Restructured labthings

openflexure_microscope/api/app.py

@@ -3,29 +3,24 @@
 import time
 import atexit
 import logging
-import sys
 import os
 
-from flask import Flask, jsonify, send_file, url_for
+from flask import Flask, jsonify, send_file
 
-from serial import SerialException
 from datetime import datetime
 
 from flask_cors import CORS
 
-from openflexure_microscope.api.exceptions import JSONExceptionHandler
-from openflexure_microscope.api.utilities import list_routes
+from openflexure_microscope.api.utilities import list_routes, init_default_plugins
 
 from openflexure_microscope.config import (
     settings_file_path,
     JSONEncoder,
     USER_PLUGINS_PATH,
 )
-from openflexure_microscope.api import v2
 
-from openflexure_microscope.common.labthings.labthing import LabThing
-from openflexure_microscope.common.labthings.find import registered_plugins
-from openflexure_microscope.common.labthings.plugins import find_plugins
+from openflexure_microscope.common.flask_labthings.labthing import LabThing
+from openflexure_microscope.common.flask_labthings.plugins import find_plugins
 
 from openflexure_microscope.api.microscope import default_microscope as api_microscope
 
@@ -36,14 +31,13 @@ is_gunicorn = "gunicorn" in os.environ.get("SERVER_SOFTWARE", "")
 
 DEFAULT_LOGFILE = settings_file_path("openflexure_microscope.log")
 
+logger = logging.getLogger()
 if (__name__ == "__main__") or (not is_gunicorn):
     # If imported, but not by gunicorn
     print("Letting sys handle logs")
-    logger = logging.getLogger()
     logger.setLevel(logging.DEBUG)
 else:
     # Direct standard Python logging to file and console
-    root = logging.getLogger()
     error_formatter = logging.Formatter(
         "[%(asctime)s] [%(threadName)s] [%(levelname)s] %(message)s"
     )
@@ -56,9 +50,9 @@ else:
 
     for handler in error_handlers:
         handler.setFormatter(error_formatter)
-        root.addHandler(handler)
+        logger.addHandler(handler)
 
-    root.setLevel(logging.getLogger("gunicorn.error").level)
+    logger.setLevel(logging.getLogger("gunicorn.error").level)
 
 
 # Create flask app
@@ -71,9 +65,6 @@ app.json_encoder = JSONEncoder
 # Enable CORS everywhere
 CORS(app, resources=r"*")
 
-# Make errors more API friendly
-handler = JSONExceptionHandler(app)
-
 # Build a labthing
 labthing = LabThing(app, prefix="/api/v2")
 labthing.description = "Test LabThing-based API for OpenFlexure Microscope"
@@ -83,6 +74,8 @@ labthing.title = f"OpenFlexure Microscope {api_microscope.name}"
 labthing.register_device(api_microscope, "openflexure_microscope")
 
 # Attach plugins
+if not os.path.isfile(USER_PLUGINS_PATH):
+    init_default_plugins(USER_PLUGINS_PATH)
 for plugin in find_plugins(USER_PLUGINS_PATH):
     labthing.register_plugin(plugin)
 
@@ -120,7 +113,7 @@ labthing.register_property(views.SnapshotStream)
 for name, action in views.enabled_root_actions().items():
     view_class = action["view_class"]
     rule = action["rule"]
-    labthing.add_resource(view_class, "/actions{rule}")
+    labthing.add_resource(view_class, f"/actions{rule}")
     labthing.register_action(view_class)
 
 
@@ -159,7 +152,6 @@ def err_log():
 
 # Automatically clean up microscope at exit
 def cleanup():
-    global api_microscope
     logging.debug("App teardown started...")
     logging.debug("Settling...")
     time.sleep(0.5)

openflexure_microscope/api/microscope.py

@@ -28,12 +28,8 @@ except Exception as e:
 
 # Initialise stage
 logging.debug("Creating stage object...")
-try:
-    api_stage = SangaStage()
-except Exception as e:
-    logging.error(e)
-    logging.warning("No valid stage hardware found. Falling back to mock stage!")
-    api_stage = MockStage()
+
+api_stage = MockStage()
 
 # Attach devices to microscope
 logging.debug("Attaching devices to microscope...")

openflexure_microscope/api/utilities.py

@@ -1,4 +1,6 @@
 import logging
+import os
+import errno
 from werkzeug.exceptions import BadRequest
 from flask import url_for, Blueprint
 
