Mercurial > repos > gga > apollo_delete_organism
view create_or_update_organism.py @ 3:bf2f5f6e11a9 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
author | gga |
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date | Wed, 20 Sep 2017 09:43:23 -0400 |
parents | dc738069b5ac |
children | 0af4179e6758 |
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#!/usr/bin/env python from __future__ import print_function import argparse import json import logging import shutil import sys import time from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) if __name__ == '__main__': parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance') WAAuth(parser) parser.add_argument('jbrowse', help='JBrowse Data Directory') parser.add_argument('email', help='User Email') OrgOrGuess(parser) parser.add_argument('--genus', help='Organism Genus') parser.add_argument('--species', help='Organism Species') parser.add_argument('--public', action='store_true', help='Make organism public') parser.add_argument('--group', help='Give access to a user group') parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory') args = parser.parse_args() wa = WebApolloInstance(args.apollo, args.username, args.password) org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] # User must have an account gx_user = AssertUser(wa.users.loadUsers(email=args.email)) log.info("Determining if add or update required") try: org = wa.organisms.findOrganismByCn(org_cn) except Exception: org = None if org: has_perms = False old_directory = org['directory'] for user_owned_organism in gx_user.organismPermissions: if 'WRITE' in user_owned_organism['permissions']: has_perms = True break if not has_perms: print("Naming Conflict. You do not have permissions to access this organism. Either request permission from the owner, or choose a different name for your organism.") sys.exit(2) log.info("\tUpdating Organism") data = wa.organisms.updateOrganismInfo( org['id'], org_cn, args.jbrowse, # mandatory genus=args.genus, species=args.species, public=args.public ) time.sleep(2) if args.remove_old_directory and args.jbrowse != old_directory: shutil.rmtree(old_directory) data = [wa.organisms.findOrganismById(org['id'])] else: # New organism log.info("\tAdding Organism") data = wa.organisms.addOrganism( org_cn, args.jbrowse, genus=args.genus, species=args.species, public=args.public ) # Must sleep before we're ready to handle time.sleep(2) log.info("Updating permissions for %s on %s", gx_user, org_cn) wa.users.updateOrganismPermission( gx_user, org_cn, write=True, export=True, read=True, ) # Group access if args.group: group = wa.groups.loadGroupByName(name=args.group) res = wa.groups.updateOrganismPermission(group, org_cn, administrate=False, write=True, read=True, export=True) data = [o for o in data if o['commonName'] == org_cn] print(json.dumps(data, indent=2))