jsonprofile 0.2.0__tar.gz → 0.2.2__tar.gz

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/PKG-INFO

@@ -1,20 +1,21 @@
 Metadata-Version: 2.3
 Name: jsonprofile
-Version: 0.2.0
+Version: 0.2.2
 Summary: Dynamic profile management for json files share same schema
-Requires-Dist: bioregistry>=0.13.64
-Requires-Dist: cachetools>=7.1.4
+Requires-Dist: bioregistry>=0.13.67
+Requires-Dist: cachetools>=7.2.8
 Requires-Dist: email-validator>=2.3.0
-Requires-Dist: httpx2>=0.28.1
+Requires-Dist: httpx2>=2.14.0
 Requires-Dist: jsonpath-ng>=1.8.0
-Requires-Dist: jsonschema-rs>=0.46.9
+Requires-Dist: jsonschema-rs>=0.60.3
 Requires-Dist: ontology-lookup>=0.1.1
-Requires-Dist: orjson>=3.11.9
-Requires-Dist: pydantic>=2.12.4
+Requires-Dist: orjson>=3.13.0
+Requires-Dist: pydantic>=2.14.0
 Requires-Dist: pyyaml>=6.0.3
 Requires-Dist: rfc3986>=2.0.0
 Requires-Dist: opa-wasmtime>=0.1.1 ; extra == 'opa'
 Requires-Python: >=3.10
+Project-URL: Repository, https://github.com/MetabolomicsHub/jsonprofile
 Provides-Extra: opa
 Description-Content-Type: text/markdown
 

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/pyproject.toml

@@ -1,23 +1,26 @@
 [project]
 name = "jsonprofile"
-version = "0.2.0"
+version = "0.2.2"
 description = "Dynamic profile management for json files share same schema"
 readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
-    "bioregistry>=0.13.64",
-    "cachetools>=7.1.4",
+    "bioregistry>=0.13.67",
+    "cachetools>=7.2.8",
     "email-validator>=2.3.0",
-    "httpx2>=0.28.1",
+    "httpx2>=2.14.0",
     "jsonpath-ng>=1.8.0",
-    "jsonschema-rs>=0.46.9",
+    "jsonschema-rs>=0.60.3",
     "ontology-lookup>=0.1.1",
-    "orjson>=3.11.9",
-    "pydantic>=2.12.4",
+    "orjson>=3.13.0",
+    "pydantic>=2.14.0",
     "pyyaml>=6.0.3",
     "rfc3986>=2.0.0",
 ]
 
+[project.urls]
+Repository = "https://github.com/MetabolomicsHub/jsonprofile"
+
 [project.optional-dependencies]
 opa = ["opa-wasmtime>=0.1.1"]
 
@@ -27,13 +30,13 @@ dev = [
     "commitizen>=4.13.9",
     "pytest>=9.0.3",
     "ruff>=0.17.00",
-    "uv-build>=0.9.8",
+    "uv-build>=0.13.0,<0.14.0",
     "mkdocs-material>=9.7.0",
 ]
 
 [tool.ruff]
 target-version = "py310"
-cache-dir = "../.cache/python/ruff"
+cache-dir = ".cache/ruff"
 src = ["src"]
 
 [tool.ruff.lint]
@@ -67,7 +70,7 @@ update_changelog_on_bump = true
 
 [tool.pytest.ini_options]
 addopts = "-v"
-cache_dir = "../.cache/python/pytest"
+cache_dir = ".cache/pytest"
 testpaths = ["tests"]
 log_cli = true
 log_cli_level = "INFO"
@@ -78,5 +81,5 @@ log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(linen
 module-name = "jsonprofile"
 
 [build-system]
-requires = ["uv_build>=0.9.8,<0.12.0"]
+requires = ["uv_build>=0.13.0,<0.14.0"]
 build-backend = "uv_build"

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/pyproject.toml.orig

@@ -1,23 +1,25 @@
 [project]
 name = "jsonprofile"
-version = "0.2.0"
+version = "0.2.2"
 description = "Dynamic profile management for json files share same schema"
 readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
-    "bioregistry>=0.13.64",
-    "cachetools>=7.1.4",
+    "bioregistry>=0.13.67",
+    "cachetools>=7.2.8",
     "email-validator>=2.3.0",
-    "httpx2>=0.28.1",
+    "httpx2>=2.14.0",
     "jsonpath-ng>=1.8.0",
-    # "jsonschema>=4.26.0",
-    "jsonschema-rs>=0.46.9",
+    "jsonschema-rs>=0.60.3",
     "ontology-lookup>=0.1.1",
-    "orjson>=3.11.9",
-    "pydantic>=2.12.4",
+    "orjson>=3.13.0",
+    "pydantic>=2.14.0",
     "pyyaml>=6.0.3",
     "rfc3986>=2.0.0",
 ]
+[project.urls]
+'Repository' = 'https://github.com/MetabolomicsHub/jsonprofile'
+
 [project.optional-dependencies]
 opa = ["opa-wasmtime>=0.1.1"]
 
@@ -27,13 +29,13 @@ dev = [
     "commitizen>=4.13.9",
     "pytest>=9.0.3",
     "ruff>=0.17.00",
-    "uv-build>=0.9.8",
+    "uv-build>=0.13.0,<0.14.0",
     "mkdocs-material>=9.7.0",
 ]
 
 [tool.ruff]
 target-version = "py310"
-cache-dir = "../.cache/python/ruff"
+cache-dir = ".cache/ruff"
 src = ["src"]
 
