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annotate planemo/lib/python3.7/site-packages/bioblend/_tests/GalaxyTestBase.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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d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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1 import os
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2
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3 import bioblend
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4 import bioblend.galaxy
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5 from . import test_util
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6 from .test_util import unittest
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8 bioblend.set_stream_logger('test', level='INFO')
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10 BIOBLEND_TEST_JOB_TIMEOUT = int(os.environ.get("BIOBLEND_TEST_JOB_TIMEOUT", "60"))
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13 @test_util.skip_unless_galaxy()
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14 class GalaxyTestBase(unittest.TestCase):
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16 def setUp(self):
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17 galaxy_key = os.environ['BIOBLEND_GALAXY_API_KEY']
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18 galaxy_url = os.environ['BIOBLEND_GALAXY_URL']
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19 self.gi = bioblend.galaxy.GalaxyInstance(url=galaxy_url, key=galaxy_key)
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21 def _test_dataset(self, history_id, contents="1\t2\t3", **kwds):
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22 tool_output = self.gi.tools.paste_content(contents, history_id, **kwds)
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23 return tool_output["outputs"][0]["id"]
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25 def _wait_and_verify_dataset(self, dataset_id, expected_contents, timeout_seconds=BIOBLEND_TEST_JOB_TIMEOUT):
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26 dataset_contents = self.gi.datasets.download_dataset(dataset_id, maxwait=timeout_seconds)
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27 self.assertEqual(dataset_contents, expected_contents)