def getDataMsgResponse(callId, timeout=None):
Web.callbackLock.acquire()
try:
callbackStruct = Web.dataCallbacks.get(callId, None)
if callbackStruct is None:
raise StateError('sendDataMsgFromThread: no callbackStruct found for callId {}'.format(callId))
finally:
Web.callbackLock.release()
# wait for semaphore signal indicating a callback for this callId has occured
signaled = callbackStruct.semaphore.acquire(timeout=timeout)
if signaled is False:
raise TimeoutError("sendDataMessage: Data Request Timed Out({}) {}".
format(timeout, callbackStruct.msg))
Web.callbackLock.acquire()
try:
# Remove from front of list not back to stay in order
# Can test removing from back of list to make sure out-of-order works too
response = callbackStruct.responses.pop(0)
if 'data' in response:
status = response.get('status', -1)
numParts = response.get('numParts', 1)
complete = (callbackStruct.numResponses == numParts and len(callbackStruct.responses) == 0)
if complete or status != 200:
# End the multipart transfer
response['incomplete'] = False
Web.dataCallbacks.pop(callId, None)
else:
response['incomplete'] = True
except IndexError:
raise StateError('sendDataMessage: callbackStruct.response is None for command {}'.
format(callbackStruct.msg))
finally:
Web.callbackLock.release()
response['callId'] = callbackStruct.callId
return response
def dataCallback(client, message):
response = json.loads(message)
if 'cmd' not in response:
raise StateError('dataCallback: cmd field missing from response: {}'.format(response))
if 'status' not in response:
raise StateError('dataCallback: status field missing from response: {}'.format(response))
if 'callId' not in response:
raise StateError('dataCallback: callId field missing from response: {}'.format(response))
status = response.get('status', -1)
callId = response.get('callId', -1)
origCmd = response.get('cmd', 'NoCommand')
logging.log(DebugLevels.L6, "callback {}: {} {}".format(callId, origCmd, status))
# Thread Synchronized Section
Web.callbackLock.acquire()
try:
callbackStruct = Web.dataCallbacks.get(callId, None)
if callbackStruct is None:
logging.error('ProjectInterface: dataCallback callId {} not found, current callId {}'
.format(callId, Web.dataSequenceNum))
return
if callbackStruct.callId != callId:
# This should never happen
raise StateError('callId mismtach {} {}'.format(callbackStruct.callId, callId))
callbackStruct.responses.append(response)
callbackStruct.numResponses += 1
callbackStruct.semaphore.release()
except Exception as err:
logging.error('ProjectInterface: dataCallback error: {}'.format(err))
raise err
finally:
Web.callbackLock.release()
if time.time() > Web.cbPruneTime:
Web.cbPruneTime = time.time() + 60
Web.pruneCallbacks()
def uploadFiles(request):
if 'cmd' not in request or request['cmd'] != "uploadFiles":
raise StateError('uploadFiles: incorrect cmd request: {}'.format(request))
if Web.wsDataConn is None:
# A remote fileWatcher hasn't connected yet
errStr = 'Waiting for fileWatcher to attach, please try again momentarily'
Web.setUserError(errStr)
return
try:
srcFile = request['srcFile']
compress = request['compress']
except KeyError as err:
Web.setUserError("UploadFiles request missing a parameter: {}".format(err))
return
# get the list of file to upload
cmd = listFilesReqStruct(srcFile)
response = Web.sendDataMsgFromThread(cmd, timeout=10)
if response.get('status') != 200:
Web.setUserError("Error listing files {}: {}".
format(srcFile, response.get('error')))
return
fileList = response.get('fileList')
if type(fileList) is not list:
Web.setUserError("Invalid fileList reponse type {}: expecting list".
