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Merge branch 'api-schema' into 'master'

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Support for plugin schemas to render GUI elements

See merge request openflexure/openflexure-microscope-server!25
This commit is contained in:
Joel Collins 2019-06-21 12:16:27 +00:00
commit 5d5ae7594e
13 changed files with 273 additions and 45 deletions
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2
openflexure_microscope/api/utilities.py
View file

@ -44,7 +44,7 @@ class JsonPayload:
else:
val = default
if convert:
if convert and (val is not None):
val = convert(val)
return val

54
openflexure_microscope/api/v1/blueprints/plugins.py
View file

@ -1,15 +1,33 @@
from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
from flask import Blueprint
from flask import Blueprint, jsonify
from openflexure_microscope.api.v1.views import MicroscopeView
import logging
import warnings
class PluginSchemaAPI(MicroscopeView):
def get(self):
"""
Return the current plugin schemas
.. :quickref: Plugin; Get schemas
"""
out = self.microscope.plugin.schemas
return jsonify(out)
def construct_blueprint(microscope_obj):
blueprint = Blueprint('plugin_blueprint', __name__)
# Create a base route to return plugin API schemas, if any exist
blueprint.add_url_rule(
'/',
view_func=PluginSchemaAPI.as_view('plugin_api_schema', microscope=microscope_obj)
)
all_routes = []
# For each plugin attached to the microscope object
@ -18,27 +36,37 @@ def construct_blueprint(microscope_obj):
# If plugin contains valid endpoints
if hasattr(plugin_obj, 'api_views') and isinstance(plugin_obj.api_views, dict):
# We'll keep a record of how each route was expanded
expanded_routes = {}
# For each defined endpoint
for view_route, view_class in plugin_obj.api_views.items():
# Remove all leading slashes from view route
while view_route[0] == '/':
view_route = view_route[1:]
cleaned_route = view_route
while cleaned_route[0] == '/':
cleaned_route = cleaned_route[1:]
# Construct a full view route from the plugin name
full_view_route = "/{}/{}".format(plugin_name, view_route)
full_view_route = "/{}/{}".format(plugin_name, cleaned_route)
logging.debug(full_view_route)
# Record how the view_route got expanded
expanded_routes[view_route] = full_view_route
# Check if endpoint name clashes
if full_view_route not in all_routes and issubclass(view_class, MicroscopeViewPlugin):
# Add route to main route dictionary
all_routes.append(full_view_route)
# Create a Python-safe name for the route
plugin_route_id = 'plugin{}'.format(full_view_route).replace('/', '_')
# Add route to the plugins blueprint
blueprint.add_url_rule(
full_view_route,
view_func=view_class.as_view(
'plugin_{}'.format(full_view_route).replace('/', '_'),
plugin_route_id,
microscope=microscope_obj,
plugin=plugin_obj
)
@ -52,9 +80,23 @@ def construct_blueprint(microscope_obj):
)
)
# If plugin includes an API schema
if hasattr(plugin_obj, 'api_schema') and isinstance(plugin_obj.api_schema, dict):
schema = plugin_obj.api_schema
# TODO: Validate schema? We need to make sure no single plugin can break all plugins.
schema['id'] = plugin_name
if 'forms' in schema and isinstance(schema['forms'], list):
for form in schema['forms']:
if 'route' in form and form['route'] in expanded_routes.keys():
form['route'] = expanded_routes[form['route']]
else:
logging.warn("No valid expandable route found for {}".format(form['route']))
# Store the complete schema in Microscope().plugin.schema
microscope_obj.plugin.schemas.append(schema)
else:
warnings.warn(
"No valid 'api_views' dictionary found in {}".format(plugin_obj)
)
return blueprint

4
openflexure_microscope/plugins/default/autofocus/api.py
View file

@ -32,9 +32,9 @@ class FastAutofocusAPI(MicroscopeViewPlugin):
# Figure out the parameters to use
dz = payload.param("dz", default=2000, convert=int)
backlash = payload.param("backlash", default=None, convert=int)
backlash = payload.param("backlash", default=0, convert=int)
if backlash < 0:
backlash = None
backlash = 0
logging.info("Running autofocus...")
task = self.microscope.task.start(self.plugin.fast_autofocus, dz, backlash=backlash)

