@galaxy-tool-util/cli 1.1.0 → 1.3.0

package/dist/commands/annotate-connections.d.ts

@@ -0,0 +1,30 @@
+/**
+ * Helper for `gxwf mermaid` / `gxwf cytoscapejs` `--annotate-connections`:
+ * runs the connection validator against a workflow and returns the
+ * `EdgeAnnotation` lookup the emitters consume.
+ */
+import { type EdgeAnnotation } from "@galaxy-tool-util/connection-validation";
+import type { ToolCache } from "@galaxy-tool-util/core";
+import type { ParsedTool } from "@galaxy-tool-util/schema";
+export interface ResolveEdgeAnnotationsOptions {
+    cacheDir?: string;
+}
+export declare function resolveEdgeAnnotations(data: Record<string, unknown>, opts?: ResolveEdgeAnnotationsOptions): Promise<Map<string, EdgeAnnotation>>;
+export declare function resolveEdgeAnnotationsWithCache(data: Record<string, unknown>, cache: ToolCache): Promise<Map<string, EdgeAnnotation>>;
+export interface ResolvedToolSpec {
+    tool_id: string;
+    tool_version: string;
+    parsed: ParsedTool;
+}
+/**
+ * Variant of `resolveEdgeAnnotationsWithCache` that also returns the
+ * `ParsedTool` specs the validator consumed, keyed by `toolId@toolVersion`.
+ * The hybrid `gxwf-web` edge-annotations response uses this so co-resident
+ * browsers can write the specs into IndexedDB and warm the client-side
+ * `useToolInfoService` for free.
+ */
+export declare function resolveEdgeAnnotationsAndSpecsWithCache(data: Record<string, unknown>, cache: ToolCache): Promise<{
+    annotations: Map<string, EdgeAnnotation>;
+    specs: Map<string, ResolvedToolSpec>;
+}>;
+//# sourceMappingURL=annotate-connections.d.ts.map

package/dist/commands/annotate-connections.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/annotate-connections.js

@@ -0,0 +1,42 @@
+/**
+ * Helper for `gxwf mermaid` / `gxwf cytoscapejs` `--annotate-connections`:
+ * runs the connection validator against a workflow and returns the
+ * `EdgeAnnotation` lookup the emitters consume.
+ */
+import { buildEdgeAnnotations, buildGetToolInfo as _buildGetToolInfo, buildWorkflowGraph, validateConnectionGraph, } from "@galaxy-tool-util/connection-validation";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { buildGetToolInfo } from "./connection-validation.js";
+import { isResolveError, loadCachedTool } from "./resolve-tool.js";
+export async function resolveEdgeAnnotations(data, opts = {}) {
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    return resolveEdgeAnnotationsWithCache(data, cache);
+}
+export async function resolveEdgeAnnotationsWithCache(data, cache) {
+    const getToolInfo = await buildGetToolInfo(data, cache);
+    const graph = buildWorkflowGraph(data, getToolInfo);
+    const [report] = validateConnectionGraph(graph);
+    return buildEdgeAnnotations(report);
+}
+/**
+ * Variant of `resolveEdgeAnnotationsWithCache` that also returns the
+ * `ParsedTool` specs the validator consumed, keyed by `toolId@toolVersion`.
+ * The hybrid `gxwf-web` edge-annotations response uses this so co-resident
+ * browsers can write the specs into IndexedDB and warm the client-side
+ * `useToolInfoService` for free.
+ */
+export async function resolveEdgeAnnotationsAndSpecsWithCache(data, cache) {
+    const specs = new Map();
+    const getToolInfo = await _buildGetToolInfo(data, async (id, version) => {
+        const r = await loadCachedTool(cache, id, version);
+        if (isResolveError(r))
+            return null;
+        const ver = r.tool.version ?? version ?? "";
+        specs.set(`${id}@${ver}`, { tool_id: id, tool_version: ver, parsed: r.tool });
+        return r.tool;
+    });
+    const graph = buildWorkflowGraph(data, getToolInfo);
+    const [report] = validateConnectionGraph(graph);
+    return { annotations: buildEdgeAnnotations(report), specs };
+}
+//# sourceMappingURL=annotate-connections.js.map

package/dist/commands/annotate-connections.js.map

@@ -0,0 +1 @@
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package/dist/commands/connection-validation.d.ts

