CHANGELOG.md

@@ -1,20 +1,30 @@
+# 6.3.0 (2026-06-29)
+
+## Changes
+
+- Automated annotation adding in write-record-endpoints has been removed.
+  The new query parameter `add_submission_tag` is added to write-record-endpoints.
+  If set to True, the server will add an automated annotation with the annotation
+  tags that  are defined in the server-configuration (the default is False).
+
+
 # 6.2.2 (2026-06-26)
 
-# Bugfixes
+## Bugfixes
 
 - Fix a bug in authentication when non-config tokens are used.
 
 
 # 6.2.1 (2026-06-26)
 
-# Bugfixes
+## Bugfixes
 
 - Fix a bug in curator-writing when non-config tokens are used.
 
 
 # 6.2.0 (2026-06-24)
 
-# New features
+## New features
 
 - Add PUT-methods to the administration endpoints `/tokens`, `/collections` and 
   `/admin_tokens`. This allows to update collections, tokens, and
@@ -31,7 +41,7 @@
 
 # 6.1.0 (2026-06-22)
 
-# New features
+## New features
 
 - Add the option: `--ignore-default-config-file`. If the option is provided
   a version 6 server will not try to initialize its configuration from the 

dump_things_service/__about__.py

@@ -1 +1 @@
-__version__ = '6.2.2'
+__version__ = '6.3.0'

dump_things_service/collection.py

@@ -84,10 +84,11 @@ _endpoint_template = """
 def {name}(
         data: {model_var_name}.{class_name} | Annotated[str, Body(media_type='text/plain')],
         api_key: str = Depends(api_key_header_scheme),
+        add_submission_tag: bool = False,
         format: Format = Format.json,
 ) -> JSONResponse | PlainTextResponse:
-    logger.info('{name}(%s, %s, %s, %s)', repr(data), repr('{class_name}'), repr({model_var_name}), repr(format))
-    return {handler}('{collection}', data, '{class_name}', {model_var_name}, format, api_key)
+    logger.info('{name}(%s, %s, %s, %s, %s)', repr(data), repr('{class_name}'), repr({model_var_name}), repr(add_submission_tag), repr(format))
+    return {handler}('{collection}', data, '{class_name}', {model_var_name}, format, add_submission_tag, api_key)
 """
 
 _endpoint_curated_template = """
@@ -536,6 +537,7 @@ def store_record(
         class_name: str,
         model: Any,
         input_format: Format,
+        add_submission_tag: bool,
         api_key: str | None = Depends(api_key_header_scheme),
 ) -> JSONResponse | PlainTextResponse:
     if input_format == Format.json and isinstance(data, str):
@@ -597,7 +599,10 @@ def store_record(
         instance_state.validators[collection].validate(record)
 
     with wrap_http_exception(CurieResolutionError):
-        stored_records = store.store_object(obj=record, submitter=user_id)
+        stored_records = store.store_object(
+            obj=record,
+            submitter=user_id if add_submission_tag else None,
+        )
 
     if input_format == Format.ttl:
         format_converter = FormatConverter(

dump_things_service/collection_endpoints.py

@@ -24,7 +24,6 @@ from dump_things_service import (
 from dump_things_service.abstract_config import (
     Configuration,
     CollectionConfig,
-    StrictModel,
     store_config,
     get_config, get_token_permissions,
 )
@@ -59,9 +58,6 @@ class TagSpec(BaseModel):
     submission_time_tag: str = 'http://semanticscience.org/resource/SIO_001083'
 
 
-from pydantic import ConfigDict, Field
-from dump_things_service.abstract_config import RecordDirBackendConfig, SQLiteBackendConfig, GitAuditBackendConfig
-
 class CollectionRequest(CollectionConfig):
     name: str
 
@@ -124,7 +120,7 @@ async def create_or_replace_collection(
 
     # Check for distinct directories.
     # TODO: we skip this currently because a number of version 5 installations
-    #  deliberately put inboxes into the same path. Those configuration cannot
+    #  deliberately put inboxes into the same path. Those configurations cannot
     #  be established if this check is performed. Instead of the `if False:`-
     #  clause, we should introduce a configuration for the server to specify
     #  whether unique directories are required.

