From 3b7281fa2008ce85c9a4a164dab19ca19edd0c8a Mon Sep 17 00:00:00 2001
From: Jakub Dylag <jjd1c23@soton.ac.uk>
Date: Fri, 7 Feb 2025 00:56:34 +0000
Subject: [PATCH] Run scripts from command line
---
medcoder/main.py | 9 ++++++---
medcoder/parse.py | 16 ++++++++--------
medcoder/trud_api.py | 12 ++++++------
pyproject.toml | 7 ++++++-
4 files changed, 26 insertions(+), 18 deletions(-)
diff --git a/medcoder/main.py b/medcoder/main.py
index ab32f81..f1868c2 100644
--- a/medcoder/main.py
+++ b/medcoder/main.py
@@ -291,8 +291,7 @@ def run_all(mapping_file, target_code_type,
error_df = error_df.sort_values(by=["SOURCE", "VOCABULARY", "CONCEPT"])
error_df.to_csv(log_errors_path, index=False)
-
-if __name__ == '__main__':
+def main():
parser = argparse.ArgumentParser(description="Script preprocess code lists and to map to given concept/phenotype",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -332,4 +331,8 @@ if __name__ == '__main__':
if not config["error_log"] == None:
params["log_errors_path"] = config["error_log"]
- run_all(**params)
\ No newline at end of file
+ run_all(**params)
+
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
diff --git a/medcoder/parse.py b/medcoder/parse.py
index a509369..8a567cf 100644
--- a/medcoder/parse.py
+++ b/medcoder/parse.py
@@ -197,15 +197,15 @@ class Icd10_code(Proto_code):
file_path=self.file_path,
cause="QA In Database"),
)
-# (
-# "ICD10 Regex",
-# lambda codes : codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Alpha, Num, Num , Dot?, 4xAlphNum*
-# lambda codes : log_invalid_code(codes,
-# codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Log non-matching rows
-# code_type="icd10_code",
-# file_path=self.file_path),
+ # (
+ # "ICD10 Regex",
+ # lambda codes : codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Alpha, Num, Num , Dot?, 4xAlphNum*
+ # lambda codes : log_invalid_code(codes,
+ # codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Log non-matching rows
+ # code_type="icd10_code",
+ # file_path=self.file_path),
-# )
+ # )
]
def trim_icd10(codes):
diff --git a/medcoder/trud_api.py b/medcoder/trud_api.py
index a7eade3..e4e5488 100644
--- a/medcoder/trud_api.py
+++ b/medcoder/trud_api.py
@@ -206,12 +206,12 @@ def main():
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument("--key", type=str, help="TRUD API Key")
-# parser.add_argument("item_ids", nargs="+", help="Item IDs to download releases for.")
-# parser.add_argument("-l", "--latest", action="store_true", help="Download only the latest release")
-# parser.add_argument("-c", "--checksum", action="store_true", help="Also download the checksum file")
-# parser.add_argument("-s", "--signature", action="store_true", help="Also download the signature file")
-# parser.add_argument("-p", "--public_key", action="store_true", help="Also download the public key file")
-
+ # parser.add_argument("item_ids", nargs="+", help="Item IDs to download releases for.")
+ # parser.add_argument("-l", "--latest", action="store_true", help="Download only the latest release")
+ # parser.add_argument("-c", "--checksum", action="store_true", help="Also download the checksum file")
+ # parser.add_argument("-s", "--signature", action="store_true", help="Also download the signature file")
+ # parser.add_argument("-p", "--public_key", action="store_true", help="Also download the public key file")
+
args = parser.parse_args()
items_latest = True
diff --git a/pyproject.toml b/pyproject.toml
index 060d7aa..40bff1b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,4 +12,9 @@ license = { file = "LICENSE" }
dependencies = [
"pandas",
"numpy"
-]
\ No newline at end of file
+]
+
+[project.scripts]
+medcoder = "medcoder.main:main"
+medcoder_install_trud = "medcoder.trud_api:main"
+medcoder_install_omop = "medcoder.omop_api:main"
\ No newline at end of file
--
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