def post(self, queryType, jobID):
job = StochOptimJobWrapper.get_by_id(int(jobID))
data = json.loads(self.request.get('data'));
#print data
#print "================================================="
parameters = data["parameters"]
modelName = job.modelName
proposedName = data["proposedName"]
model = ModelManager.getModelByName(self, modelName);
del model["id"]
if ModelManager.getModelByName(self, proposedName):
self.response.write(json.dumps({"status" : False,
"msg" : "Model name must be unique"}))
return
if not model:
self.response.write(json.dumps({"status" : False,
"msg" : "Model '{0}' does not exist anymore. Possibly deleted".format(modelName) }))
return
model["name"] = proposedName
parameterByName = {}
for parameter in model["parameters"]:
parameterByName[parameter["name"]] = parameter
for parameter in parameters:
parameterByName[parameter]["value"] = str(parameters[parameter])
if ModelManager.updateModel(self, model):
self.response.write(json.dumps({"status" : True,
"msg" : "Model created",
"url" : "/modeleditor?model_edited={0}".format(proposedName) }))
return
else:
self.response.write(json.dumps({"status" : False,
"msg" : "Model failed to be created, check logs"}))
return
def post(self, queryType, jobID):
job = StochOptimJobWrapper.get_by_id(int(jobID))
data = json.loads(self.request.get('data'));
#print data
#print "================================================="
parameters = data["parameters"]
modelName = job.modelName
proposedName = data["proposedName"]
model = ModelManager.getModelByName(self, modelName);
del model["id"]
if ModelManager.getModelByName(self, proposedName):
self.response.write(json.dumps({"status" : False,
"msg" : "Model name must be unique"}))
return
if not model:
self.response.write(json.dumps({"status" : False,
"msg" : "Model '{0}' does not exist anymore. Possibly deleted".format(modelName) }))
return
model["name"] = proposedName
parameterByName = {}
for parameter in model["parameters"]:
parameterByName[parameter["name"]] = parameter
for parameter in parameters:
parameterByName[parameter]["value"] = str(parameters[parameter])
if ModelManager.updateModel(self, model):
self.response.write(json.dumps({"status" : True,
"msg" : "Model created",
"url" : "/modeleditor?model_edited={0}".format(proposedName) }))
return
else:
self.response.write(json.dumps({"status" : False,
"msg" : "Model failed to be created, check logs"}))
return
def get(self, queryType = None, jobID = None):
logging.info("JobID: {0}".format(jobID));
jobID = int(jobID)
output = { "jobID" : jobID }
if queryType == None:
self.render_response('stochoptimvisualization.html', **output)
return
optimization = StochOptimJobWrapper.get_by_id(jobID)
service = backend.backendservice.backendservices(self.user_data)
# Might need to download the cloud data
if optimization.resource in backendservices.SUPPORTED_CLOUD_RESOURCES:
# if optimization.status == "Finished":
if optimization.status == "Finished" and optimization.has_final_cloud_data():
# Nothing more to do
pass
elif optimization.status == "Finished" and not optimization.has_final_cloud_data():
# Download the final data and mark it finished
cloud_result = self.__fetch_cloud_output(optimization)
if cloud_result["status"]:
optimization.mark_final_cloud_data()
else:
# Download current progress
cloud_result = self.__fetch_cloud_output(optimization)
# else:
# logging.error("Failed to download final output data of {0} with reason {1}".format(
# optimization.name,
# cloud_result["msg"]
# ))
result = status.getJobStatus(service, optimization)
try:
fd = os.open("{0}/stdout".format(optimization.outData), os.O_RDONLY)
f = os.fdopen(fd)
output["stdout"] = f.read().strip()
f.close()
except:
output["stdout"] = ""
if len(output["stdout"]) == 0:
if optimization.status == 'Running':
output["stdout"] = "(Job running, no output available yet)"
else:
output["stdout"] = "(empty)"
if queryType.lower() == "debug":
try:
fd = os.open("{0}/stderr".format(optimization.outData), os.O_RDONLY)
f = os.fdopen(fd)
output["stderr"] = f.read().strip()
f.close()
except:
output["stderr"] = ""
if len(output["stderr"]) == 0:
output["stderr"] = "(empty)"
# print optimization.nameToIndex
# print optimization.indata
output["nameToIndex"] = json.loads(optimization.nameToIndex)
output["status"] = result["status"]
output["jobName"] = optimization.name
output["modelName"] = optimization.modelName
output["resource"] = optimization.resource
output["activate"] = json.loads(optimization.indata)["activate"]
self.response.content_type = 'application/json'
self.response.write(json.dumps(output))
return
def runCloud(self, data):
modelDb = StochKitModelWrapper.get_by_id(data["modelID"])
berniemodel = StochOptimModel()
success, msgs = berniemodel.fromStochKitModel(modelDb.createStochKitModel())
if not success:
raise Exception(msgs)
path = os.path.abspath(os.path.dirname(__file__))
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
job = StochOptimJobWrapper()
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.indata = json.dumps(data)
job.modelName = modelDb.name
job.outData = dataDir
job.status = "Pending"
data["exec"] = "'bash'"
data["steps"] = ("C" if data["crossEntropyStep"] else "") + ("E" if data["emStep"] else "") + ("U" if data["uncertaintyStep"] else "")
# data["cores"] = 4
data["options"] = ""
cmd = "exec/mcem2.r --steps {steps} --seed {seed} --K.ce {Kce} --K.em {Kem} --K.lik {Klik} --K.cov {Kcov} --rho {rho} --perturb {perturb} --alpha {alpha} --beta {beta} --gamma {gamma} --k {k} --pcutoff {pcutoff} --qcutoff {qcutoff} --numIter {numIter} --numConverge {numConverge} --command {exec}".format(**data)
# cmd = "exec/mcem2.r --K.ce 1000 --K.em 100 --rho .01 --pcutoff .05"
stringModel, nameToIndex = berniemodel.serialize(data["activate"], True)
job.nameToIndex = json.dumps(nameToIndex)
jFileData = fileserver.FileManager.getFile(self, data["trajectoriesID"], noFile = False)
iFileData = fileserver.FileManager.getFile(self, data["initialDataID"], noFile = False)
job.put()
cloud_params = {
"job_id" : job.key().id(),
"job_type": "mcem2",
# "cores": data["cores"],
"paramstring": cmd,
"model_file": stringModel,
"model_data": {
"content": self.addWeightColumnIfNecessary(iFileData["data"]),
"extension": "txt"
},
"final_data": {
"content": self.addWeightColumnIfNecessary(jFileData["data"]),
"extension": "txt"
},
"key_prefix": self.user.user_id(),
"credentials": self.user_data.getCredentials(),
"bucketname": self.user_data.getBucketName()
}
# # execute cloud task
try:
service = backend.backendservice.backendservices(self.user_data)
cloud_result = service.submit_cloud_task(params=cloud_params)
if not cloud_result["success"]:
raise Exception(cloud_result["reason"])
job.cloudDatabaseID = cloud_result["db_id"]
job.resource = cloud_result['resource']
job.celeryPID = cloud_result["celery_pid"]
# job.pollProcessPID = int(cloud_result["poll_process_pid"])
# job.pid = handle.pid
job.put()
except Exception as e:
job.status='Failed'
job.delete(self)
raise
return job
def runLocal(self, data):
'''
'''
modelDb = StochKitModelWrapper.get_by_id(data["modelID"])
berniemodel = StochOptimModel()
success, msgs = berniemodel.fromStochKitModel(modelDb.createStochKitModel())
if not success:
raise Exception(msgs)
path = os.path.abspath(os.path.dirname(__file__))
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
job = StochOptimJobWrapper()
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.indata = json.dumps(data)