dump_things_service/store/model_store.py

@@ -45,7 +45,7 @@ class _ModelStore:
     def store_object(
             self,
             obj: BaseModel,
-            submitter: str,
+            submitter: str | None,
     ) -> Iterable[tuple[str, dict]]:
         if obj.__class__.__name__ == 'Thing' and 'dlthings:placeholder' in (obj.annotations or dict()):
             return []
@@ -72,7 +72,7 @@ class _ModelStore:
     def _store_flat_object(
             self,
             obj: BaseModel,
-            submitter: str,
+            submitter: str | None,
     ) -> dict:
         iri = self.pid_to_iri(obj.pid)
         class_name = obj.__class__.__name__
@@ -83,7 +83,9 @@ class _ModelStore:
         )
 
         # Add the submitter id to the record annotations
-        self.annotate(json_object, submitter)
+        if submitter:
+            self.annotate(json_object, submitter)
+
         self.backend.add_record(
             iri=iri,
             class_name=class_name,

dump_things_service/tests/test_basic.py

@@ -202,9 +202,7 @@ def test_store_record(fastapi_client_simple):
             headers={'x-dumpthings-token': token},
         )
         assert response.status_code == HTTP_200_OK
-        assert (
-            cleaned_json(response.json(), remove_keys=('annotations',)) == extra_record
-        )
+        assert response.json() == extra_record
 
     # Check that other collections do not report the new record
     for i in range(3, 6):
@@ -223,13 +221,12 @@ def test_store_record(fastapi_client_simple):
             f'/collection_{i}/records/Thing',
             headers={'x-dumpthings-token': token},
         )
-        cleaned_response = cleaned_json(response.json(), remove_keys=('annotations',))
-        assert extra_record in cleaned_response
+        assert extra_record in response.json()
         assert {
             'schema_type': 'abc:Person',
             'pid': pid,
             'given_name': given_name,
-        } in cleaned_response
+        } in response.json()
 
     # Check pagination
     for i, token in basic_write_locations:
@@ -240,14 +237,12 @@ def test_store_record(fastapi_client_simple):
         assert response.status_code == HTTP_200_OK
         for key in ('items', 'total', 'page', 'size', 'pages'):
             assert key in response.json()
-        records = response.json()['items']
-        cleaned_response = cleaned_json(records, remove_keys=('annotations',))
-        assert extra_record in cleaned_response
+        assert extra_record in response.json()['items']
         assert {
             'schema_type': 'abc:Person',
             'pid': pid,
             'given_name': given_name,
-        } in cleaned_response
+        } in response.json()['items']
 
 
 def test_encoding(fastapi_client_simple):

dump_things_service/tests/test_collection_administration.py

@@ -144,7 +144,7 @@ def test_collection_adding(fastapi_client_simple):
         headers={'x-dumpthings-token': new_token_representation},
     )
     assert response.status_code == HTTP_200_OK
-    assert cleaned_json(response.json()[0], ('annotations',)) == new_record
+    assert response.json()[0] == new_record
 
     # Remove the token
     response = test_client.delete(

dump_things_service/tests/test_roundtrip.py

@@ -24,6 +24,30 @@ ttl_result_record_a = """@prefix abc: <http://example.org/person-schema/abc/> .
 @prefix oxo: <http://purl.obolibrary.org/obo/> .
 @prefix xyz: <http://example.org/person-schema/xyz/> .
 
