From 36334ed743f848c85690de9cf6eb48a5daf2b766 Mon Sep 17 00:00:00 2001 From: jtc42 Date: Fri, 17 Jan 2020 15:13:32 +0000 Subject: [PATCH] Moved to a LabThings dependency for server --- docs/make.bat | 2 + docs/source/plugins/class.rst | 2 +- docs/source/plugins/example/plugin.py | 2 +- docs/source/plugins/hardware.rst | 8 +- docs/source/plugins/structure.rst | 10 +- openflexure_microscope/__init__.py | 1 - openflexure_microscope/api/app.py | 4 +- .../api/default_extensions/autofocus.py | 8 +- .../picamera_autocalibrate/extension.py | 10 +- .../api/default_extensions/scan.py | 10 +- .../api/default_extensions/zip_builder.py | 8 +- .../api/example_extensions/ev_gui.py | 6 +- .../api/v2/views/actions/__init__.py | 8 +- .../api/v2/views/actions/camera.py | 8 +- .../api/v2/views/actions/stage.py | 8 +- .../api/v2/views/actions/system.py | 4 +- .../api/v2/views/captures.py | 12 +- openflexure_microscope/api/v2/views/state.py | 8 +- .../api/v2/views/streams.py | 8 +- openflexure_microscope/camera/base.py | 4 +- openflexure_microscope/common/__init__.py | 2 - .../common/flask_labthings/__init__.py | 1 - .../common/flask_labthings/decorators.py | 178 ------ .../common/flask_labthings/exceptions.py | 37 -- .../common/flask_labthings/extensions.py | 148 ----- .../common/flask_labthings/fields.py | 2 - .../common/flask_labthings/find.py | 50 -- .../common/flask_labthings/labthing.py | 288 ---------- .../common/flask_labthings/names.py | 3 - .../common/flask_labthings/quick.py | 41 -- .../common/flask_labthings/schema.py | 93 --- .../common/flask_labthings/spec/__init__.py | 164 ------ .../common/flask_labthings/spec/paths.py | 50 -- .../common/flask_labthings/types.py | 66 --- .../common/flask_labthings/utilities.py | 29 - .../common/flask_labthings/view.py | 27 - .../common/flask_labthings/views/__init__.py | 0 .../flask_labthings/views/docs/__init__.py | 113 ---- .../views/docs/static/favicon-16x16.png | Bin 665 -> 0 bytes .../views/docs/static/favicon-32x32.png | Bin 628 -> 0 bytes .../views/docs/static/index.html | 60 -- .../views/docs/static/oauth2-redirect.html | 68 --- .../views/docs/static/swagger-ui-bundle.js | 134 ----- .../docs/static/swagger-ui-bundle.js.map | 1 - .../static/swagger-ui-standalone-preset.js | 22 - .../swagger-ui-standalone-preset.js.map | 1 - .../views/docs/static/swagger-ui.css | 4 - .../views/docs/static/swagger-ui.css.map | 1 - .../views/docs/static/swagger-ui.js | 9 - .../views/docs/static/swagger-ui.js.map | 1 - .../views/docs/templates/swagger-ui.html | 38 -- .../flask_labthings/views/extensions.py | 28 - .../common/flask_labthings/views/tasks.py | 51 -- .../common/labthings_core/__init__.py | 0 .../common/labthings_core/lock.py | 76 --- .../common/labthings_core/tasks/__init__.py | 25 - .../common/labthings_core/tasks/pool.py | 145 ----- .../common/labthings_core/tasks/thread.py | 200 ------- .../common/labthings_core/utilities.py | 71 --- openflexure_microscope/devel/__init__.py | 4 +- openflexure_microscope/exceptions.py | 4 - openflexure_microscope/microscope.py | 4 +- openflexure_microscope/stage/base.py | 4 +- poetry.lock | 530 ++++++++++++++++-- pyproject.toml | 6 +- 65 files changed, 546 insertions(+), 2364 deletions(-) delete mode 100644 openflexure_microscope/common/__init__.py delete mode 100644 openflexure_microscope/common/flask_labthings/__init__.py delete mode 100644 openflexure_microscope/common/flask_labthings/decorators.py delete mode 100644 openflexure_microscope/common/flask_labthings/exceptions.py delete mode 100644 openflexure_microscope/common/flask_labthings/extensions.py delete mode 100644 openflexure_microscope/common/flask_labthings/fields.py delete mode 100644 openflexure_microscope/common/flask_labthings/find.py delete mode 100644 openflexure_microscope/common/flask_labthings/labthing.py delete mode 100644 openflexure_microscope/common/flask_labthings/names.py delete mode 100644 openflexure_microscope/common/flask_labthings/quick.py delete mode 100644 openflexure_microscope/common/flask_labthings/schema.py delete mode 100644 openflexure_microscope/common/flask_labthings/spec/__init__.py delete mode 100644 openflexure_microscope/common/flask_labthings/spec/paths.py delete mode 100644 openflexure_microscope/common/flask_labthings/types.py delete mode 100644 openflexure_microscope/common/flask_labthings/utilities.py delete mode 100644 openflexure_microscope/common/flask_labthings/view.py delete mode 100644 openflexure_microscope/common/flask_labthings/views/__init__.py delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/__init__.py delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/favicon-16x16.png delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/favicon-32x32.png delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/index.html delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/oauth2-redirect.html delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/swagger-ui-bundle.js delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/swagger-ui-bundle.js.map delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/swagger-ui-standalone-preset.js delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/swagger-ui-standalone-preset.js.map delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/swagger-ui.css delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/swagger-ui.css.map delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/swagger-ui.js delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/static/swagger-ui.js.map delete mode 100644 openflexure_microscope/common/flask_labthings/views/docs/templates/swagger-ui.html delete mode 100644 openflexure_microscope/common/flask_labthings/views/extensions.py delete mode 100644 openflexure_microscope/common/flask_labthings/views/tasks.py delete mode 100644 openflexure_microscope/common/labthings_core/__init__.py delete mode 100644 openflexure_microscope/common/labthings_core/lock.py delete mode 100644 openflexure_microscope/common/labthings_core/tasks/__init__.py delete mode 100644 openflexure_microscope/common/labthings_core/tasks/pool.py delete mode 100644 openflexure_microscope/common/labthings_core/tasks/thread.py delete mode 100644 openflexure_microscope/common/labthings_core/utilities.py diff --git a/docs/make.bat b/docs/make.bat index 4d9eb83d..b713a4e8 100644 --- a/docs/make.bat +++ b/docs/make.bat @@ -10,6 +10,8 @@ if "%SPHINXBUILD%" == "" ( set SOURCEDIR=source set BUILDDIR=build +set SPHINXOPTS="-E" + if "%1" == "" goto help %SPHINXBUILD% >NUL 2>NUL diff --git a/docs/source/plugins/class.rst b/docs/source/plugins/class.rst index 6f6002ef..891d72db 100644 --- a/docs/source/plugins/class.rst +++ b/docs/source/plugins/class.rst @@ -3,5 +3,5 @@ Classes and Modules Extension class --------------- -.. autoclass:: openflexure_microscope.common.flask_labthings.extensions.BaseExtension +.. autoclass:: labthings.server.extensions.BaseExtension :members: diff --git a/docs/source/plugins/example/plugin.py b/docs/source/plugins/example/plugin.py index 0ea51b23..e1241cfe 100644 --- a/docs/source/plugins/example/plugin.py +++ b/docs/source/plugins/example/plugin.py @@ -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.labthings_core.tasks import taskify +from labthings.core.tasks import taskify import os import time diff --git a/docs/source/plugins/hardware.rst b/docs/source/plugins/hardware.rst index cd2f0a70..63bfa8bd 100644 --- a/docs/source/plugins/hardware.rst +++ b/docs/source/plugins/hardware.rst @@ -21,7 +21,7 @@ Tasks are introduced to manage long-running functions in a way that does not blo the use of tasks, long-running functions would block an HTTP response until the function returns, often resulting in a timeout. -To prevent this, any function can be offloaded to a background task. This is done through the :py:meth:`openflexure_microscope.common.tasks.taskify` +To prevent this, any function can be offloaded to a background task. This is done through the :py:meth:`labthings.tasks.taskify` function, by calling ``taskify()(*args, **kwargs)``. Internally, the ``tasks`` submodule stores a list of all requested tasks, which themselves contain a ``state`` dictionary. This dictionary stores the status of the task (if it is idle, running, error, or success), information about the start and end times, a unique task ID, and the return value of @@ -38,7 +38,7 @@ An example of a long running task may look like: .. code-block:: python from openflexure_microscope.plugins import MicroscopeViewPlugin - from openflexure_microscope.common.tasks import taskify + from labthings.tasks import taskify class MyPlugin(MicroscopeViewPlugin): def post(self): @@ -63,7 +63,7 @@ the microscope hardware. For example, even if the stage is not actively moving ( within a tile scan), another user should not be able to move the microscope, interrupting the task. Thread locks act to prevent this. -The camera and stage both contain an instance of :py:class:`openflexure_microscope.common.lock.StrictLock`, named ``lock``. +The camera and stage both contain an instance of :py:class:`labthings.lock.StrictLock`, named ``lock``. Built-in functions such as capture and move will always acquire this lock for the duration of the function. This ensures that, for example, simultaneous attemps to move do not occur. @@ -77,7 +77,7 @@ For example, a timelapse plugin may look like: from openflexure_microscope.api.v1.views import MicroscopeViewPlugin from openflexure_microscope.api.utilities import JsonResponse - from openflexure_microscope.common.tasks import taskify + from labthings.tasks import taskify ### MICROSCOPE PLUGIN ### diff --git a/docs/source/plugins/structure.rst b/docs/source/plugins/structure.rst index c5f1c53f..ab04412d 100644 --- a/docs/source/plugins/structure.rst +++ b/docs/source/plugins/structure.rst @@ -1,17 +1,17 @@ Basic extension structure ========================= -An extension starts as a simple instance of :py:class:`openflexure_microscope.common.flask_labthings.extensions.BaseExtension`. +An extension starts as a simple instance of :py:class:`labthings.server.extensions.BaseExtension`. Each extension is described by a single ``BaseExtension`` instance, containing any number of methods, API views, and additional hardware components. -In order to access the currently running microscope object, use the :py:func:`openflexure_microscope.common.flask_labthings.find` function, with the argument ``"org.openflexure.microscope"``. Likewise, any new components attached by other extensions can be found using their full name, as above. +In order to access the currently running microscope object, use the :py:func:`labthings.server.find` function, with the argument ``"org.openflexure.microscope"``. Likewise, any new components attached by other extensions can be found using their full name, as above. A simple extension file, with no API views but application-available methods may look like: .. code-block:: python - from openflexure_microscope.common.flask_labthings.extensions import BaseExtension - from openflexure_microscope.common.flask_labthings.find import find_component + from labthings.server.extensions import BaseExtension + from labthings.server.find import find_component def identify(): @@ -50,7 +50,7 @@ Once this extension is loaded, any other extensions will have access to your met .. code-block:: python - from openflexure_microscope.common.flask_labthings.find import find_extension + from labthings.server.find