add function that creates neccessary "mountpoints"

Author: sjanssen2

qiita_db/environment_manager.py

@@ -7,6 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from os.path import abspath, dirname, join, exists, basename, splitext
+from shutil import copytree
 from functools import partial
 from os import mkdir
 import gzip
@@ -126,6 +127,34 @@ def _download_reference_files():
 
         _insert_processed_params(ref)
 
+def create_mountpoints():
+    r"""In a fresh qiita setup, sub-directories under qiita_config.base_data_dir
+        might not yet exist. To avoid failing in 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
+                 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)
+
+        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)))
 
 def make_environment(load_ontologies, download_reference, add_demo_user):
     r"""Creates the new environment specified in the configuration
@@ -397,6 +426,9 @@ def patch(patches_dir=PATCHES_DIR, verbose=False, test=False):
         with qdb.sql_connection.TRN:
             _populate_test_db()
 
+    # create mountpoints as subdirectories in BASE_DATA_DIR
+    create_mountpoints()
+
     patch_update_sql = "UPDATE settings SET current_patch = %s"
     for sql_patch_fp in sql_patch_files[next_patch_index:]:
         sql_patch_filename = basename(sql_patch_fp)