Merge branch 'v2.1.0-dev' into stage-calibration

openflexure_microscope/api/app.py

@@ -1,4 +1,8 @@
 #!/usr/bin/env python
+from gevent import monkey
+
+# Patch most system modules. Leave threads untouched so we can still use them normally if needed.
+monkey.patch_all(thread=False)
 
 import time
 import atexit
@@ -60,6 +64,7 @@ app, labthing = create_app(
     prefix="/api/v2",
     title=f"OpenFlexure Microscope {api_microscope.name}",
     description="Test LabThing-based API for OpenFlexure Microscope",
+    types=["org.openflexure.microscope"],
     version=pkg_resources.get_distribution("openflexure_microscope").version,
     flask_kwargs={"static_url_path": ""},
 )
@@ -167,5 +172,9 @@ def cleanup():
 
 atexit.register(cleanup)
 
+# Start the app
 if __name__ == "__main__":
-    app.run(host="0.0.0.0", port="5000", threaded=True, debug=True, use_reloader=False)
+    from labthings.server.wsgi import Server
+
+    server = Server(app)
+    server.run(host="0.0.0.0", port=5000, debug=False)

openflexure_microscope/api/default_extensions/__init__.py

@@ -14,3 +14,5 @@ except Exception as e:
     logging.error(
         f"Exception loading builtin extension picamera_autocalibrate: \n{traceback.format_exc()}"
     )
+
+from ..example_extensions.custom_element import customelement_extension_v2

openflexure_microscope/api/default_extensions/autostorage.py

@@ -241,6 +241,7 @@ def dynamic_form():
     return {
         "icon": "sd_storage",
         "title": "Storage",
+        "viewPanel": "gallery",
         "forms": [
             {
                 "name": "Autostorage",

openflexure_microscope/api/example_extensions/custom_element/__init__.py

@@ -0,0 +1,57 @@
+from labthings.server.extensions import BaseExtension
+from labthings.server.view import View
+from labthings.server.decorators import ThingProperty, PropertySchema, use_args
+from labthings.server import fields
+from labthings.server.find import find_component
+from labthings.core.utilities import path_relative_to
+
+from openflexure_microscope.paths import settings_file_path, check_rw
+from openflexure_microscope.config import OpenflexureSettingsFile
+from openflexure_microscope.camera.base import BASE_CAPTURE_PATH
+from openflexure_microscope.camera.capture import build_captures_from_exif
+
+from openflexure_microscope.api.utilities.gui import build_gui
+
+from flask import abort, url_for
+import logging
+import os
+import psutil
+
+from sys import platform
+
+
+class CustomElementExtension(BaseExtension):
+    def __init__(self):
+        BaseExtension.__init__(
+            self,
+            "org.openflexure.customelement",
+            description="Testing HTML components in an extension",
+            static_folder=path_relative_to(__file__, "static"),
+        )
+
+        # Register the on_microscope function to run when the microscope is attached
+        self.on_component("org.openflexure.microscope", self.on_microscope)
+
+    def on_microscope(self, microscope_obj):
+        """Function to automatically call when the parent LabThing has a microscope attached."""
+        logging.debug(f"CustomElementExtension found microscope {microscope_obj}")
+
+
+customelement_extension_v2 = CustomElementExtension()
+
+
+def wc_func():
+    return {
+        "href": customelement_extension_v2.static_file_url("my-custom-element.min.js"),
+        "name": "my-custom-element",
+    }
+
+
+def gui_func():
+    return {"icon": "pets", "title": "Element", "viewPanel": "stream", "wc": wc_func()}
+
+
+customelement_extension_v2.add_meta("wc", wc_func)
+customelement_extension_v2.add_meta(
+    "gui", build_gui(gui_func, customelement_extension_v2)
+)

openflexure_microscope/api/v2/views/captures.py

@@ -207,7 +207,7 @@ class CaptureTags(View):
 
         return jsonify(capture_obj.tags)
 
-    def delete(self, capture_id):
+    def delete(self, id):
         """
         Delete tags from a single image capture
         """

openflexure_microscope/api/v2/views/streams.py

@@ -18,7 +18,16 @@ class MjpegStream(View):
     @doc_response(200, mimetype="multipart/x-mixed-replace")
     def get(self):
         """
-        MJPEG stream from the microscope camera
+        MJPEG stream from the microscope camera.
+
+        Note: While the code actually getting frame data from a camera and storing it in
+        camera.frame runs in a thread, the gen(microscope.camera) generator does not.
+        This response is therefore blocking. The generator just yields the most recent
+        frame from the camera object, passed to the Flask response, and then repeats until
+        the connection is closed.
+
+        Without monkey patching with gevent, or using a native threaded server, the stream
+        will block all proceeding requests.
         """
         microscope = find_component("org.openflexure.microscope")
         # Restart stream worker thread