import find_extension def test_extension_method(): # Find your extension. Returns None if it hasn't been found. diff --git a/openflexure_microscope/__init__.py b/openflexure_microscope/__init__.py index 85af80b2..d8fd15ec 100644 --- a/openflexure_microscope/__init__.py +++ b/openflexure_microscope/__init__.py @@ -4,4 +4,3 @@ __version__ = "0.1.0" from .microscope import Microscope from . import config from . import utilities -from . import common diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py index dbe4c073..6ca80e75 100644 --- a/openflexure_microscope/api/app.py +++ b/openflexure_microscope/api/app.py @@ -22,8 +22,8 @@ from openflexure_microscope.paths import ( settings_file_path, ) -from openflexure_microscope.common.flask_labthings.quick import create_app -from openflexure_microscope.common.flask_labthings.extensions import find_extensions +from labthings.server.quick import create_app +from labthings.server.extensions import find_extensions from openflexure_microscope.api.microscope import default_microscope as api_microscope diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py index 2832835a..510272b7 100644 --- a/openflexure_microscope/api/default_extensions/autofocus.py +++ b/openflexure_microscope/api/default_extensions/autofocus.py @@ -1,7 +1,7 @@ -from openflexure_microscope.common.flask_labthings.find import find_component -from openflexure_microscope.common.flask_labthings.extensions import BaseExtension -from openflexure_microscope.common.flask_labthings.view import View -from openflexure_microscope.common.flask_labthings.decorators import ( +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, ) diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py index fb0d71d7..2ac16466 100644 --- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py +++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py @@ -1,12 +1,12 @@ -from openflexure_microscope.common.flask_labthings.view import View -from openflexure_microscope.common.flask_labthings.find import find_component -from openflexure_microscope.common.flask_labthings.extensions import BaseExtension -from openflexure_microscope.common.flask_labthings.decorators import ( +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, ) -from openflexure_microscope.common.labthings_core.tasks import taskify +from labthings.core.tasks import taskify from flask import abort diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py index 3b25e2e0..de57511e 100644 --- a/openflexure_microscope/api/default_extensions/scan.py +++ b/openflexure_microscope/api/default_extensions/scan.py @@ -5,21 +5,21 @@ from typing import Tuple from functools import reduce from openflexure_microscope.camera.base import generate_basename -from openflexure_microscope.common.flask_labthings.find import ( +from labthings.server.find import ( find_component, find_extension, ) -from openflexure_microscope.common.flask_labthings.extensions import BaseExtension -from openflexure_microscope.common.flask_labthings.decorators import ( +from labthings.server.extensions import BaseExtension +from labthings.server.decorators import ( marshal_task, use_args, ThingAction, ) -from openflexure_microscope.common.flask_labthings import fields +from labthings.server import fields from openflexure_microscope.devel import taskify, abort, update_task_progress -from openflexure_microscope.common.flask_labthings.view import View +from labthings.server.view import View import time diff --git a/openflexure_microscope/api/default_extensions/zip_builder.py b/openflexure_microscope/api/default_extensions/zip_builder.py index 67bac694..2b2514f6 100644 --- a/openflexure_microscope/api/default_extensions/zip_builder.py +++ b/openflexure_microscope/api/default_extensions/zip_builder.py @@ -14,10 +14,10 @@ import zipfile import tempfile import logging -from openflexure_microscope.common.flask_labthings.find import find_component -from openflexure_microscope.common.flask_labthings.view import View -from openflexure_microscope.common.flask_labthings.extensions import BaseExtension -from openflexure_microscope.common.flask_labthings.decorators import ( +from labthings.server.find import find_component +from labthings.server.view import View +from labthings.server.extensions import BaseExtension +from labthings.server.decorators import ( ThingAction, ThingProperty, ) diff --git a/openflexure_microscope/api/example_extensions/ev_gui.py b/openflexure_microscope/api/example_extensions/ev_gui.py index 9a7c1552..1acb3f9f 100644 --- a/openflexure_microscope/api/example_extensions/ev_gui.py +++ b/openflexure_microscope/api/example_extensions/ev_gui.py @@ -1,6 +1,6 @@ -from openflexure_microscope.common.flask_labthings.view import View -from openflexure_microscope.common.flask_labthings.extensions import BaseExtension -from openflexure_microscope.common.flask_labthings.decorators import ( +from labthings.server.view import View +from labthings.server.extensions import BaseExtension +from labthings.server.decorators import ( ThingAction, ThingProperty, ) diff --git a/openflexure_microscope/api/v2/views/actions/__init__.py b/openflexure_microscope/api/v2/views/actions/__init__.py index 6640a07b..b256c60b 100644 --- a/openflexure_microscope/api/v2/views/actions/__init__.py +++ b/openflexure_microscope/api/v2/views/actions/__init__.py @@ -4,10 +4,10 @@ Top-level representation of enabled actions from . import camera, stage, system -from openflexure_microscope.common.flask_labthings.view import View -from openflexure_microscope.common.flask_labthings.find import current_labthing -from openflexure_microscope.common.flask_labthings.utilities import description_from_view -from openflexure_microscope.common.flask_labthings.decorators import Tag +from labthings.server.view import View +from labthings.server.find import current_labthing +from labthings.server.utilities import description_from_view +from labthings.server.decorators import Tag _actions = { "capture": { diff --git a/openflexure_microscope/api/v2/views/actions/camera.py b/openflexure_microscope/api/v2/views/actions/camera.py index cbb539f7..ec4445e2 100644 --- a/openflexure_microscope/api/v2/views/actions/camera.py +++ b/openflexure_microscope/api/v2/views/actions/camera.py @@ -1,7 +1,7 @@ from openflexure_microscope.api.utilities import get_bool, JsonResponse -from openflexure_microscope.common.flask_labthings.view import View -from openflexure_microscope.common.flask_labthings.find import find_component -from openflexure_microscope.common.flask_labthings.decorators import ( +from labthings.server.view import View +from labthings.server.find import find_component +from labthings.server.decorators import ( use_args, marshal_with, doc, @@ -10,7 +10,7 @@ from openflexure_microscope.common.flask_labthings.decorators import ( doc_response, ) -from openflexure_microscope.common.flask_labthings import fields +from labthings.server import fields from openflexure_microscope.utilities import filter_dict from openflexure_microscope.api.v2.views.captures import capture_schema diff --git a/openflexure_microscope/api/v2/views/actions/stage.py b/openflexure_microscope/api/v2/views/actions/stage.py index 35795781..446e719e 100644 --- a/openflexure_microscope/api/v2/views/actions/stage.py +++ b/openflexure_microscope/api/v2/views/actions/stage.py @@ -1,13 +1,13 @@ from openflexure_microscope.api.utilities import JsonResponse -from openflexure_microscope.common.flask_labthings.view import View -from openflexure_microscope.common.flask_labthings.find import find_component -from openflexure_microscope.common.flask_labthings.decorators import ( +from labthings.server.view import View +from labthings.server.find import find_component +from labthings.server.decorators import ( use_args, marshal_with, doc, ThingAction, ) -from openflexure_microscope.common.flask_labthings import fields +from labthings.server import fields from openflexure_microscope.utilities import axes_to_array, filter_dict diff --git a/openflexure_microscope/api/v2/views/actions/system.py b/openflexure_microscope/api/v2/views/actions/system.py index a370d05e..43cf0ead 100644 --- a/openflexure_microscope/api/v2/views/actions/system.py +++ b/openflexure_microscope/api/v2/views/actions/system.py @@ -1,9 +1,9 @@ -from openflexure_microscope.common.flask_labthings.view import View +from labthings.server.view import View import subprocess import os from sys import platform -from openflexure_microscope.common.flask_labthings.decorators import ( +from labthings.server.decorators import ( ThingAction, doc_response, ) diff --git a/openflexure_microscope/api/v2/views/captures.py b/openflexure_microscope/api/v2/views/captures.py index 4cb82325..e97e8765 100644 --- a/openflexure_microscope/api/v2/views/captures.py +++ b/openflexure_microscope/api/v2/views/captures.py @@ -3,15 +3,15 @@ from flask import abort, request, redirect, url_for, send_file, jsonify from openflexure_microscope.api.utilities import get_bool, JsonResponse -from openflexure_microscope.common.flask_labthings.schema import Schema -from openflexure_microscope.common.flask_labthings import fields -from openflexure_microscope.common.flask_labthings.view import View -from openflexure_microscope.common.flask_labthings.utilities import ( +from labthings.server.schema import Schema +from labthings.server import fields +from labthings.server.view import View +from labthings.server.utilities import ( description_from_view, ) -from openflexure_microscope.common.flask_labthings.decorators import marshal_with, doc_response, Tag, ThingProperty +from labthings.server.decorators import marshal_with, doc_response, Tag, ThingProperty -from openflexure_microscope.common.flask_labthings.find import find_component +from labthings.server.find import find_component from marshmallow import pre_dump diff --git a/openflexure_microscope/api/v2/views/state.py b/openflexure_microscope/api/v2/views/state.py index b46b4e63..6aa7f958 100644 --- a/openflexure_microscope/api/v2/views/state.py +++ b/openflexure_microscope/api/v2/views/state.py @@ -1,15 +1,15 @@ from openflexure_microscope.api.utilities import JsonResponse -from openflexure_microscope.common.labthings_core.utilities import ( +from labthings.core.utilities import ( get_by_path, set_by_path, create_from_path, ) -from openflexure_microscope.common.flask_labthings.find import find_component -from openflexure_microscope.common.flask_labthings.view import View +from labthings.server.find import find_component +from labthings.server.view import View -from openflexure_microscope.common.flask_labthings.decorators import ThingProperty, Tag, doc_response +from labthings.server.decorators import ThingProperty, Tag, doc_response from flask import jsonify, request, abort import logging diff --git a/openflexure_microscope/api/v2/views/streams.py b/openflexure_microscope/api/v2/views/streams.py index 8234d52f..3061af62 100644 --- a/openflexure_microscope/api/v2/views/streams.py +++ b/openflexure_microscope/api/v2/views/streams.py @@ -1,14 +1,14 @@ from openflexure_microscope.api.utilities import gen, JsonResponse -from openflexure_microscope.common.labthings_core.utilities import ( +from labthings.core.utilities import ( get_by_path, set_by_path, create_from_path, ) -from openflexure_microscope.common.flask_labthings.find import find_component -from openflexure_microscope.common.flask_labthings.view import View -from openflexure_microscope.common.flask_labthings.decorators