Type and bug fixes for api/extended_metadata.py.

lib/galaxy/webapps/galaxy/api/extended_metadata.py

@@ -2,13 +2,14 @@
 API operations on annotations.
 """
 import logging
+from typing import Generic, Optional, TypeVar
 
 from galaxy import (
     managers,
-    web
+    model,
+    web,
 )
 from galaxy.webapps.base.controller import (
-    HTTPNotImplemented,
     UsesExtendedMetadataMixin,
     UsesLibraryMixinItems,
     UsesStoredWorkflowMixin
@@ -17,10 +18,16 @@ from . import BaseGalaxyAPIController, depends
 
 log = logging.getLogger(__name__)
 
+T = TypeVar('T')
 
-class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin):
 
-    @web.legacy_expose_api
+class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin, Generic[T]):
+    exmeta_item_id: str
+
+    def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[T]:
+        ...
+
+    @web.expose_api
     def index(self, trans, **kwd):
         idnum = kwd[self.exmeta_item_id]
         item = self._get_item_from_id(trans, idnum, check_writable=False)
@@ -29,7 +36,7 @@ class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetada
             if ex_meta is not None:
                 return ex_meta.data
 
-    @web.legacy_expose_api
+    @web.expose_api
     def create(self, trans, payload, **kwd):
         idnum = kwd[self.exmeta_item_id]
         item = self._get_item_from_id(trans, idnum, check_writable=True)
@@ -41,26 +48,12 @@ class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetada
             ex_obj = self.create_extended_metadata(trans, payload)
             self.set_item_extended_metadata_obj(trans, item, ex_obj)
 
-    @web.legacy_expose_api
-    def delete(self, trans, **kwd):
-        idnum = kwd[self.tagged_item_id]
-        item = self._get_item_from_id(trans, idnum, check_writable=True)
-        if item is not None:
-            ex_obj = self.get_item_extended_metadata_obj(trans, item)
-            if ex_obj is not None:
-                self.unset_item_extended_metadata_obj(trans, item)
-                self.delete_extended_metadata(trans, ex_obj)
 
-    @web.legacy_expose_api
-    def undelete(self, trans, **kwd):
-        raise HTTPNotImplemented()
-
-
-class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController):
+class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController[model.LibraryDatasetDatasetAssociation]):
     controller_name = "library_dataset_extended_metadata"
     exmeta_item_id = "library_content_id"
 
-    def _get_item_from_id(self, trans, idstr, check_writable=True):
+    def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[model.LibraryDatasetDatasetAssociation]:
         if check_writable:
             item = self.get_library_dataset_dataset_association(trans, idstr)
             if trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), item):
@@ -72,12 +65,12 @@ class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController):
         return None
 
 
-class HistoryDatasetExtendMetadataController(BaseExtendedMetadataController):
+class HistoryDatasetExtendMetadataController(BaseExtendedMetadataController[model.HistoryDatasetAssociation]):
     controller_name = "history_dataset_extended_metadata"
     exmeta_item_id = "history_content_id"
     hda_manager: managers.hdas.HDAManager = depends(managers.hdas.HDAManager)
 
-    def _get_item_from_id(self, trans, idstr, check_writable=True):
+    def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[model.HistoryDatasetAssociation]:
         decoded_idstr = self.decode_id(idstr)
         if check_writable:
             return self.hda_manager.get_owned(decoded_idstr, trans.user, current_history=trans.history)

setup.cfg

@@ -751,8 +751,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.webapps.galaxy.api.genomes]
 check_untyped_defs = False
-[mypy-galaxy.webapps.galaxy.api.extended_metadata]
-check_untyped_defs = False
 [mypy-galaxy.webapps.galaxy.api.datasets]
 check_untyped_defs = False
 [mypy-galaxy.webapps.galaxy.api.authenticate]