Package: ont-fast5-api / 4.1.3+dfsg-1

disable-tests-needing-root.patch Patch series | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
Author: Nilesh Patra <nilesh@debian.org>
Description: 4 tests need root access to execute. But enabling root just to pass 4 tests is not justified.
Last-Changed: Thursday, June 18, 2020
--- a/test/test_compress_fast5.py
+++ b/test/test_compress_fast5.py
@@ -1,6 +1,7 @@
 import h5py
 import os
 import shutil
+import unittest
 from unittest.mock import patch
 
 from ont_fast5_api.compression_settings import VBZ, GZIP
@@ -18,6 +19,7 @@
 class TestVbzReadWrite(TestFast5ApiHelper):
     run_id = "123abc"
 
+    @unittest.skip("Tries to create dataset - permission denied")
     def test_write_vbz_directly(self):
         input_data = range(10)
         with h5py.File(os.path.join(self.save_path, 'h5py.fast5'), 'w') as fast5:
@@ -138,12 +140,14 @@
             output_read = output_f5.get_read(read_id)
             self.assertEqual(check_read_compression(output_read), VBZ)
 
+    @unittest.skip("Permission Denied - to open folder")
     @patch('ont_fast5_api.conversion_tools.compress_fast5.get_progress_bar')
     def test_conversion_script_multi(self, mock_pbar):
         input_folder = os.path.join(test_data, 'multi_read')
         compress_batch(input_folder=input_folder, output_folder=self.save_path, target_compression=VBZ)
         self.assertCompressed(self.save_path, VBZ, read_count=4, file_count=1)
 
+    @unittest.skip("Permission Denied - to open folder")
     @patch('ont_fast5_api.conversion_tools.compress_fast5.get_progress_bar')
     def test_conversion_script_single(self, mock_pbar):
         input_folder = os.path.join(test_data, 'single_reads')
@@ -201,6 +205,7 @@
 
         self.assert_all_files_retain_end_reason_enumeration_metadata()
 
+    @unittest.skip("Permission Denied - to open folder")
     @patch('ont_fast5_api.conversion_tools.compress_fast5.get_progress_bar')
     def test_compress_in_place(self, mock_pbar):
         for input_file in os.listdir(os.path.join(test_data, 'single_reads')):
--- a/test/test_fast5_converter.py
+++ b/test/test_fast5_converter.py
@@ -1,3 +1,4 @@
+import unittest
 from unittest.mock import patch
 
 import os
@@ -14,6 +15,7 @@
 
 class TestFast5Converter(TestFast5ApiHelper):
 
+    @unittest.skip("Permission Denied - to open folder")
     @patch('ont_fast5_api.conversion_tools.single_to_multi_fast5.get_progress_bar')
     def test_single_to_multi(self, mock_pbar):
         input_folder = os.path.join(test_data, "single_reads")