import os
import tempfile
import shutil
-import unittest
+from unittest import TestCase
from htsworkflow.pipelines import firecrest
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 *
f.write(eland_result)
f.close()
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
"""
Test components of the runfolder processing code
which includes firecrest, bustard, and gerald
self.failUnlessEqual(b.date, b2.date )
self.failUnlessEqual(b.user, b2.user)
self.failUnlessEqual(len(b.phasing), len(b2.phasing))
- for key in b.phasing.keys():
+ for key in list(b.phasing.keys()):
self.failUnlessEqual(b.phasing[key].lane,
b2.phasing[key].lane)
self.failUnlessEqual(b.phasing[key].phasing,
self.failUnlessEqual(g.software, 'GERALD')
self.failUnlessEqual(g.version, '1.68.2.2')
self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
- self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
- self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+ self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+ self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))
# list of genomes, matches what was defined up in
# do it all again after extracting from the xml file
self.failUnlessEqual(g.version, g2.version)
self.failUnlessEqual(g.date, g2.date)
- self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
- self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+ self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+ self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))
# test lane specific parameters from gerald config file
for i in range(1,9):
g2_results.reads)
self.failUnlessEqual(len(g_results.mapped_reads),
len(g2_results.mapped_reads))
- for k in g_results.mapped_reads.keys():
+ for k in list(g_results.mapped_reads.keys()):
self.failUnlessEqual(g_results.mapped_reads[k],
g2_results.mapped_reads[k])
self.failUnlessEqual(len(g_results.match_codes),
len(g2_results.match_codes))
- for k in g_results.match_codes.keys():
+ for k in list(g_results.match_codes.keys()):
self.failUnlessEqual(g_results.match_codes[k],
g2_results.match_codes[k])
self.failUnlessEqual(l1.lane_id, l2.lane_id)
self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
self.failUnlessEqual(len(l1.mapped_reads), 3)
- for k in l1.mapped_reads.keys():
+ for k in list(l1.mapped_reads.keys()):
self.failUnlessEqual(l1.mapped_reads[k],
l2.mapped_reads[k])
self.failUnlessEqual(len(l1.match_codes), 9)
self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
- for k in l1.match_codes.keys():
+ for k in list(l1.match_codes.keys()):
self.failUnlessEqual(l1.match_codes[k],
l2.match_codes[k])
# do we get the flowcell id from the filename?
self.failUnlessEqual(len(runs), 1)
- self.failUnlessEqual(runs[0].name, 'run_207BTAAXX_2008-04-19.xml')
+ self.failUnlessEqual(runs[0].serialization_filename, 'run_207BTAAXX_2008-04-19.xml')
# do we get the flowcell id from the FlowcellId.xml file
make_flowcell_id(self.runfolder_dir, '207BTAAXY')
runs = runfolder.get_runs(self.runfolder_dir)
self.failUnlessEqual(len(runs), 1)
- self.failUnlessEqual(runs[0].name, 'run_207BTAAXY_2008-04-19.xml')
+ self.failUnlessEqual(runs[0].serialization_filename, 'run_207BTAAXY_2008-04-19.xml')
r1 = runs[0]
xml = r1.get_elements()
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__":
- unittest.main(defaultTest="suite")
+if __name__ == "__main__":
+ from unittest import main
+ main(defaultTest="suite")