@galaxy-tool-util/schema 1.13.1 → 1.14.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (57) hide show
  1. package/dist/index.d.ts +4 -2
  2. package/dist/index.d.ts.map +1 -1
  3. package/dist/index.js +4 -2
  4. package/dist/index.js.map +1 -1
  5. package/dist/test-format/tests.schema.generated.d.ts +47 -0
  6. package/dist/test-format/tests.schema.generated.d.ts.map +1 -1
  7. package/dist/test-format/tests.schema.generated.js +62 -0
  8. package/dist/test-format/tests.schema.generated.js.map +1 -1
  9. package/dist/workflow/draft-checks.d.ts.map +1 -1
  10. package/dist/workflow/draft-checks.js +105 -59
  11. package/dist/workflow/draft-checks.js.map +1 -1
  12. package/dist/workflow/index.d.ts +4 -2
  13. package/dist/workflow/index.d.ts.map +1 -1
  14. package/dist/workflow/index.js +4 -2
  15. package/dist/workflow/index.js.map +1 -1
  16. package/dist/workflow/layout-properties.d.ts +10 -0
  17. package/dist/workflow/layout-properties.d.ts.map +1 -0
  18. package/dist/workflow/layout-properties.js +112 -0
  19. package/dist/workflow/layout-properties.js.map +1 -0
  20. package/dist/workflow/layout.d.ts +84 -0
  21. package/dist/workflow/layout.d.ts.map +1 -0
  22. package/dist/workflow/layout.js +356 -0
  23. package/dist/workflow/layout.js.map +1 -0
  24. package/dist/workflow/lint-rules.d.ts +6 -0
  25. package/dist/workflow/lint-rules.d.ts.map +1 -1
  26. package/dist/workflow/lint-rules.js +6 -0
  27. package/dist/workflow/lint-rules.js.map +1 -1
  28. package/dist/workflow/lint.d.ts +1 -1
  29. package/dist/workflow/lint.d.ts.map +1 -1
  30. package/dist/workflow/lint.js +83 -15
  31. package/dist/workflow/lint.js.map +1 -1
  32. package/dist/workflow/lint_profiles.yml +1 -0
  33. package/dist/workflow/normalized/expanded.d.ts +12 -0
  34. package/dist/workflow/normalized/expanded.d.ts.map +1 -1
  35. package/dist/workflow/normalized/expanded.js +42 -1
  36. package/dist/workflow/normalized/expanded.js.map +1 -1
  37. package/dist/workflow/normalized/index.d.ts +2 -2
  38. package/dist/workflow/normalized/index.d.ts.map +1 -1
  39. package/dist/workflow/normalized/index.js +2 -2
  40. package/dist/workflow/normalized/index.js.map +1 -1
  41. package/dist/workflow/normalized/labels.d.ts +7 -0
  42. package/dist/workflow/normalized/labels.d.ts.map +1 -1
  43. package/dist/workflow/normalized/labels.js +11 -0
  44. package/dist/workflow/normalized/labels.js.map +1 -1
  45. package/dist/workflow/normalized/toFormat2.d.ts +1 -0
  46. package/dist/workflow/normalized/toFormat2.d.ts.map +1 -1
  47. package/dist/workflow/normalized/toFormat2.js +4 -12
  48. package/dist/workflow/normalized/toFormat2.js.map +1 -1
  49. package/dist/workflow/normalized/toNative.d.ts +16 -1
  50. package/dist/workflow/normalized/toNative.d.ts.map +1 -1
  51. package/dist/workflow/normalized/toNative.js +23 -6
  52. package/dist/workflow/normalized/toNative.js.map +1 -1
  53. package/dist/workflow/semantic-validators.d.ts +9 -0
  54. package/dist/workflow/semantic-validators.d.ts.map +1 -1
  55. package/dist/workflow/semantic-validators.js +27 -14
  56. package/dist/workflow/semantic-validators.js.map +1 -1
  57. package/package.json +1 -1
@@ -0,0 +1 @@
1
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@@ -12,4 +12,10 @@ export declare class NativeStepKeyNotInteger extends Linter {
12
12
  static applies_to: readonly ["native"];
13
13
  static profile: string;
14
14
  }
15
+ /** Step labels (including inputs) must be unique within a workflow; Galaxy refuses duplicates at import. */
16
+ export declare class StepLabelNotUnique extends Linter {
17
+ static severity: "error";
18
+ static applies_to: readonly ["format2", "native"];
19
+ static profile: string;
20
+ }
15
21
  //# sourceMappingURL=lint-rules.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"lint-rules.d.ts","sourceRoot":"","sources":["../../src/workflow/lint-rules.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAEtC,4EAA4E;AAC5E,qBAAa,uBAAwB,SAAQ,MAAM;IACjD,MAAM,CAAC,QAAQ,EAAG,OAAO,CAAU;IACnC,MAAM,CAAC,UAAU,sBAAuB;IACxC,MAAM,CAAC,OAAO,SAAgB;CAC/B"}
1
+ {"version":3,"file":"lint-rules.d.ts","sourceRoot":"","sources":["../../src/workflow/lint-rules.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAEtC,4EAA4E;AAC5E,qBAAa,uBAAwB,SAAQ,MAAM;IACjD,MAAM,CAAC,QAAQ,EAAG,OAAO,CAAU;IACnC,MAAM,CAAC,UAAU,sBAAuB;IACxC,MAAM,CAAC,OAAO,SAAgB;CAC/B;AAED,4GAA4G;AAC5G,qBAAa,kBAAmB,SAAQ,MAAM;IAC5C,MAAM,CAAC,QAAQ,EAAG,OAAO,CAAU;IACnC,MAAM,CAAC,UAAU,iCAAkC;IACnD,MAAM,CAAC,OAAO,SAAgB;CAC/B"}
@@ -12,4 +12,10 @@ export class NativeStepKeyNotInteger extends Linter {
