cleanup for v0.15.0 release (wip) (#1933)

CHANGELOG.rst

@@ -11,6 +11,8 @@ Unreleased
 Added
 -----
 
+- **General**
+    - Cyberduck documentation (#1931)
 - **Isatemplates**
     - ``isatemplates`` app for custom ISA-Tab template management (#1961)
     - ``isatemplates_backend`` plugin for template retrieval (#1961)
@@ -38,6 +40,7 @@ Changed
     - ``index`` arg in ``SampleSheetAssayPluginPoint.update_row()`` (#1957)
     - Hide template output dir field by default (#1960)
     - Improve ``StudyLinksAjaxView`` return data (#1963, #1966)
+    - Optimize ``irodsbackend`` API retrieval in ``plugins`` (#1952)
 - **Taskflowbackend**
     - Increase default for ``TASKFLOW_IRODS_CONN_TIMEOUT`` (#1900)
     - Disable lock requirement for role and project update flows (#1948)

docs_manual/source/admin_settings.rst

@@ -35,7 +35,6 @@ Documentation on settings is linked below.
 - `Projectroles (the core project and site framework) <https://sodar-core.readthedocs.io/en/latest/app_projectroles_settings.html#general-site-settings>`_
 - `Admin Alerts <https://sodar-core.readthedocs.io/en/latest/app_adminalerts.html#optional-settings>`_
 - `App Alerts <https://sodar-core.readthedocs.io/en/latest/app_appalerts.html#django-settings>`_
-- `Taskflow Backend <https://sodar-core.readthedocs.io/en/latest/app_taskflow.html#django-settings>`_
 - `Timeline <https://sodar-core.readthedocs.io/en/latest/app_timeline_install.html#optional-settings>`_
 
 .. _admin_settings_backend:

docs_manual/source/ui_user_profile.rst

@@ -20,6 +20,10 @@ Sample Sheet Table Height
     from a set of options. In browsing mode, table height will fit the table
     content if the height of content is lower than the setting. In edit mode,
     the chosen table height will be maintained regardless of content.
+Display Template Output Directory Field
+    Display or hide the "output directory" field in sample sheet template
+    creation form. This can be enabled if there is need to control the output
+    directory in sample sheet ISA-Tab exports. Defaults to false.
 Display Project UUID Copying Link
     Enabling this will add an icon next to the project title on each project
     view. Clicking it will copy the project identifier (UUID) into the

irodsbackend/plugins.py

@@ -41,7 +41,7 @@ class BackendPlugin(BackendPluginPoint):
     #: Title (used in templates)
     title = 'iRODS Backend'
 
-    #: FontAwesome icon ID string
+    #: Iconify icon
     icon = 'mdi:database-search'
 
     #: Description string

landingzones/plugins.py

@@ -158,27 +158,27 @@ def get_statistics(self):
         """
         return {
             'zones_total': {
-                'label': 'Total zones',
+                'label': 'Total Zones',
                 'value': LandingZone.objects.count(),
             },
             'zones_active': {
-                'label': 'Active zones',
+                'label': 'Active Zones',
                 'value': LandingZone.objects.filter(
                     status__in=STATUS_ALLOW_UPDATE
                 ).count(),
                 'description': 'Landing zones available for use (active or '
                 'failed)',
             },
             'zones_finished': {
-                'label': 'Finished zones',
+                'label': 'Finished Zones',
                 'value': LandingZone.objects.filter(
                     status__in=STATUS_FINISHED
                 ).count(),
                 'description': 'Landing zones finished successfully, deleted '
                 'or not created',
             },
             'zones_busy': {
-                'label': 'Busy zones',
+                'label': 'Busy Zones',
                 'value': LandingZone.objects.filter(
                     status__in=STATUS_BUSY
                 ).count(),

landingzones/views.py

@@ -639,7 +639,7 @@ class ZoneDeleteView(
     http_method_names = ['get', 'post']
     template_name = 'landingzones/landingzone_confirm_delete.html'
     zone_action = 'delete'
-    # NOTE: permission_required comes from ZoneUpdateRequiredPermissionMixin
+    # NOTE: permission_required comes from ZoneModifyPermissionMixin
 
     def get_context_data(self, *args, **kwargs):
         context = super().get_context_data(*args, **kwargs)
@@ -706,7 +706,7 @@ class ZoneMoveView(
     http_method_names = ['get', 'post']
     template_name = 'landingzones/landingzone_confirm_move.html'
     zone_action = 'move'
-    # NOTE: permission_required comes from ZoneUpdateRequiredPermissionMixin
+    # NOTE: permission_required comes from ZoneModifyPermissionMixin
 
     def get_context_data(self, *args, **kwargs):
         context = super().get_context_data(*args, **kwargs)

ontologyaccess/plugins.py

@@ -42,7 +42,7 @@ class BackendPlugin(BackendPluginPoint):
     #: Title (used in templates)
     title = 'Ontology Access Backend'
 
-    #: FontAwesome icon ID string
+    #: Iconify icon
     icon = 'mdi:tags'
 
     #: Description string
@@ -58,11 +58,11 @@ def get_api(self, **kwargs):
     def get_statistics(self):
         return {
             'obo_ontology_count': {
-                'label': 'OBO ontologies',
+                'label': 'OBO Ontologies',
                 'value': OBOFormatOntology.objects.count(),
             },
             'obo_term_count': {
-                'label': 'OBO ontology terms',
+                'label': 'OBO Ontology Terms',
                 'value': OBOFormatOntologyTerm.objects.count(),
             },
         }

ontologyaccess/templates/ontologyaccess/list.html

@@ -52,7 +52,7 @@ <h2><i class="iconify" data-icon="mdi:tags"></i> Ontology Access</h2>
 
 <div class="container-fluid sodar-page-container">
   {% if object_list.count > 0 %}
-    <div class="card" id="sodar-oa-alert-list">
+    <div class="card" id="sodar-oa-ontology-list">
       <div class="card-header">
         <h4><i class="iconify" data-icon="mdi:tag"></i> OBO Format Ontologies</h4>
       </div>
@@ -77,7 +77,8 @@ <h4><i class="iconify" data-icon="mdi:tag"></i> OBO Format Ontologies</h4>
                 <td class="text-right">{{ o.terms.all.count }}</td>
                 <td>{{ o.date_created | date:'Y-m-d H:i' }}</td>
                 <td>
-                  <div class="btn-group sodar-list-btn-group" id="sodar-oa-alert-buttons-{{ a.pk }}">
+                  <div class="btn-group sodar-list-btn-group"
+                       id="sodar-oa-item-dropdown-{{ a.pk }}">
                     <button class="btn btn-secondary dropdown-toggle sodar-list-dropdown"
                             type="button" data-toggle="dropdown" aria-expanded="false">
                       <i class="iconify" data-icon="mdi:cog"></i>

ontologyaccess/views.py

@@ -25,8 +25,6 @@ class OBOFormatOntologyListView(LoggedInPermissionMixin, ListView):
 
     model = OBOFormatOntology
     permission_required = 'ontologyaccess.view_list'
-    slug_url_kwarg = 'bioontology'
-    slug_field = 'sodar_uuid'
     template_name = 'ontologyaccess/list.html'
 
     def get_queryset(self):