Initial 0.7.0 conversion

openflexure_microscope/api/default_extensions/autofocus.py

@@ -1,7 +1,7 @@
 from labthings.server.find import find_component
 from labthings.server.extensions import BaseExtension
 from labthings.server.view import View, ActionView, PropertyView
-from labthings.server.decorators import ThingAction, ThingProperty
+from labthings.server import fields
 
 from openflexure_microscope.devel import JsonResponse, request, abort
 from openflexure_microscope.utilities import set_properties
@@ -336,7 +336,9 @@ class AutofocusAPI(ActionView):
     """
     Run a standard autofocus
     """
-    def post(self):
+    args = {"dz": fields.List(fields.Int())}
+
+    def post(self, args):
         payload = JsonResponse(request)
         microscope = find_component("org.openflexure.microscope")
 
@@ -344,7 +346,7 @@ class AutofocusAPI(ActionView):
             abort(503, "No microscope connected. Unable to autofocus.")
 
         # Figure out the range of z values to use
-        dz = payload.param("dz", default=np.linspace(-300, 300, 7), convert=np.array)
+        dz = np.array(args.get("dz", np.linspace(-300, 300, 7)))
 
         if microscope.has_real_stage():
             logging.debug("Running autofocus...")
@@ -360,18 +362,20 @@ class FastAutofocusAPI(ActionView):
     """
     Run a fast autofocus
     """
-    def post(self):
+    args = {
-        payload = JsonResponse(request)
+        "dz": fields.Int(default=2000),
+        "backlash": fields.Int(default=25, minimum=0)
+    }
+
+    def post(self, args):
         microscope = find_component("org.openflexure.microscope")
 
         if not microscope:
             abort(503, "No microscope connected. Unable to autofocus.")
 
         # Figure out the parameters to use
-        dz = payload.param("dz", default=2000, convert=int)
+        dz = args.get("dz")
-        backlash = payload.param("backlash", default=25, convert=int)
+        backlash = args.get("backlash")
-        if backlash < 0:
-            backlash = 0
 
         if microscope.has_real_stage():
             logging.debug("Running autofocus...")

openflexure_microscope/api/default_extensions/autostorage.py

@@ -1,6 +1,5 @@
 from labthings.server.extensions import BaseExtension
 from labthings.server.view import View, PropertyView
-from labthings.server.decorators import ThingProperty, PropertySchema, use_args
 from labthings.server import fields
 from labthings.server.find import find_component
 
@@ -198,8 +197,9 @@ class GetLocationsView(PropertyView):
         return autostorage_extension_v2.get_locations()
 
 
-@PropertySchema(fields.String(required=True, example="Default"))
 class PreferredLocationView(PropertyView):
+    schema = fields.String(required=True, example="Default")
+
     def get(self):
         global autostorage_extension_v2
 
@@ -219,7 +219,8 @@ class PreferredLocationView(PropertyView):
 
 
 class PreferredLocationGUIView(View):
-    @use_args({"new_path_title": fields.String(required=True)})
+    args = {"new_path_title": fields.String(required=True)}
+
     def post(self, args):
         global autostorage_extension_v2
 

openflexure_microscope/api/default_extensions/scan.py

@@ -8,7 +8,6 @@ from functools import reduce
 from openflexure_microscope.captures.capture_manager import generate_basename
 from labthings.server.find import find_component, find_extension
 from labthings.server.extensions import BaseExtension
-from labthings.server.decorators import use_args
 from labthings.server import fields
 
 from openflexure_microscope.devel import abort, update_task_progress
@@ -91,7 +90,7 @@ class ScanExtension(BaseExtension):
     def __init__(self):
         self._images_to_be_captured: int = 1
         self._images_captured_so_far: int = 0
-        return BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")
+        BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")
 
     def progress(self):
         progress = (self._images_captured_so_far / self._images_to_be_captured) * 100
@@ -289,24 +288,23 @@ class ScanExtension(BaseExtension):
 scan_extension_v2 = ScanExtension()
 
