From 765286c599607181d73abadc4c0a50d55a0b45ac Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 2 Dec 2020 15:28:12 -0600
Subject: [PATCH] Fix upload execution run ci unit test
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 55c6d4a..a6a703e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -356,15 +356,15 @@ uploadExecutionRun:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- >
exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Workflow=18-DT5T/Reference_Genome=17-BPD4/Input_Bag=18-MHWC/Replicate=18-MJ3A) &&
+ cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
+ cookie=${cookie:11:-1} &&
if [ "${exist}" == "[]" ]; then
- cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
- cookie=${cookie:11:-1} &&
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) &&
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 Error -d 'Run in process' -o dev.gudmap.org -c ${cookie} -u ${rid}) &&
echo ${rid} test execution run already exists
fi
--
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