Fix triple clinvar filter

CHANGELOG.md

@@ -19,6 +19,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Empty custom_images dicts in case load config do not crash
 - Tracks missing alignment files are now properly skipped on generating IGV views
 - ClinVar form to accept MedGen phenotypes
+- Filtering variants by ClinVar significance, CLINSIG Confident and ClinVar hits at the same time
 
 ## [4.90.1]
 ### Fixed

scout/adapter/mongo/query.py

@@ -329,11 +329,18 @@ def build_query(
                 secondary_terms = True
 
         if primary_terms is True:
-            clinsign_filter = self.clinsig_query(query, mongo_query)
+            clinsign_filter = self.clinsig_query(query)
 
         # Secondary, excluding filter criteria will hide variants in general,
         # but can be overridden by an including, major filter criteria
         # such as a Pathogenic ClinSig.
+
+        """
+        if criterion == "clinvar_tag":
+            mongo_secondary_query.append({"clnsig": {"$exists": True}})
+            mongo_secondary_query.append({"clnsig": {"$ne": None}})
+        """
+
         if secondary_terms is True:
             secondary_filter = self.secondary_query(query, mongo_query)
             # If there are no primary criteria given, all secondary criteria are added as a
@@ -404,60 +411,44 @@ def affected_inds_query(self, mongo_query, case_id, gt_query):
         ]:  # Consider situation where all individuals are unaffected
             mongo_query["samples"] = affected_query
 
-    def clinsig_query(self, query, mongo_query):
-        """Add clinsig filter values to the mongo query object
-
-        Args:
-            query(dict): a dictionary of query filters specified by the users
-            mongo_query(dict): the query that is going to be submitted to the database
-
-        Returns:
-            clinsig_query(dict): a dictionary with clinsig key-values
-
-        """
+    def clinsig_query(self, query: dict):
+        """Add clinsig filter values to the mongo query object"""
         LOG.debug("clinsig is a query parameter")
         trusted_revision_level = TRUSTED_REVSTAT_LEVEL
         rank = []
         str_rank = []
-        clnsig_query = {}
 
         for item in query["clinsig"]:
             rank.append(int(item))
             # search for human readable clinsig values in newer cases
             rank.append(CLINSIG_MAP[int(item)])
             str_rank.append(CLINSIG_MAP[int(item)])
 
-        if query.get("clinsig_confident_always_returned") is True:
-            LOG.debug("add CLINSIG filter with trusted_revision_level")
+        elem_match_or = {
+            "$or": [
+                {"value": {"$in": rank}},
+                {"value": re.compile("|".join(str_rank))},
+            ]
+        }
 
+        if query.get("clinsig_confident_always_returned") is True:
             clnsig_query = {
                 "clnsig": {
                     "$elemMatch": {
                         "$and": [
-                            {
-                                "$or": [
-                                    {"value": {"$in": rank}},
-                                    {"value": re.compile("|".join(str_rank))},
-                                ]
-                            },
+                            elem_match_or,
                             {"revstat": re.compile("|".join(trusted_revision_level))},
                         ]
                     }
                 }
             }
         else:
-            LOG.debug("add CLINSIG filter for rank: %s" % ", ".join(str(query["clinsig"])))
+            clnsig_query = {"clnsig": {"$elemMatch": elem_match_or}}
+
+        if query.get("clinvar_tag"):
+            clnsig_query["clnsig"]["$exists"] = True
+            clnsig_query["clnsig"]["$ne"] = None
 
-            clnsig_query = {
-                "clnsig": {
-                    "$elemMatch": {
-                        "$or": [
-                            {"value": {"$in": rank}},
-                            {"value": re.compile("|".join(str_rank))},
-                        ]
-                    }
-                }
-            }
         return clnsig_query
 
     def coordinate_filter(self, query, mongo_query):
@@ -777,10 +768,6 @@ def secondary_query(self, query, mongo_query, secondary_filter=None):
             if criterion == "mvl_tag":
                 mongo_secondary_query.append({"mvl_tag": {"$exists": True}})
 
-            if criterion == "clinvar_tag":
-                mongo_secondary_query.append({"clnsig": {"$exists": True}})
-                mongo_secondary_query.append({"clnsig": {"$ne": None}})
-
             if criterion == "cosmic_tag":
                 mongo_secondary_query.append({"cosmic_ids": {"$exists": True}})
                 mongo_secondary_query.append({"cosmic_ids": {"$ne": None}})

scout/constants/query_terms.py

@@ -53,7 +53,6 @@
     "somatic_score",
     "control_frequency",
     "mvl_tag",
-    "clinvar_tag",
     "cosmic_tag",
     "tumor_frequency",
     "fusion_score",