Merge pull request #3845 from broadinstitute/grch37-variant-search

properly handle 37 variant ids
broadinstitute · Jan 30, 2024 · a300f5b · a300f5b
2 parents 8b1e49e + 54776fb
commit a300f5b
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/hail_search/queries/mito.py b/hail_search/queries/mito.py
@@ -189,7 +189,7 @@ def _parse_variant_keys(self, variant_ids=None, **kwargs):
 
         return [
             hl.struct(
-                locus=hl.locus(f'chr{chrom}', pos, reference_genome=self.GENOME_VERSION),
+                locus=hl.locus(f'chr{chrom}' if self._should_add_chr_prefix() else chrom, pos, reference_genome=self.GENOME_VERSION),
                 alleles=[ref, alt],
             ) for chrom, pos, ref, alt in variant_ids
         ]

diff --git a/hail_search/test_search.py b/hail_search/test_search.py
@@ -644,7 +644,13 @@ async def test_variant_lookup(self):
         async with self.client.request('POST', '/lookup', json=body) as resp:
             self.assertEqual(resp.status, 404)
 
-        body.update({'variant_id': ['M', 4429, 'G', 'A'], 'data_type': 'MITO'})
+        body.update({'genome_version': 'GRCh37', 'variant_id': ['7', 143270172, 'A', 'G']})
+        async with self.client.request('POST', '/lookup', json=body) as resp:
+            self.assertEqual(resp.status, 200)
+            resp_json = await resp.json()
+        self.assertDictEqual(resp_json, {**GRCH37_VARIANT, 'familyGuids': [], 'genotypes': {}, 'genotypeFilters': ''})
+
+        body.update({'variant_id': ['M', 4429, 'G', 'A'], 'data_type': 'MITO', 'genome_version': 'GRCh38'})
         async with self.client.request('POST', '/lookup', json=body) as resp:
             self.assertEqual(resp.status, 200)
             resp_json = await resp.json()