def testDefaults(self):
"""Test the default case of using only dictionary content."""
try:
dictApi = self.__dP.getApiByLocators(dictLocators=[self.__pathPdbxDictionaryFile])
ok = dictApi.testCache()
self.assertTrue(ok)
sdi = ContentDefinition(dictApi)
nS = sdi.getSchemaNames()
logger.debug("schema name length %d", len(nS))
self.assertGreaterEqual(len(nS), 600)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testHelper(self):
"""Test the dictionary content supplemented by helper function"""
try:
cH = ContentDefinitionHelper(cfgOb=self.__cfgOb)
dictApi = self.__dP.getApiByLocators(dictLocators=[self.__pathPdbxDictionaryFile])
sdi = ContentDefinition(dictApi, databaseName="chem_comp", contentDefHelper=cH)
catNameL = sdi.getCategories()
cfD = {}
afD = {}
for catName in catNameL:
cfD[catName] = sdi.getCategoryFeatures(catName)
afD[catName] = sdi.getAttributeFeatures(catName)
#
logger.debug("Dictionary category name length %d", len(catNameL))
self.assertGreaterEqual(len(catNameL), 600)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __getContentFeatures(self):
"""Get category and attribute features"""
try:
cH = ContentDefinitionHelper(cfgOb=self.__cfgOb)
dictApi = self.__dP.getApiByLocators(dictLocators=[
self.__pathPdbxDictionaryFile, self.__pathRcsbDictionaryFile
])
# logger.info("units = %r", dictApi.getUnits("pdbx_nmr_spectrometer", "manufacturer"))
sdi = ContentDefinition(dictApi,
databaseName="pdbx_core",
contentDefHelper=cH)
catNameL = sdi.getCategories()
cfD = {}
afD = {}
for catName in catNameL:
cfD[catName] = sdi.getCategoryFeatures(catName)
afD[catName] = sdi.getAttributeFeatures(catName)
#
return cfD, afD
except Exception as e:
logger.exception("Failing with %s", str(e))
return None, None