merge v1.0.2 release

CHANGELOG.rst

@@ -5,6 +5,55 @@ Changelog for the **SODAR Core** Django app package. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+v1.0.2 (2024-09-09)
+===================
+
+Added
+-----
+
+- **General**
+    - ``python3.11-gdbm`` dependency (#1491)
+- **Projectroles**
+    - ``get_user_by_uuid()`` common template tag (#1478)
+    - ``ProjectInvite.get_url()`` helper (#1485)
+    - ``ProjectInvite.refresh_date_expire()`` helper (#1486)
+
+Changed
+-------
+
+- **General**
+    - Upgrade minimum Django version to v4.2.16 (#1481)
+- **Projectroles**
+    - Truncate app setting values in ``remoteproject_sync.html`` (#1474)
+    - JSON app setting value rendering in ``remoteproject_sync.html`` (#1472)
+    - Change ``AppSettingAPI.compare_value()`` into public method (#1479)
+    - Refactor ``AppLinkContent`` (#1470, #1483)
+- **Userprofile**
+    - Improve user settings list layout (#1490)
+
+Fixed
+-----
+
+- **General**
+    - Celery process raising ``dbm.error`` (#1491)
+    - Celery process raising ``broker_connection_retry`` warning (#1493)
+- **Bgjobs**
+    - Non-migrated changes reported by squashed migrations (#1475)
+- **Projectroles**
+    - Incorrect app plugin link order in ``get_project_app_links()`` (#1468)
+    - Remote sync crash on updating user with additional email (#1476)
+    - User scope app setting display in ``remoteproject_sync.html`` (#1478)
+    - Incorrect boolean comparison in ``AppSettingAPI._compare_value()`` with string value (#1473)
+    - Boolean app setting update status in remote sync (#1473)
+
+Removed
+-------
+
+- **Projectroles**
+    - ``build_invite_url()`` utility method (#1485)
+    - ``get_expiry_date()`` utility method (#1486)
+
+
 v1.0.1 (2024-08-08)
 ===================
 

README.rst

@@ -117,7 +117,7 @@ and breaking changes are possible.
 
 .. code-block:: console
 
-    pip install django-sodar-core==1.0.1
+    pip install django-sodar-core==1.0.2
 
 For installing a development version you can point your dependency to a specific
 commit ID in GitHub. Note that these versions may not be stable.

bgjobs/migrations/0001_squashed_0006_auto_20200526_1657.py

@@ -81,14 +81,12 @@ class Migration(migrations.Migration):
                     'date_created',
                     models.DateTimeField(
                         auto_now_add=True,
-                        default=django.utils.timezone.now,
                         help_text='DateTime of creation',
                     ),
                 ),
                 (
                     'user',
                     models.ForeignKey(
-                        default=1,
                         on_delete=django.db.models.deletion.CASCADE,
                         related_name='background_jobs',
                         to=settings.AUTH_USER_MODEL,

codemeta.json

@@ -42,10 +42,10 @@
   "codeRepository": "https://github.com/bihealth/sodar-core",
   "datePublished": "2023-12-06",
   "dateModified": "2023-12-06",
-  "dateCreated": "2024-08-08",
+  "dateCreated": "2024-09-09",
   "description": "SODAR Core: A Django-based framework for scientific data management and analysis web apps",
   "keywords": "Python, Django, scientific data managmenent, software library",
   "license": "MIT",
   "title": "SODAR Core",
-  "version": "v1.0.1"
+  "version": "v1.0.2"
 }

config/settings/base.py

@@ -314,6 +314,8 @@
 CELERYD_TASK_TIME_LIMIT = 5 * 60
 # http://docs.celeryproject.org/en/latest/userguide/configuration.html#task-soft-time-limit
 CELERYD_TASK_SOFT_TIME_LIMIT = 60
+# https://docs.celeryq.dev/en/latest/userguide/configuration.html#broker-connection-retry-on-startup
+CELERY_BROKER_CONNECTION_RETRY_ON_STARTUP = False
 
 
 # Django REST framework

docs/source/app_projectroles_api_rest.rst

@@ -101,6 +101,25 @@ field upon a successfully processed request.
 For creation views, the ``sodar_uuid`` of the created object is returned
 along with other object fields.
 
