Fix TypeOnlyAvailableAsAwaitable exception

galaxyproject · Dec 12, 2023 · fc44060 · fc44060
1 parent 4a7b187
commit fc44060
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Showing 4 changed files with 15 additions and 15 deletions.
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
@@ -122,7 +122,7 @@
 from galaxy.tool_util.deps.dependencies import AppInfo
 from galaxy.tool_util.deps.views import DependencyResolversView
 from galaxy.tool_util.edam_util import (
-    EdamDictType,
+    EdamDict,
     load_edam_tree,
 )
 from galaxy.tool_util.verify.test_data import TestDataResolver
@@ -696,7 +696,7 @@ def __init__(self, **kwargs) -> None:
             # Load edam data
             edam_ontology_path = self.config.edam_toolbox_ontology_path
             self.edam = self._register_singleton(
-                EdamDictType,
+                EdamDict,
                 load_edam_tree(
                     None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path,
                     "format_",
@@ -706,10 +706,7 @@ def __init__(self, **kwargs) -> None:
                 ),
             )
         else:
-            self.edam = self._register_singleton(
-                EdamDictType,
-                {},
-            )
+            self.edam = self._register_singleton(EdamDict, EdamDict())
         self._configure_toolbox()
         # Load Data Manager
         self.data_managers = self._register_singleton(DataManagers)  # type: ignore[type-abstract]

diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
@@ -16,7 +16,7 @@
 )
 from galaxy.datatypes.data import Data
 from galaxy.datatypes.registry import Registry
-from galaxy.tool_util.edam_util import EdamDictType
+from galaxy.tool_util.edam_util import EdamDict
 
 
 def view_index(
@@ -91,7 +91,7 @@ def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
     return parse_obj_as(DatatypeConverterList, converters)
 
 
-def _get_edam_details(edam: EdamDictType, edam_ids: Dict[str, str]) -> Dict[str, Dict]:
+def _get_edam_details(edam: EdamDict, edam_ids: Dict[str, str]) -> Dict[str, Dict]:
     details_dict = {}
     for format, edam_iri in edam_ids.items():
         edam_details = edam.get(edam_iri, {})
@@ -106,7 +106,7 @@ def _get_edam_details(edam: EdamDictType, edam_ids: Dict[str, str]) -> Dict[str,
 
 
 def view_edam_formats(
-    edam: EdamDictType, datatypes_registry: Registry, detailed: Optional[bool] = False
+    edam: EdamDict, datatypes_registry: Registry, detailed: Optional[bool] = False
 ) -> Union[Dict[str, str], Dict[str, Dict[str, str]]]:
     if detailed:
         return _get_edam_details(edam, datatypes_registry.edam_formats)
@@ -115,7 +115,7 @@ def view_edam_formats(
 
 
 def view_edam_data(
-    edam: EdamDictType, datatypes_registry: Registry, detailed: Optional[bool] = False
+    edam: EdamDict, datatypes_registry: Registry, detailed: Optional[bool] = False
 ) -> Union[Dict[str, str], Dict[str, Dict[str, str]]]:
     if detailed:
         return _get_edam_details(edam, datatypes_registry.edam_data)

diff --git a/lib/galaxy/tool_util/edam_util.py b/lib/galaxy/tool_util/edam_util.py
@@ -15,10 +15,13 @@
 ROOT_OPERATION = "operation_0004"
 ROOT_TOPIC = "topic_0003"
 
-EdamDictType = Dict[str, Dict[str, str]]
 
+class EdamDict(dict):
+    # Exists only for lagom + python3.8
+    pass
 
-def load_edam_tree(path: Optional[str] = None, *included_terms: str) -> EdamDictType:
+
+def load_edam_tree(path: Optional[str] = None, *included_terms: str) -> EdamDict:
     if path is not None:
         assert os.path.exists(path), f"Failed to load EDAM tabular data at [{path}] path does not exist."
         handle = open(path)
@@ -27,7 +30,7 @@ def load_edam_tree(path: Optional[str] = None, *included_terms: str) -> EdamDict
             tabular_stream is not None
         ), "Failed to load optional import from edam-ontology package, install using [pip install edam-ontology]."
         handle = tabular_stream()
-    return load_edam_tree_from_tsv_stream(handle, *included_terms)
+    return EdamDict(**load_edam_tree_from_tsv_stream(handle, *included_terms))
 
 
 def load_edam_tree_from_tsv_stream(tsv_stream: TextIO, *included_terms: str):

diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -26,7 +26,7 @@
     view_mapping,
     view_sniffers,
 )
-from galaxy.tool_util.edam_util import EdamDictType
+from galaxy.tool_util.edam_util import EdamDict
 from . import (
     depends,
     Router,
@@ -58,7 +58,7 @@
 @router.cbv
 class FastAPIDatatypes:
     datatypes_registry: Registry = depends(Registry)
-    edam: EdamDictType = depends(EdamDictType)
+    edam: EdamDict = depends(EdamDict)
 
     @router.get(
         "/api/datatypes",