job.outData = dataDir
job.modelName = modelDb.name
job.resource = "local"
job.status = "Running"
# Convert model and write to file
model_file_file = tempfile.mktemp(prefix = 'modelFile', suffix = '.R', dir = dataDir)
mff = open(model_file_file, 'w')
stringModel, nameToIndex = berniemodel.serialize(data["activate"], True)
job.nameToIndex = json.dumps(nameToIndex)
mff.write(stringModel)
mff.close()
data["model_file_file"] = model_file_file
model_data_file = tempfile.mktemp(prefix = 'dataFile', suffix = '.txt', dir = dataDir)
mdf = open(model_data_file, 'w')
jFileData = fileserver.FileManager.getFile(self, data["trajectoriesID"], noFile = False)
mdf.write(self.addWeightColumnIfNecessary(jFileData["data"]))
mdf.close()
data["model_data_file"] = model_data_file
model_initial_data_file = tempfile.mktemp(prefix = 'dataFile', suffix = '.txt', dir = dataDir)
midf = open(model_initial_data_file, 'w')
iFileData = fileserver.FileManager.getFile(self, data["initialDataID"], noFile = False)
midf.write(self.addWeightColumnIfNecessary(iFileData["data"]))
midf.close()
data["model_initial_data_file"] = model_initial_data_file
data["exec"] = "\"bash&\""
data["steps"] = ("C" if data["crossEntropyStep"] else "") + ("E" if data["emStep"] else "") + ("U" if data["uncertaintyStep"] else "")
try:
import multiprocessing
data["cores"] = multiprocessing.cpu_count()
except:
data["cores"] = 1
data["options"] = ""
data["path"] = path
cmd = "Rscript --vanilla {path}/../../stochoptim/exec/mcem2.r --model {model_file_file} --data {model_initial_data_file} --finalData {model_data_file} --steps {steps} --seed {seed} --cores {cores} --K.ce {Kce} --K.em {Kem} --K.lik {Klik} --K.cov {Kcov} --rho {rho} --perturb {perturb} --alpha {alpha} --beta {beta} --gamma {gamma} --k {k} --pcutoff {pcutoff} --qcutoff {qcutoff} --numIter {numIter} --numConverge {numConverge} --command {exec}".format(**data)
exstring = '{0}/backend/wrapper.py {1}/stdout {1}/stderr {1}/return_code {2}'.format(basedir, dataDir, cmd)
handle = subprocess.Popen(exstring, shell=True, preexec_fn=os.setsid)
job.pid = handle.pid
job.put()
return job
def post(self):
reqType = self.request.get('reqType')
self.response.content_type = 'application/json'
if reqType == 'newJob':
data = json.loads(self.request.get('data'))
job = db.GqlQuery("SELECT * FROM StochOptimJobWrapper WHERE user_id = :1 AND name = :2",
self.user.user_id(),
data["jobName"].strip()).get()
if job != None:
self.response.write(json.dumps({"status" : False,
"msg" : "Job name must be unique"}))
return
try:
if data["resource"] == "local":
# This function takes full responsibility for writing responses out to the world. This is probably a bad design mechanism
result = self.runLocal(data)
else:
# cloud
result = self.runCloud(data=data)
return self.response.write(json.dumps({
"status": True,
"msg": "Job launched",
"id": result.key().id()
}))
except Exception as e:
logging.exception(e)
result = {'status':False,
'msg':'Error: {0}'.format(e)}
self.response.write(json.dumps(result))
return
elif reqType == 'stopJob':
jobID = json.loads(self.request.get('id'))
jobID = int(jobID)
job = StochOptimJobWrapper.get_by_id(jobID)
if job.user_id == self.user.user_id():
if job.resource in backendservices.SUPPORTED_CLOUD_RESOURCES:
# try:
# logging.info("Stopping StochOptim poll task pid={0}".format(job.pollProcessPID))
# os.kill(job.pollProcessPID, signal.SIGTERM)
# except Exception as e:
# logging.error("StochOptimPage.post.stopJob(): exception during kill process: {0}".format(e))
success = job.stop(self)
if not success:
return self.response.write(json.dumps({
'status': False,
'msg': 'Could not stop the job '+job.name +'. Unexpected error.'
