Include 'mixin' in names of many common controller mixins.

lib/galaxy/tools/genome_index/__init__.py

@@ -3,7 +3,7 @@ from galaxy import model, util
 from galaxy.web.framework.helpers import to_unicode
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.util.json import *
-from galaxy.web.base.controller import UsesHistory
+from galaxy.web.base.controller import UsesHistoryMixin
 from galaxy.tools.data import ToolDataTableManager
 
 log = logging.getLogger(__name__)
@@ -63,8 +63,6 @@ class GenomeIndexToolWrapper( object ):
 
         if gitd:
             destination = None
-            alldone = True
-            indexjobs = gitd.deferred.params[ 'indexjobs' ]
             tdtman = ToolDataTableManager()
             xmltree = tdtman.load_from_config_file(app.config.tool_data_table_config_path)
             for node in xmltree:
@@ -165,14 +163,6 @@ class GenomeIndexToolWrapper( object ):
                         self._check_link( fasta, target )
             for line in location:
                 self._add_line( line[ 'file' ], line[ 'line' ] )
-            for indexjob in indexjobs:
-                js = sa_session.query( model.Job ).filter_by( id=indexjob ).first()
-                if js.state not in [ 'ok', 'done', 'error' ]:
-                    alldone = False
-            if alldone:
-                gitd.deferred.state = 'ok'
-                sa_session.add( gitd.deferred )
-                sa_session.flush()
         
     def _check_link( self, targetfile, symlink ):
         target = os.path.relpath( targetfile, os.path.dirname( symlink ) )

lib/galaxy/tools/imp_exp/__init__.py

@@ -4,7 +4,7 @@ from galaxy.tools.parameters.basic import UnvalidatedValue
 from galaxy.web.framework.helpers import to_unicode
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.util.json import *
-from galaxy.web.base.controller import UsesHistory
+from galaxy.web.base.controller import UsesHistoryMixin
 
 log = logging.getLogger(__name__)
 
@@ -42,7 +42,7 @@ def load_history_imp_exp_tools( toolbox ):
     toolbox.tools_by_id[ history_imp_tool.id ] = history_imp_tool
     log.debug( "Loaded history import tool: %s", history_imp_tool.id )
     
-class JobImportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ):
+class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ):
     """ 
         Class provides support for performing jobs that import a history from
         an archive.
@@ -263,7 +263,7 @@ class JobImportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ):
                 jiha.job.stderr += "Error cleaning up history import job: %s" % e
                 db_session.flush()
 
-class JobExportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ):
+class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ):
     """ 
         Class provides support for performing jobs that export a history to an
         archive. 

lib/galaxy/web/api/datasets.py

@@ -10,7 +10,7 @@ from galaxy.model.orm import *
 
 log = logging.getLogger( __name__ )
 
-class DatasetsController( BaseAPIController, UsesHistoryDatasetAssociation ):
+class DatasetsController( BaseAPIController, UsesHistoryMixinDatasetAssociationMixin ):
 
     @web.expose_api
     def index( self, trans, hda_id, **kwd ):

lib/galaxy/web/api/histories.py

@@ -12,7 +12,7 @@ from galaxy.util.bunch import Bunch
 
 log = logging.getLogger( __name__ )
 
-class HistoriesController( BaseAPIController, UsesHistory ):
+class HistoriesController( BaseAPIController, UsesHistoryMixin ):
 
     @web.expose_api
     def index( self, trans, deleted='False', **kwd ):
@@ -153,7 +153,7 @@ class HistoriesController( BaseAPIController, UsesHistory ):
         POST /api/histories/deleted/{encoded_quota_id}/undelete
         Undeletes a quota
         """
-        history = self.get_history( trans, id, check_ownership=True, check_accessible=False, deleted=True )
+        history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False, deleted=True )
         history.deleted = False
         trans.sa_session.add( history )
         trans.sa_session.flush()

lib/galaxy/web/api/history_contents.py

@@ -12,7 +12,7 @@ import routes
 
 log = logging.getLogger( __name__ )
 
-class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociation, UsesHistory, UsesLibrary, UsesLibraryItems ):
+class HistoryContentsController( BaseAPIController, UsesHistoryMixinDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems ):
 
