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Commit 2acecec8 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Update test execution run rid for ci

parent 70fd9253
2 merge requests!58Develop,!56Resolve "Detect error in inferMetadata for tracking"
Pipeline #8776 failed with stages
in 2 minutes and 4 seconds
...@@ -388,7 +388,7 @@ uploadQC: ...@@ -388,7 +388,7 @@ uploadQC:
done done
echo all old mRNA QC RIDs deleted echo all old mRNA QC RIDs deleted
fi fi
rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BTG4 -p "Single Read" -s forward -l 35 -w 5 -f 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F) rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BVDJ -p "Single Read" -s forward -l 35 -w 5 -f 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
echo ${rid} test mRNA QC created echo ${rid} test mRNA QC created
uploadProcessedFile: uploadProcessedFile:
...@@ -402,8 +402,8 @@ uploadProcessedFile: ...@@ -402,8 +402,8 @@ uploadProcessedFile:
script: script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- echo THIS IS A TEST FILE > 17-BTFJ_test.csv - echo THIS IS A TEST FILE > 17-BTFJ_test.csv
- mkdir -p ./deriva/Seq/pipeline/17-BTFE/17-BTG4/ - mkdir -p ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/
- mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BTG4/17-BTFJ_test.csv - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/17-BTFJ_test.csv
- > - >
exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) && exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
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