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
parser.add_argument('email', help='User Email')
parser.add_argument('share_with', help='Share with this user (by email)')
parser.add_argument('--write',
action='store_true',
help='Write permission')
parser.add_argument('--export',
action='store_true',
help='Export permission')
parser.add_argument('--read', action='store_true', help='Read permission')
OrgOrGuess(parser)
args = parser.parse_args()
wa = WebApolloInstance(args.apollo, args.username, args.password)
# User must have an account
gx_user = AssertUser(wa.users.loadUsers(email=args.email))
# Get organism
org_cn = GuessOrg(args, wa)[0]
# Fetch all organisms
all_orgs = wa.organisms.findAllOrganisms()
# Figure out which are accessible to the user
# filter out common names
orgs = [d[0] for d in accessible_organisms(gx_user, all_orgs)]
# This user MUST be allowed to access an organism before they can
# modify permissions on it.
assert org_cn in orgs
org = wa.organisms.findOrganismByCn(org_cn)