Add GitHub actions

.github/workflows/ci.yml

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+# push will run on every pushed commit to any branch (so this will rerun the tests
+# once a branch gets merged to main in addition to any new commits on any branch)
+on: push
+
+name: CI
+
+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: 'true'
+    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'
+      use-cache: true
+
+  # this creates linter settings and uploads to an artifact so the configs can be pulled and used across jobs
+  LintConfig:
+    name: Get Lint Config
+    uses: uc-cdis/.github/.github/workflows/lint-create-config.yaml@master
+    with:
+      python-module-name: "gen3Dictionary"
+
+  RequiredLint:
+    name: Run Required Linters
+    needs: [ LintConfig ]
+    uses: uc-cdis/.github/.github/workflows/required_lint_check.yaml@master
+    with:
+      python-version: '3.9'
+      use-cache: true
+
+  InformationalLint:
+   name: Run Informational Linters
+   needs: [ LintConfig ] #TODO Add UnitTest
+   if: github.ref != 'refs/heads/main'
+   uses: uc-cdis/.github/.github/workflows/optional_lint_check.yaml@master
+   with:
+     python-version: '3.9'
+     use-cache: true

.github/workflows/pypi.yaml

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+name: PyPI
+on:
+  push:
+    tags:
+      - '*'
+jobs:
+  PyPIPoetryPublish:
+    name: PyPI Poetry Publish
+    uses: uc-cdis/.github/.github/workflows/python_package_index_publish.yaml@master
+    with:
+        PYTHON_VERSION: '3.9'
+        # This will attempt push to test PyPI first and only push to prod if it works
+        DO_TEST_PUBLISH_FIRST: true
+    secrets:
+      PYPI_TEST_API_TOKEN: ${{ secrets.PYPI_TEST_API_TOKEN }}
+      PYPI_PROD_API_TOKEN: ${{ secrets.PYPI_PROD_API_TOKEN }}

.github/workflows/wool.yaml

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+on:
+  pull_request
+
+name: Wool
+
+jobs:
+  runWool:
+    name: Run black
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+
+    - uses: uc-cdis/wool@master
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.pre-commit-config.yaml

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+repos:
+  - repo: [email protected]:Yelp/detect-secrets
+    rev: v1.5.0
+    hooks:
+      - id: detect-secrets
+        args: [ '--baseline', '.secrets.baseline' ]
+        exclude: poetry.lock
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: ^(gdcdictionary/schemas/|gdcdictionary/examples/valid/)
+      - id: end-of-file-fixer
+        exclude: ^(gdcdictionary/schemas/|gdcdictionary/examples/valid/)
+      - id: no-commit-to-branch
+        args: [ --branch, develop, --branch, master, --pattern, release/.* ]
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+      - id: black

