comparison util/subtools.py @ 2:4be6fcac4bf2 draft default tip

planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894

1:78af01d73add

    p = _handleExceptionAndCheckCall(array_call)
    j = json.loads(p)
    if "userId" in j:
        return j['userId']
    elif "error" in j:
        logging.error("User %s already exist", user_email)
        raise Exception(j['error'])
        
        
def arrow_delete_user(user_email):
    array_call = ['arrow', 'users', 'delete_user', user_email]
    p = _handleExceptionAndCheckCall(array_call)
    j = json.loads(p)
    if "error" in j:
        raise Exception(j['error'])

def arrow_add_to_group(groupname, user_email):
    if not arrow_get_groups(groupname):
        arrow_create_group(groupname)
    array_call = ['arrow', 'users', 'add_to_group', groupname, user_email]
    p = _handleExceptionAndCheckCall(array_call)
    j = json.loads(p)
    if j != dict():
        raise Exception("Error add user %s to group %s", user_email, groupname)


def arrow_remove_from_group(groupname, user_email):
    if arrow_get_groups(groupname):
        array_call = ['arrow', 'users', 'remove_from_group', groupname, user_email]
        p = _handleExceptionAndCheckCall(array_call)
    else:
        raise Exception("Group %s doesn't exist. Check if you spell the name correctly", groupname)

def arrow_create_group(groupname):
    if arrow_get_groups(groupname):
        raise Exception("Group %s already exist. Create a group with another name.", groupname)
    array_call = ['arrow', 'groups', 'create_group', groupname]
    p = _handleExceptionAndCheckCall(array_call)

def arrow_get_groups(groupname):
    array_call = ['arrow', 'groups', 'get_groups']

def arrow_get_users(user_email):
    array_call = ['arrow', 'users', 'get_users']
    p = _handleExceptionAndCheckCall(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)

def arrow_get_organism(organism_name):
    array_call= ['arrow', 'organisms', 'get_organisms']
    p = _handleExceptionAndCheckCall(array_call)
    all_organisms = json.loads(p)
    for org in all_organisms:
        if org['commonName'] == organism_name:
            return org['id']
    

def arrow_delete_organism(organism_id):
    array_call = ['arrow', 'organisms', 'delete_organism', organism_id]
    p = _handleExceptionAndCheckCall(array_call)
    return p
    
def verify_user_login(username, password, apollo_host):
    user_info = {'username': username, 'password': password}

2:4be6fcac4bf2

    p = _handleExceptionAndCheckCall(array_call)
    j = json.loads(p)
    if "userId" in j:
        return j['userId']
    elif "error" in j:
        logging.error("Got error message: %s", j['error'])
        exit(-1)
        
        
def arrow_delete_user(user_email):
    array_call = ['arrow', 'users', 'delete_user', user_email]
    p = _handleExceptionAndCheckCall(array_call)
    j = json.loads(p)
    if "error" in j:
        logging.error("Got error message: %s", j['error'])
        exit(-1)

def arrow_add_to_group(groupname, user_email):
    if not arrow_get_groups(groupname):
        arrow_create_group(groupname)
    array_call = ['arrow', 'users', 'add_to_group', groupname, user_email]
    p = _handleExceptionAndCheckCall(array_call)
    j = json.loads(p)
    if j != dict():
        logging.error("Error add user %s to group %s. The user doesn't exist", user_email, groupname)


def arrow_remove_from_group(groupname, user_email):
    if arrow_get_groups(groupname):
        array_call = ['arrow', 'users', 'remove_from_group', groupname, user_email]
        p = _handleExceptionAndCheckCall(array_call)
        j = json.loads(p)
        if j != dict():
            logging.error("Error remove user %s to group %s. The user doesn't exist", user_email, groupname)
    else:
        logging.error("Group %s doesn't exist. Check if you spell the name correctly", groupname)

def arrow_create_group(groupname):
    if arrow_get_groups(groupname):
        logging.error("Group %s already exist. Create a group with another name.", groupname)
    array_call = ['arrow', 'groups', 'create_group', groupname]
    p = _handleExceptionAndCheckCall(array_call)

def arrow_get_groups(groupname):
    array_call = ['arrow', 'groups', 'get_groups']

def arrow_get_users(user_email):
    array_call = ['arrow', 'users', 'get_users']
    p = _handleExceptionAndCheckCall(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)

def arrow_get_organism(organism_name):
    array_call= ['arrow', 'organisms', 'get_organisms', '--common_name', organism_name]
    p = _handleExceptionAndCheckCall(array_call)
    org = json.loads(p)
    if 'error' not in org:
        return org[0]['id']
    else:
        logging.debug("Got error msg %s when look for organism %s.", org['error'], organism_name)

def arrow_delete_organism(organism_id):
    array_call = ['arrow', 'organisms', 'delete_organism', str(organism_id)]
    p = _handleExceptionAndCheckCall(array_call)
    return p
    
def verify_user_login(username, password, apollo_host):
    user_info = {'username': username, 'password': password}