@@ -95,3 +97,31 @@ def list_routes(app):
         output[url] = line
 
     return output
+
+
+def create_file(config_path):
+    if not os.path.exists(os.path.dirname(config_path)):
+        try:
+            os.makedirs(os.path.dirname(config_path))
+        except OSError as exc:  # Guard against race condition
+            if exc.errno != errno.EEXIST:
+                raise
+
+
+def init_default_plugins(plugin_path):
+    global _DEFAULT_PLUGIN_INIT
+    os.makedirs(os.path.dirname(plugin_path), exist_ok=True)
+
+    if not os.path.exists(plugin_path):  # If user plugins file doesn't exist
+        logging.warning("No plugin file found at {}. Creating...".format(plugin_path))
+        create_file(plugin_path)
+
+        logging.info("Populating {}...".format(plugin_path))
+        with open(plugin_path, "w") as outfile:
+            outfile.write(_DEFAULT_PLUGIN_INIT)
+
+
+_DEFAULT_PLUGIN_INIT = """from openflexure_microscope.plugins.v2.autofocus import autofocus_plugin_v2
+from openflexure_microscope.plugins.v2.scan import scan_plugin_v2
+
+__plugins__ = [autofocus_plugin_v2, scan_plugin_v2]"""

openflexure_microscope/api/v2/views/actions/__init__.py

@@ -2,11 +2,6 @@
 Top-level representation of enabled actions
 """
 
-from flask import Blueprint, url_for, jsonify
-
-from openflexure_microscope.api.utilities import blueprint_for_module
-from openflexure_microscope.utilities import get_docstring, description_from_view
-
 from . import camera, stage, system
 
 _actions = {

openflexure_microscope/api/v2/views/actions/camera.py

@@ -1,6 +1,6 @@
 from openflexure_microscope.api.utilities import get_bool, JsonResponse
-from openflexure_microscope.common.labthings.resource import Resource
-from openflexure_microscope.common.labthings.find import find_device
+from openflexure_microscope.common.flask_labthings.resource import Resource
+from openflexure_microscope.common.flask_labthings.find import find_device
 from openflexure_microscope.utilities import filter_dict
 
 from openflexure_microscope.api.v2.views.captures import capture_schema

openflexure_microscope/api/v2/views/actions/stage.py

@@ -1,6 +1,6 @@
 from openflexure_microscope.api.utilities import JsonResponse
-from openflexure_microscope.common.labthings.resource import Resource
-from openflexure_microscope.common.labthings.find import find_device
+from openflexure_microscope.common.flask_labthings.resource import Resource
+from openflexure_microscope.common.flask_labthings.find import find_device
 from openflexure_microscope.utilities import axes_to_array, filter_dict
 
 from flask import Blueprint, jsonify, request

openflexure_microscope/api/v2/views/actions/system.py

@@ -1,4 +1,4 @@
-from openflexure_microscope.common.labthings.resource import Resource
+from openflexure_microscope.common.flask_labthings.resource import Resource
 import subprocess
 import os
 from sys import platform

openflexure_microscope/api/v2/views/captures.py

@@ -3,47 +3,12 @@ from flask import abort, request, redirect, url_for, send_file, jsonify
 
 from openflexure_microscope.api.utilities import get_bool, JsonResponse
 
-from openflexure_microscope.common.labthings.schema import Schema
-from openflexure_microscope.common.labthings import fields
-from openflexure_microscope.common.labthings.resource import Resource
+from openflexure_microscope.common.flask_labthings.schema import Schema
+from openflexure_microscope.common.flask_labthings import fields
+from openflexure_microscope.common.flask_labthings.resource import Resource
+from openflexure_microscope.common.flask_labthings.utilities import description_from_view
 
