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authorBonfaceKilz2021-05-11 17:00:26 +0300
committerBonfaceKilz2021-05-13 11:18:57 +0300
commit378d0fc7f4ff5df5e8e77617c37bcef2b26ddf02 (patch)
tree59b6170f45c0857b0a7ba643e1746fdf5fc4c67a
parent53f27b547e7220d46bdc2e92debb38a8739e511c (diff)
downloadgenenetwork3-378d0fc7f4ff5df5e8e77617c37bcef2b26ddf02.tar.gz
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...
-rw-r--r--gn3/api/gemma.py4
-rw-r--r--gn3/api/general.py2
-rw-r--r--gn3/computations/gemma.py2
-rw-r--r--gn3/fs_helpers.py (renamed from gn3/file_utils.py)0
-rw-r--r--tests/unit/test_file_utils.py20
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"""