12
12
  static applies_to = ["native"];
13
13
  static profile = "structural";
14
14
  }
15
+ /** Step labels (including inputs) must be unique within a workflow; Galaxy refuses duplicates at import. */
16
+ export class StepLabelNotUnique extends Linter {
17
+ static severity = "error";
18
+ static applies_to = ["format2", "native"];
19
+ static profile = "structural";
20
+ }
15
21
  //# sourceMappingURL=lint-rules.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"lint-rules.js","sourceRoot":"","sources":["../../src/workflow/lint-rules.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAEtC,4EAA4E;AAC5E,MAAM,OAAO,uBAAwB,SAAQ,MAAM;IACjD,MAAM,CAAC,QAAQ,GAAG,OAAgB,CAAC;IACnC,MAAM,CAAC,UAAU,GAAG,CAAC,QAAQ,CAAU,CAAC;IACxC,MAAM,CAAC,OAAO,GAAG,YAAY,CAAC"}
1
+ {"version":3,"file":"lint-rules.js","sourceRoot":"","sources":["../../src/workflow/lint-rules.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAEtC,4EAA4E;AAC5E,MAAM,OAAO,uBAAwB,SAAQ,MAAM;IACjD,MAAM,CAAC,QAAQ,GAAG,OAAgB,CAAC;IACnC,MAAM,CAAC,UAAU,GAAG,CAAC,QAAQ,CAAU,CAAC;IACxC,MAAM,CAAC,OAAO,GAAG,YAAY,CAAC;;AAGhC,4GAA4G;AAC5G,MAAM,OAAO,kBAAmB,SAAQ,MAAM;IAC5C,MAAM,CAAC,QAAQ,GAAG,OAAgB,CAAC;IACnC,MAAM,CAAC,UAAU,GAAG,CAAC,SAAS,EAAE,QAAQ,CAAU,CAAC;IACnD,MAAM,CAAC,OAAO,GAAG,YAAY,CAAC"}
@@ -29,7 +29,7 @@ export declare function lintWorkflow(workflowDict: Record<string, unknown>): Lin
29
29
  export declare function lintBestPracticesFormat2(workflowDict: Record<string, unknown>): LintResult;
30
30
  /**
31
31
  * Lint best practices for a native Galaxy workflow.
32
- * Runs shared format2 best practices plus native-specific checks.
32
+ * Runs top-level checks on the format2 view and step checks on native steps.
33
33
  */
34
34
  export declare function lintBestPracticesNative(workflowDict: Record<string, unknown>): LintResult;
35
35
  //# sourceMappingURL=lint.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"lint.d.ts","sourceRoot":"","sources":["../../src/workflow/lint.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAQH,OAAO,EAAe,KAAK,UAAU,EAAE,MAAM,cAAc,CAAC;AAG5D,OAAO,EACL,WAAW,EACX,WAAW,EACX,MAAM,EACN,WAAW,EACX,UAAU,EACV,KAAK,SAAS,EACd,KAAK,UAAU,EACf,KAAK,SAAS,EACd,KAAK,WAAW,GACjB,MAAM,cAAc,CAAC;AAqNtB;;;GAGG;AACH,wBAAgB,UAAU,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAU5E;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAU7E;AAED;;;GAGG;AACH,wBAAgB,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAG9E;AA6HD;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAY1F;AAED;;;GAGG;AACH,wBAAgB,uBAAuB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAyBzF"}
1
+ {"version":3,"file":"lint.d.ts","sourceRoot":"","sources":["../../src/workflow/lint.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAQH,OAAO,EAAe,KAAK,UAAU,EAAE,MAAM,cAAc,CAAC;AAI5D,OAAO,EACL,WAAW,EACX,WAAW,EACX,MAAM,EACN,WAAW,EACX,UAAU,EACV,KAAK,SAAS,EACd,KAAK,UAAU,EACf,KAAK,SAAS,EACd,KAAK,WAAW,GACjB,MAAM,cAAc,CAAC;AA4QtB;;;GAGG;AACH,wBAAgB,UAAU,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAU5E;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAU7E;AAED;;;GAGG;AACH,wBAAgB,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAG9E;AA+ID;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAe1F;AAED;;;GAGG;AACH,wBAAgB,uBAAuB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAuBzF"}
@@ -9,7 +9,8 @@ import { normalizedNative } from "./normalized/native.js";
9
9
  import { ensureFormat2 } from "./normalized/ensure.js";
10
10
  import { detectFormat } from "./detect-format.js";
11
11
  import { LintContext } from "./linting.js";
12
- import { NativeStepKeyNotInteger } from "./lint-rules.js";
12
+ import { nativeInputLabel, nativeStepLabel } from "./normalized/toNative.js";
13
+ import { NativeStepKeyNotInteger, StepLabelNotUnique } from "./lint-rules.js";
13
14
  export { LintContext, LintMessage, Linter, LEVEL_ERROR, LEVEL_WARN, } from "./linting.js";
14
15
  function toLintResult(ctx) {
15
16
  return {
@@ -41,6 +42,34 @@ function validateReport(ctx, report) {
41
42
  }
42
43
  // Note: Galaxy markdown validation (```galaxy directives) not yet ported
43
44
  }
45
+ function nativeStepContext(ctx, stepKey) {
46
+ return ctx.child("steps").child(stepKey);
47
+ }
48
+ /**
49
+ * Error on step labels shared by more than one step, as Galaxy rejects these at import.
50
+ *
51
+ * `labeledSteps` holds `[label, description, labelContext]` for each step of one
52
+ * workflow level (subworkflows have their own label namespace); `labelContext`
53
+ * locates the label, or `undefined` to report at `ctx`. Empty labels are
54
+ * ignored, matching Galaxy.
