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annotate planemo/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyDatasets.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 import shutil
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2 import tempfile
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3
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4 from . import (
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5 GalaxyTestBase,
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6 test_util
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7 )
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8
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9
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10 class TestGalaxyDatasets(GalaxyTestBase.GalaxyTestBase):
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11
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12 def setUp(self):
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13 super().setUp()
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14 self.history_id = self.gi.histories.create_history(name='TestShowDataset')['id']
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15 self.dataset_contents = "line 1\nline 2\rline 3\r\nline 4"
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16 self.dataset_id = self._test_dataset(self.history_id, contents=self.dataset_contents)
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17
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18 def tearDown(self):
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19 self.gi.histories.delete_history(self.history_id, purge=True)
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20
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21 @test_util.skip_unless_galaxy('release_19.05')
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22 def test_show_nonexistent_dataset(self):
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23 with self.assertRaises(Exception):
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24 self.gi.datasets.show_dataset('nonexistent_id')
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25
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26 def test_show_dataset(self):
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27 self.gi.datasets.show_dataset(self.dataset_id)
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28
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29 def test_download_dataset(self):
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30 with self.assertRaises(Exception):
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31 self.gi.datasets.download_dataset(None)
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32 expected_contents = ("\n".join(self.dataset_contents.splitlines()) + "\n").encode()
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33 # download_dataset() with file_path=None is already tested in TestGalaxyTools.test_paste_content()
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34 # self._wait_and_verify_dataset(self.dataset_id, expected_contents)
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35 tempdir = tempfile.mkdtemp(prefix='bioblend_test_')
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36 try:
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37 downloaded_dataset = self.gi.datasets.download_dataset(
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38 self.dataset_id, file_path=tempdir,
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39 maxwait=GalaxyTestBase.BIOBLEND_TEST_JOB_TIMEOUT * 2)
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40 self.assertTrue(downloaded_dataset.startswith(tempdir))
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41 with open(downloaded_dataset, 'rb') as f:
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42 self.assertEqual(f.read(), expected_contents)
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43 finally:
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44 shutil.rmtree(tempdir)
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45 with tempfile.NamedTemporaryFile(prefix='bioblend_test_') as f:
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46 download_filename = self.gi.datasets.download_dataset(
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47 self.dataset_id, file_path=f.name, use_default_filename=False,
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48 maxwait=GalaxyTestBase.BIOBLEND_TEST_JOB_TIMEOUT)
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49 self.assertEqual(download_filename, f.name)
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50 f.flush()
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51 self.assertEqual(f.read(), expected_contents)
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52
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53 @test_util.skip_unless_galaxy('release_19.05')
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54 def test_get_datasets(self):
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55 datasets = self.gi.datasets.get_datasets()
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56 dataset_ids = [dataset['id'] for dataset in datasets]
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57 assert self.dataset_id in dataset_ids
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58 datasets = self.gi.datasets.get_datasets(limit=0)
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59 assert datasets == []