fix: removed case_insensetivity form find and replace which cause unexpected behaiviour

__init__.py

@@ -1,26 +1,51 @@
 import argparse
-from table_handler.serializer import TableSerializer
+import os
 from logger import logger 
 
+from table_handler.serializer import TableSerializer
 import instructions.countings_formater as countings_formater
 import instructions.ring_formater as ring_formater
 
+from concurrent.futures import ProcessPoolExecutor, as_completed
+
+
+
+
+def process_file(input_file, output_file, xlsx_type):
+    # Select formatter
+    if xlsx_type == "ring":
+        formatter = ring_formater
+        row_instructions = ring_formater.ROW_INSTRUCTIONS
+    else:
+        formatter = countings_formater
+        row_instructions = countings_formater.ROW_INSTRUCTION
+
+    logger.info(f"Processing: {input_file}")
+
+    serializer = TableSerializer(
+        input_file,
+        formatter.EXPECTED_INPUT_TABLE_SCHEMA,
+        formatter.EXPECTED_OUTPUT_TABLE_SCHEMA
+    )
+
+    serializer.run(
+        formatter.COL_INSTRUCTIONS,
+        row_instructions
+    )
+
+    serializer.write_output(output_file)
+
 
 def main():
-
     parser = argparse.ArgumentParser(description="Serialize Excel tables.")
 
-    parser.add_argument(
-        "-i", "--input",
-        required=True,
-        help="Input Excel file"
-    )
+    # Single file mode (optional fallback)
+    parser.add_argument("-i", "--input", help="Input Excel file")
+    parser.add_argument("-o", "--output", help="Output Excel file")
 
-    parser.add_argument(
-        "-o", "--output",
-        required=True,
-        help="Output Excel file"
-    )
+    # Directory mode
+    parser.add_argument("--input-dir", help="Input directory")
+    parser.add_argument("--output-dir", help="Output directory")
 
     parser.add_argument(
         "-t", "--type",
@@ -31,31 +56,48 @@ def main():
 
     args = parser.parse_args()
 
-    # Select formatter based on type
-    if args.type == "ring":
-        formatter = ring_formater
-        row_instructions = ring_formater.ROW_INSTRUCTIONS
+    # directory
+    if args.input_dir and args.output_dir:
+        logger.info("Running in directory mode")
+
+        tasks = []
+
+        for root, _, files in os.walk(args.input_dir):
+            for file in files:
+                if not file.endswith((".xlsx", ".xls")):
+                    continue
+
+                input_path = os.path.join(root, file)
+
+                relative_path = os.path.relpath(root, args.input_dir)
+                output_root = os.path.join(args.output_dir, relative_path)
+                os.makedirs(output_root, exist_ok=True)
+
+                output_path = os.path.join(output_root, file)
+
+                tasks.append((input_path, output_path, args.type))
+
+        max_workers = os.cpu_count() or 1
+        logger.info(f"Processing {len(tasks)} files using {max_workers} workers")
+
+        with ProcessPoolExecutor(max_workers=max_workers) as executor:
+            futures = [executor.submit(process_file, *task) for task in tasks]
+
+            for future in as_completed(futures):
+                try:
+                    future.result()
+                except Exception as e:
+                    logger.error(f"Error processing file: {e}")
+        # single file
+    elif args.input and args.output:
+        logger.info("Running in single file mode")
+        process_file(args.input, args.output, args.type)
+
     else:
-        formatter = countings_formater
-        row_instructions = countings_formater.ROW_INSTRUCTION
-
-    logger.info("Reading file, building serializer...")
-    serializer = TableSerializer(
-        args.input,
-        formatter.EXPECTED_INPUT_TABLE_SCHEMA,
-        formatter.EXPECTED_OUTPUT_TABLE_SCHEMA
-    )
-
-    logger.info("Starting transformation")
-    serializer.run(
-        formatter.COL_INSTRUCTIONS,
-        row_instructions
-    )
-
-    logger.info("Writing transformations")
-    serializer.write_output(args.output)
+        parser.error("You must provide either input/output files or input-dir/output-dir")
 
     logger.info("Done")
 
+
 if __name__ == "__main__":
     main()

instructions/mappings.py

@@ -6,6 +6,7 @@ SPICIES = {
         "bbar",
         "Barbastella",
         "barbastellus",
+        "Bbararar",
         "B.b.",
         "B.b",
         "BB",
@@ -37,6 +38,7 @@ SPICIES = {
         "P.pip.",
         "P.pip",
         "PPIP",
+        "P.p."
         "ppip",
         "Pipistrellus pipistrellus",
     ],
@@ -155,6 +157,7 @@ SPICIES = {
         "P.nat.",
         "P.nat",
         "PNAT",
+        "Pnatatat",
         "pnat",
         "Pipistrellus nathusii",
         "P.n.",
@@ -177,6 +180,7 @@ SPICIES = {
         "unbekannt",
         "unb.",
         "Unbestimmt",
+        "Mspecbech"
     ],
     "Malc": [
         "M.alc.",
@@ -227,6 +231,7 @@ SPICIES = {
         "MSPEC",
         "mspec",
         "Myotis",
+        "Mspec.Mspec",
         "M.spe.",
         "M.spe",
         "MSPE",
@@ -251,6 +256,7 @@ SPICIES = {
         "MMYO",
         "mmyo",
         "Myotis Myotis",
+        "Mspec.bech"
         "M.m.",
         "M.m",
         "MM",

instructions/ring_formater.py

@@ -77,7 +77,4 @@ ROW_INSTRUCTIONS = [
         "target": "Wiederfunde",
         "value": "TRUE",
     }
-    #{
-    #    "command": "ROW_COPY_REMAINING"
-    #}
 ]

table_handler/commands/find_and_replace.py

@@ -2,19 +2,13 @@ import re
 from copy import deepcopy
 
 class FindAndReplace:
-    def __init__(self, map: dict[str, list[str]], case_sensitive: bool = False):
+    def __init__(self, map: dict[str, list[str]]):
         self.map = map
-        self.case_sensitive = case_sensitive
 
     def execute_on_cell(self, entry) -> str:
         res = deepcopy(entry.value)
 
         for species, alternatives in self.map.items():
             for old_version in alternatives:
-                if self.case_sensitive:
                 res = res.replace(old_version, species)
-                else:
-                    pattern = re.compile(re.escape(old_version), re.IGNORECASE)
-                    res = pattern.sub(species, res)
-
         return res

table_handler/serializer.py

@@ -37,6 +37,7 @@ class TableSerializer:
         if not self.ws:
             raise ValueError("No active worksheet found in the workbook.")
         
+        self.file = file
         self.data = self._serialize_table(expected_input_schema)
         self.serialized_output = {}
         self.seperator = ", "
@@ -147,7 +148,7 @@ class TableSerializer:
         amount_working_rows = self.vertical_len +2
         for rid in range(2, amount_working_rows):
             if rid % 1000 == 0:
-                logger.info(f"Working on row {rid}/{amount_working_rows} ")
+                logger.info(f"{self.file} Working on row {rid}/{amount_working_rows} ")
             working_row = {}
             source_row = self.get_row_as_dict(rid)
             for source_cols, instructions in list(col_instructions.items()) + [