1 files changed, 73 insertions, 0 deletions
diff --git a/uploader/publications/models.py b/uploader/publications/models.py
new file mode 100644
index 0000000..3fc9542
--- /dev/null
+++ b/uploader/publications/models.py
@@ -0,0 +1,73 @@
+"""Module to handle persistence and retrieval of publication to/from MariaDB"""
+import logging
+
+from MySQLdb.cursors import DictCursor
+
+from gn_libs.mysqldb import Connection, debug_query
+
+logger = logging.getLogger(__name__)
+
+
+def fetch_phenotype_publications(
+        conn: Connection,
+        ids: tuple[tuple[int, int], ...]
+) -> tuple[dict, ...]:
+    """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())
+
+
+def create_new_publications(
+        conn: Connection,
+        publications: tuple[dict, ...]
+) -> tuple[dict, ...]:
+    if len(publications) > 0:
+        with conn.cursor(cursorclass=DictCursor) as cursor:
+            cursor.executemany(
+                ("INSERT INTO "
+                 "Publication( "
+                 "PubMed_ID, Abstract, Authors, Title, Journal, Volume, Pages, "
+                 "Month, Year"
+                 ") "
+                 "VALUES("
+                 "%(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"]
+            } for row in cursor.fetchall())
+        return tuple()
+
+
+def update_publications(conn: Connection , publications: tuple[dict, ...]) -> tuple[dict, ...]:
+    """Update details for multiple publications"""
+    if len(publications) > 0:
+        with conn.cursor(cursorclass=DictCursor) as cursor:
+            logger.debug("UPDATING PUBLICATIONS: %s", publications)
+            cursor.executemany(
+                ("UPDATE Publication SET "
+                 "PubMed_ID=%(pubmed_id)s, Abstract=%(abstract)s, "
+                 "Authors=%(authors)s, Title=%(title)s, Journal=%(journal)s, "
+                 "Volume=%(volume)s, Pages=%(pages)s, Month=%(month)s, "
+                 "Year=%(year)s "
+                 "WHERE Id=%(publication_id)s"),
+                publications)
+            debug_query(cursor, logger)
+            return publications
+        return tuple()
+    return tuple()