def setup_class(cls):
utils.installLoggers(logging.DEBUG, logging.DEBUG, filename='logs/tests.log')
# Start a projectInterface thread running
params = StructDict({'fmriPyScript': 'projects/sample/sample.py',
'filesremote': True,
'port': 8921,
})
cfg = StructDict({'sessionId': "test",
'subjectName': "test_sample",
'subjectNum': 1,
'subjectDay': 1,
'sessionNum': 1})
cls.webThread = threading.Thread(name='webThread', target=Web.start, args=(params, cfg, True))
cls.webThread.setDaemon(True)
cls.webThread.start()
time.sleep(.1)
# Start a fileWatcher thread running
cls.fileThread = threading.Thread(
name='fileThread',
target=WsFileWatcher.runFileWatcher,
args=('localhost:8921',),
kwargs={
'retryInterval': 0.1,
'allowedDirs': ['/tmp', testDir, samplePath],
'allowedTypes': fileTypeList,
'username': '******',
'password': '******',
'testMode': True
}
)
cls.fileThread.setDaemon(True)
cls.fileThread.start()
time.sleep(1)
"-s <server>", "-u <username>", "-p <password>", "--test",
"-i <retry-connection-interval>"
webSocketChannelName: The websocket url extension used to connect and communicate
to the remote projectServer, 'wsData' will connect to 'ws://server:port/wsData'
"""
self.exampleInterface = ExampleInterface(dataRemote=False)
self.wsRemoteService = WsRemoteService(args, webSocketChannelName)
self.wsRemoteService.addHandlerClass(ExampleInterface,
self.exampleInterface)
def runDetached(self):
"""Starts the receiver in its own thread."""
self.recvThread = threading.Thread(
name='recvThread', target=self.wsRemoteService.runForever)
self.recvThread.setDaemon(True)
self.recvThread.start()
if __name__ == "__main__":
installLoggers(logging.INFO,
logging.INFO,
filename='logs/ExampleService.log')
# parse connection args
# These include: "-s <server>", "-u <username>", "-p <password>", "--test",
# "-i <retry-connection-interval>"
connectionArgs = parseConnectionArgs()
exampleService = ExampleService(connectionArgs)
exampleService.wsRemoteService.runForever()
def readFileData(filename):
data = None
fileExtension = Path(filename).suffix
if fileExtension == '.dcm':
# Anonymize Dicom files
dicomImg = readDicomFromFile(filename)
dicomImg = anonymizeDicom(dicomImg)
data = writeDicomToBuffer(dicomImg)
else:
with open(filename, 'rb') as fp:
data = fp.read()
return data
if __name__ == "__main__":
installLoggers(logging.INFO, logging.INFO, filename='logs/fileWatcher.log')
# do arg parse for server to connect to
parser = argparse.ArgumentParser()
parser.add_argument('-s',
action="store",
dest="server",
default="localhost:8888",
help="Server Address with Port [server:port]")
parser.add_argument('-i',
action="store",
dest="interval",
type=int,
default=5,
help="Retry connection interval (seconds)")
parser.add_argument(
'-d',
currPath = os.path.dirname(os.path.realpath(__file__))
rootPath = os.path.dirname(os.path.dirname(currPath))
sys.path.append(rootPath)
from rtCommon.utils import loadConfigFile, installLoggers
from rtCommon.structDict import StructDict
from rtCommon.projectInterface import Web
# HERE: Set the path to the fMRI Python script to run here
scriptToRun = 'projects/sample/sample.py'
initScript = 'projects/sample/initialize.py'
finalizeScript = 'projects/sample/finalize.py'
defaultConfig = os.path.join(currPath, 'conf/sample.toml')
if __name__ == "__main__":
installLoggers(logging.INFO,
logging.INFO,
filename=os.path.join(currPath, 'logs/sample.log'))
argParser = argparse.ArgumentParser()
argParser.add_argument('--filesremote',
'-x',
default=False,
action='store_true',
help='dicom files retrieved from remote server')
argParser.add_argument('--config',
'-c',
default=defaultConfig,
type=str,
help='experiment file (.json or .toml)')
argParser.add_argument(
'--test',
'-t',
action='store_true',
help='start webServer in test mode, unsecure')
args = argParser.parse_args()
if args.projectName is None:
raise InvocationError('Must specify project name using -p parameter')
if args.projectDir is None:
args.projectDir = os.path.join(rootPath, 'projects', args.projectName)
if args.config is None:
args.config = os.path.join(args.projectDir,
f'conf/{args.projectName}.toml')
if args.mainScript is None:
args.mainScript = os.path.join(args.projectDir,
f'{args.projectName}.py')
if args.initScript is None:
args.initScript = os.path.join(args.projectDir, 'initialize.py')
if args.finalizeScript is None:
args.finalizeScript = os.path.join(args.projectDir, 'finalize.py')
if args.remote is True:
args.dataRemote = True
args.subjectRemote = True
installLoggers(logging.INFO,
logging.INFO,
filename=os.path.join(currPath,
f'logs/{args.projectName}.log'))
# start the projectServer
projectServer = ProjectServer(args)
projectServer.start()
to the remote projectServer, e.g. 'wsData' would connect to 'ws://server:port/wsData'
"""
self.bidsInterface = BidsInterface(dataRemote=False)
self.wsRemoteService = WsRemoteService(args, webSocketChannelName)
self.wsRemoteService.addHandlerClass(BidsInterface, self.bidsInterface)
def runDetached(self):
"""Starts the receiver in it's own thread."""
