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/Markdown.vue

@@ -22,10 +22,10 @@
                     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 v-if="title" class="text-break align-middle">
+                        Title: {{ title }}
                     </h1>
                     <h2 v-if="workflowVersions" class="text-break align-middle">
                         Workflow Checkpoint: {{ workflowVersions.version }}
@@ -34,7 +34,7 @@
             </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/Tool/ToolReport.vue

@@ -0,0 +1,42 @@
+<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",

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/markdown_util.py

@@ -900,7 +900,7 @@ def _remap(container, line):
             )
         if container == "history_link":
             return (f"history_link(history_id={invocation.history.id})\n", False)
-        if container == "invocation_time":
+        elif container == "invocation_time":
             return (f"invocation_time(invocation_id={invocation.id})\n", False)
         ref_object_type = None
         output_match = re.search(OUTPUT_LABEL_PATTERN, line)
@@ -953,6 +953,70 @@ def find_non_empty_group(match):
     return galaxy_markdown
 
 
+def resolve_job_markdown(trans, job, job_markdown):
+    """Resolve job objects to convert tool markdown to 'internal' representation.
+
+    Replace references to abstract workflow parts with actual galaxy object IDs corresponding
+    to the actual executed workflow. For instance:
+
+        convert output=name -to- history_dataset_id=<id> | history_dataset_collection_id=<id>
+        convert input=name -to- history_dataset_id=<id> | history_dataset_collection_id=<id>
+        convert argument-less job directives to job
+    """
+    io_dicts = job.io_dicts()
+
+    def _remap(container, line):
+        if container == "history_link":
+            return (f"history_link(history_id={job.history.id})\n", False)
+        elif container == "tool_stdout":
+            return (f"tool_stdout(job_id={job.id})\n", False)
+        elif container == "tool_stderr":
+            return (f"tool_stderr(job_id={job.id})\n", False)
+        elif container == "job_parameters":
+            return (f"job_parameters(job_id={job.id})\n", False)
+        elif container == "job_metrics":
+            return (f"job_metrics(job_id={job.id})\n", False)
+        ref_object_type = None
+        output_match = re.search(OUTPUT_LABEL_PATTERN, line)
+        input_match = re.search(INPUT_LABEL_PATTERN, line)
+
+        def find_non_empty_group(match):
+            for group in match.groups():
+                if group:
+                    return group
+
+        target_match: Optional[Match]
+        ref_object: Optional[Any]
+        if output_match:
+            target_match = output_match
+            name = find_non_empty_group(target_match)
+            if name in io_dicts.out_data:
+                ref_object = io_dicts.out_data[name]
+            elif name in io_dicts.out_collections:
+                ref_object = io_dicts.out_collections[name]
+            else:
+                raise Exception("Unknown exception")
+        elif input_match:
+            target_match = input_match
+            name = find_non_empty_group(target_match)
+            ref_object = io_dicts.inp_data[name]
+        else:
+            target_match = None
+            ref_object = None
+        if ref_object:
+            assert target_match  # tell type system, this is set when ref_object is set
+            if ref_object_type is None:
+                if ref_object.history_content_type == "dataset":
+                    ref_object_type = "history_dataset"
+                else:
+                    ref_object_type = "history_dataset_collection"
+            line = line.replace(target_match.group(), f"{ref_object_type}_id={ref_object.id}")
+        return (line, False)
+
+    galaxy_markdown = _remap_galaxy_markdown_calls(_remap, job_markdown)
+    return galaxy_markdown
+
+
 def _remap_galaxy_markdown_containers(func, markdown):
     new_markdown = markdown
 

lib/galaxy/schema/schema.py

@@ -3846,6 +3846,13 @@ class PageDetails(PageSummary):
     model_config = ConfigDict(extra="allow")
 
