Updated to new Action tasks (eaf4cf09) · Commits · OpenFlexure / openflexure-microscope-server

docs/source/extensions/example_extension/06_tasks_locks.py

+3 −8

Original line number	Diff line number	Diff line
		@@ -9,7 +9,6 @@ from labthings.server.decorators import (
		PropertySchema,
		ThingAction,
		doc_response,
		marshal_task,
		)
		from labthings.server.schema import Schema
		from labthings.server import fields
		@@ -70,10 +69,8 @@ def timelapse(microscope, n_images, t_between):
		@ThingAction
		class TimelapseAPI(View):
		"""
		Take a series of images in a timelapse, running as a background task
		Take a series of images in a timelapse
		"""

		@marshal_task # Shorthand for marshaling with a pre-made Task object schema
		@use_args(
		{
		"n_images": fields.Integer(
		@@ -88,13 +85,11 @@ class TimelapseAPI(View):
		# Find our microscope component
		microscope = find_component("org.openflexure.microscope")

		# Create and start "timelapse", running in a background task
		task = taskify(timelapse)(
		# Start "timelapse"
		return timelapse(
		microscope, args.get("n_images"), args.get("t_between")
		)

		return task


		## Create extension

docs/source/extensions/example_extension/07_ev_gui.py

+1 −6

Original line number	Diff line number	Diff line
		@@ -9,7 +9,6 @@ from labthings.server.decorators import (
		PropertySchema,
		ThingAction,
		doc_response,
		marshal_task,
		)
		from labthings.server.schema import Schema
		from labthings.server import fields
		@@ -74,8 +73,6 @@ class TimelapseAPI(View):
		"""
		Take a series of images in a timelapse, running as a background task
		"""

		@marshal_task # Shorthand for marshaling with a pre-made Task object schema
		@use_args(
		{
		"n_images": fields.Integer(
		@@ -91,12 +88,10 @@ class TimelapseAPI(View):
		microscope = find_component("org.openflexure.microscope")

		# Create and start "timelapse", running in a background task
		task = taskify(timelapse)(
		return timelapse(
		microscope, args.get("n_images"), args.get("t_between")
		)

		return task


		## Extension GUI (OpenFlexure eV)
		# Alternate form without any dynamic parts

docs/source/extensions/tasks_locks.rst

+6 −8

Original line number	Diff line number	Diff line
		@@ -15,7 +15,7 @@ We get around these issues by making use of background tasks, and component lock
		Background tasks
		----------------

		Tasks are introduced to manage long-running functions in a way that does not block HTTP requests. Any function can be offloaded to a background task, and this is done through the :py:meth:`labthings.tasks.taskify` function, by calling ``taskify(<long_running_function>)(args, *kwargs)``.
		Tasks are introduced to manage long-running functions in a way that does not block HTTP requests. Any API Action will automatically run as a background task (that is, any View that subclasses `ActionView`, or uses the `@ThingAction` decorator).

		Internally, the ``tasks`` submodule stores a list of all requested tasks, and their states. This state stores the running status of the task (if itis idle, running, error, or success), information about the start and end times, a unique task ID, and, upon completion, the return value of the long-running function.

		@@ -23,7 +23,7 @@ By using tasks, a function can be started in the background, and it's return val

		API routes have been created to allow checking the state of all tasks (GET ``/tasks``), a particular task by ID (GET ``/tasks/<task_id>``), and terminating or removing individual tasks (DELETE ``/tasks/<task_id>``).

		A special ``@marshal_task`` decorator provides shorthand for automatically returning a serialized representation of the task, when your POST request returns.
		All Actions will return a serialized representation of the task, when your POST request returns. If the task completes within a default timeout period (usually 1 second) then the completed Task representation will be returned. If the task is still running after this timeout period, the "in-progress" Task representation will be returned. The final output value can then be retrieved at a later time.

		An example of a long running task may look like:

		@@ -31,15 +31,13 @@ An example of a long running task may look like:

		...
		from labthings.tasks import taskify
		from labthings.server.decorators import marshal_task
		from labthings.server.decorators import ThingAction

		@ThingAction
		class SlowAPI(View):
		@marshal_task
		def post(self):
		# Run the long-running function as a task
		task = taskify(long_running_function)(function_argument_1, function_argument_2)
		# Return the task object. Let @marshal_task handle serialization
		return task
		# Return the task object.
		return long_running_function(function_argument_1, function_argument_2)

		After some time, once the task has completed, it could be retreived using:

openflexure_microscope/api/default_extensions/autofocus.py

+6 −12

Original line number	Diff line number	Diff line
		from labthings.server.find import find_component
		from labthings.server.extensions import BaseExtension
		from labthings.server.view import View
		from labthings.server.decorators import ThingAction, ThingProperty, marshal_task
		from labthings.server.decorators import ThingAction, ThingProperty

		from openflexure_microscope.devel import JsonResponse, request, taskify, abort
		from openflexure_microscope.devel import JsonResponse, request, abort
		from openflexure_microscope.utilities import set_properties

		import time
		@@ -337,8 +337,6 @@ class AutofocusAPI(View):
		"""
		Run a standard autofocus
		"""

		@marshal_task
		def post(self):
		payload = JsonResponse(request)
		microscope = find_component("org.openflexure.microscope")
		@@ -351,10 +349,9 @@ class AutofocusAPI(View):

		if microscope.has_real_stage():
		logging.debug("Running autofocus...")
		task = taskify(autofocus)(microscope, dz)

		# return a handle on the autofocus task
		return task
		return autofocus(microscope, dz)

		else:
		abort(503, "No stage connected. Unable to autofocus.")
		@@ -365,8 +362,6 @@ class FastAutofocusAPI(View):
		"""
		Run a fast autofocus
		"""

		@marshal_task
		def post(self):
		payload = JsonResponse(request)
		microscope = find_component("org.openflexure.microscope")
		@@ -382,12 +377,11 @@ class FastAutofocusAPI(View):

		if microscope.has_real_stage():
		logging.debug("Running autofocus...")
		task = taskify(fast_up_down_up_autofocus)(
		microscope, dz=dz, mini_backlash=backlash
		)

		# return a handle on the autofocus task
		return task
		return fast_up_down_up_autofocus(
		microscope, dz=dz, mini_backlash=backlash
		)

		else:
		abort(503, "No stage connected. Unable to autofocus.")

openflexure_microscope/api/default_extensions/camera_stage_mapping/extension.py

+2 −10

Original line number	Diff line number	Diff line
		@@ -7,14 +7,12 @@ from labthings.server.view import View
		from labthings.server.find import find_component
		from labthings.server.extensions import BaseExtension
		from labthings.server.decorators import (
		marshal_task,
		ThingAction,
		use_args,
		ThingProperty,
		)
		from labthings.server import fields

		from labthings.core.tasks import taskify
		from labthings.core.utilities import get_by_path, set_by_path, create_from_path


		@@ -146,15 +144,12 @@ class Calibrate1DView(View):
		@use_args(
		{"direction": fields.List(fields.Float(), required=True, example=[1, 0, 0])}
		)
		@marshal_task
		def post(self, args):
		"""Calibrate one axis of the microscope stage against the camera."""

		direction = np.array(args.get("direction"))

		task = taskify(csm_extension.calibrate_1d)(direction)

		return task
		return csm_extension.calibrate_1d(direction)


		csm_extension.add_view(Calibrate1DView, "/calibrate_1d", endpoint="calibrate_1d")
		@@ -162,12 +157,9 @@ csm_extension.add_view(Calibrate1DView, "/calibrate_1d", endpoint="calibrate_1d"

		@ThingAction
		class CalibrateXYView(View):
		@marshal_task
		def post(self):
		"""Calibrate both axes of the microscope stage against the camera."""
		task = taskify(csm_extension.calibrate_xy)()

		return task
		return csm_extension.calibrate_xy()


		csm_extension.add_view(CalibrateXYView, "/calibrate_xy", endpoint="calibrate_xy")