 [tool.commitizen]
@@ -58,7 +60,7 @@ known-first-party = ["jsonprofile"]
 
 [tool.pytest.ini_options]
 addopts = "-v"
-cache_dir = "../.cache/python/pytest"
+cache_dir = ".cache/pytest"
 testpaths = ["tests"]
 log_cli = true
 log_cli_level = "INFO"
@@ -66,7 +68,7 @@ log_cli_date_format = "%Y-%m-%d %H:%M:%S"
 log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)"
 
 [build-system]
-requires = ["uv_build>=0.9.8,<0.12.0"]
+requires = ["uv_build>=0.13.0,<0.14.0"]
 build-backend = "uv_build"
 
 [tool.uv.build-backend]

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/src/jsonprofile/__init__.py

@@ -1,6 +1,6 @@
 from jsonprofile import profile, utils, validator
 
-__version__ = "v0.2.0"
+__version__ = "v0.2.2"
 
 
 __all__ = ["profile", "validator", "utils", "cv_term_search"]

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/src/jsonprofile/jsonprofile.schema.json

@@ -1,6 +1,7 @@
 {
   "$defs": {
     "BaseCvTerm": {
+      "additionalProperties": false,
       "description": "A lightweight reference to a controlled vocabulary (CV) term.\n\nUsed within constraint definitions to identify specific CV terms\nby their label, accession, or human-readable name.",
       "properties": {
         "cv_label": {
@@ -47,6 +48,7 @@
       "type": "object"
     },
     "BooleanConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a value is boolean.",
       "properties": {
         "validator": {
@@ -260,6 +262,7 @@
       "type": "object"
     },
     "CVListConstraint": {
+      "additionalProperties": false,
       "description": "Restricts CV terms to those from specific controlled vocabularies.\n\nThe ``allowed_cv_list`` field specifies which CV namespace labels are\nallowed (e.g. ``['MS', 'UO']``).",
       "properties": {
         "validator": {
@@ -496,6 +499,7 @@
       "type": "object"
     },
     "CVTermConstraint": {
+      "additionalProperties": false,
       "description": "Base constraint for values that must be controlled vocabulary terms.\n\nSubclasses refine which CV terms are acceptable (by list, by parent\nterm, or by CV namespace). This class captures the common options\nshared across all CV term constraints.",
       "properties": {
         "validator": {
@@ -715,6 +719,7 @@
       "type": "object"
     },
     "CVTermEnumConstraint": {
+      "additionalProperties": false,
       "description": "Restricts the value to a specific set of CV terms.\n\nUnlike ``CVListConstraint`` which filters by CV namespace, this\nconstraint enumerates the exact terms that are acceptable.",
       "properties": {
         "validator": {
@@ -946,6 +951,7 @@
       "type": "object"
     },
     "CVTermValueConstraint": {
+      "additionalProperties": false,
       "description": "Validates the value slot of a specific CV term.\n\nWhen a field contains a CV term matching ``key_cv_term``, its\nvalue is validated against the nested ``value_constraint``.\nThis enables context-dependent validation (e.g. a numeric range\nthat only applies when a specific CV term is used).",
       "properties": {
         "validator": {
@@ -1209,6 +1215,7 @@
       "type": "object"
     },
     "CollectionConstraint": {
+      "additionalProperties": false,
       "description": "Validates collection size and item matches against reference values.",
       "properties": {
         "validator": {
@@ -1591,6 +1598,7 @@
       "type": "object"
     },
     "ConstraintGroup": {
+      "additionalProperties": false,
       "description": "Combines multiple constraints using boolean or valid-count logic.",
       "properties": {
         "validator": {
@@ -1875,6 +1883,7 @@
       "type": "object"
     },
     "CustomConstraint": {
+      "additionalProperties": false,
       "description": "Runs a named custom constraint checker.",
       "properties": {
         "validator": {
@@ -2083,6 +2092,7 @@
       "type": "object"
     },
     "CvTerm": {
+      "additionalProperties": false,
       "description": "Controlled vocabulary term with an optional user-provided value.",
       "properties": {
         "cv_label": {
@@ -2142,6 +2152,7 @@
       "type": "object"
     },
     "CvTermFieldMapping": {
+      "additionalProperties": false,
       "properties": {
         "label_field": {
           "anyOf": [
@@ -2196,6 +2207,7 @@
       "type": "object"
     },
     "DateTimeConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a string value represents a valid date, time,\nor datetime.\n\nWhen ``format`` is provided, the value must match that specific\npattern (e.g. ISO-8601). When omitted, ISO-8601 is accepted.",
       "properties": {
         "validator": {
@@ -2376,7 +2388,8 @@
       "type": "object"
     },
     "DecimalConstraint": {
-      "description": "Validates that a value is a valid floating-point number.\n\nSupports optional range bounds, scientific notation control,\nand decimal precision limits.",
+      "additionalProperties": false,
+      "description": "Validates that a value is a valid decimal number.\n\nSupports optional range bounds, scientific notation control,\nand decimal precision limits.",
       "properties": {
         "validator": {
           "anyOf": [
@@ -2541,6 +2554,8 @@
         "minimum": {
           "anyOf": [
             {
+              "maximum": 7.922816251426434e+28,
+              "minimum": -7.922816251426434e+28,
               "type": "number"
             },
             {
@@ -2557,6 +2572,8 @@
         "maximum": {
           "anyOf": [
             {
+              "maximum": 7.922816251426434e+28,
+              "minimum": -7.922816251426434e+28,
               "type": "number"
             },
             {
@@ -2629,6 +2646,7 @@
       "type": "object"
     },
     "EmailConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a string value is a well-formed email address.",
       "properties": {
         "validator": {
@@ -2820,6 +2838,7 @@
       "type": "string"
     },
     "Evaluation": {
+      "additionalProperties": false,
       "description": "Evaluates a constraint against either the current value or another JSONPath.",
       "properties": {
         "root_value_evaluation": {
@@ -3005,6 +3024,7 @@
       "type": "object"
     },
     "ExtendedCvTerm": {
+      "additionalProperties": false,
       "description": "Controlled vocabulary term whose value may be another CV term.",
       "properties": {
         "cv_label": {
@@ -3067,6 +3087,7 @@
       "type": "object"
     },
     "FieldRequirement": {
+      "additionalProperties": false,
       "description": "Validation rules that apply to one profiled JSON field.",
       "properties": {
         "code": {
@@ -3239,6 +3260,7 @@
       "type": "object"
