From 573fde064fdf039e08375a2b3419c121948e59a6 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:39:39 -0400
Subject: [PATCH 01/39] Ensure that vega dom is available when changes are to
 be applied

---
 client/src/components/Common/VegaWrapper.vue | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/client/src/components/Common/VegaWrapper.vue b/client/src/components/Common/VegaWrapper.vue
index c75d5b920629..90abd6808fc4 100644
--- a/client/src/components/Common/VegaWrapper.vue
+++ b/client/src/components/Common/VegaWrapper.vue
@@ -3,14 +3,14 @@
         <b-alert v-if="errorMessage" class="p-2" variant="danger" show>
             {{ errorMessage }}
         </b-alert>
-        <div ref="chartContainer" :style="style" />
+        <div ref="chartContainer" :class="fillWidth && 'w-100'" />
     </div>
 </template>
 
 <script setup lang="ts">
 import { useResizeObserver } from "@vueuse/core";
 import embed, { type VisualizationSpec } from "vega-embed";
-import { computed, onBeforeUnmount, ref, watch } from "vue";
+import { nextTick, onBeforeUnmount, onMounted, ref, watch } from "vue";
 
 export interface VisSpec {
     spec: VisualizationSpec;
@@ -21,13 +21,6 @@ const props = withDefaults(defineProps<VisSpec>(), {
     fillWidth: true,
 });
 
-const style = computed(() => {
-    if (props.fillWidth) {
-        return { width: "100%" };
-    }
-    return {};
-});
-
 const chartContainer = ref<HTMLDivElement | null>(null);
 const errorMessage = ref<string>("");
 
@@ -35,6 +28,7 @@ let vegaView: any;
 
 async function embedChart() {
     try {
+        await nextTick();
         if (vegaView) {
             vegaView.finalize();
         }
@@ -48,13 +42,16 @@ async function embedChart() {
     }
 }
 
-watch(props, embedChart, { deep: true, immediate: true });
+watch(props, embedChart, { deep: true });
+
 useResizeObserver(chartContainer, () => {
     if (vegaView) {
         vegaView.resize();
     }
 });
 
+onMounted(() => embedChart());
+
 // Cleanup the chart when the component is unmounted
 onBeforeUnmount(() => {
     if (vegaView) {

From 8b0d19c209e331b06188ab54cd814f531c463d4c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:42:41 -0400
Subject: [PATCH 02/39] Switch template filter to rely on yaml instead of json

---
 .../Markdown/Editor/CellAdd.test.js           | 16 +++------
 .../components/Markdown/Editor/CellAdd.vue    | 33 ++++++++++---------
 2 files changed, 22 insertions(+), 27 deletions(-)

diff --git a/client/src/components/Markdown/Editor/CellAdd.test.js b/client/src/components/Markdown/Editor/CellAdd.test.js
index 240931001095..7fac5e7813d2 100644
--- a/client/src/components/Markdown/Editor/CellAdd.test.js
+++ b/client/src/components/Markdown/Editor/CellAdd.test.js
@@ -8,19 +8,11 @@ import DelayedInput from "@/components/Common/DelayedInput.vue";
 import Popper from "@/components/Popper/Popper.vue";
 
 jest.mock("./templates", () => ({
-    cellTemplates: [
-        {
-            name: "Category 1",
-            templates: [
-                { title: "Option A", description: "Desc A", cell: { id: 1 } },
-                { title: "Option B", description: "Desc B", cell: { id: 2 } },
-            ],
-        },
-        {
-            name: "Category 2",
-            templates: [{ title: "Option C", description: "Desc C", cell: { id: 3 } }],
-        },
+    "Category 1": [
+        { title: "Option A", description: "Desc A", cell: { id: 1 } },
+        { title: "Option B", description: "Desc B", cell: { id: 2 } },
     ],
+    "Category 2": [{ title: "Option C", description: "Desc C", cell: { id: 3 } }],
 }));
 
 const createContainer = (tag = "div") => {
diff --git a/client/src/components/Markdown/Editor/CellAdd.vue b/client/src/components/Markdown/Editor/CellAdd.vue
index cb383751dd07..fedf3341a458 100644
--- a/client/src/components/Markdown/Editor/CellAdd.vue
+++ b/client/src/components/Markdown/Editor/CellAdd.vue
@@ -4,18 +4,19 @@
         <Popper v-if="buttonRef" :reference-el="buttonRef.$el" trigger="click" placement="right" mode="light">
             <DelayedInput class="p-1" :delay="100" placeholder="Search" @change="query = $event" />
             <div class="cell-add-categories overflow-auto">
-                <div v-if="filteredTemplates.length > 0">
-                    <div v-for="(category, categoryIndex) of filteredTemplates" :key="categoryIndex">
+                <div v-if="Object.keys(filteredTemplates).length > 0">
+                    <div v-for="(templates, categoryName) of filteredTemplates" :key="categoryName">
                         <hr class="solid m-0" />
                         <span class="d-flex justify-content-between">
-                            <small class="my-1 mx-3 text-info">{{ category.name }}</small>
+                            <small class="my-1 mx-3 text-info">{{ categoryName }}</small>
                         </span>
-                        <div v-if="category.templates.length > 0" class="cell-add-options popper-close">
+                        <div v-if="templates.length > 0" class="cell-add-options popper-close">
                             <CellOption
-                                v-for="(option, optionIndex) of category.templates"
+                                v-for="(option, optionIndex) of templates"
                                 :key="optionIndex"
                                 :title="option.title"
                                 :description="option.description"
+                                :logo="option.logo"
                                 @click="$emit('click', { configure: false, toggle: true, ...option.cell })" />
                         </div>
                     </div>
@@ -31,8 +32,8 @@ import { faPlus } from "@fortawesome/free-solid-svg-icons";
 import { BAlert } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import { cellTemplates } from "./templates";
-import type { CellType, TemplateCategory } from "./types";
+import cellTemplates from "./templates.yml";
+import type { CellType, TemplateEntry } from "./types";
 
 import CellButton from "./CellButton.vue";
 import CellOption from "./CellOption.vue";
@@ -46,20 +47,22 @@ defineEmits<{
 const buttonRef = ref();
 const query = ref("");
 
+const allTemplates = computed(() => {
+    const result = { ...(cellTemplates as Record<string, Array<TemplateEntry>>) };
+    return result;
+});
+
 const filteredTemplates = computed(() => {
-    const filteredCategories: Array<TemplateCategory> = [];
-    cellTemplates.forEach((category) => {
-        const matchedTemplates = category.templates.filter(
+    const filteredCategories: Record<string, TemplateEntry[]> = {};
+    Object.entries(allTemplates.value).forEach(([categoryName, templates]) => {
+        const matchedTemplates = templates.filter(
             (template) =>
-                category.name.toLowerCase().includes(query.value.toLowerCase()) ||
+                categoryName.toLowerCase().includes(query.value.toLowerCase()) ||
                 template.title.toLowerCase().includes(query.value.toLowerCase()) ||
                 template.description.toLowerCase().includes(query.value.toLowerCase())
         );
         if (matchedTemplates.length > 0) {
-            filteredCategories.push({
-                name: category.name,
-                templates: matchedTemplates,
-            });
+            filteredCategories[categoryName] = matchedTemplates;
         }
     });
     return filteredCategories;

From 242d3098a642bf70eeaaf319c699abfcb9e63a54 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:45:39 -0400
Subject: [PATCH 03/39] Accept workflow labels in cell editor

---
 client/src/components/Markdown/Editor/CellEditor.vue | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Markdown/Editor/CellEditor.vue b/client/src/components/Markdown/Editor/CellEditor.vue
index aea676bdf7d4..7aacda50d4ec 100644
--- a/client/src/components/Markdown/Editor/CellEditor.vue
+++ b/client/src/components/Markdown/Editor/CellEditor.vue
@@ -6,9 +6,10 @@
             <CellWrapper
                 :cell-index="cellIndex"
                 :cell-total="cells.length"
-                :name="cell.name"
                 :content="cell.content"
                 :configure="cell.configure"
+                :labels="labels"
+                :name="cell.name"
                 :toggle="cell.toggle"
                 @configure="onConfigure(cellIndex)"
                 @change="onChange(cellIndex, $event)"
@@ -27,13 +28,14 @@ import { nextTick, ref } from "vue";
 
 import { parseMarkdown } from "@/components/Markdown/parse";
 
-import type { CellType } from "./types";
+import type { CellType, WorkflowLabel } from "./types";
 
 import CellAdd from "./CellAdd.vue";
 import CellWrapper from "./CellWrapper.vue";
 
 const props = defineProps<{
     markdownText: string;
+    labels?: Array<WorkflowLabel>;
 }>();
 
 const emit = defineEmits(["update"]);

From bbda56821fc89722d909cbed3ba7bd234d363663 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:46:26 -0400
Subject: [PATCH 04/39] Add icons and logos to dropdown options

---
 .../components/Markdown/Editor/CellOption.vue | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Markdown/Editor/CellOption.vue b/client/src/components/Markdown/Editor/CellOption.vue
index 3b49883055d7..107b0b231e62 100644
--- a/client/src/components/Markdown/Editor/CellOption.vue
+++ b/client/src/components/Markdown/Editor/CellOption.vue
@@ -4,19 +4,24 @@
             <div class="font-weight-bold">{{ title }}</div>
             <small v-if="description" class="d-inline-block text-wrap text-break">{{ description }}</small>
         </div>
-        <div v-if="icon" class="my-2 mx-3 align-self-center">
-            <FontAwesomeIcon :icon="icon" />
+        <div v-if="icon" class="my-2 mx-3 align-self-start">
+            <FontAwesomeIcon :icon="icon" class="cell-option-icon" />
+        </div>
+        <div v-else-if="logo" class="my-2 mx-3 align-self-start">
+            <Img class="cell-option-logo" :src="logo" :alt="title" />
         </div>
     </span>
 </template>
 
 <script setup lang="ts">
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import type { IconDefinition } from "font-awesome-6";
 
 defineProps<{
     title: string;
-    description?: string;
-    icon?: any;
+    description: string;
+    icon?: IconDefinition;
+    logo?: string;
 }>();
 
 defineEmits<{
@@ -38,5 +43,11 @@ defineEmits<{
     small {
         color: $text-muted;
     }
+    .cell-option-icon {
+        font-size: 1rem;
+    }
+    .cell-option-logo {
+        width: 2rem;
+    }
 }
 </style>

From 761d823b786417725010a7fa32934e713189c98e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:48:51 -0400
Subject: [PATCH 05/39] Move cell rendering to separate section wrapper
 component

---
 .../Markdown/Editor/CellWrapper.vue           | 28 ++++++++++++-------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/client/src/components/Markdown/Editor/CellWrapper.vue b/client/src/components/Markdown/Editor/CellWrapper.vue
index c2aaadd436cf..88790a9e0f51 100644
--- a/client/src/components/Markdown/Editor/CellWrapper.vue
+++ b/client/src/components/Markdown/Editor/CellWrapper.vue
@@ -8,13 +8,12 @@
                 <CellButton v-if="toggle" title="Collapse" :icon="faAngleDoubleUp" />
                 <CellButton v-else title="Expand" :icon="faAngleDoubleDown" />
             </div>
-            <div class="w-100">
-                <div class="m-2">
-                    <MarkdownDefault v-if="name === 'markdown'" :content="content" />
-                    <MarkdownGalaxy v-else-if="name === 'galaxy'" :content="content" />
-                    <b-alert v-else variant="danger" show> This cell type `{{ name }}` is not available. </b-alert>
-                </div>
-            </div>
+            <SectionWrapper
+                class="m-2 w-100"
+                :name="name"
+                :content="content"
+                :labels="labels"
+                @change="$emit('change', $event)" />
         </div>
         <div v-if="toggle" class="d-flex">
             <div class="d-flex flex-column" :class="{ 'cell-wrapper-hover': hover }">
@@ -34,9 +33,16 @@
                     v-if="name === 'galaxy' && configure"
                     :name="name"
                     :content="content"
+                    :labels="labels"
                     @cancel="$emit('configure')"
                     @change="handleConfigure($event)" />
-                <CellCode :key="name" class="mt-1" :value="content" :mode="mode" @change="$emit('change', $event)" />
+                <CellCode
+                    :key="name"
+                    class="mt-1"
+                    :value="content"
+                    :max-lines="30"
+                    :mode="mode"
+                    @change="$emit('change', $event)" />
                 <small class="cell-wrapper-type position-absolute">
                     {{ VALID_TYPES.includes(name) ? name : "unknown" }}
                 </small>
@@ -49,12 +55,13 @@
 import { faAngleDoubleDown, faAngleDoubleUp } from "@fortawesome/free-solid-svg-icons";
 import { computed, ref } from "vue";
 
