Source code for schrodinger.application.phase.packages.hypo_refine.job_utils

"""
Module with phase_hypo_refine job control functionality.

Copyright Schrodinger LLC, All Rights Reserved.
"""

from schrodinger.application.phase.packages import phase_utils
from schrodinger.application.phase.packages.hypo_refine import project_utils
from schrodinger.infra import phase
from schrodinger.job import jobcontrol
from schrodinger.utils import fileutils


def get_common_args(args):
    """
    Returns a command containing arguments that are common to all subjobs.

    :param args: argparser.Namespace with command line options
    :type args: argparser.Namespace

    :return: Command with common arguments
    :rtype: list(str)
    """

    common_args = []
    for key, value in args.__dict__.items():
        if key not in ("hypo", "actives", "decoys", "host"):
            flag = "-" + key
            if value is not None:
                if value is True:
                    common_args.append(flag)
                elif value is not False:
                    common_args.extend([flag, str(value)])

    return common_args


def get_input_files(args):
    """
    Returns the names of the input files for the current job/subjob.

    :param args: Command line arguments
    :type args: argparse.Namespace

    :return: Input file names
    :rtype: list(str)
    """

    input_files = []
    if args.subjob:
        input_files.append(args.subjob + phase.PHASE_HYPO_FILE_EXT)
        input_files.append(args.actives)
        input_files.append(args.decoys)
    else:
        input_files.append(args.hypo)
        for key, infile in project_utils.get_screen_dict(args).items():
            input_files.append(infile)

    return input_files


def get_output_hypo(args):
    """
    Returns the name of the hypothesis file to create.

    :param args: Command line arguments
    :type args: argparse.Namespace

    :return: Output hypothesis file name
    :rtype: str
    """

    if args.subjob:
        hypo_out = args.subjob + "-out" + phase.PHASE_HYPO_FILE_EXT
    else:
        hypo_out = args.o
        if not hypo_out:
            jobname = phase_utils.get_jobname(args, args.hypo)
            hypo_out = jobname + "-out" + phase.PHASE_HYPO_FILE_EXT

    return hypo_out


def get_output_projects(args):
    """
    Returns the names of any zipped projects that would be created.

    :param args: Command line arguments
    :type args: argparse.Namespace

    :return: Output zipped project names
    :rtype: list(str)
    """

    zipped_projects = []
    for key, infile in project_utils.get_screen_dict(args).items():
        if not phase_utils.is_phase_project_path(infile, zipped=True):
            zipped_projects.append(
                project_utils.derive_project_name(infile, zipped=True))

    return zipped_projects


def remove_output_files(args):
    """
    Removes output files that would be created in the launch directory by the
    parent job.

    :param args: Command line arguments
    :type args: argparse.Namespace
    """

    if not jobcontrol.under_job_control():
        jobname = phase_utils.get_jobname(args, args.hypo)
        fileutils.force_remove(jobname + ".log")

        # Don't remove output hypothesis if the job is being run solely to
        # create zipped active/decoy projects.
        if not args.exit:
            fileutils.force_remove(get_output_hypo(args))

        # Remove any zipped projects that would be returned.
        if args.save_projects:
            for zipped_project in get_output_projects(args):
                fileutils.force_remove(zipped_project)


def save_hypo_for_job(args, hypo):
    """
    Saves the provided hypothesis as <jobname>.phypo and replaces args.hypo
    with this file name.

    :param args: Command line arguments
    :type args: argparse.Namespace

    :param hypo: Hypothesis
    :type hypo: phase.PhpHypoAdaptor
    """

    jobname = phase_utils.get_jobname(args, args.hypo)
    args.hypo = jobname + phase.PHASE_HYPO_FILE_EXT
    hypo.save(args.hypo, True)