upgrade dependencies, reformat with black v24.3 (#1930)

.github/ISSUE_TEMPLATE/release_cleanup.md

@@ -20,6 +20,7 @@ TBA
 - [ ] Review code style and cleanup
 - [ ] Review and update docs entries
 - [ ] Update `SODAR_API_DEFAULT_VERSION` and `SODAR_API_ALLOWED_VERSIONS`
+- [ ] Run `npx update-browserslist-db@latest` for Vue app
 - [ ] Update Vue app version with `npm version`
 - [ ] Update version in CHANGELOG and SODAR Release Notes doc
 - [ ] Update version in docs conf.py

CHANGELOG.rst

@@ -5,6 +5,18 @@ Changelog for the SODAR project. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+Unreleased
+==========
+
+Changed
+-------
+
+- **General**
+    - Upgrade critical Vue app dependencies (#1930)
+    - Upgrade to black v24.3.0 (#1930)
+    - Reformat with black (#1930)
+
+
 v0.14.2 (2024-03-15)
 ====================
 

config/settings/base.py

@@ -375,9 +375,9 @@
     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:
-        AUTH_LDAP_CONNECTION_OPTIONS[
-            ldap.OPT_X_TLS_CACERTFILE
-        ] = AUTH_LDAP_CA_CERT_FILE
+        AUTH_LDAP_CONNECTION_OPTIONS[ldap.OPT_X_TLS_CACERTFILE] = (
+            AUTH_LDAP_CA_CERT_FILE
+        )
         AUTH_LDAP_CONNECTION_OPTIONS[ldap.OPT_X_TLS_NEWCTX] = 0
     AUTH_LDAP_USER_FILTER = env.str(
         'AUTH_LDAP_USER_FILTER', '(sAMAccountName=%(user)s)'
@@ -408,9 +408,9 @@
         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:
-            AUTH_LDAP2_CONNECTION_OPTIONS[
-                ldap.OPT_X_TLS_CACERTFILE
-            ] = AUTH_LDAP2_CA_CERT_FILE
+            AUTH_LDAP2_CONNECTION_OPTIONS[ldap.OPT_X_TLS_CACERTFILE] = (
+                AUTH_LDAP2_CA_CERT_FILE
+            )
             AUTH_LDAP2_CONNECTION_OPTIONS[ldap.OPT_X_TLS_NEWCTX] = 0
         AUTH_LDAP2_USER_FILTER = env.str(
             'AUTH_LDAP2_USER_FILTER', '(sAMAccountName=%(user)s)'

config/wsgi.py

@@ -13,6 +13,7 @@
 framework.
 
 """
+
 import os
 import sys
 

docs_manual/source/conf.py

@@ -26,7 +26,7 @@
 author = 'BIH Core Unit Bioinformatics'
 
 # The full version, including alpha/beta/rc tags
-release = '0.14.2'
+release = '0.14.3-WIP'
 
 
 # -- General configuration ---------------------------------------------------

docs_manual/source/sodar_release_notes.rst

@@ -8,6 +8,16 @@ list of changes in current and previous releases, see the
 :ref:`full changelog<sodar_changelog>`.
 
 
+v0.14.3 (WIP)
+=============
+
+Release for minor updates, maintenance and bug fixes.
+
+- Add Cyberduck documentation
+- Upgrade critical dependencies
+- Minor updates and bug fixes
+
+
 v0.14.2 (2024-03-15)
 ====================
 

irodsbackend/api.py

@@ -82,9 +82,9 @@ def _init_irods(self):
         # Set up additional iRODS environment variables
         irods_env = dict(settings.IRODS_ENV_DEFAULT)
         if settings.IRODS_CERT_PATH:
-            irods_env[
-                'irods_ssl_ca_certificate_file'
-            ] = settings.IRODS_CERT_PATH
+            irods_env['irods_ssl_ca_certificate_file'] = (
+                settings.IRODS_CERT_PATH
+            )
         irods_env.update(dict(settings.IRODS_ENV_BACKEND))
         # HACK: Clean up environment to avoid python-irodsclient crash
         irods_env = self.format_env(irods_env)
@@ -304,9 +304,9 @@ def get_path(cls, obj):
                     user=obj.user.username,
                     study_assay=cls.get_sub_path(obj.assay, landing_zone=True),
                     zone_title=obj.title,
-                    zone_config='_' + obj.configuration
-                    if obj.configuration
-                    else '',
+                    zone_config=(
+                        '_' + obj.configuration if obj.configuration else ''
+                    ),
                 )
             )
         return path

landingzones/forms.py

@@ -67,9 +67,9 @@ def __init__(
         self.fields['assay'].to_field_name = 'sodar_uuid'
         # Set suffix
         self.fields['title_suffix'].label = 'Title suffix'
-        self.fields[
-            'title_suffix'
-        ].help_text = 'Zone title suffix (optional, maximum 64 characters)'
+        self.fields['title_suffix'].help_text = (
+            'Zone title suffix (optional, maximum 64 characters)'
+        )
         self.fields['description'].widget.attrs['rows'] = 4
 