import doc_response, ThingProperty +from labthings.server.find import find_component +from labthings.server.view import View +from labthings.server.decorators import doc_response, ThingProperty from flask import Response diff --git a/openflexure_microscope/camera/base.py b/openflexure_microscope/camera/base.py index 796c5c6b..e6395e1f 100644 --- a/openflexure_microscope/camera/base.py +++ b/openflexure_microscope/camera/base.py @@ -10,7 +10,7 @@ from abc import ABCMeta, abstractmethod from .capture import CaptureObject from openflexure_microscope.utilities import entry_by_uuid -from openflexure_microscope.common.labthings_core.lock import StrictLock +from labthings.core.lock import StrictLock from openflexure_microscope.paths import data_file_path @@ -95,7 +95,7 @@ class BaseCamera(metaclass=ABCMeta): Attributes: thread: Background thread reading frames from camera camera: Camera object - lock (:py:class:`openflexure_microscope.common.lock.StrictLock`): Strict lock controlling thread + lock (:py:class:`labthings.lock.StrictLock`): Strict lock controlling thread access to stage hardware frame (bytes): Current frame is stored here by background thread last_access (time): Time of last client access to the camera diff --git a/openflexure_microscope/common/__init__.py b/openflexure_microscope/common/__init__.py deleted file mode 100644 index fee1e74e..00000000 --- a/openflexure_microscope/common/__init__.py +++ /dev/null @@ -1,2 +0,0 @@ -from . import flask_labthings -from .labthings_core import tasks, lock diff --git a/openflexure_microscope/common/flask_labthings/__init__.py b/openflexure_microscope/common/flask_labthings/__init__.py deleted file mode 100644 index 1d3f44bd..00000000 --- a/openflexure_microscope/common/flask_labthings/__init__.py +++ /dev/null @@ -1 +0,0 @@ -EXTENSION_NAME = "flask-labthings" diff --git a/openflexure_microscope/common/flask_labthings/decorators.py b/openflexure_microscope/common/flask_labthings/decorators.py deleted file mode 100644 index 7d6bf2c6..00000000 --- a/openflexure_microscope/common/flask_labthings/decorators.py +++ /dev/null @@ -1,178 +0,0 @@ -from webargs import flaskparser -from functools import wraps, update_wrapper -from flask import make_response -from http import HTTPStatus - -from openflexure_microscope.common.labthings_core.utilities import rupdate - -from .spec import update_spec -from .schema import TaskSchema - - -def unpack(value): - """Return a three tuple of data, code, and headers""" - if not isinstance(value, tuple): - return value, 200, {} - - try: - data, code, headers = value - return data, code, headers - except ValueError: - pass - - try: - data, code = value - return data, code, {} - except ValueError: - pass - - return value, 200, {} - - -class marshal_with(object): - def __init__(self, schema, code=200): - """ - :param schema: a dict of whose keys will make up the final - serialized response output - """ - self.schema = schema - self.code = code - - def __call__(self, f): - # Pass params to call function attribute for external access - update_spec(f, {"_schema": {self.code: self.schema}}) - # Wrapper function - @wraps(f) - def wrapper(*args, **kwargs): - resp = f(*args, **kwargs) - if isinstance(resp, tuple): - data, code, headers = unpack(resp) - return make_response(self.schema.jsonify(data), code, headers) - else: - return make_response(self.schema.jsonify(resp)) - - return wrapper - - -def marshal_task(f): - # Pass params to call function attribute for external access - update_spec(f, {"responses": {201: {"description": "Task started successfully"}}}) - update_spec(f, {"_schema": {201: TaskSchema()}}) - # Wrapper function - @wraps(f) - def wrapper(*args, **kwargs): - resp = f(*args, **kwargs) - if isinstance(resp, tuple): - data, code, headers = unpack(resp) - return make_response(TaskSchema().jsonify(data), code, headers) - else: - return make_response(TaskSchema().jsonify(resp)) - - return wrapper - - -def ThingAction(viewcls): - # Pass params to call function attribute for external access - update_spec(viewcls, {"tags": ["actions"]}) - update_spec(viewcls, {"_groups": ["actions"]}) - return viewcls - - -thing_action = ThingAction - - -def ThingProperty(viewcls): - # Pass params to call function attribute for external access - update_spec(viewcls, {"tags": ["properties"]}) - update_spec(viewcls, {"_groups": ["properties"]}) - return viewcls - - -thing_property = ThingProperty - - -class use_args(object): - def __init__(self, schema, **kwargs): - """ - Equivalent to webargs.flask_parser.use_args - """ - self.schema = schema - self.wrapper = flaskparser.use_args(schema, **kwargs) - - def __call__(self, f): - # Pass params to call function attribute for external access - update_spec(f, {"_params": self.schema}) - # Wrapper function - update_wrapper(self.wrapper, f) - return self.wrapper(f) - - -class use_kwargs(use_args): - def __init__(self, schema, **kwargs): - """ - Equivalent to webargs.flask_parser.use_kwargs - """ - kwargs["as_kwargs"] = True - use_args.__init__(self, schema, **kwargs) - - -class Doc(object): - def __init__(self, **kwargs): - self.kwargs = kwargs - - def __call__(self, f): - # Pass params to call function attribute for external access - update_spec(f, self.kwargs) - return f - - -doc = Doc - - -class Tag(object): - def __init__(self, tags): - if isinstance(tags, str): - self.tags = [tags] - elif isinstance(tags, list) and all([isinstance(e, str) for e in tags]): - self.tags = tags - else: - raise TypeError("Tags must be a string or list of strings") - - def __call__(self, f): - # Pass params to call function attribute for external access - update_spec(f, {"tags": self.tags}) - return f - - -tag = Tag - - -class doc_response(object): - def __init__(self, code, description=None, mimetype=None, **kwargs): - self.code = code - self.description = description - self.kwargs = kwargs - self.mimetype = mimetype - - self.response_dict = { - "responses": { - self.code: { - "description": self.description or HTTPStatus(self.code).phrase, - **self.kwargs, - } - } - } - - if self.mimetype: - self.response_dict.update({ - "responses": { - self.code: { - "content": {self.mimetype: {}} - } - } - }) - - def __call__(self, f): - # Pass params to call function attribute for external access - update_spec(f, self.response_dict) - return f diff --git a/openflexure_microscope/common/flask_labthings/exceptions.py b/openflexure_microscope/common/flask_labthings/exceptions.py deleted file mode 100644 index bbb83d1e..00000000 --- a/openflexure_microscope/common/flask_labthings/exceptions.py +++ /dev/null @@ -1,37 +0,0 @@ -from flask import jsonify, escape -from werkzeug.exceptions import default_exceptions -from werkzeug.exceptions import HTTPException - - -class JSONExceptionHandler(object): - - """ - A class to be registered as a Flask error handler, - converts error codes into a JSON response - """ - - def __init__(self, app=None): - if app: - self.init_app(app) - - def std_handler(self, error): - if isinstance(error, HTTPException): - message = error.description - elif hasattr(error, "message"): - message = error.message - else: - message = str(error) - - status_code = error.code if isinstance(error, HTTPException) else 500 - - response = {"code": status_code, "message": escape(message)} - return jsonify(response), status_code - - def init_app(self, app): - self.app = app - self.register(HTTPException) - for code, v in default_exceptions.items(): - self.register(code) - - def register(self, exception_or_code, handler=None): - self.app.errorhandler(exception_or_code)(handler or self.std_handler) diff --git a/openflexure_microscope/common/flask_labthings/extensions.py b/openflexure_microscope/common/flask_labthings/extensions.py deleted file mode 100644 index 11b7b083..00000000 --- a/openflexure_microscope/common/flask_labthings/extensions.py +++ /dev/null @@ -1,148 +0,0 @@ -import logging -import collections -import copy -import traceback - -from importlib import util -import sys -import os -import glob - -from openflexure_microscope.common.labthings_core.utilities import ( - get_docstring, - camel_to_snake, - snake_to_spine, -) - - -class BaseExtension: - """ - Parent class for all extensions. - - Handles binding route views and forms. - """ - - # TODO: Allow adding components to extensions - - def __init__(self, name: str, description="", version="0.0.0"): - self._views = ( - {} - ) # Key: Full, Python-safe ID. Val: Original rule, and view class - self._rules = {} # Key: Original rule. Val: View class - self._meta = {} # Extra metadata to add to the extension description - - self._cls = str(self) # String description of extension instance - - self.actions = [] - self.properties = [] - - self._name = name - self.description = get_docstring(self) - self.version = str(version) - - self.methods = {} - - @property - def views(self): - return self._views - - def add_view(self, view_class, rule, **kwargs): - # Remove all leading slashes from view route - cleaned_rule = rule - while cleaned_rule[0] == "/": - cleaned_rule = cleaned_rule[1:] - - # Expand the rule to include extension name - full_rule = "/{}/{}".format(self._name_uri_safe, cleaned_rule) - - view_id = cleaned_rule.replace("/", "_").replace("<", "").replace(">", "") - - # Store route information in a dictionary - d = {"rule": full_rule, "view": view_class, "kwargs": kwargs} - - # Add view to private views dictionary - self._views[view_id] = d - # Store the rule expansion information - self._rules[rule] = self._views[view_id] - - @property - def meta(self): - d = {} - for k, v in self._meta.items(): - if callable(v): - d[k] = v() - else: - d[k] = v - return d - - def add_meta(self, key, val): - self._meta[key] = val - - @property - def name(self): - return self._name - - @property - def _name_python_safe(self): - name = camel_to_snake(self._name) # Camel to snake - name = name.replace(" ", "_") # Spaces to snake - return name - - @property - def _name_uri_safe(self): - return snake_to_spine(self._name_python_safe) - - def add_method(self, method, method_name): - self.methods[method_name] = method - - if not hasattr(self, method_name): - setattr(self, method_name, method) - else: - logging.warning( - "Unable to bind method to extension. Method name already exists." - ) - - -def find_instances_in_module(module, class_to_find): - objs = [] - for attribute in dir(module): - if not attribute.startswith("__"): - if isinstance(getattr(module, attribute), class_to_find): - logging.debug(f"Found extension {getattr(module, attribute).name}") - objs.append(getattr(module, attribute)) - return objs - - -def find_extensions_in_file(extension_path: str, module_name="extensions") -> list: - logging.debug(f"Loading extensions from {extension_path}") - - spec = util.spec_from_file_location(module_name, extension_path) - mod = util.module_from_spec(spec) - sys.modules[spec.name] = mod - - try: - spec.loader.exec_module(mod) - except Exception as e: - logging.error( - f"Exception in extension path {extension_path}: \n{traceback.format_exc()}" - ) - return [] - else: - if hasattr(mod, "__extensions__"): - return [getattr(mod, ext_name) for ext_name in mod.