Fixes to ChEBI workflow #47
Workflow file for this run
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| name: chebi | ||
| on: | ||
| workflow_dispatch: | ||
| pull_request: # tests whether it is working on PR | ||
| schedule: | ||
| - cron: "0 0 1,15 * *" # Run the workflow on the 1st and 15th day of each month | ||
| permissions: | ||
| contents: write | ||
| pages: write | ||
| id-token: write | ||
| jobs: | ||
| check_release: | ||
| runs-on: ubuntu-latest | ||
| name: Check latest release date | ||
| steps: | ||
| # checkout the repository | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| # Download current version from Zenodo | ||
| - name: Download file from Zenodo | ||
| env: | ||
| zenodo_token: ${{ secrets.ZENODO }} | ||
| run: | | ||
| # Set up variables | ||
| chmod +x datasources/chebi/config | ||
| datasources/chebi/config . | ||
| zenodo_file_id="8348142" | ||
| file_name=$to_check_from_zenodo | ||
| echo file name: $file_name | ||
| echo "Dowloading from: https://zenodo.org/api/files/${zenodo_file_id}/${file_name}" | ||
| echo ZENODO_FILE_NAME=$file_name >>$GITHUB_ENV | ||
| # Request Zenodo API to download the file | ||
| curl -H "Authorization: Bearer $zenodo_token" -LJO "https://zenodo.org/api/files/${zenodo_file_id}/${file_name}" | ||
| # Verify the downloaded file | ||
| ls -l $FILE_NAME | ||
| # check the release date for the latest ChEBI release | ||
| - name: Check for new ChEBI release | ||
| run: | | ||
| echo 'Accessing the ChEBI archive' | ||
| wget https://ftp.ebi.ac.uk/pub/databases/chebi/archive/ | ||
| ## Read config | ||
| . datasources/chebi/config . | ||
| ## Check date for last element in index | ||
| string=$(tail -4 index.html | head -1) | ||
| ##Extract the date from the latest release (up to the day) | ||
| date_new=$(echo "$string" | grep -oP '<td align="right">\K[0-9-]+\s[0-9:]+(?=\s+</td>)' | awk '{print $1}') | ||
| release=$(echo "$string" | grep -oP '(?<=a href="rel)\d\d\d') | ||
| echo "RELEASE=$release" >>$GITHUB_ENV | ||
| echo "DATE_NEW=$date_new" >> $GITHUB_ENV | ||
| ##Extract the date from the ChEBI README file | ||
| date_old=$date | ||
| ##Compare the dates and set GITHUB_ENV variable if date_new is more recent | ||
| timestamp1=$(date -d "$date_new" +%s) | ||
| timestamp2=$(date -d "$date_old" +%s) | ||
| if [ "$timestamp1" -gt "$timestamp2" ]; then | ||
| echo "DOWNLOAD_FILE=true" >> $GITHUB_ENV | ||
| echo 'New release available', '${ 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" | ||
| ##Clean up | ||
| rm index.htm* | ||
| process_file: | ||
| needs: check_release | ||
| name: Download and test latest ChEBI release | ||
| if: ${{ github.DOWNLOAD_FILE }} == 'true' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Download data | ||
| run: | | ||
| ##Download ChEBI SDF file | ||
| wget https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel223/SDF/ChEBI_complete_3star.sdf.gz | ||
| ##Unzip gz file: | ||
| gunzip ChEBI_complete_3star.sdf.gz | ||
| ##Check file size if available | ||
| ls | ||
| ##Print file size | ||
| FILENAME=ChEBI_complete_3star.sdf | ||
| FILESIZE=$(stat -c%s "$FILENAME") | ||
| echo "Size of $FILENAME = $FILESIZE bytes." | ||
| ##Create temp. folder to store the data in | ||
| mkdir -p mapping_preprocessing/datasources/chebi/data | ||
| ##Move the SDF file to the expected location | ||
| mv ChEBI_complete_3star.sdf mapping_preprocessing/datasources/chebi/data | ||
| # step 3: run the R script for ChEBI preprocessing (to be made into a separate job) | ||
| - name: Run R script to process SDF data | ||
