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Merge remote-tracking branch 'origin/master' into v2.1.0-dev

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Joel Collins 2020-03-25 17:00:55 +00:00
commit 6476778673
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41
docs/source/extensions/example_extension/01b_basic_structure_subclass.py Normal file
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@ -0,0 +1,41 @@
from labthings.server.extensions import BaseExtension
from labthings.server.find import find_component
# Create the extension class
class MyExtension(BaseExtension):
def __init__(self):
# Create some instance variable
self.state_variable = "An example of a persistant instance variable"
# Superclass init function
super().__init__("com.myname.myextension", version="0.0.0")
def identify(self):
"""
Demonstrate access to Microscope.camera, and Microscope.stage
"""
microscope = find_component("org.openflexure.microscope")
response = (
f"My name is {microscope.name}. "
f"My parent camera is {microscope.camera}, "
f"and my parent stage is {microscope.stage}."
)
return response
def rename(self, new_name):
"""
Rename the microscope
"""
microscope = find_component("org.openflexure.microscope")
microscope.name = new_name
microscope.save_settings()
# Create your extension object
my_extension = MyExtension()

53
docs/source/extensions/lifecycle_hooks.rst Normal file
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@ -0,0 +1,53 @@
Lifecycle Hooks
===============
Introduction
------------
In some cases it is useful to have functions triggered by events in an extensions lifecycle. Currently two such lifecycle events can be used, ``on_register``, and ``on_component``.
``on_register``
---------------
The ``on_register`` method can be used to have a function call as soon as the extension has been successfully registered to the microscope. For example:
.. code-block:: python
class MyExtension(BaseExtension):
def __init__(self):
# Track if the extension has been registered
self.registered = False
# Add lifecycle hooks
self.on_register(self.on_register_handler, args=(), kwargs={})
# Superclass init function
super().__init__("com.myname.myextension", version="0.0.0")
def on_register_handler(self, *args, **kwargs):
self.registered = True
print("Extension has been registered!")
``on_component``
----------------
The ``on_component`` method can be used to have a function call as soon as a particular LabThings component has been added. This can be used, for example, to get information about the microscope instance as soon as it is available. For example:
.. code-block:: python
class MyExtension(BaseExtension):
def __init__(self):
# Hold a reference to the microscope object as soon as it is available
self.microscope = None
# Add lifecycle hooks
self.on_component("com.myname.myextension", self.on_microscope_handler)
# Superclass init function
super().__init__("org.openflexure.microscope", version="0.0.0")
def on_microscope_handler(self, microscope_object):
print("Microscope object has been found!")
self.microscope = microscope_object

14
docs/source/extensions/structure.rst
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@ -4,7 +4,7 @@ Basic extension structure
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:`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.
In order to access the currently running microscope object, use the :py:func:`labthings.server.find.find_component` 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:
@ -23,4 +23,14 @@ Once this extension is loaded, any other extensions will have access to your met
# Call a function from your extension
if my_found_extension:
my_found_extension.identify()
my_found_extension.identify()
Subclassing ``BaseExtension``
-------------------------------
The syntax used above allows novice programmers to easily start building extensions, without having to deal with subclassing. However, for more complex extensions which require persistent state, subclassing :py:class:`labthings.server.extensions.BaseExtension` is recommended.
The same simple extension as seen above can be written using subclassing:
.. literalinclude:: ./example_extension/01b_basic_structure_subclass.py

8
docs/source/extensions/views.rst
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@ -20,15 +20,15 @@ Request arguments
For POST and PUT requests, data usually needs to be provided to the view in order to perform its function. In this example, our ``rename`` view requires a new microscope name to be passed. We make use of the ``@use_body`` decorator to provide this functionality.
``@use_body`` defines the type of data expected in the request body. In this example, we ``String`` type data. The arguments of ``fields.String`` allow us to provide additional information, such as the parameter being required, and example values to appear in API documentation.
``@use_body`` defines the type of data expected in the request body. In this example, we use ``String`` type data. The arguments of ``fields.String`` allow us to provide additional information, such as the parameter being required, and example values to appear in API documentation.
Adding additional fields, and the meaning of the field types, will be discussed further in the next section.
When a POST request is made to our API view, the request body is converted to processed by ``@use_body``, and passed as a positional argument to our ``post`` function.
When a POST request is made to our API view, the ``@use_body`` converts the body of the request into a ``String``, and passes it as a positional argument to our ``post`` function.
Swagger documentation
+++++++++++++++++++++
At this point, it is useful to introduce the automatically generated Swagger documentation. From any web browser, go to ``http://microscope.local/api/v2/swagger-ui`` (or replace ``microscope.local`` with your microscopes IP address on incompatible systems).
At this point, it is useful to introduce the automatically generated Swagger documentation. From any web browser, go to ``http://microscope.local/api/v2/swagger-ui`` (or replace ``microscope.local`` with your microscope's IP address if ``microscope.local`` doesn't work for your system).
This page uses `SwaggerUI <https://swagger.io/tools/swagger-ui/>`_ to provide visual, interactive API documentation. Find your extensions URL in the documentation under the ``extensions`` group. Basic documentation about the parameters required for your POST method should be visible, as well as an interactive example filled out with the example request given in ``@use_body``.
This page uses `SwaggerUI <https://swagger.io/tools/swagger-ui/>`_ to provide visual, interactive API documentation. Find your extensions URL in the documentation under the ``extensions`` group. Basic documentation about the parameters required for your POST method should be visible, as well as an interactive example filled out with the example request given in ``@use_body``.