@@ -0,0 +1,20 @@
+/**
+ * CLI integration for connection validation.
+ *
+ * Walks a workflow dict to collect every tool reference (recursing into
+ * subworkflows), preloads each tool from the cache, and runs
+ * `validateConnectionsReport`. The connection validator wants a sync
+ * `GetToolInfo` lookup, so async cache fetches happen up front.
+ *
+ * The walker + preloader live in `@galaxy-tool-util/connection-validation`
+ * (`collectToolRefs`, `buildGetToolInfo`); this module is a thin wrapper that
+ * adapts the CLI's on-disk `ToolCache` to the lifted helper's `AsyncToolFetcher`.
+ */
+import { collectToolRefs, type GetToolInfo } from "@galaxy-tool-util/connection-validation";
+import type { ToolCache } from "@galaxy-tool-util/core";
+import type { ConnectionValidationReport } from "@galaxy-tool-util/schema";
+export { collectToolRefs };
+export type { ToolRef } from "@galaxy-tool-util/connection-validation";
+export declare function buildConnectionReport(data: Record<string, unknown>, cache: ToolCache): Promise<ConnectionValidationReport>;
+export declare function buildGetToolInfo(data: Record<string, unknown>, cache: ToolCache): Promise<GetToolInfo>;
+//# sourceMappingURL=connection-validation.d.ts.map

package/dist/commands/connection-validation.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"connection-validation.d.ts","sourceRoot":"","sources":["../../src/commands/connection-validation.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAEL,eAAe,EAEf,KAAK,WAAW,EACjB,MAAM,yCAAyC,CAAC;AACjD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACxD,OAAO,KAAK,EAAE,0BAA0B,EAAE,MAAM,0BAA0B,CAAC;AAI3E,OAAO,EAAE,eAAe,EAAE,CAAC;AAC3B,YAAY,EAAE,OAAO,EAAE,MAAM,yCAAyC,CAAC;AAEvE,wBAAsB,qBAAqB,CACzC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,GACf,OAAO,CAAC,0BAA0B,CAAC,CAGrC;AAED,wBAAsB,gBAAgB,CACpC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,GACf,OAAO,CAAC,WAAW,CAAC,CAKtB"}

package/dist/commands/connection-validation.js

@@ -0,0 +1,26 @@
+/**
+ * CLI integration for connection validation.
+ *
+ * Walks a workflow dict to collect every tool reference (recursing into
+ * subworkflows), preloads each tool from the cache, and runs
+ * `validateConnectionsReport`. The connection validator wants a sync
+ * `GetToolInfo` lookup, so async cache fetches happen up front.
+ *
+ * The walker + preloader live in `@galaxy-tool-util/connection-validation`
+ * (`collectToolRefs`, `buildGetToolInfo`); this module is a thin wrapper that
+ * adapts the CLI's on-disk `ToolCache` to the lifted helper's `AsyncToolFetcher`.
+ */
+import { buildGetToolInfo as _buildGetToolInfo, collectToolRefs, validateConnectionsReport, } from "@galaxy-tool-util/connection-validation";
+import { isResolveError, loadCachedTool } from "./resolve-tool.js";
+export { collectToolRefs };
+export async function buildConnectionReport(data, cache) {
+    const getToolInfo = await buildGetToolInfo(data, cache);
+    return validateConnectionsReport(data, getToolInfo);
+}
+export async function buildGetToolInfo(data, cache) {
+    return _buildGetToolInfo(data, async (id, version) => {
+        const r = await loadCachedTool(cache, id, version);
+        return isResolveError(r) ? null : r.tool;
+    });
+}
+//# sourceMappingURL=connection-validation.js.map

package/dist/commands/connection-validation.js.map

@@ -0,0 +1 @@
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package/dist/commands/cytoscapejs/_template-bundled.d.ts

