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import json
import os
import uuid
from gn3.commands import run_cmd
def create_dirs_if_not_exists(dirs: list):
for dir_ in dirs:
if not os.path.exists(dir_):
os.makedirs(dir_)
def remove_insignificant_edits(diff_data, epsilon=0.001):
_mod = []
for mod in diff_data.get("Modifications"):
original = mod.get("Original").split(",")
current = mod.get("Current").split(",")
for i, (x, y) in enumerate(zip(original, current)):
if all([
x.replace('.', '').isdigit(),
y.replace('.', '').isdigit(),
abs(float(x) - float(y)) < epsilon,
]):
current[i] = x
if not (__o := ",".join(original)) == (__c := ",".join(current)):
_mod.append({
"Original": __o,
"Current": __c,
})
diff_data['Modifications'] = _mod
return diff_data
def csv_diff(base_csv, delta_csv, tmp_dir="/tmp"):
base_csv_list = base_csv.strip().split("\n")
delta_csv_list = delta_csv.strip().split("\n")
_header1, _header2 = "", ""
for i, line in enumerate(base_csv_list):
if line.startswith("Strain Name,Value,SE,Count"):
_header1, _header2 = line, delta_csv_list[i]
break
if _header1 != _header2:
header = max(_header1, _header2)
base_csv = base_csv.replace("Strain Name,Value,SE,Count",
header, 1)
delta_csv = delta_csv.replace("Strain Name,Value,SE,Count",
header, 1)
file_name1 = os.path.join(tmp_dir, str(uuid.uuid4()))
file_name2 = os.path.join(tmp_dir, str(uuid.uuid4()))
with open(file_name1, "w") as f_:
f_.write(base_csv)
with open(file_name2, "w") as f_:
f_.write(delta_csv)
# Now we can run the diff!
_r = run_cmd(cmd=("csvdiff "
f"'{file_name1}' '{file_name2}' "
"--format json"))
if _r.get("code") == 0:
_r["output"] = json.loads(_r.get("output"))
# Clean Up!
if os.path.exists(file_name1):
os.remove(file_name1)
if os.path.exists(file_name2):
os.remove(file_name2)
return _r
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