Outliers query inclusive of missing fields

CHANGELOG.md

@@ -20,6 +20,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Tests for cli command to update VCF files not running (#5888)
 - Gene in panels search results broken layout - overflow when a panel has many panel versions containing the gene (#5899)
 - ACMG evaluation PDF export, both style and colors (#5879)
+- Include outliers with missing p-value fields in filtering logic (#5903)
 
 ## [4.106]
 ### Added

scout/adapter/mongo/query.py

@@ -582,9 +582,6 @@ def secondary_query(self, query: dict) -> list:
 
         if query.get("padjust") or query.get("p_adjust_gene"):
             mongo_secondary_query.append(_get_outlier_query(query))
-            LOG.info(
-                f"using padjust for filtering - query was {query}, secondary filter is {mongo_secondary_query}"
-            )
 
         for criterion in SECONDARY_CRITERIA:
             if not query.get(criterion):
@@ -849,9 +846,16 @@ def _get_outlier_query(query: dict) -> dict:
 
     outlier_padjust_query = {"$or": []}
 
+    mutual_exclusion = {
+        "padjust": "p_adjust_gene",
+        "p_adjust_gene": "padjust",
+    }
+
     for pval_name in {"padjust", "p_adjust_gene"}:
-        if pval := query.get(pval_name):
-            pval_struct = {pval_name: {"$lt": pval}}
+        provided_pval = query.get(pval_name)
+
+        if provided_pval is not None:
+            pval_struct = {pval_name: {"$lt": provided_pval}}
 
             if (abs_delta_psi := query.get("delta_psi")) and pval_name == "p_adjust_gene":
                 pval_struct = {
@@ -866,7 +870,12 @@ def _get_outlier_query(query: dict) -> dict:
                     ]
                 }
 
-            outlier_padjust_query["$or"].append(pval_struct)
+            outlier_padjust_query["$or"].append(
+                {"$and": [pval_struct, {mutual_exclusion[pval_name]: {"$exists": False}}]}
+            )
+
+        else:
+            outlier_padjust_query["$or"].append({pval_name: {"$exists": False}})
 
     return outlier_padjust_query