55
+ */
56
+ function lintDuplicateStepLabels(ctx, labeledSteps) {
57
+ const stepsByLabel = new Map();
58
+ for (const [label, description, labelContext] of labeledSteps) {
59
+ if (!label)
60
+ continue;
61
+ const steps = stepsByLabel.get(label);
62
+ if (steps)
63
+ steps.push([description, labelContext]);
64
+ else
65
+ stepsByLabel.set(label, [[description, labelContext]]);
66
+ }
67
+ for (const [label, steps] of stepsByLabel) {
68
+ if (steps.length < 2)
69
+ continue;
70
+ (steps[1][1] ?? ctx).error(`Duplicated step label '${label}' (${steps.map(([d]) => d).join(", ")})`, { linter: StepLabelNotUnique });
71
+ }
72
+ }
44
73
  // ---------------------------------------------------------------------------
45
74
  // Native workflow linting
46
75
  // ---------------------------------------------------------------------------
@@ -66,11 +95,16 @@ function lintNativeWorkflow(ctx, nnw, rawDict) {
66
95
  }
67
96
  let foundOutputs = false;
68
97
  let foundOutputWithoutLabel = false;
98
+ lintDuplicateStepLabels(ctx, Object.entries(nnw.steps).map(([key, step]) => [
99
+ step.label,
100
+ `step ${key}`,
101
+ nativeStepContext(ctx, key).child("label"),
102
+ ]));
69
103
  for (const [orderIndex, step] of Object.entries(nnw.steps)) {
104
+ const stepContext = nativeStepContext(ctx, orderIndex);
70
105
  if (!/^\d+$/.test(orderIndex)) {
71
- ctx.error(`expected step_key to be integer not [${orderIndex}]`, {
106
+ stepContext.error(`expected step_key to be integer not [${orderIndex}]`, {
72
107
  linter: NativeStepKeyNotInteger,
73
- json_pointer: `/steps/${orderIndex}`,
74
108
  });
75
109
  }
76
110
  for (const wo of step.workflow_outputs) {
@@ -85,7 +119,7 @@ function lintNativeWorkflow(ctx, nnw, rawDict) {
85
119
  ctx.error("subworkflow is missing steps or steps are empty");
86
120
  }
87
121
  else {
88
- lintNativeWorkflow(ctx, step.subworkflow);
122
+ lintNativeWorkflow(stepContext.child("subworkflow"), step.subworkflow);
89
123
  }
90
124
  }
91
125
  lintStepErrors(ctx, step.errors);
@@ -166,6 +200,19 @@ function lintFormat2Workflow(ctx, nf2, rawDict) {
166
200
  ctx.error("expected to find key [class] but absent");
167
201
  }
168
202
  }
203
+ // Check the labels conversion will assign to the native steps.
204
+ lintDuplicateStepLabels(ctx, [
205
+ ...nf2.inputs.map((inp, i) => [
206
+ nativeInputLabel(inp, i),
207
+ `input ${inp.id || i}`,
208
+ undefined,
209
+ ]),
210
+ ...nf2.steps.map((step) => [
211
+ nativeStepLabel(step),
212
+ `step ${step.id}`,
213
+ undefined,
214
+ ]),
215
+ ]);
169
216
  for (const step of nf2.steps) {
170
217
  lintStepErrors(ctx, step.errors);
171
218
  lintToolIfPresent(ctx, step.tool_id);
@@ -276,6 +323,10 @@ function lintStepBestPractices(ctx, step) {
276
323
  ctx.warn(`Workflow step ${stepId} specifies an untyped parameter in the post-job actions.`);
277
324
  }
278
325
  }
326
+ /**
327
+ * Native step best-practice checks on native fields, so messages reference
328
+ * native ids / labels rather than format2 sentinels like `_unlabeled_step_1`.
329
+ */
279
330
  function lintNativeStepBestPractices(ctx, step) {
280
331
  const stepId = step.label || step.annotation || String(step.id);
281
332
  // disconnected inputs
@@ -286,14 +337,34 @@ function lintNativeStepBestPractices(ctx, step) {
286
337
  }
287
338
  }
288
339
  }
340
+ // missing metadata
341
+ if (!step.annotation) {
342
+ ctx.warn(`Workflow step ${stepId} has no annotation.`);
343
+ }
344
+ if (!step.label) {
345
+ ctx.warn(`Workflow step ${stepId} has no label.`);
346
+ }
347
+ // untyped params in tool_state
348
+ let toolState = step.tool_state;
349
+ if (typeof toolState === "string") {
350
+ try {
351
+ toolState = JSON.parse(toolState);
352
+ }
353
+ catch {
354
+ toolState = {};
355
+ }
356
+ }
357
+ if (toolState && typeof toolState === "object" && checkJsonForUntypedParams(toolState)) {
358
+ ctx.warn(`Workflow step ${stepId} specifies an untyped parameter as an input.`);
359
+ }
289
360
  // untyped params in post_job_actions
290
361
  if (step.post_job_actions && Object.keys(step.post_job_actions).length > 0) {
291
362
  if (checkJsonForUntypedParams(step.post_job_actions)) {
292
- ctx.warn(`Workflow step with ID ${step.id} specifies an untyped parameter in the post-job actions.`);
363
+ ctx.warn(`Workflow step ${stepId} specifies an untyped parameter in the post-job actions.`);
293
364
  }
294
365
  }
295
366
  }
296
- function lintBestPractices(ctx, nf2, rawDict) {
367
+ function lintWorkflowTopLevel(ctx, nf2, rawDict) {
297
368
  // annotation/doc
298
369
  if (!nf2.doc || !nf2.doc.trim()) {
299
370
  ctx.warn("Workflow is not annotated.");
@@ -322,10 +393,6 @@ function lintBestPractices(ctx, nf2, rawDict) {
322
393
  if (!nf2.license) {
323
394
  ctx.warn("Workflow does not specify a license.");
324
395
  }
325
- // step-level
326
- for (const step of nf2.steps) {
327
- lintStepBestPractices(ctx, step);
328
- }
329
396
  }
330
397
  /**
331
398
  * Lint best practices for a Format2 Galaxy workflow.
@@ -342,17 +409,19 @@ export function lintBestPracticesFormat2(workflowDict) {
342
409
  nf2 = null;
343
410
  }
344
411
  if (nf2) {
345
- lintBestPractices(ctx, nf2, workflowDict);
412
+ lintWorkflowTopLevel(ctx, nf2, workflowDict);
413
+ for (const step of nf2.steps) {
414
+ lintStepBestPractices(ctx, step);
415
+ }
346
416
  }
347
417
  return toLintResult(ctx);
348
418
  }
349
419
  /**
350
420
  * Lint best practices for a native Galaxy workflow.
