From 9ad65c654ceeff1ce487f897067578432df15ae8 Mon Sep 17 00:00:00 2001 From: Ian Boyes Date: Fri, 6 May 2022 10:53:03 -0700 Subject: [PATCH] fix: support terminated job state Upgrade to `virtool-workflow==4.0.3` which supports this feature. BREAKING CHANGE: Changes to the workflow API mean container configurations need to be updated. --- Dockerfile | 2 +- poetry.lock | 97 +++++++++++++++++++++++++++++++++++++++++++++----- pyproject.toml | 2 +- 3 files changed, 90 insertions(+), 11 deletions(-) diff --git a/Dockerfile b/Dockerfile index 24bd927..dd4e821 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM virtool/workflow:2.1.0 +FROM virtool/workflow:4.0.2 WORKDIR /workflow COPY workflow.py /workflow/workflow.py diff --git a/poetry.lock b/poetry.lock index ee92d19..96797b7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -82,6 +82,14 @@ docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] +[[package]] +name = "certifi" +version = "2021.10.8" +description = "Python package for providing Mozilla's CA Bundle." +category = "main" +optional = false +python-versions = "*" + [[package]] name = "charset-normalizer" version = "2.0.12" @@ -95,10 +103,21 @@ unicode_backport = ["unicodedata2"] [[package]] name = "click" -version = "7.1.2" +version = "8.1.3" description = "Composable command line interface toolkit" category = "main" optional = false +python-versions = ">=3.7" + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + +[[package]] +name = "colorama" +version = "0.4.4" +description = "Cross-platform colored terminal text." +category = "main" +optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] @@ -192,6 +211,36 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +[[package]] +name = "sentry-sdk" +version = "1.5.11" +description = "Python client for Sentry (https://sentry.io)" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +certifi = "*" +urllib3 = ">=1.10.0" + +[package.extras] +aiohttp = ["aiohttp (>=3.5)"] +beam = ["apache-beam (>=2.12)"] +bottle = ["bottle (>=0.12.13)"] +celery = ["celery (>=3)"] +chalice = ["chalice (>=1.16.0)"] +django = ["django (>=1.8)"] +falcon = ["falcon (>=1.4)"] +flask = ["flask (>=0.11)", "blinker (>=1.1)"] +httpx = ["httpx (>=0.16.0)"] +pure_eval = ["pure-eval", "executing", "asttokens"] +pyspark = ["pyspark (>=2.4.4)"] +quart = ["quart (>=0.16.1)", "blinker (>=1.1)"] +rq = ["rq (>=0.6)"] +sanic = ["sanic (>=0.8)"] +sqlalchemy = ["sqlalchemy (>=1.2)"] +tornado = ["tornado (>=5)"] + [[package]] name = "six" version = "1.16.0" @@ -208,6 +257,19 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "urllib3" +version = "1.26.9" +description = "HTTP library with thread-safe connection pooling, file post, and more." +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" + +[package.extras] +brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"] +secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"] +socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] + [[package]] name = "virtool-core" version = "0.4.0" @@ -226,7 +288,7 @@ pydantic = ">=1.8.2,<2.0.0" [[package]] name = "virtool-workflow" -version = "2.1.0" +version = "4.0.2" description = "A framework for developing bioinformatics workflows for Virtool." category = "main" optional = false @@ -236,8 +298,9 @@ python-versions = ">=3.8,<4.0" aiofiles = ">=0.7.0,<0.8.0" aiohttp = ">=3.8.1,<4.0.0" aioredis = "1.3.1" -click = ">=7.1.2,<8.0.0" -PyYAML = ">=5.4.1,<6.0.0" +click = ">=8.0.0,<9.0.0" +PyYAML = ">=5.4.0,<6.0.0" +sentry-sdk = ">=1.5.7,<2.0.0" virtool-core = ">=0.4.0,<0.5.0" [[package]] @@ -255,7 +318,7 @@ multidict = ">=4.0" [metadata] lock-version = "1.1" python-versions = "^3.8" -content-hash = "99b9c6f02921f4e2ebb118aec2dbc57cb6649b225fb48ed545d8dd3998e1dae3" +content-hash = "ec133f425c13339d123f6cf615ce56227b5e31ee5f3d4c1ba80f722c10d799b7" [metadata.files] aiofiles = [ @@ -356,13 +419,21 @@ attrs = [ {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"}, {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"}, ] +certifi = [ + {file = "certifi-2021.10.8-py2.py3-none-any.whl", hash = "sha256:d62a0163eb4c2344ac042ab2bdf75399a71a2d8c7d47eac2e2ee91b9d6339569"}, + {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"}, +] charset-normalizer = [ {file = "charset-normalizer-2.0.12.tar.gz", hash = "sha256:2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597"}, {file = "charset_normalizer-2.0.12-py3-none-any.whl", hash = "sha256:6881edbebdb17b39b4eaaa821b438bf6eddffb4468cf344f09f89def34a8b1df"}, ] click = [ - {file = "click-7.1.2-py2.py3-none-any.whl", hash = "sha256:dacca89f4bfadd5de3d7489b7c8a566eee0d3676333fbb50030263894c38c0dc"}, - {file = "click-7.1.2.tar.gz", hash = "sha256:d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a"}, + {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"}, + {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"}, +] +colorama = [ + {file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"}, + {file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"}, ] dictdiffer = [ {file = "dictdiffer-0.8.1-py2.py3-none-any.whl", hash = "sha256:d79d9a39e459fe33497c858470ca0d2e93cb96621751de06d631856adfd9c390"}, @@ -643,6 +714,10 @@ pyyaml = [ {file = "PyYAML-5.4.1-cp39-cp39-win_amd64.whl", hash = "sha256:c20cfa2d49991c8b4147af39859b167664f2ad4561704ee74c1de03318e898db"}, {file = "PyYAML-5.4.1.tar.gz", hash = "sha256:607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e"}, ] +sentry-sdk = [ + {file = "sentry-sdk-1.5.11.tar.gz", hash = "sha256:6c01d9d0b65935fd275adc120194737d1df317dce811e642cbf0394d0d37a007"}, + {file = "sentry_sdk-1.5.11-py2.py3-none-any.whl", hash = "sha256:c17179183cac614e900cbd048dab03f49a48e2820182ec686c25e7ce46f8548f"}, +] six = [ {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"}, {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, @@ -651,13 +726,17 @@ typing-extensions = [ {file = "typing_extensions-4.1.1-py3-none-any.whl", hash = "sha256:21c85e0fe4b9a155d0799430b0ad741cdce7e359660ccbd8b530613e8df88ce2"}, {file = "typing_extensions-4.1.1.tar.gz", hash = "sha256:1a9462dcc3347a79b1f1c0271fbe79e844580bb598bafa1ed208b94da3cdcd42"}, ] +urllib3 = [ + {file = "urllib3-1.26.9-py2.py3-none-any.whl", hash = "sha256:44ece4d53fb1706f667c9bd1c648f5469a2ec925fcf3a776667042d645472c14"}, + {file = "urllib3-1.26.9.tar.gz", hash = "sha256:aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e"}, +] virtool-core = [ {file = "virtool-core-0.4.0.tar.gz", hash = "sha256:e8313c0cd11f5b17eb16395debc9300387a57933e5bb7f8518646c0273c1379e"}, {file = "virtool_core-0.4.0-py3-none-any.whl", hash = "sha256:3fd38d8d97c86ded02c1a9d3cfe770d459195084caba0223c6f247bbe8acafcc"}, ] virtool-workflow = [ - {file = "virtool-workflow-2.1.0.tar.gz", hash = "sha256:94c17e00ce3ae831f74f253b0fba924d428213f19bdf3bbd53218b65f5b056e7"}, - {file = "virtool_workflow-2.1.0-py3-none-any.whl", hash = "sha256:4b85f8e2ec4b7d90cb19fb0b6ceed4a5ce2e8b23af17c88f3a6e4117b54ab121"}, + {file = "virtool-workflow-4.0.2.tar.gz", hash = "sha256:bd50ae5fea4b3876ed158c16ce0a9e5de402384a3e351642a406dab7c2235837"}, + {file = "virtool_workflow-4.0.2-py3-none-any.whl", hash = "sha256:21b04252d83330efb0c62b659d5ddd6a5a42537a71b57a74a07edad269847c94"}, ] yarl = [ {file = "yarl-1.7.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f2a8508f7350512434e41065684076f640ecce176d262a7d54f0da41d99c5a95"}, diff --git a/pyproject.toml b/pyproject.toml index 587442c..88c78f0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ authors = ["Ian Boyes "] [tool.poetry.dependencies] python = "^3.8" -virtool-workflow = "^2.0.0" +virtool-workflow = "^4.0.0" [tool.poetry.dev-dependencies]