-import MarkdownDefault from "../Sections/MarkdownDefault.vue";
-import MarkdownGalaxy from "../Sections/MarkdownGalaxy.vue";
+import type { WorkflowLabel } from "./types";
+
 import CellAction from "./CellAction.vue";
 import CellButton from "./CellButton.vue";
 import CellCode from "./CellCode.vue";
 import ConfigureGalaxy from "./Configurations/ConfigureGalaxy.vue";
+import SectionWrapper from "@/components/Markdown/Sections/SectionWrapper.vue";
 
 const VALID_TYPES = ["galaxy", "markdown", "vega", "visualization", "vitessce"];
 
@@ -63,6 +70,7 @@ const props = defineProps<{
     cellTotal: number;
     configure?: boolean;
     content: string;
+    labels?: Array<WorkflowLabel>;
     name: string;
     toggle?: boolean;
 }>();

From 3176f65605d6f80018277d208614b1afd3e22050 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:49:50 -0400
Subject: [PATCH 06/39] Adjust configuration requirement handler to consume yml
 instead of json

---
 .../Markdown/Editor/Configurations/ConfigureGalaxy.vue    | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Markdown/Editor/Configurations/ConfigureGalaxy.vue b/client/src/components/Markdown/Editor/Configurations/ConfigureGalaxy.vue
index bdd5c1d61d73..74cfe23c07b6 100644
--- a/client/src/components/Markdown/Editor/Configurations/ConfigureGalaxy.vue
+++ b/client/src/components/Markdown/Editor/Configurations/ConfigureGalaxy.vue
@@ -5,7 +5,7 @@
         :argument-type="requirement"
         :argument-name="contentObject?.name"
         :argument-payload="contentObject?.args"
-        :useLabels="false"
+        :labels="labels"
         @onInsert="$emit('change', $event)"
         @onCancel="$emit('cancel')" />
     <b-alert v-else v-localize variant="info" show>
@@ -16,14 +16,16 @@
 <script setup lang="ts">
 import { computed, type Ref, ref, watch } from "vue";
 
+import type { WorkflowLabel } from "@/components/Markdown/Editor/types";
 import { getArgs } from "@/components/Markdown/parse";
 
-import REQUIREMENTS from "./requirements";
+import REQUIREMENTS from "./requirements.yml";
 
 import MarkdownDialog from "@/components/Markdown/MarkdownDialog.vue";
 
 const props = defineProps<{
     content: string;
+    labels?: Array<WorkflowLabel>;
 }>();
 
 defineEmits<{
@@ -43,7 +45,7 @@ const requirement = computed(() => {
     const name = contentObject.value?.name || "";
     if (name) {
         for (const [key, values] of Object.entries(REQUIREMENTS)) {
-            if (values.includes(name)) {
+            if (Array.isArray(values) && values.includes(name)) {
                 return key;
             }
         }

From 1df79c7b7b4e912ecd124429bacb578322aaa55d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:51:20 -0400
Subject: [PATCH 07/39] Replace requirements.json by requirements.yml in
 markdown editor

---
 .../Editor/Configurations/requirements.ts     | 19 -------------
 .../Editor/Configurations/requirements.yml    | 28 +++++++++++++++++++
 2 files changed, 28 insertions(+), 19 deletions(-)
 delete mode 100644 client/src/components/Markdown/Editor/Configurations/requirements.ts
 create mode 100644 client/src/components/Markdown/Editor/Configurations/requirements.yml

diff --git a/client/src/components/Markdown/Editor/Configurations/requirements.ts b/client/src/components/Markdown/Editor/Configurations/requirements.ts
deleted file mode 100644
index 3d3a25b40e0f..000000000000
--- a/client/src/components/Markdown/Editor/Configurations/requirements.ts
+++ /dev/null
@@ -1,19 +0,0 @@
-export default {
-    history_dataset_collection_id: ["history_dataset_collection_display"],
-    history_dataset_id: [
-        "history_dataset_display",
-        "history_dataset_info",
-        "history_dataset_index",
-        "history_dataset_type",
-        "history_dataset_embedded",
-        "history_dataset_as_table",
-        "history_dataset_as_image",
-        "history_dataset_link",
-        "history_dataset_name",
-        "history_dataset_peek",
-    ],
-    history_id: ["history_link"],
-    invocation_id: ["invocation_time"],
-    job_id: ["job_metrics", "job_parameters", "tool_stderr", "tool_stdout"],
-    workflow_id: ["workflow_display", "workflow_image", "workflow_license"],
-};
diff --git a/client/src/components/Markdown/Editor/Configurations/requirements.yml b/client/src/components/Markdown/Editor/Configurations/requirements.yml
new file mode 100644
index 000000000000..fb953ba1c9e9
--- /dev/null
+++ b/client/src/components/Markdown/Editor/Configurations/requirements.yml
@@ -0,0 +1,28 @@
+history_dataset_collection_id:
+  - history_dataset_collection_display
+history_dataset_id:
+  - history_dataset_display
+  - history_dataset_info
+  - history_dataset_index
+  - history_dataset_type
+  - history_dataset_embedded
+  - history_dataset_as_table
+  - history_dataset_as_image
+  - history_dataset_link
+  - history_dataset_name
+  - history_dataset_peek
+history_id:
+  - history_link
+invocation_id:
+  - invocation_inputs
+  - invocation_outputs
+  - invocation_time
+job_id:
+  - job_metrics
+  - job_parameters
+  - tool_stderr
+  - tool_stdout
+workflow_id:
+  - workflow_display
+  - workflow_image
+  - workflow_license

From b4a225df820f2d1a326ccb89a6821b098d1671a6 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:52:21 -0400
Subject: [PATCH 08/39] Remove unused types module

---
 .../Markdown/Editor/Configurations/types.ts           | 11 -----------
 1 file changed, 11 deletions(-)
 delete mode 100644 client/src/components/Markdown/Editor/Configurations/types.ts

diff --git a/client/src/components/Markdown/Editor/Configurations/types.ts b/client/src/components/Markdown/Editor/Configurations/types.ts
deleted file mode 100644
index 534d3128b237..000000000000
--- a/client/src/components/Markdown/Editor/Configurations/types.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-export type ApiResponse = Array<any> | undefined;
-
-export interface ContentType {
-    dataset_id: string;
-    dataset_name?: string;
-}
-
-export interface OptionType {
-    id: string | null | undefined;
-    name: string | null | undefined;
-}

From c39704cd6abd20e97c6ea4b9f0932423601303c5 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:53:47 -0400
Subject: [PATCH 09/39] Replace templates.json with template.yml

---
 .../components/Markdown/Editor/templates.ts   | 290 ------------------
 .../components/Markdown/Editor/templates.yml  | 196 ++++++++++++
 2 files changed, 196 insertions(+), 290 deletions(-)
 delete mode 100644 client/src/components/Markdown/Editor/templates.ts
 create mode 100644 client/src/components/Markdown/Editor/templates.yml

diff --git a/client/src/components/Markdown/Editor/templates.ts b/client/src/components/Markdown/Editor/templates.ts
deleted file mode 100644
index 1f8dcdfa9b07..000000000000
--- a/client/src/components/Markdown/Editor/templates.ts
+++ /dev/null
@@ -1,290 +0,0 @@
-import type { TemplateCategory } from "./types";
-
-export const cellTemplates: Array<TemplateCategory> = [
-    {
-        name: "Markdown",
-        templates: [
-            {
-                title: "Heading 1",
-                description: "Main headline",
-                cell: {
-                    name: "markdown",
-                    content: "# Heading 1",
-                },
-            },
-            {
-                title: "Heading 2",
-                description: "Section headline",
-                cell: {
-                    name: "markdown",
-                    content: "## Heading 2",
-                },
-            },
-            {
-                title: "Heading 3",
-                description: "Subhead",
-                cell: {
-                    name: "markdown",
-                    content: "### Heading 3",
-                },
-            },
-        ],
-    },
-    {
-        name: "Galaxy",
-        templates: [
-            {
-                title: "Collection",
-                description: "Display a Collection",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_collection_display()",
-                },
-            },
-            {
-                title: "Dataset",
-                description: "Display a Dataset",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_display()",
-                },
-            },
-            {
-                title: "Dataset Details",
-                description: "Display a Dataset Information",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_info()",
-                },
-            },
-            {
-                title: "Dataset Index",
-                description: "Display a Dataset Index",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_index()",
-                },
-            },
-            {
-                title: "Dataset Type",
-                description: "Display a Dataset Type",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_type()",
-                },
-            },
-            {
-                title: "Embedded Dataset",
-                description: "Embed a Dataset",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_embedded()",
-                },
-            },
-            {
-                title: "Embedded Dataset as Table",
-                description: "Embed a Dataset as Table",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_as_table()",
-                },
-            },
-            {
-                title: "Image",
-                description: "Embed an Image",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_as_image()",
-                },
-            },
-            {
-                title: "Link to Dataset",
-                description: "Create link to a Dataset",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_link()",
-                },
-            },
-            {
-                title: "Link to Import",
-                description: "Link to Import a History",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_link()",
-                },
-            },
-            {
-                title: "Name of Dataset",
-                description: "Display a Dataset name",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_name()",
-                },
-            },
-            {
-                title: "Peek into Dataset",
-                description: "Display a Dataset peek",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "history_dataset_peek()",
-                },
-            },
-            {
-                title: "Job Metrics as Table",
-                description: "Display job resource consumption",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "job_metrics()",
-                },
-            },
-            {
-                title: "Job Parameters as Table",
-                description: "Display the input parameters of a Job",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "job_parameters()",
-                },
-            },
-            {
-                title: "Tool Error of Job run",
-                description: "Display Tool errors",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "tool_stderr()",
-                },
-            },
-            {
-                title: "Tool Output of Job run",
-                description: "Display Tool standard output",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "tool_stdout()",
-                },
-            },
-            {
-                title: "Display a Workflow",
-                description: "Display all Workflow steps",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "workflow_display()",
-                },
-            },
-            {
-                title: "Time a Workflow was invoked",
-                description: "Inovcation time of a Workflow run",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "invocation_time()",
-                },
-            },
-            {
-                title: "Workflow (as image)",
-                description: "A static image of a Workflow",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "workflow_image()",
-                },
-            },
-            {
-                title: "Workflow License",
-                description: "Usage license of a Workflow",
-                cell: {
-                    name: "galaxy",
-                    configure: true,
-                    content: "workflow_license()",
-                },
-            },
-            {
-                title: "Access",
-                description: "Link used to access this Galaxy",
-                cell: {
-                    name: "galaxy",
-                    content: "instance_access_link()",
-                },
-            },
-            {
-                title: "Citation",
-                description: "Link describing how to cite this Galaxy instance",
-                cell: {
-                    name: "galaxy",
-                    content: "instance_citation_link()",
-                },
-            },
-            {
-                title: "Help",
-                description: "Link describing how to cite this Galaxy instance",
-                cell: {
-                    name: "galaxy",
-                    content: "instance_help_link()",
-                },
-            },
-            {
-                title: "Organization",
-                description: "Link describing how to cite this Galaxy instance",
-                cell: {
-                    name: "galaxy",
-                    content: "instance_organization_link()",
-                },
-            },
-            {
-                title: "Resources",
-                description: "Link for more information about this Galaxy",
-                cell: {
-                    name: "galaxy",
-                    content: "instance_resources_link()",
-                },
-            },
-            {
-                title: "Support",
-                description: "Link describing how to cite this Galaxy instance",
-                cell: {
-                    name: "galaxy",
-                    content: "instance_support_link()",
-                },
-            },
-            {
-                title: "Terms and Conditions",
-                description: "Link describing terms and conditions for using this Galaxy instance",
-                cell: {
-                    name: "galaxy",
-                    content: "instance_terms_link()",
-                },
-            },
-            {
-                title: "Current Time",
-                description: "as text",
-                cell: {
-                    name: "galaxy",
-                    content: "generate_time()",
-                },
-            },
-            {
-                title: "Galaxy Version",
-                description: "as text",
-                cell: {
-                    name: "galaxy",
-                    content: "generate_galaxy_version()",
-                },
-            },
-        ],
-    },
-];
diff --git a/client/src/components/Markdown/Editor/templates.yml b/client/src/components/Markdown/Editor/templates.yml
new file mode 100644
index 000000000000..dd40e6ba4b6e
--- /dev/null
+++ b/client/src/components/Markdown/Editor/templates.yml
@@ -0,0 +1,196 @@
+Markdown:
+  - title: "Heading 1"
+    description: "Main headline"
+    cell:
+      name: "markdown"
+      content: "# Heading 1"
+  - title: "Heading 2"
+    description: "Section headline"
+    cell:
+      name: "markdown"
+      content: "## Heading 2"
+  - title: "Heading 3"
+    description: "Subhead"
+    cell:
+      name: "markdown"
+      content: "### Heading 3"
+  - title: "Link"
+    description: "Resource Link"
+    cell:
+      name: "markdown"
+      content: "[title](https://www.example.com)"
+  - title: "List"
+    description: "Unordered List"
+    cell:
+      name: "markdown"
+      content: |
+        - First item
+        - Second item
+        - Third item
+
+Galaxy:
+  - title: "Collection"
+    description: "Display a Collection"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_collection_display()"
+  - title: "Dataset"
+    description: "Display a Dataset"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_display()"
+  - title: "Dataset Details"
+    description: "Display a Dataset Information"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_info()"
+  - title: "Dataset Index"
+    description: "Display a Dataset Index"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_index()"
+  - title: "Dataset Type"
+    description: "Display a Dataset Type"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_type()"
+  - title: "Embedded Dataset"
+    description: "Embed a Dataset"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_embedded()"
+  - title: "Embedded Dataset as Table"
+    description: "Embed a Dataset as Table"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_as_table()"
+  - title: "Image"
+    description: "Embed an Image"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_as_image()"
+  - title: "Link to Dataset"
+    description: "Create link to a Dataset"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_link()"
+  - title: "Link to Import"
+    description: "Link to Import a History"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_link()"
+  - title: "Name of Dataset"
+    description: "Display a Dataset name"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_name()"
+  - title: "Peek into Dataset"
+    description: "Display a Dataset peek"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "history_dataset_peek()"
+  - title: "Job Metrics as Table"
+    description: "Display job resource consumption"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "job_metrics()"
+  - title: "Job Parameters as Table"
+    description: "Display the input parameters of a Job"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "job_parameters()"
+  - title: "Tool Error of Job run"
+    description: "Display Tool errors"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "tool_stderr()"
+  - title: "Tool Output of Job run"
+    description: "Display Tool standard output"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "tool_stdout()"
+  - title: "Display a Workflow"
+    description: "Display all Workflow steps"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "workflow_display()"
+  - title: "Time a Workflow was invoked"
+    description: "Invocation time of a Workflow run"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "invocation_time()"
+  - title: "Workflow (as image)"
+    description: "A static image of a Workflow"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "workflow_image()"
+  - title: "Workflow License"
+    description: "Usage license of a Workflow"
+    cell:
+      name: "galaxy"
+      configure: true
+      content: "workflow_license()"
+  - title: "Access"
+    description: "Link used to access this Galaxy"
+    cell:
+      name: "galaxy"
+      content: "instance_access_link()"
+  - title: "Citation"
+    description: "Link describing how to cite this Galaxy instance"
+    cell:
+      name: "galaxy"
+      content: "instance_citation_link()"
+  - title: "Help"
+    description: "Help link for this Galaxy instance"
+    cell:
+      name: "galaxy"
+      content: "instance_help_link()"
+  - title: "Organization"
+    description: "Organization link for this Galaxy instance"
+    cell:
+      name: "galaxy"
+      content: "instance_organization_link()"
+  - title: "Resources"
+    description: "Link for more information about this Galaxy"
+    cell:
+      name: "galaxy"
+      content: "instance_resources_link()"
+  - title: "Support"
+    description: "Support link for this Galaxy instance"
+    cell:
+      name: "galaxy"
+      content: "instance_support_link()"
+  - title: "Terms and Conditions"
+    description: "Terms and conditions for using this Galaxy instance"
+    cell:
+      name: "galaxy"
+      content: "instance_terms_link()"
+  - title: "Current Time"
+    description: "as text"
+    cell:
+      name: "galaxy"
+      content: "generate_time()"
+  - title: "Galaxy Version"
+    description: "as text"
+    cell:
+      name: "galaxy"
+      content: "generate_galaxy_version()"

