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feat: hemizygote counts not displayed in variant details (#1836) #1860

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stolpeo
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@stolpeo stolpeo commented Aug 2, 2024

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@stolpeo stolpeo linked an issue Aug 2, 2024 that may be closed by this pull request
@stolpeo stolpeo enabled auto-merge (squash) August 2, 2024 13:56
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github-actions bot commented Aug 2, 2024

deps-report 🔍

Commit scanned: 79dcbe1
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

36 outdated dependencies found (including 16 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
billiard (transitive) 3.6.4.0 4.2.0
crispy-bootstrap4 (transitive) 2022.1 2024.1
django 3.2.25 5.0.7
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 2.0.31
unidecode (transitive) 0.4.21 1.3.8
xmlschema (transitive) 2.5.1 3.3.2
Dependency Installed version Latest version
botocore (transitive) 1.34.131 1.34.152
celery (transitive) 5.2.7 5.4.0
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 26.1.0
markdown (transitive) 3.4.1 3.6
requests-http-signature 0.2.0 0.7.1
rules (transitive) 3.3 3.4
versioneer (transitive) 0.28 0.29
wheel (transitive) 0.40.0 0.43.0

Logs

@stolpeo stolpeo changed the title feat: hemizygous count is not displayed in varfish variant detail (#1… feat: hemizygote counts not displayed in variant details (#1836) Aug 2, 2024
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codecov bot commented Aug 2, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91%. Comparing base (44edb7e) to head (c18073c).
Report is 1 commits behind head on main.

Additional details and impacted files
@@          Coverage Diff          @@
##            main   #1860   +/-   ##
=====================================
  Coverage     91%     91%           
=====================================
  Files        653     653           
  Lines      36856   36856           
=====================================
  Hits       33741   33741           
  Misses      3115    3115           

@stolpeo stolpeo force-pushed the 1836-hemizygous-count-is-not-displayed-in-varfish-variant-detail branch from c18073c to 79dcbe1 Compare August 2, 2024 14:13
@stolpeo stolpeo merged commit 066e2f9 into main Aug 2, 2024
16 checks passed
@stolpeo stolpeo deleted the 1836-hemizygous-count-is-not-displayed-in-varfish-variant-detail branch August 2, 2024 14:27
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hemizygous count is not displayed in varfish variant detail
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