Create and mount application level data direcory rather than just a scan directory
This commit is contained in:
Julian Stirling
parent
2c2a52cb97
commit
45903f92a6
12 changed files with 187 additions and 166 deletions
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@ -36,7 +36,7 @@ def main() -> None:
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with open(config, "r", encoding="utf-8") as file_obj:
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config_dict = json.load(file_obj)
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config_dict["things"]["smart_scan"]["kwargs"]["scans_folder"] = "/tmp/scans"
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config_dict["application_config"]["data_folder"] = "/tmp/data"
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server = lt.ThingServer(things=config_dict["things"])
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test_client = TestClient(server.app)
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@ -14,7 +14,6 @@
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"smart_scan": {
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"class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
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"kwargs": {
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"scans_folder": "/var/openflexure/scans/",
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"default_workflow": "histo_scan_workflow"
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}
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},
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@ -26,5 +25,9 @@
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"bg_channel_deviations_luv": "openflexure_microscope_server.things.background_detect:ChannelDeviationLUV"
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},
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"settings_folder": "/var/openflexure/settings/",
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"log_folder": "/var/openflexure/logs/"
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"application_config": {
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"log_folder": "/var/openflexure/logs/",
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"data_folder": "/var/openflexure/data/"
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}
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}
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@ -4,5 +4,8 @@
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"system": "openflexure_microscope_server.things.system:OpenFlexureSystem"
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},
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"settings_folder": "./openflexure/settings/",
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"log_folder": "./openflexure/logs/"
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"application_config": {
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"log_folder": "./openflexure/logs/",
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"data_folder": "./openflexure/data/"
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}
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}
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@ -9,7 +9,6 @@
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"smart_scan": {
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"class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
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"kwargs": {
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"scans_folder": "./openflexure/scans/",
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"default_workflow": "histo_scan_workflow"
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}
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},
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@ -20,5 +19,8 @@
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"bg_channel_deviations_luv": "openflexure_microscope_server.things.background_detect:ChannelDeviationLUV"
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},
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"settings_folder": "./openflexure/settings/",
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"log_folder": "./openflexure/logs/"
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"application_config": {
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"log_folder": "./openflexure/logs/",
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"data_folder": "./openflexure/data/"
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}
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}
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@ -11,7 +11,8 @@ from pathlib import Path
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from typing import Any, Callable, Optional
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import uvicorn
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from fastapi.middleware.cors import CORSMiddleware # vue3 migration
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from fastapi.middleware.cors import CORSMiddleware
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from pydantic import BaseModel
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from uvicorn.main import Server
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import labthings_fastapi as lt
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@ -35,6 +36,15 @@ DEVELOPER_MODE = os.getenv("OFM_SERVER_DEV_MODE", "false").lower() == "true"
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_TEMPLATE_PATH = Path(__file__).with_name("fallback.html.jinja")
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class OFMApplicationData(BaseModel):
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"""Application data for the OpenFlexure Microscope."""
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log_folder: str
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"""The directory to save the logs in."""
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data_folder: str
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"""The directory for Things to save data in."""
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def set_shutdown_function(shutdown_function: Callable[[], None]) -> None:
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"""Ensure a function is called before the shutdown.
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@ -62,10 +72,10 @@ def set_shutdown_function(shutdown_function: Callable[[], None]) -> None:
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def customise_server(
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server: lt.ThingServer, log_folder: str, scans_folder: Optional[str]
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server: lt.ThingServer, application_config: OFMApplicationData
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) -> None:
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"""Customise the server with additional endpoints, etc."""
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configure_logging(log_folder)
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configure_logging(application_config.log_folder)
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if DEVELOPER_MODE:
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# Allow CORS in developer mode for easier testing with the webapp
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@ -78,27 +88,13 @@ def customise_server(
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)
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add_v2_endpoints(server)
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add_static_files(server.app, scans_folder)
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add_static_files(server.app, application_config.data_folder)
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# Add an endpoint to get the logs - (directly calling the FastAPI decorator)
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server.app.get("/log/")(retrieve_log)
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server.app.get("/logfile/")(retrieve_log_from_file)
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def _get_scans_dir(config: dict) -> Optional[str]:
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"""Read the config and return the scans directory.
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Return is None if there is no smart_scan thing loaded.
