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feat: splitting recessive_parent into recessive_{father,mother} (#1867) #1868

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holtgrewe
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@Gregoor could you review the frontend part that you wrote?

@holtgrewe holtgrewe requested a review from Gregoor August 5, 2024 10:38
@holtgrewe holtgrewe linked an issue Aug 5, 2024 that may be closed by this pull request
@holtgrewe
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@Gregoor afterwards we should merge

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github-actions bot commented Aug 5, 2024

deps-report 🔍

Commit scanned: 5de7f07
ℹ️ Python version 3.10 is used by your project but the latest version is 3.12.

Vulnerable dependencies

5 dependencies have vulnerabilities 😱
Dependency Advisory Versions impacted
djangorestframework (transitive) Affected versions of the package djangorestframework are vulnerable to Cross-site Scripting (XSS) via the break_long_headers template filter due to improper input sanitization before splitting and joining with
tags.
<3.15.2
jinja2 (transitive) In Jinja2, the from_string function is prone to Server Side Template Injection (SSTI) where it takes the "source" parameter as a template object, renders it, and then returns it. The attacker can exploit it with {{INJECTION COMMANDS}} in a URI. NOTE: The maintainer and multiple third parties believe that this vulnerability isn't valid because users shouldn't use untrusted templates without sandboxing. >=0
pyopenssl (transitive) CVE-2023-6129 affects PyOpenSSL versions starting from 22.0.0 due to a vulnerability in the POLY1305 MAC algorithm on PowerPC CPUs. This issue could lead to state corruption in applications, causing inaccurate outcomes or service disruptions. Attackers need specific conditions to exploit this flaw, including the ability to manipulate the algorithm's use and reliance on certain system registers by the application. >=22.0.0
setuptools (transitive) Affected versions of Setuptools allow for remote code execution via its download functions. These functions, which are used to download packages from URLs provided by users or retrieved from package index servers, are susceptible to code injection. If these functions are exposed to user-controlled inputs, such as package URLs, they can execute arbitrary commands on the system. <70.0.0
sqlalchemy Sqlalchemy 2.0.0b1 avoids leaking cleartext passwords to the open for careless uses of str(engine.URL()) in logs and prints. sqlalchemy/sqlalchemy#8563 <2.0.0b1

Outdated dependencies

48 outdated dependencies found (including 17 outdated major versions)😢
Dependency Installed version Latest version
alabaster (transitive) 0.7.16 1.0.0
argon2-cffi (transitive) 21.3.0 23.1.0
attrs 23.2.0 24.2.0
billiard (transitive) 3.6.4.0 4.2.0
crispy-bootstrap4 (transitive) 2022.1 2024.1
django 3.2.25 5.0.8
django-rest-knox (transitive) 4.2.0 5.0.1
django-sodar-core 0.13.4 1.0.0
mistune (transitive) 2.0.5 3.0.2
packaging (transitive) 23.2 24.1
protobuf 3.20.3 5.27.3
setuptools (transitive) 67.6.1 72.1.0
sphinx (transitive) 6.2.1 8.0.2
sphinx-rtd-theme (transitive) 1.2.2 2.0.0
sqlalchemy 1.4.53 2.0.32
unidecode (transitive) 0.4.21 1.3.8
xmlschema (transitive) 2.5.1 3.3.2
Dependency Installed version Latest version
aiohttp (transitive) 3.10.0 3.10.1
black 24.4.2 24.8.0
botocore (transitive) 1.34.131 1.34.155
celery (transitive) 5.2.7 5.4.0
cffi (transitive) 1.16.0 1.17.0
coverage (dev,transitive) 7.6.0 7.6.1
django-autocomplete-light (transitive) 3.9.4 3.11.0
django-crispy-forms (transitive) 2.0 2.3
django-db-file-storage (transitive) 0.5.5 0.5.6.1
django-debug-toolbar 4.3.0 4.4.6
django-environ (transitive) 0.10.0 0.11.2
django-iconify (transitive) 0.1.1 0.4
django-model-utils (transitive) 4.3.1 4.5.1
django-plugins-bihealth 0.4.0 0.5.2
django-postgres-copy 2.3.7 2.7.4
djangorestframework (transitive) 3.14.0 3.15.2
docutils (transitive) 0.18.1 0.21.2
drf-keyed-list-bihealth 0.1.1 0.2.1
faker 26.0.0 26.2.0
flake8 (dev) 7.1.0 7.1.1
kombu (transitive) 5.3.7 5.4.0
markdown (transitive) 3.4.1 3.6
pycodestyle (dev,transitive) 2.12.0 2.12.1
pydantic-core (transitive) 2.20.1 2.21.0
pyyaml 6.0.1 6.0.2
requests-http-signature 0.2.0 0.7.1
rpds-py (transitive) 0.19.1 0.20.0
rules (transitive) 3.3 3.4
trio (dev,transitive) 0.26.0 0.26.1
versioneer (transitive) 0.28 0.29
wheel (transitive) 0.40.0 0.44.0

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codecov bot commented Aug 5, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91%. Comparing base (193b62f) to head (5de7f07).
Report is 5 commits behind head on main.

Additional details and impacted files
@@          Coverage Diff          @@
##            main   #1868   +/-   ##
=====================================
  Coverage     91%     91%           
=====================================
  Files        653     653           
  Lines      36856   36880   +24     
=====================================
+ Hits       33741   33765   +24     
  Misses      3115    3115           
Files Coverage Δ
backend/seqvars/models.py 98% <100%> (+<1%) ⬆️
backend/seqvars/tests/test_models.py 99% <ø> (ø)

... and 1 file with indirect coverage changes

Gregoor
Gregoor previously approved these changes Aug 5, 2024
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@Gregoor Gregoor left a comment

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Looks good to me! I am a bit domain-confused that it is possible to select e.g. two biological fathers, but I suppose that works as intended?

On a UI level I'm now leaning towards replacing the radio group with a dropdown to retain the same filter sidebar width. Wdyt?

@holtgrewe
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Actually, the backend will throw an error for more than one father or mother.

@Gregoor Gregoor merged commit c5fb09b into main Aug 7, 2024
17 checks passed
@Gregoor Gregoor deleted the 1867-split-recessive_parent-into-recessive_fathermother-in-seqvars branch August 7, 2024 10:51
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Split recessive_parent into recessive_{father,mother} in seqvars
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