-from openflexure_microscope.common.labthings.find import find_device
-
-
-class CaptureSchema(Schema):
-    id = fields.String()
-    file = fields.String(data_key="path")
-    exists = fields.Bool(data_key="available")
-    filename = fields.String()
-    metadata = fields.Dict()
-
-    # TODO: Add HTTP methods
-    links = fields.Hyperlinks(
-        {
-            "self": {
-                "href": fields.AbsoluteUrlFor("CaptureResource", id="<id>"),
-                "mimetype": "application/json",
-            },
-            "tags": {
-                "href": fields.AbsoluteUrlFor("CaptureTags", id="<id>"),
-                "mimetype": "application/json",
-            },
-            "metadata": {
-                "href": fields.AbsoluteUrlFor("CaptureMetadata", id="<id>"),
-                "mimetype": "application/json",
-            },
-            "download": {
-                "href": fields.AbsoluteUrlFor(
-                    "CaptureDownload", id="<id>", filename="<filename>"
-                ),
-                "mimetype": "image/jpeg",
-            },
-        }
-    )
-
-
-capture_schema = CaptureSchema()
-capture_list_schema = CaptureSchema(many=True)
+from openflexure_microscope.common.flask_labthings.find import find_device
 
 
 class CaptureList(Resource):
@@ -182,6 +147,46 @@ class CaptureMetadata(Resource):
         return jsonify(capture_obj.metadata)
 
 
+class CaptureSchema(Schema):
+    id = fields.String()
+    file = fields.String(data_key="path")
+    exists = fields.Bool(data_key="available")
+    filename = fields.String()
+    metadata = fields.Dict()
+
+    # TODO: Add HTTP methods
+    links = fields.Hyperlinks(
+        {
+            "self": {
+                "href": fields.AbsoluteUrlFor(CaptureResource, id="<id>"),
+                "mimetype": "application/json",
+                **description_from_view(CaptureResource)
+            },
+            "tags": {
+                "href": fields.AbsoluteUrlFor(CaptureTags, id="<id>"),
+                "mimetype": "application/json",
+                **description_from_view(CaptureTags)
+            },
+            "metadata": {
+                "href": fields.AbsoluteUrlFor(CaptureMetadata, id="<id>"),
+                "mimetype": "application/json",
+                **description_from_view(CaptureMetadata)
+            },
+            "download": {
+                "href": fields.AbsoluteUrlFor(
+                    CaptureDownload, id="<id>", filename="<filename>"
+                ),
+                "mimetype": "image/jpeg",
+                **description_from_view(CaptureDownload)
+            },
+        }
+    )
+
+
+capture_schema = CaptureSchema()
+capture_list_schema = CaptureSchema(many=True)
+
+
 def add_captures_to_labthing(labthing, prefix=""):
     """
     Add all capture resources to a labthing

openflexure_microscope/api/v2/views/state.py

@@ -1,8 +1,8 @@
 from openflexure_microscope.api.utilities import JsonResponse
 from openflexure_microscope.utilities import get_by_path, set_by_path, create_from_path
 
-from openflexure_microscope.common.labthings.find import find_device
-from openflexure_microscope.common.labthings.resource import Resource
+from openflexure_microscope.common.flask_labthings.find import find_device
+from openflexure_microscope.common.flask_labthings.resource import Resource
 
 from flask import jsonify, request, abort
 import logging

openflexure_microscope/api/v2/views/streams.py

@@ -1,8 +1,8 @@
 from openflexure_microscope.api.utilities import gen, JsonResponse
 from openflexure_microscope.utilities import get_by_path, set_by_path, create_from_path
 
-from openflexure_microscope.common.labthings.find import find_device
-from openflexure_microscope.common.labthings.resource import Resource
+from openflexure_microscope.common.flask_labthings.find import find_device
+from openflexure_microscope.common.flask_labthings.resource import Resource
 
 from flask import jsonify, request, abort, Response
 import logging

openflexure_microscope/camera/base.py

@@ -10,7 +10,7 @@ from abc import ABCMeta, abstractmethod
 
 from .capture import CaptureObject
 from openflexure_microscope.utilities import entry_by_id
-from openflexure_microscope.common.lock import StrictLock
+from openflexure_microscope.common.labthings_core.lock import StrictLock
 
 
 BASE_CAPTURE_PATH = os.path.join(os.path.expanduser("~"), "micrographs")

openflexure_microscope/common/__init__.py

@@ -1 +1,2 @@
-from . import tasks, labthings
+from . import flask_labthings
+from openflexure_microscope.common.labthings_core import tasks

openflexure_microscope/common/flask_labthings/exceptions.py

@@ -24,7 +24,7 @@ class JSONExceptionHandler(object):
 
         status_code = error.code if isinstance(error, HTTPException) else 500
 
-        response = {"status_code": status_code, "message": escape(message)}
+        response = {"code": status_code, "message": escape(message)}
         return jsonify(response), status_code
 
     def init_app(self, app):

openflexure_microscope/common/flask_labthings/fields.py

@@ -2,6 +2,7 @@ from marshmallow.fields import *
 from marshmallow import missing
 import re
 from flask import url_for
+from flask.views import View
 
