From c00c296dff59e8acf12457a7e52ae39568e16512 Mon Sep 17 00:00:00 2001 From: George Thomas <98996322+george42-ctds@users.noreply.github.com> Date: Fri, 3 Nov 2023 16:16:10 -0700 Subject: [PATCH 1/4] Update flask (#205) --- .github/workflows/ci.yaml | 23 + .secrets.baseline | 73 +- .travis.yml | 39 - peregrine/api.py | 1 - poetry.lock | 1554 ++++++++++++++++------------------- pyproject.toml | 10 +- tests/ci_commands_script.sh | 8 + 7 files changed, 776 insertions(+), 932 deletions(-) create mode 100644 .github/workflows/ci.yaml delete mode 100644 .travis.yml create mode 100644 tests/ci_commands_script.sh diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml new file mode 100644 index 0000000..3c78740 --- /dev/null +++ b/.github/workflows/ci.yaml @@ -0,0 +1,23 @@ +name: CI +on: + push: + pull_request: + types: [opened, reopened] +concurrency: + group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}' + cancel-in-progress: true +jobs: + Security: + name: Security Pipeline + uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master + with: + python-poetry: 'false' + secrets: inherit + + UnitTest: + name: Python Unit Test with Postgres + uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master + with: + python-version: '3.9' + test-script: 'tests/ci_commands_script.sh' + run-coveralls: true diff --git a/.secrets.baseline b/.secrets.baseline index ef11d15..48b7352 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -7,6 +7,9 @@ { "name": "AWSKeyDetector" }, + { + "name": "AzureStorageKeyDetector" + }, { "name": "Base64HighEntropyString", "limit": 4.5 @@ -17,9 +20,15 @@ { "name": "CloudantDetector" }, + { + "name": "DiscordBotTokenDetector" + }, + { + "name": "GitHubTokenDetector" + }, { "name": "HexHighEntropyString", - "limit": 3 + "limit": 3.0 }, { "name": "IbmCloudIamDetector" @@ -37,15 +46,24 @@ { "name": "MailchimpDetector" }, + { + "name": "NpmDetector" + }, { "name": "PrivateKeyDetector" }, + { + "name": "SendGridDetector" + }, { "name": "SlackDetector" }, { "name": "SoftlayerDetector" }, + { + "name": "SquareOAuthDetector" + }, { "name": "StripeDetector" }, @@ -57,10 +75,6 @@ { "path": "detect_secrets.filters.allowlist.is_line_allowlisted" }, - { - "path": "detect_secrets.filters.common.is_baseline_file", - "filename": ".secrets.baseline" - }, { "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies", "min_level": 2 @@ -94,13 +108,22 @@ } ], "results": { + ".github/workflows/ci.yaml": [ + { + "type": "Secret Keyword", + "filename": ".github/workflows/ci.yaml", + "hashed_secret": "3e26d6750975d678acb8fa35a0f69237881576b0", + "is_verified": false, + "line_number": 15 + } + ], "bin/settings.py": [ { "type": "Basic Auth Credentials", "filename": "bin/settings.py", "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", "is_verified": false, - "line_number": 44 + "line_number": 46 } ], "peregrine/blueprints/coremetadata.py": [ @@ -118,8 +141,7 @@ "filename": "peregrine/dev_settings.example.py", "hashed_secret": "739155dcfcb1fc7f98aa38d18ea3d2213ae62b54", "is_verified": false, - "line_number": 62, - "is_secret": false + "line_number": 62 }, { "type": "Secret Keyword", @@ -135,8 +157,7 @@ "filename": "peregrine/dev_settings.py", "hashed_secret": "739155dcfcb1fc7f98aa38d18ea3d2213ae62b54", "is_verified": false, - "line_number": 69, - "is_secret": false + "line_number": 69 }, { "type": "Secret Keyword", @@ -152,8 +173,7 @@ "filename": "peregrine/test_settings.py", "hashed_secret": "27d0f93fe951bda5dc3973ca2a5b420c7dfc387f", "is_verified": false, - "line_number": 11, - "is_secret": false + "line_number": 11 }, { "type": "Secret Keyword", @@ -183,8 +203,7 @@ "filename": "tests/data/files.json", "hashed_secret": "d13c66cc793960cb8d97a4d64d1deb6d2288e4fc", "is_verified": false, - "line_number": 6, - "is_secret": false + "line_number": 6 } ], "tests/graphql/data/biospec1.json": [ @@ -193,24 +212,21 @@ "filename": "tests/graphql/data/biospec1.json", "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3", "is_verified": false, - "line_number": 63, - "is_secret": false + "line_number": 63 }, { "type": "Hex High Entropy String", "filename": "tests/graphql/data/biospec1.json", "hashed_secret": "e65fd5600e42643c6d77f3c5c3a60114e0d3165d", "is_verified": false, - "line_number": 72, - "is_secret": false + "line_number": 72 }, { "type": "Hex High Entropy String", "filename": "tests/graphql/data/biospec1.json", "hashed_secret": "922282cd0fad4bf8ca1c93de95863177d57a55c1", "is_verified": false, - "line_number": 81, - "is_secret": false + "line_number": 81 } ], "tests/graphql/data/biospec2.json": [ @@ -219,16 +235,14 @@ "filename": "tests/graphql/data/biospec2.json", "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3", "is_verified": false, - "line_number": 18, - "is_secret": false + "line_number": 18 }, { "type": "Hex High Entropy String", "filename": "tests/graphql/data/biospec2.json", "hashed_secret": "e65fd5600e42643c6d77f3c5c3a60114e0d3165d", "is_verified": false, - "line_number": 27, - "is_secret": false + "line_number": 27 } ], "tests/graphql/data/databundle1.json": [ @@ -237,8 +251,7 @@ "filename": "tests/graphql/data/databundle1.json", "hashed_secret": "b87375c47433817ed4310ab448cda0f74670ee71", "is_verified": false, - "line_number": 28, - "is_secret": false + "line_number": 28 } ], "tests/graphql/data/file.json": [ @@ -247,8 +260,7 @@ "filename": "tests/graphql/data/file.json", "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3", "is_verified": false, - "line_number": 9, - "is_secret": false + "line_number": 9 } ], "tests/graphql/data/submitted_unaligned_reads.json": [ @@ -257,10 +269,9 @@ "filename": "tests/graphql/data/submitted_unaligned_reads.json", "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3", "is_verified": false, - "line_number": 10, - "is_secret": false + "line_number": 10 } ] }, - "generated_at": "2023-05-12T17:31:54Z" + "generated_at": "2023-11-01T14:27:13Z" } diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 93ac0ca..0000000 --- a/.travis.yml +++ /dev/null @@ -1,39 +0,0 @@ -dist: xenial -sudo: false -language: python - -python: - - "3.9" - -cache: - - pip - - apt - -addons: - postgresql: '9.4' - -before_install: - # bust only the the part of the cache that we are frequently changing - - pip uninstall --yes gdcdictionary gdcdatamodel || true - # resolve https://github.com/travis-ci/travis-ci/issues/7940 - - export BOTO_CONFIG=/dev/null - -# command to install dependencies -install: - - pip install poetry - - poetry install -vv - -before_script: - - poetry run python bin/setup_test_database.py - - mkdir -p tests/resources/keys; cd tests/resources/keys; openssl genrsa -out test_private_key.pem 2048; openssl rsa -in test_private_key.pem -pubout -out test_public_key.pem; cd - - -# command to run tests -script: - - poetry run pytest -vv --cov=peregrine --cov-report xml tests - -after_script: - - python-codacy-coverage -r coverage.xml - -env: - global: - - GDC_ES_HOST=localhost diff --git a/peregrine/api.py b/peregrine/api.py index 287d112..372c5da 100644 --- a/peregrine/api.py +++ b/peregrine/api.py @@ -6,7 +6,6 @@ from flask import Flask, jsonify from flask_cors import CORS -from flask_sqlalchemy_session import flask_scoped_session from psqlgraph import PsqlGraphDriver from authutils import AuthError diff --git a/poetry.lock b/poetry.lock index 9859e45..18c613f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -14,74 +14,74 @@ files = [ [[package]] name = "anyio" -version = "3.6.2" +version = "4.0.