     },
     "FieldRequirementGroup": {
+      "additionalProperties": false,
       "description": "Group of requirements combined by valid-count bounds.",
       "properties": {
         "code": {
@@ -3334,6 +3356,7 @@
       "type": "object"
     },
     "IntegerConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a value is a valid integer within an optional range.\n\nUse ``PositiveIntegerConstraint`` or ``NonNegativeIntegerConstraint``\nfor common presets.",
       "properties": {
         "validator": {
@@ -3499,6 +3522,8 @@
         "minimum": {
           "anyOf": [
             {
+              "maximum": 9223372036854775807,
+              "minimum": -9223372036854775808,
               "type": "integer"
             },
             {
@@ -3512,6 +3537,8 @@
         "maximum": {
           "anyOf": [
             {
+              "maximum": 9223372036854775807,
+              "minimum": -9223372036854775808,
               "type": "integer"
             },
             {
@@ -3527,6 +3554,7 @@
       "type": "object"
     },
     "IntegerEnumConstraint": {
+      "additionalProperties": false,
       "description": "Validates that an integer value is one of a fixed set of allowed options.\n\nEach option maps an integer value to a display value, integer code,\nor ``ExtendedCvTerm`` metadata.",
       "properties": {
         "validator": {
@@ -3715,6 +3743,7 @@
       "type": "object"
     },
     "JsonProfileConfiguration": {
+      "additionalProperties": false,
       "description": "Optional configuration shared by validators for a profile.",
       "properties": {
         "cv_term_field_mapping": {
@@ -3866,6 +3895,7 @@
       "type": "object"
     },
     "NonNegativeIntegerConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a value is a non-negative integer (>= 0).\n\nConvenience subclass of ``IntegerConstraint`` with ``minimum=0``.",
       "properties": {
         "validator": {
@@ -4031,6 +4061,8 @@
         "minimum": {
           "anyOf": [
             {
+              "maximum": 9223372036854775807,
+              "minimum": -9223372036854775808,
               "type": "integer"
             },
             {
@@ -4044,6 +4076,8 @@
         "maximum": {
           "anyOf": [
             {
+              "maximum": 9223372036854775807,
+              "minimum": -9223372036854775808,
               "type": "integer"
             },
             {
@@ -4059,6 +4093,7 @@
       "type": "object"
     },
     "NotNullConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a value is not null or one of the configured null values.",
       "properties": {
         "validator": {
@@ -4239,6 +4274,7 @@
       "type": "object"
     },
     "OpaFieldRequirement": {
+      "additionalProperties": false,
       "description": "Requirement will be evaluated and messages are produced by OPA engine",
       "properties": {
         "code": {
@@ -4306,6 +4342,7 @@
       "type": "object"
     },
     "OpaPolicyConstraint": {
+      "additionalProperties": false,
       "description": "Evaluates an Open Policy Agent policy against the input value.",
       "properties": {
         "validator": {
@@ -4494,6 +4531,7 @@
       "type": "object"
     },
     "ParentCVTermConstraint": {
+      "additionalProperties": false,
       "description": "Restricts the value to CV terms that are descendants of\nspecified parent terms in the ontology hierarchy.\n\nSupports exclusion of specific terms or name patterns to\nfilter out unwanted branches of the ontology tree.",
       "properties": {
         "validator": {
@@ -4746,6 +4784,7 @@
       "type": "object"
     },
     "PositiveIntegerConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a value is a positive integer (>= 1).\n\nConvenience subclass of ``IntegerConstraint`` with ``minimum=1``.",
       "properties": {
         "validator": {
@@ -4911,6 +4950,8 @@
         "minimum": {
           "anyOf": [
             {
+              "maximum": 9223372036854775807,
+              "minimum": -9223372036854775808,
               "type": "integer"
             },
             {
@@ -4924,6 +4965,8 @@
         "maximum": {
           "anyOf": [
             {
+              "maximum": 9223372036854775807,
+              "minimum": -9223372036854775808,
               "type": "integer"
             },
             {
@@ -4939,6 +4982,7 @@
       "type": "object"
     },
     "Precondition": {
+      "additionalProperties": false,
       "description": "Condition that controls whether a constraint should be evaluated.",
       "properties": {
         "evaluations": {
@@ -4995,6 +5039,7 @@
       "type": "object"
     },
     "ProfileValidatorDefinition": {
+      "additionalProperties": false,
       "description": "Definition of a profile validator implementation.",
       "properties": {
         "label": {
@@ -5038,6 +5083,7 @@
       "type": "object"
     },
     "RegexConstraint": {
+      "additionalProperties": false,
       "description": "Validates a string value against a regular expression pattern.\n\nUse for structured identifiers or format patterns that can be\nexpressed as a single regex (e.g. ORCID, adduct ion notation).",
       "properties": {
         "validator": {
@@ -5227,6 +5273,7 @@
       "type": "object"
     },
     "StringConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a string value's length falls within a range.\n\nAt least one of ``minimum`` or ``maximum`` should be set.",
       "properties": {
         "validator": {
@@ -5422,6 +5469,7 @@
       "type": "object"
     },
     "StringEnumConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a string value is one of a fixed set of allowed options.\n\nOptions may be a simple list of strings or a mapping from a string key\nto a display value, integer code, or ``ExtendedCvTerm`` metadata.",
       "properties": {
         "validator": {
@@ -5620,6 +5668,7 @@
       "type": "object"
     },
     "UriConstraint": {
+      "additionalProperties": false,
       "description": "Validates that a string value is a well-formed URI.\n\nOptionally restricts accepted URI schemes (e.g. only ``https``,\n``ftp``).",
       "properties": {
         "validator": {
@@ -5803,6 +5852,7 @@
       "type": "object"
     },
     "WasmFileDefinition": {
+      "additionalProperties": false,
       "description": "Configuration for an Open Policy Agent policy module.",
       "properties": {
         "wasm_file_download_url": {
@@ -5830,6 +5880,7 @@
       "type": "object"
     }
   },
+  "additionalProperties": false,
   "description": "A JSON profile containing metadata, configuration, and field requirements.",
   "properties": {
     "id": {

