diff --git a/main.py b/main.py new file mode 100644 index 0000000000000000000000000000000000000000..72f244394afab48ae90749b83fa51afe79d4534b --- /dev/null +++ b/main.py @@ -0,0 +1,59 @@ +from bioblend import galaxy +import argparse + +""" + + + +""" + +parser = argparse.ArgumentParser(description="Input genus, species, strain, version") +parser.add_argument("--name", help="Sample species name, format: genus-species",type=str, required=True) +parser.add_argument("--strain", help="Strain of the sample species", type=str, required=True) +parser.add_argument("--version", help="Data version (e.g 1.0, 1.2, ...)", type=str, required=True) +parser.add_argument("--common-name", help="Vernacular/common name of the species",type=str, required=False) + +user_arguments = parser.parse_args() + +genus = user_arguments.name.split('-')[0] +species = user_arguments.name.split('-')[1] +strain = user_arguments.strain +vernacular = user_arguments.common_name +instance_url = "http://localhost/sp/" + genus + "_" + species + "/galaxy/" + +print("Species: " + genus + " " + species + " (Wakame)" + + "\nStrain: " + strain + + "\nAccessing " + instance_url + "...") + +gi = galaxy.GalaxyInstance(url=instance_url, + key="291ec50b48dd1f006985b32e39bc3696", + email="alebars@sb-roscoff.fr", + password="pouet", + verify=True) + +# gi = galaxy.GalaxyInstance(url="http://localhost/sp/undaria_pinnatifida/galaxy/", +# # key="291ec50b48dd1f006985b32e39bc3696", +# email="alebars@sb-roscoff.fr", +# password="pouet", +# verify=True) + +# gi = galaxy.GalaxyInstance(url="http://localhost/sp/undaria_pinnatifida/galaxy/", +# key="291ec50b48dd1f006985b32e39bc3696", +# email="alebars@sb-roscoff.fr", +# password="pouet", +# verify=True) + +# gi = galaxy.GalaxyInstance(url="http://abims-gga.sb-roscoff.fr/sp/ectocarpus_species1/galaxy/", +# key="84dfbee3c0efa9155518f01fbeff57c8", +# email="gga@sb-roscoff.fr", +# password="Mmo,55k") + +try: + hl = gi.histories.get_histories() +except ConnectionError: + print("Cannot connect to GGA instance @ " + instance_url + "") + + + + +