def testExtractEntities(self):
"""Test case - extract entities"""
try:
obEx = ObjectExtractor(
self.__cfgOb,
databaseName="pdbx_core",
collectionName="pdbx_core_polymer_entity",
cacheFilePath=os.path.join(self.__workPath,
"entity-data-test-cache.json"),
useCache=False,
keyAttribute="entity",
uniqueAttributes=["rcsb_id"],
cacheKwargs=self.__testEntryCacheKwargs,
objectLimit=self.__objectLimitTest,
)
eCount = obEx.getCount()
logger.info("Entity count is %d", eCount)
self.assertGreaterEqual(eCount, self.__objectLimitTest)
objD = obEx.getObjects()
for _, obj in objD.items():
obEx.genPathList(obj, path=None)
#
pL = obEx.getPathList(filterList=False)
logger.debug("Path list (unfiltered) %r", pL)
#
pL = obEx.getPathList()
logger.debug("Path list %r", pL)
obEx.setPathList(pL)
if self.__verbose:
for ky, obj in objD.items():
obEx.genValueList(obj, path=None)
tD = obEx.getValues()
logger.info("Index object %r %s", ky,
pprint.pformat(tD, indent=3, width=120))
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()