Add reports to validators

src/sssom/validators.py

@@ -1,7 +1,7 @@
 """Validators."""
 
 import logging
-from typing import List
+from typing import Dict, List
 
 from jsonschema import ValidationError
 
@@ -18,7 +18,45 @@
 from .constants import SCHEMA_YAML, SchemaValidationType
 
 
-def validate(msdf: MappingSetDataFrame, validation_types: List[SchemaValidationType]) -> None:
+class ValidationResult:
+    """An individual validation result from a validation system."""
+
+    def __init__(self, category: str):
+        """Initialise the validation result.
+
+        :param category: Name of the category this validation result belongs to.
+        """
+        self.message = ""
+        self.category = category
+        self.check = ""
+        self.data: Dict = {}
+
+
+class ValidationReport:
+    """A validation report that contains the results of various validation methods."""
+
+    def __init__(self, name: str):
+        """Initialise the validation report.
+
+        :param name: Name of the category this validation report corresponds to.
+        """
+        self.name = name
+        self.results: List[ValidationResult] = []
+
+    def add_result(self, result: ValidationResult):
+        """Add result to the validation report."""
+        self.results.append(result)
+
+    def print_report(self):
+        """Print the all results of the report."""
+        print(f"Validation Report: {self.name}")
+        for result in self.results:
+            print(f"Category: {result.category}, Message: {result.message}")
+
+
+def validate(
+    msdf: MappingSetDataFrame, validation_types: List[SchemaValidationType]
+) -> List[ValidationReport]:
     """Validate SSSOM files against `sssom-schema` using linkML's validator function.
 
     :param msdf: MappingSetDataFrame.
@@ -29,21 +67,35 @@ def validate(msdf: MappingSetDataFrame, validation_types: List[SchemaValidationT
         SchemaValidationType.Shacl: validate_shacl,
         SchemaValidationType.PrefixMapCompleteness: check_all_prefixes_in_curie_map,
     }
+    results = []
     for vt in validation_types:
-        validation_methods[vt](msdf)
+        result = validation_methods[vt](msdf)
+        results.append(result)
+    return results
 
 
-def validate_json_schema(msdf: MappingSetDataFrame) -> None:
+def validate_json_schema(msdf: MappingSetDataFrame, fail_hard=False) -> ValidationReport:
     """Validate JSON Schema using linkml's JsonSchemaDataValidator.
 
     :param msdf: MappingSetDataFrame to eb validated.
+    :param fail_hard:
     """
     validator = ReferenceValidator(SchemaView(SCHEMA_YAML))
     mapping_set = to_mapping_set_document(msdf).mapping_set
-    validator.validate(mapping_set, MappingSet)
-
-
-def validate_shacl(msdf: MappingSetDataFrame) -> None:
+    results = validator.validate(mapping_set, MappingSet)
+    validation_results = ValidationReport("sssom_linkml_reference_validator")
+    if fail_hard and results:
+        raise ValidationError(f"Mapping set has validation errors: {results}.")
+    for res in results.results:
+        r = ValidationResult("sssom_linkml_reference_validator")
+        r.check = "TBD"
+        r.data = res
+        r.message = str(res)
+        validation_results.add_result(r)
+    return validation_results
+
+
+def validate_shacl(msdf: MappingSetDataFrame) -> ValidationReport:
     """Validate SCHACL file.
 
     :param msdf: TODO: https://github.com/linkml/linkml/issues/850 .
@@ -52,23 +104,11 @@ def validate_shacl(msdf: MappingSetDataFrame) -> None:
     raise NotImplementedError
 
 
-def validate_sparql(msdf: MappingSetDataFrame) -> None:
-    """Validate SPARQL file.
-
-    :param msdf: MappingSetDataFrame
-    :raises NotImplementedError: Not yet implemented.
-    """
-    # queries = {}
-    # validator = SparqlDataValidator(SCHEMA_YAML,queries=queries)
-    # mapping_set = to_mapping_set_document(msdf).mapping_set
-    # TODO: Complete this function
-    raise NotImplementedError
-
-
-def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame) -> None:
+def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame, fail_hard=True) -> ValidationReport:
     """Check all `EntityReference` slots are mentioned in 'curie_map'.
 
     :param msdf: MappingSetDataFrame
+    :param fail_hard: If true, validation will fail on first error
     :raises ValidationError: If all prefixes not in curie_map.
     """
     prefixes = get_all_prefixes(msdf)
@@ -84,5 +124,7 @@ def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame) -> None:
     for pref in prefixes:
         if pref != "" and pref not in list(msdf.prefix_map.keys()):
             missing_prefixes.append(pref)
-    if missing_prefixes:
+    if missing_prefixes and fail_hard:
         raise ValidationError(f"The prefixes in {missing_prefixes} are missing from 'curie_map'.")
+    report = ValidationReport("sssom_missing_prefixes")
+    return report

tests/test_validate.py

@@ -27,7 +27,8 @@ 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))
+        results = validate(self.correct_msdf1, self.validation_types)
+        self.assertEqual(len(results), 2)
 
     def test_validate_json_fail(self):
         """