diff --git a/.github/workflows/main-CI.yml b/.github/workflows/main-CI.yml index d20bcbc2..da7e142f 100644 --- a/.github/workflows/main-CI.yml +++ b/.github/workflows/main-CI.yml @@ -18,7 +18,7 @@ jobs: # This workflow contains a single job called "build" build: # The type of runner that the job will run on - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 # Steps represent a sequence of tasks that will be executed as part of the job steps: @@ -26,7 +26,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: '3.7' + python-version: '3.11' - name: Install Deps run: pip install poetry diff --git a/.github/workflows/main-publish.yml b/.github/workflows/main-publish.yml index cb524906..eb60bcc9 100644 --- a/.github/workflows/main-publish.yml +++ b/.github/workflows/main-publish.yml @@ -26,7 +26,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: 3.6 + python-version: 3.11 - name: Install Python dependencies for publish run: python -m pip install dcicutils - name: Publish diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c7d3bb71..eef790ad 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,20 +7,29 @@ foursight-cgap Change Log ---------- +4.0.0 +===== + +* Update to Python 3.11. + 3.6.1 ===== + * Add ingestion type to POST body for VCF ingestion action 3.6.0 ===== + * Changes (to foursight-core) to the access key check; making sure the action does not run every single day. 3.5.0 ===== + * Changes in foursight-core (4.3.0) to fix access key check. 3.4.5 ===== + * Minor UI fixes for display of status text for checks/actions - in foursight-core. * Added UI warning for registered action functions with no associated check - in foursight-core. * Added UI display of Redis info on INFO page - in foursight-core. @@ -28,17 +37,20 @@ Change Log 3.4.4 ===== + * Update foursight-core 4.1.2. Fixes for check arguments not being converted (from string) to int/float/etc as appropriate in the React version only (was not calling query_params_to_literals). 3.4.2 ===== + * Version changes related to foursight-core changes for SSL certificate and Portal access key checking. * Using new dcicutils.scripts.publish_to_pypi for publish. 3.3.3 ===== + * Dependency updates to update magma + tibanna_ff to fix cost updates on MWFRs * Lifecycle policy tweaks * Remove default deletion of "long term" storage options @@ -46,19 +58,23 @@ Change Log 3.3.2 ===== + * Update to foursight-core 3.3.2 (and dcicutils 6.8.0). 3.3.0 ===== + * Changes related editing user projects/institutions. * Removed the trigger_codebuild_run check (in foursight-core now). 3.2.0 ===== + * Changes related to support for running actions in Foursight React. 3.1.0 ===== + * Updated foursight-core version; changes there related to /accounts page. Not actually used currently here, only in foursight. * Moved lookup of check_setup.json (and accounts.json) to foursight-core, @@ -66,6 +82,7 @@ Change Log 2.2.0 ===== + * Changes related to Foursight React. * Renamed chalicelib directory to chalicelib_cgap. * Renamed target package (pyproject.toml) from chalicelib to chalicelib_cgap. @@ -82,23 +99,28 @@ Change Log 2.1.4 ===== + * Bring in mamga v1.1.0 2.1.3 ===== + * Lifecycle management: Only check files with ``project.lifecycle_management_active=true``. Furthermore, exclude files with status ``uploading`` and ``to be uploaded by workflow`` from the check. 2.1.2 ===== + * Assign correct action status when patch_file_lifecycle_status fails. 2.1.1 ===== + * Move lifecycle checks to separate group in UI. * Automatically run action for lifecycle checks. 2.1.0 ===== + * Spruced up Foursight UI a bit (virtually all in foursight-core but mentioning here). * New header/footer. * Different looks for Foursight-CGAP (blue header) and Foursight-Fourfront (green header). @@ -111,9 +133,11 @@ Change Log 2.0.1 ===== + * Work to spruce up the UI a bit. 2.0.0 ===== + * Created this CHANGELOG.rst file. * New version of foursight-core (1.0.0) for work related to C4-826 (IDENTITY-izing Foursight). diff --git a/chalicelib_cgap/scripts/local_check_execution.py b/chalicelib_cgap/scripts/local_check_execution.py new file mode 100644 index 00000000..4898eb26 --- /dev/null +++ b/chalicelib_cgap/scripts/local_check_execution.py @@ -0,0 +1,12 @@ +from foursight_core.captured_output import captured_output +from foursight_core.scripts.local_check_execution import local_check_execution +with captured_output(): + from chalicelib_cgap.app_utils import app_utils_obj as app_utils + + +def main(): + local_check_execution(app_utils) + + +if __name__ == "__main__": + main() diff --git a/poetry.lock b/poetry.lock index