Update how the application configuration is read for LabThings 0.0.17

pyproject.toml

@@ -18,7 +18,7 @@ classifiers = [
   "Operating System :: OS Independent",
 ]
 dependencies = [
-  "labthings-fastapi==0.0.14",
+  "labthings-fastapi==0.0.17",
   "sangaboard",
   "camera-stage-mapping ~= 0.1.10",
   "opencv-python-headless ~= 4.13.0",

src/openflexure_microscope_server/server/__init__.py

@@ -75,8 +75,6 @@ def customise_server(
     server: lt.ThingServer, application_config: OFMApplicationData
 ) -> None:
     """Customise the server with additional endpoints, etc."""
-    configure_logging(application_config.log_folder)
-
     if DEVELOPER_MODE:
         # Allow CORS in developer mode for easier testing with the webapp
         server.app.add_middleware(
@@ -108,7 +106,12 @@ def serve_from_cli(argv: Optional[list[str]] = None) -> None:
     lt_config = None
     server = None
     try:
-        lt_config, application_config = _full_config_from_args(args)
+        lt_config = _full_config_from_args(args)
+        # Validate our application data
+        if lt_config.application_config is None:
+            raise ValueError("No application configuration was supplied.")
+        application_config = OFMApplicationData(**lt_config.application_config)
+        configure_logging(application_config.log_folder)
 
         server = lt.ThingServer.from_config(lt_config)
         customise_server(server, application_config)
@@ -166,25 +169,18 @@ def serve_from_cli(argv: Optional[list[str]] = None) -> None:
             raise e
 
 
-def _full_config_from_args(
-    args: Namespace,
-) -> tuple[ThingServerConfig, OFMApplicationData]:
+def _full_config_from_args(args: Namespace) -> ThingServerConfig:
     """Load configuration from LabThings args allowing patching.
 
-    This returns the labthings ThingServerConfig model and a dictionary of the config
-    for the microscope.
+    This returns the labthings ThingServerConfig model.
 
     This provides similar functionarlity to lt.cli.config_from_args except allows the
     configuration file to specify a base config, and optionally patches.
     """
-    # Don't allow configuration to be set as an argument as then we cannot handle
-    # application_config
     if not args.config:
         raise RuntimeError(
             "OpenFlexure Microscope Server must have a configuration file specified."
         )
 
     patched_config = load_patched_config(args.config)
-    application_config = OFMApplicationData(**patched_config.pop("application_config"))
-
-    return ThingServerConfig(**patched_config), application_config
+    return ThingServerConfig(**patched_config)

src/openflexure_microscope_server/things/__init__.py

@@ -7,9 +7,6 @@ with other Things and including them in the LabThings-FastAPI config file.
 import posixpath
 from typing import Optional, Self
 
-from starlette.routing import Mount
-from starlette.staticfiles import StaticFiles
-
 import labthings_fastapi as lt
 
 
@@ -20,7 +17,13 @@ class OFMThing(lt.Thing):
 
     def __enter__(self) -> Self:
         """Set the data directory when the Thing is entered."""
-        self._data_dir = get_data_directory_from_server(self)
+        # Note that the `application_config` was already validated when the
+        # server initialised.
+        application_config = self._thing_server_interface.application_config
+        if application_config is None:
+            raise ValueError("No application configuration was supplied.")
+        app_data_dir = application_config["data_folder"]
+        self._data_dir = posixpath.join(str(app_data_dir), self.path.strip("/"))
         return self
 
     @property
@@ -31,31 +34,3 @@ class OFMThing(lt.Thing):
                 "No data directory set. Has the LabThings server been started?"
             )
         return self._data_dir
-
-
-def get_data_directory_from_server(thing: lt.Thing) -> str:
-    """Get the data directory from the server.
-
-    :param thing: The Thing to get the data directory for.
-
-    :return: The data directory as a string:
-    :raise RuntimeError: If not able to get the data directory for any reason.
-    """
-    server = thing._thing_server_interface._server()
-    if server is None:
-        raise RuntimeError("No server found to communicate with.")
-    routes = server.app.routes
-    try:
-        route_paths = [route.path if hasattr(route, "path") else "" for route in routes]
-        data_index = route_paths.index("/data")
-    except ValueError as e:
-        raise RuntimeError("Could not find data directory") from e
-    mount = routes[data_index]
-    if not isinstance(mount, Mount):
-        raise RuntimeError("Data directory isn't a starlette.routing.Mount.")
-    if not isinstance(mount.app, StaticFiles):
-        raise RuntimeError("Data is not mounted as static files.")
-    app_data_dir = mount.app.directory
-    if app_data_dir is None:
-        raise RuntimeError("Data directory is not set.")
-    return posixpath.join(str(app_data_dir), thing.path.strip("/"))

src/openflexure_microscope_server/things/camera/__init__.py

@@ -604,7 +604,7 @@ class BaseCamera(lt.Thing):
         return self._background_detector_name
 
