def test_nbadapter_repo():
from nb2workflow.nbadapter import NotebookAdapter, find_notebooks
from nb2workflow import ontology
nbas = find_notebooks(test_notebook_repo)
logger.info(ontology.service_semantic_signature(nbas))
def test_nbadapter_repo():
from nb2workflow.nbadapter import NotebookAdapter, find_notebooks
nbas=find_notebooks(test_notebook_repo)
assert len(nbas) == 2
for nba_name,nba in nbas.items():
print("notebook",nba_name)
continue
parameters=nba.extract_parameters()
print(parameters)
assert len(parameters)==4
if os.path.exists(nba.output_notebook_fn):
os.remove(nba.output_notebook_fn)
if os.path.exists(nba.preproc_notebook_fn):
os.remove(nba.preproc_notebook_fn)
nba.execute(dict())
output=nba.extract_output()
print(output)
def main():
import argparse
parser = argparse.ArgumentParser(description='Process some integers.')
parser.add_argument('notebook', metavar='notebook', type=str)
parser.add_argument('--host', metavar='host', type=str, default="127.0.0.1")
parser.add_argument('--port', metavar='port', type=int, default=9191)
#parser.add_argument('--tmpdir', metavar='tmpdir', type=str, default=None)
parser.add_argument('--publish', metavar='upstream-url', type=str, default=None)
parser.add_argument('--publish-as', metavar='published url', type=str, default=None)
parser.add_argument('--profile', metavar='service profile', type=str, default="oda")
parser.add_argument('--debug', action="store_true")
args = parser.parse_args()
if args.debug:
logging.getLogger("nb2workflow").setLevel(level=logging.DEBUG)
logging.getLogger("flask").setLevel(level=logging.DEBUG)
app.notebook_adapters = find_notebooks(args.notebook)
setup_routes(app)
app.service_semantic_signature=ontology.service_semantic_signature(app.notebook_adapters)
if args.publish:
logger.info("publishing to %s",args.publish)
if args.publish_as:
s = args.publish_as.split(":")
publish_host, publish_port = ":".join(s[:-1]), int(s[-1])
else:
publish_host, publish_port = args.host, args.port
for nba_name, nba in app.notebook_adapters.items():
publish.publish(args.publish, nba_name, publish_host, publish_port)
# for rule in app.url_map.iter_rules():
# logger.debug("==>> %s %s %s %s",rule,rule.endpoint,rule.__class__,rule.__dict__)
app.run(host=args.host,port=args.port)
def main():
parser = argparse.ArgumentParser(description='Process some integers.')
parser.add_argument('repo', metavar='repo', type=str)
parser.add_argument('--run', action='store_true')
parser.add_argument('--build', action='store_true')
parser.add_argument('--job', action='store_true')
parser.add_argument('--name', metavar='TAG', type=str, default="nb2worker")
parser.add_argument('--from-image',
metavar='FROM IMAGE',
type=str,
default="python:3.6")
parser.add_argument('--tag-image', metavar='TAG', type=str, default="")
parser.add_argument('--host',
metavar='host',
type=str,
default="127.0.0.1")
parser.add_argument('--port', metavar='port', type=int, default=9191)
parser.add_argument('--nb2wrev', metavar='TAG', type=str, default="master")
parser.add_argument('--nb2wpath', metavar='PATH', type=str)
parser.add_argument('--volume', metavar='mount:mount', type=str, nargs="*")
parser.add_argument('--docker-run-prefix', type=str, default="")
parser.add_argument('--store-dockerfile',
metavar='location',
type=str,
default=None)
parser.add_argument('--docker-command', type=str, default=None)
args = parser.parse_args()
repo_path = args.repo
tag_image = args.tag_image
if args.tag_image == "":
tag_image = os.path.basename(os.path.abspath(repo_path))
tempdir = prepare_image(repo_path,
args.from_image,
service=not args.job,
nb2w_path=args.nb2wpath,
runprefix=args.docker_run_prefix)
if args.store_dockerfile:
shutil.copy(os.path.join(tempdir, "Dockerfile"), args.store_dockerfile)
print("stored Dockerfile as", args.store_dockerfile)
if args.build:
build_result = build_image(tempdir, tag_image, args.nb2wrev)
if build_result is None:
raise Exception("failed to build")
print("built:", build_result)
if args.job:
for n, nba in find_notebooks(repo_path).items():
nb2cwl_container(tag_image,
nba.notebook_fn,
n + ".cwl",
command=args.docker_command)
if args.run:
if not args.job:
print("running", tag_image, "service on", args.port)
cli = docker.from_env()
c = cli.containers.run(
tag_image,
user=os.getuid(),
ports={9191: (args.host, args.port)},
name=args.name,
detach=True,
volumes=dict([
(os.getcwd(), {
"bind": "/workdir",
"mode": "rw"
}),
] + [v.split(":", 1) for v in args.volume]),
)
for r in c.attach(stream=True):
print(c, r.strip())
else:
print("running", tag_image)
cli = docker.from_env()
c = cli.containers.run(
tag_image,
user=os.getuid(),
name=args.name,
detach=True,
volumes=dict([
(os.getcwd(), {
"bind": "/workdir",
"mode": "rw"
}),
] + [v.split(":", 1) for v in args.volume]),
entrypoint=["nbrun", "/repo/*ipynb"],
)
for r in c.attach(stream=True):
print(c, r.strip())