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"""
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if "smart_scan" in config["things"]:
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try:
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return config["things"]["smart_scan"]["kwargs"]["scans_folder"]
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except KeyError as e:
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msg = "Configuration error: smart scan should have scans_folder kwarg set"
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raise RuntimeError(msg) from e
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return None
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def serve_from_cli(argv: Optional[list[str]] = None) -> None:
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"""Start the server from the command line."""
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args = lt.cli.parse_args(argv)
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@ -112,12 +108,10 @@ def serve_from_cli(argv: Optional[list[str]] = None) -> None:
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lt_config = None
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server = None
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try:
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lt_config, internal_config = _full_config_from_args(args)
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lt_config, application_config = _full_config_from_args(args)
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server = lt.ThingServer.from_config(lt_config)
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customise_server(
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server, internal_config["log_folder"], internal_config["scans_folder"]
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)
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customise_server(server, application_config)
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def shutdown_call() -> None:
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try:
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@ -172,7 +166,9 @@ def serve_from_cli(argv: Optional[list[str]] = None) -> None:
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raise e
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def _full_config_from_args(args: Namespace) -> tuple[ThingServerConfig, dict[str, Any]]:
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def _full_config_from_args(
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args: Namespace,
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) -> tuple[ThingServerConfig, OFMApplicationData]:
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"""Load configuration from LabThings args allowing patching.
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This returns the labthings ThingServerConfig model and a dictionary of the config
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@ -181,16 +177,14 @@ def _full_config_from_args(args: Namespace) -> tuple[ThingServerConfig, dict[str
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This provides similar functionarlity to lt.cli.config_from_args except allows the
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configuration file to specify a base config, and optionally patches.
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"""
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internal_config = {"log_folder": "./openflexure/logs", "scans_folder": None}
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# If no config file specified let LabThings handle it.
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# Don't allow configuration to be set as an argument as then we cannot handle
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# application_config
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if not args.config:
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return lt.cli.config_from_args(args), internal_config
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raise RuntimeError(
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"OpenFlexure Microscope Server must have a configuration file specified."
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)
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patched_config = load_patched_config(args.config)
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log_folder = patched_config.pop("log_folder", None)
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if log_folder is not None:
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internal_config["log_folder"] = log_folder
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scans_folder = _get_scans_dir(patched_config)
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if scans_folder is not None:
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internal_config["scans_folder"] = scans_folder
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return ThingServerConfig(**patched_config), internal_config
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application_config = OFMApplicationData(**patched_config.pop("application_config"))
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return ThingServerConfig(**patched_config), application_config
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@ -1,7 +1,6 @@
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"""Add endpoints for static files to the underlying FastAPI server."""
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import os
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from typing import Optional
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from fastapi import FastAPI
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from fastapi.responses import FileResponse, RedirectResponse
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@ -36,7 +35,7 @@ def add_static_file(app: FastAPI, fname: str, folder: str) -> None:
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)
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def add_static_files(app: FastAPI, scans_folder: Optional[str]) -> None:
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def add_static_files(app: FastAPI, data_folder: str) -> None:
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"""Add the static files responsible for the webapp app to the FastAPI app.
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Note that any file in the root of the static dir will not be cached. However, the
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@ -45,7 +44,7 @@ def add_static_files(app: FastAPI, scans_folder: Optional[str]) -> None:
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important file not to cache is "index.html".
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:param app: The FastAPI app to add to, in this case the OpenFlexure server
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:param scans_folder: The directory for the scans.
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:param data_folder: The directory for any data.
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"""
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check_static_dir()
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@ -65,15 +64,16 @@ def add_static_files(app: FastAPI, scans_folder: Optional[str]) -> None:
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name=f"static_{fname}",
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)
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# If scans folder is None, there is not smart scan thing. So nothing to mount.
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if scans_folder is not None:
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# Mount the scan directory to .../scans/, to allow dzi viewing
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if not os.path.isdir(scans_folder):
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os.makedirs(scans_folder)
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# We need a data folder
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if data_folder is None:
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raise ValueError("No data folder is set, cannot start server")
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# Mount the scan directory to .../data/, to allow dzi viewing
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if not os.path.isdir(data_folder):
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os.makedirs(data_folder)
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app.mount(
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"/scans/",
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StaticFiles(directory=scans_folder),
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name="scans",
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"/data/",
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StaticFiles(directory=data_folder),
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name="data",
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)
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@ -3,3 +3,59 @@
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The microscope can be extended to be used with other hardware by creating a package
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with other Things and including them in the LabThings-FastAPI config file.