From 33790820caef4099f2d356b1e83ce02aa134c41b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:54:52 -0400
Subject: [PATCH 10/39] Adjust markdown editor types

---
 .../src/components/Markdown/Editor/types.ts   | 22 ++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Markdown/Editor/types.ts b/client/src/components/Markdown/Editor/types.ts
index 2e1a93c31936..bc00bce83ffb 100644
--- a/client/src/components/Markdown/Editor/types.ts
+++ b/client/src/components/Markdown/Editor/types.ts
@@ -5,13 +5,29 @@ export interface CellType {
     toggle?: boolean;
 }
 
-export interface TemplateCategory {
-    name: string;
-    templates: Array<TemplateEntry>;
+export interface DatasetLabel {
+    invocation_id: string;
+    input?: string;
+    output?: string;
+}
+
+export interface Invocation {
+    history_id: string;
+    inputs: Record<string, { label?: string; id?: string }>;
+    outputs: Record<string, { id?: string }>;
+    steps: { workflow_step_label?: string; job_id?: string; implicit_collection_jobs_id?: string }[];
+    workflow_id: string;
 }
 
 export interface TemplateEntry {
     title: string;
     description: string;
+    icon?: string;
+    logo?: string;
     cell: CellType;
 }
+
+export interface WorkflowLabel {
+    label: string;
+    type: "input" | "output" | "step";
+}

From e6c31368d9ae8de30ffbf93e7aceb05ed34137c7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:55:59 -0400
Subject: [PATCH 11/39] Use types in label selector

---
 client/src/components/Markdown/LabelSelector.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Markdown/LabelSelector.vue b/client/src/components/Markdown/LabelSelector.vue
index 333bafc103ca..f2219e93f51f 100644
--- a/client/src/components/Markdown/LabelSelector.vue
+++ b/client/src/components/Markdown/LabelSelector.vue
@@ -1,9 +1,9 @@
 <script setup lang="ts">
-import { type WorkflowLabel } from "./labels";
+import { type WorkflowLabel } from "./Editor/types";
 
 interface LabelSelectorProps {
     hasLabels: boolean;
-    labels: WorkflowLabel[];
+    labels: Array<WorkflowLabel>;
     value?: WorkflowLabel;
     labelTitle: string;
 }

From 2527fdc3c4ccf12f86c312a07f06f03b1effaca4 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 10:56:55 -0400
Subject: [PATCH 12/39] Revise markdown viewer, move and fix updated date to
 bottom, align styles, use section wrapper

---
 client/src/components/Markdown/Markdown.vue | 98 +++++++++++----------
 1 file changed, 53 insertions(+), 45 deletions(-)

diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index 0ddd458cc357..43cc27598104 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -1,25 +1,27 @@
 <script setup lang="ts">
 import { faEdit } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton } from "bootstrap-vue";
 import { computed, onMounted, ref, watch } from "vue";
 
 import { parseMarkdown } from "./parse";
 
-import MarkdownDefault from "./Sections/MarkdownDefault.vue";
-import MarkdownGalaxy from "./Sections/MarkdownGalaxy.vue";
+import Heading from "@/components/Common/Heading.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
+import SectionWrapper from "@/components/Markdown/Sections/SectionWrapper.vue";
 import StsDownloadButton from "@/components/StsDownloadButton.vue";
 
 // Props
 interface MarkdownConfig {
-    generate_time?: string;
-    generate_version?: string;
     content?: string;
-    markdown?: string;
     errors?: Array<{ error?: string; line?: string }>;
+    generate_time?: string;
+    generate_version?: string;
     id?: string;
-    title?: string;
+    markdown?: string;
     model_class?: string;
+    title?: string;
+    update_time?: string;
 }
 
 const props = defineProps<{
@@ -38,8 +40,8 @@ const loading = ref(true);
 // Computed properties
 const effectiveExportLink = computed(() => (props.enable_beta_markdown_export ? props.exportLink : null));
 
-const time = computed(() => {
-    const generateTime = props.markdownConfig.generate_time;
+const updateTime = computed(() => {
+    const generateTime = props.markdownConfig.update_time;
     if (generateTime) {
         const formattedTime = generateTime.endsWith("Z") ? generateTime : `${generateTime}Z`;
         const date = new Date(formattedTime);
@@ -53,11 +55,9 @@ const time = computed(() => {
             timeZoneName: "short",
         });
     }
-    return "unavailable";
+    return "";
 });
 
-const version = computed(() => props.markdownConfig.generate_version || "Unknown Galaxy Version");
-
 // Methods
 function initConfig() {
     const config = props.markdownConfig;
@@ -81,49 +81,57 @@ onMounted(() => {
 <template>
     <div class="markdown-wrapper">
         <LoadingSpan v-if="loading" />
-        <div v-else>
-            <div>
-                <StsDownloadButton
-                    v-if="effectiveExportLink"
-                    class="float-right markdown-pdf-export"
-                    :fallback-url="exportLink"
-                    :download-endpoint="downloadEndpoint"
-                    size="sm"
-                    title="Generate PDF" />
-                <b-button
-                    v-if="!readOnly"
-                    v-b-tooltip.hover
-                    class="float-right markdown-edit mr-2"
-                    role="button"
-                    size="sm"
-                    title="Edit Markdown"
-                    @click="$emit('onEdit')">
-                    Edit
-                    <FontAwesomeIcon :icon="faEdit" />
-                </b-button>
-                <h1 class="float-right align-middle mr-2 mt-1 h-md">Galaxy {{ markdownConfig.model_class }}</h1>
-                <span class="float-left font-weight-light">
-                    <h1 class="text-break align-middle">
-                        Title: {{ markdownConfig.title || markdownConfig.model_class }}
-                    </h1>
-                </span>
+        <div v-else class="d-flex flex-column">
+            <div class="markdown-wrapper-header d-flex flex-column sticky-top bg-white">
+                <div class="d-flex">
+                    <Heading v-localize h1 separator inline size="md" class="flex-grow-1">
+                        {{ markdownConfig.title || markdownConfig.model_class }}
+                    </Heading>
+                    <div>
+                        <StsDownloadButton
+                            v-if="effectiveExportLink"
+                            class="markdown-pdf-export"
+                            :fallback-url="exportLink"
+                            :download-endpoint="downloadEndpoint"
+                            size="sm"
+                            title="Generate PDF"
+                            variant="outline-primary" />
+                        <BButton
+                            v-if="!readOnly"
+                            v-b-tooltip.hover
+                            class="markdown-edit"
+                            role="button"
+                            size="sm"
+                            title="Edit Markdown"
+                            variant="outline-primary"
+                            @click="$emit('onEdit')">
+                            Edit
+                            <FontAwesomeIcon :icon="faEdit" />
+                        </BButton>
+                    </div>
+                </div>
             </div>
-            <b-badge variant="info" class="w-100 rounded mb-3 white-space-normal">
-                <div class="float-left m-1 text-break">Generated with Galaxy {{ version }} on {{ time }}</div>
-                <div class="float-right m-1">Identifier: {{ markdownConfig.id }}</div>
-            </b-badge>
-            <div>
+            <div class="flex-grow-1 w-75 mx-auto">
                 <b-alert v-if="markdownErrors.length > 0" variant="warning" show>
                     <div v-for="(obj, index) in markdownErrors" :key="index" class="mb-1">
                         <h2 class="h-text">{{ obj.error || "Error" }}</h2>
                         {{ obj.line }}
                     </div>
                 </b-alert>
+                <div v-for="(obj, index) in markdownObjects" :key="index" class="markdown-component py-2">
+                    <SectionWrapper :name="obj.name" :content="obj.content" />
+                </div>
             </div>
-            <div v-for="(obj, index) in markdownObjects" :key="index" class="markdown-component">
-                <MarkdownDefault v-if="obj.name === 'markdown'" :content="obj.content" />
-                <MarkdownGalaxy v-else-if="obj.name === 'galaxy'" :content="obj.content" />
+            <div class="d-flex justify-content-between p-1">
+                <small v-if="updateTime" class="text-break">Last updated on {{ updateTime }}</small>
+                <small class="text-break">Identifier: {{ markdownConfig.id }}</small>
             </div>
         </div>
     </div>
 </template>
+
+<style scoped>
+.markdown-wrapper-header {
+    z-index: 1001;
+}
+</style>

From 209c4460300da0e6937927e514a0bdd9bb53ceec Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:04:00 -0400
Subject: [PATCH 13/39] Revise Markdown Dialog wrapper to use updated types

---
 .../components/Markdown/MarkdownDialog.vue    | 31 ++++++++++---------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/client/src/components/Markdown/MarkdownDialog.vue b/client/src/components/Markdown/MarkdownDialog.vue
index e40ad7144d72..f54e6a6dc061 100644
--- a/client/src/components/Markdown/MarkdownDialog.vue
+++ b/client/src/components/Markdown/MarkdownDialog.vue
@@ -5,7 +5,7 @@ import Vue, { computed, ref } from "vue";
 
 import { useHistoryStore } from "@/stores/historyStore";
 
