diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/integration/test_general.py | 11 | ||||
| -rw-r--r-- | tests/unit/test_file_utils.py | 20 |
2 files changed, 21 insertions, 10 deletions
diff --git a/tests/integration/test_general.py b/tests/integration/test_general.py index 99c4824..8fc2b43 100644 --- a/tests/integration/test_general.py +++ b/tests/integration/test_general.py @@ -46,3 +46,14 @@ class GeneralAPITest(unittest.TestCase): self.assertEqual(response.get_json(), {"status": 128, "error": "gzip failed to unpack file"}) + + @mock.patch("gn3.api.general.run_cmd") + def test_run_r_qtl(self, mock_run_cmd): + """Test correct upload of file""" + mock_run_cmd.return_value = "Random results from STDOUT" + response = self.app.post("/api/qtl/run/" + "geno_file_test/" + "pheno_file_test") + self.assertEqual(response.status_code, 201) + self.assertEqual(response.get_json(), + "Random results from STDOUT") 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""" |