htsworkflow/pipelines/test/test_summary.py

   1 #!/usr/bin/env python
   2 from __future__ import absolute_import
   3
   4 import os
   5 from six.moves import StringIO
   6 from unittest import TestCase
   7
   8 from htsworkflow.pipelines import summary
   9 from .simulate_runfolder import TESTDATA_DIR
  10
  11 class SummaryTests(TestCase):
  12     """Test elements of the summary file parser
  13     """
  14     def test_is_xml(self):
  15         xmlfile = StringIO('<?xml version="1.0"?>\n<tag>\n')
  16         htmlfile = StringIO('<html>\n<head></head>\n<body><p></p></body>\n</html>')
  17
  18         self.failUnlessEqual(summary.isxml_stream(xmlfile), True)
  19         self.failUnlessEqual(xmlfile.tell(), 0)
  20
  21         self.failUnlessEqual(summary.isxml_stream(htmlfile), False)
  22
  23     def test_xml_summary_file(self):
  24         pathname = os.path.join(TESTDATA_DIR, 'Summary-casava1.7.xml')
  25         s = summary.SummaryGA(pathname)
  26         self.failUnlessEqual(len(s.lane_results[0]), 8)
  27         self.failUnlessEqual(s.lane_results[0][1].cluster, (1073893, 146344))
  28
  29     def test_html_summary_file(self):
  30         pathname = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
  31         s = summary.SummaryGA(pathname)
  32         self.failUnlessEqual(len(s.lane_results[0]), 8)
  33         self.failUnlessEqual(s.lane_results[0][1].cluster, (126910, 4300))
  34
  35     def test_hiseq_sample_summary_file(self):
  36         pathname = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
  37         s = summary.SummaryGA(pathname)
  38
  39
  40 def suite():
  41     from unittest import TestSuite, defaultTestLoader
  42     suite = TestSuite()
  43     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SummaryTests))
  44     return suite
  45
  46
  47 if __name__ == "__main__":
  48     from unittest import main
  49     main(defaultTest="suite")