models for tool landing request state...

lib/galaxy/tool_util/parameters/__init__.py

@@ -5,6 +5,8 @@
     encode,
     encode_test,
     fill_static_defaults,
+    landing_decode,
+    landing_encode,
 )
 from .factory import (
     from_input_source,
@@ -50,8 +52,10 @@
     ToolParameterT,
     validate_against_model,
     validate_internal_job,
+    validate_internal_landing_request,
     validate_internal_request,
     validate_internal_request_dereferenced,
+    validate_landing_request,
     validate_request,
     validate_test_case,
     validate_workflow_step,
@@ -60,6 +64,8 @@
 )
 from .state import (
     JobInternalToolState,
+    LandingRequestInternalToolState,
+    LandingRequestToolState,
     RequestInternalDereferencedToolState,
     RequestInternalToolState,
     RequestToolState,
@@ -119,8 +125,10 @@
     "ValidationFunctionT",
     "validate_against_model",
     "validate_internal_job",
+    "validate_internal_landing_request",
     "validate_internal_request",
     "validate_internal_request_dereferenced",
+    "validate_landing_request",
     "validate_request",
     "validate_test_case",
     "validate_workflow_step",
@@ -134,6 +142,8 @@
     "RequestToolState",
     "RequestInternalToolState",
     "RequestInternalDereferencedToolState",
+    "LandingRequestToolState",
+    "LandingRequestInternalToolState",
     "flat_state_path",
     "keys_starting_with",
     "visit_input_values",
@@ -143,6 +153,8 @@
     "encode",
     "encode_test",
     "fill_static_defaults",
+    "landing_decode",
+    "landing_encode",
     "dereference",
     "WorkflowStepToolState",
     "WorkflowStepLinkedToolState",

lib/galaxy/tool_util/parameters/convert.py

@@ -40,6 +40,8 @@
 )
 from .state import (
     JobInternalToolState,
+    LandingRequestInternalToolState,
+    LandingRequestToolState,
     RequestInternalDereferencedToolState,
     RequestInternalToolState,
     RequestToolState,
@@ -67,7 +69,7 @@
 def decode(
     external_state: RequestToolState, input_models: ToolParameterBundle, decode_id: Callable[[str], int]
 ) -> RequestInternalToolState:
-    """Prepare an external representation of tool state (request) for storing in the database (request_internal)."""
+    """Prepare an internal representation of tool state (request_internal) for storing in the database."""
 
     external_state.validate(input_models)
     decode_callback = _decode_callback_for(decode_id)
@@ -83,21 +85,55 @@ def decode(
 
 
 def encode(
-    external_state: RequestInternalToolState, input_models: ToolParameterBundle, encode_id: EncodeFunctionT
+    internal_state: RequestInternalToolState, input_models: ToolParameterBundle, encode_id: EncodeFunctionT
 ) -> RequestToolState:
-    """Prepare an external representation of tool state (request) for storing in the database (request_internal)."""
+    """Prepare an external representation of tool state (request) from persisted state in the database (request_internal)."""
 
     encode_callback = _encode_callback_for(encode_id)
     request_state_dict = visit_input_values(
         input_models,
-        external_state,
+        internal_state,
         encode_callback,
     )
     request_state = RequestToolState(request_state_dict)
     request_state.validate(input_models)
     return request_state
 
 
+def landing_decode(
+    external_state: LandingRequestToolState, input_models: ToolParameterBundle, decode_id: Callable[[str], int]
+) -> LandingRequestInternalToolState:
+    """Prepare an external representation of tool state (request) for storing in the database (request_internal)."""
+
+    external_state.validate(input_models)
+    decode_callback = _decode_callback_for(decode_id)
+    internal_state_dict = visit_input_values(
+        input_models,
+        external_state,
+        decode_callback,
+    )
+
+    internal_request_state = LandingRequestInternalToolState(internal_state_dict)
+    internal_request_state.validate(input_models)
+    return internal_request_state
+
+
+def landing_encode(
+    internal_state: LandingRequestInternalToolState, input_models: ToolParameterBundle, encode_id: EncodeFunctionT
+) -> LandingRequestToolState:
+    """Prepare an external representation of tool state (request) for storing in the database (request_internal)."""
+
+    encode_callback = _encode_callback_for(encode_id)
+    request_state_dict = visit_input_values(
+        input_models,
+        internal_state,
+        encode_callback,
+    )
+    request_state = LandingRequestToolState(request_state_dict)
+    request_state.validate(input_models)
+    return request_state
+
+
 def dereference(
     internal_state: RequestInternalToolState, input_models: ToolParameterBundle, dereference: DereferenceCallable
 ) -> RequestInternalDereferencedToolState:

lib/galaxy/tool_util/parameters/models.py

@@ -64,6 +64,8 @@
     "request",
     "request_internal",
     "request_internal_dereferenced",
+    "landing_request",
+    "landing_request_internal",
     "job_internal",
     "test_case_xml",
     "workflow_step",
@@ -219,6 +221,8 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
         requires_value = self.request_requires_value
         if state_representation == "job_internal":
             requires_value = True
+        elif _is_landing_request(state_representation):
+            requires_value = False
         return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
 
     @property
@@ -240,7 +244,12 @@ 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)
-        return dynamic_model_information_from_py_type(self, py_type)
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+        elif _is_landing_request(state_representation):
+            requires_value = False
+        return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
 
     @property
     def request_requires_value(self) -> bool:
@@ -405,10 +414,19 @@ def py_type_test_case(self) -> Type:
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
         if state_representation == "request":
             return allow_batching(dynamic_model_information_from_py_type(self, self.py_type), BatchDataInstance)
+        if state_representation == "landing_request":
+            return allow_batching(
+                dynamic_model_information_from_py_type(self, self.py_type, requires_value=False), BatchDataInstance
+            )
         elif state_representation == "request_internal":
             return allow_batching(
                 dynamic_model_information_from_py_type(self, self.py_type_internal), BatchDataInstanceInternal
             )
+        elif state_representation == "landing_request_internal":
+            return allow_batching(
+                dynamic_model_information_from_py_type(self, self.py_type_internal, requires_value=False),
+                BatchDataInstanceInternal,
+            )
         elif state_representation == "request_internal_dereferenced":
             return allow_batching(
                 dynamic_model_information_from_py_type(self, self.py_type_internal_dereferenced),
@@ -455,6 +473,12 @@ def py_type_internal(self) -> Type:
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
         if state_representation == "request":
             return allow_batching(dynamic_model_information_from_py_type(self, self.py_type))
+        elif state_representation == "landing_request":
+            return allow_batching(dynamic_model_information_from_py_type(self, self.py_type, requires_value=False))
+        elif state_representation == "landing_request_internal":
+            return allow_batching(
+                dynamic_model_information_from_py_type(self, self.py_type_internal, requires_value=False)
+            )
         elif state_representation in ["request_internal", "request_internal_dereferenced"]:
             return allow_batching(dynamic_model_information_from_py_type(self, self.py_type_internal))
         elif state_representation == "job_internal":
@@ -600,7 +624,10 @@ def py_type(self) -> Type:
         return AnyUrl
 
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
-        return dynamic_model_information_from_py_type(self, self.py_type)
+        requires_value = self.request_requires_value
+        if _is_landing_request(state_representation):
+            requires_value = False
+        return dynamic_model_information_from_py_type(self, self.py_type, requires_value=requires_value)
 
     @property
     def request_requires_value(self) -> bool:
@@ -1080,9 +1107,14 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
         instance_class: Type[BaseModel] = create_field_model(
             self.parameters, f"Repeat_{self.name}", state_representation
         )
+        min_length = self.min
+        max_length = self.max
         requires_value = self.request_requires_value
         if state_representation == "job_internal":
             requires_value = True
+        elif _is_landing_request(state_representation):
+            requires_value = False
+            min_length = 0  # in a landing request - parameters can be partially filled
 
         initialize_repeat: Any
         if requires_value:
@@ -1091,7 +1123,7 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
             initialize_repeat = None
 
         class RepeatType(RootModel):
-            root: List[instance_class] = Field(initialize_repeat, min_length=self.min, max_length=self.max)  # type: ignore[valid-type]
+            root: List[instance_class] = Field(initialize_repeat, min_length=min_length, max_length=max_length)  # type: ignore[valid-type]
 
         return DynamicModelInformation(
             self.name,
@@ -1382,6 +1414,8 @@ def create_method(tool: ToolParameterBundle, name: str = DEFAULT_MODEL_NAME) ->
 create_request_model = create_model_factory("request")
 create_request_internal_model = create_model_factory("request_internal")
 create_request_internal_dereferenced_model = create_model_factory("request_internal_dereferenced")
+create_landing_request_model = create_model_factory("landing_request")
+create_landing_request_internal_model = create_model_factory("landing_request_internal")
 create_job_internal_model = create_model_factory("job_internal")
 create_test_case_model = create_model_factory("test_case_xml")
 create_workflow_step_model = create_model_factory("workflow_step")
@@ -1413,6 +1447,10 @@ def create_field_model(
     return pydantic_model
 
 
+def _is_landing_request(state_representation: StateRepresentationT):
+    return state_representation in ["landing_request", "landing_request_internal"]
+
+
 def validate_against_model(pydantic_model: Type[BaseModel], parameter_state: Dict[str, Any]) -> None:
     try:
         pydantic_model(**parameter_state)
@@ -1441,6 +1479,8 @@ def validate_request(tool: ToolParameterBundle, request: Dict[str, Any], name: s
 validate_request = validate_model_type_factory("request")
 validate_internal_request = validate_model_type_factory("request_internal")
 validate_internal_request_dereferenced = validate_model_type_factory("request_internal_dereferenced")
+validate_landing_request = validate_model_type_factory("landing_request")
+validate_internal_landing_request = validate_model_type_factory("landing_request_internal")
 validate_internal_job = validate_model_type_factory("job_internal")
 validate_test_case = validate_model_type_factory("test_case_xml")
 validate_workflow_step = validate_model_type_factory("workflow_step")

lib/galaxy/tool_util/parameters/state.py

@@ -15,6 +15,8 @@
 
 from .models import (
     create_job_internal_model,
+    create_landing_request_internal_model,
+    create_landing_request_model,
     create_request_internal_dereferenced_model,
     create_request_internal_model,
     create_request_model,
@@ -84,6 +86,22 @@ def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel
         return create_request_internal_model(parameters)
 
 
+class LandingRequestToolState(ToolState):
+    state_representation: Literal["landing_request"] = "landing_request"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel]:
+        return create_landing_request_model(parameters)
+
+
+class LandingRequestInternalToolState(ToolState):
+    state_representation: Literal["landing_request_internal"] = "landing_request_internal"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel]:
+        return create_landing_request_internal_model(parameters)
+
+
 class RequestInternalDereferencedToolState(ToolState):
     state_representation: Literal["request_internal_dereferenced"] = "request_internal_dereferenced"
 

lib/galaxy/tools/parameters/basic.py

@@ -187,7 +187,6 @@ def __init__(self, tool, input_source, context=None):
         self.hidden = input_source.get_bool("hidden", False)
         self.refresh_on_change = input_source.get_bool("refresh_on_change", False)
         self.optional = input_source.parse_optional()
-        self.optionality_inferred = False
         self.is_dynamic = False
         self.label = input_source.parse_label()
         self.help = input_source.parse_help()
@@ -352,6 +351,7 @@ def parse_name(input_source):
 class SimpleTextToolParameter(ToolParameter):
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
+        self.optionality_inferred = False
         super().__init__(tool, input_source)
         optional = input_source.get("optional", None)
         if optional is not None:
@@ -405,6 +405,7 @@ class TextToolParameter(SimpleTextToolParameter):
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
+        self.profile = tool.profile
         self.datalist = []
         for title, value, _ in input_source.parse_static_options():
             self.datalist.append({"label": title, "value": value})
@@ -420,6 +421,16 @@ def validate(self, value, trans=None):
         ):
             return super().validate(value, trans)
 
+    @property
+    def wrapper_default() -> Optional[str]:
+        """Handle change in default handling pre and post 23.0 profiles."""
+        profile = self.profile
+        legacy_behavior = (profile is None or Version(str(profile)) < Version("23.0"))
+        default_value = None
+        if self.optional and self.optionality_inferred and legacy_behavior:
+            default_value = ""
+        return default_value
+
     def to_dict(self, trans, other_values=None):
         d = super().to_dict(trans)
         other_values = other_values or {}

lib/galaxy/tools/wrappers.py

@@ -19,7 +19,6 @@
     Union,
 )
 
-from packaging.version import Version
 from typing_extensions import TypeAlias
 
 from galaxy.model import (
@@ -33,7 +32,10 @@
 from galaxy.model.metadata import FileParameter
 from galaxy.model.none_like import NoneDataset
 from galaxy.security.object_wrapper import wrap_with_safe_string
-from galaxy.tools.parameters.basic import BooleanToolParameter
+from galaxy.tools.parameters.basic import (
+    BooleanToolParameter,
+    TextToolParameter,
+)
 from galaxy.tools.parameters.wrapped_json import (
     data_collection_input_to_staging_path_and_source_path,
     data_input_to_staging_path_and_source_path,
@@ -126,15 +128,9 @@ def __init__(
         profile: Optional[float] = None,
     ) -> None:
         self.input = input
-        if (
-            value is None
-            and input.type == "text"
-            and input.optional
-            and input.optionality_inferred
-            and (profile is None or Version(str(profile)) < Version("23.0"))
-        ):
+        if value is None and input.type == "text":
             # Tools with old profile versions may treat an optional text parameter as `""`
-            value = ""
+            value = cast(TextToolParameter, input).wrapper_default()
         self.value = value
         self._other_values: Dict[str, str] = other_values or {}