def main(args=None):
parser = ArgParser(description=Description)
if __name__ != '__main__':
parser.prog += " " + __name__.rsplit('.', 1)[-1]
args = parser.parse_args(args)
test()
def main(args=None):
parser = ArgParser(description=Description + \
', to the latest version of its image')
if __name__ != '__main__':
parser.prog += " " + __name__.rsplit('.', 1)[-1]
args = parser.parse_args(args)
sync()
def main(args=None):
parser = ArgParser(description=Description+\
" to reflect the latest method snapshot")
if __name__ != '__main__':
parser.prog += " " + __name__.rsplit('.', 1)[-1]
args = parser.parse_args(args)
config()
def main(args=None):
initialize_logging()
initialize_user_dir()
logfile = ConfigLoader().config.All.Logfile
if logfile is not None:
log_to_logfile(logfile)
parser = ArgParser(description="Hydrant: a tool which aims to "\
"simplify and accelerate the development and maintenance of workflows"\
" for FireCloud (FC).")
parser.add_argument('-V',
'--version',
action='version',
version='%(prog)s ' + __version__)
subparsers = parser.add_subparsers(dest='subcmd')
subparsers.required = True
install_commands(subparsers, ['init', 'build', 'push', 'validate', 'test'])
install_commands(subparsers, ['tutorial', 'sync', 'install', 'config'])
args, argv = parser.parse_known_args(args)
args.func(argv)
def main(args=None):
parser = ArgParser(description=Description)
# Because parser.prog is initialized to the name of the top-level calling
# module, it needs to be modified here to be consistent.
# (i.e. so hydrant init -h returns a usage that begins with hydrant init
# rather than only hydrant)
if __name__ != '__main__':
parser.prog += " " + __name__.rsplit('.', 1)[-1]
parser.add_argument('-p',
'--package',
action='store_true',
help='include packaging tools')
parser.add_argument('-n',
'--num_tasks',
type=int,
default=1,
help='Number of empty tasks to create')
parser.add_argument('-c',
'--config',
type=task_config,
help='Config file with [Task <task_name>] sections ' +
'that may contain Src=<path/to/src>, ' +
'Image=<[registry/]namespcae/repo[:tag]>, and ' +
'any [Docker] section arguments to initialize ' +
'tasks with specified names, then copy source ' +
"code to each task's src directory and " +
"initialize each task's hydrant.cfg, or " +
'initialize WDL with prexisting docker image(s)')
parser.add_argument('workflow',
type=new_folder,
help='Name of template folder')
parser.add_argument('task',
nargs='*',
type=user_task,
help='Name of existing locally written task to ' +
'initialize with in the format of ' +
'<workflow>.<task|*>, with "<workflow>.*" ' +
'indicating all tasks in <workflow>')
args = parser.parse_args(args)
user_tasks = process_user_tasks(args.task, args.workflow)
generate_workflow(args.workflow, args.num_tasks, user_tasks, args.config
or ConfigLoader().config, args.package)
def main(args=None):
# TODO: allow bulk pushes from the workspace level like with build
docker_cfg = ConfigLoader().config.Docker
parser = ArgParser(description=Description)
# Because parser.prog is initialized to the name of the top-level calling
# module, it needs to be modified here to be consistent.
# (i.e. so hydrant docker push -h returns a usage that begins with
# hydrant docker push rather than only hydrant)
if __name__ != '__main__':
parser.prog += " " + __name__.rsplit('.', 1)[-1]
repo = os.path.basename(os.getcwd())
client = connect_to_daemon()
try:
registry, namespace = find_registry_namespace(client, repo, docker_cfg)
except Exception as e:
logging.exception(str(e))
sys.exit(1)
registry = registry or docker_cfg.Registry
namespace = namespace or docker_cfg.Namespace
reg_kwargs = {'help': "Host[:port] of registry if not at Docker Hub"}
if registry is not None:
add_default_arg(registry, reg_kwargs)
parser.add_argument('-R', '--registry', **reg_kwargs)
ns_kwargs = {'help': 'Namespace under which the repository resides'}
if namespace is None:
ns_kwargs['required'] = True
else:
add_default_arg(namespace, ns_kwargs)
parser.add_argument('-n', '--namespace', **ns_kwargs)
parser.add_argument('-r', '--repository', default=repo,
help='Repository name (default: %(default)s)')
tag = docker_cfg.Tag
parser.add_argument('-t', '--tag', help="Version of the image or task " + \
"(default: {})".format(tag or 'latest'), default=tag)
args = parser.parse_args(args)
repo = args.namespace + '/' + args.repository
if args.registry is not None:
repo = args.registry + '/' + repo
push_kwargs = {'stream': True}
if args.tag is not None:
push_kwargs['tag'] = args.tag
push_image(client, repo, push_kwargs)
def main(args=None):
repos = {repo: version for repo, version in docker_repos()}
docker_cfg = ConfigLoader().config.Docker
# TODO: allow multiple registries and namespaces from the workspace folder
# level.
reg_kwargs = {'help': "Host[:port] of registry if not at Docker Hub"}
if docker_cfg.Registry is not None:
add_default_arg(docker_cfg.Registry, reg_kwargs)
ns_kwargs = {'help': 'Namespace under which the repository resides'}
if docker_cfg.Namespace is not None:
add_default_arg(docker_cfg.Namespace, ns_kwargs)
else:
