diff --git a/client/src/components/Markdown/MarkdownToolBox.vue b/client/src/components/Markdown/MarkdownToolBox.vue
index 1cee7281fd4d..e7ae9a362e69 100644
--- a/client/src/components/Markdown/MarkdownToolBox.vue
+++ b/client/src/components/Markdown/MarkdownToolBox.vue
@@ -46,67 +46,48 @@ import ToolSection from "components/Panels/Common/ToolSection";
import { getAppRoot } from "onload/loadConfig";
import Vue from "vue";
+import { directiveEntry } from "./directives.ts";
import MarkdownDialog from "./MarkdownDialog";
Vue.use(BootstrapVue);
-const historySharedElements = [
- {
- id: "history_dataset_display",
- name: "Dataset",
- emitter: "onHistoryDatasetId",
- },
- {
- id: "history_dataset_collection_display",
- name: "Collection",
- emitter: "onHistoryCollectionId",
- },
- {
- id: "history_dataset_as_image",
- name: "Image",
- emitter: "onHistoryDatasetId",
- },
- {
- id: "history_dataset_index",
- name: "Dataset Index",
- emitter: "onHistoryDatasetId",
- },
- {
- id: "history_dataset_embedded",
- name: "Embedded Dataset",
- emitter: "onHistoryDatasetId",
- },
- {
- id: "history_dataset_as_table",
- name: "Embedded Dataset (as table)",
- emitter: "onHistoryDatasetId",
- },
- {
- id: "history_dataset_type",
- name: "Dataset Type",
- emitter: "onHistoryDatasetId",
- },
- {
- id: "history_dataset_link",
- name: "Link to Dataset",
- emitter: "onHistoryDatasetId",
- },
- {
- id: "history_dataset_name",
- name: "Name of Dataset",
- emitter: "onHistoryDatasetId",
- },
- {
- id: "history_dataset_peek",
- name: "Peek into Dataset",
- emitter: "onHistoryDatasetId",
- },
- {
- id: "history_dataset_info",
- name: "Dataset Details",
- emitter: "onHistoryDatasetId",
- },
-];
+function historySharedElements(mode) {
+ return [
+ directiveEntry("history_dataset_display", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ directiveEntry("history_dataset_collection_display", mode, {
+ emitter: "onHistoryCollectionId",
+ }),
+ directiveEntry("history_dataset_as_image", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ directiveEntry("history_dataset_index", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ directiveEntry("history_dataset_embedded", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ directiveEntry("history_dataset_as_table", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ directiveEntry("history_dataset_type", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ directiveEntry("history_dataset_link", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ directiveEntry("history_dataset_name", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ directiveEntry("history_dataset_peek", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ directiveEntry("history_dataset_info", mode, {
+ emitter: "onHistoryDatasetId",
+ }),
+ ];
+}
export default {
components: {
@@ -132,127 +113,45 @@ export default {
title: "History",
name: "history",
elems: [
- ...historySharedElements,
- {
- id: "history_link",
- name: "Link to Import",
+ ...historySharedElements("page"),
+ directiveEntry("history_link", "page", {
emitter: "onHistoryId",
- },
+ }),
],
},
historyInEditorSection: {
title: "History",
name: "history",
- elems: [
- ...historySharedElements,
- {
- id: "history_link",
- name: "Link to Import",
- },
- ],
- },
- jobSection: {
- title: "Jobs",
- name: "jobs",
- elems: [
- {
- id: "job_metrics",
- name: "Job Metrics",
- description: "as table",
- emitter: "onJobId",
- },
- {
- id: "job_parameters",
- name: "Job Parameters",
- description: "as table",
- emitter: "onJobId",
- },
- {
- id: "tool_stdout",
- name: "Tool Output",
- description: "of job run",
- emitter: "onJobId",
- },
- {
- id: "tool_stderr",
- name: "Tool Error",
- description: "of job run",
- emitter: "onJobId",
- },
- ],
+ elems: [...historySharedElements("report"), directiveEntry("history_link", "report")],
},
workflowSection: {
title: "Workflow",
name: "workflow",
elems: [
- {
- id: "invocation_time",
- name: "Invocation Time",
+ directiveEntry("invocation_time", "page", {
emitter: "onInvocationId",
- },
- {
- id: "workflow_display",
- name: "Workflow Display",
+ }),
+ directiveEntry("workflow_display", "page", {
emitter: "onWorkflowId",
- },
- {
- id: "workflow_license",
- name: "Workflow License",
+ }),
+ directiveEntry("workflow_license", "page", {
emitter: "onWorkflowId",
- },
- {
- id: "workflow_image",
- name: "Workflow Image",
+ }),
+ directiveEntry("workflow_image", "page", {
emitter: "onWorkflowId",
- },
+ }),
],
},
workflowInEditorSection: {
