Feature/gravy valet integration

CHANGELOG

@@ -2,7 +2,20 @@
 
 We follow the CalVer (https://calver.org/) versioning scheme: YY.MINOR.MICRO.
 
-24.01.0 (2024-04-30)
+24.03.0 (2024-07-08)
+====================
+- Preprints into Ember OSF Web, Phase 2 Backend Release
+
+24.03.0 (2024-07-08)
+====================
+- Allow AbstractProviders to specify Discover page presence
+- Update get_auth
+- Expand Addons Service support functionality, waffled
+- Set default Resource Type General for Registrations
+- Bug fix: Archiver Unicode edge cases
+- Bug fix: RelationshipField during project creation
+
+24.02.0 (2024-04-30)
 ====================
 - Initial Addons Service work, Waffled
 - Improve default `description` for Google Dataset Discovery

addons/base/views.py

@@ -166,7 +166,7 @@ def get_addon_user_config(**kwargs):
 
  return addon.to_json(user)
 
-
+ 
 def make_auth(user):
  if user is not None:
  return {
@@ -207,9 +207,10 @@ def get_auth(auth, **kwargs):
  waterbutler_data = _decrypt_and_decode_jwt_payload()
  resource = _get_authenticated_resource(waterbutler_data['nid'])
 
+
  action = waterbutler_data['action']
  _check_resource_permissions(resource, auth, action)
-
+ 
  provider_name = waterbutler_data['provider']
  file_version = file_node = None
  if provider_name == 'osfstorage':
@@ -221,6 +222,7 @@ def get_auth(auth, **kwargs):
  resource=resource, provider_name=provider_name, file_version=file_version,
  )
 
+
  _enqueue_metrics(file_version=file_version, file_node=file_node, action=action, auth=auth)
 
  # Construct the response payload including the JWT
@@ -230,8 +232,8 @@ def get_auth(auth, **kwargs):
  credentials=waterbutler_credentials,
  waterbutler_settings=waterbutler_settings
  )
-
-
+ 
+ 
 def _decrypt_and_decode_jwt_payload():
  try:
  payload_encrypted = request.args.get('payload', '').encode('utf-8')

api/nodes/views.py

@@ -156,6 +156,7 @@
  File,
  Folder,
  CedarMetadataRecord,
+ Preprint,
 )
 from addons.osfstorage.models import Region
 from osf.utils.permissions import ADMIN, WRITE_NODE
@@ -1514,6 +1515,8 @@ def id(self):
 
  @property
  def root_folder(self):
+ if isinstance(self.resource, Preprint):
+ return self.target.root_folder
  if self.provider_settings:
  return self.provider_settings.root_node
  return None

api/preprints/serializers.py

@@ -111,6 +111,7 @@ class PreprintSerializer(TaxonomizableSerializerMixin, MetricsSerializerMixin, J
  date_modified = VersionedDateTimeField(source='modified', read_only=True)
  date_published = VersionedDateTimeField(read_only=True)
  original_publication_date = VersionedDateTimeField(required=False, allow_null=True)
+ custom_publication_citation = ser.CharField(required=False, allow_blank=True, allow_null=True)
  doi = ser.CharField(source='article_doi', required=False, allow_null=True)
  title = ser.CharField(required=True, max_length=512)
  description = ser.CharField(required=False, allow_blank=True, allow_null=True)
@@ -222,6 +223,11 @@ def subjects_view_kwargs(self):
  # Overrides TaxonomizableSerializerMixin
  return {'preprint_id': '<_id>'}
 
+ @property
+ def subjects_self_view(self):
+ # Overrides TaxonomizableSerializerMixin
+ return 'preprints:preprint-relationships-subjects'
+
  def get_preprint_url(self, obj):
  return absolute_reverse('preprints:preprint-detail', kwargs={'preprint_id': obj._id, 'version': self.context['request'].parser_context['kwargs']['version']})
 
@@ -326,6 +332,10 @@ def update(self, preprint, validated_data):
  preprint.original_publication_date = validated_data['original_publication_date'] or None
  save_preprint = True
 
