Used is_zip as param

Author: tkakar

src/vitessce/constants.py

@@ -164,7 +164,7 @@ class FileType(DocEnum):
     ANNDATA_ZARR = "anndata.zarr", "Joint file type for AnnData objects"
     SPATIALDATA_ZARR = "spatialdata.zarr", "Joint file type for SpatialData objects"
     ANNDATA_H5AD = "anndata.h5ad", "Joint file type for AnnData objects"
-    ANNDATA_ZIPPED_ZARR = "anndata.zarr.zip", "Joint file type for AnnData objects that are zipped together"
+    ANNDATA_ZARR_ZIP = "anndata.zarr.zip", "Joint file type for AnnData object in a Zarr directory store that has been zipped"
     OBS_EMBEDDING_CSV = 'obsEmbedding.csv', "File type for obsEmbedding values stored in a CSV file"
     OBS_LOCATIONS_CSV = 'obsLocations.csv', "File type for obsLocations values stored in a CSV file"
     OBS_LABELS_CSV = 'obsLabels.csv', "File type for obsLabels values stored in a CSV file"

src/vitessce/wrappers.py

@@ -1192,7 +1192,7 @@ def raise_error_if_more_than_one(inputs):
 
 
 class AnnDataWrapper(AbstractWrapper):
-    def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_artifact=None, ref_path=None, ref_url=None, ref_artifact=None, obs_feature_matrix_path=None, feature_filter_path=None, initial_feature_filter_path=None, obs_set_paths=None, obs_set_names=None, obs_locations_path=None, obs_segmentations_path=None, obs_embedding_paths=None, obs_embedding_names=None, obs_embedding_dims=None, obs_spots_path=None, obs_points_path=None, feature_labels_path=None, obs_labels_path=None, convert_to_dense=True, coordination_values=None, obs_labels_paths=None, obs_labels_names=None, **kwargs):
+    def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_artifact=None, ref_path=None, ref_url=None, ref_artifact=None, obs_feature_matrix_path=None, feature_filter_path=None, initial_feature_filter_path=None, obs_set_paths=None, obs_set_names=None, obs_locations_path=None, obs_segmentations_path=None, obs_embedding_paths=None, obs_embedding_names=None, obs_embedding_dims=None, obs_spots_path=None, obs_points_path=None, feature_labels_path=None, obs_labels_path=None, convert_to_dense=True, coordination_values=None, obs_labels_paths=None, obs_labels_names=None, is_zip=None, **kwargs):
         """
         Wrap an AnnData object by creating an instance of the ``AnnDataWrapper`` class.
 
@@ -1220,6 +1220,7 @@ def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_arti
         :param list[str] obs_labels_names: The optional display names of columns containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store.
         :param bool convert_to_dense: Whether or not to convert `X` to dense the zarr store (dense is faster but takes more disk space).
         :param coordination_values: Coordination values for the file definition.
+        :param is_zip: Boolean indicating whether the Zarr store is in a zipped format.
         :type coordination_values: dict or None
         :param \\*\\*kwargs: Keyword arguments inherited from :class:`~vitessce.wrappers.AbstractWrapper`
         """
@@ -1229,7 +1230,7 @@ def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_arti
         self._adata_url = adata_url
         self._adata_store = adata_store
         self._adata_artifact = adata_artifact
-        self.is_zip = False
+        self.is_zip = is_zip
 
         # For reference spec JSON with .h5ad files
         self._ref_path = ref_path
@@ -1251,14 +1252,13 @@ def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_arti
             self.is_remote = False
             self.is_store = False
             self.zarr_folder = 'anndata.zarr'
-            if '.zip' in str(adata_path):
+            if is_zip is not None and '.zip' in str(adata_path):
                 self.is_zip = True
-                # self.zarr_folder = 'anndata.zarr.zip'
         elif adata_url is not None or adata_artifact is not None:
             self.is_remote = True
             self.is_store = False
             self.zarr_folder = None
-            if '.zip' in str(adata_url):
+            if is_zip is not None and '.zip' in str(adata_url):
                 self.is_zip = True
             # Store artifacts on AbstractWrapper.artifacts for downstream access,
             # e.g. in lamindb.save_vitessce_config
@@ -1362,7 +1362,7 @@ def get_anndata_zarr(base_url):
                 if self.is_h5ad:
                     options["refSpecUrl"] = self.get_ref_url(base_url, dataset_uid, obj_i)
                 obj_file_def = {
-                    "fileType": ft.ANNDATA_ZIPPED_ZARR.value if self.is_zip else ft.ANNDATA_H5AD.value if self.is_h5ad else ft.ANNDATA_ZARR.value,
+                    "fileType": ft.ANNDATA_ZARR_ZIP.value if self.is_zip else ft.ANNDATA_H5AD.value if self.is_h5ad else ft.ANNDATA_ZARR.value,
                     "url": self.get_zarr_url(base_url, dataset_uid, obj_i) if not self.is_h5ad else self.get_h5ad_url(base_url, dataset_uid, obj_i),
                     "options": options
                 }

tests/test_config.py

@@ -82,6 +82,7 @@ def test_config_add_anndata_zip_url():
         AnnDataWrapper(
             adata_url="http://example.com/adata.zarr.zip",
             obs_set_paths=["obs/louvain"],
+            is_zip=True
         )
     )
 

tests/test_wrappers.py

@@ -211,6 +211,7 @@ def test_obs_segmentations_ome_zarr(self):
     def test_anndata_with_zip(self):
         adata_path = data_path / 'test.zarr.zip'
         w = AnnDataWrapper(adata_path,
+                           is_zip=True,
                            obs_set_paths=['obs/CellType'], obs_set_names=['Cell Type'],
                            obs_labels_names=['Cell Label'], obs_labels_paths=['obs/CellLabel'],
                            obs_embedding_paths=['obsm/X_umap'], obs_embedding_names=['UMAP'])