Adding vaildation checks for --batch-id option

mpox-seek

@@ -51,7 +51,8 @@ from src.utils import (
     exists,
     fatal,
     permissions,
-    require
+    require,
+    valid_directory
 )
 
 
@@ -641,7 +642,7 @@ def parsed_arguments(name, description):
     # Batch Identifer
     subparser_run.add_argument(
         '--batch-id',
-        type = lambda option: option.replace(' ', '_'),
+        type = lambda option: valid_directory(parser, option.replace(' ', '_')),
         required = False,
         default = '',
         help = argparse.SUPPRESS

src/utils.py

@@ -4,7 +4,7 @@
 # Python standard library
 from __future__ import print_function
 from shutil import copytree, copyfileobj
-import os, sys, hashlib
+import os, sys, hashlib, re
 import subprocess, json
 
 
@@ -58,6 +58,42 @@ def permissions(parser, path, *args, **kwargs):
     return os.path.abspath(path)
 
 
+
+def valid_directory(parser, batch_id, *args, **kwargs):
+    """Checks if the value provided to '--batch-id' option is valid.
+    Check if the string consists of only alphanumeric characters, 
+    hypens, and underscores.
+    @param parser <argparse.ArgumentParser() object>:
+        Argparse parser object
+    @param batch_id <str>:
+        Value provided to '--batch-id' option
+    @return path <str>:
+        Returns batch_id if it is valid, else error is raised
+    """
+    # Check for default argparser value, if so return
+    # default --batch-id value is set to ''.
+    if batch_id == '':
+        # --batch-id is not provided, 
+        # return default value back
+        return batch_id
+
+    # Check if the batch id is a single hypen or underscore
+    # i.e --batch-id '-' or --batch-id '_' was given
+    if batch_id == '-' or batch_id == '_':
+        parser.error(
+            "Error: --batch-id '{}' is invalid! A batch identifer cannot be a single hypen or underscore.".format(batch_id)
+        )
+    # Check if the batch id is valid, enforce only alphanumeric 
+    # characters, hypens, and underscores
+    if not re.match(r'^[A-Za-z0-9\-_]+$', batch_id):
+        parser.error(
+            "Error: --batch-id '{}' is invalid! A batch identifer must consist of only alphanumeric characters, hypens, and underscores.".format(batch_id)
+        )
+
+    return batch_id
+
+
+
 def standard_input(parser, path, *args, **kwargs):
     """Checks for standard input when provided or permissions using permissions().
     @param parser <argparse.ArgumentParser() object>: