From ec081f62d4b9231ddb9e80de96caf472828ac612 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 26 Sep 2023 09:14:07 -0400 Subject: [PATCH 01/25] j --- .github/workflows/main.yml | 2 +- CHANGELOG.rst | 12 + poetry.lock | 988 +++++++++++++--------------- pyproject.toml | 26 +- src/encoded/schemas/access_key.json | 69 -- src/encoded/tests/test_schemas.py | 2 +- src/encoded/types/access_key.py | 161 ----- 7 files changed, 474 insertions(+), 786 deletions(-) delete mode 100644 src/encoded/schemas/access_key.json delete mode 100644 src/encoded/types/access_key.py diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d56ad37ef9..f87dd0e470 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -27,7 +27,7 @@ jobs: matrix: test_type: ['UNIT', 'INDEX', 'DOCKER'] # We are really not set up for these next two to be multiplicative, so be careful adding more. - python_version: ['3.8'] + python_version: ['3.8', '3.11'] node_version: ['18'] # Steps represent a sequence of tasks that will be executed as part of the job diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 9917db09f5..3286beaba3 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,18 @@ cgap-portal Change Log ---------- +15.0.0 +====== +* Upgrade to Python 3.11. +* Changed pyyaml version to ^6.0.1. +* Removed types/access_key.py and schemas/access_key.json as the ones in snovault are sufficient. +* Added generate-local-access-key script (from snovault) to pyproject.toml; + orignally created for smaht-portal since early in development no way to + create an access-key normally using the UI; but generall useful/convenient. +* Added generate-local-access-key script (defined in snovault). +* Added view-local-object script (defined in snovault). + + 14.3.1 ====== `PR 753: Auth0 Symlink Bugfix `_ diff --git a/poetry.lock b/poetry.lock index 21354ad540..83738c61e6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,22 +1,20 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. [[package]] name = "apipkg" -version = "3.0.1" +version = "3.0.2" description = "apipkg: namespace control and lazy-import mechanism" -category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "apipkg-3.0.1-py3-none-any.whl", hash = "sha256:6c4e654de1be834c66579003abc992121745209c2d12561a0dd5888feb06906f"}, - {file = "apipkg-3.0.1.tar.gz", hash = "sha256:f8c021adafc9132ac2fba9fd3c5768365d0a8c10aa375fb15e329f1fce8a5f01"}, + {file = "apipkg-3.0.2-py3-none-any.whl", hash = "sha256:a16984c39de280701f3f6406ed3af658f2a1965011fe7bb5be34fbb48423b411"}, + {file = "apipkg-3.0.2.tar.gz", hash = "sha256:c7aa61a4f82697fdaa667e70af1505acf1f7428b1c27b891d204ba7a8a3c5e0d"}, ] [[package]] name = "arrow" version = "1.2.3" description = "Better dates & times for Python" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -29,21 +27,19 @@ python-dateutil = ">=2.7.0" [[package]] name = "async-timeout" -version = "4.0.2" +version = "4.0.3" description = "Timeout context manager for asyncio programs" -category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "async-timeout-4.0.2.tar.gz", hash = "sha256:2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15"}, - {file = "async_timeout-4.0.2-py3-none-any.whl", hash = "sha256:8ca1e4fcf50d07413d66d1a5e416e42cfdf5851c981d679a09851a6853383b3c"}, + {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"}, + {file = "async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"}, ] [[package]] name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -62,7 +58,6 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte 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 = [ @@ -75,18 +70,17 @@ requests = ">=0.14.0" [[package]] name = "awscli" -version = "1.29.22" +version = "1.29.54" description = "Universal Command Line Environment for AWS." -category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "awscli-1.29.22-py3-none-any.whl", hash = "sha256:031ce6bcb58fa4f8817dd94043a64af0174f82a3d5df7abf4d511120e8b8398e"}, - {file = "awscli-1.29.22.tar.gz", hash = "sha256:2a289197a51ba5cde621fc197efc17871cdf3034132d053d8d0af3e5cb338d13"}, + {file = "awscli-1.29.54-py3-none-any.whl", hash = "sha256:53531f3625bb5a586c4a8fefac0247e3cc92bb59ddbcad90b61a66efe6b8a788"}, + {file = "awscli-1.29.54.tar.gz", hash = "sha256:de6e406749d69b1d01602100534a1d72dcd001200d1434296f3f8d2514f8a030"}, ] [package.dependencies] -botocore = "1.31.22" +botocore = "1.31.54" colorama = ">=0.2.5,<0.4.5" docutils = ">=0.10,<0.17" PyYAML = ">=3.10,<6.1" @@ -97,7 +91,6 @@ s3transfer = ">=0.6.0,<0.7.0" name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" -category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -116,7 +109,6 @@ lxml = ["lxml"] name = "bitarray" version = "2.8.1" description = "efficient arrays of booleans -- C extension" -category = "main" optional = false python-versions = "*" files = [ @@ -226,18 +218,17 @@ files = [ [[package]] name = "boto3" -version = "1.28.22" +version = "1.28.54" description = "The AWS SDK for Python" -category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.22-py3-none-any.whl", hash = "sha256:0c1c1d19232018ac49fd2c0a94aa0b802f5d222e89448ff50734626bce454b32"}, - {file = "boto3-1.28.22.tar.gz", hash = "sha256:af1ce129f462cdc8dfb1a1c559d7ed725e51344fb0ae4a56d9453196bf416555"}, + {file = "boto3-1.28.54-py3-none-any.whl", hash = "sha256:3cb2aee317a1b8686e3b23674e4099b8ff7451bd8acc61b9719acff86fa024d1"}, + {file = 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"sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"}, + {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"}, ] [[package]] name = "uptime" version = "3.0.1" description = "Cross-platform uptime library" -category = "main" optional = false python-versions = "*" files = [ @@ -3811,7 +3731,6 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3826,7 +3745,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "urllib3" version = "1.26.16" 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.*, !=3.5.*" files = [ @@ -3843,7 +3761,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "venusian" version = "1.2.0" description = "A library for deferring decorator actions" -category = "main" optional = false python-versions = "*" files = [ @@ -3859,7 +3776,6 @@ 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 = [ @@ -3875,7 +3791,6 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3891,7 +3806,6 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "main" optional = false python-versions = "*" files = [ @@ -3903,7 +3817,6 @@ 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 = [ @@ -3917,18 +3830,17 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] [[package]] name = "websocket-client" -version = "1.6.1" +version = "1.6.3" 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-1.6.3.tar.gz", hash = "sha256:3aad25d31284266bcfcfd1fd8a743f63282305a364b8d0948a43bd606acc652f"}, + {file = "websocket_client-1.6.3-py3-none-any.whl", hash = "sha256:6cfc30d051ebabb73a5fa246efdcc14c8fbebbd0330f8984ac3bb6d9edd2ad03"}, ] [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"] @@ -3936,7 +3848,6 @@ test = ["websockets"] name = "webtest" version = "2.0.35" description = "Helper to test WSGI applications" -category = "main" optional = false python-versions = "*" files = [ @@ -3958,7 +3869,6 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu name = "werkzeug" version = "2.1.2" description = "The comprehensive WSGI web application library." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3971,14 +3881,13 @@ watchdog = ["watchdog"] [[package]] name = "wheel" -version = "0.41.1" +version = "0.41.2" description = "A built-package format for Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "wheel-0.41.1-py3-none-any.whl", hash = "sha256:473219bd4cbedc62cea0cb309089b593e47c15c4a2531015f94e4e3b9a0f6981"}, - {file = "wheel-0.41.1.tar.gz", hash = "sha256:12b911f083e876e10c595779709f8a88a59f45aacc646492a67fe9ef796c1b47"}, + {file = "wheel-0.41.2-py3-none-any.whl", hash = "sha256:75909db2664838d015e3d9139004ee16711748a52c8f336b52882266540215d8"}, + {file = "wheel-0.41.2.tar.gz", hash = "sha256:0c5ac5ff2afb79ac23ab82bab027a0be7b5dbcf2e54dc50efe4bf507de1f7985"}, ] [package.extras] @@ -3988,7 +3897,6 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"] name = "wsgiproxy2" version = "0.4.2" description = "UNKNOWN" -category = "main" optional = false python-versions = "*" files = [ @@ -4003,7 +3911,6 @@ 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 = [ @@ -4015,7 +3922,6 @@ files = [ name = "xmltodict" version = "0.13.0" description = "Makes working with XML feel like you are working with JSON" -category = "dev" optional = false python-versions = ">=3.4" files = [ @@ -4025,25 +3931,23 @@ files = [ [[package]] name = "zipp" -version = "3.16.2" +version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"}, - {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"}, + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [[package]] name = "zope-deprecation" version = "4.4.0" description = "Zope Deprecation Infrastructure" -category = "main" optional = false python-versions = "*" files = [ @@ -4062,7 +3966,6 @@ test = ["zope.testrunner"] name = "zope-interface" version = "5.5.2" description = "Interfaces for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -4116,7 +4019,6 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] name = "zope-sqlalchemy" version = "1.6" description = "Minimal Zope/SQLAlchemy transaction integration" -category = "main" optional = false python-versions = "*" files = [ @@ -4135,5 +4037,5 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" -python-versions = ">=3.8.1,<3.10" -content-hash = "cbc358e65b7b5edfa5adc017d40aedb489dcfff4fa0efb9934283c4ff14ac740" +python-versions = ">=3.8.1,<3.12" +content-hash = "9b305b474c03a00950ce920400a1e568aa40595988f6eb93ddbf6b9a0ef1948b" diff --git a/pyproject.toml b/pyproject.toml index 2ce17448f8..ba57dd55f3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "cgap-portal". name = "encoded" -version = "14.3.1" +version = "14.3.1.1b1" # TODO: To become 15.0.0 description = "Computational Genome Analysis Platform" authors = ["4DN-DCIC Team "] license = "MIT" @@ -33,13 +33,16 @@ classifiers = [ 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', + 'Programming Language :: Python :: 3.9', + 'Programming Language :: Python :: 3.10', + 'Programming Language :: Python :: 3.11', ] [tool.poetry.dependencies] -python = ">=3.8.1,<3.10" -awscli = ">=1.27.79" -boto3 = "^1.26.133" -botocore = "^1.29.79" +python = ">=3.8.1,<3.12" +awscli = ">=1.29.54" +boto3 = "^1.28.54" +botocore = "^1.31.54" certifi = ">=2021.5.30" chardet = "3.0.4" codeguru-profiler-agent = "^1.2.4" @@ -49,8 +52,8 @@ codeguru-profiler-agent = "^1.2.4" cryptography = "39.0.2" colorama = "0.3.3" dcicpyvcf = "1.0.0.1b0" # "^1.0.0" -dcicsnovault = "^10.0.2" -dcicutils = "^7.7.0" +dcicsnovault = "10.0.4.1b17" +dcicutils = "7.12.0.2b6" elasticsearch = "7.13.4" execnet = "1.4.1" future = ">=0.18.2,<1" @@ -88,7 +91,7 @@ python-dateutil = "^2.8.2" # python-magic is presently pinned to 0.4.15 in lockstep with dcicsnovault's requirements. See explanation there. python_magic = ">=0.4.24,<1" pytz = ">=2021.3" -PyYAML = "5.3.1" +PyYAML = "^6.0.1" rdflib = "^4.2.2" rdflib-jsonld = ">=0.5.0,<1.0.0" # repoze.debug is needed to use pyramid.pserve - Will Feb 17 2022 @@ -122,12 +125,11 @@ WSGIProxy2 = "0.4.2" "zope.deprecation" = "^4.4.0" "zope.interface" = ">=4.7.2,<6" "zope.sqlalchemy" = "1.6" -pyyaml = "5.3.1" [tool.poetry.dev-dependencies] # PyCharm says