implement NGFF source validation (#136)

Implement NGFF source validation --------- Co-authored-by: Martin Schorb <[email protected]>
mobie · Mar 5, 2024 · d1ac181 · d1ac181
1 parent 7613641
commit d1ac181
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/mobie/validation/metadata.py b/mobie/validation/metadata.py
@@ -1,3 +1,4 @@
+import json
 import os
 
 # from elf.io import open_file
@@ -21,10 +22,12 @@ def _check_bdv_n5_s3(xml, assert_true):
 
 def _check_ome_zarr_s3(address, name, assert_true, assert_equal, channel):
     try:
-        load_json_from_s3(os.path.join(address, ".zattrs"))
+        zattrs = load_json_from_s3(os.path.join(address, ".zattrs"))
     except Exception:
         assert_true(False, f"Can't find ome.zarr..s3file at {address}")
 
+    validate_with_schema(zattrs, "NGFF")
+
     # we disable the name check for the time being since it seems to not be necessary,
     # AND restricting the name in this fashion prevents embedding existing ome.zarr files in mobie projects
     #  if channel is None:
@@ -63,6 +66,14 @@ def bdv_check():
         path = os.path.join(dataset_folder, storage["relativePath"])
         assert_true(os.path.exists(path), f"Could not find data for {name} at {path}")
 
+        attr_path = os.path.join(path, ".zattrs")
+        assert_true(os.path.exists(attr_path), f"Could not find metadata for {name} at {path}")
+
+        with open(attr_path) as f:
+            zattrs = json.load(f)
+
+        validate_with_schema(zattrs, "NGFF")
+
         # we disable the name check for the time being since it seems to not be necessary,
         # AND restricting the name in this fashion prevents embedding existing ome.zarr files in mobie projects
         # with open_file(path, "r", ext=".zarr") as f:

diff --git a/mobie/validation/utils.py b/mobie/validation/utils.py
@@ -13,6 +13,7 @@
     "source": "https://raw.githubusercontent.com/mobie/mobie.github.io/master/schema/source.schema.json",
     "view": "https://raw.githubusercontent.com/mobie/mobie.github.io/master/schema/view.schema.json",
     "views": "https://raw.githubusercontent.com/mobie/mobie.github.io/master/schema/views.schema.json",
+    "NGFF": "https://raw.githubusercontent.com/ome/ngff/main/0.4/schemas/image.schema"
 }