+Pagination
+----------
+
+From SODAR Core V1.0 onwards, list views support pagination unless otherwise
+specified. Pagination can be enabled by providing the ``?page=x`` query string
+in the API request. This will change the return data into a paginated format.
+Example:
+
+.. code-block:: python
+
+    {
+        'count' 170,
+        'next': 'api/url?page=3',
+        'previous': 'api/url?page=1',
+        'results': [
+            # ...
+        ]
+    }
+
 
 Projectroles REST API Versioning
 ================================

docs/source/app_projectroles_integration.rst

@@ -81,11 +81,11 @@ chapter.
 
 First, add the ``django-sodar-core`` dependency into your
 ``requirements/base.txt`` file. Make sure you are pointing to the desired
-release tag or commit ID.
+release tag.
 
 .. code-block:: console
 
-    django-sodar-core==1.0.1
+    django-sodar-core==x.y.z
 
 Install the requirements for development:
 

docs/source/conf.py

@@ -29,7 +29,7 @@
 # The short X.Y version
 version = '1.0'
 # The full version, including alpha/beta/rc tags
-release = '1.0.1'
+release = '1.0.2'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/getting_started.rst

@@ -12,12 +12,13 @@ Installation
 ============
 
 The ``django-sodar-core`` package can be installed into your Django project
-from PyPI as follows. It is strongly recommended to specify a version tag, as
-the package is under active development and breaking changes are expected.
+from PyPI as follows. It is strongly recommended to pin the import to a specific
+version tag, as the package is under active development and breaking changes are
+expected.
 
 .. code-block:: console
 
-    pip install django-sodar-core==1.0.1
+    pip install django-sodar-core==x.y.z
 
 Please note that the django-sodar-core package only installs
 :term:`Django apps<Django App>`, which you need to include in a

docs/source/major_changes.rst

@@ -10,6 +10,32 @@ older SODAR Core version. For a complete list of changes in current and previous
 releases, see the :ref:`full changelog<changelog>`.
 
 
+v1.0.2 (2024-09-09)
+*******************
+
+Release Highlights
+==================
+
+- Update app setting rendering in remote sync UI
+- Fix project sidebar and dropdown app plugin link order
+- Fix remote sync crash on updating user with additional email
+- Fix Celery process issues
+- General bug fixes and minor updates
+
+Breaking Changes
+================
+
+System Prerequisites
+--------------------
+
+Django Version
+    The minimum Django version has been bumped to v4.2.16.
+Celery Support
+    It is recommended to install the ``python3.11-gdbm`` package (or equivalent
+    for the Python version in use) to ensure full compatibility of the current
+    Celery implementation.
+
+
 v1.0.1 (2024-08-08)
 *******************
 

projectroles/app_settings.py

@@ -302,24 +302,6 @@ def _get_json_value(cls, value):
         except Exception:
             raise ValueError('Value is not valid JSON: {}'.format(value))
 
-    @classmethod
-    def _compare_value(cls, obj, input_value):
-        """
-        Compare input value to value in an AppSetting object. Return True if
-        values match, False if there is a mismatch.
-
-        :param obj: AppSetting object
-        :param input_value: Input value (string, int, bool or dict)
-        :return: Bool
-        """
-        if obj.type == 'JSON':
-            return (
-                not obj.value_json and not input_value
-            ) or obj.value_json == cls._get_json_value(input_value)
-        elif obj.type == 'BOOLEAN':
-            return bool(int(obj.value)) == input_value
-        return obj.value == str(input_value)
-
     @classmethod
     def _log_set_debug(
         cls, action, plugin_name, setting_name, value, project, user
@@ -587,7 +569,7 @@ def set(
             else:
                 q_kwargs['app_plugin'] = None
             setting = AppSetting.objects.get(**q_kwargs)
-            if cls._compare_value(setting, value):
+            if cls.compare_value(setting, value):
                 return False
             if validate:
                 cls.validate(
@@ -912,6 +894,26 @@ def get_global_value(cls, setting_def):
             return not setting_def['local']  # Inverse value
         return setting_def.get('global', APP_SETTING_GLOBAL_DEFAULT)
 
+    @classmethod
+    def compare_value(cls, obj, input_value):
+        """
+        Compare input value to value in an AppSetting object. Return True if
+        values match, False if there is a mismatch.
+
+        :param obj: AppSetting object
+        :param input_value: Input value (string, int, bool or dict)
+        :return: Bool
+        """
+        if obj.type == 'JSON':
+            return (
+                not obj.value_json and not input_value
+            ) or obj.value_json == cls._get_json_value(input_value)
+        elif obj.type == 'BOOLEAN':
+            if isinstance(input_value, str):
+                input_value = bool(int(input_value))
+            return bool(int(obj.value)) == input_value
+        return obj.value == str(input_value)
+
 
 def get_example_setting_default(project=None, user=None):
     """

projectroles/email.py

@@ -12,7 +12,7 @@
 from projectroles.app_settings import AppSettingAPI
 from projectroles.models import SODARUserAdditionalEmail
 from projectroles.plugins import get_app_plugin
-from projectroles.utils import build_invite_url, get_display_name
+from projectroles.utils import get_display_name
 
 
 app_settings = AppSettingAPI()
@@ -502,12 +502,11 @@ def send_invite_mail(invite, request):
     :param request: HttpRequest object
     :return: Amount of sent email (int)
     """
-    invite_url = build_invite_url(invite, request)
     message = get_invite_body(
         project=invite.project,
         issuer=invite.issuer,
         role_name=invite.role.name,
-        invite_url=invite_url,
+        invite_url=invite.get_url(request),
         date_expire_str=localtime(invite.date_expire).strftime(
             '%Y-%m-%d %H:%M'
         ),

projectroles/management/commands/batchupdateroles.py

@@ -18,7 +18,7 @@
     SODAR_CONSTANTS,
 )
 from projectroles.views import RoleAssignmentModifyMixin, ProjectInviteMixin
-from projectroles.utils import get_expiry_date, build_secret
+from projectroles.utils import build_secret
 
 
 logger = ManagementCommandLogger(__name__)
@@ -116,7 +116,6 @@ def _invite_user(self, email, project, role):
             project=project,
             role=role,
             issuer=self.issuer,
-            date_expire=get_expiry_date(),
             secret=build_secret(),
         )
         self.handle_invite(invite, self.request, add_message=False)

projectroles/models.py

@@ -11,6 +11,7 @@
 from django.db import models
 from django.db.models import Q
 from django.urls import reverse
+from django.utils import timezone
 from django.utils.translation import gettext_lazy as _
 
 from djangoplugins.models import Plugin
@@ -1101,6 +1102,22 @@ def __repr__(self):
         values = (self.project.title, self.email, self.role.name, self.active)
         return 'ProjectInvite({})'.format(', '.join(repr(v) for v in values))
 
+    @classmethod
+    def _get_date_expire(cls):
+        """
+        Return expiry date based on current date + INVITE_EXPIRY_DAYS
+
+        :return: DateTime object
+        """
+        return timezone.now() + timezone.timedelta(
+            days=settings.PROJECTROLES_INVITE_EXPIRY_DAYS
+        )
+
+    def save(self, *args, **kwargs):
+        if not self.pk and not self.date_expire:  # Set date_expire on create
+            self.date_expire = self._get_date_expire()
+        super().save(*args, **kwargs)
+
     # Custom row-level functions
 
     def is_ldap(self):
@@ -1126,6 +1143,27 @@ def is_ldap(self):
             return True
         return False
 
+    def get_url(self, request):
+        """
+        Return invite URL for a project invitation.
+
+        :param request: HttpRequest object
+        :return: URL (string)
+        """
+        return request.build_absolute_uri(
+            reverse(
+                'projectroles:invite_accept', kwargs={'secret': self.secret}
+            )
+        )
+
+    def reset_date_expire(self):
+        """
+        Reset date_expire to current date plus defined expiry days. Saves the
+        object.
+        """
+        self.date_expire = self._get_date_expire()
+        self.save()
+
 
 # RemoteSite -------------------------------------------------------------------