def _parseOverrides(overrides):
global scriptlogger
setting_overrides = {}
# parse overrides
if len(overrides) == 0:
scriptlogger.debug('No overrides found')
return setting_overrides
scriptlogger.debug('Reading parameter schema')
schemaFile, schemaFuncs = radiomics.getParameterValidationFiles()
with open(schemaFile) as schema:
settingsSchema = yaml.load(schema)['mapping']['setting']['mapping']
# parse single value function
def parse_value(value, value_type):
if value_type == 'str':
return value # no conversion
elif value_type == 'int':
return int(value)
elif value_type == 'float':
return float(value)
elif value_type == 'bool':
return value == '1' or value.lower() == 'true'
else:
raise ValueError('Cannot understand value_type %s' % value_type)
for setting in overrides: # setting = "setting_key:setting_value"
if ':' not in setting:
scriptlogger.warning('Incorrect format for override setting "%s", missing ":"', setting)
# split into key and value
setting_key, setting_value = setting.split(':', 2)
# Check if it is a valid PyRadiomics Setting
if setting_key not in settingsSchema:
scriptlogger.warning('Did not recognize override %s, skipping...', setting_key)
continue
# Try to parse the value by looking up its type in the settingsSchema
try:
setting_def = settingsSchema[setting_key]
setting_type = 'str' # If type is omitted in the schema, treat it as string (no conversion)
if 'seq' in setting_def:
# Multivalued setting
if len(setting_def['seq']) > 0 and 'type' in setting_def['seq'][0]:
setting_type = setting_def['seq'][0]['type']
setting_overrides[setting_key] = [parse_value(val, setting_type) for val in setting_value.split(',')]
scriptlogger.debug('Parsed "%s" as list (element type "%s"); value: %s',
setting_key, setting_type, setting_overrides[setting_key])
else:
if 'type' in setting_def:
setting_type = setting_def['type']
setting_overrides[setting_key] = parse_value(setting_value, setting_type)
scriptlogger.debug('Parsed "%s" as type "%s"; value: %s', setting_key, setting_type, setting_overrides[setting_key])
except Exception:
scriptlogger.warning('Could not parse value %s for setting %s, skipping...', setting_value, setting_key)
return setting_overrides
def test_files_with_unicode_content_failing(self, tmpdir):
"""
These tests should fail with the specified exception
"""
# To trigger schema exception we must pass in a source file
fail_data_2f_yaml = {
'schema': {
'type': 'map',
'mapping': {
'msg': {
'type': 'int',
},
}
},
'data': {
'msg': 'Foobar',
},
'errors': ["Value 'Foobar' is not of type 'int'. Path: '/msg'"]
}
source_f = tmpdir.join(u"2få.json")
source_f.write(yaml.safe_dump(fail_data_2f_yaml, allow_unicode=True))
_fail_tests = [
# Test mapping with unicode key and value but wrong type
(u"1f.yaml", SchemaError),
# Test unicode filename with validation errors.
# It is not possible to package a file with unicode characters
# like åäö in the filename in some python versions.
# Mock a file with åäö during testing to properly simulate this again.
(unicode(source_f), SchemaError),
# Test unicode data inside seq but wrong type
(u"3f.yaml", SchemaError),
]
for failing_test, exception_type in _fail_tests:
f = self.f(failing_test)
with open(f, "r") as stream:
yaml_data = yaml.load(stream)
data = yaml_data["data"]
schema = yaml_data["schema"]
errors = yaml_data["errors"]
try:
print(u"Running test files: {0}".format(f))
c = Core(source_data=data, schema_data=schema)
c.validate()
except exception_type:
pass # OK
else:
raise AssertionError(
u"Exception {0} not raised as expected... FILES: {1} : {2}"
.format(exception_type, exception_type))
compare(sorted(c.validation_errors),
sorted(errors),
prefix=u"Wrong validation errors when parsing files : {0}".