+xyz:HenryAdams a abc:Person ;
+    abc:annotations [ a abc:Annotation ;
+            abc:annotation_tag <http://semanticscience.org/resource/SIO_001083> ;
+            abc:annotation_value "1970-01-01T00:00:00" ] ;
+    abc:given_name "Henryöäß" ;
+    abc:schema_type "abc:Person" .
+"""
+
+ttl_result_record_b = """@prefix abc: <http://example.org/person-schema/abc/> .
+@prefix oxo: <http://purl.obolibrary.org/obo/> .
+@prefix xyz: <http://example.org/person-schema/xyz/> .
+
+xyz:HenryAdams a abc:Person ;
+    abc:annotations [ a abc:Annotation ;
+            abc:annotation_tag oxo:NCIT_C54269 ;
+            abc:annotation_value "test_user_1" ] ;
+    abc:given_name "Henryöäß" ;
+    abc:schema_type "abc:Person" .
+"""
+
+ttl_result_record_with_annotations_a = """@prefix abc: <http://example.org/person-schema/abc/> .
+@prefix oxo: <http://purl.obolibrary.org/obo/> .
+@prefix xyz: <http://example.org/person-schema/xyz/> .
+
 xyz:HenryAdams a abc:Person ;
     abc:annotations [ a abc:Annotation ;
             abc:annotation_tag <http://semanticscience.org/resource/SIO_001083> ;
@@ -35,7 +59,7 @@ xyz:HenryAdams a abc:Person ;
     abc:schema_type "abc:Person" .
 """
 
-ttl_result_record_b = """@prefix abc: <http://example.org/person-schema/abc/> .
+ttl_result_record_with_annotations_b = """@prefix abc: <http://example.org/person-schema/abc/> .
 @prefix oxo: <http://purl.obolibrary.org/obo/> .
 @prefix xyz: <http://example.org/person-schema/xyz/> .
 

dump_things_service/tests/test_roundtrip_flatsocial.py

@@ -35,7 +35,23 @@ dlflatsocial:test_john_ttl a dlflatsocial:Person ;
     dlsocialmx:given_name "Johnöüß" .
 """
 
-ttl_output_record_a = """@prefix dlflat: <https://concepts.datalad.org/s/flat/unreleased/> .
+ttl_output_record_a = """@prefix dlflatsocial: <https://concepts.datalad.org/s/flat-social/unreleased/> .
+@prefix dlsocialmx: <https://concepts.datalad.org/s/social-mixin/unreleased/> .
+
+dlflatsocial:another_john_ttl a dlflatsocial:Person ;
+    dlsocialmx:given_name "Johnöüß" .
+"""
+
+
+ttl_output_record_b = """@prefix dlflatsocial: <https://concepts.datalad.org/s/flat-social/unreleased/> .
+@prefix dlsocialmx: <https://concepts.datalad.org/s/social-mixin/unreleased/> .
+
+dlflatsocial:another_john_ttl a dlflatsocial:Person ;
+    dlsocialmx:given_name "Johnöüß" .
+"""
+
+
+ttl_output_record_with_annotation_a = """@prefix dlflat: <https://concepts.datalad.org/s/flat/unreleased/> .
 @prefix dlflatsocial: <https://concepts.datalad.org/s/flat-social/unreleased/> .
 @prefix dlsocialmx: <https://concepts.datalad.org/s/social-mixin/unreleased/> .
 @prefix dlthings: <https://concepts.datalad.org/s/things/v1/> .
@@ -52,7 +68,7 @@ dlflatsocial:another_john_ttl a dlflatsocial:Person ;
 """
 
 
-ttl_output_record_b = """@prefix dlflat: <https://concepts.datalad.org/s/flat/unreleased/> .
+ttl_output_record_with_annotation_b = """@prefix dlflat: <https://concepts.datalad.org/s/flat/unreleased/> .
 @prefix dlflatsocial: <https://concepts.datalad.org/s/flat-social/unreleased/> .
 @prefix dlsocialmx: <https://concepts.datalad.org/s/social-mixin/unreleased/> .
 @prefix dlthings: <https://concepts.datalad.org/s/things/v1/> .
@@ -108,7 +124,7 @@ def test_json_ttl_json_dlflatsocial(fastapi_client_simple):
             headers={'x-dumpthings-token': 'token-all'},
         )
         assert response.status_code == HTTP_200_OK
-        json_object = cleaned_json(response.json(), remove_keys=('annotations',))
+        json_object = response.json()
         assert cleaned_json(json_object, remove_keys=('schema_type',)) != json_record
         json_object['pid'] = json_record['pid']
         assert json_object == json_record_out

dump_things_service/validate.py

@@ -38,6 +38,7 @@ def validate_record(
         class_name: str,
         model: Any,
         input_format: Format,
+        _: bool,
         api_key: str | None = Depends(api_key_header_scheme),
 ) -> JSONResponse: