Save/Create new phenotypes in the database.

1 files changed, 24 insertions, 1 deletions

diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index 9ff89ae..fe4ccac 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -1,12 +1,13 @@
 """Database and utility functions for phenotypes."""
 import logging
-from typing import Optional
 from functools import reduce
 from datetime import datetime
+from typing import Optional, Iterable
 
 import MySQLdb as mdb
 from MySQLdb.cursors import Cursor, DictCursor
 
+from functional_tools import take
 from gn_libs.mysqldb import debug_query
 
 logger = logging.getLogger(__name__)
@@ -287,3 +288,25 @@ def phenotypes_data_by_ids(
         debug_query(cursor, logger)
         return tuple(
             reduce(__organise_by_phenotype__, cursor.fetchall(), {}).values())
+
+
+def create_new_phenotypes(conn: mdb.Connection,
+                          phenotypes: Iterable[dict]) -> tuple[dict, ...]:
+    """Add entirely new phenotypes to the database."""
+    _phenos = tuple()
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        for batch in take(phenotypes, 1000):
+            cursor.executemany(
+                ("INSERT INTO "
+                 "Phenotypes(Pre_publication_description, Original_description, Units, Authorized_Users) "
+                 "VALUES (%(id)s, %(description)s, %(units)s, 'robwilliams') "
+                 "RETURNING *"),
+                tuple(batch))
+            _phenos = _phenos + tuple({
+                "phenotype_id": row["Id"],
+                "id": row["Pre_publication_description"],
+                "description": row["Original_description"],
+                "units": row["Units"]
+            } for row in cursor.fetchall())
+
+    return _phenos