""" Utility classes and functions.
"""
"""
BSD 3-Clause License
Copyright (c) 2019, Andrew Riha
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""
import datetime
import gzip
import io
import logging
from multiprocessing import Pool
import os
import re
import shutil
import tempfile
import zipfile
from atomicwrites import atomic_write
import pandas as pd
import snps
logger = logging.getLogger(__name__)
[docs]
class Parallelizer:
[docs]
def __init__(self, parallelize=False, processes=os.cpu_count()):
"""Initialize a `Parallelizer`.
Parameters
----------
parallelize : bool
utilize multiprocessing to speedup calculations
processes : int
processes to launch if multiprocessing
"""
self._parallelize = parallelize
self._processes = processes
def __call__(self, f, tasks):
"""Optionally parallelize execution of a function.
Parameters
----------
f : func
function to execute
tasks : list of dict
tasks to pass to `f`
Returns
-------
list
results of each call to `f`
"""
if self._parallelize:
with Pool(self._processes) as p:
return p.map(f, tasks)
else:
return map(f, tasks)
[docs]
class Singleton(type):
# https://stackoverflow.com/a/6798042
_instances = {}
def __call__(cls, *args, **kwargs):
if cls not in cls._instances:
cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs)
return cls._instances[cls]
[docs]
def create_dir(path):
"""Create directory specified by `path` if it doesn't already exist.
Parameters
----------
path : str
path to directory
Returns
-------
bool
True if `path` exists
"""
# https://stackoverflow.com/a/5032238
os.makedirs(path, exist_ok=True)
if os.path.exists(path):
return True
else:
return False
[docs]
def get_utc_now():
"""Get current UTC time.
Returns
-------
datetime.datetime
"""
try:
utc_now = datetime.datetime.now(datetime.UTC)
except AttributeError:
# For versions of Python without datetime.UTC
utc_now = datetime.datetime.utcnow()
return utc_now
[docs]
def save_df_as_csv(
df, path, filename, comment="", prepend_info=True, atomic=True, **kwargs
):
"""Save dataframe to a CSV file.
Parameters
----------
df : pandas.DataFrame
dataframe to save
path : str
path to directory where to save CSV file
filename : str or buffer
filename for file to save or buffer to write to
comment : str
header comment(s); one or more lines starting with '#'
prepend_info : bool
prepend file generation information as comments
atomic : bool
atomically write output to a file on local filesystem
**kwargs
additional parameters to `pandas.DataFrame.to_csv`
Returns
-------
str or buffer
path to saved file or buffer (empty str if error)
"""
buffer = False
if isinstance(filename, io.IOBase):
buffer = True
if isinstance(df, pd.DataFrame) and len(df) > 0:
if not buffer and not create_dir(path):
return ""
if buffer:
destination = filename
else:
destination = os.path.join(path, filename)
logger.info(f"Saving {os.path.relpath(destination)}")
if prepend_info:
s = (
f"# Generated by snps v{snps.__version__}, https://pypi.org/project/snps/\n"
f'# Generated at {get_utc_now().strftime("%Y-%m-%d %H:%M:%S")} UTC\n'
)
else:
s = ""
s += comment
if "na_rep" not in kwargs:
kwargs["na_rep"] = "--"
if buffer:
if not isinstance(destination, io.TextIOBase):
s = s.encode()
destination.write(s)
df.to_csv(destination, **kwargs)
destination.seek(0)
elif atomic:
fd, tmp_path = tempfile.mkstemp(dir=path)
with open(fd, mode="w") as f:
f.write(s)
# https://stackoverflow.com/a/29233924
df.to_csv(tmp_path, mode="a", **kwargs)
os.rename(tmp_path, destination)
else:
with open(destination, mode="w") as f:
f.write(s)
df.to_csv(destination, mode="a", **kwargs)
return destination
else:
logger.warning("no data to save...")
return ""
[docs]
def clean_str(s):
"""Clean a string so that it can be used as a Python variable name.
Parameters
----------
s : str
string to clean
Returns
-------
str
string that can be used as a Python variable name
"""
# http://stackoverflow.com/a/3305731
# https://stackoverflow.com/a/52335971
return re.sub(r"\W|^(?=\d)", "_", s)
[docs]
def zip_file(src, dest, arcname):
"""Zip a file.
Parameters
----------
src : str
path to file to zip
dest : str
path to output zip file
arcname : str
name of file in zip archive
Returns
-------
str
path to zipped file
"""
with atomic_write(dest, mode="wb", overwrite=True) as f:
with zipfile.ZipFile(f, "w") as f_zip:
# https://stackoverflow.com/a/16104667
f_zip.write(src, arcname=arcname)
return dest
[docs]
def gzip_file(src, dest):
"""Gzip a file.
Parameters
----------
src : str
path to file to gzip
dest : str
path to output gzip file
Returns
-------
str
path to gzipped file
"""
with open(src, "rb") as f_in:
with atomic_write(dest, mode="wb", overwrite=True) as f_out:
with gzip.open(f_out, "wb") as f_gzip:
shutil.copyfileobj(f_in, f_gzip)
return dest