Improvements to workflow parameter validators.

- Allow specifying a min/max for integer and float parameters. - Swap language from regex to "Regular Expression" and synchronize help with regular expression fields in rule builder. - Extend regular expression help. - Improve default message for in_range validator. Probably a reversion in some ways introduced with #19027.
galaxyproject · Nov 7, 2024 · 1f1c118 · 1f1c118
1 parent 8a8fa85
commit 1f1c118
Show file tree

Hide file tree

Showing 9 changed files with 157 additions and 26 deletions.
diff --git a/client/src/components/Form/FormElement.vue b/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>
 

diff --git a/client/src/components/Form/FormElementHelpMarkdown.vue b/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>
diff --git a/client/src/components/Form/FormInputs.vue b/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"

diff --git a/client/src/components/Help/HelpPopover.vue b/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>
diff --git a/client/src/components/Help/terms.yml b/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: |

diff --git a/client/src/components/RuleBuilder/RegularExpressionInput.vue b/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>
diff --git a/lib/galaxy/tool_util/parser/parameter_validators.py b/lib/galaxy/tool_util/parser/parameter_validators.py
@@ -218,7 +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}"
 
 
@@ -466,7 +468,7 @@ def default_message(self) -> str:
 ]
 
 
-DiscriminatedAnyValidatorModel = TypeAdapter(AnyValidatorModel)
+DiscriminatedAnyValidatorModel = TypeAdapter(AnyValidatorModel)  # type:ignore[var-annotated]
 
 
 def parse_dict_validators(validator_dicts: List[Dict[str, Any]], trusted: bool) -> List[AnyValidatorModel]:

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
@@ -179,7 +179,7 @@ class ToolParameter(UsesDictVisibleKeys):
     """
 
     name: str
-    dict_collection_visible_keys = ["name", "argument", "type", "label", "help", "refresh_on_change"]
+    dict_collection_visible_keys = ["name", "argument", "type", "label", "help", "help_format", "refresh_on_change"]
 
     def __init__(self, tool, input_source, context=None):
         input_source = ensure_input_source(input_source)
@@ -193,6 +193,7 @@ def __init__(self, tool, input_source, context=None):
         self.is_dynamic = False
         self.label = input_source.parse_label()
         self.help = input_source.parse_help()
+        self.help_format = input_source.get("help_format") or "html"
         if (sanitizer_elem := input_source.parse_sanitizer_elem()) is not None:
             self.sanitizer = ToolParameterSanitizer.from_element(sanitizer_elem)
         else:

diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
@@ -78,7 +78,9 @@
     BooleanToolParameter,
     DataCollectionToolParameter,
     DataToolParameter,
+    FloatToolParameter,
     HiddenToolParameter,
+    IntegerToolParameter,
     parameter_types,
     raw_to_galaxy,
     SelectToolParameter,
@@ -1282,7 +1284,7 @@ def get_inputs(self):
                 specify_multiple = BooleanToolParameter(None, specify_multiple_source)
 
                 add_validators_repeat = Repeat("validators")
-                add_validators_repeat._title = "Add validator to restrict valid input"
+                add_validators_repeat.title = "Add validator to restrict valid input"
                 add_validators_repeat.min = 0
                 add_validators_repeat.max = math.inf
                 add_validators_repeat.inputs = {
@@ -1291,8 +1293,9 @@ def get_inputs(self):
                         {
                             "optional": False,
                             "name": "regex_match",
-                            "label": "Specify regex",
-                            "help": "Provided regex must match input value for input to be valid",
+                            "label": "Specify regular expression",
+                            "help": "Provided [regular expression](gxhelp://programming.python.reg.ex) must match input value for input to be valid",
+                            "help_format": "markdown",
                         },
                     ),
                     "regex_doc": TextToolParameter(
@@ -1301,7 +1304,7 @@ def get_inputs(self):
                             "optional": False,
                             "name": "regex_doc",
                             "label": "Specify a message",
-                            "help": "This message will be shown if the regex does not match the input",
+                            "help": "This message will be shown if the regular does not match the input",
                         },
                     ),
                 }
@@ -1389,6 +1392,45 @@ def get_inputs(self):
                 restrictions_cond.cases = restrictions_cond_cases
                 when_this_type.inputs["restrictions"] = restrictions_cond
 
+            if param_type == "integer":
+                when_this_type.inputs["min"] = IntegerToolParameter(
+                    None,
+                    {
+                        "name": "min",
+                        "optional": True,
+                        "value": parameter_def.get("min", ""),
+                        "label": "Set a minimum value for this input",
+                    },
+                )
+                when_this_type.inputs["max"] = IntegerToolParameter(
+                    None,
+                    {
+                        "name": "max",
+                        "optional": True,
+                        "value": parameter_def.get("max", ""),
+                        "label": "Set a maximum value for this input",
+                    },
+                )
+            if param_type == "float":
+                when_this_type.inputs["min"] = FloatToolParameter(
+                    None,
+                    {
+                        "name": "min",
+                        "optional": True,
+                        "value": parameter_def.get("min", ""),
+                        "label": "Set a minimum value for this input",
+                    },
+                )
+                when_this_type.inputs["max"] = FloatToolParameter(
+                    None,
+                    {
+                        "name": "max",
+                        "optional": True,
+                        "value": parameter_def.get("max", ""),
+                        "label": "Set a maximum value for this input",
+                    },
+                )
+
             cases.append(when_this_type)
 
         parameter_type_cond.cases = cases
@@ -1503,7 +1545,7 @@ def _parameter_def_list_to_options(parameter_value):
             parameter_kwds["options"] = _parameter_def_list_to_options(restriction_values)
             restricted_inputs = True
 
-        if is_text and parameter_def.get("validators"):
+        if parameter_def.get("validators"):
             parameter_kwds["validators"] = parameter_def["validators"]
 
         client_parameter_type = parameter_type
@@ -1614,13 +1656,17 @@ def step_state_to_tool_state(self, state):
             # the form definition can change from Galaxy to Galaxy fairly freely, but the source validators are persisted
             # and need to be consistent - here we convert the persisted/YAML tool definition version to the "tool form" version.
             for i, source_validator in enumerate(source_validators):
-                form_validators.append(
-                    {
-                        "__index__": i,
-                        "regex_doc": source_validator.get("message"),
-                        "regex_match": source_validator.get("expression"),
-                    }
-                )
+                source_type = source_validator["type"]
+                if source_type == "regex":
+                    form_validators.append(
+                        {
+                            "regex_doc": source_validator.get("message"),
+                            "regex_match": source_validator.get("expression"),
+                        }
+                    )
+                elif source_type == "in_range":
+                    state["parameter_definition"]["min"] = source_validator.get("min")
+                    state["parameter_definition"]["max"] = source_validator.get("max")
             state["parameter_definition"]["validators"] = form_validators
         state["parameter_definition"]["restrictions"] = {}
         state["parameter_definition"]["restrictions"]["how"] = restrictions_how
@@ -1665,9 +1711,21 @@ def _parse_state_into_dict(self):
                 optional = False
             if "multiple" in parameters_def:
                 rval["multiple"] = parameters_def["multiple"]
+            source_validators = []
+            if "min" in parameters_def or "max" in parameters_def:
+                min = parameters_def.get("min")
+                max = parameters_def.get("max")
+                source_validators.append(
+                    {
+                        "min": min,
+                        "max": max,
+                        "negate": False,
+                        "type": "in_range",
+                    }
+                )
+
             if "validators" in parameters_def:
                 form_validators = parameters_def["validators"]
-                source_validators = []
                 # convert the current tool form structure to the persisted YAML-definition style
                 for form_validator in form_validators:
                     source_validators.append(
@@ -1678,7 +1736,7 @@ def _parse_state_into_dict(self):
                             "type": "regex",
                         }
                     )
-                rval["validators"] = source_validators
+            rval["validators"] = source_validators
             restrictions_cond_values = parameters_def.get("restrictions")
             if restrictions_cond_values: