diff --git a/.github/workflows/chebi.yml b/.github/workflows/chebi.yml index 8926d57b..2c28ccd8 100644 --- a/.github/workflows/chebi.yml +++ b/.github/workflows/chebi.yml @@ -60,12 +60,12 @@ jobs: if [ "$timestamp1" -gt "$timestamp2" ]; then echo "DOWNLOAD_FILE=true" >> $GITHUB_ENV - echo 'New release (rel${release}) available' + echo 'New release available', '${ release} else echo "DOWNLOAD_FILE=false" >> $GITHUB_ENV echo 'No new release available' fi - echo "Date of latest release: $date_new", "Date of release of the current version: $date_old", "Download: ${{ github.DOWNLOAD_FILE }}" + echo "Date of latest release: $date_new", "Date of release of the current version: $date_old" ##Clean up rm index.htm* @@ -133,8 +133,8 @@ jobs: - name: Diff versions run: | - old=$GITHUB.ZENODO_FILE_NAME - new=mapping_preprocessing/datasources/chebi/data/$GITHUB.ZENODO_FILE_NAME + old=$env.ZENODO_FILE_NAME + new=mapping_preprocessing/datasources/chebi/data/$env.ZENODO_FILE_NAME column_name="secondaryID" # Extract the secondaryID column from both files and sort them ids_old=$(cut -f 2 "$old" | sort | tr -d "\r") @@ -166,14 +166,14 @@ jobs: - uses: actions/checkout@v3 - run: | echo "---" >> issue.md - echo "title: Update ChEBI - release on ${{ GITHUB.NEW_DATE }}" >> issue.md + echo "title: Update ChEBI - release on ${{ env.NEW_DATE }}" >> issue.md echo "assignees: tabbassidaloii" >> issue.md echo "---" >> issue.md - echo "[New release for ChEBI](https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${{ GITHUB.RELEASE }}/SDF/) available from ${{ GITHUB.NEW_DATE }}." >> issue.md + echo "[New release for ChEBI](https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${{ env.RELEASE }}/SDF/) available from ${{ env.NEW_DATE }}." >> issue.md echo ## Removed secondary IDs - echo $github.REMOVED + echo $env.REMOVED echo ## Added secondary IDs - echo $github.ADDED + echo $env.ADDED - uses: JasonEtco/create-an-issue@v2 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -192,10 +192,10 @@ jobs: - uses: actions/checkout@v3 - run: | echo "---" >> issue.md - echo "title: Failed ChEBI processing for release ${{ GITHUB.RELEASE }}" >> issue.md + echo "title: Failed ChEBI processing for release ${{ env.RELEASE }}" >> issue.md echo "assignees: tabbassidaloii" >> issue.md echo "---" >> issue.md - echo "Processing failed for the [new release for ChEBI](https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${{ GITHUB.RELEASE }}/SDF/) available from ${{ GITHUB.NEW_DATE }}." >> issue.md + echo "Processing failed for the [new release for ChEBI](https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${{ env.RELEASE }}/SDF/) available from ${{ env.NEW_DATE }}." >> issue.md - uses: JasonEtco/create-an-issue@v2 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}