351
- * Runs shared format2 best practices plus native-specific checks.
421
+ * Runs top-level checks on the format2 view and step checks on native steps.
352
422
  */
353
423
  export function lintBestPracticesNative(workflowDict) {
354
424
  const ctx = new LintContext();
355
- // Shared best practices on format2 view
356
425
  let nf2;
357
426
  try {
358
427
  nf2 = ensureFormat2(workflowDict);
@@ -361,9 +430,8 @@ export function lintBestPracticesNative(workflowDict) {
361
430
  nf2 = null;
362
431
  }
363
432
  if (nf2) {
364
- lintBestPractices(ctx, nf2, workflowDict);
433
+ lintWorkflowTopLevel(ctx, nf2, workflowDict);
365
434
  }
366
- // Native-specific checks
367
435
  let nnw;
368
436
  try {
369
437
  nnw = normalizedNative(workflowDict);
@@ -1 +1 @@
1
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@@ -10,6 +10,7 @@ structural:
10
10
  description: "Checks that prevent execution or indicate structural breakage."
11
11
  rules:
12
12
  - NativeStepKeyNotInteger
13
+ - StepLabelNotUnique
13
14
  - StepExportError
14
15
  - StepUsesTestToolshed
15
16
  - WorkflowHasNoOutputs
@@ -44,6 +44,18 @@ export interface ExpansionOptions {
44
44
  export declare const MAX_EXPANSION_DEPTH = 10;
45
45
  /** Check if a URL matches the GA4GH TRS v2 tools/versions pattern. */
46
46
  export declare function isTrsUrl(url: string): boolean;
47
+ /**
48
+ * Build the GA4GH TRS `GALAXY` descriptor URL for a TRS tool version URL.
49
+ *
50
+ * The tool id may be percent-encoded or not (Galaxy and planemo emit it
51
+ * unencoded, e.g. `.../tools/#workflow/github.com/org/repo/main/versions/v1`),
52
+ * so it is unquoted and re-encoded to keep `#` and `/` from being misread as
53
+ * URL syntax. Any trailing path (such as `/GALAXY/descriptor`) is ignored.
54
+ * Returns `null` if `url` is not a TRS URL.
55
+ *
56
+ * Port of gxformat2/options.py trs_descriptor_url (mirrors Galaxy's trs_proxy).
57
+ */
58
+ export declare function trsDescriptorUrl(url: string): string | null;
47
59
  /**
48
60
  * Normalize and expand a Format2 workflow.
49
61
  *
@@ -1 +1 @@
1
- {"version":3,"file":"expanded.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/expanded.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAEV,yBAAyB,EACzB,qBAAqB,EACtB,MAAM,cAAc,CAAC;AAEtB,OAAO,KAAK,EAAE,wBAAwB,EAAE,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAUlF,MAAM,MAAM,uBAAuB,GAAG,yBAAyB,CAAC;AAChE,MAAM,MAAM,mBAAmB,GAAG,qBAAqB,CAAC;AACxD,MAAM,MAAM,sBAAsB,GAAG,wBAAwB,CAAC;AAC9D,MAAM,MAAM,kBAAkB,GAAG,oBAAoB,CAAC;AAEtD;;;;;;;;GAQG;AACH,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;AAE5E;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B;;;;;;;;;;OAUG;IACH,QAAQ,CAAC,EAAE,WAAW,CAAC;CACxB;AAID,eAAO,MAAM,mBAAmB,KAAK,CAAC;AAMtC,sEAAsE;AACtE,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAE7C;AA8DD;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,uBAAuB,CAAC,CAQlC;AAED;;;;;GAKG;AACH,wBAAsB,cAAc,CAClC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,sBAAsB,CAAC,CAQjC"}
1
+ {"version":3,"file":"expanded.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/expanded.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAEV,yBAAyB,EACzB,qBAAqB,EACtB,MAAM,cAAc,CAAC;AAEtB,OAAO,KAAK,EAAE,wBAAwB,EAAE,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAUlF,MAAM,MAAM,uBAAuB,GAAG,yBAAyB,CAAC;AAChE,MAAM,MAAM,mBAAmB,GAAG,qBAAqB,CAAC;AACxD,MAAM,MAAM,sBAAsB,GAAG,wBAAwB,CAAC;AAC9D,MAAM,MAAM,kBAAkB,GAAG,oBAAoB,CAAC;AAEtD;;;;;;;;GAQG;AACH,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;AAE5E;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B;;;;;;;;;;OAUG;IACH,QAAQ,CAAC,EAAE,WAAW,CAAC;CACxB;AAID,eAAO,MAAM,mBAAmB,KAAK,CAAC;AAStC,sEAAsE;AACtE,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAE7C;AAwBD;;;;;;;;;;GAUG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAQ3D;AA8DD;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,uBAAuB,CAAC,CAQlC;AAED;;;;;GAKG;AACH,wBAAsB,cAAc,CAClC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,sBAAsB,CAAC,CAQjC"}
@@ -14,12 +14,53 @@ import { toFormat2 } from "./toFormat2.js";
14
14
  import { toNative } from "./toNative.js";
15
15
  // --- Constants ---
16
16
  export const MAX_EXPANSION_DEPTH = 10;
17
- const TRS_URL_REGEX = /^https?:\/\/.+\/ga4gh\/trs\/v2\/tools\/.+\/versions\/[^/]+/;
17
+ const TRS_URL_REGEX = /^(?<trsBaseUrl>https?:\/\/.+)\/ga4gh\/trs\/v2\/tools\/(?<toolId>.+)\/versions\/(?<versionId>[^/]+)/;
18
+ const GA4GH_GALAXY_DESCRIPTOR = "GALAXY";
18
19
  // --- Helpers ---
19
20
  /** Check if a URL matches the GA4GH TRS v2 tools/versions pattern. */
20
21
  export function isTrsUrl(url) {
21
22
  return TRS_URL_REGEX.test(url);
22
23
  }
24
+ /**
25
+ * Percent-decode `%XX` runs (Python's `unquote`). A run that isn't valid UTF-8
26
+ * is left as-is, so it ends up double-encoded (`%25XX`) where Python would emit
27
+ * U+FFFD. Real TRS ids are ASCII; parity there isn't worth a TextDecoder.
28
+ */
29
+ function _unquote(value) {
30
+ return value.replace(/(?:%[0-9A-Fa-f]{2})+/g, (run) => {
31
+ try {
32
+ return decodeURIComponent(run);
33
+ }
34
+ catch {
35
+ return run;
36
+ }
37
+ });
38
+ }
39
+ /** Percent-encode like Python's `quote_plus`: only `A-Za-z0-9_.-~` kept, space as `+`. */
40
+ function _quotePlus(value) {
41
+ return encodeURIComponent(value)
42
+ .replace(/[!'()*]/g, (c) => `%${c.charCodeAt(0).toString(16).toUpperCase()}`)
43
+ .replace(/%20/g, "+");
44
+ }
45
+ /**
46
+ * Build the GA4GH TRS `GALAXY` descriptor URL for a TRS tool version URL.
47
+ *
48
+ * The tool id may be percent-encoded or not (Galaxy and planemo emit it
49
+ * unencoded, e.g. `.../tools/#workflow/github.com/org/repo/main/versions/v1`),
50
+ * so it is unquoted and re-encoded to keep `#` and `/` from being misread as
51
+ * URL syntax. Any trailing path (such as `/GALAXY/descriptor`) is ignored.
52
+ * Returns `null` if `url` is not a TRS URL.
53
+ *
54
+ * Port of gxformat2/options.py trs_descriptor_url (mirrors Galaxy's trs_proxy).
55
+ */
56
+ export function trsDescriptorUrl(url) {
57
+ const match = TRS_URL_REGEX.exec(url);
58
+ if (!match?.groups)
59
+ return null;
60
+ const { trsBaseUrl, toolId, versionId } = match.groups;
61
+ return (`${trsBaseUrl}/ga4gh/trs/v2/tools/${_quotePlus(_unquote(toolId))}` +
62
+ `/versions/${versionId}/${GA4GH_GALAXY_DESCRIPTOR}/descriptor`);
63
+ }
23
64
  /** Check if a content_id is a URL that can be fetched. */
24
65
  function _isResolvableUrl(contentId) {
25
66
  return (contentId.startsWith("http://") ||
@@ -1 +1 @@
1
- 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+ 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@@ -6,7 +6,7 @@ export { toFormat2Stateful, type StepConversionStatus, type StatefulExportResult
6
6
  export type { StepConversionFailureClass } from "./stateful-runner.js";
7
7
  export { toNativeStateful, type StatefulNativeResult } from "./toNativeStateful.js";
8
8
  export { ensureFormat2, ensureNative } from "./ensure.js";
9
- export { expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, } from "./expanded.js";
9
+ export { expandedFormat2, expandedNative, isTrsUrl, trsDescriptorUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, } from "./expanded.js";
10
10
  export { flattenCommentData, unflattenCommentData } from "./comments.js";
11
- export { resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./labels.js";
11
+ export { resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, unlabeledNodeId, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./labels.js";
12
12
  //# sourceMappingURL=index.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,wBAAwB,EACxB,mBAAmB,EACnB,KAAK,kBAAkB,EACvB,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB,EAC1B,KAAK,sBAAsB,EAC3B,KAAK,uBAAuB,EAC5B,KAAK,0BAA0B,EAC/B,KAAK,2BAA2B,GACjC,MAAM,cAAc,CAAC;AAEtB,OAAO,EACL,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EACnB,KAAK,wBAAwB,EAC7B,KAAK,oBAAoB,EACzB,KAAK,aAAa,GACnB,MAAM,aAAa,CAAC;AAErB,OAAO,EAAE,SAAS,EAAE,KAAK,gBAAgB,EAAE,KAAK,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAC7F,OAAO,EAAE,QAAQ,EAAE,KAAK,eAAe,EAAE,MAAM,eAAe,CAAC;AAC/D,OAAO,EACL,iBAAiB,EACjB,KAAK,oBAAoB,EACzB,KAAK,oBAAoB,EACzB,KAAK,kBAAkB,GACxB,MAAM,wBAAwB,CAAC;AAChC,YAAY,EAAE,0BAA0B,EAAE,MAAM,sBAAsB,CAAC;AACvE,OAAO,EAAE,gBAAgB,EAAE,KAAK,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AACpF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,eAAe,EACf,cAAc,EACd,QAAQ,EACR,mBAAmB,EACnB,KAAK,uBAAuB,EAC5B,KAAK,mBAAmB,EACxB,KAAK,sBAAsB,EAC3B,KAAK,kBAAkB,EACvB,KAAK,WAAW,EAChB,KAAK,gBAAgB,GACtB,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACzE,OAAO,EACL,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EACrB,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,aAAa,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,wBAAwB,EACxB,mBAAmB,EACnB,KAAK,kBAAkB,EACvB,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB,EAC1B,KAAK,sBAAsB,EAC3B,KAAK,uBAAuB,EAC5B,KAAK,0BAA0B,EAC/B,KAAK,2BAA2B,GACjC,MAAM,cAAc,CAAC;AAEtB,OAAO,EACL,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EACnB,KAAK,wBAAwB,EAC7B,KAAK,oBAAoB,EACzB,KAAK,aAAa,GACnB,MAAM,aAAa,CAAC;AAErB,OAAO,EAAE,SAAS,EAAE,KAAK,gBAAgB,EAAE,KAAK,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAC7F,OAAO,EAAE,QAAQ,EAAE,KAAK,eAAe,EAAE,MAAM,eAAe,CAAC;AAC/D,OAAO,EACL,iBAAiB,EACjB,KAAK,oBAAoB,EACzB,KAAK,oBAAoB,EACzB,KAAK,kBAAkB,GACxB,MAAM,wBAAwB,CAAC;AAChC,YAAY,EAAE,0BAA0B,EAAE,MAAM,sBAAsB,CAAC;AACvE,OAAO,EAAE,gBAAgB,EAAE,KAAK,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AACpF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,eAAe,EACf,cAAc,EACd,QAAQ,EACR,gBAAgB,EAChB,mBAAmB,EACnB,KAAK,uBAAuB,EAC5B,KAAK,mBAAmB,EACxB,KAAK,sBAAsB,EAC3B,KAAK,kBAAkB,EACvB,KAAK,WAAW,EAChB,KAAK,gBAAgB,GACtB,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACzE,OAAO,EACL,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EACrB,eAAe,EACf,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,aAAa,CAAC"}
@@ -5,7 +5,7 @@ export { toNative } from "./toNative.js";
5
5
  export { toFormat2Stateful, } from "./toFormat2Stateful.js";
6
6
  export { toNativeStateful } from "./toNativeStateful.js";
7
7
  export { ensureFormat2, ensureNative } from "./ensure.js";
