Rename file_utils to fs_helpers

Generally avoid naming things with a "utils" prefix/ suffix since it
encourages contributors to dump any new functions there; and over time, as the
code grows, things get messy...

5 files changed, 14 insertions, 14 deletions

diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 81e185d..6b0b20e 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -9,8 +9,8 @@ from flask import request
 
 from gn3.commands import queue_cmd
 from gn3.commands import run_cmd
-from gn3.file_utils import cache_ipfs_file
-from gn3.file_utils import jsonfile_to_dict
+from gn3.fs_helpers import cache_ipfs_file
+from gn3.fs_helpers import jsonfile_to_dict
 from gn3.computations.gemma import generate_gemma_cmd
 from gn3.computations.gemma import do_paths_exist
 
diff --git a/gn3/api/general.py b/gn3/api/general.py
index 38e6154..a9a8da2 100644
--- a/gn3/api/general.py
+++ b/gn3/api/general.py
@@ -5,7 +5,7 @@ from flask import current_app
 from flask import jsonify
 from flask import request
 
-from gn3.file_utils import extract_uploaded_file
+from gn3.fs_helpers import extract_uploaded_file
 
 
 general = Blueprint("general", __name__)
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 5f9d5a3..0b22d3c 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -7,7 +7,7 @@ from typing import Dict
 from typing import List
 from typing import ValuesView
 from gn3.commands import compose_gemma_cmd
-from gn3.file_utils import get_hash_of_files
+from gn3.fs_helpers import get_hash_of_files
 
 
 def generate_hash_of_string(unhashed_str: str) -> str:
diff --git a/gn3/file_utils.py b/gn3/fs_helpers.py
index 73f6567..73f6567 100644
--- a/gn3/file_utils.py
+++ b/gn3/fs_helpers.py
diff --git a/tests/unit/test_file_utils.py b/tests/unit/test_file_utils.py
index cc842d5..75be4f6 100644
--- a/tests/unit/test_file_utils.py
+++ b/tests/unit/test_file_utils.py
@@ -1,14 +1,14 @@
-"""Test cases for procedures defined in file_utils.py"""
+"""Test cases for procedures defined in fs_helpers.py"""
 import os
 import unittest
 
 from dataclasses import dataclass
 from typing import Callable
 from unittest import mock
-from gn3.file_utils import extract_uploaded_file
-from gn3.file_utils import get_dir_hash
-from gn3.file_utils import jsonfile_to_dict
-from gn3.file_utils import cache_ipfs_file
+from gn3.fs_helpers import extract_uploaded_file
+from gn3.fs_helpers import get_dir_hash
+from gn3.fs_helpers import jsonfile_to_dict
+from gn3.fs_helpers import cache_ipfs_file
 
 
 @dataclass
@@ -19,7 +19,7 @@ class MockFile:
 
 
 class TestFileUtils(unittest.TestCase):
-    """Test cases for procedures defined in file_utils.py"""
+    """Test cases for procedures defined in fs_helpers.py"""
 
     def test_get_dir_hash(self):
         """Test that a directory is hashed correctly"""
@@ -45,8 +45,8 @@ non-existent"""
         self.assertRaises(FileNotFoundError, jsonfile_to_dict,
                           "/non-existent-dir")
 
-    @mock.patch("gn3.file_utils.tarfile")
-    @mock.patch("gn3.file_utils.secure_filename")
+    @mock.patch("gn3.fs_helpers.tarfile")
+    @mock.patch("gn3.fs_helpers.secure_filename")
     def test_extract_uploaded_file(self, mock_file, mock_tarfile):
         """Test that the gzip file is extracted to the right location"""
         mock_file.return_value = "upload-data.tar.gz"
@@ -65,7 +65,7 @@ non-existent"""
         mock_file.assert_called_once_with("upload-data.tar.gz")
         self.assertEqual(result, {"status": 0, "token": "abcdef-abcdef"})
 
-    @mock.patch("gn3.file_utils.secure_filename")
+    @mock.patch("gn3.fs_helpers.secure_filename")
     def test_extract_uploaded_file_non_existent_gzip(self, mock_file):
         """Test that the right error message is returned when there is a problem
 extracting the file"""
@@ -96,7 +96,7 @@ extracting the file"""
         os.rmdir(test_dir)
         self.assertEqual(file_loc, f"{test_dir}/genotype.txt")
 
-    @mock.patch("gn3.file_utils.ipfshttpclient")
+    @mock.patch("gn3.fs_helpers.ipfshttpclient")
     def test_cache_ipfs_file_cache_miss(self,
                                         mock_ipfs):
         """Test that a file is cached if there's a cache miss"""