Merge remote-tracking branch 'origin/master' into deltastage
This commit is contained in:
Samuel McDermott
commit
5e9e8cb2a3
222 changed files with 30104 additions and 7329 deletions
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@ -1,207 +1,190 @@
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#!/usr/bin/env python
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import sys
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import time
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import atexit
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import logging
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import sys
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import logging, logging.handlers
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# Look for debug flag
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if "-d" in sys.argv or "--debug" in sys.argv:
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log_level = logging.DEBUG
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else:
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log_level = logging.INFO
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# Set root logger level
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root_log = logging.getLogger()
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root_log.setLevel(log_level)
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import os
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import pkg_resources
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from flask import (
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Flask, jsonify, send_file)
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from flask import Flask, send_file, abort
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from serial import SerialException
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from datetime import datetime
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from flask_cors import CORS
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from flask_cors import CORS, cross_origin
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from openflexure_microscope.api.exceptions import JSONExceptionHandler
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from openflexure_microscope.api.utilities import list_routes
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from openflexure_microscope.api.utilities import list_routes, init_default_extensions
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from openflexure_microscope import Microscope
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from openflexure_microscope.config import JSONEncoder
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from openflexure_microscope.paths import (
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OPENFLEXURE_VAR_PATH,
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OPENFLEXURE_EXTENSIONS_PATH,
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settings_file_path,
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logs_file_path,
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)
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from openflexure_microscope.camera.capture import build_captures_from_exif
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from openflexure_microscope.config import USER_CONFIG_DIR
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from openflexure_microscope.api.v1 import blueprints
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from labthings import create_app
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from labthings.extensions import find_extensions
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# Import device modules
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# NB this will eventually be handled by the RC file, so you can choose what device
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# class should be attached.
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try:
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from openflexure_microscope.camera.pi import PiCameraStreamer
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except ImportError:
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logging.warning("Unable to import PiCameraStreamer")
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from openflexure_microscope.camera.mock import MockStreamer
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from openflexure_microscope.stage.sanga import SangaStage, SangaDeltaStage
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from openflexure_microscope.stage.mock import MockStage
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from openflexure_microscope.api.microscope import default_microscope as api_microscope
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from openflexure_microscope.api.v2 import views
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# Handle logging
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is_gunicorn = "gunicorn" in os.environ.get("SERVER_SOFTWARE", "")
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access_log = logging.getLogger('werkzeug')
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# Block the access logs from propagating up to the root logger
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access_log.propagate = False
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DEFAULT_LOGFILE = os.path.join(USER_CONFIG_DIR, 'openflexure_microscope.log')
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ROOT_LOGFILE = logs_file_path("openflexure_microscope.log")
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ACCESS_LOGFILE = logs_file_path("openflexure_microscope.access.log")
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if (__name__ == "__main__") or (not is_gunicorn):
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# If imported, but not by gunicorn
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print("Letting sys handle logs")
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logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
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else:
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# Direct standard Python logging to file and console
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root = logging.getLogger()
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error_formatter = logging.Formatter("[%(asctime)s] [%(threadName)s] [%(levelname)s] %(message)s")
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rotating_logfile = logging.handlers.RotatingFileHandler(
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DEFAULT_LOGFILE,
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maxBytes=1000000,
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backupCount=7
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)
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error_handlers = [
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rotating_logfile,
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logging.StreamHandler()
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]
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for handler in error_handlers:
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handler.setFormatter(error_formatter)
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root.addHandler(handler)
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root.setLevel(logging.getLogger("gunicorn.error").level)
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# Create a dummy microscope object, with no hardware attachments
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api_microscope = Microscope()
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# Rebuild the capture list
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# TODO: Offload to a thread?