format(type(fileList)))
return
if len(fileList) == 0:
response = {'cmd': 'uploadProgress', 'file': 'No Matching Files'}
Web.sendUserMsgFromThread(json.dumps(response))
return
for file in fileList:
try:
cmd = getFileReqStruct(file, compress=compress)
data = handleDataRequest(cmd)
# write the returned data out to a file
filename = response.get('filename')
if filename is None:
if 'data' in response: del response['data']
raise StateError('sendDataRequestToFile: filename field not in response: {}'.format(response))
# prepend with common output path and write out file
# note: can't just use os.path.join() because if two or more elements
# have an aboslute path it discards the earlier elements
global CommonOutputDir
outputFilename = os.path.normpath(CommonOutputDir + filename)
dirName = os.path.dirname(outputFilename)
if not os.path.exists(dirName):
os.makedirs(dirName)
writeFile(outputFilename, data)
response['filename'] = outputFilename
except Exception as err:
Web.setUserError(
"Error uploading file {}: {}".format(file, str(err)))
return
response = {'cmd': 'uploadProgress', 'file': file}
Web.sendUserMsgFromThread(json.dumps(response))
response = {'cmd': 'uploadProgress', 'file': '------upload complete------'}
Web.sendUserMsgFromThread(json.dumps(response))
def callback(self, client, message):
"""Recieve a callback from the client and match it to the original request that was sent."""
response = json.loads(message)
if 'cmd' not in response:
raise StateError(
'dataCallback: cmd field missing from response: {}'.format(
response))
if 'status' not in response:
raise StateError(
'dataCallback: status field missing from response: {}'.format(
response))
if 'callId' not in response:
raise StateError(
'dataCallback: callId field missing from response: {}'.format(
response))
status = response.get('status', -1)
callId = response.get('callId', -1)
origCmd = response.get('cmd', 'NoCommand')
logging.log(DebugLevels.L6,
"callback {}: {} {}".format(callId, origCmd, status))
# numParts = response.get('numParts')
# partId = response.get('partId')
# print(f'callback {callId}: {origCmd} {status} numParts {numParts} partId {partId}')
# Thread Synchronized Section
self.callbackLock.acquire()
try:
callbackStruct = self.dataCallbacks.get(callId, None)
if callbackStruct is None:
# print(f'webServer: dataCallback callId {callId} not found, current callId {self.dataSequenceNum}')
logging.error(
'webServer: dataCallback callId {} not found, current callId {}'
.format(callId, self.dataSequenceNum))
return
if callbackStruct.callId != callId:
# This should never happen
raise StateError('callId mismtach {} {}'.format(
callbackStruct.callId, callId))
callbackStruct.responses.append(response)
callbackStruct.numResponses += 1
callbackStruct.semaphore.release()
except Exception as err:
logging.error('webServer: dataCallback error: {}'.format(err))
raise err
finally:
self.callbackLock.release()
if time.time() > self.cbPruneTime:
self.cbPruneTime = time.time() + 60
self.pruneCallbacks()
def sendDataMsgFromThreadAsync(msg):
if Web.wsDataConn is None:
raise StateError("ProjectInterface: FileServer not connected. Please run the fileServer.")
callId = msg.get('callId')
if not callId:
callbackStruct = StructDict()
callbackStruct.dataConn = Web.wsDataConn
callbackStruct.numResponses = 0
callbackStruct.responses = []
callbackStruct.semaphore = threading.Semaphore(value=0)
callbackStruct.timeStamp = time.time()
callbackStruct.msg = msg.copy()
if 'data' in callbackStruct.msg:
del callbackStruct.msg['data']
Web.callbackLock.acquire()
try:
Web.dataSequenceNum += 1
callId = Web.dataSequenceNum
callbackStruct.callId = callId
msg['callId'] = callId
Web.dataCallbacks[callId] = callbackStruct
finally:
Web.callbackLock.release()
Web.ioLoopInst.add_callback(Web.sendDataMessage, msg)
return callId
def watchFile(self, filename: str, timeout: int = 5) -> bytes:
"""Watches for a specific file to be created and returns the file data.
InitWatch() must be called first, before watching for specific files.
If filename includes the full path, the path must match that used in initWatch().
"""
data = None
if not self.initWatchSet:
raise StateError(
"DataInterface: watchFile() called without an initWatch()")
# check filename dir matches initWatch dir
fileDir, fileCheck = os.path.split(filename)
if fileDir not in ('', None):
if fileDir != self.watchDir:
raise RequestError(
"DataInterface: watchFile: filepath doesn't match "
f"watch directory: {fileDir}, {self.watchDir}")
self._checkAllowedDirs(fileDir)
self._checkAllowedFileTypes(fileCheck)
self.fileWatchLock.acquire()
try:
foundFilename = self.fileWatcher.waitForFile(
filename, timeout=timeout, timeCheckIncrement=0.2)
finally:
self.fileWatchLock.release()
if foundFilename is None:
raise TimeoutError("WatchFile: Timeout {}s: {}".format(
timeout, filename))
else:
with open(foundFilename, 'rb') as fp:
data = fp.read()
return data
def parseDicomVolume(dicomImg, sliceDim):
"""
The raw dicom file coming from the scanner will be a 2-dimensional picture
made of up multiple image slices that are tiled together. This function
separates the image slices to form a single volume.
Used externally.
"""
sliceWidth = sliceDim
sliceHeight = sliceDim
image = dicomImg.pixel_array
dicomHeight, dicomWidth = image.shape
numSlicesPerRow = dicomWidth // sliceWidth
numSlicesPerCol = dicomHeight // sliceHeight
max_slices = numSlicesPerRow * numSlicesPerCol
volume = np.full((sliceWidth, sliceHeight, max_slices), np.nan)
sliceNum = 0
for row in range(numSlicesPerCol):
for col in range(numSlicesPerRow):
if sliceNum >= max_slices:
raise StateError(
'parseDicomVolume: sliceNum {} exceeds max_slices {}'.
format(sliceNum, max_slices))
rpos = row * sliceHeight
cpos = col * sliceWidth
slice = image[rpos:rpos + sliceHeight, cpos:cpos + sliceWidth]
volume[:, :, sliceNum] = slice
sliceNum += 1
return volume
def initFileNotifier(self,
dir: str,
filePattern: str,
minFileSize: int,
demoStep: int = 0) -> None:
"""
Initialize the file watcher to watch for files in the specified directory.
Note: inotify doesn't use filepatterns
Args:
dir (str): Directory to watch in
filePattern (str): ignored by inotify implementation
minFileSize (int): Minimum file size necessary to consider the file is wholely written.
Below this size the filewatcher will assume file is paritally written and continue
to wait.
demoStep (int): If non-zero then it will space out file notifications by demoStep seconds.
This is used when the image files are pre-existing but we want to simulate as if
the arrive from the scanner every few seconds (demoStep seconds).
"""
self.demoStep = demoStep
self.minFileSize = minFileSize
if dir is None:
raise StateError('initFileNotifier: dir is None')
if not os.path.exists(dir):
raise NotADirectoryError("No such directory: %s" % (dir))
if dir != self.watchDir:
if self.watchDir is not None:
self.notifier.remove_watch(self.watchDir)
self.watchDir = dir
self.notifier.add_watch(self.watchDir,
mask=inotify.constants.IN_CLOSE_WRITE)
def parseDicomVolume(dicomImg, sliceDim):
'''The raw dicom file will be a 2D picture with multiple slices tiled together.
We need to separate the slices and form a volume from them.
'''
sliceWidth = sliceDim
sliceHeight = sliceDim
image = dicomImg.pixel_array
dicomHeight, dicomWidth = image.shape
numSlicesPerRow = dicomWidth // sliceWidth
numSlicesPerCol = dicomHeight // sliceHeight
max_slices = numSlicesPerRow * numSlicesPerCol
volume = np.full((sliceWidth, sliceHeight, max_slices), np.nan)
sliceNum = 0
for row in range(numSlicesPerCol):
for col in range(numSlicesPerRow):
if sliceNum >= max_slices:
raise StateError('parseDicomVolume: sliceNum {} exceeds max_slices {}'
.format(sliceNum, max_slices))
rpos = row * sliceHeight
cpos = col * sliceWidth
slice = image[rpos: rpos+sliceHeight, cpos: cpos+sliceWidth]
volume[:, :, sliceNum] = slice
sliceNum += 1
return volume
def _uploadFilesHandler(self, request):
"""Handle requests from the web interface to upload files to this computer."""
global CommonOutputDir
if 'cmd' not in request or request['cmd'] != "uploadFiles":
raise StateError(
'uploadFiles: incorrect cmd request: {}'.format(request))
try:
srcFile = request['srcFile']
compress = request['compress'] # TODO use compress parameter
except KeyError as err:
self._setError(
"UploadFiles request missing a parameter: {}".format(err))
return
# get handle to dataInterface
dataInterface = ProjectRPCService.exposed_DataInterface
# get the list of file to upload
fileList = dataInterface.listFiles(srcFile)
if len(fileList) == 0:
# TODO - make sendUploadProgress() command
self.webUI.sendUploadStatus('No Matching Files')
return
uploadFilesFromList(dataInterface, fileList, CommonOutputDir)
# TODO - break long fileList into parts and provide periodic progress message
# self.webUI.sendUploadStatus(fileName)
self.webUI.sendUploadStatus('------upload complete------')
def registerSubjectCommFunction(commFunction):
"""
Register the function call to forward an RPC subject requests over websockets. This is the
communication for the second hop (described above) to the remote service.