8
- export { expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, } from "./expanded.js";
8
+ export { expandedFormat2, expandedNative, isTrsUrl, trsDescriptorUrl, MAX_EXPANSION_DEPTH, } from "./expanded.js";
9
9
  export { flattenCommentData, unflattenCommentData } from "./comments.js";
10
- export { resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./labels.js";
10
+ export { resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, unlabeledNodeId, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./labels.js";
11
11
  //# sourceMappingURL=index.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/workflow/normalized/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,wBAAwB,EACxB,mBAAmB,GAQpB,MAAM,cAAc,CAAC;AAEtB,OAAO,EACL,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,GAIpB,MAAM,aAAa,CAAC;AAErB,OAAO,EAAE,SAAS,EAAoD,MAAM,gBAAgB,CAAC;AAC7F,OAAO,EAAE,QAAQ,EAAwB,MAAM,eAAe,CAAC;AAC/D,OAAO,EACL,iBAAiB,GAIlB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EAAE,gBAAgB,EAA6B,MAAM,uBAAuB,CAAC;AACpF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,eAAe,EACf,cAAc,EACd,QAAQ,EACR,mBAAmB,GAOpB,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACzE,OAAO,EACL,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EACrB,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,aAAa,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/workflow/normalized/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,wBAAwB,EACxB,mBAAmB,GAQpB,MAAM,cAAc,CAAC;AAEtB,OAAO,EACL,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,GAIpB,MAAM,aAAa,CAAC;AAErB,OAAO,EAAE,SAAS,EAAoD,MAAM,gBAAgB,CAAC;AAC7F,OAAO,EAAE,QAAQ,EAAwB,MAAM,eAAe,CAAC;AAC/D,OAAO,EACL,iBAAiB,GAIlB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EAAE,gBAAgB,EAA6B,MAAM,uBAAuB,CAAC;AACpF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,eAAe,EACf,cAAc,EACd,QAAQ,EACR,gBAAgB,EAChB,mBAAmB,GAOpB,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACzE,OAAO,EACL,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EACrB,eAAe,EACf,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,aAAa,CAAC"}
@@ -5,6 +5,13 @@
5
5
  */
6
6
  export declare const UNLABELED_INPUT_PREFIX = "_unlabeled_input_";
7
7
  export declare const UNLABELED_STEP_PREFIX = "_unlabeled_step_";
8
+ /**
9
+ * Node id for a native step: its label, else a synthetic unlabeled sentinel.
10
+ *
11
+ * Shared by native→Format2 conversion and layout position matching so the two
12
+ * cannot drift.
13
+ */
14
+ export declare function unlabeledNodeId(label: string | null | undefined, stepId: string | number, isInput: boolean): string;
8
15
  export declare function isUnlabeledInput(label: string): boolean;
9
16
  export declare function isUnlabeledStep(label: string): boolean;
10
17
  export declare function isUnlabeled(label: string): boolean;
@@ -1 +1 @@
1
- {"version":3,"file":"labels.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/labels.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,eAAO,MAAM,sBAAsB,sBAAsB,CAAC;AAC1D,eAAO,MAAM,qBAAqB,qBAAqB,CAAC;AAExD,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEvD;AAED,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEtD;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAElD;AAED,wBAAgB,sBAAsB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAAG,OAAO,CAEhF;AAED;;GAEG;AACH,qBAAa,MAAM;IACjB,OAAO,CAAC,UAAU,CAAqB;IACvC,OAAO,CAAC,eAAe,CAAK;IAE5B,oBAAoB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAAG,MAAM;CAQ/D;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAAC,EAAE,EAAE,MAAM,CAAA;CAAE,GAAG,MAAM,CAEtF;AAED;;;;;;GAMG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAU5E;AAED;;;;;GAKG;AACH,wBAAgB,sBAAsB,CACpC,KAAK,EAAE,MAAM,EACb,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,GAAG,CAAC,MAAM,CAAC,GAC7C,CAAC,MAAM,EAAE,MAAM,CAAC,CAkBlB"}
1
+ {"version":3,"file":"labels.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/labels.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,eAAO,MAAM,sBAAsB,sBAAsB,CAAC;AAC1D,eAAO,MAAM,qBAAqB,qBAAqB,CAAC;AAExD;;;;;GAKG;AACH,wBAAgB,eAAe,CAC7B,KAAK,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,EAChC,MAAM,EAAE,MAAM,GAAG,MAAM,EACvB,OAAO,EAAE,OAAO,GACf,MAAM,CAGR;AAED,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEvD;AAED,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEtD;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAElD;AAED,wBAAgB,sBAAsB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAAG,OAAO,CAEhF;AAED;;GAEG;AACH,qBAAa,MAAM;IACjB,OAAO,CAAC,UAAU,CAAqB;IACvC,OAAO,CAAC,eAAe,CAAK;IAE5B,oBAAoB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAAG,MAAM;CAQ/D;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAAC,EAAE,EAAE,MAAM,CAAA;CAAE,GAAG,MAAM,CAEtF;AAED;;;;;;GAMG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAU5E;AAED;;;;;GAKG;AACH,wBAAgB,sBAAsB,CACpC,KAAK,EAAE,MAAM,EACb,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,GAAG,CAAC,MAAM,CAAC,GAC7C,CAAC,MAAM,EAAE,MAAM,CAAC,CAkBlB"}
@@ -5,6 +5,17 @@
5
5
  */
6
6
  export const UNLABELED_INPUT_PREFIX = "_unlabeled_input_";
7
7
  export const UNLABELED_STEP_PREFIX = "_unlabeled_step_";
8
+ /**
9
+ * Node id for a native step: its label, else a synthetic unlabeled sentinel.
