def test_wrapperTable_setattr_setitem(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_2"],
"NEW_ID",
preserve_token_order=True)
# # dot notation access
cif_wrapper._test_category_1["test_value_2"] = ["a", "b", "c", "d"]
self.assertEqual(
cif_wrapper._test_category_1["test_value_2"],
["a", "b", "c", "d"],
"Conventional attribute setter failed or gave inconsistent results",
)
cif_wrapper._test_category_1["test_value_2"] = "FOO"
self.assertEqual(
cif_wrapper._test_category_1["test_value_2"],
[
"FOO",
],
"Attribute setter failed to overwrite or gave inconsistent results",
)
cif_wrapper._test_category_1.test_value_3 = "Bundy"
self.assertEqual(
cif_wrapper._test_category_1["test_value_3"],
[
"Bundy",
],
"Dot-notation attribute setting failed to overwrite or gave inconsistent results",
)
def test_write_ciffile_after_cifwrapper_dictionary_import(self):
# Test write CifFile initialized by CIFWrapper and dictionary import
unit_test_file = "io_testcase_2.cif"
cfw = CifFileWriter(
file_path=os.path.join(self.FILE_ROOT, unit_test_file))
cif_obj = dict((k, CIFWrapper(v, preserve_token_order=True))
for k, v in list(self.raw_dictionary.items()))
cif_wrapper = CIFWrapper(
{"TEST_BLOCK_1": self.raw_dictionary["TEST_BLOCK_1"]},
preserve_token_order=True,
)
cfw.write(cif_wrapper)
cif_wrapper = CIFWrapper(
{"TEST_BLOCK_2": self.raw_dictionary["TEST_BLOCK_2"]},
preserve_token_order=True,
)
cfw.write(cif_wrapper)
del cfw
cfr = CifFileReader(input="data", preserve_order=True)
test_file = cfr.read(os.path.join(self.FILE_ROOT, unit_test_file),
output="cif_wrapper")
data_block_ids = list(test_file.keys())
data_block_ids.sort()
self.assertEqual(
data_block_ids,
["TEST_BLOCK_1", "TEST_BLOCK_2"],
"Datablock(s) were not written correctly",
)
self.assertEqual(
test_file["TEST_BLOCK_1"]._test_category_2.test_value_1,
["1", "2", "3", "4"],
"mmCIF data was not written correctly",
)
def test_listContents(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_1"],
preserve_token_order=True)
categories = cif_wrapper.contents()
categories.sort()
assert_equal(
categories,
["_test_category_1", "_test_category_2"],
"Item list for the category is incorrect",
)
def test_wrapperTableContains(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_2"],
"NEW_ID",
preserve_token_order=True)
self.assertIsInstance(
cif_wrapper,
CIFWrapper,
"Failed to instantiate CIFWrapper from 2-level mmCIF-like dictionary",
)
self.assertEqual(cif_wrapper.data_id, "NEW_ID",
"'NEW_ID' not set correctly as datablock ID")
self.assertFalse("bogus" in cif_wrapper,
"CIFWrapper.__contains__ not returning boolean")
self.assertTrue(
"_test_category_1" in cif_wrapper,
"CIFWrapper.__contains__ not returning boolean",
)
test_category_1 = cif_wrapper._test_category_1
self.assertFalse(
"bogus" in test_category_1,
"CIFWrapperTable.__contains__ not returning boolean",
)
self.assertTrue(
"test_value_1" in test_category_1,
"CIFWrapperTable.__contains__ not returning boolean",
)
def test_iter(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_1"],
preserve_token_order=True)
rows_in = [
{
"test_value_3": "A ->\nLINE = A",
"test_value_2": "Sleepy",
"test_value_1": 1,
},
{
"test_value_3": "B ->\nLINE = B",
"test_value_2": "Dopey",
"test_value_1": 2,
},
{
"test_value_3": "C ->\nLINE = C",
"test_value_2": "Bashful",
"test_value_1": 3,
},
{
"test_value_3": "D ->\nLINE = D",
"test_value_2": "Grumpy",
"test_value_1": 4,
},
]
rows_out = [row for row in cif_wrapper._test_category_2]
self.assertEqual(rows_out, rows_in,
"Row iteration failed or gave inconsistent results")
def test_init_2_level_dictionary(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_1"],
preserve_token_order=True)
self.assertIsInstance(
cif_wrapper,
CIFWrapper,
"Failed to instantiate CIFWrapper from 2-level mmCIF-like dictionary",
)
assert_equal(cif_wrapper.data_id, "", "datablock ID should be ''")
def test_listContents(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_1"],
preserve_token_order=True)
