BUG: Fix problem with default basedir

qiita_core/configuration_manager.py

@@ -144,8 +144,8 @@ def __init__(self):
     def _get_main(self, config):
         """Get the configuration of the main section"""
         self.test_environment = config.getboolean('main', 'TEST_ENVIRONMENT')
-        default_base_data_dir = join(dirname(abspath(__file__)),
-                                     '..', 'qiita_db', 'support_files',
+        install_dir = dirname(dirname(abspath(__file__)))
+        default_base_data_dir = join(install_dir, 'qiita_db', 'support_files',
                                      'test_data')
         self.base_data_dir = config.get('main', 'BASE_DATA_DIR') or \
             default_base_data_dir

qiita_db/support_files/patches/31.sql

@@ -0,0 +1,3 @@
+-- August 24, 2015
+-- Delete all occurrences of '..' in the base_data_dir entry
+SELECT 42;

qiita_db/support_files/patches/python_patches/31.py

@@ -0,0 +1,11 @@
+from os.path import realpath
+from qiita_db.sql_connection import TRN
+
+with TRN:
+    TRN.add('SELECT base_data_dir FROM settings')
+    path = TRN.execute_fetchlast()
+
+    # if the path is non-canonical (it contains .. or other redundant symbols)
+    # this will update it, else it will leave as is
+    TRN.add("UPDATE settings SET base_data_dir = %s", (realpath(path),))
+    TRN.execute()