Merge pull request #499 from will-moore/ome_zarr_view_no_images

ome_zarr view doesn't try to check for images

Author: will-moore

docs/source/cli.rst

@@ -28,10 +28,13 @@ Local data::
 view
 ====
 
-Use the `ome_zarr` command to view Zarr data in the https://ome.github.io/ome-ngff-validator::
+Use the `ome_zarr` command to serve local Zarr data and view in the https://ome.github.io/ome-ngff-validator::
 
     ome_zarr view 6001240.zarr/
 
+    # Use -f or --force to open in browser even if no valid data is found
+    ome_zarr view 6001240.zarr/ -f
+
 finder
 ======
 

ome_zarr/cli.py

@@ -35,7 +35,7 @@ def info(args: argparse.Namespace) -> None:
 def view(args: argparse.Namespace) -> None:
     """Wrap the :func:`~ome_zarr.utils.view` method."""
     config_logging(logging.WARNING, args)
-    zarr_view(args.path, args.port)
+    zarr_view(args.path, args.port, force=args.force)
 
 
 def finder(args: argparse.Namespace) -> None:
@@ -133,6 +133,12 @@ def main(args: list[str] | None = None) -> None:
     parser_view.add_argument(
         "--port", type=int, default=8000, help="Port to serve the data (default: 8000)"
     )
+    parser_view.add_argument(
+        "--force",
+        "-f",
+        action="store_true",
+        help="Force open in browser. Don't check for OME-Zarr data first.",
+    )
     parser_view.set_defaults(func=view)
 
     # finder (open a dir of images in BioFile Finder in a browser)

ome_zarr/utils.py

@@ -73,21 +73,24 @@ def info(path: str, stats: bool = False) -> Iterator[Node]:
         yield node
 
 
-def view(input_path: str, port: int = 8000, dry_run: bool = False) -> None:
+def view(
+    input_path: str, port: int = 8000, dry_run: bool = False, force: bool = False
+) -> None:
     # serve the parent directory in a simple server with CORS. Open browser
     # dry_run is for testing, so we don't open the browser or start the server
 
-    zarrs = []
-    if (Path(input_path) / ".zattrs").exists() or (
-        Path(input_path) / "zarr.json"
-    ).exists():
-        zarrs = find_multiscales(Path(input_path))
-    if len(zarrs) == 0:
-        print(
-            f"No OME-Zarr images found in {input_path}. "
-            f"Try $ ome_zarr finder {input_path}"
-        )
-        return
+    if not force:
+        zarrs = []
+        if (Path(input_path) / ".zattrs").exists() or (
+            Path(input_path) / "zarr.json"
+        ).exists():
+            zarrs = find_multiscales(Path(input_path))
+        if len(zarrs) == 0:
+            print(
+                f"No OME-Zarr images found in {input_path}. "
+                f"Try $ ome_zarr finder {input_path} or use -f to force open in browser."
+            )
+            return
 
     parent_dir, image_name = os.path.split(input_path)
     if len(image_name) == 0:

tests/test_cli.py

@@ -153,6 +153,10 @@ def _rotate_and_test(self, *hierarchy: Path, reverse: bool = True):
             self._rotate_and_test(*list(secondpass), reverse=False)
 
     def test_view(self):
+        # view empty dir for code coverage
+        view(str(self.path), 8000, True)
+        view(str(self.path), 8000, True, force=True)
+
         filename = f"{self.path}-4"
         main(["create", "--method=astronaut", filename])
         # CLI doesn't support the dry_run option yet