add tests and fix bugs

broadinstitute · Feb 13, 2024 · 0b3a872 · 0b3a872
1 parent 03332b0
commit 0b3a872
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Showing 2 changed files with 16 additions and 1 deletion.
diff --git a/hail_search/queries/sv.py b/hail_search/queries/sv.py
@@ -76,7 +76,7 @@ def _parse_annotations(self, annotations, *args, **kwargs):
 
     def _get_family_passes_quality_filter(self, quality_filter, parsed_annotations=None, **kwargs):
         passes_quality = super()._get_family_passes_quality_filter(quality_filter)
-        if not parsed_annotations[NEW_SV_FIELD]:
+        if not (parsed_annotations or {}).get(NEW_SV_FIELD):
             return passes_quality
 
         entries_has_new_call = lambda entries: entries.any(lambda x: x.concordance.new_call)

diff --git a/hail_search/test_search.py b/hail_search/test_search.py
@@ -662,6 +662,11 @@ async def test_variant_lookup(self):
             resp_json = await resp.json()
         self.assertDictEqual(resp_json, {**SV_VARIANT4, 'familyGuids': [], 'genotypes': {}, 'genotypeFilters': ''})
 
+        async with self.client.request('POST', '/lookup', json={**body, 'sample_data': SV_WGS_SAMPLE_DATA['SV_WGS']}) as resp:
+            self.assertEqual(resp.status, 200)
+            resp_json = await resp.json()
+        self.assertDictEqual(resp_json, SV_VARIANT4)
+
         body.update({'variant_id': 'suffix_140608_DUP', 'data_type': 'SV_WES'})
         async with self.client.request('POST', '/lookup', json=body) as resp:
             self.assertEqual(resp.status, 200)
@@ -670,6 +675,16 @@ async def test_variant_lookup(self):
             **GCNV_VARIANT4, 'numExon': 8, 'end': 38736268, 'familyGuids': [], 'genotypes': {}, 'genotypeFilters': '',
         })
 
+        async with self.client.request('POST', '/lookup', json={**body, 'sample_data': EXPECTED_SAMPLE_DATA['SV_WES']}) as resp:
+            self.assertEqual(resp.status, 200)
+            resp_json = await resp.json()
+        self.assertDictEqual(resp_json, {
+            **GCNV_VARIANT4, 'numExon': 8, 'end': 38736268, 'genotypes': {
+                individual: {k: v for k, v in genotype.items() if k not in {'start', 'end', 'numExon', 'geneIds'}}
+                for individual, genotype in GCNV_VARIANT4['genotypes'].items()
+            }
+        })
+
     async def test_frequency_filter(self):
         sv_callset_filter = {'sv_callset': {'af': 0.05}}
         await self._assert_expected_search(