 
+class ToolReportForDataset(BaseModel):
+    content: Optional[str] = ContentField
+    generate_version: Optional[str] = GenerateVersionField
+    generate_time: Optional[str] = GenerateTimeField
+    model_config = ConfigDict(extra="allow")
+
+
 class PageSummaryList(RootModel):
     root: List[PageSummary] = Field(
         default=[],

lib/galaxy/webapps/galaxy/api/datasets.py

@@ -39,6 +39,7 @@
     AsyncTaskResultSummary,
     DatasetAssociationRoles,
     DatasetSourceType,
+    ToolReportForDataset,
 )
 from galaxy.util.zipstream import ZipstreamWrapper
 from galaxy.webapps.base.api import GalaxyFileResponse
@@ -503,6 +504,17 @@ def compute_hash(
     ) -> AsyncTaskResultSummary:
         return self.service.compute_hash(trans, dataset_id, payload, hda_ldda=hda_ldda)
 
+    @router.get(
+        "/api/datasets/{dataset_id}/report",
+        summary="Return JSON content Galaxy will use to render Markdown reports",
+    )
+    def report(
+        self,
+        dataset_id: HistoryDatasetIDPathParam,
+        trans=DependsOnTrans,
+    ) -> ToolReportForDataset:
+        return self.service.report(trans, dataset_id)
+
     @router.put(
         "/api/datasets/{dataset_id}/object_store_id",
         summary="Update an object store ID for a dataset you own.",

lib/galaxy/webapps/galaxy/buildapp.py

@@ -280,6 +280,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     webapp.add_client_route("/datasets/{dataset_id}/error")
     webapp.add_client_route("/datasets/{dataset_id}/details")
     webapp.add_client_route("/datasets/{dataset_id}/preview")
+    webapp.add_client_route("/datasets/{dataset_id}/report")
     webapp.add_client_route("/datasets/{dataset_id}/show_params")
     webapp.add_client_route("/collection/{collection_id}/edit")
     webapp.add_client_route("/jobs/submission/success")

lib/galaxy/webapps/galaxy/services/datasets.py

@@ -47,6 +47,10 @@
     HistoryContentsManager,
 )
 from galaxy.managers.lddas import LDDAManager
+from galaxy.managers.markdown_util import (
+    ready_galaxy_markdown_for_export,
+    resolve_job_markdown,
+)
 from galaxy.model.base import transaction
 from galaxy.objectstore.badges import BadgeDict
 from galaxy.schema import (
@@ -70,6 +74,7 @@
     DatasetSourceType,
     EncodedDatasetSourceId,
     Model,
+    ToolReportForDataset,
     UpdateDatasetPermissionsPayload,
 )
 from galaxy.schema.tasks import ComputeDatasetHashTaskRequest
@@ -506,6 +511,18 @@ def compute_hash(
         result = compute_dataset_hash.delay(request=request, task_user_id=getattr(trans.user, "id", None))
         return async_task_summary(result)
 
+    def report(self, trans: ProvidesHistoryContext, dataset_id: DecodedDatabaseIdField) -> ToolReportForDataset:
+        dataset_instance = self.hda_manager.get_accessible(dataset_id, trans.user)
+        self.hda_manager.ensure_dataset_on_disk(trans, dataset_instance)
+        file_path = trans.app.object_store.get_filename(dataset_instance.dataset)
+        raw_content = open(file_path).read()
+        internal_markdown = resolve_job_markdown(trans, dataset_instance.creating_job, raw_content)
+        content, extra_attributes = ready_galaxy_markdown_for_export(trans, internal_markdown)
+        return ToolReportForDataset(
+            content=content,
+            **extra_attributes,
+        )
+
     def drs_dataset_instance(self, object_id: str) -> Tuple[int, DatasetSourceType]:
         if object_id.startswith("hda-"):
             decoded_object_id = self.decode_id(object_id[len("hda-") :], kind="drs")

lib/tool_shed/webapp/frontend/src/components/RepositoriesForOwner.vue

@@ -48,5 +48,10 @@ const rows = computed(() => {
 <template>
     <loading-div v-if="loading" />
     <error-banner error="Failed to load repositories" v-else-if="error"> </error-banner>
-    <repositories-grid :title="`Repositories for ${username}`" :rows="rows" :on-scroll="onScroll" />
+    <repositories-grid
+        :title="`Repositories for ${username}`"
+        :rows="rows"
+        :on-scroll="onScroll"
+        :allow-search="true"
+    />
 </template>