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"""
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import posixpath
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from typing import Optional, Self
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from starlette.routing import Mount
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from starlette.staticfiles import StaticFiles
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import labthings_fastapi as lt
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class OFMThing(lt.Thing):
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"""A custom LabThings Thing class for the OpenFlexure Microscope."""
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_data_dir: Optional[str] = None
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def __enter__(self) -> Self:
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"""Set the data directory when the Thing is entered."""
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self._data_dir = get_data_directory_from_server(self)
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return self
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@property
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def data_dir(self) -> str:
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"""The data directory for this thing."""
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if self._data_dir is None:
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raise RuntimeError(
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"No data directory set. Has the LabThings server been started?"
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)
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return self._data_dir
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def get_data_directory_from_server(thing: lt.Thing) -> str:
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"""Get the data directory from the server.
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:param thing: The Thing to get the data directory for.
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:return: The data directory as a string:
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:raise RuntimeError: If not able to get the data directory for any reason.
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"""
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server = thing._thing_server_interface._server()
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if server is None:
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raise RuntimeError("No server found to communicate with.")
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routes = server.app.routes
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try:
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route_paths = [route.path if hasattr(route, "path") else "" for route in routes]
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data_index = route_paths.index("/data")
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except ValueError as e:
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raise RuntimeError("Could not find data directory") from e
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mount = routes[data_index]
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if not isinstance(mount, Mount):
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raise RuntimeError("Data directory isn't a starlette.routing.Mount.")
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if not isinstance(mount.app, StaticFiles):
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raise RuntimeError("Data is not mounted as static files.")
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app_data_dir = mount.app.directory
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if app_data_dir is None:
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raise RuntimeError("Data directory is not set.")
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return posixpath.join(str(app_data_dir), thing.path.strip("/"))
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@ -32,6 +32,7 @@ from pydantic import BaseModel, PlainSerializer
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import labthings_fastapi as lt
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from openflexure_microscope_server import scan_directories, stitching
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from openflexure_microscope_server.things import OFMThing
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from openflexure_microscope_server.utilities import coerce_thing_selector
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# Things
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@ -120,7 +121,7 @@ def _scan_running(
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return scan_running_wrapper
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class SmartScanThing(lt.Thing):
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class SmartScanThing(OFMThing):
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"""A Thing for scanning samples and interacting with past scans.
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SmartScanThing exposes all functionality for automatically scanning samples,
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@ -135,23 +136,22 @@ class SmartScanThing(lt.Thing):
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def __init__(
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self,
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thing_server_interface: lt.ThingServerInterface,
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scans_folder: str,
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default_workflow: str,
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) -> None:
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"""Initialise a SmartScanThing saving to and loading from the input directory.
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:param scans_folder: This is the path to the directory where all scans will be
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saved. Any scans already in this directory will be accessible through the
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HTTP interface.
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:param default_workflow: The default workflows that smart scan uses if nothing
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is set in settings.
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"""
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super().__init__(thing_server_interface)
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self._scan_dir_manager = scan_directories.ScanDirectoryManager(scans_folder)
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self._scan_lock = threading.Lock()
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self._default_workflow = default_workflow
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self._workflow_name = default_workflow
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def __enter__(self) -> Self:
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"""Open hardware connection when the Thing context manager is opened."""
