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Toward declarative help for Galaxy markdown directives.
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@jmchilton
jmchilton committed Jan 11, 2024
1 parent 5f3d617 commit ada344b
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Showing 5 changed files with 276 additions and 158 deletions.
246 changes: 89 additions & 157 deletions client/src/components/Markdown/MarkdownToolBox.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -47,67 +47,48 @@ 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: {
Expand All @@ -133,127 +114,45 @@ 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"),
],
},
linksSection: {
Expand Down Expand Up @@ -309,9 +208,42 @@ 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();
Expand Down
64 changes: 64 additions & 0 deletions client/src/components/Markdown/directives.ts
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Original file line number Diff line number Diff line change
@@ -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;
}
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