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/src/jsonprofile/profile/base.py

@@ -35,6 +35,7 @@ class JsonProfileBaseModel(BaseModel):
     """Base model configuration shared by JSON Profile schemas."""
 
     model_config = ConfigDict(
+        extra="forbid",
         populate_by_name=True,
         str_strip_whitespace=True,
         validate_default=True,

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/src/jsonprofile/profile/constraints/constraints.py

@@ -14,6 +14,28 @@ from jsonprofile.profile.base import (
     JsonProfileBaseModel,
 )
 
+INT64_MIN = -(2**63)
+INT64_MAX = 2**63 - 1
+DECIMAL_MAX_COEFFICIENT = 2**96 - 1
+DECIMAL_MAX_SCALE = 28
+
+
+def decimal_fits_shared_range(value: Decimal) -> bool:
+    """Return whether a finite Decimal fits Rust Decimal's 96-bit representation."""
+    if not value.is_finite():
+        return False
+    parts = value.as_tuple()
+    coefficient = int("".join(map(str, parts.digits)) or "0")
+    exponent = parts.exponent
+    scale = max(0, -exponent)
+    if scale > DECIMAL_MAX_SCALE:
+        return False
+    if exponent > 0 and coefficient:
+        if len(str(coefficient)) + exponent > len(str(DECIMAL_MAX_COEFFICIENT)):
+            return False
+        coefficient *= 10**exponent
+    return coefficient <= DECIMAL_MAX_COEFFICIENT
+
 
 class Precondition(JsonProfileBaseModel):
     """Condition that controls whether a constraint should be evaluated."""
@@ -306,6 +328,13 @@ class IntegerEnumConstraint(Constraint):
         ),
     ]
 
+    @field_validator("options")
+    @classmethod
+    def int64_option_keys(cls, value):
+        if any(key < INT64_MIN or key > INT64_MAX for key in value):
+            raise ValueError("integer-enum option keys must fit signed 64-bit range")
+        return value
+
 
 class IntegerConstraint(Constraint):
     """Validates that a value is a valid integer within an optional range.
@@ -320,13 +349,17 @@ class IntegerConstraint(Constraint):
     minimum: Annotated[
         Optional[int],
         Field(
-            description="Minimum allowed value (inclusive). None means no lower bound."
+            description="Minimum allowed value (inclusive). None means no lower bound.",
+            ge=INT64_MIN,
+            le=INT64_MAX,
         ),
     ] = None
     maximum: Annotated[
         Optional[int],
         Field(
-            description="Maximum allowed value (inclusive). None means no upper bound."
+            description="Maximum allowed value (inclusive). None means no upper bound.",
+            ge=INT64_MIN,
+            le=INT64_MAX,
         ),
     ] = None
 
@@ -342,7 +375,11 @@ class PositiveIntegerConstraint(IntegerConstraint):
     )
     minimum: Annotated[
         Optional[int],
-        Field(description="Minimum allowed value (inclusive). Defaults to 1."),
+        Field(
+            description="Minimum allowed value (inclusive). Defaults to 1.",
+            ge=INT64_MIN,
+            le=INT64_MAX,
+        ),
     ] = 1
 
 
@@ -357,7 +394,11 @@ class NonNegativeIntegerConstraint(IntegerConstraint):
     )
     minimum: Annotated[
         Optional[int],
-        Field(description="Minimum allowed value (inclusive). Defaults to 0."),
+        Field(
+            description="Minimum allowed value (inclusive). Defaults to 0.",
+            ge=INT64_MIN,
+            le=INT64_MAX,
+        ),
     ] = 0
 
 
@@ -385,7 +426,7 @@ class BooleanConstraint(Constraint):
 
 
 class DecimalConstraint(Constraint):
-    """Validates that a value is a valid floating-point number.
+    """Validates that a value is a valid decimal number.
 