20
openflexure_microscope/plugins/default/camera_calibration/plugin.py
View file

@ -7,27 +7,9 @@ import logging
from .recalibrate_utils import recalibrate_camera, auto_expose_and_freeze_settings
API_SCHEMA = {
'icon': 'lifesaver',
'requireConnection': True,
'forms': [
{
'route': '/recalibrate',
'schema': [
{
'fieldType': "htmlBlock",
'name': "heading",
'content': "<b>This is different form in a plugin!</b>"
}
]
}
]
}
class RecalibrateAPIView(MicroscopeViewPlugin):
def post(self):
payload = JsonPayload(request)
logging.info("Starting microscope recalibration...")
task = self.microscope.task.start(self.plugin.recalibrate)
@ -44,8 +26,6 @@ class Plugin(MicroscopePlugin):
'/recalibrate': RecalibrateAPIView,
}
api_schema = API_SCHEMA
def recalibrate(self):
"""Reset the camera's settings.

1
openflexure_microscope/plugins/default/scan/plugin.py
View file

@ -2,6 +2,7 @@ import time
import numpy as np
from typing import Tuple
import uuid
import itertools
import logging
from openflexure_microscope.camera.base import generate_basename

3
openflexure_microscope/plugins/loader.py
View file

@ -126,7 +126,8 @@ class PluginMount(object):
"""
def __init__(self, parent):
self.parent = parent
self.plugins = []
self.plugins = [] # List of plugin objects
self.schemas = [] # List of plugin schemas
logging.info("Creating plugin mount")
@property

1
openflexure_microscope/plugins/testing/__init__.py
View file

@ -1 +0,0 @@
from .plugin import Plugin

13
openflexure_microscope/plugins/testing/plugin.py
View file

@ -1,13 +0,0 @@
from openflexure_microscope.plugins import MicroscopePlugin
class Plugin(MicroscopePlugin):
"""
A set of default plugins
"""
def identify(self):
"""
Tests for access to Microscope.camera, and Microscope.stage
"""
return self.microscope.camera, self.microscope.stage

2
openflexure_microscope/plugins/testing/schema_example/__init__.py Normal file
View file

@ -0,0 +1,2 @@
from .plugin import ExamplePlugin
from . import api

64
openflexure_microscope/plugins/testing/schema_example/api.py Normal file
View file

@ -0,0 +1,64 @@
from openflexure_microscope.api.utilities import JsonPayload
from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
from openflexure_microscope.exceptions import TaskDeniedException
from flask import request, Response, escape, jsonify
import logging
class DoAPI(MicroscopeViewPlugin):
"""
A simple example API plugin
"""
def get(self):
return jsonify(self.plugin.get_values_dict())
def post(self):
# Get payload JSON
payload = JsonPayload(request)
# Extract a values from the JSON payload.
val_int = payload.param('val_int', default=None, convert=int)
val_str = payload.param('val_str', default=None, convert=str)
val_radio = payload.param('val_radio', default=None)
val_check = payload.param('val_check', default=None)
val_select = payload.param('val_select', default=None)
val_disposable = payload.param('val_disposable', default=None)
self.plugin.set_values(
val_int,
val_str,
val_radio,
val_check,
val_select,
val_disposable
)
print(self.plugin.get_values_dict())
return jsonify({
'response': 'completed'
})
class TaskAPI(MicroscopeViewPlugin):
"""
A task example API plugin
"""
def get(self):
return jsonify({
'run_time': self.plugin.run_time
})
def post(self):
# Get payload JSON
payload = JsonPayload(request)
# Extract a values from the JSON payload.
val_int = payload.param('run_time', default=5, convert=int)
logging.info("Running task...")
task = self.microscope.task.start(self.plugin.generate_random_numbers_for_a_while, val_int)
# return a handle on the autofocus task
return jsonify(task.state), 202

