1 files changed, 25 insertions, 14 deletions
diff --git a/uploader/publications/models.py b/uploader/publications/models.py
index 7d2862d..dcfa02b 100644
--- a/uploader/publications/models.py
+++ b/uploader/publications/models.py
@@ -30,6 +30,7 @@ def create_new_publications(
         conn: Connection,
         publications: tuple[dict, ...]
 ) -> tuple[dict, ...]:
+    """Create new publications in the database."""
     if len(publications) > 0:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             cursor.executemany(
@@ -42,17 +43,13 @@ def create_new_publications(
                  "%(pubmed_id)s, %(abstract)s, %(authors)s, %(title)s, "
                  "%(journal)s, %(volume)s, %(pages)s, %(month)s, %(year)s"
                  ") "
-                 "ON DUPLICATE KEY UPDATE "
-                 "Abstract=VALUES(Abstract), Authors=VALUES(Authors), "
-                 "Title=VALUES(Title), Journal=VALUES(Journal), "
-                 "Volume=VALUES(Volume), Pages=VALUES(pages), "
-                 "Month=VALUES(Month), Year=VALUES(Year) "
                  "RETURNING *"),
                 publications)
             return tuple({
-                **row, "PublicationId": row["Id"]
+                **row, "publication_id": row["Id"]
             } for row in cursor.fetchall())
-        return tuple()
+
+    return tuple()
 
 
 def update_publications(conn: Connection , publications: tuple[dict, ...]) -> tuple[dict, ...]:
@@ -74,12 +71,25 @@ def update_publications(conn: Connection , publications: tuple[dict, ...]) -> tu
     return tuple()
 
 
-def fetch_publications(conn: Connection) -> Iterable[dict]:
-    """Fetch publications from the database."""
-    with conn.cursor(cursorclass=DictCursor) as cursor:
-        cursor.execute("SELECT * FROM Publication")
-        for row in cursor.fetchall():
-            yield dict(row)
+def delete_publications(conn: Connection , publications: tuple[dict, ...]):
+    """Delete multiple publications"""
+    publications = tuple(pub for pub in publications if bool(pub))
+    if len(publications) > 0:
+        _pub_ids = tuple(pub["Id"] for pub in publications)
+        _paramstr = ", ".join(["%s"] * len(_pub_ids))
+        _phenos_query = (
+            "SELECT PublicationId, COUNT(PhenotypeId) FROM PublishXRef "
+            f"WHERE PublicationId IN ({_paramstr}) GROUP BY PublicationId;")
+
+        with conn.cursor(cursorclass=DictCursor) as cursor:
+            cursor.execute(_phenos_query, _pub_ids)
+            _linked_phenos = cursor.fetchall()
+            if len(_linked_phenos) > 0:
+                raise Exception(# pylint: disable=[broad-exception-raised]
+                    "Cannot delete publications with linked phenotypes.")
+
+            cursor.execute(
+                f"DELETE FROM Publication WHERE Id IN ({_paramstr})", _pub_ids)
 
 
 def fetch_publication_by_id(conn: Connection, publication_id: int) -> dict:
@@ -87,7 +97,8 @@ def fetch_publication_by_id(conn: Connection, publication_id: int) -> dict:
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute("SELECT * FROM Publication WHERE Id=%s",
                        (publication_id,))
-        return dict(cursor.fetchone())
+        _res = cursor.fetchone()
+        return dict(_res) if _res else {}
 
 
 def fetch_publication_phenotypes(