From 5c4e252925521b31623521fdafc3dc4027921001 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 30 Jul 2020 12:48:58 -0500
Subject: [PATCH] Add pytest for parseMetadata: expect fail #54

---
 .gitlab-ci.yml                       | 17 +++++++++--------
 workflow/tests/test_parseMetadata.py | 24 ++++++++++++++++++++++++
 2 files changed, 33 insertions(+), 8 deletions(-)
 create mode 100644 workflow/tests/test_parseMetadata.py

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8f71ff4..8320a0d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -29,14 +29,15 @@ getData:
 parseMetadata:
   stage: unit
   script:
-  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID
-  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID
-  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID
-  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta
-  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual
-  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded
-  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike
-  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species
+  - rep=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID
+  - exp=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID
+  - study=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID
+  - endsMeta=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta
+  - endsManual=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual
+  - stranded=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded
+  - spike=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike
+  - species=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species
+  - pytest -m pareseMetadata
 
 inferMetadata:
   stage: unit
diff --git a/workflow/tests/test_parseMetadata.py b/workflow/tests/test_parseMetadata.py
new file mode 100644
index 0000000..a87d244
--- /dev/null
+++ b/workflow/tests/test_parseMetadata.py
@@ -0,0 +1,24 @@
+#!/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.parseMetadata
+def test_parseMetadata():
+    assert os.path.exists(os.path.join(test_output_path, 'design.csv'))
+    assert readLine(os.path.join(test_output_path, 'design.csv'))
+
+def readLine(fileName):
+    data = False
+    file = open(fileName, "r")
+    for line in file:
+        if file.readlines() == "uk,se,no,no,Homo sapiens,Experiment_RID,Study_RID,Replicate_RID":
+            data = True
+            break
+
+    return data
-- 
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