Mercurial > repos > shellac > sam_consensus_v3
comparison env/lib/python3.9/site-packages/bioblend/_tests/TestGalaxyDatasets.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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-1:000000000000 | 0:4f3585e2f14b |
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1 import shutil | |
2 import tempfile | |
3 | |
4 from . import ( | |
5 GalaxyTestBase, | |
6 test_util | |
7 ) | |
8 | |
9 | |
10 class TestGalaxyDatasets(GalaxyTestBase.GalaxyTestBase): | |
11 | |
12 def setUp(self): | |
13 super().setUp() | |
14 self.history_id = self.gi.histories.create_history(name='TestShowDataset')['id'] | |
15 self.dataset_contents = "line 1\nline 2\rline 3\r\nline 4" | |
16 self.dataset_id = self._test_dataset(self.history_id, contents=self.dataset_contents) | |
17 | |
18 def tearDown(self): | |
19 self.gi.histories.delete_history(self.history_id, purge=True) | |
20 | |
21 @test_util.skip_unless_galaxy('release_19.05') | |
22 def test_show_nonexistent_dataset(self): | |
23 with self.assertRaises(Exception): | |
24 self.gi.datasets.show_dataset('nonexistent_id') | |
25 | |
26 def test_show_dataset(self): | |
27 self.gi.datasets.show_dataset(self.dataset_id) | |
28 | |
29 def test_download_dataset(self): | |
30 with self.assertRaises(Exception): | |
31 self.gi.datasets.download_dataset(None) | |
32 expected_contents = ("\n".join(self.dataset_contents.splitlines()) + "\n").encode() | |
33 # download_dataset() with file_path=None is already tested in TestGalaxyTools.test_paste_content() | |
34 # self._wait_and_verify_dataset(self.dataset_id, expected_contents) | |
35 tempdir = tempfile.mkdtemp(prefix='bioblend_test_') | |
36 try: | |
37 downloaded_dataset = self.gi.datasets.download_dataset( | |
38 self.dataset_id, file_path=tempdir, | |
39 maxwait=GalaxyTestBase.BIOBLEND_TEST_JOB_TIMEOUT * 2) | |
40 self.assertTrue(downloaded_dataset.startswith(tempdir)) | |
41 with open(downloaded_dataset, 'rb') as f: | |
42 self.assertEqual(f.read(), expected_contents) | |
43 finally: | |
44 shutil.rmtree(tempdir) | |
45 with tempfile.NamedTemporaryFile(prefix='bioblend_test_') as f: | |
46 download_filename = self.gi.datasets.download_dataset( | |
47 self.dataset_id, file_path=f.name, use_default_filename=False, | |
48 maxwait=GalaxyTestBase.BIOBLEND_TEST_JOB_TIMEOUT) | |
49 self.assertEqual(download_filename, f.name) | |
50 f.flush() | |
51 self.assertEqual(f.read(), expected_contents) | |
52 | |
53 @test_util.skip_unless_galaxy('release_19.05') | |
54 def test_get_datasets(self): | |
55 datasets = self.gi.datasets.get_datasets() | |
56 dataset_ids = [dataset['id'] for dataset in datasets] | |
57 assert self.dataset_id in dataset_ids | |
58 datasets = self.gi.datasets.get_datasets(limit=0) | |
59 assert datasets == [] |