@galaxy-tool-util/cli 0.1.0 → 0.4.0

package/dist/workflow/_templates-bundled.js

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+// AUTO-GENERATED by scripts/bundle-templates.mjs — do not edit.
+export const BUNDLED_TEMPLATES = {
+    "_macros.md.j2": `{#-
+  Shared macros for workflow_state report templates.
+
+  IMPORTANT: every construct used here must also be valid in Nunjucks so
+  the TypeScript mirror can render identical markdown. That means: only
+  \`for\`, \`if\`, \`set\`, \`macro\`, \`import\`, \`include\`, and the shared-subset
+  filters (\`length\`, \`default\`, \`upper\`, \`lower\`, \`replace\`, \`join\`,
+  \`sort\`, \`selectattr\`). No custom filters, no globals.
+-#}
+
+{#-
+  status_badge(label)
+  Renders the summary-line badge shared across every report header.
+-#}
+{% macro status_badge(label) -%}
+**Status:** {{ label }}
+{%- endmacro %}
+
+{#-
+  kv_summary(summary)
+  Render a dict-of-counts as \`\`key: value, key: value\`\` (insertion order
+  is preserved by Pydantic \`\`model_dump\`\`, so upstream models control
+  ordering). Used under the status badge in every report header.
+-#}
+{% macro kv_summary(summary) -%}
+{% for key, value in summary.items() -%}
+{{ key }}: {{ value }}{% if not loop.last %}, {% endif %}
+{%- endfor %}
+{%- endmacro %}
+
+{#-
+  workflow_state_cells(r)
+  Renders the 5 trailing cells of a workflow table row — handling the
+  error / skipped / ok three-branch logic that every current
+  \`\`format_*_markdown\`\` reimplements. \`\`r\`\` is the json-dumped
+  workflow result dict.
+
+  Expected columns (Total | OK | Fail | Skip | Details). Callers provide
+  the leading \`\`| name\`\` cell themselves so they can choose how to label
+  it (basename, relative_path, etc.).
+-#}
+{% macro workflow_state_cells(r) -%}
+{% if r.skipped_reason -%}
+- | - | - | - | SKIPPED: {{ r.skipped_reason }}
+{%- elif r.error -%}
+- | - | - | - | ERROR: {{ r.error }}
+{%- else -%}
+{% set s = r.summary %}
+{{ (r.results | length) }} | {{ s.ok }} | {{ s.fail }} | {{ s.skip }} |
+{%- endif %}
+{%- endmacro %}
+
+{#-
+  failure_bullet(f)
+  Renders a single \`\`all_failures\`\` entry as a markdown bullet. The input
+  dict has keys \`\`workflow\`\`, \`\`step\`\`, \`\`tool_id\`\`, \`\`message\`\`.
+-#}
+{% macro failure_bullet(f) -%}
+- **{{ f.workflow }}** Step {{ f.step }} ({{ f.tool_id }}): {{ f.message }}
+{%- endmacro %}
+`,
+    "clean_tree.md.j2": `{#-
+  Tree-level report for \`\`gxwf-state-clean\`\`.
+
+  Three sections: affected-workflows table, clean-workflows banner, and
+  per-workflow detail bullets. Uses \`\`selectattr("removed_keys")\`\` and
+  \`\`selectattr("total_removed")\`\` for filtering, \`\`loop.first\`\` to gate
+  the Per-Workflow Details header, and the \`\`steps_affected\`\` +
+  \`\`display_label\`\` computed fields landed in step 1.
+
+  Context:
+    report — TreeCleanReport as json-dumped dict (\`\`results\`\` → \`\`workflows\`\`)
+    meta   — ignored here; kept for uniform signature
+-#}
+# Stale State Cleaning Report
+
+Root: \`{{ report.root }}\`
+Workflows: {{ report.workflows | length }} | {{ report.summary.total_keys }} stale key(s) across {{ report.summary.affected }} workflow(s)
+
+{% if report.summary.affected > 0 or report.summary.errors > 0 %}
+## Affected Workflows
+
+| Workflow | Steps Affected | Keys Removed | Details |
+| --- | --- | --- | --- |
+{% for r in report.workflows %}
+{% if r.error %}
+| {{ r.path }} | - | - | ERROR: {{ r.error }} |
+{% elif r.total_removed > 0 %}
+| {{ r.path }} | {{ r.steps_affected }} | {{ r.total_removed }} | {% for sr in r.results | selectattr("removed_keys") %}Step {{ sr.step }} ({{ sr.tool_id }}): {{ sr.removed_keys | join(", ") }}{% if not loop.last %}; {% endif %}{% endfor %} |
+{% endif %}
+{% endfor %}
+
+{% endif %}
+{% if report.summary.clean > 0 %}
+## Clean Workflows ({{ report.summary.clean }})
+
+All other workflows have no stale keys.
+
+{% endif %}
+{% for r in report.workflows | selectattr("total_removed") %}
+{% if loop.first %}
+## Per-Workflow Details
+
+{% endif %}
+### {{ r.path }}
+{% for sr in r.results | selectattr("removed_keys") %}
+- Step {{ sr.step }} ({{ sr.display_label }}): Removed \`{{ sr.removed_keys | join("\`, \`") }}\`
+{% endfor %}
+
+{% endfor %}
+`,
+    "connection_section.md.j2": `{#-
+  Connection validation section.
+
+  Ported verbatim from \`\`validate.format_connection_markdown\`\`. Standalone
+  renderer today; also an include target for \`\`validate_tree.md.j2\`\` when a
+  workflow carries a \`\`connection_report\`\`.
+
+  Context:
+    report — ConnectionValidationReport as json-dumped dict
+-#}
+{% set s = report.summary %}
+{% set valid_label = "VALID" if report.valid else "INVALID" %}
+## Connection Validation
+
+**Status:** {{ valid_label }}
+**Connections:** {{ s.ok | default(0) }} OK, {{ s.invalid | default(0) }} INVALID, {{ s.skip | default(0) }} SKIP
+{% if report.has_details %}
+
+| Source | Target | Status | Mapping | Errors |
+| --- | --- | --- | --- | --- |
+{% for sr in report.step_results %}
+{%   for cr in sr.connections %}
+{%     set mapping_cell = cr.mapping if cr.mapping else "-" %}
+{%     set errors_cell = cr.errors | join("; ") if cr.errors else "-" %}
+| {{ cr.source_step }}/{{ cr.source_output }} | {{ cr.target_step }}/{{ cr.target_input }} | {{ cr.status }} | {{ mapping_cell }} | {{ errors_cell }} |
+{%   endfor %}
+{%   for err in sr.errors %}
+{%     set step_label = (sr.step ~ " (" ~ sr.tool_id ~ ")") if sr.tool_id else sr.step %}
+| - | {{ step_label }} | error | - | {{ err }} |
+{%   endfor %}
+{% endfor %}
+{% endif %}
+`,
+    "export_tree.md.j2": `{#-
+  Tree-level report for \`\`gxwf-to-format2-stateful\`\`.
+
+  Pure port of \`\`export_format2._format_tree_markdown\`\`. Content improvements
+  (category grouping, per-tool fallback aggregation, skipped appendix) are
+  deferred to follow-up commits — per the plan, per-tool fallback aggregation
+  needs step-level \`\`tool_id\`\` plumbing that is out of scope here.
+
+  Context:
+    report — ExportTreeReport as json-dumped dict (\`\`results\`\` → \`\`workflows\`\`)
+    meta   — ignored here; kept for uniform signature
+-#}
+# Export Report: {{ report.root }}
+
+{% for r in report.workflows %}
+{% if r.error %}
+- **{{ r.path }}**: ERROR ({{ r.error }})
+{% elif r.skipped_reason %}
+- **{{ r.path }}**: SKIPPED ({{ r.skipped_reason }})
+{% elif r.ok %}
+- **{{ r.path }}**: OK ({{ r.steps_converted }} steps)
+{% else %}
+- **{{ r.path }}**: PARTIAL ({{ r.steps_fallback }} fallbacks)
+{% endif %}
+{% endfor %}
+
+**Summary**: {{ report.summary.ok }} OK, {{ report.summary.fail }} errors, {{ report.summary.skipped }} skipped
+`,
+    "lint_tree.md.j2": `{#-
+  Tree-level report for \`\`gxwf-lint-stateful\`\`.
+
+  Pure port of \`\`lint_stateful._format_lint_tree_markdown\`\` — single wide
+  table with one row per workflow. Uses the \`\`step_counts\`\` computed field
+  on \`\`LintWorkflowResult\`\` instead of re-looping \`\`results\`\`.
+
+  Content improvements deferred — surfacing lint messages and exit-code
+  meaning needs model + pipeline changes called out in the plan's
+  Step 1 "out of scope" list.
+
+  Context:
+    report — LintTreeReport as json-dumped dict (\`\`results\`\` → \`\`workflows\`\`)
+    meta   — ignored here; kept for uniform signature
+-#}
+# Lint Report
+
+Root: \`{{ report.root }}\`
+Workflows: {{ report.workflows | length }} | Lint: {{ report.summary.lint_errors }} errors, {{ report.summary.lint_warnings }} warnings | State: {{ report.summary.state_ok }} OK, {{ report.summary.state_fail }} FAIL, {{ report.summary.state_skip }} SKIP
+
+| Workflow | Lint Errors | Lint Warnings | State OK | State Fail | State Skip |
+| --- | --- | --- | --- | --- | --- |
+{% for r in report.workflows %}
+{% if r.error %}
+| {{ r.path }} | - | - | - | - | ERROR: {{ r.error }} |
+{% elif r.skipped_reason %}
+| {{ r.path }} | - | - | - | - | SKIPPED |
+{% else %}
+| {{ r.path }} | {{ r.lint_errors }} | {{ r.lint_warnings }} | {{ r.step_counts.ok }} | {{ r.step_counts.fail }} | {{ r.step_counts.skip }} |
+{% endif %}
+{% endfor %}
+`,
+    "roundtrip_tree.md.j2": `{#-
+  Tree-level report for \`\`gxwf-roundtrip-validate-tree\`\`.
+
+  Pure port of \`\`roundtrip.format_roundtrip_markdown\`\`. Flat bullet list
+  per workflow with sub-bullets for conversion failures and error diffs.
+
+  Context:
+    report — RoundTripTreeReport as json-dumped dict (\`\`results\`\` → \`\`workflows\`\`)
+    meta   — ignored here; kept for uniform signature
+-#}
+{% set s = report.summary %}
+# Roundtrip Validation: {{ report.root }}
+
+**{{ report.total }} workflows:** {{ s.clean }} clean, {{ s.benign_only }} benign, {{ s.fail }} fail, {{ s.error }} error, {{ s.skipped }} skipped
+
+{% for r in report.workflows %}
+{% set benign = r.benign_diffs | length %}
+{% set error_count = r.error_diffs | length %}
+{% set detail = "" %}
+{% if benign %}{% set detail = detail ~ " (" ~ benign ~ " benign)" %}{% endif %}
+{% if error_count %}{% set detail = detail ~ " (" ~ error_count ~ " errors)" %}{% endif %}
+- **{{ r.workflow_path }}**: {{ r.status | upper }}{{ detail }}
+{% for line in r.conversion_failure_lines %}
+  - {{ line }}
+{% endfor %}
+{% for d in r.error_diffs %}
+  - {{ d.step_path }}: {{ d.description }}
+{% endfor %}
+{% endfor %}
+`,
+    "to_native_tree.md.j2": `{#-
+  Tree-level report for \`\`gxwf-to-native-stateful\`\`.
+
