Hi Ted,
This looks like a good solution to me. I'll add your contributions to the
Galaxy code base as soon as I get a chance.
Thanks for all of your efforts on this!
Greg Von Kuster
On Jan 7, 2013, at 3:22 PM, Ted Goldstein wrote:
> Hi Greg and James,
> This has become a plumbing project. What starts off as fixing a leaky faucet
> ends being a $200 bill replacing the entire sink ;-). But I don't see anyway
> around it.
>
> Yes, there is a lot of power in the allowed method since it uses a function
> or a lambda. There are two problems with this: idea (1) it feels wrong to
> have a predicate method called allowed modify the state of the object.
> and worse,(2) the Python context that the lambda is capturing is at global
> instantiation time. But the data that I need captured and saved in the page
> exist only after the user has made a set of choices. Thus it only exists in a
> previous call to thePage.list() method.
>
> Another problem.
> Since this is a multi operation, the state that needs to be passed cannot go
> into the form URL itself of the form. I see that the call to get the URL of
> the form in grid_base.mako at line 702 does not take any operation arguments.
> Which is correct. Normally the submit button on an HTML form does not
> modify the form's URL The usual solution from an HTML perspective is to have
> hidden input fields on an HTML form. So the solution would be to extend the
> Grid class to generate and use hidden input fields. This would be done on a
> copy of the grid object;. So there needs to be a new Grid method.
>
> (my changes in bold)
>
> class Grid
> ...
> def clone_with_pass_through_data(self, data_dict):
> # make a copy of myself for use in passing though data
> clone = deepcopy(self)
> clone.pass_through_data = data_dict
> return clone
>
>
> my example use in Page.list()
> # Clone a copy of grid to have the pageids.
> grid =
> self._libraries_selection_grid.clone_with_pass_through_data({"pageids":
> pageidsraw});
> return trans.fill_template(
> "page/library_datasets_select_grid.mako", pagetitles=pagetitles, grid=grid,
> **kwargs)
>
> pass_through_data has a three line implementation in grid_base.mako
> <form action="${url()}" method="post" onsubmit="return false;">
> <input type="hidden" name="webapp" value="${webapp}"/>
>
> %for pass_name, pass_value in grid.pass_through_data.items():
> <input type="hidden" name="${pass_name}" value="${pass_value}"/>
> %endfor
> ..
>
> But nothing is simple, form parameters arguments are more complex than they
> sem at first.
>
>
> function go_to_URL() {
> // Not async request.
> url_args['async'] = false;
>
> // Build argument string.
> var arg_str = "";
> for (var arg in url_args) {
> arg_str = arg_str + arg + "=" + url_args[arg] + "&";
> }
>
> // add in hidden fields
> $('input[type=hidden]').each(function() {
> if (this.name == "webapp" || this.name ==
> "select_all_checkbox")
> return
> else
> arg_str = arg_str + this.name + "=" + this.value + "&";
> })
>
>
> // Go.
> window.location = encodeURI( "${h.url_for()}?" + arg_str );
> }
>
>
> What do you think of this idea?
>
> Ted
>
>
>
> On Jan 7, 2013, at 7:00 AM, James Taylor wrote:
>
>> 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")
>>>>
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
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>>>> and other Galaxy lists, please use the interface at:
>>>>
>>>> http://lists.bx.psu.edu/
>>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>>
>
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