Initial port to python3

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

diff --git a/htsworkflow/pipelines/test/test_retrive_config.py b/htsworkflow/pipelines/test/test_retrive_config.py
index cb5650191e79f886da243c9837bcfa61291fbb1f..6e6155c915c814cabc3c05ab2bc5ea0bd188fc09 100644 (file)
--- a/htsworkflow/pipelines/test/test_retrive_config.py
+++ b/htsworkflow/pipelines/test/test_retrive_config.py
@@ -1,11 +1,11 @@
 import csv
 import os
 import re
-from StringIO import StringIO
+from io import StringIO
 
 try:
     import json
-except ImportError, e:
+except ImportError as e:
     import simplejson as json
 
 from django.test import TestCase
@@ -28,7 +28,7 @@ class RetrieveTestCases(TestCase):
         flowcell_info = json.loads(flowcell_request.content)
 
         options = getCombinedOptions(['-f','FC12150','-g',os.getcwd()])
-        genome_map = {u'Homo sapiens': '/tmp/hg18' }
+        genome_map = {'Homo sapiens': '/tmp/hg18' }
 
         config = format_gerald_config(options, flowcell_info, genome_map)
         config_lines = config.split('\n')
@@ -54,19 +54,33 @@ class RetrieveTestCases(TestCase):
 
         output = StringIO()
         save_sample_sheet(output, options, flowcell_info)
+        print(output.buf)
+
         output.seek(0)
         sheet = list(csv.DictReader(output))
-        expected = [{'SampleProject': '12044_index1', 'Index': 'ATCACG'},
-                    {'SampleProject': '12044_index2', 'Index': 'CGATGT'},
-                    {'SampleProject': '12044_index3', 'Index': 'TTAGGC'},
-                    {'SampleProject': '11045_index1', 'Index': 'ATCACG'},
+        expected = [{'SampleProject': '12044_index1',
+                     'Index': 'ATCACG',
+                     'Lane': '3',
+                     },
+                    {'SampleProject': '12044_index2',
+                     'Index': 'CGATGT',
+                     'Lane': '3',
+                     },
+                    {'SampleProject': '12044_index3',
+                     'Index': 'TTAGGC',
+                     'Lane': '3',
+                     },
+                    {'SampleProject': '11045_index1',
+                     'Index': 'ATCACG',
+                     'Lane': '3',
+                     },
+                    {'SampleProject': '13044_indexN701-N501',
+                     'Index': 'TAAGGCGA-TAGATCGC',
+                     'Lane': '4',
+                     }
                     ]
-        for i in range(4):
-            self.assertEqual(sheet[i]['SampleProject'],
-                             expected[i]['SampleProject'])
-            self.assertEqual(sheet[i]['Index'],
-                             expected[i]['Index'])
-            self.assertEqual(sheet[i]['FCID'], fcid)
-            self.assertEqual(sheet[i]['Lane'], '3')
-
-
+        self.failUnlessEqual(len(sheet), len(expected))
+        for s, e in zip(sheet, expected):
+            for key in list(e.keys()):
+                self.failUnlessEqual(s[key], e[key],
+                  "%s != %s for key %s" % (s[key],e[key], key))