From 13483e6b31e048ad55dfd216610fdab5093da906 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 7 Dec 2020 10:32:18 -0600
Subject: [PATCH] Fix upload output bag ci unit test
---
.gitlab-ci.yml | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1a97d09..2bf89a8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -303,7 +303,7 @@ uploadInputBag:
cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt) &&
- rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie}) &&
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o dev.gudmap.org -c ${cookie}) &&
echo ${rid} test input bag created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
@@ -325,12 +325,12 @@ uploadExecutionRun:
cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" == "[]" ]; then
- rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 18-MJ3A -w 18-DT5T -g 17-BPD4 -i 18-MHWC -s Error -d 'Run in process' -o dev.gudmap.org -c ${cookie} -u F) &&
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 18-MJ3A -w 18-DT5T -g 17-BPD4 -i 18-MHWC -s Success -d 'This is a test execution run' -o dev.gudmap.org -c ${cookie} -u F) &&
echo ${rid} test execution run created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
rid=${rid:7:-6} &&
- rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 18-MJ3A -w 18-DT5T -g 17-BPD4 -i 18-MHWC -s Error -d 'Run in process' -o dev.gudmap.org -c ${cookie} -u ${rid}) &&
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 18-MJ3A -w 18-DT5T -g 17-BPD4 -i 18-MHWC -s Success -d 'This is a test execution run' -o dev.gudmap.org -c ${cookie} -u ${rid}) &&
echo ${rid} test execution run already exists
fi
@@ -348,12 +348,12 @@ uploadQC:
cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" == "[]" ]; then
- rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 18-MJ3A -e 18-MJ3C -p "Single Read" -s forward -l 35 -w 5 -f 1 -o dev.gudmap.org -c ${cookie} -u F) &&
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 18-MJ3A -e 18-MJ3C -p "Single Read" -s forward -l 35 -w 5 -f 1 -n 'This is a test mRNA QC' -o dev.gudmap.org -c ${cookie} -u F) &&
echo ${rid} test execution run created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
rid=${rid:7:-6} &&
- rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 18-MJ3A -e 18-MJ3C -p "Single Read" -s forward -l 35 -w 5 -f 1 -o dev.gudmap.org -c ${cookie} -u ${rid}) &&
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 18-MJ3A -e 18-MJ3C -p "Single Read" -s forward -l 35 -w 5 -f 1 -n 'This is a test mRNA QC' -o dev.gudmap.org -c ${cookie} -u ${rid}) &&
echo ${rid} test execution run already exists
fi
@@ -382,7 +382,7 @@ uploadOutputBag:
cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt) &&
- rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie}) &&
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -e -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o dev.gudmap.org -c ${cookie}) &&
echo ${rid} test output bag created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
--
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