__extensions__] - else: - return find_instances_in_module(mod, BaseExtension) - - -def find_extensions(extension_dir: str, module_name="extensions"): - logging.debug(f"Loading extensions from {extension_dir}") - - extensions = [] - extension_paths = glob.glob(os.path.join(extension_dir, "*.py")) - - for extension_path in extension_paths: - extensions.extend( - find_extensions_in_file(extension_path, module_name=module_name) - ) - - return extensions diff --git a/openflexure_microscope/common/flask_labthings/fields.py b/openflexure_microscope/common/flask_labthings/fields.py deleted file mode 100644 index 68149fcd..00000000 --- a/openflexure_microscope/common/flask_labthings/fields.py +++ /dev/null @@ -1,2 +0,0 @@ -# Marshmallow fields -from marshmallow.fields import * diff --git a/openflexure_microscope/common/flask_labthings/find.py b/openflexure_microscope/common/flask_labthings/find.py deleted file mode 100644 index b866f992..00000000 --- a/openflexure_microscope/common/flask_labthings/find.py +++ /dev/null @@ -1,50 +0,0 @@ -import logging -from flask import current_app - -from . import EXTENSION_NAME - - -def current_labthing(): - app = current_app._get_current_object() - if not app: - return None - logging.debug("Active app extensions:") - logging.debug(app.extensions) - logging.debug("Active labthing:") - logging.debug(app.extensions[EXTENSION_NAME]) - return app.extensions[EXTENSION_NAME] - - -def registered_extensions(labthing_instance=None): - if not labthing_instance: - labthing_instance = current_labthing() - return labthing_instance.extensions - - -def registered_components(labthing_instance=None): - if not labthing_instance: - labthing_instance = current_labthing() - return labthing_instance.components - - -def find_component(device_name, labthing_instance=None): - if not labthing_instance: - labthing_instance = current_labthing() - - if device_name in labthing_instance.components: - return labthing_instance.components[device_name] - else: - return None - - -def find_extension(extension_name, labthing_instance=None): - if not labthing_instance: - labthing_instance = current_labthing() - - logging.debug("Current labthing:") - logging.debug(current_labthing()) - - if extension_name in labthing_instance.extensions: - return labthing_instance.extensions[extension_name] - else: - return None diff --git a/openflexure_microscope/common/flask_labthings/labthing.py b/openflexure_microscope/common/flask_labthings/labthing.py deleted file mode 100644 index ce1e17f3..00000000 --- a/openflexure_microscope/common/flask_labthings/labthing.py +++ /dev/null @@ -1,288 +0,0 @@ -from flask import url_for, jsonify -from apispec import APISpec -from apispec.ext.marshmallow import MarshmallowPlugin - -from . import EXTENSION_NAME # TODO: Move into .names -from .names import TASK_ENDPOINT, TASK_LIST_ENDPOINT, EXTENSION_LIST_ENDPOINT -from .extensions import BaseExtension -from .utilities import description_from_view -from .spec import rule2path, get_spec -from .decorators import tag - -from .views.extensions import ExtensionList -from .views.tasks import TaskList, TaskView -from .views.docs import docs_blueprint, SwaggerUIView, W3CThingDescriptionView - -from openflexure_microscope.common.labthings_core.utilities import get_docstring - -import logging - - -class LabThing(object): - def __init__( - self, - app=None, - prefix: str = "", - title: str = "", - description: str = "", - version: str = "0.0.0", - ): - self.app = app - - self.components = {} - - self.extensions = {} - - self.views = [] - self.properties = {} - self.actions = {} - - self.custom_root_links = {} - - self.endpoints = set() - - self.url_prefix = prefix - self._description = description - self._title = title - self._version = version - - # Store handlers for things like errors and CORS - self.handlers = {} - - self.spec = APISpec( - title=self.title, - version=self.version, - openapi_version="3.0.2", - plugins=[MarshmallowPlugin()], - ) - - if app is not None: - self.init_app(app) - - @property - def description(self,): - return self._description - - @description.setter - def description(self, description: str): - self._description = description - self.spec.description = description - - @property - def title(self,): - return self._title - - @title.setter - def title(self, title: str): - self._title = title - self.spec.title = title - - @property - def version(self,): - return str(self._version) - - @version.setter - def version(self, version: str): - self._version = version - self.spec.version = version - - ### Flask stuff - - def init_app(self, app): - app.teardown_appcontext(self.teardown) - - # Register Flask extension - app.extensions = getattr(app, "extensions", {}) - app.extensions[EXTENSION_NAME] = self - - # Add resources, if registered before tying to a Flask app - if len(self.views) > 0: - for resource, urls, endpoint, kwargs in self.views: - self._register_view(app, resource, *urls, endpoint=endpoint, **kwargs) - - # Create base routes - self._create_base_routes() - - def teardown(self, exception): - pass - - def _create_base_routes(self): - # Add root representation - self.app.add_url_rule(self._complete_url("/", ""), "rootrep", self.rootrep) - # Add thing descriptions - self.app.register_blueprint(docs_blueprint, url_prefix=self.url_prefix) - - # Add extension overview - self.add_view(ExtensionList, "/extensions", endpoint=EXTENSION_LIST_ENDPOINT) - # Add task routes - self.add_view(TaskList, "/tasks", endpoint=TASK_LIST_ENDPOINT) - self.add_view(TaskView, "/tasks/", endpoint=TASK_ENDPOINT) - - ### Device stuff - - def add_component(self, device_object, device_name: str): - self.components[device_name] = device_object - - ### Extension stuff - - def register_extension(self, extension_object): - if isinstance(extension_object, BaseExtension): - self.extensions[extension_object.name] = extension_object - else: - raise TypeError("Extension object must be an instance of BaseExtension") - - for extension_view_id, extension_view in extension_object.views.items(): - # Add route to the extensions blueprint - self.add_view( - tag("extensions")(extension_view["view"]), - "/extensions" + extension_view["rule"], - **extension_view["kwargs"], - ) - - ### Resource stuff - - def _complete_url(self, url_part, registration_prefix): - """This method is used to defer the construction of the final url in - the case that the Api is created with a Blueprint. - :param url_part: The part of the url the endpoint is registered with - :param registration_prefix: The part of the url contributed by the - blueprint. Generally speaking, BlueprintSetupState.url_prefix - """ - parts = [registration_prefix, self.url_prefix, url_part] - return "".join([part for part in parts if part]) - - def add_view(self, resource, *urls, endpoint=None, **kwargs): - """Adds a view to the api. - :param resource: the class name of your resource - :type resource: :class:`Type[Resource]` - :param urls: one or more url routes to match for the resource, standard - flask routing rules apply. Any url variables will be - passed to the resource method as args. - :type urls: str - :param endpoint: endpoint name (defaults to :meth:`Resource.__name__` - Can be used to reference this route in :class:`fields.Url` fields - :type endpoint: str - :param resource_class_args: args to be forwarded to the constructor of - the resource. - :type resource_class_args: tuple - :param resource_class_kwargs: kwargs to be forwarded to the constructor - of the resource. - :type resource_class_kwargs: dict - Additional keyword arguments not specified above will be passed as-is - to :meth:`flask.Flask.add_url_rule`. - Examples:: - api.add_resource(HelloWorld, '/', '/hello') - api.add_resource(Foo, '/foo', endpoint="foo") - api.add_resource(FooSpecial, '/special/foo', endpoint="foo") - """ - endpoint = endpoint or resource.__name__.lower() - - logging.debug(f"{endpoint}: {type(resource)}") - - if self.app is not None: - self._register_view(self.app, resource, *urls, endpoint=endpoint, **kwargs) - - self.views.append((resource, urls, endpoint, kwargs)) - - def view(self, *urls, **kwargs): - def decorator(cls): - self.add_view(cls, *urls, **kwargs) - return cls - - return decorator - - def _register_view(self, app, view, *urls, endpoint=None, **kwargs): - endpoint = endpoint or view.__name__.lower() - self.endpoints.add(endpoint) - resource_class_args = kwargs.pop("resource_class_args", ()) - resource_class_kwargs = kwargs.pop("resource_class_kwargs", {}) - - # NOTE: 'view_functions' is cleaned up from Blueprint class in Flask 1.0 - if endpoint in getattr(app, "view_functions", {}): - previous_view_class = app.view_functions[endpoint].__dict__["view_class"] - - # if you override the endpoint with a different class, avoid the collision by raising an exception - if previous_view_class != view: - raise ValueError( - "This endpoint (%s) is already set to the class %s." - % (endpoint, previous_view_class.__name__) - ) - - view.endpoint = endpoint - resource_func = view.as_view( - endpoint, *resource_class_args, **resource_class_kwargs - ) - - for url in urls: - # If we've got no Blueprint, just build a url with no prefix - rule = self._complete_url(url, "") - # Add the url to the application or blueprint - app.add_url_rule(rule, view_func=resource_func, **kwargs) - # Add the resource to our API spec - #self.spec.path(**view2path(rule, view, self.spec)) - - # TEST: Getting Flask rule objects - flask_rules = app.url_map._rules_by_endpoint.get(endpoint) - for flask_rule in flask_rules: - self.spec.path(**rule2path(flask_rule, view, self.spec)) - - # Handle resource groups listed in API spec - view_spec = get_spec(view) - view_groups = view_spec.get("_groups", {}) - if "actions" in view_groups: - self.actions[view.endpoint] = view - if "properties" in view_groups: - self.properties[view.endpoint] = view - - ### Utilities - - def url_for(self, view, **values): - """Generates a URL to the given resource. - Works like :func:`flask.url_for`.""" - endpoint = view.endpoint - return url_for(endpoint, **values) - - def owns_endpoint(self, endpoint): - return endpoint in self.endpoints - - def add_root_link(self, view, title, kwargs={}): - self.custom_root_links[title] = (view, kwargs) - - ### Description - def rootrep(self): - """ - Root representation - """ - # TODO: Allow custom root representations - - rr = { - "id": url_for("rootrep", _external=True), - "title": self.title, - "description": self.description, - "links": { - "thingDescription": { - "href": url_for("labthings_docs.w3c_td", _external=True), - "description": get_docstring(W3CThingDescriptionView), - }, - "swaggerUI": { - "href": url_for("labthings_docs.swagger_ui", _external=True), - **description_from_view(SwaggerUIView), - }, - "extensions": { - "href": self.url_for(ExtensionList, _external=True), - **description_from_view(ExtensionList), - }, - "tasks": { - "href": self.url_for(TaskList, _external=True), - **description_from_view(TaskList), - }, - }, - } - - for title, (view, kwargs) in self.custom_root_links.items(): - rr["links"][title] = { - "href": self.url_for(view, **kwargs, _external=True), - **description_from_view(view), - } - - return jsonify(rr) diff --git a/openflexure_microscope/common/flask_labthings/names.py b/openflexure_microscope/common/flask_labthings/names.py deleted file mode 100644 index 417c5138..00000000 --- a/openflexure_microscope/common/flask_labthings/names.py +++ /dev/null @@ -1,3 +0,0 @@ -TASK_ENDPOINT = "labthing_task" -TASK_LIST_ENDPOINT = "labthing_task_list" -EXTENSION_LIST_ENDPOINT = "labthing_extension_list" diff --git a/openflexure_microscope/common/flask_labthings/quick.py b/openflexure_microscope/common/flask_labthings/quick.py