RF: replace use of "identifiers" with "alternateIdentifiers"

Situation with "identifiers" is messy. We relied on it but it was not in datacite schema, but was allowed by API: https://support.datacite.org/docs/what-is-the-identifiers-attribute-in-the-rest-api > When creating or updating DOI alternateIdentifier metadata, the REST API accepts values in either the alternateIdentifiers or identifiers attributes. Including metadata in either attribute will populate the identifiers and alternateIdentifiers attributes in the REST API response and the alternateIdentifiers property in DataCite XML. And in jsonschema serialization of 4.5 "identifiers" was removed, see more in inveniosoftware/datacite#81 (comment) and there in. But I guess currently used 4.3 from datacite (not inveniosoftware) is still requiring identifiers, and hence this commit/solution is incomplete since does fail validation (see below). "identifiers" was removed from required only in 4.5 from inveniosoftware. ❯ python -m pytest -s -v dandischema/tests/test_datacite.py ============================================================= test session starts ============================================================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 -- /home/yoh/proj/dandi/dandischema/venv/3/bin/python cachedir: .pytest_cache rootdir: /home/yoh/proj/dandi/dandischema configfile: tox.ini plugins: rerunfailures-14.0, cov-6.0.0 collected 14 items dandischema/tests/test_datacite.py::test_datacite[000004] FAILED dandischema/tests/test_datacite.py::test_datacite[000008] FAILED dandischema/tests/test_datacite.py::test_dandimeta_datacite[additional_meta0-datacite_checks0] FAILED dandischema/tests/test_datacite.py::test_dandimeta_datacite[additional_meta1-datacite_checks1] FAILED dandischema/tests/test_datacite.py::test_dandimeta_datacite[additional_meta2-datacite_checks2] FAILED dandischema/tests/test_datacite.py::test_dandimeta_datacite[additional_meta3-datacite_checks3] FAILED dandischema/tests/test_datacite.py::test_dandimeta_datacite[additional_meta4-datacite_checks4] FAILED dandischema/tests/test_datacite.py::test_dandimeta_datacite[additional_meta5-datacite_checks5] FAILED dandischema/tests/test_datacite.py::test_dandimeta_datacite[additional_meta6-datacite_checks6] FAILED dandischema/tests/test_datacite.py::test_datacite_publish PASSED dandischema/tests/test_datacite.py::test_datacite_related_res_url[related_res_url0-related_ident_exp0] PASSED dandischema/tests/test_datacite.py::test_datacite_related_res_url[related_res_url1-related_ident_exp1] PASSED dandischema/tests/test_datacite.py::test_datacite_related_res_url[related_res_url2-related_ident_exp2] PASSED dandischema/tests/test_datacite.py::test_datacite_related_res_url[related_res_url3-related_ident_exp3] PASSED =================================================================== FAILURES =================================================================== ____________________________________________________________ test_datacite[000004] _____________________________________________________________ dandischema/tests/test_datacite.py:160: in test_datacite datacite = to_datacite(meta=meta, validate=True) dandischema/datacite.py:238: in to_datacite validate_datacite(datacite_dict) dandischema/datacite.py:258: in validate_datacite validator.validate(datacite_dict["data"]["attributes"]) venv/3/lib/python3.12/site-packages/jsonschema/validators.py:451: in validate raise error E jsonschema.exceptions.ValidationError: 'identifiers' is a required property E E Failed validating 'required' in schema: E {'$schema': 'http://json-schema.org/draft-07/schema#', E 'definitions': {'nameType': {'type': 'string', E 'enum': ['Organizational', 'Personal']}, E 'nameIdentifiers': {'type': 'array', E 'items': {'type': 'object', E 'properties': {'nameIdentifier': {'type': 'string'}, E 'nameIdentifierScheme': {'type': 'string'}, E 'schemeURI': {'type': 'string', E 'format': 'uri'}}, E 'required': ['nameIdentifier', E 'nameIdentifierScheme']},
dandi · Nov 4, 2024 · 610ac77 · 610ac77
1 parent 7074582
commit 610ac77
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Showing 2 changed files with 16 additions and 13 deletions.
diff --git a/dandischema/datacite.py b/dandischema/datacite.py
@@ -69,16 +69,19 @@ def to_datacite(
     if publish:
         attributes["event"] = "publish"
 
-    attributes["identifiers"] = [
+    attributes["alternateIdentifiers"] = [
         # TODO: the first element is ignored, not sure how to fix it...
-        {"identifier": f"https://doi.org/{meta.doi}", "identifierType": "DOI"},
         {
-            "identifier": f"https://identifiers.org/{meta.id}",
-            "identifierType": "URL",
+            "alternateIdentifier": f"https://doi.org/{meta.doi}",
+            "alternateIdentifierType": "DOI",
         },
         {
-            "identifier": str(meta.url),
-            "identifierType": "URL",
+            "alternateIdentifier": f"https://identifiers.org/{meta.id}",
+            "alternateIdentifierType": "URL",
+        },
+        {
+            "alternateIdentifier": str(meta.url),
+            "alternateIdentifierType": "URL",
         },
     ]
 

diff --git a/dandischema/tests/test_datacite.py b/dandischema/tests/test_datacite.py
@@ -469,24 +469,24 @@ def test_datacite_publish(metadata_basic: Dict[str, Any]) -> None:
                     {"description": "testing", "descriptionType": "Abstract"}
                 ],
                 "doi": f"10.80507/dandi.{dandi_id_noprefix}/{version}",
-                "identifiers": [
+                "alternateIdentifiers": [
                     {
-                        "identifier": (
+                        "alternateIdentifier": (
                             f"https://doi.org/10.80507"
                             f"/dandi.{dandi_id_noprefix}/{version}"
                         ),
-                        "identifierType": "DOI",
+                        "alternateIdentifierType": "DOI",
                     },
                     {
-                        "identifier": f"https://identifiers.org/{dandi_id}/{version}",
-                        "identifierType": "URL",
+                        "alternateIdentifier": f"https://identifiers.org/{dandi_id}/{version}",
+                        "alternateIdentifierType": "URL",
                     },
                     {
-                        "identifier": (
+                        "alternateIdentifier": (
                             f"https://dandiarchive.org/dandiset"
                             f"/{dandi_id_noprefix}/{version}"
                         ),
-                        "identifierType": "URL",
+                        "alternateIdentifierType": "URL",
                     },
                 ],
                 "publicationYear": "1970",