+ if 'custom_publication_citation' in validated_data:
+ preprint.custom_publication_citation = validated_data['custom_publication_citation'] or None
+ save_preprint = True
+
  if 'has_coi' in validated_data:
  try:
  preprint.update_has_coi(auth, validated_data['has_coi'])

api/preprints/urls.py

@@ -16,6 +16,7 @@
  re_path(r'^(?P<preprint_id>\w+)/files/osfstorage/$', views.PreprintFilesList.as_view(), name=views.PreprintFilesList.view_name),
  re_path(r'^(?P<preprint_id>\w+)/identifiers/$', views.PreprintIdentifierList.as_view(), name=views.PreprintIdentifierList.view_name),
  re_path(r'^(?P<preprint_id>\w+)/relationships/node/$', views.PreprintNodeRelationship.as_view(), name=views.PreprintNodeRelationship.view_name),
+ re_path(r'^(?P<preprint_id>\w+)/relationships/subjects/$', views.PreprintSubjectsRelationship.as_view(), name=views.PreprintSubjectsRelationship.view_name),
  re_path(r'^(?P<preprint_id>\w+)/review_actions/$', views.PreprintActionList.as_view(), name=views.PreprintActionList.view_name),
  re_path(r'^(?P<preprint_id>\w+)/requests/$', views.PreprintRequestListCreate.as_view(), name=views.PreprintRequestListCreate.view_name),
  re_path(r'^(?P<preprint_id>\w+)/subjects/$', views.PreprintSubjectsList.as_view(), name=views.PreprintSubjectsList.view_name),

api/preprints/views.py

@@ -58,7 +58,7 @@
 from api.requests.permissions import PreprintRequestPermission
 from api.requests.serializers import PreprintRequestSerializer, PreprintRequestCreateSerializer
 from api.requests.views import PreprintRequestMixin
-from api.subjects.views import BaseResourceSubjectsList
+from api.subjects.views import BaseResourceSubjectsList, SubjectRelationshipBaseView
 from api.base.metrics import PreprintMetricsViewMixin
 from osf.metrics import PreprintDownload, PreprintView
 
@@ -456,6 +456,37 @@ class PreprintSubjectsList(BaseResourceSubjectsList, PreprintMixin):
  def get_resource(self):
  return self.get_preprint()
 
+
+class PreprintSubjectsRelationship(SubjectRelationshipBaseView, PreprintMixin):
+ """The documentation for this endpoint can be found [here](https://developer.osf.io/#operation/preprint_subjects_list).
+ """
+ permission_classes = (
+ drf_permissions.IsAuthenticatedOrReadOnly,
+ base_permissions.TokenHasScope,
+ ModeratorIfNeverPublicWithdrawn,
+ ContributorOrPublic,
+ PreprintPublishedOrWrite,
+ )
+
+ required_read_scopes = [CoreScopes.PREPRINTS_READ]
+ required_write_scopes = [CoreScopes.PREPRINTS_WRITE]
+
+ view_category = 'preprints'
+ view_name = 'preprint-relationships-subjects'
+
+ def get_resource(self, check_object_permissions=True):
+ return self.get_preprint(check_object_permissions=check_object_permissions)
+
+ def get_object(self):
+ resource = self.get_resource(check_object_permissions=False)
+ obj = {
+ 'data': resource.subjects.all(),
+ 'self': resource,
+ }
+ self.check_object_permissions(self.request, resource)
+ return obj
+
+
 class PreprintActionList(JSONAPIBaseView, generics.ListCreateAPIView, ListFilterMixin, PreprintMixin):
  """Action List *Read-only*
 

api_tests/files/views/test_file_detail.py

@@ -31,6 +31,9 @@
 
 SessionStore = import_module(django_conf_settings.SESSION_ENGINE).SessionStore
 
+from addons.base.views import _get_authenticated_resource
+from framework.exceptions import HTTPError
+
 # stolen from^W^Winspired by DRF
 # rest_framework.fields.DateTimeField.to_representation
 def _dt_to_iso8601(value):
@@ -705,6 +708,48 @@ def test_load_and_property(self, app, user, file):
  expect_errors=True, auth=user.auth,
  ).status_code == 405
 
+ def test_retracted_file_returns_410(self, app, user, file_url, file):
+ resource = RegistrationFactory(is_public=True)
+ retraction = resource.retract_registration(
+ user=resource.creator,
+ justification='Justification for retraction',
+ save=True,
+ moderator_initiated=False
+ )
+
+ retraction.accept()
+ resource.save()
+ resource.refresh_from_db()
+
+ file.target = resource
+ file.save()
+
+ res = app.get(file_url, auth=user.auth, expect_errors=True)
+ assert res.status_code == 410
+
+ def test_get_authenticated_resource_retracted(self):
+ resource = RegistrationFactory(is_public=True)
+
+ assert resource.is_retracted is False
+
+ retraction = resource.retract_registration(
+ user=resource.creator,
+ justification='Justification for retraction',
+ save=True,
+ moderator_initiated=False
+ )
+
+ retraction.accept()
+ resource.save()
+ resource.refresh_from_db()
+
+ assert resource.is_retracted is True
+
+ with pytest.raises(HTTPError) as excinfo:
+ _get_authenticated_resource(resource._id)
+
+ assert excinfo.value.code == 410
+
 
 @pytest.mark.django_db
 class TestFileTagging:

api_tests/preprints/views/test_preprint_detail.py

@@ -305,6 +305,19 @@ def test_update_original_publication_date_to_none(self, app, preprint, url):
  preprint.reload()
  assert preprint.original_publication_date is None
 
+ def test_update_custom_publication_citation_to_none(self, app, preprint, url):
+ write_contrib = AuthUserFactory()
+ preprint.add_contributor(write_contrib, WRITE, save=True)
+ preprint.custom_publication_citation = 'fake citation'
+ preprint.save()
+ update_payload = build_preprint_update_payload(
+ preprint._id, attributes={'custom_publication_citation': None}
+ )
+ res = app.patch_json_api(url, update_payload, auth=write_contrib.auth)
+ assert res.status_code == 200
+ preprint.reload()
+ assert preprint.custom_publication_citation is None
+
  @responses.activate
  @mock.patch('osf.models.preprint.update_or_enqueue_on_preprint_updated', mock.Mock())
  def test_update_preprint_permission_write_contrib(self, app, preprint, url):
@@ -536,6 +549,16 @@ def test_update_original_publication_date(self, app, user, preprint, url):
  preprint.reload()
  assert preprint.original_publication_date == date
 
+ def test_update_custom_publication_citation(self, app, user, preprint, url):
+ citation = 'fake citation'
+ update_payload = build_preprint_update_payload(
+ preprint._id, attributes={'custom_publication_citation': citation}
+ )
+ res = app.patch_json_api(url, update_payload, auth=user.auth)
+ assert res.status_code == 200
+ preprint.reload()
+ assert preprint.custom_publication_citation == citation
+
  @responses.activate
  @mock.patch('osf.models.preprint.update_or_enqueue_on_preprint_updated', mock.Mock())
  def test_update_article_doi(self, app, user, preprint, url):

osf/external/gravy_valet/translations.py

@@ -117,7 +117,6 @@ def create_waterbutler_log(self, *args, **kwargs):
  def save(self):
  pass
 
-
 @dataclasses.dataclass
 class EphemeralUserSettings:
  '''Minimalist dataclass for storing the actually used properties of UserSettings.'''

osf/migrations/0021_preprint_custom_publication_citation.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.17 on 2024-05-15 15:07
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('osf', '0020_abstractprovider_advertise_on_discover_page'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='preprint',
+ name='custom_publication_citation',
+ field=models.TextField(blank=True, null=True),
+ ),
+ ]

osf/models/mixins.py

@@ -3,6 +3,8 @@
 import markupsafe
 import logging
 
+import waffle
+
 from django.apps import apps
 from django.contrib.auth.models import Group, AnonymousUser
 from django.core.exceptions import ObjectDoesNotExist, ValidationError

osf/models/preprint.py

@@ -152,6 +152,7 @@ class Preprint(DirtyFieldsMixin, GuidMixin, IdentifierMixin, ReviewableMixin, Ba
  is_published = models.BooleanField(default=False, db_index=True)
  date_published = NonNaiveDateTimeField(null=True, blank=True)
  original_publication_date = NonNaiveDateTimeField(null=True, blank=True)
+ custom_publication_citation = models.TextField(null=True, blank=True)
  license = models.ForeignKey('osf.NodeLicenseRecord',
  on_delete=models.SET_NULL, null=True, blank=True)
 