}))
else:
job.stop(self)
else:
self.response.write(json.dumps({"status" : False,
"msg" : "No permissions to delete this job (this should never happen)"}))
return
elif reqType == 'delJob':
jobID = json.loads(self.request.get('id'))
jobID = int(jobID)
job = StochOptimJobWrapper.get_by_id(jobID)
if job.user_id == self.user.user_id():
job.delete(self)
else:
self.response.write(json.dumps({"status" : False,
"msg" : "No permissions to delete this job (this should never happen)"}))
return
elif reqType == 'getDataLocal':
jobID = json.loads(self.request.get('id'))
jobID = int(jobID)
job = StochOptimJobWrapper.get_by_id(jobID)
if not job.zipFileName:
szip = exportimport.SuperZip(os.path.abspath(os.path.dirname(__file__) + '/../static/tmp/'), preferredName = job.name + "_")
job.zipFileName = szip.getFileName()
szip.addStochOptimJob(job, True)
szip.close()
# Save the updated status
job.put()
relpath = '/' + os.path.relpath(job.zipFileName, os.path.abspath(os.path.dirname(__file__) + '/../'))
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps({ 'status' : True,
'msg' : 'Job prepared',
'url' : relpath }))
return
self.response.write(json.dumps({ 'status' : True,
'msg' : 'Success'}))
def get(self, queryType = None, jobID = None):
logging.info("JobID: {0}".format(jobID));
jobID = int(jobID)
output = { "jobID" : jobID }
if queryType == None:
self.render_response('stochoptimvisualization.html', **output)
return
optimization = StochOptimJobWrapper.get_by_id(jobID)
service = backend.backendservice.backendservices(self.user_data)
# Might need to download the cloud data
if optimization.resource in backendservices.SUPPORTED_CLOUD_RESOURCES:
# if optimization.status == "Finished":
if optimization.status == "Finished" and optimization.has_final_cloud_data():
# Nothing more to do
pass
elif optimization.status == "Finished" and not optimization.has_final_cloud_data():
# Download the final data and mark it finished
cloud_result = self.__fetch_cloud_output(optimization)
if cloud_result["status"]:
optimization.mark_final_cloud_data()
else:
# Download current progress
cloud_result = self.__fetch_cloud_output(optimization)
# else:
# logging.error("Failed to download final output data of {0} with reason {1}".format(
# optimization.name,
# cloud_result["msg"]
# ))
try:
fd = os.open("{0}/stdout".format(optimization.outData), os.O_RDONLY)
f = os.fdopen(fd)
output["stdout"] = f.read().strip()
f.close()
except:
output["stdout"] = ""
if len(output["stdout"]) == 0:
if optimization.status == 'Running':
output["stdout"] = "(Job running, no output available yet)"
else:
output["stdout"] = "(empty)"
if queryType.lower() == "debug":
try:
fd = os.open("{0}/stderr".format(optimization.outData), os.O_RDONLY)
f = os.fdopen(fd)
output["stderr"] = f.read().strip()
f.close()
except:
output["stderr"] = ""
if len(output["stderr"]) == 0:
output["stderr"] = "(empty)"
# print optimization.nameToIndex
# print optimization.indata
output["nameToIndex"] = json.loads(optimization.nameToIndex)
output["status"] = optimization.status
output["jobName"] = optimization.name
output["modelName"] = optimization.modelName
output["resource"] = optimization.resource
output["activate"] = json.loads(optimization.indata)["activate"]
self.response.content_type = 'application/json'
self.response.write(json.dumps(output))
return
def runCloud(self, data):
modelDb = StochKitModelWrapper.get_by_id(data["modelID"])
berniemodel = StochOptimModel()
success, msgs = berniemodel.fromStochKitModel(modelDb.createStochKitModel())
if not success:
raise Exception(msgs)
path = os.path.abspath(os.path.dirname(__file__))
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
job = StochOptimJobWrapper()
