@galaxy-tool-util/cli 1.1.0 → 1.3.0

package/dist/programs/galaxy-tool-cache.js

@@ -1,66 +1,24 @@
-import { Command } from "commander";
 import { runAdd } from "../commands/add.js";
 import { runList } from "../commands/list.js";
 import { runInfo } from "../commands/info.js";
 import { runClear } from "../commands/clear.js";
 import { runPopulateWorkflow } from "../commands/populate-workflow.js";
 import { runSchema } from "../commands/schema.js";
+import { runSummarize } from "../commands/summarize.js";
 import { runStructuralSchema } from "../commands/structural-schema.js";
+import { buildProgramFromSpec } from "../spec/build-program.js";
+import { galaxyToolCacheSpec } from "../meta/specs.js";
+const handlers = {
+    add: runAdd,
+    list: runList,
+    info: runInfo,
+    clear: runClear,
+    schema: runSchema,
+    summarize: runSummarize,
+    populateWorkflow: runPopulateWorkflow,
+    structuralSchema: runStructuralSchema,
+};
 export function buildGalaxyToolCacheProgram() {
-    const program = new Command();
-    program
-        .name("galaxy-tool-cache")
-        .description("Cache and inspect Galaxy tool metadata")
-        .version("1.0.0");
-    program
-        .command("add")
-        .description("Fetch a tool from ToolShed/Galaxy and cache it")
-        .argument("<tool_id>", "Tool ID (full toolshed path or TRS ID)")
-        .option("--version <ver>", "Tool version")
-        .option("--cache-dir <dir>", "Cache directory")
-        .option("--galaxy-url <url>", "Galaxy instance URL for fallback")
-        .action(runAdd);
-    program
-        .command("list")
-        .description("List cached tools")
-        .option("--json", "Output as JSON")
-        .option("--cache-dir <dir>", "Cache directory")
-        .action(runList);
-    program
-        .command("info")
-        .description("Show metadata for a cached tool")
-        .argument("<tool_id>", "Tool ID")
-        .option("--version <ver>", "Tool version")
-        .option("--cache-dir <dir>", "Cache directory")
-        .action(runInfo);
-    program
-        .command("clear")
-        .description("Clear cached tools")
-        .argument("[prefix]", "Only clear tools matching this prefix")
-        .option("--cache-dir <dir>", "Cache directory")
-        .action(runClear);
-    program
-        .command("schema")
-        .description("Export JSON Schema for a cached tool's parameters")
-        .argument("<tool_id>", "Tool ID")
-        .option("--version <ver>", "Tool version")
-        .option("--representation <rep>", "State representation (e.g., workflow_step)", "workflow_step")
-        .option("--output <file>", "Output file (default: stdout)")
-        .option("--cache-dir <dir>", "Cache directory")
-        .action(runSchema);
-    program
-        .command("populate-workflow")
-        .description("Scan a workflow and cache all referenced tools")
-        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-        .option("--cache-dir <dir>", "Cache directory")
-        .option("--galaxy-url <url>", "Galaxy instance URL for fallback")
-        .action(runPopulateWorkflow);
-    program
-        .command("structural-schema")
-        .description("Export the structural JSON Schema for Galaxy workflows")
-        .option("--format <fmt>", "Workflow format: format2 (default) or native", "format2")
-        .option("--output <file>", "Output file (default: stdout)")
-        .action(runStructuralSchema);
-    return program;
+    return buildProgramFromSpec(galaxyToolCacheSpec, handlers);
 }
 //# sourceMappingURL=galaxy-tool-cache.js.map

package/dist/programs/galaxy-tool-cache.js.map

@@ -1 +1 @@
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+{"version":3,"file":"galaxy-tool-cache.js","sourceRoot":"","sources":["../../src/programs/galaxy-tool-cache.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAClD,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,oBAAoB,EAAwB,MAAM,0BAA0B,CAAC;AACtF,OAAO,EAAE,mBAAmB,EAAE,MAAM,kBAAkB,CAAC;AAEvD,MAAM,QAAQ,GAAoB;IAChC,GAAG,EAAE,MAAM;IACX,IAAI,EAAE,OAAO;IACb,IAAI,EAAE,OAAO;IACb,KAAK,EAAE,QAAQ;IACf,MAAM,EAAE,SAAS;IACjB,SAAS,EAAE,YAAY;IACvB,gBAAgB,EAAE,mBAAmB;IACrC,gBAAgB,EAAE,mBAAmB;CACtC,CAAC;AAEF,MAAM,UAAU,2BAA2B;IACzC,OAAO,oBAAoB,CAAC,mBAAmB,EAAE,QAAQ,CAAC,CAAC;AAC7D,CAAC"}