"""
if ProjectRPCService.exposed_SubjectInterface is None:
raise StateError("exposed_SubjectInterface not instatiated yet")
ProjectRPCService.exposed_SubjectInterface.registerCommFunction(commFunction)
def clientSendCmd(commPipes, cmd):
'''Send a request using named pipes to the projectInterface for handling.
This allows a separate client process to make requests of the projectInterface process.
It writes the request on fd_out and recieves the reply on fd_in.
'''
data = None
savedError = None
incomplete = True
while incomplete:
commPipes.fd_out.write(json.dumps(cmd) + os.linesep)
msg = commPipes.fd_in.readline()
if len(msg) == 0:
# fifo closed
raise StateError('commPipe closed')
response = json.loads(msg)
status = response.get('status', -1)
if status != 200:
raise RequestError(
'clientSendCmd: Cmd: {} status {}: error {}'.format(
cmd.get('cmd'), status, response.get('error')))
if 'data' in response:
try:
data = unpackDataMessage(response)
except Exception as err:
# The call may be incomplete, save the error and keep receiving as needed
logging.error('clientSendCmd: {}'.format(err))
if savedError is None:
savedError = err
cmd['callId'] = response.get('callId', -1)
# Check if need to continue to get more parts
incomplete = response.get('incomplete', False)
if savedError:
raise RequestError('clientSendCmd: {}'.format(savedError))
retVals = StructDict()
retVals.statusCode = response.get('status', -1)
if 'filename' in response:
retVals.filename = response['filename']
if 'fileList' in response:
retVals.fileList = response['fileList']
if 'fileTypes' in response:
retVals.fileTypes = response['fileTypes']
if data:
retVals.data = data
if retVals.filename is None:
raise StateError('clientSendCmd: filename field is None')
return retVals
def processPyScriptRequest(request):
if 'cmd' not in request:
raise StateError('handleFifoRequests: cmd field not in request: {}'.format(request))
cmd = request['cmd']
route = request.get('route')
localtimeout = request.get('timeout', 10) + 5
response = StructDict({'status': 200})
if route == 'dataserver':
try:
response = Web.sendDataMsgFromThread(request, timeout=localtimeout)
if response is None:
raise StateError('handleFifoRequests: Response None from sendDataMessage')
if 'status' not in response:
raise StateError('handleFifoRequests: status field missing from response: {}'.format(response))
if response['status'] not in (200, 408):
if 'error' not in response:
raise StateError('handleFifoRequests: error field missing from response: {}'.format(response))
Web.setUserError(response['error'])
logging.error('handleFifo status {}: {}'.format(response['status'], response['error']))
except Exception as err:
errStr = 'SendDataMessage Exception type {}: error {}:'.format(type(err), str(err))
response = {'status': 400, 'error': errStr}
Web.setUserError(errStr)
logging.error('handleFifo Excpetion: {}'.format(errStr))
raise err
else:
if cmd == 'webCommonDir':
response.filename = CommonOutputDir
elif cmd == 'resultValue':
try:
# forward to bioFeedback Display
Web.sendBiofeedbackMsgFromThread(json.dumps(request))
# forward to main browser window
Web.sendUserMsgFromThread(json.dumps(request))
# Accumulate results locally to resend to browser as needed
Web.addResultValue(request)
except Exception as err:
errStr = 'SendClassification Exception type {}: error {}:'.format(type(err), str(err))
response = {'status': 400, 'error': errStr}
Web.setUserError(errStr)
