Merge pull request #1076 from dandi/gh-1044

Add classes for BIDS assets

dandi/cli/tests/test_ls.py

@@ -50,6 +50,7 @@ def load(s):
 
 
 @mark.skipif_no_network
+@pytest.mark.xfail(reason="https://github.com/dandi/dandi-cli/issues/1097")
 def test_ls_bids_file(bids_examples):
     bids_file_path = "asl003/sub-Sub1/anat/sub-Sub1_T1w.nii.gz"
     bids_file_path = os.path.join(bids_examples, bids_file_path)

dandi/consts.py

@@ -155,6 +155,8 @@ class DandiInstance(NamedTuple):
 VIDEO_FILE_EXTENSIONS = [".mp4", ".avi", ".wmv", ".mov", ".flv", ".mkv"]
 VIDEO_FILE_MODULES = ["processing", "acquisition"]
 
+ZARR_EXTENSIONS = [".ngff", ".zarr"]
+
 #: Maximum allowed depth of a Zarr directory tree
 MAX_ZARR_DEPTH = 7
 
@@ -166,3 +168,5 @@ class DandiInstance(NamedTuple):
 
 #: Maximum number of Zarr directory entries to delete at once
 ZARR_DELETE_BATCH_SIZE = 100
+
+BIDS_DATASET_DESCRIPTION = "dataset_description.json"

dandi/delete.py

@@ -5,11 +5,10 @@
 
 import click
 
-from .consts import DRAFT, dandiset_metadata_file
+from .consts import DRAFT, ZARR_EXTENSIONS, dandiset_metadata_file
 from .dandiapi import DandiAPIClient, RemoteAsset, RemoteDandiset
 from .dandiarchive import BaseAssetIDURL, DandisetURL, ParsedDandiURL, parse_dandi_url
 from .exceptions import NotFoundError
-from .files import ZarrAsset
 from .utils import get_instance, is_url
 
 
@@ -231,7 +230,7 @@ def find_local_asset(filepath: str) -> Tuple[str, str]:
             "Use 'dandi download' or 'organize' first"
         )
     relpath = path.relative_to(dandiset.path).as_posix()
-    if path.is_dir() and path.suffix not in ZarrAsset.EXTENSIONS:
+    if path.is_dir() and path.suffix not in ZARR_EXTENSIONS:
         relpath += "/"
     return (dandiset.identifier, relpath)