package/dist/programs/gxwf.d.ts

@@ -1,3 +1,9 @@
-import { Command } from "commander";
+/**
+ * `gxwf` commander program — built at runtime from `spec/gxwf.json`
+ * plus the handler registry below. The JSON spec is the source of truth
+ * for the command surface; this file just wires action functions to
+ * spec entries by name.
+ */
+import type { Command } from "commander";
 export declare function buildGxwfProgram(): Command;
 //# sourceMappingURL=gxwf.d.ts.map

package/dist/programs/gxwf.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"gxwf.d.ts","sourceRoot":"","sources":["../../src/programs/gxwf.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAoBpC,wBAAgB,gBAAgB,IAAI,OAAO,CAsQ1C"}
+{"version":3,"file":"gxwf.d.ts","sourceRoot":"","sources":["../../src/programs/gxwf.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAuEzC,wBAAgB,gBAAgB,IAAI,OAAO,CAE1C"}

package/dist/programs/gxwf.js

@@ -1,4 +1,3 @@
-import { Command } from "commander";
 import { runClean } from "../commands/clean.js";
 import { runCleanTree } from "../commands/clean-tree.js";
 import { runConvert } from "../commands/convert.js";
@@ -7,6 +6,7 @@ import { runRoundtrip } from "../commands/roundtrip.js";
 import { runRoundtripTree } from "../commands/roundtrip-tree.js";
 import { runLint } from "../commands/lint.js";
 import { runMermaid } from "../commands/mermaid.js";
+import { runCytoscapeJs } from "../commands/cytoscapejs.js";
 import { runLintTree } from "../commands/lint-tree.js";
 import { runValidateWorkflow } from "../commands/validate-workflow.js";
 import { runValidateTests } from "../commands/validate-tests.js";
@@ -16,189 +16,41 @@ import { runToolSearch } from "../commands/tool-search.js";
 import { runToolVersions } from "../commands/tool-versions.js";
 import { runToolRevisions } from "../commands/tool-revisions.js";
 import { runRepoSearch } from "../commands/repo-search.js";
-import { addStrictOptions } from "../commands/strict-options.js";
+import { buildProgramFromSpec } from "../spec/build-program.js";
+import { gxwfSpec } from "../meta/specs.js";
+const handlers = {
+    validateWorkflow: runValidateWorkflow,
+    validateTests: runValidateTests,
+    clean: runClean,
+    lint: runLint,
+    convert: runConvert,
+    roundtrip: runRoundtrip,
+    mermaid: (file, output, opts) => runMermaid(file, {
+        output,
+        comments: opts.comments,
+        annotateConnections: opts.annotateConnections,
+        cacheDir: opts.cacheDir,
+    }),
+    cytoscapeJs: (file, output, opts) => runCytoscapeJs(file, {
+        output,
+        html: opts.html,
+        json: opts.json,
+        annotateConnections: opts.annotateConnections,
+        cacheDir: opts.cacheDir,
+        layout: opts.layout,
+    }),
+    validateTree: runValidateTree,
+    lintTree: runLintTree,
+    cleanTree: runCleanTree,
+    convertTree: runConvertTree,
+    roundtripTree: runRoundtripTree,
+    validateTestsTree: runValidateTestsTree,
+    toolSearch: runToolSearch,
+    toolVersions: runToolVersions,
+    toolRevisions: runToolRevisions,
+    repoSearch: runRepoSearch,
+};
 export function buildGxwfProgram() {
-    const program = new Command();
-    program
-        .name("gxwf")
-        .description("Galaxy workflow operations — validate, clean, lint, convert (single-file and tree)")
-        .version("1.0.0");
-    addStrictOptions(program
-        .command("validate")
-        .description("Validate Galaxy workflow files (structure + optional tool state)")
-        .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)")
-        .option("--json", "Output structured JSON report")
-        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runValidateWorkflow);
-    program
-        .command("validate-tests")
-        .description("Validate a workflow-test file (*-tests.yml, *.gxwf-tests.yml) against the Galaxy Tests schema")
-        .argument("<file>", "Tests file (*-tests.yml)")
-        .option("--json", "Output structured JSON report")
-        .option("--workflow <path>", "Cross-check job inputs + output assertions against a workflow (.ga / .gxwf.yml)")
-        .action(runValidateTests);
-    program
-        .command("clean")
-        .description("Strip stale keys and decode legacy tool_state encoding")
-        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-        .option("--output <file>", "Write cleaned workflow to file (default: stdout)")
-        .option("--diff", "Show diff of changes instead of writing output")
-        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-        .option("--json", "Output structured JSON report")
-        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")
-        .option("--skip-uuid", "Skip stripping uuid fields (errors are always stripped)")
-        .action(runClean);
-    addStrictOptions(program
-        .command("lint")
