Fixing WTF failures

Author: josenavas

qiita_db/metadata_template/prep_template.py

@@ -140,7 +140,7 @@ def create(cls, md_template, raw_data, study, data_type,
             "prep_template_id", (data_type_id, raw_data.id,
                                  investigation_type))[0]
 
-        cls._add_commoneation_steps_to_queue(md_template, prep_id,
+        cls._add_common_creation_steps_to_queue(md_template, prep_id,
                                                 conn_handler, queue_name)
 
         try:
@@ -418,10 +418,16 @@ def create_qiime_mapping_file(self):
         rename_cols = {
             'barcode': 'BarcodeSequence',
             'primer': 'LinkerPrimerSequence',
-            'reverselinkerprimer': 'ReverseLinkerPrimer',
             'description': 'Description',
         }
 
+        if 'reverselinkerprimer' in self.categories():
+            rename_cols['reverselinkerprimer'] = 'ReverseLinkerPrimer'
+            new_cols = ['BarcodeSequence', 'LinkerPrimerSequence',
+                        'ReverseLinkerPrimer']
+        else:
+            new_cols = ['BarcodeSequence', 'LinkerPrimerSequence']
+
         # getting the latest sample template
         conn_handler = SQLConnectionHandler()
         sql = """SELECT filepath_id, filepath
@@ -475,7 +481,6 @@ def create_qiime_mapping_file(self):
         cols.remove('BarcodeSequence')
         cols.remove('LinkerPrimerSequence')
         cols.remove('Description')
-        new_cols = ['BarcodeSequence', 'LinkerPrimerSequence']
         new_cols.extend(cols)
         new_cols.append('Description')
         mapping = mapping[new_cols]