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Moved to a LabThings dependency for server

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This commit is contained in:
jtc42 2020-01-17 15:13:32 +00:00
parent a1223d8b28
commit 36334ed743
65 changed files with 546 additions and 2364 deletions
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2
docs/make.bat
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@ -10,6 +10,8 @@ if "%SPHINXBUILD%" == "" (
set SOURCEDIR=source
set BUILDDIR=build
set SPHINXOPTS="-E"
if "%1" == "" goto help
%SPHINXBUILD% >NUL 2>NUL

2
docs/source/plugins/class.rst
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@ -3,5 +3,5 @@ Classes and Modules
Extension class
---------------
.. autoclass:: openflexure_microscope.common.flask_labthings.extensions.BaseExtension
.. autoclass:: labthings.server.extensions.BaseExtension
:members:

2
docs/source/plugins/example/plugin.py
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@ -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

8
docs/source/plugins/hardware.rst
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@ -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(<long_running_function>)(*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 ###

10
docs/source/plugins/structure.rst
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@ -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.

1
openflexure_microscope/__init__.py
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@ -4,4 +4,3 @@ __version__ = "0.1.0"
from .microscope import Microscope
from . import config
from . import utilities
from . import common

4
openflexure_microscope/api/app.py
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@ -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

8
openflexure_microscope/api/default_extensions/autofocus.py
View file

@ -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,
)

10
openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
View file

@ -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

10
openflexure_microscope/api/default_extensions/scan.py
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@ -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

8
openflexure_microscope/api/default_extensions/zip_builder.py
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@ -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,
)

6
openflexure_microscope/api/example_extensions/ev_gui.py
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@ -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,
)

8
openflexure_microscope/api/v2/views/actions/__init__.py
View file

@ -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": {

8
openflexure_microscope/api/v2/views/actions/camera.py
View file

@ -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

8
openflexure_microscope/api/v2/views/actions/stage.py
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@ -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

4
openflexure_microscope/api/v2/views/actions/system.py
View file

@ -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,
)

12
openflexure_microscope/api/v2/views/captures.py
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@ -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

8
openflexure_microscope/api/v2/views/state.py
View file

@ -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

8
openflexure_microscope/api/v2/views/streams.py
View file

@ -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

4
openflexure_microscope/camera/base.py
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@ -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

2
openflexure_microscope/common/__init__.py
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@ -1,2 +0,0 @@
from . import flask_labthings
from .labthings_core import tasks, lock

1
openflexure_microscope/common/flask_labthings/__init__.py
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@ -1 +0,0 @@
EXTENSION_NAME = "flask-labthings"

178
openflexure_microscope/common/flask_labthings/decorators.py
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@ -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

37
openflexure_microscope/common/flask_labthings/exceptions.py
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@ -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)

148
openflexure_microscope/common/flask_labthings/extensions.py
View file

@ -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

2
openflexure_microscope/common/flask_labthings/fields.py
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@ -1,2 +0,0 @@
# Marshmallow fields
from marshmallow.fields import *

50
openflexure_microscope/common/flask_labthings/find.py
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@ -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

288
openflexure_microscope/common/flask_labthings/labthing.py
View file

@ -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/<id>", 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)

3
openflexure_microscope/common/flask_labthings/names.py
View file

@ -1,3 +0,0 @@
TASK_ENDPOINT = "labthing_task"
TASK_LIST_ENDPOINT = "labthing_task_list"
EXTENSION_LIST_ENDPOINT = "labthing_extension_list"

41
openflexure_microscope/common/flask_labthings/quick.py
View file

@ -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

93
openflexure_microscope/common/flask_labthings/schema.py
View file

@ -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

164
openflexure_microscope/common/flask_labthings/spec/__init__.py
View file

@ -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}

50
openflexure_microscope/common/flask_labthings/spec/paths.py
View file

@ -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

66
openflexure_microscope/common/flask_labthings/types.py
View file

@ -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

29
openflexure_microscope/common/flask_labthings/utilities.py
View file

@ -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

27
openflexure_microscope/common/flask_labthings/view.py
View file

@ -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

0
openflexure_microscope/common/flask_labthings/views/__init__.py
View file

113
openflexure_microscope/common/flask_labthings/views/docs/__init__.py
View file

