invenio-vocabularies 6.10.1__tar.gz → 7.0.0__tar.gz

invenio_vocabularies-7.0.0/.github/workflows/pypi-publish.yml

@@ -0,0 +1,13 @@
+name: Publish
+
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+  build-n-publish:
+    uses: inveniosoftware/workflows/.github/workflows/pypi-publish.yml@master
+    secrets: inherit
+    with:
+      babel-compile-catalog: true

{invenio-vocabularies-6.10.1 → invenio_vocabularies-7.0.0}/CHANGES.rst

@@ -1,5 +1,6 @@
 ..
     Copyright (C) 2020-2024 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
@@ -8,6 +9,23 @@
 Changes
 =======
 
+Version v7.0.0 (released 2025-02-13)
+
+- Promote to stable release
+- jobs: apply code upgrades
+
+Version v7.0.0.dev2 (released 2025-01-23)
+
+Version v7.0.0.dev1 (released 2024-12-12)
+
+- comp: make compatible to flask-sqlalchemy>=3.1
+- setup: change to reusable workflows
+- setup: bump major dependencies
+
+Version v6.11.0 (released 2024-12-13)
+
+- names: fix acronym in marshamllow schema
+
 Version v6.10.1 (released 2024-12-12)
 
 - names: drop unique id on the internal id

invenio_vocabularies-7.0.0/PKG-INFO

@@ -0,0 +1,429 @@
+Metadata-Version: 2.2
+Name: invenio-vocabularies
+Version: 7.0.0
+Summary: Invenio module for managing vocabularies.
+Home-page: https://github.com/inveniosoftware/invenio-vocabularies
+Author: CERN
+Author-email: info@inveniosoftware.org
+License: MIT
+Keywords: invenio vocabulary management
+Platform: any
+Classifier: Development Status :: 5 - Production/Stable
+Requires-Python: >=3.7
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: invenio-i18n<4.0.0,>=3.0.0
+Requires-Dist: invenio-records-resources<8.0.0,>=7.0.0
+Requires-Dist: invenio-administration<4.0.0,>=3.0.0
+Requires-Dist: invenio-jobs<4.0.0,>=3.0.0
+Requires-Dist: lxml>=4.5.0
+Requires-Dist: pycountry<23.0.0,>=22.3.5
+Requires-Dist: PyYAML>=5.4.1
+Requires-Dist: regex>=2024.7.24
+Requires-Dist: SPARQLWrapper>=2.0.0
+Provides-Extra: s3fs
+Requires-Dist: s3fs>=2024.6.1; extra == "s3fs"
+Provides-Extra: oaipmh
+Requires-Dist: invenio-oaipmh-scythe>=0.13.0; extra == "oaipmh"
+Provides-Extra: rdf
+Requires-Dist: rdflib>=7.0.0; extra == "rdf"
+Provides-Extra: sparql
+Requires-Dist: SPARQLWrapper>=2.0.0; extra == "sparql"
+Provides-Extra: tests
+Requires-Dist: pytest-black-ng>=0.4.0; extra == "tests"
+Requires-Dist: invenio-app<3.0.0,>=2.0.0; extra == "tests"
+Requires-Dist: invenio-db[mysql,postgresql]<3.0.0,>=2.0.0; extra == "tests"
+Requires-Dist: pytest_httpserver>=1.0.10; extra == "tests"
+Requires-Dist: pytest-invenio<4.0.0,>=3.0.0; extra == "tests"
+Requires-Dist: Sphinx>=4.5; extra == "tests"
+Provides-Extra: elasticsearch7
+Requires-Dist: invenio-search[elasticsearch7]<4.0.0,>=3.0.0; extra == "elasticsearch7"
+Provides-Extra: opensearch1
+Requires-Dist: invenio-search[opensearch1]<4.0.0,>=3.0.0; extra == "opensearch1"
+Provides-Extra: opensearch2
+Requires-Dist: invenio-search[opensearch2]<4.0.0,>=3.0.0; extra == "opensearch2"
+Provides-Extra: mysql
+Provides-Extra: postgresql
+Provides-Extra: sqlite
+
+..
+    Copyright (C) 2020-2021 CERN.
+
+    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.
+
+======================
+ Invenio-Vocabularies
+======================
+
+.. image:: https://github.com/inveniosoftware/invenio-vocabularies/workflows/CI/badge.svg
+        :target: https://github.com/inveniosoftware/invenio-vocabularies/actions?query=workflow%3ACI
+
+.. image:: https://img.shields.io/coveralls/inveniosoftware/invenio-vocabularies.svg
+        :target: https://coveralls.io/r/inveniosoftware/invenio-vocabularies
+
+.. image:: https://img.shields.io/github/tag/inveniosoftware/invenio-vocabularies.svg
+        :target: https://github.com/inveniosoftware/invenio-vocabularies/releases
+
+.. image:: https://img.shields.io/pypi/dm/invenio-vocabularies.svg
+        :target: https://pypi.python.org/pypi/invenio-vocabularies
+
+.. image:: https://img.shields.io/github/license/inveniosoftware/invenio-vocabularies.svg
+        :target: https://github.com/inveniosoftware/invenio-vocabularies/blob/master/LICENSE
+
+Invenio module for managing vocabularies, based on Invenio-Records and Invenio-Records-Resources. This module provides:
+
+- Factories for easily generating models, record API classes, services, and resources
+- Helpers for importing vocabularies
+
+Further documentation is available on
+https://invenio-vocabularies.readthedocs.io/
+
+..
+    Copyright (C) 2020-2024 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
+    details.
+
+Changes
+=======
+
+Version v7.0.0 (released 2025-02-13)
+
+- Promote to stable release
+- jobs: apply code upgrades
+
+Version v7.0.0.dev2 (released 2025-01-23)
+
+Version v7.0.0.dev1 (released 2024-12-12)
+