boto3-stubs contains useful type hints -boto3-stubs = "^1.26.79" -botocore-stubs = "^1.29.79" +boto3-stubs = "^1.28.54" +botocore-stubs = "^1.31.54" coverage = ">=6.2" codacy-coverage = ">=1.3.11" coveralls = ">=3.3.1" @@ -179,6 +181,7 @@ dis2pheno = "encoded.commands.parse_hpoa:main" es-index-data = "snovault.commands.es_index_data:main" export-data = "encoded.commands.export_data:main" extract-test-data = "encoded.commands.extract_test_data:main" +generate-local-access-key = "snovault.commands.generate_local_access_key:main" import-data = "encoded.commands.import_data:main" jsonld-rdf = "encoded.commands.jsonld_rdf:main" load-access-keys = "encoded.commands.load_access_keys:main" @@ -203,6 +206,7 @@ submission-test = "encoded.commands.submission_test:main" # submit-metadata-bundle = "encoded.commands.submit_metadata_bundle:main" update-inserts-from-server = "encoded.commands.update_inserts_from_server:main" verify-item = "encoded.commands.verify_item:main" +view-local-object= "snovault.commands.view_local_object:main" # cgap-specific commands clear-variants-and-genes = "encoded.commands.clear_variants_and_genes:main" gene-table-intake = "encoded.commands.gene_table_intake:main" diff --git a/src/encoded/schemas/access_key.json b/src/encoded/schemas/access_key.json deleted file mode 100644 index af8c34dca7..0000000000 --- a/src/encoded/schemas/access_key.json +++ /dev/null @@ -1,69 +0,0 @@ -{ - "title": "Admin access key", - "$id": "/profiles/access_key.json", - "$schema": "https://json-schema.org/draft/2020-12/schema", - "required": [], - "additionalProperties": false, - "mixinProperties": [ - { - "$ref": "mixins.json#/schema_version" - }, - { - "$ref": "mixins.json#/uuid" - }, - { - "$ref": "mixins.json#/submitted" - }, - { - "$ref": "mixins.json#/modified" - } - ], - "type": "object", - "properties": { - "schema_version": { - "default": "1" - }, - "status": { - "title": "Status", - "type": "string", - "default": "current", - "enum": [ - "current", - "deleted" - ] - }, - "user": { - "title": "User", - "comment": "Only admins are allowed to set this value.", - "type": "string", - "linkTo": "User" - }, - "description": { - "title": "Description", - "type": "string", - "formInput": "textarea" - }, - "access_key_id": { - "title": "Access key ID", - "comment": "Only admins are allowed to set this value.", - "type": "string", - "uniqueKey": true - }, - "secret_access_key_hash": { - "title": "Secret access key Hash", - "comment": "Only admins are allowed to set this value.", - "type": "string" - }, - "expiration_date": { - "Title": "Expiration Date", - "comment": "Only admins are allowed to set this value.", - "type": "string", - "permission": "restricted_fields" - } - }, - "facets": { - "user.display_title": { - "title": "User Name" - } - } -} diff --git a/src/encoded/tests/test_schemas.py b/src/encoded/tests/test_schemas.py index 1fbe466fb9..16f0a08c53 100644 --- a/src/encoded/tests/test_schemas.py +++ b/src/encoded/tests/test_schemas.py @@ -249,7 +249,7 @@ def test_linkTo_saves_uuid(root, bgm_user, institution): def test_mixinProperties(): - schema = load_schema('encoded:schemas/access_key.json') + schema = load_schema('snovalt:schemas/access_key.json') assert schema['properties']['uuid']['type'] == 'string' diff --git a/src/encoded/types/access_key.py b/src/encoded/types/access_key.py deleted file mode 100644 index 5fe8e01ee1..0000000000 --- a/src/encoded/types/access_key.py +++ /dev/null @@ -1,161 +0,0 @@ -"""Access_key types file.""" - -from pyramid.view import view_config -from pyramid.security import ( - Allow, - Deny, - Authenticated, - Everyone, -) -from pyramid.settings import asbool -import datetime -from .base import ( - Item, - DELETED_ACL, - ONLY_ADMIN_VIEW_ACL, -) -from ..authentication import ( - generate_password, - generate_user, - CRYPT_CONTEXT, -) -from snovault import ( - collection, - load_schema, -) -from snovault.crud_views import ( - collection_add, - item_edit, -) -from snovault.validators import ( - validate_item_content_post, -) -from snovault.util import debug_log - -@collection( - name='access-keys', - unique_key='access_key:access_key_id', - properties={ - 'title': 'Access keys', - 'description': 'Programmatic access keys', - }, - acl=[ - (Allow, Authenticated, 'add'), - (Allow, 'group.admin', 'list'), - (Allow, 'group.read-only-admin', 'list'), - (Allow, 'remoteuser.INDEXER', 'list'), - (Allow, 'remoteuser.EMBED', 'list'), - (Deny, Everyone, 'list'), - ]) -class AccessKey(Item): - """AccessKey class.""" - ACCESS_KEY_EXPIRATION_TIME = 90 # days - item_type = 'access_key' - schema = load_schema('encoded:schemas/access_key.json') - name_key = 'access_key_id' - embedded_list = [] - - STATUS_ACL = { - 'current': [(Allow, 'role.owner', ['view', 'edit'])] + ONLY_ADMIN_VIEW_ACL, - 'deleted': DELETED_ACL, - } - - @classmethod - def create(cls, registry, uuid, properties, sheets=None): - """ Sets the access key timeout 90 days from creation. """ - properties['expiration_date'] = (datetime.datetime.utcnow() + datetime.timedelta( - days=cls.ACCESS_KEY_EXPIRATION_TIME)).isoformat() - return super().create(registry, uuid, properties, sheets) - - def __ac_local_roles__(self): - """grab and return user as owner.""" - owner = 'userid.%s' % self.properties['user'] - return {owner: 'role.owner'} - - def __json__(self, request): - """delete the secret access key has from the object when used.""" - properties = super(AccessKey, self).__json__(request) - del properties['secret_access_key_hash'] - return properties - - def update(self, properties, sheets=None): - """smth.""" - # make sure PUTs preserve the secret access key hash - if 'secret_access_key_hash' not in properties: - new_properties = self.properties.copy() - new_properties.update(properties) - properties = new_properties - # set new expiration - properties['expiration_date'] = (datetime.datetime.utcnow() + datetime.timedelta( - days=self.ACCESS_KEY_EXPIRATION_TIME)).isoformat() - self._update(properties, sheets) - - class Collection(Item.Collection): - pass - - -# access keys have view permissions for update so readonly admin and the like -# can create access keys to download files. -@view_config(context=AccessKey.Collection, request_method='POST', - permission='add', - validators=[validate_item_content_post]) -@debug_log -def access_key_add(context, request): - """smth.""" - crypt_context = request.registry[CRYPT_CONTEXT] - - if 'access_key_id' not in request.validated: - request.validated['access_key_id'] = generate_user() - - if 'user' not in request.validated: - request.validated['user'], = [ - principal.split('.', 1)[1] - for principal in request.effective_principals - if principal.startswith('userid.') - ] - - password = None - if 'secret_access_key_hash' not in request.validated: - password = generate_password() - request.validated['secret_access_key_hash'] = crypt_context.hash(password) - - result = collection_add(context, request) - - if password is None: - result['secret_access_key'] = None - else: - result['secret_access_key'] = password - - result['access_key_id'] = request.validated['access_key_id'] - result['description'] = request.validated.get('description', "") - return result - - -@view_config(name='reset-secret', context=AccessKey, - permission='add', - request_method='POST', subpath_segments=0) -@debug_log -def access_key_reset_secret(context, request): - """smth.""" - request.validated = context.properties.copy() - crypt_context = request.registry[CRYPT_CONTEXT] - password = generate_password() - new_hash = crypt_context.hash(password) - request.validated['secret_access_key_hash'] = new_hash - result = item_edit(context, request, render=False) - result['access_key_id'] = request.validated['access_key_id'] - result['secret_access_key'] = password - return result - - -@view_config(context=AccessKey, permission='view_raw', request_method='GET', - name='raw') -@debug_log -def access_key_view_raw(context, request): - """smth.""" - if asbool(request.params.get('upgrade', True)): - properties = context.upgrade_properties() - else: - properties = context.properties.copy() - del properties['secret_access_key_hash'] - return properties From f21581748bfedabb8eaab73a7d46f4dda8ce1019 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 26 Sep 2023 09:17:36 -0400 Subject: [PATCH 02/25] Comments in CHANGELOG.rst --- CHANGELOG.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 3286beaba3..6af5dd6bb6 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -10,6 +10,7 @@ Change Log ====== * Upgrade to Python 3.11. * Changed pyyaml version to ^6.0.1. +* Updated boto versions. * Removed types/access_key.py and schemas/access_key.json as the ones in snovault are sufficient. * Added generate-local-access-key script (from snovault) to pyproject.toml; orignally created for smaht-portal since early in development no way to From 0f5dc2ee22c45f2b12783af0f6ebfda9acfcd26f Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 26 Sep 2023 09:33:00 -0400 Subject: [PATCH 03/25] Changed import of Mapping from collections to collections.abc --- src/encoded/ingestion/table_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/encoded/ingestion/table_utils.py b/src/encoded/ingestion/table_utils.py index 3a9c825267..f5714680f5 100644 --- a/src/encoded/ingestion/table_utils.py +++ b/src/encoded/ingestion/table_utils.py @@ -3,7 +3,7 @@ import io import json import logging -from collections import Mapping +from collections.abc import Mapping from ..util import resolve_file_path logger = logging.getLogger(__name__) From 7dbf212103ed8cb30ed048176a01f22ddcb0e01d Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 26 Sep 2023 10:03:27 -0400 Subject: [PATCH 04/25] Typo! --- src/encoded/tests/test_schemas.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/encoded/tests/test_schemas.py b/src/encoded/tests/test_schemas.py index 16f0a08c53..0599a93a72 100644 --- a/src/encoded/tests/test_schemas.py +++ b/src/encoded/tests/test_schemas.py @@ -249,7 +249,7 @@ def test_linkTo_saves_uuid(root, bgm_user, institution): def test_mixinProperties(): - schema = load_schema('snovalt:schemas/access_key.json') + schema = load_schema('snovault:schemas/access_key.json') assert schema['properties']['uuid']['type'] == 'string' From e5f396d4e8ec2031bd707f86f89741f3c458b4e8 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 26 Sep 2023 13:56:21 -0400 Subject: [PATCH 05/25] Update snovault version --- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index 83738c61e6..422e8a8c38 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1105,13 +1105,13 @@ setuptools = "*" [[package]] name = "dcicsnovault" -version = "10.0.4.1b17" +version = "10.0.4.1b18" description = "Storage support for 4DN Data Portals." optional = false python-versions = ">=3.8.1,<3.12" files = [ - {file = "dcicsnovault-10.0.4.1b17-py3-none-any.whl", hash = "sha256:ac0ef9bff3d790b26eb6f167c7f38f1ac550bed2daa5e7e7792e88ca98614973"}, - {file = "dcicsnovault-10.0.4.1b17.tar.gz", hash = "sha256:8c8e3fd44094d597904cbf361d35bdafcf0b08df53a0dbeb0f380b1f710cd2fb"}, + {file = "dcicsnovault-10.0.4.1b18-py3-none-any.whl", hash = "sha256:d245313c33ceaf728d045b3d9f873225e546824e6209e2b3c980f893dc97c371"}, + {file = "dcicsnovault-10.0.4.1b18.tar.gz", hash = "sha256:a5412c43b73f6a474ea84f0b63490ef33cf00684fa4b953076647211ce60b6d8"}, ] [package.dependencies] @@ -4038,4 +4038,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "9b305b474c03a00950ce920400a1e568aa40595988f6eb93ddbf6b9a0ef1948b" +content-hash = "a97dd739971e451990982686a55b3d9f3f589ac93ddcd0ad330c5589ba9fd202" diff --git a/pyproject.toml b/pyproject.toml index ba57dd55f3..b436414aa2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,7 +52,7 @@ codeguru-profiler-agent = "^1.2.4" cryptography = "39.0.2" colorama = "0.3.3" dcicpyvcf = "1.0.0.1b0" # "^1.0.0" -dcicsnovault = "10.0.4.1b17" +dcicsnovault = "10.0.4.1b18" dcicutils = "7.12.0.2b6" elasticsearch = "7.13.4" execnet = "1.4.1" From 9f262986c805e6579019d96a00cea2ed630fcbb1 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 26 Sep 2023 15:54:04 -0400 Subject: [PATCH 06/25] update version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b436414aa2..3521153d94 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "cgap-portal". name = "encoded" -version = "14.3.1.1b1" # TODO: To become 15.0.0 +version = "14.3.1.1b2" # TODO: To become 15.0.0 description = "Computational Genome Analysis Platform" authors = ["4DN-DCIC Team "] license = "MIT" From 27f5a7872e51b73ffe359397ff925633adb20702 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 26 Sep 2023 17:01:59 -0400 Subject: [PATCH 07/25] TEMPORARILY putting access_key.py/json back to debug GA failure. --- src/encoded/schemas/access_key.json | 69 ++++++++++++ src/encoded/tests/test_schemas.py | 2 +- src/encoded/types/access_key.py | 161 ++++++++++++++++++++++++++++ 3 files changed, 231 insertions(+), 1 deletion(-) create mode 100644 src/encoded/schemas/access_key.json create mode 100644 src/encoded/types/access_key.py diff --git a/src/encoded/schemas/access_key.json b/src/encoded/schemas/access_key.json new file mode 100644 index 0000000000..af8c34dca7 --- /dev/null +++ b/src/encoded/schemas/access_key.json @@ -0,0 +1,69 @@ +{ + "title": "Admin access key", + "$id": "/profiles/access_key.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", + "required": [], + "additionalProperties": false, + "mixinProperties": [ + { + "$ref": "mixins.json#/schema_version" + }, + { + "$ref": "mixins.json#/uuid" + }, + { + "$ref": "mixins.json#/submitted" + }, + { + "$ref": "mixins.json#/modified" + } + ], + "type": "object", + "properties": { + "schema_version": { + "default": "1" + }, + "status": { + "title": "Status", + "type": "string", + "default": "current", + "enum": [ + "current", + "deleted" + ] + }, + "user": { + "title": "User", + "comment": "Only admins are allowed to set this value.", + "type": "string", + "linkTo": "User" + }, + "description": { + "title": "Description", + "type": "string", + "formInput": "textarea" + }, + "access_key_id": { + "title": "Access key ID", + "comment": "Only admins are allowed to set this value.", + "type": "string", + "uniqueKey": true + }, + "secret_access_key_hash": { + "title": "Secret access key Hash", + "comment": "Only admins are allowed to set this value.", + "type": "string" + }, + "expiration_date": { + "Title": "Expiration Date", + "comment": "Only admins are allowed to set this value.", + "type": "string", + "permission": "restricted_fields" + } + }, + "facets": { + "user.display_title": { + "title": "User Name" + } + } +} diff --git a/src/encoded/tests/test_schemas.py b/src/encoded/tests/test_schemas.py index 0599a93a72..1fbe466fb9 100644 --- a/src/encoded/tests/test_schemas.py +++ b/src/encoded/tests/test_schemas.py @@ -249,7 +249,7 @@ def test_linkTo_saves_uuid(root, bgm_user, institution): def test_mixinProperties(): - schema = load_schema('snovault:schemas/access_key.json') + schema = load_schema('encoded:schemas/access_key.json') assert schema['properties']['uuid']['type'] == 'string' diff --git a/src/encoded/types/access_key.py b/src/encoded/types/access_key.py new file mode 100644 index 0000000000..5fe8e01ee1 --- /dev/null +++ b/src/encoded/types/access_key.py @@ -0,0 +1,161 @@ +"""Access_key types file.""" + +from pyramid.view import view_config +from pyramid.security import ( + Allow, + Deny, + Authenticated, + Everyone, +) +from pyramid.settings import asbool +import datetime +from .base import ( + Item, + DELETED_ACL, + ONLY_ADMIN_VIEW_ACL, +) +from ..authentication import ( + generate_password, + generate_user, + CRYPT_CONTEXT, +) +from snovault import ( + collection, + load_schema, +) +from snovault.crud_views import ( + collection_add, + item_edit, +) +from snovault.validators import ( + validate_item_content_post, +) +from snovault.util import debug_log + +@collection( + name='access-keys', + unique_key='access_key:access_key_id', + properties={ + 'title': 'Access keys', + 'description': 'Programmatic access keys', + }, + acl=[ + (Allow, Authenticated, 'add'), + (Allow, 'group.admin', 'list'), + (Allow, 'group.read-only-admin', 'list'), + (Allow, 'remoteuser.INDEXER', 'list'), + (Allow, 'remoteuser.EMBED', 'list'), + (Deny, Everyone, 'list'), + ]) +class AccessKey(Item): + """AccessKey class.""" + ACCESS_KEY_EXPIRATION_TIME = 90 # days + item_type = 'access_key' + schema = load_schema('encoded:schemas/access_key.json') + name_key = 'access_key_id' + embedded_list = [] + + STATUS_ACL = { + 'current': [(Allow, 'role.owner', ['view', 'edit'])] + ONLY_ADMIN_VIEW_ACL, + 'deleted': DELETED_ACL, + } + + @classmethod + def create(cls, registry, uuid, properties, sheets=None): + """ Sets the access key timeout 90 days from creation. """ + properties['expiration_date'] = (datetime.datetime.utcnow() + datetime.timedelta( + days=cls.ACCESS_KEY_EXPIRATION_TIME)).isoformat() + return super().create(registry, uuid, properties, sheets) + + def __ac_local_roles__(self): + """grab and return user as owner.""" + owner = 'userid.%s' % self.properties['user'] + return {owner: 'role.owner'} + + def __json__(self, request): + """delete the secret access key has from the object when used.""" + properties = super(AccessKey, self).__json__(request) + del properties['secret_access_key_hash'] + return properties + + def update(self, properties, sheets=None): + """smth.""" + # make sure PUTs preserve the secret access key hash + if 'secret_access_key_hash' not in properties: + new_properties = self.properties.copy() + new_properties.update(properties) + properties = new_properties + # set new expiration + properties['expiration_date'] = (datetime.datetime.utcnow() + datetime.timedelta( + days=self.ACCESS_KEY_EXPIRATION_TIME)).isoformat() + self._update(properties, sheets) + + class Collection(Item.Collection): + pass + + +# access keys have view permissions for update so readonly admin and the like +# can create access keys to download files. +@view_config(context=AccessKey.Collection, request_method='POST', + permission='add', + validators=[validate_item_content_post]) +@debug_log +def access_key_add(context, request): + """smth.""" + crypt_context = request.registry[CRYPT_CONTEXT] + + if 'access_key_id' not in request.validated: + request.validated['access_key_id'] = generate_user() + + if 'user' not in request.validated: + request.validated['user'], = [ + principal.split('.', 1)[1] + for principal in request.effective_principals + if principal.startswith('userid.') + ] + + password = None + if 'secret_access_key_hash' not in request.validated: + password = generate_password() + request.validated['secret_access_key_hash'] = crypt_context.hash(password) + + result = collection_add(context, request) + + if password is None: + result['secret_access_key'] = None + else: + result['secret_access_key'] = password + + result['access_key_id'] = request.validated['access_key_id'] + result['description'] = request.validated.get('description', "") + return result + + +@view_config(name='reset-secret', context=AccessKey, + permission='add', + request_method='POST', subpath_segments=0) +@debug_log +def access_key_reset_secret(context, request): + """smth.""" + request.validated = context.properties.copy() + crypt_context = request.registry[CRYPT_CONTEXT] + password = generate_password() + new_hash = crypt_context.hash(password) + request.validated['secret_access_key_hash'] = new_hash + result = item_edit(context, request, render=False) + result['access_key_id'] = request.validated['access_key_id'] + result['secret_access_key'] = password + return result + + +@view_config(context=AccessKey, permission='view_raw', request_method='GET', + name='raw') +@debug_log +def access_key_view_raw(context, request): + """smth.""" + if asbool(request.params.get('upgrade', True)): + properties = context.upgrade_properties() + else: + properties = context.properties.copy() + del properties['secret_access_key_hash'] + return properties From 74db13e6d4241d1cfa0eb31fa554eda62b5c5b73 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Wed, 27 Sep 2023 05:52:45 -0400 Subject: [PATCH 08/25] Update access_key.{json,py} back. --- src/encoded/schemas/access_key.json | 69 ------------ src/encoded/types/access_key.py | 161 ---------------------------- 2 files changed, 230 deletions(-) delete mode 100644 src/encoded/schemas/access_key.json delete mode 100644 src/encoded/types/access_key.py diff --git a/src/encoded/schemas/access_key.json b/src/encoded/schemas/access_key.json deleted file mode 100644 index af8c34dca7..0000000000 --- a/src/encoded/schemas/access_key.json +++ /dev/null @@ -1,69 +0,0 @@ -{ - "title": "Admin access key", - "$id": "/profiles/access_key.json", - "$schema": "https://json-schema.org/draft/2020-12/schema", - "required": [], - "additionalProperties": false, - "mixinProperties": [ - { - "$ref": "mixins.json#/schema_version" - }, - { - "$ref": "mixins.json#/uuid" - }, - { - "$ref": "mixins.json#/submitted" - }, - { - "$ref": "mixins.json#/modified" - } - ], - "type": "object", - "properties": { - "schema_version": { - "default": "1" - }, - "status": { - "title": "Status", - "type": "string", - "default": "current", - "enum": [ - "current", - "deleted" - ] - }, - "user": { - "title": "User", - "comment": "Only admins are allowed to set this value.", - "type": "string", - "linkTo": "User" - }, - "description": { - "title": "Description", - "type": "string", - "formInput": "textarea" - }, - "access_key_id": { - "title": "Access key ID", - "comment": "Only admins are allowed to set this value.", - "type": "string", - "uniqueKey": true - }, - "secret_access_key_hash": { - "title": "Secret access key Hash", - "comment": "Only admins are allowed to set this value.", - "type": "string" - }, - "expiration_date": { - "Title": "Expiration Date", - "comment": "Only admins are allowed to set this value.", - "type": "string", - "permission": "restricted_fields" - } - }, - "facets": { - "user.display_title": { - "title": "User Name" - } - } -} diff --git a/src/encoded/types/access_key.py b/src/encoded/types/access_key.py deleted file mode 100644 index 5fe8e01ee1..0000000000 --- a/src/encoded/types/access_key.py +++ /dev/null @@ -1,161 +0,0 @@ -"""Access_key types file.""" - -from pyramid.view import view_config -from pyramid.security import ( - Allow, - Deny, - Authenticated, - Everyone, -) -from pyramid.settings import asbool -import datetime -from .base import ( - Item, - DELETED_ACL, - ONLY_ADMIN_VIEW_ACL, -) -from ..authentication import ( - generate_password, - generate_user, - CRYPT_CONTEXT, -) -from snovault import ( - collection, - load_schema, -) -from snovault.crud_views import ( - collection_add, - item_edit, -) -from snovault.validators import ( - validate_item_content_post, -) -from snovault.util import debug_log - -@collection( - name='access-keys', - unique_key='access_key:access_key_id', - properties={ - 'title': 'Access keys', - 'description': 'Programmatic access keys', - }, - acl=[ - (Allow, Authenticated, 'add'), - (Allow, 'group.admin', 'list'), - (Allow, 'group.read-only-admin', 'list'), - (Allow, 'remoteuser.INDEXER', 'list'), - (Allow, 'remoteuser.EMBED', 'list'), - (Deny, Everyone, 'list'), - ]) -class AccessKey(Item): - """AccessKey class.""" - ACCESS_KEY_EXPIRATION_TIME = 90 # days - item_type = 'access_key' - schema = load_schema('encoded:schemas/access_key.json') - name_key = 'access_key_id' - embedded_list = [] - - STATUS_ACL = { - 'current': [(Allow, 'role.owner', ['view', 'edit'])] + ONLY_ADMIN_VIEW_ACL, - 'deleted': DELETED_ACL, - } - - @classmethod - def create(cls, registry, uuid, properties, sheets=None): - """ Sets the access key timeout 90 days from creation. """ - properties['expiration_date'] = (datetime.datetime.utcnow() + datetime.timedelta( - days=cls.ACCESS_KEY_EXPIRATION_TIME)).isoformat() - return super().create(registry, uuid, properties, sheets) - - def __ac_local_roles__(self): - """grab and return user as owner.""" - owner = 'userid.