merge v0.14.1 release

.github/workflows/build.yml

@@ -34,6 +34,7 @@ jobs:
         ports:
           - 6379:6379
       irods:
+        # TODO: Update image to 4.3 once its made default
         image: ghcr.io/bihealth/irods-docker:4.2.11-1
         env:
           IRODS_AUTHENTICATION_SCHEME: native

CHANGELOG.rst

@@ -5,6 +5,67 @@ Changelog for the SODAR project. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+v0.14.1 (2023-12-12)
+====================
+
+Added
+-----
+
+- **Irodsbackend**
+    - ``get_version()`` helper (#1592, #1817, #1831)
+    - ``get_access_lookup()`` helper (#1832)
+- **Irodsinfo**
+    - iRODS v4.3 auth scheme support in client environment (#1834)
+- **Samplesheets**
+    - Custom validation for ``sheet_sync_url`` and ``sheet_sync_token`` (#1310, #1384)
+    - ``hpo.jax.org`` in ``SHEETS_ONTOLOGY_URL_SKIP`` (#1821)
+    - Missing Django settings in siteinfo (#1830)
+- **Taskflowbackend**
+    - iRODS v4.3 support (#1592, #1817, #1832)
+    - ``BatchCalculateChecksumTask`` exception logging (#1843)
+
+Changed
+-------
+
+- **General**
+    - Upgrade to Django v3.2.23 (#1811)
+    - Upgrade to django-sodar-core v0.13.3 (#1810)
+- **Irodsbackend**
+    - iRODS collection modal copy button icon (#1851)
+- **Landingzones**
+    - Disable locked zone controls in template for non-superusers (#1808)
+    - Rename and refactor ``disable_zone_ui()`` template tag (#1808)
+- **Samplesheets**
+    - Upgrade Vue app dependencies (#1811)
+    - Change default IGV genome to ``b37_1kg`` (#1812)
+    - Update existing ``b37`` IGV genome settings with a migration (#1812)
+- **Taskflowbackend**
+    - Improve ``landing_zone_move`` zone status info messages for validation (#1840)
+
+Fixed
+-----
+
+- **General**
+    - Add workaround for ``AUTH_LDAP_CONNECTION_OPTIONS`` duplication (#1853)
+- **Irodsbackend**
+    - Opening redundant iRODS connection in server version retrieval (#1831)
+- **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)
+
+Removed
+-------
+
+- **Taskflowbackend**
+    - Duplicate ``SetAccessTask`` tests (#1833)
+
+
 v0.14.0 (2023-09-27)
 ====================
 

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=[])
 
@@ -356,13 +356,17 @@
     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 = {
         'first_name': 'givenName',
         'last_name': 'sn',
         'email': 'mail',
     }
+    # Temporarily disable cert checking (see issue #1853)
+    ldap.set_option(ldap.OPT_X_TLS_REQUIRE_CERT, ldap.OPT_X_TLS_NEVER)
 
     # Primary LDAP server
     AUTH_LDAP_SERVER_URI = env.str('AUTH_LDAP_SERVER_URI', None)
@@ -371,7 +375,7 @@
     AUTH_LDAP_START_TLS = env.str('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
@@ -406,7 +410,7 @@
         AUTH_LDAP2_START_TLS = env.str('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
@@ -608,7 +612,7 @@ 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 +632,7 @@ 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(
@@ -793,7 +798,7 @@ def set_logging(level=None):
 )
 # Skip URL template modification if substring found in accession
 SHEETS_ONTOLOGY_URL_SKIP = env.list(
-    'SHEETS_ONTOLOGY_URL_SKIP', default=['bioontology.org']
+    'SHEETS_ONTOLOGY_URL_SKIP', default=['bioontology.org', 'hpo.jax.org']
 )
 
 # Labels and URL patterns for external link columns

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

@@ -41,9 +41,9 @@ the SODAR API:
     # Token authorization header (required)
     auth_header = {'Authorization': 'token {}'.format(api_token)}
     # Use core_headers for project management API endpoints
-    core_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar-core+json; version=0.13.2'}
+    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_projectroles.rst

@@ -23,4 +23,4 @@ in the current SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar-core+json; version=0.13.2
+    Accept: application/vnd.bihealth.sodar-core+json; version=0.13.3

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 = '0.14.0'
+release = '0.14.1'
 
 
 # -- General configuration ---------------------------------------------------

docs_manual/source/sodar_release_notes.rst

@@ -8,6 +8,38 @@ list of changes in current and previous releases, see the
 :ref:`full changelog<sodar_changelog>`.
 
