initial commit

.dockerignore

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+# Ignore unnecessary files inside allowed directories
+# This should go after the allowed directories
+**/*.pyc
+**/*.egg-info
+**/__pycache__

.github/dependabot.yml

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+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 10

.github/workflows/ci.yml

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+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:
+       test-script: 'tests/test.sh'
+       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: "gen3workflow"
+
+  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, UnitTest]
+    if: github.ref != 'refs/heads/master'
+    uses: uc-cdis/.github/.github/workflows/optional_lint_check.yaml@master
+    with:
+      python-version: '3.9'
+      use-cache: true
+
+  ImageBuildAndPush:
+    name: Build Image and Push
+    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    needs: [RequiredLint, Security, UnitTest]
+    with:
+      BUILD_PLATFORMS: "linux/amd64"
+    secrets:
+      ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
+      ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
+      QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
+      QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}

.github/workflows/validate_markdown.yaml

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+name: Markdown validation
+
+on:
+  pull_request:
+    types:
+    - opened
+    - reopened
+    - synchronize
+    paths:
+    - .github/workflows/validate_markdown.yaml
+    - "**.md"
+
+jobs:
+  markdown_validation:
+    name: Markdown validation
+    uses: uc-cdis/.github/.github/workflows/validate_markdown.yaml@master

.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 }}

.gitignore

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+#
+.DS_Store
+chroma/
+cache/
+tests/prof/
+prof/
+bin/library
+tmp/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+_coverage/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# PyCharm
+.idea/
+
+# Docker db
+postgres-data/
+
+# VSCode
+.vscode/
+.dccache
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.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: v2.5.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: no-commit-to-branch
+        args: [--branch, master]
+-   repo: https://github.com/psf/black
+    rev: 24.8.0
+    hooks:
+    -   id: black