def _form_upload_post(self, send_status):
"""Process the POST request and create new Model resource from form data.
:param send_status: callback method to signal completion
"""
import time
data = self.application.data
ctx = yield self._create_upload_context()
now = time.clock()
content_type = self.handler.request.headers["Content-Type"]
if not content_type.startswith("multipart/form-data;"):
send_status(415, ctx)
return
ctx.model["lattice_id"] = self.handler.get_argument("lattice_id", "")
if len(ctx.model["lattice_id"]) == 0:
ctx.errors["lattice_id"] = "Lattice is required"
else:
ctx.model["lattice_id"] = ObjectId(ctx.model["lattice_id"])
for lattice in ctx.lattices:
if lattice._id == ctx.model["lattice_id"]:
break
else:
ctx.errors["lattice_id"] = "Lattice not found"
ctx.model.name = self.handler.get_argument("name", "")
if len(ctx.model.name) == 0:
ctx.errors.name = "Name is required"
ctx.model.description = self.handler.get_argument("description", "")
ctx.model.status_type = self.handler.get_argument("status_type", "")
ctx.model.created_by = self.handler.current_user
ctx.model.created_date = datetime.now()
ctx.model._id = ObjectId()
ctx.model.files = []
file_content = {}
request_files = self.handler.request.files
modelfiles = {
"fort18":"model_fort18",
"fort24":"model_fort24",
"fort25":"model_fort25",
"fort26":"model_fort26"
}
modelargs = {}
for key, name in modelfiles.iteritems():
if name in request_files and len(request_files[name]) > 0:
modelargs[key] = StringIO(request_files[name][0].body)
# find a unique file ID
while True:
file_id=_create_file_id()
if file_id not in file_content:
break
ctx.model.files.append(ObjectDict(
id=file_id,
name="ModelData",
size=len(request_files[name][0].body),
filename=request_files[name][0].filename,
location=_create_file_location(request_files[name][0])
))
file_content[file_id] = request_files[name][0].body
else:
ctx.errors[name] = "Model data file is required"
if ctx.errors:
send_status(400, ctx)
return
for p in lattice.properties:
if p.name == "OutputMode":
outputMode = p.value
break
else:
ctx.errors.lattice_id = "Lattice missing 'OutputMode' property"
send_status(400, ctx)
return
if outputMode not in [1, 2, 3, 4, 5, 6]:
ctx.errors.lattice_id = "Lattice 'OutputMode' unsupported"
send_status(400, ctx)
return
try:
model = build_result(**modelargs)
except Exception as e:
LOGGER.warning("Error building model: %s", e)
ctx.errors._global = "Model invalid format"
send_status(400, ctx)
return
ctx.model.properties = []
if "attachments" in request_files:
for attachment_file in request_files["attachments"]:
while True:
file_id=_create_file_id()
if file_id not in file_content:
break
ctx.model.files.append(ObjectDict(
id=file_id,
name="Attachment",
size=len(attachment_file.body),
filename=attachment_file.filename,
location=_create_file_location(attachment_file)
))
file_content[file_id] = attachment_file.body
attachment_path = self.settings.get("attachment_path", "")
if len(attachment_path) == 0:
LOGGER.warn("setting 'attachment_path' not found")
ctx.errors._global = "Attachment directory not specified"
send_status(500, ctx)
return
try:
yield data.validate_model(ctx.model)
except Exception as e:
LOGGER.error("model validation error: %s", e)
ctx.errors._global = "Model validation error"
send_status(500, ctx)
return
idx = -1
if outputMode in [1, 2]:
