Change unittest2 back into unittest.

[htsworkflow.git] / htsworkflow / pipelines / test / test_run_xml.py

diff --git a/htsworkflow/pipelines/test/test_run_xml.py b/htsworkflow/pipelines/test/test_run_xml.py
index a694ed4b498ea9dda1e4a0fc968f7acd78908bfb..42dedf9be9ed160fc2c6308ce88e3036e98fd1f6 100644 (file)
--- a/htsworkflow/pipelines/test/test_run_xml.py
+++ b/htsworkflow/pipelines/test/test_run_xml.py
@@ -1,21 +1,24 @@
 import os
-import unittest
+from unittest import TestCase
 from StringIO import StringIO
 
 from simulate_runfolder import TESTDATA_DIR
 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
 
-class testLoadRunXML(unittest.TestCase):
+from htsworkflow.pipelines.eland import SampleKey
 
-    def _check_run_xml(self, run_xml_name, results):
+
+class testLoadRunXML(TestCase):
+    def _check_run_xml(self, run_xml_name, results, eland_results=8):
         run_xml_path = os.path.join(TESTDATA_DIR, run_xml_name)
         run = load_pipeline_run_xml(run_xml_path)
-        
+
         self.failUnlessEqual(run.image_analysis.start, results['cycle_start'])
         self.failUnlessEqual(run.image_analysis.stop, results['cycle_stop'])
-        
-        eland_summary_by_lane = run.gerald.eland_results.results[0]
-        self.failUnlessEqual(len(eland_summary_by_lane), 8)
+
+        query = SampleKey(read=1)
+        eland_summary_by_lane = run.gerald.eland_results.find_keys(query)
+        self.failUnlessEqual(len(list(eland_summary_by_lane)), eland_results)
 
         runfolder_name = results['runfolder_name']
         self.failUnlessEqual(run.runfolder_name, runfolder_name)
@@ -24,10 +27,10 @@ class testLoadRunXML(unittest.TestCase):
         for (end, lane), lane_results in results['lane_results'].items():
             for name, test_value in lane_results.items():
                 xml_value = getattr(run.gerald.summary[end][lane], name)
-                
+
                 self.failUnlessEqual(xml_value, test_value,
                     "%s[%s][%s]: %s %s != %s" % (run_xml_name, end, lane, name, xml_value, test_value))
-        
+
     def testVersion0(self):
         run_xml_name = 'run_FC12150_2007-09-27.xml'
         results = {'runfolder_name': '070924_USI-EAS44_0022_FC12150',
@@ -47,7 +50,7 @@ class testLoadRunXML(unittest.TestCase):
                            }
                        }
                    }
-        self._check_run_xml(run_xml_name, results)
+        self._check_run_xml(run_xml_name, results, eland_results=0)
 
     def testVersion1(self):
 
@@ -59,7 +62,7 @@ class testLoadRunXML(unittest.TestCase):
                        # end, lane
                        }
                    }
-        self._check_run_xml(run_xml_name, results)
+        self._check_run_xml(run_xml_name, results, eland_results=8)
 
     def testVersion2(self):
         run_xml_name = 'run_62DJMAAXX_2011-01-09.xml'
@@ -90,10 +93,16 @@ class testLoadRunXML(unittest.TestCase):
                            }
                        }
                    }
-        self._check_run_xml(run_xml_name, results)
+        self._check_run_xml(run_xml_name, results, eland_results=8)
+
 
 def suite():
-    return unittest.makeSuite(testLoadRunXML,'test')
+    from unittest import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testLoadRunXML))
+    return suite
+
 
 if __name__ == "__main__":
-    unittest.main(defaultTest="suite")
+    from unittest import main
+    main(defaultTest="suite")