@@ -0,0 +1,2 @@
+export declare const CYTOSCAPE_HTML_TEMPLATE = "<!doctype html>\n\n<html>\n\n<head>\n    <title>Galaxy Workflow</title>\n    <script src=\"https://unpkg.com/cytoscape@3.33.2/dist/cytoscape.min.js\"></script>\n    <script src=\"https://unpkg.com/dagre@0.8.5/dist/dagre.min.js\"></script>\n    <script src=\"https://unpkg.com/cytoscape-dagre@2.5.0/cytoscape-dagre.js\"></script>\n    <script src=\"https://unpkg.com/@popperjs/core@2.11.8/dist/umd/popper.min.js\"></script>\n    <script src=\"https://unpkg.com/cytoscape-popper@2.0.0/cytoscape-popper.js\"></script>\n    <script src=\"https://unpkg.com/tippy.js@6.3.7/dist/tippy.umd.min.js\"></script>\n    <link rel=\"stylesheet\" href=\"https://unpkg.com/tippy.js@6.3.7/dist/tippy.css\" />\n    <script>\ndocument.addEventListener(\"DOMContentLoaded\", function() {\n    var requestedLayout = $layout;\n    var dagreReady = (typeof cytoscapeDagre !== 'undefined');\n    if (dagreReady && cytoscape.use) {\n        try { cytoscape.use(cytoscapeDagre); } catch (e) { /* already registered */ }\n    }\n    var layoutConfig = (function(name) {\n        if (name === 'dagre') {\n            return dagreReady\n                ? { name: 'dagre', rankDir: 'LR', nodeSep: 40, rankSep: 80 }\n                : { name: 'preset' };\n        }\n        if (name === 'breadthfirst') return { name: 'breadthfirst', directed: true, spacingFactor: 1.2 };\n        if (name === 'grid') return { name: 'grid' };\n        if (name === 'cose') return { name: 'cose' };\n        if (name === 'random') return { name: 'random' };\n        if (name === 'topological') return { name: 'preset' };\n        return { name: 'preset' };\n    })(requestedLayout);\n    var cy = cytoscape({\n        container: document.getElementById('cy'),\n        elements: $elements,\n        layout: layoutConfig,\n        // so we can see the ids\n        style: [\n            {\n                selector: 'node',\n                style: {\n                    'label': 'data(label)'\n                }\n            },\n            {\n                selector: 'edge',\n                style: {\n                    'curve-style': 'bezier',\n                    'target-arrow-shape': 'vee',\n                    'arrow-scale': 2\n                }\n            },\n            {\n                selector: \".input\",\n                style: {\n                    shape: 'diamond',\n                    'background-color': '#d0bb46'\n                }\n            },\n            {\n                selector: \".runnable\",\n                style: {\n                    shape: 'round-rectangle',\n                    'background-color': '#2c3143'\n                }\n            },\n            {\n                selector: 'edge.mapover_1',\n                style: { width: 4, 'line-color': '#5a8' }\n            },\n            {\n                selector: 'edge.mapover_2',\n                style: { width: 6, 'line-color': '#5a8' }\n            },\n            {\n                selector: 'edge.mapover_3',\n                style: { width: 8, 'line-color': '#5a8' }\n            },\n            {\n                selector: 'edge.reduction',\n                style: {\n                    'line-style': 'dashed',\n                    'line-color': '#a55',\n                    'target-arrow-shape': 'tee',\n                    'target-arrow-color': '#a55'\n                }\n            }\n        ]\n      });\n\n  function makePopper(ele) {\n    let ref = ele.popperRef(); // used only for positioning\n    let dummyDomEle = document.createElement('div');\n\n    ele.tippy = tippy(dummyDomEle, { // tippy options:\n      getReferenceClientRect: ref.getBoundingClientRect.bind(ref),\n      content: function() {\n        let content = document.createElement('div');\n\n        let innerHTML = '';\n        if(ele.isNode()) {\n            let stepType = ele.data(\"step_type\");\n            innerHTML +=  \"<p><i>Step Type:</i> \" + stepType + \"</p>\";\n            let toolId = ele.data(\"tool_id\");\n            if (toolId) {\n                innerHTML +=  \"<p><i>ToolID:</i> \" + toolId + \"</p>\";\n            }\n            let repoLink = ele.data(\"repo_link\");\n            if (repoLink) {\n                innerHTML += \"<a href=\" + repoLink + '\">Visit Tool Shed Repository</a>';\n            }\n            let doc = ele.data('doc');\n            if (doc) {\n                innerHTML += \"<p>\" + doc + \"</p>\";\n            }\n        } else {\n            let output = ele.data(\"output\");\n            let input = ele.data(\"input\");\n            if(output) {\n                innerHTML += \"Output named \" + output + \" connects to \" + input;\n            } else {\n                innerHTML += \"Connected to input \" + input;\n            }\n            let mapDepth = ele.data(\"map_depth\");\n            if (mapDepth) {\n                let mapping = ele.data(\"mapping\");\n                innerHTML += \"<p><i>Map depth:</i> \" + mapDepth + (mapping ? \" (\" + mapping + \")\" : \"\") + \"</p>\";\n            }\n            if (ele.data(\"reduction\")) {\n                innerHTML += \"<p><i>Reduction:</i> list \u2192 multi-data</p>\";\n            }\n        }\n        content.innerHTML = innerHTML;\n\n        return content;\n      },\n      delay: [0,1000],\n      interactive: true,\n      placement: 'bottom',\n      trigger: 'manual', // probably want manual mode\n      appendTo: document.body\n    });\n  }\n\n cy.ready(function() {\n    cy.elements().forEach(function(ele) {\n      makePopper(ele);\n    });\n  });\n\n  cy.elements().unbind('mouseover');\n  cy.elements().bind('mouseover', function(event) { event.target.tippy.show(); });\n\n  cy.elements().unbind('mouseout');\n  cy.elements().bind('mouseout', function(event) { event.target.tippy.hide(); });\n  // document.querySelector('#cypng').setAttribute('src', cy.png());\n});\n\n    </script>\n</head>\n\n<style>\n    #cy {\n        width: 100%;\n        height: 100%;\n        position: absolute;\n        top: 0px;\n        left: 0px;\n    }\n    a {\n        color: #d0bb46\n    }\n</style>\n\n<body>\n    <div id=\"cy\"></div>\n</body>\n</html>\n";
+//# sourceMappingURL=_template-bundled.d.ts.map

package/dist/commands/cytoscapejs/_template-bundled.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"_template-bundled.d.ts","sourceRoot":"","sources":["../../../src/commands/cytoscapejs/_template-bundled.ts"],"names":[],"mappings":"AACA,eAAO,MAAM,uBAAuB,s/LAmLnC,CAAC"}

