diff --git a/pybis/src/python/pybis/cli.py b/pybis/src/python/pybis/cli.py index ce2ba3fe5cbb8b2b0e756249bba24f07cf245035..3447052c7276df8649faeb2a708c2d5193db30fe 100644 --- a/pybis/src/python/pybis/cli.py +++ b/pybis/src/python/pybis/cli.py @@ -1,5 +1,4 @@ import os -<<<<<<< HEAD import syslog from datetime import datetime @@ -10,13 +9,6 @@ from tabulate import tabulate from . import pybis syslog.openlog("pyBIS") -======= -import click -from tabulate import tabulate -from . import pybis -from datetime import datetime -from dateutil.relativedelta import relativedelta ->>>>>>> 033729a6ad (add cli) def openbis_conn_options(func): @@ -25,17 +17,10 @@ def openbis_conn_options(func): click.option("-u", "--username", help="Username OPENBIS_USERNAME"), click.option("-p", "--password", help="Password OPENBIS_PASSWORD"), click.option( -<<<<<<< HEAD "--ignore-certificate", is_flag=True, default=True, help="Ignore SSL certificate of openBIS host", -======= - "--verify-certificate", - is_flag=True, - default=True, - help="Verify SSL certificate of openBIS host", ->>>>>>> 033729a6ad (add cli) ), ] # we use reversed(options) to keep the options order in --help @@ -48,17 +33,10 @@ def login_options(func): options = [ click.argument("hostname"), click.option( -<<<<<<< HEAD "--ignore-certificate", is_flag=True, default=True, help="Ignore SSL certificate of openBIS host", -======= - "--verify-certificate", - is_flag=True, - default=True, - help="Verify SSL certificate of openBIS host", ->>>>>>> 033729a6ad (add cli) ), ] # we use reversed(options) to keep the options order in --help @@ -71,11 +49,7 @@ def get_openbis( hostname=None, username=None, password=None, -<<<<<<< HEAD ignore_certificate=False, -======= - verify_certificate=True, ->>>>>>> 033729a6ad (add cli) session_token_needed=False, ): """Order of priorities: @@ -94,22 +68,14 @@ def get_openbis( if not hostname: hostname = config.get("hostname") if not hostname: -<<<<<<< HEAD hostname = click.prompt("openBIS hostname") -======= - hostname = click.prompt("openBIS hostname:") ->>>>>>> 033729a6ad (add cli) token = pybis.get_token_for_hostname( hostname, session_token_needed=session_token_needed ) openbis = pybis.Openbis( url=hostname, -<<<<<<< HEAD verify_certificates=not ignore_certificate, -======= - verify_certificates=verify_certificate, ->>>>>>> 033729a6ad (add cli) ) if token: try: @@ -139,17 +105,13 @@ def get_openbis( @click.group() -<<<<<<< HEAD @click.version_option() -======= ->>>>>>> 033729a6ad (add cli) def cli(): """pybis - command line access to openBIS""" @cli.group() @click.pass_obj -<<<<<<< HEAD def space(ctx): """manage spaces""" pass @@ -303,8 +265,6 @@ def download_dataset_in_collection(identifier, **kwargs): @cli.group() @click.pass_obj -======= ->>>>>>> 033729a6ad (add cli) def sample(ctx): """manage samples""" pass @@ -314,7 +274,6 @@ def sample(ctx): @openbis_conn_options @click.argument("identifier", required=True) def get_sample(identifier, **kwargs): -<<<<<<< HEAD """get sample by its identifier or permId""" openbis = get_openbis(**kwargs) try: @@ -382,9 +341,6 @@ def download_datasets_in_sample(identifier, **kwargs): syslog.LOG_INFO, f"{openbis.hostname} | {openbis.username} | {dataset.permId}", ) -======= - """get a sample by its identifier or permId""" ->>>>>>> 033729a6ad (add cli) @cli.group() @@ -398,7 +354,6 @@ def dataset(ctx): @openbis_conn_options @click.argument("permid", required=True) def get_dataset(permid, **kwargs): -<<<<<<< HEAD """get dataset meta-information by its permId""" openbis = get_openbis(**kwargs) try: @@ -450,20 +405,6 @@ def download_dataset(permid, destination, fileno, **kwargs): syslog.LOG_INFO, f"{openbis.hostname} | {openbis.username} | {dataset.permId}", ) -======= - """get a dataset by its permId""" - print(permid) - print(kwargs) - openbis = get_openbis(**kwargs) - print(openbis) - - -@dataset.command("download") -@click.argument("permid", required=True) -def download_dataset(permid, **kwargs): - """download a dataset by permId""" - click.echo(permid) ->>>>>>> 033729a6ad (add cli) @cli.command("local", context_settings=dict(ignore_unknown_options=True))