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stored_image_list = build_captures_from_exif()
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# Basic log format
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formatter = logging.Formatter(
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"[%(asctime)s] [%(threadName)s] [%(levelname)s] %(message)s"
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)
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# Generate API URI based on version from filename
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def uri(suffix, api_version, base=None):
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if not base:
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base = "/api/{}".format(api_version)
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return_uri = base + suffix
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logging.debug("Created app route: {}".format(return_uri))
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return return_uri
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# Create file handler
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fh = logging.handlers.RotatingFileHandler(
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ROOT_LOGFILE, maxBytes=1_000_000, backupCount=5
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)
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fh.setFormatter(formatter)
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fh.setLevel(logging.DEBUG)
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fh.propagate = False
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# Create access log file handler
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afh = logging.handlers.RotatingFileHandler(
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ACCESS_LOGFILE, maxBytes=1_000_000, backupCount=5
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)
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afh.setFormatter(formatter)
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afh.setLevel(logging.DEBUG)
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afh.propagate = False
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# Add file handler to root logger
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root_log.addHandler(fh)
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access_log.addHandler(afh)
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# Log server paths being used
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logging.info(f"Running with data path {OPENFLEXURE_VAR_PATH}")
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logging.info("Creating app")
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# Create flask app
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app = Flask(__name__)
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app.url_map.strict_slashes = False
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app, labthing = create_app(
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__name__,
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prefix="/api/v2",
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title=f"OpenFlexure Microscope {api_microscope.name}",
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description="Test LabThing-based API for OpenFlexure Microscope",
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types=["org.openflexure.microscope"],
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version=pkg_resources.get_distribution("openflexure-microscope-server").version,
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flask_kwargs={"static_url_path": "", "static_folder": "static/dist"},
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)
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CORS(app, resources=r'/api/*')
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# Enable CORS for some routes outside of LabThings
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cors = CORS(app)
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# Make errors more API friendly
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handler = JSONExceptionHandler(app)
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# Use custom JSON encoder
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labthing.json_encoder = JSONEncoder
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app.json_encoder = JSONEncoder
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# Attach lab devices
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labthing.add_component(api_microscope, "org.openflexure.microscope")
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# Attach extensions
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if not os.path.isfile(OPENFLEXURE_EXTENSIONS_PATH):
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init_default_extensions(OPENFLEXURE_EXTENSIONS_PATH)
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for extension in find_extensions(OPENFLEXURE_EXTENSIONS_PATH):
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labthing.register_extension(extension)
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# Attach captures resources
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labthing.add_view(views.CaptureList, f"/captures")
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labthing.add_root_link(views.CaptureList, "captures")
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labthing.add_view(views.CaptureView, f"/captures/<id>")
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labthing.add_view(views.CaptureDownload, f"/captures/<id>/download/<filename>")
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labthing.add_view(views.CaptureTags, f"/captures/<id>/tags")
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labthing.add_view(views.CaptureAnnotations, f"/captures/<id>/annotations")
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# Attach settings and state resources
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labthing.add_view(views.SettingsProperty, f"/instrument/settings")
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labthing.add_root_link(views.SettingsProperty, "instrumentSettings")
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labthing.add_view(views.NestedSettingsProperty, "/instrument/settings/<path:route>")
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labthing.add_view(views.StateProperty, "/instrument/state")
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labthing.add_view(views.NestedStateProperty, "/instrument/state/<path:route>")
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labthing.add_root_link(views.StateProperty, "instrumentState")
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labthing.add_view(views.ConfigurationProperty, "/instrument/configuration")
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labthing.add_view(
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views.NestedConfigurationProperty, "/instrument/configuration/<path:route>"
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)
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labthing.add_root_link(views.ConfigurationProperty, "instrumentConfiguration")
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# After app starts, but before first request, attach hardware to global microscope
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@app.before_first_request
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def attach_microscope():
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# Create the microscope object globally (common to all spawned server threads)
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global api_microscope, stored_image_list
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logging.debug("First request made. Populating microscope with hardware...")
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# Attach streams resources
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labthing.add_view(views.MjpegStream, f"/streams/mjpeg")
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labthing.add_view(views.SnapshotStream, f"/streams/snapshot")
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# Initialise camera
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logging.debug("Creating camera object...")
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try:
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api_camera = PiCameraStreamer()
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except Exception as e:
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logging.error(e)
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logging.warning("No valid camera hardware found. Falling back to mock camera!")
