From 3e0130a4e99db43a9b656b2bf4edbd49ce8f3b16 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 21 Jul 2021 17:42:26 -0500
Subject: [PATCH] Use CI variables for uploadProcessedFiles CI
---
.gitlab-ci.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9206432..2c449ba 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -505,11 +505,11 @@ uploadProcessedFile:
- derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
- echo ${dir}${derivaImg}_${derivaVar}.sif
- 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-BVDJ/
- - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/17-BTFJ_test.csv
+ - echo THIS IS A TEST FILE > ${ci_staging_rid_test_rep}_test.csv
+ - mkdir -p ./deriva/Seq/pipeline/${ci_staging_rid_test_study}/${ci_staging_rid_test_erun}/
+ - mv ${ci_staging_rid_test_rep}_test.csv ./deriva/Seq/pipeline/${ci_staging_rid_test_study}/${ci_staging_rid_test_erun}/${ci_staging_rid_test_rep}_test.csv
- >
- exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
+ exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=${ci_staging_rid_test_study}) &&
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" != "[]" ]; then
--
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