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super().__enter__()
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self._scan_dir_manager = scan_directories.ScanDirectoryManager(self.data_dir)
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valid_name = coerce_thing_selector(
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thing_mapping=self._all_workflows,
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selected=self.workflow_name,
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@ -81,7 +81,7 @@ def test_add_static_with_no_static_dir(mocker):
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)
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# Should raise as the mock static dir does not exist
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with pytest.raises(FileNotFoundError):
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serve_static_files.add_static_files(mock_app, scans_folder=None)
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serve_static_files.add_static_files(mock_app, data_folder=None)
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assert mock_app.get.call_count == 0
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@ -126,7 +126,8 @@ def test_add_static_files(mock_static_dir, mocker):
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)
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# Get the wrapper function from the mocked decorator
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wrapper = mock_app.get.return_value
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serve_static_files.add_static_files(mock_app, scans_folder=None)
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with tempfile.TemporaryDirectory() as datadir:
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serve_static_files.add_static_files(mock_app, data_folder=datadir)
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# Get should have been called twice to create a route for index
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assert mock_app.get.call_count == 2
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@ -151,23 +152,11 @@ def test_add_static_files(mock_static_dir, mocker):
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assert second_wrapped().headers["Pragma"] == "no-cache"
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# Also should have mounted both dirs
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assert mock_app.mount.call_count == 1
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mounted_path = mock_app.mount.call_args.args[0]
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mounted_dir = mock_app.mount.call_args.args[1].directory
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assert mock_app.mount.call_count == 2
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mounted_path = mock_app.mount.call_args_list[0].args[0]
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mounted_dir = mock_app.mount.call_args_list[0].args[1].directory
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assert "/assets/" in mounted_path
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assert os.path.join(mock_static_dir, "assets") in mounted_dir
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def test_add_static_files_with_scan_dir(mock_static_dir, mocker):
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"""Check the scan dir mounts if supplied."""
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mock_app = mocker.Mock()
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mocker.patch(
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"openflexure_microscope_server.server.serve_static_files.STATIC_PATH",
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mock_static_dir,
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)
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with tempfile.TemporaryDirectory() as scandir:
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serve_static_files.add_static_files(mock_app, scans_folder=scandir)
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# The scan dir should be the last to mount so can use call args. It should mount
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# at /scans/
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assert mock_app.mount.call_args.args[0] == "/scans/"
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assert mock_app.mount.call_args.args[1].directory == scandir
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assert mock_app.mount.call_args_list[1].args[0] == "/data/"
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assert mock_app.mount.call_args_list[1].args[1].directory == datadir
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@ -15,7 +15,8 @@ from .test_server_config import SIM_CONFIG
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def test_no_config():
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"""Check that an error is thrown if no configuration is set for the microspe via CLI."""
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with pytest.raises(RuntimeError, match="No configuration"):
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msg = "OpenFlexure Microscope Server must have a configuration file specified."
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with pytest.raises(RuntimeError, match=msg):
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ofm_server.serve_from_cli([])
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@ -1,9 +1,7 @@
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"""Test server booting and shut down."""
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import json
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import os
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from argparse import Namespace
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from copy import deepcopy
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import pytest
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@ -12,11 +10,13 @@ from labthings_fastapi.server.config_model import ThingServerConfig
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# Import as ofm server to attempt to minimise confusion with server as a var in other
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# functions and also FastAPI `Server`.
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from openflexure_microscope_server import server as ofm_server
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from openflexure_microscope_server.server import OFMApplicationData
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THIS_DIR = os.path.dirname(os.path.abspath(__file__))
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REPO_ROOT = os.path.dirname(os.path.dirname(THIS_DIR))
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FULL_CONFIG = os.path.join(REPO_ROOT, "ofm_config_full.json")
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SIM_CONFIG = os.path.join(REPO_ROOT, "ofm_config_simulation.json")
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MANUAL_CONFIG = os.path.join(REPO_ROOT, "ofm_config_manual.json")
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@pytest.mark.parametrize("side_effect", [None, RuntimeError("Mock")])
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@ -68,8 +68,11 @@ def test_customise_server(mocker):
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# The wrapper returned for app.get so we can see what functions are decorated.
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wrapper = mock_app.get.return_value
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||||
application_data = OFMApplicationData(
|
||||
log_folder="mock_log_folder", data_folder="mock_data_folder"
|
||||
)
|
||||
# Finally we can run it!
|
||||
ofm_server.customise_server(mock_server, "mock_log_folder", "mock_scan_folder")
|
||||
ofm_server.customise_server(mock_server, application_data)
|
||||
|
||||
# Check each internal customisation function is called
|
||||
assert mocked_add_static.call_count == 1
|
||||
|
|
@ -88,67 +91,26 @@ def test_customise_server(mocker):
|
|||
assert mocked_retrieve_log_file
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
("config_file", "expected_scan_dir"),
|
||||
[(FULL_CONFIG, "/var/openflexure/scans/"), (SIM_CONFIG, "./openflexure/scans/")],
|
||||
)
|
||||
def test_get_scans_dir_ok(config_file, expected_scan_dir):
|
||||
"""Test the _get_scans_dir function and also check the standard config files."""
