Upgrade JS package version. Update SpatialDataWrapper class (#460)

* Update SpatialDataWrapper. Bump js version

* Update spatialdata notebooks

* Lint

* Bump js version

Author: keller-mark

docs/notebooks/spatial_data.ipynb

@@ -86,7 +86,7 @@
    "outputs": [],
    "source": [
     "vc = VitessceConfig(\n",
-    "    schema_version=\"1.0.16\",\n",
+    "    schema_version=\"1.0.18\",\n",
     "    name='Visium SpatialData Demo (visium_associated_xenium_io)',\n",
     ")\n",
     "# Add data to the configuration:\n",

docs/notebooks/spatial_data_blobs.ipynb

@@ -29,7 +29,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import spatialdata"
+    "import spatialdata\n",
+    "from os.path import join"
    ]
   },
   {
@@ -41,15 +42,6 @@
     "sdata = spatialdata.datasets.blobs()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from os.path import join"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -65,16 +57,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sdata.write(spatialdata_filepath)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "sdata.table.uns"
+    "sdata.write(spatialdata_filepath, overwrite=True)"
    ]
   },
   {
@@ -109,15 +92,15 @@
    "outputs": [],
    "source": [
     "vc = VitessceConfig(\n",
-    "    schema_version=\"1.0.17\",\n",
+    "    schema_version=\"1.0.18\",\n",
     "    name='Visium SpatialData Demo (blobs)',\n",
     ")\n",
     "# Add data to the configuration:\n",
     "wrapper = SpatialDataWrapper(\n",
     "    sdata_store=spatialdata_filepath,\n",
     "    # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
     "    image_path=\"images/blobs_image\",\n",
-    "    labels_path=\"labels/blobs_labels\",\n",
+    "    obs_segmentations_path=\"labels/blobs_labels\",\n",
     "    coordinate_system=\"global\",\n",
     "    coordination_values={\n",
     "        \"obsType\": \"blob\",\n",
@@ -185,6 +168,13 @@
     "vw = vc.widget()\n",
     "vw"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

docs/notebooks/spatial_data_kpmp_vis.ipynb

@@ -71,7 +71,7 @@
    "outputs": [],
    "source": [
     "# Create a VitessceConfig instance.\n",
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"SpatialData\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"SpatialData\")\n",
     "\n",
     "t_obstype = \"Tubule\"\n",
     "a_obstype = \"Artery\"\n",
@@ -93,7 +93,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_tubules\",\n",
-    "        labels_path=\"labels/labels_tubules\",\n",
+    "        obs_segmentations_path=\"labels/labels_tubules\",\n",
     "        obs_feature_matrix_path=\"tables/table_tubules/X\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
@@ -106,7 +106,7 @@
     ").add_object(\n",
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
-    "        labels_path=\"labels/labels_arteries_arterioles\",\n",
+    "        obs_segmentations_path=\"labels/labels_arteries_arterioles\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
     "          \"fileUid\": \"labels_arteries_arterioles\",\n",
@@ -119,7 +119,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_cortical_interstitia\",\n",
-    "        labels_path=\"labels/labels_cortical_interstitia\",\n",
+    "        obs_segmentations_path=\"labels/labels_cortical_interstitia\",\n",
     "        obs_feature_matrix_path=\"tables/table_cortical_interstitia/X\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
@@ -133,7 +133,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_globally_sclerotic_glomeruli\",\n",
-    "        labels_path=\"labels/labels_globally_sclerotic_glomeruli\",\n",
+    "        obs_segmentations_path=\"labels/labels_globally_sclerotic_glomeruli\",\n",
     "        obs_feature_matrix_path=\"tables/table_globally_sclerotic_glomeruli/X\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
@@ -147,7 +147,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_non_globally_sclerotic_glomeruli\",\n",
-    "        labels_path=\"labels/labels_non_globally_sclerotic_glomeruli\",\n",
+    "        obs_segmentations_path=\"labels/labels_non_globally_sclerotic_glomeruli\",\n",
     "        obs_feature_matrix_path=\"tables/table_non_globally_sclerotic_glomeruli/X\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
@@ -161,7 +161,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_interstitialfibrosis_and_tubular_atrophy\",\n",
-    "        labels_path=\"labels/labels_interstitialfibrosis_and_tubular_atrophy\",\n",
+    "        obs_segmentations_path=\"labels/labels_interstitialfibrosis_and_tubular_atrophy\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
     "          \"fileUid\": \"labels_interstitialfibrosis_and_tubular_atrophy\",\n",
@@ -174,7 +174,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_peritubular_capillaries\",\n",
-    "        labels_path=\"labels/labels_peritubular_capillaries\",\n",
+    "        obs_segmentations_path=\"labels/labels_peritubular_capillaries\",\n",
     "        obs_feature_matrix_path=\"tables/table_peritubular_capillaries/X\",\n",
     "        obs_set_paths=[\n",
     "            \"tables/table_peritubular_capillaries/obs/cortex_ifta_set\",\n",

docs/notebooks/spatial_data_merfish.ipynb

@@ -64,7 +64,7 @@
    "outputs": [],
    "source": [
     "vc = VitessceConfig(\n",
-    "    schema_version=\"1.0.17\",\n",
+    "    schema_version=\"1.0.18\",\n",
     "    name='SpatialData with MERFISH data',\n",
     ")\n",
     "# Add data to the configuration:\n",
@@ -80,7 +80,7 @@
     ")).add_object(SpatialDataWrapper(\n",
     "    sdata_url=sdata_url,\n",
     "    # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
-    "    labels_path=\"labels/dapi_labels\",\n",
+    "    obs_segmentations_path=\"labels/dapi_labels\",\n",
     "    coordinate_system=\"global\",\n",
     "    coordination_values={\n",
     "        \"obsType\": \"nucleus\",\n",
@@ -89,7 +89,7 @@
     ")).add_object(SpatialDataWrapper(\n",
     "    sdata_url=sdata_url,\n",
     "    # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
-    "    labels_path=\"labels/membrane_labels\",\n",
+    "    obs_segmentations_path=\"labels/membrane_labels\",\n",
     "    coordinate_system=\"global\",\n",
     "    coordination_values={\n",
     "        \"obsType\": \"cell\",\n",

docs/notebooks/spatial_data_merfish_2.ipynb

@@ -86,7 +86,7 @@
    "outputs": [],
    "source": [
     "vc = VitessceConfig(\n",
-    "    schema_version=\"1.0.17\",\n",
+    "    schema_version=\"1.0.18\",\n",
     "    name='MERFISH SpatialData Demo',\n",
     ")\n",
     "# Add data to the configuration:\n",

docs/notebooks/spatial_data_mouseliver.ipynb

@@ -248,15 +248,15 @@
    "outputs": [],
    "source": [
     "# Create a VitessceConfig instance.\n",
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"SpatialData Demo\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"SpatialData Demo\")\n",
     "\n",
     "# Instantiate the wrapper class, specifying data fields of interest.\n",
     "wrapper = SpatialDataWrapper(\n",
     "    sdata_path=spatialdata_filepath,\n",
     "    # The following paths are relative to the root of the SpatialData Zarr store on-disk.\n",
     "    table_path=\"tables/table\",\n",
     "    image_path=\"images/raw_image\",\n",
-    "    labels_path=\"labels/segmentation_mask\",\n",
+    "    obs_segmentations_path=\"labels/segmentation_mask\",\n",
     "    obs_feature_matrix_path=\"tables/table/X\",\n",
     "    obs_set_paths=[\"tables/table/obs/annotation\"],\n",
     "    obs_set_names=[\"Annotation\"],\n",
@@ -434,7 +434,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"AnnData (zarr)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"AnnData (zarr)\")\n",
     "# Add data.\n",
     "wrapper = AnnDataWrapper(\n",
     "    adata_path=adata_zarr_filepath,\n",
@@ -481,7 +481,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"AnnData (h5ad)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"AnnData (h5ad)\")\n",
     "# Add data.\n",
     "wrapper = AnnDataWrapper(\n",
     "    adata_path=adata_h5ad_filepath,\n",
@@ -613,7 +613,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Image (ome-zarr)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"Image (ome-zarr)\")\n",
     "\n",
     "# Add data.\n",
     "img_wrapper = ImageOmeZarrWrapper(\n",
@@ -696,7 +696,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Image and segmentations (ome-tiff)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"Image and segmentations (ome-tiff)\")\n",
     "# Add data.\n",
     "wrapper = ImageOmeTiffWrapper(\n",
     "    img_path=ome_tiff_filepath,\n",

