Convert async custom message handlers to sync (#506)

* Convert async custom message handlers to sync

* Lint

* Update

Author: keller-mark

.coveragerc_omit

@@ -8,6 +8,7 @@ omit =
     src/vitessce/wrappers.py
     src/vitessce/repr.py
     src/vitessce/utils.py
+    src/vitessce/sync_store.py
     src/vitessce/data_utils/anndata.py
     src/vitessce/data_utils/ome.py
     src/vitessce/data_utils/entities.py

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.9.1"
+version = "3.9.2"
 authors = [
   { name="Mark Keller", email="mark_keller@hms.harvard.edu" },
 ]

src/vitessce/sync_store.py

@@ -0,0 +1,68 @@
+# Copied from zarr-python
+# Reference: https://github.com/zarr-developers/zarr-python/blob/fe229107f9915f05817f7a664d3550695ff9ca44/src/zarr/testing/stateful.py#L438
+
+import builtins
+from typing import Any
+import zarr
+from zarr.abc.store import Store
+from zarr.core.buffer import Buffer, BufferPrototype
+
+
+class SyncStoreWrapper(zarr.core.sync.SyncMixin):
+    def __init__(self, store: Store) -> None:
+        """Synchronous Store wrapper
+
+        This class holds synchronous methods that map to async methods of Store classes.
+        The synchronous wrapper is needed because hypothesis' stateful testing infra does
+        not support asyncio so we redefine sync versions of the Store API.
+        https://github.com/HypothesisWorks/hypothesis/issues/3712#issuecomment-1668999041
+        """
+        self.store = store
+
+    @property
+    def read_only(self) -> bool:
+        return self.store.read_only
+
+    def set(self, key: str, data_buffer: Buffer) -> None:
+        return self._sync(self.store.set(key, data_buffer))
+
+    def list(self) -> builtins.list[str]:
+        return self._sync_iter(self.store.list())
+
+    def get(self, key: str, prototype: BufferPrototype, **kwargs) -> Buffer | None:
+        return self._sync(self.store.get(key, prototype=prototype, **kwargs))
+
+    def get_partial_values(
+        self, key_ranges: builtins.list[Any], prototype: BufferPrototype
+    ) -> builtins.list[Buffer | None]:
+        return self._sync(self.store.get_partial_values(prototype=prototype, key_ranges=key_ranges))
+
+    def delete(self, path: str) -> None:
+        return self._sync(self.store.delete(path))
+
+    def is_empty(self, prefix: str) -> bool:
+        return self._sync(self.store.is_empty(prefix=prefix))
+
+    def clear(self) -> None:
+        return self._sync(self.store.clear())
+
+    def exists(self, key: str) -> bool:
+        return self._sync(self.store.exists(key))
+
+    def list_dir(self, prefix: str) -> None:
+        raise NotImplementedError
+
+    def list_prefix(self, prefix: str) -> None:
+        raise NotImplementedError
+
+    @property
+    def supports_listing(self) -> bool:
+        return self.store.supports_listing
+
+    @property
+    def supports_writes(self) -> bool:
+        return self.store.supports_writes
+
+    @property
+    def supports_deletes(self) -> bool:
+        return self.store.supports_deletes

src/vitessce/widget.py

@@ -7,9 +7,9 @@
 import anywidget
 from traitlets import Unicode, Dict, List, Int, Bool
 
-import asyncio
 from zarr.abc.store import RangeByteRequest, SuffixByteRequest
 from zarr.core.buffer.core import default_buffer_prototype
+from .sync_store import SyncStoreWrapper
 
 
 MAX_PORT_TRIES = 1000
@@ -912,11 +912,11 @@ def close(self):
         super().close()
 
