From a7da9606a8bad77eaa504f48571945c71ce54bea Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 19:01:38 -0600
Subject: [PATCH] Use staging execution run rid in ci
---
.gitlab-ci.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 69d4f52..2a4894a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -338,7 +338,7 @@ uploadQC:
done
echo all old mRNA QC RIDs deleted
fi
- rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 17-BTFJ -e -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/uploadQC.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) &&
echo ${rid} test mRNA QC created
uploadProcessedFile:
@@ -351,8 +351,8 @@ uploadProcessedFile:
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- echo THIS IS A TEST FILE > 17-BTFJ_test.csv
- - mkdir -p ./deriva/Seq/pipeline/17-BTFA//
- - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFA//17-BTFJ_test.csv
+ - mkdir -p ./deriva/Seq/pipeline/17-BTFA/17-BTG4/
+ - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFA/17-BTG4/17-BTFJ_test.csv
- >
exist=$(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) &&
cookie=$(cat credential.json | grep -A 1 '"staging.gudmap.org\: {' | grep -o '"cookie": ".*"') &&
@@ -390,7 +390,7 @@ uploadOutputBag:
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
- rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -e 18-MJ3C -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -e 17-BTG4 -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
echo ${rid} test output bag created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
--
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