util.py

# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.
"""
Helper functions for the JobCore and GenericJob objects
"""
import os
import posixpath
import psutil
import tarfile
import stat
import shutil
from typing import Optional, Union
from pyiron_base.utils.instance import static_isinstance
from pyiron_base.utils.safetar import safe_extract

__author__ = "Jan Janssen"
__copyright__ = (
    "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH - "
    "Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "Jan Janssen"
__email__ = "janssen@mpie.de"
__status__ = "production"
__date__ = "Nov 28, 2020"


def _copy_database_entry(new_job_core, job_copied_id):
    """
    Copy database entry from previous job

    Args:
        new_job_core (GenericJob): Copy of the job object
        job_copied_id (int): Job id of the copied job
    """
    db_entry = new_job_core.project.db.get_item_by_id(job_copied_id)
    if db_entry is not None:
        db_entry["job"] = new_job_core.job_name
        db_entry["subjob"] = new_job_core.project_hdf5.h5_path
        db_entry["project"] = new_job_core.project_hdf5.project_path
        db_entry["projectpath"] = new_job_core.project_hdf5.root_path
        del db_entry["id"]
        job_id = new_job_core.project.db.add_item_dict(db_entry)
        new_job_core.reset_job_id(job_id=job_id)


def _copy_to_delete_existing(project_class, job_name, delete_job):
    """
    Check if the job exists already in the project, if that is the case either
    delete it or reload it depending on the setting of delete_job

    Args:
        project_class (Project): The project to copy the job to.
            (Default is None, use the same project.)
        job_name (str): The new name to assign the duplicate job. Required if the project is `None` or the same
            project as the copied job. (Default is None, try to keep the same name.)
        delete_job (bool): Delete job if it exists already

    Returns:
        GenericJob/ None
    """
    job_table = project_class.job_table(recursive=False)
    if len(job_table) > 0 and job_name in job_table.job.values:
        if not delete_job:
            return project_class.load(job_name)
        else:
            project_class.remove_job(job_name)
            return None


def _get_project_for_copy(job, project, new_job_name):
    """
    Internal helper function to generate a project and hdf5 project for copying

    Args:
        job (JobCore): Job object used for comparison
        project (JobCore/ProjectHDFio/Project/None): The project to copy the job to.
            (Default is None, use the same project.)
        new_job_name (str): The new name to assign the duplicate job. Required if the
            project is `None` or the same project as the copied job. (Default is None,
            try to keep the same name.)

    Returns:
        Project, ProjectHDFio
    """
    if static_isinstance(
        obj=project.__class__, obj_type="pyiron_base.jobs.job.core.JobCore"
    ):
        file_project = project.project
        hdf5_project = project.project_hdf5.open(new_job_name)
    elif isinstance(project, job.project.__class__):
        file_project = project
        hdf5_project = job.project_hdf5.__class__(
            project=project, file_name=new_job_name, h5_path="/" + new_job_name
        )
    elif isinstance(project, job.project_hdf5.__class__):
        file_project = project.project
        hdf5_project = project.open(new_job_name)
    elif project is None:
        file_project = job.project
        hdf5_project = job.project_hdf5.__class__(
            project=file_project, file_name=new_job_name, h5_path="/" + new_job_name
        )
    else:
        raise ValueError("Project should be JobCore/ProjectHDFio/Project/None")
    return file_project, hdf5_project


_special_symbol_replacements = {
    ".": "d",
    "-": "m",
    "+": "p",
    ",": "c",
    " ": "_",
}


def _get_safe_job_name(
    name: Union[str, tuple],
    ndigits: Optional[int] = 8,
    special_symbols: Optional[dict] = None,
):
    """
    Sanitize a job name, optionally appending numeric values.

    Args:
        name (str|tuple): The name to sanitize, or a tuple of the name and any number
            of numeric values to append with '_' in between.
        ndigits (int|None): How many digits to round any floating point values in a
            `name` tuple to. (Default is 8; to not round at all use None.)
        special_symbols (dict|None): Conversions of special symbols to apply. This will
            be applied to the default conversion dict, which contains:
            DEFAULT_CONV_DICT

