Integrate static validators into Pydantic models...

lib/galaxy/tool_util/parameters/_types.py

@@ -6,6 +6,7 @@
 """
 
 from typing import (
+    Any,
     cast,
     List,
     Optional,
@@ -15,6 +16,7 @@
 
 # https://stackoverflow.com/questions/56832881/check-if-a-field-is-typing-optional
 from typing_extensions import (
+    Annotated,
     get_args,
     get_origin,
 )
@@ -46,3 +48,14 @@ def cast_as_type(arg) -> Type:
 
 def is_optional(field) -> bool:
     return get_origin(field) is Union and type(None) in get_args(field)
+
+
+def expand_annotation(field: Type, new_annotations: List[Any]) -> Type:
+    is_annotation = get_origin(field) is Annotated
+    new_args: List[Any]
+    if is_annotation:
+        args = get_args(field)
+        new_args = [args[0], *args[1:], *new_annotations]
+    else:
+        new_args = [field, *new_annotations]
+    return Annotated[tuple(new_args)]

lib/galaxy/tool_util/parameters/factory.py

@@ -14,6 +14,11 @@
     PagesSource,
     ToolSource,
 )
+from galaxy.tool_util.parser.parameter_validators import (
+    InRangeParameterValidatorModel,
+    LengthParameterValidatorModel,
+    static_validators,
+)
 from galaxy.tool_util.parser.util import parse_profile_version
 from galaxy.util import string_as_bool
 from .models import (
@@ -42,10 +47,12 @@
     HiddenParameterModel,
     IntegerParameterModel,
     LabelValue,
+    NumberCompatiableValidators,
     RepeatParameterModel,
     RulesParameterModel,
     SectionParameterModel,
     SelectParameterModel,
+    TextCompatiableValidators,
     TextParameterModel,
     ToolParameterBundle,
     ToolParameterBundleModel,
@@ -82,7 +89,12 @@ def _from_input_source_galaxy(input_source: InputSource, profile: float) -> Tool
                 int_value = None
             else:
                 raise ParameterDefinitionError()
-            return IntegerParameterModel(name=input_source.parse_name(), optional=optional, value=int_value)
+            static_validator_models = static_validators(input_source.parse_validators())
+            validators: List[NumberCompatiableValidators] = []
+            for static_validator in static_validator_models:
+                if static_validator.type == "in_range":
+                    validators.append(cast(InRangeParameterValidatorModel, static_validator))
+            return IntegerParameterModel(name=input_source.parse_name(), optional=optional, value=int_value, validators=validators)
         elif param_type == "boolean":
             nullable = input_source.parse_optional()
             value = input_source.get_bool_or_none("checked", None if nullable else False)
@@ -93,9 +105,15 @@ def _from_input_source_galaxy(input_source: InputSource, profile: float) -> Tool
             )
         elif param_type == "text":
             optional = input_source.parse_optional()
+            static_validator_models = static_validators(input_source.parse_validators())
+            validators: List[TextCompatiableValidators] = []
+            for static_validator in static_validator_models:
+                if static_validator.type == "length":
+                    validators.append(cast(LengthParameterValidatorModel, static_validator))
             return TextParameterModel(
                 name=input_source.parse_name(),
                 optional=optional,
+                validators=validators,
             )
         elif param_type == "float":
             optional = input_source.parse_optional()
@@ -107,10 +125,16 @@ def _from_input_source_galaxy(input_source: InputSource, profile: float) -> Tool
                 float_value = None
             else:
                 raise ParameterDefinitionError()
+            static_validator_models = static_validators(input_source.parse_validators())
+            validators: List[NumberCompatiableValidators] = []
+            for static_validator in static_validator_models:
+                if static_validator.type == "in_range":
+                    validators.append(cast(InRangeParameterValidatorModel, static_validator))
             return FloatParameterModel(
                 name=input_source.parse_name(),
                 optional=optional,
                 value=float_value,
+                validators=validators,
             )
         elif param_type == "hidden":
             optional = input_source.parse_optional()

lib/galaxy/tool_util/parameters/models.py

@@ -24,6 +24,7 @@
     Field,
     field_validator,
     HttpUrl,
+    PlainValidator,
     RootModel,
     StrictBool,
     StrictFloat,
@@ -44,8 +45,14 @@
     JsonTestCollectionDefDict,
     JsonTestDatasetDefDict,
 )
+from galaxy.tool_util.parser.parameter_validators import (
+    InRangeParameterValidatorModel,
+    LengthParameterValidatorModel,
+    StaticValidatorModel,
+)
 from ._types import (
     cast_as_type,
+    expand_annotation,
     is_optional as is_python_type_optional,
     list_type,
     optional,
@@ -179,11 +186,34 @@ class LabelValue(BaseModel):
     selected: bool
 
 
+TextCompatiableValidators = Union[
+    LengthParameterValidatorModel,
+]
+
+
+def pydantic_validator_for(validator_model: StaticValidatorModel):
+
+    def validator(v: Any) -> Any:
+        validator_model.validate(v)
+        return v
+
+    return PlainValidator(validator)
+
+
+# actual typing will require generics and a typevar I think...
+def static_tool_validators_to_pydantic(static_tool_param_validators: List[StaticValidatorModel]):
+    pydantic_validators = []
+    for static_validator in static_tool_param_validators:
+        pydantic_validators.append(pydantic_validator_for(static_validator))
+    return pydantic_validators
+
+
 class TextParameterModel(BaseGalaxyToolParameterModelDefinition):
     parameter_type: Literal["gx_text"] = "gx_text"
     area: bool = False
     default_value: Optional[str] = Field(default=None, alias="value")
     default_options: List[LabelValue] = []
+    validators: List[TextCompatiableValidators] = []
 
     @property
     def py_type(self) -> Type:
@@ -196,19 +226,28 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
         requires_value = self.request_requires_value
         if state_representation == "job_internal":
             requires_value = True
+        validators = static_tool_validators_to_pydantic(self.validators)
+        if validators:
+            py_type = expand_annotation(py_type, validators)
         return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
 
     @property
     def request_requires_value(self) -> bool:
         return False
 
 
+NumberCompatiableValidators = Union[
+    InRangeParameterValidatorModel,
+]
+
+
 class IntegerParameterModel(BaseGalaxyToolParameterModelDefinition):
     parameter_type: Literal["gx_integer"] = "gx_integer"
     optional: bool
     value: Optional[int] = None
     min: Optional[int] = None
     max: Optional[int] = None
+    validators: List[NumberCompatiableValidators] = None
 
     @property
     def py_type(self) -> Type:
@@ -223,6 +262,9 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
             requires_value = True
         elif _is_landing_request(state_representation):
             requires_value = False
+        validators = static_tool_validators_to_pydantic(self.validators)
+        if validators:
+            py_type = expand_annotation(py_type, validators)
         return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
 
     @property
@@ -235,6 +277,7 @@ class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
     value: Optional[float] = None
     min: Optional[float] = None
     max: Optional[float] = None
+    validators: List[NumberCompatiableValidators] = None
 
     @property
     def py_type(self) -> Type:
@@ -244,6 +287,9 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
         py_type = self.py_type
         if state_representation == "workflow_step_linked":
             py_type = allow_connected_value(py_type)
+        validators = static_tool_validators_to_pydantic(self.validators)
+        if validators:
+            py_type = expand_annotation(py_type, validators)
         return dynamic_model_information_from_py_type(self, py_type)
 
     @property

test/functional/tools/parameters/gx_int_validation_range.xml

@@ -0,0 +1,15 @@
+<tool id="gx_int_validation_range" name="gx_int_validation_range" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" value="1" type="integer">
+            <validator type="in_range" min="0" max="10" exclude_min="false" exclude_max="true" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>

test/functional/tools/parameters/gx_text_length_validation.xml

@@ -0,0 +1,20 @@
+<tool id="gx_text_length_validation" name="gx_text_length_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text">
+            <validator type="length" min="2" max="10" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>

test/functional/tools/parameters/gx_text_length_validation_negate.xml

@@ -0,0 +1,20 @@
+<tool id="gx_text_length_validation" name="gx_text_length_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text">
+            <validator type="length" min="2" max="10" negate="true" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>

test/unit/tool_util/parameter_specification.yml

@@ -191,6 +191,16 @@ gx_int_required: &gx_int_required
 gx_int_required_via_empty_string:
   <<: *gx_int_required
 
+
+gx_int_validation_range:
+  request_valid:
+  - parameter: 1
+  - parameter: 9
+  request_invalid:
+  - parameter: -1
+  - parameter: 11
+  - parameter: 10
+
 gx_text:
   request_valid: &gx_text_request_valid
     - parameter: moocow
@@ -294,6 +304,21 @@ gx_text_optional:
     - parameter: {}
     - parameter: { "moo": "cow" }
 
+gx_text_length_validation: 
+  request_valid:
+  - parameter: "mytext"
+  - parameter: "mytext123"
+  request_invalid:
+  - parameter: "s"  # too short
+  - parameter: "mytext1231231231sd"  # too long
+
+gx_text_length_validation_negate: 
+  request_valid:
+  - parameter: "m"
+  - parameter: "mytext123mocowdowees"
+  request_invalid:
+  - parameter: "goldilocks"
+
 gx_select:
   request_valid:
   - parameter: "--ex1"