comparison fetch_organism_jbrowse.py @ 5:696a1962212e draft

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

4:aee984715db1

import os
import subprocess
import sys
import time

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


def are_dir_trees_equal(dir1, dir2):

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
    WAAuth(parser)
    OrgOrGuess(parser)
    parser.add_argument('target_dir', help='Target directory')

    args = parser.parse_args()

    wa = WebApolloInstance(args.apollo, args.username, args.password)
    # User must have an account
    org_cn = GuessOrg(args, wa)
    if isinstance(org_cn, list):
        org_cn = org_cn[0]
    org = wa.organisms.findOrganismByCn(org_cn)

    if not os.path.exists(args.target_dir):
        os.makedirs(args.target_dir)

    if not os.path.exists(os.path.join(org['directory'], 'seq')):

5:696a1962212e

import os
import subprocess
import sys
import time

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


def are_dir_trees_equal(dir1, dir2):

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
    WAAuth(parser)
    OrgOrGuess(parser)
    parser.add_argument('target_dir', help='Target directory')
    parser.add_argument('email', help='User Email')

    args = parser.parse_args()

    wa = WebApolloInstance(args.apollo, args.username, args.password)
    # User must have an account
    org_cn = GuessOrg(args, wa)
    if isinstance(org_cn, list):
        org_cn = org_cn[0]
    org = wa.organisms.findOrganismByCn(org_cn)

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

    # User must have READ access

    if not PermissionCheck(gx_user, org_cn, "READ"):
        raise Exception("READ permissions are required for this action")

    if not os.path.exists(args.target_dir):
        os.makedirs(args.target_dir)

    if not os.path.exists(os.path.join(org['directory'], 'seq')):