.   You might want to chsnge the code in
> repository.py
>
> Best regards,
>
> Ted
>
>
> On Jan 6, 2013, at 4:12 PM, Greg Von Kuster wrote:
>
> Hi Ted,
>
> If I understand what your trying to do, I believe I've implemented grid
> operations similar to what your attempting in several places in the Galaxy
> tool shed, so checking the various grid classes and associated methods in
> /lib/galaxy/webapps/community/controllers will give you some examples.
>
> The trick is that you need to define the grid operations outside of the
> grid class itself, but in the method that calls the grid (but just before
> the call to display it) so the request parameters will include the selected
> page ids.
>
> For an example of what I'm talking about, see the following method on
> about line #740 in my
> ~/lib/galaxy/webapps/community/controllers/repository.py code file.
>
> Here is the relevant snippet of code.
>
> def browse_valid_repositories( self, trans, **kwd ):
> ...irrelevant code not displayed...
>         repository_id = None
>         for k, v in kwd.items():
>             changset_revision_str = 'changeset_revision_'
>             if k.startswith( changset_revision_str ):
>                 repository_id = trans.security.encode_id( int( k.lstrip(
> changset_revision_str ) ) )
>                 repository = suc.get_repository_in_tool_shed( trans,
> repository_id )
>                 if repository.tip( trans.app ) != v:
>                     return trans.response.send_redirect( web.url_for(
> controller='repository',
>
> action='preview_tools_in_changeset',
>
> repository_id=trans.security.encode_id( repository.id ),
>
> changeset_revision=v ) )
>         url_args = dict( action='browse_valid_repositories',
>                          operation='preview_tools_in_changeset',
>                          repository_id=repository_id )
>         self.valid_repository_grid.operations = [ grids.GridOperation( 
> "Preview
> and install",
>
> url_args=url_args,
>
> allow_multiple=False,
>
> async_compatible=False ) ]
>         return self.valid_repository_grid( trans, **kwd )
>
> Sorry if I misunderstood your dilemma and this does not help you.
>
> Greg Von Kuster
>
> On Jan 6, 2013, at 4:52 PM, Ted Goldstein wrote:
>
> Hi,
> Based on a suggestion by James Taylor, I am working on extending the
> security model so that pages can use the same RBAC permission system used
> in libraries. In fact, many of my pages have assets (images, etc) which are
> stored in a library. So this is a natural model. Therefore I want to make a
> connection between Pages and Libraries. that is visible to the user and
> extends the security model of page access. The owner of the page
> essentially grants anyone with access to a library access to the page as
> well. This part is going well.  It is few lines of code in the page access
> security code.
>
> The implementation is to that I created a many-to-many relationship table
> LibraryPageAssociation, that  "Connects" Page objects to Library Objects.
>  Grid objects provide a convenient interface to selecting multiple of each.
> In fact, I just extend the  regular PageListGrid  instantiated  by the
> /page/list  action  to select the pages by adding a  new GridOperation
> labeled "Select Libraries"  which then brings up new Grid LibrarySelectGrid
> (similar to the one visualization.py, but simpler) it has one GridOperation
> labeled "Connect Pages to Libraries"   (allows_multi=True).
>
> Here is the problem:  I can pass the page ids (enoded) into the mako page
> that carries the LibrarySelectGrid.  But I don't see a way to
> parametriize  "Connect Pages to Libraries"  GridOperation to pass anything
> out of the page except the Grid Sttate itself.   Do I have to extend
> GridOperation or am I missing something?  I have tried a number of things
> with url_args and global_operation lambda.  But these execute at controller
> instantiation time -- much too early. I need the page_ids that the user
> selects in the PageListGrid.
>
> See the ???? in the bold region below.
>
> Thanks,
> Ted
>
>
> diff -r 13098c7dc32a lib/galaxy/webapps/galaxy/controllers/page.py
> --- a/lib/galaxy/webapps/galaxy/controllers/page.py Sat Jan 05 17:40:49
> 2013 -0800
> +++ b/lib/galaxy/webapps/galaxy/controllers/page.py Sun Jan 06 13:47:05
> 2013 -0800
> @@ -1,3 +1,4 @@
> +import pdb
>  from sqlalchemy import desc, and_
>  from galaxy import model, web
>  from galaxy.web import error, url_for
> @@ -8,9 +9,6 @@
>  from galaxy.util.odict import odict
>  from galaxy.util.json import from_json_string
>  from galaxy.web.base.controller import *
> -"""
> -from galaxy.webapps.galaxy.controllers.library import LibraryListGrid;
> -"""
>
>
>  def format_bool( b ):
> @@ -54,6 +52,7 @@
>          grids.GridOperation( "Edit content", allow_multiple=False,
> url_args=dict( action='edit_content') ),
>          grids.GridOperation( "Edit attributes", allow_multiple=False,
> url_args=dict( action='edit') ),
>          grids.GridOperation( "Share or Publish", allow_multiple=False,
> condition=( lambda item: not item.deleted ), async_compatible=False ),
> +        grids.GridOperation( "Select Library", allow_multiple=True,
>  condition=( lambda item: not item.deleted ), async_compatible=False ),
>          grids.GridOperation( "Delete", confirm="Are you sure you want to
> delete this page?" ),
>      ]
>      def apply_query_filter( self, trans, query, **kwargs ):
> @@ -198,24 +197,37 @@
>          key="free-text-search", visible=False, filterable="standard" )
>                  )
>
> -"""
> -class PageLibrariesSelectionGrid( LibraryListGrid ):
> -    ""
> -    Grid enables user to select multiple Libraries, which are then
> connected to the page.
