Merge branch 'main' into time-alignment-ui

src/electron/frontend/core/components/utils/progress.js

@@ -88,7 +88,7 @@ export const createProgressPopup = async (options, tqdmCallback) => {
     return { ...commonReturnValue, id, close };
 };
 
-const eventsURL = new URL("/neuroconv/events", baseUrl).href;
+const progressEventsUrl = new URL("/neuroconv/events/progress", baseUrl).href;
 
 class ProgressHandler {
     constructor(props) {
@@ -112,4 +112,4 @@ class ProgressHandler {
     removeEventListener = (...args) => this.source.removeEventListener(...args);
 }
 
-export const progressHandler = new ProgressHandler({ url: eventsURL });
+export const progressHandler = new ProgressHandler({ url: progressEventsUrl });

src/pyflask/manageNeuroconv/__init__.py

@@ -12,8 +12,9 @@
     inspect_multiple_filesystem_objects,
     inspect_nwb_file,
     inspect_nwb_folder,
-    listen_to_neuroconv_events,
+    listen_to_neuroconv_progress_events,
     locate_data,
+    progress_handler,
     upload_folder_to_dandi,
     upload_multiple_filesystem_objects_to_dandi,
     upload_project_to_dandi,

src/pyflask/manageNeuroconv/info/__init__.py

@@ -1,4 +1,4 @@
-from .sse import announcer, format_sse
+from .sse import format_sse
 from .urls import (
     CONVERSION_SAVE_FOLDER_PATH,
     GUIDE_ROOT_FOLDER,

src/pyflask/manageNeuroconv/info/sse.py

@@ -1,30 +1,8 @@
 import json
-import queue
 
 
 def format_sse(data: str, event=None) -> str:
     msg = f"data: {json.dumps(data)}\n\n"
     if event is not None:
         msg = f"event: {event}\n{msg}"
     return msg
-
-
-class MessageAnnouncer:
-    def __init__(self):
-        self.listeners = []
-
-    def listen(self):
-        q = queue.Queue(maxsize=5)
-        self.listeners.append(q)
-        return q
-
-    def announce(self, msg, event=None):
-        msg = format_sse(msg, event)
-        for i in reversed(range(len(self.listeners))):
-            try:
-                self.listeners[i].put_nowait(msg)
-            except queue.Full:
-                del self.listeners[i]
-
-
-announcer = MessageAnnouncer()

src/pyflask/manageNeuroconv/manage_neuroconv.py

@@ -11,12 +11,12 @@
 from shutil import copytree, rmtree
 from typing import Any, Dict, List, Optional, Union
 
-from .info import (
-    CONVERSION_SAVE_FOLDER_PATH,
-    GUIDE_ROOT_FOLDER,
-    STUB_SAVE_FOLDER_PATH,
-    announcer,
-)
+from tqdm_publisher import TQDMProgressHandler
+
+from .info import CONVERSION_SAVE_FOLDER_PATH, GUIDE_ROOT_FOLDER, STUB_SAVE_FOLDER_PATH
+from .info.sse import format_sse
+
+progress_handler = TQDMProgressHandler()
 
 EXCLUDED_RECORDING_INTERFACE_PROPERTIES = ["contact_vector", "contact_shapes", "group", "location"]
 
@@ -859,15 +859,12 @@ def convert_to_nwb(info: dict) -> str:
         alignment_info=info.get("alignment", dict()),
     )
 
-    def update_conversion_progress(**kwargs):
-        announcer.announce(dict(**kwargs, nwbfile_path=nwbfile_path), "conversion_progress")
-
     # Assume all interfaces have the same conversion options for now
     available_options = converter.get_conversion_options_schema()
     options = (
         {
             interface: (
-                {"stub_test": info["stub_test"]}  # , "iter_opts": {"report_hook": update_conversion_progress}}
+                {"stub_test": info["stub_test"]}
                 if available_options.get("properties").get(interface).get("properties", {}).get("stub_test")
                 else {}
             )
@@ -1046,11 +1043,11 @@ def upload_project_to_dandi(
 
 
 # Create an events endpoint
-def listen_to_neuroconv_events():
-    messages = announcer.listen()  # returns a queue.Queue
+def listen_to_neuroconv_progress_events():
+    messages = progress_handler.listen()  # returns a queue.Queue
     while True:
         msg = messages.get()  # blocks until a new message arrives
-        yield msg
+        yield format_sse(msg)
 
 
 def generate_dataset(input_path: str, output_path: str) -> dict:
@@ -1173,9 +1170,7 @@ def inspect_all(url, config):
 
     nwbfile_paths = list(Path(path).rglob("*.nwb"))
 
