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) print(delta_csv) 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: data.append( ",".join((_n:=line.split(",")) + [value] * (width - len(_n)))) return "\n".join(data)