cleanup and prepare v0.14.1 release (#1826)

CHANGELOG.rst

@@ -5,8 +5,8 @@ Changelog for the SODAR project. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
-Unreleased
-==========
+v0.14.1 (2023-12-12)
+====================
 
 Added
 -----
@@ -50,6 +50,9 @@ Fixed
 - **Landingzones**
     - No wait for async ``CurrentUserRetrieveAPIView`` call result (#1732, #1807)
     - ``BaseLandingZoneStatusTask.set_status()`` failure with concurrent sheet replacing (#1839)
+- **Samplesheets**
+    - ``ColumnToggleModal`` study checkbox states rendered under assay (#1848)
+    - ``ColumnToggleModal`` group toggle not updating checkboxes in UI (#1849)
 - **Taskflowbackend**
     - ``project_create`` timeline event user reference (bihealth/sodar_core#1301, #1819)
     - Incorrect write access messages in ``landing_zone_move`` when validating only (#1845)

config/settings/base.py

@@ -347,7 +347,7 @@
 # Enable LDAP if configured
 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, default=[])
 
@@ -356,6 +356,8 @@
     import ldap
     from django_auth_ldap.config import LDAPSearch
 
+    if LDAP_DEBUG:
+        ldap.set_option(ldap.OPT_DEBUG_LEVEL, 255)
     # Default values
     LDAP_DEFAULT_CONN_OPTIONS = {ldap.OPT_REFERRALS: 0}
     LDAP_DEFAULT_ATTR_MAP = {
@@ -608,7 +610,7 @@ def set_logging(level=None):
 
 
 # General API settings
-SODAR_API_DEFAULT_VERSION = '0.14.0'
+SODAR_API_DEFAULT_VERSION = '0.14.1'
 SODAR_API_ALLOWED_VERSIONS = [
     '0.7.0',
     '0.7.1',
@@ -628,6 +630,7 @@ def set_logging(level=None):
     '0.13.3',
     '0.13.4',
     '0.14.0',
+    '0.14.1',
 ]
 SODAR_API_MEDIA_TYPE = 'application/vnd.bihealth.sodar+json'
 SODAR_API_DEFAULT_HOST = env.url(

docs_manual/source/admin_ontologyaccess.rst

@@ -86,8 +86,10 @@ Title
     Optional title for the ontology, mostly for easy recognizing in the Ontology
     Access UI.
 Term URL
-    The URL for linking terms to their online specifications. This expects two
-    parameters, ``{id_space}`` and ``{local_id}}``.
+    The URL pattern for linking terms to their online specifications. This
+    expects two parameters, ``{id_space}`` and ``{local_id}}``. If the ontology
+    can be found in obolibrary, it is recommended to provide the pattern in the
+    form of ``http://purl.obolibrary.org/obo/{id_space}_{local_id}``.
 
 .. figure:: _static/admin/ontologyaccess_form.png
     :align: center

docs_manual/source/api_examples.rst

@@ -43,7 +43,7 @@ the SODAR API:
     # Use core_headers for project management API endpoints
     core_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar-core+json; version=0.13.3'}
     # Use sodar_headers for sample sheet and landing zone API endpoints
-    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.14.0'}
+    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.14.1'}
 
 .. note::
 

docs_manual/source/api_irodsinfo.rst

@@ -22,4 +22,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.14.0
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.1

docs_manual/source/api_landingzones.rst

@@ -32,4 +32,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.14.0
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.1

docs_manual/source/api_samplesheets.rst

@@ -68,4 +68,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.14.0
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.1

docs_manual/source/app_samplesheets_browse.rst

@@ -145,10 +145,10 @@ displayed in the screenshot below.
 
     Table header with column visibility toggle button highlighted
 
-Clicking the button opens a modal in which you can hide or unhide columns by
-clicking the accompanying check boxes. Columns can be toggled individually
-or by an entire node. The node name columns, or protocol columns in the case of
-unnamed processes, will always be displayed.
+Clicking the button opens a modal in which you can hide or unhide columns using
+the accompanying checkboxes. Columns can be toggled individually or for an
+entire material or process. Name columns, or protocol columns in the case of
+unnamed processes, will always be displayed and can't be hidden.
 
 .. figure:: _static/app_samplesheets/column_toggle_modal.png
     :align: center

docs_manual/source/app_samplesheets_edit.rst

@@ -379,9 +379,12 @@ variables. The modal content varies based on the column type, but all share a
 few common elements:
 
 - Configuration copy/paste elements in the top right corner
-- The *Editable* checkbox for enabling or disabling editing for this column
-- The *Cancel* and *Update* buttons for committing the configuration change or
-  cancelling it.
+- The :guilabel:`Editable` checkbox for enabling or disabling editing for this
+  column. This is disabled by default. When disabled, users are only able to
+  enter data in mandatory fields such as material names or process protocols
+  when inserting new rows.
+- The :guilabel:`Cancel` and :guilabel:`Update` buttons for committing the
+  configuration change or cancelling it.
 
 Upon first importing or creating the sample sheets, the initial type and
 configuration of a column is automatically determined by SODAR. The modal

docs_manual/source/conf.py

@@ -26,7 +26,7 @@
 author = 'BIH Core Unit Bioinformatics'
 
 # The full version, including alpha/beta/rc tags
-release = '0.14.1-WIP'
+release = '0.14.1'
 
 
 # -- General configuration ---------------------------------------------------

docs_manual/source/sodar_release_notes.rst

@@ -8,8 +8,8 @@ list of changes in current and previous releases, see the
 :ref:`full changelog<sodar_changelog>`.
 
 
-v0.14.1 (WIP)
-=============
+v0.14.1 (2023-12-12)
+====================
 
 Release for minor updates, maintenance and bug fixes.
 
@@ -18,6 +18,7 @@ Release for minor updates, maintenance and bug fixes.
 - Change default IGV genome to "b37_1kg"
 - Fix landing zone locking controls for non-superusers
 - Fix access to new HP ontology URLs
+- Fix sheet column toggle modal UI issues
 - Minor updates and bug fixes
 - Upgrade to SODAR Core v0.13.3
 

ontologyaccess/templates/ontologyaccess/list.html

@@ -14,27 +14,23 @@
       width: 170px;
       white-space: nowrap;
     }
-
     table#sodar-oa-list-table thead tr th:nth-child(6),
     table#sodar-oa-list-table tbody tr td:nth-child(6) {
       width: 75px;
     }
-
     /* Responsive modifications */
     @media screen and (max-width: 1200px) {
       table#sodar-oa-list-table thead tr th:nth-child(5),
       table#sodar-oa-list-table tbody tr td:nth-child(5) {
         display: none;
       }
     }
-
     @media screen and (max-width: 1100px) {
       table#sodar-oa-list-table thead tr th:nth-child(4),
       table#sodar-oa-list-table tbody tr td:nth-child(4) {
         display: none;
       }
     }
-
     @media screen and (max-width: 650px) {
       table#sodar-oa-list-table thead tr th:nth-child(3),
       table#sodar-oa-list-table tbody tr td:nth-child(3) {
@@ -44,20 +40,17 @@
   </style>
 {% endblock css %}
 
-
 {% block projectroles %}
 
 <div class="row sodar-subtitle-container bg-white sticky-top">
   <h2><i class="iconify" data-icon="mdi:tags"></i> Ontology Access</h2>
-
   <a role="button" class="btn btn-primary ml-auto"
      href="{% url 'ontologyaccess:obo_import' %}">
-    <i class="iconify" data-icon="mdi:upload"></i> Import  Ontology
+    <i class="iconify" data-icon="mdi:upload"></i> Import Ontology
   </a>
 </div>
 
 <div class="container-fluid sodar-page-container">
-
   {% if object_list.count > 0 %}
     <div class="card" id="sodar-oa-alert-list">
       <div class="card-header">
@@ -109,15 +102,13 @@ <h4><i class="iconify" data-icon="mdi:tag"></i> OBO Format Ontologies</h4>
         </table>
       </div>
     </div>
-
   {% else %} {# if object_list.count == 0 #}
     <div class="container-fluid">
       <div class="alert alert-info" role="alert">
         No imported ontologies found.
       </div>
     </div>
   {% endif %}
-
 </div>
 
