Initial port to python3

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

diff --git a/htsworkflow/pipelines/test/test_runfolder_pair.py b/htsworkflow/pipelines/test/test_runfolder_pair.py
index b159c5fd9d953e5eff625a996b84ca9b7d9fa6f3..0b9d070ba23065d903907d23ea1de2f0b6deeed9 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_pair.py
+++ b/htsworkflow/pipelines/test/test_runfolder_pair.py
@@ -4,14 +4,14 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
-from unittest2 import TestCase
+from unittest import TestCase
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import gerald
 from htsworkflow.pipelines.eland import SampleKey
 from htsworkflow.pipelines import runfolder
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
 
 from htsworkflow.pipelines.test.simulate_runfolder import *
 
@@ -115,7 +115,7 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(b.date,    b2.date )
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
-        for key in b.phasing.keys():
+        for key in list(b.phasing.keys()):
             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,
@@ -130,8 +130,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
-        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
@@ -157,7 +157,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator
-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):
           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)
@@ -189,8 +189,8 @@ 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):
@@ -218,13 +218,13 @@ class RunfolderTests(TestCase):
                                          g2_results.reads)
                     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])
 
@@ -287,13 +287,13 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 17)
-            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])
 
@@ -304,33 +304,33 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(len(runs), 1)
         # firecrest's date depends on filename not the create time.
         name = 'run_207BTAAXX_2009-02-22.xml'
-        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, '207BTAAXY')
         runs = runfolder.get_runs(self.runfolder_dir)
         self.failUnlessEqual(len(runs), 1)
         name = 'run_207BTAAXY_2009-02-22.xml'
-        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)
 
 
 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")