format(f))
def test_files_with_unicode_content_success(self, tmpdir):
"""
These tests should pass with no exception raised
"""
fail_data_2s_yaml = {
'schema': {
'type': 'map',
'mapping': {
'msg': {
'type': 'int',
},
}
},
'data': {
'msg': 123,
},
'errors': []
}
source_f = tmpdir.join(u"2så.json")
source_f.write(yaml.safe_dump(fail_data_2s_yaml, allow_unicode=True))
_pass_tests = [
# Test mapping with unicode key and value
u"1s.yaml",
# # Test unicode filename.
# It is not possible to package a file with unicode characters
# like åäö in the filename in some python versions.
# Mock a file with åäö during testing to properly simulate this again.
unicode(source_f),
# Test sequence with unicode keys
u"3s.yaml",
]
for passing_test_files in _pass_tests:
f = self.f(passing_test_files)
with open(f, "r") as stream:
yaml_data = yaml.load(stream)
data = yaml_data["data"]
schema = yaml_data["schema"]
try:
print(u"Running test files: {0}".format(f))
c = Core(source_data=data, schema_data=schema)
c.validate()
compare(c.validation_errors, [],
prefix="No validation errors should exist...")
except Exception as e:
print(u"ERROR RUNNING FILES: {0}".format(f))
raise e
# This serve as an extra schema validation that tests more complex structures then testrule.py do
compare(
c.root_rule.schema_str,
schema,
prefix=
u"Parsed rules is not correct, something have changed... files : {0}"
.format(f))
def test_files_with_unicode_content_failing(self, tmpdir):
"""
These tests should fail with the specified exception
"""
# To trigger schema exception we must pass in a source file
fail_data_2f_yaml = {
'schema': {
'type': 'map',
'mapping': {
'msg': {
'type': 'int',
},
}
},
'data': {
'msg': 'Foobar',
},
'errors': ["Value 'Foobar' is not of type 'int'. Path: '/msg'"]
}
source_f = tmpdir.join(u"2få.json")
source_f.write(yaml.safe_dump(fail_data_2f_yaml, allow_unicode=True))
_fail_tests = [
# Test mapping with unicode key and value but wrong type
(u"1f.yaml", SchemaError),
# Test unicode filename with validation errors.
# It is not possible to package a file with unicode characters
# like åäö in the filename in some python versions.
# Mock a file with åäö during testing to properly simulate this again.
(unicode(source_f), SchemaError),
# Test unicode data inside seq but wrong type
(u"3f.yaml", SchemaError),
]
for failing_test, exception_type in _fail_tests:
f = self.f(failing_test)
with open(f, "r") as stream:
yaml_data = yaml.load(stream)
data = yaml_data["data"]
schema = yaml_data["schema"]
errors = yaml_data["errors"]
try:
print(u"Running test files: {}".format(f))
c = Core(source_data=data, schema_data=schema)
c.validate()
except exception_type:
pass # OK
else:
raise AssertionError(u"Exception {} not raised as expected... FILES: {} : {}".format(exception_type, exception_type))
compare(sorted(c.validation_errors), sorted(errors), prefix=u"Wrong validation errors when parsing files : {}".format(f))
def test_files_with_unicode_content_success(self, tmpdir):
"""
These tests should pass with no exception raised
"""
fail_data_2s_yaml = {
'schema': {
'type': 'map',
'mapping': {
'msg': {
'type': 'int',
},
}
},
'data': {
'msg': 123,
},
'errors': []
}
source_f = tmpdir.join(u"2så.json")
source_f.write(yaml.safe_dump(fail_data_2s_yaml, allow_unicode=True))
_pass_tests = [
# Test mapping with unicode key and value
u"1s.yaml",
# # Test unicode filename.
# It is not possible to package a file with unicode characters
# like åäö in the filename in some python versions.
# Mock a file with åäö during testing to properly simulate this again.
unicode(source_f),
# Test sequence with unicode keys
u"3s.yaml",
]
for passing_test_files in _pass_tests:
f = self.f(passing_test_files)
with open(f, "r") as stream:
yaml_data = yaml.load(stream)
data = yaml_data["data"]
schema = yaml_data["schema"]
try:
print(u"Running test files: {}".format(f))
c = Core(source_data=data, schema_data=schema)
c.validate()
compare(c.validation_errors, [], prefix="No validation errors should exist...")
except Exception as e:
print(u"ERROR RUNNING FILES: {}".format(f))
raise e
# This serve as an extra schema validation that tests more complex structures then testrule.py do
compare(c.root_rule.schema_str, schema, prefix=u"Parsed rules is not correct, something have changed... files : {}".format(f))
def __init__(self, source_file=None, schema_files=[], source_data=None, schema_data=None, extensions=[]):
"""
:param extensions:
List of paths to python files that should be imported and available via 'func' keywork.
This list of extensions can be set manually or they should be provided by the `--extension`
flag from the cli. This list should not contain files specified by the `extensions` list keyword
that can be defined at the top level of the schema.
"""
log.debug(u"source_file: %s", source_file)
log.debug(u"schema_file: %s", schema_files)
log.debug(u"source_data: %s", source_data)
log.debug(u"schema_data: %s", schema_data)
log.debug(u"extension files: %s", extensions)
self.source = None
self.schema = None
self.validation_errors = None
self.validation_errors_exceptions = None
self.root_rule = None
self.extensions = extensions
self.errors = []
if source_file is not None:
if not os.path.exists(source_file):
raise CoreError(u"Provided source_file do not exists on disk: {}".format(source_file))
with open(source_file, "r") as stream:
if source_file.endswith(".json"):
try:
self.source = json.load(stream)
except Exception:
raise CoreError(u"Unable to load any data from source json file")
elif source_file.endswith(".yaml") or source_file.endswith('.yml'):
try:
self.source = yaml.load(stream)
except Exception:
raise CoreError(u"Unable to load any data from source yaml file")
else:
raise CoreError(u"Unable to load source_file. Unknown file format of specified file path: {}".format(source_file))
if not isinstance(schema_files, list):
raise CoreError(u"schema_files must be of list type")
# Merge all schema files into one single file for easy parsing
if len(schema_files) > 0:
schema_data = {}
for f in schema_files:
if not os.path.exists(f):
raise CoreError(u"Provided source_file do not exists on disk : {0}".format(f))
with open(f, "r") as stream:
if f.endswith(".json"):
try:
data = json.load(stream)
except Exception:
raise CoreError(u"No data loaded from file : {}".format(f))
elif f.endswith(".yaml") or f.endswith(".yml"):
data = yaml.load(stream)
if not data:
raise CoreError(u"No data loaded from file : {}".format(f))
else:
raise CoreError(u"Unable to load file : {} : Unknown file format. Supported file endings is [.json, .yaml, .yml]")
for key in data.keys():
if key in schema_data.keys():
raise CoreError(u"Parsed key : {} : two times in schema files...".format(key))
schema_data = dict(schema_data, **data)
self.schema = schema_data
# Nothing was loaded so try the source_data variable
if self.source is None:
log.debug(u"No source file loaded, trying source data variable")
self.source = source_data
if self.schema is None:
log.debug(u"No schema file loaded, trying schema data variable")
self.schema = schema_data
# Test if anything was loaded
if self.source is None:
raise CoreError(u"No source file/data was loaded")
if self.schema is None:
raise CoreError(u"No schema file/data was loaded")
# Merge any extensions defined in the schema with the provided list of extensions from the cli
for f in self.schema.get('extensions', []):
self.extensions.append(f)
if not isinstance(self.extensions, list) and all([isinstance(e, str) for e in self.extensions]):
raise CoreError(u"Specified extensions must be a list of file paths")
self._load_extensions()
def _parseOverrides(self):
setting_overrides = {}
# parse overrides
if len(self.args.setting) == 0:
self.logger.debug('No overrides found')
return setting_overrides
self.logger.debug('Reading parameter schema')
schemaFile, schemaFuncs = radiomics.getParameterValidationFiles()
with open(schemaFile) as schema:
settingsSchema = yaml.load(schema)['mapping']['setting']['mapping']
# parse single value function
def parse_value(value, value_type):
if value_type == 'str':
return value # no conversion
elif value_type == 'int':
return int(value)
elif value_type == 'float':
return float(value)
elif value_type == 'bool':
return value == '1' or value.lower() == 'true'
else:
raise ValueError('Cannot understand value_type "%s"' % value_type)
for setting in self.args.setting: # setting = "setting_key:setting_value"
if ':' not in setting:
self.logger.warning('Incorrect format for override setting "%s", missing ":"', setting)
continue
# split into key and value
setting_key, setting_value = setting.split(':', 2)
# Check if it is a valid PyRadiomics Setting
if setting_key not in settingsSchema:
self.logger.warning('Did not recognize override "%s", skipping...', setting_key)
continue
# Try to parse the value by looking up its type in the settingsSchema
try:
setting_def = settingsSchema[setting_key]
setting_type = 'str' # If type is omitted in the schema, treat it as string (no conversion)
if 'seq' in setting_def:
# Multivalued setting
if len(setting_def['seq']) > 0 and 'type' in setting_def['seq'][0]:
setting_type = setting_def['seq'][0]['type']
setting_overrides[setting_key] = [parse_value(val, setting_type) for val in setting_value.split(',')]
self.logger.debug('Parsed "%s" as list (element type "%s"); value: %s',
setting_key, setting_type, setting_overrides[setting_key])
else:
if 'type' in setting_def:
setting_type = setting_def['type']
setting_overrides[setting_key] = parse_value(setting_value, setting_type)
self.logger.debug('Parsed "%s" as type "%s"; value: %s', setting_key, setting_type,
setting_overrides[setting_key])
except (KeyboardInterrupt, SystemExit):
raise
except Exception:
self.logger.warning('Could not parse value "%s" for setting "%s", skipping...', setting_value, setting_key)
# Section for deprecated argument label
if self.args.label is not None:
self.logger.warning(
'Argument "label" is deprecated. To specify a custom label, use argument "setting" as follows:'
'"--setting=label:N", where N is the a label value.')
setting_overrides['label'] = self.args.label
# End deprecated section
return setting_overrides
def test_core_files(self):
# These tests should pass with no exception raised
pass_tests = [
# Test sequence with only string values
"1s.yaml",
# Test sequence where the only valid items is integers
"2s.yaml",
# Test sequence with only booleans
"3s.yaml",
# Test mapping with different types of data and some extra conditions
"4s.yaml",
# Test sequence with mapping with valid mapping
"5s.yaml",
# Test mapping with sequence with mapping and valid data
"6s.yaml",
# Test most of the implemented functions
"7s.yaml",
# This will test the unique constraint
"8s.yaml",
#
"9s.yaml",
#
"10s.yaml",
#
"11s.yaml",
# This tests number validation rule
"12s.yaml",
# This test the text validation rule
"13s.yaml",
# This test the any validation rule
"14s.yaml",
#
"15s.yaml",
#
# TODO: Currently slightly broken
# # "16s.yaml",
# This test that a regex that will compile
"17s.yaml",
# Test that type can be set to 'None' and it will validate ok
"18s.yaml",
# Test that range validates with map
"19s.yaml",
# Test that range validates with seq
"20s.yaml",
# Test that 'seq' can use seq instead of 'sequence'
"21s.yaml",
# Test that 'map' can be used instead of 'mapping'
"22s.yaml",
# Test that 're' can be used instead of 'regex'
"23s.yaml",