# First line of data file is initial
# values BEFORE the first element.
idx = 0
model_elements = []
lattice_elements = yield data.find_lattice_elements_by_lattice_id(
ctx.model.lattice_id)
for lattice_element in lattice_elements:
for p in lattice_element.properties:
if p.name == "ITYPE":
elem_itype = p.value
break
else:
ctx.errors._global = ("Lattice Element ({}) missing ITYPE property"
.format(lattice_element.order))
send_status(400, ctx)
return
for p in lattice_element.properties:
if p.name == "STEPS":
elem_steps = p.value
break
else:
ctx.errors._global = ("Lattice Element ({}) missing STEPS property"
.format(lattice_element.order))
send_status(400, ctx)
return
if outputMode in [1, 2]:
loop = elem_steps
if elem_itype in [ -2, 4 ]:
# no output for these elements
loop = 0
elif elem_itype < 0:
loop = elem_steps + 1
elif outputMode in [3, 4]:
loop = 0
if elem_itype == -28:
# only output from monitor
loop = 1
elif outputMode in [5, 6]:
loop = 1
for _ in range(loop):
idx += 1
try:
model_element = ObjectDict()
model_element._id = ObjectId()
model_element.order = idx+1
model_element.model_id = ctx.model._id
model_element.lattice_element_id = lattice_element._id
model_element.position = model.getSPosition(idx)
model_element.properties = []
model_element.properties.append(dict(
name="BeamCenterX",
value=model.getOrbit("X", idx),
unit="mm"
))
model_element.properties.append(dict(
name="BeamCenterY",
value=model.getOrbit("Y", idx),
unit="mm"
))
model_element.properties.append(dict(
name="BeamEnergy",
value=model.getEnergy(idx),
unit="eV"
))
model_element.properties.append(dict(
name="BeamMomentumCenterX",
value=model.getBeamMomentumCentroid("X", idx),
unit="rad"
))
model_element.properties.append(dict(
name="BeamMomentumCenterY",
value=model.getBeamMomentumCentroid("Y", idx),
unit="rad"
))
model_element.properties.append(dict(
name="BeamMomentumCenterZ",
value=model.getBeamMomentumCentroid("Z", idx),
unit="MeV"
))
model_element.properties.append(dict(
name="BeamRMSX",
value=model.getBeamRms("X", idx),
unit="mm"
))
model_element.properties.append(dict(
name="BeamRMSY",
value=model.getBeamRms("Y", idx),
unit="mm"
))
model_element.properties.append(dict(
name="BeamRMSZ",
value=model.getBeamRms("Z", idx),
unit="deg"
))
model_element.properties.append(dict(
name="BeamMomentumRMSX",
value=model.getMomentumRms("X", idx),
unit="rad"
))
model_element.properties.append(dict(
name="BeamMomentumRMSY",
value=model.getMomentumRms("Y", idx),
unit="rad"
))
model_element.properties.append(dict(
name="BeamMomentumRMSZ",
value=model.getMomentumRms("Z", idx),
unit="MeV"
))
model_element.properties.append(dict(
name="EmittanceX",
value=model.getEmittance("X", idx),
unit="m-rad"
))
model_element.properties.append(dict(
name="EmittanceY",
value=model.getEmittance("Y", idx),
unit="m-rad"
))
model_element.properties.append(dict(
name="EmittanceZ",
value=model.getEmittance("Z", idx),
unit="m-rad"
))
model_element.properties.append(dict(
name="TwissBetaX",
value=model.getTwissBeta("X", idx),
unit=""
))
model_element.properties.append(dict(
name="TwissBetaY",
value=model.getTwissBeta("Y", idx),
unit=""
))
model_element.properties.append(dict(
name="TwissBetaZ",
value=model.getTwissBeta("Z", idx),
unit=""
))
model_element.properties.append(dict(
name="TwissAlphaX",
value=model.getTwissAlpha("X", idx),
unit=""
))
model_element.properties.append(dict(
name="TwissAlphaY",
value=model.getTwissAlpha("Y", idx),
unit=""
))
model_element.properties.append(dict(
name="TwissAlphaZ",
value=model.getTwissAlpha("Z", idx),
unit=""
))
except IndexError:
ctx.errors._global = ("Model data not found at index: {}".format(idx))
send_status(400, ctx)
return
try:
data.validate_model_element(model_element)
except:
LOGGER.exception("model element validation error: %s", e)
ctx.errors._global = "Model Element validation error"
send_status(500, ctx)
return
model_elements.append(model_element)
try:
yield data.insert_model(ctx.model, validate=False)
except Exception as e:
LOGGER.error("lattice database insert error: %s", e)
ctx.errors._global = "Lattice database insert error"
send_status(500, ctx)
return
try:
for model_element in model_elements:
#lattice_element.lattice_id = lattice_id
data.insert_model_element(model_element, validate=False)
except Exception as e:
LOGGER.error("model element database insert error: %s", e)
ctx.errors._global = "Mattice element database insert error"
# Rollback?
send_status(500, ctx)
return
try:
for f in ctx.model.files:
_write_file_content(attachment_path, f.location, file_content[f.id])
except Exception as e:
LOGGER.error("model attachment write error: %s", e)
ctx.errors._global = "Model attachment write error"
#Rollback?
send_status(500, ctx)
return
LOGGER.debug("model processing complete: %ss", (time.clock() - now))
send_status(201, ctx)
return
def _form_upload_post(self, send_status):
"""Process the request and create new Lattice resource.
