From eaaef016e3339a42a3be1ec075116d7644fe27f3 Mon Sep 17 00:00:00 2001
From: garion0000 <michele.garioni@unibas.ch>
Date: Wed, 8 Dec 2021 13:53:52 +0100
Subject: [PATCH] fix: add testing for cli
---
tests/test_sampleinput.py | 42 +++++++++++++++++++++++++++++++++++----
1 file changed, 38 insertions(+), 4 deletions(-)
diff --git a/tests/test_sampleinput.py b/tests/test_sampleinput.py
index c03630f..70d8eea 100644
--- a/tests/test_sampleinput.py
+++ b/tests/test_sampleinput.py
@@ -2,11 +2,20 @@
import pytest
import pandas as pd
+import os
+import importlib.util
+from pathlib import Path
+import sys
-from src.sample_from_input import sample_from_input
+from src.sample_from_input import (
+ sample_from_input,
+ main
+ )
+
+PACKAGE_DIR = Path(__file__).resolve().parents[1] / 'src'
-def test_sampleinput(tmpdir):
+def test_sample_from_input(tmpdir):
"""Tests the output, input file name and separator."""
sample_from_input(
input_file='./tests/resources/Transcript2.tsv',
@@ -14,9 +23,34 @@ def test_sampleinput(tmpdir):
sep='\t',
n=142958
)
- t1=pd.read_table(tmpdir / 'test1.csv', header=None, sep=',')
- assert t1[1].sum()==142958
+ t1 = pd.read_table(tmpdir / 'test1.csv', header=None, sep=',')
+ assert t1[1].sum() == 142958
with pytest.raises(IndexError):
sample_from_input(input_file='./tests/resources/Transcript2.tsv')
with pytest.raises(IOError):
sample_from_input(input_file='file_not_existing.txt')
+
+
+def test_main_with_args(monkeypatch, tmpdir):
+ """Call with args."""
+ monkeypatch.setattr(
+ sys, 'argv', [
+ 'sample_from_input',
+ './tests/resources/Transcript1.csv',
+ '-o',
+ str(tmpdir / 'test1.csv'),
+ ]
+ )
+ ret_val = main()
+ assert ret_val is None
+
+
+def test_main_as_script():
+ """Run as script."""
+ main_file = PACKAGE_DIR / "sample_from_input.py"
+ fl = os.path.join(os.path.dirname(__file__), main_file)
+ spec = importlib.util.spec_from_file_location('__main__', fl)
+ module = importlib.util.module_from_spec(spec)
+ with pytest.raises(SystemExit) as exc:
+ spec.loader.exec_module(module)
+ assert exc.value.code != 0
\ No newline at end of file
--
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