+  Pure port of \`\`to_native_stateful._format_tree_markdown\`\`. Structure is
+  identical to \`\`export_tree.md.j2\`\` — same four branches, only the H1 and
+  the OK-branch count field (\`\`steps_encoded\`\` vs \`\`steps_converted\`\`)
+  differ. Content improvements deferred, same rationale as export.
+
+  Context:
+    report — ToNativeTreeReport as json-dumped dict (\`\`results\`\` → \`\`workflows\`\`)
+    meta   — ignored here; kept for uniform signature
+-#}
+# Conversion Report: {{ report.root }}
+
+{% for r in report.workflows %}
+{% if r.error %}
+- **{{ r.path }}**: ERROR ({{ r.error }})
+{% elif r.skipped_reason %}
+- **{{ r.path }}**: SKIPPED ({{ r.skipped_reason }})
+{% elif r.ok %}
+- **{{ r.path }}**: OK ({{ r.steps_encoded }} steps)
+{% else %}
+- **{{ r.path }}**: PARTIAL ({{ r.steps_fallback }} fallbacks)
+{% endif %}
+{% endfor %}
+
+**Summary**: {{ report.summary.ok }} OK, {{ report.summary.fail }} errors, {{ report.summary.skipped }} skipped
+`,
+    "validate_tree.md.j2": `{#-
+  Tree-level report for \`\`gxwf-state-validate\`\`.
+
+  Pure port of \`\`validate.format_tree_markdown\`\`. Per-category tables with
+  a Details column showing failure counts, a Failure Details appendix using
+  \`\`report.all_failures\`\`, and per-workflow connection sections via
+  \`\`{% include "connection_section.md.j2" %}\`\`.
+
+  The \`\`workflow_state_cells\`\` macro is NOT used here because the validate
+  table has a 6th "Details" column whose content varies (failure count for
+  normal rows, SKIPPED/ERROR for exceptional rows) — inlining the 3-branch
+  logic keeps the template straightforward.
+
+  Context:
+    report — TreeValidationReport as json-dumped dict (\`\`results\`\` → \`\`workflows\`\`)
+    meta   — ignored here; kept for uniform signature
+-#}
+{% import "_macros.md.j2" as m %}
+{% set s = report.summary %}
+# Workflow Validation Report
+
+Root: \`{{ report.root }}\`
+Workflows: {{ report.workflows | length }} | Steps: {{ s.ok }} OK, {{ s.fail }} FAIL, {{ s.skip }} SKIP, {{ s.error }} ERROR{% if s.skipped %} | {{ s.skipped }} workflow(s) skipped{% endif %}
+
+
+{% for cat in report.categories %}
+## {{ cat.name }} ({{ cat.results | length }} workflows)
+
+| Workflow | Steps | OK | Fail | Skip | Details |
+| --- | --- | --- | --- | --- | --- |
+{% for r in cat.results %}
+{% if r.skipped_reason %}
+| {{ r.name }} | - | - | - | - | SKIPPED: {{ r.skipped_reason }} |
+{% elif r.error %}
+| {{ r.name }} | - | - | - | - | ERROR: {{ r.error }} |
+{% else %}
+{% set fail_count = r.failures | length %}
+| {{ r.name }} | {{ r.results | length }} | {{ r.summary.ok }} | {{ r.summary.fail }} | {{ r.summary.skip }} | {% if fail_count %}{{ fail_count }} failure(s){% endif %} |
+{% endif %}
+{% endfor %}
+
+{% endfor %}
+{% if report.all_failures %}
+## Failure Details
+
+{% for f in report.all_failures %}
+{{ m.failure_bullet(f) }}
+{% endfor %}
+
+{% endif %}
+{% for r in report.workflows | selectattr("connection_report") %}
+## Connections: {{ r.path }}
+
+{% set report = r.connection_report %}
+{% include "connection_section.md.j2" %}
+
+{% endfor %}
+`,
+};
+//# sourceMappingURL=_templates-bundled.js.map

