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GUDMAP_RBK
RNA-seq
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e618a23f
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Commit
e618a23f
authored
4 years ago
by
Gervaise Henry
🤠
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Fix upload processed file ci unit
parent
686d27d4
2 merge requests
!58
Develop
,
!53
Resolve "process_derivaUpload"
Pipeline
#8615
canceled with stages
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.gitlab-ci.yml
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e618a23f
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@@ -357,14 +357,14 @@ uploadProcessedFile:
...
@@ -357,14 +357,14 @@ uploadProcessedFile:
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\": \".*\"') &&
cookie=${cookie:11:-1}
cookie=${cookie:11:-1}
if [ "${exist}" != "[]" ]; then
if [ "${exist}" != "[]" ]; then
rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//')
rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//')
&&
for rid in ${rids}; do
for rid in ${rids}; do
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/deleteEntry.py -r ${rid} -t Processed_File -o $staging.gudmap.org -c ${cookie}
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/deleteEntry.py -r ${rid} -t Processed_File -o $staging.gudmap.org -c ${cookie}
echo old processed file RID deleted - ${rid}
echo old processed file RID deleted - ${rid}
done
done
echo all old processed file RIDs deleted
echo all old processed file RIDs deleted
fi
fi
-
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-upload-cli --catalog 2 --token ${cookie} staging.gudmap.org ./deriva
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-upload-cli --catalog 2 --token ${cookie} staging.gudmap.org ./deriva
-
echo test processed file uploaded
-
echo test processed file uploaded
-
mkdir test
-
mkdir test
-
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag test --archiver zip
-
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag test --archiver zip
...
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