 class TileScanAPI(ActionView):
-    @use_args(
+    args = {
-        {
+        "filename": fields.String(missing=None, example=None),
-            "filename": fields.String(missing=None, example=None),
+        "temporary": fields.Boolean(missing=False),
-            "temporary": fields.Boolean(missing=False),
+        "stride_size": fields.List(
-            "stride_size": fields.List(
+            fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
-                fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
+        ),
-            ),
+        "grid": fields.List(fields.Integer, missing=[3, 3, 3], example=[3, 3, 3]),
-            "grid": fields.List(fields.Integer, missing=[3, 3, 3], example=[3, 3, 3]),
+        "style": fields.String(missing="raster"),
-            "style": fields.String(missing="raster"),
+        "autofocus_dz": fields.Integer(missing=50),
-            "autofocus_dz": fields.Integer(missing=50),
+        "fast_autofocus": fields.Boolean(missing=False),
-            "fast_autofocus": fields.Boolean(missing=False),
+        "use_video_port": fields.Boolean(missing=False),
-            "use_video_port": fields.Boolean(missing=False),
+        "bayer": fields.Boolean(missing=False),
-            "bayer": fields.Boolean(missing=False),
+        "annotations": fields.Dict(missing={}, example={"Foo": "Bar"}),
-            "annotations": fields.Dict(missing={}, example={"Foo": "Bar"}),
+        "tags": fields.List(fields.String, missing=[]),
-            "tags": fields.List(fields.String, missing=[]),
+        "resize": fields.Dict(missing=None),  # TODO: Validate keys
-            "resize": fields.Dict(missing=None),  # TODO: Validate keys
+    }
-        }
+
-    )
     def post(self, args):
         microscope = find_component("org.openflexure.microscope")
 

openflexure_microscope/api/default_extensions/zip_builder.py

@@ -14,16 +14,10 @@ import logging
 
 from labthings.server.find import find_component
 from labthings.server.view import View, ActionView, PropertyView
-from labthings.server.schema import Schema
+from labthings.server.schema import Schema, pre_dump
 from labthings.server import fields
 from labthings.server.extensions import BaseExtension
 from labthings.server.utilities import description_from_view
-from labthings.server.decorators import (
-    ThingAction,
-    ThingProperty,
-    marshal_with,
-    pre_dump,
-)
 
 
 class ZipObjectSchema(Schema):
@@ -140,7 +134,6 @@ default_zip_manager = ZipManager()
 
 class ZipBuilderAPIView(ActionView):
     def post(self):
-
         ids = list(JsonResponse(request).json)
         microscope = find_component("org.openflexure.microscope")
 
@@ -151,7 +144,8 @@ class ZipBuilderAPIView(ActionView):
 
 
 class ZipListAPIView(PropertyView):
-    @marshal_with(ZipObjectSchema(many=True))
+    schema = ZipObjectSchema(many=True)
+
     def get(self):
         return default_zip_manager.session_zips.values()
 

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

@@ -58,7 +58,6 @@ def enabled_root_actions():
     return {k: v for k, v in _actions.items() if v["conditions"]}
 
 
-# @Tag("actions")
 class ActionsView(View):
     def get(self):
         """

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

@@ -1,19 +1,11 @@
 from openflexure_microscope.api.utilities import get_bool, JsonResponse
 from labthings.server.view import View, ActionView
 from labthings.server.find import find_component
-from labthings.server.decorators import (
-    use_args,
-    marshal_with,
-    doc,
-    tag,
-    ThingAction,
-    doc_response,
-)
 
 from labthings.server import fields
 from openflexure_microscope.utilities import filter_dict
 
-from openflexure_microscope.api.v2.views.captures import capture_schema
+from openflexure_microscope.api.v2.views.captures import CaptureSchema
 
 import logging
 import io
@@ -25,24 +17,23 @@ class CaptureAPI(ActionView):
     Create a new image capture. 
     """
 
-    @use_args(
+    args = {
-        {
+        "filename": fields.String(example="MyFileName"),
-            "filename": fields.String(example="MyFileName"),
+        "temporary": fields.Boolean(
-            "temporary": fields.Boolean(
+            missing=False, description="Delete capture on shutdown"
-                missing=False, description="Delete capture on shutdown"
+        ),
-            ),
+        "use_video_port": fields.Boolean(missing=False),
-            "use_video_port": fields.Boolean(missing=False),
+        "bayer": fields.Boolean(
-            "bayer": fields.Boolean(
+            missing=False, description="Store raw bayer data in file"
-                missing=False, description="Store raw bayer data in file"
+        ),
-            ),
+        "annotations": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
-            "annotations": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
+        "tags": fields.List(fields.String, missing=[], example=["docs"]),
-            "tags": fields.List(fields.String, missing=[], example=["docs"]),
+        "resize": fields.Dict(
-            "resize": fields.Dict(
+            missing=None, example={"width": 640, "height": 480}
-                missing=None, example={"width": 640, "height": 480}
+        ),  # TODO: Validate keys
-            ),  # TODO: Validate keys
+    }
-        }
+    schema = CaptureSchema()
-    )
+
-    @marshal_with(capture_schema)
     def post(self, args):
         """
         Create a new capture
@@ -78,18 +69,22 @@ class RAMCaptureAPI(ActionView):
     Take a non-persistant image capture.
     """
 
