comparison delete_features.py @ 6:83f07a884301 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2

5:9e7b56138937

import argparse
import logging
import random

from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, retry
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


if __name__ == '__main__':

    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)
    if isinstance(org_cn, list):
        org_cn = org_cn[0]

    # TODO: Check user perms on org.
    org = wa.organisms.findOrganismByCn(org_cn)

    sequences = wa.organisms.getSequencesForOrganism(org['id'])
    for sequence in sequences['sequences']:
        log.info("Processing %s %s", org['commonName'], sequence['name'])

6:83f07a884301

import argparse
import logging
import random

from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance, retry
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


if __name__ == '__main__':

    args = parser.parse_args()

    wa = WebApolloInstance(args.apollo, args.username, args.password)
    # User must have an account
    gx_user = wa.users.assertOrCreateUser(args.email)

    # Get organism
    org_cn = GuessOrg(args, wa)
    if isinstance(org_cn, list):
        org_cn = org_cn[0]

    if not PermissionCheck(gx_user, org_cn, "WRITE"):
        raise Exception("Action not permitted")
    org = wa.organisms.findOrganismByCn(org_cn)

    sequences = wa.organisms.getSequencesForOrganism(org['id'])
    for sequence in sequences['sequences']:
        log.info("Processing %s %s", org['commonName'], sequence['name'])