-    request_id = config.get("request_id")
-    if request_id:
-        config.pop("request_id")
+    request_id = config.pop("request_id", None)
 
     n_jobs = config.get("n_jobs", -2)  # Default to all but one CPU
     n_jobs = calculate_number_of_cpu(requested_cpu=n_jobs)
@@ -1200,7 +1195,7 @@ def inspect_all(url, config):
         # Announce directly
         def on_progress_update(message):
             message["progress_bar_id"] = request_id  # Ensure request_id matches
-            announcer.announce(
+            progress_handler.announce(
                 dict(
                     request_id=request_id,
                     **message,
@@ -1218,7 +1213,6 @@ def on_progress_update(message):
         i = 0
         for future in inspection_iterable:
             i += 1
-            # on_progress_update(dict(progress_bar_id=request_id, format_dict=dict(total=len(futures), n=i)))
             for message in future.result():
                 messages.append(message)
 
@@ -1228,25 +1222,15 @@ def on_progress_update(message):
 def inspect_nwb_folder(url, payload) -> dict:
     from pickle import PicklingError
 
-    from nwbinspector import load_config
     from nwbinspector.inspector_tools import format_messages, get_report_header
     from nwbinspector.nwbinspector import InspectorOutputJSONEncoder
 
-    kwargs = dict(
-        ignore=[
-            "check_description",
-            "check_data_orientation",
-        ],  # TODO: remove when metadata control is exposed
-        config=load_config(filepath_or_keyword="dandi"),
-        **payload,
-    )
-
     try:
-        messages = inspect_all(url, kwargs)
+        messages = inspect_all(url, payload)
     except PicklingError as exception:
         if "attribute lookup auto_parse_some_output on nwbinspector.register_checks failed" in str(exception):
-            del kwargs["n_jobs"]
-            messages = inspect_all(url, kwargs)
+            del payload["n_jobs"]
+            messages = inspect_all(url, payload)
         else:
             raise exception
     except Exception as exception:

src/pyflask/namespaces/neuroconv.py

@@ -13,14 +13,14 @@
     inspect_multiple_filesystem_objects,
     inspect_nwb_file,
     inspect_nwb_folder,
-    listen_to_neuroconv_events,
+    listen_to_neuroconv_progress_events,
     locate_data,
+    progress_handler,
     upload_folder_to_dandi,
     upload_multiple_filesystem_objects_to_dandi,
     upload_project_to_dandi,
     validate_metadata,
 )
-from manageNeuroconv.info import announcer
 
 neuroconv_namespace = Namespace("neuroconv", description="Neuroconv neuroconv_namespace for the NWB GUIDE.")
 
@@ -158,17 +158,16 @@ def post(self):
 class InspectNWBFolder(Resource):
     @neuroconv_namespace.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
-        url = f"{request.url_root}neuroconv/announce"
+        url = f"{request.url_root}neuroconv/announce/progress"
         return inspect_nwb_folder(url, neuroconv_namespace.payload)
 
 
-@neuroconv_namespace.route("/announce")
+@neuroconv_namespace.route("/announce/progress")
 class InspectNWBFolder(Resource):
     @neuroconv_namespace.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         data = neuroconv_namespace.payload
-        announcer.announce(data)
-
+        progress_handler.announce(data)
         return True
 
 
@@ -178,7 +177,7 @@ class InspectNWBFolder(Resource):
     def post(self):
         from os.path import isfile
 
-        url = f"{request.url_root}neuroconv/announce"
+        url = f"{request.url_root}neuroconv/announce/progress"
 
         paths = neuroconv_namespace.payload["paths"]
 
@@ -207,9 +206,8 @@ def post(self):
 
 
 # Create an events endpoint
-# announcer.announce('test', 'publish')
-@neuroconv_namespace.route("/events", methods=["GET"])
-class Events(Resource):
+@neuroconv_namespace.route("/events/progress", methods=["GET"])
+class ProgressEvents(Resource):
     @neuroconv_namespace.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def get(self):
-        return Response(listen_to_neuroconv_events(), mimetype="text/event-stream")
+        return Response(listen_to_neuroconv_progress_events(), mimetype="text/event-stream")