     Supports optional range bounds, scientific notation control,
     and decimal precision limits.
@@ -397,15 +438,29 @@ class DecimalConstraint(Constraint):
     minimum: Annotated[
         Optional[Decimal],
         Field(
-            description="Minimum allowed value (inclusive). None means no lower bound."
+            description="Minimum allowed value (inclusive). None means no lower bound.",
+            ge=Decimal(-DECIMAL_MAX_COEFFICIENT),
+            le=Decimal(DECIMAL_MAX_COEFFICIENT),
         ),
     ] = None
     maximum: Annotated[
         Optional[Decimal],
         Field(
-            description="Maximum allowed value (inclusive). None means no upper bound."
+            description="Maximum allowed value (inclusive). None means no upper bound.",
+            ge=Decimal(-DECIMAL_MAX_COEFFICIENT),
+            le=Decimal(DECIMAL_MAX_COEFFICIENT),
         ),
     ] = None
+
+    @field_validator("minimum", "maximum")
+    @classmethod
+    def bounds_fit_shared_decimal_range(cls, value):
+        if value is not None and not decimal_fits_shared_range(value):
+            raise ValueError(
+                "decimal bounds must fit a 96-bit coefficient and scale <= 28"
+            )
+        return value
+
     allow_scientific_notation: Annotated[
         Optional[bool],
         Field(

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/src/jsonprofile/validator/abstract_checker.py

@@ -9,6 +9,7 @@ import jsonpath_ng
 from jsonprofile.profile.base import JsonPath, JsonProfileBaseModel
 from jsonprofile.profile.constraints.constraints import (
     Constraint,
+    CustomConstraint,
     DecimalConstraint,
 )
 
@@ -204,22 +205,39 @@ class ConstraintChecker(abc.ABC):
 
             sub_value = self.get_json_path_value(constraint, value, context)
             if success:
-                is_valid, message = checker.validate(
-                    constraint, sub_value, root=root, context=context
-                )
+                if isinstance(constraint, CustomConstraint):
+                    null_value = sub_value is None or (
+                        constraint.null_values
+                        and str(sub_value) in constraint.null_values
+                    )
+                    exceptional = constraint.exceptional_values or []
+                    if sub_value in exceptional or (null_value and None in exceptional):
+                        is_valid, message = True, "value is in exceptional list"
+                    else:
+                        is_valid, message = checker.validate(
+                            constraint,
+                            None if null_value else sub_value,
+                            root=root,
+                            context=context,
+                        )
+                    if constraint.negated:
+                        is_valid = not is_valid
+                    message = message or ""
+                else:
+                    is_valid, message = checker.validate(
+                        constraint, sub_value, root=root, context=context
+                    )
             else:
                 is_valid = True
                 message = f"Precondition does not meet: {message}"
             return ConstraintValidationResult(
                 is_valid=is_valid,
                 message=message,
-                constraint_name=getattr(constraint, "name", "unknown"),
             )
 
         return ConstraintValidationResult(
             is_valid=False,
             message=f"Unknown constraint type: {type(constraint)}",
-            constraint_name=getattr(constraint, "name", "unknown"),
         )
 
     def get_json_path_value(

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/src/jsonprofile/validator/checkers/default_checker.py

@@ -19,6 +19,8 @@ from jsonprofile.profile.base import (
     ValidationRuntimeConfiguration,
 )
 from jsonprofile.profile.constraints.constraints import (
+    INT64_MAX,
+    INT64_MIN,
     BooleanConstraint,
     CollectionConstraint,
     ConstraintGroup,
@@ -40,6 +42,7 @@ from jsonprofile.profile.constraints.constraints import (
     StringConstraint,
     StringEnumConstraint,
     UriConstraint,
+    decimal_fits_shared_range,
 )
 from jsonprofile.profile.model import (
     JsonProfileConfiguration,
@@ -52,6 +55,14 @@ from jsonprofile.validator.decorators import constraint_checker
 logger = logging.getLogger(__name__)
 
 
+def _parse_int64(value: str) -> int | None:
+    try:
+        parsed = int(value)
+    except (ValueError, TypeError, OverflowError):
+        return None
+    return parsed if INT64_MIN <= parsed <= INT64_MAX else None
+
+
 def _extract_cv_info(value: Any, mapping: CvTermFieldMapping) -> CvTerm:
     """Extracts label, accession, name, and value from a CvTerm or dict."""
     if isinstance(value, CvTerm):
@@ -95,16 +106,23 @@ class NotNullConstraintChecker(ConstraintChecker):
     ) -> Tuple[bool, Optional[str]]:
         evaluation = False
         messages = []
+        is_exceptional = bool(
+            constraint.exceptional_values and value in constraint.exceptional_values
+        )
         if value is not None and constraint.null_values:
             str_val = str(value) if constraint.case_sensitive else str(value).lower()
             if str_val in constraint.null_values:
                 messages.append("value is in null value list")
                 value = None
         message = ""
-        if value is not None:
+        if is_exceptional:
+            evaluation = True
+            message = "value is in exceptional list"
+        elif value is not None:
             evaluation = True
             message = f"{value} is not null"
-        message = ". ".join(messages)
+        elif messages:
+            message = ". ".join(messages)
 