+- comp: make compatible to flask-sqlalchemy>=3.1
+- setup: change to reusable workflows
+- setup: bump major dependencies
+
+Version v6.11.0 (released 2024-12-13)
+
+- names: fix acronym in marshamllow schema
+
+Version v6.10.1 (released 2024-12-12)
+
+- names: drop unique id on the internal id
+
+Version v6.10.0 (released 2024-12-12)
+
+- names: add internal id column to the name_metadata db
+
+Version v6.9.0 (released 2024-12-09)
+
+- schema: added identifiers in affiliations relation
+
+Version v6.8.0 (released 2024-12-09)
+
+- names: extract affiliation identifiers from employments
+- names: optimize memory usage on ORCID sync
+- subjects: improve search with CompositeSuggestQueryParser
+- subjects: added datastream for bodc
+
+Version v6.7.0 (released 2024-11-27)
+
+- contrib: improve search accuracy for names, funders, affiliations
+- names: add affiliation acronym in mappings and schema
+    * Dereferences the affiliation `acronym` when indexing names and serving
+      REST API results. This is useful for disambiguating authors in search.
+- affiliations: move RDF and SPARQL as extra dependencies
+    * Moves `rdflib` and `SPARQLWrapper` to extras.
+- affiliation: refactored edmo datastreams
+- subjects: added datastream for GEMET vocabulary
+- awards/schema.py: read app config for alternate funding validation (#429)
+- awards: fix description field and mappings
+- awards: add fields start/end date and description
+
+Version v6.6.0 (released 2024-11-15)
+
+- mesh: add title en if not present
+- subjects: add subject to search fields
+- jobs: add ORCID job
+- global: Add unlisted tag
+    * This adds a new tag to the vocabularies to allow for unlisted
+      vocabularies. This is useful for vocabularies that are not meant to be
+      displayed in the UI.
+    * This requires to update the names mapping to add the props.
+
+Version v6.5.0 (released 2024-10-31)
+
+- subjects: euroscivoc: change default to latest version-less URL
+- Rename patched filters so the normalizer uses the default ones (#409)
+    * rename patched filters so the normalizer uses the default ones
+
+Version v6.4.1 (released 2024-10-15)
+
+- fix: exclude unknown fields when updating awards with subjects
+- fix: revert generic writer and define OpenAIRE awards writer logic
+
+Version v6.4.0 (released 2024-10-15)
+
+- jobs: add import awards OpenAIRE; Update CORDIS
+- awards: rollback to use the 2nd part of funding stream as program
+
+Version v6.3.1 (released 2024-10-11)
+
+- jobs: pass since as string to task
+
+Version v6.3.0 (released 2024-10-11)
+
+- awards: get program from CORDIS
+- fix: add 'en' title if missing ROR
+- fix: since not passed to args
+- jobs: add process funders job
+
+Version v6.2.1 (released 2024-10-10)
+
+- webpack: bump react-searchkit due to axios upgrade
+
+Version v6.2.0 (released 2024-10-10)
+
+- tests: update axios version (needed only for local js tests)
+
+Version v6.1.0 (released 2024-10-10)
+
+- jobs: define invenio job wrapper for ROR affiliation data stream
+- awards: remove subj props from jsonschema
+
+Version v6.0.0 (released 2024-10-03)
+
+- datastreams: writers: add option to not insert
+- subjects: added euroscivoc datastream
+- affiliations: OpenAIRE transformer and writer adding PIC identifier
+- awards: added subjects and participating organizations from CORDIS datastreams
+- names: add permission check to names search
+
+Version v5.1.0 (released 2024-09-25)
+
+- funders: tune search boost for acronyms
+    * Add and `acronym.keyword` field to the funders mapping.
+    * Apply to funders the same field boosting as in affiliations.
+
+Version v5.0.3 (released 2024-09-06)
+
+- services: skip index rebuilding
+
+Version v5.0.2 (released 2024-08-28)
+
+- ror: use datePublished as fallback date for dataset timestamp
+
+Version v5.0.1 (released 2024-08-27)
+
+- mapping: fix normalizer
+
+Version v5.0.0 (released 2024-08-22)
+
+- affiliations: dd analyzers and filters to improve results when searching affiliations
+
+Version v4.4.0 (released 2024-08-09)
+
+- services: use and adjust vnd.inveniordm.v1+json http accept header
+
+Version v4.3.0 (released 2024-08-05)
+
+- names: make names_exclude_regex configurable
+- names: validate entry full names
+- names: add orcid public data sync
+
+Version v4.2.0 (released 2024-07-24)
+
+- ror: check last update; use ld+json for metadata (#367)
+- tasks: remove import funders task
+- funders: add and export custom transformer
+- affiliations: add and export custom transformer
+- datastreams: implement asynchronous writer
+
+Version v4.1.1 (released 2024-07-15)
+
+- installation: use invenio-oaipmh-scythe from PyPI
+
+Version v4.1.0 (released 2024-07-15)
+
+- readers: make OAI-PMH an optional extra
