Merge 06b5259 into 51cefe9

qiita_db/data.py

@@ -83,16 +83,15 @@
 
 from __future__ import division
 from datetime import datetime
-from future.builtins import zip
-from os.path import join, basename
-from shutil import copy
+from os.path import join
 from functools import partial
 
+
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from .base import QiitaObject
 from .sql_connection import SQLConnectionHandler
-from .util import (exists_dynamic_table, get_db_files_base_dir, scrub_data,
-                   compute_checksum)
+from .util import (exists_dynamic_table, get_db_files_base_dir,
+                   compute_checksum, insert_filepaths)
 
 
 class BaseData(QiitaObject):
@@ -116,54 +115,6 @@ class BaseData(QiitaObject):
     _data_filepath_table = None
     _data_filepath_column = None
 
-    def _insert_filepaths(self, filepaths, conn_handler):
-        r"""Inserts `filepaths` in the DB connected with `conn_handler`. Since
-        the files live outside the database, the directory in which the files
-        lives is controlled by the database, so it copies the filepaths from
-        its original location to the controlled directory.
-
-        Parameters
-        ----------
-        filepaths : iterable of tuples (str, int)
-            The list of paths to the raw files and its filepath type identifier
-        conn_handler : SQLConnectionHandler
-            The connection handler object connected to the DB
-
-        Returns
-        -------
-        list
-            The filepath_id in the database for each added filepath
-        """
-        # Get the base directory in which the type of data is stored
-        base_data_dir = join(get_db_files_base_dir(), self._table)
-        # Generate the new fileapths. Format: DataId_OriginalName
-        # Keeping the original name is useful for checking if the RawData
-        # alrady exists on the DB
-        db_path = partial(join, base_data_dir)
-        new_filepaths = [
-            (db_path("%s_%s" % (self.id, basename(path))), id)
-            for path, id in filepaths]
-        # Copy the original files to the controlled DB directory
-        for old_fp, new_fp in zip(filepaths, new_filepaths):
-            copy(old_fp[0], new_fp[0])
-
-        paths_w_checksum = [(path, id, compute_checksum(path))
-                            for path, id in new_filepaths]
-
-        # Create the list of SQL values to add
-        values = ["('%s', %s, '%s', %s)" % (scrub_data(path), id, checksum, 1)
-                  for path, id, checksum in paths_w_checksum]
-        # Insert all the filepaths at once and get the filepath_id back
-        ids = conn_handler.execute_fetchall(
-            "INSERT INTO qiita.{0} (filepath, filepath_type_id, checksum, "
-            "checksum_algorithm_id) VALUES {1} "
-            "RETURNING filepath_id".format(self._filepath_table,
-                                           ', '.join(values)))
-
-        # we will receive a list of lists with a single element on it (the id),
-        # transform it to a list of ids
-        return [id[0] for id in ids]
-
     def _link_data_filepaths(self, fp_ids, conn_handler):
         r"""Links the data `data_id` with its filepaths `fp_ids` in the DB
         connected with `conn_handler`
@@ -195,7 +146,8 @@ def _add_filepaths(self, filepaths, conn_handler):
         `self` objects with these filepaths"""
         self._check_subclass()
         # Add the filepaths to the database
-        fp_ids = self._insert_filepaths(filepaths, conn_handler)
+        fp_ids = insert_filepaths(filepaths, self._id, self._table,
+                                  self._filepath_table, conn_handler)
         # Connect the raw data with its filepaths
         self._link_data_filepaths(fp_ids, conn_handler)