Provide solution to correct metadata corruption due to improper migration for "Organization" -> "Affiliation" change

dandischema/tests/test_utils.py

@@ -1,9 +1,10 @@
-from typing import Dict, List, Optional, Union
+from typing import Any, Dict, List, Optional, Union
 
 import pytest
 
 from ..utils import (
     _ensure_newline,
+    find_objs,
     name2title,
     sanitize_value,
     strip_top_level_optional,
@@ -88,3 +89,151 @@ def test_sanitize_value() -> None:
     assert sanitize_value("A;B") == "A-B"
     assert sanitize_value("A\\/B") == "A--B"
     assert sanitize_value("A\"'B") == "A--B"
+
+
+@pytest.mark.parametrize(
+    "instance, schema_key, expected",
+    [
+        # Single matching object.
+        pytest.param(
+            {"schemaKey": "Test", "data": 123},
+            "Test",
+            [{"schemaKey": "Test", "data": 123}],
+            id="single-match",
+        ),
+        # No match.
+        pytest.param(
+            {"schemaKey": "NotMatch", "data": 123},
+            "Test",
+            [],
+            id="no-match",
+        ),
+        # Empty dictionary should return an empty list.
+        pytest.param(
+            {},
+            "Test",
+            [],
+            id="empty-dict",
+        ),
+        # Empty list should return an empty list.
+        pytest.param(
+            [],
+            "Test",
+            [],
+            id="empty-list",
+        ),
+        # Nested dictionary: the matching object is nested within another dictionary.
+        pytest.param(
+            {"level1": {"schemaKey": "Test", "info": "nested"}},
+            "Test",
+            [{"schemaKey": "Test", "info": "nested"}],
+            id="nested-dict",
+        ),
+        # List of dictionaries: only those with matching schema key are returned.
+        pytest.param(
+            [
+                {"schemaKey": "Test", "data": 1},
+                {"schemaKey": "Test", "data": 2},
+                {"schemaKey": "NotTest", "data": 3},
+            ],
+            "Test",
+            [
+                {"schemaKey": "Test", "data": 1},
+                {"schemaKey": "Test", "data": 2},
+            ],
+            id="list-of-dicts",
+        ),
+        # Mixed structure: nested dictionaries and lists.
+        pytest.param(
+            {
+                "a": {"schemaKey": "Test", "value": 1},
+                "b": [
+                    {"schemaKey": "NotTest", "value": 2},
+                    {"schemaKey": "Test", "value": 3},
+                ],
+                "c": "irrelevant",
+                "d": [{"e": {"schemaKey": "Test", "value": 4}}],
+            },
+            "Test",
+            [
+                {"schemaKey": "Test", "value": 1},
+                {"schemaKey": "Test", "value": 3},
+                {"schemaKey": "Test", "value": 4},
+            ],
+            id="mixed-structure",
+        ),
+        # Non-collection type: integer.
+        pytest.param(
+            42,
+            "Test",
+            [],
+            id="non-collection-int",
+        ),
+        # Non-collection type: string.
+        pytest.param(
+            "some string",
+            "Test",
+            [],
+            id="non-collection-string",
+        ),
+        # Non-collection type: float.
+        pytest.param(
+            3.14,
+            "Test",
+            [],
+            id="non-collection-float",
+        ),
+        # Non-collection type: None.
+        pytest.param(
+            None,
+            "Test",
+            [],
+            id="non-collection-None",
+        ),
+        # Nested child: an object with the schema key contains a nested child that also
+        # has the schema key.
+        pytest.param(
+            {"schemaKey": "Test", "child": {"schemaKey": "Test", "data": "child"}},
+            "Test",
+            [
+                {"schemaKey": "Test", "child": {"schemaKey": "Test", "data": "child"}},
+                {"schemaKey": "Test", "data": "child"},
+            ],
+            id="nested-child",
+        ),
+        # List in field:
+        # The object with the given schema key has a field whose value is a list
+        # containing objects, some of which also have the given schema key.
+        pytest.param(
+            {
+                "schemaKey": "Test",
+                "items": [
+                    {"schemaKey": "Test", "data": "item1"},
+                    {"schemaKey": "Other", "data": "item2"},
+                    {"schemaKey": "Test", "data": "item3"},
+                ],
+            },
+            "Test",
+            [
+                # The outer object is returned first...
+                {
+                    "schemaKey": "Test",
+                    "items": [
+                        {"schemaKey": "Test", "data": "item1"},
+                        {"schemaKey": "Other", "data": "item2"},
+                        {"schemaKey": "Test", "data": "item3"},
+                    ],
+                },
+                # ...followed by the matching objects within the list.
+                {"schemaKey": "Test", "data": "item1"},
+                {"schemaKey": "Test", "data": "item3"},
+            ],
+            id="list-in-field",
+        ),
+    ],
+)
+def test_find_objs_parametrized(
+    instance: Any, schema_key: str, expected: list[dict]
+) -> None:
+    result = find_objs(instance, schema_key)
+    assert result == expected

dandischema/utils.py

@@ -136,3 +136,30 @@ def sanitize_value(value: str, field: str = "non-extension", sub: str = "-") ->
     if field != "extension":
         value = value.replace(".", sub)
     return value
+
+
+def find_objs(instance: Any, schema_key: str) -> list[dict]:
+    """
+    Find JSON objects, represented as dictionaries, that possess a specified schema key
+    as the value of their `"schemaKey"` field, from a data instance
+
+    :param instance: The data instance to fetch JSON objects from
+    :param schema_key: The schema key
+    :return: The list of JSON objects with the specified schema key in the data instance
+    """
+
+    def find_objs_(data: Any) -> None:
+        if isinstance(data, dict):
+            if "schemaKey" in data and data["schemaKey"] == schema_key:
+                objs.append(data)
+            for value in data.values():
+                find_objs_(value)
+        elif isinstance(data, list):
+            for item in data:
+                find_objs_(item)
+        else:
+            return
+
+    objs: list[dict] = []
+    find_objs_(instance)
+    return objs