def create_calc(self, params):
body = getBodyJson()
if 'cjson' not in body and ('fileId' not in body
or 'format' not in body):
raise RestException('Either cjson or fileId is required.')
user = getCurrentUser()
cjson = body.get('cjson')
props = body.get('properties', {})
molecule_id = body.get('moleculeId', None)
geometry_id = body.get('geometryId', None)
public = body.get('public', True)
notebooks = body.get('notebooks', [])
image = body.get('image')
input_parameters = body.get('input', {}).get('parameters')
if input_parameters is None:
input_parameters = body.get('inputParameters', {})
file_id = None
file_format = body.get('format', 'cjson')
if 'fileId' in body:
file = File().load(body['fileId'], user=getCurrentUser())
file_id = file['_id']
cjson = self._file_to_cjson(file, file_format)
if molecule_id is None:
mol = create_molecule(json.dumps(cjson),
'cjson',
user,
public,
parameters=input_parameters)
molecule_id = mol['_id']
calc = CalculationModel().create_cjson(
user,
cjson,
props,
molecule_id,
geometry_id=geometry_id,
image=image,
input_parameters=input_parameters,
file_id=file_id,
notebooks=notebooks,
public=public)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] \
= '/calculations/%s' % (str(calc['_id']))
return CalculationModel().filter(calc, user)
def ingest_calc(self, calculation, body, detectBonds=None):
self.requireParams(['fileId', 'format'], body)
file = File().load(body['fileId'], user=getCurrentUser())
cjson = self._file_to_cjson(file, body['format'])
calc_props = calculation['properties']
# The calculation is no longer pending
if 'pending' in calc_props:
del calc_props['pending']
# Add bonds if they were not there already
if detectBonds is None:
detectBonds = False
bonds = cjson.get('bonds')
if bonds is None and detectBonds:
new_cjson = openbabel.autodetect_bonds(cjson)
if new_cjson.get('bonds') is not None:
cjson['bonds'] = new_cjson['bonds']
calculation['properties'] = calc_props
calculation['cjson'] = cjson
calculation['fileId'] = file['_id']
image = body.get('image')
if image is not None:
calculation['image'] = image
scratch_folder_id = body.get('scratchFolderId')
if scratch_folder_id is not None:
calculation['scratchFolderId'] = scratch_folder_id
return CalculationModel().save(calculation)
def find_calc(self,
moleculeId=None,
geometryId=None,
imageName=None,
inputParameters=None,
inputGeometryHash=None,
name=None,
inchi=None,
inchikey=None,
smiles=None,
formula=None,
creatorId=None,
pending=None,
limit=None,
offset=None,
sort=None):
return CalculationModel().findcal(
molecule_id=moleculeId,
geometry_id=geometryId,
image_name=imageName,
input_parameters=inputParameters,
input_geometry_hash=inputGeometryHash,
name=name,
inchi=inchi,
inchikey=inchikey,
smiles=smiles,
formula=formula,
creator_id=creatorId,
pending=pending,
limit=limit,
offset=offset,
sort=sort,
user=getCurrentUser())
def ingest_calc(self, calculation, body, detectBonds=None):
self.requireParams(['fileId', 'format'], body)
file = File().load(body['fileId'], user=getCurrentUser())
cjson = self._file_to_cjson(file, body['format'])
calc_props = calculation['properties']
# The calculation is no longer pending
if 'pending' in calc_props:
del calc_props['pending']
# Add bonds if they were not there already
if detectBonds is None:
detectBonds = False
bonds = cjson.get('bonds')
if bonds is None and detectBonds:
new_cjson = openbabel.autodetect_bonds(cjson)
if new_cjson.get('bonds') is not None:
cjson['bonds'] = new_cjson['bonds']
calculation['properties'] = calc_props
calculation['cjson'] = cjson
calculation['fileId'] = file['_id']
image = body.get('image')
if image is not None:
calculation['image'] = image
code = body.get('code')
if code is not None:
calculation['code'] = code
scratch_folder_id = body.get('scratchFolderId')
if scratch_folder_id is not None:
calculation['scratchFolderId'] = scratch_folder_id
# If this was a geometry optimization, create a geometry from it
task = parse('input.parameters.task').find(calculation)
if task and task[0].value == 'optimize':
moleculeId = calculation.get('moleculeId')
provenanceType = 'calculation'
provenanceId = calculation.get('_id')
# The cjson will be whitelisted
geometry = GeometryModel().create(getCurrentUser(), moleculeId,
cjson, provenanceType,
provenanceId)
calculation['optimizedGeometryId'] = geometry.get('_id')
return CalculationModel().save(calculation)
def add_notebooks(self, calculation, notebooks):
notebooks = notebooks.get('notebooks')
if notebooks is not None:
CalculationModel().add_notebooks(calculation, notebooks)