From 7357a9e8b0e24489583b85eef0d672a897277852 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Fri, 12 Dec 2025 15:13:11 +0100
Subject: [PATCH 1/2] chore(rpextractsink.py): retry connecting to MetNetX when
 it fails

---
 rptools/rpextractsink/rpextractsink.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/rptools/rpextractsink/rpextractsink.py b/rptools/rpextractsink/rpextractsink.py
index a71ca8c..ebce4eb 100644
--- a/rptools/rpextractsink/rpextractsink.py
+++ b/rptools/rpextractsink/rpextractsink.py
@@ -11,6 +11,7 @@
 from os             import path          as os_path
 from requests import get as r_get
 from re import search as re_search
+from time import sleep
 
 from rr_cache import rrCache
 from rptools.rpfba import cobra_format
@@ -135,6 +136,25 @@ def get_inchi_from_crossid(
     except Exception as e:
         logger.warning(f'Connection lost from {url_search}')
         return ''
+    logger.debug(f'Page retrieved from MetaNetX for {id}: {page.url}')
+    logger.debug(f'Page content: {page.text}')
+    # If server 'too busy', wait and retry 3 times
+    retries = 3
+    wait_time = 5  # seconds
+    attempt = 0
+    while 'please try again' in page.text.lower() and attempt < retries:
+        logger.debug(f'Server is too busy. Retrying in {wait_time} seconds... (Attempt {attempt + 1} of {retries})')
+        sleep(wait_time)
+        try:
+            page = r_get(f'{url_search}?query={id}')
+        except Exception as e:
+            logger.warning(f'Connection lost from {url_search}')
+            return ''
+        attempt += 1
+    if 'please try again' in page.text.lower():
+        logger.debug('Server is still too busy after multiple attempts. Aborting retrieval.')
+        return ''
+    logger.debug(f'Final page content after retries: {page.text}')
     url_crossid = re_search(r'/chem_info/\w+', page.text).group()
     return get_inchi_from_url(f'{url_mnx}{url_crossid}', logger)
 

From 37a2f1ab14829a795d76fc9f9cbe7f8dfcfe0822 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Fri, 12 Dec 2025 15:17:19 +0100
Subject: [PATCH 2/2] chore(rpcompletion.py): catch exception when file not
 found

---
 rptools/rpcompletion/rpcompletion.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rptools/rpcompletion/rpcompletion.py b/rptools/rpcompletion/rpcompletion.py
index f16addb..b2fa7c4 100644
--- a/rptools/rpcompletion/rpcompletion.py
+++ b/rptools/rpcompletion/rpcompletion.py
@@ -548,8 +548,8 @@ def __read_pathways(
 
     try:
         df = pd.read_csv(infile)
-    except pd.errors.EmptyDataError as e:
-        logger.error(f'File {infile} is empty: {e}')
+    except (pd.errors.EmptyDataError, FileNotFoundError) as e:
+        logger.error(f'File {infile} is empty or does not exist: {e}')
         return {}, {}
 
     check = __check_pathways(df)