Merge pull request #20761 from mvdbeek/user_defined_tools_configfiles (af2d2408) · Commits · NDIP / Galaxy

client/src/api/schema/schema.ts

+59 −1

Original line number	Diff line number	Diff line
		@@ -14066,6 +14066,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -14108,6 +14113,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -14150,6 +14160,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -14306,7 +14321,10 @@ export interface components {
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/** Optional */
		/**
		* Optional
		* @default false
		*/
		optional: boolean;
		/**
		* Parameter Type
		@@ -18103,6 +18121,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -20200,6 +20223,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -20729,6 +20757,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -21800,6 +21833,11 @@ export interface components {
		* @enum {string}
		*/
		class: "GalaxyUserTool";
		/**
		* Configfiles
		* @description A list of config files for this tool.
		*/
		configfiles?: components["schemas"]["YamlTemplateConfigFile"][] \| null;
		/**
		* Container
		* @description Container image to use for this tool.
		@@ -21882,6 +21920,11 @@ export interface components {
		* @constant
		*/
		class: "GalaxyUserTool";
		/**
		* Configfiles
		* @description A list of config files for this tool.
		*/
		configfiles?: components["schemas"]["YamlTemplateConfigFile"][] \| null;
		/**
		* Container
		* @description Container image to use for this tool.
		@@ -22797,6 +22840,21 @@ export interface components {
		*/
		namespace: string;
		};
		/** YamlTemplateConfigFile */
		YamlTemplateConfigFile: {
		/** Content */
		content: string;
		/**
		* Eval Engine
		* @default ecmascript
		* @constant
		*/
		eval_engine: "ecmascript";
		/** Filename */
		filename?: string \| null;
		/** Name */
		name?: string \| null;
		};
		/** Organization */
		galaxy__schema__drs__Organization: {
		/**

client/src/components/Markdown/Sections/Elements/Workflow/WorkflowDisplay.vue

+1 −0

Original line number	Diff line number	Diff line
		@@ -125,6 +125,7 @@ watch(
		:tool-version="step.tool_version" />
		<WorkflowStepTitle
		:step-tool-id="step.tool_id"
		:step-tool-uuid="step.tool_uuid"
		:step-subworkflow-id="step.subworkflow_id"
		:step-label="step.label"
		:step-type="step.type"

client/src/components/Panels/UserToolPanel.vue

+10 −0

Original line number	Diff line number	Diff line
		<script setup lang="ts">
		import { faEdit, faPlus, faWrench } from "@fortawesome/free-solid-svg-icons";
		import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
		import { faCancel } from "font-awesome-6";
		import { storeToRefs } from "pinia";
		import { computed } from "vue";
		import { useRoute, useRouter } from "vue-router/composables";
		@@ -88,6 +89,15 @@ function getToolBadges(tool: UnprivilegedToolResponse) {

		function getToolSecondaryActions(tool: UnprivilegedToolResponse) {
		return [
		{
		id: "deactivate",
		label: "Deactivate",
		icon: faCancel,
		title: "Deactivate this custom tool",
		handler: () => {
		unprivilegedToolStore.deactivateTool(tool.uuid);
		},
		},
		{
		id: "edit",
		label: "Edit",

client/src/components/Tool/CustomToolEditor.vue

+16 −2

Original line number	Diff line number	Diff line
		<script setup lang="ts">
		import { faSave } from "@fortawesome/free-regular-svg-icons";
		import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
		import { loader, useMonaco, VueMonacoEditor } from "@guolao/vue-monaco-editor";
		import * as monaco from "monaco-editor";
		import { nextTick, onUnmounted, ref, watch } from "vue";
		@@ -75,7 +77,9 @@ if (props.toolUuid) {
		})
		.then(({ data, error }) => {
		if (!error) {
		yamlRepresentation.value = stringify(data.representation);
		yamlRepresentation.value = stringify(data.representation, {
		blockQuote: "literal",
		});
		}
		});
		}
		@@ -104,9 +108,19 @@ async function saveTool() {

		<template>
		<div>
		<b-alert v-if="errorMsg" variant="danger" show dismissible>
		{{ errorMsg }}
		</b-alert>
		<div class="d-flex flex-gapx-1">
		<Heading h1 separator inline size="lg" class="flex-grow-1 mb-2">Tool Editor</Heading>
		<b-button variant="primary" size="m" @click="saveTool">Save</b-button>
		<b-button
		variant="primary"
		size="m"
		title="Save Custom Tool"
		data-description="save custom tool"
		@click="saveTool"
		><FontAwesomeIcon :icon="faSave"
		/></b-button>
		</div>
		<VueMonacoEditor
		v-model="yamlRepresentation"

client/src/components/Tool/ToolForm.vue

+1 −1

Original line number	Diff line number	Diff line
		@@ -307,7 +307,7 @@ export default {
		this.disabled = true;
		this.loading = true;

		return getToolFormData(this.id, this.currentVersion, this.job_id, this.history_id)
		return getToolFormData(this.id \|\| this.toolUuid, this.currentVersion, this.job_id, this.history_id)
		.then((data) => {
		this.currentVersion = data.version;
		this.formConfig = data;

Admin message