package/dist/commands/cytoscapejs/_template-bundled.js

@@ -0,0 +1,182 @@
+// AUTO-GENERATED by scripts/bundle-templates.mjs — do not edit.
+export const CYTOSCAPE_HTML_TEMPLATE = `<!doctype html>
+
+<html>
+
+<head>
+    <title>Galaxy Workflow</title>
+    <script src="https://unpkg.com/cytoscape@3.33.2/dist/cytoscape.min.js"></script>
+    <script src="https://unpkg.com/dagre@0.8.5/dist/dagre.min.js"></script>
+    <script src="https://unpkg.com/cytoscape-dagre@2.5.0/cytoscape-dagre.js"></script>
+    <script src="https://unpkg.com/@popperjs/core@2.11.8/dist/umd/popper.min.js"></script>
+    <script src="https://unpkg.com/cytoscape-popper@2.0.0/cytoscape-popper.js"></script>
+    <script src="https://unpkg.com/tippy.js@6.3.7/dist/tippy.umd.min.js"></script>
+    <link rel="stylesheet" href="https://unpkg.com/tippy.js@6.3.7/dist/tippy.css" />
+    <script>
+document.addEventListener("DOMContentLoaded", function() {
+    var requestedLayout = $layout;
+    var dagreReady = (typeof cytoscapeDagre !== 'undefined');
+    if (dagreReady && cytoscape.use) {
+        try { cytoscape.use(cytoscapeDagre); } catch (e) { /* already registered */ }
+    }
+    var layoutConfig = (function(name) {
+        if (name === 'dagre') {
+            return dagreReady
+                ? { name: 'dagre', rankDir: 'LR', nodeSep: 40, rankSep: 80 }
+                : { name: 'preset' };
+        }
+        if (name === 'breadthfirst') return { name: 'breadthfirst', directed: true, spacingFactor: 1.2 };
+        if (name === 'grid') return { name: 'grid' };
+        if (name === 'cose') return { name: 'cose' };
+        if (name === 'random') return { name: 'random' };
+        if (name === 'topological') return { name: 'preset' };
+        return { name: 'preset' };
+    })(requestedLayout);
+    var cy = cytoscape({
+        container: document.getElementById('cy'),
+        elements: $elements,
+        layout: layoutConfig,
+        // so we can see the ids
+        style: [
+            {
+                selector: 'node',
+                style: {
+                    'label': 'data(label)'
+                }
+            },
+            {
+                selector: 'edge',
+                style: {
+                    'curve-style': 'bezier',
+                    'target-arrow-shape': 'vee',
+                    'arrow-scale': 2
+                }
+            },
+            {
+                selector: ".input",
+                style: {
+                    shape: 'diamond',
+                    'background-color': '#d0bb46'
+                }
+            },
+            {
+                selector: ".runnable",
+                style: {
+                    shape: 'round-rectangle',
+                    'background-color': '#2c3143'
+                }
+            },
+            {
+                selector: 'edge.mapover_1',
+                style: { width: 4, 'line-color': '#5a8' }
+            },
+            {
+                selector: 'edge.mapover_2',
+                style: { width: 6, 'line-color': '#5a8' }
+            },
+            {
+                selector: 'edge.mapover_3',
+                style: { width: 8, 'line-color': '#5a8' }
+            },
+            {
+                selector: 'edge.reduction',
+                style: {
+                    'line-style': 'dashed',
+                    'line-color': '#a55',
+                    'target-arrow-shape': 'tee',
+                    'target-arrow-color': '#a55'
+                }
+            }
+        ]
+      });
+
+  function makePopper(ele) {
+    let ref = ele.popperRef(); // used only for positioning
+    let dummyDomEle = document.createElement('div');
+
+    ele.tippy = tippy(dummyDomEle, { // tippy options:
+      getReferenceClientRect: ref.getBoundingClientRect.bind(ref),
+      content: function() {
+        let content = document.createElement('div');
+
+        let innerHTML = '';
+        if(ele.isNode()) {
+            let stepType = ele.data("step_type");
+            innerHTML +=  "<p><i>Step Type:</i> " + stepType + "</p>";
+            let toolId = ele.data("tool_id");
+            if (toolId) {
+                innerHTML +=  "<p><i>ToolID:</i> " + toolId + "</p>";
+            }
+            let repoLink = ele.data("repo_link");
+            if (repoLink) {
+                innerHTML += "<a href=" + repoLink + '">Visit Tool Shed Repository</a>';
+            }
+            let doc = ele.data('doc');
+            if (doc) {
+                innerHTML += "<p>" + doc + "</p>";
+            }
+        } else {
+            let output = ele.data("output");
+            let input = ele.data("input");
+            if(output) {
+                innerHTML += "Output named " + output + " connects to " + input;
+            } else {
+                innerHTML += "Connected to input " + input;
+            }
+            let mapDepth = ele.data("map_depth");
+            if (mapDepth) {
+                let mapping = ele.data("mapping");
+                innerHTML += "<p><i>Map depth:</i> " + mapDepth + (mapping ? " (" + mapping + ")" : "") + "</p>";
+            }
+            if (ele.data("reduction")) {
+                innerHTML += "<p><i>Reduction:</i> list → multi-data</p>";
+            }
+        }
+        content.innerHTML = innerHTML;
+
+        return content;
+      },
+      delay: [0,1000],
+      interactive: true,
+      placement: 'bottom',
+      trigger: 'manual', // probably want manual mode
+      appendTo: document.body
+    });
+  }
+
+ cy.ready(function() {
+    cy.elements().forEach(function(ele) {
+      makePopper(ele);
+    });
+  });
+
+  cy.elements().unbind('mouseover');
+  cy.elements().bind('mouseover', function(event) { event.target.tippy.show(); });
+
+  cy.elements().unbind('mouseout');
+  cy.elements().bind('mouseout', function(event) { event.target.tippy.hide(); });
+  // document.querySelector('#cypng').setAttribute('src', cy.png());
+});
+
+    </script>
+</head>
+
+<style>
+    #cy {
+        width: 100%;
+        height: 100%;
+        position: absolute;
+        top: 0px;
+        left: 0px;
+    }
+    a {
+        color: #d0bb46
+    }
+</style>
+
+<body>
+    <div id="cy"></div>
+</body>
+</html>
+`;
+//# sourceMappingURL=_template-bundled.js.map

