Merge branch 'develop' of https://github.com/CenterForOpenScience/osf.io

 into summary-reporter-for-insti-dashboard

* 'develop' of https://github.com/CenterForOpenScience/osf.io:
  Clean up local-ci
  Remove calls to mark_safe
  Update changelog and bump version
  [ENG-5028] [ENG-5920] Preprints Affiliation Project PR (BE) (#10745)

# Conflicts:
#	api/institutions/serializers.py

.github/workflows/test-build.yml

@@ -39,7 +39,7 @@ jobs:
       postgres:
         image: postgres
         env:
-          POSTGRES_PASSWORD: postgres
+          POSTGRES_PASSWORD: ${{ env.OSF_DB_PASSWORD }}
         options: >-
           --health-cmd pg_isready
           --health-interval 10s
@@ -66,7 +66,7 @@ jobs:
       postgres:
         image: postgres
         env:
-          POSTGRES_PASSWORD: postgres
+          POSTGRES_PASSWORD: ${{ env.OSF_DB_PASSWORD }}
         options: >-
           --health-cmd pg_isready
           --health-interval 10s
@@ -93,7 +93,7 @@ jobs:
       postgres:
         image: postgres
         env:
-          POSTGRES_PASSWORD: postgres
+          POSTGRES_PASSWORD: ${{ env.OSF_DB_PASSWORD }}
         options: >-
           --health-cmd pg_isready
           --health-interval 10s
@@ -122,7 +122,7 @@ jobs:
       postgres:
         image: postgres
         env:
-          POSTGRES_PASSWORD: postgres
+          POSTGRES_PASSWORD: ${{ env.OSF_DB_PASSWORD }}
         options: >-
           --health-cmd pg_isready
           --health-interval 10s
@@ -150,7 +150,7 @@ jobs:
         image: postgres
 
         env:
-          POSTGRES_PASSWORD: postgres
+          POSTGRES_PASSWORD: ${{ env.OSF_DB_PASSWORD }}
         options: >-
           --health-cmd pg_isready
           --health-interval 10s

CHANGELOG

@@ -2,6 +2,11 @@
 
 We follow the CalVer (https://calver.org/) versioning scheme: YY.MINOR.MICRO.
 
+24.07.0 (2024-09-19)
+====================
+
+- Preprints Affiliation Project BE Release
+
 24.06.0 (2024-09-12)
 ====================
 

admin/base/filters.py

@@ -1,5 +1,4 @@
 from django import template
-from django.utils.safestring import mark_safe
 import json
 
 
@@ -8,4 +7,4 @@
 
 @register.filter
 def jsonify(o):
-    return mark_safe(json.dumps(o))
+    return json.dumps(o)

admin/base/templatetags/filters.py

@@ -1,10 +1,9 @@
 # h/t https://djangosnippets.org/snippets/1250/
 from django import template
-from django.utils.safestring import mark_safe
 import json
 
 register = template.Library()
 
 @register.filter
 def jsonify(o):
-    return mark_safe(json.dumps(o))
+    return json.dumps(o)

api/base/permissions.py

@@ -8,8 +8,10 @@
 from framework.auth import oauth_scopes
 from framework.auth.cas import CasResponse
 
-from osf.models import ApiOAuth2Application, ApiOAuth2PersonalToken
+from osf.models import ApiOAuth2Application, ApiOAuth2PersonalToken, Preprint
+from osf.utils import permissions as osf_permissions
 from website.util.sanitize import is_iterable_but_not_string
+from api.base.utils import get_user_auth
 
 
 # Implementation built on django-oauth-toolkit, but  with more granular control over read+write permissions
@@ -160,3 +162,17 @@ def has_object_permission(self, request, view, obj):
             obj = self.get_object(request, view, obj)
             return super().has_object_permission(request, view, obj)
     return Perm
+
+
+class WriteOrPublicForRelationshipInstitutions(permissions.BasePermission):
+    def has_object_permission(self, request, view, obj):
+        assert isinstance(obj, dict)
+        auth = get_user_auth(request)
+        resource = obj['self']
+
+        if request.method in permissions.SAFE_METHODS:
+            return resource.is_public or resource.can_view(auth)
+        else:
+            if isinstance(resource, Preprint):
+                return resource.can_edit(auth=auth)
+            return resource.has_permission(auth.user, osf_permissions.WRITE)

api/base/settings/local-ci.py

@@ -5,7 +5,7 @@
 ENABLE_VARNISH = True
 ENABLE_ESI = False
 
-OSF_DB_PASSWORD = 'postgres'
+OSF_DB_PASSWORD = os.environ.get('OSF_DB_PASSWORD')
 
 SESSION_ENGINE = 'django.contrib.sessions.backends.db'
 

api/draft_registrations/serializers.py

@@ -8,7 +8,6 @@
 from api.nodes.serializers import (
     DraftRegistrationLegacySerializer,
     DraftRegistrationDetailLegacySerializer,
-    update_institutions,
     get_license_details,
     NodeSerializer,
     NodeLicenseSerializer,
@@ -18,6 +17,7 @@
     NodeContributorDetailSerializer,
     RegistrationSchemaRelationshipField,
 )
+from api.institutions.utils import update_institutions
 from api.taxonomies.serializers import TaxonomizableSerializerMixin
 from osf.exceptions import DraftRegistrationStateError
 from osf.models import Node

api/institutions/serializers.py

@@ -144,7 +144,7 @@ def create(self, validated_data):
             if not node.has_permission(user, osf_permissions.WRITE):
                 raise exceptions.PermissionDenied(detail='Write permission on node {} required'.format(node_dict['_id']))
             if not node.is_affiliated_with_institution(inst):
-                node.add_affiliated_institution(inst, user, save=True)
+                node.add_affiliated_institution(inst, user)
                 changes_flag = True
 
         if not changes_flag:
@@ -155,11 +155,19 @@ def create(self, validated_data):
             'self': inst,
         }
 
+
+class InstitutionRelated(JSONAPIRelationshipSerializer):
+    id = ser.CharField(source='_id', required=False, allow_null=True)
+    class Meta:
+        type_ = 'institutions'
+
+
 class RegistrationRelated(JSONAPIRelationshipSerializer):
     id = ser.CharField(source='_id', required=False, allow_null=True)
     class Meta:
         type_ = 'registrations'
 
+
 class InstitutionRegistrationsRelationshipSerializer(BaseAPISerializer):
     data = ser.ListField(child=RegistrationRelated())
     links = LinksField({
@@ -189,7 +197,7 @@ def create(self, validated_data):
             if not registration.has_permission(user, osf_permissions.WRITE):
                 raise exceptions.PermissionDenied(detail='Write permission on registration {} required'.format(registration_dict['_id']))
             if not registration.is_affiliated_with_institution(inst):
-                registration.add_affiliated_institution(inst, user, save=True)
+                registration.add_affiliated_institution(inst, user)
                 changes_flag = True
 
         if not changes_flag:
@@ -313,7 +321,6 @@ def get_absolute_url(self, obj):
             },
         )
 
-
 class NewInstitutionUserMetricsSerializer(JSONAPISerializer):
     '''serializer for institution-users metrics
 

api/institutions/utils.py

@@ -0,0 +1,58 @@
+from rest_framework import exceptions
+
+from api.base.serializers import relationship_diff
+from osf.models import Institution
+from osf.utils import permissions as osf_permissions
+
+
+def get_institutions_to_add_remove(institutions, new_institutions):
+    diff = relationship_diff(
+        current_items={inst._id: inst for inst in institutions.all()},
+        new_items={inst['_id']: inst for inst in new_institutions},
+    )
+
+    insts_to_add = []
+    for inst_id in diff['add']:
+        inst = Institution.load(inst_id)
+        if not inst:
+            raise exceptions.NotFound(detail=f'Institution with id "{inst_id}" was not found')
+        insts_to_add.append(inst)
+
+    return insts_to_add, diff['remove'].values()
+
+
+def update_institutions(resource, new_institutions, user, post=False):
+    add, remove = get_institutions_to_add_remove(
+        institutions=resource.affiliated_institutions,
+        new_institutions=new_institutions,
+    )
+
+    if not post:
+        for inst in remove:
+            if not user.is_affiliated_with_institution(inst) and not resource.has_permission(user, osf_permissions.ADMIN):
+                raise exceptions.PermissionDenied(detail=f'User needs to be affiliated with {inst.name}')
+            resource.remove_affiliated_institution(inst, user)
+
+    for inst in add:
+        if not user.is_affiliated_with_institution(inst):
+            raise exceptions.PermissionDenied(detail=f'User needs to be affiliated with {inst.name}')
+        resource.add_affiliated_institution(inst, user)
+
+
+def update_institutions_if_user_associated(resource, desired_institutions_data, user):
+    """Update institutions only if the user is associated with the institutions. Otherwise, raise an exception."""
+
+    desired_institutions = Institution.objects.filter(_id__in=[item['_id'] for item in desired_institutions_data])
+
+    # If a user wants to affiliate with a resource check that they have it.
+    for inst in desired_institutions:
+        if user.is_affiliated_with_institution(inst):
+            resource.add_affiliated_institution(inst, user)
+        else:
+            raise exceptions.PermissionDenied(detail=f'User needs to be affiliated with {inst.name}')
+
+    # If a user doesn't include an affiliation they have, then remove it.
+    resource_institutions = resource.affiliated_institutions.all()
+    for inst in user.get_affiliated_institutions():
+        if inst in resource_institutions and inst not in desired_institutions:
+            resource.remove_affiliated_institution(inst, user)

api/nodes/permissions.py

@@ -294,18 +294,6 @@ def has_object_permission(self, request, view, obj):
         return True
 
 
-class WriteOrPublicForRelationshipInstitutions(permissions.BasePermission):
-    def has_object_permission(self, request, view, obj):
-        assert isinstance(obj, dict)
-        auth = get_user_auth(request)
-        node = obj['self']
-
-        if request.method in permissions.SAFE_METHODS:
-            return node.is_public or node.can_view(auth)
-        else:
-            return node.has_permission(auth.user, osf_permissions.WRITE)
-
-
 class ReadOnlyIfRegistration(permissions.BasePermission):
     """Makes PUT and POST forbidden for registrations."""
 

api/nodes/serializers.py

@@ -7,11 +7,10 @@
 )
 from api.base.serializers import (
     VersionedDateTimeField, HideIfRegistration, IDField,
-    JSONAPIRelationshipSerializer,
     JSONAPISerializer, LinksField,
     NodeFileHyperLinkField, RelationshipField,
     ShowIfVersion, TargetTypeField, TypeField,
-    WaterbutlerLink, relationship_diff, BaseAPISerializer,
+    WaterbutlerLink, BaseAPISerializer,
     HideIfWikiDisabled, ShowIfAdminScopeOrAnonymous,
     ValuesListField, TargetField,
 )
@@ -21,6 +20,7 @@
     get_user_auth, is_truthy,
 )
 from api.base.versioning import get_kebab_snake_case_field
+from api.institutions.utils import update_institutions
 from api.taxonomies.serializers import TaxonomizableSerializerMixin
 from django.apps import apps
 from django.conf import settings
@@ -34,7 +34,7 @@
 from addons.osfstorage.models import Region
 from osf.exceptions import NodeStateError
 from osf.models import (
-    Comment, DraftRegistration, ExternalAccount, Institution,
+    Comment, DraftRegistration, ExternalAccount,
     RegistrationSchema, AbstractNode, PrivateLink, Preprint,
     RegistrationProvider, OSFGroup, NodeLicense, DraftNode,
     Registration, Node,
@@ -52,44 +52,6 @@ def to_internal_value(self, data):
         return self.get_object(data)
 
 
-def get_institutions_to_add_remove(institutions, new_institutions):
-    diff = relationship_diff(
-        current_items={inst._id: inst for inst in institutions.all()},
-        new_items={inst['_id']: inst for inst in new_institutions},
-    )
-
-    insts_to_add = []
-    for inst_id in diff['add']:
-        inst = Institution.load(inst_id)
-        if not inst:
-            raise exceptions.NotFound(detail=f'Institution with id "{inst_id}" was not found')
-        insts_to_add.append(inst)
-
-    return insts_to_add, diff['remove'].values()
-
-
-def update_institutions(node, new_institutions, user, post=False):
-    add, remove = get_institutions_to_add_remove(
-        institutions=node.affiliated_institutions,
-        new_institutions=new_institutions,
-    )
-
-    if not post:
-        for inst in remove:
-            if not user.is_affiliated_with_institution(inst) and not node.has_permission(user, osf_permissions.ADMIN):
-                raise exceptions.PermissionDenied(
-                    detail=f'User needs to be affiliated with {inst.name}',
-                )
-            node.remove_affiliated_institution(inst, user)
-
-    for inst in add:
-        if not user.is_affiliated_with_institution(inst):
-            raise exceptions.PermissionDenied(
-                detail=f'User needs to be affiliated with {inst.name}',
-            )
-        node.add_affiliated_institution(inst, user)
-
-
 class RegionRelationshipField(RelationshipField):
 
     def to_internal_value(self, data):
@@ -1479,13 +1441,10 @@ def get_storage_addons_url(self, obj):
             },
         )
 
-class InstitutionRelated(JSONAPIRelationshipSerializer):
-    id = ser.CharField(source='_id', required=False, allow_null=True)
-    class Meta:
-        type_ = 'institutions'
-
 
 class NodeInstitutionsRelationshipSerializer(BaseAPISerializer):
+    from api.institutions.serializers import InstitutionRelated  # Avoid circular import
+
     data = ser.ListField(child=InstitutionRelated())
     links = LinksField({
         'self': 'get_self_url',

api/nodes/views.py

@@ -57,6 +57,7 @@
     WaterButlerMixin,
 )
 from api.base.waffle_decorators import require_flag
+from api.base.permissions import WriteOrPublicForRelationshipInstitutions
 from api.cedar_metadata_records.serializers import CedarMetadataRecordsListSerializer
 from api.cedar_metadata_records.utils import can_view_record
 from api.citations.utils import render_citation
@@ -87,7 +88,6 @@
     NodeGroupDetailPermissions,
     IsContributorOrGroupMember,
     AdminDeletePermissions,
-    WriteOrPublicForRelationshipInstitutions,
     ExcludeWithdrawals,
     NodeLinksShowIfVersion,
     ReadOnlyIfWithdrawn,

api/preprints/permissions.py

@@ -137,3 +137,30 @@ def has_object_permission(self, request, view, obj):
                 raise exceptions.PermissionDenied(detail='Withdrawn preprints may not be edited')
             return True
         raise exceptions.NotFound
+
+
+class PreprintInstitutionPermissionList(permissions.BasePermission):
+    """
+    Custom permission class for checking access to a list of institutions
+    associated with a preprint.
+
+    Permissions:
+    - Allows safe methods (GET, HEAD, OPTIONS) for public preprints.
+    - For private preprints, checks if the user has read permissions.
+
+    Methods:
+    - has_object_permission: Raises MethodNotAllowed for non-safe methods and
+      checks if the user has the necessary permissions to access private preprints.
+    """
+    def has_object_permission(self, request, view, obj):
+        if request.method not in permissions.SAFE_METHODS:
+            raise exceptions.MethodNotAllowed(method=request.method)
+
+        if obj.is_public:
+            return True
+
+        auth = get_user_auth(request)
+        if not auth.user:
+            return False
+        else:
+            return obj.has_permission(auth.user, osf_permissions.READ)