def build(args):
context = {
'dbsnp_build': args.dbsnp_build,
'genome_build': args.genome_build,
'prefix': args.prefix,
'target': args.target,
}
context['db_name'] = '{prefix}_{dbsnp_build}_{genome_build}'.format(**context)
context['db_user'] = '******'
log.info(colored(pformat(context), 'blue'))
with cd(DBSNP_HOME):
force('createuser {db_user}'.format(**context))
force('createdb --owner={db_user} {db_name}'.format(**context))
target = [DBSNP_HOME] if 'core' in args.target else []
target += [os.path.join(DBSNP_HOME, 'contrib', x) for x in set(args.target) if x != 'core']
for src in target:
with cd(src):
run('pwd')
if glob.glob('02_drop_create_table.*'):
context.update(src=src)
run('./01_fetch_data.sh -d {dbsnp_build} -r {genome_build} {src}/data'.format(**context))
run('./02_drop_create_table.sh {db_name} {db_user} {src}'.format(**context))
run('./03_import_data.sh {db_name} {db_user} {src} {src}/data'.format(**context))
log.info('Done')
log.info('To connect via psql, run:')
log.info('')
log.info(colored('$ psql {db_name} -U {db_user}'.format(**context), 'blue', attrs=['bold']))
log.info('')
def restore(args):
context = {
'dbsnp_build': args.dbsnp_build,
'genome_build': args.genome_build,
'prefix': args.prefix,
'tag': args.tag,
}
context['db_src_name'] = 'dbsnp_{dbsnp_build}_{genome_build}'.format(**context)
context['db_name'] = '{prefix}_{dbsnp_build}_{genome_build}'.format(**context)
context['db_user'] = '******'
log.info(colored(pformat(context), 'blue'))
with cd(DBSNP_HOME):
force('createuser {db_user}'.format(**context))
run('./script/pg_restore.sh {db_src_name} {db_name} {db_user} {tag}'.format(**context))
log.info('Done')
log.info('To connect via psql, run:')
log.info('')
log.info(colored('$ psql {db_name} -U {db_user}'.format(**context), 'blue', attrs=['bold']))
log.info('')
def init_demo(args):
context = {
'db_user': args.demo_db_user,
'db_name': args.demo_db_name,
}
log.info(colored(pformat(context), 'blue'))
with cd(DBSNP_HOME):
force('createuser {db_user}'.format(**context))
force('createdb --owner={db_user} {db_name}'.format(**context))
for src in [DBSNP_HOME] + glob.glob(DBSNP_HOME + '/contrib/*'):
with cd(src):
run('pwd')
if glob.glob('02_drop_create_table.*'):
context.update(src=src)
run('./02_drop_create_table.sh {db_name} {db_user} {src}'.format(**context))
run('./03_import_data.sh {db_name} {db_user} {src} {src}/test/data'.format(**context))
log.info('Done')
log.info('To connect via psql, run:')
log.info('')
log.info(colored('$ psql {} -U {}'.format(args.demo_db_name, args.demo_db_user), 'blue', attrs=['bold']))
log.info('')