docs/notebooks/spatial_data_mouseliver_remote.ipynb

@@ -212,15 +212,15 @@
    "outputs": [],
    "source": [
     "# Create a VitessceConfig instance.\n",
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"SpatialData Demo\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"SpatialData Demo\")\n",
     "\n",
     "# Instantiate the wrapper class, specifying data fields of interest.\n",
     "wrapper = SpatialDataWrapper(\n",
     "    sdata_url=spatialdata_filepath,\n",
     "    # The following paths are relative to the root of the SpatialData Zarr store on-disk.\n",
     "    table_path=\"tables/table\",\n",
     "    image_path=\"images/raw_image\",\n",
-    "    labels_path=\"labels/segmentation_mask\",\n",
+    "    obs_segmentations_path=\"labels/segmentation_mask\",\n",
     "    obs_feature_matrix_path=\"tables/table/X\",\n",
     "    obs_set_paths=[\"tables/table/obs/annotation\"],\n",
     "    obs_set_names=[\"Annotation\"],\n",
@@ -349,7 +349,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"AnnData (zarr)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"AnnData (zarr)\")\n",
     "# Add data.\n",
     "wrapper = AnnDataWrapper(\n",
     "    adata_url=adata_zarr_filepath,\n",
@@ -396,7 +396,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"AnnData (h5ad)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"AnnData (h5ad)\")\n",
     "# Add data.\n",
     "wrapper = AnnDataWrapper(\n",
     "    adata_url=adata_h5ad_filepath,\n",
@@ -451,7 +451,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Image (ome-zarr)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"Image (ome-zarr)\")\n",
     "\n",
     "# Add data.\n",
     "img_wrapper = ImageOmeZarrWrapper(\n",
@@ -534,7 +534,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Image and segmentations (ome-tiff)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"Image and segmentations (ome-tiff)\")\n",
     "# Add data.\n",
     "wrapper = ImageOmeTiffWrapper(\n",
     "    img_url=ome_tiff_filepath,\n",

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.6.6"
+version = "3.6.7"
 authors = [
   { name="Mark Keller", email="[email protected]" },
 ]

src/vitessce/file_def_utils.py

@@ -3,8 +3,6 @@
 from functools import partial
 from typing import Optional
 
-import numpy as np
-
 
 def gen_obs_embedding_schema(options: dict, paths: Optional[list[str]] = None, names: Optional[list[str]] = None, dims: Optional[list[list[int]]] = None):
     if paths is not None:
@@ -127,29 +125,25 @@ def gen_path_schema(key: str, path: Optional[str], options: dict):
 gen_feature_labels_schema = partial(gen_path_schema, "featureLabels")
 
 
-def gen_sdata_image_schema(options, path: str, coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None) -> dict:
+def gen_sdata_image_schema(options, path: str, coordinate_system: Optional[str] = None) -> dict:
     if path is not None:
         options["image"] = {
             "path": path
         }
-        if affine_transformation is not None:
-            options["image"]['coordinateTransformations'] = affine_transformation
         if coordinate_system is not None:
             options["image"]['coordinateSystem'] = coordinate_system
     return options
 
 
-def gen_sdata_labels_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None) -> dict:
+def gen_sdata_obs_segmentations_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None) -> dict:
     if path is not None:
-        options["labels"] = {
+        options["obsSegmentations"] = {
             "path": path
         }
         if table_path is not None:
-            options["labels"]['tablePath'] = table_path
-        if affine_transformation is not None:
-            options["labels"]['coordinateTransformations'] = affine_transformation
+            options["obsSegmentations"]['tablePath'] = table_path
         if coordinate_system is not None:
-            options["labels"]['coordinateSystem'] = coordinate_system
+            options["obsSegmentations"]['coordinateSystem'] = coordinate_system
     return options
 
 

src/vitessce/widget.py

@@ -131,6 +131,11 @@ def launch_vitessce_io(config, theme='light', port=None, base_url=None, host_nam
         port, DEFAULT_PORT, proxy=proxy, base_url=base_url, host_name=host_name)
     config_dict = config.to_dict(base_url=base_url)
     routes = config.get_routes()
+
+    stores = config.get_stores(base_url=base_url)
+    if len(stores) > 0:
+        raise ValueError('One or more files in this configuration have been provided via Zarr store, which can only be loaded via the widget. Either use VitessceConfig.widget or VitessceConfig.display (instead of .web_app), or provide the files via _path or _url (rather than _store) parameters.')
+
     serve_routes(config, routes, use_port)
     vitessce_url = f"http://vitessce.io/#?theme={theme}&url=data:," + quote_plus(
         json.dumps(config_dict))
@@ -626,7 +631,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.7').tag(sync=True)
+    js_package_version = Unicode('3.6.9').tag(sync=True)
     js_dev_mode = Bool(False).tag(sync=True)
     custom_js_url = Unicode('').tag(sync=True)
     plugin_esm = List(trait=Unicode(''), default_value=[]).tag(sync=True)
@@ -639,7 +644,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     store_urls = List(trait=Unicode(''), default_value=[]).tag(sync=True)
 
-    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.6.7', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.6.9', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True):
         """
         Construct a new Vitessce widget.
 
@@ -775,7 +780,7 @@ def _plugin_command(self, params, buffers):
 # Launch Vitessce using plain HTML representation (no ipywidgets)
 
 
-def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.6.7', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.6.9', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None):
     from IPython.display import display, HTML
     uid_str = "vitessce" + get_uid_str(uid)