Implement tool markdown reports.

client/src/api/schema/schema.ts

@@ -615,6 +615,23 @@ export interface paths {
         patch?: never;
         trace?: never;
     };
+    "/api/datasets/{dataset_id}/report": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Return JSON content Galaxy will use to render Markdown reports */
+        get: operations["report_api_datasets__dataset_id__report_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
     "/api/datasets/{dataset_id}/storage": {
         parameters: {
             query?: never;
@@ -17047,6 +17064,27 @@ export interface components {
              */
             values: string;
         };
+        /** ToolReportForDataset */
+        ToolReportForDataset: {
+            /**
+             * Content
+             * @description Raw text contents of the last page revision (type dependent on content_format).
+             * @default
+             */
+            content: string | null;
+            /**
+             * Galaxy Version
+             * @description The version of Galaxy this object was generated with.
+             */
+            generate_time?: string | null;
+            /**
+             * Galaxy Version
+             * @description The version of Galaxy this object was generated with.
+             */
+            generate_version?: string | null;
+        } & {
+            [key: string]: unknown;
+        };
         /** ToolStep */
         ToolStep: {
             /**
@@ -20320,7 +20358,10 @@ export interface operations {
     };
     get_content_as_text_api_datasets__dataset_id__get_content_as_text_get: {
         parameters: {
-            query?: never;
+            query?: {
+                /** @description If non-null, get the specified filename from the extra files for this dataset. */
+                filename?: string | null;
+            };
             header?: {
                 /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
@@ -20653,6 +20694,50 @@ export interface operations {
             };
         };
     };
+    report_api_datasets__dataset_id__report_get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["ToolReportForDataset"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
     show_storage_api_datasets__dataset_id__storage_get: {
         parameters: {
             query?: {

client/src/components/Dataset/DatasetAsImage/DatasetAsImage.vue

@@ -15,9 +15,9 @@ const { datasetPathDestination } = useDatasetPathDestination();
 
 const props = defineProps<Props>();
 
-const pathDestination = computed<PathDestination | null>(() =>
-    datasetPathDestination.value(props.historyDatasetId, props.path)
-);
+const pathDestination = computedAsync<PathDestination | null>(async () => {
+    return await datasetPathDestination.value(props.historyDatasetId, props.path);
+}, null);
 
 const imageUrl = computed(() => {
     if (props.path === undefined || props.path === "undefined") {

client/src/components/Dataset/DatasetIndex/DatasetIndex.vue

@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { computedAsync } from "@vueuse/core";
 import { computed } from "vue";
 
 import type { DatasetExtraFiles } from "@/api/datasets";
@@ -13,7 +14,7 @@ const { datasetPathDestination } = useDatasetPathDestination();
 
 const props = defineProps<Props>();
 
-const pathDestination = computed<PathDestination | null>(() =>
+const pathDestination = computedAsync<PathDestination | null>(() =>
     datasetPathDestination.value(props.historyDatasetId, props.path)
 );
 

client/src/components/Dataset/DatasetLink/DatasetLink.vue

@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { computedAsync } from "@vueuse/core";
 import { computed } from "vue";
 
 import { hasDetails } from "@/api";
@@ -16,7 +17,7 @@ const { getDataset } = useDatasetStore();
 
 const props = defineProps<Props>();
 
-const pathDestination = computed<PathDestination | null>(() =>
+const pathDestination = computedAsync<PathDestination | null>(() =>
     datasetPathDestination.value(props.historyDatasetId, props.path)
 );
 

client/src/components/History/Content/ContentItem.vue

@@ -171,8 +171,12 @@ const itemUrls = computed<ItemUrls>(() => {
                     : null,
         };
     }
+    let display = `/datasets/${id}/preview`;
+    if (props.item.extension == "tool_markdown") {
+        display = `/datasets/${id}/report`;
+    }
     return {
-        display: `/datasets/${id}/preview`,
+        display: display,
         edit: `/datasets/${id}/edit`,
         showDetails: `/datasets/${id}/details`,
         reportError: `/datasets/${id}/error`,

client/src/components/Markdown/Markdown.vue

@@ -30,6 +30,7 @@ const props = defineProps<{
     downloadEndpoint: string;
     readOnly?: boolean;
     exportLink?: string;
+    showIdentifier?: boolean;
 }>();
 