-    @use_args(
+    args = {
-        {
+        "use_video_port": fields.Boolean(missing=True),
-            "use_video_port": fields.Boolean(missing=True),
+        "bayer": fields.Boolean(
-            "bayer": fields.Boolean(
+            missing=False, description="Return with raw bayer data"
-                missing=False, description="Return with raw bayer data"
+        ),
-            ),
+        "resize": fields.Dict(
-            "resize": fields.Dict(
+            missing=None, example={"width": 640, "height": 480}
-                missing=None, example={"width": 640, "height": 480}
+        ),  # TODO: Validate keys
-            ),  # TODO: Validate keys
+    }
+    
+    responses = {
+        200: {
+            "content_type": "image/jpeg"
         }
-    )
+    }
-    @doc_response(200, mimetype="image/jpeg")
+
     def post(self, args):
         """
         Take a non-persistant image capture.
@@ -128,9 +123,8 @@ class GPUPreviewStartAPI(ActionView):
     in the format ``[x, y, width, height]``.
     """
 
-    @use_args(
+    args = {"window": fields.List(fields.Integer, missing=[], example=[0, 0, 640, 480])}
-        {"window": fields.List(fields.Integer, missing=[], example=[0, 0, 640, 480])}
+
-    )
     def post(self, args):
         """
         Start the onboard GPU preview.

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

@@ -1,7 +1,6 @@
 from openflexure_microscope.api.utilities import JsonResponse
 from labthings.server.view import View, ActionView
 from labthings.server.find import find_component
-from labthings.server.decorators import use_args, marshal_with, doc, ThingAction
 from labthings.server import fields
 
 from openflexure_microscope.utilities import axes_to_array, filter_dict
@@ -12,16 +11,15 @@ import logging
 
 
 class MoveStageAPI(ActionView):
-    @use_args(
+    args = {
-        {
+        "absolute": fields.Boolean(
-            "absolute": fields.Boolean(
+            default=False, example=False, description="Move to an absolute position"
-                default=False, example=False, description="Move to an absolute position"
+        ),
-            ),
+        "x": fields.Int(default=0, example=100),
-            "x": fields.Int(default=0, example=100),
+        "y": fields.Int(default=0, example=100),
-            "y": fields.Int(default=0, example=100),
+        "z": fields.Int(default=0, example=20),
-            "z": fields.Int(default=0, example=20),
+    }
-        }
+
-    )
     def post(self, args):
         """
         Move the microscope stage in x, y, z

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

@@ -3,8 +3,6 @@ import subprocess
 import os
 from sys import platform
 
-from labthings.server.decorators import ThingAction, doc_response
-
 
 def is_raspberrypi(raise_on_errors=False):
     """
@@ -19,7 +17,6 @@ class ShutdownAPI(ActionView):
     Attempt to shutdown the device 
     """
 
-    @doc_response(201)
     def post(self):
         """
         Attempt to shutdown the device
@@ -31,7 +28,7 @@ class ShutdownAPI(ActionView):
         )
 
         out, err = p.communicate()
-        return {"out": out, "err": err}, 201
+        return {"out": out, "err": err}
 
 
 class RebootAPI(ActionView):
@@ -39,7 +36,6 @@ class RebootAPI(ActionView):
     Attempt to reboot the device 
     """
 
-    @doc_response(201)
     def post(self):
         """
         Attempt to reboot the device
@@ -51,4 +47,4 @@ class RebootAPI(ActionView):
         )
 
         out, err = p.communicate()
-        return {"out": out, "err": err}, 201
+        return {"out": out, "err": err}

openflexure_microscope/api/v2/views/captures.py

@@ -7,7 +7,6 @@ from labthings.server.schema import Schema
 from labthings.server import fields
 from labthings.server.view import View, PropertyView
 from labthings.server.utilities import description_from_view
-from labthings.server.decorators import marshal_with, doc_response, Tag, ThingProperty
 
 from labthings.server.find import find_component
 
@@ -84,16 +83,10 @@ class CaptureSchema(Schema):
         return data
 
 
-capture_schema = CaptureSchema()
-capture_list_schema = CaptureSchema(many=True)
-
-
-from pprint import pprint
-
-
-@Tag("captures")
 class CaptureList(PropertyView):
-    @marshal_with(CaptureSchema(many=True))
+    tags = ["captures"]
+    schema = CaptureSchema(many=True)
+
     def get(self):
         """
         List all image captures
@@ -103,9 +96,10 @@ class CaptureList(PropertyView):
         return image_list
 
