Mercurial > repos > shellac > sam_consensus_v3
annotate 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 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 == [] |