@nfdi4plants/arctrl 3.1.0 → 3.1.1

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 (89) hide show
  1. package/dist/ts/ts/CWL/CWLTypes.d.ts +162 -45
  2. package/dist/ts/ts/CWL/CWLTypes.d.ts.map +1 -1
  3. package/dist/ts/ts/CWL/CWLTypes.js +495 -104
  4. package/dist/ts/ts/CWL/Decode.d.ts +291 -48
  5. package/dist/ts/ts/CWL/Decode.d.ts.map +1 -1
  6. package/dist/ts/ts/CWL/Decode.js +911 -568
  7. package/dist/ts/ts/CWL/DynamicObjHelpers.d.ts +37 -0
  8. package/dist/ts/ts/CWL/DynamicObjHelpers.d.ts.map +1 -0
  9. package/dist/ts/ts/CWL/DynamicObjHelpers.js +57 -0
  10. package/dist/ts/ts/CWL/Encode.d.ts +117 -2
  11. package/dist/ts/ts/CWL/Encode.d.ts.map +1 -1
  12. package/dist/ts/ts/CWL/Encode.js +399 -163
  13. package/dist/ts/ts/CWL/ExpressionToolDescription.d.ts +2 -0
  14. package/dist/ts/ts/CWL/ExpressionToolDescription.d.ts.map +1 -1
  15. package/dist/ts/ts/CWL/ExpressionToolDescription.js +7 -0
  16. package/dist/ts/ts/CWL/Inputs.d.ts +65 -14
  17. package/dist/ts/ts/CWL/Inputs.d.ts.map +1 -1
  18. package/dist/ts/ts/CWL/Inputs.js +194 -51
  19. package/dist/ts/ts/CWL/OperationDescription.d.ts +2 -0
  20. package/dist/ts/ts/CWL/OperationDescription.d.ts.map +1 -1
  21. package/dist/ts/ts/CWL/OperationDescription.js +7 -0
  22. package/dist/ts/ts/CWL/Outputs.d.ts +51 -12
  23. package/dist/ts/ts/CWL/Outputs.d.ts.map +1 -1
  24. package/dist/ts/ts/CWL/Outputs.js +152 -76
  25. package/dist/ts/ts/CWL/ParameterReference.d.ts +4 -1
  26. package/dist/ts/ts/CWL/ParameterReference.d.ts.map +1 -1
  27. package/dist/ts/ts/CWL/ParameterReference.js +17 -6
  28. package/dist/ts/ts/CWL/Requirements.d.ts +140 -51
  29. package/dist/ts/ts/CWL/Requirements.d.ts.map +1 -1
  30. package/dist/ts/ts/CWL/Requirements.js +458 -128
  31. package/dist/ts/ts/CWL/ToolDescription.d.ts +27 -2
  32. package/dist/ts/ts/CWL/ToolDescription.d.ts.map +1 -1
  33. package/dist/ts/ts/CWL/ToolDescription.js +74 -4
  34. package/dist/ts/ts/CWL/WorkflowDescription.d.ts +2 -0
  35. package/dist/ts/ts/CWL/WorkflowDescription.d.ts.map +1 -1
  36. package/dist/ts/ts/CWL/WorkflowDescription.js +7 -0
  37. package/dist/ts/ts/CWL/WorkflowSteps.d.ts +50 -19
  38. package/dist/ts/ts/CWL/WorkflowSteps.d.ts.map +1 -1
  39. package/dist/ts/ts/CWL/WorkflowSteps.js +152 -23
  40. package/dist/ts/ts/ContractIO/ContractIO.d.ts.map +1 -1
  41. package/dist/ts/ts/ContractIO/ContractIO.js +4 -1
  42. package/dist/ts/ts/Conversion/Assay.d.ts.map +1 -1
  43. package/dist/ts/ts/Conversion/Assay.js +4 -3
  44. package/dist/ts/ts/Conversion/Investigation.js +2 -2
  45. package/dist/ts/ts/Conversion/Person.d.ts +1 -1
  46. package/dist/ts/ts/Conversion/Person.d.ts.map +1 -1
  47. package/dist/ts/ts/Conversion/Person.js +27 -11
  48. package/dist/ts/ts/Conversion/Run.d.ts.map +1 -1
  49. package/dist/ts/ts/Conversion/Run.js +3 -2