10
+ *
11
+ * Shared by native→Format2 conversion and layout position matching so the two
12
+ * cannot drift.
13
+ */
14
+ export function unlabeledNodeId(label, stepId, isInput) {
15
+ if (label != null)
16
+ return label;
17
+ return `${isInput ? UNLABELED_INPUT_PREFIX : UNLABELED_STEP_PREFIX}${stepId}`;
18
+ }
8
19
  export function isUnlabeledInput(label) {
9
20
  return label.startsWith(UNLABELED_INPUT_PREFIX);
10
21
  }
@@ -1 +1 @@
1
- {"version":3,"file":"labels.js","sourceRoot":"","sources":["../../../src/workflow/normalized/labels.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,MAAM,CAAC,MAAM,sBAAsB,GAAG,mBAAmB,CAAC;AAC1D,MAAM,CAAC,MAAM,qBAAqB,GAAG,kBAAkB,CAAC;AAExD,MAAM,UAAU,gBAAgB,CAAC,KAAa;IAC5C,OAAO,KAAK,CAAC,UAAU,CAAC,sBAAsB,CAAC,CAAC;AAClD,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,KAAa;IAC3C,OAAO,KAAK,CAAC,UAAU,CAAC,qBAAqB,CAAC,CAAC;AACjD,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAa;IACvC,OAAO,gBAAgB,CAAC,KAAK,CAAC,IAAI,eAAe,CAAC,KAAK,CAAC,CAAC;AAC3D,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,KAAgC;IACrE,OAAO,CAAC,KAAK,IAAI,KAAK,CAAC,UAAU,CAAC,oBAAoB,CAAC,CAAC;AAC1D,CAAC;AAED;;GAEG;AACH,MAAM,OAAO,MAAM;IACT,UAAU,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,eAAe,GAAG,CAAC,CAAC;IAE5B,oBAAoB,CAAC,KAAgC;QACnD,IAAI,KAAK,IAAI,IAAI,EAAE,CAAC;YAClB,IAAI,CAAC,eAAe,IAAI,CAAC,CAAC;YAC1B,KAAK,GAAG,qBAAqB,IAAI,CAAC,eAAe,EAAE,CAAC;QACtD,CAAC;QACD,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;QAC3B,OAAO,KAAK,CAAC;IACf,CAAC;CACF;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,kBAAkB,CAAC,IAA2C;IAC5E,OAAO,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,EAAE,CAAC;AAC/B,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,qBAAqB,CAAC,IAAa,EAAE,OAAe;IAClE,IACE,OAAO,IAAI,KAAK,QAAQ;QACxB,IAAI,KAAK,IAAI;QACb,OAAQ,IAAgC,CAAC,KAAK,KAAK,QAAQ;QACzD,IAAgC,CAAC,KAAgB,CAAC,MAAM,GAAG,CAAC,EAC9D,CAAC;QACD,OAAQ,IAAgC,CAAC,KAAe,CAAC;IAC3D,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,sBAAsB,CACpC,KAAa,EACb,WAA8C;IAE9C,MAAM,SAAS,GAAG,WAAW,YAAY,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC;IAC1F,yDAAyD;IACzD,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC;IAE9C,KAAK,MAAM,KAAK,IAAI,SAAS,EAAE,CAAC;QAC9B,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;YACpB,OAAO,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC;QAC3B,CAAC;QACD,IAAI,KAAK,CAAC,UAAU,CAAC,KAAK,GAAG,GAAG,CAAC,EAAE,CAAC;YAClC,OAAO,CAAC,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC;QAChD,CAAC;IACH,CAAC;IACD,IAAI,KAAK,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,GAAG,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;QAC/B,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,KAAK,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC;IACrD,CAAC;IACD,OAAO,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC;AAC3B,CAAC"}
1
+ {"version":3,"file":"labels.js","sourceRoot":"","sources":["../../../src/workflow/normalized/labels.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,MAAM,CAAC,MAAM,sBAAsB,GAAG,mBAAmB,CAAC;AAC1D,MAAM,CAAC,MAAM,qBAAqB,GAAG,kBAAkB,CAAC;AAExD;;;;;GAKG;AACH,MAAM,UAAU,eAAe,CAC7B,KAAgC,EAChC,MAAuB,EACvB,OAAgB;IAEhB,IAAI,KAAK,IAAI,IAAI;QAAE,OAAO,KAAK,CAAC;IAChC,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,qBAAqB,GAAG,MAAM,EAAE,CAAC;AAChF,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,KAAa;IAC5C,OAAO,KAAK,CAAC,UAAU,CAAC,sBAAsB,CAAC,CAAC;AAClD,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,KAAa;IAC3C,OAAO,KAAK,CAAC,UAAU,CAAC,qBAAqB,CAAC,CAAC;AACjD,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAa;IACvC,OAAO,gBAAgB,CAAC,KAAK,CAAC,IAAI,eAAe,CAAC,KAAK,CAAC,CAAC;AAC3D,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,KAAgC;IACrE,OAAO,CAAC,KAAK,IAAI,KAAK,CAAC,UAAU,CAAC,oBAAoB,CAAC,CAAC;AAC1D,CAAC;AAED;;GAEG;AACH,MAAM,OAAO,MAAM;IACT,UAAU,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,eAAe,GAAG,CAAC,CAAC;IAE5B,oBAAoB,CAAC,KAAgC;QACnD,IAAI,KAAK,IAAI,IAAI,EAAE,CAAC;YAClB,IAAI,CAAC,eAAe,IAAI,CAAC,CAAC;YAC1B,KAAK,GAAG,qBAAqB,IAAI,CAAC,eAAe,EAAE,CAAC;QACtD,CAAC;QACD,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;QAC3B,OAAO,KAAK,CAAC;IACf,CAAC;CACF;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,kBAAkB,CAAC,IAA2C;IAC5E,OAAO,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,EAAE,CAAC;AAC/B,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,qBAAqB,CAAC,IAAa,EAAE,OAAe;IAClE,IACE,OAAO,IAAI,KAAK,QAAQ;QACxB,IAAI,KAAK,IAAI;QACb,OAAQ,IAAgC,CAAC,KAAK,KAAK,QAAQ;QACzD,IAAgC,CAAC,KAAgB,CAAC,MAAM,GAAG,CAAC,EAC9D,CAAC;QACD,OAAQ,IAAgC,CAAC,KAAe,CAAC;IAC3D,