def _validateParam(self, name, descParam, value):
"""
Validates and transforms a single parameter that was passed. Raises
RestException if the passed value is invalid.
:param name: The name of the param.
:type name: str
:param descParam: The formal parameter in the Description.
:type descParam: dict
:param value: The value passed in for this param for the current request.
:returns: The value transformed
"""
type = descParam.get('type')
# Coerce to the correct data type
if type == 'string':
value = self._handleString(name, descParam, value)
elif type == 'boolean':
value = toBool(value)
elif type == 'integer':
value = self._handleInt(name, descParam, value)
elif type == 'number':
value = self._handleNumber(name, descParam, value)
# Enum validation (should be afer type coercion)
if 'enum' in descParam and value not in descParam['enum']:
raise RestException(
'Invalid value for %s: "%s". Allowed values: %s.' %
(name, value, ', '.join(str(v) for v in descParam['enum'])))
return value
def _validateParam(self, name, descParam, value):
"""
Validates and transforms a single parameter that was passed. Raises
RestException if the passed value is invalid.
:param name: The name of the param.
:type name: str
:param descParam: The formal parameter in the Description.
:type descParam: dict
:param value: The value passed in for this param for the current request.
:returns: The value transformed
"""
type = descParam.get('type')
# Coerce to the correct data type
if type == 'string':
value = self._handleString(name, descParam, value)
elif type == 'boolean':
value = toBool(value)
elif type == 'integer':
value = self._handleInt(name, descParam, value)
elif type == 'number':
value = self._handleNumber(name, descParam, value)
# Enum validation (should be after type coercion)
if 'enum' in descParam and value not in descParam['enum']:
raise RestException('Invalid value for %s: "%s". Allowed values: %s.' % (
name, value, ', '.join(str(v) for v in descParam['enum'])))
return value
def boolParam(self, key, params, default=None):
"""
Coerce a parameter value from a str to a bool.
:param key: The parameter key to test.
:type key: str
:param params: The request parameters.
:type params: dict
:param default: The default value if no key is passed.
:type default: bool or None
"""
if key not in params:
return default
return toBool(params[key])
def boolParam(self, key, params, default=None):
"""
Coerce a parameter value from a str to a bool.
:param key: The parameter key to test.
:type key: str
:param params: The request parameters.
:type params: dict
:param default: The default value if no key is passed.
:type default: bool or None
"""
if key not in params:
return default
return toBool(params[key])
def find_calc(self, moleculeId=None, imageName=None, inputParametersHash=None, inputGeometryHash=None, pending=None, offset=0, limit=None, sort=None):
user = getCurrentUser()
query = { }
if moleculeId:
query['moleculeId'] = ObjectId(moleculeId)
if imageName:
repository, tag = oc.parse_image_name(imageName)
query['image.repository'] = repository
query['image.tag'] = tag
if inputParametersHash:
query['input.parametersHash'] = inputParametersHash
if inputGeometryHash:
query['input.geometryHash'] = inputGeometryHash
if pending is not None:
pending = toBool(pending)
query['properties.pending'] = pending
# The absence of the field mean the calculation is not pending ...
if not pending:
query['properties.pending'] = {
'$ne': True
}
fields = ['image', 'input',
'cjson', 'cjson.vibrations.modes', 'cjson.vibrations.intensities',
'cjson.vibrations.frequencies', 'properties', 'fileId', 'access',
'moleculeId', 'public']
calcs = self._model.find(query, fields=fields, sort=sort)
calcs = self._model.filterResultsByPermission(calcs, user,
AccessType.READ, limit=limit)
calcs = [self._model.filter(x, user) for x in calcs]
return calcs
def _validateBoolean(doc):
doc['value'] = toBool(doc['value'])
def find_calc(self, params):
user = getCurrentUser()
query = {}
if 'moleculeId' in params:
query['moleculeId'] = ObjectId(params['moleculeId'])
if 'calculationType' in params:
calculation_type = params['calculationType']
if not isinstance(calculation_type, list):
calculation_type = [calculation_type]
query['properties.calculationTypes'] = {'$all': calculation_type}
if 'functional' in params:
query['properties.functional'] = params.get('functional').lower()
if 'theory' in params:
query['properties.theory'] = params.get('theory').lower()
if 'basis' in params:
query['properties.basisSet.name'] = params.get('basis').lower()
if 'pending' in params:
pending = toBool(params['pending'])
query['properties.pending'] = pending
# The absence of the field mean the calculation is not pending ...
if not pending:
query['properties.pending'] = {'$ne': True}
limit = params.get('limit', 50)
fields = [
'cjson.vibrations.modes', 'cjson.vibrations.intensities',
'cjson.vibrations.frequencies', 'properties', 'fileId', 'access',
'public'
]
sort = None
sort_by_theory = toBool(params.get('sortByTheory', False))
if sort_by_theory:
sort = [('properties.theoryPriority', pymongo.DESCENDING)]
# Exclude calculations that don't have a theoryPriority,
# otherwise they will appear first in the list.
query['properties.theoryPriority'] = {'$exists': True}
calcs = self._model.find(query, fields=fields, sort=sort)
calcs = self._model.filterResultsByPermission(calcs,
user,
AccessType.READ,
limit=int(limit))
calcs = [self._model.filter(x, user) for x in calcs]
not_sortable = []
if sort_by_theory and len(calcs) < int(limit):
# Now select any calculations without theoryPriority
query['properties.theoryPriority'] = {'$exists': False}
not_sortable = self._model.find(query, fields=fields)
not_sortable = self._model.filterResultsByPermission(
not_sortable,
user,
AccessType.READ,
limit=int(limit) - len(calcs))
not_sortable = [self._model.filter(x, user) for x in not_sortable]
return calcs + not_sortable
def _validateBoolean(doc):
doc['value'] = toBool(doc['value'])