a8b83dd8..75f2ab0e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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request and response object" -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*" files = [ @@ -1867,18 +1791,17 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] [[package]] name = "websocket-client" -version = "1.6.1" +version = "1.6.4" description = "WebSocket client for Python with low level API options" -category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "websocket-client-1.6.1.tar.gz", hash = "sha256:c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd"}, - {file = "websocket_client-1.6.1-py3-none-any.whl", hash = "sha256:f1f9f2ad5291f0225a49efad77abf9e700b6fef553900623060dad6e26503b9d"}, + {file = "websocket-client-1.6.4.tar.gz", hash = "sha256:b3324019b3c28572086c4a319f91d1dcd44e6e11cd340232978c684a7650d0df"}, + {file = "websocket_client-1.6.4-py3-none-any.whl", hash = "sha256:084072e0a7f5f347ef2ac3d8698a5e0b4ffbfcab607628cadabc650fc9a83a24"}, ] [package.extras] -docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"] +docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] optional = ["python-socks", "wsaccel"] test = ["websockets"] @@ -1886,7 +1809,6 @@ test = ["websockets"] name = "webtest" version = "2.0.35" description = "Helper to test WSGI applications" -category = "main" optional = false python-versions = "*" files = [ @@ -1906,36 +1828,19 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu [[package]] name = "wheel" -version = "0.40.0" +version = "0.41.2" description = "A built-package format for Python" -category = "dev" -optional = false -python-versions = ">=3.7" -files = [ - {file = "wheel-0.40.0-py3-none-any.whl", hash = "sha256:d236b20e7cb522daf2390fa84c55eea81c5c30190f90f29ae2ca1ad8355bf247"}, - {file = "wheel-0.40.0.tar.gz", hash = "sha256:cd1196f3faee2b31968d626e1731c94f99cbdb67cf5a46e4f5656cbee7738873"}, -] - -[package.extras] -test = ["pytest (>=6.0.0)"] - -[[package]] -name = "zipp" -version = "3.15.0" -description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"}, - {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"}, + {file = "wheel-0.41.2-py3-none-any.whl", hash = "sha256:75909db2664838d015e3d9139004ee16711748a52c8f336b52882266540215d8"}, + {file = "wheel-0.41.2.tar.gz", hash = "sha256:0c5ac5ff2afb79ac23ab82bab027a0be7b5dbcf2e54dc50efe4bf507de1f7985"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +test = ["pytest (>=6.0.0)", "setuptools (>=65)"] [metadata] lock-version = "2.0" -python-versions = ">=3.7.1,<3.8" -content-hash = "b5ebf03d4a1d9495530a0ce430694198cb14f7dad71f25d90215d45dd380406c" +python-versions = ">=3.8,<3.12" +content-hash = "bb819ec8749404753ecd78c6b2051e48b0dbcb1393a96a7a959e11f34da3ff50" diff --git a/pyproject.toml b/pyproject.toml index 12b125de..d2e473a7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "foursight-cgap" -version = "3.6.1" +version = "4.0.0" description = "Serverless Chalice Application for Monitoring" authors = ["4DN-DCIC Team "] license = "MIT" @@ -9,34 +9,40 @@ packages = [ ] [tool.poetry.dependencies] -# Cannot go to Python 3.8 because cgap-pipeilne is stuck on Python 3.7. -python = ">=3.7.1,<3.8" -#dcicutils = "^7.5.1" -dcicutils = "7.6.0.1b4" +python = ">=3.8,<3.12" +cron-descriptor = "^1.4.0" +dcicutils = "^8.0.0" click = "^7.1.2" PyJWT = "^2.5.0" -Jinja2 = "2.10.1" +Jinja2 = "^3.1.2" google-api-python-client = "^1.12.5" geocoder = "1.38.1" -elasticsearch = "^7.13.4" +# elasticsearch 7.17.9 (at least) has a problem: +# Error: "The client noticed that the server is not Elasticsearch and we do not support this unknown product" +# https://stackoverflow.com/questions/68802324/elasticsearch-in-go-err-the-client-noticed-that-the-server-is-not-elasticsear +elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" gitpython = "^3.1.2" pytz = "^2020.1" -magma-suite = "^1.2.2" -tibanna-ff = "^1.3.0" -MarkupSafe = "1.1.1" -foursight-core = "4.4.0" +magma-suite = "^2.0.0" +tibanna-ff = "^3.1.1" +MarkupSafe = "^2.1.3" +foursight-core = "^5.0.0" # use below for tests but not for deployment #foursight-core = { git = "https://github.com/4dn-dcic/foursight-core.git", branch="core2" } -cgap-pipeline-utils = "23.0" -pytest = "5.1.2" +#portal-pipeline-utils = "2.1.0.1b1" +# Need pytest-redis 3.0.2 or higher for pytest 7.4.2 (or higher). +pytest = "^7.4.2" +pytest-redis = "^3.0.2" +tzlocal = "^5.1" [tool.poetry.dev-dependencies] chalice = "^1.21.6" -pytest-cov = "2.7.1" +pytest-cov = "^4.1.0" flaky = "3.6.1" [tool.poetry.scripts] +local-check-execution = "chalicelib_cgap.scripts.local_check_execution:main" publish-to-pypi = "dcicutils.scripts.publish_to_pypi:main" [build-system]