@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.
- package/dist/index.d.ts +4 -2
- package/dist/index.d.ts.map +1 -1
- package/dist/index.js +4 -2
- package/dist/index.js.map +1 -1
- package/dist/test-format/tests.schema.generated.d.ts +47 -0
- package/dist/test-format/tests.schema.generated.d.ts.map +1 -1
- package/dist/test-format/tests.schema.generated.js +62 -0
- package/dist/test-format/tests.schema.generated.js.map +1 -1
- package/dist/workflow/draft-checks.d.ts.map +1 -1
- package/dist/workflow/draft-checks.js +105 -59
- package/dist/workflow/draft-checks.js.map +1 -1
- package/dist/workflow/index.d.ts +4 -2
- package/dist/workflow/index.d.ts.map +1 -1
- package/dist/workflow/index.js +4 -2
- package/dist/workflow/index.js.map +1 -1
- package/dist/workflow/layout-properties.d.ts +10 -0
- package/dist/workflow/layout-properties.d.ts.map +1 -0
- package/dist/workflow/layout-properties.js +112 -0
- package/dist/workflow/layout-properties.js.map +1 -0
- package/dist/workflow/layout.d.ts +84 -0
- package/dist/workflow/layout.d.ts.map +1 -0
- package/dist/workflow/layout.js +356 -0
- package/dist/workflow/layout.js.map +1 -0
- package/dist/workflow/lint-rules.d.ts +6 -0
- package/dist/workflow/lint-rules.d.ts.map +1 -1
- package/dist/workflow/lint-rules.js +6 -0
- package/dist/workflow/lint-rules.js.map +1 -1
- package/dist/workflow/lint.d.ts +1 -1
- package/dist/workflow/lint.d.ts.map +1 -1
- package/dist/workflow/lint.js +83 -15
- package/dist/workflow/lint.js.map +1 -1
- package/dist/workflow/lint_profiles.yml +1 -0
- package/dist/workflow/normalized/expanded.d.ts +12 -0
- package/dist/workflow/normalized/expanded.d.ts.map +1 -1
- package/dist/workflow/normalized/expanded.js +42 -1
- package/dist/workflow/normalized/expanded.js.map +1 -1
- package/dist/workflow/normalized/index.d.ts +2 -2
- package/dist/workflow/normalized/index.d.ts.map +1 -1
- package/dist/workflow/normalized/index.js +2 -2
- package/dist/workflow/normalized/index.js.map +1 -1
- package/dist/workflow/normalized/labels.d.ts +7 -0
- package/dist/workflow/normalized/labels.d.ts.map +1 -1
- package/dist/workflow/normalized/labels.js +11 -0
- package/dist/workflow/normalized/labels.js.map +1 -1
- package/dist/workflow/normalized/toFormat2.d.ts +1 -0
- package/dist/workflow/normalized/toFormat2.d.ts.map +1 -1
- package/dist/workflow/normalized/toFormat2.js +4 -12
- package/dist/workflow/normalized/toFormat2.js.map +1 -1
- package/dist/workflow/normalized/toNative.d.ts +16 -1
- package/dist/workflow/normalized/toNative.d.ts.map +1 -1
- package/dist/workflow/normalized/toNative.js +23 -6
- package/dist/workflow/normalized/toNative.js.map +1 -1
- package/dist/workflow/semantic-validators.d.ts +9 -0
- package/dist/workflow/semantic-validators.d.ts.map +1 -1
- package/dist/workflow/semantic-validators.js +27 -14
- package/dist/workflow/semantic-validators.js.map +1 -1
- package/package.json +1 -1
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@@ -12,4 +12,10 @@ export declare class NativeStepKeyNotInteger extends Linter {
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12
12
|
static applies_to: readonly ["native"];
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13
13
|
static profile: string;
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14
14
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}
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15
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+
/** Step labels (including inputs) must be unique within a workflow; Galaxy refuses duplicates at import. */
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16
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+
export declare class StepLabelNotUnique extends Linter {
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17
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+
static severity: "error";
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18
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+
static applies_to: readonly ["format2", "native"];
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+
static profile: string;
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}
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//# sourceMappingURL=lint-rules.d.ts.map
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@@ -1 +1 @@
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1
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-
{"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"}
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1
