From 1f06bc2be765d23c098419b2ceafbd30cff64e9f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 21 Jul 2021 16:41:57 -0500
Subject: [PATCH] Use CI variables for uploadExecutionRun CI
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 83a4dfe..13e548d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -456,12 +456,12 @@ uploadExecutionRun:
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" == "[]" ]; then
- rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
+ rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_execution_run.py -r ${ci_staging_rid_test_rep} -w ${ci_staging_rid_wf} -g ${ci_staging_rid_genome} -i ${ci_staging_rid_test_ibag} -s Success -d 'This is a test execution run' -o staging.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 ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
+ rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_execution_run.py -r ${ci_staging_rid_test_rep} -w ${ci_staging_rid_wf} -g ${ci_staging_rid_genome} -i ${ci_staging_rid_test_ibag} -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
echo ${rid} test execution run already exists
fi
--
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