utilities.py

#!/usr/bin/python
# -*- coding: utf-8 -*-

import yaml
import logging
import sys

def parse_input(input_file):
    """
    Parse the yml input file to extract data to create the SpeciesData objects
    Return a list of dictionaries. Each dictionary contains data tied to a species

    :param input_file:
    :return:
    """

    parsed_sp_dict_list = []

    if str(input_file).endswith("yml") or str(input_file).endswith("yaml"):
        logging.debug("Input format used: YAML")
    else:
        logging.critical("Error, please input a YAML file")
        sys.exit()
    with open(input_file, 'r') as stream:
        try:
            yaml_dict = yaml.safe_load(stream)
            for k, v in yaml_dict.items():
                if k == "config":
                    pass
                parsed_sp_dict_list.append(v)
        except yaml.YAMLError as exit_code:
            logging.critical(exit_code + " (YAML input file might be incorrect)")
            sys.exit()
    return parsed_sp_dict_list

def filter_empty_not_empty_items(li):
    ret = {"empty": [], "not_empty": []}
    for i in li:
        if i is None or i == "":
            ret["empty"].append(i)
        else:
            ret["not_empty"].append(i)
    return ret