Merge remote-tracking branch 'origin/dev' into feature_stdout_live_re…

…porting
galaxyproject · Nov 18, 2024 · a69031b · a69031b
2 parents be11412 + 4a7c220
commit a69031b
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diff --git a/client/gulpfile.js b/client/gulpfile.js
@@ -15,7 +15,6 @@ const xml2js = require("xml2js");
 const STATIC_PLUGIN_BUILD_IDS = [
     "annotate_image",
     "chiraviz",
-    "cytoscape",
     "drawrna",
     "editor",
     "example",
@@ -28,17 +27,15 @@ const STATIC_PLUGIN_BUILD_IDS = [
     "mvpapp",
     "nora",
     "nvd3/nvd3_bar",
-    "openlayers",
     "openseadragon",
     "PCA_3Dplot",
     "phylocanvas",
     "pv",
     "scatterplot",
     "tiffviewer",
     "ts_visjs",
-    "venn",
 ];
-const INSTALL_PLUGIN_BUILD_IDS = ["ngl", "msa"]; // todo: derive from XML
+const INSTALL_PLUGIN_BUILD_IDS = ["cytoscape", "ngl", "msa", "openlayers", "venn", "vizarr"]; // todo: derive from XML
 const DIST_PLUGIN_BUILD_IDS = ["new_user"];
 const PLUGIN_BUILD_IDS = Array.prototype.concat(DIST_PLUGIN_BUILD_IDS, STATIC_PLUGIN_BUILD_IDS);
 

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
@@ -11963,6 +11963,21 @@ 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: {
             /**
@@ -12044,7 +12059,8 @@ export interface components {
             | components["schemas"]["InvocationFailureExpressionEvaluationFailedResponse"]
             | components["schemas"]["InvocationFailureWhenNotBooleanResponse"]
             | components["schemas"]["InvocationUnexpectedFailureResponse"]
-            | components["schemas"]["InvocationEvaluationWarningWorkflowOutputNotFoundResponse"];
+            | components["schemas"]["InvocationEvaluationWarningWorkflowOutputNotFoundResponse"]
+            | components["schemas"]["InvocationFailureWorkflowParameterInvalidResponse"];
         /** InvocationOutput */
         InvocationOutput: {
             /**

diff --git a/client/src/components/Common/ButtonSpinner.vue b/client/src/components/Common/ButtonSpinner.vue
@@ -11,12 +11,14 @@ interface Props {
     wait?: boolean;
     tooltip?: string;
     disabled?: boolean;
+    size?: string;
 }
 
 withDefaults(defineProps<Props>(), {
     wait: false,
     tooltip: undefined,
     disabled: false,
+    size: "md",
 });
 </script>
 
@@ -25,6 +27,7 @@ withDefaults(defineProps<Props>(), {
         v-if="wait"
         v-b-tooltip.hover.bottom
         disabled
+        :size="size"
         variant="info"
         title="Please Wait..."
         class="d-flex flex-nowrap align-items-center text-nowrap">
@@ -38,6 +41,7 @@ withDefaults(defineProps<Props>(), {
         class="d-flex flex-nowrap align-items-center text-nowrap"
         :title="tooltip"
         :disabled="disabled"
+        :size="size"
         @click="$emit('onClick')">
         <FontAwesomeIcon :icon="faPlay" class="mr-2" />
         {{ title }}

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/Grid/GridInvocation.vue b/client/src/components/Grid/GridInvocation.vue
@@ -109,7 +109,7 @@ function refreshTable() {
             :extra-props="extraProps"
             :embedded="forStoredWorkflow || forHistory || forBatch">
             <template v-slot:expanded="{ rowData }">
-                <span class="position-absolute ml-4" :data-invocation-id="rowData.id">
+                <span class="mb-2" :data-invocation-id="rowData.id">
                     <small>
                         <b>Last updated: <UtcDate :date="rowData.update_time" mode="elapsed" />; Invocation ID:</b>
                     </small>

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/History/SwitchToHistoryLink.vue b/client/src/components/History/SwitchToHistoryLink.vue
@@ -86,7 +86,7 @@ function viewHistoryInNewTab(history: HistorySummary) {
 <template>
     <div>
         <LoadingSpan v-if="!history" />
-        <div v-else class="history-link">
+        <div v-else class="history-link" data-description="switch to history link">
             <BLink
                 v-b-tooltip.hover.top.noninteractive.html
                 data-description="switch to history link"

diff --git a/client/src/components/JobMetrics/JobMetrics.test.js b/client/src/components/JobMetrics/JobMetrics.test.js
@@ -6,6 +6,8 @@ import { getLocalVue } from "tests/jest/helpers";
 
 import JobMetrics from "./JobMetrics";
 