     @web.expose_api
     def index( self, trans, history_id, **kwd ):

lib/galaxy/web/api/library_contents.py

@@ -10,7 +10,7 @@ from galaxy.model.orm import *
 
 log = logging.getLogger( __name__ )
 
-class LibraryContentsController( BaseAPIController, UsesLibrary, UsesLibraryItems ):
+class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ):
 
     @web.expose_api
     def index( self, trans, library_id, **kwd ):

lib/galaxy/web/api/quotas.py

@@ -2,7 +2,7 @@
 API operations on Quota objects.
 """
 import logging
-from galaxy.web.base.controller import BaseAPIController, Admin, UsesQuota, url_for
+from galaxy.web.base.controller import BaseAPIController, Admin, UsesQuotaMixin, url_for
 from galaxy import web, util
 from elementtree.ElementTree import XML
 
@@ -14,7 +14,7 @@ from galaxy.exceptions import *
 
 log = logging.getLogger( __name__ )
 
-class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuota, QuotaParamParser ):
+class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuotaMixin, QuotaParamParser ):
     @web.expose_api
     @web.require_admin
     def index( self, trans, deleted='False', **kwd ):

lib/galaxy/web/base/controller.py

@@ -177,7 +177,11 @@ class BaseAPIController( BaseController ):
     def not_implemented( self, trans, **kwd ):
         raise HTTPNotImplemented()
 
-class SharableItemSecurity:
+#        
+# -- Mixins for working with Galaxy objects. --
+#
+
+class SharableItemSecurityMixin:
     """ Mixin for handling security for sharable items. """
     def security_check( self, trans, item, check_ownership=False, check_accessible=False ):
         """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """
@@ -197,11 +201,7 @@ class SharableItemSecurity:
                     raise ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' )
         return item
 
-#
-# TODO: need to move UsesHistory, etc. mixins to better location - perhaps lib/galaxy/model/XXX ?
-#
-
-class UsesHistoryDatasetAssociation:
+class UsesHistoryMixinDatasetAssociationMixin:
     """ Mixin for controllers that use HistoryDatasetAssociation objects. """
     def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False ):
         """ Get an HDA object by id. """
@@ -259,14 +259,14 @@ class UsesHistoryDatasetAssociation:
                 truncated = False
         return truncated, dataset_data
 
-class UsesLibrary:
+class UsesLibraryMixin:
     def get_library( self, trans, id, check_ownership=False, check_accessible=True ):
         l = self.get_object( trans, id, 'Library' )
         if check_accessible and not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), l ) ):
             error( "LibraryFolder is not accessible to the current user" )
         return l
 
-class UsesLibraryItems( SharableItemSecurity ):
+class UsesLibraryMixinItems( SharableItemSecurityMixin ):
     def get_library_folder( self, trans, id, check_ownership=False, check_accessible=True ):
         return self.get_object( trans, id, 'LibraryFolder', check_ownership=False, check_accessible=check_accessible )
     def get_library_dataset_dataset_association( self, trans, id, check_ownership=False, check_accessible=True ):
@@ -274,7 +274,7 @@ class UsesLibraryItems( SharableItemSecurity ):
     def get_library_dataset( self, trans, id, check_ownership=False, check_accessible=True ):
         return self.get_object( trans, id, 'LibraryDataset', check_ownership=False, check_accessible=check_accessible )
 
-class UsesVisualization( SharableItemSecurity ):
+class UsesVisualizationMixin( SharableItemSecurityMixin ):
     """ Mixin for controllers that use Visualization objects. """
     
     viz_types = [ "trackster", "circos" ]
@@ -522,7 +522,7 @@ class UsesVisualization( SharableItemSecurity ):
 
         return visualization
 
-class UsesStoredWorkflow( SharableItemSecurity ):
+class UsesStoredWorkflowMixin( SharableItemSecurityMixin ):
     """ Mixin for controllers that use StoredWorkflow objects. """
     def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ):
         """ Get a StoredWorkflow from the database by id, verifying ownership. """
@@ -560,7 +560,7 @@ class UsesStoredWorkflow( SharableItemSecurity ):
             # Connections by input name
             step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
 