deleted file mode 100644 index 2f9f5ed4..00000000 --- a/openflexure_microscope/common/flask_labthings/quick.py +++ /dev/null @@ -1,41 +0,0 @@ -from flask import Flask -from flask_cors import CORS - -from .labthing import LabThing -from .exceptions import JSONExceptionHandler - - -def create_app( - import_name, - prefix: str = "", - title: str = "", - description: str = "", - version: str = "0.0.0", - handle_errors: bool = True, - handle_cors: bool = True, - flask_kwargs: dict = {}, -): - app = Flask(import_name, **flask_kwargs) - app.url_map.strict_slashes = False - - # Handle CORS - if handle_cors: - cors_handler = CORS(app, resources=f"{prefix}/*") - - # Handle errors - if handle_errors: - error_handler = JSONExceptionHandler() - error_handler.init_app(app) - - # Create a LabThing - labthing = LabThing( - app, prefix=prefix, title=title, description=description, version=str(version) - ) - - # Store references to added-in handlers - if cors_handler: - labthing.handlers["cors"] = cors_handler - if error_handler: - labthing.handlers["error"] = error_handler - - return app, labthing diff --git a/openflexure_microscope/common/flask_labthings/schema.py b/openflexure_microscope/common/flask_labthings/schema.py deleted file mode 100644 index 7a8166e7..00000000 --- a/openflexure_microscope/common/flask_labthings/schema.py +++ /dev/null @@ -1,93 +0,0 @@ -# -*- coding: utf-8 -*- -from flask import jsonify, url_for -import marshmallow - -from .names import TASK_ENDPOINT, TASK_LIST_ENDPOINT, EXTENSION_LIST_ENDPOINT -from .utilities import view_class_from_endpoint, description_from_view -from . import fields - -MARSHMALLOW_VERSION_INFO = tuple( - [int(part) for part in marshmallow.__version__.split(".") if part.isdigit()] -) - -sentinel = object() - - -class Schema(marshmallow.Schema): - """Base serializer with which to define custom serializers. - See `marshmallow.Schema` for more details about the `Schema` API. - """ - - def jsonify(self, obj, many=sentinel, *args, **kwargs): - """Return a JSON response containing the serialized data. - :param obj: Object to serialize. - :param bool many: Whether `obj` should be serialized as an instance - or as a collection. If unset, defaults to the value of the - `many` attribute on this Schema. - :param kwargs: Additional keyword arguments passed to `flask.jsonify`. - .. versionchanged:: 0.6.0 - Takes the same arguments as `marshmallow.Schema.dump`. Additional - keyword arguments are passed to `flask.jsonify`. - .. versionchanged:: 0.6.3 - The `many` argument for this method defaults to the value of - the `many` attribute on the Schema. Previously, the `many` - argument of this method defaulted to False, regardless of the - value of `Schema.many`. - """ - if many is sentinel: - many = self.many - if MARSHMALLOW_VERSION_INFO[0] >= 3: - data = self.dump(obj, many=many) - else: - data = self.dump(obj, many=many).data - return jsonify(data, *args, **kwargs) - - -class TaskSchema(Schema): - _ID = fields.String(data_key="id") - target_string = fields.String(data_key="function") - _status = fields.String(data_key="status") - progress = fields.String() - data = fields.Raw() - _return_value = fields.Raw(data_key="return") - _start_time = fields.String(data_key="start_time") - _end_time = fields.String(data_key="end_time") - - links = fields.Dict() - - @marshmallow.pre_dump - def generate_links(self, data, **kwargs): - data.links = { - "self": { - "href": url_for(TASK_ENDPOINT, id=data.id, _external=True), - "mimetype": "application/json", - **description_from_view(view_class_from_endpoint(TASK_ENDPOINT)), - } - } - return data - - -class ExtensionSchema(Schema): - name = fields.String(data_key="title") - _name_python_safe = fields.String(data_key="pythonName") - _cls = fields.String(data_key="pythonObject") - meta = fields.Dict() - description = fields.String() - - links = fields.Dict() - - @marshmallow.pre_dump - def generate_links(self, data, **kwargs): - d = {} - for view_id, view_data in data.views.items(): - view_cls = view_data["view"] - view_rule = view_data["rule"] - # Make links dictionary if it doesn't yet exist - d[view_id] = { - "href": url_for(EXTENSION_LIST_ENDPOINT, _external=True) + view_rule, - **description_from_view(view_cls), - } - - data.links = d - - return data diff --git a/openflexure_microscope/common/flask_labthings/spec/__init__.py b/openflexure_microscope/common/flask_labthings/spec/__init__.py deleted file mode 100644 index eb5bef96..00000000 --- a/openflexure_microscope/common/flask_labthings/spec/__init__.py +++ /dev/null @@ -1,164 +0,0 @@ -from ..view import View -from apispec import APISpec -from apispec.ext.marshmallow import MarshmallowPlugin - -from openflexure_microscope.common.labthings_core.utilities import ( - get_docstring, - get_summary, - rupdate, -) - -from ..fields import Field -from marshmallow import Schema as BaseSchema - -from .paths import rule_to_path, rule_to_params - -from werkzeug.routing import Rule -from collections import Mapping -from http import HTTPStatus - - -def update_spec(obj, spec): - obj.__apispec__ = obj.__dict__.get("__apispec__", {}) - rupdate(obj.__apispec__, spec) - return obj.__apispec__ - - -def get_spec(obj): - obj.__apispec__ = obj.__dict__.get("__apispec__", {}) - return obj.__apispec__ - - -def rule2path(rule: Rule, view: View, spec: APISpec): - params = { - "path": rule_to_path(rule), - "operations": view2operations(view, spec), - "description": get_docstring(view), - "summary": get_summary(view), - } - - # Add URL arguments - if rule.arguments: - for op in params.get("operations").keys(): - params["operations"][op].update({ - "parameters": rule_to_params(rule) - }) - - # Add extra parameters - if hasattr(view, "__apispec__"): - # Recursively update params - rupdate(params, view.__apispec__) - - return params - - -def view2operations(view: View, spec: APISpec): - # Operations inherit tags from parent - inherited_tags = [] - if hasattr(view, "__apispec__"): - inherited_tags = getattr(view, "__apispec__").get("tags", []) - - # Build dictionary of operations (HTTP methods) - ops = {} - for method in View.methods: - if hasattr(view, method): - ops[method] = {} - - rupdate( - ops[method], - { - "description": get_docstring(getattr(view, method)), - "summary": get_summary(getattr(view, method)), - "tags": inherited_tags, - }, - ) - - rupdate(ops[method], method2operation(getattr(view, method), spec)) - - return ops - - -def method2operation(method: callable, spec: APISpec): - if hasattr(method, "__apispec__"): - apispec = getattr(method, "__apispec__") - else: - apispec = {} - - op = {} - if "_params" in apispec: - rupdate( - op, - { - "requestBody": { - "content": { - "application/json": { - "schema": convert_schema(apispec.get("_params"), spec) - } - } - } - }, - ) - - if "_schema" in apispec: - for code, schema in apispec.get("_schema", {}).items(): - rupdate( - op, - { - "responses": { - code: { - "description": HTTPStatus(code).phrase, - "content": { - "application/json": { - "schema": convert_schema(schema, spec) - } - }, - } - } - }, - ) - else: - # If no explicit responses are known, populate with defaults - rupdate( - op, - { - "responses": { - 200: {"description": get_summary(method) or HTTPStatus(200).phrase} - } - }, - ) - - # Bung in any extra swagger fields supplied - for key, val in apispec.items(): - if not key in ["_params", "_schema"]: - rupdate(op, {key: val}) - - return op - - -def convert_schema(schema, spec: APISpec): - if isinstance(schema, BaseSchema): - return schema - elif isinstance(schema, Mapping): - return map2properties(schema, spec) - else: - raise TypeError( - "Unsupported schema type. Ensure schema is a Schema class, or dictionary of Field objects" - ) - - -def map2properties(schema, spec: APISpec): - marshmallow_plugin = next( - plugin for plugin in spec.plugins if isinstance(plugin, MarshmallowPlugin) - ) - converter = marshmallow_plugin.converter - - d = {} - for k, v in schema.items(): - if isinstance(v, Field): - d[k] = converter.field2property(v) - elif isinstance(v, Mapping): - d[k] = map2properties(v, spec) - else: - d[k] = v - - return {"properties": d} diff --git a/openflexure_microscope/common/flask_labthings/spec/paths.py b/openflexure_microscope/common/flask_labthings/spec/paths.py deleted file mode 100644 index 6c70c2c4..00000000 --- a/openflexure_microscope/common/flask_labthings/spec/paths.py +++ /dev/null @@ -1,50 +0,0 @@ -# -*- coding: utf-8 -*- - -import re - -import werkzeug.routing - -PATH_RE = re.compile(r'<(?:[^:<>]+:)?([^<>]+)>') - - -def rule_to_path(rule): - return PATH_RE.sub(r'{\1}', rule.rule) - - -# Conversion map of werkzeug rule converters to Javascript schema types -CONVERTER_MAPPING = { - werkzeug.routing.UnicodeConverter: ('string', None), - werkzeug.routing.IntegerConverter: ('integer', 'int32'), - werkzeug.routing.FloatConverter: ('number', 'float'), -} - -DEFAULT_TYPE = ('string', None) - - -def rule_to_params(rule, overrides=None): - overrides = (overrides or {}) - result = [ - argument_to_param(argument, rule, overrides.get(argument, {})) - for argument in rule.arguments - ] - for key in overrides.keys(): - if overrides[key].get('in') in ('header', 'query'): - overrides[key]['name'] = overrides[key].get('name', key) - result.append(overrides[key]) - return result - - -def argument_to_param(argument, rule, override=None): - param = { - 'in': 'path', - 'name': argument, - 'required': True, - } - type_, format_ = CONVERTER_MAPPING.get(type(rule._converters[argument]), DEFAULT_TYPE) - param['type'] = type_ - if format_ is not None: - param['format'] = format_ - if rule.defaults and argument in rule.defaults: - param['default'] = rule.defaults[argument] - param.update(override or {}) - return param diff --git a/openflexure_microscope/common/flask_labthings/types.py b/openflexure_microscope/common/flask_labthings/types.py deleted file mode 100644 index b0304368..00000000 --- a/openflexure_microscope/common/flask_labthings/types.py +++ /dev/null @@ -1,66 +0,0 @@ -# Marshmallow fields to JSON schema types -# Note: We shouldn't ever need to use this directly. We should go via the apispec converter -from apispec.ext.marshmallow.field_converter import DEFAULT_FIELD_MAPPING - -from . import fields - -# Extra standard library Python types -from datetime import date, datetime, time, timedelta -from decimal import Decimal -from typing import Dict, List, Tuple, Union -from uuid import UUID - -""" -TODO: Use this to convert arbitrary dictionary into its own schema, for W3C TD - -First: Convert Python non-builtins to builtins using DEFAULT_BUILTIN_CONVERSIONS -Then match types of each element to Field using DEFAULT_TYPE_MAPPING -Finally convert Fields to JSON using converter (preferred due to extra metadata), or DEFAULT_FIELD_MAPPING -""" -# Python types to Marshmallow fields -DEFAULT_TYPE_MAPPING = { - bool: fields.Boolean, - date: fields.Date, - datetime: fields.DateTime, - Decimal: fields.Decimal, - float: fields.Float, - int: fields.Integer, - str: fields.String, - time: fields.Time, - timedelta: fields.TimeDelta, - UUID: fields.UUID, - dict: fields.Dict, - Dict: fields.Dict, -} - -# Functions to handle conversion of common Python types into serialisable Python types - - -def ndarray_to_list(o): - return o.tolist() - - -def to_int(o): - return int(o) - - -def to_float(o): - return float(o) - - -def to_string(o): - return str(o) - - -# Map of Python type conversions -DEFAULT_BUILTIN_CONVERSIONS = { - "numpy.ndarray": ndarray_to_list, - "numpy.int": to_int, - "fractions.Fraction": to_float, -} - -# TODO: Deserialiser with inverse defaults -# TODO: Option to switch to .npy serialisation/deserialisation (or look for a better common array format) - -# Use with [x.