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Updated ChEBI SDF files name #263

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Merged
DeniseSl22 merged 2 commits into from
Jan 28, 2026
Merged

Updated ChEBI SDF files name #263

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c134b75
Updated ChEBI SDF files name
DeniseSl22 Jan 15, 2026
08299df
Fix artifact name from ChEBI_priIDs.tsv to ChEBI_priID.tsv
DeniseSl22 Jan 15, 2026
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10 changes: 5 additions & 5 deletions .github/workflows/chebi.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ jobs:
success=false

while [ $retry_count -lt $max_retries ]; do
response=$(curl -o /dev/null -s -w "%{http_code}" "http://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${release}/SDF/ChEBI_complete_3star.sdf.gz")
response=$(curl -o /dev/null -s -w "%{http_code}" "http://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${release}/SDF/chebi_3_stars.sdf.gz")
curl_exit_code=$?

if [ $curl_exit_code -eq 0 ] && [ "$response" -eq 200 ]; then
Expand Down Expand Up @@ -123,9 +123,9 @@ jobs:
echo "CURRENT_RELEASE_NUMBER=$CURRENT_RELEASE_NUMBER" >> $GITHUB_ENV
url_release="http://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel$RELEASE_NUMBER/SDF/"
echo "URL_RELEASE=$url_release" >> $GITHUB_ENV
wget "http://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${RELEASE_NUMBER}/SDF/ChEBI_complete_3star.sdf.gz"
wget "http://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel${RELEASE_NUMBER}/SDF/chebi_3_stars.sdf.gz"
##Unzip gz file:
gunzip ChEBI_complete_3star.sdf.gz #TODO replace by config var
gunzip chebi_3_stars.sdf.gz #TODO replace by config var
##Check file size if available
ls
##Print file size
Expand Down Expand Up @@ -155,7 +155,7 @@ jobs:
- name: Test SDF processing
id: sdf_process
run: |
inputFile="ChEBI_complete_3star.sdf"
inputFile="chebi_3_stars.sdf"
mkdir new
cd java
mvn clean install assembly:single
Expand Down Expand Up @@ -274,7 +274,7 @@ jobs:
- name: 'Upload processed data as artifacts priIDs'
uses: actions/upload-artifact@v4
with:
name: ChEBI_priIDs.tsv
name: ChEBI_priID.tsv
path: datasources/chebi/recentData/ChEBI_priIDs.tsv

- name: 'Upload processed data as artifacts secID2priID'
Expand Down