remove flask upper pin

invenio_vocabularies/datastreams/writers.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 # Copyright (C) 2021-2024 CERN.
+# Copyright (C) 2024 Graz University of Technology.
 #
 # Invenio-Vocabularies is free software; you can redistribute it and/or
 # modify it under the terms of the MIT License; see LICENSE file for more
@@ -96,12 +97,13 @@ def write(self, stream_entry, *args, **kwargs):
 
         try:
             if self._insert:
-                try:
-                    return StreamEntry(self._service.create(self._identity, entry))
-                except PIDAlreadyExists:
-                    if not self._update:
-                        raise WriterError([f"Vocabulary entry already exists: {entry}"])
-                    return self._do_update(entry)
+                ret = StreamEntry(self._service.create(self._identity, entry))
+
+                # with that state management it is avoidable to check if pid
+                # exists and run into possible rollback problems
+                if self._update:
+                    self._insert = False
+                return ret
             elif self._update:
                 try:
                     return self._do_update(entry)
@@ -112,6 +114,8 @@ def write(self, stream_entry, *args, **kwargs):
                     ["Writer wrongly configured to not insert and to not update"]
                 )
 
+        except PIDAlreadyExists:
+            raise WriterError([f"Vocabulary entry already exists: {entry}"])
         except ValidationError as err:
             raise WriterError([{"ValidationError": err.messages}])
         except InvalidRelationValue as err:

invenio_vocabularies/records/systemfields/pid.py

@@ -2,6 +2,7 @@
 #
 # Copyright (C) 2020-2021 CERN.
 # Copyright (C) 2020 Northwestern University.
+# Copyright (C) 2024 Graz University of Technology.
 #
 # Invenio-Records-Resources is free software; you can redistribute it and/or
 # modify it under the terms of the MIT License; see LICENSE file for more
@@ -100,7 +101,9 @@ def resolve(self, pid_value):
     def get_pid_type(self, type_id):
         """Get the PID type for a vocabulary type."""
         # Get type based on name.
-        vocab_type = VocabularyType.query.filter_by(id=type_id).one_or_none()
+        vocab_type = (
+            db.session.query(VocabularyType).filter_by(id=type_id).one_or_none()
+        )
         if vocab_type is None:
             raise PIDDoesNotExistError(None, None)
         return vocab_type.pid_type

invenio_vocabularies/services/components.py

@@ -1,13 +1,15 @@
 # -*- coding: utf-8 -*-
 #
 # Copyright (C) 2020-2021 CERN.
+# Copyright (C) 2024 Graz University of Technology.
 #
 # Invenio-Vocabularies is free software; you can redistribute it and/or
 # modify it under the terms of the MIT License; see LICENSE file for more
 # details.
 
 """Vocabulary components."""
 
+from invenio_db import db
 from invenio_i18n import lazy_gettext as _
 from invenio_records_resources.services.records.components import ServiceComponent
 from marshmallow import ValidationError
@@ -23,7 +25,10 @@ def _set_type(self, data, record):
         type_id = data.pop("type", None)
         if type_id:
             try:
-                record.type = VocabularyType.query.filter_by(id=type_id["id"]).one()
+
+                record.type = (
+                    db.session.query(VocabularyType).filter_by(id=type_id["id"]).one()
+                )
             except NoResultFound:
                 raise ValidationError(
                     _("The vocabulary type does not exists."),

invenio_vocabularies/services/service.py

@@ -3,6 +3,7 @@
 # Copyright (C) 2024 CERN.
 # Copyright (C) 2021 Northwestern University.
 # Copyright (C) 2024 University of Münster.
+# Copyright (C) 2024 Graz University of Technology.
 #
 # Invenio-Vocabularies is free software; you can redistribute it and/or
 # modify it under the terms of the MIT License; see LICENSE file for more
@@ -12,6 +13,7 @@
 
 import sqlalchemy as sa
 from invenio_cache import current_cache
+from invenio_db import db
 from invenio_records_resources.services import LinksTemplate, RecordService
 from invenio_records_resources.services.base.utils import map_search_params
 from invenio_records_resources.services.records.schema import ServiceSchemaWrapper
@@ -42,7 +44,8 @@ def search(self, identity, params=None):
             filters.extend([VocabularyType.id.ilike(f"%{query_param}%")])
 
         vocabulary_types = (
-            VocabularyType.query.filter(sa.or_(*filters))
+            db.session.query(VocabularyType)
+            .filter(sa.or_(*filters))
             .order_by(
                 search_params["sort_direction"](
                     sa.text(",".join(search_params["sort"]))
@@ -87,7 +90,7 @@ def search(
         self.require_permission(identity, "search")
 
