Use GraphQL client instead of custom model and IO

setup.cfg

@@ -31,12 +31,13 @@ project_urls =
 [options]
 packages = find:
 install_requires =
+    cryoet_data_portal
+    fsspec[http,s3]
     npe2
     numpy
     napari_ome_zarr
     ndjson
     qtpy
-    s3fs
     superqt
 
 python_requires = >=3.8

src/napari_cryoet_data_portal/__init__.py

@@ -2,10 +2,11 @@
     from ._version import version as __version__
 except ImportError:
     __version__ = "unknown"
-from ._logging import logger
 from ._reader import (
     points_annotations_reader,
-    read_points_annotations_json,
+    read_annotation,
+    read_points_annotations_ndjson,
+    read_tomogram,
     read_tomogram_ome_zarr,
     tomogram_ome_zarr_reader,
 )
@@ -14,7 +15,9 @@
 __all__ = (
     "DataPortalWidget",
     "points_annotations_reader",
+    "read_annotation",
+    "read_tomogram",
     "read_tomogram_ome_zarr",
-    "read_points_annotations_json",
+    "read_points_annotations_ndjson",
     "tomogram_ome_zarr_reader",
 )

src/napari_cryoet_data_portal/_listing_widget.py

@@ -1,4 +1,4 @@
-from typing import Generator, Optional
+from typing import Generator, List, Optional, Tuple
 
 from qtpy.QtCore import Qt
 from qtpy.QtWidgets import (
@@ -8,11 +8,10 @@
     QVBoxLayout,
     QWidget,
 )
+from cryoet_data_portal import Client, Dataset, Tomogram
 
-from napari_cryoet_data_portal._io import list_dir
 from napari_cryoet_data_portal._listing_tree_widget import ListingTreeWidget
 from napari_cryoet_data_portal._logging import logger
-from napari_cryoet_data_portal._model import Dataset
 from napari_cryoet_data_portal._progress_widget import ProgressWidget
 from napari_cryoet_data_portal._vendored.superqt._searchable_tree_widget import (
     _update_visible_items,
@@ -44,37 +43,37 @@ def __init__(self, parent: Optional[QWidget] = None) -> None:
         layout.addStretch(0)
         self.setLayout(layout)
 
-    def load(self, path: str) -> None:
-        """Lists the datasets and tomograms at the given data portal path."""
-        logger.debug("ListingWidget.load: %s", path)
+    def load(self, uri: str) -> None:
+        """Lists the datasets and tomograms using the given portal URI."""
+        logger.debug("ListingWidget.load: %s", uri)
         self.tree.clear()
         self.show()
-        self._progress.submit(path)
+        self._progress.submit(uri)
 
     def cancel(self) -> None:
         """Cancels the last listing."""
         logger.debug("ListingWidget.cancel")
         self._progress.cancel()
 
-    def _loadDatasets(self, path: str) -> Generator[Dataset, None, None]:
-        logger.debug("ListingWidget._loadDatasets: %s", path)
-        # TODO: only list non-hidden directories.
-        dataset_names = tuple(
-            p for p in list_dir(path) if not p.startswith(".")
-        )
-        if len(dataset_names) == 0:
-            logger.debug("No datasets found")
-        for name in dataset_names:
-            yield Dataset.from_data_path_and_name(path, name)
+    def _loadDatasets(self, uri: str) -> Generator[Tuple[Dataset, List[Tomogram]], None, None]:
+        logger.debug("ListingWidget._loadDatasets: %s", uri)
+        client = Client(uri)
+        for dataset in Dataset.find(client):
+            tomograms: List[Tomogram] = []
+            for run in dataset.runs:
+                for spacing in run.tomogram_voxel_spacings:
+                    tomograms.extend(spacing.tomograms)
+            yield dataset, tomograms
 
-    def _onDatasetLoaded(self, dataset: Dataset) -> None:
-        logger.debug("ListingWidget._onDatasetLoaded: %s", dataset.name)
-        text = f"{dataset.name} ({len(dataset.tomograms)})"
+    def _onDatasetLoaded(self, result: Tuple[Dataset, List[Tomogram]]) -> None:
+        dataset, tomograms = result
+        logger.debug("ListingWidget._onDatasetLoaded: %s", dataset.id)
+        text = f"{dataset.id} ({len(tomograms)})"
         item = QTreeWidgetItem((text,))
         item.setData(0, Qt.ItemDataRole.UserRole, dataset)
-        for s in dataset.tomograms:
-            tomogram_item = QTreeWidgetItem((s.name,))
-            tomogram_item.setData(0, Qt.ItemDataRole.UserRole, s)
+        for tomogram in tomograms:
+            tomogram_item = QTreeWidgetItem((tomogram.name,))
+            tomogram_item.setData(0, Qt.ItemDataRole.UserRole, tomogram)
             item.addChild(tomogram_item)
         _update_visible_items(item, self.tree.last_filter)
         self.tree.addTopLevelItem(item)

src/napari_cryoet_data_portal/_metadata_widget.py

@@ -5,10 +5,9 @@
     QVBoxLayout,
     QWidget,
 )
+from cryoet_data_portal import Dataset, Tomogram
 
-from napari_cryoet_data_portal._io import read_json
 from napari_cryoet_data_portal._logging import logger
-from napari_cryoet_data_portal._model import Dataset, Tomogram
 from napari_cryoet_data_portal._progress_widget import ProgressWidget
 from napari_cryoet_data_portal._vendored.superqt._searchable_tree_widget import (
     QSearchableTreeWidget,
@@ -39,7 +38,8 @@ def load(self, data: Union[Dataset, Tomogram]) -> None:
         """Loads the JSON metadata of the given dataset or tomogram."""
         logger.debug("MetadataWidget.load: %s", data)
         self._main.tree.clear()
-        self.setTitle(f"Metadata: {data.name}")
+        name = data.id if isinstance(data, Dataset) else data.name
+        self.setTitle(f"Metadata: {name}")
         self.show()
         self._progress.submit(data)
 
@@ -50,14 +50,7 @@ def cancel(self) -> None:
 
     def _loadMetadata(self, data: Union[Dataset, Tomogram]) -> Dict[str, Any]:
         logger.debug("MetadataWidget._loadMetadata: %s", data)
-        path = ""
-        if isinstance(data, Dataset):
-            path = data.metadata_path
-        elif isinstance(data, Tomogram):
-            path = data.tomogram_metadata_path
-        else:
-            raise AssertionError("Expected Dataset or Tomogram data")
-        return read_json(path)
+        return data.to_dict()
 
     def _onMetadataLoaded(self, metadata: Dict[str, Any]) -> None:
         logger.debug("MetadataWidget._onMetadataLoaded: %s", metadata)