merge v0.13.4 release

.github/workflows/build.yml

@@ -40,6 +40,8 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Checkout repository
         uses: actions/checkout@v3
+      - name: Fetch all history for all tags and branches
+        run: git fetch --prune --unshallow
       - name: Install project Python dependencies
         run: |
           pip install "wheel>=0.38.4, <0.39"

CHANGELOG.rst

@@ -5,6 +5,49 @@ Changelog for the **SODAR Core** Django app package. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+v0.13.4 (2024-02-16)
+====================
+
+Added
+-----
+
+- **Projectroles**
+    - ``LoggedInPermissionMixin`` login message customization (#1360)
+    - Base UI classses in Django API documentation (#1363)
+- **Siteinfo**
+    - Missing LDAP Django settings (#1347)
+
+Changed
+-------
+
+- **General**
+    - Upgrade minimum Django version to v3.2.24 (#1348)
+    - Upgrade LDAP dependencies (#1348)
+- **Projectroles**
+    - Improve remote site deletion UI text labels (#1349)
+    - Store remote sync app setting foreign key UUIDs as strings (#1356)
+    - Do not create timeline event for re-accepting project invite (#1352)
+    - Improve user message for re-accepting project invite (#1354)
+    - Redirect to ``ProjectDetailView`` from re-accepting project invite (#1361)
+    - Do not display login error on invite accept (#1360)
+    - Clarify login error message for unauthenticated user (#1362)
+
+Fixed
+-----
+
+- **General**
+    - Invalid env var retrieval for ``AUTH_LDAP*_START_TLS`` (#1351)
+    - Versioneer version not available in CI (#1357)
+- **Projectroles**
+    - Remote sync ``user_name`` crash with <0.13.3 target sites (#1355)
+
+Removed
+-------
+
+- **Timeline**
+    - Unused ``collect_extra_data()`` template tag (#1359)
+
+
 v0.13.3 (2023-12-06)
 ====================
 

README.rst

@@ -115,7 +115,7 @@ and breaking changes are possible.
 
 .. code-block:: console
 
-    pip install django-sodar-core==0.13.3
+    pip install django-sodar-core==0.13.4
 
 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.

codemeta.json

@@ -42,10 +42,10 @@
   "codeRepository": "https://github.com/bihealth/sodar-core",
   "datePublished": "2023-12-06",
   "dateModified": "2023-12-06",
-  "dateCreated": "2019-06-26",
+  "dateCreated": "2024-02-16",
   "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": "v0.13.3"
+  "version": "v0.13.4"
 }

config/settings/base.py

@@ -340,9 +340,8 @@
 ENABLE_LDAP = env.bool('ENABLE_LDAP', False)
 ENABLE_LDAP_SECONDARY = env.bool('ENABLE_LDAP_SECONDARY', False)
 LDAP_DEBUG = env.bool('LDAP_DEBUG', False)
-
 # Alternative domains for detecting LDAP access by email address
-LDAP_ALT_DOMAINS = env.list('LDAP_ALT_DOMAINS', None, [])
+LDAP_ALT_DOMAINS = env.list('LDAP_ALT_DOMAINS', None, default=[])
 
