From a308569ff57a226d5a33b9bb40f3be53fcacc820 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 14:38:34 -0600
Subject: [PATCH] Fix upload processed file process
---
workflow/rna-seq.nf | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d3b3c6b..b09ee5f 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1528,7 +1528,7 @@ process uploadProcessedFile {
cp ${counts} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
- cookie=\${cookie:20:-1}
+ cookie=\${cookie:11:-1}
exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=${repRID})
if [ "\${exist}" != "[]" ]
@@ -1537,15 +1537,14 @@ process uploadProcessedFile {
for rid in \${rids}
do
python3 deleteEntry.py -r \${rid} -t Processed_File -o ${source} -c \${cookie}
- echo LOG: old processed file RID deleted - \${rid} >> ${repRID}.uploadQC.log
done
echo LOG: all old processed file RIDs deleted >> ${repRID}.uploadQC.log
fi
- deriva-upload-cli --catalog 2 --token \${cookie} ${source} ./deriva
+ deriva-upload-cli --catalog 2 --token \${cookie:9} ${source} ./deriva
echo LOG: processed files uploaded >> ${repRID}.outputBag.log
- deriva-download-cli --catalog 2 --token \${cookie} ${source} ${executionRunExportConfig} . rid=${executionRunRID}
+ deriva-download-cli --catalog 2 --token \${cookie:9} ${source} ${executionRunExportConfig} . rid=${executionRunRID}
echo LOG: execution run bag downloaded >> ${repRID}.outputBag.log
echo -e "### Run Details" >> runDetails.md
--
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