logging.error('handleFifo Excpetion: {}'.format(errStr))
raise err
elif cmd == 'subjectDisplay':
logging.info('subjectDisplay projectInterface Callback')
return response
def close_pending_requests(self, channelName):
"""Close out all pending RPC requests when a connection is disconnected"""
handler = self.handlers.get(channelName)
if handler is None:
raise StateError(f'RPC Handler {channelName} not registered')
try:
handler.close_pending_requests()
except Exception as err:
self.setError('close_pending_requests: ' + format(err))
def subjectWsCallback(self, client, message):
"""Callback for requests sent to remote service over the wsSubject channel"""
handler = self.handlers.get('wsSubject')
if handler is None:
raise StateError(f'RPC Handler wsSubject not registered')
try:
handler.callback(client, message)
except Exception as err:
self.setError('subjectWsCallback: ' + format(err))
def allowedFileTypes(self):
if self.local:
return ['*']
else:
cmd = projUtils.allowedFileTypesReqStruct()
retVals = projUtils.clientSendCmd(self.commPipes, cmd)
fileTypes = retVals.get('fileTypes')
if type(fileTypes) is not list:
errStr = "Invalid fileTypes reponse type {}: expecting list".format(type(fileTypes))
raise StateError(errStr)
return fileTypes
def validateRequestedFile(dir, file, cmd):
textFileTypeOnly = False
wildcardAllowed = False
if cmd in ('putTextFile', 'dataLog'):
textFileTypeOnly = True
if cmd in ('listFiles'):
wildcardAllowed = True
# Restrict requests to certain directories and file types
WsFileWatcher.validationError = None
if WsFileWatcher.allowedDirs is None or WsFileWatcher.allowedTypes is None:
raise StateError(
'FileServer: Allowed Directories or File Types is not set')
if file is not None and file != '':
fileDir, filename = os.path.split(file)
fileExtension = Path(filename).suffix
if textFileTypeOnly:
if fileExtension != '.txt':
WsFileWatcher.validationError = \
'Only .txt files allowed with command putTextFile() or dataLog()'
return False
if wildcardAllowed:
pass # wildcard searches will be filtered for filetype later
elif fileExtension not in WsFileWatcher.allowedTypes:
WsFileWatcher.validationError = \
"File type {} not in list of allowed file types {}. " \
"Specify allowed filetypes with FileServer -f parameter.". \
format(fileExtension, WsFileWatcher.allowedTypes)
return False
if fileDir is not None and fileDir != '': # and os.path.isabs(fileDir):
dirMatch = False
for allowedDir in WsFileWatcher.allowedDirs:
if fileDir.startswith(allowedDir):
dirMatch = True
break
if dirMatch is False:
WsFileWatcher.validationError = \
"Path {} not within list of allowed directories {}. " \
"Make sure you specified a full (absolute) path. " \
"Specify allowed directories with FileServer -d parameter.". \
format(fileDir, WsFileWatcher.allowedDirs)
return False
if dir is not None and dir != '':
for allowedDir in WsFileWatcher.allowedDirs:
if dir.startswith(allowedDir):
return True
WsFileWatcher.validationError = \
"Path {} not within list of allowed directories {}. " \
"Make sure you specified a full (absolute) path. " \
"Specify allowed directories with FileServer -d parameter.". \
format(dir, WsFileWatcher.allowedDirs)
return False
# default case
return True
def registerDataCommFunction(commFunction):
"""
Register the function call to forward an RPC data requests over websockets. This is the
communication for the second hop (described above) to the remote service.