+- schema: add administration UI attributes
+- ror: fix duplicate acronymns and aliases
+- affiliations: fix title search
+- datastreams: have yaml writer output utf8
+- datastreams: add configs for funders and affiliations
+- affiliations: add datastreams
+- datastreams: move ror transformer to common
+- vocabulary-types: services, resources, and administration UI (#310)
+- config: add OpenAIRE mapping for "Latvian Council of Science"
+- funders: fix country name display (#343)
+- Initial implementation of OAIPMHReader (#329)
+- global: add "tags" field to all vocabularies
+
+Version 4.0.0 (released 2024-06-04)
+
+- datastreams: implement factories for generating vocabulary configurations
+- datastreams: added ROR HTTP reader
+- funders: use ROR v2 dump instead of v1
+- datastreams: added celery task for funders using ROR HTTP reader
+- datastreams: add OpenAIRE Project HTTP Reader
+- datastreams: fix OpenAIRE graph dataset parsing
+- installation: upgrade invenio-records-resources
+
+Version 3.4.0 (released 2024-04-19)
+
+- templates: add subject fields UI template (#303)
+
+Version 3.3.0 (released 2024-04-16)
+
+- assets: add overridable awards and funding
+
+Version 3.2.0 (released 2024-03-22)
+
+- funding: add country and ror to funder search results
+- init: move record_once to finalize_app (removes deprecation on `before_first_request`)
+- installation: upgrade invenio-app
+
+
+Version 3.1.0 (released 2024-03-05)
+
+- custom_fields: added subject field
+- custom_fields: add pid_field to custom fields
+- mappings: change "dynamic" values to string
+- ci: upgrade tests matrix
+- bumps react-invenio-forms
+
+Version 3.0.0 (released 2024-01-30)
+
+- installation: bump invenio-records-resources
+
+Version 2.4.0 (2023-12-07)
+
+- schema: add validation for affiliations
+- mappings: add a text subfield for award acronyms
+- config: add new TWCF funder
+
+Version 2.3.1 (2023-11-01)
+
+- contrib: add affiliation suggestion by id
+
+Version 2.3.0 (2023-10-25)
+
+- contrib: allow search funders by id
+- contrib: funders and awards fix TransportError in OS caused by suggestion search in too many fields
+
+Version 2.2.4 (2023-10-19)
+
+- search: decrease number of searching fields
+
+Version 2.2.3 (2023-10-08)
+
+- contrib: fix ``name`` serialization for the Names vocabulary.
+
+Version 2.2.2 (2023-10-06)
+
+- alembic rcp: set explicit dependency on pidstore create table
+
+Version 2.2.1 (2023-10-02)
+
+- facets: change caching strategy by caching each vocabulary by id. Replace
+  lru_cache with invenio-cache to ensure that cache expiration uses a TTL that
+  is correctly computed.
+
+Version 2.2.0 (2023-09-19)
+
+- facets: implement in-memory cache
+
+Version 2.1.1 (2023-09-19)
+
+- funding: fixed accessiblity issues
+
+Version 2.1.0 (2023-09-15)
+
+- custom_fields: allow to pass schema to the VocabularyCF
+- affiliations: add facet labels
+
+Version 2.0.0 (2023-09-14)
+
+- contrib-awards: add "program" to schema fields
+- global: switch names and affiliations to model PID field
+- ci: update matrix
+- awards: add "program" field
+- config: update awards funders mapping
+- service: add sort option to load vocabs
+
+Version 1.6.0 (2023-09-12)
+
+- awards: add acronym to schema
+
+Version 1.5.1 (2023-07-07)
+
+- fix string type columns for mysql
+
+Version 1.5.0 (2023-04-25)
+
+- upgrade invenio-records-resources
+
+Version 1.4.0 (2023-04-20)
+
+- upgrade invenio-records-resources
+
+Version 1.3.0 (2023-04-20)
+
+- add UI deposit contrib components
+
+Version 1.2.0 (2023-03-24)
+
+- bump invenio-records-resources to v2.0.0
+
+Version 1.1.0 (released 2023-03-02)
+
+- serializers: deprecate marshamllow JSON
+- mappings: add dynamic template for i18n titles and descriptions
+- remove deprecated flask-babelex dependency and imports
+
+Version 1.0.4 (released 2023-01-20)
+
+- funders: Add ROR to identifiers for all funders in datastream
+- facets: add not found facet exception (when facet is configured but not provided in setup)
+- facets: handle non existing vocabulary type
+
+Version 1.0.3 (released 2022-11-25)
+
+- Add i18n translations.
+
+Version 1.0.2 (released 2022-11-14)
+
+- Fix missing field_args in VocabularyCF
+
+Version 1.0.1 (released 2022-11-14)
+
+- Allow kwargs in VocabularyCF
+
+Version 1.0.0 (released 2022-11-04)
+
+- Bump invenio-records-resources
+
+Version 0.1.5 (released 2020-12-11)
+
+- Bug fixes in contrib vocabulary
+
+Version 0.1.4 (released 2020-12-11)
+
+- Add subjects vocabulary
+
+Version 0.1.3 (released 2020-12-11)
+
+- Include csv vocabularies data
+
+Version 0.1.2 (released 2020-12-11)
+
+- CI changes
+
+Version 0.1.1 (released 2020-12-11)
+
+- Add vocabulary import command
+
+Version 0.1.0 (released 2020-12-08)
+
+- Initial public release.

{invenio-vocabularies-6.10.1 → invenio_vocabularies-7.0.0}/invenio_vocabularies/__init__.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 # Copyright (C) 2020-2024 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
@@ -10,6 +11,6 @@
 
 from .ext import InvenioVocabularies
 
-__version__ = "6.10.1"
+__version__ = "7.0.0"
 
 __all__ = ("__version__", "InvenioVocabularies")

{invenio-vocabularies-6.10.1 → invenio_vocabularies-7.0.0}/invenio_vocabularies/contrib/names/schema.py

@@ -11,7 +11,14 @@
 from functools import partial
 
 from invenio_i18n import lazy_gettext as _
-from marshmallow import ValidationError, fields, post_dump, post_load, validates_schema
+from marshmallow import (
+    EXCLUDE,
+    ValidationError,
+    fields,
+    post_dump,
+    post_load,
+    validates_schema,
+)
 from marshmallow_utils.fields import IdentifierSet, SanitizedUnicode
 from marshmallow_utils.schemas import IdentifierSchema
 
@@ -27,6 +34,11 @@ class AffiliationRelationSchema(BaseAffiliationRelationSchema):
 
     acronym = SanitizedUnicode(dump_only=True)
 
+    class Meta:
+        """Meta class."""
+
+        unknown = EXCLUDE
+
 
 class NameSchema(BaseVocabularySchema, ModePIDFieldVocabularyMixin):
     """Service schema for names.

