annotate env/lib/python3.9/site-packages/bioblend/_tests/GalaxyTestBase.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

import os

import bioblend
import bioblend.galaxy
from . import test_util
from .test_util import unittest

bioblend.set_stream_logger('test', level='INFO')

BIOBLEND_TEST_JOB_TIMEOUT = int(os.environ.get("BIOBLEND_TEST_JOB_TIMEOUT", "60"))


@test_util.skip_unless_galaxy()
class GalaxyTestBase(unittest.TestCase):

    def setUp(self):
        galaxy_key = os.environ['BIOBLEND_GALAXY_API_KEY']
        galaxy_url = os.environ['BIOBLEND_GALAXY_URL']
        self.gi = bioblend.galaxy.GalaxyInstance(url=galaxy_url, key=galaxy_key)

    def _test_dataset(self, history_id, contents="1\t2\t3", **kwds):
        tool_output = self.gi.tools.paste_content(contents, history_id, **kwds)
        return tool_output["outputs"][0]["id"]

    def _wait_and_verify_dataset(self, dataset_id, expected_contents, timeout_seconds=BIOBLEND_TEST_JOB_TIMEOUT):
        dataset_contents = self.gi.datasets.download_dataset(dataset_id, maxwait=timeout_seconds)
        self.assertEqual(dataset_contents, expected_contents)