.secrets.baseline

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+{
+  "version": "1.5.0",
+  "plugins_used": [
+    {
+      "name": "ArtifactoryDetector"
+    },
+    {
+      "name": "AWSKeyDetector"
+    },
+    {
+      "name": "AzureStorageKeyDetector"
+    },
+    {
+      "name": "Base64HighEntropyString",
+      "limit": 4.5
+    },
+    {
+      "name": "BasicAuthDetector"
+    },
+    {
+      "name": "CloudantDetector"
+    },
+    {
+      "name": "DiscordBotTokenDetector"
+    },
+    {
+      "name": "GitHubTokenDetector"
+    },
+    {
+      "name": "GitLabTokenDetector"
+    },
+    {
+      "name": "HexHighEntropyString",
+      "limit": 3.0
+    },
+    {
+      "name": "IbmCloudIamDetector"
+    },
+    {
+      "name": "IbmCosHmacDetector"
+    },
+    {
+      "name": "IPPublicDetector"
+    },
+    {
+      "name": "JwtTokenDetector"
+    },
+    {
+      "name": "KeywordDetector",
+      "keyword_exclude": ""
+    },
+    {
+      "name": "MailchimpDetector"
+    },
+    {
+      "name": "NpmDetector"
+    },
+    {
+      "name": "OpenAIDetector"
+    },
+    {
+      "name": "PrivateKeyDetector"
+    },
+    {
+      "name": "PypiTokenDetector"
+    },
+    {
+      "name": "SendGridDetector"
+    },
+    {
+      "name": "SlackDetector"
+    },
+    {
+      "name": "SoftlayerDetector"
+    },
+    {
+      "name": "SquareOAuthDetector"
+    },
+    {
+      "name": "StripeDetector"
+    },
+    {
+      "name": "TelegramBotTokenDetector"
+    },
+    {
+      "name": "TwilioKeyDetector"
+    }
+  ],
+  "filters_used": [
+    {
+      "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
+      "min_level": 2
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_indirect_reference"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_likely_id_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_lock_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_potential_uuid"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_sequential_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_swagger_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_templated_secret"
+    }
+  ],
+  "results": {
+    ".github/workflows/ci.yml": [
+      {
+        "type": "Secret Keyword",
+        "filename": ".github/workflows/ci.yml",
+        "hashed_secret": "3e26d6750975d678acb8fa35a0f69237881576b0",
+        "is_verified": false,
+        "line_number": 17
+      }
+    ],
+    ".travis.yml": [
+      {
+        "type": "Base64 High Entropy String",
+        "filename": ".travis.yml",
+        "hashed_secret": "a5550bd57663a78c1cd9ffd31148627d780a5e94",
+        "is_verified": false,
+        "line_number": 9
+      },
+      {
+        "type": "Base64 High Entropy String",
+        "filename": ".travis.yml",
+        "hashed_secret": "9367bab27f27511665862beae3dad6468998f4a5",
+        "is_verified": false,
+        "line_number": 10
+      }
+    ],
+    "gdcdictionary/examples/valid/aligned_reads_index.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/aligned_reads_index.json",
+        "hashed_secret": "a1ba33896d16eda8522e531edbaf3b625c1f4c31",
+        "is_verified": false,
+        "line_number": 6
+      }
+    ],
+    "gdcdictionary/examples/valid/experimental_metadata.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/experimental_metadata.json",
+        "hashed_secret": "daef34f66b6e909f3a22ffd063d48eb428067b6e",
+        "is_verified": false,
+        "line_number": 6
+      }
+    ],
+    "gdcdictionary/examples/valid/slide_image.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/slide_image.json",
+        "hashed_secret": "daef34f66b6e909f3a22ffd063d48eb428067b6e",
+        "is_verified": false,
+        "line_number": 6
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_aligned_reads.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_aligned_reads.json",
+        "hashed_secret": "e3f181b6b92d74e30d524d03029e785d0c7c7535",
+        "is_verified": false,
+        "line_number": 7
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_copy_number.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_copy_number.json",
+        "hashed_secret": "e3f181b6b92d74e30d524d03029e785d0c7c7535",
+        "is_verified": false,
+        "line_number": 6
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_methylation.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_methylation.json",
+        "hashed_secret": "e3f181b6b92d74e30d524d03029e785d0c7c7535",
+        "is_verified": false,
+        "line_number": 7
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_somatic_mutation.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_somatic_mutation.json",
+        "hashed_secret": "a1ba33896d16eda8522e531edbaf3b625c1f4c31",
+        "is_verified": false,
+        "line_number": 9
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_unaligned_reads.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_unaligned_reads.json",
+        "hashed_secret": "88e3a7adc1779a311467797f00d2edc5e9697d9c",
+        "is_verified": false,
+        "line_number": 7
+      }
+    ]
+  },
+  "generated_at": "2025-01-10T20:22:28Z"
+}

NOTICE

@@ -1 +1,18 @@
-Copyright 2015 University of Chicago, Ontario Institute for Cancer ResearchLicensed under the Apache License, Version 2.0 (the "License");you may not use this file except in compliance with the License.You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing,software distributed under the License is distributed on an "AS IS" BASIS,WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.See the License for the specific language governing permissions andlimitations under the License.Portions of this work, authored by University of Chicago andOntario Institute for Cancer Research employees, was funded in whole or in partby National Cancer Institute, National Institutes of Healthunder U.S. Government contract HHSN261200800001E.
+Copyright 2015 University of Chicago, Ontario Institute for Cancer Research
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing,
+software distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+Portions of this work, authored by University of Chicago and
+Ontario Institute for Cancer Research employees, was funded in whole or in part
+by National Cancer Institute, National Institutes of Health
+under U.S. Government contract HHSN261200800001E.