@ -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")
)

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<!-- HTML for static distribution bundle build -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Swagger UI</title>
<link rel="stylesheet" type="text/css" href="./swagger-ui.css" >
<link rel="icon" type="image/png" href="./favicon-32x32.png" sizes="32x32" />
<link rel="icon" type="image/png" href="./favicon-16x16.png" sizes="16x16" />
<style>
html
{
box-sizing: border-box;
overflow: -moz-scrollbars-vertical;
overflow-y: scroll;
}
*,
*:before,
*:after
{
box-sizing: inherit;
}
body
{
margin:0;
background: #fafafa;
}
</style>
</head>
<body>
<div id="swagger-ui"></div>
<script src="./swagger-ui-bundle.js"> </script>
<script src="./swagger-ui-standalone-preset.js"> </script>
<script>
window.onload = function() {
// Begin Swagger UI call region
const ui = SwaggerUIBundle({
url: "https://petstore.swagger.io/v2/swagger.json",
dom_id: '#swagger-ui',
deepLinking: true,
presets: [
SwaggerUIBundle.presets.apis,
SwaggerUIStandalonePreset
],
plugins: [
SwaggerUIBundle.plugins.DownloadUrl
],
layout: "StandaloneLayout"
})
// End Swagger UI call region
window.ui = ui
}
</script>
</body>
</html>

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openflexure_microscope/common/flask_labthings/views/docs/static/oauth2-redirect.html vendored
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@ -1,68 +0,0 @@
<!doctype html>
<html lang="en-US">
<title>Swagger UI: OAuth2 Redirect</title>
<body onload="run()">
</body>
</html>
<script>
'use strict';
function run () {
var oauth2 = window.opener.swaggerUIRedirectOauth2;
var sentState = oauth2.state;
var redirectUrl = oauth2.redirectUrl;
var isValid, qp, arr;
if (/code|token|error/.test(window.location.hash)) {
qp = window.location.hash.substring(1);
} else {
qp = location.search.substring(1);
}
arr = qp.split("&")
arr.forEach(function (v,i,_arr) { _arr[i] = '"' + v.replace('=', '":"') + '"';})
qp = qp ? JSON.parse('{' + arr.join() + '}',
function (key, value) {
return key === "" ? value : decodeURIComponent(value)
}
) : {}
isValid = qp.state === sentState
if ((
oauth2.auth.schema.get("flow") === "accessCode"||
oauth2.auth.schema.get("flow") === "authorizationCode"
) && !oauth2.auth.code) {
if (!isValid) {
oauth2.errCb({
authId: oauth2.auth.name,
source: "auth",
level: "warning",
message: "Authorization may be unsafe, passed state was changed in server Passed state wasn't returned from auth server"
});
}
if (qp.code) {
delete oauth2.state;
oauth2.auth.code = qp.code;
oauth2.callback({auth: oauth2.auth, redirectUrl: redirectUrl});
} else {
let oauthErrorMsg
if (qp.error) {
oauthErrorMsg = "["+qp.error+"]: " +
(qp.error_description ? qp.error_description+ ". " : "no accessCode received from the server. ") +
(qp.error_uri ? "More info: "+qp.error_uri : "");
}
oauth2.errCb({
authId: oauth2.auth.name,
source: "auth",
level: "error",
message: oauthErrorMsg || "[Authorization failed]: no accessCode received from the server"
});
}
} else {
oauth2.callback({auth: oauth2.auth, token: qp, isValid: isValid, redirectUrl: redirectUrl});
}
window.close();
}
</script>

