From 59308fac944c1fb574bb27574d190d379906616e Mon Sep 17 00:00:00 2001 From: David Michaels Date: Fri, 11 Oct 2024 10:50:40 -0400 Subject: [PATCH 1/3] update dcictuils to 8.16.1 for vulnerabilities --- CHANGELOG.rst | 6 ++ poetry.lock | 275 +++++++++---------------------------------------- pyproject.toml | 4 +- 3 files changed, 57 insertions(+), 228 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 3b530707e..a4ada9a95 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,6 +7,12 @@ smaht-portal Change Log ---------- +0.104.0 +======= +* dmichaels / 2024-10-11 +* Updated dcicutils version (8.16.1) for vulnerabilities. + + 0.103.0 ======= diff --git a/poetry.lock b/poetry.lock index f3ad74103..cd8f9f332 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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= ">=1.34.147,<2.0.0" chardet = ">=5.2.0,<6.0.0" +cryptography = ">=43.0.1,<44.0.0" docker = ">=7.1.0,<8.0.0" elasticsearch = "7.13.4" gitpython = ">=3.1.2,<4.0.0" @@ -1114,7 +1094,7 @@ jsonschema = ">=4.22.0,<5.0.0" openpyxl = ">=3.1.2,<4.0.0" opensearch-py = ">=2.0.1,<3.0.0" PyJWT = ">=2.6.0,<3.0.0" -pyOpenSSL = ">=23.1.1,<24.0.0" +pyopenssl = ">=24.2.1,<25.0.0" pyperclip = ">=1.8.2,<2.0.0" pyramid = "1.10.8" pytz = ">=2020.4" @@ -1134,7 +1114,6 @@ webtest = ">=2.0.34,<3.0.0" name = "docker" version = "7.1.0" description = "A Python library for the Docker Engine API." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1157,7 +1136,6 @@ websockets = ["websocket-client (>=1.3.0)"] name = "docopt" version = "0.6.2" description = "Pythonic argument parser, that will make you smile" -category = "dev" optional = false python-versions = "*" files = [ @@ -1168,7 +1146,6 @@ files = [ name = "docutils" version = "0.21.2" description = "Docutils -- Python Documentation Utilities" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -1180,7 +1157,6 @@ files = [ name = "elasticsearch" version = "7.13.4" description = "Python client for Elasticsearch" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4" files = [ @@ -1202,7 +1178,6 @@ requests = ["requests (>=2.4.0,<3.0.0)"] name = "elasticsearch-dsl" version = "7.4.1" description = "Python client for Elasticsearch" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1222,7 +1197,6 @@ develop = ["coverage (<5.0.0)", "mock", "pytest (>=3.0.0)", "pytest-cov", "pytes name = "encoded-core" version = "0.9.6" description = "Core data models for Park Lab ENCODE based projects" -category = "main" optional = false python-versions = "<3.13,>=3.9.0" files = [ @@ -1270,7 +1244,6 @@ WSGIProxy2 = "0.4.2" name = "et-xmlfile" version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1282,7 +1255,6 @@ files = [ name = "events" version = "0.5" description = "Bringing the elegance of C# EventHandler to Python" -category = "main" optional = false python-versions = "*" files = [ @@ -1293,7 +1265,6 @@ files = [ name = "exceptiongroup" version = "1.2.2" description = "Backport of PEP 654 (exception groups)" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1308,7 +1279,6 @@ test = ["pytest (>=6)"] name = "execnet" version = "1.4.1" description = "execnet: rapid multi-Python deployment" -category = "main" optional = false python-versions = "*" files = [ @@ -1323,7 +1293,6 @@ apipkg = ">=1.4" name = "fakeredis" version = "2.23.3" description = "Python implementation of redis API, can be used for testing purposes." -category = "dev" optional = false python-versions = "<4.0,>=3.7" files = [ @@ -1347,7 +1316,6 @@ probabilistic = ["pyprobables (>=0.6,<0.7)"] name = "flake8" version = "7.1.0" description = "the modular source code checker: pep8 pyflakes and co" -category = "dev" optional = false python-versions = ">=3.8.1" files = [ @@ -1364,7 +1332,6 @@ pyflakes = ">=3.2.0,<3.3.0" name = "flaky" version = "3.8.1" description = "Plugin for pytest that automatically reruns flaky tests." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1376,7 +1343,6 @@ files = [ name = "fqdn" version = "1.5.1" description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" -category = "main" optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" files = [ @@ -1388,7 +1354,6 @@ files = [ name = "future" version = "0.18.3" description = "Clean single-source support for Python 3 and 2" -category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1399,7 +1364,6 @@ files = [ name = "gitdb" version = "4.0.11" description = "Git Object Database" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1414,7 +1378,6 @@ smmap = ">=3.0.1,<6" name = "gitpython" version = "3.1.43" description = "GitPython is a Python library used to interact with Git repositories" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1433,7 +1396,6 @@ test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", name = "google" version = "3.0.0" description = "Python bindings to the Google search engine." -category = "main" optional = false python-versions = "*" files = [ @@ -1448,7 +1410,6 @@ beautifulsoup4 = "*" name = "google-api-core" version = "2.19.1" description = "Google API client core library" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1472,7 +1433,6 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] name = "google-api-python-client" version = "2.138.0" description = "Google API Client Library for Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1481,7 +1441,7 @@ files = [ ] [package.dependencies] -google-api-core = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0.dev0" +google-api-core = ">=1.31.5,<2.0.dev0 || >2.3.0,<3.0.0.dev0" google-auth = ">=1.32.0,<2.24.0 || >2.24.0,<2.25.0 || >2.25.0,<3.0.0.dev0" google-auth-httplib2 = ">=0.2.0,<1.0.0" httplib2 = ">=0.19.0,<1.dev0" @@ -1491,7 +1451,6 @@ uritemplate = ">=3.0.1,<5" name = "google-auth" version = "2.32.0" description = "Google Authentication Library" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1515,7 +1474,6 @@ requests = ["requests (>=2.20.0,<3.0.0.dev0)"] name = "google-auth-httplib2" version = "0.2.0" description = "Google Authentication Library: httplib2 transport" -category = "main" optional = false python-versions = "*" files = [ @@ -1531,7 +1489,6 @@ httplib2 = ">=0.19.0" name = "google-auth-oauthlib" version = "1.2.1" description = "Google Authentication Library" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1550,7 +1507,6 @@ tool = ["click (>=6.0.0)"] name = "google-pasta" version = "0.2.0" description = "pasta is an AST-based Python refactoring library" -category = "main" optional = false python-versions = "*" files = [ @@ -1566,7 +1522,6 @@ six = "*" name = "googleapi" version = "0.1.0" description = "A high-level python interface to Google APIs" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1590,7 +1545,6 @@ oauthlib = ">=3.0.1" name = "googleapis-common-protos" version = "1.63.2" description = "Common protobufs used in Google APIs" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1608,7 +1562,6 @@ grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"] name = "greenlet" version = "3.0.3" description = "Lightweight in-process concurrent programming" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1680,7 +1633,6 @@ test = ["objgraph", "psutil"] name = "html5lib" version = "1.1" description = "HTML parser based on the WHATWG HTML specification" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1702,7 +1654,6 @@ lxml = ["lxml"] name = "httplib2" version = "0.22.0" description = "A comprehensive HTTP client library." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1717,7 +1668,6 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0 name = "humanfriendly" version = "1.44.9" description = "Human friendly output for text interfaces using Python" -category = "main" optional = false python-versions = "*" files = [ @@ -1729,7 +1679,6 @@ files = [ name = "hupper" version = "1.12.1" description = "Integrated process monitor for developing and reloading daemons." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1745,7 +1694,6 @@ testing = ["mock", "pytest", "pytest-cov", "watchdog"] name = "idna" version = "2.10" description = "Internationalized Domain Names in Applications (IDNA)" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1757,7 +1705,6 @@ files = [ name = "importlib-metadata" version = "8.2.0" description = "Read metadata from Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1777,7 +1724,6 @@ test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "p name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1789,7 +1735,6 @@ files = [ name = "isodate" version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" -category = "main" optional = false python-versions = "*" files = [ @@ -1804,7 +1749,6 @@ six = "*" name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1819,7 +1763,6 @@ arrow = ">=0.15.0" name = "jmespath" version = "0.9.0" description = "JSON Matching Expressions" -category = "main" optional = false python-versions = "*" files = [ @@ -1831,7 +1774,6 @@ files = [ name = "joblib" version = "1.4.2" description = "Lightweight pipelining with Python functions" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1843,7 +1785,6 @@ files = [ name = "jsonc-parser" version = "1.1.5" description = "A lightweight, native tool for parsing .jsonc files" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -1855,7 +1796,6 @@ files = [ name = "jsonpointer" version = "3.0.0" description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1867,7 +1807,6 @@ files = [ name = "jsonschema" version = "4.23.0" description = "An implementation of JSON Schema validation for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1897,7 +1836,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.12.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1912,7 +1850,6 @@ referencing = ">=0.31.0" name = "loremipsum" version = "1.0.5" description = "A Lorem Ipsum text generator" -category = "main" optional = false python-versions = "*" files = [ @@ -1924,7 +1861,6 @@ files = [ name = "markdown" version = "3.6" description = "Python implementation of John Gruber's Markdown." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1943,7 +1879,6 @@ testing = ["coverage", "pyyaml"] name = "mccabe" version = "0.7.0" description = "McCabe checker, plugin for flake8" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1955,7 +1890,6 @@ files = [ name = "netaddr" version = "0.10.1" description = "A network address manipulation library for Python" -category = "main" optional = false python-versions = "*" files = [ @@ -1967,7 +1901,6 @@ files = [ name = "numpy" version = "1.26.4" description = "Fundamental package for array computing in Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2013,7 +1946,6 @@ files = [ name = "oauth2client" version = "4.1.3" description = "OAuth 2.0 client library" -category = "main" optional = false python-versions = "*" files = [ @@ -2032,7 +1964,6 @@ six = ">=1.6.1" name = "oauthlib" version = "3.2.2" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2049,7 +1980,6 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"] name = "openpyxl" version = "3.1.5" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2064,7 +1994,6 @@ et-xmlfile = "*" name = "opensearch-py" version = "2.6.0" description = "Python client for OpenSearch" -category = "main" optional = false python-versions = "<4,>=3.8" files = [ @@ -2093,7 +2022,6 @@ kerberos = ["requests-kerberos"] name = "packaging" version = "24.1" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2105,7 +2033,6 @@ files = [ name = "pandas" version = "2.2.2" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2179,7 +2106,6 @@ xml = ["lxml (>=4.9.2)"] name = "passlib" version = "1.7.4" description = "comprehensive password hashing framework supporting over 30 schemes" -category = "main" optional = false python-versions = "*" files = [ @@ -2197,7 +2123,6 @@ totp = ["cryptography"] name = "pastedeploy" version = "3.1.0" description = "Load, configure, and compose WSGI applications and servers" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2214,7 +2139,6 @@ testing = ["Paste", "pytest", "pytest-cov"] name = "patsy" version = "0.5.6" description = "A Python package for describing statistical models and for building design matrices." -category = "main" optional = false python-versions = "*" files = [ @@ -2233,7 +2157,6 @@ test = ["pytest", "pytest-cov", "scipy"] name = "pbkdf2" version = "1.3" description = "PKCS#5 v2.0 PBKDF2 Module" -category = "main" optional = false python-versions = "*" files = [ @@ -2244,7 +2167,6 @@ files = [ name = "pillow" version = "9.5.0" description = "Python Imaging Library (Fork)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2324,7 +2246,6 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa name = "pip" version = "24.1.2" description = "The PyPA recommended tool for installing Python packages." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2336,7 +2257,6 @@ files = [ name = "pip-licenses" version = "3.5.5" description = "Dump the software license list of Python packages installed with pip." -category = "dev" optional = false python-versions = "~=3.7" files = [ @@ -2354,7 +2274,6 @@ test = ["docutils", "pytest-cov", "pytest-pycodestyle", "pytest-runner"] name = "pipdeptree" version = "2.23.1" description = "Command line utility to show dependency tree of packages." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2374,7 +2293,6 @@ test = ["covdefaults (>=2.3)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pyte name = "plaster" version = "1.0" description = "A loader interface around multiple config file formats." -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2393,7 +2311,6 @@ testing = ["pytest", "pytest-cov"] name = "plaster-pastedeploy" version = "0.6" description = "A loader implementing the PasteDeploy syntax to be used by plaster." -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2412,7 +2329,6 @@ testing = ["pytest", "pytest-cov"] name = "pluggy" version = "1.5.0" description = "plugin and hook calling mechanisms for python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2428,7 +2344,6 @@ testing = ["pytest", "pytest-benchmark"] name = "pmdarima" version = "2.0.4" description = "Python's forecast::auto.arima equivalent" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2480,7 +2395,6 @@ urllib3 = "*" name = "proto-plus" version = "1.24.0" description = "Beautiful, Pythonic protocol buffers." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2498,7 +2412,6 @@ testing = ["google-api-core (>=1.31.5)"] name = "protobuf" version = "5.27.2" description = "" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2519,7 +2432,6 @@ files = [ name = "psutil" version = "5.9.8" description = "Cross-platform lib for process and system monitoring in Python." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -2548,7 +2460,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "psycopg2-binary" version = "2.9.9" description = "psycopg2 - Python-PostgreSQL Database Adapter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2630,7 +2541,6 @@ files = [ name = "ptable" version = "0.9.2" description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format" -category = "dev" optional = false python-versions = "*" files = [ @@ -2641,7 +2551,6 @@ files = [ name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2653,7 +2562,6 @@ files = [ name = "pyasn1" version = "0.6.0" description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2665,7 +2573,6 @@ files = [ name = "pyasn1-modules" version = "0.4.0" description = "A collection of ASN.1-based protocols modules" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2680,7 +2587,6 @@ pyasn1 = ">=0.4.6,<0.7.0" name = "pybrowserid" version = "0.14.0" description = "Python library for the BrowserID Protocol" -category = "main" optional = false python-versions = "*" files = [ @@ -2695,7 +2601,6 @@ requests = "*" name = "pycodestyle" version = "2.12.0" description = "Python style guide checker" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2707,7 +2612,6 @@ files = [ name = "pycparser" version = "2.18" description = "C parser in Python" -category = "main" optional = false python-versions = "*" files = [ @@ -2718,7 +2622,6 @@ files = [ name = "pyflakes" version = "3.2.0" description = "passive checker of Python programs" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2730,7 +2633,6 @@ files = [ name = "pygments" version = "2.18.0" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2745,7 +2647,6 @@ windows-terminal = ["colorama (>=0.4.6)"] name = "pyjwt" version = "2.8.0" description = "JSON Web Token implementation in Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2761,28 +2662,26 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"] [[package]] name = "pyopenssl" -version = "23.3.0" +version = "24.2.1" description = "Python wrapper module around the OpenSSL library" -category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "pyOpenSSL-23.3.0-py3-none-any.whl", hash = "sha256:6756834481d9ed5470f4a9393455154bc92fe7a64b7bc6ee2c804e78c52099b2"}, - {file = "pyOpenSSL-23.3.0.tar.gz", hash = "sha256:6b2cba5cc46e822750ec3e5a81ee12819850b11303630d575e98108a079c2b12"}, + {file = "pyOpenSSL-24.2.1-py3-none-any.whl", hash = "sha256:967d5719b12b243588573f39b0c677637145c7a1ffedcd495a487e58177fbb8d"}, + {file = "pyopenssl-24.2.1.tar.gz", hash = "sha256:4247f0dbe3748d560dcbb2ff3ea01af0f9a1a001ef5f7c4c647956ed8cbf0e95"}, ] [package.dependencies] -cryptography = ">=41.0.5,<42" +cryptography = ">=41.0.5,<44" [package.extras] docs = ["sphinx (!=5.2.0,!=5.2.0.post0,!