         # If not found, NoResultFound is raised (caught by the resource).
-        vocabulary_type = VocabularyType.query.filter_by(id=type).one()
+        vocabulary_type = db.session.query(VocabularyType).filter_by(id=type).one()
 
         # Prepare and execute the search
         params = params or {}
@@ -123,7 +126,7 @@ def read_all(self, identity, fields, type, cache=True, extra_filter="", **kwargs
 
         if not results:
             # If not found, NoResultFound is raised (caught by the resource).
-            vocabulary_type = VocabularyType.query.filter_by(id=type).one()
+            vocabulary_type = db.session.query(VocabularyType).filter_by(id=type).one()
             vocab_id_filter = dsl.Q("term", type__id=vocabulary_type.id)
             if extra_filter:
                 vocab_id_filter = vocab_id_filter & extra_filter
@@ -150,7 +153,7 @@ def read_all(self, identity, fields, type, cache=True, extra_filter="", **kwargs
     def read_many(self, identity, type, ids, fields=None, **kwargs):
         """Search for records matching the querystring filtered by ids."""
         search_query = dsl.Q("match_all")
-        vocabulary_type = VocabularyType.query.filter_by(id=type).one()
+        vocabulary_type = db.session.query(VocabularyType).filter_by(id=type).one()
         vocab_id_filter = dsl.Q("term", type__id=vocabulary_type.id)
         filters = []
 

tests/conftest.py

@@ -3,6 +3,7 @@
 # Copyright (C) 2020-2024 CERN.
 # Copyright (C) 2021 TU Wien.
 # Copyright (C) 2024 California Institute of Technology.
+# Copyright (C) 2024 Graz University of Technology.
 #
 # Invenio-Vocabularies is free software; you can redistribute it and/or
 # modify it under the terms of the MIT License; see LICENSE file for more
@@ -76,7 +77,7 @@ def extra_entry_points():
 @pytest.fixture(scope="module")
 def app_config(app_config):
     """Mimic an instance's configuration."""
-    app_config["JSONSCHEMAS_HOST"] = "localhost"
+    app_config["JSONSCHEMAS_HOST"] = "not-used"
     app_config["BABEL_DEFAULT_LOCALE"] = "en"
     app_config["I18N_LANGUAGES"] = [("da", "Danish")]
     app_config["RECORDS_REFRESOLVER_CLS"] = (
@@ -119,11 +120,11 @@ def service(app):
     return app.extensions["invenio-vocabularies"].vocabularies_service
 
 
-@pytest.fixture()
+@pytest.fixture(scope="function")
 def lang_type(db):
     """Get a language vocabulary type."""
     v = VocabularyType.create(id="languages", pid_type="lng")
-    db.session.commit()
+    db.session.add(v)
     return v
 
 
@@ -158,7 +159,6 @@ def example_record(db, identity, service, example_data):
     vocabulary_type_licenses = VocabularyType(name="licenses")
     db.session.add(vocabulary_type_languages)
     db.session.add(vocabulary_type_licenses)
-    db.session.commit()
 
     record = service.create(
         identity=identity,
@@ -192,7 +192,7 @@ def user(app, db):
             password=hash_password("password"),
             active=True,
         )
-    db.session.commit()
+
     return _user
 
 
@@ -203,7 +203,6 @@ def role(app, db):
         datastore = app.extensions["security"].datastore
         role = datastore.create_role(name="admin", description="admin role")
 
-    db.session.commit()
     return role
 
 

tests/contrib/affiliations/test_affiliations_resource.py

@@ -2,6 +2,7 @@
 #
 # This file is part of Invenio.
 # Copyright (C) 2021-2024 CERN.
+# Copyright (C) 2024 Graz University of Technology.
 #
 # Invenio-Vocabularies is free software; you can redistribute it and/or
 # modify it under the terms of the MIT License; see LICENSE file for more
@@ -30,7 +31,6 @@ def example_affiliation(
     """Example affiliation."""
     aff = service.create(identity, affiliation_full_data)
     Affiliation.index.refresh()  # Refresh the index
-
     return aff
 
 
@@ -41,7 +41,7 @@ def test_affiliations_invalid(client, h, prefix):
     assert res.status_code == 404
 
 
-def test_affiliations_forbidden(
+def test_affiliations_forbidden_a(
     client, h, prefix, example_affiliation, affiliation_full_data
 ):
     """Test invalid type."""
@@ -53,11 +53,22 @@ def test_affiliations_forbidden(
     )
     assert res.status_code == 403
 
