def testLoadFiles(self):
"""Test case - create batch load files for all chemical component definition data files -"""
self.__lfh.write("\nStarting ChemCompLoaderTests testLoadFiles\n")
startTime = time.time()
try:
ccsd = ChemCompSchemaDef()
sml = SchemaDefLoader(schemaDefObj=ccsd,
ioObj=self.__ioObj,
dbCon=None,
workPath=".",
cleanUp=False,
warnings="default",
verbose=self.__verbose,
log=self.__lfh)
pathList = self.__makeComponentPathList()
containerNameList, tList = sml.makeLoadFiles(pathList,
append=False)
for tId, fn in tList:
self.__lfh.write("\nCreated table %s load file %s\n" %
(tId, fn))
#
endTime1 = time.time()
self.__lfh.write("\nBatch files created in %.2f seconds\n" %
(endTime1 - startTime))
self.open(dbName=ccsd.getDatabaseName())
sdl = SchemaDefLoader(schemaDefObj=ccsd,
ioObj=self.__ioObj,
dbCon=self.__dbCon,
workPath=".",
cleanUp=False,
warnings="default",
verbose=self.__verbose,
log=self.__lfh)
sdl.loadBatchFiles(loadList=tList,
containerNameList=containerNameList,
deleteOpt="all")
self.close()
endTime2 = time.time()
self.__lfh.write("\nLoad completed in %.2f seconds\n" %
(endTime2 - endTime1))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
endTime = time.time()
self.__lfh.write(
"\nCompleted ChemCompLoaderTests testLoadFiles at %s (%.2f seconds)\n"
% (time.strftime("%Y %m %d %H:%M:%S",
time.localtime()), endTime - startTime))
def testConnect(self):
"""Test case - for creating a test connection"""
self.__lfh.write("\nStarting ChemCompLoaderTests testConnect\n")
startTime = time.time()
try:
ccsd = ChemCompSchemaDef()
self.open(dbName=ccsd.getDatabaseName())
self.close()
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
endTime = time.time()
self.__lfh.write(
"\nCompleted ChemCompLoaderTests testConnect at %s (%.2f seconds)\n"
% (time.strftime("%Y %m %d %H:%M:%S",
time.localtime()), endTime - startTime))
def loadBatchFilesMulti(self, dataList, procName, optionsD, workingDir): # pylint: disable=unused-argument
ccsd = ChemCompSchemaDef()
self.open(dbName=ccsd.getDatabaseName())
sdl = SchemaDefLoader(schemaDefObj=ccsd,
ioObj=self.__ioObj,
dbCon=self.__dbCon,
workPath=".",
cleanUp=False,
warnings="default",
verbose=self.__verbose,
log=self.__lfh)
#
sdl.loadBatchFiles(loadList=dataList,
containerNameList=None,
deleteOpt=None)
self.close()
return dataList, dataList, []
def testSchemaCreate(self):
"""Create table schema for BIRD, chemical component, and PDBx data."""
sd = BirdSchemaDef()
self.__schemaCreate(schemaDefObj=sd)
#
sd = ChemCompSchemaDef()
self.__schemaCreate(schemaDefObj=sd)
#
sd = PdbxSchemaDef()
self.__schemaCreate(schemaDefObj=sd)
def testLoadChemCompExamples(self):
startTime = time.time()
self.__lfh.write("\nStarting SchemaDefLoaderDbTest testLoadChemCompExamples at %s\n" % time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
try:
sd = ChemCompSchemaDef()
self.__schemaCreate(schemaDefObj=sd)
inputPathList = [os.path.join(self.__ccPath, fn) for fn in self.__ccFileList]
sdl = SchemaDefLoader(schemaDefObj=sd, ioObj=self.__ioObj, dbCon=self.__dbCon, workPath=".", cleanUp=False, warnings="default", verbose=self.__verbose, log=self.__lfh)
sdl.load(inputPathList=inputPathList, loadType="batch-insert", deleteOpt="selected")
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
endTime = time.time()
self.__lfh.write(
"\nCompleted SchemaDefLoaderDbTest testLoadChemCompExamples at %s (%.2f seconds)\n" % (time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - startTime)
)
def testLoadFilesMulti(self):
"""Test case - create batch load files for all chemical component definition data files - (multiproc test)"""
self.__lfh.write("\nStarting ChemCompLoaderTests testLoadFilesMulti\n")
startTime = time.time()
numProc = 8
try:
dataS = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
dataList = [a for a in dataS]
mpu = MultiProcUtil(verbose=True)
mpu.set(workerObj=self, workerMethod="makeComponentPathListMulti")
_ok, _failList, retLists, _diagList = mpu.runMulti(
dataList=dataList, numProc=numProc, numResults=1)
pathList = retLists[0]
endTime0 = time.time()
self.__lfh.write("\nPath list length %d in %.2f seconds\n" %
(len(pathList), endTime0 - startTime))
# self.__lfh.write("\nPath list %r\n" % pathList[:20])
# pathList=self.__makeComponentPathList()
ccsd = ChemCompSchemaDef()
sml = SchemaDefLoader(schemaDefObj=ccsd,
ioObj=self.__ioObj,
dbCon=None,
workPath=".",
cleanUp=False,
warnings="default",
verbose=self.__verbose,
log=self.__lfh)
#
mpu = MultiProcUtil(verbose=True)
mpu.set(workerObj=sml, workerMethod="makeLoadFilesMulti")
_ok, _failList, retLists, _diagList = mpu.runMulti(
dataList=pathList, numProc=numProc, numResults=2)
#
containerNameList = retLists[0]
tList = retLists[1]
for tId, fn in tList:
self.__lfh.write("\nCreated table %s load file %s\n" %
(tId, fn))
#
endTime1 = time.time()
self.__lfh.write("\nBatch files created in %.2f seconds\n" %
(endTime1 - endTime0))
self.open(dbName=ccsd.getDatabaseName())
sdl = SchemaDefLoader(schemaDefObj=ccsd,
ioObj=self.__ioObj,
dbCon=self.__dbCon,
workPath=".",
cleanUp=False,
warnings="default",
verbose=self.__verbose,
log=self.__lfh)
#
for tId, fn in tList:
sdl.delete(tId,
containerNameList=containerNameList,
deleteOpt="all")
self.close()
#
mpu = MultiProcUtil(verbose=True)
mpu.set(workerObj=self, workerMethod="loadBatchFilesMulti")
_ok, _failList, retLists, _diagList = mpu.runMulti(dataList=tList,
numProc=numProc,
numResults=1)
endTime2 = time.time()
self.__lfh.write("\nLoad completed in %.2f seconds\n" %
(endTime2 - endTime1))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
endTime = time.time()
self.__lfh.write(
"\nCompleted ChemCompLoaderTests testLoadFilesMulti at %s (%.2f seconds)\n"
% (time.strftime("%Y %m %d %H:%M:%S",
time.localtime()), endTime - startTime))
def testChemCompSchema(self):
"""Test case - chemCompSchema test"""
sd = ChemCompSchemaDef()
self.__dotest(sd)