=7.2.5)", "sphinx-rtd-theme"] -test = ["flaky", "pretend", "pytest (>=3.0.1)"] +test = ["pretend", "pytest (>=3.0.1)", "pytest-rerunfailures"] [[package]] name = "pyparsing" version = "3.1.2" description = "pyparsing module - Classes and methods to define and execute parsing grammars" -category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -2797,7 +2696,6 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pyperclip" version = "1.9.0" description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)" -category = "main" optional = false python-versions = "*" files = [ @@ -2808,7 +2706,6 @@ files = [ name = "pyramid" version = "1.10.8" description = "The Pyramid Web Framework, a Pylons project" -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2835,7 +2732,6 @@ testing = ["coverage", "nose", "virtualenv", "webtest (>=1.3.1)", "zope.componen name = "pyramid-localroles" version = "0.1" description = "Local roles authorization policy for Pyramid" -category = "main" optional = false python-versions = "*" files = [ @@ -2849,7 +2745,6 @@ pyramid = "*" name = "pyramid-multiauth" version = "0.9.0" description = "pyramid_multiauth" -category = "main" optional = false python-versions = "*" files = [ @@ -2864,7 +2759,6 @@ pyramid = "*" name = "pyramid-retry" version = "1.0" description = "An execution policy for Pyramid that supports retrying requests after certain failure exceptions." -category = "main" optional = false python-versions = "*" files = [ @@ -2884,7 +2778,6 @@ testing = ["WebTest", "pytest", "pytest-cov"] name = "pyramid-tm" version = "2.5" description = "A package which allows Pyramid requests to join the active transaction" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2904,7 +2797,6 @@ testing = ["WebTest", "coverage (>=5.0)", "pytest", "pytest-cov"] name = "pyramid-translogger" version = "0.1" description = "access log logger tween (almost stolen from Paste.translogger)" -category = "main" optional = false python-versions = "*" files = [ @@ -2918,7 +2810,6 @@ setuptools = "*" name = "pytest" version = "7.4.4" description = "pytest: simple powerful testing with Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2941,7 +2832,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-cov" version = "5.0.0" description = "Pytest plugin for measuring coverage." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2960,7 +2850,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"] name = "pytest-instafail" version = "0.5.0" description = "pytest plugin to show failures instantly" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2975,7 +2864,6 @@ pytest = ">=5" name = "pytest-mock" version = "3.14.0" description = "Thin-wrapper around the mock package for easier use with pytest" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2993,7 +2881,6 @@ dev = ["pre-commit", "pytest-asyncio", "tox"] name = "pytest-timeout" version = "2.3.1" description = "pytest plugin to abort hanging tests" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3008,7 +2895,6 @@ pytest = ">=7.0.0" name = "pytest-xdist" version = "3.5.0" description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3029,7 +2915,6 @@ testing = ["filelock"] name = "python-dateutil" version = "2.9.0.post0" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -3044,7 +2929,6 @@ six = ">=1.5" name = "python-magic" version = "0.4.27" description = "File type identification using libmagic" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3056,7 +2940,6 @@ files = [ name = "pytz" version = "2024.1" description = "World timezone definitions, modern and historical" -category = "main" optional = false python-versions = "*" files = [ @@ -3068,7 +2951,6 @@ files = [ name = "pywin32" version = "307" description = "Python for Window Extensions" -category = "main" optional = false python-versions = "*" files = [ @@ -3096,7 +2978,6 @@ files = [ name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3157,7 +3038,6 @@ files = [ name = "rdflib" version = "4.2.2" description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information." -category = "main" optional = false python-versions = "*" files = [ @@ -3177,7 +3057,6 @@ sparql = ["SPARQLWrapper"] name = "rdflib-jsonld" version = "0.6.0" description = "rdflib extension adding JSON-LD parser and serializer" -category = "main" optional = false python-versions = "*" files = [ @@ -3192,7 +3071,6 @@ rdflib = "*" name = "redis" version = "4.6.0" description = "Python client for Redis database and key-value store" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3211,7 +3089,6 @@ ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)" name = "referencing" version = "0.35.1" description = "JSON Referencing + Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3227,7 +3104,6 @@ rpds-py = ">=0.7.0" name = "repoze-debug" version = "1.1" description = "Forensic debugging WSGI middleware" -category = "main" optional = false python-versions = "*" files = [ @@ -3246,7 +3122,6 @@ testing = ["WebOb", "coverage", "nose"] name = "requests" version = "2.31.0" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3268,7 +3143,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "requests-oauthlib" version = "2.0.0" description = "OAuthlib authentication support for Requests." -category = "main" optional = false python-versions = ">=3.4" files = [ @@ -3287,7 +3161,6 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"] name = "rfc3339-validator" version = "0.1.4" description = "A pure python RFC3339 validator" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3302,7 +3175,6 @@ six = "*" name = "rfc3986" version = "1.5.0" description = "Validating URI References per RFC 3986" -category = "main" optional = false python-versions = "*" files = [ @@ -3317,7 +3189,6 @@ idna2008 = ["idna"] name = "rfc3986-validator" version = "0.1.1" description = "Pure python rfc3986 validator" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3329,7 +3200,6 @@ files = [ name = "rpds-py" version = "0.19.1" description = "Python bindings to Rust's persistent data structures (rpds)" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3442,7 +3312,6 @@ files = [ name = "rsa" version = "3.3" description = "Pure-Python RSA implementation" -category = "main" optional = false python-versions = "*" files = [ @@ -3457,7 +3326,6 @@ pyasn1 = ">=0.1.3" name = "rutter" version = "0.4" description = "Py3k-compatible fork of Paste's urlmap" -category = "main" optional = false python-versions = "*" files = [ @@ -3475,7 +3343,6 @@ testing = ["WebTest", "coverage", "pytest", "pytest-cov"] name = "s3transfer" version = "0.10.2" description = "An Amazon S3 Transfer Manager" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3493,7 +3360,6 @@ crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"] name = "scikit-learn" version = "1.5.1" description = "A set of python modules for machine learning and data mining" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3539,7 +3405,6 @@ tests = ["black (>=24.3.0)", "matplotlib (>=3.3.4)", "mypy (>=1.9)", "numpydoc ( name = "scipy" version = "1.13.1" description = "Fundamental algorithms for scientific computing in Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3582,7 +3447,6 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po name = "sentry-sdk" version = "1.45.1" description = "Python client for Sentry (https://sentry.io)" -category = "main" optional = false python-versions = "*" files = [ @@ -3630,7 +3494,6 @@ tornado = ["tornado (>=5)"] name = "setuptools" version = "71.1.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3641,13 +3504,12 @@ files = [ [package.extras] core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"] -test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (>=1.11.0,<1.12.0)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] [[package]] name = "shortuuid" version = "1.0.13" description = "A generator library for concise, unambiguous and URL-safe UUIDs." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3659,7 +3521,6 @@ files = [ name = "simplejson" version = "3.19.2" description = "Simple, fast, extensible JSON encoder/decoder for Python" -category = "main" optional = false python-versions = ">=2.5, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3767,7 +3628,6 @@ files = [ name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3779,7 +3639,6 @@ files = [ name = "smmap" version = "5.0.1" description = "A pure Python implementation of a sliding window memory map manager" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3791,7 +3650,6 @@ files = [ name = "sortedcontainers" version = "2.4.0" description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" -category = "dev" optional = false python-versions = "*" files = [ @@ -3803,7 +3661,6 @@ files = [ name = "soupsieve" version = "2.5" description = "A modern CSS selector implementation for Beautiful Soup." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3815,7 +3672,6 @@ files = [ name = "sparqlwrapper" version = "1.8.5" description = "SPARQL Endpoint interface to Python" -category = "main" optional = false python-versions = "*" files = [ @@ -3834,7 +3690,6 @@ keepalive = ["keepalive (>=0.5)"] name = "sqlalchemy" version = "1.4.41" description = "Database Abstraction Library" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -3882,7 +3737,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and platform_machine == \"aarch64\" or python_version >= \"3\" and platform_machine == \"ppc64le\" or python_version >= \"3\" and platform_machine == \"x86_64\" or python_version >= \"3\" and platform_machine == \"amd64\" or python_version >= \"3\" and platform_machine == \"AMD64\" or python_version >= \"3\" and platform_machine == \"win32\" or python_version >= \"3\" and platform_machine == \"WIN32\""} +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} [package.extras] aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] @@ -3909,7 +3764,6 @@ sqlcipher = ["sqlcipher3-binary"] name = "statsmodels" version = "0.14.2" description = "Statistical computations and models for Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3955,7 +3809,6 @@ docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "n name = "structlog" version = "19.2.0" description = "Structured Logging for Python" -category = "main" optional = false python-versions = "*" files = [ @@ -3976,7 +3829,6 @@ tests = ["coverage", "freezegun (>=0.2.8)", "pretend", "pytest (>=3.3.0)", "pyth name = "subprocess-middleware" version = "0.3" description = "Subprocess WSGI middleware and Pyramid tween." -category = "main" optional = false python-versions = "*" files = [ @@ -3993,7 +3845,6 @@ test = ["WebTest", "pyramid", "pytest"] name = "supervisor" version = "4.2.5" description = "A system for controlling process state under UNIX" -category = "main" optional = false python-versions = "*" files = [ @@ -4011,7 +3862,6 @@ testing = ["pytest", "pytest-cov"] name = "threadpoolctl" version = "3.5.0" description = "threadpoolctl" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4023,7 +3873,6 @@ 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 = [ @@ -4035,7 +3884,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4047,7 +3895,6 @@ files = [ name = "tqdm" version = "4.66.4" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4068,7 +3915,6 @@ 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 = [ @@ -4088,7 +3934,6 @@ 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 = [ @@ -4100,7 +3945,6 @@ files = [ name = "types-awscrt" version = "0.21.2" description = "Type annotations and code completion for awscrt" -category = "dev" optional = false python-versions = "<4.0,>=3.7" files = [ @@ -4112,7 +3956,6 @@ 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 = [ @@ -4124,7 +3967,6 @@ 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 = [ @@ -4136,7 +3978,6 @@ 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 = [ @@ -4148,7 +3989,6 @@ files = [ name = "tzdata" version = "2024.1" description = "Provider of IANA time zone data" -category = "main" optional = false python-versions = ">=2" files = [ @@ -4160,7 +4000,6 @@ files = [ name = "uptime" version = "3.0.1" description = "Cross-platform uptime library" -category = "main" optional = false python-versions = "*" files = [ @@ -4171,7 +4010,6 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4186,7 +4024,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "uritemplate" version = "4.1.1" description = "Implementation of RFC 6570 URI Templates" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -4198,7 +4035,6 @@ files = [ 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 = [ @@ -4215,7 +4051,6 @@ 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 = [ @@ -4231,7 +4066,6 @@ 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 = [ @@ -4247,7 +4081,6 @@ 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 = [ @@ -4263,7 +4096,6 @@ tests = ["coverage[toml]"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "main" optional = false python-versions = "*" files = [ @@ -4275,7 +4107,6 @@ 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 = [ @@ -4291,7 +4122,6 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] name = "webtest" version = "2.0.35" description = "Helper to test WSGI applications" -category = "main" optional = false python-versions = "*" files = [ @@ -4313,7 +4143,6 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu name = "wheel" version = "0.43.0" description = "A built-package format for Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -4328,7 +4157,6 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"] name = "wsgiproxy2" version = "0.4.2" description = "UNKNOWN" -category = "main" optional = false python-versions = "*" files = [ @@ -4343,7 +4171,6 @@ 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 = [ @@ -4355,7 +4182,6 @@ 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 = [ @@ -4371,7 +4197,6 @@ 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 = [ @@ -4390,7 +4215,6 @@ test = ["zope.testrunner"] name = "zope-interface" version = "4.7.2" description = "Interfaces for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -4447,7 +4271,6 @@ testing = ["coverage", "nose", "zope.event"] name = "zope-sqlalchemy" version = "1.6" description = "Minimal Zope/SQLAlchemy transaction integration" -category = "main" optional = false python-versions = "*" files = [ @@ -4467,4 +4290,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9.1,<3.13" -content-hash = "f6bb54437e66b59eced8bd57b5aedefe5d3a9dd2b4ed335691b706741c23e356" +content-hash = "6a94b6d9a0aa928861fb978ad2855f4df2f11de8e3c075b053b33c12b7a474cf" diff --git a/pyproject.toml b/pyproject.toml index e15d9b274..5ab3cac79 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "encoded" -version = "0.103.0" +version = "0.104.0" description = "SMaHT Data Analysis Portal" authors = ["4DN-DCIC Team "] license = "MIT" @@ -45,7 +45,7 @@ chardet = "^5.0.0" codeguru-profiler-agent = "^1.2.4" colorama = "0.3.3" dcicsnovault = "^11.21.1" -dcicutils = "^8.16.0" +dcicutils = "^8.16.1" docutils = ">=0.16,<1" encoded-core = "^0.9.6" elasticsearch = "7.13.4" From 57ce0fb750dd6e541863275f946741113ef3d825 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Sat, 12 Oct 2024 07:57:04 -0400 Subject: [PATCH 2/3] comments --- CHANGELOG.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index a4ada9a95..bcd1ce6c6 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -9,7 +9,7 @@ Change Log 0.104.0 ======= -* dmichaels / 2024-10-11 +* 2024-10-11/dmichaels * Updated dcicutils version (8.16.1) for vulnerabilities. From b344a1f7f4fe81f6476fea0a5f6be6b503fa2d89 Mon Sep 17 00:00:00 2001 From: sarahgonicholson Date: Tue, 15 Oct 2024 14:31:09 -0400 Subject: [PATCH 3/3] SN Enzymes optional (#272) * Remove exlusive enzyme restriction * Update changelog * Add mechanical enum --- CHANGELOG.rst | 6 ++++++ pyproject.toml | 2 +- src/encoded/schemas/library_preparation.json | 8 +------- src/encoded/tests/test_schema_library_preparation.py | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index bcd1ce6c6..9a70f1ea5 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,6 +7,12 @@ smaht-portal Change Log ---------- +0.104.1 +======= +`PR 272: SN Enzymes optional `_ +* Make property `enzymes` in LibraryPreparation optional if `fragmentation_method` does not contain "Transposase" or "Restriction Enzyme", otherwise required + + 0.104.0 ======= * 2024-10-11/dmichaels diff --git a/pyproject.toml b/pyproject.toml index 5ab3cac79..0d0862604 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "encoded" -version = "0.104.0" +version = "0.104.1" description = "SMaHT Data Analysis Portal" authors = ["4DN-DCIC Team "] license = "MIT" diff --git a/src/encoded/schemas/library_preparation.json b/src/encoded/schemas/library_preparation.json index 8a6e717f2..f6fcc1e14 100644 --- a/src/encoded/schemas/library_preparation.json +++ b/src/encoded/schemas/library_preparation.json @@ -100,6 +100,7 @@ "items": { "type": "string", "enum": [ + "Mechanical", "Sonication", "Restriction Enzyme", "Transposase", @@ -200,13 +201,6 @@ }, "then": { "required": ["enzymes"] - }, - "else": { - "not": { - "required": [ - "enzymes" - ] - } } } ] diff --git a/src/encoded/tests/test_schema_library_preparation.py b/src/encoded/tests/test_schema_library_preparation.py index 8a0343fdb..b117c03fb 100644 --- a/src/encoded/tests/test_schema_library_preparation.py +++ b/src/encoded/tests/test_schema_library_preparation.py @@ -24,12 +24,12 @@ def test_library_preparation( @pytest.mark.parametrize( "patch_body,status", [ - ({"enzymes": ["AluI"]}, 422), + ({"enzymes": ["AluI"]}, 200), ({"fragmentation_method": ["Sonication"]}, 200), ({"fragmentation_method": ["Restriction Enzyme"]}, 422), ({"fragmentation_method": ["Restriction Enzyme"], "enzymes": ["AluI"]}, 200), - ({"fragmentation_method": ["Transposase"], "enzymes": ["Tn5"]}, 200), - ({"fragmentation_method": ["Sonication"], "enzymes": ["AluI"]}, 422), + ({"fragmentation_method": ["Transposase"]}, 422), + ({"fragmentation_method": ["Sonication"], "enzymes": ["AluI"]}, 200), ], ) def test_enzyme_conditional(