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feat: upgrade to sodar core v1 (#1973) #2010

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feat: upgrade to sodar core v1 (#1973) #2010

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8 changes: 4 additions & 4 deletions .github/workflows/main.yml
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Expand Up @@ -14,7 +14,7 @@ jobs:
- 6379:6379

postgres:
image: postgres:14
image: postgres:16
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💡 Codebase verification

Update remaining PostgreSQL references to version 16

The PostgreSQL version has been upgraded to 16 in .github/workflows/main.yml, but references to version 14 still exist in the following files:

  • CHANGELOG.md
  • utils/docker/Dockerfile

Please update all PostgreSQL references to ensure consistency and compatibility across the codebase.

🔗 Analysis chain

Verify compatibility with PostgreSQL 16.

The PostgreSQL image has been upgraded from version 14 to 16. This is a major version upgrade that may introduce breaking changes.

Please ensure that:

  1. The application is compatible with PostgreSQL 16.
  2. All database migrations have been tested with the new version.
  3. Performance impact, if any, has been evaluated.

Run the following script to check for any PostgreSQL version-specific code or comments in the codebase:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Search for PostgreSQL version-specific code or comments
rg -i 'postgres(ql)?\s*(9|10|11|12|13|14|15)' --type py

Length of output: 518

Script:

#!/bin/bash
# Search for PostgreSQL version-specific code or comments across all files
rg -i 'postgres(ql)?\s*(9|10|11|12|13|14|15)'

Length of output: 166

env:
POSTGRES_DB: varfish_web
POSTGRES_USER: varfish_web
Expand Down Expand Up @@ -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: |
Expand Down Expand Up @@ -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
Expand All @@ -182,7 +182,7 @@ jobs:
- name: Install Python
uses: actions/setup-python@v5
with:
python-version: "3.10"
python-version: "3.11"
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⚠️ Potential issue

Remove duplicate Python setup step.

This step is a duplicate of the Python setup performed at line 174. To simplify the workflow and improve maintainability, consider removing this redundant step.

Apply this diff to remove the duplicate step:

-      - name: Install Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"

Committable suggestion was skipped due to low confidence.


- name: Install pip and Pipenv
run: pip install pip pipenv
Expand Down
11 changes: 7 additions & 4 deletions backend/Makefile
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Expand Up @@ -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:
Expand Down
15 changes: 8 additions & 7 deletions backend/Pipfile
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Expand Up @@ -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"
Expand Down Expand Up @@ -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 = "*"
Expand Down Expand Up @@ -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.

Expand All @@ -109,4 +110,4 @@ django-storages = "*"
django_redis = "*"

[requires]
python_version = "3.10"
python_version = "3.11"
2,048 changes: 963 additions & 1,085 deletions backend/Pipfile.lock
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8 changes: 4 additions & 4 deletions backend/beaconsite/tests/test_permissions.py
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@@ -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

Expand All @@ -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)
Expand Down Expand Up @@ -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)
Expand Down
6 changes: 3 additions & 3 deletions backend/beaconsite/tests/test_permissions_ajax.py
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@@ -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
Expand Down Expand Up @@ -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
Expand Down
6 changes: 3 additions & 3 deletions backend/beaconsite/tests/test_permissions_api.py
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Expand Up @@ -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

Expand Down Expand Up @@ -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()
Expand Down Expand Up @@ -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()
Expand Down
4 changes: 2 additions & 2 deletions backend/beaconsite/tests/test_views_ajax.py
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Expand Up @@ -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):
Expand Down
60 changes: 30 additions & 30 deletions backend/beaconsite/urls.py
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@@ -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",
),
Expand Down
4 changes: 2 additions & 2 deletions backend/cases/tests/test_permissions.py
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@@ -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):
Expand Down
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