Merge pull request #20425 from jdavcs/25.0_trigger

[25.0] Update triggers

Author: mvdbeek

lib/galaxy/model/migrations/alembic/versions_gxy/a91ea1d97111_update_trigger_to_use_clock_timestamp_.py

@@ -0,0 +1,77 @@
+"""Update postgresql trigger to use clock_timestamp function
+
+NOTE: This migration will not be applied on SQLIte.
+
+Revision ID: a91ea1d97111
+Revises: f070559879f1
+Create Date: 2025-06-09 12:21:53.427419
+
+"""
+
+from alembic import op
+
+from galaxy.model.migrations.util import _is_sqlite
+
+# revision identifiers, used by Alembic.
+revision = "a91ea1d97111"
+down_revision = "f070559879f1"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    if not _is_sqlite():
+        create_functions_and_triggers("clock_timestamp()")
+
+
+def downgrade():
+    if not _is_sqlite():
+        create_functions_and_triggers("CURRENT_TIMESTAMP")
+
+
+def create_functions_and_triggers(timestamp):
+    version_info = op.get_bind().engine.dialect.server_version_info
+    # For offline mode (version_info is None), we assume that version > 10
+    if version_info and version_info[0] > 10 or not version_info:
+        trigger_fn = statement_trigger_fn
+    else:
+        trigger_fn = row_trigger_fn
+
+    for id_field in ["history_id", "id"]:
+        function_name = f"fn_audit_history_by_{id_field}"
+        stmt = trigger_fn(function_name, id_field, timestamp)
+        op.execute(stmt)
+
+
+def statement_trigger_fn(function_name, id_field, timestamp):
+    return f"""
+        CREATE OR REPLACE FUNCTION {function_name}()
+            RETURNS TRIGGER
+            LANGUAGE 'plpgsql'
+        AS $BODY$
+            BEGIN
+                INSERT INTO history_audit (history_id, update_time)
+                SELECT DISTINCT {id_field}, {timestamp} AT TIME ZONE 'UTC'
+                FROM new_table
+                WHERE {id_field} IS NOT NULL
+                ON CONFLICT DO NOTHING;
+                RETURN NULL;
+            END;
+        $BODY$
+    """
+
+
+def row_trigger_fn(function_name, id_field, timestamp):
+    return f"""
+        CREATE OR REPLACE FUNCTION {function_name}()
+            RETURNS TRIGGER
+            LANGUAGE 'plpgsql'
+        AS $BODY$
+            BEGIN
+                INSERT INTO history_audit (history_id, update_time)
+                VALUES (NEW.{id_field}, {timestamp} AT TIME ZONE 'UTC')
+                ON CONFLICT DO NOTHING;
+                RETURN NULL;
+            END;
+        $BODY$
+    """

lib/galaxy/model/migrations/dbscript.py

@@ -46,8 +46,8 @@
     "24.1": "04288b6a5b25",
     "release_24.2": "a4c3ef999ab5",
     "24.2": "a4c3ef999ab5",
-    "release_25.0": "f070559879f1",
-    "25.0": "f070559879f1",
+    "release_25.0": "a91ea1d97111",
+    "25.0": "a91ea1d97111",
 }
 
 

lib/galaxy/model/triggers/history_update_time_field.py

@@ -1,4 +1,4 @@
-from galaxy.model.triggers.utils import execute_statements
+from sqlalchemy import DDL
 
 # function name prefix
 fn_prefix = "fn_audit_history_by"
@@ -56,7 +56,7 @@ def statement_trigger_fn(id_field):
             AS $BODY$
                 BEGIN
                     INSERT INTO history_audit (history_id, update_time)
-                    SELECT DISTINCT {id_field}, CURRENT_TIMESTAMP AT TIME ZONE 'UTC'
+                    SELECT DISTINCT {id_field}, clock_timestamp() AT TIME ZONE 'UTC'
                     FROM new_table
                     WHERE {id_field} IS NOT NULL
                     ON CONFLICT DO NOTHING;
@@ -75,7 +75,7 @@ def row_trigger_fn(id_field):
             AS $BODY$
                 BEGIN
                     INSERT INTO history_audit (history_id, update_time)
-                    VALUES (NEW.{id_field}, CURRENT_TIMESTAMP AT TIME ZONE 'UTC')
+                    VALUES (NEW.{id_field}, clock_timestamp() AT TIME ZONE 'UTC')
                     ON CONFLICT DO NOTHING;
                     RETURN NULL;
                 END;
@@ -174,3 +174,11 @@ def get_trigger_name(label, operation, when, statement=False):
     when_initial = when.lower()[0]
     rs = "s" if statement else "r"
     return f"trigger_{label}_{when_initial}{op_initial}{rs}"
+
+
+def execute_statements(engine, raw_sql):
+    statements = raw_sql if isinstance(raw_sql, list) else [raw_sql]
+    with engine.begin() as connection:
+        for sql in statements:
+            cmd = DDL(sql)
+            connection.execute(cmd)