Merge pull request #1331 from dandi/bf-1307

Fix uploading Zarr within a BIDS dataset

Author: yarikoptic

dandi/dandiapi.py

@@ -1450,7 +1450,10 @@ def get_content_url(
                     else:
                         break
         except requests.HTTPError as e:
-            url = e.request.url
+            if e.request is not None and isinstance(e.request.url, str):
+                url = e.request.url
+            else:
+                raise  # reraise since we need to figure out how to handle such a case
         if strip_query:
             url = urlunparse(urlparse(url)._replace(query=""))
         return url

dandi/files/bids.py

@@ -235,7 +235,7 @@ def get_metadata(
         )
 
 
-class ZarrBIDSAsset(BIDSAsset, ZarrAsset):
+class ZarrBIDSAsset(ZarrAsset, BIDSAsset):
     """
     .. versionadded:: 0.46.0
 

dandi/tests/fixtures.py

@@ -628,6 +628,22 @@ def bids_nwb_dandiset(
     return new_dandiset
 
 
+# TODO: refactor: avoid duplication and come up with some fixture helper which would
+# just need specify bids example name
+@pytest.fixture()
+def bids_zarr_dandiset(
+    new_dandiset: SampleDandiset, bids_examples: Path
+) -> SampleDandiset:
+    shutil.copytree(
+        bids_examples / "micr_SEMzarr",
+        new_dandiset.dspath,
+        dirs_exist_ok=True,
+        ignore=shutil.ignore_patterns(dandiset_metadata_file),
+    )
+    (new_dandiset.dspath / "CHANGES").write_text("0.1.0 2014-11-03\n")
+    return new_dandiset
+
+
 @pytest.fixture()
 def bids_dandiset_invalid(
     new_dandiset: SampleDandiset, bids_error_examples: Path

dandi/tests/test_upload.py

@@ -292,6 +292,19 @@ def test_upload_zarr(new_dandiset: SampleDandiset) -> None:
     new_dandiset.upload()
 
 
+# identical to above, but different scenaior/fixture and path. TODO: avoid duplication
+def test_upload_bids_zarr(bids_zarr_dandiset: SampleDandiset) -> None:
+    bids_zarr_dandiset.upload()
+    assets = list(bids_zarr_dandiset.dandiset.get_assets())
+    assert len(assets) > 10  # it is a bigish dataset
+    (asset,) = [a for a in assets if a.path.endswith(".zarr")]
+    assert isinstance(asset, RemoteZarrAsset)
+    assert asset.asset_type is AssetType.ZARR
+    assert asset.path.endswith(".zarr")
+    # Test that uploading again without any changes works:
+    bids_zarr_dandiset.upload()
+
+
 def test_upload_different_zarr(tmp_path: Path, zarr_dandiset: SampleDandiset) -> None:
     asset = zarr_dandiset.dandiset.get_asset_by_path("sample.zarr")
     assert isinstance(asset, RemoteZarrAsset)