quiet output for cleaner log debug

sec2pri · Jul 15, 2024 · f838a62 · f838a62
1 parent 99e1d3a
commit f838a62
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Showing 2 changed files with 21 additions and 21 deletions.
diff --git 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
@@ -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