         if constraint.negated:
             evaluation = not evaluation
@@ -275,7 +293,9 @@ class CollectionConstraintChecker(ConstraintChecker):
             message = "value is not defined"
         elif not isinstance(collection_values, list):
             message = f"{constraint.json_path} is not a collection."
-            return False, message
+            if constraint.negated:
+                return True, self.format_message(constraint, message)
+            return False, self.format_message(constraint, message)
         else:
             val = collection_values
             if constraint.exceptional_values and (
@@ -526,10 +546,7 @@ class IntegerEnumConstraintChecker(ConstraintChecker):
             ):
                 evaluation = True
             else:
-                try:
-                    int_val = int(val)
-                except:  # noqa: E722
-                    int_val = None
+                int_val = _parse_int64(val)
                 if int_val is not None:
                     if int_val in constraint.options:
                         evaluation = True
@@ -575,10 +592,7 @@ class IntegerConstraintChecker(ConstraintChecker):
                 min_req = True
                 max_req = True
             else:
-                try:
-                    int_val = int(val)
-                except:  # noqa: E722
-                    int_val = None
+                int_val = _parse_int64(val)
                 if int_val is not None:
                     min_req = (
                         True
@@ -724,13 +738,18 @@ class DecimalConstraintChecker(ConstraintChecker):
                     pass
                 if decimal_val is not None:
                     if decimal_val.is_finite():
-                        if (
-                            not constraint.allow_scientific_notation
+                        if not decimal_fits_shared_range(decimal_val):
+                            message = (
+                                "value is outside the shared decimal range "
+                                "(96-bit coefficient, scale <= 28)"
+                            )
+                        elif (
+                            constraint.allow_scientific_notation is False
                             and "e" in val.lower()
                         ):
                             message = "scientific notation is not allowed"
                         else:
-                            scale = -decimal_val.as_tuple().exponent
+                            scale = max(0, -decimal_val.as_tuple().exponent)
                             min_scale_req = (
                                 True
                                 if constraint.min_scale is None
@@ -966,40 +985,34 @@ class CVTermConstraintChecker(ConstraintChecker):
                     and param.cv_label in constraint.exceptional_cv_list
                 ):
                     message = "CV source is in exception list"
-                    return True, self.format_message(constraint, message)
-                is_user_defined = (
-                    not param.cv_label
-                    and not param.cv_accession
-                    and param.name
-                    and len(param.name) > 0
-                )
-                if is_user_defined:
-                    if constraint.allow_user_defined_terms:
-                        name_req = True
-                        message = "User-defined terms is allowed."
-                    else:
-                        message = "User-defined terms is not allowed."
+                    name_req = True
                 else:
-                    if param.name:
-                        if not param.cv_label or not param.cv_accession:
-                            message = f"invalid cv term label or accession. {param}"
+                    is_user_defined = (
+                        not param.cv_label
+                        and not param.cv_accession
+                        and param.name
+                        and len(param.name) > 0
+                    )
+                    if is_user_defined:
+                        if constraint.allow_user_defined_terms:
+                            name_req = True
+                            message = "User-defined terms is allowed."
                         else:
-                            if runtime_config and runtime_config.offline_mode:
+                            message = "User-defined terms is not allowed."
+                    else:
+                        if param.name:
+                            if not param.cv_label or not param.cv_accession:
+                                message = f"invalid cv term label or accession. {param}"
+                            elif runtime_config and runtime_config.offline_mode:
                                 name_req = True
                                 message = "term is valid."
                             else:
-                                verified, message = cv_term_search.check_cv_term(
+                                name_req, message = cv_term_search.check_cv_term(
                                     param,
-                                    allow_synonym_search=True
-                                    if constraint.allow_synonym
-                                    else False,
+                                    allow_synonym_search=bool(constraint.allow_synonym),
                                 )
-                                return verified, self.format_message(
-                                    constraint, message
-                                )
-
-                    else:
-                        message = f"invalid cv term name: {param}"
+                        else:
+                            message = f"invalid cv term name: {param}"
 
                 messages = [message] if message else []
 
@@ -1063,6 +1076,13 @@ class CVListConstraintChecker(ConstraintChecker):
                                 message = (
                                     f"'{param}' term is in exception cv term list."
                                 )
+                        if (
+                            not name_req
+                            and constraint.exceptional_cv_list
+                            and param.cv_label in constraint.exceptional_cv_list
+                        ):
+                            name_req = True
+                            message = "CV source is in exception list"
                         if not name_req:
                             if constraint.allowed_cv_list:
                                 if param.cv_label.upper() in [
@@ -1080,9 +1100,7 @@ class CVListConstraintChecker(ConstraintChecker):
                                                 else False,
                                             )
                                         )
-                                        return verified, self.format_message(
-                                            constraint, message
-                                        )
+                                        name_req = verified
                                 else:
                                     message = (
                                         f"'{param}' not in the selected cv list: "
@@ -1099,9 +1117,7 @@ class CVListConstraintChecker(ConstraintChecker):
                                         if constraint.allow_synonym
                                         else False,
                                     )
-                                    return verified, self.format_message(
-                                        constraint, message
-                                    )
+                                    name_req = verified
 