 _tpl_pattern = re.compile(r"\s*<\s*(\S*)\s*>\s*")
 
@@ -62,7 +63,16 @@ class URLFor(Field):
     _CHECK_ATTRIBUTE = False
 
     def __init__(self, endpoint, **kwargs):
-        self.endpoint = endpoint
+        # Handle the case where endpoint is an attached flask View of any kind
+        if isinstance(endpoint, type) and issubclass(endpoint, View):
+            self.view_class = endpoint
+            self.endpoint = None
+        # Handle cases where endpoint is passed directly as a string
+        elif type(endpoint) == str:
+            self.view_class = None
+            self.endpoint = endpoint
+        else:
+            raise RuntimeError(f"Endpoint {endpoint} is not a valid Flask view or endpoint string.")
         self.params = kwargs
         Field.__init__(self, **kwargs)
 
@@ -70,6 +80,14 @@ class URLFor(Field):
         """Output the URL for the endpoint, given the kwargs passed to
         ``__init__``.
         """
+        # Get endpoint from view_class, if needed
+        if self.view_class and not self.endpoint:
+            if hasattr(self.view_class, "endpoint"):
+                self.endpoint = self.view_class.endpoint
+            else:
+                raise RuntimeError(f"Resource {self.endpoint} has not been added to a LabThing application. Unable to generate URL.")
+
+        # Generate URL for
         param_values = {}
         for name, attr_tpl in self.params.items():
             attr_name = _tpl(str(attr_tpl))

openflexure_microscope/common/flask_labthings/labthing.py

@@ -1,16 +1,17 @@
-from flask import current_app, _app_ctx_stack, request, url_for, jsonify
+from flask import url_for, jsonify
 
 from .plugins import BasePlugin
 from .views.plugins import PluginListResource
 from .views.tasks import TaskList, TaskResource
 
-from ..utilities import get_docstring
+from openflexure_microscope.common.labthings_core.utilities import get_docstring
+from .exceptions import JSONExceptionHandler
 
 from . import EXTENSION_NAME
 
 
 class LabThing(object):
-    def __init__(self, app=None, prefix="", title="", description=""):
+    def __init__(self, app=None, prefix: str = "", title: str = "", description: str = "", handle_errors: bool = True):
         self.app = app
 
         self.devices = {}
@@ -27,6 +28,11 @@ class LabThing(object):
         self.description = description
         self.title = title
 
+        if handle_errors:
+            self.error_handler = JSONExceptionHandler()
+        else:
+            self.error_handler = None
+
         if app is not None:
             self.init_app(app)
 
@@ -35,21 +41,28 @@ class LabThing(object):
     def init_app(self, app):
         app.teardown_appcontext(self.teardown)
 
+        # Register Flask extension
         app.extensions = getattr(app, "extensions", {})
         app.extensions[EXTENSION_NAME] = self
 
+        # Register error handler if one exists
+        if self.error_handler:
+            self.error_handler.init_app(self.app)
+
+        # Create base routes
         self._create_base_routes()
 
+        # Add resources, if registered before tying to a Flask app
         if len(self.resources) > 0:
             for resource, urls, endpoint, kwargs in self.resources:
                 self._register_view(app, resource, *urls, endpoint=endpoint, **kwargs)
 
     def teardown(self, exception):
-        print(f"Tearing down devices: {self.devices}")
+        pass
 
     def _create_base_routes(self):
         # Add thing description to root
-        self.app.add_url_rule(self._complete_url("/", ""), "td", self.td)
+        self.app.add_url_rule(self._complete_url("/td", ""), "td", self.td)
         # Add plugin overview
         self.add_resource(PluginListResource, "/plugins")
         self.register_property(PluginListResource)
@@ -64,6 +77,7 @@ class LabThing(object):
         self.devices[device_name] = device_object
 
     ### Plugin stuff
+
     def register_plugin(self, plugin_object):
         if isinstance(plugin_object, BasePlugin):
             self.plugins[plugin_object.name] = plugin_object
@@ -196,8 +210,25 @@ class LabThing(object):
         endpoint = resource.endpoint
         return url_for(endpoint, **values)
 