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.indata = json.dumps(data)
job.modelName = modelDb.name
job.outData = dataDir
job.status = "Pending"
data["exec"] = "'bash'"
data["steps"] = ("C" if data["crossEntropyStep"] else "") + ("E" if data["emStep"] else "") + ("U" if data["uncertaintyStep"] else "")
# data["cores"] = 4
data["options"] = ""
cmd = "exec/mcem2.r --steps {steps} --seed {seed} --K.ce {Kce} --K.em {Kem} --K.lik {Klik} --K.cov {Kcov} --rho {rho} --perturb {perturb} --alpha {alpha} --beta {beta} --gamma {gamma} --k {k} --pcutoff {pcutoff} --qcutoff {qcutoff} --numIter {numIter} --numConverge {numConverge} --command {exec}".format(**data)
# cmd = "exec/mcem2.r --K.ce 1000 --K.em 100 --rho .01 --pcutoff .05"
stringModel, nameToIndex = berniemodel.serialize(data["activate"], True)
job.nameToIndex = json.dumps(nameToIndex)
jFileData = fileserver.FileManager.getFile(self, data["trajectoriesID"], noFile = False)
iFileData = fileserver.FileManager.getFile(self, data["initialDataID"], noFile = False)
job.put()
cloud_params = {
"job_id" : job.key().id(),
"job_type": "mcem2",
# "cores": data["cores"],
"paramstring": cmd,
"model_file": stringModel,
"model_data": {
"content": self.addWeightColumnIfNecessary(iFileData["data"]),
"extension": "txt"
},
"final_data": {
"content": self.addWeightColumnIfNecessary(jFileData["data"]),
"extension": "txt"
},
"key_prefix": self.user.user_id(),
"credentials": self.user_data.getCredentials(),
"bucketname": self.user_data.getBucketName()
}
# # execute cloud task
try:
service = backend.backendservice.backendservices(self.user_data)
cloud_result = service.submit_cloud_task(params=cloud_params)
if not cloud_result["success"]:
raise Exception(cloud_result["reason"])
job.cloudDatabaseID = cloud_result["db_id"]
job.resource = cloud_result['resource']
job.celeryPID = cloud_result["celery_pid"]
# job.pollProcessPID = int(cloud_result["poll_process_pid"])
# job.pid = handle.pid
job.put()
except Exception as e:
job.status='Failed'
job.delete(self)
raise
return job
def runLocal(self, data):
'''
'''
modelDb = StochKitModelWrapper.get_by_id(data["modelID"])
berniemodel = StochOptimModel()
success, msgs = berniemodel.fromStochKitModel(modelDb.createStochKitModel())
if not success:
raise Exception(msgs)
path = os.path.abspath(os.path.dirname(__file__))
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
job = StochOptimJobWrapper()
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.indata = json.dumps(data)
job.outData = dataDir
job.modelName = modelDb.name
job.resource = "local"
job.status = "Running"
# Convert model and write to file
model_file_file = tempfile.mktemp(prefix = 'modelFile', suffix = '.R', dir = dataDir)
mff = open(model_file_file, 'w')
stringModel, nameToIndex = berniemodel.serialize(data["activate"], True)
job.nameToIndex = json.dumps(nameToIndex)
mff.write(stringModel)
mff.close()
data["model_file_file"] = model_file_file
model_data_file = tempfile.mktemp(prefix = 'dataFile', suffix = '.txt', dir = dataDir)
mdf = open(model_data_file, 'w')
jFileData = fileserver.FileManager.getFile(self, data["trajectoriesID"], noFile = False)
mdf.write(self.addWeightColumnIfNecessary(jFileData["data"]))
mdf.close()
data["model_data_file"] = model_data_file
model_initial_data_file = tempfile.mktemp(prefix = 'dataFile', suffix = '.txt', dir = dataDir)
midf = open(model_initial_data_file, 'w')
iFileData = fileserver.FileManager.getFile(self, data["initialDataID"], noFile = False)
midf.write(self.addWeightColumnIfNecessary(iFileData["data"]))
midf.close()
data["model_initial_data_file"] = model_initial_data_file
data["exec"] = "\"bash&\""