  50. package/dist/ts/ts/Conversion/ScholarlyArticle.d.ts.map +1 -1
  51. package/dist/ts/ts/Conversion/ScholarlyArticle.js +2 -1
  52. package/dist/ts/ts/Conversion/Study.d.ts.map +1 -1
  53. package/dist/ts/ts/Conversion/Study.js +5 -4
  54. package/dist/ts/ts/Conversion/Workflow.d.ts.map +1 -1
  55. package/dist/ts/ts/Conversion/Workflow.js +13 -12
  56. package/dist/ts/ts/Conversion.d.ts +14 -10
  57. package/dist/ts/ts/Conversion.d.ts.map +1 -1
  58. package/dist/ts/ts/Conversion.js +18 -11
  59. package/dist/ts/ts/Core/ArcTypes.d.ts.map +1 -1
  60. package/dist/ts/ts/Core/ArcTypes.js +18 -0
  61. package/dist/ts/ts/Json.d.ts +2 -2
  62. package/dist/ts/ts/Json.d.ts.map +1 -1
  63. package/dist/ts/ts/Json.js +3 -3
  64. package/dist/ts/ts/WorkflowGraph/ReferenceParsing.d.ts.map +1 -1
  65. package/dist/ts/ts/WorkflowGraph/ReferenceParsing.js +2 -1
  66. package/dist/ts/ts/Yaml/ValidationPackage.d.ts +1 -1
  67. package/dist/ts/ts/Yaml/ValidationPackage.d.ts.map +1 -1
  68. package/dist/ts/ts/Yaml/ValidationPackage.js +5 -5
  69. package/dist/ts/ts/Yaml/ValidationPackagesConfig.d.ts +1 -1
  70. package/dist/ts/ts/Yaml/ValidationPackagesConfig.d.ts.map +1 -1
  71. package/dist/ts/ts/Yaml/ValidationPackagesConfig.js +5 -5
  72. package/dist/ts/ts/Yaml.js +1 -1
  73. package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/Decode.fs.js +5 -33
  74. package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/Persil.fs.js +11 -159
  75. package/dist/ts/ts/fable_modules/YAMLicious.1.0.0-alpha.11/Preprocessing.fs.js +319 -0
  76. package/dist/ts/ts/fable_modules/YAMLicious.1.0.0-alpha.11/Reader.fs.js +1867 -0
  77. package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/Regex.fs.js +1 -1
  78. package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/RegexActivePatterns.fs.js +2 -2
  79. package/dist/ts/ts/fable_modules/YAMLicious.1.0.0-alpha.11/Syntax.fs.js +819 -0
  80. package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/Writer.fs.js +75 -48
  81. package/package.json +1 -1
  82. package/dist/ts/ts/fable_modules/YAMLicious.1.0.0-alpha.7/FlowToBlock.fs.js +0 -956
  83. package/dist/ts/ts/fable_modules/YAMLicious.1.0.0-alpha.7/Preprocessing.fs.js +0 -181
  84. package/dist/ts/ts/fable_modules/YAMLicious.1.0.0-alpha.7/Reader.fs.js +0 -1493
  85. /package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/Encode.fs.js +0 -0
  86. /package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/Escapes.fs.js +0 -0
  87. /package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/Interop/JsInterop.fs.js +0 -0
  88. /package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/StringBuffer.fs.js +0 -0
  89. /package/dist/ts/ts/fable_modules/{YAMLicious.1.0.0-alpha.7 → YAMLicious.1.0.0-alpha.11}/YAMLiciousTypes.fs.js +0 -0
@@ -4,6 +4,7 @@ import { forAll, toList, delay, collect, singleton, map as map$2 } from '../../.
4
4
  import { map as map$1, ofArray, isEmpty, empty, head, tail, cons, reverse, singleton as singleton$1 } from '../../../node_modules/@fable-org/fable-library-js/List.js';
5
5
  import { replace, join, trimEnd, substring, split } from '../../../node_modules/@fable-org/fable-library-js/String.js';
6
6
  import { int32ToString } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
7
+ import { Line_normalizeNewlines } from './Syntax.fs.js';
7
8
  import { write as write$1 } from './Preprocessing.fs.js';
8
9
 
9
10
  function StyleVerifier_isInlineSimpleScalar(v) {
@@ -87,9 +88,6 @@ function Formatting_escapeSingleQuoted(s) {
87
88
  function Formatting_escapeDoubleQuoted(s) {
88
89
  return replace(replace(replace(replace(replace(replace(replace(replace(replace(replace(replace(replace(replace(replace(replace(s, "\\", "\\\\"), '"', '\\"'), "\0", "\\0"), "\x07", "\\a"), "\b", "\\b"), " ", "\\t"), "\v", "\\v"), "\f", "\\f"), "\r", "\\r"), "\x1B", "\\e"), "…", "\\N"), " ", "\\_"), "\u2028", "\\L"), "\u2029", "\\P"), "\n", "\\n");
89
90
  }
90
- function Formatting_normalizeNewlines(s) {
91
- return replace(s, "\r\n", "\n");
92
- }
93
91
  function Formatting_resolveBlockStyle(options, content) {
94
92
  const matchValue_1 = content.Style;
95
93
  let matchResult, chomp, indent, style;
@@ -239,7 +237,7 @@ function Formatting_mkBlockHeader(style, chomp, indent) {
239
237
  2 ? "+" : "-");
240
238
  }
241
239
  function Formatting_bodyTextForChomping(chomp, value) {
242
- const normalized = Formatting_normalizeNewlines(value);
240
+ const normalized = Line_normalizeNewlines(value);
243
241
  switch (chomp.tag) {
244
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  case /* Clip */
245
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  1:
@@ -258,7 +256,7 @@ function Formatting_splitPreservingEmpty(s) {
258
256
  return ofArray(split(s, ["\n"], void 0, 0));
259
257
  }
260
258
  function Formatting_plainMultilineLines(content) {
261
- return Formatting_splitPreservingEmpty(Formatting_normalizeNewlines(content.Value));
259
+ return Formatting_splitPreservingEmpty(Line_normalizeNewlines(content.Value));
262
260
  }
263
261
  function Formatting_mkPlainMultilineNode(mkHeader, lines) {
264
262
  const patternInput = isEmpty(lines) ? ["", empty()] : [head(lines), tail(lines)];
@@ -365,14 +363,21 @@ function detokenizeWithOptions(options, ele) {
365
363
  0: {
366
364
  const key = ele_1.fields[0];
367
365
  const v = ele_1.fields[1];
368
- let matchResult, value_6, value_7, value_8, a, items_5, value_10, value_11, value_12, seq_1, anyElse;
366
+ let matchResult, value_6, value_7, value_8, a, items_6, value_10, value_11, value_12, seq_2, seq_3, anyElse;
369
367
  if (key.Comment != null) {
370
368
  matchResult = 0;
371
369
  } else {
372
370
  switch (v.tag) {
373
371
  case /* Object */
374
372
  3: {
375
- if (!isEmpty(v.fields[0])) {
373
+ if (isEmpty(v.fields[0])) {
374
+ if (Formatting_tryLegacyPlainMultilineContent(v.fields[0]) != null) {
375
+ matchResult = 5;
376
+ items_6 = v.fields[0];
377
+ } else {
378
+ matchResult = 11;
379
+ }
380
+ } else {
376
381
  switch (head(v.fields[0]).tag) {
377
382
  case /* Value */
378
383
  1: {
@@ -389,9 +394,9 @@ function detokenizeWithOptions(options, ele) {
389
394
  }
390
395
  } else if (Formatting_tryLegacyPlainMultilineContent(v.fields[0]) != null) {
391
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  matchResult = 5;
392
- items_5 = v.fields[0];
397
+ items_6 = v.fields[0];
393
398
  } else {
394
- matchResult = 10;
399
+ matchResult = 12;
395
400
  anyElse = v;
396
401
  }
397
402
  break;
@@ -403,9 +408,28 @@ function detokenizeWithOptions(options, ele) {
403
408
  a = head(v.fields[0]).fields[0];
404
409
  } else if (Formatting_tryLegacyPlainMultilineContent(v.fields[0]) != null) {
405
410
  matchResult = 5;
406
- items_5 = v.fields[0];
411
+ items_6 = v.fields[0];
407
412
  } else {
408
- matchResult = 10;
413
+ matchResult = 12;
414
+ anyElse = v;
415
+ }
416
+ break;
417
+ }
418
+ case /* Sequence */
419
+ 2: {
420
+ if (Formatting_tryLegacyPlainMultilineContent(v.fields[0]) != null) {
421
+ matchResult = 5;
422
+ items_6 = v.fields[0];
423
+ } else if (isEmpty(tail(v.fields[0]))) {
424
+ if (StyleVerifier_checkInlineSequence(head(v.fields[0]).fields[0])) {
425
+ matchResult = 9;
426
+ seq_2 = head(v.fields[0]).fields[0];
427
+ } else {
428
+ matchResult = 12;
429
+ anyElse = v;
430
+ }
431
+ } else {
432
+ matchResult = 12;
409
433
  anyElse = v;
410
434
  }
411
435
  break;
@@ -413,18 +437,12 @@ function detokenizeWithOptions(options, ele) {
413
437
  default:
414
438
  if (Formatting_tryLegacyPlainMultilineContent(v.fields[0]) != null) {
415
439
  matchResult = 5;
416
- items_5 = v.fields[0];
440
+ items_6 = v.fields[0];
417
441
  } else {
418
- matchResult = 10;
442
+ matchResult = 12;
419
443
  anyElse = v;
420
444
  }
421
445
  }
422
- } else if (Formatting_tryLegacyPlainMultilineContent(v.fields[0]) != null) {
423
- matchResult = 5;
424
- items_5 = v.fields[0];
425
- } else {
426
- matchResult = 10;
427
- anyElse = v;
428
446
  }
429
447
  break;
430
448
  }
@@ -445,16 +463,16 @@ function detokenizeWithOptions(options, ele) {
445
463
  case /* Sequence */
446
464
  2: {
447
465
  if (StyleVerifier_checkInlineSequence(v.fields[0])) {
448
- matchResult = 9;
449
- seq_1 = v.fields[0];
450
- } else {
451
466
  matchResult = 10;
467
+ seq_3 = v.fields[0];
468
+ } else {
469
+ matchResult = 12;
452
470
  anyElse = v;
453
471
  }
454
472
  break;
455
473
  }
456
474
  default: {
457
- matchResult = 10;
475
+ matchResult = 12;
458
476
  anyElse = v;
459
477
  }
460
478
  }
@@ -471,7 +489,7 @@ function detokenizeWithOptions(options, ele) {
471
489
  case 4:
472
490
  return PreprocessorElement_Line(Formatting_mkMappingKey(options, key) + " *" + a);
473
491
  case 5:
474
- return Formatting_mkPlainMultilineMapping(options, key, value(Formatting_tryLegacyPlainMultilineContent(items_5)));
492
+ return Formatting_mkPlainMultilineMapping(options, key, value(Formatting_tryLegacyPlainMultilineContent(items_6)));
475
493
  case 6:
476
494
  return Formatting_mkBlockScalarMapping(options, key, value_10);
477
495
  case 7:
@@ -479,7 +497,11 @@ function detokenizeWithOptions(options, ele) {
479
497
  case 8:
480
498
  return PreprocessorElement_Line(Formatting_mkMappingKey(options, key) + " " + Formatting_mkInlineContent(options, value_12));
481
499
  case 9:
482
- return PreprocessorElement_Line(Formatting_mkMappingKey(options, key) + " " + Formatting_mkInlineSequence(options, seq_1));
500
+ return PreprocessorElement_Line(Formatting_mkMappingKey(options, key) + " " + Formatting_mkInlineSequence(options, seq_2));
501
+ case 10:
502
+ return PreprocessorElement_Line(Formatting_mkMappingKey(options, key) + " " + Formatting_mkInlineSequence(options, seq_3));
503
+ case 11:
504
+ return PreprocessorElement_Line(Formatting_mkMappingKey(options, key) + " {}");
483
505
  default:
484
506
  return PreprocessorElement_Level(ofArray([PreprocessorElement_Line(Formatting_mkMappingKey(options, key)), PreprocessorElement_Intendation(singleton$1(loop(anyElse)))]));
485
507
  }
@@ -487,11 +509,13 @@ function detokenizeWithOptions(options, ele) {
487
509
  case /* Object */
488
510
  3:
489
511
  if (Formatting_tryLegacyPlainMultilineContent(ele_1.fields[0]) != null) {
490
- const items_6 = ele_1.fields[0];
491
- return Formatting_mkPlainMultilineRoot(options, value(Formatting_tryLegacyPlainMultilineContent(items_6)));
512
+ const items_7 = ele_1.fields[0];
513
+ return Formatting_mkPlainMultilineRoot(options, value(Formatting_tryLegacyPlainMultilineContent(items_7)));
514
+ } else if (isEmpty(ele_1.fields[0])) {
515
+ return PreprocessorElement_Line("{}");
492
516
  } else {
493
- const seq_2 = ele_1.fields[0];
494
- return PreprocessorElement_Level(toList(delay(() => map$2(loop, seq_2))));
517
+ const seq_4 = ele_1.fields[0];
518
+ return PreprocessorElement_Level(toList(delay(() => map$2(loop, seq_4))));
495
519
  }
496
520
  case /* Value */
497
521
  1:
@@ -507,14 +531,21 @@ function detokenizeWithOptions(options, ele) {
507
531
  }
508
532
  case /* Sequence */
509
533
  2: {
510
- const seq_3 = ele_1.fields[0];
534
+ const seq_5 = ele_1.fields[0];
511
535
  return PreprocessorElement_Level(toList(delay(() => collect((element_1) => {
512
536
  const matchValue = element_1;
513
- let matchResult_1, value_21, value_22, value_23, a_1, items_11, value_25, value_26, value_27, nested_1, anyElse_1;
537
+ let matchResult_1, value_21, value_22, value_23, a_1, items_12, value_25, value_26, value_27, nested_1, anyElse_1;
514
538
  switch (matchValue.tag) {
515
539
  case /* Object */
516
540
  3: {
517
- if (!isEmpty(matchValue.fields[0])) {
541
+ if (isEmpty(matchValue.fields[0])) {
542
+ if (Formatting_tryLegacyPlainMultilineContent(matchValue.fields[0]) != null) {
543
+ matchResult_1 = 4;
544
+ items_12 = matchValue.fields[0];
545
+ } else {
546
+ matchResult_1 = 9;
547
+ }
548
+ } else {
518
549
  switch (head(matchValue.fields[0]).tag) {
519
550
  case /* Value */
520
551
  1: {
@@ -531,9 +562,9 @@ function detokenizeWithOptions(options, ele) {
531
562
  }
532
563
  } else if (Formatting_tryLegacyPlainMultilineContent(matchValue.fields[0]) != null) {
533
564
  matchResult_1 = 4;
534
- items_11 = matchValue.fields[0];
565
+ items_12 = matchValue.fields[0];
535
566
  } else {
536
- matchResult_1 = 9;
567
+ matchResult_1 = 10;
537
568
  anyElse_1 = matchValue;
538
569
  }
539
570
  break;
@@ -545,9 +576,9 @@ function detokenizeWithOptions(options, ele) {
545
576
  a_1 = head(matchValue.fields[0]).fields[0];
546
577
  } else if (Formatting_tryLegacyPlainMultilineContent(matchValue.fields[0]) != null) {
547
578
  matchResult_1 = 4;
548
- items_11 = matchValue.fields[0];
579
+ items_12 = matchValue.fields[0];
549
580
  } else {
550
- matchResult_1 = 9;
581
+ matchResult_1 = 10;
551
582
  anyElse_1 = matchValue;
552
583
  }
553
584
  break;
@@ -555,18 +586,12 @@ function detokenizeWithOptions(options, ele) {
555
586
  default:
556
587
  if (Formatting_tryLegacyPlainMultilineContent(matchValue.fields[0]) != null) {
557
588
  matchResult_1 = 4;
558
- items_11 = matchValue.fields[0];
589
+ items_12 = matchValue.fields[0];
559
590
  } else {
560
- matchResult_1 = 9;
591
+ matchResult_1 = 10;
561
592
  anyElse_1 = matchValue;
562
593
  }
563
594
  }
564
- } else if (Formatting_tryLegacyPlainMultilineContent(matchValue.fields[0]) != null) {
565
- matchResult_1 = 4;
566
- items_11 = matchValue.fields[0];
567
- } else {
568
- matchResult_1 = 9;
569
- anyElse_1 = matchValue;
570
595
  }
571
596
  break;
572
597
  }
@@ -590,13 +615,13 @@ function detokenizeWithOptions(options, ele) {
590
615
  matchResult_1 = 8;
591
616
  nested_1 = matchValue.fields[0];
592
617
  } else {
593
- matchResult_1 = 9;
618
+ matchResult_1 = 10;
594
619
  anyElse_1 = matchValue;
595
620
  }
596
621
  break;
597
622
  }
598
623
  default: {
599
- matchResult_1 = 9;
624
+ matchResult_1 = 10;
600
625
  anyElse_1 = matchValue;
601
626
  }
602
627
  }
@@ -610,7 +635,7 @@ function detokenizeWithOptions(options, ele) {
610
635
  case 3:
611
636
  return singleton(PreprocessorElement_Line("- *" + a_1));
612
637
  case 4:
613
- return singleton(Formatting_mkPlainMultilineSequenceItem(options, value(Formatting_tryLegacyPlainMultilineContent(items_11))));
638
+ return singleton(Formatting_mkPlainMultilineSequenceItem(options, value(Formatting_tryLegacyPlainMultilineContent(items_12))));
614
639
  case 5:
615
640
  return singleton(Formatting_mkPlainMultilineSequenceItem(options, value_25));
616
641
  case 6:
@@ -619,10 +644,12 @@ function detokenizeWithOptions(options, ele) {
619
644
  return singleton(PreprocessorElement_Line(Formatting_mkMinusLine(Formatting_mkInlineContent(options, value_27))));
620
645
  case 8:
621
646
  return singleton(PreprocessorElement_Line(Formatting_mkMinusLine(Formatting_mkInlineSequence(options, nested_1))));
647
+ case 9:
648
+ return singleton(PreprocessorElement_Line("- {}"));
622
649
  default:
623
650
  return singleton(PreprocessorElement_Level(ofArray([PreprocessorElement_Line("-"), PreprocessorElement_Intendation(singleton$1(loop(anyElse_1)))])));
624
651
  }
625
- }, seq_3))));
652
+ }, seq_5))));
626
653
  }
627
654
  case /* Comment */
628
655
  4: {
package/package.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "type": "module",
3
3
  "name": "@nfdi4plants/arctrl",
4
- "version": "3.1.0",
4
+ "version": "3.1.1",
5
5
  "description": "Top level ARC DataModel and API function descriptions.",
6
6
  "repository": {
7
7
  "type": "git",