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"""Procedures related gemma computations"""
import os
import random
import string
from base64 import b64encode
from hashlib import md5
from typing import List
from typing import ValuesView
def generate_random_n_string(n_length: int) -> str:
"""Generate a random string that is N chars long"""
return ''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(n_length))
def generate_hash_of_string(unhashed_str: str) -> str:
"""Given an UNHASHED_STRING, generate it's md5 hash while removing the '==' at
the end"""
hashed_str = md5(unhashed_str.encode("utf-8")).digest()
return b64encode(hashed_str).decode("utf-8").replace("==", "")
def generate_pheno_txt_file(trait_filename: str,
values: List,
tmpdir: str = "/tmp") -> str:
"""Given VALUES, and TMPDIR, generate a valid traits file"""
if not os.path.isdir(f"{tmpdir}/gn2/"):
os.mkdir(f"{tmpdir}/gn2/")
ext = trait_filename.partition(".")[-1]
if ext:
trait_filename = trait_filename.replace(f".{ext}", "")
ext = f".{ext}"
trait_filename += f"_{generate_hash_of_string(''.join(values))}{ext}"
# Early return if this already exists!
if os.path.isfile(f"{tmpdir}/gn2/{trait_filename}"):
return f"{tmpdir}/gn2/{trait_filename}"
with open(f"{tmpdir}/gn2/{trait_filename}", "w") as _file:
for value in values:
if value == "x":
_file.write("NA\n")
else:
_file.write(f"{value}\n")
return f"{tmpdir}/gn2/{trait_filename}"
def do_paths_exist(paths: ValuesView) -> bool:
"""Given a list of PATHS, return False if any of them do not exist."""
for path in paths:
if not os.path.isfile(path):
return False
return True
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