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+
{"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"}
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@@ -12,4 +12,10 @@ export class NativeStepKeyNotInteger extends Linter {
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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"];
|
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19
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+
static profile = "structural";
|
|
20
|
+
}
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15
21
|
//# sourceMappingURL=lint-rules.js.map
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@@ -1 +1 @@
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|
|
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"}
|
package/dist/workflow/lint.d.ts
CHANGED
|
@@ -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
|
|
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;
|
|
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"}
|
package/dist/workflow/lint.js
CHANGED
|
@@ -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 {
|
|
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
|
-
|
|
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(
|
|
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
|
|
363
|
+
ctx.warn(`Workflow step ${stepId} specifies an untyped parameter in the post-job actions.`);
|
|
293
364
|
}
|
|
294
365
|
}
|
|
295
366
|
}
|
|
296
|
-
function
|
|
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
|
-
|
|
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
|
|
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
|
-
|
|
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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|
|
1
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+
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@@ -44,6 +44,18 @@ export interface ExpansionOptions {
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44
44
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export declare const MAX_EXPANSION_DEPTH = 10;
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45
45
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/** Check if a URL matches the GA4GH TRS v2 tools/versions pattern. */
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46
46
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export declare function isTrsUrl(url: string): boolean;
|
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47
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+
/**
|
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48
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+
* Build the GA4GH TRS `GALAXY` descriptor URL for a TRS tool version URL.
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49
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+
*
|
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50
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+
* The tool id may be percent-encoded or not (Galaxy and planemo emit it
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51
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+
* unencoded, e.g. `.../tools/#workflow/github.com/org/repo/main/versions/v1`),
|
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52
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+
* so it is unquoted and re-encoded to keep `#` and `/` from being misread as
|
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53
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+
* URL syntax. Any trailing path (such as `/GALAXY/descriptor`) is ignored.
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54
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+
* Returns `null` if `url` is not a TRS URL.
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55
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+
*
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56
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+
* Port of gxformat2/options.py trs_descriptor_url (mirrors Galaxy's trs_proxy).
|
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57
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+
*/
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58
|
+
export declare function trsDescriptorUrl(url: string): string | null;
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47
59
|
/**
|
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48
60
|
* Normalize and expand a Format2 workflow.
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49