-import { type WorkflowLabel, type WorkflowLabels } from "./labels";
+import { type WorkflowLabel } from "./Editor/types";
 import { getHistories, getInvocations, getJobs, getWorkflows } from "./services";
 
 import MarkdownSelector from "./MarkdownSelector.vue";
@@ -20,8 +20,7 @@ interface MarkdownDialogProps {
     argumentName?: string;
     argumentType?: string;
     argumentPayload?: object;
-    labels?: WorkflowLabels;
-    useLabels: boolean;
+    labels?: Array<WorkflowLabel>;
 }
 
 const props = withDefaults(defineProps<MarkdownDialogProps>(), {
@@ -42,12 +41,12 @@ interface SelectTitles {
 
 type SelectType = "job_id" | "invocation_id" | "history_dataset_id" | "history_dataset_collection_id";
 
-const effectiveLabels = computed<WorkflowLabels>(() => {
+const effectiveLabels = computed<Array<WorkflowLabel>>(() => {
     if (!props.labels) {
-        return [] as WorkflowLabels;
+        return [] as Array<WorkflowLabel>;
     }
     const selectSteps = props.argumentType == "job_id";
-    const filteredLabels: WorkflowLabels = [];
+    const filteredLabels: Array<WorkflowLabel> = [];
     for (const label of props.labels) {
         if (selectSteps && label.type == "step") {
             filteredLabels.push(label);
@@ -58,6 +57,8 @@ const effectiveLabels = computed<WorkflowLabels>(() => {
     return filteredLabels;
 });
 
+const hasLabels = computed(() => props.labels && props.labels.length > 0);
+
 const selectorConfig = {
     job_id: {
         labelTitle: "Step",
@@ -139,25 +140,25 @@ function onOk(selectedLabel: WorkflowLabel | undefined) {
     }
 
     if (props.argumentType == "history_dataset_id") {
-        if (props.useLabels) {
+        if (hasLabels.value) {
             onInsertArgument();
         } else {
             dataShow.value = true;
         }
     } else if (props.argumentType == "history_dataset_collection_id") {
-        if (props.useLabels) {
+        if (hasLabels.value) {
             onInsertArgument();
         } else {
             dataCollectionShow.value = true;
         }
     } else if (props.argumentType == "job_id") {
-        if (props.useLabels) {
+        if (hasLabels.value) {
             onInsertArgument();
         } else {
             jobShow.value = true;
         }
     } else if (props.argumentType == "invocation_id") {
-        if (props.useLabels) {
+        if (hasLabels.value) {
             onInsertArgument();
         } else {
             invocationShow.value = true;
@@ -181,25 +182,25 @@ if (props.argumentType == "workflow_id") {
 } else if (props.argumentType == "history_id") {
     historyShow.value = true;
 } else if (props.argumentType == "history_dataset_id") {
-    if (props.useLabels) {
+    if (hasLabels.value) {
         selectedShow.value = true;
     } else {
         dataShow.value = true;
     }
 } else if (props.argumentType == "history_dataset_collection_id") {
-    if (props.useLabels) {
+    if (hasLabels.value) {
         selectedShow.value = true;
     } else {
         dataCollectionShow.value = true;
     }
 } else if (props.argumentType == "invocation_id") {
-    if (props.useLabels) {
+    if (hasLabels.value) {
         selectedShow.value = true;
     } else {
         invocationShow.value = true;
     }
 } else if (props.argumentType == "job_id") {
-    if (props.useLabels) {
+    if (hasLabels.value) {
         selectedShow.value = true;
     } else {
         jobShow.value = true;
@@ -224,7 +225,7 @@ if (props.argumentType == "workflow_id") {
             :argument-name="argumentName"
             :argument-payload="argumentPayload"
             :labels="effectiveLabels"
-            :use-labels="useLabels"
+            :use-labels="hasLabels"
             :history="currentHistoryId"
             @onOk="onVisualization"
             @onCancel="onCancel" />

From 08b41cb2cfd74b4e1e8c1e5897dba65f6b82b618 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:06:02 -0400
Subject: [PATCH 14/39] Revise error handling in collection display component

---
 .../HistoryDatasetCollection/CollectionDisplay.vue    | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Markdown/Sections/Elements/HistoryDatasetCollection/CollectionDisplay.vue b/client/src/components/Markdown/Sections/Elements/HistoryDatasetCollection/CollectionDisplay.vue
index 725ab3025330..52668e1d03de 100644
--- a/client/src/components/Markdown/Sections/Elements/HistoryDatasetCollection/CollectionDisplay.vue
+++ b/client/src/components/Markdown/Sections/Elements/HistoryDatasetCollection/CollectionDisplay.vue
@@ -1,5 +1,8 @@
 <template>
-    <b-card body-class="p-0">
+    <b-alert v-if="!!errorText" variant="warning" show>
+        {{ errorText }}
+    </b-alert>
+    <b-card v-else body-class="p-0">
         <b-card-header>
             <span class="float-right">
                 <b-button
@@ -67,6 +70,7 @@ const currentHistoryId = computed(() => historyStore.currentHistoryId);
 
 const itemContent = ref<any>(null);
 const loading = ref(true);
+const errorText = ref<string>("");
 const messageText = ref<string>("");
 const messageVariant = ref<string>("");
 
@@ -91,10 +95,9 @@ const getContent = async () => {
         },
     });
     if (error) {
-        messageVariant.value = "danger";
-        messageText.value = `Failed to retrieve content. ${error}`;
+        errorText.value = `Failed to retrieve content. ${error.err_msg}`;
     } else {
-        messageText.value = "";
+        errorText.value = "";
     }
     itemContent.value = data;
     loading.value = false;

From b35f764fdd740f1a8b1e3a954bfaf1fe1d19a7a7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:06:51 -0400
Subject: [PATCH 15/39] Add history dataset details test

---
 .../Elements/HistoryDatasetDetails.test.js    | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 client/src/components/Markdown/Sections/Elements/HistoryDatasetDetails.test.js

diff --git a/client/src/components/Markdown/Sections/Elements/HistoryDatasetDetails.test.js b/client/src/components/Markdown/Sections/Elements/HistoryDatasetDetails.test.js
new file mode 100644
index 000000000000..80330c78177e
--- /dev/null
+++ b/client/src/components/Markdown/Sections/Elements/HistoryDatasetDetails.test.js
@@ -0,0 +1,55 @@
+import { createTestingPinia } from "@pinia/testing";
+import { mount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { getLocalVue } from "tests/jest/helpers";
+
+import { useServerMock } from "@/api/client/__mocks__";
+import { testDatatypesMapper } from "@/components/Datatypes/test_fixtures";
+import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
+
+import HistoryDatasetDetails from "./HistoryDatasetDetails.vue";
+
+const localVue = getLocalVue();
+
+const { server, http } = useServerMock();
+
+const tabularMetaData = {
+    metadata_columns: 2,
+    metadata_data_lines: 4,
+    misc_blurb: "tabular_misc_blurb",
+    extension: "tabular",
+    name: "tabular_name",
+    peek: "tabular_peek",
+    state: "ok",
+};
+
+function setUpDatatypesStore() {
+    const pinia = createTestingPinia({ stubActions: false });
+    const datatypesStore = useDatatypesMapperStore();
+    datatypesStore.datatypesMapper = testDatatypesMapper;
+    return pinia;
+}
+
+async function mountTarget(propsData = {}) {
+    server.use(http.get("/api/datasets/{dataset_id}", ({ response }) => response(200).json(tabularMetaData)));
+    const wrapper = mount(HistoryDatasetDetails, {
+        localVue,
+        propsData,
+        pinia: setUpDatatypesStore(),
+    });
+    await flushPromises();
+    return wrapper;
+}
+
+describe("HistoryDatasetDetails.vue", () => {
+    it("should render details", async () => {
+        const wrapper = await mountTarget({ datasetId: "datasetId", name: "history_dataset_peek" });
+        expect(wrapper.text()).toBe("tabular_peek");
+        await wrapper.setProps({ name: "history_dataset_name" });
+        expect(wrapper.text()).toBe("tabular_name");
+        await wrapper.setProps({ name: "history_dataset_info" });
+        expect(wrapper.text()).toBe("tabular_misc_blurb");
+        await wrapper.setProps({ name: "history_dataset_type" });
+        expect(wrapper.text()).toBe("tabular");
+    });
+});

From 8fa1835f2acc1b6fcc0a7c88be7280989e8616f6 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:07:21 -0400
Subject: [PATCH 16/39] Fix history dataset details display

---
 .../Sections/Elements/HistoryDatasetDetails.vue      | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Markdown/Sections/Elements/HistoryDatasetDetails.vue b/client/src/components/Markdown/Sections/Elements/HistoryDatasetDetails.vue
index 993cc18e0201..7a1c53ed34d0 100644
--- a/client/src/components/Markdown/Sections/Elements/HistoryDatasetDetails.vue
+++ b/client/src/components/Markdown/Sections/Elements/HistoryDatasetDetails.vue
@@ -4,20 +4,20 @@ import { computed } from "vue";
 
 import { useDatasetStore } from "@/stores/datasetStore";
 
-type AttributeType = "name" | "info" | "peek" | "file_ext";
+type AttributeType = "name" | "misc_blurb" | "peek" | "extension";
 
 const ATTRIBUTES: Record<string, AttributeType> = {
     history_dataset_name: "name",
-    history_dataset_info: "info",
+    history_dataset_info: "misc_blurb",
     history_dataset_peek: "peek",
-    history_dataset_type: "file_ext",
+    history_dataset_type: "extension",
 };
 
 interface Dataset {
     name?: string;
-    info?: string;
+    misc_blurb?: string;
     peek?: string;
-    file_ext?: string;
+    extension?: string;
 }
 
 const { getDatasetError, getDataset } = useDatasetStore();
@@ -44,5 +44,5 @@ const getClass = computed(() => `dataset-${ATTRIBUTES[props.name || ""]}`);
 
 <template>
     <BAlert v-if="error" show variant="warning">{{ error }}</BAlert>
-    <pre v-else><code :class="getClass">{{ attributeValue }}</code></pre>
+    <pre v-else :class="getClass" class="m-0" v-html="attributeValue" />
 </template>

From 4e0cee79663c21591e24f859acc21e6e923522c4 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:07:52 -0400
Subject: [PATCH 17/39] Adjust invocation time wrapper

---
 .../components/Markdown/Sections/Elements/InvocationTime.vue    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Markdown/Sections/Elements/InvocationTime.vue b/client/src/components/Markdown/Sections/Elements/InvocationTime.vue
index 6e3f6ce612f1..1fb2b41a50c9 100644
--- a/client/src/components/Markdown/Sections/Elements/InvocationTime.vue
+++ b/client/src/components/Markdown/Sections/Elements/InvocationTime.vue
@@ -31,6 +31,6 @@ watch(
 
 <template>
     <div class="invocation-time">
-        <pre><code>{{ invocationTime }}</code></pre>
+        <pre class="m-0">{{ invocationTime }}</pre>
     </div>
 </template>

From 9053d573584e14b43ccb583f2e4b98e0da146f8c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:08:20 -0400
Subject: [PATCH 18/39] Remove debug statement from job parameters component

---
 .../src/components/Markdown/Sections/Elements/JobParameters.vue  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/src/components/Markdown/Sections/Elements/JobParameters.vue b/client/src/components/Markdown/Sections/Elements/JobParameters.vue
index 4dbabff3c63a..e98dca5a0a5c 100644
--- a/client/src/components/Markdown/Sections/Elements/JobParameters.vue
+++ b/client/src/components/Markdown/Sections/Elements/JobParameters.vue
@@ -72,7 +72,6 @@ watch(
             :implicit-collection-jobs-id="implicitCollectionJobsId"
             :select-job-options="selectJobOptions">
             <JobParameters class="job-parameters" :job-id="targetJobId" :param="param" :include-title="false" />
-            {{ targetJobId }}
         </JobSelection>
         <b-card-footer v-if="footer">
             {{ footer }}

From 5331d8e23e3b8e87564677df61335d253c7621ca Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:09:16 -0400
Subject: [PATCH 19/39] Parse labels to markdown wrapper

---
 .../Markdown/Sections/MarkdownGalaxy.vue      | 25 ++++++++++++-------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/client/src/components/Markdown/Sections/MarkdownGalaxy.vue b/client/src/components/Markdown/Sections/MarkdownGalaxy.vue
index 4300a32ec0bd..c340a8108141 100644
--- a/client/src/components/Markdown/Sections/MarkdownGalaxy.vue
+++ b/client/src/components/Markdown/Sections/MarkdownGalaxy.vue
@@ -36,6 +36,10 @@ const props = defineProps({
         type: String,
         required: true,
     },
+    labels: {
+        type: Array,
+        required: false,
+    },
 });
 
 const attributes = ref({});
@@ -51,6 +55,7 @@ const args = computed(() => {
     }
 });
 
+const hasLabels = computed(() => props.labels !== undefined);
 const invocation = computed(() => invocationId.value && getInvocationById(invocationId.value));
 const invocationId = computed(() => attributes.value.args?.invocation_id);
 const invocationLoading = computed(() => isLoadingInvocation(invocationId.value));
@@ -59,7 +64,6 @@ const isCollapsible = computed(() => args.value?.collapse !== undefined);
 const isLoading = computed(() => invocationLoading.value || workflowLoading.value);
 const isVisible = computed(() => !isCollapsible.value || toggle.value);
 const name = computed(() => attributes.value.name);
-const version = computed(() => config.version_major);
 const workflowId = computed(() => invocation.value && getStoredWorkflowIdByInstanceId(invocation.value.workflow_id));
 
 async function fetchWorkflow() {
@@ -99,10 +103,13 @@ watch(
 </script>
 
 <template>
-    <BAlert v-if="error" v-localize variant="danger" show>
+    <BAlert v-if="error" v-localize variant="danger" class="m-0" show>
         {{ error }}
     </BAlert>
-    <BAlert v-else-if="invocationLoadError" v-localize variant="danger" show>
+    <BAlert v-else-if="hasLabels && !invocationId" v-localize variant="info" class="m-0" show>
+        Data for rendering this <b>{{ name }}</b> is not yet available.
+    </BAlert>
+    <BAlert v-else-if="invocationLoadError" v-localize variant="danger" class="m-0" show>
         {{ invocationLoadError }}
     </BAlert>
     <LoadingSpan v-else-if="isLoading" />
@@ -111,12 +118,12 @@ watch(
             {{ args.collapse }}
         </BLink>
         <BCollapse :visible="isVisible">
-            <div v-if="name == 'generate_galaxy_version'" class="galaxy-version">
-                <pre><code>{{ version }}</code></pre>
-            </div>
-            <div v-else-if="name == 'generate_time'" class="galaxy-time">
-                <pre><code>{{ new Date().toUTCString() }}</code></pre>
-            </div>
+            <pre
+                v-if="name == 'generate_galaxy_version'"
+                class="galaxy-version m-0"><code>Galaxy Version {{ config.version_major }}</code></pre>
+            <pre
+                v-else-if="name == 'generate_time'"
+                class="galaxy-time m-0"><code>{{ new Date().toUTCString() }}</code></pre>
             <HistoryDatasetAsImage
                 v-else-if="name == 'history_dataset_as_image'"
                 :dataset-id="args.history_target_id || args.history_dataset_id"

From 901d5141024fcb4089205edf5dd8a8350a549bb5 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:10:37 -0400
Subject: [PATCH 20/39] Add markdown component section wrapper

---
 .../Markdown/Sections/SectionWrapper.vue      | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 client/src/components/Markdown/Sections/SectionWrapper.vue

diff --git a/client/src/components/Markdown/Sections/SectionWrapper.vue b/client/src/components/Markdown/Sections/SectionWrapper.vue
new file mode 100644
index 000000000000..9f864996a225
--- /dev/null
+++ b/client/src/components/Markdown/Sections/SectionWrapper.vue
@@ -0,0 +1,20 @@
+<template>
+    <MarkdownDefault v-if="name === 'markdown'" :content="content" />
+    <MarkdownGalaxy v-else-if="name === 'galaxy'" :content="content" :labels="labels" />
+    <b-alert v-else variant="danger" show> This cell type `{{ name }}` is not available. </b-alert>
+</template>
+
+<script setup lang="ts">
+import type { WorkflowLabel } from "@/components/Markdown/Editor/types";
+
+import MarkdownDefault from "../Sections/MarkdownDefault.vue";
+import MarkdownGalaxy from "../Sections/MarkdownGalaxy.vue";
+
+defineProps<{
+    content: string;
+    labels?: Array<WorkflowLabel>;
+    name: string;
+}>();
+
+defineEmits(["change"]);
+</script>

From 493a821e47df8d3d11817d1c0f93e3b8b5b03581 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:11:24 -0400
Subject: [PATCH 21/39] Modularize markdown invocation label parser

---
 .../Markdown/Utilities/parseInvocation.ts     | 65 +++++++++++--------
 1 file changed, 39 insertions(+), 26 deletions(-)

diff --git a/client/src/components/Markdown/Utilities/parseInvocation.ts b/client/src/components/Markdown/Utilities/parseInvocation.ts
index bf6474e7c383..97f7b2df1b15 100644
--- a/client/src/components/Markdown/Utilities/parseInvocation.ts
+++ b/client/src/components/Markdown/Utilities/parseInvocation.ts
@@ -1,10 +1,4 @@
-interface Invocation {
-    history_id: string;
-    inputs: Record<string, { label?: string; id?: string }>;
-    outputs: Record<string, { id?: string }>;
-    steps: { workflow_step_label?: string; job_id?: string; implicit_collection_jobs_id?: string }[];
-    workflow_id: string;
-}
+import type { Invocation } from "@/components/Markdown/Editor/types";
 
 interface ParsedAttributes {
     history_id?: string;
@@ -19,35 +13,54 @@ interface ParsedAttributes {
     workflow_id?: string;
 }
 
+export function parseInput(invocation: Invocation, name: string | undefined) {
+    if (name && invocation.inputs) {
+        const inputs = Object.values(invocation.inputs);
+        const input = inputs.find((i) => i.label && i.label === name);
+        return input?.id;
+    }
+}
+
+export function parseOutput(invocation: any, name: string | undefined) {
+    if (name && invocation.outputs) {
+        const output = invocation.outputs[name];
+        return output?.id;
+    }
+}
+
+export function parseStep(invocation: Invocation, name: string | undefined) {
+    if (name && invocation.steps) {
+        const step = invocation.steps.find((s) => s.workflow_step_label === name);
+        if (step) {
+            return {
+                job_id: step.job_id,
+                implicit_collection_jobs_id: step.implicit_collection_jobs_id,
+            };
+        }
+    }
+}
+
 export function parseInvocation(
     invocation: Invocation,
     workflowId: string,
     name: string,
     attributes: ParsedAttributes
 ): ParsedAttributes {
-    const result: ParsedAttributes = { ...attributes };
-    result.invocation = invocation;
+    const result: ParsedAttributes = { ...attributes, invocation };
+    const inputId = parseInput(invocation, result.input);
+    const outputId = parseOutput(invocation, result.output);
+    const step = parseStep(invocation, result.step);
     if (name === "history_link") {
         result.history_id = invocation.history_id;
     } else if (["workflow_display", "workflow_image", "workflow_license"].includes(name)) {
         result.workflow_id = workflowId;
-    } else if (result.input && invocation.inputs) {
-        const inputs = Object.values(invocation.inputs);
-        const input = inputs.find((i) => i.label && i.label === result?.input);
-        if (input) {
-            result.history_target_id = input.id;
-        }
-    } else if (result.output && invocation.outputs) {
-        const output = invocation.outputs[result.output];
-        if (output) {
-            result.history_target_id = output.id;
-        }
-    } else if (result.step && invocation.steps) {
-        const step = invocation.steps.find((s) => s.workflow_step_label === result.step);
-        if (step) {
-            result.job_id = step.job_id;
-            result.implicit_collection_jobs_id = step.implicit_collection_jobs_id;
-        }
+    } else if (inputId) {
+        result.history_target_id = inputId;
+    } else if (outputId) {
+        result.history_target_id = outputId;
+    } else if (step) {
+        result.job_id = step.job_id;
+        result.implicit_collection_jobs_id = step.implicit_collection_jobs_id;
     }
     return result;
 }

From 24fc22a7b688327fc178fd4f4c6337152801754e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:16:34 -0400
Subject: [PATCH 22/39] Move labels parser to modules, remove unused prop from
 selection dialog

---
 client/src/components/Markdown/labels.ts      | 48 -------------------
 .../SelectionDialog/HistoryDatasetPicker.vue  |  1 -
 .../src/components/Workflow/Editor/Index.vue  |  6 ++-
 .../Workflow/Editor/modules/labels.ts         | 44 +++++++++++++++++
 4 files changed, 49 insertions(+), 50 deletions(-)
 delete mode 100644 client/src/components/Markdown/labels.ts
 create mode 100644 client/src/components/Workflow/Editor/modules/labels.ts

diff --git a/client/src/components/Markdown/labels.ts b/client/src/components/Markdown/labels.ts
deleted file mode 100644
index 10048e834573..000000000000
--- a/client/src/components/Markdown/labels.ts
+++ /dev/null
@@ -1,48 +0,0 @@
-// abstractions for dealing with workflows labels and
-// connecting them to the Markdown editor
-
-type WorkflowLabelKind = "input" | "output" | "step";
-
-export interface WorkflowLabel {
-    label: string;
-    type: WorkflowLabelKind;
-}
-
-interface StepOutput {
-    label?: string;
-}
-
-interface Step {
-    label?: string;
-    type: string;
-    workflow_outputs: StepOutput[];
-}
-
-export type WorkflowLabels = WorkflowLabel[];
-
-export function fromSteps(steps?: Step[]): WorkflowLabels {
-    const labels: WorkflowLabels = [];
-
-    if (!steps) {
-        return labels;
-    }
-
-    Object.values(steps).forEach((step) => {
-        const stepType = step.type;
-        if (step.label) {
-            const isInput = ["data_input", "data_collection_input", "parameter_input"].indexOf(stepType) >= 0;
-            if (isInput) {
-                labels.push({ type: "input", label: step.label });
-            } else {
-                labels.push({ type: "step", label: step.label });
-            }
-        }
-        step.workflow_outputs.forEach((workflowOutput) => {
-            if (workflowOutput.label) {
-                labels.push({ type: "output", label: workflowOutput.label });
-            }
-        });
-    });
-
-    return labels;
-}
diff --git a/client/src/components/SelectionDialog/HistoryDatasetPicker.vue b/client/src/components/SelectionDialog/HistoryDatasetPicker.vue
index 7958c0a661ef..bd2eb978362a 100644
--- a/client/src/components/SelectionDialog/HistoryDatasetPicker.vue
+++ b/client/src/components/SelectionDialog/HistoryDatasetPicker.vue
@@ -19,7 +19,6 @@ interface HistoryRecord extends SelectionItem {
 }
 
 interface Props {
-    folderId: string;
     title?: string;
     actionButtonText?: string;
 }
diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index e7855ba29e26..500790acd4e7 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -111,7 +111,7 @@
                 :markdown-text="report.markdown"
                 mode="report"
                 :title="'Workflow Report: ' + name"
-                :steps="steps"
+                :labels="getLabels"
                 @insert="insertMarkdown"
                 @update="onReportUpdate">
                 <template v-slot:buttons>
@@ -224,6 +224,7 @@ import { CopyIntoWorkflowAction, SetValueActionHandler } from "./Actions/workflo
 import { defaultPosition } from "./composables/useDefaultStepPosition";
 import { useActivityLogic, useSpecialWorkflowActivities, workflowEditorActivities } from "./modules/activities";
 import { getWorkflowInputs } from "./modules/inputs";
+import { fromSteps } from "./modules/labels";
 import { fromSimple } from "./modules/model";
 import { getModule, getVersions, loadWorkflow, saveWorkflow } from "./modules/services";
 import { getStateUpgradeMessages } from "./modules/utilities";
@@ -510,6 +511,8 @@ export default {
             }))
         );
 
+        const getLabels = computed(() => fromSteps(steps.value));
+
         const saveWorkflowTitle = computed(() =>
             hasInvalidConnections.value
                 ? "Workflow has invalid connections, review and remove invalid connections"
@@ -536,6 +539,7 @@ export default {
             setName,
             report,
             license,
+            getLabels,
             setLicense,
             creator,
             setCreator,
diff --git a/client/src/components/Workflow/Editor/modules/labels.ts b/client/src/components/Workflow/Editor/modules/labels.ts
new file mode 100644
index 000000000000..5c4cdb4d36fb
--- /dev/null
+++ b/client/src/components/Workflow/Editor/modules/labels.ts
@@ -0,0 +1,44 @@
+// abstractions for dealing with workflows labels and
+// connecting them to the Markdown editor
+
+type WorkflowLabelKind = "input" | "output" | "step";
+
+export interface WorkflowLabel {
+    label: string;
+    type: WorkflowLabelKind;
+}
+
+interface StepOutput {
+    label?: string;
+}
+
+interface Step {
+    label?: string;
+    type: string;
+    workflow_outputs: StepOutput[];
+}
+
+export type WorkflowLabels = WorkflowLabel[];
+
+export function fromSteps(steps?: Step[]): WorkflowLabels {
+    const labels: WorkflowLabels = [];
+    if (steps) {
+        Object.values(steps).forEach((step) => {
+            const stepType = step.type;
+            if (step.label) {
+                const isInput = ["data_input", "data_collection_input", "parameter_input"].indexOf(stepType) >= 0;
+                if (isInput) {
+                    labels.push({ type: "input", label: step.label });
+                } else {
+                    labels.push({ type: "step", label: step.label });
+                }
+            }
+            step.workflow_outputs.forEach((workflowOutput) => {
+                if (workflowOutput.label) {
+                    labels.push({ type: "output", label: workflowOutput.label });
+                }
+            });
+        });
+    }
+    return labels;
+}

From 3125e5db7378b29001330b21128860a84448c31a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:17:36 -0400
Subject: [PATCH 23/39] Remove unused styles

---
 client/src/style/scss/base.scss     | 1 -
 client/src/style/scss/markdown.scss | 6 ------
 2 files changed, 7 deletions(-)
 delete mode 100644 client/src/style/scss/markdown.scss

diff --git a/client/src/style/scss/base.scss b/client/src/style/scss/base.scss
index 748868bf1b34..c3e1e0d98127 100644
--- a/client/src/style/scss/base.scss
+++ b/client/src/style/scss/base.scss
@@ -35,7 +35,6 @@ $fa-font-path: "../../../node_modules/@fortawesome/fontawesome-free/webfonts/";
 @import "flex.scss";
 @import "charts.scss";
 @import "message.scss";
-@import "markdown.scss";
 @import "multiselect.scss";
 @import "icon-btn.scss";
 @import "peek-columns.scss";
diff --git a/client/src/style/scss/markdown.scss b/client/src/style/scss/markdown.scss
deleted file mode 100644
index 62292052aee4..000000000000
--- a/client/src/style/scss/markdown.scss
+++ /dev/null
@@ -1,6 +0,0 @@
-.markdown-wrapper {
-    @extend .px-4;
-    .markdown-components {
-        @extend .py-2;
-    }
-}

From f8edc63b154b1b63b58175950421c2d6f0e53a3e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:25:12 -0400
Subject: [PATCH 24/39] Update and correct visualization xmls embeddable flag
 setting

---
 .../plugins/visualizations/PCA_3Dplot/config/PCA_3Dplot.xml   | 2 +-
 .../visualizations/annotate_image/config/annotate_image.xml   | 2 +-
 config/plugins/visualizations/cytoscape/config/cytoscape.xml  | 4 ++--
 config/plugins/visualizations/editor/config/editor.xml        | 2 +-
 config/plugins/visualizations/example/config/example.xml      | 2 +-
 .../fits_graph_viewer/config/fits_graph_viewer.xml            | 2 +-
 .../fits_image_viewer/config/fits_image_viewer.xml            | 2 +-
 config/plugins/visualizations/h5web/config/h5web.xml          | 2 +-
 config/plugins/visualizations/heatmap/config/heatmap.xml      | 4 ++--
 config/plugins/visualizations/ngl/config/ngl.xml              | 4 ++--
 .../plugins/visualizations/openlayers/config/openlayers.xml   | 4 ++--
 .../plugins/visualizations/phylocanvas/config/phylocanvas.xml | 4 ++--
 config/plugins/visualizations/plotly/config/plotly.xml        | 4 ++--
 .../plugins/visualizations/plotly_box/config/plotly_box.xml   | 2 +-
 .../plotly_histogram/config/plotly_histogram.xml              | 2 +-
 .../plugins/visualizations/tiffviewer/config/tiffviewer.xml   | 2 +-
 config/plugins/visualizations/trackster/config/trackster.xml  | 2 +-
 config/plugins/visualizations/ts_visjs/config/ts_visjs.xml    | 2 +-
 config/plugins/visualizations/venn/config/venn.xml            | 4 ++--
 config/plugins/visualizations/vizarr/config/vizarr.xml        | 2 +-
 20 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/config/plugins/visualizations/PCA_3Dplot/config/PCA_3Dplot.xml b/config/plugins/visualizations/PCA_3Dplot/config/PCA_3Dplot.xml
index 933e57f03238..fb5dae15fe42 100644
--- a/config/plugins/visualizations/PCA_3Dplot/config/PCA_3Dplot.xml
+++ b/config/plugins/visualizations/PCA_3Dplot/config/PCA_3Dplot.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="PCA 3D plot" embeddable="false">
+<visualization name="PCA 3D plot">
     <description>Plotly-based 3D PCA visualization plugin.</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/annotate_image/config/annotate_image.xml b/config/plugins/visualizations/annotate_image/config/annotate_image.xml
index b5bcfe76a7ab..5d9f82c73ed3 100644
--- a/config/plugins/visualizations/annotate_image/config/annotate_image.xml
+++ b/config/plugins/visualizations/annotate_image/config/annotate_image.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Image annotator" embeddable="false">
+<visualization name="Image annotator">
     <description>An image annotater built using PaperJS at https://github.com/paperjs/paper.js.</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/cytoscape/config/cytoscape.xml b/config/plugins/visualizations/cytoscape/config/cytoscape.xml
index 79de685142fa..39b9933de02f 100644
--- a/config/plugins/visualizations/cytoscape/config/cytoscape.xml
+++ b/config/plugins/visualizations/cytoscape/config/cytoscape.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Cytoscape">
+<visualization name="Cytoscape" embeddable="true">
     <description>A viewer based on graph theory/ network library for analysis and visualisation hosted at http://js.cytoscape.org.</description>
     <data_sources>
         <data_source>
@@ -14,7 +14,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.3" package="@galaxyproject/cytoscape"/>
+        <requirement type="npm" version="0.0.7" package="@galaxyproject/cytoscape"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
diff --git a/config/plugins/visualizations/editor/config/editor.xml b/config/plugins/visualizations/editor/config/editor.xml
index 8038f9fd2e88..b6a50718b687 100644
--- a/config/plugins/visualizations/editor/config/editor.xml
+++ b/config/plugins/visualizations/editor/config/editor.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Editor" embeddable="false">
+<visualization name="Editor">
     <description>Manually edit text</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/example/config/example.xml b/config/plugins/visualizations/example/config/example.xml
index 7ebf2f643a12..7c052c1ee539 100644
--- a/config/plugins/visualizations/example/config/example.xml
+++ b/config/plugins/visualizations/example/config/example.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Minimal Example" embeddable="false">
+<visualization name="Minimal Example">
     <description>Welcome to the Minimal JS-Based Example Plugin.</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/fits_graph_viewer/config/fits_graph_viewer.xml b/config/plugins/visualizations/fits_graph_viewer/config/fits_graph_viewer.xml
index 4d67c16da013..a8c455130dfe 100644
--- a/config/plugins/visualizations/fits_graph_viewer/config/fits_graph_viewer.xml
+++ b/config/plugins/visualizations/fits_graph_viewer/config/fits_graph_viewer.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="FITS Graph viewer" embeddable="false">
+<visualization name="FITS Graph viewer">
     <description>Basic plugin for fits file table visualization</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/fits_image_viewer/config/fits_image_viewer.xml b/config/plugins/visualizations/fits_image_viewer/config/fits_image_viewer.xml
index 9affd764bb58..90bdbc75e317 100644
--- a/config/plugins/visualizations/fits_image_viewer/config/fits_image_viewer.xml
+++ b/config/plugins/visualizations/fits_image_viewer/config/fits_image_viewer.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="FITS Aladin viewer" embeddable="false">
+<visualization name="FITS Aladin viewer">
     <description>Basic plugin for fits file visualization with aladin-lite viewer</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/h5web/config/h5web.xml b/config/plugins/visualizations/h5web/config/h5web.xml
index 48a767d8bf2a..a06faaabe49c 100644
--- a/config/plugins/visualizations/h5web/config/h5web.xml
+++ b/config/plugins/visualizations/h5web/config/h5web.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="H5Web" embeddable="false">
+<visualization name="H5Web" embeddable="true">
     <description>HDF5 data visualization and exploration</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/heatmap/config/heatmap.xml b/config/plugins/visualizations/heatmap/config/heatmap.xml
index e69a5ffb1b58..398557e11a40 100644
--- a/config/plugins/visualizations/heatmap/config/heatmap.xml
+++ b/config/plugins/visualizations/heatmap/config/heatmap.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Heatmap" embeddable="false">
+<visualization name="Heatmap" embeddable="true">
     <description>Renders a heatmap from matrix data provided in 3-column format (x, y, observation).</description>
     <requirements>
-        <requirement type="npm" version="0.0.8" package="@galaxyproject/heatmap"/>
+        <requirement type="npm" version="0.0.12" package="@galaxyproject/heatmap"/>
     </requirements>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/ngl/config/ngl.xml b/config/plugins/visualizations/ngl/config/ngl.xml
index 18607ed2c427..4ef14bb4d556 100644
--- a/config/plugins/visualizations/ngl/config/ngl.xml
+++ b/config/plugins/visualizations/ngl/config/ngl.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="NGL Viewer">
+<visualization name="NGL Viewer" embeddable="true">
     <description>NGL Viewer is a WebGL based molecular visualization hosted at http://arose.github.io/ngl/.</description>
     <data_sources>
         <data_source>
@@ -13,7 +13,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.11" package="@galaxyproject/ngl"/>
+        <requirement type="npm" version="0.0.29" package="@galaxyproject/ngl"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
diff --git a/config/plugins/visualizations/openlayers/config/openlayers.xml b/config/plugins/visualizations/openlayers/config/openlayers.xml
index 2fb0ae6ca428..e54f99b7dd44 100644
--- a/config/plugins/visualizations/openlayers/config/openlayers.xml
+++ b/config/plugins/visualizations/openlayers/config/openlayers.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="OpenLayers map">
+<visualization name="OpenLayers map" embeddable="true">
     <description>A viewer to show maps using OpenLayers from https://openlayers.org/</description>
     <data_sources>
         <data_source>
@@ -14,7 +14,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.0" package="@galaxyproject/openlayers"/>
+        <requirement type="npm" version="0.0.4" package="@galaxyproject/openlayers"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
diff --git a/config/plugins/visualizations/phylocanvas/config/phylocanvas.xml b/config/plugins/visualizations/phylocanvas/config/phylocanvas.xml
index f1346e14059c..ff84ecfcfb45 100644
--- a/config/plugins/visualizations/phylocanvas/config/phylocanvas.xml
+++ b/config/plugins/visualizations/phylocanvas/config/phylocanvas.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Phylogenetic Tree Visualization">
+<visualization name="Phylogenetic Tree Visualization" embeddable="true">
     <description>A performant, reusable, and extensible tree visualisation from the Centre for Genomic Pathogen Surveillance at https://www.phylocanvas.gl</description>
     <data_sources>
         <data_source>
@@ -14,7 +14,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.3" package="@galaxyproject/phylocanvas"/>
+        <requirement type="npm" version="0.0.7" package="@galaxyproject/phylocanvas"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
diff --git a/config/plugins/visualizations/plotly/config/plotly.xml b/config/plugins/visualizations/plotly/config/plotly.xml
index d361cd5cdf47..82cb52b592e2 100644
--- a/config/plugins/visualizations/plotly/config/plotly.xml
+++ b/config/plugins/visualizations/plotly/config/plotly.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar, Line and Scatter (plotly.js)">
+<visualization name="Bar, Line and Scatter (plotly.js)" embeddable="true">
     <description>Basic Diagrams from Plotly Graphing Library.</description>
     <data_sources>
         <data_source>
@@ -14,7 +14,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.0" package="@galaxyproject/plotly"/>
+        <requirement type="npm" version="0.0.11" package="@galaxyproject/plotly"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
diff --git a/config/plugins/visualizations/plotly_box/config/plotly_box.xml b/config/plugins/visualizations/plotly_box/config/plotly_box.xml
index 57d8a2d32227..dbab0290472f 100644
--- a/config/plugins/visualizations/plotly_box/config/plotly_box.xml
+++ b/config/plugins/visualizations/plotly_box/config/plotly_box.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Box Plot (plotly.js)">
+<visualization name="Box Plot (plotly.js)" embeddable="true">
     <description>Box Plot from Plotly Graphing Library.</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/plotly_histogram/config/plotly_histogram.xml b/config/plugins/visualizations/plotly_histogram/config/plotly_histogram.xml
index ce16b868b546..35780e2faebd 100644
--- a/config/plugins/visualizations/plotly_histogram/config/plotly_histogram.xml
+++ b/config/plugins/visualizations/plotly_histogram/config/plotly_histogram.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Histogram (plotly.js)">
+<visualization name="Histogram (plotly.js)" embeddable="true">
     <description>Histogram from Plotly Graphing Library.</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml b/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml
index 84d14366f62c..4d8f0bed2818 100644
--- a/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml
+++ b/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Tiff Viewer">
+<visualization name="Tiff Viewer" embeddable="true">
     <description>Tiff Image Viewer</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/trackster/config/trackster.xml b/config/plugins/visualizations/trackster/config/trackster.xml
index 585ce3f73be7..ac0cb8a41b9a 100644
--- a/config/plugins/visualizations/trackster/config/trackster.xml
+++ b/config/plugins/visualizations/trackster/config/trackster.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name=" Trackster" embeddable="false">
+<visualization name=" Trackster">
     <description>Fast, interactive visualization for large, NGS/HTS datasets using only a web browser.</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/ts_visjs/config/ts_visjs.xml b/config/plugins/visualizations/ts_visjs/config/ts_visjs.xml
index 697ee498551b..d4d775e68908 100644
--- a/config/plugins/visualizations/ts_visjs/config/ts_visjs.xml
+++ b/config/plugins/visualizations/ts_visjs/config/ts_visjs.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Transition system visualization" embeddable="false">
+<visualization name="Transition system visualization">
     <description>- visjs-based interactive visualization of transition system in graph form.</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/venn/config/venn.xml b/config/plugins/visualizations/venn/config/venn.xml
index 1e9140135ea9..d8b7d48561b2 100644
--- a/config/plugins/visualizations/venn/config/venn.xml
+++ b/config/plugins/visualizations/venn/config/venn.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Venn Diagram (Benfred)">
+<visualization name="Venn Diagram (Benfred)" embeddable="true">
     <description>A javascript library for laying out area proportional venn and euler diagrams hosted at https://github.com/benfred/venn.js.</description>
     <data_sources>
         <data_source>
@@ -14,7 +14,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.3" package="@galaxyproject/venn"/>
+        <requirement type="npm" version="0.0.7" package="@galaxyproject/venn"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <tracks>
diff --git a/config/plugins/visualizations/vizarr/config/vizarr.xml b/config/plugins/visualizations/vizarr/config/vizarr.xml
index a6bc313c20de..5c4196460108 100644
--- a/config/plugins/visualizations/vizarr/config/vizarr.xml
+++ b/config/plugins/visualizations/vizarr/config/vizarr.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Vizarr Viewer">
+<visualization name="Vizarr Viewer" embeddable="true">
     <description>Basic visualization for Zarr-based images like OME-Zarr</description>
     <requirements>
         <requirement type="npm" version="0.1.6" package="@galaxyproject/vizarr"/>