title: "Workflow",
name: "workflow",
elems: [
- {
- id: "invocation_inputs",
- name: "Invocation Inputs",
- },
- {
- id: "invocation_outputs",
- name: "Invocation Output",
- },
- {
- id: "invocation_time",
- name: "Time a Workflow",
- description: "was invoked",
- },
- {
- id: "workflow_display",
- name: "Current Workflow",
- description: "containing all steps",
- },
- {
- id: "workflow_image",
- name: "Current Workflow Image",
- },
- {
- id: "workflow_license",
- name: "Current Workflow License",
- },
- ],
- },
- otherSection: {
- title: "Miscellaneous",
- name: "others",
- elems: [
- {
- id: "generate_galaxy_version",
- name: "Galaxy Version",
- description: "as text",
- },
- {
- id: "generate_time",
- name: "Current Time",
- description: "as text",
- },
+ directiveEntry("invocation_inputs", "report"),
+ directiveEntry("invocation_outputs", "report"),
+ directiveEntry("invocation_time", "report"),
+ directiveEntry("workflow_display", "report"),
+ directiveEntry("workflow_license", "report"),
+ directiveEntry("workflow_image", "report"),
],
},
visualizationSection: {
@@ -266,9 +165,42 @@ export default {
isWorkflow() {
return !!this.steps;
},
+ mode() {
+ return this.isWorkflow ? "report" : "page";
+ },
hasVisualizations() {
return this.visualizationSection.elems.length > 0;
},
+ otherSection() {
+ return {
+ title: "Miscellaneous",
+ name: "others",
+ elems: [
+ directiveEntry("generate_galaxy_version", this.mode),
+ directiveEntry("generate_time", this.mode),
+ ],
+ };
+ },
+ jobSection() {
+ return {
+ title: "Jobs",
+ name: "jobs",
+ elems: [
+ directiveEntry("job_metrics", this.mode, {
+ emitter: "onJobId",
+ }),
+ directiveEntry("job_parameters", this.mode, {
+ emitter: "onJobId",
+ }),
+ directiveEntry("tool_stdout", this.mode, {
+ emitter: "onJobId",
+ }),
+ directiveEntry("tool_stderr", this.mode, {
+ emitter: "onJobId",
+ }),
+ ],
+ };
+ },
},
created() {
this.getVisualizations();
diff --git a/client/src/components/Markdown/directives.ts b/client/src/components/Markdown/directives.ts
new file mode 100644
index 000000000000..256537b5d0fe
--- /dev/null
+++ b/client/src/components/Markdown/directives.ts
@@ -0,0 +1,64 @@
+import RAW_DIRECTIVE_DATA from "./directives.yml";
+
+type DirectiveMode = "page" | "report";
+
+type DirectiveMetadataValueByMode = {
+ [key: string]: string;
+};
+
+interface DirectiveMetadata {
+ side_panel_name: string | DirectiveMetadataValueByMode;
+ side_panel_description?: string | DirectiveMetadataValueByMode;
+ help?: string | DirectiveMetadataValueByMode;
+}
+
+type DirectivesMetadata = {
+ [key: string]: DirectiveMetadata;
+};
+
+type SidePanelEntry = {
+ [key: string]: string;
+};
+
+const DIRECTIVE_METADATA = RAW_DIRECTIVE_DATA as DirectivesMetadata;
+
+export function directiveEntry(
+ directiveId: string,
+ mode: DirectiveMode,
+ baseEntry: SidePanelEntry = {}
+): SidePanelEntry {
+ const directiveMetadataData: DirectiveMetadata | undefined = DIRECTIVE_METADATA[directiveId];
+ if (directiveMetadataData == undefined) {
+ throw Error(`Client logic error, cannot find directive metadata for ${directiveId}`);
+ }
+ let name = directiveMetadataData.side_panel_name;
+ if (name && !(typeof name == "string")) {
+ const modeName = name[mode];
+ if (modeName == undefined) {
+ throw Error(`Client logic error, cannot find directive metadata for ${directiveId}`);
+ }
+ name = modeName;
+ }
+ let description = directiveMetadataData.side_panel_description;
+ if (description && !(typeof description == "string")) {
+ description = description[mode];
+ }
+ let help = directiveMetadataData.help;
+ if (help && !(typeof help == "string")) {
+ help = help[mode];
+ }
+ if (help) {
+ help = help.replace(/%MODE%/g, mode);
+ }
+ const entry: SidePanelEntry = { id: directiveId, ...baseEntry };
+ if (name) {
+ entry.name = name;
+ }
+ if (description) {
+ entry.description = description;
+ }
+ if (help) {
+ entry.help = help;
+ }
+ return entry;
+}
diff --git a/client/src/components/Markdown/directives.yml b/client/src/components/Markdown/directives.yml
new file mode 100644
index 000000000000..51ae5ebeed0c
--- /dev/null
+++ b/client/src/components/Markdown/directives.yml
@@ -0,0 +1,111 @@
+---
+history_dataset_display:
+ side_panel_name: Dataset
+ help: |
+ Display a dataset and relevant options for viewing, importing, downloading,
+ and visualization in the resulting document. To embed a dataset directly
+ into the document use the "history_dataset_embedded" / "Embedded Dataset"
+ directive.