> -    ""
> -    title = "Select Librariies"
> -    template='/tracks/history_select_grid.mako'
> +class LibrarySelectionGrid( ItemSelectionGrid ):
> +    """ Grid for selecting library. """
> +    # Grid definition.
> +    title = "Select Libraries "
>      model_class = model.Library
> -    datasets_action = 'list_library_datasets'
> -    datasets_param = "f-library"
>      columns = [
> -        NameColumn( "Library Name", key="name", filterable="standard" )
> +       grids.TextColumn( "Library Name", key="name",
> filterable="standard" ),
> +       grids.TextColumn( "Description", key="description",
> filterable="advanced" ),
> +       grids.TextColumn( "Synopsis", key="synopsis",
> filterable="advanced" )
>      ]
> -    num_rows_per_page = 10
> -    use_async = True
> -    use_paging = True
> -"""
> -
> *+    operations = [*
> *+            grids.GridOperation( "Connect to Library",
> allow_multiple=True,*
> *+                url_args=???????????,*
> *+                async_compatible=False ),*
> *+    ]*
> +
> +    def apply_query_filter( self, trans, query, **kwargs ):
> +        """Return all data libraries that the received user can access"""
> +        user = trans.user
> +        current_user_role_ids = [ role.id for role in user.all_roles() ]
> +        library_access_action =
> trans.app.model.Library.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 )
> ) ) ]
> +        # Filter to get libraries accessible by the current user.  Get
> both
> +        # public libraries and restricted libraries accessible by the
> current user.
> +        return query.filter( and_( trans.model.Library.table.c.deleted ==
> False, ( or_( not_( trans.model.Library.table.c.id.in_(
> restricted_library_ids ) ), trans.model.Library.table.c.id.in_(
> accessible_restricted_library_ids ) ) ) ) )  .order_by(
> trans.app.model.Library.name )
> +
>
>  @ -309,16 +321,28 @@
>      _datasets_selection_grid = HistoryDatasetAssociationSelectionGrid()
>      _page_selection_grid = PageSelectionGrid()
>      _visualization_selection_grid = VisualizationSelectionGrid()
> -    """
> -    _libraries_selection_grid = LibrariesSelectionGrid()
> -    """
> +    _libraries_selection_grid = LibrarySelectionGrid()
>
>      @web.expose
>      @web.require_login()
>      def list( self, trans, *args, **kwargs ):
>          """ List user's pages. """
>          # Handle operation
> -        if 'operation' in kwargs and 'id' in kwargs:
> +
> +
> +        # library connect step 1
> +        if 'operation' in kwargs and kwargs['operation'] == 'select
> library':
> +            ids = util.listify( kwargs['id'] )
> +            session = trans.sa_session
> +            pages = [session.query( model.Page ).get(
> trans.security.decode_id( id ) ) for id in ids]
> +            return trans.fill_template(
> "page/library_datasets_select_grid.mako",  pages=pages,
> grid=self._libraries_selection_grid, **kwargs)
> +
> +        # library connect step 2
> +        elif 'operation' in kwargs and kwargs['operation'] == 'connect to
> library':
> +            # TBD
> +            pdb.set_trace()
> +
> +        elif 'operation' in kwargs and 'id' in kwargs:
>              session = trans.sa_session
>              operation = kwargs['operation'].lower()
>              ids = util.listify( kwargs['id'] )
> @@ -765,14 +789,12 @@
>          # Render the list view
>          return self._workflow_selection_grid( trans, **kwargs )
>
> -    """
>      @web.expose
>      @web.require_login("select libraries from all accessible libraries")
>      def list_libraries_for_selection( self, trans, **kwargs ):
>          " Returns HTML that enables a user to select one or more
> libraries. "
>          # Render the list view
>          return self._libraries_selection_grid( trans, **kwargs )
> -    """
>
>      @web.expose
>      @web.require_login("select a visualization from saved visualizations")
>
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