diff options
| -rw-r--r-- | wqflask/wqflask/correlation/pre_computes.py | 27 |
1 files changed, 9 insertions, 18 deletions
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py index aacc3071..b8a78a45 100644 --- a/wqflask/wqflask/correlation/pre_computes.py +++ b/wqflask/wqflask/correlation/pre_computes.py @@ -1,3 +1,4 @@ +import csv import json import os import hashlib @@ -174,10 +175,10 @@ def fetch_text_file(dataset_name, conn, text_dir=TEXTDIR): """fetch textfiles with strain vals if exists""" with conn.cursor() as cursor: - query = 'SELECT Id, FullName FROM ProbeSetFreeze WHERE Name = "%s"' % dataset_name - cursor.execute(query) + cursor.execute( + 'SELECT Id, FullName FROM ProbeSetFreeze WHERE Name = "%s"' % dataset_name) results = cursor.fetchone() - if (results): + if results: try: for file in os.listdir(text_dir): if file.startswith(f"ProbeSetFreezeId_{results[0]}_"): @@ -188,16 +189,6 @@ def fetch_text_file(dataset_name, conn, text_dir=TEXTDIR): def read_text_file(sample_dict, file_path): - def parse_line_csv(line): - return_list = line.split('","') - return_list[-1] = return_list[-1][:-2] - return_list[0] = return_list[0][1:] - return return_list - - def filter_line_with_index(line, index): - lst = parse_line_csv(line) - return ",".join([lst[i] for i in index]) - def __fetch_id_positions__(all_ids, target_ids): _vals = [] _posit = [0] # alternative for parsing @@ -208,9 +199,9 @@ def read_text_file(sample_dict, file_path): _posit.append(idx) return (_posit, _vals) - with open(file_path, "r") as file_handler: - all_ids = file_handler.readline() + + with open(file_path) as csv_file: + csv_reader = csv.reader(csv_file, delimiter=',') _posit, sample_vals = __fetch_id_positions__( - parse_line_csv(all_ids)[1:], sample_dict) - return (sample_vals, [filter_line_with_index(line, _posit) - for line in file_handler.readlines()]) + next(csv_reader)[1:], sample_dict) + return (sample_vals, [",".join([line[i] for i in _posit]) for line in csv_reader]) |