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/exceptions.py

@@ -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 = {"status_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)

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