Commit e86ffbb3 authored by Médéric Boquien's avatar Médéric Boquien
Browse files

So far no validation was made on the input parameters provided in pcigale.ini....

So far no validation was made on the input parameters provided in pcigale.ini. This could lead to runtime crashes when an argument took an unexpected value. As we are using the ConfigObj module to handle the configuration file, we can also use the validate module that comes with it. However the standard validation functions are not precise enough in our case. This file defines two validation functions for input parameters, and a new exception that will be used in a subsequent patch.
parent e40d9852
# -*- coding: utf-8 -*-
# Copyright (C) 2016 Universidad de Antofagasta
# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt
# Author: Médéric Boquien
import numpy as np
import validate as vdt
class VdtValueRepeatedError(vdt.VdtValueError):
"""The value supplied was repeated."""
def __init__(self, value):
>>> raise VdtValueRepeatedError('jedie')
Traceback (most recent call last):
VdtValueRepeatedError: the value "jedie" is too long.
vdt.ValidateError.__init__(self, 'the value {} is repeated.'.format(value))
def is_cigale_list(inobject, dtype='float', minvalue=None, maxvalue=None,
"""Function that returns a list made of float or int numpy. It also checks
if any element is lower/high then a set minimum/maximum value or if any
does not belong to a predefined list. If any of the tests fails, an
exception is thrown. All the parameters besides "value" are strings because
configobj/validate pass arguments as such.
inobject: list or string
Object that we need to convert and verify
dtype: string
Desired type of the object
minvalue: string
Minimum value of all the elements
maxvalue: string
Maximum value of all the elements
options: string
All the values that the array can take
outobject: list
List of the requested type and respecting the constraints
if dtype == 'float':
dtype = float
conv_type = lambda x: float(x)
elif dtype == 'int':
dtype = int
conv_type = lambda x: int(float(x))
raise Exception("Unsupported data type. Only float and int are "
if isinstance(inobject, str):
if inobject.startswith('eval '):
outobject = eval(inobject[4:])
# If the evaluation lead to a single value, we put it in a list.
if not isinstance(outobject, Iterable):
outobject = [outobject]
elif inobject.startswith('range '):
start, stop, step = [conv_type(item) for item in inobject[5:].split()]
outobject = np.arange(start, stop+step, step)
# We need to return a list to combine the list of possible values
# for each parameter.
outobject = [inobject]
outobject = inobject
try: # We convert to an array as it is more convenient for tests
outobject = np.asarray(outobject, dtype)
except ValueError:
raise vdt.VdtValueError(inobject)
# Test if there are two identical elements
unique_outobject, counts = np.unique(outobject, return_counts=True)
if outobject.size > unique_outobject.size:
raise VdtValueRepeatedError(unique_outobject[counts > 1])
# Test if any value is smaller than the minimum value
if minvalue is not None:
minvalue = conv_type(minvalue)
if np.any(outobject < minvalue):
raise vdt.VdtValueTooSmallError(outobject[outobject < minvalue])
# Test if any value is larger than the maximum value
if maxvalue is not None:
maxvalue = conv_type(maxvalue)
if np.any(outobject > maxvalue):
raise vdt.VdtValueTooBigError(outobject[outobject > maxvalue])
# Test if any value is not in the list of allowed options
if options is not None:
options = {conv_type(option) for option in options.split('&')}
if not set(outobject).issubset(options):
raise vdt.VdtValueError(set(outobject) - options)
return list(outobject)
def is_cigale_string_list(inobject):
"""Function that returns a list of strings. If inobject is already a list,
it is returned as is. Otherwise the string is put into a list. If the
string is empty, it returns an empty list.
inobject: list or string
Object that we need to convert and verify
outobject: list
Object transformed into a list
if isinstance(inobject, str):
if len(inobject) == 0:
return []
return [inobject]
return inobject
# Dictionary of functions that are to be passed to the validator so it knows
# about extra tests that are not covered with the base functions
functions = {'cigale_list': is_cigale_list,
'cigale_string_list': is_cigale_string_list}
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