From d6566fb7c2db9039c26103df6afdc54a56333007 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Thu, 20 Apr 2023 00:29:55 +0200
Subject: [PATCH] chore: add error handler

---
 retropath2_wrapper/Args.py       |  3 ++-
 retropath2_wrapper/RetroPath2.py | 12 +++++++++---
 retropath2_wrapper/__main__.py   |  3 +++
 3 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/retropath2_wrapper/Args.py b/retropath2_wrapper/Args.py
index 9933e70..e95a549 100644
--- a/retropath2_wrapper/Args.py
+++ b/retropath2_wrapper/Args.py
@@ -23,7 +23,8 @@
     # Errors
     'FileNotFound': 1,
     'OSError': 2,
-    'InChI': 3
+    'InChI': 3,
+    'SinkFileMalformed': 4,
 }
 __PACKAGE_FOLDER = os_path.dirname(
     os_path.realpath(__file__)
diff --git a/retropath2_wrapper/RetroPath2.py b/retropath2_wrapper/RetroPath2.py
index d3a2225..17f47da 100644
--- a/retropath2_wrapper/RetroPath2.py
+++ b/retropath2_wrapper/RetroPath2.py
@@ -153,6 +153,8 @@ def check_input(
         return RETCODES['SrcInSink'], None
     elif r_code == RETCODES['FileNotFound']:
         return RETCODES['FileNotFound'], None
+    elif r_code == RETCODES['SinkFileMalformed']:
+        return RETCODES['SinkFileMalformed'], None
 
     return RETCODES['OK'], inchi
 
@@ -185,9 +187,13 @@ def check_src_in_sink_1(
     try:
         with open(sink_file, 'r') as f:
             for row in csv_reader(f, delimiter=',', quotechar='"'):
-                if source_inchi == row[1]:
-                    logger.error('        source has been found in sink')
-                    return RETCODES['SrcInSink']
+                try:
+                    if source_inchi == row[1]:
+                        logger.error('        source has been found in sink')
+                        return RETCODES['SrcInSink']
+                except IndexError:
+                    # logger.error('        sink file is not well-formed')
+                    return RETCODES['SinkFileMalformed']
 
     except FileNotFoundError as e:
         logger.error(e)
diff --git a/retropath2_wrapper/__main__.py b/retropath2_wrapper/__main__.py
index 665ff6c..9ad217c 100644
--- a/retropath2_wrapper/__main__.py
+++ b/retropath2_wrapper/__main__.py
@@ -118,6 +118,9 @@ def _cli():
     elif r_code == RETCODES['SrcInSink']:
         logger.warning('It seems that the target product is already in the chassis.')
         logger.warning('Exiting...')
+    elif r_code == RETCODES['SinkFileMalformed']:
+        logger.error('The sink file is malformed.')
+        logger.error('Exiting...')
     else:
         logger.error(f'The following error occured: {r_code}')
         logger.error('Exiting...')