Merge pull request #3130 from antgonza/insert_filepaths-copy-files-

making sure the files are copied when copy in insert_filepaths

Author: adswafford

qiita_db/test/test_util.py

@@ -228,7 +228,8 @@ def test_insert_filepaths_copy(self):
             qdb.sql_connection.TRN.add(
                 "SELECT last_value FROM qiita.filepath_filepath_id_seq")
             exp_new_id = 1 + qdb.sql_connection.TRN.execute_fetchflatten()[0]
-        obs = qdb.util.insert_filepaths([(fp, 1)], 2, "raw_data", copy=True)
+        obs = qdb.util.insert_filepaths([(fp, 1)], 2, "raw_data",
+                                        move_files=False, copy=True)
         self.assertEqual(obs, [exp_new_id])
 
         # Check that the files have been copied correctly
@@ -247,6 +248,19 @@ def test_insert_filepaths_copy(self):
         exp = [[exp_new_id, exp_fp, 1, '852952723', 1, 5, 1]]
         self.assertEqual(obs, exp)
 
+        # let's do that again but with move_files = True
+        exp_new_id += 1
+        obs = qdb.util.insert_filepaths([(fp, 1)], 2, "raw_data",
+                                        move_files=True, copy=True)
+        self.assertEqual(obs, [exp_new_id])
+
+        # Check that the files have been copied correctly
+        exp_fp = join(qdb.util.get_db_files_base_dir(), "raw_data",
+                      "2_%s" % basename(fp))
+        self.assertTrue(exists(exp_fp))
+        self.assertTrue(exists(fp))
+        self.files_to_remove.append(exp_fp)
+
         qdb.util.purge_filepaths()
 
     def test_insert_filepaths_string(self):

qiita_db/util.py

@@ -610,7 +610,7 @@ def insert_filepaths(filepaths, obj_id, table, move_files=True, copy=False):
         dd_id, mp, subdir = get_mountpoint(table, retrieve_subdir=True)[0]
         base_fp = join(get_db_files_base_dir(), mp)
 
-        if move_files:
+        if move_files or copy:
             db_path = partial(join, base_fp)
             if subdir:
                 # Generate the new filepaths, format: