From d65d19ec0979b285482afb3da4445b8f2f45d4cb Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 12 Aug 2020 15:20:39 -0500
Subject: [PATCH] Add unit test for outputBag
---
.gitlab-ci.yml | 10 ++++++++--
workflow/tests/test_outputBag.py | 13 +++++++++++++
2 files changed, 21 insertions(+), 2 deletions(-)
create mode 100644 workflow/tests/test_outputBag.py
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index dc2eab1..19f279a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -130,6 +130,13 @@ dataQC:
echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.1_indev' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
- pytest -m dataQC
+outputBag:
+ stage: unit
+ script:
+ - mkdir test
+ - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bdbag test --archiver zip
+ - pytest -m outputBag
+
integration_se:
stage: integration
@@ -181,5 +188,4 @@ consistency:
- assignedPE.txt
- assignedExpectSE.txt
- assignedExpectPE.txt
- expire_in: 7 days
-
+ expire_in: 7 days
\ No newline at end of file
diff --git a/workflow/tests/test_outputBag.py b/workflow/tests/test_outputBag.py
new file mode 100644
index 0000000..4132d83
--- /dev/null
+++ b/workflow/tests/test_outputBag.py
@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+ '/../../'
+
+@pytest.mark.outputBag
+def test_outputBag():
+ assert os.path.exists(os.path.join(test_output_path, 'test.zip'))
--
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