def updateBody():
print request.content_type
bodyArray = []
dvidEnv = None
#dvidServer = getDefaultDvidServer()
#uuid = getDefaultUuid()
option = None
if request.content_type == 'application/x-www-form-urlencoded':
bodyIdStr = request.forms.get('bodyId')
dvidName = request.forms.get('database')
dvidEnv = dvidEnvMap[dvidName]
bodyArray = [int(bodyId) for bodyId in bodyIdStr.split()]
elif request.content_type == 'application/json':
print request.json
jsonObj = request.json
try:
schema = getSchema('update_body', 'post')
#print schema
jsonschema.validate(jsonObj, json.loads(schema))
except jsonschema.exceptions.ValidationError as inst:
print 'Invalid json input'
print inst
return '<p>Update for ' + str(bodyArray) + ' failed.</p>'
bodyArray = jsonObj.get('bodies')
#dvidServer = jsonObj.get('dvid-server')
option = jsonObj.get('option')
#uuid = jsonObj['uuid']
#config = {'dvid-server': dvidServer, 'uuid': uuid}
dvidEnv = DvidEnv()
dvidEnv.loadServerConfig(jsonObj)
print dvidEnv
if not option:
option = "update"
for bodyId in bodyArray:
if option == "delete":
event = fd.DataEvent(fd.DataEvent.DATA_DELETE,
fd.DataId(fd.DataId.DATA_BODY, bodyId),
dvidEnv)
eventQueue.put(event)
print "+++Event added:", event
if option == "update" or option == "invalidate":
event = fd.DataEvent(fd.DataEvent.DATA_INVALIDATE,
fd.DataId(fd.DataId.DATA_BODY, bodyId),
dvidEnv)
eventQueue.put(event)
print "+++Event added:", event
if option == "update" or option == "add":
event = fd.DataEvent(fd.DataEvent.DATA_UPDATE,
fd.DataId(fd.DataId.DATA_SKELETON, bodyId),
dvidEnv)
eventQueue.put(event)
print "+++Event added:", event
class Skeletonizer:
def __init__(self):
self.dvidEnv = None
self.processMap = {}
def setDvidEnv(self, env):
self.dvidEnv = env
def getDvidEnv(self):
return self.dvidEnv
def loadDvidConfig(self, config):
self.dvidEnv = DvidEnv()
self.dvidEnv.loadServerConfig(config)
def loadFlyEmConfig(self, config):
self.dvidEnv = DvidEnv()
self.dvidEnv.loadFlyEmConfig(config)
def skeletonize(self, bodyId, bg=False, forceUpdate=False):
if bodyId < 1:
raise Exception("Invalid body ID")
if self.dvidEnv and self.dvidEnv.isValid():
print self.dvidEnv.getNeuTuInput()
args = [
"/opt/bin/neutu", "--command", "--skeletonize",
self.dvidEnv.getNeuTuInput(), "--bodyid",
str(bodyId)
]
if forceUpdate:
args.append("--force")
print args
p = subprocess.Popen(args)
if not bg:
p.wait()
return p
else:
raise Exception("Invalid DVID env")
skl = Skeletonizer()
socket.setdefaulttimeout(1000)
configFile = "../../json/flyem_config.json"
with open(configFile, "r") as fp:
flyemConfig = json.load(fp)
dvidEnvMap = {}
eventQueue = Queue()
#eventLock = Lock()
dvidWriter = DvidWriter()
for config in flyemConfig["dvid repo"]:
if config.get("user_name") != "[]":
dvidEnv = DvidEnv()
print config
dvidEnv.loadFlyEmConfig(config)
dvidEnvMap[config["name"]] = dvidEnv
def processEvent(event):
print "Processing event ..."
