Added tests

Author: tkakar

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.5.9"
+version = "3.6.0"
 authors = [
   { name="Mark Keller", email="[email protected]" },
 ]

src/vitessce/constants.py

@@ -164,6 +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"
     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

@@ -1229,6 +1229,7 @@ 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
 
         # For reference spec JSON with .h5ad files
         self._ref_path = ref_path
@@ -1250,11 +1251,15 @@ 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):
+                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):
+                self.is_zip = True
             # Store artifacts on AbstractWrapper.artifacts for downstream access,
             # e.g. in lamindb.save_vitessce_config
             if adata_artifact is not None:
@@ -1358,7 +1363,7 @@ def get_anndata_zarr(base_url):
                     options["refSpecUrl"] = self.get_ref_url(base_url, dataset_uid, obj_i)
 
                 obj_file_def = {
-                    "fileType": ft.ANNDATA_ZARR.value if not self.is_h5ad else ft.ANNDATA_H5AD.value,
+                    "fileType": ft.ANNDATA_ZIPPED_ZARR.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

@@ -75,6 +75,50 @@ def test_config_add_dataset():
         "initStrategy": "auto"
     }
 
+def test_config_add_anndata_zip_url():
+    vc = VitessceConfig(schema_version="1.0.15")
+    vc.add_dataset(name='My Dataset').add_object(
+        AnnDataWrapper(
+            adata_url="http://example.com/adata.h5ad.zarr.zip",
+            obs_set_paths=["obs/louvain"],
+        )
+    )
+
+    vc_dict = vc.to_dict()
+
+    assert vc_dict == {
+        "version": "1.0.15",
+        "name": "",
+        "description": "",
+        "datasets": [
+            {
+                'uid': 'A',
+                'name': 'My Dataset',
+                'files': [
+                    {
+                        "fileType": "anndata.zarr.zip",
+                        "url": "http://example.com/adata.h5ad.zarr.zip",
+                        "options": {
+                            "obsSets": [
+                                {
+                                    "name": "louvain",
+                                    "path": "obs/louvain",
+                                }
+                            ]
+                        }
+                    }
+                ]
+            }
+        ],
+        'coordinationSpace': {
+            'dataset': {
+                'A': 'A'
+            },
+        },
+        "layout": [],
+        "initStrategy": "auto"
+    }
+
 
 def test_config_add_anndata_url():
     vc = VitessceConfig(schema_version="1.0.15")

tests/test_wrappers.py

@@ -208,6 +208,23 @@ def test_obs_segmentations_ome_zarr(self):
             'url': 'http://localhost:8000/A/0/test.ome.zarr'
         })
 
+    def test_anndata_with_zip(self):
+        adata_path = data_path / 'test.h5ad.zarr.zip'
+        w = AnnDataWrapper(adata_path,
+                           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'])
+        w.local_dir_uid = 'anndata.zarr.zip'
+
+        file_def_creator = w.make_file_def_creator('A', 0)
+        file_def = file_def_creator('http://localhost:8000')
+        self.assertEqual(file_def, {'fileType': 'anndata.zarr.zip', 'url': 'http://localhost:8000/A/0/anndata.zarr.zip',
+                                    'options': {
+                                        'obsEmbedding': [{'path': 'obsm/X_umap', 'embeddingType': 'UMAP', 'dims': [0, 1]}],
+                                        'obsSets': [{'path': 'obs/CellType', 'name': 'Cell Type'}],
+                                        'obsLabels': [{'path': 'obs/CellLabel', 'obsLabelsType': 'Cell Label'}]
+                                    }})
+
     def test_anndata(self):
         adata_path = data_path / 'test.h5ad.zarr'
         w = AnnDataWrapper(adata_path,