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https://github.com/galaxyproject/galaxy.git
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More merging
This commit is contained in:
Nate Coraor
@@ -461,6 +461,7 @@ class Admin( BaseController ):
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galaxy.model.GroupDatasetAssociation.table.c.permitted_actions ] )
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for row2 in q2.execute():
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total_datasets = row2.total_datasets
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libraries = []
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permitted_actions = []
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# There may not yet be any GroupDatasetAssociations, in which case no
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# actions will be found
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@@ -468,16 +469,42 @@ class Admin( BaseController ):
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for action in row2.permitted_actions:
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permitted_actions.append( action.encode( 'ascii' ) )
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permitted_actions.sort()
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# If we have permitted actions, then we have at least 1 GroupDatasetAssociation, in
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# which case, we can see if we have any Libraries that the user can access
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libs = trans.app.model.Library.select()
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for library in libs:
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folder = library.root_folder
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components = list( folder.folders ) + list( folder.datasets )
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for component in components:
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if self.renderable( trans, component, row2.group_id ):
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libraries.append( library.id )
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break
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groups.append( ( row.group_id,
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escape( row.group_name, entities ),
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row.group_priority,
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row2.total_datasets,
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permitted_actions ) )
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permitted_actions,
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libraries ) )
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return trans.fill_template( '/admin/dataset_security/specified_users_groups.mako',
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user_id=user_id,
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user_email=escape( user_email, entities ),
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groups=groups,
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groups=groups,
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msg=msg )
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@web.expose
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def specified_users_group_libraries( self, trans, **kwd ):
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if not self.user_is_admin( trans ):
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return trans.show_error_message( no_privilege_msg )
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params = util.Params( kwd )
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msg = params.msg
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library_ids = params.library_ids.split( ',' )
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libraries = []
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for id in library_ids:
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library = trans.app.model.Library.get( id )
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libraries.append( library )
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return trans.fill_template( '/admin/library/specified_users_group_libraries.mako',
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user_email=params.user_email,
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group_name=params.group_name,
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libraries=libraries )
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# Galaxy Library Stuff
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@web.expose
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@@ -794,3 +821,28 @@ class Admin( BaseController ):
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err=None )
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else:
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return trans.show_error_message( "Invalid dataset specified" )
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def renderable( self, trans, component, group_id ):
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render = False
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if isinstance( component, trans.app.model.LibraryFolder ):
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# Check the folder's datasets to see what can be rendered
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for library_folder_dataset_assoc in component.datasets:
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if render:
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break
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dataset = trans.app.model.Dataset.get( library_folder_dataset_assoc.dataset_id )
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for group_dataset_assoc in dataset.groups:
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if group_dataset_assoc.group_id == group_id:
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render = True
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break
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# Check the folder's sub-folders to see what can be rendered
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if not render:
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for library_folder in component.folders:
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self.renderable( trans, library_folder, group_id )
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elif isinstance( component, trans.app.model.LibraryFolderDatasetAssociation ):
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render = False
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dataset = trans.app.model.Dataset.get( component.dataset_id )
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for group_dataset_assoc in dataset.groups:
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if group_dataset_assoc.group_id == group_id:
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render = True
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break
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return render
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@@ -33,64 +33,46 @@ class Library( BaseController ):
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group_ids.append( user_group_assoc.group_id )
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library = trans.app.model.Library.get( library_id )
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return trans.fill_template( '/library/library.mako', library=library, group_ids=group_ids )
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if user:
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# Only display libraries that contain datasets associated with the user's groups
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group_ids = []
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for user_group_assoc in user.groups:
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group = trans.app.model.Group.get( user_group_assoc.group_id )
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group_ids.append( group.id )
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else:
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if user:
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# Only display libraries that contain datasets associated with the user's groups
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group_ids = []
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for user_group_assoc in user.groups:
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group = trans.app.model.Group.get( user_group_assoc.group_id )
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group_ids.append( group.id )
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else:
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# Only display libraries that contain datasets associated with the public group
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group_ids = [ trans.app.model.Group.select_by( name='public' )[0].id ]
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libs = trans.app.model.Library.select()
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for library in libs:
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user_can_access = False
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# Check for public datasets in the Library's root folder
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for library_folder_dataset_assoc in library.root_folder.datasets:
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if user_can_access:
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folder = library.root_folder
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components = list( folder.folders ) + list( folder.datasets )
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for component in components:
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if self.renderable( trans, component, group_ids ):
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libraries.append( library )
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break
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dataset = trans.app.model.Dataset.get( library_folder_dataset_assoc.dataset_id )
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for group_dataset_assoc in dataset.groups:
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if group_dataset_assoc.group_id in group_ids:
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libraries.append( library )
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user_can_access = True
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break
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for folder in library.root_folder.folders:
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if user_can_access:
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break
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for library_folder_dataset_assoc in folder.datasets:
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if user_can_access:
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break
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dataset = trans.app.model.Dataset.get( library_folder_dataset_assoc.dataset_id )
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for group_dataset_assoc in dataset.groups:
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if group_dataset_assoc.group_id in group_ids:
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libraries.append( library )
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user_can_access = True
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break
