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feat: init

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chuan
2025-12-04 16:07:30 +08:00
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# Copyright (c) 2021-2025 The University of Texas Southwestern Medical Center.
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted for academic and research use only (subject to the
# limitations in the disclaimer below) provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the copyright holders nor the names of its
# contributors may be used to endorse or promote products derived from this
# software without specific prior written permission.
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
# Standard library imports
import unittest
import os
from datetime import datetime
import json
# Third party imports
# Local application imports
from navigate.tools.file_functions import (
create_save_path,
save_yaml_file,
delete_folder,
load_yaml_file,
)
class CreateSavePathTestCase(unittest.TestCase):
def setUp(self) -> None:
self.save_root = "test_dir"
os.mkdir(self.save_root)
self.date_string = str(datetime.now().date())
def tearDown(self) -> None:
delete_folder("test_dir")
def test_existing_root_directory_no_existing_cell_directories(self):
"""Test 1: Testing with existing root directory and no existing cell
directories."""
saving_settings = {
"root_directory": self.save_root,
"user": "John Doe",
"tissue": "Liver",
"celltype": "Hepatocyte",
"label": "Sample1",
"prefix": "Cell_",
}
expected_save_directory = os.path.join(
self.save_root,
"John-Doe",
"Liver",
"Hepatocyte",
"Sample1",
self.date_string,
"Cell_001",
)
save_directory = create_save_path(saving_settings)
# Assert that the save directory is correct
self.assertEqual(save_directory, expected_save_directory)
# Assert that the save directory and cell directory are created
self.assertTrue(os.path.exists(save_directory))
# Delete the created directory
self.tearDown()
def test_existing_root_directory_existing_cell_directories(self):
"""Test 2: Testing with existing root directory and existing cell
sub-directory."""
os.makedirs(
os.path.join(
self.save_root,
"John-Doe",
"Liver",
"Hepatocyte",
"Sample1",
self.date_string,
"Cell_001",
)
)
saving_settings = {
"root_directory": self.save_root,
"user": "John Doe",
"tissue": "Liver",
"celltype": "Hepatocyte",
"label": "Sample1",
"prefix": "Cell_",
}
save_directory = create_save_path(saving_settings)
# Assert that the save directory is correct
self.assertEqual(
save_directory,
os.path.join(
self.save_root,
"John-Doe",
"Liver",
"Hepatocyte",
"Sample1",
self.date_string,
"Cell_002",
),
)
# Assert that the save directory and cell directory are created
self.assertTrue(os.path.exists(save_directory))
# Delete the created directory
self.tearDown()
def test_spaces_in_strings(self):
saving_settings = {
"root_directory": self.save_root,
"user": "John Doe",
"tissue": "Liver Tissue",
"celltype": "Hepatocyte Cell Type",
"label": "Sample 1",
"prefix": "Cell_",
}
save_directory = create_save_path(saving_settings)
expected_save_directory = os.path.join(
self.save_root,
"John-Doe",
"Liver-Tissue",
"Hepatocyte-Cell-Type",
"Sample-1",
self.date_string,
"Cell_001",
)
# Assert that the save directory is correct
self.assertEqual(save_directory, expected_save_directory)
# Assert that the save directory and cell directory are created
self.assertTrue(os.path.exists(save_directory))
# Delete the created directory
self.tearDown()
class SaveYAMLFileTestCase(unittest.TestCase):
def setUp(self) -> None:
os.mkdir("test_dir")
self.save_root = "test_dir"
def tearDown(self) -> None:
delete_folder("test_dir")
def test_save_yaml_file_success(self):
content_dict = {"name": "John Doe", "age": 30, "location": "New York"}
result = save_yaml_file(self.save_root, content_dict)
# Assert that the file was saved successfully
self.assertTrue(result)
# Assert that the file exists
file_path = os.path.join(self.save_root, "experiment.yml")
self.assertTrue(os.path.exists(file_path))
# Assert that the file content is correct
with open(file_path, "r") as f:
saved_content = json.load(f)
self.assertEqual(saved_content, content_dict)
def test_save_yaml_file_failure(self):
# Test with non-existing directory
content_dict = {"name": "John Doe", "age": 30, "location": "New York"}
result = save_yaml_file(
os.path.join(self.save_root, "does-not-exist"), content_dict
)
# Assert that the file save failed
self.assertFalse(
result,
"File save should have failed. Function does not "
"create the path if it does not exist.",
)
# Assert that the file does not exist
file_path = os.path.join(self.save_root, "experiment.yml")
self.assertFalse(os.path.exists(file_path))
class TestDeleteFolder(unittest.TestCase):
def setUp(self) -> None:
os.mkdir("test_dir")
self.save_root = "test_dir"
def test_delete_folder(self):
delete_folder(self.save_root)
self.assertFalse(os.path.exists(self.save_root))
class TestLoadYamlFile(unittest.TestCase):
def setUp(self) -> None:
os.mkdir("test_dir")
self.save_root = "test_dir"
def tearDown(self) -> None:
delete_folder("test_dir")
def test_load_existing_yaml_file(self):
content_dict = {"name": "John Doe", "age": 30, "location": "New York"}
result = save_yaml_file(self.save_root, content_dict, "test.yml")
file_path = os.path.join(self.save_root, "test.yml")
result = load_yaml_file(file_path)
self.assertIsNotNone(result)
self.assertIsInstance(result, dict)
assert result == content_dict
def test_load_nonexistent_yaml_file(self):
file_path = os.path.join(self.save_root, "test.yml")
result = load_yaml_file(file_path)
self.assertIsNone(result)
def test_load_invalid_yaml_file(self):
file_path = os.path.join(self.save_root, "test.yml")
with open(file_path, "w") as f:
f.write(
"""
{"name": "John Doe", "age": 30, "locati
"""
)
result = load_yaml_file(file_path)
self.assertIsNone(result)
if __name__ == "__main__":
unittest.main()