From 6925ae4d2480c583c50cb308291fb8f156306fff Mon Sep 17 00:00:00 2001
From: asherpasha <asher.pasha@utoronto.ca>
Date: Mon, 3 Nov 2025 15:27:48 -0500
Subject: [PATCH] More fixes.

---
 api/resources/gaia.py | 58 ++++++++++++++++++++++++++-----------------
 1 file changed, 35 insertions(+), 23 deletions(-)

diff --git a/api/resources/gaia.py b/api/resources/gaia.py
index 4098a34..51ba417 100644
--- a/api/resources/gaia.py
+++ b/api/resources/gaia.py
@@ -19,24 +19,27 @@ def get(self, identifier=""):
 
         # Is it valid
         if BARUtils.is_gaia_alias(identifier):
+            query_ids = []
+            data = []
 
             # Check if alias exists
             # Note: This check can be done in on query, but optimizer is not using indexes for some reason
-            # Also, GAIA only uses the first result
             query = db.select(Aliases.genes_id, Aliases.alias).filter(Aliases.alias == identifier)
-            row = db.session.execute(query).fetchone()
+            rows = db.session.execute(query).fetchall()
 
-            if row:
-                # Alias exists. Get the genes_id
-                query_id = row.genes_id
+            if rows and len(rows) > 0:
+                # Alias exists. Get the genes_ids
+                for row in rows:
+                    query_ids.append(row.genes_id)
 
             else:
-                # Alias doesn't exist. Get the genes_id if it's locus or ncbi id
+                # Alias doesn't exist. Get the ids if it's locus or ncbi id
                 query = db.select(Genes.id).filter(or_(Genes.locus == identifier, Genes.geneid == identifier))
-                row = db.session.execute(query).fetchone()
+                rows = db.session.execute(query).fetchall()
 
-                if row:
-                    query_id = row.id
+                if rows and len(rows) > 0:
+                    for row in rows:
+                        query_ids.append(row.id)
                 else:
                     return BARUtils.error_exit("Nothing found"), 404
 
@@ -45,23 +48,32 @@ def get(self, identifier=""):
                 db.select(Genes.species, Genes.locus, Genes.geneid, func.json_arrayagg(Aliases.alias).label("aliases"))
                 .select_from(Genes)
                 .outerjoin(Aliases, Aliases.genes_id == Genes.id)
-                .filter(Genes.id == query_id)
+                .filter(Genes.id.in_(query_ids))
+                .group_by(Genes.species, Genes.locus, Genes.geneid)
             )
 
-            result = db.session.execute(query).fetchone()
+            rows = db.session.execute(query).fetchall()
 
-            # See if aliases exists
-            if result.aliases:
-                aliases = json.loads(result.aliases)
-            else:
-                aliases = []
-
-            data = {
-                "species": result.species,
-                "locus": result.locus,
-                "geneid": result.geneid,
-                "aliases": aliases,
-            }
+            if rows and len(rows) > 0:
+                for row in rows:
+
+                    # JSONify aliases
+                    if row.aliases:
+                        aliases = json.loads(row.aliases)
+                    else:
+                        aliases = []
+
+                    record = {
+                        "species": row.species,
+                        "locus": row.locus,
+                        "geneid": row.geneid,
+                        "aliases": aliases,
+                    }
+
+                    # Add the record to data
+                    data.append(record)
+
+            # Return final data
             return BARUtils.success_exit(data)
 
         else: