robot_utils.py

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

import os
import subprocess # Source: https://docs.python.org/2/library/subprocess.html#popen-constructor

def initialize_robot(path:str) -> list:
    '''
    This initializes ROBOT with necessary configuration.

    :param path: Path to ROBOT files.
    :return: A list consisting of robot shell script name and environment variables.
    '''
     # Declare variables
    robot_file = os.path.join(path, 'robot')

     # Declare environment variables
    env = dict(os.environ)
    #(JDK compatibility issue: https://stackoverflow.com/questions/49962437/unrecognized-vm-option-useparnewgc-error-could-not-create-the-java-virtual)
    #env['ROBOT_JAVA_ARGS'] = '-Xmx8g -XX:+UseConcMarkSweepGC' # for JDK 9 and older 
    env['ROBOT_JAVA_ARGS'] = '-Xmx12g -XX:+UseG1GC' # For JDK 10 and over
    env['PATH'] = os.environ['PATH']
    env['PATH'] += os.pathsep + path

    return [robot_file, env]

def convert_to_json(path:str, ont:str):
    """
    This method converts owl to JSON using ROBOT and the subprocess library

    :param path: Path to ROBOT files
    :param ont: Ontology
    :return: None
    """
   
    robot_file, env = initialize_robot(path)
    input_owl = os.path.join(path, ont.lower()+'.owl')
    output_json = os.path.join(path, ont.lower()+'.json')
    if not os.path.isfile(output_json):
        # Setup the arguments for ROBOT through subprocess
        call = ['bash', robot_file, 'convert', \
                                    '--input', input_owl, \
                                    '--output', output_json, \
                                    '-f', 'json']

        subprocess.call(call, env=env)
    
    return None

def extract_convert_to_json(path:str, ont_name:str, terms:str, mode:str):
    """
    This method extracts all children of provided CURIE.

    :param path: path of file to be converted
    :param ont_name: Name of the ontology
    :param terms: Either CURIE or a file of CURIEs list
    :param mode: Method options as listed below.
    :return: None

    ROBOT Method options:

    -   STAR: The STAR-module contains mainly the terms in the seed and the inter-relations between them (not necessarily sub- and super-classes).

    -   TOP: The TOP-module contains mainly the terms in the seed, plus all their sub-classes and the inter-relations between them. 

    -   BOT: The BOT, or BOTTOM, -module contains mainly the terms in the seed, plus all their super-classes and the inter-relations between them. 

    -   MIREOT : The MIREOT method preserves the hierarchy of the input ontology (subclass and subproperty relationships), but does not try to preserve the full set of logical entailments.

    """

    robot_file, env = initialize_robot(path)
    input_owl = os.path.join(path, ont_name.lower()+'.owl')
    output_json = os.path.join(path, ont_name.lower()+'.json')
    output_owl = os.path.join(path, ont_name.lower()+'_extracted_subset.owl')
    
    if ':' in terms:
        call = ['bash', robot_file, 'extract', \
                                '--method', mode, \
                                '--input', input_owl, \
                                '--output', output_owl, \
                                '--term', terms, \
                                'convert', \
                                '--output', output_json, \
                                '-f', 'json']
    else:
        call = ['bash', robot_file, 'extract', \
                                    '--method', mode, \
                                    '--input', input_owl, \
                                    '--output', output_owl, \
                                    '--term-file', terms, \
                                    'convert', \
                                    '--output', output_json, \
                                    '-f', 'json']
    
    subprocess.call(call, env=env)

    return None