Merge pull request #112 from uc-cdis/feat/add-vlmd-submission-tools-cli

Feat/add vlmd submission tools cli

.github/workflows/build_vlmd_submission_python_image.yml

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+name: Build Python Image and Push to Quay and ECR
+
+on:
+  push:
+    paths:
+    - vlmd-submission-tools/**
+    - .github/workflows/build_vlmd_submission_python_image.yml
+
+jobs:
+  ci:
+    name: Build Image and Push to Quay
+    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    with:
+      DOCKERFILE_LOCATION: "./vlmd-submission-tools/Dockerfile"
+      DOCKERFILE_BUILD_CONTEXT: "./vlmd-submission-tools"
+      OVERRIDE_REPO_NAME: "vlmd-submission-tools"
+      OVERRIDE_TAG_NAME: "vlmd-submission-tools-$(echo ${GITHUB_REF#refs/*/} | tr / _)"
+    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/ci_vlmd.yaml

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+name: CI Workflow
+
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - vlmd-submission-tools/
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+    - uses: actions/cache@v3
+      with:
+        path: ~/.cache/pypoetry/virtualenvs
+        key: ${{ runner.os }}-poetry-${{ hashFiles(format('{0}{1}', github.workspace, '/poetry.lock')) }}
+        restore-keys: |
+          ${{ runner.os }}-poetry-
+    - name: Install dependencies
+      working-directory: ./vlmd-submission-tools
+      run: |
+        python -m pip install --upgrade pip poetry
+        poetry install
+    - name: Test with unittest
+      working-directory: ./vlmd-submission-tools
+      run: |
+        poetry run python -m unittest discover -v -s tests/

vlmd-submission-tools/.dockerignore

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+venv/*
+.git/*

vlmd-submission-tools/.gitignore

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+vlmd_submission_tools/common/*cred*.json
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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
+
+# Pyre type checker
+.pyre/

vlmd-submission-tools/.pre-commit-config.yaml

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+default_stages: [commit, push]
+
+repos:
+  - repo: [email protected]:Yelp/detect-secrets
+    rev: v1.2.0
+    hooks:
+      - id: detect-secrets
+        args: ['--baseline', '.secrets.baseline']
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+      - id: trailing-whitespace
+      - id: detect-aws-credentials
+        args: ["--allow-missing-credentials"]
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: no-commit-to-branch
+        args: [--branch, develop, --branch, master, --branch, main, --pattern, release/.*]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        name: isort
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black

vlmd-submission-tools/Dockerfile

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+FROM quay.io/cdis/python:python3.9-buster-master
+
+RUN pip install --upgrade pip poetry
+
+WORKDIR /opt
+COPY poetry.lock /opt/
+COPY pyproject.toml /opt/
+COPY vlmd_submission_tools/__main__.py /opt/vlmd_submission_tools/__main__.py
+RUN python -m venv /env \
+    && . /env/bin/activate \
+    && poetry install --only main --no-interaction
+COPY . /opt/
+
+ENTRYPOINT ["/env/bin/vlmd-submission-tools"]