:param send_status: callback method to signal completion
"""
data = self.application.data
ctx = yield self._create_upload_context()
content_type = self.handler.request.headers["Content-Type"]
if not content_type.startswith("multipart/form-data;"):
send_status(415)
return
ctx.lattice.particle_type = self.handler.get_argument("particle_type", "")
if len(ctx.lattice.particle_type) == 0:
ctx.errors.particle_type = "Particle Type is required"
else:
for p in ctx.particle_types:
if p["type"] == ctx.lattice.particle_type:
particle_type = ObjectDict(p)
break
else:
ctx.errors.particle_type = "Particle Type '{}' is invalid" \
.format(ctx.lattice.particle_type)
ctx.lattice.name = self.handler.get_argument("name", "")
if len(ctx.lattice.name) == 0:
ctx.errors.name = "Name is required"
ctx.lattice.branch = self.handler.get_argument("branch", "")
if len(ctx.lattice.branch) == 0:
ctx.errors.branch = "Branch is required"
if self.handler.get_argument("autoversion", "off") == "on":
ctx.lattice_autoversion = True
else:
ctx.lattice_autoversion = False
ctx.lattice.version = self.handler.get_argument("version", "")
if not ctx.lattice_autoversion:
if len(ctx.lattice.version) == 0:
ctx.errors.version = "Version is required"
else:
try:
ctx.lattice.version = int(ctx.lattice.version)
except ValueError:
ctx.lattice.version = self._INITIAL_VERSION
ctx.errors.version = "Version must be an integer"
if ctx.lattice.version <= 0:
ctx.errors.version = "Version must be greater than zero"
ctx.lattice.description = self.handler.get_argument("description", "")
ctx.lattice.status_type = self.handler.get_argument("status_type", "")
ctx.lattice.created_by = self.handler.current_user
ctx.lattice.created_date = datetime.now()
ctx.lattice._id = ObjectId()
request_files = self.handler.request.files
if "lattice_file" not in request_files:
ctx.errors.lattice_file = "Lattice File is required"
elif len(request_files["lattice_file"]) == 0:
ctx.errors.lattice_file = "Lattice File is required"
if ctx.errors:
send_status(400, ctx)
return
# check for another lattice with name, branch and version
if ctx.lattice_autoversion:
lattice = yield data.find_lattice_by_name(ctx.lattice.name,
ctx.lattice.branch)
else:
lattice = yield data.find_lattice_by_name(ctx.lattice.name,
ctx.lattice.branch, ctx.lattice.version)
if ctx.lattice_autoversion:
if lattice:
ctx.lattice.version = lattice.version + 1
else:
ctx.lattice.version = self._INITIAL_VERSION
else:
if lattice:
ctx.errors.version = "Version already exists"
if ctx.errors:
send_status(400, ctx)
return
lattice_file = request_files["lattice_file"][0]
try:
lattice = read_lattice(StringIO(lattice_file.body))
except Exception as e:
LOGGER.warning("Error reading lattice: %s", e)
ctx.errors.lattice_file = "Lattice File invalid format"
if ctx.errors:
send_status(400, ctx)
return
ctx.lattice.properties = []
ctx.lattice.properties.append(dict(
name="ParticleMass",
value=lattice.particleMass,
unit="MeV/c^2"
))
ctx.lattice.properties.append(dict(
name="ParticleCount",
value=lattice.nparticles
))
ctx.lattice.properties.append(dict(
name="ParticleCurrent",
value=lattice.current,
unit="A"
))
ctx.lattice.properties.append(dict(
name="PositionMismatch",
value=lattice.mismatch
))
ctx.lattice.properties.append(dict(
name="EnergyMismatch",
value=lattice.emismatch
))
ctx.lattice.properties.append(dict(
name="PositionOffset",
value=lattice.offset
))
ctx.lattice.properties.append(dict(
name="EnergyOffset",
value=lattice.eoffset
))
ctx.lattice.properties.append(dict(
name="DistSigma",
value=lattice.distSigma
))
ctx.lattice.properties.append(dict(
name="DistLambda",
value=lattice.distLambda
))
ctx.lattice.properties.append(dict(
name="DistMu",
value=lattice.distMu
))
ctx.lattice.properties.append(dict(
name="OutputMode",
value=lattice.outputMode
))