| run: | | ||
| ##Check R version: | ||
| R --version | ||
| ##Install the readr package: | ||
| #Rscript -e 'install.packages("readr")' | ||
| ##Running the R script: | ||
| #Rscript r/chebi_processing.R | ||
| #echo "R preprocessing of ChEBI data is done" | ||
| # step 4: run the Java .jar for ChEBI preprocessing (to be made into a separate job) | ||
| - name: Set up Java | ||
| uses: actions/setup-java@v2 | ||
| with: | ||
| java-version: '11' | ||
| distribution: 'adopt' | ||
| - name: Test SDF processing | ||
| run: | | ||
| inputFile="mapping_preprocessing/datasources/chebi/data/ChEBI_complete_3star.sdf" | ||
| outputDir="mapping_preprocessing/datasources/chebi/data" | ||
| # Run Java program and capture its exit code | ||
| java -cp target/mapping_prerocessing-0.0.1-jar-with-dependencies.jar org.sec2pri.chebi_sdf "$inputFile" "$outputDir" | ||
| # Check the exit status of the Java program | ||
| if [ $? -eq 0 ]; then | ||
| # Java program succeeded | ||
| echo "Java preprocessing of ChEBI data is done." | ||
| echo "FAILED=false" >>$GITHUB_ENV | ||
| else | ||
| # Java program failed | ||
| echo "Java preprocessing of ChEBI data failed." | ||
| echo "FAILED=true" >>$GITHUB_ENV | ||
| fi | ||
| - name: Diff versions | ||
| run: | | ||
| old=$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 "$old" | sort | tr -d "\r") | ||
| ids_new=$(cut -f 2 "$new" | sort | tr -d "\r") | ||
| # Perform a diff between the sorted lists of secondaryIDs | ||
| diff_output=$(diff -u <(echo "$ids_old") <(echo "$ids_new")) | ||
| # Store the output | ||
| output_file="diff_output.txt" | ||
| # Additions | ||
| added=$(grep '^+CHEBI' "$output_file") | ||
| echo ADDED=$added >>$GITHUB_ENV | ||
| # Removals | ||
| removed=$(grep '^-CHEBI' "$output_file") | ||
| echo REMOVED=$removed >>$GITHUB_ENV | ||
| post-issue_update: | ||
| needs: process_file | ||
| name: Post issue about updating data | ||
| runs-on: ubuntu-latest | ||
| if: github.DOWNLOAD_FILE == 'true' | ||
| permissions: | ||
| contents: read | ||
| issues: write | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - run: | | ||
| echo "---" >> issue.md | ||
| echo "title: Update ChEBI - release on ${{ env.DATE_NEW }}" >> issue.md | ||
| echo "assignees: tabbassidaloii" >> issue.md | ||
| echo "---" >> issue.md | ||
| echo "[New release for ChEBI](https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${{ env.RELEASE }}/SDF/) available from ${{ env.DATE_NEW }}." >> issue.md | ||
| echo ## Removed secondary IDs | ||
| echo $env.REMOVED | ||
| echo ## Added secondary IDs | ||
| echo $env.ADDED | ||
| - uses: JasonEtco/create-an-issue@v2 | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
| filename: issue.md | ||
| post-issue-fail: | ||
| needs: process_file | ||
| if: $ {{ github.FAILED == 'true' }} | ||
|
Check failure on line 186 in .github/workflows/chebi.yml
|
||
| name: Post issue about failed test | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: read | ||
| issues: write | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - run: | | ||
| echo "---" >> issue.md | ||
| echo "title: Failed ChEBI processing for release ${{ env.RELEASE }}" >> issue.md | ||
| echo "assignees: tabbassidaloii" >> issue.md | ||
| echo "---" >> issue.md | ||
| echo "Processing failed for the [new release for ChEBI](https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${{ env.RELEASE }}/SDF/) available from ${{ env.DATE_NEW }}." >> issue.md | ||
| - uses: JasonEtco/create-an-issue@v2 | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
| filename: issue.md | ||
