From de33d175474927938647f9af68c4cdadfc0548dd Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 14 Feb 2020 20:50:39 -0600
Subject: [PATCH] Test bdbag fetch on text file
---
.gitlab-ci.yml | 4 ++--
workflow/tests/test_getData.py | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9043d72..bf9231c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,5 +1,5 @@
before_script:
- - module add python/3.6.1-2-anaconda
+ - module add python/3.6.4-anaconda
- pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
- module load singularity/3.0.2
- module load nextflow/19.09.0
@@ -23,7 +23,7 @@ getData:
script:
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- unzip ./test_data/bagit/Replicate_16-1ZX4
- - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4 TEST
+ - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' bash ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4 TEST
- pytest -m getData
parseMetadata:
diff --git a/workflow/tests/test_getData.py b/workflow/tests/test_getData.py
index 36d0b22..f84a30f 100644
--- a/workflow/tests/test_getData.py
+++ b/workflow/tests/test_getData.py
@@ -11,4 +11,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.getData
def test_getData():
assert os.path.exists(os.path.join(test_output_path, 'Replicate_16-1ZX4/bagit.txt'))
- assert os.path.exists(os.path.join(test_output_path, '16-1ZX4.R1.fastq.gz'))
\ No newline at end of file
+ assert os.path.exists(os.path.join(test_output_path, 'Study_Q-Y4H0/data/assets/Study/Q-Y4H0/Experiment/Q-Y4BY/Replicate/Q-Y5F8/hMARIS_SIX2+_RiboDep#1.gene.rpkm.txt'))
\ No newline at end of file
--
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