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https://github.com/chanzuckerberg/cellxgene.git
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59f989d26f
* initial support for corpora schema conventions * remove debugging print * add corpora util module * tests * lint * PR review edits * PR changes * more PR changes * more PR chnages * PR fixes * formatting * PR updates * lint * PR review
74 lines
2.9 KiB
Python
74 lines
2.9 KiB
Python
import unittest
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import anndata
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import json
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from server.common.corpora import (
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corpora_get_versions_from_anndata,
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corpora_is_version_supported,
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corpora_get_props_from_anndata,
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)
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from server.test import PROJECT_ROOT
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class CorporaAPITest(unittest.TestCase):
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def test_corpora_get_versions_from_anndata(self):
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adata = self._get_h5ad()
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if "version" in adata.uns:
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del adata.uns["version"]
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self.assertIsNone(corpora_get_versions_from_anndata(adata))
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# something bogus
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adata.uns["version"] = 99
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self.assertIsNone(corpora_get_versions_from_anndata(adata))
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# something legit
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adata.uns["version"] = {"corpora_schema_version": "0.0.0", "corpora_encoding_version": "9.9.9"}
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self.assertEqual(corpora_get_versions_from_anndata(adata), ["0.0.0", "9.9.9"])
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def test_corpora_is_version_supported(self):
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self.assertTrue(corpora_is_version_supported("1.0.0", "0.1.0"))
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self.assertFalse(corpora_is_version_supported("0.0.0", "0.1.0"))
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self.assertFalse(corpora_is_version_supported("1.0.0", "0.0.0"))
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def test_corpora_get_props_from_anndata(self):
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adata = self._get_h5ad()
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if "version" in adata.uns:
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del adata.uns["version"]
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self.assertIsNone(corpora_get_props_from_anndata(adata))
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# something bogus
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adata.uns["version"] = 99
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self.assertIsNone(corpora_get_props_from_anndata(adata))
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# unsupported version, but missing required values
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adata.uns["version"] = {"corpora_schema_version": "99.0.0", "corpora_encoding_version": "32.1.0"}
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with self.assertRaises(ValueError):
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corpora_get_props_from_anndata(adata)
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# legit version, but missing required values
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adata.uns["version"] = {"corpora_schema_version": "1.0.0", "corpora_encoding_version": "0.1.0"}
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with self.assertRaises(KeyError):
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corpora_get_props_from_anndata(adata)
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some_fields = {
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"version": {"corpora_schema_version": "1.0.0", "corpora_encoding_version": "0.1.0"},
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"title": "title",
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"layer_descriptions": "layer_descriptions",
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"organism": "organism",
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"organism_ontology_term_id": "organism_ontology_term_id",
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"project_name": "project_name",
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"project_description": "project_description",
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"contributors": json.dumps([{"contributors": "contributors"}]),
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"project_links": json.dumps([{"link_name": "link_name", "link_url": "link_url", "link_type": "SUMMARY"}]),
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}
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for k in some_fields:
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adata.uns[k] = some_fields[k]
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some_fields["contributors"] = json.loads(some_fields["contributors"])
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some_fields["project_links"] = json.loads(some_fields["project_links"])
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self.assertEqual(corpora_get_props_from_anndata(adata), some_fields)
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def _get_h5ad(self):
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return anndata.read_h5ad(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
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