|
||||
with open(config_file, "r", encoding="utf-8") as f_obj:
|
||||
config_dict = json.load(f_obj)
|
||||
assert ofm_server._get_scans_dir(config_dict) == expected_scan_dir
|
||||
|
||||
|
||||
def test_get_scans_dir_no_smart_scan():
|
||||
"""Test _get_scans_dir with no SmartScanThing."""
|
||||
# Load the standard config dict
|
||||
with open(FULL_CONFIG, "r", encoding="utf-8") as f_obj:
|
||||
config_dict = json.load(f_obj)
|
||||
# Delete smart scan
|
||||
del config_dict["things"]["smart_scan"]
|
||||
# No SmartScanThing, should return None
|
||||
assert ofm_server._get_scans_dir(config_dict) is None
|
||||
|
||||
|
||||
def test_get_scans_dir_bad_smart_scan_config():
|
||||
"""Test _get_scans_dir with a SmartScanThing that doesn't set a config dir."""
|
||||
# Load the standard config dict
|
||||
with open(FULL_CONFIG, "r", encoding="utf-8") as f_obj:
|
||||
config_dict = json.load(f_obj)
|
||||
|
||||
# Copy the dictionary
|
||||
broken_config = deepcopy(config_dict)
|
||||
# Delete all the smart scan kwargs
|
||||
del broken_config["things"]["smart_scan"]["kwargs"]
|
||||
# Creates an Error
|
||||
with pytest.raises(RuntimeError):
|
||||
ofm_server._get_scans_dir(broken_config)
|
||||
|
||||
# Same thing should happen if just the scans_folder key is deleted
|
||||
broken_config = deepcopy(config_dict)
|
||||
del broken_config["things"]["smart_scan"]["kwargs"]
|
||||
# Creates an Error
|
||||
with pytest.raises(RuntimeError):
|
||||
ofm_server._get_scans_dir(broken_config)
|
||||
|
||||
|
||||
def test_full_config_from_args_json():
|
||||
"""Check that _full_config_from_args returns as expected if json is supplied."""
|
||||
"""Check that _full_config_from_args errors if json config is supplied."""
|
||||
msg = "OpenFlexure Microscope Server must have a configuration file specified."
|
||||
args = Namespace(
|
||||
config=None,
|
||||
json='{"things":{"example": "labthings_fastapi.example_things:MyThing"}}',
|
||||
)
|
||||
lt_conf, ofm_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 "log_folder" in ofm_conf
|
||||
assert ofm_conf["log_folder"] == "./openflexure/logs"
|
||||
assert "scans_folder" in ofm_conf
|
||||
assert ofm_conf["scans_folder"] is None
|
||||
with pytest.raises(RuntimeError, match=msg):
|
||||
ofm_server._full_config_from_args(args)
|
||||
|
||||
|
||||
def test_full_config_from_args_full(mocker):
|
||||
@pytest.mark.parametrize(
|
||||
("config", "log_dir", "data_dir"),
|
||||
[
|
||||
(FULL_CONFIG, "/var/openflexure/logs/", "/var/openflexure/data/"),
|
||||
(SIM_CONFIG, "./openflexure/logs/", "./openflexure/data/"),
|
||||
(MANUAL_CONFIG, "./openflexure/logs/", "./openflexure/data/"),
|
||||
],
|
||||
)
|
||||
def test_full_config_from_args(config, log_dir, data_dir, mocker):
|
||||
"""Check that _full_config_from_args returns as expected if json is supplied."""
