def main(argv=None):
"""
This is the main function that is called when you run 'intialize.py'.
Here, you will load the configuration settings specified in the toml configuration
file, initiate the class dataInterface, and set up some directories and other
important things through 'initialize()'
"""
# define the parameters that will be recognized later on to set up fileIterface
argParser = argparse.ArgumentParser()
argParser.add_argument('--config',
'-c',
default=defaultConfig,
type=str,
help='experiment config file (.json or .toml)')
argParser.add_argument('--runs',
'-r',
default='',
type=str,
help='Comma separated list of run numbers')
argParser.add_argument('--scans',
'-s',
default='',
type=str,
help='Comma separated list of scan number')
args = argParser.parse_args(argv)
print('Initializing directories and configurations')
# establish the RPC connection to the projectInterface
clientInterface = ClientInterface()
dataInterface = clientInterface.dataInterface
args.dataRemote = clientInterface.isDataRemote()
# load the experiment configuration file
cfg = utils.loadConfigFile(args.config)
cfg = initialize(cfg, args)
# build subject folders on server
if args.dataRemote:
print('Files Remote Case')
buildSubjectFoldersOnServer(cfg)
# next, transfer transformation files from local --> server for online processing
uploadFolderToCloud(dataInterface, cfg.local.wf_dir, cfg.server.wf_dir)
# upload ROI folder to cloud server - we would need to do this if we were using
# a standard mask, but we're not in this case
#uploadFolderToCloud(dataInterface, cfg.local.maskDir, cfg.server.maskDir)
# upload all transformed masks to the cloud
uploadFilesFromList(dataInterface, cfg.local_MASK_transformed,
cfg.subject_reg_dir)
print('Initialization Complete!')
return 0
def test_runWithInitWatch(self):
print("\nSampleProject::test_runWithDataRemote")
TestSampleProject.serversForTests.stopServers()
TestSampleProject.serversForTests.startServers(
allowedDirs=allowedDirs,
allowedFileTypes=allowedFileTypes,
dataRemote=True)
client = ClientInterface()
assert client.isDataRemote() == True
argv = ['--useInitWatch', '--noVerbose']
ret = sample.main(argv)
assert ret == 0
def test_runWithDataRemote(self):
print("\nOpenNeuroClient::test_runWithDataRemote")
TestOpenNeuroClient.serversForTests.stopServers()
TestOpenNeuroClient.serversForTests.startServers(
allowedDirs=allowedDirs,
allowedFileTypes=allowedFileTypes,
dataRemote=True,
projectArgs=openNeuroArgs)
client = ClientInterface()
assert client.isDataRemote() == True
argv = ['--archive']
ret = openNeuroClient.main(argv)
assert ret == 0
def test_rpyclocalDataInterface(self, dicomTestFilename, bigTestFile):
# Use a remote (RPC) client to the dataInterface
TestDataInterface.serversForTests.stopServers()
TestDataInterface.serversForTests.startServers(allowedDirs=allowedDirs,
allowedFileTypes=allowedFileTypes,
dataRemote=False,
subjectRemote=False)
clientInterface = ClientInterface()
dataInterface = clientInterface.dataInterface
assert clientInterface.isDataRemote() == False
assert dataInterface.isRemote == False
runDataInterfaceMethodTests(dataInterface, dicomTestFilename)
runReadWriteFileTest(dataInterface, bigTestFile)
return