From cf071e889af2e6e20c995d5d294be95ec07aea26 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 30 Nov 2020 16:55:33 -0600
Subject: [PATCH] Test CI unit uploadInputBag
---
.gitlab-ci.yml | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 33d0844..60a094f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -290,9 +290,7 @@ uploadInputBag:
- >
hatrac=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o /TESTX$) &&
echo ${hatrac} &&
- if [ -z "${hatrac}" ]; then
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TESTX
- fi
+ if [ -z "${hatrac}" ]; then singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TESTX; fi
- echo THIS IS A TEST FILE > test.txt
- >
md5=$(md5sum ./test.txt | awk '{ print $1 }') &&
@@ -303,7 +301,7 @@ uploadInputBag:
cookie=$(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) &&
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie}
+ 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}
fi
--
GitLab