# Test that 'req' can be used instead of 'required'
"24s.yaml",
# Test that there is no need to specify 'type: seq' or 'type: map'
"25s.yaml",
# Test that the different types of timestamps can be validated
"26s.yaml",
# Test that multiple sequence values is supported
"27s.yaml",
# Test that multiple sequence values with matching 'all' is supported
"28s.yaml",
# Test that multiple sequence values with matching '*' is supported
"29s.yaml",
# Test that multiple sequence values with nested data structures work
"30s.yaml",
# Test that multiple sequence vlaues with nested lists works
"31s.yaml",
# Test Complex tree with many different structures
"32s.yaml",
# Test float range
"33s.yaml",
# Test float range with negative boundary
"34s.yaml",
# Test keyword regex default matching-rule any
"35s.yaml",
# Test keyword regex declared matching-rule any
"36s.yaml",
# Test keyword regex declared matching-rule all
"37s.yaml",
# Test mixed keyword regex and normal keyword
"38s.yaml",
]
_fail_tests = [
# Test sequence with defined string content type but data only has integers
("1f.yaml", SchemaError),
# Test sequence with defined string content type but data only has booleans
("2f.yaml", SchemaError),
# Test sequence with defined booleans but with one integer
("3f.yaml", SchemaError),
# Test sequence with strings and and lenght on each string
("4f.yaml", SchemaError),
# Test mapping that do not work
("5f.yaml", SchemaError),
# Test sequence with mapping with missing required key
("6f.yaml", SchemaError),
# Test mapping with sequence with mapping and invalid data
("7f.yaml", SchemaError),
#
("8f.yaml", SchemaError),
# TODO: The reverse unique do not currently work proper # This will test the unique constraint but should fail
("9f.yaml", SchemaError),
# This tests number validation rule with wrong data
("10f.yaml", SchemaError),
# This test the text validation rule with wrong data
("11f.yaml", SchemaError),
# This test that typechecking works when value in map is None
("12f.yaml", SchemaError),
# Test that range validates on 'map' raise correct error
("13f.yaml", SchemaError),
# Test that range validates on 'seq' raise correct error
("14f.yaml", SchemaError),
# Test timestamps that should throw errors
("15f.yaml", SchemaError),
# Test multiple sequence values with wrong sub type and 'any' matching rule
("16f.yaml", SchemaError),
# Test multiple sequence values with wrong sub type and 'all' matching rule
("17f.yaml", SchemaError),
# Test multiple nested sequence values with error in level 2 with 'any' matching rule
("18f.yaml", SchemaError),
# Test float range value out of range
("19f.yaml", SchemaError),
# Test float range value out of range (min-ex)
("20f.yaml", SchemaError),
# Test keyword regex using default matching-rule 'any'
("21f.yaml", SchemaError),
# Test keyword regex using declared matching-rule 'any'
("22f.yaml", SchemaError),
# Test keyword regex using declared matching-rule 'all'
("23f.yaml", SchemaError),
# Test that True/False is not valid integers
("24f.yaml", SchemaError),
]
# Add override magic to make it easier to test a specific file
if "S" in os.environ:
pass_tests = [os.environ["S"]]
_fail_tests = []
elif "F" in os.environ:
pass_tests = []
_fail_tests = [(os.environ["F"], SchemaError)]
for passing_test_file in pass_tests:
f = self.f(os.path.join("success", passing_test_file))
with open(f, "r") as stream:
yaml_data = yaml.load(stream)
data = yaml_data["data"]
schema = yaml_data["schema"]
try:
print("Running test files: {}".format(f))
c = Core(source_data=data, schema_data=schema)
c.validate()
compare(c.validation_errors, [], prefix="No validation errors should exist...")
except Exception as e:
print("ERROR RUNNING FILES: {}".format(f))
raise e
# This serve as an extra schema validation that tests more complex structures then testrule.py do
compare(c.root_rule.schema_str, schema, prefix="Parsed rules is not correct, something have changed... files : {}".format(f))
for failing_test, exception_type in _fail_tests:
f = self.f(os.path.join("fail", failing_test))
with open(f, "r") as stream:
yaml_data = yaml.load(stream)
data = yaml_data["data"]
schema = yaml_data["schema"]
errors = yaml_data["errors"]
try:
print("Running test files: {}".format(f))
c = Core(source_data=data, schema_data=schema)
c.validate()
except exception_type:
pass # OK
else:
raise AssertionError("Exception {} not raised as expected... FILES: {} : {}".format(exception_type, exception_type))
compare(sorted(c.validation_errors), sorted(errors), prefix="Wrong validation errors when parsing files : {}".format(f))
def __init__(self, source_file=None, schema_files=None, source_data=None, schema_data=None, extensions=None, strict_rule_validation=False,
fix_ruby_style_regex=False, allow_assertions=False,):
"""
:param extensions:
List of paths to python files that should be imported and available via 'func' keywork.
This list of extensions can be set manually or they should be provided by the `--extension`
flag from the cli. This list should not contain files specified by the `extensions` list keyword
that can be defined at the top level of the schema.
"""
if schema_files is None:
schema_files = []
if extensions is None:
extensions = []
log.debug(u"source_file: %s", source_file)
log.debug(u"schema_file: %s", schema_files)
log.debug(u"source_data: %s", source_data)
log.debug(u"schema_data: %s", schema_data)
log.debug(u"extension files: %s", extensions)
self.source = None
self.schema = None
self.validation_errors = None
self.validation_errors_exceptions = None
self.root_rule = None
self.extensions = extensions
self.errors = []
self.strict_rule_validation = strict_rule_validation
self.fix_ruby_style_regex = fix_ruby_style_regex
self.allow_assertions = allow_assertions
if source_file is not None:
if not os.path.exists(source_file):
raise CoreError(u"Provided source_file do not exists on disk: {0}".format(source_file))
with open(source_file, "r") as stream:
if source_file.endswith(".json"):
try:
self.source = json.load(stream)
except Exception:
raise CoreError(u"Unable to load any data from source json file")
elif source_file.endswith(".yaml") or source_file.endswith('.yml'):
try:
self.source = yaml.load(stream)
except Exception:
raise CoreError(u"Unable to load any data from source yaml file")
else:
raise CoreError(u"Unable to load source_file. Unknown file format of specified file path: {0}".format(source_file))
if not isinstance(schema_files, list):
raise CoreError(u"schema_files must be of list type")
# Merge all schema files into one single file for easy parsing
if len(schema_files) > 0:
schema_data = {}
for f in schema_files:
if not os.path.exists(f):
raise CoreError(u"Provided source_file do not exists on disk : {0}".format(f))
with open(f, "r") as stream:
if f.endswith(".json"):
try:
data = json.load(stream)
except Exception:
raise CoreError(u"No data loaded from file : {0}".format(f))
elif f.endswith(".yaml") or f.endswith(".yml"):
data = yaml.load(stream)
if not data:
raise CoreError(u"No data loaded from file : {0}".format(f))
else:
raise CoreError(u"Unable to load file : {0} : Unknown file format. Supported file endings is [.json, .yaml, .yml]")
for key in data.keys():
if key in schema_data.keys():
raise CoreError(u"Parsed key : {0} : two times in schema files...".format(key))
schema_data = dict(schema_data, **data)
self.schema = schema_data
# Nothing was loaded so try the source_data variable
if self.source is None:
log.debug(u"No source file loaded, trying source data variable")
self.source = source_data
if self.schema is None:
log.debug(u"No schema file loaded, trying schema data variable")
self.schema = schema_data
# Test if anything was loaded
if self.source is None:
raise CoreError(u"No source file/data was loaded")
if self.schema is None:
raise CoreError(u"No schema file/data was loaded")
# Merge any extensions defined in the schema with the provided list of extensions from the cli
for f in self.schema.get('extensions', []):
self.extensions.append(f)
if not isinstance(self.extensions, list) and all(isinstance(e, str) for e in self.extensions):
raise CoreError(u"Specified extensions must be a list of file paths")
self._load_extensions()
if self.strict_rule_validation:
log.info("Using strict rule keywords validation...")