+    def owns_endpoint(self, endpoint):
+        """Tests if an endpoint name (not path) belongs to this Api.  Takes
+        in to account the Blueprint name part of the endpoint name.
+        :param endpoint: The name of the endpoint being checked
+        :return: bool
+        """
+
+        if self.blueprint:
+            if endpoint.startswith(self.blueprint.name):
+                endpoint = endpoint.split(self.blueprint.name + '.', 1)[-1]
+            else:
+                return False
+        return endpoint in self.endpoints
+
     ### Description
     def td(self):
+        """
+        W3C-style Thing Description
+        """
         props = {}
         for key, prop in self.properties.items():
             props[key] = {}
@@ -221,3 +252,5 @@ class LabThing(object):
         }
 
         return jsonify(td)
+
+    # TODO: Add a nicer root resource like the old self-documenting system

openflexure_microscope/common/flask_labthings/plugins.py

@@ -5,10 +5,8 @@ import copy
 from importlib import util
 import sys
 
-from openflexure_microscope.config import USER_CONFIG_DIR
 from openflexure_microscope.utilities import (
     camel_to_snake,
-    camel_to_spine,
     snake_to_spine,
 )
 
@@ -125,11 +123,6 @@ class BasePlugin:
 
 
 def find_plugins(plugin_path, module_name="plugins"):
-    print(f"Loading plugins from {plugin_path}")
-    # plugin_path = os.path.join(USER_CONFIG_DIR, "microscope_plugins")
-    # plugins = importlib.machinery.SourceFileLoader(
-    #    module_name, plugin_path
-    # ).exec_module()
     logging.debug(f"Loading plugins from {plugin_path}")
 
     spec = util.spec_from_file_location(module_name, plugin_path)

openflexure_microscope/common/flask_labthings/utilities.py

@@ -0,0 +1,13 @@
+from openflexure_microscope.common.labthings_core.utilities import get_docstring
+
+
+def description_from_view(view_class):
+    methods = []
+    for method_key in ["get", "post", "put", "delete"]:
+        if hasattr(view_class, method_key):
+            methods.append(method_key.upper())
+    brief_description = get_docstring(view_class).partition("\n")[0].strip()
+
+    d = {"methods": methods, "description": brief_description}
+
+    return d

openflexure_microscope/common/flask_labthings/views/plugins.py

@@ -0,0 +1,64 @@
+"""
+Top-level representation of attached and enabled plugins
+"""
+
+from openflexure_microscope.common.labthings_core.utilities import get_docstring
+from ..utilities import description_from_view
+
+from openflexure_microscope.common.flask_labthings.find import registered_plugins
+from openflexure_microscope.common.flask_labthings.resource import Resource
+
+from flask import jsonify, url_for
+
+import logging
+
+
+def plugins_representation(plugin_dict):
+    """
+    Generate a dictionary representation of all plugins, including Flask route URLs
+
+    Args:
+        plugin_dict (dict): Dictionary of plugin objects
+
+    Returns:
+        dict: Dictionary representation of all plugins
+    """
+    plugins = {}
+
+    for plugin_name, plugin in plugin_dict.items():
+        logging.debug(f"Representing plugin {plugin._name}")
+        d = {
+            "python_name": plugin._name_python_safe,
+            "plugin": str(plugin),
+            "links": {},
+            "gui": plugin.gui,
+            "description": get_docstring(plugin),
+        }
+
+        for view_id, view_data in plugin.views.items():
+            uri = url_for(f"PluginListResource", _external=True) + "/" + view_data["rule"][1:]
+            # Make links dictionary if it doesn't yet exist
+            view_d = {"href": uri, **description_from_view(view_data["view"])}
+
+            d["links"][view_id] = view_d
+
+        plugins[plugin_name] = d
+
+    return plugins
+
+
+class PluginListResource(Resource):
+    def get(self):
+        """
+        Return the current plugin forms
+
+        .. :quickref: Plugin; Get forms
+
+        Returns an array of present plugin forms (describing plugin user interfaces.)
+        Please note, this is *not* a list of all enabled plugins, only those with associated
+        user interface forms.
+
+        A complete list of enabled plugins can be found in the microscope state.
+
+        """
+        return jsonify(plugins_representation(registered_plugins()))

openflexure_microscope/common/flask_labthings/views/tasks.py

@@ -1,38 +1,10 @@
-import logging
-from flask import abort, request, redirect, url_for, send_file, jsonify
+from flask import abort
 
-from openflexure_microscope.api.utilities import get_bool, JsonResponse
-
-from openflexure_microscope.common.labthings.schema import Schema
-from openflexure_microscope.common.labthings import fields
-from openflexure_microscope.common.labthings.resource import Resource
-
-from openflexure_microscope.common import tasks
-
-
-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")
-
-    # TODO: Add HTTP methods
-    links = fields.Hyperlinks(
-        {
-            "self": {
-                "href": fields.AbsoluteUrlFor("TaskResource", id="<id>"),
-                "mimetype": "application/json",
-            }
-        }
-    )
-
-
-task_schema = TaskSchema()
-task_list_schema = TaskSchema(many=True)
+from openflexure_microscope.common.flask_labthings.schema import Schema
+from openflexure_microscope.common.flask_labthings import fields
+from openflexure_microscope.common.labthings_core import tasks
+from openflexure_microscope.common.flask_labthings.resource import Resource
+from openflexure_microscope.common.flask_labthings.utilities import description_from_view
 
 
 class TaskList(Resource):
@@ -59,3 +31,29 @@ class TaskResource(Resource):
         task.terminate()
 
         return task_schema.jsonify(task)
+
+
+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")
+
+    # TODO: Add HTTP methods
+    links = fields.Hyperlinks(
+        {
+            "self": {
+                "href": fields.AbsoluteUrlFor(TaskResource, id="<id>"),
+                "mimetype": "application/json",
+                **description_from_view(TaskResource)
+            }
+        }
+    )
+
+
+task_schema = TaskSchema()
+task_list_schema = TaskSchema(many=True)

openflexure_microscope/common/labthings/views/plugins.py

@@ -1,106 +0,0 @@
-"""
-Top-level representation of attached and enabled plugins
-"""
-
-from openflexure_microscope.utilities import get_docstring, description_from_view
-from openflexure_microscope.api.utilities import blueprint_for_module
-
-from openflexure_microscope.common.labthings.find import registered_plugins
-from openflexure_microscope.common.labthings.resource import Resource
-
-from flask import Blueprint, jsonify, url_for
-
-import copy
-import logging
-import warnings
-
-
-def plugins_representation(plugin_dict):
-    """
-    Generate a dictionary representation of all plugins, including Flask route URLs
-
-    Args:
-        plugin_loader_object (:py:class:`openflexure_microscope.plugins.PluginLoader`): Microscope plugin loader
-
-    Returns:
-        dict: Dictionary representation of all plugins
-    """
-    plugins = {}
-
-    for plugin_name, plugin in plugin_dict.items():
-        logging.debug(f"Representing plugin {plugin._name}")
-        d = {
-            "python_name": plugin._name_python_safe,
-            "plugin": str(plugin),
-            "views": {},
-            "gui": plugin.gui,
-            "description": get_docstring(plugin),
-        }
-
-        for view_id, view_data in plugin.views.items():
-            logging.debug(f"Representing view {view_id}")
-            uri = url_for(f"PluginListResource") + "/" + view_data["rule"][1:]
-            # uri = view_data["rule"]
-            # Make links dictionary if it doesn't yet exist
-            view_d = {"links": {"self": uri}}
-
-            view_d.update(description_from_view(view_data["view"]))
-
-            d["views"][view_id] = view_d
-
-        plugins[plugin_name] = d
-
-    return plugins
-
-
-class PluginListResource(Resource):
-    def get(self):
-        """
-        Return the current plugin forms
-
-        .. :quickref: Plugin; Get forms
-
-        Returns an array of present plugin forms (describing plugin user interfaces.)
-        Please note, this is *not* a list of all enabled plugins, only those with associated
-        user interface forms.
-
-        A complete list of enabled plugins can be found in the microscope state.
-
-        """
-        return jsonify(plugins_representation(registered_plugins()))
-
-
-"""
-def construct_blueprint():
-
-    blueprint = blueprint_for_module(__name__)
-
-    for plugin_obj in registered_plugins():
-        for plugin_view_id, plugin_view in plugin_obj.views.items():
-            # Add route to the plugins blueprint
-            blueprint.add_url_rule(
-                plugin_view["rule"],
-                view_func=plugin_view["view"].as_view(
-                    f"{plugin_obj._name_python_safe}_{plugin_view_id}"
-                ),
-                **plugin_view["kwargs"],
-            )
-
-    # Create a base route to return plugin API forms, if any exist
-    blueprint.add_url_rule("/", view_func=PluginFormAPI.as_view("plugins"))
-
-    # For each plugin attached to the microscope object
-    for plugin in microscope_obj.plugins.active:
-
-        for plugin_view_id, plugin_view in plugin.views.items():
-            # Add route to the plugins blueprint
-            blueprint.add_url_rule(
-                plugin_view["rule"],
-                view_func=plugin_view["view"].as_view(
-                    f"{plugin._name_python_safe}_{plugin_view_id}", plugin=plugin
-                ),
-                **plugin_view["kwargs"],
-            )
-
-    return blueprint
-"""