     # @anywidget.experimental.command
-    async def _zarr_get(self, params, buffers):
+    def _zarr_get(self, params, buffers):
         [store_url, key] = params
-        store = self._stores[store_url]
+        store = SyncStoreWrapper(self._stores[store_url])
         try:
-            result = await store.get(key.lstrip("/"), prototype=default_buffer_prototype())
+            result = store.get(key.lstrip("/"), prototype=default_buffer_prototype())
             if result is None:
                 buffers = []
             else:
@@ -927,9 +927,9 @@ async def _zarr_get(self, params, buffers):
         return {"success": len(buffers) == 1}, buffers
 
     # @anywidget.experimental.command
-    async def _zarr_get_range(self, params, buffers):
+    def _zarr_get_range(self, params, buffers):
         [store_url, key, range_query] = params
-        store = self._stores[store_url]
+        store = SyncStoreWrapper(self._stores[store_url])
         try:
             range_param = None
             # Reference: https://github.com/manzt/zarrita.js/blob/f63a2521e2b46b22aa26af4146822e4d827dff83/packages/%40zarrita-storage/src/types.ts#L3
@@ -943,7 +943,7 @@ async def _zarr_get_range(self, params, buffers):
             else:
                 raise ValueError(f"Invalid range query: {range_query}. Must contain either 'suffixLength' or both 'offset' and 'length'.")
 
-            result = await store.get(key, byte_range=range_param, prototype=default_buffer_prototype())
+            result = store.get(key, byte_range=range_param, prototype=default_buffer_prototype())
             if result is None:
                 buffers = []
             else:
@@ -954,16 +954,16 @@ async def _zarr_get_range(self, params, buffers):
         return {"success": len(buffers) == 1}, buffers
 
     # @anywidget.experimental.command
-    async def _zarr_get_multi(self, params_arr, buffers):
+    def _zarr_get_multi(self, params_arr, buffers):
         # This variant of _zarr_get and _zarr_get_range supports batching.
         result_dicts = []
         result_buffers = []
         for params in params_arr:
             result_dict, result_buffer_arr = {}, []
             if len(params) == 2:
-                result_dict, result_buffer_arr = await self._zarr_get(params, buffers)
+                result_dict, result_buffer_arr = self._zarr_get(params, buffers)
             elif len(params) == 3:
-                result_dict, result_buffer_arr = await self._zarr_get_range(params, buffers)
+                result_dict, result_buffer_arr = self._zarr_get_range(params, buffers)
             else:
                 raise ValueError("Expected params to have len 2 or 3 in _zarr_get_multi")
             if result_dict["success"] and len(result_buffer_arr) == 1:
@@ -986,28 +986,21 @@ def _handle_msg(self, msg: dict) -> None:
         if content.get("kind") != "anywidget-command":
             super()._handle_msg(msg)
             return
-        try:
-            loop = asyncio.get_event_loop()
-        except RuntimeError:
-            return
-        if loop.is_running():
-            loop.create_task(self._dispatch_command(content, buffers))
-        else:
-            loop.run_until_complete(self._dispatch_command(content, buffers))
+        self._dispatch_command(content, buffers)
 
-    async def _dispatch_command(self, msg: dict, buffers: list[bytes]) -> None:
+    def _dispatch_command(self, msg: dict, buffers: list[bytes]) -> None:
         name = msg.get("name")
         params = msg.get("msg")
         msg_id = msg.get("id")
         try:
             if name == "_zarr_get":
-                response, result_buffers = await self._zarr_get(params, buffers)
+                response, result_buffers = self._zarr_get(params, buffers)
             elif name == "_zarr_get_range":
-                response, result_buffers = await self._zarr_get_range(params, buffers)
+                response, result_buffers = self._zarr_get_range(params, buffers)
             elif name == "_zarr_get_multi":
-                response, result_buffers = await self._zarr_get_multi(params, buffers)
+                response, result_buffers = self._zarr_get_multi(params, buffers)
             elif name == "_plugin_command":
-                response, result_buffers = await self._plugin_command(params, buffers)
+                response, result_buffers = self._plugin_command(params, buffers)
             else:
                 return
         except Exception as exc:  # noqa: BLE001