package/dist/workflow/_templates-bundled.js.map

@@ -0,0 +1 @@
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package/dist/workflow/report-templates.d.ts

@@ -0,0 +1,13 @@
+export interface ReportMeta {
+    generated_at?: string;
+    tool_util_version?: string;
+}
+/**
+ * Render a Markdown report template by name.
+ *
+ * @param templateName - e.g. `"validate_tree.md.j2"`
+ * @param report - the tree report object (plain JSON-serialisable value)
+ * @param meta - optional metadata (generated_at, tool_util_version)
+ */
+export declare function renderReport(templateName: string, report: unknown, meta?: ReportMeta): Promise<string>;
+//# sourceMappingURL=report-templates.d.ts.map

package/dist/workflow/report-templates.d.ts.map

@@ -0,0 +1 @@
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package/dist/workflow/report-templates.js

@@ -0,0 +1,91 @@
+/**
+ * Nunjucks renderer for workflow_state tree-level Markdown reports.
+ *
+ * Mirrors Python's `_report_templates.py`. Templates are the synced `.md.j2`
+ * files under `templates/reports/`. The Nunjucks environment aliases
+ * `_macros.md.j2` to the bundled macro file so body templates remain unchanged.
+ *
+ * Nunjucks/Jinja2 compatibility note:
+ * The synced `_macros.md.j2` uses `summary.items()` in `kv_summary`. This is
+ * valid Jinja2 but NOT Nunjucks — use plain `for k, v in obj` in Nunjucks.
+ * `kv_summary` is currently unused by all body templates, so this is latent.
+ * If a future sync adds a template that calls `kv_summary`, the `.items()` call
+ * will fail at render time. Fix in `_macros.md.j2` (TS-side) by using plain
+ * iteration; for the Python-side file the issue upstream with Python first.
+ */
+import nunjucks from "nunjucks";
+import { readFileSync } from "node:fs";
+import { join, dirname } from "node:path";
+import { fileURLToPath } from "node:url";
+// ── Template loader ──────────────────────────────────────────────────
+/**
+ * Custom Nunjucks loader that resolves templates from an in-memory map
+ * (bundled mode) with a filesystem fallback (dev/test mode).
+ */
+class ReportTemplateLoader extends nunjucks.Loader {
+    async = false;
+    bundled;
+    fsDir;
+    constructor(bundled, fsDir) {
+        super();
+        this.bundled = bundled;
+        this.fsDir = fsDir;
+    }
+    getSource(name) {
+        if (this.bundled[name] !== undefined) {
+            return { src: this.bundled[name], path: name, noCache: false };
+        }
+        // Filesystem fallback (dev/test without a prior build)
+        const fsPath = join(this.fsDir, name);
+        const src = readFileSync(fsPath, "utf-8");
+        return { src, path: fsPath, noCache: true };
+    }
+}
+// ── Lazy singleton environment ───────────────────────────────────────
+let _mdEnv;
+/** Path to `templates/reports/` resolved relative to this source file. */
+function getTemplatesDir() {
+    return join(dirname(fileURLToPath(import.meta.url)), "templates/reports");
+}
+async function loadBundled() {
+    try {
+        // Dynamic import so the module is optional (not present before `pnpm build`)
+        const mod = await import("./_templates-bundled.js");
+        return mod.BUNDLED_TEMPLATES;
+    }
+    catch {
+        return {};
+    }
+}
+async function getMdEnv() {
+    if (_mdEnv)
+        return _mdEnv;
+    const bundled = await loadBundled();
+    const loader = new ReportTemplateLoader(bundled, getTemplatesDir());
+    _mdEnv = new nunjucks.Environment(loader, {
+        autoescape: false,
+        trimBlocks: true,
+        lstripBlocks: true,
+    });
+    return _mdEnv;
+}
+// ── Public API ───────────────────────────────────────────────────────
+/**
+ * Render a Markdown report template by name.
+ *
+ * @param templateName - e.g. `"validate_tree.md.j2"`
+ * @param report - the tree report object (plain JSON-serialisable value)
+ * @param meta - optional metadata (generated_at, tool_util_version)
+ */
+export async function renderReport(templateName, report, meta) {
+    const env = await getMdEnv();
+    return new Promise((resolve, reject) => {
+        env.render(templateName, { report, meta }, (err, result) => {
+            if (err)
+                reject(err);
+            else
+                resolve(result ?? "");
+        });
+    });
+}
+//# sourceMappingURL=report-templates.js.map

