def testDDLApi(self):
"""Test case - DDL API linkage counts"""
try:
myIo = IoAdapter(raiseExceptions=True)
containerList = myIo.readFile(
inputFilePath=self.__pathDdlGeneratedDictionary)
dApi = DictionaryApi(containerList=containerList,
consolidate=True,
expandItemLinked=True)
cL = dApi.getCategoryList()
logger.info("Category length %r", len(cL))
self.assertGreaterEqual(len(cL), 63)
cL = dApi.getFullChildList("category", "id")
logger.info("Children of category.id (%d)", len(cL))
self.assertGreaterEqual(len(cL), 11)
#
cL = dApi.getFullDescendentList("category", "id")
logger.info("Descendents of category.id (%d)", len(cL))
self.assertGreaterEqual(len(cL), 13)
#
cL = dApi.getFullChildList("item", "name")
logger.info("Children of item.name (%d)", len(cL))
self.assertGreaterEqual(len(cL), 36)
cL = dApi.getFullDescendentList("item", "name")
logger.info("Descendents of item.name (%d)", len(cL))
self.assertGreaterEqual(len(cL), 38)
#
val = dApi.getDictionaryVersion()
self.assertEqual(val, "2.2.2")
val = dApi.getDictionaryTitle()
self.assertEqual(val, "mmcif_ddl.dic")
val = dApi.getDictionaryUpdate(order="reverse")
self.assertEqual(val, "2020-06-05")
val = dApi.getDictionaryRevisionCount()
self.assertGreaterEqual(val, 78)
valL = dApi.getDictionaryHistory(order="reverse")
self.assertGreaterEqual(len(valL), 78)
#
val = dApi.getDictionaryComponentCount()
self.assertGreaterEqual(val, 6)
#
valL = dApi.getDictionaryComponentDetails()
self.assertGreaterEqual(len(valL), 6)
valL = dApi.getDictionaryComponents()
self.assertGreaterEqual(len(valL), 6)
for dictionaryComponentId in dApi.getDictionaryComponents():
valL = dApi.getDictionaryComponentHistory(
dictionaryComponentId, order="reverse")
self.assertGreaterEqual(len(valL), 2)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testConsolidateDictionary(self):
"""Test case - dump methods for dictionary metadata"""
try:
myIo = IoAdapter(raiseExceptions=True)
self.__containerList = myIo.readFile(inputFilePath=self.__pathPdbxDictionary)
dApi = DictionaryApi(containerList=self.__containerList, consolidate=True, expandItemLinked=False, verbose=self.__verbose)
for itemName in [
"_entity.id",
"_entity_poly_seq.num",
"_atom_site.label_asym_id",
"_struct_asym.id",
"_chem_comp.id",
"chem_comp_atom.comp_id",
"chem_comp_bond.comp_id",
]:
categoryName = CifName.categoryPart(itemName)
attributeName = CifName.attributePart(itemName)
logger.debug("Full parent list for %s : %s\n", itemName, dApi.getFullParentList(categoryName, attributeName))
logger.debug("Full child list for %s : %s\n", itemName, dApi.getFullChildList(categoryName, attributeName))
logger.debug("Ultimate parent for %s : %s\n", itemName, dApi.getUltimateParent(categoryName, attributeName))
logger.debug("Type code for %s : %s\n", itemName, dApi.getTypeCode(categoryName, attributeName))
self.assertIsNotNone(dApi.getTypeCode(categoryName, attributeName))
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def test_consolidate_dictionary(self, api_paths):
myIo = IoAdapter(raiseExceptions=True)
containerList = myIo.readFile(
inputFilePath=str(api_paths['pathPdbxDictionary']))
dApi = DictionaryApi(containerList=containerList, consolidate=True)
for itemName in [
'_entity.id', '_entity_poly_seq.num',
'_atom_site.label_asym_id', '_struct_asym.id', '_chem_comp.id',
'chem_comp_atom.comp_id', 'chem_comp_bond.comp_id'
]:
categoryName = CifName.categoryPart(itemName)
attributeName = CifName.attributePart(itemName)
print("Full parent list for %s : %s\n" %
(itemName, dApi.getFullParentList(categoryName,
attributeName)))
print(
"Full child list for %s : %s\n" %
(itemName, dApi.getFullChildList(categoryName, attributeName)))
print("Ultimate parent for %s : %s\n" %
(itemName, dApi.getUltimateParent(categoryName,
attributeName)))
print("Type code for %s : %s\n" %
(itemName, dApi.getTypeCode(categoryName, attributeName)))
assert dApi.getTypeCode(categoryName, attributeName) is not None