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openflexure_microscope/common/flask_labthings/views/docs/templates/swagger-ui.html vendored
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@ -1,38 +0,0 @@
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title>Swagger UI</title>
<link rel="icon" type="image/png" href="{{ url_for('labthings_docs.static', filename='favicon-32x32.png') }}"
sizes="32x32" />
<link rel="icon" type="image/png" href="{{ url_for('labthings_docs.static', filename='favicon-16x16.png') }}"
sizes="16x16" />
<link href="{{ url_for('labthings_docs.static', filename='swagger-ui.css') }}" rel="stylesheet" type="text/css" />
</head>
<body class="swagger-section">
<div id="message-bar" class="swagger-ui-wrap" data-sw-translate>&nbsp;</div>
<div id="swagger-ui-container" class="swagger-ui-wrap"></div>
<script src="{{ url_for('labthings_docs.static', filename='swagger-ui-bundle.js') }}" type="text/javascript"></script>
<script src="{{ url_for('labthings_docs.static', filename='swagger-ui-standalone-preset.js') }}"
type="text/javascript"></script>
<script type="text/javascript">
var ui = SwaggerUIBundle({
url: "{{ url_for('labthings_docs.swagger_json') }}",
dom_id: '#swagger-ui-container',
deepLinking: true,
presets: [
SwaggerUIBundle.presets.apis,
SwaggerUIStandalonePreset
],
plugins: [
SwaggerUIBundle.plugins.DownloadUrl
],
layout: "BaseLayout"
})
window.ui = ui
</script>
</body>
</html>

28
openflexure_microscope/common/flask_labthings/views/extensions.py
View file

@ -1,28 +0,0 @@
"""
Top-level representation of attached and enabled Extensions
"""
from ..view import View
from ..find import registered_extensions
from ..schema import ExtensionSchema
from ..decorators import marshal_with, ThingProperty
@ThingProperty
class ExtensionList(View):
"""
List and basic documentation for all enabled Extensions
"""
@marshal_with(ExtensionSchema(many=True))
def get(self):
"""
Return the current Extension forms
Returns an array of present Extension forms (describing Extension user interfaces.)
Please note, this is *not* a list of all enabled Extensions, only those with associated
user interface forms.
A complete list of enabled Extensions can be found in the microscope state.
"""
return registered_extensions().values()

51
openflexure_microscope/common/flask_labthings/views/tasks.py
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@ -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

0
openflexure_microscope/common/labthings_core/__init__.py
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76
openflexure_microscope/common/labthings_core/lock.py
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@ -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()

25
openflexure_microscope/common/labthings_core/tasks/__init__.py
View file

@ -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

145
openflexure_microscope/common/labthings_core/tasks/pool.py
View file

@ -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()

200
openflexure_microscope/common/labthings_core/tasks/thread.py
View file

@ -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

71
openflexure_microscope/common/labthings_core/utilities.py
View file

@ -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("_", "-")

4
openflexure_microscope/devel/__init__.py
View file

@ -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

4
openflexure_microscope/exceptions.py
View file

@ -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.",

4
openflexure_microscope/microscope.py
View file

@ -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

4
openflexure_microscope/stage/base.py
View file

@ -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
"""

