Switch to lxml for parsing the summary file.

[htsworkflow.git] / htsworkflow / pipelines / test / test_summary.py
diff --git a/htsworkflow/pipelines/test/test_summary.py b/htsworkflow/pipelines/test/test_summary.py

new file mode 100644 (file)

index 0000000..ab9f962
--- /dev/null
+++ b/htsworkflow/pipelines/test/test_summary.py
@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+import os
+from StringIO import StringIO
+import unittest
+
+from htsworkflow.pipelines import summary
+from simulate_runfolder import TESTDATA_DIR
+
+class SummaryTests(unittest.TestCase):
+    """Test elements of the summary file parser
+    """
+    def test_is_xml(self):
+        xmlfile = StringIO('<?xml version="1.0"?>\n<tag>\n')
+        htmlfile = StringIO('<html>\n<head></head>\n<body><p></p></body>\n</html>')
+
+        self.failUnlessEqual(summary.isxml_stream(xmlfile), True)
+        self.failUnlessEqual(xmlfile.tell(), 0)
+
+        self.failUnlessEqual(summary.isxml_stream(htmlfile), False)
+
+    def test_xml_summary_file(self):
+        pathname = os.path.join(TESTDATA_DIR, 'Summary-casava1.7.xml')
+        s = summary.Summary(pathname)
+        self.failUnlessEqual(len(s.lane_results[0]), 8)
+        self.failUnlessEqual(s.lane_results[0][1].cluster, (1073893, 146344))
+
+    def test_html_summary_file(self):
+        pathname = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
+        s = summary.Summary(pathname)
+        self.failUnlessEqual(len(s.lane_results[0]), 8)
+        self.failUnlessEqual(s.lane_results[0][1].cluster, (126910, 4300))
+
+    def test_hiseq_sample_summary_file(self):
+        pathname = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
+        s = summary.Summary(pathname)
+
+def suite():
+    return unittest.makeSuite(SummaryTests,'test')
+
+if __name__ == "__main__":
+    unittest.main(defaultTest="suite")