update example to deal with multiple files

from bioblend import galaxy

from bioblend.galaxy.tools.inputs import inputs

def wait_for_dataset(result_dataset_id, galaxy_instance, dataset_client):

    wait_res = dataset_client.wait_for_dataset(result_dataset_id, check=False)

    if wait_res["state"] == "ok":

        print("register successful")

        print("dataset is now in history under id: ", wait_res["hid"])

    else:

        details = galaxy_instance.histories.show_dataset_provenance(history_id, result_dataset_id)

        raise Exception("register failed", details)

galaxy_url = os.getenv("GALAXY_URL")

galaxy_user_api_key = os.getenv("GALAXY_API_KEY")

file_to_register = sys.argv[1]

files_to_register = sys.argv[1:]

# connect to a Galaxy instance, create dataset client

galaxy_instance = galaxy.GalaxyInstance(url=galaxy_url, key=galaxy_user_api_key)

# history_id = galaxy_instance.histories.create_history(name="New history")["id"]

# set tool inputs, run tool and wait it finishes

# The neutrons_register tool takes a filepath

# and returns a single output file (hence ['outputs'][0]['id'])

tool_inputs = inputs().set("input", file_to_register)

result_dataset_id = galaxy_instance.tools.run_tool(history_id, 'neutrons_register', tool_inputs)['outputs'][0]['id']

res = dataset_client.wait_for_dataset(result_dataset_id, check=False)

# The neutrons_register tool takes a list of filepaths

# and returns multiple output files

n_files = len(files_to_register)

tool_inputs = inputs()

for i in range(n_files):

    tool_inputs = tool_inputs.set_param(f"series_{i}|input", files_to_register[i])

meta = galaxy_instance.tools.run_tool(history_id, 'neutrons_register', tool_inputs)

for output in meta['outputs']:

    wait_for_dataset(output['id'], galaxy_instance, dataset_client)

if res["state"] == "ok":

    print("register successful")

    print("dataset is now in history under id: ", res["hid"])

else:

    details = galaxy_instance.histories.show_dataset_provenance(history_id, result_dataset_id)

    raise Exception("register failed", details)

# uncomment to delete history and all data, purge=True might be not allowed by Galaxy admin

# galaxy_instance.histories.delete_history(history_id, purge=True)