feat: upgrade to sodar core v1 (#1973)

[stolpeo]

Summary by CodeRabbit

• New Features

  • Updated PostgreSQL Docker image version to enhance testing environment.
  • Added new targets in the build process for improved clarity in migrations and coverage reporting.
  • Introduced new dependencies for better functionality and compatibility.

• Bug Fixes

  • Improved URL routing by replacing deprecated regex patterns with modern path converters for better readability and maintainability.

• Refactor

  • Standardized base classes for permission testing across various test files to enhance consistency and maintainability.

• Style

  • Improved code formatting and variable declarations for better clarity and maintainability in frontend components.

• Chores

  • Enhanced database migration commands in the Docker entrypoint script for better management of variant summaries during deployment.

[github-actions[bot]]

deps-report 🔍

Commit scanned: 8c43d97 ℹ️ Python version 3.11 is used by your project but the latest version is 3.13.

Vulnerable dependencies

1 dependencies have vulnerabilities 😱

Dependency	Advisory	Versions impacted
sqlalchemy	Sqlalchemy 2.0.0b1 avoids leaking cleartext passwords to the open for careless uses of str(engine.URL()) in logs and prints. https://github.com/sqlalchemy/sqlalchemy/pull/8563	<2.0.0b1

Outdated dependencies

32 outdated dependencies found (including 13 outdated major versions)😢

Dependency	Installed version	Latest version
alabaster (transitive)	0.7.16	1.0.0
aldjemy	2.6	3.2
argon2-cffi (transitive)	21.3.0	23.1.0
django	4.2.19	5.1.6
django-model-utils (transitive)	4.4.0	5.0.0
django-rest-knox (transitive)	4.2.0	5.0.2
packaging (transitive)	23.2	24.2
protobuf	3.20.3	5.29.3
setuptools (transitive)	70.0.0	75.8.2
sphinx (transitive)	7.2.6	8.3.0
sphinx-rtd-theme (transitive)	2.0.0	3.0.2
sqlalchemy	1.4.54	2.0.38
unidecode (transitive)	0.4.21	1.3.8

Dependency	Installed version	Latest version
aiohappyeyeballs (transitive)	2.4.6	2.4.8
botocore (transitive)	1.37.1	1.37.5
celery (transitive)	5.3.6	5.4.0
clinvar-this	0.18.3	0.18.5
crispy-bootstrap4 (transitive)	2024.1	2024.10
django-autocomplete-light (transitive)	3.11.0	3.12.1
django-crispy-forms (transitive)	2.1	2.3
django-environ (transitive)	0.11.2	0.12.0
django-iconify (transitive)	0.3	0.4.1
django-postgres-copy	2.3.7	2.7.6
django-sodar-core	1.0.5	1.1.0
docutils (transitive)	0.20.1	0.21.2
markdown (transitive)	3.5.2	3.7
mistune (transitive)	3.0.2	3.1.2
mypy-protobuf (dev)	3.3.0	3.6.0
pydantic-core (transitive)	2.27.2	2.30.0
requests-http-signature	0.2.0	0.7.1
rules (transitive)	3.3	3.5
wheel (transitive)	0.42.0	0.45.1

_Logs

[holtgrewe]

@coderabbitai full review

[coderabbitai[bot]]

:white_check_mark: Actions performed

Full review triggered.

[coderabbitai[bot]]

Walkthrough

The changes in this pull request involve updates across various files, primarily focusing on modifying test classes to use a new base class for permission testing, updating URL routing definitions to utilize the path() function instead of the deprecated url() function, and enhancing GitHub Actions workflow configurations. Additionally, there are updates to the Makefile for improved clarity in migration commands, adjustments to the Pipfile for dependency versions, and modifications to executor logic in the case import process. The Dockerfile has also been updated to use newer base images for PostgreSQL and Python.

Changes

File	Change Summary
.github/workflows/main.yml	Updated PostgreSQL Docker image from postgres:14 to postgres:16 in Python-Test job; updated Python version from 3.10.15 to 3.11 in Python-Test and Python-Lint jobs; minor indentation adjustments.
backend/Makefile	Renamed _migrate to _makemigrations; added makemigrations target; modified migrate target to run migration command directly; corrected indentation in docs target; added coverage target.
backend/Pipfile	Updated package versions for django-plugins-bihealth, django-sodar-core, djangorestframework, drf-keyed-list-bihealth, django-auth-ldap; changed Python version from 3.10 to 3.11.
backend/beaconsite/tests/test_permissions.py	Changed base class for TestIndexView, TestConsortiumViews, TestSiteViews from TestProjectPermissionBase to ProjectPermissionTestBase.
backend/beaconsite/tests/test_permissions_ajax.py	Changed base class for TestOrganisationAjaxViews, TestBeaconQueryAjaxView from TestProjectAPIPermissionBase to ProjectAPIPermissionTestBase.
backend/beaconsite/tests/test_permissions_api.py	Changed base class for TestBeaconInfoApiView, TestBeaconQueryApiView from TestProjectAPIPermissionBase to ProjectAPIPermissionTestBase.
backend/beaconsite/urls.py	Replaced url() function with path() function for all URL patterns, simplifying regex patterns to use path converters.
backend/cases/tests/test_permissions.py	Changed base class for TestCasesViews from TestProjectPermissionBase to ProjectPermissionTestBase.
backend/cases/tests/test_permissions_ajax.py	Changed base class for multiple test classes from TestProjectAPIPermissionBase to ProjectAPIPermissionTestBase.
backend/cases/tests/test_permissions_api.py	Changed base class for multiple test classes from TestProjectAPIPermissionBase to ProjectAPIPermissionTestBase.
backend/cases/urls.py	Replaced url() function with path() function for all URL patterns, simplifying regex patterns to use path converters.
backend/cohorts/tests/test_permissions_ajax.py	Changed base class for multiple test classes from TestProjectAPIPermissionBase to ProjectAPIPermissionTestBase.
backend/cohorts/tests/test_permissions_api.py	Changed base class for multiple test classes from TestProjectAPIPermissionBase to ProjectAPIPermissionTestBase.
utils/docker/Dockerfile	Updated PostgreSQL client version from postgresql-client-12 to postgresql-client-14; updated Python version from 3.10.15 to 3.11.
backend/cases_import/models/executors.py	Changed keyword argument in _build_fs_options method from "app_name" to "plugin_name".
frontend/src/variants/components/FilterForm/FrequencyPane.vue	Minor formatting adjustment in the template section.
frontend/src/variants/components/FilterForm/GenesRegionsPane.vue	Enhanced conditional rendering logic for genomic region and gene allow list sections; minor adjustments in the template.
frontend/src/variants/components/FilterForm/QualityPane.vue	Removed conditional rendering check for the <table> element, allowing it to render unconditionally.
frontend/src/variants/components/QueryPresets/SetEditor.vue	Changed variable declarations from var to const for better immutability.
frontend/src/variants/components/QueryPresets/SetProperties.vue	Reordered class and type attributes in checkbox input for defaultPresetSetModel.
backend/cohorts/migrations/0008_alter_cohort_user.py	Modified user field in cohort model to allow blank and null values.
backend/varfish/templates/users/login.html	Extended from projectroles/login.html, removing all custom content.

Poem

In the garden of code, we hop and play,
With updates and changes brightening the day.
From PostgreSQL to Vue, we dance with delight,
Each line a new story, each function takes flight.
So let’s celebrate progress, both big and small,
For every little change makes our project stand tall! 🐇✨

---

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[holtgrewe]

@stolpeo just taking the CodeRabbit AI for a test drive here just for fun ;-)

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 92.54237% with 22 lines in your changes missing coverage. Please review.

Project coverage is 91%. Comparing base (5b7f4fd) to head (8c43d97). Report is 26 commits behind head on main.

Files with missing lines	Patch %	Lines
backend/config/settings/base.py	28%	10 Missing :warning:
backend/variants/models/maintenance.py	40%	6 Missing :warning:
...d/variants/migrations/0110_drop_variant_summary.py	82%	4 Missing :warning:
backend/config/urls.py	75%	1 Missing :warning:
...variants/migrations/0111_create_variant_summary.py	90%	1 Missing :warning:

Additional details and impacted files

@@          Coverage Diff           @@
##            main   #2010    +/-   ##
======================================
  Coverage     91%     91%            
======================================
  Files        678     684     +6     
  Lines      38537   38600    +63     
======================================
+ Hits       35140   35297   +157     
+ Misses      3397    3303    -94     

Files with missing lines	Coverage Δ
backend/beaconsite/tests/test_permissions.py	100% <100%> (ø)
backend/beaconsite/tests/test_permissions_ajax.py	100% <100%> (ø)
backend/beaconsite/tests/test_permissions_api.py	100% <100%> (ø)
backend/beaconsite/tests/test_views_ajax.py	50% <100%> (ø)
backend/beaconsite/urls.py	100% <100%> (ø)
backend/cases/tests/test_permissions.py	100% <100%> (ø)
backend/cases/tests/test_permissions_ajax.py	100% <100%> (ø)
backend/cases/tests/test_permissions_api.py	100% <100%> (ø)
backend/cases/tests/test_views.py	100% <100%> (ø)
backend/cases/tests/test_views_ajax.py	100% <100%> (ø)
... and 55 more

... and 2 files with indirect coverage changes