fix: update search pattern to find new lines in cells

EBI-Metabolights · Nov 20, 2024 · bcf703a · bcf703a
1 parent 1d68f25
commit bcf703a
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Showing 2 changed files with 4 additions and 6 deletions.
diff --git a/metabolights_utils/isatab/default/parser/common.py b/metabolights_utils/isatab/default/parser/common.py
@@ -168,16 +168,14 @@ def read_table_file(
             )
         )
         file_content = re.sub(r"[\r\n][\r\n]+", r"\n", file_content)
-
-    find_matches = re.findall(r'\t"([^\t]*)([\r\n]+)([^\t]*)"\t', file_content)
+    pattern = r'(^|\t)"([^"\t]*)([\r\n]+)([^"\t]*)"(\t|\n\|\r|$)'
+    find_matches = re.findall(pattern, file_content)
 
     if find_matches:
         max_iteration = 10
         iteration = 0
         while True:
-            new_file_content = re.sub(
-                r'\t"([^\t]*)([\r\n]+)([^\t]*)"\t', r'\t"\1\3"\t', file_content
-            )
+            new_file_content = re.sub(pattern, r'\1"\2\4"\5', file_content)
             if new_file_content == file_content:
                 break
             if iteration < 1:

diff --git a/metabolights_utils/isatab/default/parser/isa_table_parser.py b/metabolights_utils/isatab/default/parser/isa_table_parser.py
@@ -61,7 +61,7 @@ def fix_isa_table_file(
                 iteration = 0
                 while True:
                     new_file_content = re.sub(
-                        new_line_in_cells_pattern, r'\t"\2\4"\t', file_content
+                        new_line_in_cells_pattern, r'\1"\2\4"\5', file_content
                     )
                     if new_file_content == file_content:
                         break