-        .description("Lint Galaxy workflow — structural checks, best practices, tool state validation")
-        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-        .option("--skip-best-practices", "Skip annotation/creator/license/label checks")
-        .option("--skip-state-validation", "Skip tool state validation against cached tool definitions")
-        .option("--cache-dir <dir>", "Tool cache directory (for state validation)")
-        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-        .option("--json", "Output structured JSON result")
-        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runLint);
-    addStrictOptions(program
-        .command("convert")
-        .description("Convert between native (.ga) and format2 (.gxwf.yml) formats")
-        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-        .option("--to <format>", "Target format: native or format2 (infers opposite by default)")
-        .option("--output <file>", "Write result to file (default: stdout)")
-        .option("--compact", "Omit position info in format2 output")
-        .option("--json", "Force JSON output")
-        .option("--yaml", "Force YAML output")
-        .option("--format <fmt>", "Force source format (auto-detected by default)")
-        .option("--stateful", "Use cached tool definitions for schema-aware state re-encoding")
-        .option("--cache-dir <dir>", "Tool cache directory (for --stateful)")).action(runConvert);
-    addStrictOptions(program
-        .command("roundtrip")
-        .description("Roundtrip-validate a native workflow: native → format2 → native, diff tool_state")
-        .argument("<file>", "Native workflow file (.ga)")
-        .option("--cache-dir <dir>", "Tool cache directory")
-        .option("--format <fmt>", "Force source format (must resolve to native)")
-        .option("--json", "Output structured JSON report")
-        .option("--errors-only", "Suppress benign diffs and clean steps from output")
-        .option("--benign-only", "Show only steps with benign diffs (no errors, no failures)")
-        .option("--brief", "Omit per-diff list; show only the one-line summary")).action(runRoundtrip);
-    program
-        .command("mermaid")
-        .description("Render a Galaxy workflow as a Mermaid flowchart diagram")
-        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-        .argument("[output]", "Output path (.mmd for raw, .md for fenced code block); stdout if omitted")
-        .option("--comments", "Render frame comments as Mermaid subgraphs")
-        .action((file, output, opts) => runMermaid(file, { output, comments: opts.comments }));
-    // -- Tree (batch) variants --
-    addStrictOptions(program
-        .command("validate-tree")
-        .description("Batch validate all workflows under a directory")
-        .argument("<dir>", "Directory to scan for workflows")
-        .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)")
-        .option("--json", "Output structured JSON report")
-        .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
-        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runValidateTree);
-    addStrictOptions(program
-        .command("lint-tree")
-        .description("Batch lint all workflows under a directory")
-        .argument("<dir>", "Directory to scan for workflows")
-        .option("--skip-best-practices", "Skip annotation/creator/license/label checks")
-        .option("--skip-state-validation", "Skip tool state validation against cached tool definitions")
-        .option("--cache-dir <dir>", "Tool cache directory (for state validation)")
-        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-        .option("--json", "Output structured JSON report")
-        .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
-        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runLintTree);
-    program
-        .command("clean-tree")
-        .description("Batch clean all workflows under a directory")
-        .argument("<dir>", "Directory to scan for workflows")
-        .option("--output-dir <dir>", "Write cleaned workflows to directory (mirrors source tree)")
-        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-        .option("--json", "Output structured JSON report")
-        .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
-        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")
-        .option("--skip-uuid", "Skip stripping uuid fields (errors are always stripped)")
-        .action(runCleanTree);
-    addStrictOptions(program
-        .command("convert-tree")
-        .description("Batch convert all workflows under a directory")
-        .argument("<dir>", "Directory to scan for workflows")
-        .option("--to <format>", "Target format: native or format2 (infers opposite by default)")
