From dc2d6631f15b7b812ac2d9ecff3ec58f80925985 Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Mon, 25 Nov 2019 12:28:37 -0600
Subject: [PATCH] Add If stattements to check materialize of bdbag
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index eae88e9..376b966 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -11,7 +11,7 @@ stages:
unit:
stage: unit
script:
- - singularity run 'docker://bicf/bdbag:1.0' bdbag --validate completeness ./test_data/File_Q-Y53P.zip
- singularity run 'docker://bicf/bdbag:1.0' bdbag --materialize ./test_data/File_Q-Y53P.zip
- - singularity run 'docker://bicf/bdbag:1.0' bdbag --validate full ./test_data/File_Q-Y53P/
- - if [ $(md5sum test_data/File_Q-Y53P/data/assets/Study/Q-Y4H0/Experiment/Q-Y4BY/Replicate/Q-Y5F8/hMARIS_SIX2+_RiboDep#1.gene.rpkm.txt | awk '{ print $1 }') != $(cat test_data/File_Q-Y53P/data/File.csv | cut -d ',' -f10 | tail -1) ]; then exit; fi;
+ - if [ $(singularity run 'docker://bicf/bdbag:1.0' bdbag --validate completeness ./test_data/File_Q-Y53P/ 2>&1 | tail -3 | head -n 1 | cut -c 34-) != 'The directory ./test_data/File_Q-Y53P is a valid bag structure' ]; then exit 21; fi;
+ - if [ $(singularity run 'docker://bicf/bdbag:1.0' bdbag --validate full ./test_data/File_Q-Y53P/ 2>&1 | tail -3 | head -n 1 | cut -c 34-) != 'Bag ./test_data/File_Q-Y53P is valid' ]; then exit 21; fi;
+ - if [ $(md5sum test_data/File_Q-Y53P/data/assets/Study/Q-Y4H0/Experiment/Q-Y4BY/Replicate/Q-Y5F8/hMARIS_SIX2+_RiboDep#1.gene.rpkm.txt | awk '{ print $1 }') != $(cat test_data/File_Q-Y53P/data/File.csv | cut -d ',' -f10 | tail -1) ]; then exit 21; fi;
--
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