import os
import tempfile
import shutil
-import unittest
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines.samplekey import SampleKey
from htsworkflow.pipelines import bustard
from htsworkflow.pipelines import gerald
from htsworkflow.pipelines import runfolder
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines.test.simulate_runfolder import *
os.mkdir(unaligned_dir)
make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id)
make_unaligned_config_1_12(unaligned_dir)
+ make_unaligned_status_1_12(unaligned_dir, flowcell_id)
aligned_dir = os.path.join(runfolder_dir, "Aligned")
os.mkdir(aligned_dir)
obj.reads = 2
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
"""
Test components of the runfolder processing code
which includes firecrest, bustard, and gerald
self.assertEqual(runs[0].flowcell_id, self.flowcell_id)
name = 'run_%s_%s.xml' % ( self.flowcell_id,
date.today().strftime('%Y-%m-%d'),)
- self.failUnlessEqual(runs[0].name, name)
+ self.failUnlessEqual(runs[0].serialization_filename, name)
bustard_dir = os.path.join(self.runfolder_dir, 'Unaligned')
r1 = runs[0]
xml_str = ElementTree.tostring(xml)
r2 = runfolder.PipelineRun(xml=xml)
- self.failUnlessEqual(r1.name, r2.name)
+ self.failUnlessEqual(r1.serialization_filename, r2.serialization_filename)
self.failIfEqual(r2.image_analysis, None)
self.failIfEqual(r2.bustard, None)
self.failIfEqual(r2.gerald, None)
def suite():
- return unittest.makeSuite(RunfolderTests,'test')
+ from unittest import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
+ return suite
-if __name__ == "__main__":
- logging.basicConfig(level=logging.WARN)
- unittest.main(defaultTest="suite")
+if __name__ == "__main__":
+ from unittest import main
+ main(defaultTest="suite")