cleanup for v0.14.2 release (wip) (#1861)

config/settings/base.py

@@ -22,7 +22,7 @@
 env = environ.Env()
 
 # .env file, should load only in development environment
-READ_DOT_ENV_FILE = env.bool('DJANGO_READ_DOT_ENV_FILE', default=False)
+READ_DOT_ENV_FILE = env.bool('DJANGO_READ_DOT_ENV_FILE', False)
 
 if READ_DOT_ENV_FILE:
     # Operating System Environment variables have precedence over variables
@@ -157,7 +157,7 @@
 # See: https://docs.djangoproject.com/en/3.2/ref/settings/#databases
 # Uses django-environ to accept uri format
 # See: https://django-environ.readthedocs.io/en/latest/#supported-types
-DATABASES = {'default': env.db('DATABASE_URL', default='postgres:///sodar')}
+DATABASES = {'default': env.db('DATABASE_URL', 'postgres:///sodar')}
 DATABASES['default']['ATOMIC_REQUESTS'] = False
 
 # Set default auto field (for Django 3.2+)

config/settings/local.py

@@ -16,7 +16,7 @@
 
 # DEBUG
 # ------------------------------------------------------------------------------
-DEBUG = env.bool('DJANGO_DEBUG', default=True)
+DEBUG = env.bool('DJANGO_DEBUG', True)
 TEMPLATES[0]['OPTIONS']['debug'] = DEBUG
 
 # SECRET CONFIGURATION
@@ -53,7 +53,7 @@
 
 # django-debug-toolbar
 # ------------------------------------------------------------------------------
-ENABLE_DEBUG_TOOLBAR = env.bool('ENABLE_DEBUG_TOOLBAR', default=True)
+ENABLE_DEBUG_TOOLBAR = env.bool('ENABLE_DEBUG_TOOLBAR', True)
 
 if ENABLE_DEBUG_TOOLBAR:
     MIDDLEWARE += ['debug_toolbar.middleware.DebugToolbarMiddleware']

config/settings/production.py

@@ -28,23 +28,23 @@
 SECURE_HSTS_SECONDS = 60
 
 SECURE_HSTS_INCLUDE_SUBDOMAINS = env.bool(
-    'DJANGO_SECURE_HSTS_INCLUDE_SUBDOMAINS', default=True
+    'DJANGO_SECURE_HSTS_INCLUDE_SUBDOMAINS', True
 )
 SECURE_CONTENT_TYPE_NOSNIFF = env.bool(
-    'DJANGO_SECURE_CONTENT_TYPE_NOSNIFF', default=True
+    'DJANGO_SECURE_CONTENT_TYPE_NOSNIFF', True
 )
 SECURE_BROWSER_XSS_FILTER = True
 SESSION_COOKIE_SECURE = True
 SESSION_COOKIE_HTTPONLY = True
-SECURE_SSL_REDIRECT = env.bool('DJANGO_SECURE_SSL_REDIRECT', default=True)
+SECURE_SSL_REDIRECT = env.bool('DJANGO_SECURE_SSL_REDIRECT', True)
 SECURE_REDIRECT_EXEMPT = env.list(
     'DJANGO_SECURE_REDIRECT_EXEMPT',
     default=['/taskflow/', r'^irodsbackend/api/auth$'],
 )
 CSRF_COOKIE_SECURE = True
 CSRF_COOKIE_HTTPONLY = True
 CSRF_TRUSTED_ORIGINS = env.list('DJANGO_CSRF_TRUSTED_ORIGINS', default=[])
-CSRF_COOKIE_DOMAIN = env.str('DJANGO_CSRF_COOKIE_DOMAIN', default=None)
+CSRF_COOKIE_DOMAIN = env.str('DJANGO_CSRF_COOKIE_DOMAIN', None)
 
 X_FRAME_OPTIONS = 'DENY'
 

docs_manual/source/conf.py

@@ -22,11 +22,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'SODAR'
-copyright = '2018-2023, BIH Core Unit Bioinformatics'
+copyright = '2018-2024, BIH Core Unit Bioinformatics'
 author = 'BIH Core Unit Bioinformatics'
 
 # The full version, including alpha/beta/rc tags
-release = '0.14.2-WIP'
+release = '0.14.2'
 
 
 # -- General configuration ---------------------------------------------------

landingzones/views.py

@@ -329,11 +329,7 @@ def submit_delete(self, zone):
         if zone_exists:  # Submit with taskflow
             flow_name = 'landing_zone_delete'
             flow_data = self.get_flow_data(
-                zone,
-                flow_name,
-                {
-                    'zone_uuid': str(zone.sodar_uuid),
-                },
+                zone, flow_name, {'zone_uuid': str(zone.sodar_uuid)}
             )
             taskflow.submit(
                 project=project,

samplesheets/templates/samplesheets/samplesheet_import_form.html

@@ -91,17 +91,11 @@ <h3>
            href="{% url 'samplesheets:project_sheets' project=project.sodar_uuid %}">
           <i class="iconify" data-icon="mdi:arrow-left-circle"></i> Cancel
         </a>
-        {% if replace_sheets %}
-          <button type="submit" class="btn btn-primary sodar-btn-submit-once"
-                  id="sodar-ss-btn-import-submit">
-            <i class="iconify" data-icon="mdi:refresh"></i> Replace
-          </button>
-        {% else %}
-          <button type="submit" class="btn btn-primary sodar-btn-submit-once"
-                  id="sodar-ss-btn-import-submit">
-            <i class="iconify" data-icon="mdi:upload"></i> Import
-          </button>
-        {% endif %}
+        <button type="submit" class="btn btn-primary sodar-btn-submit-once"
+                id="sodar-ss-btn-import-submit">
+          <i class="iconify" data-icon="mdi:upload"></i>
+          {% if replace_sheets %}Replace{% else %}Import{% endif %}
+        </button>
       </div>
     </div>
   </form>

samplesheets/views.py

@@ -1472,12 +1472,8 @@ def get_context_data(self, *args, **kwargs):
     def get_form_kwargs(self):
         """Pass kwargs to form"""
         kwargs = super().get_form_kwargs()
-        kwargs.update(
-            {
-                'project': self.get_project(),
-                'sheet_tpl': self._get_sheet_template(),
-            }
-        )
+        kwargs['project'] = self.get_project()
+        kwargs['sheet_tpl'] = self._get_sheet_template()
         return kwargs
 
     def form_valid(self, form):

samplesheets/vueapp/src/App.vue

@@ -1062,8 +1062,7 @@ export default {
                 groupId = cols[startIdx].originalParent.groupId
                 // Update newRow for source cells
                 for (let i = 1; i < startIdx; i++) {
-                  const value = rowNode.data[cols[i].colId]
-                  value.newRow = false
+                  rowNode.data[cols[i].colId].newRow = false
                 }
               }
 

taskflowbackend/flows/landing_zone_delete.py

@@ -54,7 +54,7 @@ def build(self, force_fail=False):
                 inject={'path': zone_path},
             )
         )
-        # Set zone status to DELETING
+        # Set zone status to DELETED
         self.add_task(
             lz_tasks.SetLandingZoneStatusTask(
                 name='Set landing zone status to DELETED',