530
poetry.lock generated
View file

@ -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", "d8b24664561d0d34ddfaec54636d502d7cea6e29c3eaf68f3df6180863e2166e"]
astroid = ["71ea07f44df9568a75d0f354c49143a4575d90645e9fead6dfb52c26a85ed13a", "840947ebfa8b58f318d42301cf8c0a20fd794a33b61cc4638e28e9e61ba32f42"]
attrs = ["08a96c641c3a74e44eb59afb61a24f2cb9f4d7188748e76ba4bb5edfa3cb7d1c", "f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"]
babel = ["1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38", "d670ea0b10f8b723672d3a6abeb87b565b244da220d76b4dba1b66269ec152d4"]
black = ["817243426042db1d36617910df579a54f1afd659adb96fc5032fcf4b36209739", "e030a9a28f542debc08acceb273f228ac422798e5215ba2a791a6ddeaaca22a5"]
certifi = ["017c25db2a153ce562900032d5bc68e9f191e44e9a0f762f373977de9df1fbb3", "25b64c7da4cd7479594d035c08c2d809eb4aab3a26e5a990ea98cc450c320f1f"]
chardet = ["84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae", "fc323ffcaeaed0e0a02bf4d117757b98aed530d9ed4531e3e15460124c106691"]
click = ["2335065e6395b9e67ca716de5f7526736bfa6ceead690adf616d925bdc622b13", "5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7"]
colorama = ["7d73d2a99753107a36ac6b455ee49046802e59d9d076ef8e47b61499fa29afff", "e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1"]
docutils = ["0c5b78adfbf7762415433f5515cd5c9e762339e23369dbe8000d84a4bf4ab3af", "c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc"]
flask = ["13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52", "45eb5a6fd193d6cf7e0cf5d8a5b31f83d5faae0293695626f539a823e93b13f6"]
flask-cors = ["72170423eb4612f0847318afff8c247b38bd516b7737adfc10d1c2cdbb382d16", "f4d97201660e6bbcff2d89d082b5b6d31abee04b1b3003ee073a6fd25ad1d69a"]
idna = ["c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407", "ea8b7f6188e6fa117537c3df7da9fc686d485087abf6ac197f9c46432f7e4a3c"]
imagesize = ["6965f19a6a2039c7d48bca7dba2473069ff854c36ae6f19d2cde309d998228a1", "b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1"]
isort = ["54da7e92468955c4fceacd0c86bd0ec997b0e1ee80d97f67c35a78b719dccab1", "6e811fcb295968434526407adb8796944f1988c5b65e8139058f2014cbe100fd"]
itsdangerous = ["321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19", "b12271b2047cb23eeb98c8b5622e2e5c5e9abd9784a153e9d8ef9cb4dd09d749"]
jinja2 = ["74320bb91f31270f9551d46522e33af46a80c3d619f4a4bf42b3164d30b5911f", "9fe95f19286cfefaa917656583d020be14e7859c6b0252588391e47db34527de"]
lazy-object-proxy = ["0c4b206227a8097f05c4dbdd323c50edf81f15db3b8dc064d08c62d37e1a504d", "194d092e6f246b906e8f70884e620e459fc54db3259e60cf69a4d66c3fda3449", "1be7e4c9f96948003609aa6c974ae59830a6baecc5376c25c92d7d697e684c08", "4677f594e474c91da97f489fea5b7daa17b5517190899cf213697e48d3902f5a", "48dab84ebd4831077b150572aec802f303117c8cc5c871e182447281ebf3ac50", "5541cada25cd173702dbd99f8e22434105456314462326f06dba3e180f203dfd", "59f79fef100b09564bc2df42ea2d8d21a64fdcda64979c0fa3db7bdaabaf6239", "8d859b89baf8ef7f8bc6b00aa20316483d67f0b1cbf422f5b4dc56701c8f2ffb", "9254f4358b9b541e3441b007a0ea0764b9d056afdeafc1a5569eee1cc6c1b9ea", "9651375199045a358eb6741df3e02a651e0330be090b3bc79f6d0de31a80ec3e", "97bb5884f6f1cdce0099f86b907aa41c970c3c672ac8b9c8352789e103cf3156", "9b15f3f4c0f35727d3a0fba4b770b3c4ebbb1fa907dbcc046a1d2799f3edd142", "a2238e9d1bb71a56cd710611a1614