From 2302dde056d6637ddac8d49990f1a05a28f8cf10 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 16 May 2024 16:39:09 +0300 Subject: [PATCH 01/12] Failing test --- tests/data/mondo-nando.sssom.tsv | 15 +++++++++++++++ tests/test_validate.py | 6 ++++++ 2 files changed, 21 insertions(+) create mode 100644 tests/data/mondo-nando.sssom.tsv diff --git a/tests/data/mondo-nando.sssom.tsv b/tests/data/mondo-nando.sssom.tsv new file mode 100644 index 00000000..af312219 --- /dev/null +++ b/tests/data/mondo-nando.sssom.tsv @@ -0,0 +1,15 @@ +#curie_map: +# NANDO: "http://nanbyodata.jp/ontology/NANDO_" +# MONDO: "http://purl.obolibrary.org/obo/MONDO_" +# orcid: "https://orcid.org/" +#creator_id: +# - "orcid:0000-0003-0011-764X" +# - "orcid:0000-0002-0170-9172" +#license: "https://creativecommons.org/licenses/by/4.0/" +#mapping_set_title: "NANDO - Mondo mappings provided by nanbyodata.jp" +#mapping_set_description: "This mapping set is manually curated by the NANDO team at nanbyodata.jp." +#mapping_provider: "http://nanbyodata.jp" +subject_id subject_label predicate_id object_id object_label mapping_justification +NANDO:1100001 Neuromuscular disease skos:exactMatch MONDO:0019056 neuromuscular disease semapv:MappingCuration +NANDO:1100004 Immune system disease skos:exactMatch MONDO:0005046 immune system disorder semapv:MappingCuration +NANDO:2200355 Isolated ACTH deficiency skos:exactMatch MONDO:0008720|MONDO:0016042 semapv:MappingCuration diff --git a/tests/test_validate.py b/tests/test_validate.py index 871edead..3ae3cf65 100644 --- a/tests/test_validate.py +++ b/tests/test_validate.py @@ -17,6 +17,7 @@ def setUp(self) -> None: """Test up the test cases with the third basic example.""" self.correct_msdf1 = parse_sssom_table(f"{data_dir}/basic.tsv") self.bad_msdf1 = parse_sssom_table(f"{data_dir}/bad_basic.tsv") + self.bad_nando = parse_sssom_table(f"{data_dir}/mondo-nando.sssom.tsv") self.validation_types = DEFAULT_VALIDATION_TYPES self.shacl_validation_types = [SchemaValidationType.Shacl] @@ -75,3 +76,8 @@ def test_validate_sparql(self): self.correct_msdf1, self.shacl_validation_types, ) + + def test_validate_nando(self): + """Test Shacl validation (Not implemented).""" + self.assertIsNone(validate(self.bad_nando, self.validation_types)) + self.assertRaises(ValidationError, validate, self.bad_nando, self.validation_types) From ef8069f32ef46bcd86d7f464a561418bd01db740 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 16 May 2024 18:35:34 +0300 Subject: [PATCH 02/12] Add new linkml validator framework --- poetry.lock | 932 +++++++++++++++++++++++++++++++--------- pyproject.toml | 3 +- src/sssom/validators.py | 17 +- 3 files changed, 751 insertions(+), 201 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4b1f010f..a951ba4a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "alabaster" @@ -25,6 +25,35 @@ files = [ [package.dependencies] typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} +[[package]] +name = "antlr4-python3-runtime" +version = "4.9.3" +description = "ANTLR 4.9.3 runtime for Python 3.7" +optional = false +python-versions = "*" +files = [ + {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, +] + +[[package]] +name = "arrow" +version = "1.3.0" +description = "Better dates & times for Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, + {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, +] + +[package.dependencies] +python-dateutil = ">=2.7.0" +types-python-dateutil = ">=2.8.10" + +[package.extras] +doc = ["doc8", "sphinx 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+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" -python-versions = "^3.8" -content-hash = "c308daded19714684f04091b38dc509dd6da0431c0c47154113f29c60993b7c5" +python-versions = "^3.8.1" +content-hash = "c703c8a2688c432d9acce58ccd7989c1f47da65d273eab42ff61c97c7ff3009c" diff --git a/pyproject.toml b/pyproject.toml index 75c318cd..15f43381 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,10 +11,11 @@ license = "MIT" readme = "README.md" [tool.poetry.dependencies] -python = "^3.8" +python = "^3.8.1" click = ">=8.1.6" curies = ">=0.7.3" linkml-runtime = "^1.7.5" +linkml = ">1.7.10" pandas = ">1.0.3" pansql = { version = ">=0.0.1", extras = ["pansql"] } sssom-schema = "^0.15.2" diff --git a/src/sssom/validators.py b/src/sssom/validators.py index 1b15787e..b74e09ab 100644 --- a/src/sssom/validators.py +++ b/src/sssom/validators.py @@ -1,15 +1,12 @@ """Validators.""" - from typing import Callable, List, Mapping from jsonschema import ValidationError -from linkml_runtime.processing.referencevalidator import ReferenceValidator -from linkml_runtime.utils.schemaview import SchemaView -from sssom_schema import MappingSet +from linkml.validator import Validator +from linkml.validator.plugins import JsonschemaValidationPlugin, RecommendedSlotsPlugin from sssom.parsers import to_mapping_set_document from sssom.util import MappingSetDataFrame, get_all_prefixes - from .constants import SCHEMA_YAML, SchemaValidationType @@ -28,9 +25,15 @@ def validate_json_schema(msdf: MappingSetDataFrame) -> None: :param msdf: MappingSetDataFrame to eb validated. """ - validator = ReferenceValidator(SchemaView(SCHEMA_YAML)) + validator = Validator( + schema=SCHEMA_YAML, + validation_plugins=[ + JsonschemaValidationPlugin(closed=True), + RecommendedSlotsPlugin() + ] + ) mapping_set = to_mapping_set_document(msdf).mapping_set - validator.validate(mapping_set, MappingSet) + validator.validate(mapping_set, "MappingSet") def validate_shacl(msdf: MappingSetDataFrame) -> None: From c5f735a50110dcff1488fa7057879164a0363485 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Fri, 17 May 2024 09:50:03 +0300 Subject: [PATCH 03/12] Fix validator --- src/sssom/validators.py | 24 ++++++++++++++++++++++-- tests/test_validate.py | 1 - 2 files changed, 22 insertions(+), 3 deletions(-) diff --git a/src/sssom/validators.py b/src/sssom/validators.py index b74e09ab..304d3f3d 100644 --- a/src/sssom/validators.py +++ b/src/sssom/validators.py @@ -1,8 +1,11 @@ """Validators.""" +import logging from typing import Callable, List, Mapping +from dataclasses import asdict from jsonschema import ValidationError -from linkml.validator import Validator +from linkml.validator import Validator, ValidationReport +from linkml.validator.report import Severity from linkml.validator.plugins import JsonschemaValidationPlugin, RecommendedSlotsPlugin from sssom.parsers import to_mapping_set_document @@ -20,6 +23,20 @@ def validate(msdf: MappingSetDataFrame, validation_types: List[SchemaValidationT VALIDATION_METHODS[vt](msdf) +def print_linkml_report(report: ValidationReport, fail_on_error: bool = True): + validation_errors = 0 + + if not report.results: + logging.info('The instance is valid!') + else: + for result in report.results: + validation_errors += 1 + if result.severity == Severity.ERROR: + logging.error(result.message) + + if fail_on_error and validation_errors: + raise ValidationError(f"You mapping set has {validation_errors} validation errors!") + def validate_json_schema(msdf: MappingSetDataFrame) -> None: """Validate JSON Schema using linkml's JsonSchemaDataValidator. @@ -33,7 +50,10 @@ def validate_json_schema(msdf: MappingSetDataFrame) -> None: ] ) mapping_set = to_mapping_set_document(msdf).mapping_set - validator.validate(mapping_set, "MappingSet") + + mapping_set_yaml = asdict(mapping_set) + report = validator.validate(mapping_set_yaml, "mapping set") + print_linkml_report(report) def validate_shacl(msdf: MappingSetDataFrame) -> None: diff --git a/tests/test_validate.py b/tests/test_validate.py index 3ae3cf65..e1ec40bd 100644 --- a/tests/test_validate.py +++ b/tests/test_validate.py @@ -79,5 +79,4 @@ def test_validate_sparql(self): def test_validate_nando(self): """Test Shacl validation (Not implemented).""" - self.assertIsNone(validate(self.bad_nando, self.validation_types)) self.assertRaises(ValidationError, validate, self.bad_nando, self.validation_types) From eb50efcfb5eb132642cc102959efb05ed493e097 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 15 Jun 2024 08:48:10 +0300 Subject: [PATCH 04/12] Update validators.py --- src/sssom/validators.py | 60 ++++++++++++++++++++++++++++++++++------- 1 file changed, 50 insertions(+), 10 deletions(-) diff --git a/src/sssom/validators.py b/src/sssom/validators.py index 304d3f3d..9e1ca19e 100644 --- a/src/sssom/validators.py +++ b/src/sssom/validators.py @@ -1,15 +1,17 @@ """Validators.""" + import