From 17622a1ce7f52b45a5b1a58e1d0241b7f8ed74ff Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 6 Jan 2022 17:17:19 -0500
Subject: [PATCH] Address existing mypy error (see note)

This is a (possible) bug that has existed on dev. To expose it, simply
change this call to init_models_from_config
(https://github.com/galaxyproject/galaxy/blob/release_21.09/lib/galaxy/config/__init__.py#L1302)
to a call directly to mapping.init(). The result will be 6 mypy errors.

The reason is that the mapping.init() method
(https://github.com/galaxyproject/galaxy/blob/release_21.09/lib/galaxy/model/mapping.py#L79)
specifies its return type as GalaxyModelMapping - which results in
several errors of this type:

lib/galaxy/app.py:178: error: Definition of "model" in base class "MinimalApp" is incompatible with definition in base class "ConfiguresGalaxyMixin"

When we call an intermediary function (that does not have a return type
specified), mypy is happy.

This should be addressed in a separate issue/PR. Removing the return
type is the simplest (temporary) solution.
---
 lib/galaxy/config/__init__.py | 20 ++++++++------------
 lib/galaxy/model/mapping.py   |  2 +-
 2 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 30be0f500d42..071e38e437d5 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -1395,7 +1395,14 @@ def _configure_models(self, check_migrate_databases=False, config_file=None):
             from galaxy.model.migrations import verify_databases
             verify_databases(engine, install_engine, self.config)
 
-        self.model = self._this_should_be_inlined(engine, combined_install_database)
+        self.model = mapping.configure_model_mapping(
+            self.config.file_path,
+            self.object_store,
+            self.config.use_pbkdf2,
+            engine,
+            combined_install_database,
+            self.config.thread_local_log
+        )
 
         if combined_install_database:
             log.info("Install database targeting Galaxy's database configuration.")  # TODO this message is ambiguous
@@ -1405,17 +1412,6 @@ def _configure_models(self, check_migrate_databases=False, config_file=None):
             self.install_model = install_mapping.configure_model_mapping(install_engine)
             log.info(f"Install database using its own connection {install_db_url}")
 
-    def _this_should_be_inlined(self, engine, combined_install_database):
-        # TODO this is WIP: see comments in method above.
-        return mapping.configure_model_mapping(
-            self.config.file_path,
-            self.object_store,
-            self.config.use_pbkdf2,
-            engine,
-            combined_install_database,
-            self.config.thread_local_log
-        )
-
     def _configure_signal_handlers(self, handlers):
         for sig, handler in handlers.items():
             signal.signal(sig, handler)
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 231b0b40e82d..28aa1ca65546 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -55,7 +55,7 @@ def configure_model_mapping(
     engine,
     map_install_models,
     thread_local_log,
-) -> GalaxyModelMapping:
+):
     _configure_model(file_path, object_store, use_pbkdf2)
     return _build_model_mapping(engine, map_install_models, thread_local_log)