Fetch existing publications from the database.

1 files changed, 14 insertions, 0 deletions

diff --git a/scripts/phenotypes_bulk_edit.py b/scripts/phenotypes_bulk_edit.py
index 8da3c77..72a901a 100644
--- a/scripts/phenotypes_bulk_edit.py
+++ b/scripts/phenotypes_bulk_edit.py
@@ -82,6 +82,20 @@ def descriptions_differences(file_data, db_data) -> dict[str, str]:
 
 
 def compute_differences(conn, file_contents, pheno_ids, pheno_xref_ids) -> tuple[tuple[dict, ...], tuple[dict, ...], tuple[dict, ...]]:
+def __fetch_publications__(conn, ids):
+    """Fetch publication from database by ID."""
+    paramstr = ",".join(["(%s, %s)"] * len(ids))
+    query = (
+        "SELECT "
+        "pxr.PhenotypeId, pxr.Id AS xref_id, pxr.PublicationId, pub.PubMed_ID "
+        "FROM PublishXRef AS pxr INNER JOIN Publication AS pub "
+        "ON pxr.PublicationId=pub.Id "
+        f"WHERE (pxr.PhenotypeId, pxr.Id) IN ({paramstr})")
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(query, tuple(item for row in ids for item in row))
+        return tuple(dict(row) for row in cursor.fetchall())
+
+
     """Compute differences between data in DB and edited data."""
     logger.info("Computing differences.")
     # 1. Basic Phenotype data differences