Merge branch '6-file-ingest-example' into 'main'

#### Description

This is a simple script to demonstrate how one can in-place register a dataset in Galaxy

without copying it to Galaxy storage. 

#### To run it:

see README in a root folder

import os,sys

from bioblend import galaxy

from bioblend.galaxy.tools.inputs import inputs

galaxy_url = os.getenv("GALAXY_URL")

galaxy_user_api_key = os.getenv("GALAXY_API_KEY")

file_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)

dataset_client = galaxy.datasets.DatasetClient(galaxy_instance)

# get active history id

history_id = galaxy_instance.histories.get_histories()[0]["id"]

# or create a new one

# 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)

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)