package/dist/commands/cytoscapejs/_template-bundled.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"_template-bundled.js","sourceRoot":"","sources":["../../../src/commands/cytoscapejs/_template-bundled.ts"],"names":[],"mappings":"AAAA,gEAAgE;AAChE,MAAM,CAAC,MAAM,uBAAuB,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAmLtC,CAAC"}

package/dist/commands/cytoscapejs.d.ts

@@ -0,0 +1,12 @@
+import type { CytoscapeElements, LayoutName } from "@galaxy-tool-util/schema";
+export interface CytoscapeJsCommandOptions {
+    output?: string;
+    html?: boolean;
+    json?: boolean;
+    annotateConnections?: boolean;
+    cacheDir?: string;
+    layout?: string;
+}
+export declare function renderHtml(elements: CytoscapeElements, layout?: LayoutName): string;
+export declare function runCytoscapeJs(filePath: string, opts: CytoscapeJsCommandOptions): Promise<void>;
+//# sourceMappingURL=cytoscapejs.d.ts.map

package/dist/commands/cytoscapejs.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"cytoscapejs.d.ts","sourceRoot":"","sources":["../../src/commands/cytoscapejs.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,0BAA0B,CAAC;AAO9E,MAAM,WAAW,yBAAyB;IACxC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,wBAAgB,UAAU,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,GAAE,UAAqB,GAAG,MAAM,CAQ7F;AAmBD,wBAAsB,cAAc,CAClC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,yBAAyB,GAC9B,OAAO,CAAC,IAAI,CAAC,CA+Bf"}

package/dist/commands/cytoscapejs.js

@@ -0,0 +1,62 @@
+/**
+ * `gxwf cytoscapejs` — render a Galaxy workflow as Cytoscape.js elements,
+ * either as JSON (default / `.json` output) or as a standalone HTML viewer
+ * (`.html` output).
+ *
+ * Port of gxformat2's `gxwf-viz` CLI; diverges from Python by defaulting to
+ * stdout JSON when no output path is given.
+ */
+import { cytoscapeElements, elementsToList, isLayoutName } from "@galaxy-tool-util/schema";
+import { writeFile } from "node:fs/promises";
+import { resolveEdgeAnnotations } from "./annotate-connections.js";
+import { CYTOSCAPE_HTML_TEMPLATE } from "./cytoscapejs/_template-bundled.js";
+import { readWorkflowFile } from "./workflow-io.js";
+export function renderHtml(elements, layout = "preset") {
+    const elementsJson = JSON.stringify(elementsToList(elements));
+    // Python uses string.Template.safe_substitute(...). Tokens are $elements
+    // and $layout (a quoted string the template embeds inside `layout: { name: ... }`).
+    return CYTOSCAPE_HTML_TEMPLATE.replaceAll("$elements", elementsJson).replaceAll("$layout", JSON.stringify(layout));
+}
+function chooseFormat(opts) {
+    if (opts.html)
+        return "html";
+    if (opts.json)
+        return "json";
+    if (opts.output?.endsWith(".html"))
+        return "html";
+    return "json";
+}
+function resolveLayout(raw) {
+    if (raw == null)
+        return "preset";
+    if (!isLayoutName(raw)) {
+        throw new Error(`Unknown --layout "${raw}". Valid values: preset, topological, dagre, breadthfirst, grid, cose, random.`);
+    }
+    return raw;
+}
+export async function runCytoscapeJs(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data)
+        return;
+    const layout = resolveLayout(opts.layout);
+    const edgeAnnotations = opts.annotateConnections
+        ? await resolveEdgeAnnotations(data, { cacheDir: opts.cacheDir })
+        : undefined;
+    const elements = cytoscapeElements(data, { edgeAnnotations, layout });
+    const format = chooseFormat(opts);
+    // JSON shape: bare list when layout=preset (Python parity), wrapped
+    // {elements, layout} when caller opted in to a non-default layout. The
+    // wrapper carries the hint so downstream consumers (e.g. gxwf-ui) can honor
+    // it without sniffing.
+    const jsonPayload = layout === "preset"
+        ? elementsToList(elements)
+        : { elements: elementsToList(elements), layout: { name: layout } };
+    const content = format === "html" ? renderHtml(elements, layout) : JSON.stringify(jsonPayload, null, 2);
+    if (!opts.output) {
+        process.stdout.write(content + "\n");
+        return;
+    }
+    await writeFile(opts.output, content + "\n", "utf-8");
+    console.error(`Cytoscape ${format.toUpperCase()} written to ${opts.output}`);
+}
+//# sourceMappingURL=cytoscapejs.js.map

package/dist/commands/cytoscapejs.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"cytoscapejs.js","sourceRoot":"","sources":["../../src/commands/cytoscapejs.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AACH,OAAO,EAAE,iBAAiB,EAAE,cAAc,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AAE3F,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAE7C,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAC;AACnE,OAAO,EAAE,uBAAuB,EAAE,MAAM,oCAAoC,CAAC;AAC7E,OAAO,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AAWpD,MAAM,UAAU,UAAU,CAAC,QAA2B,EAAE,SAAqB,QAAQ;IACnF,MAAM,YAAY,GAAG,IAAI,CAAC,SAAS,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAC;IAC9D,yEAAyE;IACzE,oFAAoF;IACpF,OAAO,uBAAuB,CAAC,UAAU,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC,UAAU,CAC7E,SAAS,EACT,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CACvB,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CAAC,IAA+B;IACnD,IAAI,IAAI,CAAC,IAAI;QAAE,OAAO,MAAM,CAAC;IAC7B,IAAI,IAAI,CAAC,IAAI;QAAE,OAAO,MAAM,CAAC;IAC7B,IAAI,IAAI,CAAC,MAAM,EAAE,QAAQ,CAAC,OAAO,CAAC;QAAE,OAAO,MAAM,CAAC;IAClD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,SAAS,aAAa,CAAC,GAAuB;IAC5C,IAAI,GAAG,IAAI,IAAI;QAAE,OAAO,QAAQ,CAAC;IACjC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC;QACvB,MAAM,IAAI,KAAK,CACb,qBAAqB,GAAG,gFAAgF,CACzG,CAAC;IACJ,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,QAAgB,EAChB,IAA+B;IAE/B,MAAM,IAAI,GAAG,MAAM,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAI;QAAE,OAAO;IAElB,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAE1C,MAAM,eAAe,GAAG,IAAI,CAAC,mBAAmB;QAC9C,CAAC,CAAC,MAAM,sBAAsB,CAAC,IAAI,EAAE,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC;QACjE,CAAC,CAAC,SAAS,CAAC;IAEd,MAAM,QAAQ,GAAG,iBAAiB,CAAC,IAAI,EAAE,EAAE,eAAe,EAAE,MAAM,EAAE,CAAC,CAAC;IACtE,MAAM,MAAM,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC;IAElC,oEAAoE;IACpE,uEAAuE;IACvE,4EAA4E;IAC5E,uBAAuB;IACvB,MAAM,WAAW,GACf,MAAM,KAAK,QAAQ;QACjB,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC;QAC1B,CAAC,CAAC,EAAE,QAAQ,EAAE,cAAc,CAAC,QAAQ,CAAC,EAAE,MAAM,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,CAAC;IAEvE,MAAM,OAAO,GACX,MAAM,KAAK,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,WAAW,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;IAE1F,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;QACjB,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC;QACrC,OAAO;IACT,CAAC;IACD,MAAM,SAAS,CAAC,IAAI,CAAC,MAAM,EAAE,OAAO,GAAG,IAAI,EAAE,OAAO,CAAC,CAAC;IACtD,OAAO,CAAC,KAAK,CAAC,aAAa,MAAM,CAAC,WAAW,EAAE,eAAe,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;AAC/E,CAAC"}

package/dist/commands/mermaid.d.ts

@@ -1,6 +1,8 @@
 export interface MermaidCommandOptions {
     output?: string;
     comments?: boolean;
+    annotateConnections?: boolean;
+    cacheDir?: string;
 }
 export declare function runMermaid(filePath: string, opts: MermaidCommandOptions): Promise<void>;
 //# sourceMappingURL=mermaid.d.ts.map

package/dist/commands/mermaid.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"mermaid.d.ts","sourceRoot":"","sources":["../../src/commands/mermaid.ts"],"names":[],"mappings":"AAOA,MAAM,WAAW,qBAAqB;IACpC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,qBAAqB,GAAG,OAAO,CAAC,IAAI,CAAC,CAgB7F"}
+{"version":3,"file":"mermaid.d.ts","sourceRoot":"","sources":["../../src/commands/mermaid.ts"],"names":[],"mappings":"AAQA,MAAM,WAAW,qBAAqB;IACpC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,qBAAqB,GAAG,OAAO,CAAC,IAAI,CAAC,CAoB7F"}