data["steps"] = ("C" if data["crossEntropyStep"] else "") + ("E" if data["emStep"] else "") + ("U" if data["uncertaintyStep"] else "")
try:
import multiprocessing
data["cores"] = multiprocessing.cpu_count()
except:
data["cores"] = 1
data["options"] = ""
data["path"] = path
cmd = "Rscript --vanilla {path}/../../stochoptim/exec/mcem2.r --model {model_file_file} --data {model_initial_data_file} --finalData {model_data_file} --steps {steps} --seed {seed} --cores {cores} --K.ce {Kce} --K.em {Kem} --K.lik {Klik} --K.cov {Kcov} --rho {rho} --perturb {perturb} --alpha {alpha} --beta {beta} --gamma {gamma} --k {k} --pcutoff {pcutoff} --qcutoff {qcutoff} --numIter {numIter} --numConverge {numConverge} --command {exec}".format(**data)
exstring = '{0}/backend/wrapper.py {1}/stdout {1}/stderr {1}/return_code {2}'.format(basedir, dataDir, cmd)
handle = subprocess.Popen(exstring, shell=True, preexec_fn=os.setsid)
job.pid = handle.pid
job.put()
return job
def post(self):
reqType = self.request.get('reqType')
self.response.content_type = 'application/json'
if reqType == 'newJob':
data = json.loads(self.request.get('data'))
job = db.GqlQuery("SELECT * FROM StochOptimJobWrapper WHERE user_id = :1 AND name = :2",
self.user.user_id(),
data["jobName"].strip()).get()
if job != None:
self.response.write(json.dumps({"status" : False,
"msg" : "Job name must be unique"}))
return
try:
if data["resource"] == "local":
# This function takes full responsibility for writing responses out to the world. This is probably a bad design mechanism
result = self.runLocal(data)
else:
# cloud
result = self.runCloud(data=data)
return self.response.write(json.dumps({
"status": True,
"msg": "Job launched",
"id": result.key().id()
}))
except Exception as e:
logging.exception(e)
result = {'status':False,
'msg':'Error: {0}'.format(e)}
self.response.write(json.dumps(result))
return
elif reqType == 'stopJob':
jobID = json.loads(self.request.get('id'))
jobID = int(jobID)
job = StochOptimJobWrapper.get_by_id(jobID)
if job.user_id == self.user.user_id():
if job.resource in backendservices.SUPPORTED_CLOUD_RESOURCES:
# try:
# logging.info("Stopping StochOptim poll task pid={0}".format(job.pollProcessPID))
# os.kill(job.pollProcessPID, signal.SIGTERM)
# except Exception as e:
# logging.error("StochOptimPage.post.stopJob(): exception during kill process: {0}".format(e))
success = job.stop(self)
if not success:
return self.response.write(json.dumps({
'status': False,
'msg': 'Could not stop the job '+job.name +'. Unexpected error.'
}))
else:
job.stop(self)
else:
self.response.write(json.dumps({"status" : False,
"msg" : "No permissions to delete this job (this should never happen)"}))
return
elif reqType == 'delJob':
jobID = json.loads(self.request.get('id'))
jobID = int(jobID)
job = StochOptimJobWrapper.get_by_id(jobID)
if job.user_id == self.user.user_id():
job.delete(self)
else:
self.response.write(json.dumps({"status" : False,
"msg" : "No permissions to delete this job (this should never happen)"}))
return
elif reqType == 'getDataLocal':
jobID = json.loads(self.request.get('id'))
jobID = int(jobID)
job = StochOptimJobWrapper.get_by_id(jobID)
if not job.zipFileName:
szip = exportimport.SuperZip(os.path.abspath(os.path.dirname(__file__) + '/../static/tmp/'), preferredName = job.name + "_")
job.zipFileName = szip.getFileName()
szip.addStochOptimJob(job, True)
szip.close()
# Save the updated status
job.put()
relpath = '/' + os.path.relpath(job.zipFileName, os.path.abspath(os.path.dirname(__file__) + '/../'))
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps({ 'status' : True,
'msg' : 'Job prepared',
'url' : relpath }))
return
self.response.write(json.dumps({ 'status' : True,
'msg' : 'Success'}))