72
openflexure_microscope/plugins/testing/schema_example/plugin.py Normal file
View file

@ -0,0 +1,72 @@
import random
import time
import os
import json
from openflexure_microscope.plugins import MicroscopePlugin
from .api import DoAPI, TaskAPI
HERE = os.path.dirname(os.path.realpath(__file__))
SCHEMA_PATH = os.path.join(HERE, "schema.json")
class ExamplePlugin(MicroscopePlugin):
"""
An example plugin using a comprehensive schema
"""
global SCHEMA_PATH
with open(SCHEMA_PATH, 'r') as sc:
api_schema = json.load(sc)
api_views = {
'/do': DoAPI,
'/task': TaskAPI
}
def __init__(self):
self.val_int = 10
self.val_str = "Hello"
self.val_radio = "First"
self.val_check = ["Foo", "Bar"]
self.val_select = "Most"
self.val_unused = "I'm an unused string, here to confuse the form parsing"
self.run_time = 5
def set_values(self, val_int, val_str, val_radio, val_check, val_select, val_disposable):
"""
Demonstrate a plugin with schema
"""
if val_int:
self.val_int = int(val_int)
if val_str:
self.val_str = str(val_str)
if val_radio:
self.val_radio = val_radio
if val_check is not None:
print(val_check)
self.val_check = val_check if (type(val_check) is list) else [val_check]
if val_select:
self.val_select = val_select
if val_disposable:
print("DISPOSABLE VALUE: {}".format(val_disposable))
def get_values_dict(self):
return {
'val_int': self.val_int,
'val_str': self.val_str,
'val_radio': self.val_radio,
'val_check': self.val_check,
'val_select': self.val_select,
'val_unused': self.val_unused
}
def generate_random_numbers_for_a_while(self, run_time: int):
self.run_time = run_time
vals = []
for _ in range(run_time):
vals.append(random.random())
time.sleep(1)
return vals

80
openflexure_microscope/plugins/testing/schema_example/schema.json Normal file
View file

@ -0,0 +1,80 @@
{
"id": "test-plugin",
"icon": "pets",
"forms": [
{
"name": "Simple request",
"isCollapsible": false,
"isTask": false,
"selfUpdate": true,
"route": "/do",
"submitLabel": "Do things",
"schema": [
[
{
"fieldType": "numberInput",
"placeholder": "Some integer",
"name": "val_int",
"label": "Number value",
"minValue": 0
},
{
"fieldType": "textInput",
"placeholder": "Some string",
"label": "String value",
"name": "val_str"
}
],
[
{
"fieldType": "radioList",
"name": "val_radio",
"label": "Radio value",
"options": ["First", "Second", "Third"]
},
{
"fieldType": "checkList",
"name": "val_check",
"label": "Checklist values",
"options": ["Foo", "Bar", "Baz"]
}
],
{
"fieldType": "htmlBlock",
"name": "html_block",
"content": "<i>This is a block of HTML in a plugin!</i><br>I can do paragraph breaks and stuff."
},
{
"fieldType": "selectList",
"name": "val_select",
"multi": false,
"label": "Some selection",
"options": ["Most", "Average", "Least"]
},
{
"fieldType": "textInput",
"placeholder": "Some string",
"label": "Non-persistent string",
"name": "val_disposable"
}
]
},
{
"name": "Task form",
"isTask": true,
"selfUpdate": true,
"route": "/task",
"submitLabel": "Start task",
"schema": [
{
"fieldType": "numberInput",
"placeholder": "",
"name": "run_time",
"label": "Run time (seconds)",
"minValue": 1
}
]
}
]
}

2
pyproject.toml
View file

@ -4,7 +4,7 @@ build-backend = "poetry.masonry.api"
[tool.poetry]
name = "openflexure_microscope"
version = "1.1.0-beta.1"
version = "1.1.0-beta.2"
description = "Python module, and Flask-based web API, to run the OpenFlexure Microscope."
authors = [