 
-@Tag("captures")
 class CaptureView(View):
-    @marshal_with(CaptureSchema())
+    tags = ["captures"]
+    schema = CaptureSchema()
+
     def get(self, id):
         """
         Description of a single image capture
@@ -136,9 +130,14 @@ class CaptureView(View):
         return "", 204
 
 
-@Tag("captures")
 class CaptureDownload(View):
-    @doc_response(200, mimetype="image/jpeg")
+    tags = ["captures"]
+    responses = {
+        200: {
+            "content_type": "image/jpeg"
+        }
+    }
+
     def get(self, id, filename):
         """
         Image data for a single image capture
@@ -172,8 +171,9 @@ class CaptureDownload(View):
         return send_file(img, mimetype="image/jpeg")
 
 
-@Tag("captures")
 class CaptureTags(View):
+    tags = ["captures"]
+
     def get(self, id):
         """
         Get tags associated with a single image capture
@@ -227,8 +227,9 @@ class CaptureTags(View):
         return capture_obj.tags
 
 
-@Tag("captures")
 class CaptureAnnotations(View):
+    tags = ["captures"]
+
     def get(self, id):
         """
         Get annotations associated with a single image capture

openflexure_microscope/api/v2/views/instrument.py

@@ -5,8 +5,6 @@ from labthings.core.utilities import get_by_path, set_by_path, create_from_path
 from labthings.server.find import find_component
 from labthings.server.view import View, PropertyView
 
-from labthings.server.decorators import ThingProperty, Tag, doc_response
-
 from flask import request, abort
 import logging
 
@@ -35,9 +33,12 @@ class SettingsProperty(PropertyView):
         return self.get()
 
 
-@Tag("properties")
 class NestedSettingsProperty(View):
-    @doc_response(404, description="Settings key cannot be found")
+    tags = ["properties"]
+    responses = {
+        404: {"description": "Settings key cannot be found"}
+    }
+
     def get(self, route):
         """
         Show a nested section of the current microscope settings
@@ -52,7 +53,6 @@ class NestedSettingsProperty(View):
 
         return value
 
-    @doc_response(404, description="Settings key cannot be found")
     def put(self, route):
         """
         Update a nested section of the current microscope settings
@@ -79,9 +79,12 @@ class StateProperty(PropertyView):
         return microscope.state
 
 
-@Tag("properties")
 class NestedStateProperty(View):
-    @doc_response(404, description="Status key cannot be found")
+    tags = ["properties"]
+    responses = {
+        404: {"description": "Status key cannot be found"}
+    }
+
     def get(self, route):
         """
         Show a nested section of the current microscope state
@@ -106,9 +109,12 @@ class ConfigurationProperty(PropertyView):
         return microscope.configuration
 
 
-@Tag("properties")
 class NestedConfigurationProperty(View):
-    @doc_response(404, description="Configuration key cannot be found")
+    tags = ["properties"]
+    responses = {
+        404: {"description": "Status key cannot be found"}
+    }
+
     def get(self, route):
         """
         Show a nested section of the current microscope state

openflexure_microscope/api/v2/views/streams.py

@@ -4,17 +4,19 @@ from labthings.core.utilities import get_by_path, set_by_path, create_from_path
 
 from labthings.server.find import find_component
 from labthings.server.view import View, PropertyView
-from labthings.server.decorators import doc_response, ThingProperty
+from labthings.server.responses import Response
-
-from flask import Response
 
 
 class MjpegStream(PropertyView):
     """
     Real-time MJPEG stream from the microscope camera
     """
+    responses = {
+        200: {
+            "content_type": "multipart/x-mixed-replace"
+        }
+    }
 
-    @doc_response(200, mimetype="multipart/x-mixed-replace")
     def get(self):
         """
         MJPEG stream from the microscope camera.
@@ -42,7 +44,13 @@ class SnapshotStream(PropertyView):
     Single JPEG snapshot from the camera stream
     """
 
-    @doc_response(200, description="Snapshot taken", mimetype="image/jpeg")
+    responses = {
+        200: {
+            "content_type": "image/jpeg",
+            "description": "Snapshot taken"
+        }
+    }
+
     def get(self):
         """
         Single snapshot from the camera stream