3
docs/source/plugins.rst
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@ -11,4 +11,5 @@ Developing API Extensions
./extensions/properties.rst
./extensions/actions.rst
./extensions/tasks_locks.rst
./extensions/ev_gui.rst
./extensions/ev_gui.rst
./extensions/lifecycle_hooks.rst

2
docs/source/quickstart.rst
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@ -21,6 +21,6 @@ For offline (i.e. no real microscope connected) development, a basic development
Managing the server
-------------------
Managing the server through the installer script's CLI is documented `on our website <https://openflexure.org/projects/microscope/install/#managing-the-microscope-server>`_.
Managing the server through the installer script's CLI is documented `on our website <https://openflexure.org/projects/microscope/install#managing-the-microscope-server>`_.
This includes starting the server as a background service, as well as starting a development server with real-time debug logging.

2
openflexure_microscope/api/default_extensions/autofocus.py
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@ -359,7 +359,7 @@ class FastAutofocusAPI(View):
autofocus_extension_v2 = BaseExtension(
"org.openflexure.autofocus", version="2.0.0-beta.1"
"org.openflexure.autofocus", version="2.0.0"
)
autofocus_extension_v2.add_method(fast_autofocus, "fast_autofocus")

2
openflexure_microscope/api/default_extensions/autostorage.py
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@ -88,7 +88,7 @@ class AutostorageExtension(BaseExtension):
BaseExtension.__init__(
self,
"org.openflexure.autostorage",
version="2.0.0-beta.1",
version="2.0.0",
description="Handle switching capture storage devices",
)

2
openflexure_microscope/api/default_extensions/scan.py
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@ -354,6 +354,6 @@ class TileScanAPI(View):
return task
scan_extension_v2 = BaseExtension("org.openflexure.scan", version="2.0.0-beta.1")
scan_extension_v2 = BaseExtension("org.openflexure.scan", version="2.0.0")
scan_extension_v2.add_view(TileScanAPI, "/tile")

2
openflexure_microscope/api/default_extensions/zip_builder.py
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@ -202,7 +202,7 @@ class ZipGetterAPIView(View):
zip_extension_v2 = BaseExtension(
"org.openflexure.zipbuilder",
version="2.0.0-beta.1",
version="2.0.0",
description="Build and download capture collections as ZIP files",
)

2
openflexure_microscope/camera/pi.py
View file

@ -531,6 +531,7 @@ class PiCameraStreamer(BaseCamera):
# Set resolution and stop stream recording if necessary
if not use_video_port:
self.stop_stream_recording()
time.sleep(0.1)
self.camera.capture(
target,
@ -540,6 +541,7 @@ class PiCameraStreamer(BaseCamera):
bayer=(not use_video_port) and bayer,
use_video_port=use_video_port,
)
time.sleep(0.1)
# Set resolution and start stream recording if necessary
if not use_video_port:

50
poetry.lock generated
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@ -324,7 +324,7 @@ description = "NumPy is the fundamental package for array computing with Python.
name = "numpy"
optional = false
python-versions = ">=3.5"
version = "1.18.1"
version = "1.18.2"
[[package]]
category = "dev"
@ -355,7 +355,6 @@ test = ["coverage", "pytest", "mock", "pillow", "numpy"]
reference = "79177fa7f28d6d5c6eab5ba814b420b1785b6b24"
type = "git"
url = "https://github.com/rwb27/picamera.git"
[[package]]
category = "main"
description = "Python Imaging Library (Fork)"
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@ -931,27 +925,27 @@ mccabe = [
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2
pyproject.toml
View file

@ -4,7 +4,7 @@ build-backend = "poetry.masonry.api"
[tool.poetry]
name = "openflexure_microscope"
version = "2.0.0-beta.6"
version = "2.0.0"
description = "Python module, and Flask-based web API, to run the OpenFlexure Microscope."
authors = [