 
+v0.14.1 (2023-12-12)
+====================
+
+Release for minor updates, maintenance and bug fixes.
+
+- Add iRODS v4.3 support
+- Add sheet sync setting validation
+- 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
+
+Migration Guide
+---------------
+
+Default IGV Genome
+    The default IGV genome for cancer and germline projects has been changed
+    from "b37" to "b37_1kg", as the former is no longer supported by new
+    versions of IGV. Existing settings referring the now-unavailble genome will
+    be automatically updated. Users should be advised to upgrade their IGV
+    software to a recent version.
+HPO Term Accession
+    The official API for the Human Phenotype Ontology has changed. It is
+    recommended to set the default URL pattern in the Ontology Access app to
+    ``https://hpo.jax.org/app/browse/term/{id_space}:{local_id}``. Furthermore,
+    ``hpo.jax.org`` should be included in ``SHEETS_ONTOLOGY_URL_SKIP`` as
+    bioontology.org-wrapped URLs to the new API do not work at the time of
+    writing.
+
+
 v0.14.0 (2023-09-27)
 ====================
 

irodsbackend/api.py

@@ -3,14 +3,14 @@
 import logging
 import math
 import os
+import pytz
 import random
 import re
 import string
 import uuid
 
 from contextlib import contextmanager
-
-import pytz
+from packaging import version
 
 from irods.api_number import api_number
 from irods.collection import iRODSCollection
@@ -490,9 +490,37 @@ def get_info(cls, irods):
             'server_host': irods.host,
             'server_port': irods.port,
             'server_zone': irods.zone,
-            'server_version': '.'.join(
-                str(x) for x in irods.pool.get_connection().server_version
-            ),
+            'server_version': cls.get_version(irods),
+        }
+
+    @classmethod
+    def get_version(cls, irods):
+        """
+        Return the version of the iRODS server SODAR is connected to.
+
+        :param irods: iRODSSession object
+        :return: String
+        """
+        return '.'.join(str(x) for x in irods.server_version)
+
+    @classmethod
+    def get_access_lookup(cls, irods):
+        """
+        Return an ACL lookup dict compatible with the currently used iRODS
+        server version (4.2 and 4.3 supported).
+
+        :param irods: iRODSSession object
+        :return: Dict
+        """
+        v = version.parse(cls.get_version(irods))
+        d = '_' if v >= version.parse('4.3') else ' '
+        return {
+            'read': 'read{}object'.format(d),
+            'read{}object'.format(d): 'read',
+            'write': 'modify{}object'.format(d),
+            'modify{}object'.format(d): 'write',
+            'null': 'null',
+            'own': 'own',
         }
 
     def get_object_stats(self, irods, path):

irodsbackend/static/irodsbackend/js/irodsbackend.js

@@ -243,7 +243,7 @@ $(document).ready(function() {
                         'title="Copy iRODS path into clipboard" data-tooltip="tooltip" ' +
                         'data-placement="top" onclick="copyModalPath(\'' + obj['path'] +
                         '\', \'' + elemId + '\')">' +
-                        '<i class="iconify" data-icon="mdi:clipboard-text-multiple"></i>' +
+                        '<i class="iconify" data-icon="mdi:console-line"></i>' +
                         '</button>';
                     var iconHtml = '<i class="iconify mr-1" data-icon="' + icon + '"' +
                         ' title="' + toolTip + '"></i>';

irodsbackend/tests/test_api_taskflow.py

@@ -76,7 +76,21 @@ def test_get_info(self):
         self.assertEqual(info['server_host'], IRODS_HOST)
         self.assertEqual(info['server_port'], IRODS_PORT)
         self.assertEqual(info['server_zone'], IRODS_ZONE)
-        self.assertIsNotNone(info['server_version'])
+        self.assertEqual(
+            info['server_version'],
+            '.'.join(
+                str(x) for x in self.irods.pool.get_connection().server_version
+            ),
+        )
+
+    def test_get_version(self):
+        """Test get_irods_version()"""
+        self.assertEqual(
+            self.irods_backend.get_version(self.irods),
+            '.'.join(
+                str(x) for x in self.irods.pool.get_connection().server_version
+            ),
+        )
 
     def test_get_objects(self):
         """Test get_objects() with files in a sample collection"""

irodsinfo/views.py

@@ -6,6 +6,7 @@
 import zipfile
 
 from irods.exception import NetworkException, CAT_INVALID_AUTHENTICATION
+from packaging import version
 
 from django.conf import settings
 from django.contrib import messages
@@ -43,7 +44,6 @@ def get_irods_client_env(user, irods_backend):
         irods_env = dict(settings.IRODS_ENV_DEFAULT)
         irods_env.update(
             {
-                'irods_authentication_scheme': 'PAM',
                 'irods_cwd': home_path,
                 'irods_home': home_path,
                 'irods_host': settings.IRODS_HOST_FQDN,
@@ -56,6 +56,14 @@ def get_irods_client_env(user, irods_backend):
             irods_env['irods_ssl_certificate_file'] = cert_file_name
         # Get optional client environment overrides
         irods_env.update(dict(settings.IRODS_ENV_CLIENT))
+        # Update authentication scheme with iRODS v4.3+ support
+        with irods_backend.get_session() as irods:
+            irods_version = irods_backend.get_version(irods)
+            if version.parse(irods_version) >= version.parse('4.3'):
+                auth_scheme = 'pam_password'
+            else:
+                auth_scheme = 'PAM'
+            irods_env['irods_authentication_scheme'] = auth_scheme
         irods_env = irods_backend.format_env(irods_env)
         logger.debug('iRODS environment: {}'.format(irods_env))
         return irods_env