From 1e5917089064fcea522d8ec1e5d5a31c6a4e20d7 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 31 Jan 2020 10:48:23 +0100
Subject: [PATCH] Use POSIX ERE for sub function (#321)

implements openwdl/wdl#243
---
 WDL/StdLib.py           | 6 ++++--
 requirements.txt        | 1 +
 stubs/regex/__init__.py | 7 +++++++
 tests/test_5stdlib.py   | 6 +++++-
 4 files changed, 17 insertions(+), 3 deletions(-)
 create mode 100644 stubs/regex/__init__.py

diff --git a/WDL/StdLib.py b/WDL/StdLib.py
index 0316016d..bfdee179 100644
--- a/WDL/StdLib.py
+++ b/WDL/StdLib.py
@@ -1,7 +1,7 @@
 # pylint: disable=protected-access,exec-used
 import math
 import os
-import re
+import regex
 import json
 import tempfile
 from typing import List, Tuple, Callable, BinaryIO, Optional
@@ -67,7 +67,9 @@ def static(
 
         @static([Type.String(), Type.String(), Type.String()], Type.String())
         def sub(input: Value.String, pattern: Value.String, replace: Value.String) -> Value.String:
-            return Value.String(re.compile(pattern.value).sub(replace.value, input.value))
+            return Value.String(
+                regex.compile(pattern.value, flags=regex.POSIX).sub(replace.value, input.value)
+            )
 
         static([Type.String(), Type.String(optional=True)], Type.String())(basename)
 
diff --git a/requirements.txt b/requirements.txt
index 9c31c821..4523faab 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -8,3 +8,4 @@ pygtail>=0.11.0
 coloredlogs
 psutil
 importlib-metadata
+regex
diff --git a/stubs/regex/__init__.py b/stubs/regex/__init__.py
new file mode 100644
index 00000000..4c0cbcc0
--- /dev/null
+++ b/stubs/regex/__init__.py
@@ -0,0 +1,7 @@
+from typing import Any
+
+POSIX: int
+
+
+def compile(pattern, flags=0, **kwargs) -> Any:
+    ...
diff --git a/tests/test_5stdlib.py b/tests/test_5stdlib.py
index a19d04c5..fb6a4476 100644
--- a/tests/test_5stdlib.py
+++ b/tests/test_5stdlib.py
@@ -220,6 +220,8 @@ def test_sub(self):
                 String chocolove = sub(chocolike, "like", "love") # I love chocolate when it's late
                 String chocoearly = sub(chocolike, "late", "early") # I like chocoearly when it's early
                 String chocolate = sub(chocolike, "late$", "early") # I like chocolate when it's early
+                String chocoearlylate = sub(chocolike, "[^ ]late", "early") # I like chocearly when it's late
+                String choco4 = sub(chocolike, " [[:alpha:]]{4} ", " 4444 ") # I 4444 chocolate 4444 it's late
             }
         }
         """)
@@ -227,7 +229,9 @@ def test_sub(self):
             "chocolike": "I like chocolate when it's late",
             "chocolove": "I love chocolate when it's late",
             "chocoearly": "I like chocoearly when it's early",
-            "chocolate": "I like chocolate when it's early"
+            "chocolate": "I like chocolate when it's early",
+            "chocoearlylate": "I like chocearly when it's late",
+            "choco4": "I 4444 chocolate 4444 it's late"
         })
         outputs = self._test_task(R"""
         task example {