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import json
import os
import uuid
from gn3.commands import run_cmd
def extract_strain_name(csv_header, data, seek="Strain Name"):
for column, value in zip(csv_header.split(","), data.split(",")):
if seek in column:
return value
return ""
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 (x.replace('.', '').isdigit() and
y.replace('.', '').isdigit() and
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")
base_csv_header, delta_csv_header, header = "", "", ""
for i, line in enumerate(base_csv_list):
if line.startswith("Strain Name,Value,SE,Count"):
header = line
base_csv_header, delta_csv_header= line, delta_csv_list[i]
break
longest_header = max(base_csv_header, delta_csv_header)
if base_csv_header != delta_csv_header:
if longest_header != base_csv_header:
base_csv = base_csv.replace("Strain Name,Value,SE,Count",
longest_header, 1)
else:
delta_csv = delta_csv.replace("Strain Name,Value,SE,Count",
longest_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_:
_l = len(longest_header.split(","))
f_.write(fill_csv(csv_text=base_csv,
width=_l))
with open(file_name2, "w") as f_:
f_.write(fill_csv(delta_csv,
width=_l))
# Now we can run the diff!
_r = run_cmd(cmd=('"csvdiff '
f'{file_name1} {file_name2} '
'--format json"'))
if _r.get("code") == 0:
_r = json.loads(_r.get("output"))
if any(_r.values()):
_r["Columns"] = max(base_csv_header, delta_csv_header)
else:
_r = {}
# Clean Up!
if os.path.exists(file_name1):
os.remove(file_name1)
if os.path.exists(file_name2):
os.remove(file_name2)
return _r
def fill_csv(csv_text, width, value="x"):
data = []
for line in csv_text.strip().split("\n"):
if line.startswith("Strain") or line.startswith("#"):
data.append(line)
elif line:
_n = line.split(",")
for i, val in enumerate(_n):
if not val.strip():
_n[i] = value
data.append(
",".join(_n + [value] * (width - len(_n))))
return "\n".join(data)
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