comparison create_or_update_organism.py @ 5:0af4179e6758 draft

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

4:a5de2095bd01

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)

    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(

5:0af4179e6758

import logging
import shutil
import sys
import time

from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, 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)

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

    # User must have an account, if not, create it
    gx_user = wa.users.assertOrCreateUser(args.email)

    log.info("Determining if add or update required")
    try:
        org = wa.organisms.findOrganismByCn(org_cn)
    except Exception:
        org = None

    if org:
        old_directory = org['directory']

        if not PermissionCheck(gx_user, org_cn, "WRITE"):
            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(