-        .option("--output-dir <dir>", "Write converted workflows to directory (required)")
-        .option("--compact", "Omit position info in format2 output")
-        .option("--report-json", "Output structured JSON report")
-        .option("--json", "Force JSON output for converted files")
-        .option("--yaml", "Force YAML output")
-        .option("--format <fmt>", "Force source format (auto-detected by default)")
-        .option("--stateful", "Use cached tool definitions for schema-aware state re-encoding")
-        .option("--cache-dir <dir>", "Tool cache directory (for --stateful)")).action(runConvertTree);
-    addStrictOptions(program
-        .command("roundtrip-tree")
-        .description("Batch roundtrip-validate native workflows under a directory")
-        .argument("<dir>", "Directory to scan for native workflows")
-        .option("--cache-dir <dir>", "Tool cache directory")
-        .option("--format <fmt>", "Force source format (must resolve to native)")
-        .option("--json", "Output structured JSON report")
-        .option("--errors-only", "List only files with errors or failures")
-        .option("--benign-only", "List only files with benign diffs (no errors, no failures)")
-        .option("--brief", "Omit per-file lines; print only the aggregate summary")
-        .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
-        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runRoundtripTree);
-    program
-        .command("validate-tests-tree")
-        .description("Batch validate workflow-test files (*-tests.yml / *.gxwf-tests.yml) under a directory")
-        .argument("<dir>", "Directory to scan for test files")
-        .option("--json", "Output structured JSON report")
-        .option("--auto-workflow", "Pair each tests file with a sibling workflow by filename convention (foo.gxwf-tests.yml ↔ foo.gxwf.yml/foo.ga) and cross-check inputs/outputs")
-        .action(runValidateTestsTree);
-    program
-        .command("tool-search")
-        .description("Search the Galaxy Tool Shed for tools matching a query")
-        .argument("<query>", "Search text (e.g. 'fastqc')")
-        .option("--page-size <n>", "Server-side page size", "20")
-        .option("--max-results <n>", "Hard cap on hits returned", "50")
-        .option("--page <n>", "Starting page (1-indexed)", "1")
-        .option("--owner <user>", "Filter hits to a single repo owner (client-side)")
-        .option("--match-name", "Drop hits where the query is not a token in the tool name")
-        .option("--json", "Emit machine-readable JSON envelope")
-        .option("--enrich", "Resolve each hit's ParsedTool and attach it as `parsedTool` (one fetch per hit; off by default)")
-        .option("--cache-dir <dir>", "Tool cache directory (used by --enrich; shared with galaxy-tool-cache)")
-        .action(runToolSearch);
-    program
-        .command("tool-versions")
-        .description("List TRS-published versions of a Tool Shed tool (newest last)")
-        .argument("<tool-id>", "TRS id (owner~repo~tool_id) or pretty form (owner/repo/tool_id)")
-        .option("--json", "Emit machine-readable JSON envelope")
-        .option("--latest", "Print only the latest version")
-        .action(runToolVersions);
-    program
-        .command("tool-revisions")
-        .description("List changeset revisions that publish a Tool Shed tool (ordered oldest→newest). " +
-        "Use for reproducible (name, owner, changeset_revision) workflow pins. " +
-        "Caveat: version strings are not monotonic — the same version can appear in multiple changesets.")
-        .argument("<tool-id>", "TRS id (owner~repo~tool_id) or pretty form (owner/repo/tool_id)")
-        .option("--tool-version <v>", "Restrict to revisions that publish this exact tool version")
-        .option("--latest", "Print only the newest matching revision")
-        .option("--json", "Emit machine-readable JSON envelope")
-        .action(runToolRevisions);
-    program
-        .command("repo-search")
-        .description("Search the Galaxy Tool Shed for repositories. Ranking is popularity-boosted; supports server-side --owner / --category filters via reserved keywords.")
-        .argument("<query>", "Search text (e.g. 'fastqc')")
-        .option("--page-size <n>", "Server-side page size", "20")
-        .option("--max-results <n>", "Hard cap on hits returned", "50")
-        .option("--page <n>", "Starting page (1-indexed)", "1")
-        .option("--owner <user>", "Restrict to a single owner (server-side `owner:` keyword)")
-        .option("--category <name>", "Restrict to a category (server-side `category:` keyword)")
-        .option("--json", "Emit machine-readable JSON envelope")
-        .action(runRepoSearch);
-    return program;
+    return buildProgramFromSpec(gxwfSpec, handlers);
 }
 //# sourceMappingURL=gxwf.js.map

package/dist/programs/gxwf.js.map

@@ -1 +1 @@
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+{"version":3,"file":"gxwf.js","sourceRoot":"","sources":["../../src/programs/gxwf.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AACzD,OAAO,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AACpD,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAC7D,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AACpD,OAAO,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC;AAC5D,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAC;AACvD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,oBAAoB,EAAE,MAAM,oCAAoC,CAAC;AAC1E,OAAO,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAC/D,OAAO,EAAE,aAAa,EAAE,MAAM,4BAA4B,CAAC;AAC3D,OAAO,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,aAAa,EAAE,MAAM,4BAA4B,CAAC;AAC3D,OAAO,EAAE,oBAAoB,EAAwB,MAAM,0BAA0B,CAAC;AACtF,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAE5C,MAAM,QAAQ,GAAoB;IAChC,gBAAgB,EAAE,mBAAmB;IACrC,aAAa,EAAE,gBAAgB;IAC/B,KAAK,EAAE,QAAQ;IACf,IAAI,EAAE,OAAO;IACb,OAAO,EAAE,UAAU;IACnB,SAAS,EAAE,YAAY;IACvB,OAAO,EAAE,CACP,IAAY,EACZ,MAA0B,EAC1B,IAA8E,EAC9E,EAAE,CACF,UAAU,CAAC,IAAI,EAAE;QACf,MAAM;QACN,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;QAC7C,QAAQ,EAAE,IAAI,CAAC,QAAQ;KACxB,CAAC;IACJ,WAAW,EAAE,CACX,IAAY,EACZ,MAA0B,EAC1B,IAMC,EACD,EAAE,CACF,cAAc,CAAC,IAAI,EAAE;QACnB,MAAM;QACN,IAAI,EAAE,IAAI,CAAC,IAAI;QACf,IAAI,EAAE,IAAI,CAAC,IAAI;QACf,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;QAC7C,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,MAAM,EAAE,IAAI,CAAC,MAAM;KACpB,CAAC;IACJ,YAAY,EAAE,eAAe;IAC7B,QAAQ,EAAE,WAAW;IACrB,SAAS,EAAE,YAAY;IACvB,WAAW,EAAE,cAAc;IAC3B,aAAa,EAAE,gBAAgB;IAC/B,iBAAiB,EAAE,oBAAoB;IACvC,UAAU,EAAE,aAAa;IACzB,YAAY,EAAE,eAAe;IAC7B,aAAa,EAAE,gBAAgB;IAC/B,UAAU,EAAE,aAAa;CAC1B,CAAC;AAEF,MAAM,UAAU,gBAAgB;IAC9B,OAAO,oBAAoB,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;AAClD,CAAC"}

package/dist/spec/build-program.d.ts

@@ -0,0 +1,12 @@
+/**
+ * Build a commander `Command` tree from a declarative `ProgramSpec` plus
+ * a name-keyed handler registry. The spec carries the static shape
+ * (commands, args, options, defaults); the registry supplies the
+ * runtime action functions.
+ */
+import { Command } from "commander";
+import type { ProgramSpec } from "../meta/spec-types.js";
+export type HandlerFn = (...args: any[]) => void | Promise<void>;
+export type HandlerRegistry = Record<string, HandlerFn>;
+export declare function buildProgramFromSpec(spec: ProgramSpec, handlers: HandlerRegistry): Command;
+//# sourceMappingURL=build-program.d.ts.map

package/dist/spec/build-program.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"build-program.d.ts","sourceRoot":"","sources":["../../src/spec/build-program.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,KAAK,EAAE,WAAW,EAA2B,MAAM,uBAAuB,CAAC;AAElF,MAAM,MAAM,SAAS,GAAG,CAAC,GAAG,IAAI,EAAE,GAAG,EAAE,KAAK,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;AACjE,MAAM,MAAM,eAAe,GAAG,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,CAAC;AAExD,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,WAAW,EAAE,QAAQ,EAAE,eAAe,GAAG,OAAO,CAS1F"}