package.json

@@ -1,6 +1,6 @@
 {
  "name": "OSF",
- "version": "24.02.0",
+ "version": "24.04.0",
  "description": "Facilitating Open Science",
  "repository": "https://github.com/CenterForOpenScience/osf.io",
  "author": "Center for Open Science",

website/identifiers/tasks.py

@@ -5,12 +5,15 @@
 from framework.celery_tasks.handlers import queued_task
 from framework import sentry
 
-
-@queued_task
-@celery_app.task(ignore_results=True)
-def update_doi_metadata_on_change(target_guid):
+@celery_app.task(bind=True, max_retries=5, acks_late=True)
+def task__update_doi_metadata_on_change(self, target_guid):
  sentry.log_message('Updating DOI for guid', extra_data={'guid': target_guid}, level=logging.INFO)
  Guid = apps.get_model('osf.Guid')
  target_object = Guid.load(target_guid).referent
  if target_object.get_identifier('doi'):
  target_object.request_identifier_update(category='doi')
+
+@queued_task
+@celery_app.task(ignore_results=True)
+def update_doi_metadata_on_change(target_guid):
+ task__update_doi_metadata_on_change(target_guid)

website/routes.py

@@ -261,15 +261,7 @@ def ember_app(path=None):
  if request.path.strip('/').startswith(k):
  ember_app = EXTERNAL_EMBER_APPS[k]
  if k == 'preprints':
- if request.path.rstrip('/').endswith('edit'):
- # Route preprint edit pages to old preprint app
- ember_app = EXTERNAL_EMBER_APPS.get('preprints', False) or ember_app
- elif request.path.rstrip('/').endswith('submit'):
- # Route preprint submit pages to old preprint app
- ember_app = EXTERNAL_EMBER_APPS.get('preprints', False) or ember_app
- else:
- # Route other preprint pages to EOW
- ember_app = EXTERNAL_EMBER_APPS.get('ember_osf_web', False) or ember_app
+ ember_app = EXTERNAL_EMBER_APPS.get('ember_osf_web', False) or ember_app
  break
 
  if not ember_app:

website/settings/defaults.py

@@ -455,7 +455,7 @@ class CeleryConfig:
  'website.mailchimp_utils',
  'website.notifications.tasks',
  'website.collections.tasks',
- 'website.identifier.tasks',
+ 'website.identifiers.tasks',
  'website.preprints.tasks',
  'website.project.tasks',
  }
@@ -516,6 +516,7 @@ class CeleryConfig:
  'website.mailchimp_utils',
  'website.notifications.tasks',
  'website.archiver.tasks',
+ 'website.identifiers.tasks',
  'website.search.search',
  'website.project.tasks',
  'scripts.populate_new_and_noteworthy_projects',

website/views.py

@@ -37,7 +37,6 @@
 from api.waffle.utils import storage_i18n_flag_active, flag_is_active
 
 logger = logging.getLogger(__name__)
-preprints_dir = os.path.abspath(os.path.join(os.getcwd(), EXTERNAL_EMBER_APPS['preprints']['path']))
 ember_osf_web_dir = os.path.abspath(os.path.join(os.getcwd(), EXTERNAL_EMBER_APPS['ember_osf_web']['path']))
 
 
@@ -331,8 +330,6 @@ def resolve_guid(guid, suffix=None):
  if isinstance(resource, Preprint):
  if resource.provider.domain_redirect_enabled:
  return redirect(resource.absolute_url, http_status.HTTP_301_MOVED_PERMANENTLY)
- if clean_suffix.endswith('edit'):
- return stream_emberapp(EXTERNAL_EMBER_APPS['preprints']['server'], preprints_dir)
  return use_ember_app()
 
  elif isinstance(resource, Registration) and (clean_suffix in ('', 'comments', 'links', 'components', 'resources',)) and flag_is_active(request, features.EMBER_REGISTRIES_DETAIL_PAGE):