                 else:
                     message = "invalid cv term name."
@@ -1240,40 +1256,34 @@ class ParentCVTermConstraintChecker(ConstraintChecker):
                             if param in constraint.exceptional_values:
                                 name_req = True
                                 message = "cv term is in exception list."
+                        if (
+                            not name_req
+                            and constraint.exceptional_cv_list
+                            and param.cv_label in constraint.exceptional_cv_list
+                        ):
+                            name_req = True
+                            message = "CV source is in exception list"
                         if not name_req:
                             if runtime_config and runtime_config.offline_mode:
                                 name_req = True
                                 message = "offline mode."
-                            else:
-                                verified_parent = None
-                                for parent in constraint.parent_cv_terms or []:
+                            elif constraint.parent_cv_terms:
+                                for parent in constraint.parent_cv_terms:
                                     verified, message = cv_term_search.check_cv_term(
                                         cv_term=param,
                                         parent_cv_term=parent,
-                                        allow_synonym_search=True
-                                        if constraint.allow_synonym
-                                        else False,
+                                        allow_synonym_search=bool(
+                                            constraint.allow_synonym
+                                        ),
                                     )
                                     if verified:
-                                        verified_parent = parent
+                                        name_req = True
+                                        message = (
+                                            f"CV term {param} is parent of {parent}."
+                                        )
                                         break
-                                if verified_parent:
-                                    name_req = True
-                                    message = (
-                                        f"CV term {param} is "
-                                        f"parent of {verified_parent}."
-                                    )
-                                else:
+                                if not name_req:
                                     message = "term in not child of the parent."
-
-                            if constraint.parent_cv_terms:
-                                input_val = BaseCvTerm.model_validate(
-                                    param, from_attributes=True
-                                )
-                                if input_val in (constraint.exceptional_values or []):
-                                    name_req = True
-                                else:
-                                    message = "not child of the parent."
                             else:
                                 name_req = True
                                 message = "not child of the parent."

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/src/jsonprofile/validator/default/ols_cv_term_search.py

@@ -15,6 +15,10 @@ logger = logging.getLogger(__name__)
 _T = TypeVar("T")
 
 
+class _OlsSearchFailure(RuntimeError):
+    """An unsuccessful OLS response that must not be kept in the result cache."""
+
+
 class _OlsSearchModel(JsonProfileBaseModel, Generic[_T]):
     page: int
     num_elements: int
@@ -53,18 +57,17 @@ class _ChildrenSearchModel(JsonProfileBaseModel):
 def _search_ols(
     url: str, params: dict, headers: dict, timeout: int = 10
 ) -> tuple[int, dict[str, Any]]:
-    try:
-        result = httpx2.get(url, params=params, headers=headers, timeout=timeout)
-        if result.status_code in {200, 201}:
-            return result.status_code, result.json()
-    except Exception as ex:
-        return 500, {"error": str(ex)}
+    result = httpx2.get(url, params=params, headers=headers, timeout=timeout)
+    if result.status_code in {200, 201}:
+        return result.status_code, result.json()
+    if result.status_code == 404:
+        return result.status_code, {}
     logger.warning(
         "Could not find CV term: %s %s",
         result.status_code,
         orjson.dumps(params, orjson.OPT_SORT_KEYS),
     )
-    return result.status_code, {}
+    raise _OlsSearchFailure(f"OLS returned HTTP {result.status_code} for {url}")
 
 
 class OlsCvTermSearch(CvTermSearch):

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/src/jsonprofile/validator/json_validator.py

@@ -125,7 +125,7 @@ class JsonValidator:
         logger.debug("Json schema will be loaded.")
         self.json_schema = None
         self.schema_validator = None
-        if json_schema:
+        if json_schema is not None:
             self.json_schema = self.load_jsonschema(json_schema)
             self.validate_jsonschema(self.json_schema)
             logger.debug("Json schema validated.")
@@ -233,7 +233,7 @@ class JsonValidator:
         elif isinstance(profile, dict):
             target_profile = JsonProfile.model_validate(profile, by_alias=True)
         if isinstance(profile, JsonProfile):
-            target_profile = profile
+            target_profile = profile.model_copy(deep=True)
         if not target_profile or not isinstance(target_profile, JsonProfile):
             raise ValueError(
                 "Json profile load failure. "
@@ -284,6 +284,8 @@ class JsonValidator:
 
     @staticmethod
     def extend_profile(parent_profile: None | JsonProfile, input_profile: JsonProfile):
+        # Merge into a detached copy because profiles may be reused or cached.
+        input_profile = input_profile.model_copy(deep=True)
         if not parent_profile:
             if not input_profile.configuration:
                 input_profile.configuration = JsonProfileConfiguration(
@@ -301,16 +303,21 @@ class JsonValidator:
             parent_profile.name,
         )
         new_requirements = input_profile.requirements or {}
-        input_profile.requirements = dict(parent_profile.requirements or {})
+        input_profile.requirements = {
+            key: value.model_copy(deep=True) if value is not None else None
+            for key, value in (parent_profile.requirements or {}).items()
+        }
 
         if not input_profile.configuration:
             input_profile.configuration = (
                 parent_profile.configuration or JsonProfileConfiguration()
-            )
+            ).model_copy(deep=True)
 
         # set configuration fields from parent if they are not defined.
         config = input_profile.configuration
-        parent_config = parent_profile.configuration or JsonProfileConfiguration()
+        parent_config = (
+            parent_profile.configuration or JsonProfileConfiguration()
+        ).model_copy(deep=True)
         for field, _ in config.__class__.model_fields.items():
             val = getattr(config, field)
             if val is None:
@@ -526,8 +533,9 @@ class JsonValidator:
         process_reporting_threshold_in_secs: float = 5.0,
     ) -> JsonValidationResult:
         id_fields = self.json_profile.configuration.object_unique_id_fields
-        if not runtime_config:
-            runtime_config = ValidationRuntimeConfiguration()
+        runtime_config = (
+            runtime_config or ValidationRuntimeConfiguration()
+        ).model_copy(deep=True)
         unique_id_objects = {}
         if id_fields:
             unique_id_objects = self.update_unique_object_dict(
@@ -973,7 +981,9 @@ class JsonValidator:
                         )
 
                 if field_requirement.value_constraint:
-                    constraint = field_requirement.value_constraint
+                    constraint = field_requirement.value_constraint.model_copy(
+                        deep=True
+                    )
                     checker = self.profile_validator_factory.get_checker(constraint)
                     skip = False
                     if runtime_config and runtime_config.skip_decimal_validations:
@@ -981,12 +991,10 @@ class JsonValidator:
                             skip = True
 
                     if not skip:
-                        if not field_requirement.value_constraint.description:
-                            field_requirement.value_constraint.description = (
-                                field_requirement.description
-                            )
+                        if not constraint.description:
+                            constraint.description = field_requirement.description
                         res = checker.validate_constraint(
-                            constraint=field_requirement.value_constraint,
+                            constraint=constraint,
                             value=x.value,
                             root=input_json,
                             context=context,