ns_kwargs['required'] = True
repo_kwargs = {'help': 'Repository name[:tag]'}
# TODO: Allow arbitrary repo names and uncomment below code. For now repo
# names must match task folder names.
# if len(repos) == 1 and cwd in repos:
# repo_kwargs['help'] += ' (default: %(default)s)'
# repo_kwargs['default'] = os.path.basename(cwd) + ':' + repos[cwd]
if len(repos) > 0:
repo_kwargs['choices'] = sorted(os.path.basename(repo) + ':' + version
for repo, version in repos.items())
if len(repos) > 1:
repo_kwargs['nargs'] = '*'
else:
repo_kwargs['nargs'] = '?'
repo_kwargs['metavar'] = repo_kwargs['choices'][0]
repo_kwargs['const'] = repo_kwargs['metavar']
repo_kwargs['default'] = repo_kwargs['metavar']
else:
repo_kwargs['help'] += ''', requires hydrant.cfg file if building
multiple images with tags other than "latest"'''
parser = ArgParser(description=Description)
# Because parser.prog is initialized to the name of the top-level calling
# module, it needs to be modified here to be consistent.
# (i.e. so hydrant docker build -h returns a usage that begins with
# hydrant docker build rather than only hydrant)
if __name__ != '__main__':
parser.prog += " " + __name__.rsplit('.', 1)[-1]
parser.add_argument('-R', '--registry', **reg_kwargs)
parser.add_argument('-n', '--namespace', **ns_kwargs)
parser.add_argument('-r', '--repository', **repo_kwargs)
parser.add_argument('-a', '--all', action='store_true',
help="Build all docker images.")
args = parser.parse_args(args)
client = connect_to_daemon()
if args.all:
for repo, version in repos.items():
tag = get_full_tag(args.registry, args.namespace,
os.path.basename(repo), version)
build_image(client, repo, tag)
elif args.repository:
all_repos = {os.path.basename(path): path for path in repos}
if isinstance(args.repository, list):
user_repos = [repo.split(':', 1)[0] for repo in args.repository]
# Only build images if all user-specified ones are available
build_images = set(user_repos).issubset(set(all_repos.keys()))
for idx, repo in enumerate(args.repository):
tag = get_full_tag(args.registry, args.namespace, repo)
user_repo = user_repos[idx]
if user_repo in all_repos:
if build_images:
build_image(client, all_repos[user_repo],
tag)
else:
logging.error("Could not find a path for %s. Please ensure" + \
" the directory containing the Dockerfile " + \
"matches the name of the repository.", tag)
if not build_images:
sys.exit(1)
else:
tag = get_full_tag(args.registry, args.namespace, args.repository)
repo = args.repository.split(':', 1)[0]
build_image(client, all_repos[repo], tag)
else:
logging.error("No repository specified.")
sys.exit(1)
def main(args=None):
method_name = os.path.basename(os.getcwd())
wdl = method_name + '.wdl'
firecloud_cfg = ConfigLoader().config.FireCloud # @UndefinedVariable
parser = ArgParser(formatter_class=ArgumentDefaultsHelpFormatter,
description=Description)
# Because parser.prog is initialized to the name of the top-level calling
# module, it needs to be modified here to be consistent.
# (i.e. so hydrant install -h returns a usage that begins with
# hydrant install rather than only hydrant)
if __name__ != '__main__':
parser.prog += " " + __name__.rsplit('.', 1)[-1]
parser.add_argument('-m', '--method', help='Method name',
default=method_name)
method_ns_kwargs = {}
if fcconfig.method_ns:
method_ns_kwargs['default'] = fcconfig.method_ns
else:
method_ns_kwargs['required'] = True
parser.add_argument('-n', '--namespace', help="Method Repo namespace.",
**method_ns_kwargs)
parser.add_argument('-d','--wdl', default=wdl, help="Method definiton, " + \
"as a file of WDL (Workflow Description Language)",
type=ValidFile)
parser.add_argument('-s', '--synopsis', help="Short (<80 chars) " + \
"description of method")
parser.add_argument('--doc', help='Optional documentation file <10Kb',
type=ValidFile)
parser.add_argument('-c', '--comment', metavar='SNAPSHOT_COMMENT',
help='Optional comment specific to this snapshot',
default='')
parser.add_argument('-o', '--owners',
**acl_kwargs('owner', firecloud_cfg.Owners))
parser.add_argument('-r', '--readers',
**acl_kwargs('reader', firecloud_cfg.Readers))
parser.add_argument('-w', '--writers',
**acl_kwargs('writer', firecloud_cfg.Writers))
args = parser.parse_args(args)
meth_new(args)
args.snapshot_id = None
set_acl('owner', args)
set_acl('reader', args)
set_acl('writer', args)