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annotate env/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyDatasets.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 import shutil
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2 import tempfile
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3
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4 import six
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5
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6 from . import (
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7 GalaxyTestBase,
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8 test_util
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9 )
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12 class TestGalaxyDatasets(GalaxyTestBase.GalaxyTestBase):
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13
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14 def setUp(self):
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15 super(TestGalaxyDatasets, self).setUp()
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16 self.history_id = self.gi.histories.create_history(name='TestShowDataset')['id']
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17 self.dataset_contents = "line 1\nline 2\rline 3\r\nline 4"
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18 self.dataset_id = self._test_dataset(self.history_id, contents=self.dataset_contents)
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19
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20 def tearDown(self):
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21 self.gi.histories.delete_history(self.history_id, purge=True)
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22
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23 @test_util.skip_unless_galaxy('release_19.05')
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24 def test_show_nonexistent_dataset(self):
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25 with self.assertRaises(Exception):
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26 self.gi.datasets.show_dataset('nonexistent_id')
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27
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28 def test_show_dataset(self):
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29 self.gi.datasets.show_dataset(self.dataset_id)
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30
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31 def test_download_dataset(self):
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32 with self.assertRaises(Exception):
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33 self.gi.datasets.download_dataset(None)
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34 expected_contents = six.b("\n".join(self.dataset_contents.splitlines()) + "\n")
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35 # download_dataset() with file_path=None is already tested in TestGalaxyTools.test_paste_content()
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36 # self._wait_and_verify_dataset(self.dataset_id, expected_contents)
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37 tempdir = tempfile.mkdtemp(prefix='bioblend_test_')
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38 try:
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39 downloaded_dataset = self.gi.datasets.download_dataset(
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40 self.dataset_id, file_path=tempdir,
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41 maxwait=GalaxyTestBase.BIOBLEND_TEST_JOB_TIMEOUT)
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42 self.assertTrue(downloaded_dataset.startswith(tempdir))
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43 with open(downloaded_dataset, 'rb') as f:
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44 self.assertEqual(f.read(), expected_contents)
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45 finally:
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46 shutil.rmtree(tempdir)
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47 with tempfile.NamedTemporaryFile(prefix='bioblend_test_') as f:
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48 download_filename = self.gi.datasets.download_dataset(
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49 self.dataset_id, file_path=f.name, use_default_filename=False,
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50 maxwait=GalaxyTestBase.BIOBLEND_TEST_JOB_TIMEOUT)
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51 self.assertEqual(download_filename, f.name)
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52 f.flush()
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53 self.assertEqual(f.read(), expected_contents)
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54
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55 def test_show_stderr(self):
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56 stderr = self.gi.datasets.show_stderr(self.dataset_id)
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57 self.assertIsNotNone(stderr)
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58
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59 def test_show_stdout(self):
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60 stdout = self.gi.datasets.show_stdout(self.dataset_id)
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61 self.assertIsNotNone(stdout)