update-event #13
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| name: Update datasources | |
| on: | |
| repository_dispatch: | |
| types: [update-event] | |
| workflow_dispatch: | |
| jobs: | |
| update-version: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| - name: Echo client-payload values | |
| run: | | |
| echo "Ref: ${{ github.event.client_payload.ref }}" | |
| echo "SHA: ${{ github.event.client_payload.sha }}" | |
| echo "Datasource: ${{ github.event.client_payload.datasource }}" | |
| echo "Processed data: ${{ github.event.client_payload.processed_data }}" | |
| echo "Release number: ${{ github.event.client_payload.version }}" | |
| echo "Date: ${{ github.event.client_payload.date }}" | |
| - name: Update data files | |
| env: | |
| PAT_TOKEN: ${{ secrets.PAT }} | |
| run: | | |
| cd inst/apps/processed_mapping_files | |
| artifact=$(echo ${{ github.event.client_payload.processed_data }} | grep -oP '[^/]*$') | |
| curl -H "Accept: application/vnd.github+json" -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -L -o processed_data.zip "https://api.github.com/repos/sec2pri/mapping_preprocessing/actions/artifacts/$artifact/zip" | |
| unzip -f processed_data.zip | |
| rm -f processed_data.zip | |
| ls | |
| cd ../../ | |
| - name: Commit new data files | |
| env: | |
| token: ${{ secrets.PAT }} | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "OmicsFixID bot" | |
| git add --all | |
| git status | |
| git commit -m "Updated data" -m "Artifact URL: ${{ github.event.client_payload.datasource }}" | |
| git push -f | |
| - name: Update dataSourceVersion | |
| run: | | |
| new_date=${{ github.event.client_payload.date }} | |
| new_version=${{ github.event.client_payload.version }} | |
| datasource=${{ github.event.client_payload.datasource }} | |
| # File containing the data | |
| cp inst/apps/processed_mapping_files/dataSourceVersion.tsv inst/apps/processed_mapping_files/dataSourceVersion-old.tsv | |
| input_file="inst/apps/processed_mapping_files/dataSourceVersion-old.tsv" | |
| output_file="inst/apps/processed_mapping_files/dataSourceVersion.tsv" | |
| # Update the file using awk | |
| awk -F'\t' -v OFS='\t' -v ds="$datasource" -v nd="$new_date" -v nv="$new_version" ' | |
| BEGIN { OFS = FS } | |
| NR==1 { print; next } | |
| $1 == ds { $2 = nv; $4 = nd } | |
| { print } | |
| ' "$input_file" > "$output_file" | |
| if [ "$(md5sum file1 | awk '{ print $1 }')" == "$(md5sum file2 | awk '{ print $1 }')" ]; then | |
| echo changes=False >> $GITHUB_ENV | |
| else | |
| echo changes=True >> $GITHUB_ENV | |
| fi | |
| rm $input_file | |
| - name: Commit datasource | |
| if: env.changes=='True' | |
| env: | |
| token: ${{ secrets.PAT }} | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "OmicsFixID bot" | |
| git add --all | |
| git status | |
| git commit -m "Updated dataSourceVersion for $datasource" | |
| git push -f |