fix spelling error in module name

diff --git a/htsworkflow/pipelines/test/test_retrieve_config.py b/htsworkflow/pipelines/test/test_retrieve_config.py
new file mode 100644 (file)
index 0000000..fd1c112
--- /dev/null
+++ b/htsworkflow/pipelines/test/test_retrieve_config.py
@@ -0,0 +1,86 @@
+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.auth import apidata
+from htsworkflow.pipelines.retrieve_config import \
+     format_gerald_config, \
+     getCombinedOptions, \
+     save_sample_sheet
+
+class RetrieveTestCases(TestCase):
+    fixtures = ['initial_data.json',
+                'test_flowcells.json']
+
+    def setUp(self):
+        pass
+
+    def test_format_gerald(self):
+        flowcell_request = self.client.get('/experiments/config/FC12150/json', apidata)
+        self.failUnlessEqual(flowcell_request.status_code, 200)
+        flowcell_info = json.loads(flowcell_request.content)
+
+        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) ]
+        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')
+        # we changed the api to force unknown genomes to be sequencing
+        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))

diff --git a/htsworkflow/pipelines/test/test_retrive_config.py b/htsworkflow/pipelines/test/test_retrive_config.py
deleted file mode 100644 (file)
index fd1c112..0000000
--- a/htsworkflow/pipelines/test/test_retrive_config.py
+++ /dev/null
@@ -1,86 +0,0 @@
-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.auth import apidata
-from htsworkflow.pipelines.retrieve_config import \
-     format_gerald_config, \
-     getCombinedOptions, \
-     save_sample_sheet
-
-class RetrieveTestCases(TestCase):
-    fixtures = ['initial_data.json',
-                'test_flowcells.json']
-
-    def setUp(self):
-        pass
-
-    def test_format_gerald(self):
-        flowcell_request = self.client.get('/experiments/config/FC12150/json', apidata)
-        self.failUnlessEqual(flowcell_request.status_code, 200)
-        flowcell_info = json.loads(flowcell_request.content)
-
-        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) ]
-        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')
-        # we changed the api to force unknown genomes to be sequencing
-        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))