         # Get options for configuration

ontologyaccess/io.py

@@ -122,9 +122,9 @@ def import_obo(cls, obo_doc, name, file, title=None, term_url=None):
                 isinstance(h, fh.PropertyValueClause)
                 and str(h.property_value.relation) in OBO_PROPERTY_MAP
             ):
-                o_kwargs[
-                    OBO_PROPERTY_MAP[str(h.property_value.relation)]
-                ] = h.property_value.value
+                o_kwargs[OBO_PROPERTY_MAP[str(h.property_value.relation)]] = (
+                    h.property_value.value
+                )
 
         if title:  # If manually enforcing a title, set here
             o_kwargs['title'] = title

requirements/test.txt

@@ -18,8 +18,7 @@ selenium==4.8.2
 beautifulsoup4==4.11.2
 
 # Black for formatting
-black==23.1.0
+black==24.3.0
 
 # Coveralls for coverage reporting
 coveralls==3.3.1
-

samplesheets/forms.py

@@ -312,9 +312,9 @@ def __init__(
             field_kwargs = {'label': label}
             # Set field and initial value
             if k == TPL_DIR_FIELD:
-                field_kwargs[
-                    'help_text'
-                ] = 'Investigation directory and assay prefix'
+                field_kwargs['help_text'] = (
+                    'Investigation directory and assay prefix'
+                )
                 self.fields[k] = forms.CharField(**field_kwargs)
                 self.initial[k] = clean_sheet_dir_name(project.title)
             elif isinstance(v, str):

samplesheets/io.py

@@ -312,9 +312,11 @@ def _import_ontology_vals(cls, vals):
         ret = {}
         for v in vals:
             ret[v.name] = {
-                'unit': cls._import_multi_val(v.unit)
-                if hasattr(v, 'unit')
-                else None,
+                'unit': (
+                    cls._import_multi_val(v.unit)
+                    if hasattr(v, 'unit')
+                    else None
+                ),
                 'value': cls._import_multi_val(v.value),
             }
         return ret
@@ -465,12 +467,16 @@ def _import_processes(
                 'performer': p.performer,
                 'perform_date': p.date if p.date else None,
                 'array_design_ref': p.array_design_ref,
-                'first_dimension': cls._import_multi_val(p.first_dimension)
-                if p.first_dimension
-                else {},
-                'second_dimension': cls._import_multi_val(p.second_dimension)
-                if p.second_dimension
-                else {},
+                'first_dimension': (
+                    cls._import_multi_val(p.first_dimension)
+                    if p.first_dimension
+                    else {}
+                ),
+                'second_dimension': (
+                    cls._import_multi_val(p.second_dimension)
+                    if p.second_dimension
+                    else {}
+                ),
                 'headers': p.headers,
                 'comments': cls._import_comments(p.comments),
             }
@@ -827,9 +833,11 @@ def import_isa(
                 tags.append('REPLACE')
             self.save_isa(
                 project=project,
-                inv_uuid=replace_uuid
-                if replace and replace_uuid
-                else db_investigation.sodar_uuid,
+                inv_uuid=(
+                    replace_uuid
+                    if replace and replace_uuid
+                    else db_investigation.sodar_uuid
+                ),
                 isa_data=isa_data,
                 tags=tags,
                 user=user,
@@ -1021,9 +1029,11 @@ def _export_characteristics(cls, characteristics):
         return tuple(
             isa_models.Characteristics(
                 name=k,
-                value=[cls._export_val(v['value'])]
-                if not isinstance(v['value'], list)
-                else cls._export_val(v['value']),
+                value=(
+                    [cls._export_val(v['value'])]
+                    if not isinstance(v['value'], list)
+                    else cls._export_val(v['value'])
+                ),
                 unit=cls._export_val(v['unit']),
             )
             for k, v in characteristics.items()
@@ -1088,9 +1098,11 @@ def _export_param_values(cls, param_values):
         return tuple(
             isa_models.ParameterValue(
                 name=k,
-                value=[cls._export_val(v['value'])]
-                if not isinstance(v['value'], list)
-                else cls._export_val(v['value']),
+                value=(
+                    [cls._export_val(v['value'])]
+                    if not isinstance(v['value'], list)
+                    else cls._export_val(v['value'])
+                ),
                 unit=cls._export_val(v['unit']),
             )
             for k, v in param_values.items()
@@ -1133,21 +1145,29 @@ def _export_materials(cls, materials, study_data=True):
             else:
                 extract_label = cls._export_val(m.extract_label)
             ret[m.unique_name] = isa_models.Material(
-                type=m.material_type
-                if m.material_type
-                else MATERIAL_TYPE_EXPORT_MAP[m.item_type],
+                type=(
+                    m.material_type
+                    if m.material_type
+                    else MATERIAL_TYPE_EXPORT_MAP[m.item_type]
+                ),
                 unique_name=m.unique_name,
                 name=m.name,
                 extract_label=extract_label,
-                characteristics=cls._export_characteristics(m.characteristics)
-                if not sample_in_assay
-                else (),
-                comments=cls._export_comments(m.comments)
-                if not sample_in_assay
-                else (),
-                factor_values=cls._export_factor_vals(m.factor_values)
-                if study_data
-                else tuple(),
+                characteristics=(
+                    cls._export_characteristics(m.characteristics)
+                    if not sample_in_assay
+                    else ()
+                ),
+                comments=(
+                    cls._export_comments(m.comments)
+                    if not sample_in_assay
+                    else ()
+                ),
+                factor_values=(
+                    cls._export_factor_vals(m.factor_values)
+                    if study_data
+                    else tuple()
+                ),
                 material_type=cls._export_val(m.extra_material_type),
                 headers=headers,
             )
@@ -1169,9 +1189,9 @@ def _export_processes(cls, processes):
             else:
                 perform_date = p.perform_date
             ret[p.unique_name] = isa_models.Process(
-                protocol_ref=p.protocol.name
-                if p.protocol
-                else PROTOCOL_UNKNOWN_NAME,
+                protocol_ref=(
+                    p.protocol.name if p.protocol else PROTOCOL_UNKNOWN_NAME
+                ),
                 unique_name=p.unique_name,
                 name=p.name,
                 name_type=p.name_type,