__module__+"."+x.__name__ for x in inspect.getmro(type(POSSIBLE_MATCHER))] -# Resulting array will contain strings with the same format as keys in DEFAULT_BUILTIN_CONVERSIONS diff --git a/openflexure_microscope/common/flask_labthings/utilities.py b/openflexure_microscope/common/flask_labthings/utilities.py deleted file mode 100644 index 86c904da..00000000 --- a/openflexure_microscope/common/flask_labthings/utilities.py +++ /dev/null @@ -1,29 +0,0 @@ -from openflexure_microscope.common.labthings_core.utilities import ( - get_docstring, - get_summary, -) - -from .view import View - -from flask import current_app - - -def description_from_view(view_class): - summary = get_summary(view_class) - - methods = [] - for method_key in View.methods: - if hasattr(view_class, method_key): - methods.append(method_key.upper()) - - # If no class summary was given, try using summaries from method functions - if not summary: - summary = get_summary(getattr(view_class, method_key)) - - d = {"methods": methods, "description": summary} - - return d - - -def view_class_from_endpoint(endpoint: str): - return current_app.view_functions[endpoint].view_class diff --git a/openflexure_microscope/common/flask_labthings/view.py b/openflexure_microscope/common/flask_labthings/view.py deleted file mode 100644 index 0998a199..00000000 --- a/openflexure_microscope/common/flask_labthings/view.py +++ /dev/null @@ -1,27 +0,0 @@ -from flask.views import MethodView - - -class View(MethodView): - """ - A LabThing Resource class should make use of functions get(), put(), post(), and delete() - corresponding to HTTP methods. - - These functions will allow for automated documentation generation - """ - - methods = ["get", "post", "put", "delete"] - endpoint = None - - def __init__(self, *args, **kwargs): - MethodView.__init__(self, *args, **kwargs) - - def doc(self): - docs = {"operations": {}} - if hasattr(self, "__apispec__"): - docs.update(self.__apispec__) - - for meth in View.methods: - if hasattr(self, meth) and hasattr(getattr(self, meth), "__apispec__"): - docs["operations"][meth] = {} - docs["operations"][meth] = getattr(self, meth).__apispec__ - return docs diff --git a/openflexure_microscope/common/flask_labthings/views/__init__.py b/openflexure_microscope/common/flask_labthings/views/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/openflexure_microscope/common/flask_labthings/views/docs/__init__.py b/openflexure_microscope/common/flask_labthings/views/docs/__init__.py deleted file mode 100644 index 4da62d29..00000000 --- a/openflexure_microscope/common/flask_labthings/views/docs/__init__.py +++ /dev/null @@ -1,113 +0,0 @@ -from flask import abort, url_for, jsonify, render_template, Blueprint, current_app, request - -from openflexure_microscope.common.labthings_core.utilities import get_docstring - -from ...view import View -from ...find import current_labthing -from ...spec import rule_to_path, rule_to_params - -import os - - -class APISpecView(View): - """ - OpenAPI v3 documentation - """ - - def get(self): - """ - OpenAPI v3 documentation - """ - return jsonify(current_labthing().spec.to_dict()) - - -class SwaggerUIView(View): - """ - Swagger UI documentation - """ - - def get(self): - return render_template("swagger-ui.html") - - -class W3CThingDescriptionView(View): - """ - W3C-style Thing Description - """ - - def get(self): - base_url = request.host_url.rstrip('/') - - props = {} - for key, prop in current_labthing().properties.items(): - prop_rules = current_app.url_map._rules_by_endpoint.get(prop.endpoint) - prop_urls = [rule_to_path(rule) for rule in prop_rules] - - props[key] = {} - props[key]["title"] = prop.__name__ - # TODO: Get description from __apispec__ preferentially - props[key]["description"] = get_docstring(prop) or ( - get_docstring(prop.get) if hasattr(prop, "get") else "" - ) - props[key]["readOnly"] = not ( - hasattr(prop, "post") or hasattr(prop, "put") or hasattr(prop, "delete") - ) - props[key]["writeOnly"] = not hasattr(prop, "get") - props[key]["links"] = [ - {"href": f"{base_url}{url}"} for url in prop_urls - ] - - props[key]["uriVariables"] = {} - for prop_rule in prop_rules: - params = rule_to_params(prop_rule) - params_dict = {} - for param in params: - params_dict.update({ - param.get("name"): { - "type": param.get("type") - } - }) - props[key]["uriVariables"].update(params_dict) - if not props[key]["uriVariables"]: - del props[key]["uriVariables"] - - actions = {} - for key, action in current_labthing().actions.items(): - action_rules = current_app.url_map._rules_by_endpoint.get(action.endpoint) - action_urls = [rule_to_path(rule) for rule in action_rules] - - actions[key] = {} - actions[key]["title"] = action.__name__ - # TODO: Get description from __apispec__ preferentially - actions[key]["description"] = get_docstring(action) or ( - get_docstring(action.post) if hasattr(action, "post") else "" - ) - actions[key]["links"] = [ - {"href": f"{base_url}{url}"} for url in action_urls - ] - - td = { - "@context": "https://www.w3.org/2019/wot/td/v1", - "id": url_for("labthings_docs.w3c_td", _external=True), - "title": current_labthing().title, - "description": current_labthing().description, - "properties": props, - "actions": actions, - } - - return jsonify(td) - - -docs_blueprint = Blueprint( - "labthings_docs", __name__, static_folder="./static", template_folder="./templates" -) - -docs_blueprint.add_url_rule( - "/swagger", view_func=APISpecView.as_view("swagger_json") -) -docs_blueprint.add_url_rule( - "/swagger-ui", view_func=SwaggerUIView.as_view("swagger_ui") -) -docs_blueprint.add_url_rule( - "/td", view_func=W3CThingDescriptionView.as_view("w3c_td") -) diff --git a/openflexure_microscope/common/flask_labthings/views/docs/static/favicon-16x16.png b/openflexure_microscope/common/flask_labthings/views/docs/static/favicon-16x16.png deleted file mode 100644 index 8b194e617af1c135e6b37939591d24ac3a5efa18..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 665 zcmeAS@N?(olHy`uVBq!ia0y~yU=RRd4rT@h1`S>QUldMA14)GCski36+dTHKW7<77a4n3d1n_{XBT-F7X?>mB~K7i_Ht4Wc2x0k zRts=ca(7blaMlcS)Q+@Q@pV-7brLai6E$%WHF6g;b`dgl6EJk*G4vGGc3@EPWH9z+ zFg9iYgVtBNEiZMNU+6SF(`|gJQ~yY>;h|pbUA>ySdS#akN-h`_oiZ#uX;^T=F#niQ z?oq?sBZfJLjj|6IW$ic0+-IDz+c;yFarzEp?_Nu_I^ZWPgTC;lP%7rthP3h}wZSgTwk&~4d z*@{4T&dKy&G3BjwcXL1TZE(? zdrYTTmp*7)B6Kk7tl#{_|Nozhlg!qe?pem~qq{Tu*c$%wDc%8Aem(1UB_I{ z%hx*X#ogN~)68dmfB1><^+&l|Vj&z4Yq_(Z^B(g2%JM<#!5)VT%SB@DzL_sSM{Zt- zp2FL|p8E^`pI-lS>-!mB7UwYdyUuy8gTe~ HDWM4fUsDF? diff --git a/openflexure_microscope/common/flask_labthings/views/docs/static/favicon-32x32.png b/openflexure_microscope/common/flask_labthings/views/docs/static/favicon-32x32.png deleted file mode 100644 index 249737fe44558e679f0b67134e274461d988fa98..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 628 zcmeAS@N?(olHy`uVBq!ia0y~yU{C;I4rT@h2A3sW#~2tGCIt9|xH2#>2pGGFnYxLY zxrv*(G3Z%|nYu|>xQd&*N!hsa8#;&>yNH5iL2680#Z28qO+bo4Tx0jvSGwY6?uzct zjZbxq)9edQ8tTV6m}lEXEj6oqpy%9RU4BJBex0dhzFpo?Bl`-Q;&TRS{!TiPj&e?} zsoPDeZt69^(D7)u^6Ikk?6C5iU|Esh`;>u!L9`^uFPK5}?3ah^GynbgC!kP%WTjhI z@b$gAUD-cM7#JAqJY5_^DsHs~-z;k~5Rg?BP7#0Pv$)zVJWt0!>^hUMd$00x?iKYC)<2bZL)F6{(by(TD#|y^8%_n zZcFTSzi~ERA^phgH=O3rj&Z7630C`h|7Z2uwJo%62H*dEF}plJYA{Ef{IJ^c*y3eN z3(Za(k!_M$`6nb|$>hwQ@JyGv@lC4t>w0Du#wBY%y}I>b!>U7UN0+>3HTzU}nAyVT zYyaXYQd7JI4cPTIRwX?@e<8rNU*Cc2s)f(97N%g;^9w%lPP|@wJJs=U>jU5TVxH7# zVmp)-xh?i{pKD%|{d4b4YCEwx*Iq?uFx$=` - 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- """ - return registered_extensions().values() diff --git a/openflexure_microscope/common/flask_labthings/views/tasks.py b/openflexure_microscope/common/flask_labthings/views/tasks.py deleted file mode 100644 index f583ba17..00000000 --- a/openflexure_microscope/common/flask_labthings/views/tasks.py +++ /dev/null @@ -1,51 +0,0 @@ -from flask import abort, url_for - -from ..decorators import marshal_with, ThingProperty, Tag -from ..view import View -from ..schema import TaskSchema - -from openflexure_microscope.common.labthings_core import tasks - - -@ThingProperty -@Tag("tasks") -class TaskList(View): - @marshal_with(TaskSchema(many=True)) - def get(self): - """ - List of all session tasks - """ - return tasks.tasks() - - -@Tag(["properties", "tasks"]) -class TaskView(View): - @marshal_with(TaskSchema()) - def get(self, id): - """ - Show status of a session task - - Includes progress and intermediate data. - """ - try: - task = tasks.dict()[id] - except KeyError: - return abort(404) # 404 Not Found - - return task - - @marshal_with(TaskSchema()) - def delete(self, id): - """ - Terminate a running task. - - If the task is finished, deletes its entry. - """ - try: - task = tasks.dict()[id] - except KeyError: - return abort(404) # 404 Not Found - - task.terminate() - - return task diff --git a/openflexure_microscope/common/labthings_core/__init__.py b/openflexure_microscope/common/labthings_core/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/openflexure_microscope/common/labthings_core/lock.py b/openflexure_microscope/common/labthings_core/lock.py deleted file mode 100644 index d96fae30..00000000 --- a/openflexure_microscope/common/labthings_core/lock.py +++ /dev/null @@ -1,76 +0,0 @@ -from threading import RLock - -from openflexure_microscope.exceptions import LockError - - -class StrictLock(object): - """ - Class that behaves like a Python RLock, but with stricter timeout conditions and custom exceptions. - - Args: - timeout (int): Time, in seconds, lock acquisition will wait before raising an exception - - Attributes: - _lock (:py:class:`threading.RLock`): Parent RLock object - timeout (int): Time, in seconds, lock acquisition will wait before raising an exception - """ - - def __init__(self, timeout=1): - self._lock = RLock() - self.timeout = timeout - - def locked(self): - return self._lock.locked() - - def acquire(self, blocking=True): - return self._lock.acquire(blocking, timeout=self.timeout) - - def __enter__(self): - result = self._lock.acquire(blocking=True, timeout=self.timeout) - if result: - return result - else: - raise LockError("ACQUIRE_ERROR", self) - - def __exit__(self, *args): - self._lock.release() - - def release(self): - self._lock.release() - - -class CompositeLock(object): - """ - Class that behaves like a :py:class:`openflexure_microscope.common.lock.StrictLock`, - but allows multiple locks to be acquired and released. - - Args: - locks (list): List of parent RLock objects - timeout (int): Time, in seconds, lock acquisition will wait before raising an exception - - Attributes: - locks (list): List of parent RLock objects - timeout (int): Time, in seconds, lock acquisition will wait before raising an exception - """ - - def __init__(self, locks, timeout=1): - self.locks = locks - self.timeout = timeout - - def acquire(self, blocking=True): - return (lock.acquire(blocking=blocking) for lock in self.locks) - - def __enter__(self): - result = (lock.acquire(blocking=True) for lock in self.locks) - if all(result): - return result - else: - raise LockError("ACQUIRE_ERROR", self) - - def __exit__(self, *args): - for lock in self.locks: - lock.release() - - def release(self): - for lock