{invenio-vocabularies-6.10.1 → invenio_vocabularies-7.0.0}/invenio_vocabularies/jobs.py

@@ -9,44 +9,19 @@
 """Jobs module."""
 
 import datetime
-from datetime import timezone
 
 from invenio_i18n import gettext as _
 from invenio_jobs.jobs import JobType
-from marshmallow import Schema, fields
-from marshmallow_utils.fields import TZDateTime
 
 from invenio_vocabularies.services.tasks import process_datastream
 
 from .contrib.names.datastreams import ORCID_PRESET_DATASTREAM_CONFIG
 
 
-class ArgsSchema(Schema):
-    """Schema of task input arguments."""
-
-    since = TZDateTime(
-        timezone=timezone.utc,
-        format="iso",
-        metadata={
-            "description": _(
-                "YYYY-MM-DD HH:mm format. "
-                "Leave field empty if it should continue since last successful run."
-            )
-        },
-    )
-    job_arg_schema = fields.String(
-        metadata={"type": "hidden"},
-        dump_default="ArgsSchema",
-        load_default="ArgsSchema",
-    )
-
-
 class ProcessDataStreamJob(JobType):
     """Generic process data stream job type."""
 
-    arguments_schema = ArgsSchema
     task = process_datastream
-    id = None
 
 
 class ProcessRORAffiliationsJob(ProcessDataStreamJob):
@@ -57,13 +32,8 @@ class ProcessRORAffiliationsJob(ProcessDataStreamJob):
     id = "process_ror_affiliations"
 
     @classmethod
-    def default_args(cls, job_obj, since=None, **kwargs):
-        """Generate default job arguments here."""
-        if since is None and job_obj.last_runs["success"]:
-            since = job_obj.last_runs["success"].started_at
-        else:
-            since = since or datetime.datetime.now()
-
+    def build_task_arguments(cls, job_obj, since=None, **kwargs):
+        """Process ROR affiliations."""
         # NOTE: Update is set to False for now given we don't have the logic to re-index dependent records yet.
         # Since jobs support custom args, update true can be passed via that.
         return {
@@ -100,13 +70,8 @@ class ProcessRORFundersJob(ProcessDataStreamJob):
     id = "process_ror_funders"
 
     @classmethod
-    def default_args(cls, job_obj, since=None, **kwargs):
-        """Generate default job arguments here."""
-        if since is None and job_obj.last_runs["success"]:
-            since = job_obj.last_runs["success"].started_at
-        else:
-            since = since or datetime.datetime.now()
-
+    def build_task_arguments(cls, job_obj, since=None, **kwargs):
+        """Process ROR funders."""
         # NOTE: Update is set to False for now given we don't have the logic to re-index dependent records yet.
         # Since jobs support custom args, update true can be passed via that.
         return {
@@ -143,8 +108,8 @@ class ImportAwardsOpenAIREJob(ProcessDataStreamJob):
     id = "import_awards_openaire"
 
     @classmethod
-    def default_args(cls, job_obj, **kwargs):
-        """Generate default job arguments."""
+    def build_task_arguments(cls, job_obj, since=None, **kwargs):
+        """Process awards OpenAIRE."""
         return {
             "config": {
                 "readers": [
@@ -178,8 +143,8 @@ class UpdateAwardsCordisJob(ProcessDataStreamJob):
     id = "update_awards_cordis"
 
     @classmethod
-    def default_args(cls, job_obj, **kwargs):
-        """Generate default job arguments."""
+    def build_task_arguments(cls, job_obj, since=None, **kwargs):
+        """Process awards Cordis."""
         return {
             "config": {
                 "readers": [
@@ -206,6 +171,6 @@ class ImportORCIDJob(ProcessDataStreamJob):
     id = "import_orcid"
 
     @classmethod
-    def default_args(cls, job_obj, **kwargs):
-        """Generate default job arguments."""
+    def build_task_arguments(cls, job_obj, since=None, **kwargs):
+        """Process ORCID data."""
         return {"config": {**ORCID_PRESET_DATASTREAM_CONFIG}}