Merge pull request #13171 from ic4f/dev_sa20warning

Enable setting SQLALCHEMY_WARN_20

.github/workflows/api.yaml

@@ -14,6 +14,7 @@ env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
   GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT: '1'
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
 concurrency:
   group: api-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/api_paste.yaml

@@ -14,6 +14,7 @@ env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_USE_UVICORN: false
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
 concurrency:
   group: api-legacy-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/integration.yaml

@@ -14,6 +14,7 @@ env:
   GALAXY_TEST_AMQP_URL: 'amqp://localhost:5672//'
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
 concurrency:
   group: integration-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/integration_selenium.yaml

@@ -12,6 +12,7 @@ env:
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
   GALAXY_TEST_SELENIUM_RETRIES: 1
   YARN_INSTALL_OPTS: --frozen-lockfile
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
 concurrency:
   group: integration-selenium-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/selenium.yaml

@@ -13,6 +13,7 @@ env:
   GALAXY_TEST_SELENIUM_RETRIES: 1
   GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR: 1
   YARN_INSTALL_OPTS: --frozen-lockfile
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
 concurrency:
   group: selenium-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/selenium_beta.yaml

@@ -14,6 +14,7 @@ env:
   GALAXY_TEST_SELENIUM_BETA_HISTORY: 1
   GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR: 1
   YARN_INSTALL_OPTS: --frozen-lockfile
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
 concurrency:
   group: selenium-beta-${{ github.ref }}
   cancel-in-progress: true

lib/galaxy/config/__init__.py

@@ -628,8 +628,36 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
         self._override_tempdir(kwargs)
+        self._configure_sqlalchemy20_warnings(kwargs)
         self._process_config(kwargs)
 
+    def _configure_sqlalchemy20_warnings(self, kwargs):
+        """
+        This method should be deleted after migration to SQLAlchemy 2.0 is complete.
+        To enable warnings, set `GALAXY_CONFIG_SQLALCHEMY_WARN_20=1`,
+        """
+        warn = string_as_bool(kwargs.get('sqlalchemy_warn_20', False))
+        if warn:
+            import sqlalchemy
+            sqlalchemy.util.deprecations.SQLALCHEMY_WARN_20 = True
+            self._setup_sqlalchemy20_warnings_filters()
+
+    def _setup_sqlalchemy20_warnings_filters(self):
+        import warnings
+        from sqlalchemy.exc import RemovedIn20Warning
+        # Always display RemovedIn20Warning warnings.
+        warnings.filterwarnings('always', category=RemovedIn20Warning)
+        # Optionally, enable filters for specific warnings (raise error, or log, etc.)
+        # messages = [
+        #     r"replace with warning text to match",
+        # ]
+        # for msg in messages:
+        #     warnings.filterwarnings('error', message=msg, category=RemovedIn20Warning)
+        #
+        # See documentation:
+        # https://docs.python.org/3.7/library/warnings.html#the-warnings-filter
+        # https://docs.sqlalchemy.org/en/14/changelog/migration_20.html#migration-to-2-0-step-three-resolve-all-removedin20warnings
+
     def _load_schema(self):
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)