comparison util/subtools.py @ 32:7b955a58d8f2 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty

31:127037c49bc8

        if tab:
            array_call.append('-tab')
    p = _handleExceptionAndCheckCall(array_call)
    return p

def arrow_add_organism(organism_name, organism_dir, public=False):
    array_call = ['arrow', 'organisms', 'add_organism', organism_name, organism_dir]
    if public:
        array_call.append('--public')
    p = subprocess.check_output(array_call)
    return p

def arrow_create_user(user_email, firstname, lastname, password, admin=False):
    """ Create a new user of Apollo, the default user_role is "user" """
    array_call = ['arrow', 'users', 'create_user', user_email, firstname, lastname, password]
    if admin:
        array_call += ['--role', 'admin']
    logging.debug("%s", array_call)
    print array_call
    p = subprocess.check_output(array_call)
    print ("p = %s", p)
    return p

def arrow_update_organism_permissions(user_id, organism, **user_permissions):
    array_call = ['arrow', 'users', 'update_organism_permissions', str(user_id), str(organism)]
    admin = user_permissions.get("admin", False)
    write = user_permissions.get("write", False)
    read = user_permissions.get("read", False)
    export = user_permissions.get("export", False)
    if admin:
        array_call.append('--administrate')
    if write:
        array_call.append('--write')
    if read:
        array_call.append('--read')
    if export:
        array_call.append('--export')
    p = subprocess.check_output(array_call)
    return p

def arrow_get_users(user_email):
    array_call = ['arrow', 'users', 'get_users']
    logging.debug("%s", array_call)
    print array_call
    p = subprocess.check_output(array_call)
    all_users = json.loads(p)
    for d  in all_users:
        if d['username'] == user_email:
            return d['userId']
    logging.error("Cannot find user %s", user_email)

32:7b955a58d8f2

        if tab:
            array_call.append('-tab')
    p = _handleExceptionAndCheckCall(array_call)
    return p