Test for broken regex in bamignore

client/cli/bam.py

@@ -163,13 +163,18 @@ class bam_config:
         if os.path.isfile(bamignore):
             with open(bamignore, 'r') as f:
                 patterns = f.read().split("\n")
-                def filter_ignore(f):
                 import re
-                    for pattern in filter_ignore.patterns:
+                try:
+                    compiled_patterns = [re.compile(p) for p in patterns]
+                except re.error:
+                    fatal("Your .bamignore file contains invalid regular expressions")
+
+                def filter_ignore(f):
+                    for pattern in filter_ignore.compiled_patterns:
                         if re.match(pattern, f):
                             return False
                     return True
-                filter_ignore.patterns = patterns
+                filter_ignore.compiled_patterns = compiled_patterns
 
                 return filter_ignore
         else:

tests/test_cli.py

@@ -1045,6 +1045,26 @@ class BamIgnoreTest(BamSessionTestCase):
         self.assertEqual("Nothing to commit!\n", stdout)
 
 
+    def test_invalid_ignore(self):
+        session_name = "mysession"
+        file_name = "testfile.txt"
+        file_data = b"hello world!\n"
+
+        # A failing regex that breaks syntax highlight as nice side effect
+        file_data_bamignore = r"""("""
+
+        proj_path, session_path = self.init_session(session_name)
+
+        # write the .bamignore in the session root
+        file_quick_write(proj_path, ".bamignore", file_data_bamignore)
+
+        # create some files
+        file_quick_write(session_path, file_name, file_data)
+
+        # now check for status
+        self.assertRaises(RuntimeError, bam_run, ["status",], session_path)
+
+
 if __name__ == '__main__':
     data = global_setup()
     unittest.main(exit=False)