{jsonprofile-0.2.0 → jsonprofile-0.2.2}/src/jsonprofile/validator/local_opa_engine.py

@@ -5,6 +5,7 @@ import re
 import shutil
 import tarfile
 import tempfile
+import threading
 import time
 from datetime import datetime, timezone
 from pathlib import Path
@@ -222,6 +223,7 @@ def _builtin_time_parse_ns(*args):
 
 class LocalOpaEngine(OpaEngine):
     def __init__(self, wasm_path: str):
+        self._evaluation_lock = threading.RLock()
         try:
             self._bundle_data = None
             if tarfile.is_tarfile(wasm_path):
@@ -396,23 +398,24 @@ class LocalOpaEngine(OpaEngine):
                 bundle data loaded from data.json is restored if available.
         """
         input_data = _sanitize_json_value(input_data)
-        if data is not None:
-            self.policy.set_data(_sanitize_json_value(data))
-        elif self._bundle_data is not None:
-            self.policy.set_data(_sanitize_json_value(self._bundle_data))
-        entrypoint = self.resolve_entrypoint(entrypoint)
-        if entrypoint is None:
-            result = self.policy.evaluate(input_data)
-        else:
-            result = self.policy.evaluate(input_data, entrypoint=entrypoint)
-        # Return the raw OPA evaluation result so callers can inspect
-        # the returned list of evaluation records
-        return result[0].get("result") if result and result[0] else []
+        with self._evaluation_lock:
+            if data is not None:
+                self.policy.set_data(_sanitize_json_value(data))
+            elif self._bundle_data is not None:
+                self.policy.set_data(_sanitize_json_value(self._bundle_data))
+            entrypoint = self.resolve_entrypoint(entrypoint)
+            if entrypoint is None:
+                result = self.policy.evaluate(input_data)
+            else:
+                result = self.policy.evaluate(input_data, entrypoint=entrypoint)
+            # Return the raw OPA evaluation result for caller inspection.
+            return result[0].get("result") if result and result[0] else []
 
 
 class LocalOpaEngineFactory(OpaEngineFactory):
     def __init__(self):
         self.engines: dict[Path, OpaEngine] = {}
+        self._engines_lock = threading.RLock()
 
     def load_from_url(self, url: str, file_path: str) -> None:
         """Download a file from a URL and save it to the given file path.
@@ -441,30 +444,31 @@ class LocalOpaEngineFactory(OpaEngineFactory):
         wasm_file_path: str,
         wasm_file_download_url: Optional[str] = None,
     ):
-        if not wasm_file_path:
-            raise ValueError("Invalid WASM file path")
-        wasm_path = Path(wasm_file_path)
-        if not wasm_path.exists():
-            alt_parent = Path("..") / wasm_path
-            alt_stripped = Path(wasm_file_path.removeprefix("../"))
-            if alt_parent.exists():
-                wasm_path = alt_parent
-                wasm_file_path = str(alt_parent)
-            elif alt_stripped.exists():
-                wasm_path = alt_stripped
-                wasm_file_path = str(alt_stripped)
-        if wasm_path in self.engines:
-            return self.engines[wasm_path]
-
-        if not wasm_path.exists() and not wasm_file_download_url:
-            raise ValueError(
-                "Invalid WASM file does not exists and URL is not defined. "
-                "Select a valid file path or a valid URL to download WASM file"
-            )
-
-        if not wasm_path.exists():
-            self.load_from_url(wasm_file_download_url, wasm_file_path)
-
-        engine = LocalOpaEngine(wasm_path=wasm_file_path)
-        self.engines[wasm_path] = engine
-        return engine
+        with self._engines_lock:
+            if not wasm_file_path:
+                raise ValueError("Invalid WASM file path")
+            wasm_path = Path(wasm_file_path)
+            if not wasm_path.exists():
+                alt_parent = Path("..") / wasm_path
+                alt_stripped = Path(wasm_file_path.removeprefix("../"))
+                if alt_parent.exists():
+                    wasm_path = alt_parent
+                    wasm_file_path = str(alt_parent)
+                elif alt_stripped.exists():
+                    wasm_path = alt_stripped
+                    wasm_file_path = str(alt_stripped)
+            if wasm_path in self.engines:
+                return self.engines[wasm_path]
+
+            if not wasm_path.exists() and not wasm_file_download_url:
+                raise ValueError(
+                    "Invalid WASM file does not exists and URL is not defined. "
+                    "Select a valid file path or a valid URL to download WASM file"
+                )
+
+            if not wasm_path.exists():
+                self.load_from_url(wasm_file_download_url, wasm_file_path)
+
+            engine = LocalOpaEngine(wasm_path=wasm_file_path)
+            self.engines[wasm_path] = engine
+            return engine