Factor out overriding tempdir into own method

lib/galaxy/config/__init__.py

@@ -348,11 +348,16 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
     def __init__(self, **kwargs):
         super(GalaxyAppConfiguration, self).__init__(**kwargs)
+        self._override_tempdir(kwargs)
         self._process_config(kwargs)
 
     def _load_schema(self):
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 
+    def _override_tempdir(self, kwargs):
+        if string_as_bool(kwargs.get("override_tempdir", "True")):
+            tempfile.tempdir = self.new_file_path
+
     def _process_config(self, kwargs):
         # Resolve paths of other config files
         self.parse_config_file_options(kwargs)
@@ -377,10 +382,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             self.thread_local_log = threading.local()
         # Install database related configuration (if different)
         self.install_database_engine_options = get_database_engine_options(kwargs, model_prefix="install_")
-
-        override_tempdir = string_as_bool(kwargs.get("override_tempdir", "True"))
-        if override_tempdir:
-            tempfile.tempdir = self.new_file_path
         self.shared_home_dir = kwargs.get("shared_home_dir")
         self.cookie_path = kwargs.get("cookie_path")
         self.tool_path = self._in_root_dir(self.tool_path)

test/unit/config/test_config_values.py

@@ -169,7 +169,8 @@ def mock_config_running_not_from_source(monkeypatch, mock_config_file):
 
 @pytest.fixture
 def appconfig(monkeypatch):
-    return config.Configuration()
+    monkeypatch.setattr(config.GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
+    return config.GalaxyAppConfiguration()
 
 
 def test_root(appconfig):
@@ -196,7 +197,8 @@ def test_common_base_config(appconfig):
 
 
 def get_config_data():
-    configuration = config.Configuration()
+    config.GalaxyAppConfiguration._override_tempdir = lambda a, b: None  # method must be mocked
+    configuration = config.GalaxyAppConfiguration()
     ev = ExpectedValues(configuration)
     items = ((k, v) for k, v in configuration.schema.app_schema.items() if k not in DO_NOT_TEST)
     for key, data in items:

test/unit/config/test_load_config.py

@@ -22,6 +22,7 @@ def get_schema(app_mapping):
 def mock_init(monkeypatch):
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
 
 def test_load_config_from_schema(mock_init):

test/unit/config/test_path_graph.py

@@ -49,6 +49,7 @@ def test_basecase(monkeypatch):
     }
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.component1_path0 == 'value0'
@@ -159,6 +160,7 @@ def test_resolves_with_empty_component(monkeypatch):
     }
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.path0 == 'value0'

test/unit/config/test_path_resolves_to.py

@@ -44,6 +44,7 @@ def test_deprecated_prefixes_set_correctly(monkeypatch):
     # Before we mock them, check that correct values are assigned
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.deprecated_dirs == {'config_dir': 'config', 'data_dir': 'database'}
@@ -53,6 +54,7 @@ def test_deprecated_prefixes_set_correctly(monkeypatch):
 def mock_init(monkeypatch):
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
     monkeypatch.setattr(GalaxyAppConfiguration, 'deprecated_dirs', MOCK_DEPRECATED_DIRS)
 
 

test/unit/config/test_reload_config.py

@@ -25,6 +25,7 @@ def mock_init(monkeypatch):
 
     monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
     monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+    monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
 
 
 def test_update_property(mock_init, monkeypatch):