-class UsesHistory( SharableItemSecurity ):
+class UsesHistoryMixin( SharableItemSecurityMixin ):
     """ Mixin for controllers that use History objects. """
     def get_history( self, trans, id, check_ownership=True, check_accessible=False, deleted=None ):
         """Get a History from the database by id, verifying ownership."""
@@ -580,7 +580,7 @@ class UsesHistory( SharableItemSecurity ):
             query = query.filter( trans.model.Dataset.purged == False )
         return query.all()
 
-class UsesFormDefinitions:
+class UsesFormDefinitionsMixin:
     """Mixin for controllers that use Galaxy form objects."""
     def get_all_forms( self, trans, all_versions=False, filter=None, form_type='All' ):
         """
@@ -1342,7 +1342,7 @@ class UsesFormDefinitions:
                                    selected_value=selected_value,
                                    refresh_on_change=True )
 
-class Sharable:
+class SharableMixin:
     """ Mixin for a controller that manages an item that can be shared. """
     
     # -- Implemented methods. --
@@ -1433,7 +1433,7 @@ class Sharable:
         """ Return item based on id. """
         raise "Unimplemented Method"
 
-class UsesQuota( object ):
+class UsesQuotaMixin( object ):
     def get_quota( self, trans, id, check_ownership=False, check_accessible=False, deleted=None ):
         return self.get_object( trans, id, 'Quota', check_ownership=False, check_accessible=False, deleted=deleted )
 

lib/galaxy/web/controllers/admin.py

@@ -428,7 +428,7 @@ class ToolVersionListGrid( grids.Grid ):
     def build_initial_query( self, trans, **kwd ):
         return trans.sa_session.query( self.model_class )
 
-class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ):
+class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaParamParser ):
     
     user_list_grid = UserListGrid()
     role_list_grid = RoleListGrid()

lib/galaxy/web/controllers/dataset.py

@@ -150,7 +150,7 @@ class HistoryDatasetAssociationListGrid( grids.Grid ):
                 .filter( model.History.deleted==False ) \
                 .filter( self.model_class.visible==True )
 
-class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHistoryDatasetAssociation, UsesItemRatings ):
+class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistoryMixin, UsesHistoryMixinDatasetAssociationMixin, UsesItemRatings ):
 
     stored_list_grid = HistoryDatasetAssociationListGrid()
 

lib/galaxy/web/controllers/external_service.py

@@ -63,7 +63,7 @@ class ExternalServiceGrid( grids.Grid ):
         grids.GridAction( "Create new external service", dict( controller='external_service', action='create_external_service' ) )
     ]
 
-class ExternalService( BaseUIController, UsesFormDefinitions ):
+class ExternalService( BaseUIController, UsesFormDefinitionsMixin ):
     external_service_grid = ExternalServiceGrid()
 
     @web.expose

lib/galaxy/web/controllers/history.py

@@ -190,7 +190,7 @@ class HistoryAllPublishedGrid( grids.Grid ):
         # 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 )
 
-class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRatings, UsesHistory ):
+class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings, UsesHistoryMixin ):
     @web.expose
     def index( self, trans ):
         return ""

lib/galaxy/web/controllers/library_common.py

@@ -68,7 +68,7 @@ except OSError:
     pass
 os.rmdir( tmpd )
 
-class LibraryCommon( BaseUIController, UsesFormDefinitions ):
+class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin ):
     @web.json
     def library_item_updates( self, trans, ids=None, states=None ):
         # Avoid caching

lib/galaxy/web/controllers/page.py

@@ -272,8 +272,8 @@ class _PageContentProcessor( _BaseHTMLProcessor ):
         # Default behavior: 
         _BaseHTMLProcessor.unknown_endtag( self, tag )
                 
-class PageController( BaseUIController, Sharable, UsesAnnotations, UsesHistory, 
-                      UsesStoredWorkflow, UsesHistoryDatasetAssociation, UsesVisualization, UsesItemRatings ):
+class PageController( BaseUIController, SharableMixin, UsesAnnotations, UsesHistoryMixin, 
+                      UsesStoredWorkflowMixin, UsesHistoryMixinDatasetAssociationMixin, UsesVisualizationMixin, UsesItemRatings ):
     
     _page_list = PageListGrid()
     _all_published_list = PageAllPublishedGrid()

lib/galaxy/web/controllers/request_type.py

@@ -72,7 +72,7 @@ class RequestTypeGrid( grids.Grid ):
         grids.GridAction( "Create new request type", dict( controller='request_type', action='create_request_type' ) )
     ]
 
-class RequestType( BaseUIController, UsesFormDefinitions ):
+class RequestType( BaseUIController, UsesFormDefinitionsMixin ):
     request_type_grid = RequestTypeGrid()
 
     @web.expose

lib/galaxy/web/controllers/requests_admin.py

@@ -94,7 +94,7 @@ class DataTransferGrid( grids.Grid ):
             return query
         return query.filter_by( sample_id=trans.security.decode_id( sample_id ) )
 
-class RequestsAdmin( BaseUIController, UsesFormDefinitions ):
+class RequestsAdmin( BaseUIController, UsesFormDefinitionsMixin ):
     request_grid = AdminRequestsGrid()
     datatx_grid = DataTransferGrid()
 

lib/galaxy/web/controllers/requests_common.py

@@ -93,7 +93,7 @@ class RequestsGrid( grids.Grid ):
                              confirm="Samples cannot be added to this request after it is submitted. Click OK to submit."  )
         ]
 
-class RequestsCommon( BaseUIController, UsesFormDefinitions ):
+class RequestsCommon( BaseUIController, UsesFormDefinitionsMixin ):
     @web.json
     def sample_state_updates( self, trans, ids=None, states=None ):
         # Avoid caching

lib/galaxy/web/controllers/root.py

@@ -11,7 +11,7 @@ from galaxy.model.item_attrs import UsesAnnotations
 
 log = logging.getLogger( __name__ )
 
-class RootController( BaseUIController, UsesHistory, UsesAnnotations ):
+class RootController( BaseUIController, UsesHistoryMixin, UsesAnnotations ):
     
     @web.expose
     def default(self, trans, target1=None, target2=None, **kwd):

lib/galaxy/web/controllers/tracks.py

@@ -163,7 +163,7 @@ class TracksterSelectionGrid( grids.Grid ):
     def apply_query_filter( self, trans, query, **kwargs ):
         return query.filter( self.model_class.user_id == trans.user.id )                    
         
-class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetAssociation, Sharable ):
+class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryMixinDatasetAssociationMixin, SharableMixin ):
     """
     Controller for track browser interface. Handles building a new browser from
     datasets in the current history, and display of the resulting browser.

lib/galaxy/web/controllers/user.py

@@ -38,7 +38,7 @@ class UserOpenIDGrid( grids.Grid ):
     def build_initial_query( self, trans, **kwd ):
         return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id )
 
-class User( BaseUIController, UsesFormDefinitions ):
+class User( BaseUIController, UsesFormDefinitionsMixin ):
     user_openid_grid = UserOpenIDGrid()
     installed_len_files = None
     

lib/galaxy/web/controllers/visualization.py

@@ -68,8 +68,8 @@ class VisualizationAllPublishedGrid( grids.Grid ):
         return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True )
 
 
-class VisualizationController( BaseUIController, Sharable, UsesAnnotations, 
-                                UsesHistoryDatasetAssociation, UsesVisualization, 
+class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations, 
+                                UsesHistoryMixinDatasetAssociationMixin, UsesVisualizationMixin, 
                                 UsesItemRatings ):
     _user_list_grid = VisualizationListGrid()
     _published_list_grid = VisualizationAllPublishedGrid()

lib/galaxy/web/controllers/workflow.py

@@ -105,7 +105,7 @@ class SingleTagContentsParser( sgmllib.SGMLParser ):
         if self.cur_tag == self.target_tag:
             self.tag_content += text
 
-class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAnnotations, UsesItemRatings ):
+class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesAnnotations, UsesItemRatings ):
     stored_list_grid = StoredWorkflowListGrid()
     published_list_grid = StoredWorkflowAllPublishedGrid()