From 63442d1d722b7b5ae0d76da34e50d44531f5acc2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 13 Sep 2023 11:58:43 +0200
Subject: [PATCH] Fix regex validation for global inline flags

Fixes https://github.com/galaxyproject/galaxy/issues/16676
---
 lib/galaxy/dependencies/pinned-requirements.txt  |  1 +
 lib/galaxy/tools/parameters/validation.py        |  5 +++--
 packages/app/setup.cfg                           |  1 +
 pyproject.toml                                   |  1 +
 test/unit/app/tools/test_parameter_validation.py | 12 ++++++++++++
 5 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index e995f6d9c2cc..3cca837b3a8b 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -153,6 +153,7 @@ pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.12"
 pyzmq==25.1.0 ; python_version >= "3.7" and python_version < "3.12"
 rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
 refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.12"
+regex==2023.8.8 ; python_version >= "3.7" and python_version < "3.12"
 repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.12"
 requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 4df3364011ec..6b67b0200cd8 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -4,7 +4,8 @@
 import abc
 import logging
 import os.path
-import re
+
+import regex
 
 from galaxy import (
     model,
@@ -143,7 +144,7 @@ def validate(self, value, trans=None):
         if not isinstance(value, list):
             value = [value]
         for val in value:
-            match = re.match(self.expression, val or "")
+            match = regex.match(self.expression, val or "")
             super().validate(match is not None, value_to_show=val)
 
 
diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
index 9743bcbcd8af..daaa99ffbb3f 100644
--- a/packages/app/setup.cfg
+++ b/packages/app/setup.cfg
@@ -66,6 +66,7 @@ install_requires =
     PyJWT
     PyYAML
     refgenconf>=0.12.0
+    regex
     requests
     SQLAlchemy>=1.4.25,<2
     sqlitedict
diff --git a/pyproject.toml b/pyproject.toml
index bba81c7104df..faf9b58666b0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -93,6 +93,7 @@ python-magic = "*"
 python-multipart = "*"  # required to support form parsing in FastAPI/Starlette
 PyYAML = "*"
 refgenconf = ">=0.12.0"
+regex = "*"
 requests = "*"
 rocrate = "*"
 Routes = "*"
diff --git a/test/unit/app/tools/test_parameter_validation.py b/test/unit/app/tools/test_parameter_validation.py
index 77fcfee7030d..a1f9da021b45 100644
--- a/test/unit/app/tools/test_parameter_validation.py
+++ b/test/unit/app/tools/test_parameter_validation.py
@@ -62,3 +62,15 @@ def test_ExpressionValidator_message(self):
             ValueError, r"Validator 'value.lower\(\) == \"foo\"' could not be evaluated on '1'"
         ):
             p.validate(1)
+
+    def test_RegexValidator_global_flag_inline(self):
+        # tests that global inline flags continue to work past python 3.10
+        p = self._parameter_for(
+            xml=r"""
+<param name="blah" type="text" value="">
+    <validator type="regex">^(?ims)\s*select\s+.*\s+from\s+.*$</validator>
+</param>"""
+        )
+        p.validate("select id from job where id = 1;")
+        with self.assertRaises(ValueError):
+            p.validate("not sql")