Move edam data out of registry and into (web) app

It's only used in API responses and the tool panels.
We surely don't want to load edam data when loading the registry while
setting metadata.

lib/galaxy/app.py

@@ -121,6 +121,10 @@
 from galaxy.tool_util.deps import containers
 from galaxy.tool_util.deps.dependencies import AppInfo
 from galaxy.tool_util.deps.views import DependencyResolversView
+from galaxy.tool_util.edam_util import (
+    EdamDictType,
+    load_edam_tree,
+)
 from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy.tools.biotools import get_galaxy_biotools_metadata_source
 from galaxy.tools.cache import ToolCache
@@ -688,6 +692,19 @@ def __init__(self, **kwargs) -> None:
         self.tool_shed_repository_cache = self._register_singleton(ToolShedRepositoryCache)
         # Watch various config files for immediate reload
         self.watchers = self._register_singleton(ConfigWatchers)
+        if self.is_webapp:
+            # Load edam data
+            edam_ontology_path = self.config.edam_toolbox_ontology_path
+            self.edam = self._register_singleton(
+                EdamDictType,
+                load_edam_tree(
+                    None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path,
+                    "format_",
+                    "data_",
+                    "operation_",
+                    "topic_",
+                ),
+            )
         self._configure_toolbox()
         # Load Data Manager
         self.data_managers = self._register_singleton(DataManagers)  # type: ignore[type-abstract]

lib/galaxy/datatypes/registry.py

@@ -46,21 +46,9 @@ class ConfigurationError(Exception):
 
 class Registry:
     def __init__(self, config=None):
-        edam_ontology_path = config.get("edam_toolbox_ontology_path", None) if config is not None else None
-        edam = {}
-        if edam_ontology_path:
-            edam = load_edam_tree(
-                None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path,
-                "format_",
-                "data_",
-                "operation_",
-                "topic_",
-            )
-
         self.log = logging.getLogger(__name__)
         self.log.addHandler(logging.NullHandler())
         self.config = config
-        self.edam = edam
         self.datatypes_by_extension = {}
         self.datatypes_by_suffix_inferences = {}
         self.mimetypes_by_extension = {}

lib/galaxy/managers/datatypes.py

@@ -16,6 +16,7 @@
 )
 from galaxy.datatypes.data import Data
 from galaxy.datatypes.registry import Registry
+from galaxy.tool_util.edam_util import EdamDictType
 
 
 def view_index(
@@ -90,10 +91,10 @@ def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
     return parse_obj_as(DatatypeConverterList, converters)
 
 
-def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]) -> Dict[str, Dict]:
+def _get_edam_details(edam: EdamDictType, edam_ids: Dict[str, str]) -> Dict[str, Dict]:
     details_dict = {}
     for format, edam_iri in edam_ids.items():
-        edam_details = datatypes_registry.edam.get(edam_iri, {})
+        edam_details = edam.get(edam_iri, {})
 
         details_dict[format] = {
             "prefix_IRI": edam_iri,
@@ -105,19 +106,19 @@ def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]) ->
 
 
 def view_edam_formats(
-    datatypes_registry: Registry, detailed: Optional[bool] = False
+    edam: EdamDictType, datatypes_registry: Registry, detailed: Optional[bool] = False
 ) -> Union[Dict[str, str], Dict[str, Dict[str, str]]]:
     if detailed:
-        return _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
+        return _get_edam_details(edam, datatypes_registry.edam_formats)
     else:
         return datatypes_registry.edam_formats
 
 
 def view_edam_data(
-    datatypes_registry: Registry, detailed: Optional[bool] = False
+    edam: EdamDictType, datatypes_registry: Registry, detailed: Optional[bool] = False
 ) -> Union[Dict[str, str], Dict[str, Dict[str, str]]]:
     if detailed:
-        return _get_edam_details(datatypes_registry, datatypes_registry.edam_data)
+        return _get_edam_details(edam, datatypes_registry.edam_data)
     else:
         return datatypes_registry.edam_data
 

lib/galaxy/tool_util/edam_util.py

@@ -15,8 +15,10 @@
 ROOT_OPERATION = "operation_0004"
 ROOT_TOPIC = "topic_0003"
 
