def test_write_mmCIF_dictionary(self):
unit_test_file = "io_testcase_5.cif"
cfr = CifFileReader(input="dictionary", preserve_order=True)
cif_file = cfr.read(self.TEST_DIC_FILE, output="cif_file")
cfw = CifFileWriter(
file_path=os.path.join(self.FILE_ROOT, unit_test_file))
cfw.write(cif_file)
test_file = cfr.read(os.path.join(self.FILE_ROOT, unit_test_file),
output="cif_file")
test_value = (test_file.getDataBlock("TEST").getSaveFrame(
"some_interesting_category").getCategory("category").getItem(
"mandatory_code").value)
self.assertEqual(test_value, "no",
"mmCIF dictionary file was not written correctly")
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_ignoreCategories(self):
cfr = CifFileReader(input="data", preserve_order=True)
cif_file = cfr.read(self.TEST_CIF_FILE,
output="cif_file",
ignore=["_test_loop_2", "_valid_CIF"])
self.assertIsInstance(
cif_file, CifFile,
"Failed to create CifFile using algorithmic parser")
self.__assertListEqual(
cif_file.getDataBlockIds(),
["TEST_CIF", "BLOCK_2"],
"DataBlocks not read correctly",
)
categories_A = cif_file.getDataBlock("TEST_CIF").getCategoryIds()
categories_A.sort()
self.assertEqual(
categories_A,
["test_keyword", "test_loop_1", "valid_cif"],
"Categories were not ignored correctly",
)
categories_B = cif_file.getDataBlock("BLOCK_2").getCategoryIds()
categories_B.sort()
self.assertEqual(
categories_B,
["equivalence_test", "extra"],
"Categories were not ignored correctly",
)
def test_inData_outDict(self):
cfr = CifFileReader(input="data", preserve_order=True)
cif_dictionary = cfr.read(self.TEST_CIF_FILE, output="cif_dictionary")
self.assertIsInstance(
cif_dictionary, dict,
"Failed to create python dictionary from cif file")
self.__assertListEqual(
list(cif_dictionary.keys()),
["TEST_CIF", "BLOCK_2"],
"DataBlocks not read correctly",
)
self.assertEqual(
cif_dictionary["BLOCK_2"]["_extra"]["strange_value"],
"Three#Blind#Mice",
"All levels of CIF file not translated to dictionary correctly",
)
def test_inDict_outFile(self):
cfr = CifFileReader(input="dictionary", preserve_order=True)
cif_file = cfr.read(self.TEST_CIF_FILE, output="cif_file")
self.assertIsInstance(cif_file, CifFile,
"Failed to create CifFile using lexical parser")
self.__assertListEqual(
cif_file.getDataBlockIds(),
["TEST_CIF", "BLOCK_2"],
"DataBlocks not read correctly",
)
self.assertEqual(
cif_file.getDataBlock("BLOCK_2").getCategory("_extra").getItem(
"strange_value").value,
"Three#Blind#Mice",
"All levels of CIF file not translated to dictionary correctly",
)
def test_inData_outWrap(self):
cfr = CifFileReader(input="data", preserve_order=True)
cif_wrapper = cfr.read(self.TEST_CIF_FILE, output="cif_wrapper")
self.assertIsInstance(
cif_wrapper["TEST_CIF"],
CIFWrapper,
"Failed to create CIFWrapper using lexical parser",
)
self.__assertListEqual(
list(cif_wrapper.keys()),
["TEST_CIF", "BLOCK_2"],
"DataBlocks not read correctly",
)
self.assertEqual(
cif_wrapper["BLOCK_2"]._extra.strange_value[0],
"Three#Blind#Mice",
"All levels of CIF file not translated to dictionary correctly",
)
def test_write_raw_dictionary_without_block_id(self):
unit_test_file = "io_testcase_4.cif"
# Test raw dictionary (WITHOUT datablock id)
cfw = CifFileWriter(
file_path=os.path.join(self.FILE_ROOT, unit_test_file))
cfw.write(self.raw_dictionary["TEST_BLOCK_1"])
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, [unit_test_file],
"Datablock(s) were not written correctly")
self.assertEqual(
test_file[unit_test_file]._test_category_2.test_value_1,
["1", "2", "3", "4"],
"mmCIF data was not written correctly",
)
def test_write_ciffile_after_ciffile_dictionary_import(self):
# Test write CifFile initialized by dictionary
unit_test_file = "io_testcase_1.cif"
cfw = CifFileWriter()
cif_file = CifFile(os.path.join(self.FILE_ROOT, unit_test_file))
cif_file.import_mmcif_data_map(self.raw_dictionary)
cfw.write(cif_file)
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",
)