+const NO_METRICS_MESSAGE = "No metrics available for this job.";
+
 // Ignore all axios calls, data is mocked locally -- just say "OKAY!"
 jest.mock("axios", () => ({
     get: async () => {
@@ -26,7 +28,8 @@ describe("JobMetrics/JobMetrics.vue", () => {
         });
 
         await wrapper.vm.$nextTick();
-        expect(wrapper.find("div").exists()).toBe(false);
+        const alert = wrapper.find(".alert-info");
+        expect(alert.text()).toBe(NO_METRICS_MESSAGE);
     });
 
     it("should group plugins by type", async () => {

diff --git a/client/src/components/JobMetrics/JobMetrics.vue b/client/src/components/JobMetrics/JobMetrics.vue
@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { BAlert } from "bootstrap-vue";
 import { computed, ref, unref, watch } from "vue";
 
 import { useJobMetricsStore } from "@/stores/jobMetricsStore";
@@ -217,4 +218,5 @@ const estimatedServerInstance = computed(() => {
             :cores-allocated="coresAllocated"
             :memory-allocated-in-mebibyte="memoryAllocatedInMebibyte" />
     </div>
+    <BAlert v-else variant="info" show> No metrics available for this job. </BAlert>
 </template>
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/client/src/components/Workflow/Invocation/InvocationScrollList.vue b/client/src/components/Workflow/Invocation/InvocationScrollList.vue
@@ -96,12 +96,10 @@ const route = useRoute();
 const router = useRouter();
 
 function cardClicked(invocation: WorkflowInvocation) {
-    let path = `/workflows/invocations/${invocation.id}`;
     if (props.inPanel) {
-        path += "?from_panel=true";
         emit("invocation-clicked");
     }
-    router.push(path);
+    router.push(`/workflows/invocations/${invocation.id}`);
 }
 
 function scrollToTop() {
@@ -204,10 +202,14 @@ function workflowName(workflowId: string) {
                         @click="() => cardClicked(invocation)">
                         <div class="overflow-auto w-100">
                             <Heading bold size="text" icon="fa-sitemap">
-                                <span class="truncate-3-lines">{{ workflowName(invocation.workflow_id) }}</span>
+                                <span class="truncate-n-lines three-lines">
+                                    {{ workflowName(invocation.workflow_id) }}
+                                </span>
                             </Heading>
                             <Heading size="text" icon="fa-hdd">
-                                <small class="text-muted">{{ historyName(invocation.history_id) }}</small>
+                                <small class="text-muted truncate-n-lines two-lines">
+                                    {{ historyName(invocation.history_id) }}
+                                </small>
                             </Heading>
                             <div class="d-flex justify-content-between">
                                 <BBadge v-b-tooltip.noninteractive.hover pill>
@@ -257,12 +259,19 @@ function workflowName(workflowId: string) {
 </template>
 
 <style scoped lang="scss">
-@import "theme/blue.scss";
-
-.truncate-3-lines {
+.truncate-n-lines {
     display: -webkit-box;
-    -webkit-line-clamp: 3;
     -webkit-box-orient: vertical;
     overflow: hidden;
+    word-break: break-word;
+    overflow-wrap: break-word;
+    &.three-lines {
+        -webkit-line-clamp: 3;
+        line-clamp: 3;
+    }
+    &.two-lines {
+        -webkit-line-clamp: 2;
+        line-clamp: 2;
+    }
 }
 </style>
diff --git a/client/src/components/Workflow/List/WorkflowIndicators.vue b/client/src/components/Workflow/List/WorkflowIndicators.vue
@@ -17,6 +17,7 @@ library.add(faFileImport, faGlobe, faShieldAlt, faUsers, faUser);
 interface Props {
     workflow: any;
     publishedView: boolean;
+    noEditTime?: boolean;
 }
 
 const props = defineProps<Props>();
@@ -118,7 +119,7 @@ function onViewUserPublished() {
             <FontAwesomeIcon :icon="faFileImport" fixed-width @click="onCopyLink" />
         </BButton>
 
-        <span class="mr-1">
+        <span v-if="!noEditTime" class="mr-1">
             <small>
                 edited
                 <UtcDate :date="workflow.update_time" mode="elapsed" />
@@ -136,8 +137,9 @@ function onViewUserPublished() {
         </BBadge>
 
         <BBadge
-            v-if="publishedView"
+            v-if="publishedView && workflow.published"
             v-b-tooltip.noninteractive.hover
+            data-description="published owner badge"
             class="outline-badge cursor-pointer mx-1"
             :title="publishedTitle"
             @click="onViewUserPublished">

diff --git a/client/src/components/Workflow/Run/WorkflowRun.vue b/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"