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else:
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# Only display libraries that contain datasets associated with the public group
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group_ids = [ trans.app.model.Group.select_by( name='public' )[0].id ]
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libs = trans.app.model.Library.select()
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for library in libs:
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public_library = False
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# Check for public datasets in the Library's root folder
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for library_folder_dataset_assoc in library.root_folder.datasets:
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if public_library:
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break
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dataset = trans.app.model.Dataset.get( library_folder_dataset_assoc.dataset_id )
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for group_dataset_assoc in dataset.groups:
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if group_dataset_assoc.group_id in group_ids:
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libraries.append( library )
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public_library = True
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break
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# Check for public datasets in the root folder's sub-folders
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for folder in library.root_folder.folders:
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if public_library:
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break
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for library_folder_dataset_assoc in folder.datasets:
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if public_library:
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break
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dataset = trans.app.model.Dataset.get( library_folder_dataset_assoc.dataset_id )
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for group_dataset_assoc in dataset.groups:
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if group_dataset_assoc.group_id in group_ids:
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libraries.append( library )
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public_library = True
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break
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return trans.fill_template( '/library/libraries.mako', group_ids=group_ids, libraries=libraries )
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def renderable( self, trans, component, group_ids ):
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render = False
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if isinstance( component, trans.app.model.LibraryFolder ):
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# Check the folder's datasets to see what can be rendered
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for library_folder_dataset_assoc in component.datasets:
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if render:
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break
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dataset = trans.app.model.Dataset.get( library_folder_dataset_assoc.dataset_id )
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for group_dataset_assoc in dataset.groups:
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if group_dataset_assoc.group_id in group_ids:
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render = True
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break
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# Check the folder's sub-folders to see what can be rendered
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if not render:
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for library_folder in component.folders:
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self.renderable( trans, library_folder, group_ids )
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elif isinstance( component, trans.app.model.LibraryFolderDatasetAssociation ):
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render = False
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dataset = trans.app.model.Dataset.get( component.dataset_id )
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for group_dataset_assoc in dataset.groups:
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if group_dataset_assoc.group_id in group_ids:
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render = True
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break
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return render
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@@ -17,20 +17,27 @@
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<h3 align="center">Groups of which '${email}' is a member</h3>
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<table align="center" class="colored">
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%if msg:
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<tr><td colspan="4"><p class="ok_bgr">${msg}</p></td></tr>
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<tr><td colspan="5"><p class="ok_bgr">${msg}</p></td></tr>
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%endif
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%if len( groups ) == 0:
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<tr><td colspan="4">User '${email}' belongs to no groups</td></tr>
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<tr><td colspan="5">User '${email}' belongs to no groups</td></tr>
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%else:
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<tr class="header">
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<td>Group</td>
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<td>Priority</td>
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<td>Datasets</td>
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<td>Permitted Actions on Datasets</td>
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<td>Containing Libraries</td>
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</tr>
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<% ctr = 0 %>
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%for group in groups:
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<% gn = unescape( group[1], unentities ) %>
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<%
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gn = unescape( group[1], unentities )
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library_ids = ''
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for library_id in group[5]:
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library_ids += "%s," % library_id
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library_ids = library_ids.rstrip( ',' )
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%>
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%if ctr % 2 == 1:
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<tr class="odd_row">
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%else:
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@@ -48,9 +55,16 @@
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${da}<br/>
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%endfor
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</td>
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<td>
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%if len( group[5] ) > 0:
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<a href="${h.url_for( controller='admin', action='specified_users_group_libraries', user_email=user_email, group_name=group[1], library_ids=library_ids )}">${len( group[5] )}</a>
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%else:
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${len( group[5] )}
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%endif
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</td>
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</tr>
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<% ctr += 1 %>
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%endfor
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%endfor
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%endif
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</table>
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</div>
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@@ -0,0 +1,27 @@
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<%inherit file="/base.mako"/>
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<%
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from galaxy.web.controllers.admin import entities, unentities
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from xml.sax.saxutils import escape, unescape
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%>
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<%def name="title()">Specified Users Group Libraries{</%def>
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<%
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gn = unescape( group_name, unentities )
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email = unescape( user_email, unentities )
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%>
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<div class="toolForm">
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<div class="form-row">
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<a href="${h.url_for( controller='admin', action='libraries' )}">Libraries</a> |
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<a href="${h.url_for( controller='admin', action='groups' )}">Groups</a> |
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<a href="${h.url_for( controller='admin', action='users' )}">Users</a>
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</div>
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<div class="toolFormTitle">Libraries containing datasets associated with group '${gn}' that user '${email}' can access</div>
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<div class="toolFormBody">
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%for library in libraries:
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<div class="form-row">
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<a href="${h.url_for( controller='admin', action='library', id=library.id )}">${library.name}</a>
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</div>
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%endfor
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</div>
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</div>
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@@ -13,7 +13,6 @@
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if group_dataset_assoc.group_id in group_ids:
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render = True
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break
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# TODO: Do we need to upgrade sqlalchemy? The following shouldn't be necessary if the mappers work correctly.
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# Check the folder's sub-folders to see what can be rendered
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for library_folder in component.folders:
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render_component( library_folder )
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