From 4aa05d83aaceb8a239d2a6310a5e7b47aa22c296 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Mon, 14 Oct 2024 09:17:43 -0400 Subject: [PATCH] update dcictuils to 8.16.1 for vulnerabilities --- CHANGELOG.rst | 6 + poetry.lock | 387 +++++++++++++------------------------------------ pyproject.toml | 7 +- 3 files changed, 108 insertions(+), 292 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index f80b3c5382..11dfc3acdb 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,12 @@ cgap-portal Change Log ---------- +15.6.0 +======= +* 2024-10-11/dmichaels +* Updated dcicutils version (8.16.1) for vulnerabilities. + + 15.5.0 ====== * Use snovault search modules rather than the local ones (in the src/encoded/search directory). diff --git a/poetry.lock b/poetry.lock index 6fcd92309a..74804ef074 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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system for controlling process state under UNIX" -category = "main" optional = false python-versions = "*" files = [ @@ -4388,7 +4243,6 @@ testing = ["pytest", "pytest-cov"] name = "threadpoolctl" version = "3.5.0" description = "threadpoolctl" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4400,7 +4254,6 @@ files = [ name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" -category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -4412,7 +4265,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4424,7 +4276,6 @@ files = [ name = "tqdm" version = "4.66.4" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4445,7 +4296,6 @@ telegram = ["requests"] name = "transaction" version = "3.1.0" description = "Transaction management for Python" -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" files = [ @@ -4465,7 +4315,6 @@ testing = ["coverage", "mock", "nose"] name = "translationstring" version = "1.3" description = "Utility library for i18n relied on by various Repoze and Pyramid packages" -category = "main" optional = false python-versions = "*" files = [ @@ -4477,7 +4326,6 @@ files = [ name = "types-awscrt" version = "0.21.0" description = "Type annotations and code completion for awscrt" -category = "dev" optional = false python-versions = "<4.0,>=3.7" files = [ @@ -4489,7 +4337,6 @@ files = [ name = "types-python-dateutil" version = "2.9.0.20240316" description = "Typing stubs for python-dateutil" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4501,7 +4348,6 @@ files = [ name = "types-s3transfer" version = "0.10.1" description = "Type annotations and code completion for s3transfer" -category = "dev" optional = false python-versions = "<4.0,>=3.8" files = [ @@ -4513,7 +4359,6 @@ files = [ name = "typing-extensions" version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4525,7 +4370,6 @@ files = [ name = "tzdata" version = "2024.1" description = "Provider of IANA time zone data" -category = "main" optional = false python-versions = ">=2" files = [ @@ -4537,7 +4381,6 @@ files = [ name = "uptime" version = "3.0.1" description = "Cross-platform uptime library" -category = "main" optional = false python-versions = "*" files = [ @@ -4548,7 +4391,6 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4563,7 +4405,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "urllib3" version = "1.26.19" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -4580,7 +4421,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "venusian" version = "3.1.0" description = "A library for deferring decorator actions" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4596,7 +4436,6 @@ testing = ["coverage", "pytest", "pytest-cov"] name = "waitress" version = "2.1.2" description = "Waitress WSGI server" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -4612,7 +4451,6 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] name = "webcolors" version = "24.6.0" description = "A library for working with the color formats defined by HTML and CSS." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4628,7 +4466,6 @@ tests = ["coverage[toml]"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "main" optional = false python-versions = "*" files = [ @@ -4640,7 +4477,6 @@ files = [ name = "webob" version = "1.8.7" description = "WSGI request and response object" -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*" files = [ @@ -4652,28 +4488,10 @@ files = [ docs = ["Sphinx (>=1.7.5)", "pylons-sphinx-themes"] testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] -[[package]] -name = "websocket-client" -version = "1.8.0" -description = "WebSocket client for Python with low level API options" -category = "main" -optional = false -python-versions = ">=3.8" -files = [ - {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"}, - {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"}, -] - -[package.extras] -docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"] -optional = ["python-socks", "wsaccel"] -test = ["websockets"] - [[package]] name = "webtest" version = "2.0.35" description = "Helper to test WSGI applications" -category = "main" optional = false python-versions = "*" files = [ @@ -4695,7 +4513,6 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu name = "werkzeug" version = "2.1.2" description = "The comprehensive WSGI web application library." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4710,7 +4527,6 @@ watchdog = ["watchdog"] name = "wheel" version = "0.43.0" description = "A built-package format for Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -4725,7 +4541,6 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"] name = "wsgiproxy2" version = "0.4.2" description = "UNKNOWN" -category = "main" optional = false python-versions = "*" files = [ @@ -4740,7 +4555,6 @@ webob = "*" name = "xlrd" version = "1.2.0" description = "Library for developers to extract data from Microsoft Excel (tm) spreadsheet files" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -4752,7 +4566,6 @@ files = [ name = "xmltodict" version = "0.13.0" description = "Makes working with XML feel like you are working with JSON" -category = "dev" optional = false python-versions = ">=3.4" files = [ @@ -4764,7 +4577,6 @@ files = [ name = "zipp" version = "3.19.2" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4780,7 +4592,6 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", name = "zope-deprecation" version = "4.4.0" description = "Zope Deprecation Infrastructure" -category = "main" optional = false python-versions = "*" files = [ @@ -4799,7 +4610,6 @@ test = ["zope.testrunner"] name = "zope-interface" version = "5.5.2" description = "Interfaces for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -4853,7 +4663,6 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] name = "zope-sqlalchemy" version = "1.6" description = "Minimal Zope/SQLAlchemy transaction integration" -category = "main" optional = false python-versions = "*" files = [ @@ -4873,4 +4682,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "e065fcaff14870d311045aab9f01f4c055f02e027aa9f9bd577be773483692ce" +content-hash = "e160ce903cf53de7ea5ae1ad2e2a7190bc5765c10d2b01e651be7fdff95047f7" diff --git a/pyproject.toml b/pyproject.toml index 5affa5d1b8..bdd4e263f1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "cgap-portal". name = "encoded" -version = "15.5.0" +version = "15.6.0" description = "Computational Genome Analysis Platform" authors = ["4DN-DCIC Team "] license = "MIT" @@ -49,11 +49,12 @@ codeguru-profiler-agent = "^1.2.4" # At least on Mac M1 if cryptography package is later than 39.x.x (i.e. 40.x.x and up) # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. -cryptography = "39.0.2" +# cryptography = "39.0.2" +cryptography = "^43.0.1" colorama = "0.3.3" dcicpyvcf = "^3.1.0" dcicsnovault = "^11.18.0" -dcicutils = "^8.13.3" +dcicutils = "^8.16.1" elasticsearch = "7.13.4" execnet = "1.4.1" future = ">=0.18.2,<1"