def test_custom_directory(self):
import tempfile
import os
import shutil
handler = Parser.DataHandler(validate=False, escape=False)
# Create a temporary directory
tmpdir = tempfile.mkdtemp()
# Set the custom directory to the temporary directory.
# This assignment statement will also initialize the local DTD and XSD directories.
handler.directory = tmpdir
# Confirm that the two temp directories are named what we want.
self.assertEqual(
handler.local_dtd_dir,
os.path.join(handler.directory, 'Bio', 'Entrez', 'DTDs'))
self.assertEqual(
handler.local_xsd_dir,
os.path.join(handler.directory, 'Bio', 'Entrez', 'XSDs'))
# And that they were created.
self.assertTrue(os.path.isdir(handler.local_dtd_dir))
self.assertTrue(os.path.isdir(handler.local_xsd_dir))
shutil.rmtree(tmpdir)
def entrez_dtd_dir(test_dir):
"""Fixes CircleCI failure to retrieve DTDs for Entrez.Parser from NCBI.
See BioPython GitHub repository for demonstration of ability to pass
Entrez.Parser a custom directory containting DTDs. Found in
Tests.test_Entrez.py classCustomDirectoryTest:
https://github.com/biopython/biopython/blob/master/Tests/test_Entrez.py
"""
dir_path = test_dir / "test_inputs" / "Bio" / "Entrez" / "DTDs"
handler = Parser.DataHandler(validate=False, escape=False)
handler.directory = dir_path
return