From 0d23777ea362d66f35fe3bab1c71def677647163 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 21 Jul 2021 20:37:50 -0500
Subject: [PATCH] Use CI variables for getBag CI
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4d0df8b..d5dcb8b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -183,7 +183,7 @@ getBag:
- 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` ~/.deriva/credential.json
- - singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
+ - singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=${ci_staging_rid_rep}
- pytest -m getBag
getData:
@@ -197,7 +197,7 @@ getData:
script:
- derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1)
- derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
- - echo ${dir}${derivaImg}_${derivaVar}.sif
+ - echo ${dir}${derivaImg}_${derivaVar}.sif
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- unzip ./test_data/bag/Q-Y5F6_inputBag_xxxxtest.zip
- singularity run ${dir}${derivaImg}_${derivaVar}.sif bash ./workflow/scripts/bdbag_fetch.sh Q-Y5F6_inputBag Q-Y5F6
@@ -548,7 +548,7 @@ uploadOutputBag:
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
loc=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
- rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_output_bag.py -e ${ci_staging_rid_test_erun} -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie} -u "F") &&
+ rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_output_bag.py -e ${ci_staging_rid_test_erun} -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie} -u "F") &&
echo ${rid} test output bag created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
--
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