%s' % self.properties['user'] - return {owner: 'role.owner'} - - def __json__(self, request): - """delete the secret access key has from the object when used.""" - properties = super(AccessKey, self).__json__(request) - del properties['secret_access_key_hash'] - return properties - - def update(self, properties, sheets=None): - """smth.""" - # make sure PUTs preserve the secret access key hash - if 'secret_access_key_hash' not in properties: - new_properties = self.properties.copy() - new_properties.update(properties) - properties = new_properties - # set new expiration - properties['expiration_date'] = (datetime.datetime.utcnow() + datetime.timedelta( - days=self.ACCESS_KEY_EXPIRATION_TIME)).isoformat() - self._update(properties, sheets) - - class Collection(Item.Collection): - pass - - -# access keys have view permissions for update so readonly admin and the like -# can create access keys to download files. -@view_config(context=AccessKey.Collection, request_method='POST', - permission='add', - validators=[validate_item_content_post]) -@debug_log -def access_key_add(context, request): - """smth.""" - crypt_context = request.registry[CRYPT_CONTEXT] - - if 'access_key_id' not in request.validated: - request.validated['access_key_id'] = generate_user() - - if 'user' not in request.validated: - request.validated['user'], = [ - principal.split('.', 1)[1] - for principal in request.effective_principals - if principal.startswith('userid.') - ] - - password = None - if 'secret_access_key_hash' not in request.validated: - password = generate_password() - request.validated['secret_access_key_hash'] = crypt_context.hash(password) - - result = collection_add(context, request) - - if password is None: - result['secret_access_key'] = None - else: - result['secret_access_key'] = password - - result['access_key_id'] = request.validated['access_key_id'] - result['description'] = request.validated.get('description', "") - return result - - -@view_config(name='reset-secret', context=AccessKey, - permission='add', - request_method='POST', subpath_segments=0) -@debug_log -def access_key_reset_secret(context, request): - """smth.""" - request.validated = context.properties.copy() - crypt_context = request.registry[CRYPT_CONTEXT] - password = generate_password() - new_hash = crypt_context.hash(password) - request.validated['secret_access_key_hash'] = new_hash - result = item_edit(context, request, render=False) - result['access_key_id'] = request.validated['access_key_id'] - result['secret_access_key'] = password - return result - - -@view_config(context=AccessKey, permission='view_raw', request_method='GET', - name='raw') -@debug_log -def access_key_view_raw(context, request): - """smth.""" - if asbool(request.params.get('upgrade', True)): - properties = context.upgrade_properties() - else: - properties = context.properties.copy() - del properties['secret_access_key_hash'] - return properties From a2ffd0f0e35e706ba058dfa68f0a7174646f3ec5 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Wed, 27 Sep 2023 07:30:22 -0400 Subject: [PATCH 09/25] debug --- src/encoded/tests/test_schemas.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/encoded/tests/test_schemas.py b/src/encoded/tests/test_schemas.py index 1fbe466fb9..0599a93a72 100644 --- a/src/encoded/tests/test_schemas.py +++ b/src/encoded/tests/test_schemas.py @@ -249,7 +249,7 @@ def test_linkTo_saves_uuid(root, bgm_user, institution): def test_mixinProperties(): - schema = load_schema('encoded:schemas/access_key.json') + schema = load_schema('snovault:schemas/access_key.json') assert schema['properties']['uuid']['type'] == 'string' From 22db0bc0490cff0c9bb8e76649661d7b6091d487 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Wed, 27 Sep 2023 09:35:02 -0400 Subject: [PATCH 10/25] Remove 3.11 from .github/workflows/main.yml for testing/debugging purposes. --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f87dd0e470..d56ad37ef9 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -27,7 +27,7 @@ jobs: matrix: test_type: ['UNIT', 'INDEX', 'DOCKER'] # We are really not set up for these next two to be multiplicative, so be careful adding more. - python_version: ['3.8', '3.11'] + python_version: ['3.8'] node_version: ['18'] # Steps represent a sequence of tasks that will be executed as part of the job From 40246359bd8e0b640fd6536fff8a5abc5238f576 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Wed, 27 Sep 2023 10:04:50 -0400 Subject: [PATCH 11/25] Put 3.11 back into .github/workflows/main.yml but removed 3.8 so only one. --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d56ad37ef9..e10c228ce7 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -27,7 +27,7 @@ jobs: matrix: test_type: ['UNIT', 'INDEX', 'DOCKER'] # We are really not set up for these next two to be multiplicative, so be careful adding more. - python_version: ['3.8'] + python_version: ['3.11'] node_version: ['18'] # Steps represent a sequence of tasks that will be executed as part of the job From 393bd255c3a821698425ae925f95ca0fec976499 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Wed, 27 Sep 2023 10:27:49 -0400 Subject: [PATCH 12/25] Now put back both 3.8 and 3.11 in .github/workflows/main.yml --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e10c228ce7..f87dd0e470 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -27,7 +27,7 @@ jobs: matrix: test_type: ['UNIT', 'INDEX', 'DOCKER'] # We are really not set up for these next two to be multiplicative, so be careful adding more. - python_version: ['3.11'] + python_version: ['3.8', '3.11'] node_version: ['18'] # Steps represent a sequence of tasks that will be executed as part of the job From 3f2b191d1e0de4c32726b8499bc2497a228421e1 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Wed, 27 Sep 2023 10:43:36 -0400 Subject: [PATCH 13/25] Again remove 3.8 from .github/workflows/main.yml so again there is only one. --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f87dd0e470..e10c228ce7 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -27,7 +27,7 @@ jobs: matrix: test_type: ['UNIT', 'INDEX', 'DOCKER'] # We are really not set up for these next two to be multiplicative, so be careful adding more. - python_version: ['3.8', '3.11'] + python_version: ['3.11'] node_version: ['18'] # Steps represent a sequence of tasks that will be executed as part of the job From 14581933c13918385dce4cebe06113358e8f2913 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Wed, 27 Sep 2023 13:47:18 -0400 Subject: [PATCH 14/25] Added back both 3.8 and 3.11 in .github/workflows/main.yml and added wait_for_index in test_create_mapping.py. --- .github/workflows/main.yml | 2 +- src/encoded/tests/test_create_mapping.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e10c228ce7..f87dd0e470 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -27,7 +27,7 @@ jobs: matrix: test_type: ['UNIT', 'INDEX', 'DOCKER'] # We are really not set up for these next two to be multiplicative, so be careful adding more. - python_version: ['3.11'] + python_version: ['3.8', '3.11'] node_version: ['18'] # Steps represent a sequence of tasks that will be executed as part of the job diff --git a/src/encoded/tests/test_create_mapping.py b/src/encoded/tests/test_create_mapping.py index a571cd453e..7f638bb910 100644 --- a/src/encoded/tests/test_create_mapping.py +++ b/src/encoded/tests/test_create_mapping.py @@ -98,8 +98,8 @@ def test_run_create_mapping_with_upgrader(mock_add_uuids, es_testapp, workbook): """ # Indexing might be out of date here. One thing that works but is heavyweight: - # from .test_static_page import wait_for_index - # wait_for_index(es_testapp) + from .test_static_page import wait_for_index + wait_for_index(es_testapp) # Another thing that might work is just to invoke the indexer in a more lightweight way and wait. es_testapp.post_json('/index', {}) time.sleep(2) From c1320f4734dca5d1805c9b05cbb6f559651ee94d Mon Sep 17 00:00:00 2001 From: David Michaels Date: Wed, 27 Sep 2023 14:36:42 -0400 Subject: [PATCH 15/25] Backed out both 3.8 and 3.11 from .github/workflows/main.yml - just 3.1 now --- .github/workflows/main.yml | 2 +- src/encoded/tests/test_create_mapping.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f87dd0e470..e10c228ce7 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -27,7 +27,7 @@ jobs: matrix: test_type: ['UNIT', 'INDEX', 'DOCKER'] # We are really not set up for these next two to be multiplicative, so be careful adding more. - python_version: ['3.8', '3.11'] + python_version: ['3.11'] node_version: ['18'] # Steps represent a sequence of tasks that will be executed as part of the job diff --git a/src/encoded/tests/test_create_mapping.py b/src/encoded/tests/test_create_mapping.py index 7f638bb910..a571cd453e 100644 --- a/src/encoded/tests/test_create_mapping.py +++ b/src/encoded/tests/test_create_mapping.py @@ -98,8 +98,8 @@ def test_run_create_mapping_with_upgrader(mock_add_uuids, es_testapp, workbook): """ # Indexing might be out of date here. One thing that works but is heavyweight: - from .test_static_page import wait_for_index - wait_for_index(es_testapp) + # from .test_static_page import wait_for_index + # wait_for_index(es_testapp) # Another thing that might work is just to invoke the indexer in a more lightweight way and wait. es_testapp.post_json('/index', {}) time.sleep(2) From 02368691703d7a10d9daf7537015beac2a21453b Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 14:36:11 -0400 Subject: [PATCH 16/25] update versions: dcicutils, dcicsnovault --- .github/workflows/main.yml | 2 +- poetry.lock | 340 ++++++++++++++++++------------------- pyproject.toml | 14 +- 3 files changed, 172 insertions(+), 184 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e10c228ce7..68b606e2d0 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -20,7 +20,7 @@ jobs: name: cgap-portal tests # The type of runner that the job will run on - runs-on: ubuntu-20.04 + 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"0.3.3" dcicpyvcf = "1.0.0.1b0" # "^1.0.0" -dcicsnovault = "10.0.4.1b18" -dcicutils = "7.12.0.2b6" +dcicsnovault = "10.0.4.1b22" +dcicutils = "7.12.0.2b9" elasticsearch = "7.13.4" execnet = "1.4.1" future = ">=0.18.2,<1" @@ -128,8 +128,8 @@ WSGIProxy2 = "0.4.2" [tool.poetry.dev-dependencies] # PyCharm says boto3-stubs contains useful type hints -boto3-stubs = "^1.28.54" -botocore-stubs = "^1.31.54" +boto3-stubs = "^1.28.56" +botocore-stubs = "^1.31.56" coverage = ">=6.2" codacy-coverage = ">=1.3.11" coveralls = ">=3.3.1" From 8d1e9e252f1c5fbdb84e8b6eadd88f4ddc70bdca Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 