+
+history_dataset_collection_display:
+ side_panel_name: Collection
+ help: |
+ Display a dataset collection and relevant options for viewing, importing, downloading
+ in the resulting documenting.
+
+history_dataset_as_image:
+ side_panel_name: Image
+ help: |
+ Embed a dataset in the resulting document as an image. This only works for simple image
+ types. This can be used to present graphs and other visual summaries of an analysis into
+ a Galaxy Markdown document summary.
+
+history_dataset_index:
+ side_panel_name: Dataset Index
+ help: |
+ For Galaxy composite datasets (datasets that consist on multiple files), this option will
+ display the contents of the composite dataset as files and folders in the resulting document.
+history_dataset_embedded:
+ side_panel_name: Embedded Dataset
+history_dataset_as_table:
+ side_panel_name: Embedded Dataset as table
+history_dataset_type:
+ side_panel_name: Dataset Type
+history_dataset_link:
+ side_panel_name: Link to Dataset
+history_dataset_name:
+ side_panel_name: Name of Dataset
+history_dataset_peek:
+ side_panel_name: Peek into Dataset
+history_dataset_info:
+ side_panel_name: Dataset Details
+
+history_link:
+ side_panel_name: Link to Import
+ help:
+ report: |
+ Add a link to import the history the workflow invocation was executed in.
+ page: |
+ Add a link to import the target history referenced by the directive.
+
+invocation_time:
+ side_panel_name:
+ report: Time Workflow
+ page: Time a Workflow
+
+ side_panel_description: was invoked
+
+invocation_inputs:
+ side_panel_name: Invocation Inputs
+
+invocation_outputs:
+ side_panel_name: Invocation Output
+
+workflow_license:
+ side_panel_name: Workflow License
+
+workflow_image:
+ side_panel_name: Workflow (as image)
+
+workflow_display:
+ side_panel_name:
+ report: Current Workflow
+ page: Display a Workflow
+ side_panel_description: containing all steps
+
+generate_galaxy_version:
+ side_panel_name: Galaxy Version
+ side_panel_description: as text
+
+ help: |
+ Report the current Galaxy version at the time %MODE% generation.
+
+ Warning: This is the Galaxy version at the time the %MODE% was generated and
+ not the time of an analysis. This option makes the most sense for PDF generation
+ of %MODE%s designed for external archiving or printing.
+
+generate_time:
+ side_panel_name: Current Time
+ side_panel_description: as text
+ help: |
+ Report the current time of %MODE% generation.
+
+ Warning: This is the time the %MODE% was generated and not the time of
+ an analysis. This option makes the most sense for PDF generation of %MODE%s
+ designed for external archiving or printing.
+
+job_metrics:
+ side_panel_name: Job Metrics
+ side_panel_description: as table
+
+job_parameters:
+ side_panel_name: Job Parameters
+ side_panel_description: as table
+
+tool_stdout:
+ side_panel_name: Tool Output
+ side_panel_description: of job run
+
+tool_stderr:
+ side_panel_name: Tool Error
+ side_panel_description: of job run
diff --git a/client/src/components/Panels/Common/Tool.vue b/client/src/components/Panels/Common/Tool.vue
index ec4ad493745f..2ed5e20820fd 100644
--- a/client/src/components/Panels/Common/Tool.vue
+++ b/client/src/components/Panels/Common/Tool.vue
@@ -4,7 +4,14 @@
{{ tool.name }}
{{ tool.description }}
-
+
![]()
{
test: /\.(txt|tmpl)$/,
loader: "raw-loader",
},
+ {
+ test: /\.ya?ml$/,
+ use: "yaml-loader",
+ },
],
},
resolveLoader: {