diff options
| -rw-r--r-- | gn3/api/gemma.py | 4 | ||||
| -rw-r--r-- | gn3/api/general.py | 2 | ||||
| -rw-r--r-- | gn3/computations/gemma.py | 2 | ||||
| -rw-r--r-- | gn3/fs_helpers.py (renamed from gn3/file_utils.py) | 0 | ||||
| -rw-r--r-- | tests/unit/test_file_utils.py | 20 |
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""" |