# -*- coding: utf-8 -*-
# pylint: disable=invalid-name
"""
Some general utility functions for the oxidation state mining project
"""
import hashlib
import json
import os
import pickle
import urllib
from collections.abc import Iterable
from functools import partial
from pathlib import Path
from typing import Union
import numpy as np
from pymatgen.core import Element
from .config import MODEL_CONFIG
[docs]def md5sum(filename: Union[str, Path]):
"""Gets the md5 hash of a file"""
with open(filename, "rb") as f:
d = hashlib.md5()
for buf in iter(partial(f.read, 128), b""):
d.update(buf)
return d.hexdigest()
[docs]def model_exists(path: Union[Path, str], md5: str):
"""Checks whether a model if the expected md5 hash
exists at the path"""
is_exist = False
if os.path.exists(path):
this_file_md5 = md5sum(path)
if this_file_md5 == md5:
is_exist = True
return is_exist
[docs]def cbk_for_urlretrieve(a, b, c):
"""
Callback function for showing process
"""
per = 100.0 * a * b / c
if per > 100:
per = 100
print("\r%.1f%% of %.2fM" % (per, c / (1024 * 1024)), end="")
[docs]def download_model(url: str, destination: Union[Path, str], md5: str):
"""Downloads file from url to destination
and checks md5 hash
Args:
url (str): URL
destination (Union[Path, str]): Path to which the downloaded file
will be saved
md5 (str): Expected md5 hash
Raises:
Exception: [description]
Exception: [description]
"""
if not model_exists(destination, md5):
print("{} does not exist or md5 is wrong.".format(destination))
print("Download file from {}".format(url))
try:
basedir = Path(destination).parent
if not os.path.exists(basedir):
os.makedirs(basedir)
urllib.request.urlretrieve(url, destination, cbk_for_urlretrieve)
this_file_md5 = md5sum(destination)
if this_file_md5 == md5:
print("\nDownload {} file successfully.".format(destination))
else:
raise Exception("Md5 wrong.")
except Exception as error:
infos = "[Error]: Download from {} failed due to {}".format(url, error)
raise Exception(infos) from error
[docs]def download_all():
"""Download model and scaler"""
for _, v in MODEL_CONFIG.items():
download_model(v["scaler"]["url"], v["scaler"]["path"], v["scaler"]["md5"])
download_model(
v["classifier"]["url"], v["classifier"]["path"], v["classifier"]["md5"]
)
[docs]def read_pickle(filepath: str):
"""Does what it says. Nothing more and nothing less.
Takes a pickle file path and unpickles it"""
with open(filepath, "rb") as fh: # pylint: disable=invalid-name
result = pickle.load(fh) # pylint: disable=invalid-name
return result
[docs]def flatten(items):
"""Yield items from any nested iterable; see Reference."""
for x in items:
if isinstance(x, Iterable) and not isinstance(x, (str, bytes)):
for sub_x in flatten(x):
yield sub_x
else:
yield x
[docs]def diff_to_18e(nvalence):
"""The number of electrons to donate to achieve 18 electrons might be an interesting descriptor,
though there are more stable electron configurations"""
return min(np.abs(nvalence - 18), nvalence)
[docs]class SymbolNameDict: # pylint: disable=too-few-public-methods
"""Parses the periodic table json and returns a dictionary with symbol: longname"""
[docs] def __init__(self):
with open(
os.path.join(
Path(__file__).absolute().parent, "assets", "periodic_table.json"
),
"r",
) as periodic_table_file:
self.pt_data = json.load(periodic_table_file)
self.symbol_name_dict = {}
[docs] def get_symbol_name_dict(self, only_metal=True):
"""
Iterates over keys and returns the symbol: name dict.
"""
for key, value in self.pt_data.items():
if only_metal:
if Element(key).is_metal:
self.symbol_name_dict[key] = value["Name"].lower()
else:
self.symbol_name_dict[key] = value["Name"].lower()
return self.symbol_name_dict
