Initial port to python3

[htsworkflow.git] / htsworkflow / frontend / experiments / test_experiments.py

diff --git a/htsworkflow/frontend/experiments/test_experiments.py b/htsworkflow/frontend/experiments/test_experiments.py
index 5878d726d7ee1d268382230a56a235aef7ca29e6..cd212332c1f06b3e0846a88406f8ae5c23ffb8f4 100644 (file)
--- a/htsworkflow/frontend/experiments/test_experiments.py
+++ b/htsworkflow/frontend/experiments/test_experiments.py
@@ -2,13 +2,13 @@ import re
 from lxml.html import fromstring
 try:
     import json
 from lxml.html import fromstring
 try:
     import json

-except ImportError, e:
+except ImportError as e:

     import simplejson as json
 import os
 import shutil
 import sys
 import tempfile
     import simplejson as json
 import os
 import shutil
 import sys
 import tempfile

-from urlparse import urljoin
+from urllib.parse import urljoin

 
 from django.conf import settings
 from django.core import mail
 
 from django.conf import settings
 from django.core import mail


@@ -24,7 +24,7 @@ from htsworkflow.util.ethelp import validate_xhtml
 
 from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
 
 
 from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
 

-LANE_SET = range(1,9)
+LANE_SET = list(range(1,9))

 
 NSMAP = {'libns':'http://jumpgate.caltech.edu/wiki/LibraryOntology#'}
 
 
 NSMAP = {'libns':'http://jumpgate.caltech.edu/wiki/LibraryOntology#'}
 


@@ -177,7 +177,7 @@ class ExperimentsTestCases(TestCase):
         """
         Check the code that packs the django objects into simple types.
         """
         """
         Check the code that packs the django objects into simple types.
         """

-        for fc_id in [u'FC12150', u"42JTNAAXX", "42JU1AAXX"]:
+        for fc_id in ['FC12150', "42JTNAAXX", "42JU1AAXX"]:

             fc_dict = experiments.flowcell_information(fc_id)
             fc_django = models.FlowCell.objects.get(flowcell_id=fc_id)
             self.assertEqual(fc_dict['flowcell_id'], fc_id)
             fc_dict = experiments.flowcell_information(fc_id)
             fc_django = models.FlowCell.objects.get(flowcell_id=fc_id)
             self.assertEqual(fc_dict['flowcell_id'], fc_id)


@@ -211,7 +211,7 @@ class ExperimentsTestCases(TestCase):
 
 
             for lane in fc_django.lane_set.all():
 
 
             for lane in fc_django.lane_set.all():

-                lane_contents = fc_json['lane_set'][unicode(lane.lane_number)]
+                lane_contents = fc_json['lane_set'][str(lane.lane_number)]

                 lane_dict = multi_lane_to_dict(lane_contents)[lane.library_id]
 
                 self.assertEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
                 lane_dict = multi_lane_to_dict(lane_contents)[lane.library_id]
 
                 self.assertEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)


@@ -235,7 +235,7 @@ class ExperimentsTestCases(TestCase):
         """
         Require logging in to retrieve meta data
         """
         """
         Require logging in to retrieve meta data
         """

-        response = self.client.get(u'/experiments/config/FC12150/json')
+        response = self.client.get('/experiments/config/FC12150/json')

         self.assertEqual(response.status_code, 403)
 
     def test_library_id(self):
         self.assertEqual(response.status_code, 403)
 
     def test_library_id(self):


@@ -268,8 +268,8 @@ class ExperimentsTestCases(TestCase):
         This tests to make sure that the value entered in the raw library id field matches
         the library id looked up.
         """
         This tests to make sure that the value entered in the raw library id field matches
         the library id looked up.
         """

-        expected_ids = [u'10981',u'11016',u'SL039',u'11060',
-                        u'11061',u'11062',u'11063',u'11064']
+        expected_ids = ['10981','11016','SL039','11060',
+                        '11061','11062','11063','11064']

         self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
         response = self.client.get('/admin/experiments/flowcell/153/')
 
         self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
         response = self.client.get('/admin/experiments/flowcell/153/')
 


@@ -322,11 +322,11 @@ class ExperimentsTestCases(TestCase):
         lane_dict = multi_lane_to_dict(lane_contents)
 
         self.assertEqual(lane_dict['12044']['index_sequence'],
         lane_dict = multi_lane_to_dict(lane_contents)
 
         self.assertEqual(lane_dict['12044']['index_sequence'],

-                         {u'1': u'ATCACG',
-                          u'2': u'CGATGT',
-                          u'3': u'TTAGGC'})
+                         {'1': 'ATCACG',
+                          '2': 'CGATGT',
+                          '3': 'TTAGGC'})

         self.assertEqual(lane_dict['11045']['index_sequence'],
         self.assertEqual(lane_dict['11045']['index_sequence'],

-                         {u'1': u'ATCACG'})
+                         {'1': 'ATCACG'})

 
 
 
 
 
 


@@ -482,7 +482,7 @@ class ExperimentsTestCases(TestCase):
         count = 0
         for r in query.execute(model):
             count += 1
         count = 0
         for r in query.execute(model):
             count += 1

-            self.assertEqual(fromTypedNode(r['flowcell_id']), u'42JU1AAXX')
+            self.assertEqual(fromTypedNode(r['flowcell_id']), '42JU1AAXX')

             lane_id = fromTypedNode(r['lane_id'])
             library_id = fromTypedNode(r['library_id'])
             self.assertTrue(library_id in expected[lane_id])
             lane_id = fromTypedNode(r['lane_id'])
             library_id = fromTypedNode(r['library_id'])
             self.assertTrue(library_id in expected[lane_id])


@@ -494,8 +494,8 @@ class TestFileType(TestCase):
         file_type_objects = models.FileType.objects
         name = 'QSEQ tarfile'
         file_type_object = file_type_objects.get(name=name)
         file_type_objects = models.FileType.objects
         name = 'QSEQ tarfile'
         file_type_object = file_type_objects.get(name=name)

-        self.assertEqual(u"QSEQ tarfile",
-                             unicode(file_type_object))
+        self.assertEqual("QSEQ tarfile",
+                             str(file_type_object))

 
     def test_find_file_type(self):
         file_type_objects = models.FileType.objects
 
     def test_find_file_type(self):
         file_type_objects = models.FileType.objects


@@ -607,7 +607,7 @@ class TestSequencer(TestCase):
         seq.instrument_name = "HWI-SEQ1"
         seq.model = "Imaginary 5000"
 
         seq.instrument_name = "HWI-SEQ1"
         seq.model = "Imaginary 5000"
 

-        self.assertEqual(unicode(seq), "Seq1 (HWI-SEQ1)")
+        self.assertEqual(str(seq), "Seq1 (HWI-SEQ1)")

 
     def test_lookup(self):
         fc = models.FlowCell.objects.get(pk=153)
 
     def test_lookup(self):
         fc = models.FlowCell.objects.get(pk=153)


@@ -698,7 +698,7 @@ def tearDownModule():
     teardown_test_environment()
 
 def suite():
     teardown_test_environment()
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     for testcase in [ClusterStationTestCases,
                      SequencerTestCases,
     suite = TestSuite()
     for testcase in [ClusterStationTestCases,
                      SequencerTestCases,


@@ -710,5 +710,5 @@ def suite():
     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")