_convert_=all required in hydra instantiation due to third party libr…

…aries not respecting list like types

kazu/krt/ontology_update_editor/utils.py

@@ -21,7 +21,7 @@ class OntologyUpdateManager:
 
     def __init__(self, parser_name: str):
         self.original_parser_cfg: DictConfig = self.name_to_parser_cfg()[parser_name]
-        self.parser = instantiate(self.original_parser_cfg)
+        self.parser = instantiate(self.original_parser_cfg, _convert_="all")
         self.new_parser_cfg: DictConfig = self.original_parser_cfg.copy()
 
     def get_downloader_args_and_types(self) -> dict[str, type]:
@@ -72,7 +72,7 @@ def modify_parser_cfg_with_new_args(self) -> None:
 
         :return:
         """
-        parser = instantiate(self.new_parser_cfg)
+        parser = instantiate(self.new_parser_cfg, _convert_="all")
         new_in_path = parser.ontology_downloader.download(parser.in_path, skip_download=True)
         with open_dict(self.new_parser_cfg):
             self.new_parser_cfg.data_origin = parser.ontology_downloader.version(parser.in_path)
@@ -83,7 +83,7 @@ def instantiate_parser_with_new_config(self) -> OntologyParser:
 
         :return:
         """
-        return cast(OntologyParser, instantiate(self.new_parser_cfg))
+        return cast(OntologyParser, instantiate(self.new_parser_cfg, _convert_="all"))
 
     @functools.cache
     def get_or_build_upgrade_report(self) -> OntologyUpgradeReport:

kazu/krt/resource_manager.py

@@ -163,7 +163,7 @@ def save(self) -> Iterable[str]:
     def _load_pipeline() -> Pipeline:
         load_config.clear()  # type: ignore[attr-defined]
         cfg = load_config()
-        pipeline: Pipeline = instantiate(cfg.Pipeline)
+        pipeline: Pipeline = instantiate(cfg.Pipeline, _convert_="all")
         return pipeline
 
     def clear_invalid_caches(self) -> None:

kazu/krt/utils.py

@@ -14,7 +14,7 @@ def load_parsers() -> list[OntologyParser]:
     cfg = load_config()
     parsers = []
     for parser in cfg.ontologies.parsers.values():
-        parsers.append(instantiate(parser))
+        parsers.append(instantiate(parser, _convert_="all"))
     return parsers