Disable HGVS strict bounds checks

This is a workaround for some liftover failures: biocommons/hgvs#717
FHIR · Apr 2, 2024 · 14de3f1 · 14de3f1
1 parent 15d9c3b
commit 14de3f1
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diff --git a/app/__init__.py b/app/__init__.py
@@ -7,6 +7,8 @@
 # Disable the hgvs LRU cache to avoid blowing up memory
 # TODO: Revisit this, since this caching might not use a ton of memory.
 hgvs.global_config.lru_cache.maxsize = 0
+# Disable HGVS strict bounds checks as a workaround for liftover failures: https://github.com/biocommons/hgvs/issues/717
+hgvs.global_config.mapping.strict_bounds = False
 
 
 def create_app():

diff --git a/tests/integration_tests/test_normalize_variant_utility.py b/tests/integration_tests/test_normalize_variant_utility.py
@@ -12,3 +12,15 @@ def test_normalize_variant_utility(client):
     response = client.get(url)
 
     assert response.status_code == 200
+
+
+def test_normalize_variant_utility_transcript_ref_disagree_position_variant(client):
+    """
+    This is a specific corner case where liftover fails if HGVS strict bounds checks are enforced
+    Details here: https://github.com/biocommons/hgvs/issues/717
+    """
+    url = tu.normalize_variant_query('variant=NC_000001.10:g.145592073A>T')
+
+    response = client.get(url)
+
+    assert response.status_code == 200