Main

.env

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+
+KGX_DATA_SETS="bdc-studies-kgx:v1.0"
+INPUT_DATA_SETS="heal-mds-studies:v1.0"
+
+LAKEFS_ACCESS_KEY=""
+LAKEFS_SECRET_KEY=""
+LAKEFS_REPO=""
+LAKEFS_BRANCH=""
+LAKEFS_URL="https://lakefs.apps.renci.org"
+
+BIOMEGATRON_URL="https://med-nemo.apps.renci.org/annotate"
+SAPBERT_URL="https://sap-qdrant.apps.renci.org/annotate"
+NODE_NORM_URL="https://nodenormalization-sri.renci.org/get_normalized_nodes?conflate=false&description=true&curie="
+NAME_RES_URL="https://name-resolution-sri.renci.org/reverse_lookup"

.github/workflows/build-push-dev-image.yml

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+# Workflow responsible for the 
+# development release processes.
+#
+name: Build-Push-Dev-Image
+on:
+  push:
+    branches:
+      - develop
+    paths-ignore:
+      - README.md
+      - .old_cicd/*
+      - .github/*
+      - .github/workflows/*
+      - LICENSE
+      - .gitignore
+      - .dockerignore
+      - .githooks
+  # Do not build another image on a pull request.
+  # Any push to develop will trigger a new build however.
+  pull_request:
+    branches-ignore:
+      - '*'
+
+jobs:
+  build-push-dev-image:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout Code
+      uses: actions/checkout@v3
+      with:
+        ref: ${{ github.head_ref }} 
+        # fetch-depth: 0 means, get all branches and commits
+        fetch-depth: 0
+
+    - name: Set short git commit SHA
+      id: vars
+      run: |
+        echo "short_sha=$(git rev-parse --short ${{ github.sha }})" >> $GITHUB_OUTPUT
+    # https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
+
+    - name: Confirm git commit SHA output
+      run: echo ${{ steps.vars.outputs.short_sha }}
+
+    # Docker Buildx is important to caching in the Build And Push Container
+    # step
+    # https://github.com/marketplace/actions/build-and-push-docker-images
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+      with:
+        driver-opts: |
+          network=host
+
+    - name: Login to DockerHub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+        logout: true
+
+    - name: Login to Container Registry
+      uses: docker/login-action@v3
+      with:
+        registry: containers.renci.org
+        username: ${{ secrets.CONTAINERHUB_USERNAME }}
+        password: ${{ secrets.CONTAINERHUB_TOKEN }}
+        logout: true
+
+
+    # Notes on Cache: 
+    # https://docs.docker.com/build/ci/github-actions/examples/#inline-cache
+    - name: Build Push Container
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: true
+        # Push to renci-registry and dockerhub here.
+        # cache comes from dockerhub.
+        tags: |
+          ${{ github.repository }}:develop
+          ${{ github.repository }}:${{ steps.vars.outputs.short_sha }}
+          containers.renci.org/${{ github.repository }}:develop
+          containers.renci.org/${{ github.repository }}:${{ steps.vars.outputs.short_sha }}
+        cache-from: type=registry,ref=${{ github.repository }}:buildcache-dev
+        cache-to: type=registry,ref=${{ github.repository }}:buildcache-dev,mode=max

