[DLMED] add allow_missing_reference (#4079)

Signed-off-by: Nic Ma <[email protected]>

Author: Nic-Ma

monai/bundle/reference_resolver.py

@@ -9,7 +9,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import os
 import re
+import warnings
 from typing import Any, Dict, Optional, Sequence, Set
 
 from monai.bundle.config_item import ConfigComponent, ConfigExpression, ConfigItem
@@ -50,6 +52,8 @@ class ReferenceResolver:
     ref = ID_REF_KEY  # reference prefix
     # match a reference string, e.g. "@id#key", "@id#key#0", "@_target_#key"
     id_matcher = re.compile(rf"{ref}(?:\w*)(?:{sep}\w*)*")
+    # if `allow_missing_reference` and can't find a reference ID, will just raise a warning and don't update the config
+    allow_missing_reference = False if os.environ.get("MONAI_ALLOW_MISSING_REFERENCE", "0") == "0" else True
 
     def __init__(self, items: Optional[Sequence[ConfigItem]] = None):
         # save the items in a dictionary with the `ConfigItem.id` as key
@@ -140,7 +144,12 @@ def _resolve_one_item(self, id: str, waiting_list: Optional[Set[str]] = None, **
                 try:
                     look_up_option(d, self.items, print_all_options=False)
                 except ValueError as err:
-                    raise ValueError(f"the referring item `@{d}` is not defined in the config content.") from err
+                    msg = f"the referring item `@{d}` is not defined in the config content."
+                    if self.allow_missing_reference:
+                        warnings.warn(msg)
+                        continue
+                    else:
+                        raise ValueError(msg) from err
                 # recursively resolve the reference first
                 self._resolve_one_item(id=d, waiting_list=waiting_list, **kwargs)
                 waiting_list.discard(d)
@@ -210,7 +219,12 @@ def update_refs_pattern(cls, value: str, refs: Dict) -> str:
         for item in result:
             ref_id = item[len(cls.ref) :]  # remove the ref prefix "@"
             if ref_id not in refs:
-                raise KeyError(f"can not find expected ID '{ref_id}' in the references.")
+                msg = f"can not find expected ID '{ref_id}' in the references."
+                if cls.allow_missing_reference:
+                    warnings.warn(msg)
+                    continue
+                else:
+                    raise KeyError(msg)
             if value_is_expr:
                 # replace with local code, will be used in the `evaluate` logic with `locals={"refs": ...}`
                 value = value.replace(item, f"{cls._vars}['{ref_id}']")

tests/test_config_parser.py

@@ -16,7 +16,7 @@
 
 from parameterized import parameterized
 
-from monai.bundle.config_parser import ConfigParser
+from monai.bundle import ConfigParser, ReferenceResolver
 from monai.data import DataLoader, Dataset
 from monai.transforms import Compose, LoadImaged, RandTorchVisiond
 from monai.utils import min_version, optional_import
@@ -86,6 +86,8 @@ def __call__(self, a, b):
     }
 ]
 
+TEST_CASE_4 = [{"A": 1, "B": "@A", "C": "@D", "E": "$'test' + '@F'"}]
+
 
 class TestConfigParser(unittest.TestCase):
     def test_config_content(self):
@@ -154,6 +156,27 @@ def test_macro_replace(self):
             parser.resolve_macro_and_relative_ids()
             self.assertEqual(str(parser.get()), str({"A": {"B": 1, "C": 2}, "D": [3, 1, 3, 4]}))
 
+    @parameterized.expand([TEST_CASE_4])
+    def test_allow_missing_reference(self, config):
+        default = ReferenceResolver.allow_missing_reference
+        ReferenceResolver.allow_missing_reference = True
+        parser = ConfigParser(config=config)
+
+        for id in config:
+            item = parser.get_parsed_content(id=id)
+            if id in ("A", "B"):
+                self.assertEqual(item, 1)
+            elif id == "C":
+                self.assertEqual(item, "@D")
+            elif id == "E":
+                self.assertEqual(item, "test@F")
+
+        # restore the default value
+        ReferenceResolver.allow_missing_reference = default
+        with self.assertRaises(ValueError):
+            parser.parse()
+            parser.get_parsed_content(id="E")
+
 
 if __name__ == "__main__":
     unittest.main()