Append_File_On_Merged_to_Main.yml

name: Adding documentation and update GitHub Page
run-name: Action on Merged main by ${{ github.actor }} 

on:
  workflow_call:
    inputs:
    
      image_to_use:
        required: true
        type: string
  
      artifact_rid:
        required: true
        type: string

      package_name:
        required: true
        type: string

      r_version:
        required: true
        type: string
        
    secrets:
      NIDAP_TOKEN:
        required: false 
      
jobs:
  Document_GitHub_Page_CD:
    name: Post Merged to Main by ${{ github.actor }}
    runs-on: ubuntu-latest
    container:
      image: ${{ inputs.image_to_use }}
      credentials:
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
         
    steps:
      - run: echo "Checking in ${{ inputs.image_to_use }}"
      - uses: actions/checkout@v3
        with:
          token: ${{secrets.GITHUB_TOKEN}}
          
      - name: Generating files with Document
        id: prepare-push 
        if: ${{ success() }}
        run: |
          bash
          ./root/miniconda3/etc/profile.d/conda.sh && conda init bash

          export current_wd="/__w/${GITHUB_REPOSITORY#*/}/${GITHUB_REPOSITORY#*/}"
          

          cd $current_wd
          
          export MY_GIT_TOKEN=${{ secrets.GITHUB_TOKEN }}
          export MY_GIT_USERNAME=${{ github.actor }}
          export MY_GIT_EMAIL=${{ github.event.pusher.email }}
          
          git config --global user.name "$MY_GIT_USERNAME"
          git config --global user.email "$MY_GIT_EMAIL"
          git config --global url."https://api:$MY_GIT_TOKEN@github.com/".insteadOf "https://github.com/"
          git config --global url."https://ssh:$MY_GIT_TOKEN@github.com/".insteadOf "ssh://git@github.com/"
          git config --global url."https://git:$MY_GIT_TOKEN@github.com/".insteadOf "git@github.com:"
          
          git config --global --add safe.directory "$current_wd"

          git clone https://github.com/fnlcr-dmap/gitflow-R.git

          cd $current_wd
          
          git clone https://github.com/${GITHUB_REPOSITORY}.git
          
          cd ${GITHUB_REPOSITORY#*/}

          BRANCH_NAME="Conda_Package"

          git checkout $BRANCH_NAME

          git checkout main

          current_version=$(grep -oP 'Version: \K.*' DESCRIPTION)

          echo "Upcoming Production Package Name: ${{ inputs.package_name }}"

          echo "Upcoming Production Package Version: $current_version"

          echo  "\nWriting Documentations Now......\n"

          R -e 'library(devtools);document()'

          if [ -d "./vignettes" ]; then
              HAS_VIGNETTES=True
          else
              HAS_VIGNETTES=False
          fi

          if [ "$HAS_VIGNETTES" = True ]; then
              mv ./vignettes ./bk_vignettes
          fi

          # ls -al /renv/library/R-4.1/x86_64-pc-linux-gnu

          R -e 'library(devtools);load_all();library(pkgdown);build_site_github_pages()'

          if [ "$HAS_VIGNETTES" = True ]; then
            mkdir -p ./docs/vignettes
            if [ -n "$(find ./bk_vignettes -maxdepth 1 -type f -name '*.html')" ]; then
              # HTML files exist, so copy them to ./docs/vignettes
              mkdir -p ./docs/vignettes && cp ./bk_vignettes/*.html ./docs/vignettes
            else
              # HTML files do not exist, display an error message or take appropriate action
              echo "No HTML files found in the ./bk_vignettes directory."
              # You can add more error handling or actions here as needed
            fi
          fi

          if [ "$HAS_VIGNETTES" = True ]; then
            mv ./bk_vignettes ./vignettes
          fi
          
          git add ./NAMESPACE ./man/* ./DESCRIPTION ./CHANGELOG.md

          echo $(git commit -a -m "docs: Adding auto-generated files") > commit_log.log
                    
          echo "Performing check now"
          export nothing_for_commit="$(grep -Po "nothing to commit" commit_log.log)"
          
          if [ -n "${nothing_for_commit}" ]; then
            echo "Commit check failed with message: $nothing_for_commit" 
          else
            echo "Pushing changes now."
            git push -f origin main
          fi

          echo "$(git log --oneline --ancestry-path ${{github.event.pull_request.head.sha}}..HEAD)" > \
              $current_wd/commit_history_log.log

          commit_log_location="$current_wd/commit_history_log.log"

          cp $(pwd)/Conda_Recipe/meta.yaml $current_wd

          conda_recipe="$current_wd/meta.yaml"
          change_log_location="$current_wd/commit_history_log.log"

          echo "conda_recipe=$conda_recipe" >> $GITHUB_ENV
          echo "commit_log_location=$commit_log_location" >> $GITHUB_ENV
          
          echo "Create release tag for Continueous Deployment"

          latest_commit_hash=$(git rev-parse HEAD)
          TAG_NAME="continuous_deployment"

          # Check if the tag exists locally
          if git rev-parse -q --verify "refs/tags/$TAG_NAME" >/dev/null; then
              echo "Local tag '$TAG_NAME' exists. Deleting..."
              git tag -d "$TAG_NAME"
          else
              echo "Local tag '$TAG_NAME' does not exist."
          fi

          # Check if the tag exists remotely
          if git ls-remote --tags origin | grep -q "refs/tags/$TAG_NAME"; then
              echo "Remote tag '$TAG_NAME' exists. Deleting..."
              git push origin ":refs/tags/$TAG_NAME"
          else
              echo "Remote tag '$TAG_NAME' does not exist."
          fi

          git tag \
            -a "$TAG_NAME" \
            -m "Automatically tagged latest commit for continuous_deployment." \
            $latest_commit_hash

          git push origin $TAG_NAME

          echo "Now pushing GitHub Page Documents"

          if [ "$HAS_VIGNETTES" = True ]; then
            cp ./vignettes/*.png ./docs/articles
          fi

          git add ./docs/*
          git add ./docs/.*

          if git diff --cached --name-only | grep -q 'commit_log.log'; then
            git reset HEAD commit_log.log
          fi


          git commit -a -m "Documenting doc files."
          
          echo $(git checkout github_page) > checkout_check.log
          
          export no_branch="$(grep -Po "did not match any file(s) known" checkout_check.log)"
          
          if [ -n "${no_branch}" ]; then
            git checkout -b github_page
          fi
          
          git checkout -f main ./docs
          
          echo $(git commit -a -m "Updating GitHub Page") > commit_log.log
          
          cat commit_log.log
          
          export nothing_for_commit="$(grep -Po "nothing to commit" commit_log.log)"
          
          if [ -n "${nothing_for_commit}" ]; then
            echo "Commit check failed with message: $nothing_for_commit" 
          else
            echo "Pushing changes now."
            git push -f origin github_page
          fi

          echo "Process completed."

      - name: Generating Conda Package
        id: prepare-conda-pkg 
        if: ${{ success() }}
        run: |

          export current_wd="/__w/${GITHUB_REPOSITORY#*/}/${GITHUB_REPOSITORY#*/}"
          cd $current_wd/${GITHUB_REPOSITORY#*/}

          git checkout main

          VERSION=$(grep -oP 'Version: \K[\d.]+' DESCRIPTION)

          cd ../
          mkdir conda_pkg_building
          cd conda_pkg_building

          CONDA_DIR=$(pwd)
          BRANCH_NAME="Conda_Package"
          
          export MY_GIT_TOKEN=${{ secrets.GITHUB_TOKEN }}
          export MY_GIT_USERNAME=${{ github.actor }}
          export MY_GIT_EMAIL=${{ github.event.pusher.email }}
          
          git config --global user.name "$MY_GIT_USERNAME"
          git config --global user.email "$MY_GIT_EMAIL"
          git config --global url."https://api:$MY_GIT_TOKEN@github.com/".insteadOf "https://github.com/"
          git config --global url."https://ssh:$MY_GIT_TOKEN@github.com/".insteadOf "ssh://git@github.com/"
          git config --global url."https://git:$MY_GIT_TOKEN@github.com/".insteadOf "git@github.com:"
          
          git config --global --add safe.directory "$current_wd"

          # Check if conda-build is installed
          # if ! command -v conda mambabuild &> /dev/null; then
          #     echo "conda mambabuild is not installed. Installing..."
          #     conda install -c conda-forge boa
          # fi

          REPO_NAME_LOWERCASE=$(echo ${GITHUB_REPOSITORY#*/} | \
                      tr '[:upper:]' '[:lower:]')

          echo "$(pwd)"
          echo "$(ls)"
          PACKAGE_NAME="${{ inputs.package_name }}"
          echo "Package Name: $PACKAGE_NAME"
          echo "New version: $VERSION"

          mkdir r-$PACKAGE_NAME

          cp -rf $current_wd/${GITHUB_REPOSITORY#*/}/Conda_Recipe/meta.yaml ./r-$PACKAGE_NAME/
          cp $current_wd/gitflow-R/src/bld.bat ./r-$PACKAGE_NAME/
          cp $current_wd/gitflow-R/src/build.sh ./r-$PACKAGE_NAME/
      
          sed -i "s/<CURRENT_VERSION>/$VERSION/g" ./r-$PACKAGE_NAME/meta.yaml

          echo "\n\n##########Current Recipe:##################\n\n" 

          cat ./r-$PACKAGE_NAME/meta.yaml

          echo "\n\n##########################################\n\n"       
          
          # Construct the package name as "r-repository_name"

          RECIPE_DIR="$(pwd)/$PACKAGE_NAME"

          echo "Recipe is now in $RECIPE_DIR."

          echo "#####################################################"

          # Build the Conda package while ignoring tests
          echo "#####################################################"
          echo "Building Conda Package Now."
          echo "#####################################################"

          # conda config --set channel_priority strict
          conda config --add channels conda-forge
          conda config --append channels file:///local_channel
          conda config --append channels bioconda
          conda config --append channels defaults
          conda config --get channels
          conda clean --all

          echo "#####################################################"

          conda build --R="${{ inputs.r_version }}" r-$PACKAGE_NAME

          echo "#####################################################"

          PKG_PATH=$(find "/conda/conda-bld" -name '*.tar.bz2')
          # --build-only \
          echo "Package build in $PKG_PATH"
          
          echo "#####################################################"
          echo "Package Built! Uploading to $BRANCH_NAME now"         

          cd $current_wd/${GITHUB_REPOSITORY#*/}

          BRANCH_NAME="Conda_Package"

          git checkout "$BRANCH_NAME"

          # Move the built package to the current directory
          echo "Moving Conda Package Now."

          PKG_NAME=$(basename "$PKG_PATH")
          DEST_NAME="$PKG_NAME"

          mv $PKG_PATH .

          git add *.tar.bz2

          current_pkg="$(basename "$PKG_PATH")"
          
          echo "current_pkg="$current_pkg"" >> $GITHUB_ENV
          echo "###############################################################"
          echo "\nCurrent package: $current_pkg"

      - name: Continuous Deployment to NIDAP
        id: nidap-cd
        if: ${{ success() }}
        run: |
          export current_wd="/__w/${GITHUB_REPOSITORY#*/}/${GITHUB_REPOSITORY#*/}"
          cd $current_wd
          cd ${GITHUB_REPOSITORY#*/}

          conda install curl
          
          echo "Package to Upload: ${{ env.current_pkg }}"

          TOKEN="${{ secrets.NIDAP_TOKEN }}"
          PACKAGE="${{ env.current_pkg }}"
          PLATFORM="linux-64" # replace with the package platform (e.g. noarch, linux-64, osx-64)
          response=$(curl \
                    -H "Authorization: Bearer $TOKEN" \
                    -H "Content-Type: application/octet-stream" \
                    --data-binary "@$PACKAGE" \
                    -XPUT "https://nidap.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.00852eef-c60b-4b78-8f14-cd48cdfde051/contents/release/conda/$PLATFORM/$PACKAGE" \
                    2>&1)
          current_datetime="$(date +"%Y-%m-%d %H:%M:%S")"
          echo "\nDatetime: $current_datetime, Version:  ${{ env.current_pkg }}"
          echo "\nDatetime: $current_datetime, Version:  ${{ env.current_pkg }}" >> README.md

          current_log_name=${{ env.current_pkg }}
          current_log_name="${current_log_name%.tar.bz2}"
          current_log_name="Commit_Log_$current_log_name.log"

          mv "${{ env.commit_log_location }}" "$current_log_name"

          git add ./$current_log_name

          echo "<br>[View Commit Log]($current_log_name)" >> README.md

          echo "#########################################################"

          # Check if the response contains an error message
          if echo "$response" | grep -q "errorCode"; then
            error_name=$(echo "$response" | grep -o '"errorName":"[^"]*' | awk -F'"' '{print $4}')
            echo "Error message: $error_name"
            echo "<br>Deployment Status: $error_name" >> README.md
          else
            echo "Update Success!"
            echo "Package ${{ env.current_pkg }} is now on NIDAP."
            echo "<br>Deployment Status: Success" >> README.md
          fi

          git commit -a -m "Automatically build conda package"

          git push -f origin $BRANCH_NAME