def test_wrong_array_from_string(self):
"""Test that parsing an array from string is throwing the expected
exception when wrong input string"""
row = {'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'quantifier': 'manual',
'elementType': 'float',
'type': 'array',
'options': None,
'name': 'test'}
input_data_string = '[ [1,2 3] [4,5,6]]'
self.assertRaises(ValueError, string2array, input_data_string, ',', row['elementType'])
input_data_string = '[ [1,2,wrong], [4, 5, 6]]'
self.assertRaises(ValueError, string2array, input_data_string, ',', row['elementType'])
row = {'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'quantifier': 'manual',
'elementType': 'str',
'type': 'array',
'options': None,
'name': 'test'}
output = string2array(input_data_string, ',', row['elementType'])
self.assertEqual(output.shape, (2, 3))
self.assertEqual(output[0][2], 'wrong', 'String data not converted properly')
input_data_string = '[ [1,2 3] [4,5,6]]'
output = string2array(input_data_string, ',', row['elementType'])
self.assertEqual(output[0][1], '2 3')
def test_wrong_array_from_string(self):
"""Test that parsing an array from string is throwing the expected
exception when wrong input string"""
row = {'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'quantifier': 'manual',
'elementType': 'float',
'type': 'array',
'options': None,
'name': 'test'}
input_data_string = '[ [1,2 3] [4,5,6]]'
self.assertRaises(ValueError, string2array, input_data_string, ',', row['elementType'])
input_data_string = '[ [1,2,wrong], [4, 5, 6]]'
self.assertRaises(ValueError, string2array, input_data_string, ',', row['elementType'])
row = {'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'quantifier': 'manual',
'elementType': 'str',
'type': 'array',
'options': None,
'name': 'test'}
output = string2array(input_data_string, ',', row['elementType'])
self.assertEqual(output.shape, (2, 3))
self.assertEqual(output[0][2], 'wrong', 'String data not converted properly')
input_data_string = '[ [1,2 3] [4,5,6]]'
output = string2array(input_data_string, ',', row['elementType'])
self.assertEqual(output[0][1], '2 3')
def test_array_from_string(self):
"""
Simple test for parse array on 1d, 2d and 3d array.
"""
row = {
'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'quantifier': 'manual',
'elementType': 'float',
'type': 'array',
'options': None,
'name': 'test'
}
input_data_string = '[ [1 2 3] [4 5 6]]'
output = string2array(input_data_string, ' ', row['elementType'])
self.assertEqual(output.shape, (2, 3),
"Dimensions not properly parsed")
for i in output[0]:
self.assertTrue(i in [1, 2, 3])
for i in output[1]:
self.assertTrue(i in [4, 5, 6])
input_data_string = '[1, 2, 3, 4, 5, 6]'
output = string2array(input_data_string, ',', row['elementType'])
self.assertEqual(output.shape, (6, ), "Dimensions not properly parsed")
for i in output:
self.assertTrue(i in [1, 2, 3, 4, 5, 6])
input_data_string = '[ [ [1,1], [2, 2] ], [ [3 ,3], [4,4] ] ]'
output = string2array(input_data_string, ',', row['elementType'])
self.assertEqual(output.shape, (2, 2, 2), "Wrong dimensions.")
for i in output[0][0]:
self.assertTrue(i == 1)
for i in output[0][1]:
self.assertTrue(i == 2)
for i in output[1][0]:
self.assertTrue(i == 3)
for i in output[1][1]:
self.assertTrue(i == 4)
row = {
'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'quantifier': 'manual',
'elementType': 'str',
'type': 'array',
'options': None,
'name': 'test'
}
input_data_string = '[1, 2, 3, 4, 5, 6]'
output = string2array(input_data_string, ',', row['elementType'])
for i in output:
self.assertTrue(i in [1, 2, 3, 4, 5, 6])
def test_array_from_string(self):
"""
Simple test for parse array on 1d, 2d and 3d array.
"""
row = {
"description": "test.",
"default": "None",
"required": True,
"label": "test: ",
"attributes": None,
"quantifier": "manual",
"elementType": "float",
"type": "array",
"options": None,
"name": "test",
}
input_data_string = "[ [1 2 3] [4 5 6]]"
output = string2array(input_data_string, " ", row["elementType"])
self.assertEqual(output.shape, (2, 3), "Dimensions not properly parsed")
for i in output[0]:
self.assertTrue(i in [1, 2, 3])
for i in output[1]:
self.assertTrue(i in [4, 5, 6])
input_data_string = "[1, 2, 3, 4, 5, 6]"
output = string2array(input_data_string, ",", row["elementType"])
self.assertEqual(output.shape, (6,), "Dimensions not properly parsed")
for i in output:
self.assertTrue(i in [1, 2, 3, 4, 5, 6])
input_data_string = "[ [ [1,1], [2, 2] ], [ [3 ,3], [4,4] ] ]"
output = string2array(input_data_string, ",", row["elementType"])
self.assertEqual(output.shape, (2, 2, 2), "Wrong dimensions.")
for i in output[0][0]:
self.assertTrue(i == 1)
for i in output[0][1]:
self.assertTrue(i == 2)
for i in output[1][0]:
self.assertTrue(i == 3)
for i in output[1][1]:
self.assertTrue(i == 4)
row = {
"description": "test.",
"default": "None",
"required": True,
"label": "test: ",
"attributes": None,
"quantifier": "manual",
"elementType": "str",
"type": "array",
"options": None,
"name": "test",
}
input_data_string = "[1, 2, 3, 4, 5, 6]"
output = string2array(input_data_string, ",", row["elementType"])
for i in output:
self.assertTrue(i in [1, 2, 3, 4, 5, 6])
def test_array_from_string(self):
"""
Simple test for parse array on 1d, 2d and 3d array.
"""
row = {
'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'elementType': 'float',
'type': 'array',
'options': None,
'name': 'test'
}
input_data_string = '[ [1 2 3] [4 5 6]]'
output = string2array(input_data_string, ' ', row['elementType'])
assert output.shape, (2, 3) == "Dimensions not properly parsed"
for i in output[0]:
assert i in [1, 2, 3]
for i in output[1]:
assert i in [4, 5, 6]
input_data_string = '[1, 2, 3, 4, 5, 6]'
output = string2array(input_data_string, ',', row['elementType'])
assert output.shape == (6, ), "Dimensions not properly parsed"
for i in output:
assert i in [1, 2, 3, 4, 5, 6]
input_data_string = '[ [ [1,1], [2, 2] ], [ [3 ,3], [4,4] ] ]'
output = string2array(input_data_string, ',', row['elementType'])
assert output.shape == (2, 2, 2), "Wrong dimensions."
for i in output[0][0]:
assert i == 1
for i in output[0][1]:
assert i == 2
for i in output[1][0]:
assert i == 3
for i in output[1][1]:
assert i == 4
row = {
'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'elementType': 'str',
'type': 'array',
'options': None,
'name': 'test'
}
input_data_string = '[1, 2, 3, 4, 5, 6]'
output = string2array(input_data_string, ',', row['elementType'])
for i in output:
assert i in [1, 2, 3, 4, 5, 6]
def test_array_from_string(self):
"""
Simple test for parse array on 1d, 2d and 3d array.
"""
row = {'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'quantifier': 'manual',
'elementType': 'float',
'type': 'array',
'options': None,
'name': 'test'}
input_data_string = '[ [1 2 3] [4 5 6]]'
output = string2array(input_data_string, ' ', row['elementType'])
self.assertEqual(output.shape, (2, 3), "Dimensions not properly parsed")
for i in output[0]:
self.assertTrue(i in [1, 2, 3])
for i in output[1]:
self.assertTrue(i in [4, 5, 6])
input_data_string = '[1, 2, 3, 4, 5, 6]'
output = string2array(input_data_string, ',', row['elementType'])
self.assertEqual(output.shape, (6,), "Dimensions not properly parsed")
for i in output:
self.assertTrue(i in [1, 2, 3, 4, 5, 6])
input_data_string = '[ [ [1,1], [2, 2] ], [ [3 ,3], [4,4] ] ]'
output = string2array(input_data_string, ',', row['elementType'])
self.assertEqual(output.shape, (2, 2, 2), "Wrong dimensions.")
for i in output[0][0]:
self.assertTrue(i == 1)
for i in output[0][1]:
self.assertTrue(i == 2)
for i in output[1][0]:
self.assertTrue(i == 3)
for i in output[1][1]:
self.assertTrue(i == 4)
row = {'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'quantifier': 'manual',
'elementType': 'str',
'type': 'array',
'options': None,
'name': 'test'}
input_data_string = '[1, 2, 3, 4, 5, 6]'
output = string2array(input_data_string, ',', row['elementType'])
for i in output:
self.assertTrue(i in [1, 2, 3, 4, 5, 6])
def test_array_from_string(self):
"""
Simple test for parse array on 1d, 2d and 3d array.
"""
row = {'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'elementType': 'float',
'type': 'array',
'options': None,
'name': 'test'}
input_data_string = '[ [1 2 3] [4 5 6]]'
output = string2array(input_data_string, ' ', row['elementType'])
assert output.shape, (2, 3) == "Dimensions not properly parsed"
for i in output[0]:
assert i in [1, 2, 3]
for i in output[1]:
assert i in [4, 5, 6]
input_data_string = '[1, 2, 3, 4, 5, 6]'
output = string2array(input_data_string, ',', row['elementType'])
assert output.shape == (6,), "Dimensions not properly parsed"
for i in output:
assert i in [1, 2, 3, 4, 5, 6]
input_data_string = '[ [ [1,1], [2, 2] ], [ [3 ,3], [4,4] ] ]'
output = string2array(input_data_string, ',', row['elementType'])
assert output.shape == (2, 2, 2), "Wrong dimensions."
for i in output[0][0]:
assert i == 1
for i in output[0][1]:
assert i == 2
for i in output[1][0]:
assert i == 3
for i in output[1][1]:
assert i == 4
row = {'description': 'test.',
'default': 'None',
'required': True,
'label': 'test: ',
'attributes': None,
'elementType': 'str',
'type': 'array',
'options': None,
'name': 'test'}
input_data_string = '[1, 2, 3, 4, 5, 6]'
output = string2array(input_data_string, ',', row['elementType'])
for i in output:
assert i in [1, 2, 3, 4, 5, 6]
def _convert_to_array(self, input_data, row):
"""
Method used when the type of an input is array, to parse or read.
If the user set an equation for computing a model parameter then the
value of that parameter will be a dictionary which contains all the data
needed for computing that parameter for each vertex from the used surface.
"""
if KEY_EQUATION in str(input_data) and KEY_FOCAL_POINTS in str(
input_data) and KEY_SURFACE_GID in str(input_data):
try:
input_data = eval(str(input_data))
# TODO move at a different level
equation_type = input_data.get(KEY_DTYPE)
if equation_type is None:
self.log.warning(
"Cannot figure out type of equation from input dictionary: %s. "
"Returning []." % input_data)
return []
eq_class = get_class_by_name(equation_type)
equation = eq_class.from_json(input_data[KEY_EQUATION])
focal_points = json.loads(input_data[KEY_FOCAL_POINTS])
surface_gid = input_data[KEY_SURFACE_GID]
surface = load_entity_by_gid(surface_gid)
return surface.compute_equation(focal_points, equation)
except Exception:
self.log.exception(
"The parameter %s was ignored. None value was returned.",
row['name'])
return None
dtype = None
if KEY_DTYPE in row:
dtype = row[KEY_DTYPE]
return string2array(str(input_data), ",", dtype)
def _convert_to_array(self, input_data, row):
"""
Method used when the type of an input is array, to parse or read.
If the user set an equation for computing a model parameter then the
value of that parameter will be a dictionary which contains all the data
needed for computing that parameter for each vertex from the used surface.
"""
if KEY_EQUATION in str(input_data) and KEY_FOCAL_POINTS in str(input_data) and KEY_SURFACE_GID in str(input_data):
try:
input_data = eval(str(input_data))
# TODO move at a different level
equation_type = input_data.get(KEY_DTYPE)
if equation_type is None:
self.log.warning("Cannot figure out type of equation from input dictionary: %s. "
"Returning []." % input_data)
return []
eq_class = get_class_by_name(equation_type)
equation = eq_class.from_json(input_data[KEY_EQUATION])
focal_points = json.loads(input_data[KEY_FOCAL_POINTS])
surface_gid = input_data[KEY_SURFACE_GID]
surface = load_entity_by_gid(surface_gid)
return surface.compute_equation(focal_points, equation)
except Exception:
self.log.exception("The parameter %s was ignored. None value was returned.", row['name'])
return None
dtype = None
if KEY_DTYPE in row:
dtype = row[KEY_DTYPE]
return string2array(str(input_data), ",", dtype)
def _convert_to_array(self, input_data, row):
"""
Method used when the type of an input is array, to parse or read.
If the user set an equation for computing a model parameter then the
value of that parameter will be a dictionary which contains all the data
needed for computing that parameter for each vertex from the used surface.
"""
if KEY_EQUATION in str(input_data) and KEY_FOCAL_POINTS in str(input_data) and KEY_SURFACE_GID in str(input_data):
try:
input_data = eval(str(input_data))
# TODO move at a different level
equation_type = input_data.get(KEY_DTYPE, None)
if equation_type is None:
self.log.warning("Cannot figure out type of equation from input dictionary: %s. "
"Returning []." % (str(input_data, )))
return []
splitted_class = equation_type.split('.')
module = '.'.join(splitted_class[:-1])
classname = splitted_class[-1]
eq_module = __import__(module, globals(), locals(), [classname])
eq_class = eval('eq_module.' + classname)
equation = eq_class.from_json(input_data[KEY_EQUATION])
focal_points = json.loads(input_data[KEY_FOCAL_POINTS])
surface_gid = input_data[KEY_SURFACE_GID]
surface = load_entity_by_gid(surface_gid)
return surface.compute_equation(focal_points, equation)
except Exception:
self.log.exception("The parameter '" + str(row['name']) + "' was ignored. None value was returned.")
return None
if xml_reader.ATT_QUATIFIER in row:
quantifier = row[xml_reader.ATT_QUATIFIER]
dtype = None
if KEY_DTYPE in row:
dtype = row[KEY_DTYPE]
if quantifier == xml_reader.QUANTIFIER_MANUAL:
return string2array(str(input_data), ",", dtype)
elif quantifier == xml_reader.QUANTIFIER_UPLOAD:
input_str = open(input_data, 'r').read()
return string2array(input_str, " ", dtype)
elif quantifier == xml_reader.QUANTIFIER_FUNTION:
return input_data
return None
def test_string2array(self):
"""
Check the string2array method for various inputs
"""
test_string_arrays = ['[1,2,3]', '1,2,3', '1 2 3']
array_separators = [',', ',', ' ']
for idx in xrange(len(test_string_arrays)):
result_array = string2array(test_string_arrays[idx], array_separators[idx])
self.assertEqual(len(result_array), 3)
self.assertEqual(result_array[0], 1)
self.assertEqual(result_array[1], 2)
self.assertEqual(result_array[2], 3)
def test_string2array(self):
"""
Check the string2array method for various inputs
"""
test_string_arrays = ['[1,2,3]', '1,2,3', '1 2 3']
array_separators = [',', ',', ' ']
for idx in range(len(test_string_arrays)):
result_array = string2array(test_string_arrays[idx], array_separators[idx])
assert len(result_array) == 3
assert result_array[0] == 1
assert result_array[1] == 2
assert result_array[2] == 3
def test_string2array(self):
"""
Check the string2array method for various inputs
"""
test_string_arrays = ['[1,2,3]', '1,2,3', '1 2 3']
array_separators = [',', ',', ' ']
for idx in xrange(len(test_string_arrays)):
result_array = string2array(test_string_arrays[idx],
array_separators[idx])
self.assertEqual(len(result_array), 3)
self.assertEqual(result_array[0], 1)
self.assertEqual(result_array[1], 2)
self.assertEqual(result_array[2], 3)
def test_wrong_array_from_string(self):
"""Test that parsing an array from string is throwing the expected
exception when wrong input string"""
row = {
"description": "test.",
"default": "None",
"required": True,
"label": "test: ",
"attributes": None,
"quantifier": "manual",
"elementType": "float",
"type": "array",
"options": None,
"name": "test",
}
input_data_string = "[ [1,2 3] [4,5,6]]"
self.assertRaises(ValueError, string2array, input_data_string, ",", row["elementType"])
input_data_string = "[ [1,2,wrong], [4, 5, 6]]"
self.assertRaises(ValueError, string2array, input_data_string, ",", row["elementType"])
row = {
"description": "test.",
"default": "None",
"required": True,
"label": "test: ",
"attributes": None,
"quantifier": "manual",
"elementType": "str",
"type": "array",
"options": None,
"name": "test",
}
output = string2array(input_data_string, ",", row["elementType"])
self.assertEqual(output.shape, (2, 3))
self.assertEqual(output[0][2], "wrong", "String data not converted properly")
input_data_string = "[ [1,2 3] [4,5,6]]"
output = string2array(input_data_string, ",", row["elementType"])
self.assertEqual(output[0][1], "2 3")
def _get_dictionary(row, **kwargs):
"""
Find all key/value pairs for the dictionary represented by name.
"""
if InputTreeManager._is_parent_not_submitted(row, kwargs):
return {}, []
name = row[xml_reader.ATT_NAME]
result_dict = {}
taken_keys = []
for key in kwargs:
if name in key and name != key:
taken_keys.append(key)
if KEY_DTYPE in row:
if row[KEY_DTYPE] == 'array':
val = string2array(kwargs[key], " ", "float")
else:
val = eval(row[KEY_DTYPE] + "('" + kwargs[key] + "')")
else:
val = str(kwargs[key])
result_dict[key.split(KEYWORD_PARAMS[1:])[-1]] = val
return result_dict, taken_keys
def _get_dictionary(row, **kwargs):
"""
Find all key/value pairs for the dictionary represented by name.
"""
if InputTreeManager._is_parent_not_submitted(row, kwargs):
return {}, []
name = row[KEY_NAME]
result_dict = {}
taken_keys = []
for key in kwargs:
if name in key and name != key:
taken_keys.append(key)
if KEY_DTYPE in row:
if row[KEY_DTYPE] == 'array':
val = string2array(kwargs[key], " ", "float")
else:
val = eval(row[KEY_DTYPE])(kwargs[key])
else:
val = str(kwargs[key])
result_dict[key.split(KEYWORD_PARAMS[1:])[-1]] = val
return result_dict, taken_keys