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,sBAAsB,CACpC,KAAa,EACb,WAA8C;IAE9C,MAAM,SAAS,GAAG,WAAW,YAAY,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC;IAC1F,yDAAyD;IACzD,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC;IAE9C,KAAK,MAAM,KAAK,IAAI,SAAS,EAAE,CAAC;QAC9B,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;YACpB,OAAO,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC;QAC3B,CAAC;QACD,IAAI,KAAK,CAAC,UAAU,CAAC,KAAK,GAAG,GAAG,CAAC,EAAE,CAAC;YAClC,OAAO,CAAC,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC;QAChD,CAAC;IACH,CAAC;IACD,IAAI,KAAK,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,GAAG,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;QAC/B,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,KAAK,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC;IACrD,CAAC;IACD,OAAO,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC;AAC3B,CAAC"}
@@ -5,6 +5,7 @@
5
5
  */
6
6
  import type { NormalizedNativeStep } from "./native.js";
7
7
  import type { NormalizedFormat2Workflow } from "./format2.js";
8
+ export declare const INPUT_STEP_TYPES: Set<string>;
8
9
  /**
9
10
  * Per-step callback result: a replacement format2 state dict + optional `in`
10
11
  * block overrides (flat path → source). Return null to fall back to the
@@ -1 +1 @@
1
- {"version":3,"file":"toFormat2.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toFormat2.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAA4B,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAElF,OAAO,KAAK,EACV,yBAAyB,EAM1B,MAAM,cAAc,CAAC;AAWtB;;;;GAIG;AACH,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,EAAE,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7B;AAED,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,CAAC,UAAU,EAAE,oBAAoB,KAAK,oBAAoB,GAAG,IAAI,CAAC;CAC1F;AAED;;GAEG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,gBAAgB,GAAG,yBAAyB,CAG7F"}
1
+ {"version":3,"file":"toFormat2.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toFormat2.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAA4B,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAElF,OAAO,KAAK,EACV,yBAAyB,EAM1B,MAAM,cAAc,CAAC;AAStB,eAAO,MAAM,gBAAgB,aAAsE,CAAC;AAEpG;;;;GAIG;AACH,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,EAAE,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7B;AAED,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,CAAC,UAAU,EAAE,oBAAoB,KAAK,oBAAoB,GAAG,IAAI,CAAC;CAC1F;AAED;;GAEG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,gBAAgB,GAAG,yBAAyB,CAG7F"}
@@ -6,11 +6,11 @@
6
6
  import { normalizedNative } from "./native.js";
7
7
  import { isGalaxyUserToolRun } from "./format2.js";
8
8
  import { flattenCommentData } from "./comments.js";
9
- import { UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, isUnlabeled, Labels } from "./labels.js";
9
+ import { isUnlabeled, Labels, unlabeledNodeId } from "./labels.js";
10
10
  // Effect schemas produce deeply-readonly types. We build plain objects
11
11
  // and cast — runtime semantics are identical.
12
12
  // Step types that represent workflow inputs
13
- const INPUT_STEP_TYPES = new Set(["data_input", "data_collection_input", "parameter_input"]);
13
+ export const INPUT_STEP_TYPES = new Set(["data_input", "data_collection_input", "parameter_input"]);
14
14
  /**
15
15
  * Convert a native Galaxy workflow to normalized Format2.
16
16
  */
@@ -22,15 +22,7 @@ function _buildFormat2Workflow(wf, options) {
22
22
  // Build label map: step key → label string
23
23
  const labelMap = new Map();
24
24
  for (const [key, step] of Object.entries(wf.steps)) {
25
- if (step.label != null) {
26
- labelMap.set(String(key), step.label);
27
- }
28
- else if (INPUT_STEP_TYPES.has(step.type)) {
29
- labelMap.set(String(key), `${UNLABELED_INPUT_PREFIX}${step.id}`);
30
- }
31
- else {
32
- labelMap.set(String(key), `${UNLABELED_STEP_PREFIX}${step.id}`);
33
- }
25
+ labelMap.set(String(key), unlabeledNodeId(step.label, step.id, INPUT_STEP_TYPES.has(step.type)));
34
26
  }
35
27
  // Build workflow outputs from step workflow_outputs
36
28
  const labels = new Labels();
@@ -99,7 +91,7 @@ function _nativeInputToFormat2Type(stepType, toolState) {
99
91
  return "data";
100
92
  }
101
93
  function _buildInputParam(step) {
102
- const stepId = step.label ?? `${UNLABELED_INPUT_PREFIX}${step.id}`;
94
+ const stepId = unlabeledNodeId(step.label, step.id, true);
103
95
  const inputType = _nativeInputToFormat2Type(step.type, step.tool_state);
104
96
  const result = { id: stepId, type: inputType };
105
97
  const ts = step.tool_state;