d1194dc10a175c1e08d75e1a7bcc250d442", "a6ae12d08c0bf9909ce12385803a543bfe99b95fe01e752536a60af2b7797c62", "ca0a928a3ddbc5725be2dd1cf895ec0a254798915fb3a36af0964a0a4149e3db", "cb2c7c57005a6804ab66f106ceb8482da55f5314b7fcb06551db1edae4ad1531", "d74bb8693bf9cf75ac3b47a54d716bbb1a92648d5f781fc799347cfc95952383", "d945239a5639b3ff35b70a88c5f2f491913eb94871780ebfabb2568bd58afc5a", "eba7011090323c1dadf18b3b689845fd96a61ba0a1dfbd7f24b921398affc357", "efa1909120ce98bbb3777e8b6f92237f5d5c8ea6758efea36a473e1d38f7d3e4", "f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0"]
markupsafe = ["00bc623926325b26bb9605ae9eae8a215691f33cae5df11ca5424f06f2d1f473", "09027a7803a62ca78792ad89403b1b7a73a01c8cb65909cd876f7fcebd79b161", "09c4b7f37d6c648cb13f9230d847adf22f8171b1ccc4d5682398e77f40309235", "1027c282dad077d0bae18be6794e6b6b8c91d58ed8a8d89a89d59693b9131db5", "24982cc2533820871eba85ba648cd53d8623687ff11cbb805be4ff7b4c971aff", "29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b", "43a55c2930bbc139570ac2452adf3d70cdbb3cfe5912c71cdce1c2c6bbd9c5d1", "46c99d2de99945ec5cb54f23c8cd5689f6d7177305ebff350a58ce5f8de1669e", "500d4957e52ddc3351cabf489e79c91c17f6e0899158447047588650b5e69183", "535f6fc4d397c1563d08b88e485c3496cf5784e927af890fb3c3aac7f933ec66", "62fe6c95e3ec8a7fad637b7f3d372c15ec1caa01ab47926cfdf7a75b40e0eac1", "6dd73240d2af64df90aa7c4e7481e23825ea70af4b4922f8ede5b9e35f78a3b1", "717ba8fe3ae9cc0006d7c451f0bb265ee07739daf76355d06366154ee68d221e", "79855e1c5b8da654cf486b830bd42c06e8780cea587384cf6545b7d9ac013a0b", "7c1699dfe0cf8ff607dbdcc1e9b9af1755371f92a68f706051cc8c37d447c905", "88e5fcfb52ee7b911e8bb6d6aa2fd21fbecc674eadd44118a9cc3863f938e735", "8defac2f2ccd6805ebf65f5eeb132adcf2ab57aa11fdf4c0dd5169a004710e7d", "98c7086708b163d425c67c7a91bad6e466bb99d797aa64f965e9d25c12111a5e", "9add70b36c5666a2ed02b43b335fe19002ee5235efd4b8a89bfcf9005bebac0d", "9bf40443012702a1d2070043cb6291650a0841ece432556f784f004937f0f32c", "ade5e387d2ad0d7ebf59146cc00c8044acbd863725f887353a10df825fc8ae21", "b00c1de48212e4cc9603895652c5c410df699856a2853135b3967591e4beebc2", "b1282f8c00509d99fef04d8ba936b156d419be841854fe901d8ae224c59f0be5", "b2051432115498d3562c084a49bba65d97cf251f5a331c64a12ee7e04dacc51b", "ba59edeaa2fc6114428f1637ffff42da1e311e29382d81b339c1817d37ec93c6", "c8716a48d94b06bb3b2524c2b77e055fb313aeb4ea620c8dd03a105574ba704f", "cd5df75523866410809ca100dc9681e301e3c27567cf498077e8551b6d20e42f", "e249096428b3ae81b08327a63a485ad0878de3fb939049038579ac0ef61e17e7"]
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6
pyproject.toml
View file

@ -28,15 +28,13 @@ Flask = "^1.0"
pyyaml = "^3.13"
numpy = "^1.17.0"
Pillow = "^5.4"
flask-cors = "^3.0"
scipy = "1.3.0" # Exact version until we can guarantee a wheel
picamera = { git = "https://github.com/rwb27/picamera.git", branch = "lens-shading", optional = true } # Lens shading requires >1.14 or RWB fork, lens-shading branch.
"RPi.GPIO" = { version = "^0.6.5", optional = true }
marshmallow = "^3.3" # LabThings
webargs = "^5.5.2" # LabThings
pyserial = "^3.4" # Used for sangaboard (basic_serial_instrument) until we move to sangaboard pip library
apispec = "^3.2" # LabThings
labthings = { git = "https://github.com/labthings/python-labthings.git", branch = "master"}
[tool.poetry.extras]
rpi = ["picamera", "RPi.GPIO"]