Merge branch 'fix-simulation' into 'v3'

Simulation fixes

See merge request openflexure/openflexure-microscope-server!279

.gitignore

@@ -79,8 +79,8 @@ packages.png
 openflexure_microscope/cobertura.xml
 
 # labthings settings
-/settings/
+settings/
-/openflexure_settings/
+openflexure_settings/
 
 # web app build
 /src/openflexure_microscope_server/static/

ofm_config_full.json

@@ -11,5 +11,6 @@
         "/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing",
         "/capture/": "openflexure_microscope_server.things.capture:CaptureThing"
     },
-    "settings_folder": "/var/openflexure/settings/"
+    "settings_folder": "/var/openflexure/settings/",
+    "log_folder": "/var/openflexure/logs/"
 }

ofm_config_simulation.json

@@ -8,8 +8,9 @@
         "/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing",
         "/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager",
         "/smart_scan/": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
-        "/background_detect/": "openflexure_microscope_server.things.smart_scan:BackgroundDetectThing",
+        "/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing",
-        "/api_test/": "openflexure_microscope_server.things.test:APITestThing"
+        "/capture/": "openflexure_microscope_server.things.capture:CaptureThing"
     },
-    "settings_folder": "./openflexure_settings/"
+    "settings_folder": "./openflexure/settings/",
+    "log_folder": "./openflexure/logs/"
 }

ofm_config_stub.json

@@ -8,8 +8,9 @@
         "/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing",
         "/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager",
         "/smart_scan/": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
-        "/background_detect/": "openflexure_microscope_server.things.smart_scan:BackgroundDetectThing",
+        "/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing",
-        "/api_test/": "openflexure_microscope_server.things.test:APITestThing"
+        "/capture/": "openflexure_microscope_server.things.capture:CaptureThing"
     },
-    "settings_folder": "./openflexure_settings/"
+    "settings_folder": "./openflexure/settings/",
+    "log_folder": "./openflexure/logs/"
 }

src/openflexure_microscope_server/logging.py

@@ -4,17 +4,19 @@ import os
 
 from fastapi.responses import PlainTextResponse
 
-OFM_LOG_FOLDER = "/var/openflexure/logs/"
+OFM_LOG_FILE = None
-OFM_LOG_FILE = os.path.join(OFM_LOG_FOLDER, "openflexure_microscope.log")
 
 
-def configure_logging():
+def configure_logging(log_folder):
     root_logger = logging.getLogger()
     root_logger.setLevel(logging.INFO)
+    # Explictly make OFM_LOG_FILE a global so it can be updated based on log settings
+    global OFM_LOG_FILE
+    OFM_LOG_FILE = os.path.join(log_folder, "openflexure_microscope.log")
 
     try:
-        if not os.path.exists(OFM_LOG_FOLDER):
+        if not os.path.exists(log_folder):
-            os.makedirs(OFM_LOG_FOLDER)
+            os.makedirs(log_folder)
         handler = RotatingFileHandler(
             filename=OFM_LOG_FILE,
             mode="a",
@@ -38,7 +40,7 @@ def configure_logging():
 
 def retrieve_log() -> PlainTextResponse:
     """
-    Returns logs since we started running the server, up to a maxiumum of
+    Returns logs since we started running the server, up to a maximum of
     250 messages. This log is the one shown in the UI and on the logging page.
 
     It does not include any of the `uvicorn.access` logs as these are emmitted
@@ -57,6 +59,10 @@ def retrieve_log_from_file() -> PlainTextResponse:
     Note this is read and then sent as otherwise it causes a RuntimeError if it
     is written to while sending through FileResponse
     """
+    if OFM_LOG_FILE is None:
+        raise RuntimeError(
+            "Cannot retrieve log file as logging directory hasn't been configured"
+        )
     with open(OFM_LOG_FILE, "r", encoding="utf-8") as logfile:
         full_log = logfile.read()
     return PlainTextResponse(full_log)
@@ -86,7 +92,6 @@ class OFMHandler(logging.Handler):
         """
         Emit will save the logged record to the log
         """
-
         # Basic filter for now that simply stops uvicorn.access logs
         # These are the logs each time an API endpoint is accessed
         # This is only the log for the UI.

src/openflexure_microscope_server/server/__init__.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from typing import Optional
+from copy import copy
 
 from labthings_fastapi.server import cli, ThingServer
 import uvicorn
@@ -9,14 +10,11 @@ from .legacy_api import add_v2_endpoints
 from ..logging import configure_logging, retrieve_log, retrieve_log_from_file
 
 
-def customise_server(server: ThingServer):
+def customise_server(server: ThingServer, log_folder: str):
     """Customise the server with additional endpoints, etc."""
-    configure_logging()
+    configure_logging(log_folder)
     add_v2_endpoints(server)
-    try:
+    add_static_files(server.app)
-        add_static_files(server.app)
-    except RuntimeError:
-        print("Failed to add static files - you will have to do without them!")
 
     # Add an endpoint to get the logs - (directly calling the FastAPI decorator)
     server.app.get("/log/")(retrieve_log)
@@ -26,19 +24,21 @@ def customise_server(server: ThingServer):
 def serve_from_cli(argv: Optional[list[str]] = None):
     """Start the server from the command line"""
     args = cli.parse_args(argv)
+
+    log_config = copy(uvicorn.config.LOGGING_CONFIG)
+    log_config["loggers"]["uvicorn"]["propagate"] = True
+    log_config["loggers"]["uvicorn.access"]["propagate"] = True
+
     try:
-        config, server = None, None
         config = cli.config_from_args(args)
+        log_folder = config.get("log_folder", "./openflexure/logs")
         server = cli.server_from_config(config)
-        customise_server(server)
+        customise_server(server, log_folder)
         uvicorn.run(
             server.app,
             host=args.host,
             port=args.port,
-            log_config={
+            log_config=log_config,
-                "version": 1,
-                "disable_existing_loggers": False,
-            },
         )
 
     except BaseException as e:
@@ -54,10 +54,7 @@ def serve_from_cli(argv: Optional[list[str]] = None):
                 app,
                 host=args.host,
                 port=args.port,
-                log_config={
+                log_config=log_config,
-                    "version": 1,
-                    "disable_existing_loggers": False,
-                },
             )
         else:
             raise e