package/dist/commands/mermaid.js

@@ -4,11 +4,15 @@
 import { workflowToMermaid } from "@galaxy-tool-util/schema";
 import { writeFile } from "node:fs/promises";
 import { readWorkflowFile } from "./workflow-io.js";
+import { resolveEdgeAnnotations } from "./annotate-connections.js";
 export async function runMermaid(filePath, opts) {
     const data = await readWorkflowFile(filePath);
     if (!data)
         return;
-    const diagram = workflowToMermaid(data, { comments: opts.comments });
+    const edgeAnnotations = opts.annotateConnections
+        ? await resolveEdgeAnnotations(data, { cacheDir: opts.cacheDir })
+        : undefined;
+    const diagram = workflowToMermaid(data, { comments: opts.comments, edgeAnnotations });
     if (!opts.output) {
         process.stdout.write(diagram + "\n");
         return;

package/dist/commands/mermaid.js.map

@@ -1 +1 @@
-{"version":3,"file":"mermaid.js","sourceRoot":"","sources":["../../src/commands/mermaid.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAC7D,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AAOpD,MAAM,CAAC,KAAK,UAAU,UAAU,CAAC,QAAgB,EAAE,IAA2B;IAC5E,MAAM,IAAI,GAAG,MAAM,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAI;QAAE,OAAO;IAElB,MAAM,OAAO,GAAG,iBAAiB,CAAC,IAAI,EAAE,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAErE,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;QACjB,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC;QACrC,OAAO;IACT,CAAC;IAED,MAAM,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC;QACzC,CAAC,CAAC,kBAAkB,OAAO,YAAY;QACvC,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC;IACnB,MAAM,SAAS,CAAC,IAAI,CAAC,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;IAC/C,OAAO,CAAC,KAAK,CAAC,8BAA8B,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;AAC7D,CAAC"}
+{"version":3,"file":"mermaid.js","sourceRoot":"","sources":["../../src/commands/mermaid.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAC7D,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AACpD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAC;AASnE,MAAM,CAAC,KAAK,UAAU,UAAU,CAAC,QAAgB,EAAE,IAA2B;IAC5E,MAAM,IAAI,GAAG,MAAM,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAI;QAAE,OAAO;IAElB,MAAM,eAAe,GAAG,IAAI,CAAC,mBAAmB;QAC9C,CAAC,CAAC,MAAM,sBAAsB,CAAC,IAAI,EAAE,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC;QACjE,CAAC,CAAC,SAAS,CAAC;IAEd,MAAM,OAAO,GAAG,iBAAiB,CAAC,IAAI,EAAE,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,eAAe,EAAE,CAAC,CAAC;IAEtF,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;QACjB,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC;QACrC,OAAO;IACT,CAAC;IAED,MAAM,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC;QACzC,CAAC,CAAC,kBAAkB,OAAO,YAAY;QACvC,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC;IACnB,MAAM,SAAS,CAAC,IAAI,CAAC,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;IAC/C,OAAO,CAAC,KAAK,CAAC,8BAA8B,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;AAC7D,CAAC"}

package/dist/commands/summarize.d.ts

@@ -0,0 +1,31 @@
+import { type ParsedTool } from "@galaxy-tool-util/schema";
+export interface SummarizeOptions {
+    version?: string;
+    output?: string;
+    cacheDir?: string;
+}
+export interface GalaxyToolSummaryManifest {
+    schema_version: 1;
+    tool_id: string;
+    tool_version: string | null;
+    cache_key: string;
+    source: {
+        kind: "toolshed" | "galaxy" | "local" | "orphan" | "unknown";
+        label: string;
+        url: string;
+        cached_at: string | null;
+    };
+    artifacts: {
+        parsed_tool_path: string;
+        raw_tool_source_path: string | null;
+    };
+    parsed_tool: ParsedTool;
+    input_schemas: {
+        workflow_step: unknown | null;
+        workflow_step_linked: unknown | null;
+    };
+    warnings: string[];
+}
+export declare function buildToolSummaryManifest(toolId: string, opts: SummarizeOptions): Promise<GalaxyToolSummaryManifest | null>;
+export declare function runSummarize(toolId: string, opts: SummarizeOptions): Promise<void>;
+//# sourceMappingURL=summarize.d.ts.map

