feat: upgrade to sodar core v1 (#1973)

.github/workflows/main.yml

@@ -14,7 +14,7 @@ jobs:
           - 6379:6379
 
       postgres:
-        image: postgres:14
+        image: postgres:16
         env:
           POSTGRES_DB: varfish_web
           POSTGRES_USER: varfish_web
@@ -119,7 +119,7 @@ jobs:
         with:
           # We need to fix the patch version here otherwise, snapshot tests
           # with randomness will / may fail.
-          python-version: "3.10.13"
+          python-version: "3.11"
 
       - name: Install pip and Pipenv
         run: |
@@ -171,7 +171,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Checkout repository
         uses: actions/checkout@v4
@@ -182,7 +182,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install pip and Pipenv
         run: pip install pip pipenv

backend/Makefile

@@ -109,13 +109,16 @@ ci: \
 docs:
 	pipenv run $(MAKE) -C ../docs clean html
 
-.PHONY: _migrate
-_migrate:
+.PHONY: _makemigrations
+_makemigrations:
 	pipenv run $(MANAGE) makemigrations
-	pipenv run $(MANAGE) migrate
+
+.PHONY: makemigrations
+makemigrations: _makemigrations format
 
 .PHONY: migrate
-migrate: _migrate format
+migrate:
+	pipenv run $(MANAGE) migrate
 
 .PHONY: shell
 shell:

backend/Pipfile

@@ -7,20 +7,21 @@ name = "pypi"
 aldjemy = "~=2.2"
 altamisa = "~=0.2.5"
 attrs = "~=24.2"
-beautifulsoup4 = "~=4.9"
+beautifulsoup4 = "~=4.12.3"
 cattrs = "*"
 django = "*"  # whatever django-sodar-core enforces
 django-clone = "*"
 django-cryptographic-fields-bihealth = "~=0.6.0"
 django-debug-toolbar = "*"
 django-extensions = "~=3.2"
 django-postgres-copy = "~=2.3.5"  # there are issues above 2.3
-django-plugins-bihealth = "~=0.4.0"
-django-sodar-core = "~=0.13.4"
+django-plugins-bihealth = "~=0.5.2"
+django-sodar-core = "~=1.0.2"
 django-su = "~=1.0.0"
 djangorestframework-httpsignature = "~=1.0"
+djangorestframework = "~=3.15"
 djproxy = "~=2.3"
-drf-keyed-list-bihealth = "~=0.1.1"
+drf-keyed-list-bihealth = "~=0.2.1"
 httpsig = "~=1.3"
 interval-binning = "~=1.0"
 intervaltree = "~=3.1"
@@ -51,10 +52,10 @@ wrapt = "~=1.16"
 xlsxwriter = "~=3.2"
 django-pydantic-field = "*"
 pydantic = "*"
+typing-extensions="*"
 universal-pathlib = "*"
 s3fs = "*"
 toml = "*"
-black = "*"
 rich = "*"
 drf-writable-nested = "*"
 django-modelcluster = "*"
@@ -96,7 +97,7 @@ django-types = "*"
 [ldap-packages]
 # Dependencies for enabling LDAP support.  You will need the system library
 # named `libldap` (or similar).
-django-auth-ldap = "~=4.1"
+django-auth-ldap = "~=4.6"
 python-ldap = "~=3.4"
 # Packages needed in production.
 
@@ -109,4 +110,4 @@ django-storages = "*"
 django_redis = "*"
 
 [requires]
-python_version = "3.10"
+python_version = "3.11"

backend/beaconsite/tests/test_permissions.py

@@ -1,5 +1,5 @@
 from django.urls import reverse
-from projectroles.tests.test_permissions import TestProjectPermissionBase
+from projectroles.tests.test_permissions import ProjectPermissionTestBase
 
 from beaconsite.tests.factories import ConsortiumFactory, SiteFactory
 
@@ -24,14 +24,14 @@ def setUp(self):
         ]
 
 
-class TestIndexView(UsersMixin, TestProjectPermissionBase):
+class TestIndexView(UsersMixin, ProjectPermissionTestBase):
     def test_index(self):
         url = reverse("beaconsite:index")
         self.assert_response(url, self.good_users, 200)
         self.assert_response(url, self.bad_users, 302)
 
 
-class TestConsortiumViews(UsersMixin, TestProjectPermissionBase):
+class TestConsortiumViews(UsersMixin, ProjectPermissionTestBase):
     def test_list(self):
         url = reverse("beaconsite:consortium-list")
         self.assert_response(url, self.good_users, 200)
@@ -59,7 +59,7 @@ def test_delete(self):
         self.assert_response(url, self.bad_users, 302)
 
 
-class TestSiteViews(UsersMixin, TestProjectPermissionBase):
+class TestSiteViews(UsersMixin, ProjectPermissionTestBase):
     def test_list(self):
         url = reverse("beaconsite:site-list")
         self.assert_response(url, self.good_users, 200)

backend/beaconsite/tests/test_permissions_ajax.py

@@ -1,14 +1,14 @@
 import cattr
 from django.urls import reverse
-from projectroles.tests.test_permissions_api import TestProjectAPIPermissionBase
+from projectroles.tests.test_permissions_api import ProjectAPIPermissionTestBase
 import requests_mock
 
 from ..models import Site
 from ..models_api import BeaconAlleleRequest
 from .factories import SiteFactory
 
 
-class TestOrganisationAjaxViews(TestProjectAPIPermissionBase):
+class TestOrganisationAjaxViews(ProjectAPIPermissionTestBase):
     @requests_mock.Mocker()
     def test_get(self, r_mock):
         _local_site = SiteFactory(role=Site.LOCAL)  # noqa: F841
@@ -57,7 +57,7 @@ def test_get(self, r_mock):
         self.assert_response(url, bad_users, 302, method="GET")  # redirect to login
 
 
-class TestBeaconQueryAjaxView(TestProjectAPIPermissionBase):
+class TestBeaconQueryAjaxView(ProjectAPIPermissionTestBase):
     @requests_mock.Mocker()
     def test_get(self, r_mock):
         _local_site = SiteFactory(role=Site.LOCAL)  # noqa: F841

backend/beaconsite/tests/test_permissions_api.py

@@ -7,7 +7,7 @@
 from django.shortcuts import reverse
 from django.utils import timezone
 import httpsig
-from projectroles.tests.test_permissions_api import TestProjectAPIPermissionBase
+from projectroles.tests.test_permissions_api import ProjectAPIPermissionTestBase
 
 from variants.tests.factories import SmallVariantFactory
 
@@ -42,7 +42,7 @@ def get_accept_header(self, media_type, version):
         return {_header_canonical(k): v for k, v in signed_headers_dict.items()}
 
 
-class TestBeaconInfoApiView(AcceptHeaderMixin, TestProjectAPIPermissionBase):
+class TestBeaconInfoApiView(AcceptHeaderMixin, ProjectAPIPermissionTestBase):
     def setUp(self):
         super().setUp()
         self.consortium = ConsortiumWithLocalAndRemoteSiteFactory()
@@ -110,7 +110,7 @@ def _get_date():
         self.get_date = old_get_date
 
 
-class TestBeaconQueryApiView(AcceptHeaderMixin, TestProjectAPIPermissionBase):
+class TestBeaconQueryApiView(AcceptHeaderMixin, ProjectAPIPermissionTestBase):
     def setUp(self):
         super().setUp()
         self.consortium = ConsortiumWithLocalAndRemoteSiteFactory()

backend/beaconsite/tests/test_views_ajax.py

@@ -2,14 +2,14 @@
 
 from django.urls import reverse
 import jsonmatch
-from projectroles.tests.test_permissions_api import TestProjectAPIPermissionBase
+from projectroles.tests.test_permissions_api import ProjectAPIPermissionTestBase
 import requests_mock
 
 RE_UUID4 = re.compile(r"^[0-9a-f-]+$")
 RE_DATETIME = re.compile(r"^\d\d\d\d-\d\d-\d\dT\d\d:\d\d:\d\dZ$")
 
 
-class TestBeaconInfoAjaxView(TestProjectAPIPermissionBase):
+class TestBeaconInfoAjaxView(ProjectAPIPermissionTestBase):
     """Permission tests for the AJAX views dealing with Organisation."""
 
     def setUp(self):

backend/beaconsite/urls.py

@@ -1,87 +1,87 @@
 """URL configuration for the ``beaconsite`` app.
 """
 
-from django.conf.urls import url
+from django.urls import path
 
 from . import views, views_ajax, views_api
 
 app_name = "beaconsite"
 
 ui_urlpatterns = [
-    url(
-        regex=r"^$",
+    path(
+        route="",
         view=views.IndexView.as_view(),
         name="index",
     ),
-    url(
-        regex=r"^consortium$",
+    path(
+        route="consortium/",
         view=views.ConsortiumListView.as_view(),
         name="consortium-list",
     ),
-    url(
-        regex=r"^consortium/(?P<consortium>[0-9a-f-]+)$",
+    path(
+        route="consortium/<uuid:consortium>/",
         view=views.ConsortiumDetailView.as_view(),
         name="consortium-detail",
     ),
-    url(
-        regex=r"^consortium/create/$",
+    path(
+        route="consortium/create/",
         view=views.ConsortiumCreateView.as_view(),
         name="consortium-create",
     ),
-    url(
-        regex=r"^consortium/update/(?P<consortium>[0-9a-f-]+)$",
+    path(
+        route="consortium/update/<uuid:consortium>/",
         view=views.ConsortiumUpdateView.as_view(),
         name="consortium-update",
     ),
-    url(
-        regex=r"^consortium/delete/(?P<consortium>[0-9a-f-]+)$",
+    path(
+        route="consortium/delete/<uuid:consortium>/",
         view=views.ConsortiumDeleteView.as_view(),
         name="consortium-delete",
     ),
-    url(
-        regex=r"^site$",
+    path(
+        route="site/",
         view=views.SiteListView.as_view(),
         name="site-list",
     ),
-    url(
-        regex=r"^site/(?P<site>[0-9a-f-]+)$",
+    path(
+        route="site/<uuid:site>/",
         view=views.SiteDetailView.as_view(),
         name="site-detail",
     ),
-    url(
-        regex=r"^site/create/$",
+    path(
+        route="site/create/",
         view=views.SiteCreateView.as_view(),
         name="site-create",
     ),
-    url(
-        regex=r"^site/update/(?P<site>[0-9a-f-]+)$",
+    path(
+        route="site/update/<uuid:site>/",
         view=views.SiteUpdateView.as_view(),
         name="site-update",
     ),
-    url(
-        regex=r"^site/delete/(?P<site>[0-9a-f-]+)$",
+    path(
+        route="site/delete/<uuid:site>/",
         view=views.SiteDeleteView.as_view(),
         name="site-delete",
     ),
 ]
 
 ajax_urlpatterns = [
-    url(
-        regex=r"^ajax/beacon/info/(?P<site>[0-9a-f-]+)$",
+    path(
+        route="ajax/beacon/info/<uuid:site>/",
         view=views_ajax.BeaconInfoAjaxView.as_view(),
         name="ajax-beacon-info",
     ),
-    url(
-        regex=r"^ajax/beacon/query/(?P<site>[0-9a-f-]+)$",
+    path(
+        route="ajax/beacon/query/<uuid:site>/",
         view=views_ajax.BeaconQueryAjaxView.as_view(),
         name="ajax-beacon-query",
     ),
 ]
 
 beacon_api_urlpatterns = [
-    url(regex=r"^endpoint/?$", view=views_api.BeaconInfoApiView.as_view(), name="beacon-api-info"),
-    url(
-        regex=r"^endpoint/query/?$",
+    path(route="endpoint", view=views_api.BeaconInfoApiView.as_view(), name="beacon-api-info"),
+    path(
+        route="endpoint/query/",
         view=views_api.BeaconQueryApiView.as_view(),
         name="beacon-api-query",
     ),

backend/cases/tests/test_permissions.py

@@ -1,8 +1,8 @@
 from django.urls import reverse
-from projectroles.tests.test_permissions import TestProjectPermissionBase
+from projectroles.tests.test_permissions import ProjectPermissionTestBase
 
 
-class TestCasesViews(TestProjectPermissionBase):
+class TestCasesViews(ProjectPermissionTestBase):
     """Permission tests for the ``cases`` views"""
 
     def test_entrypoint(self):