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" category = "main" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.8" files = [ - {file = "anyio-3.6.2-py3-none-any.whl", hash = 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(>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [metadata] lock-version = "2.0" -python-versions = "3.9.*" -content-hash = "2a3f126d05258a9d68a8be139705826e73c71d8d01997173f3457e33e0c2cf4a" +python-versions = ">=3.9,<3.10" +content-hash = "3229dfe50611245140fb1912ce32aad48cffc20e2f33a3877cb221eb4e25973f" diff --git a/pyproject.toml b/pyproject.toml index 06b26ad..f9f805e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,7 @@ include = [ ] [tool.poetry.dependencies] -python = "3.9.*" +python = ">=3.9,<3.10" authutils = ">=6.2.0" datamodelutils = ">=1.0" defusedxml = ">=0.5" @@ -19,10 +19,10 @@ dictionaryutils = ">=3.0" gen3dictionary = ">=2.0" simplejson = ">=3.8" stopit = ">=1.1" -Flask = ">=1.1" +Flask = ">=2.2.5" Flask-Cors = ">=3.0.9" gen3authz = ">=0.2" -PyYAML = ">=5.1" +PyYAML = "~5.3.1" dicttoxml = ">=1.5" SQLAlchemy = "1.3.5" graphene = ">=2.0,<3" @@ -40,7 +40,9 @@ mock = ">=1.0" pytest-flask = ">=0.15" pytest-cov = ">=2.8" indexclient = ">=2.1.1" -sheepdog = {git = "https://git@github.com/uc-cdis/sheepdog.git", rev = "5.1.0"} +# TODO: Sheepdog tests have been temporarily disabled until Sheepdog (and indirectly Indexd) are updated to +# a more recent version of Flask. +# sheepdog = {git = "https://git@github.com/uc-cdis/sheepdog.git", branch = "fix/flask-upgrade"} [tool.poetry.plugins."peregrine.modules"] "system" = "peregrine=peregrine.api:main" diff --git a/tests/ci_commands_script.sh b/tests/ci_commands_script.sh new file mode 100644 index 0000000..3993328 --- /dev/null +++ b/tests/ci_commands_script.sh @@ -0,0 +1,8 @@ +#!/usr/bin/env bash + +# Set up database +poetry run python bin/setup_test_database.py +mkdir -p tests/resources/keys; cd tests/resources/keys; openssl genrsa -out test_private_key.pem 2048; openssl rsa -in test_private_key.pem -pubout -out test_public_key.pem; cd - + +# run tests +poetry run pytest -vv --cov=peregrine --cov-report xml tests From a08e5599c52951c11794a42f2a08db011c16cdf0 Mon Sep 17 00:00:00 2001 From: George Thomas <98996322+george42-ctds@users.noreply.github.com> Date: Wed, 15 Nov 2023 13:22:01 -0800 Subject: [PATCH 2/4] fix: pull in recent tag of sheepdog (#207) --- poetry.lock | 373 +++++++++++++++++++++++++++++++++---------------- pyproject.toml | 4 +- 2 files changed, 251 insertions(+), 126 deletions(-) diff --git a/poetry.lock b/poetry.lock index 18c613f..e6954f7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "aniso8601" version = "7.0.0" description = "A library for parsing ISO 8601 strings." -category = "main" optional = false python-versions = "*" files = [ @@ -16,7 +15,6 @@ files = [ name = "anyio" version = "4.0.