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/README.md b/README.md index 1aa6fb4..c2f1ff6 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,7 @@ # Peregrine [![Build Status](https://travis-ci.org/uc-cdis/peregrine.svg?branch=master)](https://travis-ci.org/uc-cdis/peregrine) -[![Codacy Badge](https://api.codacy.com/project/badge/Grade/f6128183864d4e5da5093eb72a3c9c97)](https://www.codacy.com/app/uc-cdis/peregrine?utm_source=github.com&utm_medium=referral&utm_content=uc-cdis/peregrine&utm_campaign=Badge_Grade) -[![Codacy Badge](https://api.codacy.com/project/badge/Coverage/f6128183864d4e5da5093eb72a3c9c97)](https://www.codacy.com/app/uc-cdis/peregrine?utm_source=github.com&utm_medium=referral&utm_content=uc-cdis/peregrine&utm_campaign=Badge_Coverage) +[![Coverage Status](https://coveralls.io/repos/github/uc-cdis/peregrine/badge.svg)](https://coveralls.io/github/uc-cdis/peregrine) Query interface to get insights into data in Gen3 Commons diff --git a/peregrine/api.py b/peregrine/api.py index 2dc3f09..658c073 100644 --- a/peregrine/api.py +++ b/peregrine/api.py @@ -7,7 +7,6 @@ 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 7a69bcc..95a9b48 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,66 +1,84 @@ +# This file is automatically @generated by Poetry 1.7.1 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 = [ + {file = "aniso8601-7.0.0-py2.py3-none-any.whl", hash = "sha256:d10a4bf949f619f719b227ef5386e31f49a2b6d453004b21f02661ccc8670c7b"}, + {file = "aniso8601-7.0.0.tar.gz", hash = "sha256:513d2b6637b7853806ae79ffaca6f3e8754bdd547048f5ccc1420aec4b714f1e"}, +] [[package]] name = "anyio" -version = "3.6.2" +version = "4.3.0" 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-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, + {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, +] [package.dependencies] +exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] -trio = ["trio (>=0.16,<0.22)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] [[package]] name = "attrs" -version = "22.2.0" +version = "23.2.0" description = "Classes Without Boilerplate" -category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" +files = [ + {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, + {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, +] [package.extras] -cov = ["attrs", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"] -dev = ["attrs"] -docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"] -tests = ["attrs", "zope.interface"] -tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist"] -tests_no_zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist"] +cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] +dev = ["attrs[tests]", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs[tests-no-zope]", "zope-interface"] +tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] +tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] [[package]] name = "authlib" -version = "0.11" -description = "The ultimate Python library in building OAuth and OpenID Connect servers." -category = "main" +version = "1.3.0" +description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." optional = false -python-versions = "*" +python-versions = ">=3.8" +files = [ + {file = "Authlib-1.3.0-py2.py3-none-any.whl", hash = "sha256:9637e4de1fb498310a56900b3e2043a206b03cb11c05422014b0302cbc814be3"}, + {file = "Authlib-1.3.0.tar.gz", hash = "sha256:959ea62a5b7b5123c5059758296122b57cd2585ae2ed1c0622c21b371ffdae06"}, +] [package.dependencies] cryptography = "*" -requests = "*" [[package]] name = "authutils" -version = "6.2.2" +version = "6.2.3" description = "Gen3 auth utility functions" -category = "main" optional = false python-versions = ">=3.9,<4.0" +files = [ + {file = "authutils-6.2.3-py3-none-any.whl", hash = "sha256:8c4e7e24183cbc1055ab91eaf9d2966f0da5b739be0fabfe380749674ba3057e"}, + {file = "authutils-6.2.3.tar.gz", hash = "sha256:c44e1f309b2b5b6db1276f69e1e18ec5c6be1ae33bfe52608a30049b8669ff7b"}, +] [package.dependencies] -authlib = "0.11.0" +authlib = ">=1.1.0" cached-property = ">=1.4,<2.0" cdiserrors = "<2.0.0" httpx = ">=0.23.0,<1.0.0" @@ -69,15 +87,17 @@ xmltodict = ">=0.9,<1.0" [package.extras] fastapi = ["fastapi (>=0.65.2,<0.66.0)"] -flask = ["Flask (>=0.10.1)"] +flask = ["Flask (<=2.3.3)"] [[package]] name = "avro" -version = "1.11.1" +version = "1.11.3" description = "Avro is a serialization and RPC framework." -category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "avro-1.11.3.tar.gz", hash = "sha256:3393bb5139f9cf0791d205756ce1e39a5b58586af5b153d6a3b5a199610e9d17"}, +] [package.extras] snappy = ["python-snappy"] @@ -87,33 +107,75 @@ 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 = [ + {file = "backoff-1.11.1-py2.py3-none-any.whl", hash = "sha256:61928f8fa48d52e4faa81875eecf308eccfb1016b018bb6bd21e05b5d90a96c5"}, + {file = "backoff-1.11.1.tar.gz", hash = "sha256:ccb962a2378418c667b3c979b504fdeb7d9e0d29c0579e3b13b86467177728cb"}, +] + +[[package]] +name = "blinker" +version = "1.7.0" +description = "Fast, simple object-to-object and broadcast signaling" +optional = false +python-versions = ">=3.8" +files = [ + {file = "blinker-1.7.0-py3-none-any.whl", hash = "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9"}, + {file = "blinker-1.7.0.tar.gz", hash = "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182"}, +] [[package]] name = "boto" version = "2.49.0" description = "Amazon Web Services Library" -category = "main" optional = false python-versions = "*" +files = [ + {file = "boto-2.49.0-py2.py3-none-any.whl", hash = "sha256:147758d41ae7240dc989f0039f27da8ca0d53734be0eb869ef16e3adcfa462e8"}, + {file = "boto-2.49.0.tar.gz", hash = "sha256:ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a"}, +] + +[[package]] +name = "botocore" +version = "1.34.51" +description = "Low-level, data-driven core of boto 3." +optional = false +python-versions = ">= 3.8" +files = [ + {file = "botocore-1.34.51-py3-none-any.whl", hash = "sha256:01d5156247f991b3466a8404e3d7460a9ecbd9b214f9992d6ba797d9ddc6f120"}, + {file = "botocore-1.34.51.tar.gz", hash = "sha256:5086217442e67dd9de36ec7e87a0c663f76b7790d5fb6a12de565af95e87e319"}, +] + +[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 (==0.19.19)"] [[package]] name = "cached-property" version = "1.5.2" description = "A decorator for caching properties in classes." -category = "main" optional = false python-versions = "*" +files = [ + {file = "cached-property-1.5.2.tar.gz", hash = "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130"}, + {file = "cached_property-1.5.2-py2.py3-none-any.whl", hash = "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"}, +] [[package]] name = "cdiserrors" version = "1.0.0" description = "Gen3 shared exceptions and utilities." -category = "main" optional = false python-versions = ">=3.6,<4.0" +files = [ + {file = "cdiserrors-1.0.0-py3-none-any.whl", hash = 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">=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"} -PyYAML = ">=5.1" -boto = "^2.36" -elasticsearch = "^1.2" +# 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" dicttoxml = ">=1.5" SQLAlchemy = "1.3.5" graphene = ">=2.0,<3" @@ -44,7 +45,7 @@ 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 = "5.1.0"} +sheepdog = {git = "https://git@github.com/uc-cdis/sheepdog.git", rev = "5.1.3" } [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