 // Refs and data
@@ -58,6 +59,10 @@ const updateTime = computed(() => {
     return "";
 });
 
+const pageTitle = computed(() => {
+    return props.markdownConfig.title || props.markdownConfig.model_class;
+});
+
 // Methods
 function initConfig() {
     const config = props.markdownConfig;
@@ -85,7 +90,7 @@ onMounted(() => {
             <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 }}
+                        {{ pageTitle }}
                     </Heading>
                     <div>
                         <StsDownloadButton

client/src/components/Markdown/Sections/Elements/HistoryDatasetAsTable.vue

@@ -11,17 +11,23 @@ interface HistoryDatasetAsTableProps {
     footer?: string;
     showColumnHeaders: boolean;
     title?: string;
+    path?: string;
 }
 
 const props = withDefaults(defineProps<HistoryDatasetAsTableProps>(), {
     compact: false,
     showColumnHeaders: true,
     title: undefined,
     footer: undefined,
+    path: undefined,
 });
 
 const itemUrl = computed(() => {
-    return `/api/datasets/${props.datasetId}/get_content_as_text`;
+    if (props.path) {
+        return `/api/datasets/${props.datasetId}/get_content_as_text?filename=${props.path}`;
+    } else {
+        return `/api/datasets/${props.datasetId}/get_content_as_text`;
+    }
 });
 
 const metaUrl = computed(() => {

client/src/components/Markdown/Sections/MarkdownGalaxy.vue

@@ -160,7 +160,8 @@ watch(
                 :dataset-id="args.history_dataset_id"
                 :footer="args.footer"
                 :show-column-headers="argToBoolean(args, 'show_column_headers', true)"
-                :title="args.title" />
+                :title="args.title"
+                :path="path" />
             <HistoryDatasetCollectionDisplay
                 v-else-if="name == 'history_dataset_collection_display'"
                 :collection-id="args.history_dataset_collection_id" />

client/src/components/Tool/ToolReport.vue

@@ -0,0 +1,39 @@
+<script setup lang="ts">
+import { computed, ref } from "vue";
+
+import { useConfig } from "@/composables/config";
+import { urlData } from "@/utils/url";
+
+import Markdown from "@/components/Markdown/Markdown.vue";
+
+interface Props {
+    datasetId: string;
+}
+
+const props = defineProps<Props>();
+
+const dataUrl = computed(() => {
+    return `/api/datasets/${props.datasetId}/report`;
+});
+
+const dataRef = ref<unknown>(null);
+
+const { config, isConfigLoaded } = useConfig(true);
+
+urlData({ url: dataUrl.value }).then((data) => {
+    dataRef.value = data;
+});
+</script>
+
+<template>
+    <div>
+        <Markdown
+            v-if="isConfigLoaded && dataRef"
+            :markdown-config="dataRef"
+            :enable-beta-markdown-export="config.enable_beta_markdown_export"
+            download-endpoint="TODO"
+            :show-identifier="false"
+            :read-only="true" />
+        <div v-else>Loading....</div>
+    </div>
+</template>

client/src/composables/datasetPathDestination.ts

@@ -20,11 +20,11 @@ export function useDatasetPathDestination() {
     const cache = ref<{ [key: string]: PathDestinationMap }>({});
 
     const datasetPathDestination = computed(() => {
-        return (dataset_id: string, path?: string) => {
+        return async (dataset_id: string, path?: string) => {
             const targetPath = path ?? "undefined";
-            const pathDestination = cache.value[dataset_id]?.[targetPath];
+            let pathDestination = cache.value[dataset_id]?.[targetPath];
             if (!pathDestination) {
-                getPathDestination(dataset_id, path);
+                pathDestination = (await getPathDestination(dataset_id, path)) ?? undefined;
             }
             return pathDestination ?? null;
         };
@@ -36,7 +36,6 @@ export function useDatasetPathDestination() {
             await datasetExtraFilesStore.fetchDatasetExtFilesByDatasetId({ id: dataset_id });
             datasetExtraFiles = datasetExtraFilesStore.getDatasetExtraFiles(dataset_id);
         }
-
         if (datasetExtraFiles === null) {
             return null;
         }
@@ -66,9 +65,7 @@ export function useDatasetPathDestination() {
             }
             pathDestination.fileLink = getCompositeDatasetLink(dataset_id, datasetEntry.path);
         }
-
         set(cache.value, dataset_id, { [path]: pathDestination });
-
         return pathDestination;
     }
 

