def testValidateExchangeObject(self):
"""Test fetch exchange objects"""
try:
#
sD = self.__mU.doImport(self.__jsonSchemaPath, "json")
#
fobj = UniProtUtils(saveText=False)
idList = self.__unpIdList1
retD, _ = fobj.fetchList(idList,
usePrimary=self.__usePrimary,
retryAltApi=self.__retryAltApi)
#
exObjD = fobj.reformat(retD, formatType="exchange")
if exObjD and self.__export:
for rId in exObjD:
self.__mU.doExport(os.path.join(self.__workPath,
rId + "-exchange.json"),
exObjD[rId],
fmt="json",
indent=3)
#
Draft4Validator.check_schema(sD)
#
valInfo = Draft4Validator(sD, format_checker=FormatChecker())
eCount = 0
for rId, dD in exObjD.items():
logger.debug("Uid %s", rId)
try:
cCount = 0
for error in sorted(valInfo.iter_errors(dD), key=str):
logger.info("%s path %s error: %s", rId, error.path,
error.message)
logger.debug(">>> failing object is %r", dD)
eCount += 1
cCount += 1
#
logger.debug("%s errors count %d", rId, cCount)
except Exception as e:
logger.exception("Validator fails %s", str(e))
#
logger.debug("Total errors count %d", eCount)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testExchangeObject(self):
"""Test fetch exchange objects"""
try:
#
fobj = UniProtUtils(saveText=False)
idList = self.__unpIdList1
retD, _ = fobj.fetchList(idList,
usePrimary=self.__usePrimary,
retryAltApi=self.__retryAltApi)
exObjD = fobj.reformat(retD, formatType="exchange")
if exObjD and self.__export:
for rId in exObjD:
self.__mU.doExport(os.path.join(self.__workPath,
rId + "-exchange.json"),
exObjD[rId],
fmt="json",
indent=3)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def getDocuments(self, formatType="exchange"):
fobj = UniProtUtils(saveText=False)
exObjD = fobj.reformat(self.__refD, formatType=formatType)
return list(exObjD.values())