Implement a client side config file generator.

[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
new file mode 100644 (file)
index 0000000..dd8f30e
--- /dev/null
+++ b/htsworkflow/pipelines/test/test_retrive_config.py
@@ -0,0 +1,43 @@
+import os
+import re
+
+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
+
+class RetrieveTestCases(TestCase):
+    fixtures = ['test_flowcells.json']
+
+    def setUp(self):
+        pass
+
+    def test_format_gerald(self):
+        flowcell_request = self.client.get('/experiments/config/303TUAAXX/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()])        
+        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) ]
+        self.failUnlessEqual(len(lane3), 1)
+        self.failUnlessEqual(lane3[0], '# Lane3: SL039 | Paired ends 99 GM12892')
+        human = [ line for line in config_lines if re.search('hg18', line) ]
+        self.failUnlessEqual(len(human), 1)
+        self.failUnlessEqual(human[0], '345678:ELAND_GENOME /tmp/hg18')
+        unknown = [ line for line in config_lines if re.search('Unknown', line) ]
+        self.failUnlessEqual(len(unknown), 2)
+                  
+
+        
+