From 37961b4044a15a1ceca382c300c5b59bb8b7ecf0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:26:26 -0400
Subject: [PATCH 25/39] Sort markdown arguments alphabetically

---
 lib/galaxy/managers/markdown_parse.py | 63 +++++++++++++--------------
 1 file changed, 31 insertions(+), 32 deletions(-)

diff --git a/lib/galaxy/managers/markdown_parse.py b/lib/galaxy/managers/markdown_parse.py
index 1cdcb2b1a090..f59fa26d2443 100644
--- a/lib/galaxy/managers/markdown_parse.py
+++ b/lib/galaxy/managers/markdown_parse.py
@@ -27,49 +27,48 @@ class DynamicArguments:
 DYNAMIC_ARGUMENTS = DynamicArguments()
 SHARED_ARGUMENTS: List[str] = ["collapse"]
 VALID_ARGUMENTS: Dict[str, Union[List[str], DynamicArguments]] = {
-    "history_link": ["history_id", "invocation_id"],
-    "history_dataset_display": ["invocation_id", "input", "output", "history_dataset_id"],
-    "history_dataset_embedded": ["invocation_id", "input", "output", "history_dataset_id"],
-    "history_dataset_as_image": ["invocation_id", "input", "output", "history_dataset_id", "path"],
+    "generate_galaxy_version": [],
+    "generate_time": [],
+    "history_dataset_as_image": ["history_dataset_id", "input", "invocation_id", "output", "path"],
     "history_dataset_as_table": [
-        "invocation_id",
+        "compact",
+        "footer",
+        "history_dataset_id",
         "input",
+        "invocation_id",
         "output",
-        "history_dataset_id",
         "path",
-        "title",
-        "footer",
         "show_column_headers",
-        "compact",
+        "title",
     ],
-    "history_dataset_peek": ["invocation_id", "input", "output", "history_dataset_id"],
-    "history_dataset_info": ["invocation_id", "input", "output", "history_dataset_id"],
-    "history_dataset_link": ["invocation_id", "input", "output", "history_dataset_id", "path", "label"],
-    "history_dataset_index": ["invocation_id", "input", "output", "history_dataset_id", "path"],
-    "history_dataset_name": ["invocation_id", "input", "output", "history_dataset_id"],
-    "history_dataset_type": ["invocation_id", "input", "output", "history_dataset_id"],
-    "history_dataset_collection_display": ["invocation_id", "input", "output", "history_dataset_collection_id"],
-    "workflow_display": ["invocation_id", "workflow_id", "workflow_checkpoint"],
-    "workflow_license": ["invocation_id", "workflow_id"],
-    "workflow_image": ["invocation_id", "workflow_id", "size", "workflow_checkpoint"],
-    "job_metrics": ["invocation_id", "step", "job_id", "implicit_collection_jobs_id"],
-    "job_parameters": ["invocation_id", "step", "job_id", "implicit_collection_jobs_id"],
-    "tool_stderr": ["invocation_id", "step", "job_id", "implicit_collection_jobs_id"],
-    "tool_stdout": ["invocation_id", "step", "job_id", "implicit_collection_jobs_id"],
-    "generate_galaxy_version": [],
-    "generate_time": [],
+    "history_dataset_collection_display": ["history_dataset_collection_id", "input", "invocation_id", "output"],
+    "history_dataset_display": ["history_dataset_id", "input", "invocation_id", "output"],
+    "history_dataset_embedded": ["history_dataset_id", "input", "invocation_id", "output"],
+    "history_dataset_index": ["history_dataset_id", "input", "invocation_id", "output", "path"],
+    "history_dataset_info": ["history_dataset_id", "input", "invocation_id", "output"],
+    "history_dataset_link": ["history_dataset_id", "input", "invocation_id", "output", "path", "label"],
+    "history_dataset_name": ["history_dataset_id", "input", "invocation_id", "output"],
+    "history_dataset_peek": ["history_dataset_id", "input", "invocation_id", "output"],
+    "history_dataset_type": ["history_dataset_id", "input", "invocation_id", "output"],
+    "history_link": ["history_id", "invocation_id"],
     "instance_access_link": [],
-    "instance_resources_link": [],
+    "instance_citation_link": [],
     "instance_help_link": [],
+    "instance_organization_link": [],
+    "instance_resources_link": [],
     "instance_support_link": [],
-    "instance_citation_link": [],
     "instance_terms_link": [],
-    "instance_organization_link": [],
-    "visualization": DYNAMIC_ARGUMENTS,
-    # Invocation Flavored Markdown
-    "invocation_time": ["invocation_id"],
-    "invocation_outputs": ["invocation_id"],
     "invocation_inputs": ["invocation_id"],
+    "invocation_outputs": ["invocation_id"],
+    "invocation_time": ["invocation_id"],
+    "job_metrics": ["implicit_collection_jobs_id", "invocation_id", "job_id", "step"],
+    "job_parameters": ["footer", "implicit_collection_jobs_id", "invocation_id", "job_id", "step"],
+    "tool_stderr": ["implicit_collection_jobs_id", "invocation_id", "job_id", "step"],
+    "tool_stdout": ["implicit_collection_jobs_id", "invocation_id", "job_id", "step"],
+    "visualization": DYNAMIC_ARGUMENTS,
+    "workflow_display": ["invocation_id", "workflow_checkpoint", "workflow_id"],
+    "workflow_image": ["invocation_id", "workflow_checkpoint", "workflow_id", "size"],
+    "workflow_license": ["invocation_id", "workflow_id"],
 }
 GALAXY_FLAVORED_MARKDOWN_CONTAINERS = list(VALID_ARGUMENTS.keys())
 GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>{})".format("|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS))

From 611dcfcd9a030b7495c65b903fd7b088073422c0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:27:42 -0400
Subject: [PATCH 26/39] Switch embeddable default in visualization xmls to
 false

---
 lib/galaxy/visualization/plugins/config_parser.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/visualization/plugins/config_parser.py b/lib/galaxy/visualization/plugins/config_parser.py
index 09ec7acc6a99..3f9330059dc9 100644
--- a/lib/galaxy/visualization/plugins/config_parser.py
+++ b/lib/galaxy/visualization/plugins/config_parser.py
@@ -75,12 +75,12 @@ def parse_visualization(self, xml_tree):
             log.info("Visualizations plugin disabled: %s. Skipping...", returned["name"])
             return None
 
-        # record the embeddable flag - defaults to true
-        returned["embeddable"] = True
+        # record the embeddable flag - defaults to False
+        returned["embeddable"] = False
         if "embeddable" in xml_tree.attrib:
             returned["embeddable"] = asbool(xml_tree.attrib.get("embeddable"))
 
-        # record the visible flag - defaults to true
+        # record the visible flag - defaults to False
         returned["hidden"] = False
         if "hidden" in xml_tree.attrib:
             returned["hidden"] = asbool(xml_tree.attrib.get("hidden"))

From 74c3cd5275e56b3753050d24400ffe6e1dd5910d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:28:42 -0400
Subject: [PATCH 27/39] Hide textarea field showing unstructured markdown text
 when moving from reports to pages

---
 lib/galaxy/webapps/galaxy/controllers/page.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index ec4ff9ca9ca7..ded11eaa191a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -52,7 +52,6 @@ def create(self, trans, payload=None, **kwd):
             title = ""
             slug = ""
             content = ""
-            content_hide = True
             if "invocation_id" in kwd:
                 invocation_id = kwd.get("invocation_id")
                 form_title = f"{form_title} from Invocation Report"
@@ -62,7 +61,6 @@ def create(self, trans, payload=None, **kwd):
                 )
                 title = invocation_report.get("title")
                 content = invocation_report.get("markdown")
-                content_hide = False
             return {
                 "title": form_title,
                 "inputs": [
@@ -93,7 +91,7 @@ def create(self, trans, payload=None, **kwd):
                         "label": "Content",
                         "area": True,
                         "value": content,
-                        "hidden": content_hide,
+                        "hidden": True,
                     },
                 ],
             }

From 72763bd635dcb1aef17ae5deff9e531c246acd87 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:53:20 -0400
Subject: [PATCH 28/39] Adjust markdown selector

---
 client/src/components/Markdown/MarkdownSelector.vue | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Markdown/MarkdownSelector.vue b/client/src/components/Markdown/MarkdownSelector.vue
index 6897962d3e19..72693aade376 100644
--- a/client/src/components/Markdown/MarkdownSelector.vue
+++ b/client/src/components/Markdown/MarkdownSelector.vue
@@ -2,17 +2,16 @@
 import { BModal } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import { type WorkflowLabel } from "./labels";
+import { type WorkflowLabel } from "./Editor/types";
 
 import LabelSelector from "./LabelSelector.vue";
 
-interface MarkdownSelectorProps {
+const props = defineProps<{
+    argumentName: string;
     labelTitle?: string;
-    labels: WorkflowLabel[];
-    argumentName?: string;
-}
+    labels: Array<WorkflowLabel>;
+}>();
 
-const props = defineProps<MarkdownSelectorProps>();
 const selectedValue = ref<WorkflowLabel | undefined>(undefined);
 const modalShow = ref(true);
 

From 1a25f02deeec567e2017a2f3162b75ffba5fb933 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 11:55:18 -0400
Subject: [PATCH 29/39] Adjust markdown toolbox labels import

---
 client/src/components/Markdown/MarkdownToolBox.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Markdown/MarkdownToolBox.vue b/client/src/components/Markdown/MarkdownToolBox.vue
index 336c5951dce1..7e770ba3f071 100644
--- a/client/src/components/Markdown/MarkdownToolBox.vue
+++ b/client/src/components/Markdown/MarkdownToolBox.vue
@@ -37,7 +37,7 @@ import { getAppRoot } from "onload/loadConfig";
 import Vue from "vue";
 
 import { directiveEntry } from "./directives.ts";
-import { fromSteps } from "./labels.ts";
+import { fromSteps } from "@/components/Workflow/Editor/modules/labels";
 import MarkdownDialog from "./MarkdownDialog";
 
 import ActivityPanel from "@/components/Panels/ActivityPanel.vue";

From 25cb212cde535a386c887d789c6225efbcc463cb Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 12:03:27 -0400
Subject: [PATCH 30/39] Fix import order

---
 client/src/components/Markdown/MarkdownToolBox.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Markdown/MarkdownToolBox.vue b/client/src/components/Markdown/MarkdownToolBox.vue
index 7e770ba3f071..c4ab527a1918 100644
--- a/client/src/components/Markdown/MarkdownToolBox.vue
+++ b/client/src/components/Markdown/MarkdownToolBox.vue
@@ -36,8 +36,9 @@ import ToolSection from "components/Panels/Common/ToolSection";
 import { getAppRoot } from "onload/loadConfig";
 import Vue from "vue";
 