samplesheets/plugins.py

@@ -312,9 +312,11 @@ def get_object_link(self, model_str, uuid):
         if obj.__class__ in [Investigation, Study, Assay]:
             return {
                 'url': obj.get_url(),
-                'label': obj.title
-                if obj.__class__ == Investigation
-                else obj.get_display_name(),
+                'label': (
+                    obj.title
+                    if obj.__class__ == Investigation
+                    else obj.get_display_name()
+                ),
             }
         url_kwargs = {'project': obj.project.sodar_uuid}
         if obj.__class__ == ISATab:
@@ -564,9 +566,9 @@ def validate_form_app_settings(self, app_settings, project=None, user=None):
             if 'sheet_sync_url' not in ret and not re.findall(
                 SYNC_URL_RE, app_settings['sheet_sync_url']
             ):
-                ret[
-                    'sheet_sync_url'
-                ] = 'URL does not point to a sheet sync endpoint'
+                ret['sheet_sync_url'] = (
+                    'URL does not point to a sheet sync endpoint'
+                )
         return ret
 
     # Project Modify API Implementation ----------------------------------------
@@ -770,9 +772,9 @@ def update_cache(self, name=None, project=None, user=None):
                 if assay_plugin:
                     plugin_shortcuts = assay_plugin.get_shortcuts(assay) or []
                     for sc in plugin_shortcuts:
-                        cache_data['shortcuts'][
-                            sc['id']
-                        ] = irods.collections.exists(sc['path'])
+                        cache_data['shortcuts'][sc['id']] = (
+                            irods.collections.exists(sc['path'])
+                        )
                 cache_data['shortcuts']['track_hubs'] = [
                     c.path
                     for c in irods_backend.get_child_colls(
@@ -1037,9 +1039,9 @@ def _update_cache_rows(self, app_name, name=None, project=None, user=None):
                 with irods_backend.get_session() as irods:
                     for path in row_paths:
                         try:
-                            cache_data['paths'][
-                                path
-                            ] = irods_backend.get_object_stats(irods, path)
+                            cache_data['paths'][path] = (
+                                irods_backend.get_object_stats(irods, path)
+                            )
                         except FileNotFoundError:
                             cache_data['paths'][path] = None
                 cache_backend.set_cache_item(
@@ -1183,18 +1185,20 @@ def get_irods_content(inv, study, irods_backend, ret_data):
                     'title': 'Track Hub',
                     'assay_plugin': False,
                     'path': track_hub,
-                    'extra_links': [
-                        {
-                            'url': ticket.get_webdav_link(),
-                            'icon': 'mdi:ticket',
-                            'id': 'ticket_access_%d' % i,
-                            'class': 'sodar-irods-ticket-access-%d-btn' % i,
-                            'title': ' iRODS Access Ticket',
-                            'enabled': ticket.is_active(),
-                        }
-                    ]
-                    if ticket
-                    else [],
+                    'extra_links': (
+                        [
+                            {
+                                'url': ticket.get_webdav_link(),
+                                'icon': 'mdi:ticket',
+                                'id': 'ticket_access_%d' % i,
+                                'class': 'sodar-irods-ticket-access-%d-btn' % i,
+                                'title': ' iRODS Access Ticket',
+                                'enabled': ticket.is_active(),
+                            }
+                        ]
+                        if ticket
+                        else []
+                    ),
                 }
             )
         for i in range(len(a_data['shortcuts'])):