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -38,7 +36,6 @@ trio = ["trio (>=0.22)"] name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -57,7 +54,6 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "authlib" version = "1.2.1" description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." -category = "main" optional = false python-versions = "*" files = [ @@ -72,7 +68,6 @@ cryptography = ">=3.2" name = "authutils" version = "6.2.3" description = "Gen3 auth utility functions" -category = "main" optional = false python-versions = ">=3.9,<4.0" files = [ @@ -96,7 +91,6 @@ flask = ["Flask (<=2.3.3)"] name = "avro" version = "1.11.3" description = "Avro is a serialization and RPC framework." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -111,7 +105,6 @@ zstandard = ["zstandard"] name = "backoff" version = "1.11.1" description = "Function decoration for backoff and retry" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -123,7 +116,6 @@ files = [ name = "blinker" version = "1.7.0" description = "Fast, simple object-to-object and broadcast signaling" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -135,7 +127,6 @@ files = [ name = "boto" version = "2.49.0" description = "Amazon Web Services Library" -category = "main" optional = false python-versions = "*" files = [ @@ -143,11 +134,29 @@ files = [ {file = "boto-2.49.0.tar.gz", hash = "sha256:ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a"}, ] +[[package]] +name = "botocore" +version = "1.32.0" +description = "Low-level, data-driven core of boto 3." +optional = false +python-versions = ">= 3.7" +files = [ + {file = "botocore-1.32.0-py3-none-any.whl", hash = "sha256:9c1e143feb6a04235cec342d2acb31a0f44df3c89f309f839e03e38a75f3f44e"}, + {file = "botocore-1.32.0.tar.gz", hash = "sha256:95fe3357b9ddc4559941dbea0f0a6b8fc043305f013b7ae2a85dff0c3b36ee92"}, +] + +[package.dependencies] +jmespath = ">=0.7.1,<2.0.0" +python-dateutil = ">=2.1,<3.0.0" +urllib3 = {version = ">=1.25.4,<1.27", markers = "python_version < \"3.10\""} + +[package.extras] +crt = ["awscrt (==0.19.12)"] + [[package]] name = "cached-property" version = "1.5.2" description = "A decorator for caching properties in classes." -category = "main" optional = false python-versions = "*" files = [ @@ -159,7 +168,6 @@ files = [ name = "cdiserrors" version = "1.0.0" description = "Gen3 shared exceptions and utilities." -category = "main" optional = false python-versions = ">=3.6,<4.0" files = [ @@ -177,7 +185,6 @@ flask = ["Flask (>=1.1.2,<2.0.0)"] name = "cdislogging" version = "1.1.1" description = "Standardized logging tool and format for cdis applications" -category = "main" optional = false python-versions = "*" files = [ @@ -188,7 +195,6 @@ files = [ name = "cdispyutils" version = "2.0.1" description = "This package includes several utility Python tools for the Gen3 stack." -category = "main" optional = false python-versions = ">=3.6,<4.0" files = [ @@ -207,7 +213,6 @@ requests = "*" name = "cdisutils" version = "1.2.2" description = "Miscellaneous utilities useful for interaction with CDIS systems." -category = "main" optional = false python-versions = "*" files = [ @@ -227,7 +232,6 @@ xmltodict = ">=0.9.2" name = "certifi" version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -239,7 +243,6 @@ 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 = [ @@ -304,7 +307,6 @@ pycparser = "*" name = "charset-normalizer" version = "3.3.2" 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 = [ @@ -404,7 +406,6 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -419,7 +420,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -431,7 +431,6 @@ files = [ name = "coverage" version = "7.3.2" description = "Code coverage measurement for Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -499,7 +498,6 @@ toml = ["tomli"] name = "cryptography" version = "41.0.5" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -545,7 +543,6 @@ test-randomorder = ["pytest-randomly"] name = "datamodelutils" version = "1.0.0" description = "" -category = "main" optional = false python-versions = "*" files = [ @@ -563,7 +560,6 @@ psqlgraph = ">=3.0.0" name = "defusedxml" version = "0.7.1" description = "XML bomb protection for Python stdlib modules" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -573,13 +569,12 @@ files = [ [[package]] name = "dictionaryutils" -version = "3.4.8" +version = "3.4.9" description = "Python wrapper and metaschema for datadictionary." -category = "main" optional = false -python-versions = ">=3.6,<3.10" +python-versions = ">=3.9,<4" files = [ - {file = "dictionaryutils-3.4.8.tar.gz", hash = "sha256:e543937306585a78f9f646457dcb0983cc26f5f0e8a8151d9354faf539caff83"}, + {file = "dictionaryutils-3.4.9.tar.gz", hash = "sha256:18bf677a123ec8fd1e6ce5f2887bc7555dd1faca245a31e3cb6b858bfade87c1"}, ] [package.dependencies] @@ -593,7 +588,6 @@ requests = ">=2.18,<3.0" name = "dicttoxml" version = "1.7.16" description = "Converts a Python dictionary or other native data type into a valid XML string." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -601,11 +595,20 @@ files = [ {file = "dicttoxml-1.7.16.tar.gz", hash = "sha256:6f36ce644881db5cd8940bee9b7cb3f3f6b7b327ba8a67d83d3e2caa0538bf9d"}, ] +[[package]] +name = "envelopes" +version = "0.4" +description = "Mailing for human beings" +optional = false +python-versions = "*" +files = [ + {file = "Envelopes-0.4.tar.gz", hash = "sha256:a4a02b4dc21467794d3a646f946d99a8c5b3311b2df8e211f96ca9e0b838e7e0"}, +] + [[package]] 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 = [ @@ -617,7 +620,6 @@ files = [ name = "exceptiongroup" version = "1.1.3" description = "Backport of PEP 654 (exception groups)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -632,7 +634,6 @@ test = ["pytest (>=6)"] name = "flask" version = "3.0.0" description = "A simple framework for building complex web applications." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -656,7 +657,6 @@ dotenv = ["python-dotenv"] name = "flask-cors" version = "4.0.0" description = "A Flask extension adding a decorator for CORS support" -category = "main" optional = false python-versions = "*" files = [ @@ -671,7 +671,6 @@ Flask = ">=0.9" name = "flask-sqlalchemy-session" version = "1.1" description = "SQL Alchemy session scoped on Flask requests." -category = "main" optional = false python-versions = "*" files = [ @@ -686,11 +685,24 @@ Werkzeug = ">=0.6.1" [package.extras] docs = ["Sphinx (>=1.2.3)", "alabaster (>=0.6.3)"] +[[package]] +name = "fuzzywuzzy" +version = "0.18.0" +description = "Fuzzy string matching in python" +optional = false +python-versions = "*" +files = [ + {file = "fuzzywuzzy-0.18.0-py2.py3-none-any.whl", hash = "sha256:928244b28db720d1e0ee7587acf660ea49d7e4c632569cad4f1cd7e68a5f0993"}, + {file = "fuzzywuzzy-0.18.0.tar.gz", hash = "sha256:45016e92264780e58972dca1b3d939ac864b78437422beecebb3095f8efd00e8"}, +] + +[package.extras] +speedup = ["python-levenshtein (>=0.12)"] + [[package]] name = "gen3authz" version = "2.1.0" description = "Gen3 authz client" -category = "main" optional = false python-versions = ">=3.6,<4.0" files = [ @@ -708,7 +720,6 @@ six = ">=1.16.0,<2.0.0" name = "gen3datamodel" version = "3.1.2" description = "" -category = "main" optional = false python-versions = "*" files = [ @@ -726,25 +737,23 @@ strict-rfc3339 = "0.7" [[package]] name = "gen3dictionary" -version = "2.0.1" -description = "Gen3 generic data dictionary" -category = "main" +version = "2.0.3" +description = "" optional = false -python-versions = "*" 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(and indirectly Indexd) are updated to -# a more recent version of Flask. -# sheepdog = {git = "https://git@github.com/uc-cdis/sheepdog.git", branch = "fix/flask-upgrade"} +sheepdog = {git = "https://git@github.com/uc-cdis/sheepdog.git", rev = "5.1.2" } [tool.poetry.plugins."peregrine.modules"] "system" = "peregrine=peregrine.api:main" From 61cb197bcf4167ff2c89ccbc08285334a037a6b7 Mon Sep 17 00:00:00 2001 From: George Thomas <98996322+george42-ctds@users.noreply.github.com> Date: Fri, 17 Nov 2023 10:32:32 -0800 Subject: [PATCH 3/4] Fix/upgrade pyyaml (#208) * (fix PXP-11163): upgrade pyyaml, gen3dictionary * (fix PXP-11163): remove broken codacy badge, add coverage * (fix PXP-11163): use latest tag for sheepdog, bump peregrine version --- README.md | 3 +- poetry.lock | 94 +++++++++++++++++++++++++++++--------------------- pyproject.toml | 10 +++--- 3 files changed, 60 insertions(+), 47 deletions(-) diff --git a/README.md b/README.md index 9ab2f48..0b8f7e8 100644 --- a/README.md +++ 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= "<2.0.0" [package.source] type = "git" url = "https://git@github.com/uc-cdis/sheepdog.git" -reference = "5.1.2" -resolved_reference = "d2893b13166ca9c6d78072bbf389752e462974aa" +reference = "5.1.3" +resolved_reference = "359c764c8b312d0ac6707b1c2bee130f4ac0b44e" [[package]] name = "simplejson" @@ -1939,4 +1953,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.10" -content-hash = "33ad2ff1caa7f2abbd6798abb6f82a9d8781c4dd10c011411063ca7627243cca" +content-hash = "5334077b7c6c00df770dde0670497df907545e06959a65c14b4aef1563fe61a3" diff --git a/pyproject.toml b/pyproject.toml index bea73f3..6b2479a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "peregrine" -version = "3.0.1" +version = "3.2.2" description = "Query interface to get insights into data in Gen3 Commons" authors = ["CTDS UChicago "] license = "Apache-2.0" @@ -15,14 +15,14 @@ python = ">=3.9,<3.10" authutils = ">=6.2.0" datamodelutils = ">=1.0" defusedxml = ">=0.5" -dictionaryutils = ">=3.0" -gen3dictionary = ">=2.0" +dictionaryutils = ">=3.4.10" +gen3dictionary = ">=2.0.3" simplejson = ">=3.8" stopit = ">=1.1" Flask = ">=2.2.5" Flask-Cors = ">=3.0.9" gen3authz = ">=0.2" -PyYAML = "~5.3.1" +PyYAML = ">=5.4.1" dicttoxml = ">=1.5" SQLAlchemy = "1.3.5" graphene = ">=2.0,<3" @@ -40,7 +40,7 @@ mock = ">=1.0" pytest-flask = ">=0.15" pytest-cov = ">=2.8" indexclient = ">=2.1.1" -sheepdog = {git = "https://git@github.com/uc-cdis/sheepdog.git", rev = "5.1.2" } +sheepdog = {git = "https://git@github.com/uc-cdis/sheepdog.git", rev = "5.1.3" } [tool.poetry.plugins."peregrine.modules"] "system" = "peregrine=peregrine.api:main" From cbdda7eecf91aa54e4b8737a0cb5c5bbc45ca08b Mon Sep 17 00:00:00 2001 From: grugna Date: Tue, 27 Feb 2024 14:57:39 -0600 Subject: [PATCH 4/4] Update pyproject.toml --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 2c6c5b3..d574d72 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,8 @@ Flask = ">=2.2.5" Flask-Cors = ">=3.0.9" gen3authz = ">=0.2" # gen3authz = {git = "https://github.com/grugna/gen3authz.git", rev = "0.2.4", subdirectory = "python"} -# gen3authz = {git = "https://github.com/grugna/gen3authz.git", rev = "1.0.6"} Need to make this changes if times out. +# ATTENTION: Need to make this changes if times out. +# gen3authz = {git = "https://github.com/grugna/gen3authz.git", rev = "1.0.6"} # boto = "^2.36" # elasticsearch = "^1.2" PyYAML = ">=5.4.1"