    Returns:
        (str): The sanitized (and possibly rounded) name.
    """
    d_special_symbols = _special_symbol_replacements.copy()
    if special_symbols is not None:
        d_special_symbols.update(special_symbols)

    def round_(value, ndigits=ndigits):
        if isinstance(value, float) and ndigits is not None:
            return round(value, ndigits=ndigits)
        return value

    if not isinstance(name, str):
        name_rounded = [round_(nn) for nn in name]
        job_name = "_".join([str(nn) for nn in name_rounded])
    else:
        job_name = name
    for k, v in d_special_symbols.items():
        job_name = job_name.replace(k, v)
    _is_valid_job_name(job_name=job_name)
    return job_name


_get_safe_job_name.__doc__ = _get_safe_job_name.__doc__.replace(
    "DEFAULT_CONV_DICT", f"{_special_symbol_replacements}"
)


def _rename_job(job, new_job_name):
    """ """
    new_job_name = _get_safe_job_name(new_job_name)
    child_ids = job.child_ids
    if child_ids:
        for child_id in child_ids:
            ham = job.project.load(child_id)
            ham.move_to(job.project.open(new_job_name + "_hdf5"))
    old_working_directory = job.working_directory
    if len(job.project_hdf5.h5_path.split("/")) > 2:
        new_location = job.project_hdf5.open("../" + new_job_name)
    else:
        new_location = job.project_hdf5.__class__(
            job.project, new_job_name, h5_path="/" + new_job_name
        )
    if job.job_id:
        job.project.db.item_update(
            {"job": new_job_name, "subjob": new_location.h5_path}, job.job_id
        )
    old_job_name = job.name
    job._name = new_job_name
    job.project_hdf5.copy_to(destination=new_location, maintain_name=False)
    job.project_hdf5.remove_file()
    job.project_hdf5 = new_location
    if os.path.exists(old_working_directory):
        shutil.move(old_working_directory, job.working_directory)
        os.rmdir("/".join(old_working_directory.split("/")[:-1]))
    if os.path.exists(os.path.join(job.working_directory, old_job_name + ".tar.bz2")):
        os.rename(
            os.path.join(job.working_directory, old_job_name + ".tar.bz2"),
            os.path.join(job.working_directory, job.job_name + ".tar.bz2"),
        )


def _is_valid_job_name(job_name):
    """
    internal function to validate the job_name - only available in Python 3.4 <

    Args:
        job_name (str): job name
    """
    if not job_name.isidentifier():
        raise ValueError(
            f'Invalid name for a pyiron object, must be letters, digits (not as first character) and "_" only, not {job_name}'
        )
    if len(job_name) > 50:
        raise ValueError(
            "Invalid name for a PyIron object: must be less then or "
            "equal to 50 characters"
        )


def _copy_restart_files(job):
    """
    Internal helper function to copy the files required for the restart job.
    """
    if not (os.path.isdir(job.working_directory)):
        raise ValueError(
            "The working directory is not yet available to copy restart files"
        )
    for i, actual_name in enumerate(
        [os.path.basename(f) for f in job.restart_file_list]
    ):
        if actual_name in job.restart_file_dict.keys():
            new_name = job.restart_file_dict[actual_name]
            shutil.copy(
                job.restart_file_list[i],
                posixpath.join(job.working_directory, new_name),
            )
        else:
            shutil.copy(job.restart_file_list[i], job.working_directory)


def _kill_child(job):
    """
    Internal helper function to kill a child process.

    Args:
        job (JobCore): job object to decompress
    """
    if (
        static_isinstance(
            obj=job.__class__, obj_type="pyiron_base.jobs.master.GenericMaster"
        )
        and not job.server.run_mode.queue
        and (job.status.running or job.status.submitted)
    ):
        for proc in psutil.process_iter():
            try:
                pinfo = proc.as_dict(attrs=["pid", "cwd"])
            except psutil.NoSuchProcess:
                pass
            else:
                if pinfo["cwd"] is not None and pinfo["cwd"].startswith(
                    job.working_directory
                ):
                    job_process = psutil.Process(pinfo["pid"])
                    job_process.kill()


def _job_compress(job, files_to_compress=None):
    """
    Compress the output files of a job object.

