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-5
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3 files changed

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src/vitessce/wrappers.py

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1274,7 +1274,6 @@ def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_arti
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12751275
self.local_dir_uid = make_unique_filename(".adata.zarr")
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self.local_file_uid = make_unique_filename(".h5ad")
1277-
self.local_file_uid_zarr = make_unique_filename('.zarr.zip')
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self.local_ref_uid = make_unique_filename(".ref.json")
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12801279
self._expression_matrix = obs_feature_matrix_path
@@ -1362,7 +1361,6 @@ def get_anndata_zarr(base_url):
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if len(options.keys()) > 0:
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if self.is_h5ad:
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options["refSpecUrl"] = self.get_ref_url(base_url, dataset_uid, obj_i)
1365-
print(ft.ANNDATA_ZIPPED_ZARR.value)
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obj_file_def = {
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"fileType": ft.ANNDATA_ZIPPED_ZARR.value if self.is_zip else ft.ANNDATA_H5AD.value if self.is_h5ad else ft.ANNDATA_ZARR.value,
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"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),

tests/test_config.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -75,11 +75,12 @@ def test_config_add_dataset():
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"initStrategy": "auto"
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}
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78+
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def test_config_add_anndata_zip_url():
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vc = VitessceConfig(schema_version="1.0.15")
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vc.add_dataset(name='My Dataset').add_object(
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AnnDataWrapper(
82-
adata_url="http://example.com/adata.h5ad.zarr.zip",
83+
adata_url="http://example.com/adata.zarr.zip",
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obs_set_paths=["obs/louvain"],
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)
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)
@@ -97,7 +98,7 @@ def test_config_add_anndata_zip_url():
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'files': [
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{
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"fileType": "anndata.zarr.zip",
100-
"url": "http://example.com/adata.h5ad.zarr.zip",
101+
"url": "http://example.com/adata.zarr.zip",
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"options": {
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"obsSets": [
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{

tests/test_wrappers.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -209,7 +209,7 @@ def test_obs_segmentations_ome_zarr(self):
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})
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211211
def test_anndata_with_zip(self):
212-
adata_path = data_path / 'test.h5ad.zarr.zip'
212+
adata_path = data_path / 'test.zarr.zip'
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w = AnnDataWrapper(adata_path,
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obs_set_paths=['obs/CellType'], obs_set_names=['Cell Type'],
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obs_labels_names=['Cell Label'], obs_labels_paths=['obs/CellLabel'],

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