"""
if (ProjectRPCService.exposed_DataInterface is None
and ProjectRPCService.exposed_BidsInterface is None):
raise StateError("ServerRPC no dataInterface instatiated yet")
if ProjectRPCService.exposed_DataInterface is not None:
ProjectRPCService.exposed_DataInterface.registerCommFunction(
commFunction)
if ProjectRPCService.exposed_BidsInterface is not None:
ProjectRPCService.exposed_BidsInterface.registerCommFunction(
commFunction)
def initFileNotifier(self, dir, filePattern, minFileSize, demoStep=0):
# inotify doesn't use filepatterns
self.demoStep = demoStep
self.minFileSize = minFileSize
if dir is None:
raise StateError('initFileNotifier: dir is None')
if not os.path.exists(dir):
raise NotADirectoryError("No such directory: %s" % (dir))
if dir != self.watchDir:
if self.watchDir is not None:
self.notifier.remove_watch(self.watchDir)
self.watchDir = dir
self.notifier.add_watch(self.watchDir,
mask=inotify.constants.IN_CLOSE_WRITE)
def watchFile(self, filename, timeout=5):
data = None
if not self.initWatchSet:
raise StateError("FileInterface: watchFile() called without an initWatch()")
if self.local:
retVal = self.fileWatcher.waitForFile(filename, timeout=timeout)
if retVal is None:
raise FileNotFoundError("WatchFile: Timeout {}s: {}".format(timeout, filename))
else:
with open(filename, 'rb') as fp:
data = fp.read()
else:
watchCmd = projUtils.watchFileReqStruct(filename, timeout=timeout)
retVals = projUtils.clientSendCmd(self.commPipes, watchCmd)
data = retVals.data
return data
def listFiles(self, filePattern):
if self.local:
if not os.path.isabs(filePattern):
errStr = "listFiles must have an absolute path: {}".format(filePattern)
raise RequestError(errStr)
fileList = []
for filename in glob.iglob(filePattern, recursive=True):
if os.path.isdir(filename):
continue
fileList.append(filename)
else:
listCmd = projUtils.listFilesReqStruct(filePattern)
retVals = projUtils.clientSendCmd(self.commPipes, listCmd)
fileList = retVals.get('fileList')
if type(fileList) is not list:
errStr = "Invalid fileList reponse type {}: expecting list".format(type(fileList))
raise StateError(errStr)
return fileList
def handleRPCRequest(self, channelName, cmd, timeout=60):
"""Process RPC requests using websocket RequestHandler to send the request"""
"""Caller will catch exceptions"""
handler = self.handlers[channelName]
if handler is None:
raise StateError(f'RPC Handler {channelName} not registered')
savedError = None
incomplete = True
# print(f'handle request {cmd}')
if cmd.get('cmd') == 'rpc':
# if cmd is rpc, check and encode any byte args as base64
cmd = encodeByteTypeArgs(cmd)
# Convert numpy arguments to native python types
cmd['args'] = npToPy(cmd.get('args', ()))
cmd['kwargs'] = npToPy(cmd.get('kwargs', {}))
while incomplete:
response = handler.doRequest(cmd, timeout)
if response.get('status') != 200:
errStr = 'handleDataRequest: status {}, err {}'.format(
response.get('status'), response.get('error'))
self.setError(errStr)
raise RequestError(errStr)
try:
data = unpackDataMessage(response)
except Exception as err:
errStr = 'handleDataRequest: unpackDataMessage: {}'.format(err)
logging.error(errStr)
if savedError is None:
savedError = errStr
incomplete = response.get('incomplete', False)
cmd['callId'] = response.get('callId', -1)
cmd['incomplete'] = incomplete
if savedError:
self.setError(savedError)
raise RequestError(savedError)
serializationType = response.get('dataSerialization')
if serializationType == 'json':
if type(data) is bytes:
data = data.decode()
data = json.loads(data)
elif serializationType == 'pickle':
data = pickle.loads(data)
return data
def close():
# Currently this should never be called
raise StateError("Web close() called")
Web.wsConnLock.acquire()
try:
if Web.wsDataConn is not None:
Web.wsDataConn.close()
Web.wsDataConn = None
for client in Web.wsBrowserMainConns[:]:
client.close()
Web.wsBrowserMainConns = []
for client in Web.wsBiofeedbackConns[:]:
client.close()
Web.wsBiofeedbackConns = []
finally:
Web.wsConnLock.release()
def sendWebSocketMessage(wsName, msg, conn=None):
"""Send messages from the web server to all clients connected on the specified wsName socket."""
websocketState.wsConnLock.acquire()
try:
connList = websocketState.wsConnectionLists.get(wsName)
if connList is not None:
if conn is None:
for client in connList:
client.write_message(msg)
else:
if conn not in connList:
raise StateError(
f'sendWebSocketMessage: {wsName} no matching connection {conn}'
)
conn.write_message(msg)
else:
logging.log(
DebugLevels.L6,
f'sendWebSocketMessage: {wsName} has no connectionList')
finally:
websocketState.wsConnLock.release()
def runRemoteCall(self, callDict):
# print(f'remoteCall {callDict}')
className = callDict.get('class')
attributeName = callDict.get('attribute')
if None in (className, attributeName):
raise RequestError(f'Malformed remote call struct: missing one of '
f'class {className}, attribute {attributeName}')
classInstance = self.classInstanceDict.get(className)
if classInstance is None:
raise StateError(
f'RemoteHandler: class {className} not registered')
attributeInstance = getattr(classInstance, attributeName)
if not callable(attributeInstance):
return attributeInstance
args = callDict.get('args', ())
if args is None: # Can happen if key 'args' exists and is set to None
args = ()
kwargs = callDict.get('kwargs', {})
if kwargs is None:
kwargs = {}
res = attributeInstance(*args, **kwargs)
return res
def prepare_request(self, msg):
"""Prepate a request to be sent, including creating a callback structure and unique ID."""