logging +from dataclasses import asdict from typing import Callable, List, Mapping -from dataclasses import asdict from jsonschema import ValidationError -from linkml.validator import Validator, ValidationReport -from linkml.validator.report import Severity +from linkml.validator import ValidationReport, Validator from linkml.validator.plugins import JsonschemaValidationPlugin, RecommendedSlotsPlugin +from linkml.validator.report import Severity from sssom.parsers import to_mapping_set_document from sssom.util import MappingSetDataFrame, get_all_prefixes + from .constants import SCHEMA_YAML, SchemaValidationType @@ -24,10 +26,15 @@ def validate(msdf: MappingSetDataFrame, validation_types: List[SchemaValidationT def print_linkml_report(report: ValidationReport, fail_on_error: bool = True): + """Print the error messages in the report. Optionally throw exception. + + :param report: A LinkML validation report + :param fail_on_error: if true, the function will throw an ValidationError exception when there are errors + """ validation_errors = 0 if not report.results: - logging.info('The instance is valid!') + logging.info("The instance is valid!") else: for result in report.results: validation_errors += 1 @@ -37,6 +44,40 @@ def print_linkml_report(report: ValidationReport, fail_on_error: bool = True): if fail_on_error and validation_errors: raise ValidationError(f"You mapping set has {validation_errors} validation errors!") + +# TODO This should not be necessary: https://github.com/linkml/linkml/issues/2117, https://github.com/orgs/linkml/discussions/1975 +def clean_dict(d): + """Recursively removes key-value pairs from a dictionary where the value is None, "null", or an empty string. + + Args: + d (dict): The dictionary to clean. + + Returns: + dict: A cleaned dictionary with unwanted values removed. + """ + if not isinstance(d, dict): + return d + + cleaned_dict = {} + for k, v in d.items(): + if isinstance(v, dict): + # Recursively clean nested dictionary + cleaned_value = clean_dict(v) + if cleaned_value: # Add only if the nested dictionary is not empty + cleaned_dict[k] = cleaned_value + elif isinstance(v, list): + # Recursively clean list elements if they are dictionaries + cleaned_list = [clean_dict(item) if isinstance(item, dict) else item for item in v] + # Filter out empty dictionaries from list + cleaned_list = [item for item in cleaned_list if item not in [None, "", "null", {}]] + if cleaned_list: # Add only if the list is not empty + cleaned_dict[k] = cleaned_list + elif v not in [None, "", "null"]: + cleaned_dict[k] = v + + return cleaned_dict + + def validate_json_schema(msdf: MappingSetDataFrame) -> None: """Validate JSON Schema using linkml's JsonSchemaDataValidator. @@ -44,16 +85,15 @@ def validate_json_schema(msdf: MappingSetDataFrame) -> None: """ validator = Validator( schema=SCHEMA_YAML, - validation_plugins=[ - JsonschemaValidationPlugin(closed=True), - RecommendedSlotsPlugin() - ] + validation_plugins=[JsonschemaValidationPlugin(closed=False), RecommendedSlotsPlugin()], ) mapping_set = to_mapping_set_document(msdf).mapping_set mapping_set_yaml = asdict(mapping_set) - report = validator.validate(mapping_set_yaml, "mapping set") - print_linkml_report(report) + mapping_set_yaml_cleaned = clean_dict(mapping_set_yaml) + + report = validator.validate(mapping_set_yaml_cleaned, "mapping set") + print_linkml_report(report, False) def validate_shacl(msdf: MappingSetDataFrame) -> None: From cd205909a5493a32290549e0bcc739fe264d81fb Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 15 Jun 2024 08:56:57 +0300 Subject: [PATCH 05/12] Update poetry.lock Using the latest version of LinkML to get latest validator features. --- poetry.lock | 339 ++++++++++++++++++++++++++-------------------------- 1 file changed, 171 insertions(+), 168 deletions(-) diff --git a/poetry.lock b/poetry.lock index a951ba4a..8048715a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[package]] name = "annotated-types" -version = "0.6.0" +version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" files = [ - {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, - {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, ] [package.dependencies] @@ -103,13 +103,13 @@ files = [ [[package]] name = "certifi" -version = "2024.2.2" +version = "2024.6.2" description = 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"jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" From 84c25a8eaab7534a8ef693300129aaa78a2eff6b Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 15 Jun 2024 09:01:47 +0300 Subject: [PATCH 06/12] Update validators.py --- src/sssom/validators.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/sssom/validators.py b/src/sssom/validators.py index 9e1ca19e..631c5569 100644 --- a/src/sssom/validators.py +++ b/src/sssom/validators.py @@ -93,6 +93,7 @@ def validate_json_schema(msdf: MappingSetDataFrame) -> None: mapping_set_yaml_cleaned = clean_dict(mapping_set_yaml) report = validator.validate(mapping_set_yaml_cleaned, "mapping set") + # TODO fail_on_error: False because of https://github.com/linkml/linkml/issues/2164 print_linkml_report(report, False) From 36c0b987e25bcd1c37ae67e50abd4a4daa28e840 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 15 Jun 2024 09:59:05 +0300 Subject: [PATCH 07/12] Refactor of validate methods In this commit we 1. Add a new parameter, fail_on_error, to all validation methods (if true, throws and exception when errors are encountered) 2. We generate ValidationResult instances fall all custom checks (reusing the LinkML validation framework) 3. Add a few missing docstrings 4. Add a new validation check, check_strict_curie_format, which looks for curies with a | character in it --- src/sssom/constants.py | 2 + src/sssom/validators.py | 94 ++++++++++++++++++++++++++++++++++------- 2 files changed, 81 insertions(+), 15 deletions(-) diff --git a/src/sssom/constants.py b/src/sssom/constants.py index 19003ac6..b2800ac3 100644 --- a/src/sssom/constants.py +++ b/src/sssom/constants.py @@ -197,11 +197,13 @@ class SchemaValidationType(str, Enum): Shacl = "Shacl" Sparql = "Sparql" PrefixMapCompleteness = "PrefixMapCompleteness" + StrictCurieFormat = "StrictCurieFormat" DEFAULT_VALIDATION_TYPES = [ SchemaValidationType.JsonSchema, SchemaValidationType.PrefixMapCompleteness, + SchemaValidationType.StrictCurieFormat, ] diff --git a/src/sssom/validators.py b/src/sssom/validators.py index 631c5569..bccbc257 100644 --- a/src/sssom/validators.py +++ b/src/sssom/validators.py @@ -7,22 +7,27 @@ from jsonschema import ValidationError from linkml.validator import ValidationReport, Validator from linkml.validator.plugins import JsonschemaValidationPlugin, RecommendedSlotsPlugin -from linkml.validator.report import Severity +from linkml.validator.report import Severity, ValidationResult from sssom.parsers import to_mapping_set_document from sssom.util import MappingSetDataFrame, get_all_prefixes -from .constants import SCHEMA_YAML, SchemaValidationType +from .constants import SCHEMA_YAML, SchemaValidationType, _get_sssom_schema_object -def validate(msdf: MappingSetDataFrame, validation_types: List[SchemaValidationType]) -> None: +def validate( + msdf: MappingSetDataFrame, + validation_types: List[SchemaValidationType], + fail_on_error: bool = True, +) -> None: """Validate SSSOM files against `sssom-schema` using linkML's validator function. :param msdf: MappingSetDataFrame. :param validation_types: SchemaValidationType + :param fail_on_error: If true, throw an error when execution of a method has failed """ for vt in validation_types: - VALIDATION_METHODS[vt](msdf) + VALIDATION_METHODS[vt](msdf, fail_on_error) def print_linkml_report(report: ValidationReport, fail_on_error: bool = True): @@ -45,8 +50,9 @@ def print_linkml_report(report: ValidationReport, fail_on_error: bool = True): raise ValidationError(f"You mapping set has {validation_errors} validation errors!") -# TODO This should not be necessary: https://github.com/linkml/linkml/issues/2117, https://github.com/orgs/linkml/discussions/1975 -def clean_dict(d): +# TODO This should not be necessary: https://github.com/linkml/linkml/issues/2117, +# https://github.com/orgs/linkml/discussions/1975 +def _clean_dict(d): """Recursively removes key-value pairs from a dictionary where the value is None, "null", or an empty string. Args: @@ -62,12 +68,12 @@ def clean_dict(d): for k, v in d.items(): if isinstance(v, dict): # Recursively clean nested dictionary - cleaned_value = clean_dict(v) + cleaned_value = _clean_dict(v) if cleaned_value: # Add only if the nested dictionary is not empty cleaned_dict[k] = cleaned_value elif isinstance(v, list): # Recursively clean list elements if they are dictionaries - cleaned_list = [clean_dict(item) if isinstance(item, dict) else item for item in v] + cleaned_list = [_clean_dict(item) if isinstance(item, dict) else item for item in v] # Filter out empty dictionaries from list cleaned_list = [item for item in cleaned_list if item not in [None, "", "null", {}]] if cleaned_list: # Add only if the list is not empty @@ -78,10 +84,11 @@ def clean_dict(d): return cleaned_dict -def validate_json_schema(msdf: MappingSetDataFrame) -> None: +def validate_json_schema(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None: """Validate JSON Schema using linkml's JsonSchemaDataValidator. :param msdf: MappingSetDataFrame to eb validated. + :param fail_on_error: if true, the function will throw an ValidationError exception when there are errors """ validator = Validator( schema=SCHEMA_YAML, @@ -90,26 +97,28 @@ def validate_json_schema(msdf: MappingSetDataFrame) -> None: mapping_set = to_mapping_set_document(msdf).mapping_set mapping_set_yaml = asdict(mapping_set) - mapping_set_yaml_cleaned = clean_dict(mapping_set_yaml) + mapping_set_yaml_cleaned = _clean_dict(mapping_set_yaml) report = validator.validate(mapping_set_yaml_cleaned, "mapping set") # TODO fail_on_error: False because of https://github.com/linkml/linkml/issues/2164 print_linkml_report(report, False) -def validate_shacl(msdf: MappingSetDataFrame) -> None: +def validate_shacl(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None: """Validate SCHACL file. :param msdf: TODO: https://github.com/linkml/linkml/issues/850 . + :param fail_on_error: if true, the function will throw an ValidationError exception when there are errors :raises NotImplementedError: Not yet implemented. """ raise NotImplementedError -def validate_sparql(msdf: MappingSetDataFrame) -> None: +def validate_sparql(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None: """Validate SPARQL file. :param msdf: MappingSetDataFrame + :param fail_on_error: if true, the function will throw an ValidationError exception when there are errors :raises NotImplementedError: Not yet implemented. """ # queries = {} @@ -119,16 +128,70 @@ def validate_sparql(msdf: MappingSetDataFrame) -> None: raise NotImplementedError -def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame) -> None: +def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None: """Check all `EntityReference` slots are mentioned in 'curie_map'. :param msdf: MappingSetDataFrame + :param fail_on_error: if true, the function will throw an ValidationError exception when there are errors :raises ValidationError: If all prefixes not in curie_map. """ msdf.clean_context() missing_prefixes = get_all_prefixes(msdf).difference(msdf.converter.bimap) - if missing_prefixes: - raise ValidationError(f"The prefixes in {missing_prefixes} are missing from 'curie_map'.") + validation_results = [] + for prefix in missing_prefixes: + validation_results.append( + ValidationResult( + type="prefix validation", + severity=Severity.ERROR, + instance=None, + instantiates=None, + message=f"Missing {prefix}", + ) + ) + report = ValidationReport(results=validation_results) + # TODO fail_on_error: False because of https://github.com/linkml/linkml/issues/2164 + print_linkml_report(report, False) + + +def check_strict_curie_format(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None: + """Check all `EntityReference` slots are formatted as unambiguous curies. + + Implemented rules: + - CURIE does not contain pipe "|" character to ensure that multivalued processing of in TSV works correctly. + :param msdf: MappingSetDataFrame + :param fail_on_error: if true, the function will throw an ValidationError exception when there are errors + :raises ValidationError: If any entity reference does not follow the strict CURIE format + """ + import itertools as itt + + import pandas as pd + + msdf.clean_context() + validation_results = [] + metadata_keys = set(msdf.metadata.keys()) + entity_reference_slots = { + slot + for slot in itt.chain(metadata_keys, msdf.df.columns.to_list()) + if slot in _get_sssom_schema_object().entity_reference_slots + if slot not in _get_sssom_schema_object().multivalued_slots + } + + for column in entity_reference_slots: + if column in msdf.df.columns: + for index, value in msdf.df[column].items(): + if pd.notna(value) and "|" in str(value): + message = f"{value} contains a pipe ('|') character (row {index + 1}, column '{column}')." + validation_results.append( + ValidationResult( + type="strict curie test", + severity=Severity.ERROR, + message=message, + ) + ) + + report = ValidationReport(results=validation_results) + # TODO fail_on_error: False because of https://github.com/linkml/linkml/issues/2164 + print_linkml_report(report, fail_on_error) VALIDATION_METHODS: Mapping[SchemaValidationType, Callable] = { @@ -136,4 +199,5 @@ def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame) -> None: SchemaValidationType.Shacl: validate_shacl, SchemaValidationType.Sparql: validate_sparql, SchemaValidationType.PrefixMapCompleteness: check_all_prefixes_in_curie_map, + SchemaValidationType.StrictCurieFormat: check_strict_curie_format, } From f5e911223225d582fc9e4fd235bcf32bd0daa053 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 15 Jun 2024 10:07:03 +0300 Subject: [PATCH 08/12] Update validators.py --- src/sssom/validators.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/sssom/validators.py b/src/sssom/validators.py index bccbc257..f2653a47 100644 --- a/src/sssom/validators.py +++ b/src/sssom/validators.py @@ -190,7 +190,6 @@ def check_strict_curie_format(msdf: MappingSetDataFrame, fail_on_error: bool = T ) report = ValidationReport(results=validation_results) - # TODO fail_on_error: False because of https://github.com/linkml/linkml/issues/2164 print_linkml_report(report, fail_on_error) From 98b9f63d038fce8952fa9a3b6a1c15d094d2bea0 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 18 Jun 2024 11:28:22 +0300 Subject: [PATCH 09/12] Update validators.py --- src/sssom/validators.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sssom/validators.py b/src/sssom/validators.py index f2653a47..e006af74 100644 --- a/src/sssom/validators.py +++ b/src/sssom/validators.py @@ -101,7 +101,7 @@ def validate_json_schema(msdf: MappingSetDataFrame, fail_on_error: bool = True) report = validator.validate(mapping_set_yaml_cleaned, "mapping set") # TODO fail_on_error: False because of https://github.com/linkml/linkml/issues/2164 - print_linkml_report(report, False) + print_linkml_report(report, fail_on_error) def validate_shacl(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None: From 66728e688f02a27bf80d5606b70df9b455d8d630 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 4 Jul 2024 15:59:00 +0300 Subject: [PATCH 10/12] Use linkml runtime for preprocessing json Previously I used dataclasses. asdict to turn a dataclass instance to a dictionary to pass to the validation framework. @pkalita-lbl explained to me why this was not a good idea (essentially, dataclass instances dont look like what the validation framework expects), and recommended the use of linkml_runtime.dumpers.json_dumper instead. Tests work fine! --- src/sssom/validators.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/src/sssom/validators.py b/src/sssom/validators.py index e006af74..5e3ba8d6 100644 --- a/src/sssom/validators.py +++ b/src/sssom/validators.py @@ -1,13 +1,13 @@ """Validators.""" import logging -from dataclasses import asdict from typing import Callable, List, Mapping from jsonschema import ValidationError from linkml.validator import ValidationReport, Validator -from linkml.validator.plugins import JsonschemaValidationPlugin, RecommendedSlotsPlugin +from linkml.validator.plugins import JsonschemaValidationPlugin from linkml.validator.report import Severity, ValidationResult +from linkml_runtime.dumpers import json_dumper from sssom.parsers import to_mapping_set_document from sssom.util import MappingSetDataFrame, get_all_prefixes @@ -92,14 +92,15 @@ def validate_json_schema(msdf: MappingSetDataFrame, fail_on_error: bool = True) """ validator = Validator( schema=SCHEMA_YAML, - validation_plugins=[JsonschemaValidationPlugin(closed=False), RecommendedSlotsPlugin()], + validation_plugins=[JsonschemaValidationPlugin(closed=False)], ) mapping_set = to_mapping_set_document(msdf).mapping_set - mapping_set_yaml = asdict(mapping_set) - mapping_set_yaml_cleaned = _clean_dict(mapping_set_yaml) + # mapping_set_yaml = asdict(mapping_set) + # mapping_set_dict = _clean_dict(mapping_set_yaml) + mapping_set_dict = json_dumper.to_dict(mapping_set) - report = validator.validate(mapping_set_yaml_cleaned, "mapping set") + report = validator.validate(mapping_set_dict, "mapping set") # TODO fail_on_error: False because of https://github.com/linkml/linkml/issues/2164 print_linkml_report(report, fail_on_error) From 0063399fc0ceb66e70a6d5c7ae62b10b4e70aa2a Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 4 Jul 2024 16:36:17 +0300 Subject: [PATCH 11/12] Update call to print_linkml_report .. to ensure that it recognises the argument fail_on_error. --- src/sssom/validators.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sssom/validators.py b/src/sssom/validators.py index 5e3ba8d6..f6c8c259 100644 --- a/src/sssom/validators.py +++ b/src/sssom/validators.py @@ -151,7 +151,7 @@ def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame, fail_on_error: bo ) report = ValidationReport(results=validation_results) # TODO fail_on_error: False because of https://github.com/linkml/linkml/issues/2164 - print_linkml_report(report, False) + print_linkml_report(report, fail_on_error) def check_strict_curie_format(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None: From c5a4439ca1efa24f9190966e6803e139a25fdd8e Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 23 Jul 2024 11:03:47 -0500 Subject: [PATCH 12/12] poetry lock file was outdated. --- poetry.lock | 559 +++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 555 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index bba8b8fc..931807db 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "alabaster" @@ -25,6 +25,35 @@ files = [ [package.dependencies] typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} +[[package]] +name = "antlr4-python3-runtime" +version = "4.9.3" +description = "ANTLR 4.9.3 runtime for Python 3.7" +optional = false +python-versions = "*" +files = [ + {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, +] + +[[package]] +name = "arrow" +version = "1.3.0" +description = "Better dates & times for Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, + {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, +] + +[package.dependencies] +python-dateutil = ">=2.7.0" +types-python-dateutil = ">=2.8.10" + +[package.extras] +doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] +test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] + [[package]] name = "attrs" version = "23.2.0" @@ -83,6 +112,19 @@ files = [ {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"}, ] +[[package]] +name = "cfgraph" +version = "0.2.1" +description = "rdflib collections flattening graph" +optional = false +python-versions = "*" +files = [ + {file = "CFGraph-0.2.1.tar.gz", hash = "sha256:b57fe7044a10b8ff65aa3a8a8ddc7d4cd77bf511b42e57289cd52cbc29f8fe74"}, +] + +[package.dependencies] +rdflib = ">=0.4.2" + [[package]] name = "chardet" version = "5.2.0" @@ -295,6 +337,17 @@ files = [ {file = "docutils-0.20.1.tar.gz", hash = "sha256:f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b"}, ] +[[package]] +name = "et-xmlfile" +version = "1.1.0" +description = "An implementation of lxml.xmlfile for the standard library" +optional = false +python-versions = ">=3.6" +files = [ + {file = "et_xmlfile-1.1.0-py3-none-any.whl", hash = "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"}, + {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"}, +] + [[package]] name = "exceptiongroup" version = "1.2.1" @@ -325,6 +378,33 @@ docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1 testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-asyncio (>=0.21)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"] typing = ["typing-extensions (>=4.8)"] +[[package]] +name = "fqdn" +version = "1.5.1" +description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" +optional = false +python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" +files = [ + {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"}, + {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"}, +] + +[[package]] +name = "graphviz" +version = "0.20.3" +description = "Simple Python interface for Graphviz" +optional = false +python-versions = ">=3.8" +files = [ + {file = "graphviz-0.20.3-py3-none-any.whl", hash = "sha256:81f848f2904515d8cd359cc611faba817598d2feaac4027b266aa3eda7b3dde5"}, + {file = "graphviz-0.20.3.zip", hash = "sha256:09d6bc81e6a9fa392e7ba52135a9d49f1ed62526f96499325930e87ca1b5925d"}, +] + +[package.extras] +dev = ["flake8", "pep8-naming", "tox (>=3)", "twine", "wheel"] +docs = ["sphinx (>=5,<7)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"] +test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"] + [[package]] name = "greenlet" version = "3.0.3" @@ -491,6 +571,20 @@ files = [ [package.dependencies] six = "*" +[[package]] +name = "isoduration" +version = "20.11.0" +description = "Operations with ISO 8601 durations" +optional = false +python-versions = ">=3.7" +files = [ + {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"}, + {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"}, +] + +[package.dependencies] +arrow = ">=0.15.0" + [[package]] name = "jinja2" version = "3.1.4" @@ -523,6 +617,17 @@ files = [ click = "*" pyyaml = "*" +[[package]] +name = "jsonasobj" +version = "1.3.1" +description = "JSON as python objects" +optional = false +python-versions = "*" +files = [ + {file = "jsonasobj-1.3.1-py3-none-any.whl", hash = "sha256:b9e329dc1ceaae7cf5d5b214684a0b100e0dad0be6d5bbabac281ec35ddeca65"}, + {file = "jsonasobj-1.3.1.tar.gz", hash = "sha256:d52e0544a54a08f6ea3f77fa3387271e3648655e0eace2f21e825c26370e44a2"}, +] + [[package]] name = "jsonasobj2" version = "1.0.4" @@ -537,6 +642,45 @@ files = [ [package.dependencies] hbreader = "*" +[[package]] +name = "jsonpatch" +version = "1.33" +description = "Apply JSON-Patches (RFC 6902)" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" +files = [ + {file = "jsonpatch-1.33-py2.py3-none-any.whl", hash = "sha256:0ae28c0cd062bbd8b8ecc26d7d164fbbea9652a1a3693f3b956c1eae5145dade"}, + {file = "jsonpatch-1.33.tar.gz", hash = "sha256:9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c"}, +] + +[package.dependencies] +jsonpointer = ">=1.9" + +[[package]] +name = "jsonpath-ng" +version = "1.6.1" +description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming." +optional = false +python-versions = "*" +files = [ + {file = "jsonpath-ng-1.6.1.tar.gz", hash = "sha256:086c37ba4917304850bd837aeab806670224d3f038fe2833ff593a672ef0a5fa"}, + {file = "jsonpath_ng-1.6.1-py3-none-any.whl", hash = "sha256:8f22cd8273d7772eea9aaa84d922e0841aa36fdb8a2c6b7f6c3791a16a9bc0be"}, +] + +[package.dependencies] +ply = "*" + +[[package]] +name = "jsonpointer" +version = "3.0.0" +description = "Identify specific nodes in a JSON document (RFC 6901)" +optional = false +python-versions = ">=3.7" +files = [ + {file = "jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942"}, + {file = "jsonpointer-3.0.0.tar.gz", hash = "sha256:2b2d729f2091522d61c3b31f82e11870f60b68f43fbc705cb76bf4b832af59ef"}, +] + [[package]] name = "jsonschema" version = "4.22.0" @@ -550,11 +694,19 @@ files = [ [package.dependencies] attrs = ">=22.2.0" +fqdn = {version = "*", optional = true, markers = "extra == \"format\""} +idna = {version = "*", optional = true, markers = "extra == \"format\""} importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""} +isoduration = {version = "*", optional = true, markers = "extra == \"format\""} +jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""} jsonschema-specifications = ">=2023.03.6" pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""} referencing = ">=0.28.4" +rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""} +rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""} rpds-py = ">=0.7.1" +uri-template = {version = "*", optional = true, markers = "extra == \"format\""} +webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\""} [package.extras] format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] @@ -575,6 +727,67 @@ files = [ importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""} referencing = 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