merge v0.13.3 release

.gitignore

@@ -98,6 +98,7 @@ flamegraph.pl
 
 # Celery
 celerybeat-schedule
+celerybeat-schedule.db
 celerybeat.pid
 
 # iRODS files

AUTHORS.rst

@@ -4,6 +4,7 @@ Credits
 * Mikko Nieminen <mikko.nieminen@bih-charite.de>
 * Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
 * Oliver Stolpe <oliver.stolpe@bih-charite.de>
+* Dzmitry Hramyka <dzmitry.hramyka@bih-charite.de>
 * Mathias Kuhring <mathias.kuhring@bih-charite.de>
 * Franziska Schumann <franziska.schumann@fu-berlin.de>
 * Tim Garrels <tim.garrels@student.hpi.uni-potsdam.de>

CHANGELOG.rst

@@ -5,6 +5,42 @@ Changelog for the SODAR project. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+v0.13.3 (2023-05-10)
+====================
+
+Added
+-----
+
+- **Samplesheets**
+    - ``ProjectIrodsFileListAPIView`` in REST API (#1619)
+    - ``SIMPLE_LINK_TEMPLATE`` helper for simple link creation
+
+Changed
+-------
+
+- **General**
+    - Upgrade to Django v3.2.19 (#1646, #1652)
+    - Upgrade Vue app dependencies (#1646)
+    - Update URL patterns to use path (#1631)
+- **Samplesheets**
+    - Refactor ``meta_ms`` to remove ``SPECIAL_FILE_LINK_HEADERS`` use (#1641)
+    - Display study and assay plugin icons to contributors and above (#1354)
+
+Fixed
+-----
+
+- **Samplesheets**
+    - Crash from ``ClearableFileInput`` with Django v3.2.19+ (#1652)
+
+Removed
+-------
+
+- **General**
+    - Unused ``sodar.users`` views and URLs (#1663)
+- **Samplesheets**
+    - ``SPECIAL_FILE_LINK_HEADERS`` hack (#817, #1641)
+
+
 v0.13.2 (2023-04-18)
 ====================
 

config/settings/base.py

@@ -586,7 +586,7 @@ def set_logging(level=None):
 
 
 # General API settings
-SODAR_API_DEFAULT_VERSION = '0.13.2'
+SODAR_API_DEFAULT_VERSION = '0.13.3'
 SODAR_API_ALLOWED_VERSIONS = [
     '0.7.0',
     '0.7.1',
@@ -603,6 +603,7 @@ def set_logging(level=None):
     '0.13.0',
     '0.13.1',
     '0.13.2',
+    '0.13.3',
 ]
 SODAR_API_MEDIA_TYPE = 'application/vnd.bihealth.sodar+json'
 SODAR_API_DEFAULT_HOST = env.url(

config/urls.py

@@ -5,8 +5,8 @@
 from django.contrib.auth import views as auth_views
 from django.contrib.staticfiles.urls import staticfiles_urlpatterns
 from django.shortcuts import render
+from django.urls import path
 from django.views import defaults as default_views
-from django.views.generic import TemplateView
 
 from projectroles.views import HomeView
 
@@ -24,77 +24,81 @@ def handler500(request, *args, **argv):
 
