Implement regex validators for text workflow parameter

client/src/api/schema/schema.ts

@@ -11556,6 +11556,21 @@ export interface components {
              */
             workflow_step_id: number;
         };
+        /** InvocationFailureWorkflowParameterInvalidResponse */
+        InvocationFailureWorkflowParameterInvalidResponse: {
+            /**
+             * Details
+             * @description Message raised by validator
+             */
+            details: string;
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            reason: "workflow_parameter_invalid";
+            /** Workflow parameter step that failed validation */
+            workflow_step_id: number;
+        };
         /** InvocationInput */
         InvocationInput: {
             /**
@@ -11637,7 +11652,8 @@ export interface components {
             | components["schemas"]["InvocationFailureExpressionEvaluationFailedResponse"]
             | components["schemas"]["InvocationFailureWhenNotBooleanResponse"]
             | components["schemas"]["InvocationUnexpectedFailureResponse"]
-            | components["schemas"]["InvocationEvaluationWarningWorkflowOutputNotFoundResponse"];
+            | components["schemas"]["InvocationEvaluationWarningWorkflowOutputNotFoundResponse"]
+            | components["schemas"]["InvocationFailureWorkflowParameterInvalidResponse"];
         /** InvocationOutput */
         InvocationOutput: {
             /**

client/src/components/Workflow/Run/WorkflowRun.vue

@@ -195,7 +195,7 @@ defineExpose({
                         Workflow submission failed: {{ submissionError }}
                     </BAlert>
                     <WorkflowRunFormSimple
-                        v-else-if="fromVariant === 'simple'"
+                        v-if="fromVariant === 'simple'"
                         :model="workflowModel"
                         :target-history="simpleFormTargetHistory"
                         :use-job-cache="simpleFormUseJobCache"

client/src/components/WorkflowInvocationState/InvocationMessage.vue

@@ -20,6 +20,7 @@ type ReasonToLevel = {
     when_not_boolean: "error";
     unexpected_failure: "error";
     workflow_output_not_found: "warning";
+    workflow_parameter_invalid: "error";
 };
 
 const level: ReasonToLevel = {
@@ -34,6 +35,7 @@ const level: ReasonToLevel = {
     when_not_boolean: "error",
     unexpected_failure: "error",
     workflow_output_not_found: "warning",
+    workflow_parameter_invalid: "error",
 };
 
 const levelClasses = {
@@ -165,6 +167,10 @@ const infoString = computed(() => {
         return `Defined workflow output '${invocationMessage.output_name}' was not found in step ${
             invocationMessage.workflow_step_id + 1
         }.`;
+    } else if (reason === "workflow_parameter_invalid") {
+        return `Workflow parameter on step ${invocationMessage.workflow_step_id + 1} failed validation: ${
+            invocationMessage.details
+        }`;
     } else {
         return reason;
     }

lib/galaxy/schema/invocation.py

@@ -77,6 +77,7 @@ class FailureReason(str, Enum):
     expression_evaluation_failed = "expression_evaluation_failed"
     when_not_boolean = "when_not_boolean"
     unexpected_failure = "unexpected_failure"
+    workflow_parameter_invalid = "workflow_parameter_invalid"
 
 
 # The reasons below are attached to the invocation and user-actionable.
@@ -212,6 +213,14 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
     )
 
 
+class GenericInvocationFailureWorkflowParameterInvalid(InvocationFailureMessageBase[DatabaseIdT], Generic[DatabaseIdT]):
+    reason: Literal[FailureReason.workflow_parameter_invalid]
+    workflow_step_id: int = Field(
+        ..., title="Workflow parameter step that failed validation", validation_alias="workflow_step_index"
+    )
+    details: str = Field(..., description="Message raised by validator")
+
+
 InvocationCancellationReviewFailed = GenericInvocationCancellationReviewFailed[int]
 InvocationCancellationHistoryDeleted = GenericInvocationCancellationHistoryDeleted[int]
 InvocationCancellationUserRequest = GenericInvocationCancellationUserRequest[int]
@@ -223,6 +232,7 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
 InvocationFailureWhenNotBoolean = GenericInvocationFailureWhenNotBoolean[int]
 InvocationUnexpectedFailure = GenericInvocationUnexpectedFailure[int]
 InvocationWarningWorkflowOutputNotFound = GenericInvocationEvaluationWarningWorkflowOutputNotFound[int]
+InvocationFailureWorkflowParameterInvalid = GenericInvocationFailureWorkflowParameterInvalid[int]
 
 InvocationMessageUnion = Union[
     InvocationCancellationReviewFailed,
@@ -236,6 +246,7 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
     InvocationFailureWhenNotBoolean,
     InvocationUnexpectedFailure,
     InvocationWarningWorkflowOutputNotFound,
+    InvocationFailureWorkflowParameterInvalid,
 ]
 
 InvocationCancellationReviewFailedResponseModel = GenericInvocationCancellationReviewFailed[EncodedDatabaseIdField]
@@ -253,6 +264,9 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
 InvocationWarningWorkflowOutputNotFoundResponseModel = GenericInvocationEvaluationWarningWorkflowOutputNotFound[
     EncodedDatabaseIdField
 ]
+InvocationFailureWorkflowParameterInvalidResponseModel = GenericInvocationFailureWorkflowParameterInvalid[
+    EncodedDatabaseIdField
+]
 
 _InvocationMessageResponseUnion = Annotated[
     Union[
@@ -267,6 +281,7 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
         InvocationFailureWhenNotBooleanResponseModel,
         InvocationUnexpectedFailureResponseModel,
         InvocationWarningWorkflowOutputNotFoundResponseModel,
+        InvocationFailureWorkflowParameterInvalidResponseModel,
     ],
     Field(discriminator="reason"),
 ]

lib/galaxy/tool_util/parser/xml.py

@@ -1337,7 +1337,34 @@ def parse_sanitizer_elem(self):
         return self.input_elem.find("sanitizer")
 
     def parse_validator_elems(self):
-        return self.input_elem.findall("validator")
+        elements = []
+        attributes = {
+            "type": str,
+            "message": str,
+            "negate": string_as_bool,
+            "check": str,
+            "table_name": str,
+            "filename": str,
+            "metadata_name": str,
+            "metadata_column": str,
+            "min": float,
+            "max": float,
+            "exclude_min": string_as_bool,
+            "exclude_max": string_as_bool,
+            "split": str,
+            "skip": str,
+            "value": str,
+            "value_json": lambda v: json.loads(v) if v else None,
+            "line_startswith": str,
+        }
+        for elem in self.input_elem.findall("validator"):
+            elem_dict = {"content": elem.text}
+            for attribute, type_cast in attributes.items():
+                val = elem.get(attribute)
+                if val:
+                    elem_dict[attribute] = type_cast(val)
+            elements.append(elem_dict)
+        return elements
 
     def parse_dynamic_options(self) -> Optional[XmlDynamicOptions]:
         """Return a XmlDynamicOptions to describe dynamic options if options elem is available."""

lib/galaxy/tool_util/parser/yaml.py

@@ -375,6 +375,21 @@ def parse_when_input_sources(self):
             sources.append((value, case_page_source))
         return sources
 
+    def parse_validator_elems(self):
+        elements = []
+        if "validators" in self.input_dict:
+            for elem in self.input_dict["validators"]:
+                if "regex_match" in elem:
+                    elements.append(
+                        {
+                            "message": elem.get("regex_doc"),
+                            "content": elem["regex_match"],
+                            "negate": elem.get("negate", False),
+                            "type": "regex",
+                        }
+                    )
+        return elements
+
     def parse_static_options(self) -> List[Tuple[str, str, bool]]:
         static_options = []
         input_dict = self.input_dict

lib/galaxy/tools/__init__.py

@@ -134,7 +134,6 @@
     DataCollectionToolParameter,
     DataToolParameter,
     HiddenToolParameter,
-    ImplicitConversionRequired,
     SelectTagParameter,
     SelectToolParameter,
     ToolParameter,
@@ -153,6 +152,7 @@
 )
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
 from galaxy.tools.parameters.meta import expand_meta_parameters
+from galaxy.tools.parameters.populate_model import populate_model
 from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.tools.parameters.wrapped_json import json_wrap
 from galaxy.util import (
@@ -2678,63 +2678,13 @@ def populate_model(self, request_context, inputs, state_inputs, group_inputs, ot
         """
         Populates the tool model consumed by the client form builder.
         """
-        other_values = ExpressionContext(state_inputs, other_values)
-        for input_index, input in enumerate(inputs.values()):
-            tool_dict = None
-            group_state = state_inputs.get(input.name, {})
-            if input.type == "repeat":
-                tool_dict = input.to_dict(request_context)
-                group_size = len(group_state)
-                tool_dict["cache"] = [None] * group_size
-                group_cache: List[List[str]] = tool_dict["cache"]
-                for i in range(group_size):
-                    group_cache[i] = []
-                    self.populate_model(request_context, input.inputs, group_state[i], group_cache[i], other_values)
-            elif input.type == "conditional":
-                tool_dict = input.to_dict(request_context)
-                if "test_param" in tool_dict:
-                    test_param = tool_dict["test_param"]
-                    test_param["value"] = input.test_param.value_to_basic(
-                        group_state.get(
-                            test_param["name"], input.test_param.get_initial_value(request_context, other_values)
-                        ),
-                        self.app,
-                    )
-                    test_param["text_value"] = input.test_param.value_to_display_text(test_param["value"])
-                    for i in range(len(tool_dict["cases"])):
-                        current_state = {}
-                        if i == group_state.get("__current_case__"):
-                            current_state = group_state
-                        self.populate_model(
-                            request_context,
-                            input.cases[i].inputs,
-                            current_state,
-                            tool_dict["cases"][i]["inputs"],
-                            other_values,
-                        )
-            elif input.type == "section":
-                tool_dict = input.to_dict(request_context)
-                self.populate_model(request_context, input.inputs, group_state, tool_dict["inputs"], other_values)
-            else:
-                try:
-                    initial_value = input.get_initial_value(request_context, other_values)
-                    tool_dict = input.to_dict(request_context, other_values=other_values)
-                    tool_dict["value"] = input.value_to_basic(
-                        state_inputs.get(input.name, initial_value), self.app, use_security=True
-                    )
-                    tool_dict["default_value"] = input.value_to_basic(initial_value, self.app, use_security=True)
-                    tool_dict["text_value"] = input.value_to_display_text(tool_dict["value"])
-                except ImplicitConversionRequired:
-                    tool_dict = input.to_dict(request_context)
-                    # This hack leads client to display a text field
-                    tool_dict["textable"] = True
-                except Exception:
-                    tool_dict = input.to_dict(request_context)
-                    log.exception("tools::to_json() - Skipping parameter expansion '%s'", input.name)
-            if input_index >= len(group_inputs):
-                group_inputs.append(tool_dict)
-            else:
-                group_inputs[input_index] = tool_dict
+        populate_model(
+            request_context=request_context,
+            inputs=inputs,
+            state_inputs=state_inputs,
+            group_inputs=group_inputs,
+            other_values=other_values,
+        )
 
     def _map_source_to_history(self, trans, tool_inputs, params):
         # Need to remap dataset parameters. Job parameters point to original

lib/galaxy/tools/parameters/basic.py

@@ -315,7 +315,7 @@ def validate(self, value, trans=None) -> None:
             try:
                 validator.validate(value, trans)
             except ValueError as e:
-                raise ValueError(f"Parameter {self.name}: {e}") from None
+                raise ParameterValueError(str(e), self.name, value) from None
 
     def to_dict(self, trans, other_values=None):
         """to_dict tool parameter. This can be overridden by subclasses."""
@@ -1982,7 +1982,7 @@ def do_validate(v):
                     try:
                         validator.validate(v, trans)
                     except ValueError as e:
-                        raise ValueError(f"Parameter {self.name}: {e}") from None
+                        raise ParameterValueError(str(e), self.name, v) from None
 
         dataset_count = 0
         if value:

lib/galaxy/tools/parameters/populate_model.py

@@ -0,0 +1,74 @@
+import logging
+from typing import (
+    Any,
+    Dict,
+    List,
+)
+
+from galaxy.util.expressions import ExpressionContext
+from .basic import ImplicitConversionRequired
+
+log = logging.getLogger(__name__)
+
+
+def populate_model(request_context, inputs, state_inputs, group_inputs: List[Dict[str, Any]], other_values=None):
+    """
+    Populates the tool model consumed by the client form builder.
+    """
+    other_values = ExpressionContext(state_inputs, other_values)
+    for input_index, input in enumerate(inputs.values()):
+        tool_dict = None
+        group_state = state_inputs.get(input.name, {})
+        if input.type == "repeat":
+            tool_dict = input.to_dict(request_context)
+            group_size = len(group_state)
+            tool_dict["cache"] = [None] * group_size
+            group_cache: List[List[Dict[str, Any]]] = tool_dict["cache"]
+            for i in range(group_size):
+                group_cache[i] = []
+                populate_model(request_context, input.inputs, group_state[i], group_cache[i], other_values)
+        elif input.type == "conditional":
+            tool_dict = input.to_dict(request_context)
+            if "test_param" in tool_dict:
+                test_param = tool_dict["test_param"]
+                test_param["value"] = input.test_param.value_to_basic(
+                    group_state.get(
+                        test_param["name"], input.test_param.get_initial_value(request_context, other_values)
+                    ),
+                    request_context.app,
+                )
+                test_param["text_value"] = input.test_param.value_to_display_text(test_param["value"])
+                for i in range(len(tool_dict["cases"])):
+                    current_state = {}
+                    if i == group_state.get("__current_case__"):
+                        current_state = group_state
+                    populate_model(
+                        request_context,
+                        input.cases[i].inputs,
+                        current_state,
+                        tool_dict["cases"][i]["inputs"],
+                        other_values,
+                    )
+        elif input.type == "section":
+            tool_dict = input.to_dict(request_context)
+            populate_model(request_context, input.inputs, group_state, tool_dict["inputs"], other_values)
+        else:
+            try:
+                initial_value = input.get_initial_value(request_context, other_values)
+                tool_dict = input.to_dict(request_context, other_values=other_values)
+                tool_dict["value"] = input.value_to_basic(
+                    state_inputs.get(input.name, initial_value), request_context.app, use_security=True
+                )
+                tool_dict["default_value"] = input.value_to_basic(initial_value, request_context.app, use_security=True)
+                tool_dict["text_value"] = input.value_to_display_text(tool_dict["value"])
+            except ImplicitConversionRequired:
+                tool_dict = input.to_dict(request_context)
+                # This hack leads client to display a text field
+                tool_dict["textable"] = True
+            except Exception:
+                tool_dict = input.to_dict(request_context)
+                log.exception("tools::to_json() - Skipping parameter expansion '%s'", input.name)
+        if input_index >= len(group_inputs):
+            group_inputs.append(tool_dict)
+        else:
+            group_inputs[input_index] = tool_dict