client/src/entry/analysis/router.js

@@ -23,6 +23,7 @@ import WorkflowLanding from "components/Landing/WorkflowLanding";
 import PageDisplay from "components/PageDisplay/PageDisplay";
 import PageForm from "components/PageDisplay/PageForm";
 import PageEditor from "components/PageEditor/PageEditor";
+import ToolReport from "components/Tool/ToolReport";
 import ToolSuccess from "components/Tool/ToolSuccess";
 import ToolsList from "components/ToolsList/ToolsList";
 import ToolsJson from "components/ToolsView/ToolsSchemaJson/ToolsJson";
@@ -236,6 +237,11 @@ export function getRouter(Galaxy) {
                             isPreview: true,
                         }),
                     },
+                    {
+                        path: "datasets/:datasetId/report",
+                        component: ToolReport,
+                        props: true,
+                    },
                     {
                         // legacy route, potentially used by 3rd parties
                         path: "datasets/:datasetId/show_params",

doc/parse_gx_xsd.py

@@ -8,12 +8,16 @@
 from io import StringIO
 
 from lxml import etree
+from yaml import safe_load
 
 with open(sys.argv[2]) as f:
     xmlschema_doc = etree.parse(f)
 
 markdown_buffer = StringIO()
 
+DIRECTIVES_PATH = "../client/src/components/Markdown/directives.yml"
+DIRECTIVES = safe_load(open(DIRECTIVES_PATH))
+
 
 def main():
     """Entry point for the function that builds Markdown help for the Galaxy XSD."""
@@ -74,6 +78,7 @@ def _build_tag(tag, hide_attributes):
     annotation_el = tag_el.find("{http://www.w3.org/2001/XMLSchema}annotation")
     text = annotation_el.find("{http://www.w3.org/2001/XMLSchema}documentation").text
     text = _replace_attribute_list(tag, text, attributes)
+    text = _expand_directives(text)
     for line in text.splitlines():
         if line.startswith("$assertions"):
             assertions_tag = xmlschema_doc.find(
@@ -127,6 +132,29 @@ def _replace_attribute_list(tag, text, attributes):
     return text
 
 
+def _build_directive_table(line: str) -> str:
+    _, directives_str = line.split(":", 1)
+    directives = directives_str.split(",")
+    attribute_table = StringIO()
+    attribute_table.write("\n\n")
+    for directive in directives:
+        header_level = 3
+        header_prefix = "#" * header_level
+        attribute_table.write(f"\n{header_prefix} {directive}\n\n")
+        directive_info = DIRECTIVES[directive]
+        if "help" in directive_info:
+            attribute_table.write(DIRECTIVES[directive]["help"])
+    return attribute_table.getvalue()
+
+
+def _expand_directives(text):
+    for line in text.splitlines():
+        if not line.startswith("$directive_list:"):
+            continue
+        text = text.replace(line, _build_directive_table(line))
+    return text
+
+
 def _get_bp_link(annotation_el):
     anchor = annotation_el.attrib.get("{http://galaxyproject.org/xml/1.0}best_practices", None)
     link = None

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -591,6 +591,7 @@
     <!-- End RGenetics Datatypes -->
     <datatype extension="ipynb" type="galaxy.datatypes.text:Ipynb" display_in_upload="true"/>
     <datatype extension="json" type="galaxy.datatypes.text:Json" display_in_upload="true"/>
+    <datatype extension="tool_markdown" type="galaxy.datatypes.text:Text"/>
     <datatype extension="expression.json" type="galaxy.datatypes.text:ExpressionJson" display_in_upload="true"/>
     <!-- graph datatypes -->
     <datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/>

lib/galaxy/datatypes/data.py

@@ -465,6 +465,7 @@ def to_archive(self, dataset: DatasetProtocol, name: str = "") -> Iterable:
     def _serve_file_download(self, headers, data, trans, to_ext, file_size, **kwd):
         composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
         composite_extensions.append("html")  # for archiving composite datatypes
+        composite_extensions.append("tool_markdown")  # basically should act as an HTML datatype in this capacity
         composite_extensions.append("data_manager_json")  # for downloading bundles if bundled.
         composite_extensions.append("directory")  # for downloading directories.
         composite_extensions.append("zarr")  # for downloading zarr directories.