diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 7e8b9e7f40..34f57a0cb8 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,13 @@ fourfront Change Log ---------- +8.2.0 +===== + +* Merged in master (2024-10-09) +* Update DRS API to return JSON always +* Update DRS download URLs to return direct downloads to Open Data where applicable + 8.1.5 ===== @@ -65,7 +72,7 @@ Change Log 7.10.1 ===== -* Bug fix to revert schema version of workflow.json back to 7 +* Bug fix to revert schema version of workflow.json back to 7 7.10.0 @@ -116,6 +123,7 @@ Change Log `Add ignored enum `_ * Add value to ignored_enum for file_type +>>>>>>> master 7.5.7 diff --git a/Makefile b/Makefile index 1d7689490e..8bd3199b35 100644 --- a/Makefile +++ b/Makefile @@ -52,6 +52,28 @@ configure: # does any pre-requisite installs pip install setuptools poetry config virtualenvs.create false --local # do not create a virtualenv - the user should have already done this -wrr 20-Sept-2021 +check-awscli: + @if ! aws --version > /dev/null 2>&1; then \ + echo "AWS CLI is not installed."; \ + exit 0; \ + else \ + echo "AWS CLI is already installed. Exiting."; \ + exit 1; \ + fi + +install-awscli: check-awscli # installs awscli v2 for use with credentialing + @echo "Installing AWS CLI v2..." + curl "https://awscli.amazonaws.com/AWSCLIV2.pkg" -o "AWSCLIV2.pkg" + sudo installer -pkg AWSCLIV2.pkg -target /usr/local/bin/ + aws --version + rm AWSCLIV2.pkg + +clear-aws: + @echo "unset AWS_ACCESS_KEY_ID" > ~/.clear_aws_env && \ + echo "unset AWS_SECRET_ACCESS_KEY" >> ~/.clear_aws_env && \ + echo "unset AWS_SESSION_TOKEN" >> ~/.clear_aws_env && \ + echo "Run 'source ~/.clear_aws_env' to finish clearing" + build-poetry: make configure poetry install @@ -111,6 +133,7 @@ kibana-stop: kill: # kills back-end processes associated with the application. Use with care. pkill -f postgres & + pkill -f opensearch & pkill -f elasticsearch & pkill -f moto_server & diff --git a/poetry.lock b/poetry.lock index 46ffd8529d..eee965e08c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. [[package]] name = "apipkg" version = "3.0.2" description = "apipkg: namespace control and lazy-import mechanism" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -15,6 +16,7 @@ files = [ name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" optional = false python-versions = "*" files = [ @@ -26,6 +28,7 @@ files = [ name = "arrow" version = "1.3.0" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -39,12 +42,13 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] +test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] [[package]] name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -56,6 +60,7 @@ files = [ name = "attrs" version = "22.2.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -74,6 +79,7 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy name = "aws-requests-auth" version = "0.4.3" description = "AWS signature version 4 signing process for the python requests module" +category = "main" optional = false python-versions = "*" files = [ @@ -88,6 +94,7 @@ requests = ">=0.14.0" name = "aws-xray-sdk" version = "0.95" description = "The AWS X-Ray SDK for Python (the SDK) enables Python developers to record and emit information from within their applications to the AWS X-Ray service." +category = "dev" optional = false python-versions = "*" files = [ @@ -102,17 +109,18 @@ wrapt = "*" [[package]] name = "awscli" -version = "1.34.11" +version = "1.35.3" description = "Universal Command Line Environment for AWS." +category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "awscli-1.34.11-py3-none-any.whl", hash = "sha256:389853d923fe083c02fd3d23d77e3f8fc610a4312511b98117d5e4cf982b4454"}, - {file = "awscli-1.34.11.tar.gz", hash = "sha256:7282c4510bceb9fd3b19d1069f54d9808342ac2ef7b65080054860f8c15b5479"}, + {file = "awscli-1.35.3-py3-none-any.whl", hash = "sha256:19fe44489e1bf863d6a1c3dcffab293a26bcb73aab18614980a61ef8b3afce87"}, + {file = "awscli-1.35.3.tar.gz", hash = "sha256:0695715914ce934c6702db7b06a889035bc1fcafeb150fa7d306054949bfb3bd"}, ] [package.dependencies] -botocore = "1.35.11" +botocore = "1.35.37" colorama = ">=0.2.5,<0.4.7" docutils = ">=0.10,<0.17" PyYAML = ">=3.10,<6.1" @@ -123,6 +131,7 @@ s3transfer = ">=0.10.0,<0.11.0" name = "beautifulsoup4" version = "4.12.3" description = "Screen-scraping library" +category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -144,6 +153,7 @@ lxml = ["lxml"] name = "blinker" version = "1.8.2" description = "Fast, simple object-to-object and broadcast signaling" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -155,6 +165,7 @@ files = [ name = "boto" version = "2.49.0" description = "Amazon Web Services Library" +category = "dev" optional = false python-versions = "*" files = [ @@ -164,17 +175,18 @@ files = [ [[package]] name = "boto3" -version = "1.35.11" +version = "1.35.37" description = "The AWS SDK for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.11-py3-none-any.whl", hash = "sha256:f5834dd908edda56c3da86b908693c7cd1c17c2f8150de736e9e90c56ecc78f6"}, - {file = "boto3-1.35.11.tar.gz", hash = "sha256:bdfb8dd2564e5cf2f5095fb8e3a0a4612202654c1196692dddd9bc48aadc7657"}, + {file 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"sha256:347a714dfc92653fdd0d8ed9801c82a01c51053c8fa0e40bcb880b39de8d06bd"}, + {file = "boto3_stubs-1.35.37-py3-none-any.whl", hash = "sha256:32b70602af1c34ddd244bbdafcc7f32b9824135c2f14dcf41d8e5a33b914b19a"}, + {file = "boto3_stubs-1.35.37.tar.gz", hash = "sha256:dc12838481a10d65802f75b4ca1e4eb334e06dbb2f0d5c565f43e0363c2037d6"}, ] [package.dependencies] @@ -198,404 +211,408 @@ types-s3transfer = "*" typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.12\""} [package.extras] -accessanalyzer = ["mypy-boto3-accessanalyzer (>=1.34.0,<1.35.0)"] -account = ["mypy-boto3-account (>=1.34.0,<1.35.0)"] -acm = ["mypy-boto3-acm (>=1.34.0,<1.35.0)"] -acm-pca = ["mypy-boto3-acm-pca (>=1.34.0,<1.35.0)"] -all = ["mypy-boto3-accessanalyzer (>=1.34.0,<1.35.0)", "mypy-boto3-account (>=1.34.0,<1.35.0)", "mypy-boto3-acm (>=1.34.0,<1.35.0)", "mypy-boto3-acm-pca (>=1.34.0,<1.35.0)", "mypy-boto3-amp (>=1.34.0,<1.35.0)", "mypy-boto3-amplify (>=1.34.0,<1.35.0)", "mypy-boto3-amplifybackend 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">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" files = [ @@ -3947,6 +4226,7 @@ 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 = [ @@ -3956,41 +4236,45 @@ files = [ [[package]] name = "types-awscrt" -version = "0.20.12" +version = "0.22.0" description = "Type annotations and code completion for awscrt" +category = "dev" optional = false -python-versions = "<4.0,>=3.7" +python-versions = ">=3.8" files = [ - {file = "types_awscrt-0.20.12-py3-none-any.whl", hash = "sha256:521ce54cc4dad9fe6480556bb0f8315a508106938ba1f2a0baccfcea7d4a4dee"}, - {file = "types_awscrt-0.20.12.tar.gz", hash = "sha256:0beabdde0205dc1da679ea464fd3f98b570ef4f0fc825b155a974fb51b21e8d9"}, + {file = "types_awscrt-0.22.0-py3-none-any.whl", hash = "sha256:b2c196bbd3226bab42d80fae13c34548de9ddc195f5a366d79c15d18e5897aa9"}, + {file = 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description = "Type annotations and code completion for s3transfer" +category = "dev" optional = false -python-versions = "<4.0,>=3.8" +python-versions = ">=3.8" files = [ - {file = "types_s3transfer-0.10.1-py3-none-any.whl", hash = "sha256:49a7c81fa609ac1532f8de3756e64b58afcecad8767933310228002ec7adff74"}, - {file = "types_s3transfer-0.10.1.tar.gz", hash = "sha256:02154cce46528287ad76ad1a0153840e0492239a0887e8833466eccf84b98da0"}, + {file = "types_s3transfer-0.10.3-py3-none-any.whl", hash = "sha256:d34c5a82f531af95bb550927136ff5b737a1ed3087f90a59d545591dfde5b4cc"}, + {file = "types_s3transfer-0.10.3.tar.gz", hash = "sha256:f761b2876ac4c208e6c6b75cdf5f6939009768be9950c545b11b0225e7703ee7"}, ] [[package]] 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 = [ @@ -4000,19 +4284,21 @@ files = [ [[package]] name = "tzdata" -version = "2024.1" +version = "2024.2" description = "Provider of IANA time zone data" +category = "main" optional = false python-versions = ">=2" files = [ - {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"}, - {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"}, + {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"}, + {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"}, ] [[package]] name = "uptime" version = "3.0.1" description = "Cross-platform uptime library" +category = "main" optional = false python-versions = "*" files = [ @@ -4023,6 +4309,7 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4035,13 +4322,14 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake [[package]] name = "urllib3" -version = "1.26.19" +version = "1.26.20" 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 = [ - {file = "urllib3-1.26.19-py2.py3-none-any.whl", hash = "sha256:37a0344459b199fce0e80b0d3569837ec6b6937435c5244e7fd73fa6006830f3"}, - {file = "urllib3-1.26.19.tar.gz", hash = "sha256:3e3d753a8618b86d7de333b4223005f68720bcd6a7d2bcb9fbd2229ec7c1e429"}, + {file = "urllib3-1.26.20-py2.py3-none-any.whl", hash = "sha256:0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e"}, + {file = "urllib3-1.26.20.tar.gz", hash = "sha256:40c2dc0c681e47eb8f90e7e27bf6ff7df2e677421fd46756da1161c39ca70d32"}, ] [package.extras] @@ -4053,6 +4341,7 @@ 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 = [ @@ -4068,6 +4357,7 @@ 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 = [ @@ -4081,13 +4371,14 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] [[package]] name = "webcolors" -version = "24.6.0" +version = "24.8.0" description = "A library for working with the color formats defined by HTML and CSS." +category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "webcolors-24.6.0-py3-none-any.whl", hash = "sha256:8cf5bc7e28defd1d48b9e83d5fc30741328305a8195c29a8e668fa45586568a1"}, - {file = "webcolors-24.6.0.tar.gz", hash = "sha256:1d160d1de46b3e81e58d0a280d0c78b467dc80f47294b91b1ad8029d2cedb55b"}, + {file = "webcolors-24.8.0-py3-none-any.whl", hash = "sha256:fc4c3b59358ada164552084a8ebee637c221e4059267d0f8325b3b560f6c7f0a"}, + {file = "webcolors-24.8.0.tar.gz", hash = "sha256:08b07af286a01bcd30d583a7acadf629583d1f79bfef27dd2c2c5c263817277d"}, ] [package.extras] @@ -4098,6 +4389,7 @@ tests = ["coverage[toml]"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" +category = "main" optional = false python-versions = "*" files = [ @@ -4107,13 +4399,14 @@ files = [ [[package]] name = "webob" -version = "1.8.7" +version = "1.8.8" description = "WSGI request and response object" +category = "main" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ - {file = "WebOb-1.8.7-py2.py3-none-any.whl", hash = "sha256:73aae30359291c14fa3b956f8b5ca31960e420c28c1bec002547fb04928cf89b"}, - {file = "WebOb-1.8.7.tar.gz", hash = "sha256:b64ef5141be559cfade448f044fa45c2260351edcb6a8ef6b7e00c7dcef0c323"}, + {file = "WebOb-1.8.8-py2.py3-none-any.whl", hash = "sha256:b60ba63f05c0cf61e086a10c3781a41fcfe30027753a8ae6d819c77592ce83ea"}, + {file = "webob-1.8.8.tar.gz", hash = "sha256:2abc1555e118fc251e705fc6dc66c7f5353bb9fbfab6d20e22f1c02b4b71bcee"}, ] [package.extras] @@ -4124,6 +4417,7 @@ 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 = [ @@ -4143,13 +4437,14 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu [[package]] name = "werkzeug" -version = "3.0.3" +version = "3.0.4" description = "The comprehensive WSGI web application library." +category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "werkzeug-3.0.3-py3-none-any.whl", hash = "sha256:fc9645dc43e03e4d630d23143a04a7f947a9a3b5727cd535fdfe155a17cc48c8"}, - {file = "werkzeug-3.0.3.tar.gz", hash = "sha256:097e5bfda9f0aba8da6b8545146def481d06aa7d3266e7448e2cccf67dd8bd18"}, + {file = "werkzeug-3.0.4-py3-none-any.whl", hash = "sha256:02c9eb92b7d6c06f31a782811505d2157837cea66aaede3e217c7c27c039476c"}, + {file = "werkzeug-3.0.4.tar.gz", hash = "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"}, ] [package.dependencies] @@ -4162,6 +4457,7 @@ watchdog = ["watchdog (>=2.3)"] name = "wheel" version = "0.40.0" description = "A built-package format for Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4176,6 +4472,7 @@ test = ["pytest (>=6.0.0)"] name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4255,6 +4552,7 @@ files = [ name = "wsgiproxy2" version = "0.4.2" description = "UNKNOWN" +category = "main" optional = false python-versions = "*" files = [ @@ -4269,6 +4567,7 @@ 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 = [ @@ -4280,6 +4579,7 @@ files = [ name = "xlwt" version = "1.2.0" description = "Library to create spreadsheet files compatible with MS Excel 97/2000/XP/2003 XLS files, on any platform, with Python 2.6, 2.7, 3.3+" +category = "main" optional = false python-versions = "*" files = [ @@ -4289,34 +4589,41 @@ files = [ [[package]] name = "xmltodict" -version = "0.13.0" +version = "0.14.1" description = "Makes working with XML feel like you are working with JSON" +category = "dev" optional = false -python-versions = ">=3.4" +python-versions = ">=3.6" files = [ - {file = "xmltodict-0.13.0-py2.py3-none-any.whl", hash = "sha256:aa89e8fd76320154a40d19a0df04a4695fb9dc5ba977cbb68ab3e4eb225e7852"}, - {file = "xmltodict-0.13.0.tar.gz", hash = "sha256:341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56"}, + {file = "xmltodict-0.14.1-py2.py3-none-any.whl", hash = "sha256:3ef4a7b71c08f19047fcbea572e1d7f4207ab269da1565b5d40e9823d3894e63"}, + {file = "xmltodict-0.14.1.tar.gz", hash = "sha256:338c8431e4fc554517651972d62f06958718f6262b04316917008e8fd677a6b0"}, ] [[package]] name = "zipp" -version = "3.19.2" +version = "3.20.2" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"}, - {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"}, + {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, + {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, ] [package.extras] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [[package]] name = "zope-deprecation" version = "4.4.0" description = "Zope Deprecation Infrastructure" +category = "main" optional = false python-versions = "*" files = [ @@ -4335,6 +4642,7 @@ 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 = [ @@ -4388,6 +4696,7 @@ 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 = [ @@ -4407,4 +4716,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "acc0c48a41c011d04e71870d0bcfe2810e25c1f0f911d43c307cddfede451e95" +content-hash = "3be646601b4b77f324d82840914fa5137a3f65fd5c4be6f5df4e2001f78c7dd8" diff --git a/pyproject.toml b/pyproject.toml index d27aad85b7..9be3844b44 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "fourfront". name = "encoded" -version = "8.1.5" +version = "8.1.5.1b1" # TODO: To become 8.2.0 description = "4DN-DCIC Fourfront" authors = ["4DN-DCIC Team "] license = "MIT" @@ -38,8 +38,8 @@ classifiers = [ ] [tool.poetry.dependencies] + python = ">=3.9,<3.13" -awscli = ">=1.29.62" boto3 = "^1.34.136" botocore = "^1.34.136" certifi = ">=2021.5.30" @@ -49,7 +49,8 @@ colorama = "0.3.3" # 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" -dcicsnovault = "^11.22.0" +# dcicsnovault = "11.21.1.0b5" +dcicsnovault = "11.22.0.1b1" dcicutils = "^8.13.3" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses diff --git a/src/encoded/tests/test_file_drs.py b/src/encoded/tests/test_file_drs.py index 9ce8412651..16fd2a237a 100644 --- a/src/encoded/tests/test_file_drs.py +++ b/src/encoded/tests/test_file_drs.py @@ -1,4 +1,5 @@ import pytest +from unittest import mock pytestmark = [pytest.mark.setone, pytest.mark.working] @@ -17,7 +18,7 @@ def mcool_file_json(award, experiment, lab, file_formats): 'md5sum': '00000000000000000000000000000000', 'content_md5sum': '00000000000000000000000000000000', 'filename': 'my.cool.mcool', - 'status': 'uploaded', + 'status': 'released', } return item @@ -32,7 +33,9 @@ def file(testapp, award, experiment, lab, file_formats): 'md5sum': '00000000000000000000000000000000', 'content_md5sum': '00000000000000000000000000000000', 'filename': 'my.fastq.gz', - 'status': 'uploaded', + 'status': 'released', + 'accession': 'TSTFI2896250', + 'uuid': '96115074-b6bd-4a1e-9564-14b708607e4c' } res = testapp.post_json('/file_fastq', item) return res.json['@graph'][0] @@ -40,37 +43,53 @@ def file(testapp, award, experiment, lab, file_formats): def validate_drs_conversion(drs_obj, meta, uri=None): """ Validates drs object structure against the metadata in the db """ - assert drs_obj['id'] == meta['@id'] + assert drs_obj['id'] == meta['accession'] assert drs_obj['created_time'] == meta['date_created'] - assert drs_obj['drs_id'] == meta['accession'] - assert drs_obj['self_uri'] == f'drs://localhost:80{meta["@id"]}@@drs' if not uri else uri + assert drs_obj['self_uri'] == f'drs://localhost:80/{meta["accession"]}' if not uri else uri assert drs_obj['version'] == meta['md5sum'] assert drs_obj['name'] == meta['filename'] assert drs_obj['aliases'] == [meta['uuid']] + assert drs_obj['access_methods'][0]['access_id'] == 'https' def test_processed_file_drs_view(testapp, mcool_file_json): """ Tests that processed mcool gives a valid DRS response """ - meta = testapp.post_json('/file_processed', mcool_file_json).json['@graph'][0] - drs_meta = testapp.get(meta['@id'] + '@@drs').json - validate_drs_conversion(drs_meta, meta) - drs_meta = testapp.get(f'{DRS_PREFIX}/{meta["uuid"]}').json - validate_drs_conversion(drs_meta, meta, uri=f'{DRS_PREFIX}/{meta["uuid"]}') + with mock.patch('encoded.types.file.File._head_s3', return_value=None): + meta = testapp.post_json('/file_processed', mcool_file_json).json['@graph'][0] + drs_meta = testapp.get(meta['@id'] + '@@drs').json + validate_drs_conversion(drs_meta, meta) + drs_meta = testapp.get(f'{DRS_PREFIX}/{meta["uuid"]}').json + validate_drs_conversion(drs_meta, meta, uri=f'{DRS_PREFIX}/{meta["uuid"]}') def test_fastq_file_drs_view(testapp, file): """ Tests that a fastq file has valid DRS response """ - drs_meta = testapp.get(file['@id'] + '@@drs').json - validate_drs_conversion(drs_meta, file) - drs_meta = testapp.get(f'{DRS_PREFIX}/{file["uuid"]}').json - validate_drs_conversion(drs_meta, file, uri=f'{DRS_PREFIX}/{file["uuid"]}') + with mock.patch('encoded.types.file.File._head_s3', return_value=None): + drs_meta = testapp.get(file['@id'] + '@@drs').json + validate_drs_conversion(drs_meta, file) + drs_meta = testapp.get(f'{DRS_PREFIX}/{file["uuid"]}').json + validate_drs_conversion(drs_meta, file, uri=f'{DRS_PREFIX}/{file["uuid"]}') def test_fastq_file_drs_access(testapp, file): """ Tests that access URLs are retrieved successfully """ - drs_meta = testapp.get(file['@id'] + '@@drs').json - drs_object_uri = drs_meta['drs_id'] - drs_object_download = testapp.get(f'/ga4gh/drs/v1/objects/{drs_object_uri}/access/').json - assert drs_object_download == { - 'url': f'https://localhost:80/{drs_object_uri}/@@download' - } + with mock.patch('encoded.types.file.File._head_s3', return_value=None): + drs_meta = testapp.get(file['@id'] + '@@drs').json + drs_object_uri = drs_meta['id'] + drs_object_download = testapp.get(f'/ga4gh/drs/v1/objects/{drs_object_uri}/access/').json + assert drs_object_download == { + 'url': f'https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/' + f'96115074-b6bd-4a1e-9564-14b708607e4c/TSTFI2896250.fastq.gz' + } + + +def test_drs_always_returns_json(htmltestapp, file): + """ DRS is a JSON only API so should never not return html """ + with mock.patch('encoded.types.file.File._head_s3', return_value=None): + drs_meta = htmltestapp.get(file['@id'] + '@@drs') + assert drs_meta.content_type == 'application/json' + + +def test_drs_without_open_data_returns_404(testapp, file): + """ Tests that without open_data_url mocked, """ + testapp.get(file['@id'] + '@@drs', status=404) diff --git a/src/encoded/types/base.py b/src/encoded/types/base.py index 68ccdffcd7..188a3e8456 100644 --- a/src/encoded/types/base.py +++ b/src/encoded/types/base.py @@ -26,18 +26,18 @@ def _award_viewing_group(award_uuid, root): # Item acls from ..acl import ( - ALLOW_CURRENT_AND_SUBMITTER_EDIT_ACL, + ALLOW_CURRENT_AND_SUBMITTER_EDIT_ACL, ALLOW_CURRENT_ACL, AWARD_MEMBER_ROLE, ALLOW_ANY_USER_ADD_ACL, - ALLOW_EVERYONE_VIEW_ACL, - ALLOW_LAB_MEMBER_VIEW_ACL, - ALLOW_LAB_SUBMITTER_EDIT_ACL, + ALLOW_EVERYONE_VIEW_ACL, + ALLOW_LAB_MEMBER_VIEW_ACL, + ALLOW_LAB_SUBMITTER_EDIT_ACL, ALLOW_LAB_VIEW_ADMIN_EDIT_ACL, ALLOW_OWNER_EDIT_ACL, ALLOW_SUBMITTER_ADD_ACL, - ALLOW_VIEWING_GROUP_LAB_SUBMITTER_EDIT_ACL, - ALLOW_VIEWING_GROUP_VIEW_ACL, + ALLOW_VIEWING_GROUP_LAB_SUBMITTER_EDIT_ACL, + ALLOW_VIEWING_GROUP_VIEW_ACL, DELETED_ACL, LAB_MEMBER_ROLE, LAB_SUBMITTER_ROLE, @@ -244,16 +244,6 @@ def _is_joint_analysis(props): roles[submitter] = OWNER_ROLE return roles - def unique_keys(self, properties): - """smth.""" - keys = super(Item, self).unique_keys(properties) - if 'accession' not in self.schema['properties']: - return keys - keys.setdefault('accession', []).extend(properties.get('alternate_accessions', [])) - if properties.get('status') != 'replaced' and 'accession' in properties: - keys['accession'].append(properties['accession']) - return keys - def _update(self, properties, sheets=None): props = {} try: diff --git a/src/encoded/types/file.py b/src/encoded/types/file.py index a8798112b0..9ab7498f1c 100644 --- a/src/encoded/types/file.py +++ b/src/encoded/types/file.py @@ -20,6 +20,7 @@ from pyramid.threadlocal import get_current_request from pyramid.traversal import resource_path from pyramid.view import view_config +from pyramid.response import Response from snovault import ( AfterModified, BeforeModified, @@ -569,7 +570,7 @@ def _get_file_experiment_info(self, request, currinfo): def track_and_facet_info(self, request, biosource_name=None): props = self.upgrade_properties() # order matters here at leat for last 2 fields - fields = ['experiment_type', 'assay_info', 'experimental_lab', 'dataset', 'condition', + fields = ['experiment_type', 'assay_info', 'experimental_lab', 'dataset', 'condition', 'biosource_name', 'replicate_info', 'experiment_bucket', 'lab_name', 'track_title'] # look for existing _props track_info = {field: props.get('override_' + field) for field in fields} @@ -1709,26 +1710,23 @@ def drs(context, request): """ DRS object implementation for file. """ rendered_object = request.embed(str(context.uuid), '@@object', as_user=True) accession = rendered_object['accession'] + open_data_url = rendered_object.get('open_data_url', None) + # TODO: implement access_id mechanism + if not open_data_url: + return Response('Access ID support planned for the future', status=404) drs_object_base = { - 'id': rendered_object['@id'], + 'id': accession, 'created_time': rendered_object['date_created'], - 'drs_id': accession, - 'self_uri': f'drs://{request.host}{request.path}', + 'self_uri': f'drs://{request.host}/{accession}', 'access_methods': [ { - # always prefer https + # always use open data 'access_url': { - 'url': f'https://{request.host}/{accession}/@@download' + 'url': open_data_url }, - 'type': 'https' - }, - { - # but provide http as well in case we are not on prod - 'access_url': { - 'url': f'http://{request.host}/{accession}/@@download' - }, - 'type': 'http' - }, + 'type': 'https', + 'access_id': 'https' + } ] } return build_drs_object_from_props(drs_object_base, rendered_object)