From eb655d33848f2711e3b0fadbd7051309a8cd8f46 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 14 Jan 2020 11:03:38 -0600
Subject: [PATCH] Add CI for getBag
---
.gitlab-ci.yml | 10 ++++------
1 file changed, 4 insertions(+), 6 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1181343..dc43b74 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,15 +2,13 @@ before_script:
- module add python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
- module load singularity/3.0.2
- - ln -sfn /project/BICF/BICF_Core/shared/gudmap/cookies/deriva-cookies.txt ./test_data/
- - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/File_Q-Y53P.zip ./test_data/
+ - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/ ./test_data/
stages:
- unit
-unit:
+getBag:
stage: unit
script:
- - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' bdbag --materialize ./test_data/File_Q-Y53P.zip
- - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' 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 21; fi;
+ - ln -sf `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
+ - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=16-1ZX4
\ No newline at end of file
--
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