|
||||
# Mock picamera library so LabThings can create its model.
|
||||
mocker.patch.dict(
|
||||
|
|
@ -159,12 +121,11 @@ def test_full_config_from_args_full(mocker):
|
|||
"picamera2.outputs": mocker.Mock(),
|
||||
},
|
||||
)
|
||||
args = Namespace(config=FULL_CONFIG, json=None)
|
||||
lt_conf, ofm_conf = ofm_server._full_config_from_args(args)
|
||||
args = Namespace(config=config, json=None)
|
||||
lt_conf, application_config = 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 "log_folder" in ofm_conf
|
||||
assert ofm_conf["log_folder"] == "/var/openflexure/logs/"
|
||||
assert "scans_folder" in ofm_conf
|
||||
assert ofm_conf["scans_folder"] == "/var/openflexure/scans/"
|
||||
assert isinstance(application_config, OFMApplicationData)
|
||||
assert application_config.log_folder == log_dir
|
||||
assert application_config.data_folder == data_dir
|
||||
|
|
|
|||
|
|
@ -51,25 +51,42 @@ def _clear_scan_dir() -> None:
|
|||
|
||||
|
||||
@pytest.fixture
|
||||
def smart_scan_thing():
|
||||
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(
|
||||
SmartScanThing,
|
||||
scans_folder=SCAN_DIR,
|
||||
default_workflow="mock-_all_workflows",
|
||||
mock_all_slots=True,
|
||||
)
|
||||
|
||||
|
||||
def custom_smart_scan_thing(default_workflow, all_workflows):
|
||||
@pytest.fixture
|
||||
def entered_smart_scan_thing(smart_scan_thing):
|
||||
"""Yield a smart scan thing as a fixture that has been entred.
|
||||
|
||||
This will make a scan directory manager. This fixture also clears the scan dir
|
||||
"""
|
||||
_clear_scan_dir()
|
||||
with smart_scan_thing:
|
||||
yield smart_scan_thing
|
||||
|
||||
|
||||
def custom_smart_scan_thing(default_workflow, all_workflows, mocker):
|
||||
"""Set up a custom smart scan thing with workflows adjusted.
|
||||
|
||||
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,
|
||||
scans_folder=SCAN_DIR,
|
||||
default_workflow=default_workflow,
|
||||
mock_all_slots=True,
|
||||
)
|
||||
|
|
@ -81,12 +98,13 @@ def custom_smart_scan_thing(default_workflow, all_workflows):
|
|||
return smart_scan_thing
|
||||
|
||||
|
||||
def test_initial_properties(smart_scan_thing):
|
||||
def test_initial_properties(entered_smart_scan_thing):
|
||||
"""Check the initial values of properties.
|
||||
|
||||
Test properties of SmartScanThing are available without a ThingServer
|
||||
and return expected default values.
|
||||
"""
|
||||
smart_scan_thing = entered_smart_scan_thing
|
||||
assert smart_scan_thing._scan_dir_manager.base_dir == SCAN_DIR
|
||||
assert smart_scan_thing.latest_scan_name is None
|
||||
|
||||
|
|
@ -168,9 +186,9 @@ SELECTOR_CASES = [
|
|||
|
||||
|
||||
@pytest.mark.parametrize("case", SELECTOR_CASES)
|
||||
def test_workflow_set_on_enter(case, check_side_effect):
|
||||
def test_workflow_set_on_enter(case, check_side_effect, mocker):
|
||||
"""Check workflow is set on enter."""
|
||||
smart_scan_thing = custom_smart_scan_thing(case.default_wf, case.workflows)
|
||||
smart_scan_thing = custom_smart_scan_thing(case.default_wf, case.workflows, mocker)
|
||||
with check_side_effect(case.side_effect, match=case.match):
|
||||
# Load in "loaded" as the sever would
|
||||
smart_scan_thing._workflow_name = case.loaded_wf
|
||||
|
|
@ -178,14 +196,13 @@ def test_workflow_set_on_enter(case, check_side_effect):
|
|||
assert smart_scan_thing._workflow_name == case.expected_wf
|
||||
|
||||
|
||||
def test_setting_workflows(caplog):
|
||||
def test_setting_workflows(caplog, mocker):
|
||||
"""Check that setting workflow works, or warns if incorrect."""
|
||||
workflows = {
|
||||
"foo": mock.MagicMock(spec=ScanWorkflow),
|
||||
"bar": mock.MagicMock(spec=ScanWorkflow),
|
||||
}
|
||||
|
||||
smart_scan_thing = custom_smart_scan_thing("foo", workflows)
|
||||
smart_scan_thing = custom_smart_scan_thing("foo", workflows, mocker)
|
||||
with caplog.at_level(logging.WARNING), smart_scan_thing:
|
||||
assert smart_scan_thing._workflow_name == "foo"
|
||||
assert smart_scan_thing._workflow is workflows["foo"]
|
||||
|
|
@ -225,15 +242,13 @@ def test_inaccessible_scan_methods(smart_scan_thing):
|
|||
smart_scan_thing.ongoing_scan
|
||||
|
||||
|
||||
def test_private_delete_scan(smart_scan_thing, caplog):
|
||||
def test_private_delete_scan(entered_smart_scan_thing, caplog):
|
||||
"""Test the private _delete_scan method deletes directories or warns if it can't."""
