Initial port to python3

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder_casava_1_7.py

diff --git a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
index ae8899eeda02df677ca79360035d1b3c4a3c09df..a511437bbe31736abdec96f58921817c4402c99a 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
+++ b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
@@ -5,7 +5,7 @@ import glob
 import os
 import tempfile
 import shutil
-from unittest2 import TestCase
+from unittest import TestCase
 
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import eland
@@ -91,8 +91,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'CASAVA')
         self.failUnlessEqual(g.version, '1.7.0')
         self.failUnlessEqual(g.date, datetime(2011,5,2,19,19,49))
-        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
@@ -128,7 +128,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*100+'y'*100)
 
         # I want to be able to use a simple iterator
-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):
           self.failUnless(l.analysis in ('sequence_pair', 'eland_pair'))
           self.failUnlessEqual(l.read_length, '100')
           self.failUnlessEqual(l.use_bases, 'Y'*100+'y'*100)
@@ -155,8 +155,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         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):
@@ -185,13 +185,13 @@ class RunfolderTests(TestCase):
                 if isinstance(g_results, eland.ElandLane):
                   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])
 
@@ -250,13 +250,13 @@ class RunfolderTests(TestCase):
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 7)
-              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])
             elif isinstance(l1, eland.SequenceLane):
@@ -268,21 +268,21 @@ class RunfolderTests(TestCase):
         # do we get the flowcell id from the filename?
         self.failUnlessEqual(len(runs), 1)
         name = 'run_%s_%s.xml' % ( FCID, date.today().strftime('%Y-%m-%d'),)
-        self.failUnlessEqual(runs[0].name, name)
+        self.failUnlessEqual(runs[0].serialization_filename, name)
 
         # do we get the flowcell id from the FlowcellId.xml file
         make_flowcell_id(self.runfolder_dir, FCID)
         runs = runfolder.get_runs(self.runfolder_dir)
         self.failUnlessEqual(len(runs), 1)
         name = 'run_%s_%s.xml' % ( FCID, date.today().strftime('%Y-%m-%d'),)
-        self.failUnlessEqual(runs[0].name, name)
+        self.failUnlessEqual(runs[0].serialization_filename, name)
 
         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)
@@ -300,12 +300,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
-    from unittest2 import main
+    from unittest import main
     main(defaultTest="suite")