in self.locks: - lock.release() diff --git a/openflexure_microscope/common/labthings_core/tasks/__init__.py b/openflexure_microscope/common/labthings_core/tasks/__init__.py deleted file mode 100644 index 282998ca..00000000 --- a/openflexure_microscope/common/labthings_core/tasks/__init__.py +++ /dev/null @@ -1,25 +0,0 @@ -__all__ = [ - "taskify", - "tasks", - "dict", - "states", - "current_task", - "update_task_progress", - "cleanup_tasks", - "remove_task", - "update_task_data", - "ThreadTerminationError", -] - -from .pool import ( - tasks, - dict, - states, - current_task, - update_task_progress, - cleanup_tasks, - remove_task, - update_task_data, - taskify, -) -from .thread import ThreadTerminationError diff --git a/openflexure_microscope/common/labthings_core/tasks/pool.py b/openflexure_microscope/common/labthings_core/tasks/pool.py deleted file mode 100644 index 6c152fa5..00000000 --- a/openflexure_microscope/common/labthings_core/tasks/pool.py +++ /dev/null @@ -1,145 +0,0 @@ -import threading -import logging -from functools import wraps - -from .thread import TaskThread - -from flask import copy_current_request_context - - -class TaskMaster: - def __init__(self, *args, **kwargs): - self._tasks = [] - - @property - def tasks(self): - """ - Returns: - list: List of TaskThread objects. - """ - return self._tasks - - @property - def dict(self): - """ - Returns: - dict: Dictionary of TaskThread objects. Key is TaskThread ID. - """ - return {str(t.id): t for t in self._tasks} - - @property - def states(self): - """ - Returns: - dict: Dictionary of TaskThread.state dictionaries. Key is TaskThread ID. - """ - return {str(t.id): t.state for t in self._tasks} - - def new(self, f, *args, **kwargs): - # copy_current_request_context allows threads to access flask current_app - task = TaskThread( - target=copy_current_request_context(f), args=args, kwargs=kwargs - ) - self._tasks.append(task) - return task - - def remove(self, task_id): - for task in self._tasks: - if (task.id == task_id) and not task.isAlive(): - del task - - def cleanup(self): - for task in self._tasks: - if not task.isAlive(): - del task - - -# Task management - - -def tasks(): - """ - List of tasks in default taskmaster - Returns: - list: List of tasks in default taskmaster - """ - global _default_task_master - return _default_task_master.tasks - - -def dict(): - """ - Dictionary of tasks in default taskmaster - Returns: - dict: Dictionary of tasks in default taskmaster - """ - global _default_task_master - return _default_task_master.dict - - -def states(): - """ - Dictionary of TaskThread.state dictionaries. Key is TaskThread ID. - Returns: - dict: Dictionary of task states in default taskmaster - """ - global _default_task_master - return _default_task_master.states - - -def cleanup_tasks(): - global _default_task_master - return _default_task_master.cleanup() - - -def remove_task(task_id: str): - global _default_task_master - return _default_task_master.remove(task_id) - - -# Operations on the current task - - -def current_task(): - current_task_thread = threading.current_thread() - if not isinstance(current_task_thread, TaskThread): - return None - return current_task_thread - - -def update_task_progress(progress: int): - if current_task(): - current_task().update_progress(progress) - else: - logging.info("Cannot update task progress of __main__ thread. Skipping.") - - -def update_task_data(data: dict): - if current_task(): - current_task().update_data(data) - else: - logging.info("Cannot update task data of __main__ thread. Skipping.") - - -# Main "taskify" functions - - -def taskify(f): - """ - A decorator that wraps the passed in function - and surpresses exceptions should one occur - """ - - @wraps(f) - def wrapped(*args, **kwargs): - task = _default_task_master.new( - f, *args, **kwargs - ) # Append to parent object's task list - task.start() # Start the function - return task - - return wrapped - - -# Create our default, protected, module-level task pool -_default_task_master = TaskMaster() diff --git a/openflexure_microscope/common/labthings_core/tasks/thread.py b/openflexure_microscope/common/labthings_core/tasks/thread.py deleted file mode 100644 index d3b06c34..00000000 --- a/openflexure_microscope/common/labthings_core/tasks/thread.py +++ /dev/null @@ -1,200 +0,0 @@ -import ctypes -import datetime -import logging -import traceback -import uuid - -import threading - -_LOG = logging.getLogger(__name__) - - -class ThreadTerminationError(SystemExit): - """Sibling of SystemExit, but specific to thread termination.""" - - -class TaskThread(threading.Thread): - def __init__(self, target=None, name=None, args=(), kwargs={}, daemon=True): - threading.Thread.__init__( - self, - group=None, - target=target, - name=name, - args=args, - kwargs=kwargs, - daemon=daemon, - ) - - # A UUID for the TaskThread (not the same as the threading.Thread ident) - self._ID = uuid.uuid4() # Task ID - - # Make _target, _args, and _kwargs available to the subclass - self._target = target - self._args = args - self._kwargs = kwargs - - # Nice string representation of target function - self.target_string = f"{self._target}(args={self._args}, kwargs={self._kwargs})" - - # Private state properties - self._status: str = "idle" # Task status - self._return_value = None # Return value - self._start_time = None # Task start time - self._end_time = None # Task end time - - # Public state properties - self.progress: int = None # Percent progress of the task - self.data = {} # Dictionary of custom data added during the task - - # Stuff for handling termination - self._running_lock = ( - threading.Lock() - ) # Lock obtained while self._target is running - self._killed = ( - threading.Event() - ) # Event triggered when thread is manually terminated - - @property - def id(self): - """ - Return ID of current TaskThread - """ - return self._ID - - @property - def state(self): - return { - "function": self.target_string, - "id": self._ID, - "status": self._status, - "progress": self.progress, - "data": self.data, - "return": self._return_value, - "start_time": self._start_time, - "end_time": self._end_time, - } - - def update_progress(self, progress: int): - # Update progress of the task - self.progress = progress - - def update_data(self, data: dict): - # Store data to be used before task finishes (eg for real-time plotting) - self.data.update(data) - - def _thread_proc(self, f): - """ - Wraps the target function to handle recording `status` and `return` to `state`. - Happens inside the task thread. - """ - - def wrapped(*args, **kwargs): - nonlocal self - - self._status = "running" - self._start_time = datetime.datetime.now().strftime("%Y-%m-%d %H-%M-%S") - try: - self._return_value = f(*args, **kwargs) - self._status = "success" - except Exception as e: - logging.error(e) - logging.error(traceback.format_exc()) - self._return_value = str(e) - self._status = "error" - finally: - self._end_time = datetime.datetime.now().strftime("%Y-%m-%d %H-%M-%S") - - return wrapped - - def run(self): - """ - Overrides default threading.Thread run() method - """ - logging.debug((self._args, self._kwargs)) - try: - with self._running_lock: - if self._killed.is_set(): - raise ThreadTerminationError() - if self._target: - self._thread_proc(self._target)(*self._args, **self._kwargs) - finally: - # Avoid a refcycle if the thread is running a function with - # an argument that has a member that points to the thread. - del self._target, self._args, self._kwargs - - def wait(self): - """ - Start waiting for the task to finish before returning - """ - print("Joining thread {}".format(self)) - self.join() - return self._return_value - - def async_raise(self, exc_type): - """Raise an exception in this thread.""" - # Should only be called on a started thread, so raise otherwise. - assert self.ident is not None, "Only started threads have thread identifier" - - # If the thread has died we don't want to raise an exception so log. - if not self.is_alive(): - _LOG.debug( - "Not raising %s because thread %s (%s) is not alive", - exc_type, - self.name, - self.ident, - ) - return - - result = ctypes.pythonapi.PyThreadState_SetAsyncExc( - ctypes.c_long(self.ident), ctypes.py_object(exc_type) - ) - if result == 0 and self.is_alive(): - # Don't raise an exception an error unnecessarily if the thread is dead. - raise ValueError("Thread ID was invalid.", self.ident) - elif result > 1: - # Something bad happened, call with a NULL exception to undo. - ctypes.pythonapi.PyThreadState_SetAsyncExc(self.ident, None) - raise RuntimeError( - "Error: PyThreadState_SetAsyncExc %s %s (%s) %s" - % (exc_type, self.name, self.ident, result) - ) - - def _is_thread_proc_running(self): - """ - Test if thread funtion (_thread_proc) is running, - by attemtping to acquire the lock _thread_proc acquires at runtime. - Returns: - bool: If _thread_proc is currently running - """ - could_acquire = self._running_lock.acquire(0) - if could_acquire: - self._running_lock.release() - return False - return True - - def terminate(self): - """ - Raise ThreadTerminatedException in the context of the given thread, - which should cause the thread to exit silently. - """ - _LOG.warning(f"Terminating thread {self}") - self._killed.set() - if not self.is_alive(): - logging.debug("Cannot kill thread that is no longer running.") - return - if not self._is_thread_proc_running(): - logging.debug( - "Thread's _thread_proc function is no longer running, " - "will not kill; letting thread exit gracefully." - ) - return - self.async_raise(ThreadTerminationError) - - # Wait for the thread for finish closing. If the threaded function has cleanup code in a try-except, - # this pause allows it to finish running before the main process can continue. - while self._is_thread_proc_running(): - pass - - # Set state to terminated - self._status = "terminated" - self.progress = None diff --git a/openflexure_microscope/common/labthings_core/utilities.py b/openflexure_microscope/common/labthings_core/utilities.py deleted file mode 100644 index 20a90796..00000000 --- a/openflexure_microscope/common/labthings_core/utilities.py +++ /dev/null @@ -1,71 +0,0 @@ -import collections.abc -import re -import base64 -import operator -from functools import reduce - - -def get_docstring(obj): - ds = obj.__doc__ - if ds: - return ds.strip() - else: - return "" - - -def get_summary(obj): - return get_docstring(obj).partition("\n")[0].strip() - - -def rupdate(d, u): - for k, v in u.items(): - # Merge lists if they're present in both objects - if isinstance(v, list): - if not k in d: - d[k] = [] - if isinstance(d[k], list): - d[k].extend(v) - # Recursively merge dictionaries if the element is a dictionary - elif isinstance(v, collections.abc.Mapping): - if not k in d: - d[k] = {} - d[k] = rupdate(d.get(k, {}), v) - # If not a list or dictionary, overwrite old value with new value - else: - d[k] = v - return d - - -def get_by_path(root, items): - """Access a nested object in root by item sequence.""" - return reduce(operator.getitem, items, root) - - -def set_by_path(root, items, value): - """Set a value in a nested object in root by item sequence.""" - get_by_path(root, items[:-1])[items[-1]] = value - - -def create_from_path(items): - tree_dict = {} - for key in reversed(items): - tree_dict = {key: tree_dict} - return tree_dict - - -def bottom_level_name(obj): - return obj.__name__.split(".")