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 apply_launcher_patches(launcher):
patches = Path('patches').absolute()
if not patches.exists():
fail('No patches')
apply = git.apply
with cd(launcher):
for p in patches.iterdir():
print('Patching', p.absolute())
if not p.is_file():
fail('Patch {} is not a file. Please remove it.'.format(p.absolute()))
if 'version.txt' == str(p.name):
continue
apply(str(p.absolute()))
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('')
def require_folder_git(src, target, branch=None):
if not target.exists():
print('Cloning', src, target)
clone = git.clone.bake(src, target)
if branch:
clone = clone.bake('--branch', branch, '--single-branch')
if clone().exit_code:
fail("Couldn't clone")
else:
try:
with cd(target):
git.pull()
git.reset('--hard', 'HEAD')
except sh.ErrorReturnCode:
import traceback
traceback.print_exc()
shutil.rmtree(str(target))
return require_folder_git(src, target, branch=branch)
return target
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 fail_if_no_changes(downloads, version, launcher_version):
msg = make_commit_message(launcher_version, version)
with cd(downloads):
last_msg = git_last_commit_message(_out=None).stdout.decode().strip()
if msg == last_msg:
fail("No changes, '{}' == '{}'".format(msg, last_msg))
def discover_launcher_version(launcher):
with cd(launcher):
return git_last_commit_sha(_out=None).stdout.decode().strip()
def upload_downloads(d, version, launcher_version):
with cd(d):
git.add('.')
git.commit('-m', make_commit_message(launcher_version, version))
git.push()
def __call__(self, *args, **kwargs):
with cd(self.dir):
return self._gradle(*args, **kwargs)