test passed

galaxyproject · Aug 7, 2024 · 18f9c8a · 18f9c8a
1 parent bbfac35
commit 18f9c8a
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Showing 3 changed files with 19 additions and 20 deletions.
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
@@ -1478,7 +1478,7 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
             dataset.metadata.url = anndata_file.attrs.get("url")
             dataset.metadata.doi = anndata_file.attrs.get("doi")
             dataset.metadata.creation_date = anndata_file.attrs.get("creation_date")
-            dataset.metadata.shape = anndata_file.attrs.get("shape", dataset.metadata.shape)
+            dataset.metadata.shape = anndata_file.attrs.get("shape")
             # none of the above appear to work in any dataset tested, but could be useful for
             # future AnnData datasets
             dataset.metadata.layers_count = len(anndata_file)
@@ -1574,7 +1574,7 @@ def _layercountsize(tmp, lennames=0):
                 dataset.metadata.shape = (int(dataset.metadata.obs_size), int(dataset.metadata.var_size))
 
     def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
-        if not dataset.dataset.purged:
+        if not dataset.file_name_ == None:
             tmp = dataset.metadata
 
             def _makelayerstrings(layer, count, names):
@@ -1596,7 +1596,7 @@ def _makelayerstrings(layer, count, names):
             peekstr += _makelayerstrings("uns", tmp.uns_count, tmp.uns_layers)
 
             dataset.peek = peekstr
-            dataset.blurb = f"Anndata file ({nice_size(dataset.get_size())})"
+            dataset.blurb = "Anndata file"
         else:
             dataset.peek = "file does not exist"
             dataset.blurb = "file purged from disk"
@@ -1605,7 +1605,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return f"Binary Anndata file ({nice_size(dataset.get_size())})"
+            return "Peek unavailable"
 
 
 @build_sniff_from_prefix

diff --git a/lib/galaxy/datatypes/test/anndata.h5ad b/lib/galaxy/datatypes/test/anndata.h5ad
diff --git a/test/unit/data/datatypes/test_h5ad_metadata.py b/test/unit/data/datatypes/test_h5ad_metadata.py
@@ -23,11 +23,8 @@ def test_h5ad_set_meta():
 
         ann.set_meta(dataset)
 
-        assert dataset.metadata.layers_count == "9"
-        assert dataset.metadata.layers_names == "['X', 'layers', 'obs', 'obsm', 'obsp', 'uns', 'var', 'varm', 'varp']"
-
-        assert ann.set_meta._layercountsize(dataset) == "['X', 'layers', 'obs', 'obsm', 'obsp', 'uns', 'var', 'varm', 'varp'], 9, 0"
-
+        assert dataset.metadata.layers_count == 9
+        assert dataset.metadata.layers_names == ['X', 'layers', 'obs', 'obsm', 'obsp', 'uns', 'var', 'varm', 'varp']
 
 
 def test_h5ad_set_peek():
@@ -42,15 +39,17 @@ def test_h5ad_set_peek():
 
         assert (
             dataset.peek
-            == """
-            [n_obs x n_vars]
-                640 x 11
-            [obs]: 2 layers
-                blobs, index
-            [var]: 1 layer
-                index
-            [obsm]: 0 layer
-            [varm]: 0 layer
-            [uns]: 0 layer
-            """
+            == 
+"""[n_obs x n_vars]
+    640 x 11
+[obs]: 2 layers
+    blobs, index
+[var]: 1 layer
+    index
+[obsm]: 2 layers
+    X_pca, X_umap
+[varm]: 1 layer
+    PCs
+[uns]: 1 layer
+    sample_data"""
         )