print event.dvidEnv
dvidWriter.setDvidEnv(event.dvidEnv)
if event.getType() == fd.DataEvent.DATA_INVALIDATE:
if event.getDataId().getType() == fd.DataId.DATA_BODY:
print "Invalidating body", event.getDataId().getBodyId()
dvidWriter.deleteSkeleton(event.getDataId().getBodyId())
dvidWriter.deleteThumbnail(event.getDataId().getBodyId())
elif event.getType() == fd.DataEvent.DATA_DELETE:
def setDvidEnv(self, dvidEnv):
self.dvidEnv = dvidEnv
self.dvidUrl = DvidUrl(dvidEnv)
def deleteSkeleton(self, bodyId):
url = self.dvidUrl.getSkeletonUrl(bodyId)
r = requests.delete(url)
print r.url
def deleteThumbnail(self, bodyId):
url = self.dvidUrl.getThumbnailUrl(bodyId)
r = requests.delete(url)
print r.url
print r.status_code
def deleteBodyAnnotation(self, bodyId):
r = requests.delete(self.dvidUrl.getBodyAnnotationUrl(bodyId))
print r.url
print r.status_code
def deleteKeyValue(self, dataName, key):
r = requests.delete(self.dvidUrl.getKeyUrl(dataName, key))
if __name__ == "__main__":
dvidWriter = DvidWriter(
DvidEnv("http://emdata1.int.janelia.org", 8500, "372c"))
#dvidWriter.dvidEnv.setBodyLabel("bodies3")
dvidWriter.deleteThumbnail(1)
dvidWriter.deleteSkeleton(1)
if self._type == DataEvent.DATA_INVALIDATE:
s += "Invalidate"
elif self._type == DataEvent.DATA_UPDATE:
s += "Update"
elif self._type == DataEvent.DATA_DELETE:
s += "Delete"
s += "|" + self.getDataId().getId()
return s
def getType(self):
return self._type
def getDataId(self):
return self.dataId
class DataValidator:
def __init__(self, dvidEnv):
self.dvidEnv = dvidEnv
def setDvidEnv(self, dvidEnv):
self.dvidEnv = dvidEnv
if __name__ == "__main__":
event = DataEvent(DataEvent.DATA_INVALIDATE, DataId(DataId.DATA_BODY, 1),
DvidEnv("emdata1.int.janelia.org", 8500, "372c"))
print event
def loadFlyEmConfig(self, config):
self.dvidEnv = DvidEnv()
self.dvidEnv.loadFlyEmConfig(config)
def loadDvidConfig(self, config):
self.dvidEnv = DvidEnv()
self.dvidEnv.loadServerConfig(config)
def skeletonize(self, bodyId, bg=False, forceUpdate=False):
if bodyId < 1:
raise Exception("Invalid body ID")
if self.dvidEnv and self.dvidEnv.isValid():
print self.dvidEnv.getNeuTuInput()
args = [
"/opt/bin/neutu", "--command", "--skeletonize",
self.dvidEnv.getNeuTuInput(), "--bodyid",
str(bodyId)
]
if forceUpdate:
args.append("--force")
print args
p = subprocess.Popen(args)
if not bg:
p.wait()
return p
else:
raise Exception("Invalid DVID env")
if __name__ == "__main__":
skeletonizer = Skeletonizer()
skeletonizer.setDvidEnv(DvidEnv("emdata1.int.janelia.org", 8500, "372c"))
dvidUrl = DvidUrl(skeletonizer.getDvidEnv())
conn = httplib.HTTPConnection(dvidUrl.getServerUrl())
#conn.request("DELETE", dvidUrl.getSkeletonEndPoint(15363212))
skeletonizer.skeletonize(15363212, bg=True, forceUpdate=True)
print "Done"
@author: zhaot
'''
import httplib
import requests
from dvidurl import DvidUrl
from dvidenv import DvidEnv
class DvidReader(object):
'''
DVID reader
'''
def __init__(self, dvidEnv=None):
'''
Constructor
'''
self.setDvidEnv(dvidEnv)
def setDvidEnv(self, dvidEnv):
self.dvidEnv = dvidEnv
self.dvidUrl = DvidUrl(dvidEnv)
def readMasterBranches(self):
r = requests.get(self.dvidUrl.getMasterBranchUrl())
print r.json
if __name__ == '__main__':
reader = DvidReader(DvidEnv("emdata1.int.janelia.org", 8500, "99ef"))