     @background_detector_name.setter
-    def _set_background_detector_name(self, name: str) -> None:
+    def _set_background_detector_name(self, name: Optional[str]) -> None:
         """Validate and set background_detector_name."""
         if name not in self._all_background_detectors:
             self.logger.warning(f"{name} is not a valid background detector name.")

tests/unit_tests/test_server_cli.py

@@ -36,6 +36,8 @@ def test_successful_start(mocker, caplog):
         "openflexure_microscope_server.server.lt.ThingServer.from_config",
         return_value=mock_server,
     )
+    # Also mock configure_logging or it will touch a load of code and log.
+    mock_log_configure = mocker.patch.object(ofm_server, "configure_logging")
     # Also mock customisation or it will try to access the hard drive and make files.
     mock_customise = mocker.patch.object(ofm_server, "customise_server")
     # And mock uvicorn.run as we don't want to start a server process
@@ -44,7 +46,9 @@ def test_successful_start(mocker, caplog):
     # Run the mock CLI
     ofm_server.serve_from_cli(["-c", SIM_CONFIG])
 
-    # Check that the server was customised and the run
+    # Check that the logging was configures, the server was customised, and uvicorn was
+    # run
+    assert mock_log_configure.call_count == 1
     assert mock_customise.call_count == 1
     assert mock_uvicorn_run.call_count == 1
     # Read the log config that was set

tests/unit_tests/test_server_config.py

@@ -60,7 +60,6 @@ def test_customise_server(mocker):
     # but also to limit excess coverage reporting.
     mocked_add_static = mocker.patch.object(ofm_server, "add_static_files")
     mocked_v2_endpoints = mocker.patch.object(ofm_server, "add_v2_endpoints")
-    mocked_configure_logging = mocker.patch.object(ofm_server, "configure_logging")
     mocked_retrieve_log = mocker.patch.object(ofm_server, "retrieve_log")
     mocked_retrieve_log_file = mocker.patch.object(ofm_server, "retrieve_log_from_file")
 
@@ -77,7 +76,6 @@ def test_customise_server(mocker):
     # Check each internal customisation function is called
     assert mocked_add_static.call_count == 1
     assert mocked_v2_endpoints.call_count == 1
-    assert mocked_configure_logging.call_count == 1
     # Check app.get adds two routes
     assert mock_app.get.call_count == 2
     assert wrapper.call_count == 2
@@ -122,10 +120,12 @@ def test_full_config_from_args(config, log_dir, data_dir, mocker):
         },
     )
     args = Namespace(config=config, json=None)
-    lt_conf, application_config = ofm_server._full_config_from_args(args)
+    lt_conf = ofm_server._full_config_from_args(args)
     # If json is supplied OFM config is default. As the json is passed dircectly to
     # The Pydantic Mocel in LabThings. No custom data allowed.
     assert isinstance(lt_conf, ThingServerConfig)
-    assert isinstance(application_config, OFMApplicationData)
+    # Check the configuration validates
+    application_config = OFMApplicationData(**lt_conf.application_config)
+    # And has the correct values
     assert application_config.log_folder == log_dir
     assert application_config.data_folder == data_dir

tests/unit_tests/test_smart_scan.py

@@ -41,7 +41,7 @@ from openflexure_microscope_server.things.smart_scan import (
 
 # Use our own dir in the root temp dir not a dynamically generated one so we
 # have some control of when it is deleted
-SCAN_DIR = os.path.join(tempfile.gettempdir(), "scans")
+SCAN_DIR = os.path.join(tempfile.gettempdir(), "smartscanthing")
 
 
 def _clear_scan_dir() -> None:
@@ -53,15 +53,15 @@ def _clear_scan_dir() -> None:
 @pytest.fixture
 def smart_scan_thing(mocker):
     """Return a smart scan thing as a fixture."""
-    mocker.patch(
-        "openflexure_microscope_server.things.get_data_directory_from_server",
-        return_value=SCAN_DIR,
-    )
-    return create_thing_without_server(
+    thing = create_thing_without_server(
         SmartScanThing,
         default_workflow="mock-_all_workflows",
         mock_all_slots=True,
     )
+    type(thing._thing_server_interface).application_config = mocker.PropertyMock(
+        return_value={"data_folder": tempfile.gettempdir()}
+    )
+    return thing
 
 
 @pytest.fixture
@@ -81,15 +81,15 @@ def custom_smart_scan_thing(default_workflow, all_workflows, mocker):
     This allows setting a default workflow and to adjust all workflows from simple
     single item mock from `mock_all_slots`.
     """
-    mocker.patch(
-        "openflexure_microscope_server.things.get_data_directory_from_server",
-        return_value=SCAN_DIR,
-    )
     smart_scan_thing = create_thing_without_server(
         SmartScanThing,
         default_workflow=default_workflow,
         mock_all_slots=True,
     )
+    interface_type = type(smart_scan_thing._thing_server_interface)
+    interface_type.application_config = mocker.PropertyMock(
+        return_value={"data_folder": tempfile.gettempdir()}
+    )
     # Pop the existing mock workflow and add specified ones (if any)
     smart_scan_thing._all_workflows.pop("mock-_all_workflows")
     for key, thing in all_workflows.items():