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api_camera = MockStreamer()
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# Initialise stage
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logging.debug("Creating stage object...")
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try:
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api_stage = SangaDeltaStage()
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except Exception as e:
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logging.error(e)
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logging.warning("No valid stage hardware found. Falling back to mock stage!")
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api_stage = MockStage()
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# Attach devices to microscope
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logging.debug("Attaching devices to microscope...")
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api_microscope.attach(
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api_camera,
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api_stage
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)
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# Restore loaded capture array to camera object
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logging.debug("Restoring captures...")
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if stored_image_list:
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api_microscope.camera.images = stored_image_list
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logging.debug("Microscope successfully attached!")
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# Attach microscope action resources
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labthing.add_view(views.actions.ActionsView, "/actions")
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labthing.add_root_link(views.actions.ActionsView, "actions")
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for name, action in views.enabled_root_actions().items():
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view_class = action["view_class"]
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rule = action["rule"]
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labthing.add_view(view_class, f"/actions{rule}")
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# WEBAPP ROUTES
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# API ROUTES
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# Base routes
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base_blueprint = blueprints.base.construct_blueprint(api_microscope)
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app.register_blueprint(base_blueprint, url_prefix=uri('', 'v1'))
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# Stage routes
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stage_blueprint = blueprints.stage.construct_blueprint(api_microscope)
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app.register_blueprint(stage_blueprint, url_prefix=uri('/stage', 'v1'))
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# Camera routes
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camera_blueprint = blueprints.camera.construct_blueprint(api_microscope)
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app.register_blueprint(camera_blueprint, url_prefix=uri('/camera', 'v1'))
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# Plugin routes
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plugin_blueprint = blueprints.plugins.construct_blueprint(api_microscope)
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app.register_blueprint(plugin_blueprint, url_prefix=uri('/plugin', 'v1'))
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# Task routes
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task_blueprint = blueprints.task.construct_blueprint(api_microscope)
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app.register_blueprint(task_blueprint, url_prefix=uri('/task', 'v1'))
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@app.route("/")
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def openflexure_ev():
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return app.send_static_file("index.html")
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@app.route('/routes')
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@app.route("/routes")
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@cross_origin()
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def routes():
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"""
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List of all connected API routes
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.. :quickref: System; Routes
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:>header Accept: application/json
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:>header Content-Type: application/json
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:status 200: stream active
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"""
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return jsonify(list_routes(app))
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return list_routes(app)
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@app.route('/log')
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@app.route("/log")
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def err_log():
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"""
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Most recent 1mb of log output
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.. :quickref: System; Log
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:>header Accept: application/json
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:>header Content-Type: application/json
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:status 200: stream active
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"""
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timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
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return send_file(
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DEFAULT_LOGFILE,
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as_attachment=True,
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attachment_filename='openflexure_microscope_{}.log'.format(timestamp)
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ROOT_LOGFILE,
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as_attachment=True,
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attachment_filename="openflexure_microscope_{}.log".format(timestamp),
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)
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@app.route("/api/v1/", defaults={"path": ""})
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@app.route("/api/v1/<path:path>")
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def api_v1_catch_all(path):
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abort(410, "API v1 is no longer in use. Please upgrade your client.")
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# Automatically clean up microscope at exit
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def cleanup():
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global api_microscope
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logging.debug("App teardown started...")
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logging.debug("Settling...")
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time.sleep(0.5)
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# Save config
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logging.debug("Saving config for teardown...")
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api_microscope.save_config(backup=True)
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api_microscope.save_settings()
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logging.debug("Settling...")
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time.sleep(0.5)
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@ -218,5 +201,9 @@ def cleanup():
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atexit.register(cleanup)
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# Start the app
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if __name__ == "__main__":
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app.run(host='0.0.0.0', port="5000", threaded=True, debug=True, use_reloader=False)
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from labthings import Server
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logging.info("Starting OpenFlexure Microscope Server...")
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server = Server(app)
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server.run(host="::", port=5000, debug=False, zeroconf=True)
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