15:25:55 -0400 Subject: [PATCH 17/25] update snovault version --- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index c0afaf8c34..b69685d1e5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1093,13 +1093,13 @@ setuptools = "*" [[package]] name = "dcicsnovault" -version = "10.0.4.1b22" +version = "10.0.4.1b23" description = "Storage support for 4DN Data Portals." optional = false python-versions = ">=3.8.1,<3.12" files = [ - {file = "dcicsnovault-10.0.4.1b22-py3-none-any.whl", hash = "sha256:8f292f21216a24f1ccd1bf828669f6c98668db56d2b37336dd15aa63a4f20ddb"}, - {file = "dcicsnovault-10.0.4.1b22.tar.gz", hash = "sha256:00d9ec6bb27079a23c3dd72cd792c01bafe51185f257f38624e755b467d67337"}, + {file = "dcicsnovault-10.0.4.1b23-py3-none-any.whl", hash = "sha256:f479c840f3e63e754b226e52a4d9d8b10dfcfc0d0352a3506da1bdb496dfe7e8"}, + {file = "dcicsnovault-10.0.4.1b23.tar.gz", hash = "sha256:18cbf8e71b0e4b1594436b7ec852aa726940fabbc12527b729dfbf0f37ef6ab9"}, ] [package.dependencies] @@ -4026,4 +4026,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "d8574f85dbe17baab4dbb567cae96c9e8afe23fbc6cede5f0a7bdf3450a0c619" +content-hash = "d7df1eab2a4d36eb63a042e9ad5673e2e49ee6612cbc72b105d822f67857cc23" diff --git a/pyproject.toml b/pyproject.toml index ecfac12c80..73677e5060 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,7 +52,7 @@ codeguru-profiler-agent = "^1.2.4" cryptography = "39.0.2" colorama = "0.3.3" dcicpyvcf = "1.0.0.1b0" # "^1.0.0" -dcicsnovault = "10.0.4.1b22" +dcicsnovault = "10.0.4.1b23" dcicutils = "7.12.0.2b9" elasticsearch = "7.13.4" execnet = "1.4.1" From 35f6670350c9b321331ef3b724b8abb9fb21cbbd Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 16:14:52 -0400 Subject: [PATCH 18/25] update versions: dcicsnovault --- poetry.lock | 44 +++++++++++++++++++++++--------------------- pyproject.toml | 2 +- 2 files changed, 24 insertions(+), 22 deletions(-) diff --git a/poetry.lock b/poetry.lock index b69685d1e5..0337dcc1a4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -70,17 +70,17 @@ requests = ">=0.14.0" [[package]] name = "awscli" -version = "1.29.56" +version = "1.29.57" description = "Universal Command Line Environment for AWS." optional = false python-versions = ">= 3.7" files = [ - {file = "awscli-1.29.56-py3-none-any.whl", hash = "sha256:c32183b90398bef6db48ea73a853df7bfc1226067dec2b025247691a7668459a"}, - {file = "awscli-1.29.56.tar.gz", hash = "sha256:2664250be92addde8a1cf12688fba19c00d1987e37bcdfd654991055f8b895b4"}, + {file = "awscli-1.29.57-py3-none-any.whl", hash = "sha256:d7291cf485e73fe4315b84ecd1a2c5d90424d150ee36379a409c7ea7e7b0f5ca"}, + {file = "awscli-1.29.57.tar.gz", hash = "sha256:fb1304e468838adc67eb5cab224884072c7fc5e31e5ccad54b6ae27c85fa0a2f"}, ] [package.dependencies] -botocore = "1.31.56" +botocore = "1.31.57" colorama = ">=0.2.5,<0.4.5" docutils = ">=0.10,<0.17" PyYAML = ">=3.10,<6.1" @@ -218,17 +218,17 @@ files = [ [[package]] name = "boto3" -version = "1.28.56" +version = "1.28.57" description = "The AWS SDK for Python" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.56-py3-none-any.whl", hash = "sha256:f5fcb27cdbd08ca38d699f2d2e32d96d1d9fab3368c15c6bc326256612d2cfd7"}, - {file = "boto3-1.28.56.tar.gz", hash = "sha256:b927a7ed335d543c33c15fa63f1076f3fa8422959771c2187da74bc4395ab6e3"}, + {file = "boto3-1.28.57-py3-none-any.whl", hash = "sha256:5ddf24cf52c7fb6aaa332eaa08ae8c2afc8f2d1e8860680728533dd573904e32"}, + {file = "boto3-1.28.57.tar.gz", hash = "sha256:e2d2824ba6459b330d097e94039a9c4f96ae3f4bcdc731d620589ad79dcd16d3"}, ] [package.dependencies] -botocore = ">=1.31.56,<1.32.0" +botocore = ">=1.31.57,<1.32.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.7.0,<0.8.0" @@ -237,13 +237,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.28.56" -description = "Type annotations for boto3 1.28.56 generated with mypy-boto3-builder 7.19.0" +version = "1.28.57" +description = "Type annotations for boto3 1.28.57 generated with mypy-boto3-builder 7.19.0" optional = false python-versions = ">=3.7" files = [ - {file = "boto3-stubs-1.28.56.tar.gz", hash = "sha256:2b77d4b9e944ffa4308822dc0327269f47cc4527a97903a3c5d14b9abed4eaad"}, - {file = "boto3_stubs-1.28.56-py3-none-any.whl", hash = "sha256:e9c1f32463cf8e6ba56588f7c0f5cae52190b87eb19744ad1067a717be1c80b3"}, + {file = "boto3-stubs-1.28.57.tar.gz", hash = "sha256:61cd792792c2a16d70801d187ebed705c39962a70e90b5dc0f33d04001fb39ae"}, + {file = "boto3_stubs-1.28.57-py3-none-any.whl", hash = "sha256:b389a693e33d75ed19d38b4a2ba99d25f4f2045a3136f816d7fec4d27a71ddb4"}, ] [package.dependencies] @@ -257,7 +257,7 @@ account = ["mypy-boto3-account (>=1.28.0,<1.29.0)"] acm = ["mypy-boto3-acm (>=1.28.0,<1.29.0)"] acm-pca = ["mypy-boto3-acm-pca (>=1.28.0,<1.29.0)"] alexaforbusiness = ["mypy-boto3-alexaforbusiness (>=1.28.0,<1.29.0)"] -all = ["mypy-boto3-accessanalyzer (>=1.28.0,<1.29.0)", "mypy-boto3-account (>=1.28.0,<1.29.0)", "mypy-boto3-acm (>=1.28.0,<1.29.0)", "mypy-boto3-acm-pca (>=1.28.0,<1.29.0)", "mypy-boto3-alexaforbusiness (>=1.28.0,<1.29.0)", "mypy-boto3-amp (>=1.28.0,<1.29.0)", 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"mypy-boto3-route53-recovery-control-config (>=1.28.0,<1.29.0)", "mypy-boto3-route53-recovery-readiness (>=1.28.0,<1.29.0)", "mypy-boto3-route53domains (>=1.28.0,<1.29.0)", "mypy-boto3-route53resolver (>=1.28.0,<1.29.0)", "mypy-boto3-rum (>=1.28.0,<1.29.0)", "mypy-boto3-s3 (>=1.28.0,<1.29.0)", "mypy-boto3-s3control (>=1.28.0,<1.29.0)", "mypy-boto3-s3outposts (>=1.28.0,<1.29.0)", "mypy-boto3-sagemaker (>=1.28.0,<1.29.0)", "mypy-boto3-sagemaker-a2i-runtime (>=1.28.0,<1.29.0)", "mypy-boto3-sagemaker-edge (>=1.28.0,<1.29.0)", "mypy-boto3-sagemaker-featurestore-runtime (>=1.28.0,<1.29.0)", "mypy-boto3-sagemaker-geospatial (>=1.28.0,<1.29.0)", "mypy-boto3-sagemaker-metrics (>=1.28.0,<1.29.0)", "mypy-boto3-sagemaker-runtime (>=1.28.0,<1.29.0)", "mypy-boto3-savingsplans (>=1.28.0,<1.29.0)", "mypy-boto3-scheduler (>=1.28.0,<1.29.0)", "mypy-boto3-schemas (>=1.28.0,<1.29.0)", "mypy-boto3-sdb (>=1.28.0,<1.29.0)", "mypy-boto3-secretsmanager (>=1.28.0,<1.29.0)", "mypy-boto3-securityhub (>=1.28.0,<1.29.0)", "mypy-boto3-securitylake (>=1.28.0,<1.29.0)", "mypy-boto3-serverlessrepo (>=1.28.0,<1.29.0)", "mypy-boto3-service-quotas (>=1.28.0,<1.29.0)", "mypy-boto3-servicecatalog (>=1.28.0,<1.29.0)", "mypy-boto3-servicecatalog-appregistry (>=1.28.0,<1.29.0)", "mypy-boto3-servicediscovery (>=1.28.0,<1.29.0)", "mypy-boto3-ses (>=1.28.0,<1.29.0)", "mypy-boto3-sesv2 (>=1.28.0,<1.29.0)", "mypy-boto3-shield (>=1.28.0,<1.29.0)", "mypy-boto3-signer (>=1.28.0,<1.29.0)", "mypy-boto3-simspaceweaver (>=1.28.0,<1.29.0)", "mypy-boto3-sms (>=1.28.0,<1.29.0)", "mypy-boto3-sms-voice (>=1.28.0,<1.29.0)", "mypy-boto3-snow-device-management (>=1.28.0,<1.29.0)", "mypy-boto3-snowball (>=1.28.0,<1.29.0)", "mypy-boto3-sns (>=1.28.0,<1.29.0)", "mypy-boto3-sqs (>=1.28.0,<1.29.0)", "mypy-boto3-ssm (>=1.28.0,<1.29.0)", "mypy-boto3-ssm-contacts (>=1.28.0,<1.29.0)", "mypy-boto3-ssm-incidents (>=1.28.0,<1.29.0)", "mypy-boto3-ssm-sap (>=1.28.0,<1.29.0)", "mypy-boto3-sso (>=1.28.0,<1.29.0)", "mypy-boto3-sso-admin (>=1.28.0,<1.29.0)", "mypy-boto3-sso-oidc (>=1.28.0,<1.29.0)", "mypy-boto3-stepfunctions (>=1.28.0,<1.29.0)", "mypy-boto3-storagegateway (>=1.28.0,<1.29.0)", "mypy-boto3-sts (>=1.28.0,<1.29.0)", "mypy-boto3-support (>=1.28.0,<1.29.0)", "mypy-boto3-support-app (>=1.28.0,<1.29.0)", "mypy-boto3-swf (>=1.28.0,<1.29.0)", "mypy-boto3-synthetics (>=1.28.0,<1.29.0)", "mypy-boto3-textract (>=1.28.0,<1.29.0)", "mypy-boto3-timestream-query (>=1.28.0,<1.29.0)", "mypy-boto3-timestream-write (>=1.28.0,<1.29.0)", "mypy-boto3-tnb (>=1.28.0,<1.29.0)", "mypy-boto3-transcribe (>=1.28.0,<1.29.0)", "mypy-boto3-transfer (>=1.28.0,<1.29.0)", "mypy-boto3-translate (>=1.28.0,<1.29.0)", "mypy-boto3-verifiedpermissions (>=1.28.0,<1.29.0)", "mypy-boto3-voice-id (>=1.28.0,<1.29.0)", "mypy-boto3-vpc-lattice (>=1.28.0,<1.29.0)", "mypy-boto3-waf (>=1.28.0,<1.29.0)", "mypy-boto3-waf-regional (>=1.28.0,<1.29.0)", "mypy-boto3-wafv2 (>=1.28.0,<1.29.0)", "mypy-boto3-wellarchitected (>=1.28.0,<1.29.0)", "mypy-boto3-wisdom (>=1.28.0,<1.29.0)", "mypy-boto3-workdocs (>=1.28.0,<1.29.0)", "mypy-boto3-worklink (>=1.28.0,<1.29.0)", "mypy-boto3-workmail (>=1.28.0,<1.29.0)", "mypy-boto3-workmailmessageflow (>=1.28.0,<1.29.0)", "mypy-boto3-workspaces (>=1.28.0,<1.29.0)", "mypy-boto3-workspaces-web (>=1.28.0,<1.29.0)", "mypy-boto3-xray (>=1.28.0,<1.29.0)"] amp = ["mypy-boto3-amp (>=1.28.0,<1.29.0)"] amplify = ["mypy-boto3-amplify (>=1.28.0,<1.29.0)"] amplifybackend = ["mypy-boto3-amplifybackend (>=1.28.0,<1.29.0)"] @@ -286,8 +286,10 @@ backup = ["mypy-boto3-backup (>=1.28.0,<1.29.0)"] backup-gateway = ["mypy-boto3-backup-gateway (>=1.28.0,<1.29.0)"] backupstorage = ["mypy-boto3-backupstorage (>=1.28.0,<1.29.0)"] batch = ["mypy-boto3-batch (>=1.28.0,<1.29.0)"] +bedrock = ["mypy-boto3-bedrock (>=1.28.0,<1.29.0)"] +bedrock-runtime = ["mypy-boto3-bedrock-runtime (>=1.28.0,<1.29.0)"] billingconductor = ["mypy-boto3-billingconductor (>=1.28.0,<1.29.0)"] -boto3 = ["boto3 (==1.28.56)", "botocore (==1.31.56)"] +boto3 = ["boto3 (==1.28.57)", "botocore (==1.31.57)"] braket = ["mypy-boto3-braket (>=1.28.0,<1.29.0)"] budgets = ["mypy-boto3-budgets (>=1.28.0,<1.29.0)"] ce = ["mypy-boto3-ce (>=1.28.0,<1.29.0)"] @@ -613,13 +615,13 @@ xray = ["mypy-boto3-xray (>=1.28.0,<1.29.0)"] [[package]] name = "botocore" -version = "1.31.56" +version = "1.31.57" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">= 3.7" files = [ - {file = "botocore-1.31.56-py3-none-any.whl", hash = "sha256:66c686e4eda7051ffcc9357d9075390c8ab2f95a2977669039618ee186fb533b"}, - {file = "botocore-1.31.56.tar.gz", hash = "sha256:70252cd8abc2fe9b791328e187620f5a3911545e2520486b01ecfad31f41b9cb"}, + {file = "botocore-1.31.57-py3-none-any.whl", hash = "sha256:af006248276ff8e19e3ec7214478f6257035eb40aed865e405486500471ae71b"}, + {file = "botocore-1.31.57.tar.gz", hash = "sha256:301436174635bec739b225b840fc365ca00e5c1a63e5b2a19ee679d204e01b78"}, ] [package.dependencies] @@ -1093,13 +1095,13 @@ setuptools = "*" [[package]] name = "dcicsnovault" -version = "10.0.4.1b23" +version = "10.0.4.1b25" description = "Storage support for 4DN Data Portals." optional = false python-versions = ">=3.8.1,<3.12" files = [ - {file = "dcicsnovault-10.0.4.1b23-py3-none-any.whl", hash = "sha256:f479c840f3e63e754b226e52a4d9d8b10dfcfc0d0352a3506da1bdb496dfe7e8"}, - {file = "dcicsnovault-10.0.4.1b23.tar.gz", hash = "sha256:18cbf8e71b0e4b1594436b7ec852aa726940fabbc12527b729dfbf0f37ef6ab9"}, + {file = "dcicsnovault-10.0.4.1b25-py3-none-any.whl", hash = "sha256:c89938c05f097f1e196b1d8ccf68b782cb6f80d65d1b988013ffb3a8dce42ff0"}, + {file = "dcicsnovault-10.0.4.1b25.tar.gz", hash = "sha256:4ebba9b8d0b0e6a04295d0dc59469117cb01e3c309e235d81507048910e5d110"}, ] [package.dependencies] @@ -4026,4 +4028,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "d7df1eab2a4d36eb63a042e9ad5673e2e49ee6612cbc72b105d822f67857cc23" +content-hash = "c00e599361d8b19d9041b150b82641bce3216dbb13fa2ab70bbc74979820227f" diff --git a/pyproject.toml b/pyproject.toml index 73677e5060..eddd33a944 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,7 +52,7 @@ codeguru-profiler-agent = "^1.2.4" cryptography = "39.0.2" colorama = "0.3.3" dcicpyvcf = "1.0.0.1b0" # "^1.0.0" -dcicsnovault = "10.0.4.1b23" +dcicsnovault = "10.0.4.1b25" dcicutils = "7.12.0.2b9" elasticsearch = "7.13.4" execnet = "1.4.1" From 123251a43983f0e4153da29f61a33b5982042e9d Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 