 if ENABLE_LDAP:
     import itertools
@@ -363,18 +362,17 @@
     AUTH_LDAP_SERVER_URI = env.str('AUTH_LDAP_SERVER_URI', None)
     AUTH_LDAP_BIND_DN = env.str('AUTH_LDAP_BIND_DN', None)
     AUTH_LDAP_BIND_PASSWORD = env.str('AUTH_LDAP_BIND_PASSWORD', None)
-    AUTH_LDAP_START_TLS = env.str('AUTH_LDAP_START_TLS', False)
+    AUTH_LDAP_START_TLS = env.bool('AUTH_LDAP_START_TLS', False)
     AUTH_LDAP_CA_CERT_FILE = env.str('AUTH_LDAP_CA_CERT_FILE', None)
     AUTH_LDAP_CONNECTION_OPTIONS = {**LDAP_DEFAULT_CONN_OPTIONS}
-    if AUTH_LDAP_CA_CERT_FILE is not None:
+    if AUTH_LDAP_CA_CERT_FILE:
         AUTH_LDAP_CONNECTION_OPTIONS[
             ldap.OPT_X_TLS_CACERTFILE
         ] = AUTH_LDAP_CA_CERT_FILE
         AUTH_LDAP_CONNECTION_OPTIONS[ldap.OPT_X_TLS_NEWCTX] = 0
     AUTH_LDAP_USER_FILTER = env.str(
         'AUTH_LDAP_USER_FILTER', '(sAMAccountName=%(user)s)'
     )
-
     AUTH_LDAP_USER_SEARCH = LDAPSearch(
         env.str('AUTH_LDAP_USER_SEARCH_BASE', None),
         ldap.SCOPE_SUBTREE,
@@ -385,7 +383,6 @@
     AUTH_LDAP_DOMAIN_PRINTABLE = env.str(
         'AUTH_LDAP_DOMAIN_PRINTABLE', AUTH_LDAP_USERNAME_DOMAIN
     )
-
     AUTHENTICATION_BACKENDS = tuple(
         itertools.chain(
             ('projectroles.auth_backends.PrimaryLDAPBackend',),
@@ -398,18 +395,17 @@
         AUTH_LDAP2_SERVER_URI = env.str('AUTH_LDAP2_SERVER_URI', None)
         AUTH_LDAP2_BIND_DN = env.str('AUTH_LDAP2_BIND_DN', None)
         AUTH_LDAP2_BIND_PASSWORD = env.str('AUTH_LDAP2_BIND_PASSWORD', None)
-        AUTH_LDAP2_START_TLS = env.str('AUTH_LDAP2_START_TLS', False)
+        AUTH_LDAP2_START_TLS = env.bool('AUTH_LDAP2_START_TLS', False)
         AUTH_LDAP2_CA_CERT_FILE = env.str('AUTH_LDAP2_CA_CERT_FILE', None)
         AUTH_LDAP2_CONNECTION_OPTIONS = {**LDAP_DEFAULT_CONN_OPTIONS}
-        if AUTH_LDAP2_CA_CERT_FILE is not None:
+        if AUTH_LDAP2_CA_CERT_FILE:
             AUTH_LDAP2_CONNECTION_OPTIONS[
                 ldap.OPT_X_TLS_CACERTFILE
             ] = AUTH_LDAP2_CA_CERT_FILE
             AUTH_LDAP2_CONNECTION_OPTIONS[ldap.OPT_X_TLS_NEWCTX] = 0
         AUTH_LDAP2_USER_FILTER = env.str(
             'AUTH_LDAP2_USER_FILTER', '(sAMAccountName=%(user)s)'
         )
-
         AUTH_LDAP2_USER_SEARCH = LDAPSearch(
             env.str('AUTH_LDAP2_USER_SEARCH_BASE', None),
             ldap.SCOPE_SUBTREE,
@@ -420,7 +416,6 @@
         AUTH_LDAP2_DOMAIN_PRINTABLE = env.str(
             'AUTH_LDAP2_DOMAIN_PRINTABLE', AUTH_LDAP2_USERNAME_DOMAIN
         )
-
         AUTHENTICATION_BACKENDS = tuple(
             itertools.chain(
                 ('projectroles.auth_backends.SecondaryLDAPBackend',),

docs/source/app_projectroles_api_django.rst

@@ -9,6 +9,45 @@ app. Included are functionalities and classes intended to be used by other
 applications when building a SODAR Core based Django site.
 
 
+.. _app_projectroles_api_django_ui:
+
+Base UI View Classes
+====================
+
+Base mixins and classes for building UI views can be found in
+``projectroles.views``.
+
+.. currentmodule:: projectroles.views
+
+.. autoclass:: LoginRequiredMixin
+    :members:
+    :show-inheritance:
+
+.. autoclass:: LoggedInPermissionMixin
+    :members:
+    :show-inheritance:
+
+.. autoclass:: ProjectAccessMixin
+    :members:
+    :show-inheritance:
+
+.. autoclass:: ProjectPermissionMixin
+    :members:
+    :show-inheritance:
+
+.. autoclass:: ProjectContextMixin
+    :members:
+    :show-inheritance:
+
+.. autoclass:: PluginContextMixin
+    :members:
+    :show-inheritance:
+
+.. autoclass:: InvalidFormMixin
+    :members:
+    :show-inheritance:
+
+
 Plugins
 =======
 

docs/source/app_projectroles_integration.rst

@@ -85,7 +85,7 @@ release tag or commit ID.
 
 .. code-block:: console
 
-    django-sodar-core==0.13.3
+    django-sodar-core==0.13.4
 
 Install the requirements for development:
 

docs/source/conf.py

@@ -23,13 +23,13 @@
 # -- Project information -----------------------------------------------------
 
 project = 'SODAR Core'
-copyright = '2018-2023, Berlin Institute of Health'
+copyright = '2018-2024, Berlin Institute of Health'
 author = 'BIH Core Unit Bioinformatics'
 
 # The short X.Y version
 version = '0.13'
 # The full version, including alpha/beta/rc tags
-release = '0.13.3'
+release = '0.13.4'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/dev_project_app.rst

@@ -372,7 +372,8 @@ The most commonly used mixins:
     your site, you **must** use this mixing instead of the original one in
     Django.
 ``LoggedInPermissionMixin``
-    Ensure correct redirection of users on no permissions.
+    Ensure correct redirection of users on no permissions. Can also be used to
+    customize messages displayed to the user.
 ``ProjectPermissionMixin``
     Provides a ``Project`` object for permission checking based on URL kwargs.
 ``ProjectContextMixin``

docs/source/getting_started.rst

@@ -17,7 +17,7 @@ the package is under active development and breaking changes are expected.
 
 .. code-block:: console
 
-    pip install django-sodar-core==0.13.3
+    pip install django-sodar-core==0.13.4
 
 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 +10,29 @@ older SODAR Core version. For a complete list of changes in current and previous
 releases, see the :ref:`full changelog<changelog>`.
 
 
+v0.13.4 (2024-02-16)
+********************
+
+Release Highlights
+==================
+
+- Add login message customization
+- Add missing LDAP settings in siteinfo
+- Improve project invite accept link reuse handling
+- Fix remote sync crash with target sites using SODAR Core <0.13.3
+- Fix LDAP settings on example site
+- General bug fixes and minor updates
+
+Breaking Changes
+================
+
+System Prerequisites
+--------------------
+
+The minimum Django version has been bumped to v3.2.24. Optional LDAP
+requirements in ``requirements/ldap.txt`` have also been upgraded.
+
+
 v0.13.3 (2023-12-06)
 ********************
 

projectroles/remote_projects.py

@@ -6,6 +6,7 @@
 import urllib
 
 from copy import deepcopy
+from packaging import version
 
 from django.conf import settings
 from django.contrib import auth
@@ -166,13 +167,14 @@ def _add_user(cls, sync_data, user):
         return sync_data
 
     @classmethod
-    def _add_app_setting(cls, sync_data, app_setting, all_defs):
+    def _add_app_setting(cls, sync_data, app_setting, all_defs, add_user_name):
         """
         Add app setting to sync data on source site.
 
         :param sync_data: Sync data to be updated (dict)
         :param app_setting: AppSetting object
         :param all_defs: All settings defs
+        :param add_user_name: Add user_name to sync data (boolean)
         :return: Updated sync_data (dict)
         """
         if app_setting.app_plugin:
@@ -193,29 +195,38 @@ def _add_app_setting(cls, sync_data, app_setting, all_defs):
             'app_plugin': app_setting.app_plugin.name
             if app_setting.app_plugin
             else None,
-            'project_uuid': app_setting.project.sodar_uuid
+            'project_uuid': str(app_setting.project.sodar_uuid)
             if app_setting.project
             else None,
-            'user_uuid': app_setting.user.sodar_uuid
-            if app_setting.user
-            else None,
-            'user_name': app_setting.user.username
+            'user_uuid': str(app_setting.user.sodar_uuid)
             if app_setting.user
             else None,
             'local': local,
         }
+        if add_user_name:
+            sync_data['app_settings'][str(app_setting.sodar_uuid)][
+                'user_name'
+            ] = (app_setting.user.username if app_setting.user else None)
         return sync_data
 
     # Source Site API functions ------------------------------------------------
 
-    def get_source_data(self, target_site):
+    def get_source_data(self, target_site, req_version=None):
         """
         Get user and project data on a source site to be synchronized into a
         target site.
 
         :param target_site: RemoteSite object for target site
+        :param req_version: Request version (string)
         :return: Dict
         """
+        # TODO: Remove user_name workaround when API backwards compatibility to
+        #       <0.13.3 is removed
+        if not req_version:
+            from projectroles.views_api import CORE_API_DEFAULT_VERSION
+
+            req_version = CORE_API_DEFAULT_VERSION
+        add_user_name = version.parse(req_version) >= version.parse('0.13.3')
         sync_data = {
             'users': {},
             'projects': {},
@@ -242,7 +253,9 @@ def get_source_data(self, target_site):
             # NOTE: Also provide global settings in case they are not yet set
             for a in AppSetting.objects.filter(project=project):
                 try:
-                    sync_data = self._add_app_setting(sync_data, a, all_defs)
+                    sync_data = self._add_app_setting(
+                        sync_data, a, all_defs, add_user_name
+                    )
                 except Exception as ex:
                     logger.error(
                         'Failed to add app setting "{}.settings.{}" '

projectroles/templates/projectroles/_remote_site_dropdown.html

@@ -26,6 +26,6 @@
   </a>
   <a class="dropdown-item text-danger"
      href="{% url 'projectroles:remote_site_delete' remotesite=site.sodar_uuid %}">
-    <i class="iconify" data-icon="mdi:close-thick"></i> Remove Site
+    <i class="iconify" data-icon="mdi:close-thick"></i> Delete Site
   </a>
 </div>

projectroles/templates/projectroles/remotesite_confirm_delete.html

@@ -4,23 +4,27 @@
 {% load crispy_forms_filters %}
 {% load projectroles_common_tags %}
 
-{% block title %}Confirm Removal of Remote Site{% endblock %}
+{% block title %}Confirm Deletion of Remote Site{% endblock %}
 
 {% block projectroles %}
 
 {% get_django_setting 'PROJECTROLES_SITE_MODE' as site_mode %}
 
 <div class="row sodar-subtitle-container">
-  <h2>Confirm Removal of Remote Site</h2>
+  <h2>Confirm Deletion of Remote Site</h2>
 </div>
 
 <div class="container-fluid sodar-page-container">
   <div class="alert alert-warning" role="alert">
-    Do you really want to remove the remote {{ object.mode | lower }} site
+    Do you really want to remove the delete {{ object.mode | lower }} site
     "<strong>{{ object.name }}</strong>"? Please note that this will also
-    remove all {% get_display_name 'PROJECT' %} access rules associated
+    delete all {% get_display_name 'PROJECT' %} access rules associated
     with the site!
   </div>
+  <div class="alert alert-warning" role="alert">
+    If the remote site is still in use, once its entry is deleted it will no
+    longer be able to sync projects to/from this site.
+  </div>
 
   <form method="post">
     {% csrf_token %}
@@ -30,7 +34,7 @@ <h2>Confirm Removal of Remote Site</h2>
         <i class="iconify" data-icon="mdi:arrow-left-circle"></i> Cancel
       </a>
       <button type="submit" class="btn btn-danger">
-        <i class="iconify" data-icon="mdi:close-thick"></i> Remove
+        <i class="iconify" data-icon="mdi:close-thick"></i> Delete
       </button>
     </div>
   </form>