package/dist/commands/summarize.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"summarize.d.ts","sourceRoot":"","sources":["../../src/commands/summarize.ts"],"names":[],"mappings":"AAGA,OAAO,EAEL,KAAK,UAAU,EAGhB,MAAM,0BAA0B,CAAC;AAIlC,MAAM,WAAW,gBAAgB;IAC/B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,yBAAyB;IACxC,cAAc,EAAE,CAAC,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE;QACN,IAAI,EAAE,UAAU,GAAG,QAAQ,GAAG,OAAO,GAAG,QAAQ,GAAG,SAAS,CAAC;QAC7D,KAAK,EAAE,MAAM,CAAC;QACd,GAAG,EAAE,MAAM,CAAC;QACZ,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;KAC1B,CAAC;IACF,SAAS,EAAE;QACT,gBAAgB,EAAE,MAAM,CAAC;QACzB,oBAAoB,EAAE,MAAM,GAAG,IAAI,CAAC;KACrC,CAAC;IACF,WAAW,EAAE,UAAU,CAAC;IACxB,aAAa,EAAE;QACb,aAAa,EAAE,OAAO,GAAG,IAAI,CAAC;QAC9B,oBAAoB,EAAE,OAAO,GAAG,IAAI,CAAC;KACtC,CAAC;IACF,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AA+BD,wBAAsB,wBAAwB,CAC5C,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,gBAAgB,GACrB,OAAO,CAAC,yBAAyB,GAAG,IAAI,CAAC,CAwC3C;AAED,wBAAsB,YAAY,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CAUxF"}

package/dist/commands/summarize.js

@@ -0,0 +1,85 @@
+import { join } from "node:path";
+import { writeFile } from "node:fs/promises";
+import { getCacheDir, makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { createFieldModel, } from "@galaxy-tool-util/schema";
+import * as JSONSchema from "effect/JSONSchema";
+import { isResolveError, loadCachedTool } from "./resolve-tool.js";
+function sourceKind(label) {
+    if (label === "api")
+        return "toolshed";
+    if (label === "galaxy" || label === "local" || label === "orphan")
+        return label;
+    return "unknown";
+}
+function inputSchemaFor(tool, rep, warnings) {
+    const bundle = {
+        parameters: tool.inputs,
+    };
+    const effectSchema = createFieldModel(bundle, rep);
+    if (effectSchema === undefined) {
+        warnings.push(`${rep} input schema could not be generated for this tool`);
+        return null;
+    }
+    try {
+        return JSONSchema.make(effectSchema);
+    }
+    catch (err) {
+        warnings.push(`${rep} input schema generation failed: ${err instanceof Error ? err.message : String(err)}`);
+        return null;
+    }
+}
+export async function buildToolSummaryManifest(toolId, opts) {
+    const cacheDir = getCacheDir(opts.cacheDir);
+    const cache = makeNodeToolCache({ cacheDir });
+    await cache.index.load();
+    const result = await loadCachedTool(cache, toolId, opts.version);
+    if (isResolveError(result)) {
+        if (result.kind === "no_version") {
+            console.error(`No version specified for tool: ${toolId}`);
+        }
+        else {
+            console.error(`Tool not found in cache: ${toolId}. Run 'galaxy-tool-cache add' first.`);
+        }
+        process.exitCode = 1;
+        return null;
+    }
+    const indexEntry = (await cache.index.listAll()).find((entry) => entry.cache_key === result.key);
+    const warnings = [];
+    const manifest = {
+        schema_version: 1,
+        tool_id: result.tool.id,
+        tool_version: result.tool.version,
+        cache_key: result.key,
+        source: {
+            kind: sourceKind(indexEntry?.source),
+            label: indexEntry?.source ?? "unknown",
+            url: indexEntry?.source_url ?? "",
+            cached_at: indexEntry?.cached_at ?? null,
+        },
+        artifacts: {
+            parsed_tool_path: join(cacheDir, `${result.key}.json`),
+            raw_tool_source_path: null,
+        },
+        parsed_tool: result.tool,
+        input_schemas: {
+            workflow_step: inputSchemaFor(result.tool, "workflow_step", warnings),
+            workflow_step_linked: inputSchemaFor(result.tool, "workflow_step_linked", warnings),
+        },
+        warnings,
+    };
+    return manifest;
+}
+export async function runSummarize(toolId, opts) {
+    const manifest = await buildToolSummaryManifest(toolId, opts);
+    if (manifest === null)
+        return;
+    const output = `${JSON.stringify(manifest, null, 2)}\n`;
+    if (opts.output) {
+        await writeFile(opts.output, output);
+        console.log(`Summary written to ${opts.output}`);
+    }
+    else {
+        process.stdout.write(output);
+    }
+}
+//# sourceMappingURL=summarize.js.map

package/dist/commands/summarize.js.map

@@ -0,0 +1 @@
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package/dist/commands/validate-workflow.d.ts

@@ -11,6 +11,7 @@ export interface ValidateWorkflowOptions extends StrictOptions {
     toolSchemaDir?: string;
     json?: boolean;
     reportHtml?: string | boolean;
+    connections?: boolean;
 }
 /** Run Effect Schema decode on raw workflow data and return structural decode failures. */
 export declare function decodeStructureErrors(data: Record<string, unknown>, format: WorkflowFormat): string[];

package/dist/commands/validate-workflow.d.ts.map

@@ -1 +1 @@
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