package/dist/workflow/report-templates.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,11 +1,11 @@
 {
   "name": "@galaxy-tool-util/cli",
-  "version": "0.1.0",
+  "version": "0.4.0",
   "description": "galaxy-tool-cache CLI — cache and inspect Galaxy tool metadata",
   "type": "module",
   "bin": {
     "galaxy-tool-cache": "dist/bin/galaxy-tool-cache.js",
-    "galaxy-workflow-validate": "dist/bin/galaxy-workflow-validate.js"
+    "gxwf": "dist/bin/gxwf.js"
   },
   "exports": {
     ".": {
@@ -27,25 +27,27 @@
     "access": "public",
     "provenance": true
   },
-  "scripts": {
-    "build": "tsc",
-    "typecheck": "tsc --noEmit",
-    "test": "tsc --noEmit && vitest run",
-    "test:watch": "vitest",
-    "lint": "eslint src/ test/",
-    "format": "prettier --check 'src/**/*.ts' 'test/**/*.ts'",
-    "format-fix": "prettier --write 'src/**/*.ts' 'test/**/*.ts'"
-  },
   "license": "MIT",
   "dependencies": {
-    "@galaxy-tool-util/core": "workspace:*",
-    "@galaxy-tool-util/schema": "workspace:*",
     "ajv": "^8.18.0",
     "commander": "^14.0.0",
     "effect": "^3.21.0",
-    "yaml": "^2.8.3"
+    "nunjucks": "^3.2.4",
+    "yaml": "^2.8.3",
+    "@galaxy-tool-util/core": "0.3.0",
+    "@galaxy-tool-util/schema": "0.4.0"
   },
   "devDependencies": {
-    "@types/node": "^25.5.0"
+    "@types/node": "^25.5.0",
+    "@types/nunjucks": "^3.2.6"
+  },
+  "scripts": {
+    "build": "node scripts/bundle-templates.mjs && tsc",
+    "typecheck": "tsc --noEmit",
+    "test": "tsc --noEmit && vitest run",
+    "test:watch": "vitest",
+    "lint": "eslint src/ test/",
+    "format": "prettier --check 'src/**/*.ts' 'test/**/*.ts'",
+    "format-fix": "prettier --write 'src/**/*.ts' 'test/**/*.ts'"
   }
-}
+}

package/dist/bin/galaxy-workflow-validate.d.ts

@@ -1,3 +0,0 @@
-#!/usr/bin/env node
-export {};
-//# sourceMappingURL=galaxy-workflow-validate.d.ts.map

package/dist/bin/galaxy-workflow-validate.d.ts.map

@@ -1 +0,0 @@
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package/dist/bin/galaxy-workflow-validate.js

@@ -1,17 +0,0 @@
-#!/usr/bin/env node
-import { Command } from "commander";
-import { runValidateWorkflow } from "../commands/validate-workflow.js";
-const program = new Command();
-program
-    .name("galaxy-workflow-validate")
-    .description("Validate Galaxy workflow files (structure + optional tool state)")
-    .version("1.0.0")
-    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-    .option("--no-tool-state", "Skip tool state validation")
-    .option("--cache-dir <dir>", "Tool cache directory")
-    .option("--mode <mode>", "Validation backend: effect (default) or json-schema", "effect")
-    .option("--tool-schema-dir <dir>", "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)")
-    .action(runValidateWorkflow);
-program.parse();
-//# sourceMappingURL=galaxy-workflow-validate.js.map

package/dist/bin/galaxy-workflow-validate.js.map

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