From 2acecec8b885426103e89bc2c639627f78f01299 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 14:25:22 -0600
Subject: [PATCH] Update test execution run rid for ci
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2d68fbc..80623ef 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -388,7 +388,7 @@ uploadQC:
done
echo all old mRNA QC RIDs deleted
fi
- rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_qc.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 ${cookie} -u F)
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BVDJ -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 ${rid} test mRNA QC created
uploadProcessedFile:
@@ -402,8 +402,8 @@ uploadProcessedFile:
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- echo THIS IS A TEST FILE > 17-BTFJ_test.csv
- - mkdir -p ./deriva/Seq/pipeline/17-BTFE/17-BTG4/
- - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BTG4/17-BTFJ_test.csv
+ - mkdir -p ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/
+ - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/17-BTFJ_test.csv
- >
exist=$(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\": \".*\"') &&
--
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