Mercurial > repos > gga > apollo_fetch_jbrowse
view delete_organism.py @ 14:b7c44671f012 draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f274d9deece87f6837ffb0a22d9231671be4542"
author | gga |
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date | Wed, 19 Aug 2020 06:58:13 -0400 |
parents | dca2fb399ee6 |
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#!/usr/bin/env python from __future__ import print_function import argparse import logging import os from apollo import accessible_organisms from apollo.util import GuessOrg, OrgOrGuess from arrow.apollo import get_apollo_instance from webapollo import UserObj, handle_credentials logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) def IsRemote(): return 'GALAXY_SHARED_DIR' not in os.environ or len(os.environ['GALAXY_SHARED_DIR'].lower().strip()) == 0 if __name__ == '__main__': parser = argparse.ArgumentParser(description='Script to completely delete an organism') parser.add_argument('email', help='User Email') OrgOrGuess(parser) args = parser.parse_args() wa = get_apollo_instance() # User must have an account gx_user = UserObj(**wa.users._assert_or_create_user(args.email)) handle_credentials(gx_user) # Get organism org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] all_orgs = wa.organisms.get_organisms() if 'error' in all_orgs: all_orgs = [] all_orgs = [org['commonName'] for org in all_orgs] if org_cn not in all_orgs: raise Exception("Could not find organism %s" % org_cn) orgs = accessible_organisms(gx_user, [org_cn], 'WRITE') if not orgs: raise Exception("You do not have write permission on this organism") org = wa.organisms.show_organism(org_cn) wa.organisms.delete_features(org['id']) if IsRemote(): print(wa.remote.delete_organism(org['commonName'])) else: print(wa.organisms.delete_organism(org['id']))