[-1] - - -def camel_to_snake(name): - s1 = re.sub("(.)([A-Z][a-z]+)", r"\1_\2", name) - return re.sub("([a-z0-9])([A-Z])", r"\1_\2", s1).lower() - - -def camel_to_spine(name): - s1 = re.sub("(.)([A-Z][a-z]+)", r"\1-\2", name) - return re.sub("([a-z0-9])([A-Z])", r"\1-\2", s1).lower() - - -def snake_to_spine(name): - return name.replace("_", "-") diff --git a/openflexure_microscope/devel/__init__.py b/openflexure_microscope/devel/__init__.py index d412d008..6ec0ebe4 100644 --- a/openflexure_microscope/devel/__init__.py +++ b/openflexure_microscope/devel/__init__.py @@ -8,15 +8,13 @@ as well as some Flask imports to simplify API route development from openflexure_microscope.api.utilities import JsonResponse # Task management -from openflexure_microscope.common.labthings_core.tasks import ( +from labthings.core.tasks import ( current_task, update_task_progress, update_task_data, taskify, ) -# Exceptions -from openflexure_microscope.exceptions import TaskDeniedException # Flask things from flask import abort, escape, jsonify, Response, request diff --git a/openflexure_microscope/exceptions.py b/openflexure_microscope/exceptions.py index c1864c80..b85196d8 100644 --- a/openflexure_microscope/exceptions.py +++ b/openflexure_microscope/exceptions.py @@ -1,10 +1,6 @@ from threading import ThreadError -class TaskDeniedException(Exception): - pass - - class LockError(ThreadError): ERROR_CODES = { "ACQUIRE_ERROR": "Unable to acquire. Lock in use by another thread.", diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py index cdf857bf..dabf7033 100644 --- a/openflexure_microscope/microscope.py +++ b/openflexure_microscope/microscope.py @@ -14,7 +14,7 @@ from openflexure_microscope.camera.mock import MockStreamer from openflexure_microscope.utilities import serialise_array_b64 from openflexure_microscope.config import user_settings -from openflexure_microscope.common.labthings_core.lock import CompositeLock +from labthings.core.lock import CompositeLock class Microscope: @@ -33,7 +33,7 @@ class Microscope: self.stage = None #: Currently connected stage object # Initialise with an empty composite lock - #: :py:class:`openflexure_microscope.common.lock.CompositeLock`: Composite lock for locking both camera and stage + #: :py:class:`labthings.lock.CompositeLock`: Composite lock for locking both camera and stage self.lock = CompositeLock([]) # Apply settings loaded from file diff --git a/openflexure_microscope/stage/base.py b/openflexure_microscope/stage/base.py index edb40158..5821cff2 100644 --- a/openflexure_microscope/stage/base.py +++ b/openflexure_microscope/stage/base.py @@ -1,12 +1,12 @@ import numpy as np from abc import ABCMeta, abstractmethod -from openflexure_microscope.common.labthings_core.lock import StrictLock +from labthings.core.lock import StrictLock class BaseStage(metaclass=ABCMeta): """ Attributes: - lock (:py:class:`openflexure_microscope.common.lock.StrictLock`): Strict lock controlling thread + lock (:py:class:`labthings.lock.StrictLock`): Strict lock controlling thread access to camera hardware """ diff --git a/poetry.lock b/poetry.lock index eac6bdec..0d12cc6d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -14,6 +14,14 @@ optional = false python-versions = ">=3.5" version = "3.2.0" +[package.extras] +dev = ["PyYAML (>=3.10)", "prance (>=0.11)", "marshmallow (>=2.19.2)", "pytest", "mock", "flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)", "tox"] +docs = ["marshmallow (>=2.19.2)", "pyyaml (5.2)", "sphinx (2.3.0)", "sphinx-issues (1.2.0)", "sphinx-rtd-theme (0.4.3)"] +lint = ["flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)"] +tests = ["PyYAML (>=3.10)", "prance (>=0.11)", "marshmallow (>=2.19.2)", "pytest", "mock"] +validation = ["prance (>=0.11)"] +yaml = ["PyYAML (>=3.10)"] + [[package]] category = "dev" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." @@ -47,6 +55,12 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" version = "19.3.0" +[package.extras] +azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"] +dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"] +docs = ["sphinx", "zope.interface"] +tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"] + [[package]] category = "dev" description = "Internationalization utilities" @@ -72,6 +86,9 @@ attrs = ">=17.4.0" click = ">=6.5" toml = ">=0.9.4" +[package.extras] +d = ["aiohttp (>=3.3.2)"] + [[package]] category = "dev" description = "Python package for providing Mozilla's CA Bundle." @@ -127,6 +144,11 @@ Werkzeug = ">=0.15" click = ">=5.1" itsdangerous = ">=0.24" +[package.extras] +dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"] +docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"] +dotenv = ["python-dotenv"] + [[package]] category = "main" description = "A Flask extension adding a decorator for CORS support" @@ -163,6 +185,12 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" version = "4.3.21" +[package.extras] +pipfile = ["pipreqs", "requirementslib"] +pyproject = ["toml"] +requirements = ["pipreqs", "pip-api"] +xdg_home = ["appdirs (>=1.4.0)"] + [[package]] category = "main" description = "Various helpers to pass data to untrusted environments and back." @@ -182,6 +210,28 @@ version = "2.10.3" [package.dependencies] MarkupSafe = ">=0.23" +[package.extras] +i18n = ["Babel (>=0.8)"] + +[[package]] +category = "main" +description = "" +name = "labthings" +optional = false +python-versions = "^3.6" +version = "0.1.0" + +[package.dependencies] +Flask = "^1.1.1" +apispec = "^3.2.0" +flask-cors = "^3.0.8" +marshmallow = "^3.3.0" +webargs = "^5.5.2" + +[package.source] +reference = "2854c2ea80fee1053d51edbe34cde8bbdb0364bb" +type = "git" +url = "https://github.com/labthings/python-labthings.git" [[package]] category = "dev" description = "A fast and thorough lazy object proxy." @@ -206,6 +256,12 @@ optional = false python-versions = ">=3.5" version = "3.3.0" +[package.extras] +dev = ["pytest", "pytz", "simplejson", "mypy (0.750)", "flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)", "tox"] +docs = ["sphinx (2.2.2)", "sphinx-issues (1.2.0)", "alabaster (0.7.12)", "sphinx-version-warning (1.1.2)"] +lint = ["mypy (0.750)", "flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)"] +tests = ["pytest", "pytz", "simplejson"] + [[package]] category = "dev" description = "McCabe checker, plugin for flake8" @@ -242,11 +298,15 @@ optional = true python-versions = "*" version = "1.13.1b0" +[package.extras] +array = ["numpy"] +doc = ["sphinx"] +test = ["coverage", "pytest", "mock", "pillow", "numpy"] + [package.source] reference = "b39c2b6e42f5f7f57bb46eafcb5c9e2bbdb5d0cb" type = "git" url = "https://github.com/rwb27/picamera.git" - [[package]] category = "main" description = "Python Imaging Library (Fork)" @@ -323,6 +383,10 @@ chardet = ">=3.0.2,<3.1.0" idna = ">=2.5,<2.9" urllib3 = ">=1.21.1,<1.25.0 || >1.25.0,<1.25.1 || >1.25.1,<1.26" +[package.extras] +security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)"] +socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"] + [[package]] category = "dev" description = "a python refactoring library..." @@ -355,8 +419,8 @@ category = "main" description = "Python 2 and 3 compatibility utilities" name = "six" optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*" -version = "1.13.0" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" +version = "1.14.0" [[package]] category = "dev" @@ -393,6 +457,10 @@ sphinxcontrib-jsmath = "*" sphinxcontrib-qthelp = "*" sphinxcontrib-serializinghtml = "*" +[package.extras] +docs = ["sphinxcontrib-websupport"] +test = ["pytest", "pytest-cov", "html5lib", "flake8 (>=3.5.0)", "flake8-import-order", "mypy (>=0.761)", "docutils-stubs"] + [[package]] category = "dev" description = "" @@ -401,6 +469,9 @@ optional = false python-versions = "*" version = "1.0.1" +[package.extras] +test = ["pytest", "flake8", "mypy"] + [[package]] category = "dev" description = "" @@ -409,6 +480,9 @@ optional = false python-versions = "*" version = "1.0.1" +[package.extras] +test = ["pytest", "flake8", "mypy"] + [[package]] category = "dev" description = "" @@ -417,6 +491,9 @@ optional = false python-versions = "*" version = "1.0.2" +[package.extras] +test = ["pytest", "flake8", "mypy", "html5lib"] + [[package]] category = "dev" description = "Sphinx domain for documenting HTTP APIs" @@ -437,6 +514,9 @@ optional = false python-versions = ">=3.5" version = "1.0.1" +[package.extras] +test = ["pytest", "flake8", "mypy"] + [[package]] category = "dev" description = "" @@ -445,6 +525,9 @@ optional = false python-versions = "*" version = "1.0.2" +[package.extras] +test = ["pytest", "flake8", "mypy"] + [[package]] category = "dev" description = "" @@ -453,6 +536,9 @@ optional = false python-versions = "*" version = "1.1.3" +[package.extras] +test = ["pytest", "flake8", "mypy"] + [[package]] category = "dev" description = "Python Library for Tom's Obvious, Minimal Language" @@ -478,6 +564,11 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4" version = "1.25.7" +[package.extras] +brotli = ["brotlipy (>=0.6.0)"] +secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"] +socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7,<2.0)"] + [[package]] category = "main" description = "Declarative parsing and validation of HTTP request objects, with built-in support for popular web frameworks, including Flask, Django, Bottle, Tornado, Pyramid, webapp2, Falcon, and aiohttp." @@ -489,6 +580,13 @@ version = "5.5.2" [package.dependencies] marshmallow = ">=2.15.2" +[package.extras] +dev = ["pytest", "mock", "webtest (2.0.33)", "Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "flake8 (3.7.8)", "pre-commit (>=1.17,<2.0)", "tox", "webtest-aiohttp (2.0.0)", "pytest-aiohttp (>=0.3.0)", "aiohttp (>=3.0.0)", "mypy (0.730)", "flake8-bugbear (19.8.0)"] +docs = ["Sphinx (2.2.0)", "sphinx-issues (1.2.0)", "sphinx-typlog-theme (0.7.3)", "Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "aiohttp (>=3.0.0)"] +frameworks = ["Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "aiohttp (>=3.0.0)"] +lint = ["flake8 (3.7.8)", "pre-commit (>=1.17,<2.0)", "mypy (0.730)", "flake8-bugbear (19.8.0)"] +tests = ["pytest", "mock", "webtest (2.0.33)", "Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "webtest-aiohttp (2.0.0)", "pytest-aiohttp (>=0.3.0)", "aiohttp (>=3.0.0)"] + [[package]] category = "main" description = "The comprehensive WSGI web application library." @@ -497,6 +595,11 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" version = "0.16.0" +[package.extras] +dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinx-issues"] +termcolor = ["termcolor"] +watchdog = ["watchdog"] + [[package]] category = "dev" description = "Module for decorators, wrappers and monkey patching." @@ -509,60 +612,373 @@ version = "1.11.2" rpi = ["picamera", "RPi.GPIO"] [metadata] -content-hash = "26681a870da7f987373db62329a0dee4b39f6be767ef86faf47815f5f35abf8b" +content-hash = "53c82daa835ef29f7aac8ac7d36048487a9d989662a58a2d05d9a70465fbc8c6" python-versions = "^3.6" -[metadata.hashes] -alabaster = ["446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359", "a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"] -apispec = ["c1625ae910f699c9adb21928693a3245b9faab6843f1b1c94ab2d505549cd78a", "f2ecb3a6534cfb42cf69b5c1222d2c0e695aab5ec3d7edde31b7354670948f05"] -appdirs = ["9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92", 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