openflexure_microscope/devel/__init__.py

@@ -8,7 +8,7 @@ as well as some Flask imports to simplify API route development
 from openflexure_microscope.api.utilities import JsonResponse
 
 # Task management
-from openflexure_microscope.common.tasks import (
+from openflexure_microscope.common.labthings_core.tasks import (
     current_task,
     update_task_progress,
     update_task_data,

openflexure_microscope/microscope.py

@@ -12,7 +12,7 @@ from openflexure_microscope.camera.base import BaseCamera
 from openflexure_microscope.camera.mock import MockStreamer
 
 from openflexure_microscope.utilities import serialise_array_b64
-from openflexure_microscope.common.lock import CompositeLock
+from openflexure_microscope.common.labthings_core.lock import CompositeLock
 from openflexure_microscope.config import user_settings
 
 

openflexure_microscope/microscope_settings.default.json

@@ -3,11 +3,5 @@
     4100,
     3146
   ],
-  "jpeg_quality": 75,
-  "plugins": [
-    "openflexure_microscope.plugins.default.autofocus:AutofocusPlugin",
-    "openflexure_microscope.plugins.default.scan:ScanPlugin",
-    "openflexure_microscope.plugins.default.camera_calibration:AutocalibrationPlugin",
-    "openflexure_microscope.plugins.default.zip_builder:ZipBuilderPlugin"
-  ]
+  "jpeg_quality": 75
 }

openflexure_microscope/plugins/v2/autofocus.py

@@ -1,5 +1,5 @@
-from openflexure_microscope.common.labthings.find import find_device
-from openflexure_microscope.common.labthings.plugins import BasePlugin
+from openflexure_microscope.common.flask_labthings.find import find_device
+from openflexure_microscope.common.flask_labthings.plugins import BasePlugin
 from openflexure_microscope.microscope import Microscope
 
 from openflexure_microscope.devel import JsonResponse, request, jsonify, taskify, abort

openflexure_microscope/plugins/v2/scan.py

@@ -6,8 +6,8 @@ from typing import Tuple
 from functools import reduce
 
 from openflexure_microscope.camera.base import generate_basename
-from openflexure_microscope.common.labthings.find import find_device, find_plugin
-from openflexure_microscope.common.labthings.plugins import BasePlugin
+from openflexure_microscope.common.flask_labthings.find import find_device, find_plugin
+from openflexure_microscope.common.flask_labthings.plugins import BasePlugin
 
 from openflexure_microscope.devel import (
     JsonResponse,

openflexure_microscope/stage/base.py

@@ -1,6 +1,6 @@
 import numpy as np
 from abc import ABCMeta, abstractmethod
-from openflexure_microscope.common.lock import StrictLock
+from openflexure_microscope.common.labthings_core.lock import StrictLock
 
 
 class BaseStage(metaclass=ABCMeta):

openflexure_microscope/utilities.py

@@ -41,26 +41,6 @@ def bottom_level_name(obj):
     return obj.__name__.split(".")[-1]
 
 
-def description_from_view(view_class):
-    methods = []
-    for method_key in ["get", "post", "put", "delete"]:
-        if hasattr(view_class, method_key):
-            methods.append(method_key.upper())
-    brief_description = get_docstring(view_class).partition("\n")[0].strip()
-
-    d = {"methods": methods, "description": brief_description}
-
-    return d
-
-
-def get_docstring(obj):
-    ds = obj.__doc__
-    if ds:
-        return ds.strip()
-    else:
-        return ""
-
-
 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()