61
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*
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@@ -1 +1 @@
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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;
|
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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"}
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@@ -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
|
|
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
|
-
{"version":3,"file":"expanded.js","sourceRoot":"","sources":["../../../src/workflow/normalized/expanded.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAOH,OAAO,EAAE,mBAAmB,EAAE,iBAAiB,EAAE,MAAM,cAAc,CAAC;AAEtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAC;AAC/C,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAyCzC,oBAAoB;AAEpB,MAAM,CAAC,MAAM,mBAAmB,GAAG,EAAE,CAAC;AAEtC,MAAM,aAAa,GAAG,
|
|
1
|
+
{"version":3,"file":"expanded.js","sourceRoot":"","sources":["../../../src/workflow/normalized/expanded.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAOH,OAAO,EAAE,mBAAmB,EAAE,iBAAiB,EAAE,MAAM,cAAc,CAAC;AAEtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAC;AAC/C,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAyCzC,oBAAoB;AAEpB,MAAM,CAAC,MAAM,mBAAmB,GAAG,EAAE,CAAC;AAEtC,MAAM,aAAa,GACjB,oGAAoG,CAAC;AAEvG,MAAM,uBAAuB,GAAG,QAAQ,CAAC;AAEzC,kBAAkB;AAElB,sEAAsE;AACtE,MAAM,UAAU,QAAQ,CAAC,GAAW;IAClC,OAAO,aAAa,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AACjC,CAAC;AAED;;;;GAIG;AACH,SAAS,QAAQ,CAAC,KAAa;IAC7B,OAAO,KAAK,CAAC,OAAO,CAAC,uBAAuB,EAAE,CAAC,GAAG,EAAE,EAAE;QACpD,IAAI,CAAC;YACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAC;QACjC,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,GAAG,CAAC;QACb,CAAC;IACH,CAAC,CAAC,CAAC;AACL,CAAC;AAED,0FAA0F;AAC1F,SAAS,UAAU,CAAC,KAAa;IAC/B,OAAO,kBAAkB,CAAC,KAAK,CAAC;SAC7B,OAAO,CAAC,UAAU,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,CAAC;SAC5E,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;AAC1B,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,gBAAgB,CAAC,GAAW;IAC1C,MAAM,KAAK,GAAG,aAAa,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,CAAC,KAAK,EAAE,MAAM;QAAE,OAAO,IAAI,CAAC;IAChC,MAAM,EAAE,UAAU,EAAE,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAC,MAAM,CAAC;IACvD,OAAO,CACL,GAAG,UAAU,uBAAuB,UAAU,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,EAAE;QAClE,aAAa,SAAS,IAAI,uBAAuB,aAAa,CAC/D,CAAC;AACJ,CAAC;AAED,0DAA0D;AAC1D,SAAS,gBAAgB,CAAC,SAAiB;IACzC,OAAO,CACL,SAAS,CAAC,UAAU,CAAC,SAAS,CAAC;QAC/B,SAAS,CAAC,UAAU,CAAC,UAAU,CAAC;QAChC,SAAS,CAAC,UAAU,CAAC,WAAW,CAAC,CAClC,CAAC;AACJ,CAAC;AAED,qEAAqE;AACrE,SAAS,iBAAiB,CAAC,GAA4B;IACrD,OAAO,GAAG,CAAC,iBAAiB,KAAK,MAAM,CAAC;AAC1C,CAAC;AAED,mFAAmF;AACnF,SAAS,cAAc,CAAC,QAAiC;IACvD,IAAI,iBAAiB,CAAC,QAAQ,CAAC,EAAE,CAAC;QAChC,OAAO,SAAS,CAAC,QAAQ,CAAC,CAAC;IAC7B,CAAC;IACD,OAAO,iBAAiB,CAAC,QAAQ,CAAC,CAAC;AACrC,CAAC;AAED,0FAA0F;AAC1F,SAAS,aAAa,CAAC,QAAiC;IACtD,IAAI,iBAAiB,CAAC,QAAQ,CAAC,EAAE,CAAC;QAChC,OAAO,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IACpC,CAAC;IACD,OAAO,QAAQ,CAAC,QAAQ,CAAC,CAAC;AAC5B,CAAC;AAED,+DAA+D;AAE/D,MAAM,gBAAgB;IACZ,SAAS,CAAc;IACvB,cAAc,CAAsB;IAE5C,YAAY,QAAqB,EAAE,gBAAqC,IAAI,GAAG,EAAE;QAC/E,IAAI,CAAC,SAAS,GAAG,QAAQ,CAAC;QAC1B,IAAI,CAAC,cAAc,GAAG,aAAa,CAAC;IACtC,CAAC;IAED,KAAK,CAAC,OAAO,CAAC,GAAW;QACvB,IAAI,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACjC,MAAM,IAAI,KAAK,CAAC,mCAAmC,GAAG,EAAE,CAAC,CAAC;QAC5D,CAAC;QACD,IAAI,IAAI,CAAC,cAAc,CAAC,IAAI,IAAI,mBAAmB,EAAE,CAAC;YACpD,MAAM,IAAI,KAAK,CAAC,wBAAwB,mBAAmB,YAAY,CAAC,CAAC;QAC3E,CAAC;QACD,OAAO,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC;IAC7B,CAAC;IAED,KAAK,CAAC,GAAW;QACf,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;QAC/C,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;QACnB,OAAO,IAAI,gBAAgB,CAAC,IAAI,CAAC,SAAS,EAAE,SAAS,CAAC,CAAC;IACzD,CAAC;CACF;AAED,8BAA8B;AAE9B;;;;;;GAMG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,GAAY,EACZ,OAA0B;IAE1B,MAAM,EAAE,GAAG,iBAAiB,CAAC,GAAG,CAAC,CAAC;IAClC,IAAI,CAAC,OAAO,EAAE,QAAQ,EAAE,CAAC;QACvB,mEAAmE;QACnE,OAAO,kBAAkB,CAAC,EAAE,CAAC,CAAC;IAChC,CAAC;IACD,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;IACnD,OAAO,cAAc,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC;AACjC,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,GAAY,EACZ,OAA0B;IAE1B,MAAM,EAAE,GAAG,gBAAgB,CAAC,GAAG,CAAC,CAAC;IACjC,IAAI,CAAC,OAAO,EAAE,QAAQ,EAAE,CAAC;QACvB,mEAAmE;QACnE,OAAO,iBAAiB,CAAC,EAAE,CAAC,CAAC;IAC/B,CAAC;IACD,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