remove some test code debugging print statements

[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 9847ffd4aea53d7a613bfe266cc882584c1c3a7d..d06508e9ed3217aa8475f9ace27c39074d0a0202 100644 (file)
--- a/htsworkflow/pipelines/test/test_retrive_config.py
+++ b/htsworkflow/pipelines/test/test_retrive_config.py
@@ -1,15 +1,20 @@
+import csv
 import os
 import re
+from StringIO import StringIO
 
 try:
     import json
 except ImportError, e:
     import simplejson as json
-    
+
 from django.test import TestCase
 
 from htsworkflow.frontend.auth import apidata
-from htsworkflow.pipelines.retrieve_config import format_gerald_config, getCombinedOptions
+from htsworkflow.pipelines.retrieve_config import \
+     format_gerald_config, \
+     getCombinedOptions, \
+     save_sample_sheet
 
 class RetrieveTestCases(TestCase):
     fixtures = ['test_flowcells.json']
@@ -18,15 +23,13 @@ class RetrieveTestCases(TestCase):
         pass
 
     def test_format_gerald(self):
-        flowcell_request = self.client.get('/experiments/config/303TUAAXX/json', apidata)
+        flowcell_request = self.client.get('/experiments/config/FC12150/json', apidata)
         self.failUnlessEqual(flowcell_request.status_code, 200)
-
-        print dir(flowcell_request)
         flowcell_info = json.loads(flowcell_request.content)
 
-        options = getCombinedOptions(['-f','303TUAAXX','-g',os.getcwd()])        
+        options = getCombinedOptions(['-f','FC12150','-g',os.getcwd()])
         genome_map = {u'Homo sapiens': '/tmp/hg18' }
-        
+
         config = format_gerald_config(options, flowcell_info, genome_map)
         config_lines = config.split('\n')
         lane3 = [ line for line in config_lines if re.search('Lane3', line) ]
@@ -39,7 +42,44 @@ class RetrieveTestCases(TestCase):
         sequencing = [ line for line in config_lines if re.search('sequence_pair', line) ]
         self.failUnlessEqual(len(sequencing), 2)
 
-                  
 
-        
-    
+    def test_format_sample_sheet(self):
+        fcid = '42JU1AAXX'
+        url = '/experiments/config/%s/json' % (fcid,)
+        flowcell_request = self.client.get(url, apidata)
+        self.failUnlessEqual(flowcell_request.status_code, 200)
+        flowcell_info = json.loads(flowcell_request.content)
+
+        options = getCombinedOptions(['-f',fcid,'-g',os.getcwd(),])
+
+        output = StringIO()
+        save_sample_sheet(output, options, flowcell_info)
+
+        output.seek(0)
+        sheet = list(csv.DictReader(output))
+        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',
+                     }
+                    ]
+        self.failUnlessEqual(len(sheet), len(expected))
+        for s, e in zip(sheet, expected):
+            for key in e.keys():
+                self.failUnlessEqual(s[key], e[key],
+                  "%s != %s for key %s" % (s[key],e[key], key))