 
 urlpatterns = [
-    url(r'^$', HomeView.as_view(), name='home'),
+    path(route='', view=HomeView.as_view(), name='home'),
     # Django Admin, use {% url 'admin:index' %}
     url(settings.ADMIN_URL, admin.site.urls),
     # Login and logout
-    url(
-        r'^login/$',
-        auth_views.LoginView.as_view(template_name='users/login.html'),
+    path(
+        route='login/',
+        view=auth_views.LoginView.as_view(template_name='users/login.html'),
         name='login',
     ),
-    url(r'^logout/$', auth_views.logout_then_login, name='logout'),
+    path(
+        route='logout/',
+        view=auth_views.logout_then_login,
+        name='logout',
+    ),
     # User Profile URLs
-    url(r'^user/', include('userprofile.urls')),
+    path('user/', include('userprofile.urls')),
     # Auth
-    url(r'api/auth/', include('knox.urls')),
+    path('api/auth/', include('knox.urls')),
     # Iconify SVG icons
-    url(r'icons/', include('dj_iconify.urls')),
+    path('icons/', include('dj_iconify.urls')),
     # General site apps
-    url(r'^alerts/adm/', include('adminalerts.urls')),
-    url(r'^alerts/app/', include('appalerts.urls')),
-    url(r'^siteinfo/', include('siteinfo.urls')),
-    url(r'^irods/', include('irodsinfo.urls')),
-    url(r'^tokens/', include('tokens.urls')),
-    url(r'^ontology/', include('ontologyaccess.urls')),
+    path('alerts/adm/', include('adminalerts.urls')),
+    path('alerts/app/', include('appalerts.urls')),
+    path('siteinfo/', include('siteinfo.urls')),
+    path('irods/', include('irodsinfo.urls')),
+    path('tokens/', include('tokens.urls')),
+    path('ontology/', include('ontologyaccess.urls')),
     # Projectroles URLs
-    url(r'^project/', include('projectroles.urls')),
+    path('project/', include('projectroles.urls')),
     # App plugin URLs
     # TODO: See if plugin URLs can be made to work now (Flynn no longer used)
     # url(r'^', include_plugins(ProjectAppPluginPoint)),
-    url(r'^timeline/', include('timeline.urls')),
-    url(r'^samplesheets/', include('samplesheets.urls')),
-    url(r'^landingzones/', include('landingzones.urls')),
+    path('timeline/', include('timeline.urls')),
+    path('samplesheets/', include('samplesheets.urls')),
+    path('landingzones/', include('landingzones.urls')),
     # Backend apps with API URLs
-    url(r'^irodsbackend/', include('irodsbackend.urls')),
+    path('irodsbackend/', include('irodsbackend.urls')),
     # Samplesheets study sub-app URLs
-    url(
-        r'^samplesheets/study/germline/',
+    path(
+        'samplesheets/study/germline/',
         include('samplesheets.studyapps.germline.urls'),
     ),
-    url(
-        r'^samplesheets/study/cancer/',
+    path(
+        'samplesheets/study/cancer/',
         include('samplesheets.studyapps.cancer.urls'),
     ),
     # Landingzones config sub-app URLs
-    url(
-        r'^landingzones/config/bih-proteomics-smb/',
+    path(
+        'landingzones/config/bih-proteomics-smb/',
         include('landingzones.configapps.bih_proteomics_smb.urls'),
     ),
     # Sodarcache URLs
-    url(r'^cache/', include('sodarcache.urls')),
+    path('cache/', include('sodarcache.urls')),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
 
 if settings.DEBUG:
     # This allows the error pages to be debugged during development, just visit
     # these url in browser to see how these error pages look like.
     urlpatterns += [
-        url(
-            r'^400/$',
-            default_views.bad_request,
+        path(
+            route='400/',
+            view=default_views.bad_request,
             kwargs={'exception': Exception('Bad Request!')},
         ),
-        url(
-            r'^403/$',
-            default_views.permission_denied,
+        path(
+            route='403/',
+            view=default_views.permission_denied,
             kwargs={'exception': Exception('Permission Denied')},
         ),
-        url(
-            r'^404/$',
-            default_views.page_not_found,
+        path(
+            route='404/',
+            view=default_views.page_not_found,
             kwargs={'exception': Exception('Page not Found')},
         ),
-        url(r'^500/$', default_views.server_error),
+        path(route='500/', view=default_views.server_error),
     ]
 
     urlpatterns += staticfiles_urlpatterns()
@@ -103,5 +107,5 @@ def handler500(request, *args, **argv):
         import debug_toolbar
 
         urlpatterns = [
-            url(r'^__debug__/', include(debug_toolbar.urls))
+            path('__debug__/', include(debug_toolbar.urls))
         ] + urlpatterns

docs_manual/source/api_documentation.rst

@@ -45,7 +45,7 @@ expected version.
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.13.2
+    Accept: application/vnd.bihealth.sodar+json; version=0.13.3
 
