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Handle schema v1.1.0 (#2002)

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Correctly display datasets that follow schema version 1.1.0
This commit is contained in:
Marcus Kinsella
2020-12-14 15:20:29 -08:00
committed by GitHub
parent 0b91371ea8
commit 46d02b1987
7 changed files with 132 additions and 9 deletions
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server/test/unit/common/test_corpora.py
+24
View File
@@ -76,6 +76,30 @@ class CorporaAPITest(unittest.TestCase):
some_fields["project_links"] = json.loads(some_fields["project_links"])
self.assertEqual(corpora_get_props_from_anndata(adata), some_fields)
def test_corpora_get_props_from_anndata_v110(self):
adata = self._get_h5ad()
if "version" in adata.uns:
del adata.uns["version"]
self.assertIsNone(corpora_get_props_from_anndata(adata))
# legit version, but missing required values
adata.uns["version"] = {"corpora_schema_version": "1.1.0", "corpora_encoding_version": "0.1.0"}
with self.assertRaises(KeyError):
corpora_get_props_from_anndata(adata)
# Metadata following schema 1.1.0, which removes some fields relative to 1.1.0
some_110_fields = {
"version": {"corpora_schema_version": "1.0.0", "corpora_encoding_version": "0.1.0"},
"title": "title",
"layer_descriptions": "layer_descriptions",
"organism": "organism",
"organism_ontology_term_id": "organism_ontology_term_id",
}
for k in some_110_fields:
adata.uns[k] = some_110_fields[k]
self.assertEqual(corpora_get_props_from_anndata(adata), some_110_fields)
def _get_h5ad(self):
return anndata.read_h5ad(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
server/test/unit/converters/test_h5ad_data_file.py
+1 -1
View File
@@ -254,7 +254,7 @@ class TestH5ADDataFile(unittest.TestCase):
for metadata_field in CorporaConstants.REQUIRED_SIMPLE_METADATA_FIELDS:
uns[metadata_field] = "random"
for metadata_field in CorporaConstants.REQUIRED_JSON_ENCODED_METADATA_FIELD:
for metadata_field in CorporaConstants.OPTIONAL_JSON_ENCODED_METADATA_FIELD:
uns[metadata_field] = json.dumps({"random_key": "random_value"})
# Need to carefully set the corpora schema versions in order for tests to pass.