Tool markdown reports.

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

@@ -14,15 +14,14 @@ 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") {
         return `${getAppRoot()}dataset/display?dataset_id=${props.historyDatasetId}`;
     }
-
     return pathDestination.value?.fileLink;
 });
 

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

@@ -189,8 +189,12 @@ 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/Elements/HistoryDatasetAsTable.vue

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

client/src/components/Markdown/Markdown.vue

@@ -22,19 +22,19 @@
                     Edit
                     <FontAwesomeIcon icon="edit" />
                 </b-button>
-                <h1 class="float-right align-middle mr-2 mt-1 h-md">Galaxy {{ markdownConfig.model_class }}</h1>
+                <h1 v-if="title" 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>
+                    <h1 v-if="title" class="text-break align-middle">Title: {{ title }}</h1>
                     <h2 v-if="workflowVersions" class="text-break align-middle">
                         Workflow Checkpoint: {{ workflowVersions.version }}
                     </h2>
                 </span>
             </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>
+                <div v-if="showIdentifier" class="float-right m-1">Identifier: {{ markdownConfig.id }}</div>
             </b-badge>
             <div>
                 <b-alert v-if="markdownErrors.length > 0" variant="warning" show>
@@ -119,6 +119,10 @@ export default {
             type: String,
             default: null,
         },
+        showIdentifier: {
+            type: Boolean,
+            default: true,
+        },
     },
     data() {
         return {
@@ -137,6 +141,9 @@ export default {
         effectiveExportLink() {
             return this.enable_beta_markdown_export ? this.exportLink : null;
         },
+        title() {
+            return this.markdownConfig.title || this.markdownConfig.model_class;
+        },
         time() {
             let generateTime = this.markdownConfig.generate_time;
             if (generateTime) {

client/src/components/Markdown/MarkdownContainer.vue

@@ -140,7 +140,8 @@ function argToBoolean(args, name, booleanDefault) {
                 :compact="argToBoolean(args, 'compact', false)"
                 :show-column-headers="argToBoolean(args, 'show_column_headers', true)"
                 :title="args.title"
-                :footer="args.footer" />
+                :footer="args.footer"
+                :path="args.path" />
             <HistoryDatasetLink v-else-if="name == 'history_dataset_link'" :args="args" />
             <HistoryDatasetIndex v-else-if="name == 'history_dataset_index'" :args="args" />
             <InvocationTime v-else-if="name == 'invocation_time'" :args="args" :invocations="invocations" />

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

@@ -21,6 +21,7 @@ import ToolLanding from "components/Landing/ToolLanding";
 import WorkflowLanding from "components/Landing/WorkflowLanding";
 import PageDisplay from "components/PageDisplay/PageDisplay";
 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";
@@ -239,6 +240,11 @@ export function getRouter(Galaxy) {
                             src: `/datasets/${route.params.datasetId}/display/?preview=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

@@ -575,6 +575,7 @@
     <!-- 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" display_in_upload="true"/>
     <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 _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("data_manager_json")  # for downloading bundles if bundled.
+        composite_extensions.append("tool_markdown")
 
         if data.extension in composite_extensions:
             return self._archive_composite_dataset(trans, data, headers, do_action=kwd.get("do_action", "zip"))

lib/galaxy/managers/hdas.py

@@ -302,13 +302,10 @@ def data_conversion_status(self, hda):
 
     # .... data
     # TODO: to data provider or Text datatype directly
-    def text_data(self, hda, preview=True):
+    def text_data(self, hda, preview=True, filename: Optional[str] = None):
         """
         Get data from text file, truncating if necessary.
         """
-        # 1 MB
-        MAX_PEEK_SIZE = 1000000
-
         truncated = False
         hda_data = None
         # For now, cannot get data from non-text datasets.
@@ -318,6 +315,11 @@ def text_data(self, hda, preview=True):
         if not os.path.exists(file_path):
             return truncated, hda_data
 
+        return self.text_data_truncated(file_path, preview=preview)
+
+    def text_data_truncated(self, file_path, preview=True):
+        # 1 MB
+        MAX_PEEK_SIZE = 1000000
         truncated = preview and os.stat(file_path).st_size > MAX_PEEK_SIZE
         with get_fileobj(file_path) as fh:
             try: