Return validation reports (#579)

Author: cthoyt

src/sssom/io.py

@@ -13,6 +13,7 @@
 import yaml
 from curies import Converter
 from deprecation import deprecated
+from linkml.validator import ValidationReport
 
 from sssom.validators import validate
 
@@ -98,17 +99,23 @@ def parse_file(
     write_table(doc, output, embedded_mode)
 
 
-def validate_file(input_path: str, validation_types: List[SchemaValidationType]) -> None:
+def validate_file(
+    input_path: str,
+    validation_types: Optional[List[SchemaValidationType]] = None,
+    fail_on_error: bool = True,
+) -> dict[SchemaValidationType, ValidationReport]:
     """Validate the incoming SSSOM TSV according to the SSSOM specification.
 
     :param input_path: The path to the input file in one of the legal formats, eg obographs, aligmentapi-xml
     :param validation_types: A list of validation types to run.
+    :param fail_on_error: Should an exception be raised on error of _any_ validator?
+    :returns: A dictionary from validation types to validation reports
     """
     # Two things to check:
     # 1. All prefixes in the DataFrame are define in prefix_map
     # 2. All columns in the DataFrame abide by sssom-schema.
     msdf = parse_sssom_table(file_path=input_path)
-    validate(msdf=msdf, validation_types=validation_types)
+    return validate(msdf=msdf, validation_types=validation_types, fail_on_error=fail_on_error)
 
 
 def split_file(input_path: str, output_directory: Union[str, Path]) -> None:

src/sssom/validators.py

@@ -1,7 +1,7 @@
 """Validators."""
 
 import logging
-from typing import Callable, List, Mapping
+from typing import Callable, List, Mapping, Optional
 
 from jsonschema import ValidationError
 from linkml.validator import ValidationReport, Validator
@@ -12,22 +12,29 @@
 from sssom.parsers import to_mapping_set_document
 from sssom.util import MappingSetDataFrame, get_all_prefixes
 
-from .constants import SCHEMA_YAML, SchemaValidationType, _get_sssom_schema_object
+from .constants import (
+    DEFAULT_VALIDATION_TYPES,
+    SCHEMA_YAML,
+    SchemaValidationType,
+    _get_sssom_schema_object,
+)
 
 
 def validate(
     msdf: MappingSetDataFrame,
-    validation_types: List[SchemaValidationType],
+    validation_types: Optional[List[SchemaValidationType]] = None,
     fail_on_error: bool = True,
-) -> None:
+) -> dict[SchemaValidationType, ValidationReport]:
     """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
+    :returns: A dictionary from validation types to validation reports
     """
-    for vt in validation_types:
-        VALIDATION_METHODS[vt](msdf, fail_on_error)
+    if validation_types is None:
+        validation_types = DEFAULT_VALIDATION_TYPES
+    return {vt: VALIDATION_METHODS[vt](msdf, fail_on_error) for vt in validation_types}
 
 
 def print_linkml_report(report: ValidationReport, fail_on_error: bool = True):
@@ -88,7 +95,7 @@ def _clean_dict(d):
     return cleaned_dict
 
 
-def validate_json_schema(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None:
+def validate_json_schema(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> ValidationReport:
     """Validate JSON Schema using linkml's JsonSchemaDataValidator.
 
     :param msdf: MappingSetDataFrame to eb validated.
@@ -106,9 +113,10 @@ def validate_json_schema(msdf: MappingSetDataFrame, fail_on_error: bool = True)
 
     report = validator.validate(mapping_set_dict, "mapping set")
     print_linkml_report(report, fail_on_error)
+    return report
 
 
-def validate_shacl(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None:
+def validate_shacl(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> ValidationReport:
     """Validate SCHACL file.
 
     :param msdf: TODO: https://github.com/linkml/linkml/issues/850 .
@@ -118,7 +126,7 @@ def validate_shacl(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> Non
     raise NotImplementedError
 
 
-def validate_sparql(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None:
+def validate_sparql(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> ValidationReport:
     """Validate SPARQL file.
 
     :param msdf: MappingSetDataFrame
@@ -132,7 +140,9 @@ def validate_sparql(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> No
     raise NotImplementedError
 
 
-def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None:
+def check_all_prefixes_in_curie_map(
+    msdf: MappingSetDataFrame, fail_on_error: bool = True
+) -> ValidationReport:
     """Check all `EntityReference` slots are mentioned in 'curie_map'.
 
     :param msdf: MappingSetDataFrame
@@ -154,9 +164,12 @@ def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame, fail_on_error: bo
         )
     report = ValidationReport(results=validation_results)
     print_linkml_report(report, fail_on_error)
+    return report
 
 
-def check_strict_curie_format(msdf: MappingSetDataFrame, fail_on_error: bool = True) -> None:
+def check_strict_curie_format(
+    msdf: MappingSetDataFrame, fail_on_error: bool = True
+) -> ValidationReport:
     """Check all `EntityReference` slots are formatted as unambiguous curies.
 
     Implemented rules:
@@ -194,9 +207,10 @@ def check_strict_curie_format(msdf: MappingSetDataFrame, fail_on_error: bool = T
 
     report = ValidationReport(results=validation_results)
     print_linkml_report(report, fail_on_error)
+    return report
 
 
-VALIDATION_METHODS: Mapping[SchemaValidationType, Callable] = {
+VALIDATION_METHODS: Mapping[SchemaValidationType, Callable[..., ValidationReport]] = {
     SchemaValidationType.JsonSchema: validate_json_schema,
     SchemaValidationType.Shacl: validate_shacl,
     SchemaValidationType.Sparql: validate_sparql,

tests/test_validate.py

@@ -28,7 +28,11 @@ def test_validate_json(self):
         Validate of the incoming file (basic.tsv) abides
         by the rules set by `sssom-schema`.
         """
-        self.assertIsNone(validate(self.correct_msdf1, self.validation_types))
+        rv = validate(self.correct_msdf1, self.validation_types)
+        self.assertIsNotNone(rv)
+        self.assertIn(SchemaValidationType.JsonSchema, rv)
+        json_validation = rv[SchemaValidationType.JsonSchema]
+        self.assertEqual([], json_validation.results)
 
     @unittest.skip(
         reason="""\