self.recvThread = threading.Thread(
name='recvThread', target=self.wsRemoteService.runForever)
self.recvThread.setDaemon(True)
self.recvThread.start()
if __name__ == "__main__":
installLoggers(logging.INFO,
logging.INFO,
filename='logs/OpenNeuroService.log')
# parse connection args
connectionArgs = parseConnectionArgs()
try:
openNeuroService = OpenNeuroService(connectionArgs)
# Use this command to run the service and not return control
openNeuroService.wsRemoteService.runForever()
# Alternately use this command to start the service in a thread and
# return control to main.
# openNeuroService.runDetached()
except Exception as err:
print(f'Exception: {err}')
"""
self.dataInterface = DataInterface(
dataRemote=False,
allowedDirs=args.allowedDirs,
allowedFileTypes=args.allowedFileTypes)
self.bidsInterface = BidsInterface(dataRemote=False,
allowedDirs=args.allowedDirs)
self.wsRemoteService = WsRemoteService(args, webSocketChannelName)
self.wsRemoteService.addHandlerClass(DataInterface, self.dataInterface)
self.wsRemoteService.addHandlerClass(BidsInterface, self.bidsInterface)
if __name__ == "__main__":
installLoggers(logging.INFO,
logging.INFO,
filename='logs/CRDataServer.log')
# parse connection args
# These include: "-s <server>", "-u <username>", "-p <password>", "--test",
# "-i <retry-connection-interval>"
connectionArgs = parseConnectionArgs()
# parse remaining args
parser = argparse.ArgumentParser()
parser.add_argument(
'-d',
action="store",
dest="allowedDirs",
default=defaultAllowedDirs,
help="Allowed directories to server files from - comma separated list")
self.subjectInterface = SubjectInterface(subjectRemote=False)
self.wsRemoteService = WsRemoteService(args, webSocketChannelName)
self.wsRemoteService.addHandlerClass(SubjectInterface,
self.subjectInterface)
def runDetached(self):
"""Starts the receiver in it's own thread."""
self.recvThread = threading.Thread(
name='recvThread', target=self.wsRemoteService.runForever)
self.recvThread.setDaemon(True)
self.recvThread.start()
if __name__ == "__main__":
installLoggers(logging.INFO,
logging.INFO,
filename='logs/SubjectService.log')
# parse connection args
# These include: "-s <server>", "-u <username>", "-p <password>", "--test",
# "-i <retry-connection-interval>"
connectionArgs = parseConnectionArgs()
subjectService = SubjectService(connectionArgs)
subjectService.runDetached()
while True:
feedbackMsg = subjectService.subjectInterface.msgQueue.get(
block=True, timeout=None)
print("Dequeue run: {}, tr: {}, value: {}, timestamp: {}".format(
feedbackMsg.get('runId'), feedbackMsg.get('trId'),
import argparse
import logging
# import project modules
# Add base project path (two directories up)
currPath = os.path.dirname(os.path.realpath(__file__))
rootPath = os.path.dirname(os.path.dirname(currPath))
sys.path.append(rootPath)
from rtCommon.utils import loadConfigFile, installLoggers
from rtCommon.structDict import StructDict
from rtCommon.projectInterface import Web
defaultConfig = os.path.join(currPath, 'conf/faceMatching_organized.toml')
if __name__ == "__main__":
installLoggers(logging.INFO,
logging.INFO,
filename=os.path.join(currPath, 'logs/webServer.log'))
argParser = argparse.ArgumentParser()
argParser.add_argument('--filesremote',
'-x',
default=False,
action='store_true',
help='dicom files retrieved from remote server')
argParser.add_argument('--config',
'-c',
default=defaultConfig,
type=str,
help='experiment file (.json or .toml)')
args = argParser.parse_args()
# HERE: Set the path to the fMRI Python script to run here