Check and test HMDB updates #40
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| name: Check and test HMDB updates | |
| on: | |
| workflow_dispatch: | |
| pull_request: # tests whether it is working on PR | |
| paths: | |
| - '.github/workflows/hmdb.yml' | |
| 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 | |
| issues: write | |
| jobs: | |
| check_new_data: | |
| runs-on: ubuntu-latest | |
| name: Check the date of the latest data | |
| outputs: | |
| DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }} | |
| DATE_OLD: ${{ steps.check_download.outputs.DATE_OLD }} | |
| NEW_RELEASE: ${{ steps.check_download.outputs.NEW_RELEASE }} | |
| steps: | |
| # step 1: check the release date for the latest hmdb files | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Check for new hmdb files | |
| id: check_download | |
| run: | | |
| ## Setup | |
| sudo apt-get install xml-twig-tools | |
| ##Extract the date from the hmdb config file | |
| date_old=$(grep -E '^date=' datasources/hmdb/config | cut -d'=' -f2) | |
| echo 'Accessing the hmdb data' | |
| wget http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip | |
| unzip hmdb_metabolites.zip | |
| head hmdb_metabolites.xml | |
| head hmdb_metabolites.xml | grep 'update_date' | sed 's/.*>\([0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\).*/\1/' | |
| date_new=$(head hmdb_metabolites.xml | grep 'update_date' | sed 's/.*>\([0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\).*/\1/') | |
| #Store dates to output | |
| echo "DATE_OLD=$date_old" >> $GITHUB_OUTPUT | |
| echo "DATE_NEW=$date_new" >> $GITHUB_OUTPUT | |
| ##Compare the dates and set variable if date_new is more recent | |
| timestamp1=$(date -d "$date_new" +%s) | |
| timestamp2=$(date -d "$date_old" +%s) | |
| if [ "$timestamp1" -gt "$timestamp2" ]; then | |
| echo 'New release available', "$release" | |
| echo "NEW_RELEASE=true" >> $GITHUB_OUTPUT | |
| else | |
| echo 'No new release available' | |
| fi | |
| echo "Date of latest release: $date_new" | |
| echo "Date of release of the current version: $date_old" | |
| test_new_data_processing: | |
| name: Processing new data and check updates | |
| needs: check_new_data | |
| outputs: | |
| ARTIFACT_ID: ${{ steps.artifact-upload.outputs.artifact-id }} | |
| env: | |
| DATE_OLD: ${{ needs.check_new_data.outputs.DATE_OLD }} | |
| DATE_NEW: ${{ needs.check_new_data.outputs.DATE_NEW }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| # step 2: download the recent data | |
| - name: Download the recent data | |
| run: | | |
| sudo apt-get install xml-twig-tools | |
| ##Store outputs from previous job in environment variables | |
| echo "$DATE_NEW=$DATE_NEW" >> $GITHUB_ENV | |
| ##Download hmdb file | |
| wget http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip | |
| unzip hmdb_metabolites.zip | |
| mkdir hmdb | |
| mv hmdb_metabolites.xml hmdb | |
| cd hmdb | |
| xml_split -v -l 1 hmdb_metabolites.xml | |
| rm hmdb_metabolites.xml | |
| cd ../ | |
| zip -r hmdb_metabolites_split.zip hmdb | |
| # step 3: run the jar for hmdb preprocessing | |
| - name: Set up Java | |
| uses: actions/setup-java@v2 | |
| with: | |
| java-version: '11' | |
| distribution: 'adopt' | |
| - name: Test XML processing | |
| id: sdf_process | |
| run: | | |
| # Set up vars from config file | |
| to_check_from_zenodo=$(grep -E '^to_check_from_zenodo=' datasources/hmdb/config | cut -d'=' -f2) | |
| inputFile=hmdb_metabolites_split.zip | |
| mkdir datasources/hmdb/recentData/ | |
| outputDir="datasources/hmdb/recentData/" | |
| # Run Java program and capture its exit code | |
| java -cp java/target/mapping_prerocessing-0.0.1-jar-with-dependencies.jar org.sec2pri.hmdb_xml "$inputFile" "$outputDir" | |
| # Check the exit status of the Java program | |
| if [ $? -eq 0 ]; then | |
| # Java program succeeded | |
| echo "Successful preprocessing of ChEBI data." | |
| echo "FAILED=false" >> $GITHUB_ENV | |
| else | |
| # Java program failed | |
| echo "Failed preprocessing of ChEBI data." | |
| echo "FAILED=true" >> $GITHUB_ENV | |
| fi | |
| # step 4: compare the new and old data | |
| - name: Diff versions | |
| if: | |
| ${{ env.FAILED == 'false' }} | |
| run: | | |
| # Set up vars from config file | |
| to_check_from_zenodo=$(grep -E '^to_check_from_zenodo=' datasources/hmdb/config | cut -d'=' -f2) | |
| old="datasources/hmdb/data/$to_check_from_zenodo" | |
| new="datasources/hmdb/recentData/$to_check_from_zenodo" | |
| # remove headers | |
| sed -i '1d' "$new" | |
| sed -i '1d' "$old" | |
| # qc integrity of IDs | |
| wget -nc https://raw.githubusercontent.com/bridgedb/datasources/main/datasources.tsv | |
| HMDB_ID=$(awk -F '\t' '$1 == "HMDB" {print $10}' datasources.tsv) | |
| # Split the file into two separate files for each column | |
| awk -F '\t' '{print $1}' $new > column1.txt | |
| awk -F '\t' '{print $2}' $new > column2.txt | |
| # Use grep to check if any line in the primary column doesn't match the pattern | |
| if grep -nqvE "$HMDB_ID" "column1.txt"; then | |
| echo "All lines in the primary column match the pattern." | |
| else | |
| echo "Error: At least one line in the primary column does not match pattern." | |
| grep -nvE "^$HMDB_ID$" "column1.txt" | |
| echo "FAILED=true" >> $GITHUB_ENV | |
| exit 1 | |
| fi | |
| # Use grep to check if any line in the secondary column doesn't match the pattern | |
| if grep -nqvE "$HMDB_ID" "column1.txt"; then | |
| echo "All lines in the secondary column match the pattern." | |
| else | |
| echo "Error: At least one line in the secondary column does not match pattern." | |
| grep -nqvE "$HMDB_ID" "column2.txt" | |
| echo "FAILED=true" >> $GITHUB_ENV | |
| exit 1 | |
| fi | |
| # sort them | |
| cat "$old" | sort | tr -d "\r" > ids_old.txt | |
| cat "$new" | sort | tr -d "\r" > ids_new.txt | |
| echo "Performing diff between the sorted lists of Symbols" | |
| # Perform a diff between the sorted lists of Symbols | |
| output_file=diff.txt | |
| diff -u ids_old.txt ids_new.txt > $output_file || true | |
| # retrieve new lines | |
| added=$(grep '^+' "$output_file" | sed 's/+//g') || true | |
| # retrieve removed lines | |
| removed=$(grep '^-' "$output_file" | sed 's/-//g') || true | |
| # Create temporary files | |
| tmp_added=$(mktemp) | |
| tmp_withdrawn=$(mktemp) | |
| tmp_removed=$(mktemp) | |
| # Write the content of the added variable to the temporary file | |
| echo "$added" > "$tmp_added" | |
| # Retrieve matches and store them in another temporary file | |
| grep 'Entry Withdrawn' "$tmp_added" > "$tmp_withdrawn" || true | |
| # Append matches to the removed variable | |
| if [ -n "$removed" ]; then | |
| echo -e "$removed\n$(cat $tmp_withdrawn)" > "$tmp_removed" | |
| else | |
| cat "$tmp_withdrawn" > "$tmp_removed" | |
| fi | |
| # Remove matching lines from the added variable | |
| sed '/Entry Withdrawn/d' "$tmp_added" > "$tmp_added.tmp" && mv "$tmp_added.tmp" "$tmp_added" | |
| # Read the updated content back into the variables | |
| added=$(cat "$tmp_added") | |
| removed=$(cat "$tmp_removed") | |
| # Clean up temporary files | |
| rm "$tmp_added" "$tmp_withdrawn" "$tmp_removed" | |
| added_filtered=$(comm -23 <(sort <<< "$added") <(sort <<< "$removed")) | |
| removed_filtered=$(comm -23 <(sort <<< "$removed") <(sort <<< "$added")) | |
| added=$added_filtered | |
| removed=$removed_filtered | |
| # count them | |
| count_removed=$(printf "$removed" | wc -l) || true | |
| count_added=$(printf "$added" | wc -l) || true | |
| # make sure we are not counting empty lines | |
| if [ -z "$removed" ]; then | |
| count_removed=0 | |
| removed="None" | |
| fi | |
| if [ -z "$added" ]; then | |
| count_added=0 | |
| added="None" | |
| fi | |
| echo ________________________________________________ | |
| echo " removed pairs " | |
| echo ________________________________________________ | |
| echo "$removed" | |
| echo ________________________________________________ | |
| echo " added pairs " | |
| echo ________________________________________________ | |
| echo "$added" | |
| echo _________________________________________________ | |
| echo "What's changed:" | |
| echo "- Added id pairs: $count_added" | |
| echo "- Removed id pairs: $count_removed" | |
| # Store to env to use in issue | |
| echo "ADDED=$count_added" >> $GITHUB_ENV | |
| echo "REMOVED=$count_removed" >> $GITHUB_ENV | |
| count=$(expr $count_added + $count_removed) || true | |
| echo "COUNT=$count" >> $GITHUB_ENV | |
| total_old=$(cat "$old" | wc -l) || true | |
| change=$((100 * count / total_old)) | |
| echo "CHANGE=$change" >> $GITHUB_ENV | |
| - name: 'Upload processed data as artifacts' | |
| id: artifact-upload | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: hmdb_processed | |
| path: datasources/hmdb/recentData/* | |
| - uses: JasonEtco/create-an-issue@v2 | |
| if: env.COUNT != 0 | |
| name: Post issue about update availability | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: "HMDB" | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md | |
| update_existing: true | |
| - uses: JasonEtco/create-an-issue@v2 | |
| name: Post issue about failing test | |
| if: ${{ env.FAILED == 'true' }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: hmdb | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md | |
| update_existing: true | |
| - name: Trigger docker release | |
| uses: peter-evans/repository-dispatch@v3 | |
| if: ${{ env.COUNT != 0 }} | |
| with: | |
| token: ${{ secrets.PING }} | |
| repository: sec2pri/omicsFixID | |
| event-type: update-event | |
| client-payload: > | |
| { | |
| "ref": "${{ github.ref }}", | |
| "sha": "${{ github.sha }}", | |
| "datasource": "HMDB", | |
| "version": "NA", | |
| "processed_data": "https://github.com/sec2pri/mapping_preprocessing/actions/runs/${{ github.run_id }}/artifacts/${{ steps.artifact-upload.outputs.artifact-id }}" | |
| } |