Merge pull request #19092 from jmchilton/min_max_regex

Implement workflow parameter validators.

client/src/api/schema/schema.ts

@@ -11941,6 +11941,21 @@ 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: {
             /**
@@ -12022,7 +12037,8 @@ 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/Form/FormElement.vue

@@ -27,6 +27,7 @@ import FormSelection from "./Elements/FormSelection.vue";
 import FormTags from "./Elements/FormTags.vue";
 import FormText from "./Elements/FormText.vue";
 import FormUpload from "./Elements/FormUpload.vue";
+import FormElementHelpMarkdown from "./FormElementHelpMarkdown.vue";
 
 interface FormElementProps {
     id?: string;
@@ -35,6 +36,7 @@ interface FormElementProps {
     title?: string;
     refreshOnChange?: boolean;
     help?: string;
+    helpFormat?: string;
     error?: string;
     warning?: string;
     disabled?: boolean;
@@ -63,6 +65,7 @@ const props = withDefaults(defineProps<FormElementProps>(), {
     connectedDisableText: "Add connection to module.",
     connectedEnableIcon: "fa fa-times",
     connectedDisableIcon: "fa fa-arrows-alt-h",
+    helpFormat: "html",
     workflowBuildingMode: false,
 });
 
@@ -337,7 +340,13 @@ function onAlert(value: string | undefined) {
         </div>
 
         <div v-if="showPreview" class="ui-form-preview pt-1 pl-2 mt-1">{{ previewText }}</div>
-        <span v-if="Boolean(helpText)" class="ui-form-info form-text text-muted" v-html="helpText" />
+        <span
+            v-if="Boolean(helpText) && helpFormat != 'markdown'"
+            class="ui-form-info form-text text-muted"
+            v-html="helpText" />
+        <span v-else-if="Boolean(helpText)" class="ui-form-info form-text text-muted"
+            ><FormElementHelpMarkdown :content="helpText"
+        /></span>
     </div>
 </template>
 

client/src/components/Form/FormElementHelpMarkdown.vue

@@ -0,0 +1,56 @@
+<script setup lang="ts">
+import { computed, onMounted, ref } from "vue";
+
+import { markup } from "@/components/ObjectStore/configurationMarkdown";
+import { getAppRoot } from "@/onload/loadConfig";
+
+import HelpPopover from "@/components/Help/HelpPopover.vue";
+
+const props = defineProps<{
+    content: string;
+}>();
+
+const markdownHtml = computed(() => markup(props.content ?? "", false));
+
+const helpHtml = ref<HTMLDivElement>();
+
+interface InternalTypeReference {
+    element: HTMLElement;
+    term: string;
+}
+
+const internalHelpReferences = ref<InternalTypeReference[]>([]);
+
+function setupPopovers() {
+    internalHelpReferences.value.length = 0;
+    if (helpHtml.value) {
+        const links = helpHtml.value.getElementsByTagName("a");
+        Array.from(links).forEach((link) => {
+            if (link.href.startsWith("gxhelp://")) {
+                const uri = link.href.substr("gxhelp://".length);
+                internalHelpReferences.value.push({ element: link, term: uri });
+                link.href = `${getAppRoot()}help/terms/${uri}`;
+                link.style.color = "inherit";
+                link.style.textDecorationLine = "underline";
+                link.style.textDecorationStyle = "dashed";
+            }
+        });
+    }
+}
+
+onMounted(setupPopovers);
+</script>
+
+<template>
+    <span>
+        <!-- Disable v-html warning because we allow markdown generated HTML
+            in various places in the Galaxy interface. Raw HTML is not allowed
+            here because admin = false in the call to markup.
+        -->
+        <!-- eslint-disable-next-line vue/no-v-html -->
+        <div ref="helpHtml" v-html="markdownHtml" />
+        <span v-for="(value, i) in internalHelpReferences" :key="i">
+            <HelpPopover :target="value.element" :term="value.term" />
+        </span>
+    </span>
+</template>

client/src/components/Form/FormInputs.vue

@@ -11,6 +11,7 @@
                         v-model="input.test_param.value"
                         :type="input.test_param.type"
                         :help="input.test_param.help"
+                        :help-format="input.test_param.help_format"
                         :refresh-on-change="false"
                         :disabled="sustainConditionals"
                         :attributes="input.test_param"
@@ -51,6 +52,7 @@
                 :error="input.error"
                 :warning="input.warning"
                 :help="input.help"
+                :help-format="input.help_format"
                 :refresh-on-change="input.refresh_on_change"
                 :attributes="input.attributes || input"
                 :collapsed-enable-text="collapsedEnableText"

client/src/components/Help/HelpPopover.vue

@@ -12,7 +12,7 @@ defineProps<Props>();
 </script>
 
 <template>
-    <BPopover :target="target" triggers="hover" placement="bottom">
+    <BPopover v-if="target" :target="target" triggers="hover" placement="bottom">
         <HelpTerm :term="term" />
     </BPopover>
 </template>

client/src/components/Help/terms.yml

@@ -27,7 +27,12 @@ unix:
     debug what is wrong with the execution of an application.
 
     More information on stack traces can be found on [Wikipedia](https://en.wikipedia.org/wiki/Stack_trace).
+programming:
+  python:
+    regex: |
+      Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in [this Python for Biologists tutorial](https://pythonforbiologists.com/tutorial/regex.html).
 
+      The website [regex101](https://regex101.com/) is a useful playground to explore regular expressions (be sure to enable "Python" as your flavor) and language models such as ChatGPT can help interactively build up and explain regular expressions from natural language prompts or examples.
 galaxy:
   collections:
     flatList: |

client/src/components/RuleBuilder/RegularExpressionInput.vue

@@ -1,7 +1,7 @@
 <template>
     <div>
-        <label v-b-tooltip.hover for="regular_expression" :title="title">{{ label }}</label>
-        <span v-b-popover.html="popoverContent" :title="popoverTitle" class="fa fa-question"></span>
+        <label ref="helpTarget" v-b-tooltip.hover for="regular_expression">{{ label }}</label>
+        <HelpPopover :target="$refs.helpTarget" term="programming.python.regex" />
         <input
             v-b-tooltip.hover.left
             :title="title"
@@ -16,7 +16,10 @@
 <script>
 import _l from "utils/localization";
 
+import HelpPopover from "@/components/Help/HelpPopover.vue";
+
 export default {
+    components: { HelpPopover },
     props: {
         target: {
             required: true,
@@ -32,11 +35,6 @@ export default {
         popoverTitle() {
             return _l("Regular Expressions");
         },
-        popoverContent() {
-            return _l(
-                `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/tutorial/regex.html">this Python for Biologists tutorial</a>.`
-            );
-        },
     },
 };
 </script>

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

@@ -199,7 +199,7 @@ 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

@@ -90,6 +90,7 @@ 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.
@@ -225,6 +226,14 @@ 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]
@@ -236,6 +245,7 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
 InvocationFailureWhenNotBoolean = GenericInvocationFailureWhenNotBoolean[int]
 InvocationUnexpectedFailure = GenericInvocationUnexpectedFailure[int]
 InvocationWarningWorkflowOutputNotFound = GenericInvocationEvaluationWarningWorkflowOutputNotFound[int]
+InvocationFailureWorkflowParameterInvalid = GenericInvocationFailureWorkflowParameterInvalid[int]
 
 InvocationMessageUnion = Union[
     InvocationCancellationReviewFailed,
@@ -249,6 +259,7 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
     InvocationFailureWhenNotBoolean,
     InvocationUnexpectedFailure,
     InvocationWarningWorkflowOutputNotFound,
+    InvocationFailureWorkflowParameterInvalid,
 ]
 
 InvocationCancellationReviewFailedResponseModel = GenericInvocationCancellationReviewFailed[EncodedDatabaseIdField]
@@ -266,6 +277,9 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
 InvocationWarningWorkflowOutputNotFoundResponseModel = GenericInvocationEvaluationWarningWorkflowOutputNotFound[
     EncodedDatabaseIdField
 ]
+InvocationFailureWorkflowParameterInvalidResponseModel = GenericInvocationFailureWorkflowParameterInvalid[
+    EncodedDatabaseIdField
+]
 
 _InvocationMessageResponseUnion = Annotated[
     Union[
@@ -280,6 +294,7 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
         InvocationFailureWhenNotBooleanResponseModel,
         InvocationUnexpectedFailureResponseModel,
         InvocationWarningWorkflowOutputNotFoundResponseModel,
+        InvocationFailureWorkflowParameterInvalidResponseModel,
     ],
     Field(discriminator="reason"),
 ]

lib/galaxy/tool_util/parser/factory.py

@@ -119,17 +119,22 @@ def get_tool_source_from_representation(tool_format, tool_representation):
         raise Exception(f"Unknown tool representation format [{tool_format}].")
 
 
-def get_input_source(content):
+def get_input_source(content, trusted: bool = True):
     """Wrap dicts or XML elements as InputSource if needed.
 
     If the supplied content is already an InputSource object,
     it is simply returned. This allow Galaxy to uniformly
     consume using the tool input source interface.
+
+    Setting trusted to false indicates that no dynamic code should be
+    executed - no eval. This should be used for user-defined tools (in
+    the future) and for workflow inputs.
     """
     if not isinstance(content, InputSource):
         if isinstance(content, dict):
-            content = YamlInputSource(content)
+            content = YamlInputSource(content, trusted=trusted)
         else:
+            assert trusted  # trust is not implemented for XML inputs
             content = XmlInputSource(content)
     return content
 

lib/galaxy/tool_util/parser/parameter_validators.py

@@ -2,6 +2,7 @@
 from typing import (
     Any,
     cast,
+    Dict,
     List,
     Optional,
     Sequence,
@@ -14,6 +15,7 @@
     Field,
     model_validator,
     PrivateAttr,
+    TypeAdapter,
 )
 from typing_extensions import (
     Annotated,
@@ -96,6 +98,9 @@ class ParameterValidatorModel(StrictModel):
     implicit: bool = False
     _static: bool = PrivateAttr(False)
     _deprecated: bool = PrivateAttr(False)
+    # validators must be explicitly set as 'safe' to operate as user-defined workflow parameters or to be used
+    # within future user-defined tool parameters
+    _safe: bool = PrivateAttr(False)
 
     @model_validator(mode="after")
     def set_default_message(self) -> Self:
@@ -163,6 +168,7 @@ class RegexParameterValidatorModel(StaticValidatorModel):
     type: Literal["regex"] = "regex"
     negate: Negate = NEGATE_DEFAULT
     expression: Annotated[str, ValidationArgument("Regular expression to validate against.", xml_body=True)]
+    _safe: bool = PrivateAttr(True)
 
     @property
     def default_message(self) -> str:
@@ -189,6 +195,7 @@ class InRangeParameterValidatorModel(StaticValidatorModel):
     exclude_min: bool = False
     exclude_max: bool = False
     negate: Negate = NEGATE_DEFAULT
+    _safe: bool = PrivateAttr(True)
 
     def statically_validate(self, value: Any):
         if isinstance(value, (int, float)):
@@ -211,7 +218,9 @@ def default_message(self) -> str:
             op1 = "<"
         if self.exclude_max:
             op2 = "<"
-        range_description_str = f"({self.min} {op1} value {op2} {self.max})"
+        min_str = str(self.min) if self.min is not None else "-infinity"
+        max_str = str(self.max) if self.max is not None else "+infinity"
+        range_description_str = f"({min_str} {op1} value {op2} {max_str})"
         return f"Value ('%s') must {'not ' if self.negate else ''}fulfill {range_description_str}"
 
 
@@ -220,6 +229,7 @@ class LengthParameterValidatorModel(StaticValidatorModel):
     min: Optional[int] = None
     max: Optional[int] = None
     negate: Negate = NEGATE_DEFAULT
+    _safe: bool = PrivateAttr(True)
 
     def statically_validate(self, value: Any):
         if isinstance(value, str):
@@ -458,6 +468,20 @@ def default_message(self) -> str:
 ]
 
 
+DiscriminatedAnyValidatorModel = TypeAdapter(AnyValidatorModel)  # type:ignore[var-annotated]
+
+
+def parse_dict_validators(validator_dicts: List[Dict[str, Any]], trusted: bool) -> List[AnyValidatorModel]:
+    validator_models = []
+    for validator_dict in validator_dicts:
+        validator = DiscriminatedAnyValidatorModel.validate_python(validator_dict)
+        if not trusted:
+            # Don't risk instantiating unsafe validators for user-defined code
+            assert validator._safe
+        validator_models.append(validator)
+    return validator_models
+
+
 def parse_xml_validators(input_elem: Element) -> List[AnyValidatorModel]:
     validator_els: List[Element] = input_elem.findall("validator") or []
     models = []