Update usage of GraphQL client to match new schema (#20)

This bumps the minimum required version of `cryoet-data-portal` to v2
that includes changes to the underlying GraphQL schema.

It also changes the readers and widgets to adapt to the corresponding
API changes, so that tomograms and points annotations are read correctly
when they are available.

setup.cfg

@@ -31,7 +31,7 @@ project_urls =
 [options]
 packages = find:
 install_requires =
-    cryoet_data_portal
+    cryoet_data_portal>=2
     fsspec[http,s3]
     npe2
     numpy

src/napari_cryoet_data_portal/_open_widget.py

@@ -165,7 +165,15 @@ def _loadTomogram(
         )
 
         for annotation in annotations:
-            yield read_annotation(annotation, tomogram=tomogram)
+            point_paths = tuple(
+                f.https_path
+                for f in annotation.files
+                if f.shape_type == "Point"
+            )
+            if len(point_paths) > 0:
+                yield read_annotation(annotation, tomogram=tomogram)
+            else:
+                logger.warn("Found no points annotations. Skipping.")
 
     def _onLayerLoaded(self, layer_data: FullLayerData) -> None:
         logger.debug("OpenWidget._onLayerLoaded")

src/napari_cryoet_data_portal/_reader.py

@@ -8,6 +8,8 @@
 from npe2.types import FullLayerData, PathOrPaths, ReaderFunction
 from cryoet_data_portal import Annotation, Tomogram
 
+from napari_cryoet_data_portal._logging import logger
+
 
 OBJECT_COLOR = {
     "ribosome": "red",
@@ -195,7 +197,14 @@ def read_annotation(annotation: Annotation, *, tomogram: Optional[Tomogram] = No
     >>> data, attrs, _ = read_annotation(annotation)
     >>> points = Points(data, **attrs)
     """
-    data, attributes, layer_type = read_points_annotations_ndjson(annotation.https_annotations_path)
+    point_paths = tuple(
+        f.https_path
+        for f in annotation.files
+        if f.shape_type == "Point"
+    )
+    if len(point_paths) > 1:
+        logger.warn("Found more than one points annotation. Using the first.")
+    data, attributes, layer_type = read_points_annotations_ndjson(point_paths[0])
     name = annotation.object_name
     if tomogram is None:
         attributes["name"] = name

src/napari_cryoet_data_portal/_sample_data.py

@@ -23,7 +23,7 @@ def tomogram_10000_ts_027() -> List[FullLayerData]:
 def _read_tomogram_from_10000(name: str) -> List[FullLayerData]:
     client = Client()
 
-    tomogram_spacing_url = f"https://files.cryoetdataportal.cziscience.com/10000/{name}/Tomograms/VoxelSpacing13.48/"
+    tomogram_spacing_url = f"https://files.cryoetdataportal.cziscience.com/10000/{name}/Tomograms/VoxelSpacing13.480/"
     tomogram_spacing = next(TomogramVoxelSpacing.find(client, [TomogramVoxelSpacing.https_prefix == tomogram_spacing_url]))
 
     tomogram: Tomogram = next(tomogram_spacing.tomograms)

src/napari_cryoet_data_portal/_tests/conftest.py

@@ -15,4 +15,4 @@ def dataset(client: Client) -> Dataset:
 
 @pytest.fixture()
 def tomogram(client: Client) -> Tomogram:
-    return next(Tomogram.find(client, [Tomogram.name == 'TS_026']))
+    return next(Tomogram.find(client, [Tomogram.name == 'TS_026', Tomogram.https_omezarr_dir.like("%13.480%")]))

src/napari_cryoet_data_portal/_tests/test_reader.py

@@ -2,16 +2,15 @@
 
 from napari import Viewer
 from napari.layers import Points
-from cryoet_data_portal import Annotation, Client
 
 from napari_cryoet_data_portal import (
     read_points_annotations_ndjson,
     read_tomogram_ome_zarr,
 )
 
 CLOUDFRONT_URI = "https://files.cryoetdataportal.cziscience.com"
-TOMOGRAM_DIR = f"{CLOUDFRONT_URI}/10000/TS_026/Tomograms/VoxelSpacing13.48"
-ANNOTATION_FILE = f"{TOMOGRAM_DIR}/Annotations/sara_goetz-ribosome-1.0.ndjson"
+TOMOGRAM_DIR = f"{CLOUDFRONT_URI}/10000/TS_026/Tomograms/VoxelSpacing13.480"
+ANNOTATION_FILE = f"{TOMOGRAM_DIR}/Annotations/101-cytosolic_ribosome-1.0_point.ndjson"
 
 
 def test_read_tomogram_ome_zarr():