def test_rule_set(self):
ruleset = validation.read_in_ruleset("test_data/test_ruleset.json")
section_names = [
'standard', 'warships', 'transports', 'dummy transport'
]
self.assertListEqual(ruleset.get_all_section_names(), section_names)
self.assertRaises(ValueError, ruleset.get_section_by_name,
'not existing')
warships_section = ruleset.get_section_by_name('warships')
self.assertEqual(warships_section.get_section_name(), "warships")
# test add rule section
new_section = Ruleset.RuleSection('new')
duplicate_section = Ruleset.RuleSection('standard')
self.assertRaises(ValueError, ruleset.add_rule_section,
duplicate_section)
ruleset.add_rule_section(new_section)
section_names.append('new')
self.assertListEqual(ruleset.get_all_section_names(), section_names)
filename = "test_data/test_data.json"
# NOTE: file are supposed to exists while testing
with open(filename) as infile:
data = json.load(infile)
ruleset.validate(data[0], "id")
def read_in_ruleset(self, ruleset_filename):
try:
self.ruleset = validation.read_in_ruleset(ruleset_filename)
except json.JSONDecodeError as message:
logger.error("Error with 'https://www.ebi.ac.uk/ols/api/': %s" %
(str(message)))
raise OntologyCacheError(
"Issue with 'https://www.ebi.ac.uk/ols/api/'")
def test_rule_section(self):
ruleset = validation.read_in_ruleset("test_data/test_ruleset.json")
warships_section = ruleset.get_section_by_name('warships')
self.assertRaises(TypeError, warships_section.add_condition, 12,
'value')
self.assertRaises(TypeError, warships_section.add_condition, True,
'value')
self.assertRaises(TypeError, warships_section.add_condition, 'field',
-12.34)
self.assertRaises(TypeError, warships_section.add_condition, 'field',
False)
expected_conditions = {'role': 'warship'}
self.assertDictEqual(warships_section.get_conditions(),
expected_conditions)
self.assertRaises(ValueError, warships_section.add_condition, 'role',
'second role')
self.assertRaises(
ValueError, warships_section.add_rule,
Ruleset.RuleField("weapon", "limited value", 'mandatory'))
rules = warships_section.get_rules()
self.assertTrue('mandatory' in rules)
self.assertTrue('weapon' in rules['mandatory'])
rule = rules['mandatory']['weapon']
self.assertTrue(type(rule) is Ruleset.RuleField)
self.assertRaises(TypeError,
warships_section.check_contain_rule_for_field, False)
self.assertRaises(TypeError,
warships_section.check_contain_rule_for_field, 12)
self.assertFalse(
warships_section.check_contain_rule_for_field('random'))
self.assertTrue(
warships_section.check_contain_rule_for_field('weapon'))
# test meet condition
filename = "test_data/test_data.json"
# NOTE: file are supposed to exists while testing
with open(filename) as infile:
data = json.load(infile)
transport_data = data[0]
warship_data = data[1]
self.assertRaises(TypeError, warships_section.meet_condition, 'dict')
self.assertRaises(TypeError, warships_section.meet_condition, 12)
self.assertRaises(KeyError, warships_section.meet_condition,
transport_data['attributes'])
self.assertFalse(warships_section.meet_condition(transport_data))
self.assertTrue(warships_section.meet_condition(warship_data))
standard_section = ruleset.get_section_by_name("standard")
self.assertTrue(standard_section.meet_condition(warship_data))
self.assertTrue(standard_section.meet_condition(transport_data))
def test_check_ruleset(self):
filename = "test_data/test_error_ruleset_missing_attributes.json"
self.assertRaises(KeyError, validation.read_in_ruleset, filename)
expected: List[str] = [
'Error: Valid units provided for field id having type as text which does not expect units',
'Error: Field crew_capacity has type as number but no valid units provided',
'Error: No valid values should be provided to field class as being of text type',
'Error: No valid terms provided to field Fake which is essential to be of ontology_id type',
'Error: There is no allowed values for field Availability being of limited value type',
'Error: No valid values should be provided to field manufacturer country as being of ontology_id type',
'Warning: Ontology terms are provided for field color. '
'Please re-consider whether it needs to change to ontology_id type.'