    Args:
        job (JobCore): job object to compress
        files_to_compress (list): list of files to compress
    """
    if not _job_is_compressed(job):
        if files_to_compress is None:
            files_to_compress = list(job.list_files())
        cwd = os.getcwd()
        try:
            os.chdir(job.working_directory)
            with tarfile.open(
                os.path.join(job.working_directory, job.job_name + ".tar.bz2"),
                "w:bz2",
            ) as tar:
                for name in files_to_compress:
                    if "tar" not in name and not stat.S_ISFIFO(os.stat(name).st_mode):
                        tar.add(name)
            for name in files_to_compress:
                if "tar" not in name:
                    fullname = os.path.join(job.working_directory, name)
                    if os.path.isfile(fullname):
                        os.remove(fullname)
                    elif os.path.isdir(fullname):
                        shutil.rmtree(fullname)
        finally:
            os.chdir(cwd)
    else:
        print("The files are already compressed!")


def _job_decompress(job):
    """
    Decompress the output files of a compressed job object.

    Args:
        job (JobCore): job object to decompress
    """
    try:
        tar_file_name = os.path.join(job.working_directory, job.job_name + ".tar.bz2")
        with tarfile.open(tar_file_name, "r:bz2") as tar:
            safe_extract(tar, job.working_directory)
        os.remove(tar_file_name)
    except IOError:
        pass


def _job_is_compressed(job):
    """
    Check if the job is already compressed or not.

    Args:
        job (JobCore): job object to check

    Returns:
        bool: [True/False]
    """
    compressed_name = job.job_name + ".tar.bz2"
    for name in job.list_files():
        if compressed_name in name:
            return True
    return False


def _job_archive(job):
    """
    Compress HDF5 file of the job object to tar-archive

    Args:
        job (JobCore): job object to archive
    """
    fpath = job.project_hdf5.file_path
    jname = job.job_name
    h5_dir_name = jname + "_hdf5"
    h5_file_name = jname + ".h5"
    cwd = os.getcwd()
    try:
        os.chdir(fpath)
        with tarfile.open(
            os.path.join(fpath, job.job_name + ".tar.bz2"), "w:bz2"
        ) as tar:
            for name in [h5_dir_name, h5_file_name]:
                tar.add(name)
        for name in [h5_dir_name, h5_file_name]:
            fullname = os.path.join(fpath, name)
            if os.path.isfile(fullname):
                os.remove(fullname)
            elif os.path.isdir(fullname):
                shutil.rmtree(fullname)
    finally:
        os.chdir(cwd)


def _job_unarchive(job):
    """
    Decompress HDF5 file of the job object from tar-archive

    Args:
        job (JobCore): job object to unarchive
    """
    fpath = job.project_hdf5.file_path
    try:
        tar_name = os.path.join(fpath, job.job_name + ".tar.bz2")
        with tarfile.open(tar_name, "r:bz2") as tar:
            safe_extract(tar, fpath)
        os.remove(tar_name)
    finally:
        pass


def _job_is_archived(job):
    """
    Check if the HDF5 file of the Job is compressed as tar-archive

    Args:
        job (JobCore): job object to check

    Returns:
        bool: [True/False]
    """
    return os.path.isfile(
        os.path.join(job.project_hdf5.file_path, job.job_name + ".tar.bz2")
    )


def _job_delete_hdf(job):
    """
    Delete HDF5 file of job object

    Args:
        job (JobCore): job object to delete
    """
    if os.path.isfile(job.project_hdf5.file_name):
        os.remove(job.project_hdf5.file_name)


def _job_delete_files(job):
    """
    Delete files in the working directory of job object

    Args:
        job (JobCore): job object to delete
    """
    working_directory = str(job.working_directory)
    if job._import_directory is None and os.path.exists(working_directory):
        shutil.rmtree(working_directory)
    else:
        job._import_directory = None


def _job_remove_folder(job):
    """
    Delete the working directory of the job object

    Args:
        job (JobCore): job object to delete
    """
    working_directory = os.path.abspath(os.path.join(str(job.working_directory), ".."))
    if os.path.exists(working_directory) and len(os.listdir(working_directory)) == 0:
        shutil.rmtree(working_directory)


def _job_store_before_copy(job):
    """
    Store job in HDF5 file for copying

    Args:
        job (GenericJob): job object to copy

    Returns:
        bool: [True/False] if the HDF5 file of the job exists already
    """
    if not job.project_hdf5.file_exists:
        delete_file_after_copy = True
    else:
        delete_file_after_copy = False
    job.to_hdf()
    return delete_file_after_copy


def _job_reload_after_copy(job, delete_file_after_copy):
    """
    Reload job from HDF5 file after copying

    Args:
        job (GenericJob): copied job object
        delete_file_after_copy (bool): delete HDF5 file after reload
    """
    job.from_hdf()
    if delete_file_after_copy:
        job.project_hdf5.remove_file()