diff --git a/.github/workflows/test_releases.yml b/.github/workflows/test_releases.yml index 208792e3..603b8f62 100644 --- a/.github/workflows/test_releases.yml +++ b/.github/workflows/test_releases.yml @@ -16,7 +16,7 @@ permissions: jobs: ################################ChEBI########################### check_new_data_chebi: - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 name: Check ChEBI outputs: RELEASE_NUMBER: ${{ steps.check_download.outputs.RELEASE_NUMBER }} @@ -39,7 +39,7 @@ jobs: DATE_OLD: ${{ needs.check_new_data_chebi.outputs.DATE_OLD }} DATE_NEW: ${{ needs.check_new_data_chebi.outputs.DATE_NEW }} CURRENT_RELEASE_NUMBER: ${{ needs.check_new_data_chebi.outputs.CURRENT_RELEASE_NUMBER }} - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 steps: - name: Checkout repository uses: actions/checkout@v4 @@ -88,7 +88,7 @@ jobs: ################################HGNC########################### check_new_data_hgnc: - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 name: Check HGNC outputs: COMPLETE_NEW: ${{ steps.check_download.outputs.COMPLETE_NEW }} @@ -109,7 +109,7 @@ jobs: DATE_NEW: ${{ needs.check_new_data_hgnc.outputs.DATE_NEW }} COMPLETE_NEW: ${{ needs.check_new_data_hgnc.outputs.COMPLETE_NEW }} WITHDRAWN_NEW: ${{ needs.check_new_data_hgnc.outputs.WITHDRAWN_NEW }} - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 steps: - name: Checkout repository uses: actions/checkout@v4 @@ -157,7 +157,7 @@ jobs: update_existing: true ################################HMDB########################### check_new_data_hmdb: - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 name: Check HMDB outputs: DATE_NEW: ${{ steps.check_new_data_hmdb.outputs.DATE_NEW }} @@ -175,7 +175,7 @@ jobs: env: DATE_OLD: ${{ needs.check_download.outputs.DATE_OLD }} DATE_NEW: ${{ needs.check_download.outputs.DATE_NEW }} - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 steps: - name: Checkout repository uses: actions/checkout@v4 @@ -221,7 +221,7 @@ jobs: update_existing: true ################################NCBI########################### check_new_data_ncbi: - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 name: Check NCBI outputs: DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }} @@ -238,7 +238,7 @@ jobs: env: DATE_OLD: ${{ needs.check_new_data_ncbi.outputs.DATE_OLD }} DATE_NEW: ${{ needs.check_new_data_ncbi.outputs.DATE_NEW }} - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 steps: - name: Checkout repository uses: actions/checkout@v4 @@ -288,7 +288,7 @@ jobs: update_existing: true ##############################UNIPROT######################### check_new_data_uniprot: - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 name: Check UniProt outputs: UNIPROT_SPROT_NEW: ${{ steps.check_download.outputs.UNIPROT_SPROT_NEW }} @@ -308,7 +308,7 @@ jobs: env: DATE_OLD: ${{ needs.check_new_data_uniprot.outputs.DATE_OLD }} DATE_NEW: ${{ needs.check_new_data_uniprot.outputs.DATE_NEW }} - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 steps: - name: Checkout repository uses: actions/checkout@v4 @@ -355,7 +355,7 @@ jobs: filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md update_existing: true #trigger-docker-update: - # runs-on: ubuntu-latest + # runs-on: ubuntu-22.04 # steps: # - name: Checkout # uses: actions/checkout@v4 diff --git a/scripts/test_new_release.sh b/scripts/test_new_release.sh index c56dedcc..00c80add 100644 --- a/scripts/test_new_release.sh +++ b/scripts/test_new_release.sh @@ -34,9 +34,9 @@ case $source in echo "CURRENT_RELEASE_NUMBER=$CURRENT_RELEASE_NUMBER" >> $GITHUB_ENV url_release="https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel$RELEASE_NUMBER/SDF/" echo "URL_RELEASE=$url_release" >> $GITHUB_ENV - wget "https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${RELEASE_NUMBER}/SDF/ChEBI_complete_3star.sdf.gz" + wget -q "https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${RELEASE_NUMBER}/SDF/ChEBI_complete_3star.sdf.gz" ##Unzip gz file: - gunzip ChEBI_complete_3star.sdf.gz #TODO replace by config var + gunzip --quiet ChEBI_complete_3star.sdf.gz #TODO replace by config var ##Check file size if available ls ##Print file size @@ -55,8 +55,8 @@ case $source in ##Create temp. folder to store the data in mkdir -p datasources/hgnc/data ##Download hgnc file - wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/quarterly/tsv/${WITHDRAWN_NEW} - wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/quarterly/tsv/${COMPLETE_NEW} + wget -q https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/quarterly/tsv/${WITHDRAWN_NEW} + wget -q https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/quarterly/tsv/${COMPLETE_NEW} mv $WITHDRAWN_NEW $COMPLETE_NEW datasources/hgnc/data ##Check file size if available ls -trlh datasources/hgnc/data @@ -70,7 +70,7 @@ case $source in ##Store outputs from previous job in environment variables echo "$DATE_NEW=$DATE_NEW" >> $GITHUB_ENV ##Download hmdb file - wget http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip + wget -q http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip unzip hmdb_metabolites.zip mkdir hmdb mv hmdb_metabolites.xml hmdb @@ -96,9 +96,9 @@ case $source in ##Create temp. folder to store the data in mkdir -p datasources/uniprot/data ##Download uniprot file - wget https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/${UNIPROT_SPROT_NEW} - wget https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/docs/${SEC_AC_NEW} - wget https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/docs/${DELAC_SP_NEW} + wget -q https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/${UNIPROT_SPROT_NEW} + wget -q https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/docs/${SEC_AC_NEW} + wget -q https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/docs/${DELAC_SP_NEW} mv $DELAC_SP_NEW $SEC_AC_NEW $UNIPROT_SPROT_NEW datasources/uniprot/data ##Check file size if available ls -trlh datasources/uniprot/data @@ -115,8 +115,8 @@ case $source in ##Create temp. folder to store the data in mkdir -p datasources/ncbi/data ##Download ncbi file - wget https://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz - wget https://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz + wget -q https://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz + wget -q https://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz mv gene_info.gz gene_history.gz datasources/ncbi/data ##Check file size if available ls -trlh datasources/ncbi/data