Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/bioblend/_tests/GalaxyTestBase.py @ 5:9b1c78e6ba9c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
comparison
equal deleted inserted replaced
4:79f47841a781 5:9b1c78e6ba9c
1 import os
2
3 import bioblend
4 import bioblend.galaxy
5 from . import test_util
6 from .test_util import unittest
7
8 bioblend.set_stream_logger('test', level='INFO')
9
10 BIOBLEND_TEST_JOB_TIMEOUT = int(os.environ.get("BIOBLEND_TEST_JOB_TIMEOUT", "60"))
11
12
13 @test_util.skip_unless_galaxy()
14 class GalaxyTestBase(unittest.TestCase):
15
16 def setUp(self):
17 galaxy_key = os.environ['BIOBLEND_GALAXY_API_KEY']
18 galaxy_url = os.environ['BIOBLEND_GALAXY_URL']
19 self.gi = bioblend.galaxy.GalaxyInstance(url=galaxy_url, key=galaxy_key)
20
21 def _test_dataset(self, history_id, contents="1\t2\t3", **kwds):
22 tool_output = self.gi.tools.paste_content(contents, history_id, **kwds)
23 return tool_output["outputs"][0]["id"]
24
25 def _wait_and_verify_dataset(self, dataset_id, expected_contents, timeout_seconds=BIOBLEND_TEST_JOB_TIMEOUT):
26 dataset_contents = self.gi.datasets.download_dataset(dataset_id, maxwait=timeout_seconds)
27 self.assertEqual(dataset_contents, expected_contents)