addressing Antonio's suggestion to use get_mountpoint

Author: sjanssen2

qiita_db/environment_manager.py

@@ -134,28 +134,29 @@ def create_mountpoints():
         later steps, they are created here.
     """
     with qdb.sql_connection.TRN:
-        # Insert the settings values to the database
-        sql = """SELECT mountpoint FROM qiita.data_directory
+        sql = """SELECT DISTINCT mountpoint FROM qiita.data_directory
                  WHERE active = TRUE"""
         qdb.sql_connection.TRN.add(sql)
         created_subdirs = []
-        for subdir in qdb.sql_connection.TRN.execute_fetchflatten():
-            if not exists(join(qiita_config.base_data_dir, subdir)):
-                if qiita_config.test_environment and \
-                   exists(get_support_file('test_data', subdir)):
-                    # if in test mode, we want to potentially fill the
-                    # new directory with according test data
-                    copytree(get_support_file('test_data', subdir),
-                             join(qiita_config.base_data_dir, subdir))
-                else:
-                    # in production mode, an empty directory is created
-                    mkdir(join(qiita_config.base_data_dir, subdir))
-                created_subdirs.append(subdir)
+        for mountpoint in qdb.sql_connection.TRN.execute_fetchflatten():
+            for (ddid, subdir) in qdb.util.get_mountpoint(mountpoint,
+                                                          retrieve_all=True):
+                if not exists(join(qiita_config.base_data_dir, subdir)):
+                    if qiita_config.test_environment and \
+                       exists(get_support_file('test_data', subdir)):
+                        # if in test mode, we want to potentially fill the
+                        # new directory with according test data
+                        copytree(get_support_file('test_data', subdir),
+                                 join(qiita_config.base_data_dir, subdir))
+                    else:
+                        # in production mode, an empty directory is created
+                        mkdir(join(qiita_config.base_data_dir, subdir))
+                    created_subdirs.append(subdir)
 
         if len(created_subdirs) > 0:
-            print("Created %i sub-directories as 'mount points' in '%s': %s"
-                  % (len(created_subdirs), qiita_config.base_data_dir,
-                     ', '.join(created_subdirs)))
+            print("Created %i sub-directories as 'mount points':\n%s"
+                  % (len(created_subdirs),
+                     ''.join(map(lambda x: ' - %s\n' % x, created_subdirs))))
 
 
 def make_environment(load_ontologies, download_reference, add_demo_user):