From 8ab276d489c121c9f53bf9b55e20188acb744ea3 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 21 Jul 2023 08:36:44 +0300
Subject: Fetch a publication by its PubMed ID

---
 gn3/db/phenotypes.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

(limited to 'gn3')

diff --git a/gn3/db/phenotypes.py b/gn3/db/phenotypes.py
index a908c41..009dc1a 100644
--- a/gn3/db/phenotypes.py
+++ b/gn3/db/phenotypes.py
@@ -141,3 +141,13 @@ def fetch_publication_by_id(conn: DBConnection, publication_id: int) -> dict:
              "WHERE Id=%(publication_id)s"),
             {"publication_id": publication_id})
         return cursor.fetchone()
+
+def fetch_publication_by_pubmed_id(conn: DBConnection, pubmed_id: int) -> dict:
+    """Fetch the publication by its PUBMED ID."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cols = ', '.join(mapping_to_query_columns(publication_mapping))
+        cursor.execute(
+            (f"SELECT Id as id, {cols} FROM Publication "
+             "WHERE PubMed_Id=%(pubmed_id)s"),
+            {"pubmed_id": pubmed_id})
+        return cursor.fetchone()
-- 
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