]
filename = "test_data/test_error_ruleset.json"
ruleset = validation.read_in_ruleset(filename)
results = validation.check_ruleset(ruleset)
self.assertListEqual(expected, results.get_messages())
print("here")
print(results.get_messages())
expected = []
ruleset = validation.read_in_ruleset(static_parameters.ruleset_filename)
results = validation.check_ruleset(ruleset)
self.assertListEqual(expected, results.get_messages())
def test_image_sample(self):
# get image test file
filename = "test_data/image_sample.json"
# NOTE: file are supposed to exists while testing
with open(filename) as infile:
sample = json.load(infile)
# read ruleset
ruleset = validation.read_in_ruleset(
static_parameters.ruleset_filename)
# now check sample
result = ruleset.validate(sample).get_messages()
self.assertEqual(result, [])
def test_validate(self):
ruleset = validation.read_in_ruleset("test_data/test_ruleset.json")
expected_result: Dict[str, List[str]] = {
"cardinality": [
'Error: Multiple values supplied for field passenger_capacity which does not allow multiple values '
'(standard section) for Record 404-T-132-4FE274A',
'Error: Mandatory field crew_capacity has empty value (standard section) for Record 404-T-132-4FE274A',
'Error: Maximum of 2 values allowed for field color but 3 values provided (standard section)'
' for Record 404-T-132-4FE274A',
'Warning: recommended field manufacturer country has empty value, '
'better remove the field (standard section) for Record 502-W-133-4FE274B',
"{'Pass': 0, 'Warning': 1, 'Error': 1}"
],
"units": [
'Error: One of km, m need to be present for the field length '
'(standard section) for Record 404-T-132-4FE274A',
'Error: g for field cargo_capacity is not in the valid units list (kg) '
'(transports section) for Record 404-T-132-4FE274A',
'Warning: No units required but person is used as unit for field id '
'(standard section) for Record 502-W-133-4FE274B',
"{'Pass': 0, 'Warning': 1, 'Error': 1}"
],
"values": [
'Error: <None> of field Availability is neither "no longer available" nor a valid URI '
'(standard section) for Record 404-T-132-4FE274A',
'Error: <purple> of field color is not in the valid values list '
'(<red>, <yellow>, <blue>) (standard section) for Record 502-W-133-4FE274B',
"{'Pass': 0, 'Warning': 0, 'Error': 2}"
],
"allowed_terms": [
'Error: Invalid URI value wrong url in field manufacturer country '
'(standard section) for Record 404-T-132-4FE274A',
'Warning: Ontology provided for field role however there is no requirement in the ruleset '
'(standard section) for Record 404-T-132-4FE274A',
'Error: Not valid ontology term PATO_0000383 in field manufacturer country'
' (standard section) for Record 502-W-133-4FE274B',
"{'Pass': 0, 'Warning': 0, 'Error': 2}"
],
"extra_and_missing_field": [
'Error: Mandatory field passenger_capacity in standard section could not be found '
'for Record 404-T-132-4FE274A',
'Warning: Column extra could not be found in ruleset for Record 502-W-133-4FE274B',
"{'Pass': 0, 'Warning': 1, 'Error': 1}"
],
"types": [
'Error: For field crew_capacity the provided value 5 is not represented as/of the expected type Number '
'(standard section) for Record 404-T-132-4FE274A',
'Error: For field instruction the provided value 5 is not of the expected type doi '
'(standard section) for Record 404-T-132-4FE274A',
'Error: Invalid URI value wrong url for field video demo '
'(standard section) for Record 404-T-132-4FE274A',
'Error: The date value 15-07-2408 does not match to the format YYYY-MM-DD '
'(standard section) for Record 404-T-132-4FE274A',
'Error: No url found for the field manufacturer country which has the type of ontology_id '
'(standard section) for Record 404-T-132-4FE274A',
'Error: Invalid DOI value supplied in the field instruction '
'(standard section) for Record 502-W-133-4FE274B',
'Error: One of YYYY-MM-DD, YYYY-MM need to be present for the field production date '
'(standard section) for Record 502-W-133-4FE274B',
'Warning: Provided iri http://wrong.iri.com/obo/NCIT_C17233 does not match '
'the iri retrieved from OLS in the field manufacturer country '
'(standard section) for Record 502-W-133-4FE274B',
"{'Pass': 0, 'Warning': 0, 'Error': 2}"
],
"types2": [
'Error: Email address must have prefix "mailto:" in the field video demo '
'(standard section) for Record 404-T-132-4FE274A',
'Warning: Provided value United kingdom has different letter case to the term '
'referenced by http://purl.obolibrary.org/obo/NCIT_C17233 (standard section) '
'for Record 404-T-132-4FE274A',
'Error: mailto must be at position 1 to be a valid email value in the field video demo '
'(standard section) for Record 502-W-133-4FE274B',
'Error: Provided value United Kingdom does not match to the provided ontology '
'http://purl.obolibrary.org/obo/NCIT_C16699 (standard section) for Record '
'502-W-133-4FE274B', "{'Pass': 0, 'Warning': 0, 'Error': 2}"
]
}
self.maxDiff = None
for error_type in expected_result.keys():
filename = "test_data/data/test_error_rule_" + error_type + ".json"
# NOTE: file are supposed to exists while testing
with open(filename) as infile:
data = json.load(infile)
submission_result: List[
ValidationResult.ValidationResultRecord] = []
actual_values: List[str] = []
for record in data:
record_result = ruleset.validate(record, "id")
if record_result.is_empty():
record_result.add_validation_result_column(
ValidationResult.ValidationResultColumn(
"Pass", "", record_result.record_id, ""))
submission_result.append(record_result)
for msg in record_result.get_messages():
actual_values.append(msg)
summary, vcr_summary, vcr_details = \
validation.deal_with_validation_results(submission_result, verbose=False)
summary_str = str(summary)
actual_values.append(summary_str)
self.assertListEqual(expected_result[error_type], actual_values)
def test_rule_set_serializer(self):
ruleset = validation.read_in_ruleset("test_data/test_ruleset.json")
# test string serialization
self.assertIsInstance(ruleset.to_json(), str)