Restructured labthings (a8a3cafa) · Commits · OpenFlexure / openflexure-microscope-server

docs/source/plugins/example/plugin.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@ from openflexure_microscope.plugins import MicroscopePlugin
		from openflexure_microscope.api.views import MicroscopeViewPlugin
		from openflexure_microscope.api.utilities import JsonResponse

		from openflexure_microscope.common.tasks import taskify
		from openflexure_microscope.common.labthings_core.tasks import taskify

		import os
		import time

openflexure_microscope/api/app.py

+10 −18

Original line number	Diff line number	Diff line
		@@ -3,29 +3,24 @@
		import time
		import atexit
		import logging
		import sys
		import os

		from flask import Flask, jsonify, send_file, url_for
		from flask import Flask, jsonify, send_file

		from serial import SerialException
		from datetime import datetime

		from flask_cors import CORS

		from openflexure_microscope.api.exceptions import JSONExceptionHandler
		from openflexure_microscope.api.utilities import list_routes
		from openflexure_microscope.api.utilities import list_routes, init_default_plugins

		from openflexure_microscope.config import (
		settings_file_path,
		JSONEncoder,
		USER_PLUGINS_PATH,
		)
		from openflexure_microscope.api import v2

		from openflexure_microscope.common.labthings.labthing import LabThing
		from openflexure_microscope.common.labthings.find import registered_plugins
		from openflexure_microscope.common.labthings.plugins import find_plugins
		from openflexure_microscope.common.flask_labthings.labthing import LabThing
		from openflexure_microscope.common.flask_labthings.plugins import find_plugins

		from openflexure_microscope.api.microscope import default_microscope as api_microscope

		@@ -36,14 +31,13 @@ is_gunicorn = "gunicorn" in os.environ.get("SERVER_SOFTWARE", "")

		DEFAULT_LOGFILE = settings_file_path("openflexure_microscope.log")

		logger = logging.getLogger()
		if (__name__ == "__main__") or (not is_gunicorn):
		# If imported, but not by gunicorn
		print("Letting sys handle logs")
		logger = logging.getLogger()
		logger.setLevel(logging.DEBUG)
		else:
		# Direct standard Python logging to file and console
		root = logging.getLogger()
		error_formatter = logging.Formatter(
		"[%(asctime)s] [%(threadName)s] [%(levelname)s] %(message)s"
		)
		@@ -56,9 +50,9 @@ else:

		for handler in error_handlers:
		handler.setFormatter(error_formatter)
		root.addHandler(handler)
		logger.addHandler(handler)

		root.setLevel(logging.getLogger("gunicorn.error").level)
		logger.setLevel(logging.getLogger("gunicorn.error").level)


		# Create flask app
		@@ -71,9 +65,6 @@ app.json_encoder = JSONEncoder
		# Enable CORS everywhere
		CORS(app, resources=r"*")

		# Make errors more API friendly
		handler = JSONExceptionHandler(app)

		# Build a labthing
		labthing = LabThing(app, prefix="/api/v2")
		labthing.description = "Test LabThing-based API for OpenFlexure Microscope"
		@@ -83,6 +74,8 @@ labthing.title = f"OpenFlexure Microscope {api_microscope.name}"
		labthing.register_device(api_microscope, "openflexure_microscope")

		# Attach plugins
		if not os.path.isfile(USER_PLUGINS_PATH):
		init_default_plugins(USER_PLUGINS_PATH)
		for plugin in find_plugins(USER_PLUGINS_PATH):
		labthing.register_plugin(plugin)

		@@ -120,7 +113,7 @@ labthing.register_property(views.SnapshotStream)
		for name, action in views.enabled_root_actions().items():
		view_class = action["view_class"]
		rule = action["rule"]
		labthing.add_resource(view_class, "/actions{rule}")
		labthing.add_resource(view_class, f"/actions{rule}")
		labthing.register_action(view_class)


		@@ -159,7 +152,6 @@ def err_log():

		# Automatically clean up microscope at exit
		def cleanup():
		global api_microscope
		logging.debug("App teardown started...")
		logging.debug("Settling...")
		time.sleep(0.5)

openflexure_microscope/api/microscope.py

+1 −5

Original line number	Diff line number	Diff line
		@@ -28,11 +28,7 @@ except Exception as e:

		# Initialise stage
		logging.debug("Creating stage object...")
		try:
		api_stage = SangaStage()
		except Exception as e:
		logging.error(e)
		logging.warning("No valid stage hardware found. Falling back to mock stage!")

		api_stage = MockStage()

		# Attach devices to microscope

openflexure_microscope/api/utilities.py

+30 −0

Original line number	Diff line number	Diff line
		import logging
		import os
		import errno
		from werkzeug.exceptions import BadRequest
		from flask import url_for, Blueprint

		@@ -95,3 +97,31 @@ def list_routes(app):
		output[url] = line

		return output


		def create_file(config_path):
		if not os.path.exists(os.path.dirname(config_path)):
		try:
		os.makedirs(os.path.dirname(config_path))
		except OSError as exc: # Guard against race condition
		if exc.errno != errno.EEXIST:
		raise


		def init_default_plugins(plugin_path):
		global _DEFAULT_PLUGIN_INIT
		os.makedirs(os.path.dirname(plugin_path), exist_ok=True)

		if not os.path.exists(plugin_path): # If user plugins file doesn't exist
		logging.warning("No plugin file found at {}. Creating...".format(plugin_path))
		create_file(plugin_path)

		logging.info("Populating {}...".format(plugin_path))
		with open(plugin_path, "w") as outfile:
		outfile.write(_DEFAULT_PLUGIN_INIT)


		_DEFAULT_PLUGIN_INIT = """from openflexure_microscope.plugins.v2.autofocus import autofocus_plugin_v2
		from openflexure_microscope.plugins.v2.scan import scan_plugin_v2

		__plugins__ = [autofocus_plugin_v2, scan_plugin_v2]"""
		No newline at end of file

openflexure_microscope/api/v2/views/actions/init.py

+0 −5

Original line number	Diff line number	Diff line
		@@ -2,11 +2,6 @@
		Top-level representation of enabled actions
		"""

		from flask import Blueprint, url_for, jsonify

		from openflexure_microscope.api.utilities import blueprint_for_module
		from openflexure_microscope.utilities import get_docstring, description_from_view

		from . import camera, stage, system

		_actions = {