;IACnD,OAAO,aAAa,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC;AAChC,CAAC;AAED,kEAAkE;AAElE,SAAS,kBAAkB,CAAC,EAA6B;IACvD,MAAM,aAAa,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE;QAC1C,IAAI,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC;YAAE,OAAO,IAAI,CAAC;QAC/C,IAAI,IAAI,CAAC,GAAG,IAAI,OAAO,IAAI,CAAC,GAAG,KAAK,QAAQ,EAAE,CAAC;YAC7C,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,EAAE,kBAAkB,CAAC,IAAI,CAAC,GAAgC,CAAC,EAAE,CAAC;QACrF,CAAC;QACD,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG,IAAI,IAAI,EAAE,CAAC;IAC5C,CAAC,CAAC,CAAC;IACH,OAAO,EAAE,GAAG,EAAE,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC;AACzC,CAAC;AAED,SAAS,iBAAiB,CAAC,EAA4B;IACrD,MAAM,aAAa,GAAyC,EAAE,CAAC;IAC/D,KAAK,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC;QACnD,IAAI,IAAI,CAAC,WAAW,IAAI,IAAI,EAAE,CAAC;YAC7B,aAAa,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,IAAI,EAAE,WAAW,EAAE,iBAAiB,CAAC,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC;QACrF,CAAC;aAAM,CAAC;YACN,aAAa,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC;QAC5B,CAAC;IACH,CAAC;IACD,OAAO,EAAE,GAAG,EAAE,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC;AACzC,CAAC;AAED,0CAA0C;AAE1C,KAAK,UAAU,cAAc,CAC3B,EAA6B,EAC7B,GAAqB;IAErB,MAAM,aAAa,GAA4B,EAAE,CAAC;IAElD,KAAK,MAAM,IAAI,IAAI,EAAE,CAAC,KAAK,EAAE,CAAC;QAC5B,IAAI,WAAW,GAA0D,IAAI,CAAC;QAE9E,IAAI,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YAClC,kDAAkD;YAClD,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC;QACzB,CAAC;aAAM,IAAI,IAAI,CAAC,GAAG,IAAI,OAAO,IAAI,CAAC,GAAG,KAAK,QAAQ,EAAE,CAAC;YACpD,wCAAwC;YACxC,WAAW,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,GAAgC,EAAE,GAAG,CAAC,CAAC;QACjF,CAAC;aAAM,IAAI,OAAO,IAAI,CAAC,GAAG,KAAK,QAAQ,EAAE,CAAC;YACxC,8CAA8C;YAC9C,MAAM,QAAQ,GAAG,MAAM,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YAC7C,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACrC,MAAM,UAAU,GAAG,cAAc,CAAC,QAAQ,CAAC,CAAC;YAC5C,WAAW,GAAG,MAAM,cAAc,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC;QAC3D,CAAC;QAED,aAAa,CAAC,IAAI,CAAC;YACjB,GAAG,IAAI;YACP,GAAG,EAAE,WAAW;SACjB,CAAC,CAAC;IACL,CAAC;IAED,OAAO,EAAE,GAAG,EAAE,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC;AACzC,CAAC;AAED,KAAK,UAAU,aAAa,CAC1B,EAA4B,EAC5B,GAAqB;IAErB,MAAM,aAAa,GAAyC,EAAE,CAAC;IAE/D,KAAK,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC;QACnD,IAAI,WAAW,GAAoC,IAAI,CAAC;QAExD,IAAI,IAAI,CAAC,WAAW,IAAI,IAAI,EAAE,CAAC;YAC7B,wCAAwC;YACxC,WAAW,GAAG,MAAM,aAAa,CAAC,IAAI,CAAC,WAAW,EAAE,GAAG,CAAC,CAAC;QAC3D,CAAC;aAAM,IAAI,IAAI,CAAC,UAAU,IAAI,gBAAgB,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE,CAAC;YAChE,8DAA8D;YAC9D,MAAM,QAAQ,GAAG,MAAM,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;YACpD,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;YAC5C,MAAM,UAAU,GAAG,aAAa,CAAC,QAAQ,CAAC,CAAC;YAC3C,WAAW,GAAG,MAAM,aAAa,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC;QAC1D,CAAC;QAED,IAAI,WAAW,IAAI,IAAI,EAAE,CAAC;YACxB,6CAA6C;YAC7C,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAC;YAC/C,aAAa,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,IAAI,EAAE,WAAW,EAAE,WAAW,EAAE,CAAC;QAC7D,CAAC;aAAM,CAAC;YACN,aAAa,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC;QAC5B,CAAC;IACH,CAAC;IAED,OAAO,EAAE,GAAG,EAAE,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC;AACzC,CAAC"}
|
|
@@ -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"}
|
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@@ -5,7 +5,7 @@ export { toNative } from "./toNative.js";
|
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|
5
5
|
export { toFormat2Stateful, } from "./toFormat2Stateful.js";
|
|
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6
|
export { toNativeStateful } from "./toNativeStateful.js";
|
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7
|
export { ensureFormat2, ensureNative } from "./ensure.js";
|
|
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|
-
export { expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, } from "./expanded.js";
|
|
8
|
+
export { expandedFormat2, expandedNative, isTrsUrl, trsDescriptorUrl, MAX_EXPANSION_DEPTH, } from "./expanded.js";
|
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9
9
|
export { flattenCommentData, unflattenCommentData } from "./comments.js";
|
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|
-
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";
|
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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";
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8