+
+def test_affiliations_forbidden_b(
+    client, h, prefix, example_affiliation, affiliation_full_data
+):
+    """Test put."""
     res = client.put(
         f"{prefix}/01ggx4157", headers=h, data=json.dumps(affiliation_full_data)
     )
+
     assert res.status_code == 403
 
+
+def test_affiliations_forbidden_c(
+    client, h, prefix, example_affiliation, affiliation_full_data
+):
+    """Test delete."""
     res = client.delete(f"{prefix}/01ggx4157")
     assert res.status_code == 403
 

tests/contrib/awards/conftest.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 # Copyright (C) 2022 CERN.
+# Copyright (C) 2024 Graz University of Technology.
 #
 # Invenio-Vocabularies is free software; you can redistribute it and/or
 # modify it under the terms of the MIT License; see LICENSE file for more
@@ -13,12 +14,14 @@
 """
 
 import pytest
-from invenio_i18n import lazy_gettext as _
 from invenio_indexer.proxies import current_indexer_registry
 from invenio_records_resources.proxies import current_service_registry
+from sqlalchemy.orm.exc import ObjectDeletedError
 
 from invenio_vocabularies.contrib.awards.api import Award
+from invenio_vocabularies.contrib.awards.models import AwardsMetadata
 from invenio_vocabularies.contrib.funders.api import Funder
+from invenio_vocabularies.contrib.funders.models import FundersMetadata
 
 
 #
@@ -38,10 +41,27 @@ def example_funder(db, identity, funders_service, funder_indexer):
     }
     funder = funders_service.create(identity, funder_data)
     Funder.index.refresh()  # Refresh the index
+
+    funder_id = funder._record.id
+    index = type("index", (), {"_name": funder._record.index._name})
+    funder_dict = type(
+        "",
+        (),
+        {
+            "index": index(),
+            "id": funder._record.id,
+            "revision_id": funder._record.revision_id,
+        },
+    )
+
     yield funder
-    funder._record.delete(force=True)
-    funder_indexer.delete(funder._record, refresh=True)
-    db.session.commit()
+
+    db.session.query(FundersMetadata).filter(FundersMetadata.id == funder_id).delete()
+
+    try:
+        funder_indexer.delete(funder._record, refresh=True)
+    except ObjectDeletedError:
+        funder_indexer.delete(funder_dict(), refresh=True)
 
 
 @pytest.fixture(scope="function")
@@ -55,10 +75,27 @@ def example_funder_ec(db, identity, funders_service, funder_indexer):
     }
     funder = funders_service.create(identity, funder_data)
     Funder.index.refresh()  # Refresh the index
+
+    funder_id = funder._record.id
+    index = type("index", (), {"_name": funder._record.index._name})
+    funder_dict = type(
+        "",
+        (),
+        {
+            "index": index(),
+            "id": funder._record.id,
+            "revision_id": funder._record.revision_id,
+        },
+    )
+
     yield funder
-    funder._record.delete(force=True)
-    funder_indexer.delete(funder._record, refresh=True)
-    db.session.commit()
+
+    db.session.query(FundersMetadata).filter(FundersMetadata.id == funder_id).delete()
+
+    try:
+        funder_indexer.delete(funder._record, refresh=True)
+    except ObjectDeletedError:
+        funder_indexer.delete(funder_dict(), refresh=True)
 
 
 @pytest.fixture(scope="module")
@@ -125,10 +162,31 @@ def example_award(db, example_funder_ec, award_full_data, identity, indexer, ser
     """Creates and hard deletes an award."""
     award = service.create(identity, award_full_data)
     Award.index.refresh()  # Refresh the index
+
+    # necessary step for the clean up part after yield
+    # award._record could be gone if there was a intended rollback
+    # in one of the test functions
+    award_id = award._record.id
+    index = type("index", (), {"_name": award._record.index._name})
+    award_dict = type(
+        "",
+        (),
+        {
+            "index": index(),
+            "id": award._record.id,
+            "revision_id": award._record.revision_id,
+        },
+    )
+
     yield award
-    award._record.delete(force=True)
-    indexer.delete(award._record, refresh=True)
-    db.session.commit()
+
+    # to clean up
+    db.session.query(AwardsMetadata).filter(AwardsMetadata.id == award_id).delete()
+
+    try:
+        indexer.delete(award._record, refresh=True)
+    except ObjectDeletedError:
+        indexer.delete(award_dict(), refresh=True)
 
 
 @pytest.fixture(scope="module")