18:17:53 -0400 Subject: [PATCH 19/25] Updated Dockerfile with python:3.11.5-slim-bullseye and install_nginx_bullseye.sh --- Dockerfile | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index ad5adaf299..a3ea5f066f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,9 @@ # CGAP-Portal (Production) Dockerfile -# Debian Buster with Python 3.8.13 -FROM python:3.8.13-slim-buster +# Bullseye with Python 3.11.5 +# 2023-09-28: Update docker image to a Python 3.11 version; +# this was previously: FROM python:3.8.13-slim-buster +FROM python:3.11.5-slim-bullseye MAINTAINER William Ronchetti "william_ronchetti@hms.harvard.edu" @@ -32,7 +34,7 @@ ENV PATH="$VIRTUAL_ENV/bin:$PATH" # Note that the ordering of these operations is intentional to minimize package footprint WORKDIR /home/nginx/.nvm ENV NVM_DIR=/home/nginx/.nvm -COPY deploy/docker/production/install_nginx.sh /install_nginx.sh +COPY deploy/docker/production/install_nginx_bullseye.sh /install_nginx.sh # Temporarily replacing # curl -sSL https://install.python-poetry.org | POETRY_HOME=/opt/venv python - && \ From 973b70dd538ab3c2ced0b29e8004b3375b109c1b Mon Sep 17 00:00:00 2001 From: David Michaels Date: Fri, 29 Sep 2023 06:11:55 -0400 Subject: [PATCH 20/25] Minro update to main.yml for GA --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 68b606e2d0..38561f970e 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -108,7 +108,7 @@ jobs: poetry run wipe-test-indices $TEST_JOB_ID search-cgap-unit-testing-opensearch-tcs45cjpwgdzoi7pafr6oewq6u.us-east-1.es.amazonaws.com:443 - name: Docker Build - if: ${{ matrix.test_type == 'DOCKER' && matrix.node_version == '18' && matrix.python_version == '3.8' }} + if: ${{ matrix.test_type == 'DOCKER' && matrix.node_version == '18' && matrix.python_version == '3.11' }} run: | touch deploy/docker/local/docker_development.ini # cheap substitute for prepare-docker to make ignored file docker build . From 0467c8be1fd8b8a86ada9d6d110e436f424ab039 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Fri, 29 Sep 2023 09:47:30 -0400 Subject: [PATCH 21/25] Removed Python 3.7 from list in pyproject.toml --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index eddd33a944..3d11194c2f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,6 @@ classifiers = [ # Specify the Python versions you support here. In particular, ensure # that you indicate whether you support Python 2, Python 3 or both. 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', From 5931f514a52b7136831cc59bf6979d813276a036 Mon Sep 17 00:00:00 2001 From: Kent Pitman Date: Wed, 4 Oct 2023 19:03:35 -0400 Subject: [PATCH 22/25] Update dcicpyvcf to use latest version (3.0.0a4). --- poetry.lock | 193 +++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 2 +- 2 files changed, 187 insertions(+), 8 deletions(-) diff --git a/poetry.lock b/poetry.lock index 0337dcc1a4..885df886de 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.5.1 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 = "arrow" version = "1.2.3" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -29,6 +31,7 @@ python-dateutil = ">=2.7.0" name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -40,6 +43,7 @@ files = [ name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -58,6 +62,7 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte 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 = [ @@ -72,6 +77,7 @@ requests = ">=0.14.0" name = "awscli" version = "1.29.57" description = "Universal Command Line Environment for AWS." +category = "main" optional = false python-versions = ">= 3.7" files = [ @@ -91,6 +97,7 @@ s3transfer = ">=0.7.0,<0.8.0" name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" +category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -109,6 +116,7 @@ lxml = ["lxml"] name = "bitarray" version = "2.8.1" description = "efficient arrays of booleans -- C extension" +category = "main" optional = false python-versions = "*" files = [ @@ -220,6 +228,7 @@ files = [ name = "boto3" version = "1.28.57" description = "The AWS SDK for Python" +category = "main" optional = false python-versions = ">= 3.7" files = [ @@ -239,6 +248,7 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] name = "boto3-stubs" version = "1.28.57" description = "Type annotations for boto3 1.28.57 generated with mypy-boto3-builder 7.19.0" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -617,6 +627,7 @@ xray = ["mypy-boto3-xray (>=1.28.0,<1.29.0)"] name = "botocore" version = "1.31.57" description = "Low-level, data-driven core of boto 3." +category = "main" optional = false python-versions = ">= 3.7" files = [ @@ -636,6 +647,7 @@ crt = ["awscrt (==0.16.26)"] name = "botocore-stubs" version = "1.31.56" description = "Type annotations and code completion for botocore" +category = "dev" optional = false python-versions = ">=3.7,<4.0" files = [ @@ -651,6 +663,7 @@ typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.9\""} name = "certifi" version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -662,6 +675,7 @@ files = [ name = "cffi" version = "1.16.0" description = "Foreign Function Interface for Python calling C code." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -726,6 +740,7 @@ pycparser = "*" name = "chardet" version = "3.0.4" description = "Universal encoding detector for Python 2 and 3" +category = "main" optional = false python-versions = "*" files = [ @@ -737,6 +752,7 @@ files = [ name = "charset-normalizer" version = "3.2.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -821,6 +837,7 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -835,6 +852,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "codacy-coverage" version = "1.3.11" description = "Codacy coverage reporter for Python" +category = "dev" optional = false python-versions = "*" files = [ @@ -853,6 +871,7 @@ test = ["coverage", "nosetests"] name = "codeguru-profiler-agent" version = "1.2.4" description = "The Python agent to be used for Amazon CodeGuru Profiler" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -867,6 +886,7 @@ boto3 = ">=1.14.0" name = "colorama" version = "0.3.3" description = "Cross-platform colored terminal text." +category = "main" optional = false python-versions = "*" files = [ @@ -877,6 +897,7 @@ files = [ name = "coverage" version = "6.5.0" description = "Code coverage measurement for Python" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -942,6 +963,7 @@ toml = ["tomli"] name = "coveralls" version = "3.3.1" description = "Show coverage stats online via coveralls.io" +category = "dev" optional = false python-versions = ">= 3.5" files = [ @@ -950,7 +972,7 @@ files = [ ] [package.dependencies] -coverage = ">=4.1,<6.0.dev0 || >6.1,<6.1.1 || >6.1.1,<7.0" +coverage = ">=4.1,<6.0.0 || >6.1,<6.1.1 || >6.1.1,<7.0" docopt = ">=0.6.1" requests = ">=1.0.0" @@ -961,6 +983,7 @@ yaml = ["PyYAML (>=3.10)"] name = "cryptography" version = "39.0.2" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1006,6 +1029,7 @@ tox = ["tox"] name = "cycler" version = "0.11.0" description = "Composable style cycles" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1017,6 +1041,7 @@ files = [ name = "cython" version = "3.0.2" description = "The Cython compiler for writing C extensions in the Python language." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1082,21 +1107,26 @@ files = [ [[package]] name = "dcicpyvcf" -version = "1.0.0.1b0" +version = "3.0.0a4" description = "Variant Call Format (VCF) parser for Python" +category = "main" optional = false -python-versions = "*" +python-versions = ">=3.8.0,<3.12" files = [ - {file = "dcicpyvcf-1.0.0.1b0.tar.gz", hash = "sha256:6303f63cd6c486ba826e7ea44428f39e00d8411ca97d46874ab9f68df8f45959"}, + {file = "dcicpyvcf-3.0.0a4-py3-none-any.whl", hash = "sha256:6145ba55dc7ddbca3222e25f82dd9cc0741d2ba19b51251b572b31e9c6f09477"}, + {file = "dcicpyvcf-3.0.0a4.tar.gz", hash = "sha256:0902758bcead6ef0df6ac184ba2952a0b2e3fe27571a2cf93265d8693d1c8b32"}, ] [package.dependencies] +cython = "*" +pysam = ">=0.21.0" setuptools = "*" [[package]] name = "dcicsnovault" version = "10.0.4.1b25" description = "Storage support for 4DN Data Portals." +category = "main" optional = false python-versions = ">=3.8.1,<3.12" files = [ @@ -1153,6 +1183,7 @@ xlrd = ">=1.0.0,<2.0.0" name = "dcicutils" version = "7.12.0.2b9" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" +category = "main" optional = false python-versions = ">=3.8,<3.12" files = [ @@ -1186,6 +1217,7 @@ webtest = ">=2.0.34,<3.0.0" name = "docker" version = "4.4.4" description = "A Python library for the Docker Engine API." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1207,6 +1239,7 @@ tls = ["cryptography (>=1.3.4)", "idna (>=2.0.0)", "pyOpenSSL (>=17.5.0)"] name = "docopt" version = "0.6.2" description = "Pythonic argument parser, that will make you smile" +category = "dev" optional = false python-versions = "*" files = [ @@ -1217,6 +1250,7 @@ files = [ name = "docutils" version = "0.16" description = "Docutils -- Python Documentation Utilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1228,6 +1262,7 @@ 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 = [ @@ -1249,6 +1284,7 @@ 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 = [ @@ -1268,6 +1304,7 @@ develop = ["coverage (<5.0.0)", "mock", "pytest (>=3.0.0)", "pytest-cov", "pytes 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 = [ @@ -1279,6 +1316,7 @@ files = [ name = "exceptiongroup" version = "1.1.3" description = "Backport of PEP 654 (exception groups)" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1293,6 +1331,7 @@ test = ["pytest (>=6)"] name = "execnet" version = "1.4.1" description = "execnet: rapid multi-Python deployment" +category = "main" optional = false python-versions = "*" files = [ @@ -1307,6 +1346,7 @@ apipkg = ">=1.4" name = "flake8" version = "6.1.0" description = "the modular source code checker: pep8 pyflakes and co" +category = "dev" optional = false python-versions = ">=3.8.1" files = [ @@ -1323,6 +1363,7 @@ pyflakes = ">=3.1.0,<3.2.0" name = "flaky" version = "3.7.0" description = "Plugin for nose or pytest that automatically reruns flaky tests." +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1334,6 +1375,7 @@ files = [ name = "flask" version = "2.1.3" description = "A simple framework for building complex web applications." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1356,6 +1398,7 @@ dotenv = ["python-dotenv"] 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 = [ @@ -1367,6 +1410,7 @@ 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 = [ @@ -1377,6 +1421,7 @@ files = [ name = "gitdb" version = "4.0.10" description = "Git Object Database" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1391,6 +1436,7 @@ smmap = ">=3.0.1,<6" name = "gitpython" version = "3.1.37" description = "GitPython is a Python library used to interact with Git repositories" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1408,6 +1454,7 @@ test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit" name = "granite-suite" version = "0.1.11b0" description = "granite is a collection of software to call, filter and work with genomic variants" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1427,6 +1474,7 @@ pytabix = ">=0.0.2" name = "greenlet" version = "2.0.2" description = "Lightweight in-process concurrent programming" +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" files = [ @@ -1500,6 +1548,7 @@ test = ["objgraph", "psutil"] name = "h5py" version = "3.9.0" description = "Read and write HDF5 files from Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1533,6 +1582,7 @@ numpy = ">=1.17.3" 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 = [ @@ -1554,6 +1604,7 @@ lxml = ["lxml"] name = "humanfriendly" version = "1.44.9" description = "Human friendly output for text interfaces using Python" +category = "main" optional = false python-versions = "*" files = [ @@ -1565,6 +1616,7 @@ files = [ name = "hupper" version = "1.5" description = "Integrated process monitor for developing and reloading daemons." +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -1580,6 +1632,7 @@ 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 = [ @@ -1591,6 +1644,7 @@ files = [ name = "importlib-metadata" version = "6.8.0" description = "Read metadata from Python packages" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1610,6 +1664,7 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs name = "importlib-resources" version = "6.1.0" description = "Read resources from Python packages" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1628,6 +1683,7 @@ testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1639,6 +1695,7 @@ files = [ name = "isodate" version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" +category = "main" optional = false python-versions = "*" files = [ @@ -1653,6 +1710,7 @@ six = "*" name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1667,6 +1725,7 @@ arrow = ">=0.15.0" name = "itsdangerous" version = "2.1.2" description = "Safely pass data to untrusted environments and back." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1678,6 +1737,7 @@ files = [ name = "jinja2" version = "3.1.2" description = "A very fast and expressive template engine." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1695,6 +1755,7 @@ i18n = ["Babel (>=2.7)"] name = "jmespath" version = "0.10.0" description = "JSON Matching Expressions" +category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1706,6 +1767,7 @@ files = [ name = "jsonpointer" version = "2.4" description = "Identify specific nodes in a JSON document (RFC 6901)" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -1717,6 +1779,7 @@ files = [ name = "jsonschema" version = "4.19.1" description = "An implementation of JSON Schema validation for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1748,6 +1811,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.7.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1763,6 +1827,7 @@ referencing = ">=0.28.0" name = "kiwisolver" version = "1.4.5" description = "A fast implementation of the Cassowary constraint solver" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1876,6 +1941,7 @@ files = [ name = "markupsafe" version = "2.1.3" description = "Safely add untrusted strings to HTML/XML markup." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1935,6 +2001,7 @@ files = [ name = "matplotlib" version = "3.3.4" description = "Python plotting package" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1977,6 +2044,7 @@ python-dateutil = ">=2.1" name = "mccabe" version = "0.7.0" description = "McCabe checker, plugin for flake8" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1988,6 +2056,7 @@ files = [ name = "moto" version = "4.0.3" description = "A library that allows your python tests to easily mock out the boto library" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2036,6 +2105,7 @@ xray = ["aws-xray-sdk (>=0.93,!=0.96)", "setuptools"] name = "negspy" version = "0.2.24" description = "Python NGS tools" +category = "main" optional = false python-versions = "*" files = [ @@ -2046,6 +2116,7 @@ files = [ name = "netaddr" version = "0.9.0" description = "A network address manipulation library for Python" +category = "main" optional = false python-versions = "*" files = [ @@ -2057,6 +2128,7 @@ files = [ name = "numpy" version = "1.24.4" description = "Fundamental package for array computing in Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2094,6 +2166,7 @@ files = [ name = "openpyxl" version = "3.1.2" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2108,6 +2181,7 @@ et-xmlfile = "*" name = "opensearch-py" version = "2.3.1" description = "Python client for OpenSearch" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4" files = [ @@ -2132,6 +2206,7 @@ kerberos = ["requests-kerberos"] name = "packaging" version = "23.1" description = "Core utilities for Python packages" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2143,6 +2218,7 @@ files = [ name = "passlib" version = "1.7.4" description = "comprehensive password hashing framework supporting over 30 schemes" +category = "main" optional = false python-versions = "*" files = [ @@ -2160,6 +2236,7 @@ totp = ["cryptography"] name = "pastedeploy" version = "1.5.2" description = "Load, configure, and compose WSGI applications and servers" +category = "main" optional = false python-versions = "*" files = [ @@ -2174,6 +2251,7 @@ paste = ["Paste"] name = "pbkdf2" version = "1.3" description = "PKCS#5 v2.0 PBKDF2 Module" +category = "main" optional = false python-versions = "*" files = [ @@ -2184,6 +2262,7 @@ files = [ name = "pillow" version = "9.5.0" description = "Python Imaging Library (Fork)" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2263,6 +2342,7 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa 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 = [ @@ -2280,6 +2360,7 @@ test = ["docutils", "pytest-cov", "pytest-pycodestyle", "pytest-runner"] name = "pipdeptree" version = "2.13.0" description = "Command line utility to show dependency tree of packages." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2295,6 +2376,7 @@ test = ["covdefaults (>=2.3)", "diff-cover (>=7.7)", "pip (>=23.2)", "pytest (>= name = "pkgutil-resolve-name" version = "1.3.10" description = "Resolve a name to an object." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2306,6 +2388,7 @@ files = [ 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 = [ @@ -2324,6 +2407,7 @@ 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 = [ @@ -2342,6 +2426,7 @@ testing = ["pytest", "pytest-cov"] name = "pluggy" version = "1.3.0" description = "plugin and hook calling mechanisms for python" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2357,6 +2442,7 @@ testing = ["pytest", "pytest-benchmark"] name = "psutil" version = "5.9.5" 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.*" files = [ @@ -2383,6 +2469,7 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "psycopg2" version = "2.9.8" description = "psycopg2 - Python-PostgreSQL Database Adapter" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2403,6 +2490,7 @@ files = [ name = "psycopg2-binary" version = "2.9.8" description = "psycopg2 - Python-PostgreSQL Database Adapter" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2472,6 +2560,7 @@ 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 = [ @@ -2482,6 +2571,7 @@ 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 = [ @@ -2493,6 +2583,7 @@ files = [ name = "pyasn1" version = "0.1.9" description = "ASN.1 types and codecs" +category = "main" optional = false python-versions = "*" files = [ @@ -2504,6 +2595,7 @@ files = [ name = "pybrowserid" version = "0.14.0" description = "Python library for the BrowserID Protocol" +category = "main" optional = false python-versions = "*" files = [ @@ -2518,6 +2610,7 @@ requests = "*" name = "pycodestyle" version = "2.11.0" description = "Python style guide checker" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2529,6 +2622,7 @@ files = [ name = "pycparser" version = "2.14" description = "C parser in Python" +category = "main" optional = false python-versions = "*" files = [ @@ -2539,6 +2633,7 @@ files = [ name = "pyflakes" version = "3.1.0" description = "passive checker of Python programs" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2550,6 +2645,7 @@ files = [ name = "pyjwt" version = "2.8.0" description = "JSON Web Token implementation in Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2567,6 +2663,7 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"] name = "pyopenssl" version = "23.2.0" description = "Python wrapper module around the OpenSSL library" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2585,6 +2682,7 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"] name = "pyparsing" version = "3.1.1" description = "pyparsing module - Classes and methods to define and execute parsing grammars" +category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -2599,6 +2697,7 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pyramid" version = "1.10.4" 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 = [ @@ -2625,6 +2724,7 @@ testing = ["coverage", "nose", "virtualenv", "webtest (>=1.3.1)", "zope.componen name = "pyramid-multiauth" version = "0.9.0" description = "pyramid_multiauth" +category = "main" optional = false python-versions = "*" files = [ @@ -2639,6 +2739,7 @@ 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 = [ @@ -2658,6 +2759,7 @@ 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 = [ @@ -2677,6 +2779,7 @@ 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 = [ @@ -2690,6 +2793,7 @@ setuptools = "*" name = "pysam" version = "0.21.0" description = "pysam - a python module for reading, manipulating and writing genomic data sets." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2723,6 +2827,7 @@ cython = "*" name = "pytabix" version = "0.1" description = "Python interface for tabix" +category = "main" optional = false python-versions = "*" files = [ @@ -2733,6 +2838,7 @@ files = [ name = "pytest" version = "7.4.2" description = "pytest: simple powerful testing with Python" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2755,6 +2861,7 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-cov" version = "4.1.0" description = "Pytest plugin for measuring coverage." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2773,6 +2880,7 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale name = "pytest-instafail" version = "0.5.0" description = "pytest plugin to show failures instantly" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2787,6 +2895,7 @@ pytest = ">=5" name = "pytest-mock" version = "3.11.1" description = "Thin-wrapper around the mock package for easier use with pytest" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2804,6 +2913,7 @@ dev = ["pre-commit", "pytest-asyncio", "tox"] name = "pytest-timeout" version = "2.1.0" description = "pytest plugin to abort hanging tests" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2818,6 +2928,7 @@ pytest = ">=5.0.0" name = "pytest-xdist" version = "3.1.0" description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2838,6 +2949,7 @@ testing = ["filelock"] name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -2852,6 +2964,7 @@ 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 = [ @@ -2863,6 +2976,7 @@ files = [ name = "pytz" version = "2023.3.post1" description = "World timezone definitions, modern and historical" +category = "main" optional = false python-versions = "*" files = [ @@ -2874,6 +2988,7 @@ files = [ name = "pywin32" version = "227" description = "Python for Window Extensions" +category = "main" optional = false python-versions = "*" files = [ @@ -2895,6 +3010,7 @@ files = [ name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2903,6 +3019,7 @@ files = [ {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938"}, {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d"}, {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = 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name = "rutter" version = "0.4" description = "Py3k-compatible fork of Paste's urlmap" +category = "main" optional = false python-versions = "*" files = [ @@ -3245,6 +3384,7 @@ testing = ["WebTest", "coverage", "pytest", "pytest-cov"] name = "s3transfer" version = "0.7.0" description = "An Amazon S3 Transfer Manager" +category = "main" optional = false python-versions = ">= 3.7" files = [ @@ -3262,6 +3402,7 @@ crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"] name = "sentry-sdk" version = "1.31.0" description = "Python client for Sentry (https://sentry.io)" +category = "main" optional = false python-versions = "*" files = [ @@ -3307,6 +3448,7 @@ tornado = ["tornado (>=5)"] name = "setuptools" version = "68.2.2" description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3323,6 +3465,7 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar name = "simplejson" 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false python-versions = "*" files = [ @@ -3468,6 +3615,7 @@ 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 = [ @@ -3515,7 +3663,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\")"} +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 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uptime library" +category = "main" optional = false python-versions = "*" files = [ @@ -3721,6 +3882,7 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3735,6 +3897,7 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "urllib3" version = "1.26.16" 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.*, !=3.5.*" files = [ @@ -3751,6 +3914,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "venusian" version = "1.2.0" description = "A library for deferring decorator actions" +category = "main" optional = false python-versions = "*" files = [ @@ -3766,6 +3930,7 @@ testing = ["coverage", "pytest", "pytest-cov"] name = "waitress" version = "2.1.2" description = "Waitress WSGI server" 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= "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 = [ @@ -3912,6 +4086,7 @@ files = [ name = "xmltodict" version = "0.13.0" description = "Makes working with XML feel like you are working with JSON" +category = "dev" optional = false python-versions = ">=3.4" files = [ @@ -3923,6 +4098,7 @@ files = [ name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3938,6 +4114,7 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p name = "zope-deprecation" version = "4.4.0" description = "Zope Deprecation Infrastructure" +category = "main" optional = false python-versions = "*" files = [ @@ -3956,6 +4133,7 @@ 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 = [ @@ -4009,6 +4187,7 @@ 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 = [ @@ -4028,4 +4207,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "c00e599361d8b19d9041b150b82641bce3216dbb13fa2ab70bbc74979820227f" +content-hash = "88c116768d782a95286cb01cd29fad54f75304b3fc219a766edeb09fddc54607" diff --git a/pyproject.toml b/pyproject.toml index 3d11194c2f..2847079031 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,7 +50,7 @@ codeguru-profiler-agent = "^1.2.4" # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" colorama = "0.3.3" -dcicpyvcf = 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= "3.0.0a4" +dcicpyvcf = "^3.0.0" dcicsnovault = "10.0.4.1b25" dcicutils = "7.12.0.2b9" elasticsearch = "7.13.4" From 3580110a9455a53b4005ea7c18cb246ede0bf0c0 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 5 Oct 2023 05:17:13 -0400 Subject: [PATCH 24/25] Update snovault version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 3d11194c2f..a40abcc8dc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -51,7 +51,7 @@ codeguru-profiler-agent = "^1.2.4" cryptography = "39.0.2" colorama = "0.3.3" dcicpyvcf = "1.0.0.1b0" # "^1.0.0" -dcicsnovault = "10.0.4.1b25" +dcicsnovault = "10.0.5.1b1" dcicutils = "7.12.0.2b9" elasticsearch = "7.13.4" execnet = "1.4.1" From af58b4b4dbe23a7d6c14d33edc918fe80881f10e Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 10 Oct 2023 14:33:42 -0400 Subject: [PATCH 25/25] Update to 15.0.0; ready for merge to master. --- poetry.lock | 278 +++++++++---------------------------------------- pyproject.toml | 16 +-- 2 files changed, 60 insertions(+), 234 deletions(-) diff --git a/poetry.lock b/poetry.lock index bc71016475..67a4bbdd4e 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 1.5.1 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 = [ @@ -16,7 +15,6 @@ files = [ name = "arrow" version = "1.2.3" description = "Better dates & times for Python" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -31,7 +29,6 @@ python-dateutil = ">=2.7.0" name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -43,7 +40,6 @@ files = [ name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -62,7 +58,6 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte 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 = [ @@ -75,18 +70,17 @@ requests = ">=0.14.0" [[package]] name = "awscli" -version = "1.29.57" +version = "1.29.62" description = "Universal Command Line Environment for AWS." -category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "awscli-1.29.57-py3-none-any.whl", hash = "sha256:d7291cf485e73fe4315b84ecd1a2c5d90424d150ee36379a409c7ea7e7b0f5ca"}, - {file = "awscli-1.29.57.tar.gz", hash = "sha256:fb1304e468838adc67eb5cab224884072c7fc5e31e5ccad54b6ae27c85fa0a2f"}, + {file = "awscli-1.29.62-py3-none-any.whl", hash = "sha256:642c2b1bfceba5af29a4b2648cce86f765fd48749fd21d79e0480cfacf0af907"}, + {file = "awscli-1.29.62.tar.gz", hash = "sha256:aef24cdcdc6d8acdb482a06620289a76ccc264424536e235c2a5705810651b2b"}, ] [package.dependencies] -botocore = "1.31.57" +botocore = "1.31.62" colorama = ">=0.2.5,<0.4.5" docutils = ">=0.10,<0.17" PyYAML = ">=3.10,<6.1" @@ -97,7 +91,6 @@ s3transfer = ">=0.7.0,<0.8.0" 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false python-versions = ">= 3.7" files = [ @@ -3416,7 +3281,6 @@ crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"] name = "sentry-sdk" version = "1.31.0" description = "Python client for Sentry (https://sentry.io)" -category = "main" optional = false python-versions = "*" files = [ @@ -3462,7 +3326,6 @@ tornado = ["tornado (>=5)"] name = "setuptools" version = "68.2.2" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3479,7 +3342,6 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar name = "simplejson" version = "3.19.1" description = "Simple, fast, extensible JSON encoder/decoder for Python" -category = "main" optional = false python-versions = ">=2.5, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3574,7 +3436,6 @@ files = [ name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false 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Logging for Python" -category = "main" optional = false python-versions = "*" files = [ @@ -3725,7 +3581,6 @@ 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 = [ @@ -3742,7 +3597,6 @@ 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 = [ @@ -3760,7 +3614,6 @@ testing = ["pytest", "pytest-cov"] 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 = [ @@ -3772,7 +3625,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3784,7 +3636,6 @@ files = [ name = "tqdm" version = "4.66.1" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3805,7 +3656,6 @@ 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 = [ @@ -3825,7 +3675,6 @@ 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 = [ @@ -3837,7 +3686,6 @@ files = [ name = "types-awscrt" version = "0.19.1" description = "Type annotations and code completion for awscrt" -category = "dev" optional = false python-versions = ">=3.7,<4.0" files = [ @@ -3849,7 +3697,6 @@ files = [ name = "types-pyyaml" 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"flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "urllib3" version = "1.26.16" 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.*, !=3.5.*" files = [ @@ -3928,7 +3770,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "venusian" version = "1.2.0" description = "A library for deferring decorator actions" -category = "main" optional = false python-versions = "*" files = [ @@ -3944,7 +3785,6 @@ 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 = [ @@ -3960,7 +3800,6 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3976,7 +3815,6 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "main" optional = false python-versions = "*" files = [ @@ -3988,7 +3826,6 @@ 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 = [ @@ -4004,7 +3841,6 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] name = "websocket-client" version = "1.6.3" description = "WebSocket client for Python with low level API options" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4021,7 +3857,6 @@ test = ["websockets"] name = "webtest" version = "2.0.35" description = "Helper to test WSGI applications" -category = "main" optional = false python-versions = "*" files = [ @@ -4043,7 +3878,6 @@ tests = ["PasteDeploy", 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working with XML feel like you are working with JSON" -category = "dev" optional = false python-versions = ">=3.4" files = [ @@ -4112,7 +3942,6 @@ files = [ name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4128,7 +3957,6 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p name = "zope-deprecation" version = "4.4.0" description = "Zope Deprecation Infrastructure" -category = "main" optional = false python-versions = "*" files = [ @@ -4147,7 +3975,6 @@ test = ["zope.testrunner"] name = "zope-interface" version = "5.5.2" description = "Interfaces for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -4201,7 +4028,6 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] name = "zope-sqlalchemy" version = "1.6" description = "Minimal Zope/SQLAlchemy transaction integration" -category = "main" optional = false python-versions = "*" files = [ @@ -4221,4 +4047,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "0e2529574aaf98ad44d28b81e59b58dfd70e501ac076491934d2aa2c8fad0f24" +content-hash = "5a09566ec0cba9d473912bfb0d325671f3e98647a8ef6b7b9c41fabd503b84af" diff --git a/pyproject.toml b/pyproject.toml index d818395c2f..a1eff08529 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "cgap-portal". name = "encoded" -version = "14.3.1.1b2" # TODO: To become 15.0.0 +version = "15.0.0" description = "Computational Genome Analysis Platform" authors = ["4DN-DCIC Team "] license = "MIT" @@ -39,9 +39,9 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.8.1,<3.12" -awscli = ">=1.29.56" -boto3 = "^1.28.56" -botocore = "^1.31.56" +awscli = ">=1.29.62" +boto3 = "^1.28.62" +botocore = "^1.31.62" certifi = ">=2021.5.30" chardet = "3.0.4" codeguru-profiler-agent = "^1.2.4" @@ -51,8 +51,8 @@ codeguru-profiler-agent = "^1.2.4" cryptography = "39.0.2" colorama = "0.3.3" dcicpyvcf = "^3.0.0" -dcicsnovault = "10.0.5.1b1" -dcicutils = "7.12.0.2b9" +dcicsnovault = "^11.0.0" +dcicutils = "^8.0.0" elasticsearch = "7.13.4" execnet = "1.4.1" future = ">=0.18.2,<1" @@ -127,8 +127,8 @@ WSGIProxy2 = "0.4.2" [tool.poetry.dev-dependencies] # PyCharm says boto3-stubs contains useful type hints -boto3-stubs = "^1.28.56" -botocore-stubs = "^1.31.56" +boto3-stubs = "^1.28.62" +botocore-stubs = "^1.31.62" coverage = ">=6.2" codacy-coverage = ">=1.3.11" coveralls = ">=3.3.1"