 Specific sections of the SODAR API may require their own accept header. See the
 exact header requirement in the respective documentation on each section of the

docs_manual/source/api_landingzones.rst

@@ -30,4 +30,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.13.2
+    Accept: application/vnd.bihealth.sodar+json; version=0.13.3

docs_manual/source/api_samplesheets.rst

@@ -21,6 +21,8 @@ API Views
 
 .. autoclass:: SampleDataFileExistsAPIView
 
+.. autoclass:: ProjectIrodsFileListAPIView
+
 
 Versioning
 ==========
@@ -30,4 +32,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.13.2
+    Accept: application/vnd.bihealth.sodar+json; version=0.13.3

docs_manual/source/conf.py

@@ -26,7 +26,7 @@
 author = 'BIH Core Unit Bioinformatics'
 
 # The full version, including alpha/beta/rc tags
-release = '0.13.2'
+release = '0.13.3'
 
 
 # -- General configuration ---------------------------------------------------

docs_manual/source/dev_apps.rst

@@ -194,7 +194,7 @@ An example of expected output for ``get_shortcut_links()``:
                 'title': 'Printable title for item type',
                 'files': [
                     {
-                        'label': 'Link label (e.g. related library name)',
+                        'label': 'Link label (e.g. related extract name)',
                         'url': some_url,
                         'title': 'Mouseover title'
                         'extra_links': {  # Additional links for the same item

docs_manual/source/metadata_advanced.rst

@@ -40,7 +40,7 @@ IGV session generation. This is determined by file name: in case of multiple
 files, the last file sorted by file name is returned. Hence to ensure the most
 recent file is returned, it is recommended to use dates in the file names.
 
-Placement of files in subcollections under the library collection does not
+Placement of files in subcollections under the row-specific collection does not
 affect study shortcuts or IGV session inclusion. This also means files can be
 freely organized within desired subcollections.
 

docs_manual/source/sodar_release_notes.rst

@@ -8,6 +8,18 @@ list of changes in current and previous releases, see the
 :ref:`full changelog<sodar_changelog>`.
 
 
+v0.13.3 (2023-05-10)
+====================
+
+Release for minor updates, maintenance and bug fixes.
+
+- Add ``ProjectIrodsFileListAPIView`` API endpoint
+- Display study and assay plugin icons to contributors and above
+- Remove ``SPECIAL_FILE_LINK_HEADERS`` hack
+- Update URL patterns
+- Upgrade dependencies, fix site for Django v3.2.19+
+
+
 v0.13.2 (2023-04-18)
 ====================
 

irodsbackend/urls.py

@@ -1,23 +1,23 @@
-from django.conf.urls import url
+from django.urls import path
 
 from . import views
 
 
 app_name = 'irodsbackend'
 
 urlpatterns = [
-    url(
-        regex=r'^ajax/stats/(?P<project>[0-9a-f-]+)$',
+    path(
+        route='ajax/stats/<uuid:project>',
         view=views.IrodsStatisticsAjaxView.as_view(),
         name='stats',
     ),
-    url(
-        regex=r'^ajax/list/(?P<project>[0-9a-f-]+)$',
+    path(
+        route='ajax/list/<uuid:project>',
         view=views.IrodsObjectListAjaxView.as_view(),
         name='list',
     ),
-    url(
-        regex=r'^api/auth$',
+    path(
+        route='api/auth',
         view=views.LocalAuthAPIView.as_view(),
         name='api_auth',
     ),

irodsinfo/urls.py

@@ -1,10 +1,18 @@
-from django.conf.urls import url
+from django.urls import path
 
 from . import views
 
 app_name = 'irodsinfo'
 
 urlpatterns = [
-    url(regex=r'^info$', view=views.IrodsInfoView.as_view(), name='info'),
-    url(regex=r'^config$', view=views.IrodsConfigView.as_view(), name='config'),
+    path(
+        route='info',
+        view=views.IrodsInfoView.as_view(),
+        name='info',
+    ),
+    path(
+        route='config',
+        view=views.IrodsConfigView.as_view(),
+        name='config',
+    ),
 ]