def test_unsuccessful_test_returns_none(self, mock_http_requests):
mock_return_value = mock.Mock()
mock_return_value.ok = False
mock_http_requests.return_value = mock_return_value
self.assertIsNone(pdb_client.get_pdb_file("5TML"))
mock_http_requests.assert_called_once_with(
"https://files.rcsb.org/download/5TML.pdb")
def test_umcompressed_pdb(self, mock_http_requests):
mock_return_value_pdb = mock.Mock()
mock_return_value_pdb.text = "fake_uncompressed_pdb"
mock_return_value_pdb.ok = True
mock_http_requests.return_value = mock_return_value_pdb
self.assertEqual("fake_uncompressed_pdb",
pdb_client.get_pdb_file("1234"))
mock_http_requests.assert_called_once_with(
"https://files.rcsb.org/download/1234.pdb")
def test_uncompressed_xml(self, mock_http_requests):
mock_return_value_pdb = mock.Mock()
mock_return_value_pdb.text = "fake_uncompressed_xml"
mock_return_value_pdb.ok = True
mock_http_requests.return_value = mock_return_value_pdb
self.assertEqual(
"fake_uncompressed_xml",
pdb_client.get_pdb_file("MI17",
pdb_client.PDBFileType.XML,
compression=False))
mock_http_requests.assert_called_once_with(
"https://files.rcsb.org/download/MI17.xml")
def test_compressed_structfact(self, mock_decompress, mock_http_requests):
mock_return_value_pdb = mock.Mock()
mock_return_value_pdb.content = "fake_compressed_structfact"
mock_return_value_pdb.ok = True
mock_http_requests.return_value = mock_return_value_pdb
mock_decompress.return_value = "fake_decompressed_structfact"
self.assertEqual(
"fake_decompressed_structfact",
pdb_client.get_pdb_file("HK97",
pdb_client.PDBFileType.STRUCTFACT,
compression=True))
mock_http_requests.assert_called_once_with(
"https://files.rcsb.org/download/HK97-sf.cif.gz")
mock_decompress.assert_called_once_with("fake_compressed_structfact")
def test_compressed_cif_file(self, mock_decompress, mock_http_requests):
mock_return_value_cif = mock.Mock()
mock_return_value_cif.ok = True
mock_return_value_cif.content = "fake_compressed_cif"
mock_http_requests.return_value = mock_return_value_cif
mock_decompress.return_value = "fake_decompressed_cif"
self.assertEqual(
"fake_decompressed_cif",
pdb_client.get_pdb_file("1A2B",
pdb_client.PDBFileType.CIF,
compression=True))
mock_http_requests.assert_called_once_with(
"https://files.rcsb.org/download/1A2B.cif.gz")
mock_decompress.assert_called_once_with("fake_compressed_cif")
def get_pdb_file(pdb_id: str, filetype='pdb', compression=False):
"""Deprecated wrapper for fetching PDB files from RCSB Database.
For new uses, please use `pypdb/clients/pdb/pdb_client.py`
"""
warnings.warn(
"The `get_pdb_file` function within pypdb.py is deprecated."
"See `pypdb/clients/pdb/pdb_client.py` for a near-identical "
"function to use", DeprecationWarning)
if filetype is 'pdb':
filetype_enum = pdb_client.PDBFileType.PDB
elif filetype is 'cif':
filetype_enum = pdb_client.PDBFileType.CIF
elif filetype is 'xml':
filetype_enum = pdb_client.PDBFileType.XML
elif filetype is 'structfact':
filetype_enum = pdb_client.PDBFileType.STRUCTFACT
else:
warnings.warn(
"Filetype specified to `get_pdb_file` appears to be invalid")
return pdb_client.get_pdb_file(pdb_id, filetype_enum, compression)