-import { directiveEntry } from "./directives.ts";
 import { fromSteps } from "@/components/Workflow/Editor/modules/labels";
+
+import { directiveEntry } from "./directives.ts";
 import MarkdownDialog from "./MarkdownDialog";
 
 import ActivityPanel from "@/components/Panels/ActivityPanel.vue";

From 741bc927f5559d4368e4419da18f1d60dda2df7e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 12:20:15 -0400
Subject: [PATCH 31/39] Remove z-index adjustment due to potential conflicts

---
 client/src/components/Markdown/Markdown.vue | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index 43cc27598104..6872c032a055 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -82,7 +82,7 @@ onMounted(() => {
     <div class="markdown-wrapper">
         <LoadingSpan v-if="loading" />
         <div v-else class="d-flex flex-column">
-            <div class="markdown-wrapper-header d-flex flex-column sticky-top bg-white">
+            <div class="d-flex flex-column sticky-top bg-white">
                 <div class="d-flex">
                     <Heading v-localize h1 separator inline size="md" class="flex-grow-1">
                         {{ markdownConfig.title || markdownConfig.model_class }}
@@ -129,9 +129,3 @@ onMounted(() => {
         </div>
     </div>
 </template>
-
-<style scoped>
-.markdown-wrapper-header {
-    z-index: 1001;
-}
-</style>

From b792aa2f5b197b5231e99b6c64c1aa88269bb27d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 12:40:12 -0400
Subject: [PATCH 32/39] Adjust markdown galaxy wrapper test

---
 .../Markdown/Sections/MarkdownGalaxy.test.js           |  8 ++++----
 .../components/Markdown/Sections/MarkdownGalaxy.vue    | 10 ++++------
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/client/src/components/Markdown/Sections/MarkdownGalaxy.test.js b/client/src/components/Markdown/Sections/MarkdownGalaxy.test.js
index cbbbf681d9bd..b8be05d5da9c 100644
--- a/client/src/components/Markdown/Sections/MarkdownGalaxy.test.js
+++ b/client/src/components/Markdown/Sections/MarkdownGalaxy.test.js
@@ -58,12 +58,12 @@ function mountComponent(propsData = {}, apiMap = {}) {
 describe("MarkdownContainer", () => {
     it("Renders version", async () => {
         const version = "test_version";
-        const wrapper = await mountComponent({
+        const wrapper = mountComponent({
             content: "generate_galaxy_version()",
         });
         const versionEl = wrapper.find(".galaxy-version");
         expect(versionEl.exists()).toBe(true);
-        expect(versionEl.find("code").text()).toBe(version);
+        expect(versionEl.text()).toContain(version);
 
         // test collapsing
         const nolink = wrapper.find("a");
@@ -81,12 +81,12 @@ describe("MarkdownContainer", () => {
     it("Renders time stamp", async () => {
         const time = new Date();
         jest.useFakeTimers().setSystemTime(time);
-        const wrapper = await mountComponent({
+        const wrapper = mountComponent({
             content: "generate_time()",
         });
         const version = wrapper.find(".galaxy-time");
         expect(version.exists()).toBe(true);
-        expect(version.find("code").text()).toBe(time.toUTCString());
+        expect(version.text()).toBe(time.toUTCString());
     });
 
     it("Renders history link", async () => {
diff --git a/client/src/components/Markdown/Sections/MarkdownGalaxy.vue b/client/src/components/Markdown/Sections/MarkdownGalaxy.vue
index c340a8108141..eca6be18d66b 100644
--- a/client/src/components/Markdown/Sections/MarkdownGalaxy.vue
+++ b/client/src/components/Markdown/Sections/MarkdownGalaxy.vue
@@ -118,12 +118,10 @@ watch(
             {{ args.collapse }}
         </BLink>
         <BCollapse :visible="isVisible">
-            <pre
-                v-if="name == 'generate_galaxy_version'"
-                class="galaxy-version m-0"><code>Galaxy Version {{ config.version_major }}</code></pre>
-            <pre
-                v-else-if="name == 'generate_time'"
-                class="galaxy-time m-0"><code>{{ new Date().toUTCString() }}</code></pre>
+            <pre v-if="name == 'generate_galaxy_version'" class="galaxy-version m-0">
+Galaxy Version {{ config.version_major }}</pre
+            >
+            <pre v-else-if="name == 'generate_time'" class="galaxy-time m-0">{{ new Date().toUTCString() }}</pre>
             <HistoryDatasetAsImage
                 v-else-if="name == 'history_dataset_as_image'"
                 :dataset-id="args.history_target_id || args.history_dataset_id"

From febaee6a449f6e61eeb10f9d9b9ed0d1799143f0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 16:37:41 -0400
Subject: [PATCH 33/39] Pass steps to markdown toolbox for now

---
 .../src/components/Markdown/MarkdownEditor.vue  | 17 +++++++----------
 client/src/components/Workflow/Editor/Index.vue |  1 +
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/client/src/components/Markdown/MarkdownEditor.vue b/client/src/components/Markdown/MarkdownEditor.vue
index d33fa1d2e163..55c66553a3e5 100644
--- a/client/src/components/Markdown/MarkdownEditor.vue
+++ b/client/src/components/Markdown/MarkdownEditor.vue
@@ -8,7 +8,7 @@
                     </div>
                     <div>
                         <b-form-radio-group
-                            v-if="!steps || steps.length === 0"
+                            v-if="!labels || labels.length === 0"
                             v-model="editor"
                             v-b-tooltip.hover.bottom
                             button-variant="outline-primary"
@@ -31,13 +31,7 @@
                     :steps="steps"
                     :mode="mode"
                     @update="$emit('update', $event)" />
-                <CellEditor
-                    v-else
-                    :title="title"
-                    :markdown-text="markdownText"
-                    :steps="steps"
-                    :mode="mode"
-                    @update="$emit('update', $event)" />
+                <CellEditor v-else :markdown-text="markdownText" :labels="labels" @update="$emit('update', $event)" />
             </div>
         </div>
         <b-modal v-model="showHelpModal" hide-footer>
@@ -56,6 +50,8 @@ import { faQuestion } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { ref } from "vue";
 
+import type { WorkflowLabel } from "./Editor/types";
+
 import CellEditor from "./Editor/CellEditor.vue";
 import TextEditor from "./Editor/TextEditor.vue";
 import MarkdownHelp from "@/components/Markdown/MarkdownHelp.vue";
@@ -64,17 +60,18 @@ library.add(faQuestion);
 
 defineProps<{
     markdownText: string;
+    mode: "report" | "page";
+    labels?: Array<WorkflowLabel>;
     steps?: Record<string, any>;
     title: string;
-    mode: "report" | "page";
 }>();
 
 const showHelpModal = ref<boolean>(false);
 
 const editor = ref("text");
 const editorOptions = ref([
+    { text: "Editor", value: "editor" },
     { text: "Text", value: "text" },
-    { text: "Cells", value: "cells" },
 ]);
 
 function onHelp() {
diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index 500790acd4e7..a8e431ac4a17 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -112,6 +112,7 @@
                 mode="report"
                 :title="'Workflow Report: ' + name"
                 :labels="getLabels"
+                :steps="steps"
                 @insert="insertMarkdown"
                 @update="onReportUpdate">
                 <template v-slot:buttons>

From ea617067254c5751f8cd682185dbe875228ad054 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 17:44:46 -0400
Subject: [PATCH 34/39] Update the heatmap visualization logo to center the
 squares

---
 config/plugins/visualizations/heatmap/static/logo.svg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/visualizations/heatmap/static/logo.svg b/config/plugins/visualizations/heatmap/static/logo.svg
index 41c80b8f2c16..7dab3d8c7567 100644
--- a/config/plugins/visualizations/heatmap/static/logo.svg
+++ b/config/plugins/visualizations/heatmap/static/logo.svg
@@ -1,4 +1,4 @@
-<svg width="200" height="200" viewBox="0 0 5 5" xmlns="http://www.w3.org/2000/svg">
+<svg width="200" height="200" viewBox="0 0 3.8 3.8" xmlns="http://www.w3.org/2000/svg">
   <rect x="0.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
   <rect x="1.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
   <rect x="2.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />

From 1027d31d70c1f6ce82d926bc4bf0afe8c9b21dd1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 17:57:37 -0400
Subject: [PATCH 35/39] Adjust has labels condition

---
 client/src/components/Markdown/MarkdownDialog.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Markdown/MarkdownDialog.vue b/client/src/components/Markdown/MarkdownDialog.vue
index f54e6a6dc061..c2728fb1848a 100644
--- a/client/src/components/Markdown/MarkdownDialog.vue
+++ b/client/src/components/Markdown/MarkdownDialog.vue
@@ -57,7 +57,7 @@ const effectiveLabels = computed<Array<WorkflowLabel>>(() => {
     return filteredLabels;
 });
 
-const hasLabels = computed(() => props.labels && props.labels.length > 0);
+const hasLabels = computed(() => props.labels !== undefined);
 
 const selectorConfig = {
     job_id: {

From 4ddb37b2ed2fb1b63df880f7331b7a357a7dc652 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 18:19:40 -0400
Subject: [PATCH 36/39] Adjust handling in legacy markdown toolbox panel

---
 client/src/components/Markdown/MarkdownToolBox.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Markdown/MarkdownToolBox.vue b/client/src/components/Markdown/MarkdownToolBox.vue
index c4ab527a1918..92b7e5d2cc19 100644
--- a/client/src/components/Markdown/MarkdownToolBox.vue
+++ b/client/src/components/Markdown/MarkdownToolBox.vue
@@ -238,7 +238,7 @@ export default {
             };
         },
         workflowLabels() {
-            return fromSteps(this.steps);
+            return this.isWorkflow ? fromSteps(this.steps) : undefined;
         },
     },
     created() {

From dd506bc15b252f328c6454145084bf267b6e84fb Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 18 Mar 2025 19:26:24 -0400
Subject: [PATCH 37/39] Update heatmap, fix tooltip color

---
 config/plugins/visualizations/heatmap/config/heatmap.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/visualizations/heatmap/config/heatmap.xml b/config/plugins/visualizations/heatmap/config/heatmap.xml
index 398557e11a40..c1a95a5c4781 100644
--- a/config/plugins/visualizations/heatmap/config/heatmap.xml
+++ b/config/plugins/visualizations/heatmap/config/heatmap.xml
@@ -3,7 +3,7 @@
 <visualization name="Heatmap" embeddable="true">
     <description>Renders a heatmap from matrix data provided in 3-column format (x, y, observation).</description>
     <requirements>
-        <requirement type="npm" version="0.0.12" package="@galaxyproject/heatmap"/>
+        <requirement type="npm" version="0.0.13" package="@galaxyproject/heatmap"/>
     </requirements>
     <data_sources>
         <data_source>

From 196b880bca8799bad11c29672551bd1551fc8370 Mon Sep 17 00:00:00 2001
From: Aysam Guerler <aysam.guerler@gmail.com>
Date: Wed, 19 Mar 2025 12:05:39 -0400
Subject: [PATCH 38/39] Update
 client/src/components/Markdown/Utilities/parseInvocation.ts
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
---
 client/src/components/Markdown/Utilities/parseInvocation.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Markdown/Utilities/parseInvocation.ts b/client/src/components/Markdown/Utilities/parseInvocation.ts
index 97f7b2df1b15..a6536fbd56d7 100644
--- a/client/src/components/Markdown/Utilities/parseInvocation.ts
+++ b/client/src/components/Markdown/Utilities/parseInvocation.ts
@@ -21,7 +21,7 @@ export function parseInput(invocation: Invocation, name: string | undefined) {
     }
 }
 
-export function parseOutput(invocation: any, name: string | undefined) {
+export function parseOutput(invocation: Invocation, name: string | undefined) {
     if (name && invocation.outputs) {
         const output = invocation.outputs[name];
         return output?.id;

From 727d6cce76b6dbc7d89fea90baac98793db58810 Mon Sep 17 00:00:00 2001
From: Aysam Guerler <aysam.guerler@gmail.com>
Date: Wed, 19 Mar 2025 12:06:11 -0400
Subject: [PATCH 39/39] Update
 client/src/components/Markdown/MarkdownDialog.vue
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
---
 client/src/components/Markdown/MarkdownDialog.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Markdown/MarkdownDialog.vue b/client/src/components/Markdown/MarkdownDialog.vue
index c2728fb1848a..0e860cbfcbdc 100644
--- a/client/src/components/Markdown/MarkdownDialog.vue
+++ b/client/src/components/Markdown/MarkdownDialog.vue
@@ -43,7 +43,7 @@ type SelectType = "job_id" | "invocation_id" | "history_dataset_id" | "history_d
 
 const effectiveLabels = computed<Array<WorkflowLabel>>(() => {
     if (!props.labels) {
-        return [] as Array<WorkflowLabel>;
+        return [];
     }
     const selectSteps = props.argumentType == "job_id";
     const filteredLabels: Array<WorkflowLabel> = [];