Merge pull request #645 from FAIRmat-NFDI/644-bug-validation-fails-with-key-error-if-link-cannot-be-resolved

handle broken links, add test

Author: lukaspie

src/pynxtools/dataconverter/validation.py

@@ -545,6 +545,7 @@ def _follow_link(
                         ValidationProblem.KeyToBeRemoved,
                         "key",
                     )
+                    keys_to_remove.append(key_path)
                     del resolved_keys[key]
                 else:
                     resolved_keys[key] = current_keys
@@ -763,6 +764,10 @@ def is_documented(key: str, tree: NexusNode) -> bool:
         if isinstance(mapping[key], dict) and "link" in mapping[key]:
             resolved_link = _follow_link({key: mapping[key]}, "")
 
+            if key not in resolved_link:
+                # Link is broken and key will be removed; no need to check further
+                return False
+
             is_mapping = isinstance(resolved_link[key], Mapping)
 
             if node.type == "group" and not is_mapping:

tests/dataconverter/test_validation.py

@@ -816,6 +816,24 @@ def listify_template(data_dict: Template):
             ],
             id="field-instead-of-named-group",
         ),
+        pytest.param(
+            alter_dict(
+                alter_dict(
+                    TEMPLATE,
+                    "/ENTRY[my_entry]/identified_calibration",
+                    {"link": "/my_entry/some_group"},
+                ),
+                "/ENTRY[my_entry]/NXODD_name[nxodd_name]/float_value",
+                {"link": "/my_entry/specified_group/some_field"},
+            ),
+            [
+                "Broken link at /ENTRY[my_entry]/identified_calibration to /my_entry/some_group.",
+                "The key /ENTRY[my_entry]/identified_calibration will not be written.",
+                "Broken link at /ENTRY[my_entry]/NXODD_name[nxodd_name]/float_value to /my_entry/specified_group/some_field.",
+                "The key /ENTRY[my_entry]/NXODD_name[nxodd_name]/float_value will not be written.",
+            ],
+            id="appdef-broken-links",
+        ),
         pytest.param(
             alter_dict(
                 alter_dict(
@@ -850,6 +868,24 @@ def listify_template(data_dict: Template):
             ],
             id="appdef-links-with-wrong-nexus-types",
         ),
+        pytest.param(
+            alter_dict(
+                alter_dict(
+                    TEMPLATE,
+                    "/ENTRY[my_entry]/SAMPLE[my_sample]",
+                    {"link": "/my_entry/some_group"},
+                ),
+                "/ENTRY[my_entry]/SAMPLE[my_sample2]/name",
+                {"link": "/my_entry/specified_group/some_field223"},
+            ),
+            [
+                "Broken link at /ENTRY[my_entry]/SAMPLE[my_sample] to /my_entry/some_group.",
+                "The key /ENTRY[my_entry]/SAMPLE[my_sample] will not be written.",
+                "Broken link at /ENTRY[my_entry]/SAMPLE[my_sample2]/name to /my_entry/specified_group/some_field223.",
+                "The key /ENTRY[my_entry]/SAMPLE[my_sample2]/name will not be written.",
+            ],
+            id="baseclass-broken-links",
+        ),
         pytest.param(
             alter_dict(
                 alter_dict(