Add auto-generated Configuration schema from Pydantic model

Makefile

@@ -92,6 +92,9 @@ reports-config-convert: ## convert old style reports ini to yaml
 reports-config-lint: ## lint reports YAML configuration file
 	$(CONFIG_MANAGE) lint reports
 
+config-generate-schema: ## build galaxy YAML configuration schema
+	$(CONFIG_MANAGE) generate_schema galaxy
+
 config-validate: ## validate galaxy YAML configuration file
 	$(CONFIG_MANAGE) validate galaxy
 

lib/galaxy/app.py

@@ -41,6 +41,7 @@
 from galaxy.managers.api_keys import ApiKeyManager
 from galaxy.managers.citations import CitationsManager
 from galaxy.managers.collections import DatasetCollectionManager
+from galaxy.managers.configuration import ConfigurationManager
 from galaxy.managers.dbkeys import GenomeBuilds
 from galaxy.managers.folders import FolderManager
 from galaxy.managers.hdas import HDAManager
@@ -244,6 +245,7 @@ def __init__(self, fsmon=False, **kwargs) -> None:
         self.is_webapp = False
         # Read config file and check for errors
         self.config = self._register_singleton(config.GalaxyAppConfiguration, config.GalaxyAppConfiguration(**kwargs))
+        ConfigurationManager.validate_config(self.config._raw_config)
         self.config.check()
         self._configure_object_store(fsmon=True)
         self._register_singleton(BaseObjectStore, self.object_store)

lib/galaxy/config/__init__.py

@@ -914,7 +914,7 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
         self.galaxy_data_manager_data_path = self.galaxy_data_manager_data_path or self.tool_data_path
         self.tool_secret = kwargs.get("tool_secret", "")
         self.metadata_strategy = kwargs.get("metadata_strategy", "directory")
-        self.use_remote_user = self.use_remote_user or self.single_user
+        self.use_remote_user = self.use_remote_user or bool(self.single_user)
         self.fetch_url_allowlist_ips = [
             ipaddress.ip_network(unicodify(ip.strip()))  # If it has a slash, assume 127.0.0.1/24 notation
             if "/" in ip

lib/galaxy/config/config_manage.py

@@ -41,6 +41,7 @@
     TOOL_SHED_CONFIG_SCHEMA_PATH,
 )
 from galaxy.config.schema import AppSchema
+from galaxy.schema.configuration import FullGalaxyConfig
 from galaxy.util import safe_makedirs
 from galaxy.util.properties import (
     nice_config_parser,
@@ -524,12 +525,23 @@ def _get_option_desc(option: Dict[str, Any]) -> str:
     return desc
 
 
+def _generate_schema(args: Namespace, app_desc: App) -> None:
+    """Generates the configuration YAML schema from the Pydantic model."""
+    if app_desc.app_name != "galaxy":
+        raise Exception("Only Galaxy is supported for configuration schema generation")
+    galaxy_config_schema = FullGalaxyConfig.schema()
+    target_path = app_desc.schema_path + ".test.yml"
+    with open(target_path, "w") as f:
+        yaml.dump(galaxy_config_schema, f)
+
+
 ACTIONS: Dict[str, Callable] = {
     "convert": _run_conversion,
     "build_sample_yaml": _build_sample_yaml,
     "validate": _validate,
     "lint": _lint,
     "build_rst": _to_rst,
+    "generate_schema": _generate_schema,
 }
 
 

lib/galaxy/managers/configuration.py

@@ -16,6 +16,7 @@
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.markdown_util import weasyprint_available
 from galaxy.schema import SerializationParams
+from galaxy.schema.configuration import FullGalaxyConfig
 from galaxy.structured_app import StructuredApp
 from galaxy.web.framework.base import server_starttime
 
@@ -84,6 +85,14 @@ def tool_conf_to_dict(conf):
     def reload_toolbox(self):
         self._app.queue_worker.send_control_task("reload_toolbox")
 
+    @staticmethod
+    def validate_config(config_dict: Dict[str, Any]):
+        """Validate the configuration against the schema model.
+
+        It will raise an exception if the configuration is invalid.
+        """
+        return FullGalaxyConfig(**config_dict)
+
 
 # TODO: this is a bit of an odd duck. It uses the serializer structure from managers
 #   but doesn't have a model like them. It might be better in config.py or a