Compare db indexes defined in mapping.py to those in the database. Call check_model.sh from galaxy root.

check_model.py

import os
import sys

sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))

from sqlalchemy import create_engine, MetaData

from galaxy.model import mapping
from galaxy.model.orm.scripts import get_config


def check_indexes():
    """
    Check for missing/extra db indexes defined in mapping.py and/or the database.
    Note: pass '-c /path/to/galaxy.yml' to use the database_connection set in galaxy.yml.
    Otherwise the default sqlite database will be used.
    """
    config = get_config(sys.argv)

    # metadata loaded from mapping.py
    md1 = mapping.metadata
    ix1 = set()
    for t in md1.tables.values():
        ix1 |= t.indexes

    # create EMPTY metadata, then load from db
    md2 = MetaData(bind=create_engine(config['db_url']))
    md2.reflect()
    ix2 = set()
    for t in md2.tables.values():
        ix2 |= t.indexes

    inames1 = {i.name for i in ix1}  # indexes in mapping
    inames2 = {i.name for i in ix2}  # indexes in db
    inames1m2 = inames1 - inames2    # indexes in mapping and not in db
    inames2m1 = inames2 - inames1    # indexes in db and not in mapping

    # print summary
    print('db_url: %s' % config['db_url'])
    print('in mapping.py: %d' % len(inames1))
    print('in db: %d' % len(inames2))
    print('in mapping.py, not in db: %d' % len(inames1m2))
    print('in db, not in mapping.py: %d' % len(inames2m1))

    # print indexes
    names = inames1
    # names = ianmes2
    # names = ianmes1m2
    # names = ianmes2m1
    for i in names:
        print(i)

    # sanity check
    # benchmark = 'ix_workflow_invocation_step_implicit_collection_jobs_id'
    # assert benchmark in inames1
    # assert benchmark not in inames2
    # assert benchmark in inames1m2


if __name__ == '__main__':
    check_indexes()

check_model.sh

#!/bin/sh

cd "$(dirname "$0")"

. ./scripts/common_startup_functions.sh

setup_python

python ./scripts/check_model.py "$@"