+EdamDictType = Dict[str, Dict[str, str]]
 
-def load_edam_tree(path: Optional[str] = None, *included_terms: str):
+
+def load_edam_tree(path: Optional[str] = None, *included_terms: str) -> EdamDictType:
     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)

lib/galaxy/tool_util/toolbox/base.py

@@ -189,6 +189,9 @@ def __init__(
         self._tool_tag_manager = self.tool_tag_manager()
         self._init_tools_from_configs(config_filenames)
 
+        if not self.app.is_webapp:
+            return
+
         if self.app.name == "galaxy" and self._integrated_tool_panel_config_has_contents:
             self._load_tool_panel()
 
@@ -223,7 +226,7 @@ def to_model(self) -> ToolPanelViewModel:
 
         for edam_view in listify(self.app.config.edam_panel_views):
             mode = EdamPanelMode[edam_view]
-            tool_panel_views_list.append(EdamToolPanelView(self.app.datatypes_registry.edam, mode=mode))
+            tool_panel_views_list.append(EdamToolPanelView(self.app.edam, mode=mode))
 
         if view_sources is not None:
             for definition in view_sources.get_definitions():
@@ -233,7 +236,7 @@ def to_model(self) -> ToolPanelViewModel:
         for tool_panel_view in tool_panel_views_list:
             self._tool_panel_views[tool_panel_view.to_model().id] = tool_panel_view
 
-        if self.app.name == "galaxy":
+        if self.app.name == "galaxy" and self.app.is_webapp:
             self._load_tool_panel_views()
         if save_integrated_tool_panel:
             self._save_integrated_tool_panel()

lib/galaxy/webapps/galaxy/api/datatypes.py

@@ -26,6 +26,7 @@
     view_mapping,
     view_sniffers,
 )
+from galaxy.tool_util.edam_util import EdamDictType
 from . import (
     depends,
     Router,
@@ -57,6 +58,7 @@
 @router.cbv
 class FastAPIDatatypes:
     datatypes_registry: Registry = depends(Registry)
+    edam: EdamDictType = depends(EdamDictType)
 
     @router.get(
         "/api/datatypes",
@@ -123,7 +125,7 @@ async def converters(self) -> DatatypeConverterList:
     )
     async def edam_formats(self) -> Dict[str, str]:
         """Gets a map of datatypes and their corresponding EDAM formats."""
-        return cast(Dict[str, str], view_edam_formats(self.datatypes_registry))
+        return cast(Dict[str, str], view_edam_formats(self.edam, self.datatypes_registry))
 
     @router.get(
         "/api/datatypes/edam_formats/detailed",
@@ -134,7 +136,7 @@ async def edam_formats(self) -> Dict[str, str]:
     async def edam_formats_detailed(self):
         """Gets a map of datatypes and their corresponding EDAM formats.
         EDAM formats contain the EDAM iri, label, and definition."""
-        return view_edam_formats(self.datatypes_registry, True)
+        return view_edam_formats(self.edam, self.datatypes_registry, True)
 
     @router.get(
         "/api/datatypes/edam_data",
@@ -143,7 +145,7 @@ async def edam_formats_detailed(self):
     )
     async def edam_data(self) -> Dict[str, str]:
         """Gets a map of datatypes and their corresponding EDAM data."""
-        return cast(Dict[str, str], view_edam_data(self.datatypes_registry))
+        return cast(Dict[str, str], view_edam_data(self.edam, self.datatypes_registry))
 
     @router.get(
         "/api/datatypes/edam_data/detailed",
@@ -154,4 +156,4 @@ async def edam_data(self) -> Dict[str, str]:
     async def edam_data_detailed(self):
         """Gets a map of datatypes and their corresponding EDAM data.
         EDAM data contains the EDAM iri, label, and definition."""
-        return view_edam_data(self.datatypes_registry, True)
+        return view_edam_data(self.edam, self.datatypes_registry, True)