.github/workflows/build-push-release.yml

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+# Workflow responsible for the 
+# major release processes.
+#
+
+name: Build-Push-Release
+on:
+  push:
+    branches:
+      - master 
+      - main
+    paths-ignore:
+      - README.md
+      - .old_cicd/*
+      - .github/*
+      - .github/workflows/*
+      - LICENSE
+      - .gitignore
+      - .dockerignore
+      - .githooks
+    tags-ignore:
+      - '*'
+jobs:
+  build-push-release:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout Code
+      uses: actions/checkout@v3
+      with:
+        ref: ${{ github.head_ref }} 
+        fetch-depth: 0
+
+    - name: Set short git commit SHA
+      id: vars
+      run: |
+        echo "short_sha=$(git rev-parse --short ${{ github.sha }})" >> $GITHUB_OUTPUT
+    # https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
+
+    - name: Confirm git commit SHA output
+      run: echo ${{ steps.vars.outputs.short_sha }}
+
+    # https://github.com/marketplace/actions/git-semantic-version
+    - name: Semver Check
+      uses: paulhatch/semantic-version@v5.0.3
+      id: version
+      with:
+        # The prefix to use to identify tags
+        tag_prefix: "v"
+        # A string which, if present in a git commit, indicates that a change represents a
+        # major (breaking) change, supports regular expressions wrapped with '/'
+        major_pattern: "/breaking:|major:/"
+        # A string which indicates the flags used by the `major_pattern` regular expression. Supported flags: idgs
+        major_regexp_flags: "ig"
+        # Same as above except indicating a minor change, supports regular expressions wrapped with '/'
+        minor_pattern: "/feat:|feature:|minor:/"
+        # A string which indicates the flags used by the `minor_pattern` regular expression. Supported flags: idgs
+        minor_regexp_flags: "ig"
+        # A string to determine the format of the version output
+        # version_format: "${major}.${minor}.${patch}-prerelease${increment}"
+        version_format: "${major}.${minor}.${patch}"
+        search_commit_body: false
+
+    # Docker Buildx is important to caching in the Build And Push Container
+    # step
+    # https://github.com/marketplace/actions/build-and-push-docker-images
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+      with:
+        driver-opts: |
+          network=host
+
+    - name: Login to DockerHub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+        logout: true
+
+    - name: Login to Container Registry
+      uses: docker/login-action@v3
+      with:
+        registry: containers.renci.org
+        username: ${{ secrets.CONTAINERHUB_USERNAME }}
+        password: ${{ secrets.CONTAINERHUB_TOKEN }}
+        logout: true
+
+    # Notes on Cache: 
+    # https://docs.docker.com/build/ci/github-actions/examples/#inline-cache
+    - name: Build Push Container
+      uses: docker/build-push-action@v5
+      with:
+        push: true
+        # Push to renci-registry and dockerhub here.
+        # cache comes from dockerhub.
+        tags: |
+          containers.renci.org/${{ github.repository }}:v${{ steps.version.outputs.version }}
+          containers.renci.org/${{ github.repository }}:latest
+          containers.renci.org/${{ github.repository }}:${{ steps.vars.outputs.short_sha }}
+          ${{ github.repository }}:v${{ steps.version.outputs.version }}
+          ${{ github.repository }}:latest
+          ${{ github.repository }}:${{ steps.vars.outputs.short_sha }}
+        cache-from: type=registry,ref=${{ github.repository }}:buildcache-release
+        cache-to: type=registry,ref=${{ github.repository }}:buildcache-release,mode=max
+
+#==========================TAG & RELEASE W/ NOTES =========================
+
+    # Note: GITHUB_TOKEN is autogenerated feature of github app
+    # which is auto-enabled when using github actions.
+    # https://docs.github.com/en/actions/security-guides/automatic-token-authentication
+    # https://docs.github.com/en/rest/git/tags?apiVersion=2022-11-28#create-a-tag-object
+    # https://docs.github.com/en/rest/git/refs?apiVersion=2022-11-28#create-a-reference
+    # This creates a "lightweight" ref tag.
+    - name: Create Tag for Release
+      run: |
+        curl \
+        -s --fail -X POST \
+        -H "Accept: application/vnd.github+json" \
+        -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+        -H "X-GitHub-Api-Version: 2022-11-28" \
+        https://api.github.com/repos/${{ github.repository }}/git/refs \
+        -d '{"ref":"refs/tags/v${{ steps.version.outputs.version }}","sha":"${{ github.sha }}"}'
+        
+#   https://cli.github.com/manual/gh_release_create
+    - name: Create Release
+      env:
+        RELEASE_VERSION: ${{ steps.version.outputs.version }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        gh release create ${{ env.RELEASE_VERSION }} \
+          -t "${{ env.RELEASE_VERSION }}" \
+          --generate-notes \
+          --latest

.github/workflows/code-checks.yml

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+# Workflow responsible for core acceptance testing.
+# Tests Currently Run:
+#     - flake8-linter
+#     - PYTest
+#     - Bandit
+# For PR Vulnerability Scanning a separate workflow will run.
+# The build-push-dev-image and build-push-release workflows
+# handle the develop and release image storage respectively.
+#
+#
+
+name: Code-Checks
+on:
+  push:
+    branches-ignore:
+      - master
+      - main
+      - develop
+  pull_request:
+    branches:
+      - develop
+      - master
+      - main
+    types: [opened, synchronize]
+    paths-ignore:
+      - README.md
+      - .old_cicd/*
+      - .github/*
+      - .github/workflows/*
+      - LICENSE
+      - .gitignore
+      - .dockerignore
+      - .githooks
+
+jobs:
+  ############################## flake8-linter ##############################
+  flake8-linter:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      # Currently actions/setup-python supports caching
+      # but the cache is not as robust as cache action.
+      # Here we cache the entire python env which speeds subsequent builds up alot. (alot being scientific term)
+      # Ref: https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
+      - uses: actions/cache@v3
+        name: Cache Python
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('pyproject.toml') }}
+
+      - name: Install Requirements
+        run: |
+          pip install -r requirements.txt
+
+      - name: Lint with flake8
+        run: |
+          pip install flake8
+          flake8 --ignore=E,W dags
+        # We continue on error here until the code is clean
+        # flake8 --ignore=E,W --exit-zero .
+        continue-on-error: true
+
+  ################################### PYTEST ###################################
+  # pytest:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #   - uses: actions/checkout@v3
+  #   - name: Set up Python
+  #     uses: actions/setup-python@v4
+  #     with:
+  #       python-version: '3.12'
+
+  #   - name: Install Requirements
+  #     run: |
+  #       pip install -r requirements.txt
+  #       pip install coverage
+  #       pip install ./tests
+
+  #   - name: Test with pytest
+  #     run: |
+  #       make test
+  ############################## test-image-build ##############################
+  test-image-build:
+    runs-on: ubuntu-latest
+    # if: ${{ github.actor == 'dependabot[bot]' }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set short git commit SHA
+        id: vars
+        run: |
+          echo "short_sha=$(git rev-parse --short ${{ github.sha }})" >> $GITHUB_OUTPUT
+      # https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
+      - name: Confirm git commit SHA output
+        run: echo ${{ steps.vars.outputs.short_sha }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+          logout: true
+
+      - name: Parse Github Reference Name
+        id: branch
+        run: |
+          REF=${{ github.ref_name }}
+          echo "GHR=${REF%/*}" >> $GITHUB_OUTPUT
+
+      # Notes on Cache:
+      # https://docs.docker.com/build/ci/github-actions/examples/#inline-cache
+      - name: Build Container
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: |
+            ${{ github.repository }}:test_${{ steps.branch.outputs.GHR }}
+          cache-from: type=registry,ref=${{ github.repository }}:buildcache
+          cache-to: type=registry,ref=${{ github.repository }}:buildcache,mode=max