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Merge pull request #20425 from jdavcs/25.0_trigger

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[25.0] Update triggers
This commit is contained in:
Marius van den Beek
2025-06-11 18:21:32 +02:00
committed by GitHub
parent db865963ca b24d8ae6dd
commit 100612b33b
5 changed files with 90 additions and 174 deletions
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lib/galaxy/model/migrations/alembic/versions_gxy/a91ea1d97111_update_trigger_to_use_clock_timestamp_.py
+77
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@@ -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
+2 -2
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@@ -46,8 +46,8 @@ REVISION_TAGS = {
"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
-160
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@@ -1,160 +0,0 @@
"""
Database trigger installation and removal
"""
from galaxy.model.triggers.utils import execute_statements
def install_timestamp_triggers(engine):
"""
Install update_time propagation triggers for history table
"""
statements = get_timestamp_install_sql(engine.name)
execute_statements(engine, statements)
def drop_timestamp_triggers(engine):
"""
Remove update_time propagation triggers for history table
"""
statements = get_timestamp_drop_sql(engine.name)
execute_statements(engine, statements)
def get_timestamp_install_sql(variant):
"""
Generate a list of SQL statements for installation of timestamp triggers
"""
sql = get_timestamp_drop_sql(variant)
if "postgres" in variant:
# PostgreSQL has a separate function definition and a trigger
# assignment. The first two statements the functions, and
# the later assign those functions to triggers on tables
fn_name = "update_history_update_time"
sql.append(build_pg_timestamp_fn(fn_name, "history", source_key="history_id"))
sql.append(build_pg_trigger("history_dataset_association", fn_name))
sql.append(build_pg_trigger("history_dataset_collection_association", fn_name))
else:
# Other database variants are more granular. Requiring separate
# statements for INSERT/UPDATE/DELETE, and the body of the trigger
# is not necessarily reusable with a function
for operation in ["INSERT", "UPDATE", "DELETE"]:
# change hda -> update history
sql.append(
build_timestamp_trigger(operation, "history_dataset_association", "history", source_key="history_id")
)
# change hdca -> update history
sql.append(
build_timestamp_trigger(
operation, "history_dataset_collection_association", "history", source_key="history_id"
)
)
return sql
def get_timestamp_drop_sql(variant):
"""
Generate a list of statements to drop the timestamp update triggers
"""
sql = []
if "postgres" in variant:
sql.append("DROP FUNCTION IF EXISTS update_history_update_time() CASCADE;")
else:
for operation in ["INSERT", "UPDATE", "DELETE"]:
for when in ["BEFORE", "AFTER"]:
sql.append(build_drop_trigger(operation, "history_dataset_association", when))
sql.append(build_drop_trigger(operation, "history_dataset_collection_association", when))
return sql
def build_pg_timestamp_fn(fn_name, target_table, source_key, target_key="id"):
"""Generates a PostgreSQL history update timestamp function"""
return f"""
CREATE OR REPLACE FUNCTION {fn_name}()
RETURNS trigger
LANGUAGE 'plpgsql'
AS $BODY$
BEGIN
IF (TG_OP = 'DELETE') THEN
UPDATE {target_table}
SET update_time = (CURRENT_TIMESTAMP AT TIME ZONE 'UTC')
WHERE {target_key} = OLD.{source_key};
RETURN OLD;
ELSEIF (TG_OP = 'UPDATE') THEN
UPDATE {target_table}
SET update_time = (CURRENT_TIMESTAMP AT TIME ZONE 'UTC')
WHERE {target_key} = NEW.{source_key} OR {target_key} = OLD.{source_key};
RETURN NEW;
ELSIF (TG_OP = 'INSERT') THEN
UPDATE {target_table}
SET update_time = (CURRENT_TIMESTAMP AT TIME ZONE 'UTC')
WHERE {target_key} = NEW.{source_key};
RETURN NEW;
END IF;
END;
$BODY$;
"""
def build_pg_trigger(source_table, fn_name, when="AFTER"):
"""Assigns a PostgreSQL trigger to indicated table, calling user-defined function"""
when_initial = when.lower()[0]
trigger_name = f"trigger_{source_table}_{when_initial}iudr"
return f"""
CREATE TRIGGER {trigger_name}
{when} INSERT OR DELETE OR UPDATE
ON {source_table}
FOR EACH ROW
EXECUTE PROCEDURE {fn_name}();
"""
def build_timestamp_trigger(operation, source_table, target_table, source_key, target_key="id", when="AFTER"):
"""Creates a non-PostgreSQL update_time trigger"""
trigger_name = get_trigger_name(operation, source_table, when)
# three different update clauses depending on update/insert/delete
clause = ""
if operation == "DELETE":
clause = f"{target_key} = OLD.{source_key}"
elif operation == "UPDATE":
clause = f"{target_key} = NEW.{source_key} OR {target_key} = OLD.{source_key}"
else:
clause = f"{target_key} = NEW.{source_key}"
return f"""
CREATE TRIGGER {trigger_name}
{when} {operation}
ON {source_table}
FOR EACH ROW
BEGIN
UPDATE {target_table}
SET update_time = CURRENT_TIMESTAMP
WHERE {clause};
END;
"""
def build_drop_trigger(operation, source_table, when="AFTER"):
"""Drops a non-PostgreSQL trigger by name"""
trigger_name = get_trigger_name(operation, source_table, when)
return f"DROP TRIGGER IF EXISTS {trigger_name}"
def get_trigger_name(operation, source_table, when):
"""Non-PostgreSQL trigger name"""
op_initial = operation.lower()[0]
when_initial = when.lower()[0]
return f"trigger_{source_table}_{when_initial}{op_initial}r"
lib/galaxy/model/triggers/update_audit_table.py
+11 -3
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@@ -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 _postgres_install(engine):
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 _postgres_install(engine):
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)
lib/galaxy/model/triggers/utils.py
-9
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@@ -1,9 +0,0 @@
from sqlalchemy import DDL
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)