From d9eb90635c2a4c17257933033696691264a4e7a8 Mon Sep 17 00:00:00 2001
From: Charlotte Mauvezin <charlotte.mauvezin@irht.cnrs.fr>
Date: Mon, 3 Jan 2022 16:04:25 +0100
Subject: [PATCH] Rebase
---
nerval/evaluate.py | 90 +++++++++++++++++++++++++++++++++++++++++-----
1 file changed, 82 insertions(+), 8 deletions(-)
diff --git a/nerval/evaluate.py b/nerval/evaluate.py
index 6601a72..ab11dde 100644
--- a/nerval/evaluate.py
+++ b/nerval/evaluate.py
@@ -1,9 +1,12 @@
# -*- coding: utf-8 -*-
import argparse
+import glob
import logging
import os
import re
+from csv import reader
+from pathlib import Path
import editdistance
import edlib
@@ -81,7 +84,11 @@ def parse_bio(path: str) -> dict:
try:
word, label = line.split()
except ValueError:
- raise (Exception(f"The file {path} given in input is not in BIO format."))
+ raise (
+ Exception(
+ f"The file {path} given in input is not in BIO format: check line {index} ({line})"
+ )
+ )
# Preserve hyphens to avoid confusion with the hyphens added later during alignment
word = word.replace("-", "§")
@@ -553,6 +560,37 @@ def run(annotation: str, prediction: str, threshold: int, verbose: bool) -> dict
return scores
+def run_multiple(file_csv, folder, threshold, verbose):
+ """Run the program for multiple files (correlation indicated in the csv file)"""
+ # Read the csv in a list
+ with open(file_csv, "r") as read_obj:
+ csv_reader = reader(read_obj)
+ list_cor = list(csv_reader)
+
+ if os.path.isdir(folder):
+ list_bio_file = glob.glob(str(folder) + "/**/*.bio", recursive=True)
+
+ for row in list_cor:
+ annot = None
+ predict = None
+
+ for file in list_bio_file:
+ if row[0] == os.path.basename(file):
+ annot = file
+ for file in list_bio_file:
+ if row[1] == os.path.basename(file):
+ predict = file
+
+ if annot and predict:
+ print(os.path.basename(predict))
+ run(annot, predict, threshold, verbose)
+ print()
+ else:
+ raise f"No file found for files {annot}, {predict}"
+ else:
+ raise Exception("the path indicated does not lead to a folder.")
+
+
def threshold_float_type(arg):
"""Type function for argparse."""
try:
@@ -571,30 +609,66 @@ def main():
parser = argparse.ArgumentParser(description="Compute score of NER on predict.")
parser.add_argument(
- "-a", "--annot", help="Annotation in BIO format.", required=True
+ "-m",
+ "--multiple",
+ help="Single if 1, multiple 2",
+ type=int,
+ required=True,
+ )
+ parser.add_argument(
+ "-a",
+ "--annot",
+ help="Annotation in BIO format.",
)
parser.add_argument(
- "-p", "--predict", help="Prediction in BIO format.", required=True
+ "-p",
+ "--predict",
+ help="Prediction in BIO format.",
)
parser.add_argument(
"-t",
"--threshold",
help="Set a distance threshold for the match between gold and predicted entity.",
- required=False,
default=THRESHOLD,
type=threshold_float_type,
)
+ parser.add_argument(
+ "-c",
+ "--csv",
+ help="Csv with the correlation between the annotation bio files and the predict bio files",
+ type=Path,
+ )
+ parser.add_argument(
+ "-f",
+ "--folder",
+ help="Folder containing the bio files referred to in the csv file",
+ type=Path,
+ )
parser.add_argument(
"-v",
"--verbose",
- help="Print only the recap if False and detailed results if True (default)",
+ help="Print only the recap if False",
action="store_false",
- default="True",
)
-
args = parser.parse_args()
- run(args.annot, args.predict, args.threshold, args.verbose)
+ if args.multiple == 1 or args.multiple == 2:
+ if args.multiple == 2:
+ if not args.folder:
+ raise argparse.ArgumentError(args.folder, "-f must be given if -m is 2")
+ if not args.csv:
+ raise argparse.ArgumentError(args.folder, "-c must be given if -m is 2")
+ if args.folder and args.csv:
+ run_multiple(args.csv, args.folder, args.threshold, args.verbose)
+ if args.multiple == 1:
+ if not args.annot:
+ raise argparse.ArgumentError(args.folder, "-a must be given if -m is 1")
+ if not args.predict:
+ raise argparse.ArgumentError(args.folder, "-p must be given if -m is 1")
+ if args.annot and args.predict:
+ run(args.annot, args.predict, args.threshold, args.verbose)
+ else:
+ raise argparse.ArgumentTypeError("Value has to be 1 or 2")
if __name__ == "__main__":
--
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