From 083a9d899e22b3b2d2d6c226a589fe76b63f7d28 Mon Sep 17 00:00:00 2001
From: Charlotte Mauvezin <charlotte.mauvezin@irht.cnrs.fr>
Date: Mon, 3 Jan 2022 11:34:21 +0100
Subject: [PATCH] Correctif Chaza
---
nerval/evaluate.py | 35 ++++++++++++++++++++++++-----------
1 file changed, 24 insertions(+), 11 deletions(-)
diff --git a/nerval/evaluate.py b/nerval/evaluate.py
index 7fa887f..00d9e43 100644
--- a/nerval/evaluate.py
+++ b/nerval/evaluate.py
@@ -568,7 +568,7 @@ def run_multiple(file_csv, folder, threshold):
else:
raise f"No file found for files {annot}, {predict}"
else:
- raise "This is no folder"
+ raise Exception("the path indicated does not lead to a folder.")
def threshold_float_type(arg):
@@ -588,23 +588,27 @@ def main():
logging.basicConfig(level=logging.INFO)
parser = argparse.ArgumentParser(description="Compute score of NER on predict.")
+ parser.add_argument(
+ "-m",
+ "--multiple",
+ help="Single if 1, multiple 2",
+ type=int,
+ required=True,
+ )
parser.add_argument(
"-a",
"--annot",
help="Annotation in BIO format.",
- required=False,
)
parser.add_argument(
"-p",
"--predict",
help="Prediction in BIO format.",
- required=False,
)
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,
)
@@ -612,24 +616,33 @@ def main():
"-c",
"--csv",
help="Csv with the correlation between the annotation bio files and the predict bio files",
- required=False,
type=Path,
)
parser.add_argument(
"-f",
"--folder",
help="Folder containing the bio files referred to in the csv file",
- required=False,
type=Path,
)
args = parser.parse_args()
- if args.csv and args.folder:
- run_multiple(args.csv, args.folder, args.threshold)
- elif args.annot and args.predict:
- run(args.annot, args.predict, args.threshold)
+ 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)
+ 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)
else:
- raise "You did not give the proper input"
+ raise argparse.ArgumentTypeError("Value has to be 1 or 2")
if __name__ == "__main__":
--
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