package/dist/spec/build-program.js

@@ -0,0 +1,102 @@
+/**
+ * Build a commander `Command` tree from a declarative `ProgramSpec` plus
+ * a name-keyed handler registry. The spec carries the static shape
+ * (commands, args, options, defaults); the registry supplies the
+ * runtime action functions.
+ */
+import { Command } from "commander";
+export function buildProgramFromSpec(spec, handlers) {
+    validateSpec(spec, handlers);
+    const program = new Command();
+    program.name(spec.name).description(spec.description).version(spec.version);
+    const groups = spec.optionGroups ?? {};
+    for (const cmd of spec.commands) {
+        program.addCommand(buildCommand(cmd, groups, handlers));
+    }
+    return program;
+}
+/**
+ * Cheap structural checks the YAML loader doesn't catch — duplicate
+ * names, dangling refs, missing handlers. Runs before commander touches
+ * the spec so errors point at the YAML, not at a confusing commander
+ * stack trace.
+ */
+function validateSpec(spec, handlers) {
+    const groups = spec.optionGroups ?? {};
+    const seenCommands = new Set();
+    for (const cmd of spec.commands) {
+        if (seenCommands.has(cmd.name)) {
+            throw new Error(`Duplicate command "${cmd.name}" in spec "${spec.name}"`);
+        }
+        seenCommands.add(cmd.name);
+        if (!handlers[cmd.handler]) {
+            throw new Error(`Missing handler "${cmd.handler}" for command "${cmd.name}"`);
+        }
+        const seenOptions = new Set();
+        const checkOptName = (flags) => {
+            const optName = attributeNameFromFlags(flags);
+            if (seenOptions.has(optName)) {
+                throw new Error(`Duplicate option "${optName}" on command "${cmd.name}"`);
+            }
+            seenOptions.add(optName);
+        };
+        for (const opt of cmd.options ?? [])
+            checkOptName(opt.flags);
+        for (const groupName of cmd.optionGroups ?? []) {
+            const group = groups[groupName];
+            if (!group) {
+                throw new Error(`Command "${cmd.name}" references unknown optionGroup "${groupName}"`);
+            }
+            for (const opt of group)
+                checkOptName(opt.flags);
+        }
+    }
+}
+/**
+ * Extract the option's attributeName the same way commander does — the
+ * first long flag, stripped of `--no-` prefix and camelCased. Used only
+ * for duplicate detection here; commander itself owns the canonical
+ * derivation at runtime.
+ */
+function attributeNameFromFlags(flags) {
+    const long = flags.split(/[ ,|]+/).find((part) => part.startsWith("--"));
+    if (!long)
+        return flags;
+    const stripped = long.replace(/^--(no-)?/, "");
+    return stripped.replace(/-([a-z])/g, (_m, c) => c.toUpperCase());
+}
+function buildCommand(spec, groups, handlers) {
+    const cmd = new Command(spec.name).description(spec.description);
+    for (const arg of spec.args ?? []) {
+        if (arg.description !== undefined)
+            cmd.argument(arg.raw, arg.description);
+        else
+            cmd.argument(arg.raw);
+    }
+    for (const opt of spec.options ?? []) {
+        addOption(cmd, opt);
+    }
+    for (const groupName of spec.optionGroups ?? []) {
+        const group = groups[groupName];
+        if (!group) {
+            throw new Error(`Command "${spec.name}" references unknown optionGroup "${groupName}"`);
+        }
+        for (const opt of group)
+            addOption(cmd, opt);
+    }
+    const handler = handlers[spec.handler];
+    if (!handler) {
+        throw new Error(`Missing handler "${spec.handler}" for command "${spec.name}"`);
+    }
+    cmd.action(handler);
+    return cmd;
+}
+function addOption(cmd, opt) {
+    if (opt.default !== undefined) {
+        cmd.option(opt.flags, opt.description, String(opt.default));
+    }
+    else {
+        cmd.option(opt.flags, opt.description);
+    }
+}
+//# sourceMappingURL=build-program.js.map

package/dist/spec/build-program.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/cli",
-  "version": "1.1.0",
+  "version": "1.3.0",
   "description": "galaxy-tool-cache CLI — cache and inspect Galaxy tool metadata",
   "type": "module",
   "bin": {
@@ -11,10 +11,15 @@
     ".": {
       "types": "./dist/index.d.ts",
       "import": "./dist/index.js"
+    },
+    "./meta": {
+      "types": "./dist/meta/index.d.ts",
+      "import": "./dist/meta/index.js"
     }
   },
   "files": [
     "dist",
+    "spec",
     "README.md",
     "LICENSE"
   ],
@@ -34,9 +39,10 @@
     "effect": "^3.21.0",
     "nunjucks": "^3.2.4",
     "yaml": "^2.8.3",
-    "@galaxy-tool-util/core": "1.1.0",
-    "@galaxy-tool-util/schema": "1.1.0",
-    "@galaxy-tool-util/search": "1.1.0"
+    "@galaxy-tool-util/connection-validation": "1.2.0",
+    "@galaxy-tool-util/core": "1.2.0",
+    "@galaxy-tool-util/schema": "1.2.0",
+    "@galaxy-tool-util/search": "1.2.0"
   },
   "devDependencies": {
     "@types/node": "^25.5.0",