 {% endblock projectroles %}

ontologyaccess/templates/ontologyaccess/obo_import_form.html

@@ -11,7 +11,6 @@
     input#id_term_url {
       font-family: monospace;
     }
-
     div.alert ul {
       margin-bottom: 0;
     }

samplesheets/plugins.py

@@ -537,7 +537,6 @@ def get_project_list_value(self, column_id, project, user):
                 )
             )
 
-    # TODO: Add tests
     def validate_form_app_settings(self, app_settings, project=None, user=None):
         """
         Validate app settings form data and return a dict of errors.

samplesheets/templates/samplesheets/_details_card.html

@@ -19,11 +19,9 @@
   table#sodar-ss-details-table tr td:nth-child(2) {
     width: 220px;
   }
-
   table#sodar-ss-details-table tr td:nth-child(3) {
     width: 110px;
   }
-
   /* Responsive modifications */
   @media screen and (max-width: 800px) {
     table#sodar-ss-details-table tr th:nth-child(2) {
@@ -37,11 +35,11 @@
 
 {% if not investigation %}
   <div class="card-body bg-faded font-italic text-center">
-    <p>No sample sheets available</p>
+    <p>No sample sheets available.</p>
   </div>
 {% elif investigation and not investigation.irods_status %}
   <div class="card-body bg-faded font-italic text-center">
-    <p>Sample sheets available, sample repository not created in iRODS</p>
+    <p>Sample sheets available, sample repository not created in iRODS.</p>
   </div>
 {% elif investigation and can_view_sheet %}
   <!-- Irodsbackend -->

samplesheets/templates/samplesheets/irods_requests.html

@@ -217,7 +217,7 @@ <h3>iRODS Delete Requests</h3>
     {% if is_contributor %}
       You don't have active iRODS delete requests for this project.
     {% else %}
-      No iRODS delete requests have been found for the sample sheets in this project.
+      No iRODS delete requests have been found for this project.
     {% endif %}
   </div>
 {% endif %}

samplesheets/tests/test_tasks_celery_taskflow.py

@@ -27,7 +27,7 @@
     CACHE_UPDATE_EVENT,
 )
 from samplesheets.tests.test_io import SampleSheetIOMixin, SHEET_DIR
-from samplesheets.tests.test_views import TestSheetRemoteSyncBase
+from samplesheets.tests.test_views import SheetRemoteSyncTestBase
 from samplesheets.tests.test_views_taskflow import (
     SampleSheetTaskflowMixin,
 )
@@ -154,7 +154,7 @@ def test_update_cache_no_user(self):
         self.assertEqual(ProjectEvent.objects.count(), 3)
 
 
-class TestSheetRemoteSyncTask(TestSheetRemoteSyncBase):
+class TestSheetRemoteSyncTask(SheetRemoteSyncTestBase):
     """Tests for periodic sample sheet sync task"""
 
     def setUp(self):

samplesheets/tests/test_views.py

@@ -1629,7 +1629,7 @@ def test_list_empty(self):
         self.assertEqual(len(response.context['object_list']), 0)
 
 
-class TestSheetRemoteSyncBase(
+class SheetRemoteSyncTestBase(
     ProjectMixin,
     RoleMixin,
     RoleAssignmentMixin,
@@ -1694,7 +1694,7 @@ def setUp(self):
         )
 
 
-class TestSheetRemoteSyncView(TestSheetRemoteSyncBase):
+class TestSheetRemoteSyncView(SheetRemoteSyncTestBase):
     """Tests for SheetRemoteSyncView"""
 
     def test_sync(self):

samplesheets/vueapp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "samplesheets",
-  "version": "0.14.1-WIP",
+  "version": "0.14.1",
   "private": true,
   "scripts": {
     "serve": "vue-cli-service serve",