htsworkflow/pipelines/test/test_summary.py

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