opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge branch 'release_25.0' into dev

Browse Source
This commit is contained in:
mvdbeek
2025-06-11 18:22:14 +02:00
parent 357356dda3 100612b33b
commit d5b883c0d1
9 changed files with 107 additions and 187 deletions
Download Patch File Download Diff File Expand all files Collapse all files
doc/source/admin/galaxy_options.rst
+7 -6
View File
@@ -1222,12 +1222,13 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Whether to enable the tool document cache. This cache stores
expanded XML strings. Enabling the tool cache results in slightly
faster startup times. The tool cache is backed by a SQLite
database, which cannot be stored on certain network disks. The
cache location is configurable with the ``tool_cache_data_dir``
tag in tool config files.
This option is deprecated, and the tool document cache will be
removed in the next release. Whether to enable the tool document
cache. This cache stores expanded XML strings. Enabling the tool
cache results in slightly faster startup times. The tool cache is
backed by a SQLite database, which cannot be stored on certain
network disks. The cache location is configurable with the
``tool_cache_data_dir`` tag in tool config files.
:Default: ``false``
:Type: bool
lib/galaxy/config/sample/galaxy.yml.sample
+7 -6
View File
@@ -935,12 +935,13 @@ galaxy:
# generated commands run in sh.
#default_job_shell: /bin/bash
# Whether to enable the tool document cache. This cache stores
# expanded XML strings. Enabling the tool cache results in slightly
# faster startup times. The tool cache is backed by a SQLite database,
# which cannot be stored on certain network disks. The cache location
# is configurable with the ``tool_cache_data_dir`` tag in tool config
# files.
# This option is deprecated, and the tool document cache will be
# removed in the next release. Whether to enable the tool document
# cache. This cache stores expanded XML strings. Enabling the tool
# cache results in slightly faster startup times. The tool cache is
# backed by a SQLite database, which cannot be stored on certain
# network disks. The cache location is configurable with the
# ``tool_cache_data_dir`` tag in tool config files.
#enable_tool_document_cache: false
# Directory in which the toolbox search index is stored. The value of
lib/galaxy/config/schemas/config_schema.yml
+2
View File
@@ -887,6 +887,8 @@ mapping:
default: false
required: false
desc: |
This option is deprecated, and the tool document cache will be removed
in the next release.
Whether to enable the tool document cache. This cache stores
expanded XML strings. Enabling the tool cache results in slightly faster startup
times. The tool cache is backed by a SQLite database, which cannot
lib/galaxy/dependencies/conditional-requirements.txt
+1 -1
View File
@@ -56,7 +56,7 @@ pygithub
influxdb
# Deep learning packages for tool recommendation
tensorflow==2.9.3
tensorflow==2.15.1
# weasyprint has problematic requirements (cairo, Pango, see:
# https://doc.courtbouillon.org/weasyprint/stable/first_steps.html#linux)
lib/galaxy/model/migrations/alembic/versions_gxy/a91ea1d97111_update_trigger_to_use_clock_timestamp_.py
+77
View File
@@ -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
View File
@@ -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
View File
@@ -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
View File
@@ -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
View File
@@ -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)