ctx.lattice.properties.append(dict(
name="IntegratorType",
value=lattice.integrator
))
nucleons = particle_type.protons + particle_type.neutrons
# lattice charge states
if isinstance(lattice.charge, (tuple, list)):
lattice_charge = []
for charge in lattice.charge:
lattice_charge.append(int(charge * lattice.particleMass * nucleons))
else:
lattice_charge = int(lattice.charge * lattice.particleMass * nucleons)
ctx.lattice.properties.append(dict(
name="ParticleCharge",
value=lattice_charge
))
ctx.lattice.files = []
file_content = {}
file_id = _create_file_id()
ctx.lattice.files.append(ObjectDict(
id=file_id,
name="LatticeFile",
size=len(lattice_file.body),
filename=lattice_file.filename,
location=_create_file_location(lattice_file)
))
file_content[file_id] = lattice_file.body
for data_file in request_files.get("data_file", []):
# find a unique file ID
while True:
file_id=_create_file_id()
if file_id not in file_content:
break
ctx.lattice.files.append(ObjectDict(
id=file_id,
name="DataFile",
size=len(data_file.body),
filename=data_file.filename,
location=_create_file_location(data_file)
))
file_content[file_id] = data_file.body
# check that all the data files specified by the
# lattice have been submitted as attachments
for filename in lattice.files:
for f in ctx.lattice.files:
if f.filename == filename:
break
else:
ctx.errors.data_file = "Missing data file: " + filename
send_status(400, ctx)
return
attachment_path = self.settings.get("attachment_path", "")
if len(attachment_path) == 0:
LOGGER.warn("setting 'attachment_path' not found")
ctx.errors._global = "Attachment directory not specified"
send_status(500, ctx)
return
if not os.path.isdir(attachment_path):
LOGGER.error("attachment path '%s' not found", attachment_path)
ctx.errors._global = "Attachment directory not found"
send_status(500, ctx)
return
try:
yield data.validate_lattice(ctx.lattice)
except Exception as e:
LOGGER.error("lattice validation error: %s", e)
ctx.errors._global = "Lattice validation error"
send_status(500, ctx)
return
lattice_elements = []
for idx, element in enumerate(lattice.elements):
lattice_element = ObjectDict()
lattice_element.lattice_id = ctx.lattice._id
lattice_element.order = idx+1
lattice_element.name = element.name
lattice_element.type = element.etype
lattice_element.length = element.length
lattice_element.position = element.position
lattice_element.properties = []
lattice_element.properties.append(dict(
name="ITYPE",
value=element.itype
))
lattice_element.properties.append(dict(
name="STEPS",
value=element.steps
))
for field in element.fields:
lattice_element.properties.append(dict(
name = field.name,
unit = field.unit,
value = element.getfield(field.name)
))
try:
yield data.validate_lattice_element(lattice_element)
except Exception as e:
LOGGER.error("lattice element validation error: %s", e)
ctx.errors._global = "Lattice element validation error"
send_status(500, ctx)
return
lattice_elements.append(lattice_element)
try:
lattice_id = yield data.insert_lattice(ctx.lattice, validate=False)
except Exception as e:
LOGGER.error("lattice database insert error: %s", e)
ctx.errors._global = "Lattice database insert error"
send_status(500, ctx)
return
try:
for lattice_element in lattice_elements:
lattice_element.lattice_id = lattice_id
data.insert_lattice_element(lattice_element, validate=False)
except Exception as e:
LOGGER.error("lattice element database insert error: %s", e)
ctx.errors._global = "Lattice element database insert error"
# Rollback?
send_status(500, ctx)
return
try:
for f in ctx.lattice.files:
_write_file_content(attachment_path, f.location, file_content[f.id])
except Exception as e:
LOGGER.exception("lattice file write error: %s", e)
ctx.errors._global = "Lattice file write error"
#Rollback?
send_status(500, ctx)
return
send_status(201, ctx)
return