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+
export declare const INPUT_STEP_TYPES: Set<string>;
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8
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/**
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9
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* Per-step callback result: a replacement format2 state dict + optional `in`
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* block overrides (flat path → source). Return null to fall back to the
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@@ -1 +1 @@
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1
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-
{"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;
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1
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+
{"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"}
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@@ -6,11 +6,11 @@
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6
6
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import { normalizedNative } from "./native.js";
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7
7
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import { isGalaxyUserToolRun } from "./format2.js";
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8
8
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import { flattenCommentData } from "./comments.js";
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9
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-
import {
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9
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+
import { isUnlabeled, Labels, unlabeledNodeId } from "./labels.js";
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10
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// Effect schemas produce deeply-readonly types. We build plain objects
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11
11
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// and cast — runtime semantics are identical.
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12
12
|
// Step types that represent workflow inputs
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13
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-
const INPUT_STEP_TYPES = new Set(["data_input", "data_collection_input", "parameter_input"]);
|
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13
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+
export const INPUT_STEP_TYPES = new Set(["data_input", "data_collection_input", "parameter_input"]);
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14
14
|
/**
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15
15
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* Convert a native Galaxy workflow to normalized Format2.
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16
16
|
*/
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|
@@ -22,15 +22,7 @@ function _buildFormat2Workflow(wf, options) {
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22
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|
// Build label map: step key → label string
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23
23
|
const labelMap = new Map();
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24
24
|
for (const [key, step] of Object.entries(wf.steps)) {
|
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25
|
-
|
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26
|
-
labelMap.set(String(key), step.label);
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27
|
-
}
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28
|
-
else if (INPUT_STEP_TYPES.has(step.type)) {
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29
|
-
labelMap.set(String(key), `${UNLABELED_INPUT_PREFIX}${step.id}`);
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30
|
-
}
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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
|
}
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|
35
27
|
// Build workflow outputs from step workflow_outputs
|
|
36
28
|
const labels = new Labels();
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|
@@ -99,7 +91,7 @@ function _nativeInputToFormat2Type(stepType, toolState) {
|
|
|
99
91
|
return "data";
|
|
100
92
|
}
|
|
101
93
|
function _buildInputParam(step) {
|
|
102
|
-
const stepId = step.label
|
|
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;
|