# Get data server connection the request will be sent on
websocketState.wsConnLock.acquire()
try:
wsConnections = websocketState.wsConnectionLists.get(self.name)
if wsConnections is None or len(wsConnections) == 0:
serviceName = 'DataService'
if self.name == 'wsSubject':
serviceName = 'SubjectService'
raise StateError(
f"RemoteService: {serviceName} not connected. Please start the remote service."
)
reqConn = wsConnections[-1] # always use most recent connection
finally:
websocketState.wsConnLock.release()
callId = msg.get('callId')
if not callId:
callbackStruct = StructDict()
callbackStruct.dataConn = reqConn
callbackStruct.numResponses = 0
callbackStruct.responses = []
callbackStruct.semaphore = threading.Semaphore(value=0)
callbackStruct.timeStamp = time.time()
callbackStruct.msg = msg.copy()
if 'data' in callbackStruct.msg:
del callbackStruct.msg['data']
self.callbackLock.acquire()
try:
self.dataSequenceNum += 1
callId = self.dataSequenceNum
callbackStruct.callId = callId
msg['callId'] = callId
self.dataCallbacks[callId] = callbackStruct
finally:
self.callbackLock.release()
# self.ioLoopInst.add_callback(Web.sendDataMessage, msg)
return callId, reqConn
def signalFifoExit(fifoThread, commPipes):
'''Under normal exit conditions the fifothread will exit when the fifo filehandles
are closed. However if the fifo filehandles were never opened by both ends then
the fifothread can be blocked waiting for them to open. To handle that case
we open both filehandles with O_NONBLOCK flag so that if the fifo thread reader
is listening it will be opened and closed, if not it will throw OSError exception
in which case the fifothread has already exited and closed the fifo filehandles.
'''
if fifoThread is None:
return
try:
pipeout = os.open(commPipes.name_out, os.O_RDONLY | os.O_NONBLOCK)
os.close(pipeout)
# trigger context swap to allow handleFifoRequests to open next pipe if needed
time.sleep(0.1)
pipein = os.open(commPipes.name_in, os.O_WRONLY | os.O_NONBLOCK)
os.close(pipein)
except OSError as err:
# No reader/writer listening on file so fifoThread already exited
# print('signalFifoExit: exception {}'.format(err))
pass
fifoThread.join(timeout=1)
if fifoThread.is_alive() is not False:
raise StateError('runSession: fifoThread not completed')
def close():
# Currently this should never be called
raise StateError("Web close() called")
def waitForFile(self, filename: str, timeout: int = 0) -> Optional[str]:
"""
Wait for a specific filename to be created in the directory specified in initFileNotifier.
Args:
filename: Name of File to watch for creation of. If filename includes a path it must
match that specified in initFileNotifier.
timeout: Max number of seconds to watch for the file creation. If timeout expires
before the file is created then None will be returned
Returns:
The filename of the created file (same as input arg) or None if timeout expires
"""
_filedir, _filename = os.path.split(filename)
if _filedir in (None, ''):
filename = os.path.join(self.watchDir, filename)
elif _filedir != self.watchDir:
raise StateError(
f"FileWatcher: file path doesn't match watch directory: {_filedir}, {self.watchDir}"
)
fileExists = os.path.exists(filename)
if not fileExists:
if self.notify_thread is None:
raise FileNotFoundError(
"No fileNotifier and dicom file not found %s" % (filename))
else:
logStr = "FileWatcher: Waiting for file {}, timeout {}s ".format(
filename, timeout)
logging.log(DebugLevels.L6, logStr)
eventLoopCount = 0
exitWithFileEvent = False
eventTimeStamp = 0
startTime = time.time()
timeToCheckForFile = time.time(
) + 1 # check if file exists at least every second
while not fileExists:
if timeout > 0 and time.time() > (startTime + timeout):
return None
# look for file creation event
eventLoopCount += 1
try:
eventfile, ts = self.fileNotifyQ.get(block=True, timeout=1.0)
except Empty:
# The timeout occured on fileNotifyQ.get()
fileExists = os.path.exists(filename)
continue
if eventfile is None:
raise StateError('waitForFile: eventfile is None')
# We may have a stale event from a previous file if multiple events
# are created per file or if the previous file eventloop
# timed out and then the event arrived later.
if eventfile == filename:
fileExists = True
exitWithFileEvent = True
eventTimeStamp = ts
continue
if time.time() > timeToCheckForFile:
# periodically check if file exists, can occur if we get
# swamped with unrelated events
fileExists = os.path.exists(filename)
timeToCheckForFile = time.time() + 1
if exitWithFileEvent is False:
# We didn't get a file-close event because the file already existed.
# Check the file size and sleep up to 300 ms waitig for full size
waitIncrement = 0.1
totalWriteWait = 0.0
fileSize = os.path.getsize(filename)
while fileSize < self.minFileSize and totalWriteWait < 0.3:
time.sleep(waitIncrement)
totalWriteWait += waitIncrement
fileSize = os.path.getsize(filename)
logging.log(
DebugLevels.L6,
"File avail: eventLoopCount %d, fileEventCaptured %s, "
"fileName %s, eventTimeStamp %d", eventLoopCount,
exitWithFileEvent, filename, eventTimeStamp)
if self.demoStep is not None and self.demoStep > 0:
self.prevEventTime = demoDelay(self.demoStep, self.prevEventTime)
return filename
def unpackDataMessage(msg):
global multiPartDataCache
try:
if msg.get('status') != 200:
# On error delete any partial transfers
fileHash = msg.get('fileHash')
if fileHash is not None and fileHash in multiPartDataCache:
del multiPartDataCache[fileHash]
raise RequestError('unpackDataMessage: {} {}'.format(
msg.get('status'), msg.get('error')))
data = decodeMessageData(msg)
multipart = msg.get('multipart', False)
numParts = msg.get('numParts', 1)
partId = msg.get('partId', 1)
logging.debug('unpackDataMessage: callid {}, part {} of {}'.format(
msg.get('callId'), partId, numParts))
if multipart is False or numParts == 1:
# All data sent in a single message
return data
else:
assert numParts > 1
assert multipart is True
if partId > numParts:
raise RequestError(
'unpackDataMessage: Inconsistent parts: partId {} exceeds numParts {}'
.format(partId, numParts))
# get the data structure for this data
fileHash = msg.get('fileHash')
if partId > 1:
partialDataStruct = multiPartDataCache.get(fileHash)
if partialDataStruct is None:
raise RequestError(
'unpackDataMessage: partialDataStruct not found')
else:
partialDataStruct = StructDict({
'cachedDataParts': [None] * numParts,
'numCachedParts': 0
})
multiPartDataCache[fileHash] = partialDataStruct
partialDataStruct.cachedDataParts[partId - 1] = data
partialDataStruct.numCachedParts += 1
if partialDataStruct.numCachedParts == numParts:
# All parts of the multipart transfer have been received
# Concatenate the data into one bytearray
data = bytearray()
for i in range(numParts):
dataPart = partialDataStruct.cachedDataParts[i]
if dataPart is None:
raise StateError(
'unpackDataMessage: missing dataPart {}'.format(i))
data.extend(dataPart)
# Check fileHash and fileSize
dataHash = hashlib.md5(data).hexdigest()
dataSize = len(data)
if dataHash != fileHash:
raise RequestError(
"unpackDataMessage: File checksum mismatch {} {}".
format(dataHash, fileHash))
if dataSize != msg.get('fileSize', 0):
raise RequestError(
"unpackDataMessage: File size mismatch {} {}".format(
dataSize, msg.get('fileSize', 0)))
# delete the multipart data cache for this item
del multiPartDataCache[fileHash]
return data
# Multi-part transfer not complete, nothing to return
return None
except Exception as err:
# removed any cached data
fileHash = msg.get('fileHash')
if fileHash and fileHash in multiPartDataCache:
del multiPartDataCache[fileHash]
raise err
