diff --git a/.travis.yml b/.travis.yml index 9d8d3a442..6bbca1c19 100644 --- a/.travis.yml +++ b/.travis.yml @@ -18,7 +18,7 @@ install: - poetry install -vv script: - - poetry run pytest -vv + - poetry run pytest -vv tests before_deploy: - poetry config pypi-token.pypi $PYPI_API_TOKEN diff --git a/example_validation.py b/example_validation.py new file mode 100644 index 000000000..9528666be --- /dev/null +++ b/example_validation.py @@ -0,0 +1,70 @@ +""" +This is an example of validating json dictionaries (e.g., gdcdictionary/examples) +against the schemas in the local yaml files. + +Example usage: +python example_validation.py gdcdictionary/examples/valid/*json +""" + +from jsonschema import ValidationError +import argparse +import json + +from gdcdictionary import gdcdictionary +from tests.utils import validate_entity + +if __name__ == '__main__': + + #################### + # Setup + #################### + + + parser = argparse.ArgumentParser(description='Validate JSON') + parser.add_argument('jsonfiles', metavar='file', + type=argparse.FileType('r'), nargs='+', + help='json files to test if (in)valid') + + parser.add_argument('--invalid', action='store_true', default=False, + help='expect the files to be invalid instead of valid') + + args = parser.parse_args() + + #################### + # Example validation + #################### + + # Load schemata + dictionary = gdcdictionary + + for f in args.jsonfiles: + doc = json.load(f) + if args.invalid: + try: + print("CHECK if {0} is invalid:".format(f.name), end=" ") + print(type(doc)) + if type(doc) == dict: + validate_entity(doc, dictionary.schema) + elif type(doc) == list: + for entity in doc: + validate_entity(entity, dictionary.schema) + else: + raise ValidationError("Invalid json") + except ValidationError as e: + print("Invalid as expected.") + pass + else: + raise Exception("Expected invalid, but validated.") + else: + print("CHECK if {0} is valid:".format(f.name), end=" ") + if type(doc) == dict: + validate_entity(doc, dictionary.schema) + elif type(doc) == list: + for entity in doc: + validate_entity(entity, dictionary.schema) + else: + print("Invalid json") + + print("Valid as expected") + + print('ok.') diff --git a/gdcdictionary/schema_test.py b/gdcdictionary/schema_test.py deleted file mode 100644 index d5d124986..000000000 --- a/gdcdictionary/schema_test.py +++ /dev/null @@ -1,201 +0,0 @@ -"""This is an example of json schema for the GDC using schemas defined -in local yaml files. - -Included are a few functions to augment jsonschema and the python -validator. - -Examples are at the end. - -""" - -from __future__ import print_function - -from jsonschema import validate, ValidationError -import copy -import yaml -import glob -import os -import argparse -import json -import unittest -from gdcdictionary import gdcdictionary - - - -def load_yaml_schema(path): - with open(path, 'r') as f: - return yaml.safe_load(f) -CUR_DIR = os.path.dirname(os.path.realpath(__file__)) -DATA_DIR = os.path.join(CUR_DIR, 'examples') -project1 = load_yaml_schema(os.path.join(CUR_DIR, 'schemas/projects/project1.yaml')) -projects = {'project1': project1} - -def merge_schemas(a, b, path=None): - """Recursively zip schemas together - - """ - path = path if path is not None else [] - for key in b: - if key in a: - if isinstance(a[key], dict) and isinstance(b[key], dict): - merge_schemas(a[key], b[key], path + [str(key)]) - elif a[key] == b[key]: - pass - else: - print("Overriding '{}':\n\t- {}\n\t+ {}".format( - '.'.join(path + [str(key)]), a[key], b[key])) - a[key] = b[key] - else: - print("Adding '{}':\n\t+ {}".format( - '.'.join(path + [str(key)]), b[key])) - a[key] = b[key] - return a - - -def get_project_specific_schema(projects, project, schema, entity_type): - """Look up the core schema for its type and override it with any - project level overrides - - """ - root = copy.deepcopy(schema) - project_overrides = projects.get(project) - if project_overrides: - overrides = project_overrides.get(entity_type) - if overrides: - merge_schemas(root, overrides, [entity_type]) - return root - - -def validate_entity(entity, schemata, project=None, name=''): - """Validate an entity by looking up the core schema for its type and - overriding it with any project level overrides - - """ - local_schema = get_project_specific_schema( - projects, project, schemata[entity['type']], entity['type']) - result = validate(entity, local_schema) - return result - - -def validate_schemata(schemata, metaschema): - # validate schemata - print('Validating schemas against metaschema... ', end=" ") - for s in schemata.values(): - validate(s, metaschema) - - def assert_link_is_also_prop(link): - assert link in s['properties'],\ - "Entity '{}' has '{}' as a link but not property".format( - s['id'], link) - - for link in [l['name'] for l in s['links'] if 'name' in l]: - assert_link_is_also_prop(link) - for subgroup in [l['subgroup'] for l in s['links'] if 'name' not in l]: - for link in [l['name'] for l in subgroup if 'name' in l]: - assert_link_is_also_prop(link) - - -class SchemaTest(unittest.TestCase): - def setUp(self): - self.dictionary = gdcdictionary - self.definitions = yaml.safe_load(open(os.path.join(CUR_DIR, 'schemas','_definitions.yaml'),'r')) - - def test_schemas(self): - validate_schemata(self.dictionary.schema, self.dictionary.metaschema) - - def test_valid_files(self): - for path in glob.glob(os.path.join(DATA_DIR, 'valid', '*.json')): - print("Validating {}".format(path)) - doc = json.load(open(path, 'r')) - print(doc) - if type(doc) == dict: - self.add_system_props(doc) - validate_entity(doc, self.dictionary.schema) - elif type(doc) == list: - for entity in doc: - self.add_system_props(entity) - validate_entity(entity, self.dictionary.schema) - else: - raise Exception("Invalid json") - - def test_invalid_files(self): - for path in glob.glob(os.path.join(DATA_DIR, 'invalid', '*.json')): - print("Validating {}".format(path)) - doc = json.load(open(path, 'r')) - if type(doc) == dict: - self.add_system_props(doc) - with self.assertRaises(ValidationError): - validate_entity(doc, self.dictionary.schema) - elif type(doc) == list: - for entity in doc: - self.add_system_props(entity) - with self.assertRaises(ValidationError): - validate_entity(entity, self.dictionary.schema) - else: - raise Exception("Invalid json") - - def add_system_props(self, doc): - schema = self.dictionary.schema[doc['type']] - for key in schema['systemProperties']: - use_def_default = ( - '$ref' in schema['properties'][key] and - key in self.definitions and - 'default' in self.definitions[key] - ) - if use_def_default: - doc[key] = self.definitions[key]['default'] - -if __name__ == '__main__': - - #################### - # Setup - #################### - - - parser = argparse.ArgumentParser(description='Validate JSON') - parser.add_argument('jsonfiles', metavar='file', - type=argparse.FileType('r'), nargs='*', - help='json files to test if (in)valid') - - parser.add_argument('--invalid', action='store_true', default=False, - help='expect the files to be invalid instead of valid') - - args = parser.parse_args() - - #################### - # Example validation - #################### - - # Load schemata - dictionary = gdcdictionary - - for f in args.jsonfiles: - doc = json.load(f) - if args.invalid: - try: - print("CHECK if {0} is invalid:".format(f.name), end=" ") - print(type(doc)) - if type(doc) == dict: - validate_entity(doc, dictionary.schema) - elif type(doc) == list: - for entity in doc: - validate_entity(entity, dictionary.schema) - else: - raise ValidationError("Invalid json") - except ValidationError as e: - print("Invalid as expected.") - pass - else: - raise Exception("Expected invalid, but validated.") - else: - print("CHECK if {0} is valid:".format(f.name), end=" ") - if type(doc) == dict: - validate_entity(doc, dictionary.schema) - elif type(doc) == list: - for entity in doc: - validate_entity(entity, dictionary.schema) - else: - print("Invalid json") - - print("Valid as expected") - print('ok.') diff --git a/poetry.lock b/poetry.lock index e10be5e65..50328d3ea 100644 --- a/poetry.lock +++ b/poetry.lock @@ -42,101 +42,127 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.3.2" +version = "3.4.0" description = "The Real First Universal Charset Detector. 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["zstandard (>=0.18.0)"] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "e3c96326f698182862e2f85020c27f612d3320a6a6e4720673b1d521069340a9" +content-hash = "c9056adf146f14bb7c5a50f52baaf9f19c9c538e77559e625e7ebc314a107263" diff --git a/pyproject.toml b/pyproject.toml index 856da3519..081e3bf49 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "gen3Dictionary" -version = "2.0.4" +version = "2.0.5" description = "" authors = ["CTDS UChicago "] license = "Apache-2.0" @@ -9,10 +9,13 @@ packages = [{include = "gdcdictionary"}] [tool.poetry.dependencies] python = "^3.9" -PyYAML = "*" +PyYAML = ">= 6.0" jsonschema = "*" dictionaryutils = "*" +[tool.poetry.dev-dependencies] +pytest = "*" + [build-system] requires = ["poetry>=0.12"] build-backend = "poetry.core.masonry.api" diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 000000000..8ebf82c18 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,23 @@ +""" + Conftest.py a configuration file for pytest +""" +import os + +import pytest +from gdcdictionary import SCHEMA_DIR, GDCDictionary +from tests.utils import load_yaml + + +@pytest.fixture(scope="session") +def dictionary(): + return GDCDictionary(root_dir=SCHEMA_DIR) + + +@pytest.fixture(scope="session") +def definitions(dictionary): + return load_yaml(os.path.join(SCHEMA_DIR, '_definitions.yaml')) + + +@pytest.fixture(scope="session") +def schema(dictionary): + return dictionary.schema diff --git a/tests/test_json_validation.py b/tests/test_json_validation.py new file mode 100644 index 000000000..0a5b2a4a1 --- /dev/null +++ b/tests/test_json_validation.py @@ -0,0 +1,52 @@ +"""This is an example of json schema for the GDC using schemas defined +in local yaml files (see gdcdictionary/examples). + +This test class is making sure the example jsons comply with the schema. + +Note this is NOT testing that the schema is sane. Just that we adhere +to it + +""" + +import json +import glob +import os + +from jsonschema import ValidationError + +from tests.utils import BaseTest, DATA_DIR, validate_entity + +def get_all_paths(subdir): + for path in sorted(glob.glob(os.path.join(DATA_DIR, subdir, '*.json'))): + yield path + + +class ExamplesTest(BaseTest): + + def test_valid_examples(self): + for path in get_all_paths('valid'): + print(f"Valid path {path}") + with open(path, 'r') as f: + doc = json.load(f) + if type(doc) == dict: + validate_entity(doc, self.dictionary.schema) + elif type(doc) == list: + for entity in doc: + validate_entity(entity, self.dictionary.schema) + else: + raise Exception("Invalid json") + + + def test_invalid_examples(self): + for path in get_all_paths('invalid'): + with open(path, 'r') as f: + doc = json.load(f) + if type(doc) == dict: + with self.assertRaises(ValidationError): + validate_entity(doc, self.dictionary.schema) + elif type(doc) == list: + for entity in doc: + with self.assertRaises(ValidationError): + validate_entity(entity, self.dictionary.schema) + else: + raise Exception("Invalid json") diff --git a/tests/test_schema.py b/tests/test_schema.py new file mode 100644 index 000000000..e28d04dfe --- /dev/null +++ b/tests/test_schema.py @@ -0,0 +1,200 @@ +"""This test verifies the schema contains no errors. + +Note the kinda weird trigger and test functions getting passed around. +This is a mechanism that can easily be expanded upon if +have more tests later that need to validate new errors found within the +schema. +""" + +import collections + +from tests.utils import BaseTest, check_for_cycles, validate_schemata + + +def _check_enum(enums): + """Check the collected enums + + Args: + enums (dict of str: list[str]): mapping from the path to the enum to the enum object + + Returns: + dict: mapping from the violations and the corresponding path (and item name if necessary) + + """ + check_result = collections.defaultdict(list) + for path, enum_list in enums.items(): + if not isinstance(enum_list, list): + check_result["enum not a list"].append(path) + + for item in enum_list: + # dictionaryutils >= 3.1.0 adds None to non-required enums. + if not isinstance(item, str) and item is not None: + check_result["enum item is not a string or None"].append(f"{path}: {item}") + + if len(set(enum_list)) < len(enum_list): + check_result["duplicates in enum"].append(path) + duplicates = [ + item for item, count in collections.Counter(enum_list).items() if count > 1 + ] + for item in duplicates: + check_result["duplicates in enum"].append(f"\t{item}") + return check_result + + +def _generate_error_message_for_enum(res_dict): + """Generate error message string for enum checks + + Args: + res_dict (dict of string: string): mapping from the violation to the list of enum path + + Returns: + str: the formatted error message + + """ + message_lines = ["Errors in enum checks:"] + for error_name, lines in res_dict.items(): + message_lines.append(error_name) + for line in lines: + message_lines.append(f"\t{line}") + return "\n".join(message_lines) + + +class SchemaTest(BaseTest): + + def test_properties_enum(self): + """Check the enums of node properties""" + # The enums in _definitions.yaml, _terms.yaml and metaschema.yaml are not checked + + enum_dict = {} + for node_name, node_schema in self.dictionary.schema.items(): + for prop_name, prop_schema in node_schema["properties"].items(): + if "enum" in prop_schema: + path_str = f"{node_name}->{prop_name}" + enum_dict[path_str] = prop_schema["enum"] + + res = _check_enum(enum_dict) + assert len(res) == 0, _generate_error_message_for_enum(res) + + + def test_schemas(self): + """Validate schema""" + validate_schemata(self.dictionary.schema, self.dictionary.metaschema) + + + def test_acyclicality(self): + """Confirm the dictionary has no (unexpected) cycles.""" + # 'file' and 'archive' both point to each other. Ignore 'archive' since it's + # less relevant than 'file'. The other types should be acyclic. + # Set ignored to empty list since 'archive' and 'file' are not included in schemas + check_for_cycles(self.dictionary.schema, []) + + + def test_acyclicalty_without_ignored_types(self): + """ + Confirm the dictionary has cycles involving the expected type(s). + + If the acyclicality check passes like this, either the algorithm is + missing something or we're ignoring types that we shouldn't. + """ + # Add this test if any cyclic schemas are added, eg, 'file' and 'archive' + # with self.assertRaisesRegex(AssertionError, 'cycle detected'): + # check_for_cycles(self.dictionary.schema) + + + def test_check_for_cycles_positive(self): + """Test the cycle detection logic with a synthetic positive case.""" + + # The below schemata cover a few real edge cases; e.g., subgroups, + # schemata with no incoming links, schemata with no outgoing links, + # and schemata that link back to themselves. + schemata = { + 'analyte': { + 'links': [ + { + 'subgroup': [ + {'target_type': 'portion'}, + {'target_type': 'sample'}, + ] + } + ] + }, + 'case': { + 'links': [ + {'target_type': 'tissue_source_site'}, + ] + }, + 'portion': { + 'links': [ + {'target_type': 'sample'}, + ] + }, + 'sample': { + 'links': [ + {'target_type': 'case'}, + {'target_type': 'sample'}, + {'target_type': 'tissue_source_site'}, + ] + }, + 'slide': { + 'links': [ + { + 'subgroup': [ + {'target_type': 'portion'}, + {'target_type': 'sample'}, + ] + } + ] + }, + 'tissue_source_site': {'links': []}, + } + + check_for_cycles(schemata) + + def test_check_for_cycles_negative(self): + """Test the cycle detection logic with a synthetic negative case.""" + + # There is one cycle involving case, sample, and analyte, and a second + # cycle that also includes portion. + schemata = { + 'analyte': { + 'links': [ + { + 'subgroup': [ + {'target_type': 'portion'}, + {'target_type': 'sample'}, + ] + } + ] + }, + 'case': { + 'links': [ + {'target_type': 'analyte'}, + ] + }, + 'portion': { + 'links': [ + {'target_type': 'sample'}, + ] + }, + 'sample': { + 'links': [ + {'target_type': 'case'}, + {'target_type': 'sample'}, + {'target_type': 'tissue_source_site'}, + ] + }, + 'slide': { + 'links': [ + { + 'subgroup': [ + {'target_type': 'portion'}, + {'target_type': 'sample'}, + ] + } + ] + }, + 'tissue_source_site': {'links': []}, + } + + with self.assertRaisesRegex(AssertionError, 'cycle detected'): + check_for_cycles(schemata) diff --git a/tests/utils.py b/tests/utils.py new file mode 100644 index 000000000..c6bd2fb0c --- /dev/null +++ b/tests/utils.py @@ -0,0 +1,143 @@ +""" A file to hold all test utilities. Note the project +specific overrides are not being used in the GDC currently. + +""" + +from collections import defaultdict +import copy +import os +import unittest +import yaml + +from jsonschema import validate + +from gdcdictionary import SCHEMA_DIR, GDCDictionary + + +def load_yaml(path): + with open(path, 'r') as f: + return yaml.safe_load(f) + + +DATA_DIR = os.path.join(os.path.dirname(SCHEMA_DIR), 'examples') +project1 = load_yaml(os.path.join(SCHEMA_DIR, 'projects/project1.yaml')) +projects = {'project1': project1} + + +class BaseTest(unittest.TestCase): + + def setUp(self): + self.dictionary = GDCDictionary(root_dir=SCHEMA_DIR) + self.definitions = load_yaml(os.path.join(SCHEMA_DIR, '_definitions.yaml')) + + +def merge_schemas(a, b, path=None): + """Recursively zip schemas together + + """ + path = path if path is not None else [] + for key in b: + if key in a: + if isinstance(a[key], dict) and isinstance(b[key], dict): + merge_schemas(a[key], b[key], path + [str(key)]) + elif a[key] == b[key]: + pass + else: + print("Overriding '{}':\n\t- {}\n\t+ {}".format( + '.'.join(path + [str(key)]), a[key], b[key])) + a[key] = b[key] + else: + print("Adding '{}':\n\t+ {}".format( + '.'.join(path + [str(key)]), b[key])) + a[key] = b[key] + return a + + +def get_project_specific_schema(projects, project, schema, entity_type): + """Look up the core schema for its type and override it with any + project level overrides + + """ + root = copy.deepcopy(schema) + project_overrides = projects.get(project) + if project_overrides: + overrides = project_overrides.get(entity_type) + if overrides: + merge_schemas(root, overrides, [entity_type]) + return root + + +def validate_entity(entity, schemata, project=None, name=''): + """Validate an entity by looking up the core schema for its type and + overriding it with any project level overrides + + """ + local_schema = get_project_specific_schema( + projects, project, schemata[entity['type']], entity['type']) + result = validate(entity, local_schema) + return result + + +def validate_schemata(schemata, metaschema): + """ Validate schemata""" + print('Validating schemas against metaschema... '), + for s in schemata.values(): + validate(s, metaschema) + + def assert_link_is_also_prop(link): + assert link in s['properties'],\ + "Entity '{}' has '{}' as a link but not property".format( + s['id'], link) + + for link in [l['name'] for l in s['links'] if 'name' in l]: + assert_link_is_also_prop(link) + for subgroup in [l['subgroup'] for l in s['links'] if 'name' not in l]: + for link in [l['name'] for l in subgroup if 'name' in l]: + assert_link_is_also_prop(link) + + +def check_for_cycles(schemata, ignored_types=None): + """Assert the given schemata contain no cycles (outside ignored types).""" + if ignored_types is None: + ignored_types = [] + + # Build a bidirectional map representing the links between schema types. + forward = defaultdict(set) + backward = defaultdict(set) + for schema_type, schema in schemata.items(): + # Ignore cycles involving types that we know don't hurt anything so we + # can detect new cycles that might actually hurt. + if schema_type in ignored_types: + continue + + for link in schema.get('links', []): + if 'subgroup' in link: + target_types = [g.get('target_type') for g in link['subgroup']] + else: + target_types = [link['target_type']] + + for target_type in target_types: + # It's fine for a type to link to itself. Ignore such links + # to avoid confusing the below cycle detection algorithm. + if target_type != schema_type: + forward[schema_type].add(target_type) + backward[target_type].add(schema_type) + + # Iteratively remove types that have no links pointing to them. + # If there are no cycles, this will continue to free up types without + # any links until the entire map is cleared out. If a cycle exists, + # this process will fail to remove all of the links. + removable_types = [ + schema_type for schema_type in forward + if schema_type not in backward + ] + + while removable_types: + schema_type = removable_types.pop() + for target_type in forward[schema_type]: + backward[target_type].remove(schema_type) + if not backward[target_type]: + removable_types.append(target_type) + del backward[target_type] + + assert not backward, 'cycle detected among {}'.format(backward.keys())