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util.py
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# 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
"""
from itertools import islice
import os
import posixpath
import psutil
import tarfile
import stat
import shutil
import monty.io
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__ = "[email protected]"
__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_compressed_name(job):
"""Return the canonical file name of a compressed job."""
return _get_compressed_job_name(working_directory=job.working_directory)
def _get_compressed_job_name(working_directory):
"""Return the canonical file name of a compressed job from the working directory."""
return os.path.join(
working_directory, os.path.basename(working_directory) + ".tar.bz2"
)
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 = job.files.list()
cwd = os.getcwd()
try:
os.chdir(job.working_directory)
with tarfile.open(_job_compressed_name(job), "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:
job.logger.info("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
"""
tar_file_name = _job_compressed_name(job)
try:
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 _working_directory_is_compressed(working_directory):
"""
Check if the working directory of a given job is already compressed or not.
Args:
working_directory (str): working directory of the job object
Returns:
bool: [True/False]
"""
compressed_name = os.path.basename(
_get_compressed_job_name(working_directory=working_directory)
)
return compressed_name in os.listdir(working_directory)
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]
"""
return _working_directory_is_compressed(working_directory=job.working_directory)
def _working_directory_list_files(working_directory, include_archive=True):
"""
Returns list of files in the jobs working directory.
If the working directory is compressed, return a list of files in the archive.
Args:
working_directory (str): working directory of the job object to inspect files in
include_archive (bool): include files in the .tag.gz archive
Returns:
list of str: file names
"""
if os.path.isdir(working_directory):
uncompressed_files_lst = os.listdir(working_directory)
if include_archive and _working_directory_is_compressed(
working_directory=working_directory
):
compressed_job_name = _get_compressed_job_name(
working_directory=working_directory
)
with tarfile.open(compressed_job_name, "r") as tar:
compressed_files_lst = [
member.name for member in tar.getmembers() if member.isfile()
]
uncompressed_files_lst.remove(os.path.basename(compressed_job_name))
return uncompressed_files_lst + compressed_files_lst
else:
return uncompressed_files_lst
return []
def _job_list_files(job):
"""
Returns list of files in the jobs working directory.
If the job is compressed, return a list of files in the archive.
Args:
job (JobCore): job object to inspect files in
Returns:
list of str: file names
"""
return _working_directory_list_files(working_directory=job.working_directory)
def _working_directory_read_file(working_directory, file_name, tail=None):
"""
Return list of lines of the given file.
Transparently decompresses the file if working directory is compressed.
If `tail` is given and job is decompressed, only read the last lines
instead of traversing the full file.
Args:
working_directory (str): working directory of the job object
file_name (str): the file to print
tail (int, optional): only return the last lines
Raises:
FileNotFoundError: if the given file name does not exist in the job folder
"""
if file_name not in _working_directory_list_files(
working_directory=working_directory
):
raise FileNotFoundError(file_name)
if _working_directory_is_compressed(
working_directory=working_directory
) and file_name not in os.listdir(working_directory):
with tarfile.open(
_get_compressed_job_name(working_directory=working_directory),
encoding="utf8",
) as f:
lines = [
line.decode("utf8") for line in f.extractfile(file_name).readlines()
]
if tail is None:
return lines
else:
return lines[-tail:]
else:
file_name = posixpath.join(working_directory, file_name)
if tail is None:
with open(file_name) as f:
return f.readlines()
else:
lines = list(
reversed(
[
l + os.linesep
for l in islice(monty.io.reverse_readfile(file_name), tail)
]
)
)
# compatibility with the other methods
# monty strips all newlines, where as reading the other ways does
# not. So if a file does not end with a newline (as most text
# files) adding it to every line like above adds an additional one.
lines[-1] = lines[-1].rstrip(os.linesep)
return lines
def _job_read_file(job, file_name, tail=None):
"""
Return list of lines of the given file.
Transparently decompresses the file if job is compressed.
If `tail` is given and job is decompressed, only read the last lines
instead of traversing the full file.
Args:
file_name (str): the file to print
tail (int, optional): only return the last lines
Raises:
FileNotFoundError: if the given file name does not exist in the job folder
"""
return _working_directory_read_file(
working_directory=job.working_directory, file_name=file_name, tail=tail
)
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()