items = cif_wrapper._test_category_1.contents()
items.sort()
self.assertEqual(
items,
["test_value_1", "test_value_2", "test_value_3"],
"Item list for the category is incorrect",
)
def test_init_2_level_dictionary_new_id(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_2"],
"NEW_ID",
preserve_token_order=True)
self.assertIsInstance(
cif_wrapper,
CIFWrapper,
"Failed to instantiate CIFWrapper from 2-level mmCIF-like dictionary",
)
assert_equal(cif_wrapper.data_id, "NEW_ID",
"'NEW_ID' not set correctly as datablock ID")
def test_search(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_1"],
preserve_token_order=True)
check_row = {
"test_value_3": "C ->\nLINE = C",
"test_value_2": "Bashful",
"test_value_1": 3,
}
result = cif_wrapper._test_category_2.search("test_value_1", 3)
self.assertEqual(
result[2], check_row,
"Category search failed or gave inconsistent results")
def test_unwrap(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_2"],
"NEW_ID",
preserve_token_order=True)
assert_equal(
cif_wrapper.unwrap(),
{"NEW_ID": {
"_test_category_1": {
"test_value_1": [1, 2, 3, 4]
}
}},
"CIFWrapper to dictionary conversion failed",
)
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_2"],
preserve_token_order=True)
for unique_id, data in list(cif_wrapper.unwrap().items()):
self.assertNotEqual(unique_id, "",
"No unique datablock id was assigned")
assert_equal(
data,
{"_test_category_1": {
"test_value_1": [1, 2, 3, 4]
}},
"CIFWrapper to dictionary conversion failed",
)
def test_wrapper_getattr(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_2"],
"NEW_ID",
preserve_token_order=True)
self.assertIsNone(
cif_wrapper._bogus,
"__getattr__ not returning None for uninitialized attribute",
)
self.assertIsInstance(
cif_wrapper._test_category_1,
CIFWrapperTable,
"__getattr__ not returning CIFWrapperTable",
)
def test_delitem(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_1"],
preserve_token_order=True)
del cif_wrapper._test_category_2["test_value_2"]
self.assertFalse(
"test_value_2" in cif_wrapper._test_category_2,
"Failed to delete item from category",
)
columns = list([k for k in cif_wrapper._test_category_2][0].keys())
columns.sort()
self.assertEqual(
columns,
["test_value_1", "test_value_3"],
"item deletion failed or gave inconsistent results",
)
def test_init_3_level_dictionary(self):
""" preserve_token_order=True ensures deterministic unittests otherwise CIF data is random access """
cif_wrapper = CIFWrapper(self.raw_dictionary,
preserve_token_order=True)
self.assertIsInstance(
cif_wrapper,
CIFWrapper,
"Failed to instantiate CIFWrapper from 3-level mmCIF-like dictionary",
)
sys.stdout.write(cif_wrapper.data_id)
self.assertEqual(
cif_wrapper.data_id,
"TEST_BLOCK_1",
"'TEST_BLOCK_1' not set correctly as datablock ID",
)
def test_wrapperTable_getattr(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_2"],
"NEW_ID",
preserve_token_order=True)
# # dot notation access
cif_wrapper._test_category_1.test_value_3 = "Bundy"
self.assertEqual(
cif_wrapper._test_category_1["test_value_3"],
[
"Bundy",
],
"Dot-notation attribute setting failed to overwrite or gave inconsistent results",
)
self.assertEqual(
cif_wrapper._test_category_1.test_value_3,
[
"Bundy",
],
"Dot-notation attribute setting failed to overwrite or gave inconsistent results",
)
def test_wrapper_delItem(self):
cif_wrapper = CIFWrapper(self.raw_dictionary["TEST_BLOCK_2"],
"NEW_ID",
preserve_token_order=True)
self.assertIsNone(
cif_wrapper._bogus,
"__getattr__ not returning None for uninitialized attribute",
)
self.assertIsInstance(
cif_wrapper._test_category_1,
CIFWrapperTable,
"__getattr__ not returning CIFWrapperTable",
)
del cif_wrapper["_test_category_1"]
self.assertIsNone(cif_wrapper._test_category_1,
"__delitem__ failed (dot notation)")
self.assertIsNone(cif_wrapper["_test_category_1"],
"__delitem__ failed (dict notation)")
self.assertIsNone(
cif_wrapper._DATA.get("_test_category_1", None),
"__delitem__ failed (direct access)",
)