upgrade to django-sodar-core v0.13.0 (wip) (#1617)

config/settings/base.py

@@ -53,6 +53,7 @@
 ]
 THIRD_PARTY_APPS = [
     'crispy_forms',  # Form layouts
+    'crispy_bootstrap4',  # Bootstrap4 theme for Crispy
     'rules.apps.AutodiscoverRulesConfig',  # Django rules engine
     'djangoplugins',  # Django plugins
     'pagedown',  # For markdown
@@ -212,6 +213,7 @@
                 'projectroles.context_processors.urls_processor',
                 'projectroles.context_processors.site_app_processor',
                 'projectroles.context_processors.app_alerts_processor',
+                'projectroles.context_processors.sidebar_processor',
             ],
         },
     }
@@ -613,6 +615,10 @@ def set_logging(level=None):
 
 # Projectroles app settings
 PROJECTROLES_SITE_MODE = env.str('PROJECTROLES_SITE_MODE', 'SOURCE')
+PROJECTROLES_TEMPLATE_INCLUDE_PATH = env.path(
+    'PROJECTROLES_TEMPLATE_INCLUDE_PATH',
+    os.path.join(APPS_DIR, 'templates', 'include'),
+)
 PROJECTROLES_SECRET_LENGTH = env.int('PROJECTROLES_SECRET_LENGTH', 32)
 PROJECTROLES_INVITE_EXPIRY_DAYS = env.int('PROJECTROLES_INVITE_EXPIRY_DAYS', 14)
 PROJECTROLES_SEND_EMAIL = env.bool('PROJECTROLES_SEND_EMAIL', False)

irodsadmin/tests/test_commands.py

@@ -10,9 +10,12 @@
 
 # Projectroles dependency
 from projectroles.constants import SODAR_CONSTANTS
-from projectroles.models import Role
 from projectroles.plugins import get_backend_api
-from projectroles.tests.test_models import ProjectMixin, RoleAssignmentMixin
+from projectroles.tests.test_models import (
+    ProjectMixin,
+    RoleMixin,
+    RoleAssignmentMixin,
+)
 
 # Landingzones dependency
 from landingzones.tests.test_models import LandingZoneMixin
@@ -25,6 +28,7 @@
 
 # SODAR constants
 PROJECT_ROLE_OWNER = SODAR_CONSTANTS['PROJECT_ROLE_OWNER']
+PROJECT_TYPE_CATEGORY = SODAR_CONSTANTS['PROJECT_TYPE_CATEGORY']
 PROJECT_TYPE_PROJECT = SODAR_CONSTANTS['PROJECT_TYPE_PROJECT']
 
 # Local constants
@@ -34,10 +38,11 @@
 
 
 class TestIrodsOrphans(
-    ProjectMixin,
     SampleSheetIOMixin,
-    RoleAssignmentMixin,
     LandingZoneMixin,
+    RoleAssignmentMixin,
+    ProjectMixin,
+    RoleMixin,
     TestCase,
 ):
     """Tests for the irodsorphans management command"""
@@ -50,10 +55,13 @@ def setUp(self):
         self.user.is_staff = True
         self.user.save()
         # Init roles
-        self.role_owner = Role.objects.get_or_create(name=PROJECT_ROLE_OWNER)[0]
+        self.init_roles()
+        # Init category with owner
         # Init project with owner
         self.project = self.make_project(
-            'TestProject', PROJECT_TYPE_PROJECT, None
+            'TestProject',
+            PROJECT_TYPE_PROJECT,
+            None,
         )
         self.owner_as = self.make_assignment(
             self.project, self.user, self.role_owner

irodsbackend/tests/test_api.py

@@ -6,8 +6,12 @@
 from test_plus.test import TestCase
 
 # Projectroles dependency
-from projectroles.models import Role, SODAR_CONSTANTS
-from projectroles.tests.test_models import ProjectMixin, RoleAssignmentMixin
+from projectroles.models import SODAR_CONSTANTS
+from projectroles.tests.test_models import (
+    ProjectMixin,
+    RoleMixin,
+    RoleAssignmentMixin,
+)
 
 # Samplesheets dependency
 from samplesheets.tests.test_io import SampleSheetIOMixin, SHEET_DIR
@@ -47,10 +51,11 @@
 
 
 class TestIrodsbackendAPI(
-    ProjectMixin,
-    RoleAssignmentMixin,
     SampleSheetIOMixin,
     LandingZoneMixin,
+    ProjectMixin,
+    RoleMixin,
+    RoleAssignmentMixin,
     TestCase,
 ):
     """Tests for the API in the irodsbackend app"""
@@ -60,27 +65,18 @@ def setUp(self):
         self.user = self.make_user('user')
         self.user.save()
         # Init roles
-        self.role_owner = Role.objects.get_or_create(name=PROJECT_ROLE_OWNER)[0]
-        self.role_delegate = Role.objects.get_or_create(
-            name=PROJECT_ROLE_DELEGATE
-        )[0]
-        self.role_contributor = Role.objects.get_or_create(
-            name=PROJECT_ROLE_CONTRIBUTOR
-        )[0]
-        self.role_guest = Role.objects.get_or_create(name=PROJECT_ROLE_GUEST)[0]
+        self.init_roles()
         # Init project with owner
         self.project = self.make_project(
             'TestProject', PROJECT_TYPE_PROJECT, None
         )
         self.owner_as = self.make_assignment(
             self.project, self.user, self.role_owner
         )
-
         # Import investigation
         self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
         self.study = self.investigation.studies.first()
         self.assay = self.study.assays.first()
-
         # Create LandingZone
         self.landing_zone = self.make_landing_zone(
             title=ZONE_TITLE,
@@ -91,7 +87,6 @@ def setUp(self):
             configuration=None,
             config_data={},
         )
-
         self.irods_backend = IrodsAPI()
 
     def test_format_env(self):
@@ -137,7 +132,7 @@ def test_sanitize_path(self):
             self.assertEqual(ex, ERROR_PATH_PARENT)
 
     def test_get_path_project(self):
-        """Test get_irods_path() with a Project object"""
+        """Test get_irods_path() with Project object"""
         expected = '/{zone}/projects/{uuid_prefix}/{uuid}'.format(
             zone=IRODS_ZONE,
             uuid_prefix=str(self.project.sodar_uuid)[:2],
@@ -148,7 +143,7 @@ def test_get_path_project(self):
 
     @override_settings(IRODS_ROOT_PATH=IRODS_ROOT_PATH)
     def test_get_path_project_root_path(self):
-        """Test get_irods_path() with a Project object and root path"""
+        """Test get_irods_path() with Project object and root path"""
         expected = '/{zone}/projects/{root_path}/{uuid_prefix}/{uuid}'.format(
             zone=IRODS_ZONE,
             root_path=IRODS_ROOT_PATH,
@@ -159,7 +154,7 @@ def test_get_path_project_root_path(self):
         self.assertEqual(expected, path)
 
     def test_get_path_study(self):
-        """Test get_irods_path() with a Study object"""
+        """Test get_irods_path() with Study object"""
         expected = (
             '/{zone}/projects/{uuid_prefix}/{uuid}/{sample_coll}'
             '/{study}'.format(
@@ -174,7 +169,7 @@ def test_get_path_study(self):
         self.assertEqual(expected, path)
 
     def test_get_path_assay(self):
-        """Test get_irods_path() with an Assay object"""
+        """Test get_irods_path() with Assay object"""
         expected = (
             '/{zone}/projects/{uuid_prefix}/{uuid}/{sample_coll}'
             '/{study}/{assay}'.format(
@@ -190,7 +185,7 @@ def test_get_path_assay(self):
         self.assertEqual(expected, path)
 
     def test_get_path_zone(self):
-        """Test get_irods_path() with a LandingZone object"""
+        """Test get_irods_path() with LandingZone object"""
         expected = (
             '/{zone}/projects/{uuid_prefix}/{uuid}/{zone_dir}'
             '/{user}/{study_assay}/{zone_title}'.format(
@@ -209,7 +204,7 @@ def test_get_path_zone(self):
         self.assertEqual(expected, path)
 
     def test_get_sample_path(self):
-        """Test get_sample_path() with a Project object"""
+        """Test get_sample_path() with Project object"""
         expected = '/{zone}/projects/{uuid_prefix}/{uuid}/{sample_coll}'.format(
             zone=IRODS_ZONE,
             uuid_prefix=str(self.project.sodar_uuid)[:2],
@@ -220,7 +215,7 @@ def test_get_sample_path(self):
         self.assertEqual(expected, path)
 
     def test_get_sample_path_no_project(self):
-        """Test get_sample_path() with a wrong type of object (should fail)"""
+        """Test get_sample_path() with wrong object type (should fail)"""
         with self.assertRaises(ValueError):
             self.irods_backend.get_sample_path(self.study)
 
@@ -247,26 +242,26 @@ def test_get_projects_path_with_root_path(self):
         self.assertEqual(self.irods_backend.get_projects_path(), expected)
 
     def test_get_uuid_from_path_assay(self):
-        """Test get_uuid_from_path() with an assay path"""
+        """Test get_uuid_from_path() with assay path"""
         path = self.irods_backend.get_path(self.assay)
         uuid = self.irods_backend.get_uuid_from_path(path, 'assay')
         self.assertEqual(uuid, str(self.assay.sodar_uuid))
 
     def test_get_uuid_from_path_project(self):
-        """Test get_uuid_from_path() for project UUID with an assay path"""
+        """Test get_uuid_from_path() for project UUID with assay path"""
         path = self.irods_backend.get_path(self.assay)
         uuid = self.irods_backend.get_uuid_from_path(path, 'project')
         self.assertEqual(uuid, str(self.project.sodar_uuid))
 
     def test_get_uuid_from_path_wrong_type(self):
-        """Test get_uuid_from_path() with an invalid type (should fail)"""
+        """Test get_uuid_from_path() with invalid type (should fail)"""
         path = self.irods_backend.get_path(self.study)
 
         with self.assertRaises(ValueError):
             self.irods_backend.get_uuid_from_path(path, 'investigation')
 
     def test_get_uuid_from_path_wrong_path(self):
-        """Test get_uuid_from_path() with a path not containing the uuid (should fail)"""
+        """Test get_uuid_from_path() on path without uuid (should fail)"""
         path = self.irods_backend.get_path(self.project)
         uuid = self.irods_backend.get_uuid_from_path(path, 'study')
         self.assertIsNone(uuid)
@@ -279,21 +274,21 @@ def test_get_uuid_from_path_root_path(self):
         self.assertEqual(uuid, str(self.assay.sodar_uuid))
 
     def test_get_user_group_name(self):
-        """Test get_user_group_name() with a Project object"""
+        """Test get_user_group_name() with Project object"""
         self.assertEqual(
             self.irods_backend.get_user_group_name(self.project),
             '{}{}'.format(USER_GROUP_PREFIX, self.project.sodar_uuid),
         )
 
     def test_get_user_group_name_uuid(self):
-        """Test get_user_group_name() with an UUID object"""
+        """Test get_user_group_name() with UUID object"""
         self.assertEqual(
             self.irods_backend.get_user_group_name(self.project.sodar_uuid),
             '{}{}'.format(USER_GROUP_PREFIX, self.project.sodar_uuid),
         )
 
     def test_get_user_group_name_uuid_str(self):
-        """Test get_user_group_name() with an UUID string"""
+        """Test get_user_group_name() with UUID string"""
         self.assertEqual(
             self.irods_backend.get_user_group_name(
                 str(self.project.sodar_uuid)

landingzones/tasks_taskflow.py

@@ -304,7 +304,7 @@ def set_status(cls, zone, flow_name, status, status_info, extra_data=None):
                 set(
                     [
                         r.user
-                        for r in zone.project.get_all_roles()
+                        for r in zone.project.get_roles()
                         if r.user != zone.user
                     ]
                 )

landingzones/tests/test_ui.py

@@ -57,7 +57,6 @@ def _assert_btn_enabled(self, element, expected=True):
     def setUp(self):
         super().setUp()
         # NOTE: Temp inherited owner override, see bihealth/sodar-core#1103
-        self.user_owner_cat = self.make_user('user_owner_cat')
         self.owner_as_cat = RoleAssignment.objects.get(
             project=self.category, role=self.role_owner
         )

requirements/base.txt

@@ -1,33 +1,34 @@
 # Wheel
 # NOTE: For best results wheel should be installed separately before other deps
-wheel==0.38.4
+wheel==0.40.0
 
 # Setuptools
-setuptools==65.6.3
+setuptools==67.6.0
 
 # Django
-django==3.2.19
+django>=3.2.18, <3.3
 
 # Configuration
-django-environ==0.9.0
+django-environ==0.10.0
 
 # Forms
-django-crispy-forms==1.14.0
+django-crispy-forms==2.0
+crispy-bootstrap4==2022.1
 
 # Models
-django-model-utils==4.2.0
+django-model-utils==4.3.1
 
 # Password storage
 argon2-cffi==21.3.0
 
 # Python-PostgreSQL Database Adapter
-psycopg2-binary==2.9.3
+psycopg2-binary==2.9.5
 
 # Unicode slugification
 awesome-slugify==1.6.5
 
 # Time zones support
-pytz==2022.2.1
+pytz==2022.7.1
 
 # Redis support
 redis>=4.5.4, <4.6
@@ -36,13 +37,13 @@ redis>=4.5.4, <4.6
 django-cprofile-middleware==1.0.5
 
 # Versioning
-versioneer==0.23
+versioneer==0.28
 
 # Online documentation via django-docs
-docutils==0.17.1
-Sphinx==5.1.1
-django-docs==0.3.1
-sphinx-rtd-theme==1.0.0
+docutils==0.18.1
+Sphinx==6.1.3
+django-docs==0.3.3
+sphinx-rtd-theme==1.2.0
 sphinxcontrib-youtube==1.2.0
 
 #####################
@@ -53,7 +54,7 @@ sphinxcontrib-youtube==1.2.0
 rules==3.3
 
 # REST framework
-djangorestframework==3.13.1
+djangorestframework==3.14.0
 
 # Keyed list addon for DRF
 # drf-keyed-list==0.0.2
@@ -66,14 +67,14 @@ django-rest-knox==4.2.0
 markdown==3.4.1
 django-markupfield==2.0.1
 django-pagedown==2.2.1
-mistune==2.0.4
+mistune==2.0.5
 
 # Django-plugins (with Django v3.0+ support)
 -e git+https://github.com/mikkonie/django-plugins.git@42e86e7904e5c09f1da32173862b26843eda5dd8#egg=django-plugins
 
 # SODAR Core
-django-sodar-core==0.12.0
-# -e git+https://github.com/bihealth/sodar-core.git@55d46268e5da4ef8a26913ce3b2c584d794d275c#egg=django-sodar-core
+# django-sodar-core==0.12.0
+-e git+https://github.com/bihealth/sodar-core.git@09881c342243e14abcc7c84ee3758d20cf8a41cf#egg=django-sodar-core
 
 # Celery
 celery==5.2.7

requirements/ldap.txt

@@ -2,4 +2,4 @@
 -r base.txt
 
 django-auth-ldap==4.1.0
-python-ldap==3.4.2
+python-ldap==3.4.3

requirements/local.txt

@@ -1,9 +1,9 @@
 # Local development dependencies go here
 -r base.txt
 
-django-extensions==3.2.0
+django-extensions==3.2.1
 Werkzeug==2.2.3
-django-debug-toolbar==3.6.0
+django-debug-toolbar==3.8.1
 
 # improved REPL
-ipdb==0.13.9
+ipdb==0.13.13