|
||||
_clear_scan_dir()
|
||||
smart_scan_thing = entered_smart_scan_thing
|
||||
with caplog.at_level(logging.INFO):
|
||||
fake_scan_name = "fake_scan_0001"
|
||||
fake_scan_path = os.path.join(SCAN_DIR, fake_scan_name)
|
||||
|
||||
# Make the outer scan dir, but not the one to delete
|
||||
os.makedirs(SCAN_DIR)
|
||||
# Attempt to delete the fake scan. Expect it to fail and provide a warning
|
||||
deleted = smart_scan_thing._delete_scan(fake_scan_name)
|
||||
assert not deleted
|
||||
|
|
@ -251,16 +266,13 @@ def test_private_delete_scan(smart_scan_thing, caplog):
|
|||
assert len(caplog.records) == 1
|
||||
|
||||
|
||||
def test_public_delete_scan(smart_scan_thing, caplog):
|
||||
def test_public_delete_scan(entered_smart_scan_thing, caplog):
|
||||
"""Test the delete_scan API call deletes directories or warns if it can't."""
|
||||
_clear_scan_dir()
|
||||
smart_scan_thing = entered_smart_scan_thing
|
||||
with caplog.at_level(logging.INFO):
|
||||
fake_scan_name = "fake_scan_0001"
|
||||
fake_scan_path = os.path.join(SCAN_DIR, fake_scan_name)
|
||||
|
||||
# Make the outer scan dir, but not the one to delete
|
||||
os.makedirs(SCAN_DIR)
|
||||
|
||||
# Attempt to delete the fake scan. Expect it to fail
|
||||
with pytest.raises(HTTPException) as exc_info:
|
||||
smart_scan_thing.delete_scan(fake_scan_name)
|
||||
|
|
@ -280,9 +292,9 @@ def test_public_delete_scan(smart_scan_thing, caplog):
|
|||
assert len(caplog.records) == 1
|
||||
|
||||
|
||||
def test_delete_all_scans(smart_scan_thing, caplog):
|
||||
def test_delete_all_scans(entered_smart_scan_thing, caplog):
|
||||
"""Check the delete_all_scan API really does delete all the scans."""
|
||||
_clear_scan_dir()
|
||||
smart_scan_thing = entered_smart_scan_thing
|
||||
with caplog.at_level(logging.INFO):
|
||||
fake_scan_names = [
|
||||
"fake_scan_0001",
|
||||
|
|
@ -346,15 +358,15 @@ def _run_only_outer_scan(
|
|||
return smart_scan_thing, exec_info
|
||||
|
||||
|
||||
def test_outer_scan(smart_scan_thing, mocker):
|
||||
def test_outer_scan(entered_smart_scan_thing, mocker):
|
||||
"""Test setup and teardown of the scan."""
|
||||
mock_ss_thing, exec_info = _run_only_outer_scan(smart_scan_thing, mocker)
|
||||
mock_ss_thing, exec_info = _run_only_outer_scan(entered_smart_scan_thing, mocker)
|
||||
assert exec_info is None
|
||||
# Checked the mocked _run_scan was run exactly once
|
||||
assert mock_ss_thing._run_scan.call_count == 1
|
||||
|
||||
|
||||
def test_outer_scan_wo_sample_skip(smart_scan_thing, mocker):
|
||||
def test_outer_scan_wo_sample_skip(entered_smart_scan_thing, mocker):
|
||||
"""Test setup and teardown of the scan."""
|
||||
|
||||
def _set_skip_background(mock_ss_thing):
|
||||
|
|
@ -363,7 +375,7 @@ def test_outer_scan_wo_sample_skip(smart_scan_thing, mocker):
|
|||
mock_ss_thing.__dict__["skip_background"] = False
|
||||
|
||||
mock_ss_thing, exec_info = _run_only_outer_scan(
|
||||
smart_scan_thing, mocker, _set_skip_background
|
||||
entered_smart_scan_thing, mocker, _set_skip_background
|
||||
)
|
||||
|
||||
assert exec_info is None
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue