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indentation fixes

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This commit is contained in:
Bjoern Gruening
2015-07-05 18:17:38 +01:00
committed by Nicola Soranzo
parent 2160a03272
commit 8b9aa5d8df
7 changed files with 25 additions and 25 deletions
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lib/galaxy/webapps/galaxy/api/datasets.py
+3 -3
View File
@@ -67,7 +67,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
# Default: return dataset as dict.
if hda_ldda == 'hda':
return self.hda_serializer.serialize_to_view( dataset,
view=kwd.get( 'view', 'detailed' ), user=trans.user, trans=trans )
view=kwd.get( 'view', 'detailed' ), user=trans.user, trans=trans )
else:
rval = dataset.to_dict()
@@ -111,7 +111,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
# If there is a chrom, check for data on the chrom.
if chrom:
data_provider = trans.app.data_provider_registry.get_data_provider( trans,
original_dataset=dataset, source='index' )
original_dataset=dataset, source='index' )
if not data_provider.has_data( chrom ):
return dataset.conversion_messages.NO_DATA
@@ -286,7 +286,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
if raw:
if filename and filename != 'index':
file_path = trans.app.object_store.get_filename( hda.dataset,
extra_dir=( 'dataset_%s_files' % hda.dataset.id ), alt_name=filename)
extra_dir=( 'dataset_%s_files' % hda.dataset.id ), alt_name=filename)
else:
file_path = hda.file_name
rval = open( file_path )
lib/galaxy/webapps/galaxy/api/group_roles.py
+4 -4
View File
@@ -56,8 +56,8 @@ class GroupRolesAPIController( BaseAPIController ):
for gra in group.roles:
if gra.role == role:
item = dict( id=role_id,
name=role.name,
url=url_for( 'group_role', group_id=group_id, id=role_id) ) # TODO Fix This
name=role.name,
url=url_for( 'group_role', group_id=group_id, id=role_id) ) # TODO Fix This
if not item:
item = "role %s not in group %s" % (role.name, group.name)
except Exception, e:
@@ -82,8 +82,8 @@ class GroupRolesAPIController( BaseAPIController ):
for gra in group.roles:
if gra.role == role:
item = dict( id=role_id,
name=role.name,
url=url_for( 'group_role', group_id=group_id, id=role_id) )
name=role.name,
url=url_for( 'group_role', group_id=group_id, id=role_id) )
if not item:
gra = trans.app.model.GroupRoleAssociation( group, role )
# Add GroupRoleAssociation
lib/galaxy/webapps/galaxy/api/group_users.py
+4 -4
View File
@@ -56,8 +56,8 @@ class GroupUsersAPIController( BaseAPIController ):
for uga in group.users:
if uga.user == user:
item = dict( id=user_id,
email=user.email,
url=url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This
email=user.email,
url=url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This
if not item:
item = "user %s not in group %s" % (user.email, group.name)
except Exception, e:
@@ -82,8 +82,8 @@ class GroupUsersAPIController( BaseAPIController ):
for uga in group.users:
if uga.user == user:
item = dict( id=user_id,
email=user.email,
url=url_for( 'group_user', group_id=group_id, id=user_id) )
email=user.email,
url=url_for( 'group_user', group_id=group_id, id=user_id) )
if not item:
uga = trans.app.model.UserGroupAssociation( user, group )
# Add UserGroupAssociations
lib/galaxy/webapps/galaxy/api/histories.py
+6 -6
View File
@@ -123,7 +123,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
rval = []
for history in histories:
history_dict = self.history_serializer.serialize_to_view( history,
user=trans.user, trans=trans, **serialization_params )
user=trans.user, trans=trans, **serialization_params )
rval.append( history_dict )
return rval
@@ -183,7 +183,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )
return self.history_serializer.serialize_to_view( history,
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
@expose_api_anonymous
def citations( self, trans, history_id, **kwd ):
@@ -249,7 +249,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
trans.sa_session.flush()
return self.history_serializer.serialize_to_view( new_history,
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
@expose_api
def delete( self, trans, id, **kwd ):
@@ -288,7 +288,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
self.history_manager.purge( history )
return self.history_serializer.serialize_to_view( history,
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
@expose_api
def undelete( self, trans, id, **kwd ):
@@ -311,7 +311,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
self.history_manager.undelete( history )
return self.history_serializer.serialize_to_view( history,
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
@expose_api
def update( self, trans, id, payload, **kwd ):
@@ -340,7 +340,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
self.history_deserializer.deserialize( history, payload, user=trans.user, trans=trans )
return self.history_serializer.serialize_to_view( history,
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
@expose_api
def archive_export( self, trans, id, **kwds ):
lib/galaxy/webapps/galaxy/api/history_contents.py
+6 -6
View File
@@ -111,7 +111,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
def __collection_dict( self, trans, dataset_collection_instance, view="collection" ):
return dictify_dataset_collection_instance( dataset_collection_instance,
security=trans.security, parent=dataset_collection_instance.history, view=view )
security=trans.security, parent=dataset_collection_instance.history, view=view )
@expose_api_anonymous
def show( self, trans, id, history_id, **kwd ):
@@ -140,7 +140,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
def __show_dataset( self, trans, id, **kwd ):
hda = self.hda_manager.get_accessible( self.decode_id( id ), trans.user )
return self.hda_serializer.serialize_to_view( hda,
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
def __show_dataset_collection( self, trans, id, history_id, **kwd ):
try:
@@ -210,7 +210,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
# examples. See also bioblend and API tests for specific examples.
history = self.history_manager.get_owned( self.decode_id( history_id ), trans.user,
current_history=trans.history )
current_history=trans.history )
type = payload.get( 'type', 'dataset' )
if type == 'dataset':
@@ -253,7 +253,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
if not hda:
return None
return self.hda_serializer.serialize_to_view( hda,
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
def __create_dataset_collection( self, trans, history, payload, **kwd ):
source = kwd.get("source", "new_collection")
@@ -344,7 +344,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
if payload.get( 'deleted', False ):
self.hda_manager.stop_creating_job( hda )
return self.hda_serializer.serialize_to_view( hda,
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
return {}
@@ -403,7 +403,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
else:
self.hda_manager.delete( hda )
return self.hda_serializer.serialize_to_view( hda,
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
def __handle_unknown_contents_type( self, trans, contents_type ):
raise exceptions.UnknownContentsType('Unknown contents type: %s' % type)
lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+1 -1
View File
@@ -120,7 +120,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
def __get_value_mapper( self, trans, tool_shed_repository ):
value_mapper = { 'id' : trans.security.encode_id( tool_shed_repository.id ),
'error_message' : tool_shed_repository.error_message or '' }
'error_message' : tool_shed_repository.error_message or '' }
return value_mapper
@expose_api
lib/galaxy/webapps/galaxy/api/visualizations.py
+1 -1
View File
@@ -63,7 +63,7 @@ class VisualizationsController( BaseAPIController, UsesVisualizationMixin, Shara
visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
dictionary = trans.security.encode_dict_ids( self.get_visualization_dict( visualization ) )
dictionary[ 'url' ] = web.url_for( controller='visualization',
action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug )
action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug )
dictionary[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, trans.user, visualization )
# need to encode ids in revisions as well