Removing display_hgmd_public_membership (varfish-org#363)

HISTORY.rst

@@ -98,6 +98,7 @@ Full Change List
 - DgvSvs and DgvGoldStandardSvs are two different data sources now
 - Adding deep linking into case details tab (#344)
 - Allowing direct update of variant annotations and ACMG ratings on case annotations details (#344)
+- Removing `display_hgmd_public_membership` (#363)
 
 -------
 v0.23.9

variants/forms.py

@@ -1098,7 +1098,6 @@ def __init__(self, *args, **kwargs):
     def clean(self):
         """Translate effect field names into ``effects`` key list"""
         cleaned_data = super().clean()
-        cleaned_data["display_hgmd_public_membership"] = True
         return cleaned_data
 
 

variants/queries.py

@@ -447,29 +447,18 @@ def __init__(self, *args, **kwargs):
             .lateral("hgmd_subquery")
         )
 
-    def _get_skip_query(self):
-        return not self.kwargs.get("require_in_hgmd_public") and not self.kwargs.get(
-            "display_hgmd_public_membership"
-        )
-
     def extend_fields(self, _query_parts):
-        if self._get_skip_query():
-            return []
         return [
             func.coalesce(self.subquery.c.hgmd_public_overlap, 0).label("hgmd_public_overlap"),
             func.coalesce(self.subquery.c.hgmd_accession, "").label("hgmd_accession"),
         ]
 
     def extend_selectable(self, query_parts):
-        if self._get_skip_query():
-            return query_parts.selectable
         return query_parts.selectable.outerjoin(self.subquery, true())
 
 
 class ExtendQueryPartsHgmdJoinAndFilter(ExtendQueryPartsHgmdJoin):
     def extend_conditions(self, _query_parts):
-        if self._get_skip_query():
-            return []
         if self.kwargs["require_in_hgmd_public"]:
             return [column("hgmd_public_overlap") > 0]
         return []

variants/tests/factories.py

@@ -81,7 +81,6 @@ class FormDataFactoryBase:
     transcripts_noncoding: bool = True
     remove_if_in_dbsnp: bool = False
     require_in_hgmd_public: bool = False
-    display_hgmd_public_membership: bool = False
     require_in_clinvar: bool = False
     clinvar_include_benign: bool = False
     clinvar_include_likely_benign: bool = False

variants/tests/test_queries.py

@@ -4408,34 +4408,12 @@ def setUp(self):
             end=self.small_vars[1].start,
         )
 
-    def test_no_hgmd_query(self):
-        self.run_query(
-            CasePrefetchQuery,
-            {"require_in_hgmd_public": False, "display_hgmd_public_membership": False},
-            2,
-        )
-
-    def test_require_in_hgmd_query(self):
-        self.run_query(
-            CasePrefetchQuery,
-            {"require_in_hgmd_public": True, "display_hgmd_public_membership": False},
-            1,
-        )
-
     def test_display_hgmd_membership_query(self):
-        res = self.run_query(
-            CasePrefetchQuery,
-            {"require_in_hgmd_public": False, "display_hgmd_public_membership": True},
-            2,
-        )
+        res = self.run_query(CasePrefetchQuery, {"require_in_hgmd_public": False}, 2,)
         self.assertEqual(res[1].hgmd_accession, self.hgmd.variation_name)
 
     def test_require_in_hgmd_and_display_membership_query(self):
-        res = self.run_query(
-            CasePrefetchQuery,
-            {"require_in_hgmd_public": True, "display_hgmd_public_membership": True},
-            1,
-        )
+        res = self.run_query(CasePrefetchQuery, {"require_in_hgmd_public": True}, 1,)
         self.assertEqual(res[0].hgmd_accession, self.hgmd.variation_name)