@galaxy-tool-util/schema 1.10.1 → 1.13.1

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 (104) hide show
  1. package/dist/index.d.ts +29 -4
  2. package/dist/index.d.ts.map +1 -1
  3. package/dist/index.js +23 -2
  4. package/dist/index.js.map +1 -1
  5. package/dist/schema/bundle-types.d.ts +6 -2
  6. package/dist/schema/bundle-types.d.ts.map +1 -1
  7. package/dist/schema/bundle-types.js.map +1 -1
  8. package/dist/schema/parameter-defaults.d.ts.map +1 -1
  9. package/dist/schema/parameter-defaults.js +7 -3
  10. package/dist/schema/parameter-defaults.js.map +1 -1
  11. package/dist/schema/parameters/base.d.ts.map +1 -1
  12. package/dist/schema/parameters/base.js +3 -1
  13. package/dist/schema/parameters/base.js.map +1 -1
  14. package/dist/schema/parameters/gx-drill-down.js +2 -1
  15. package/dist/schema/parameters/gx-drill-down.js.map +1 -1
  16. package/dist/schema/parameters/gx-text.js +2 -2
  17. package/dist/schema/parameters/gx-text.js.map +1 -1
  18. package/dist/schema/parsed-tool.d.ts +180 -10
  19. package/dist/schema/parsed-tool.d.ts.map +1 -1
  20. package/dist/schema/parsed-tool.js +56 -2
  21. package/dist/schema/parsed-tool.js.map +1 -1
  22. package/dist/schema/state-representations.js +1 -1
  23. package/dist/schema/state-representations.js.map +1 -1
  24. package/dist/tool-state-validator.d.ts +2 -2
  25. package/dist/tool-state-validator.d.ts.map +1 -1
  26. package/dist/tool-state-validator.js +4 -4
  27. package/dist/tool-state-validator.js.map +1 -1
  28. package/dist/trs/index.d.ts +110 -0
  29. package/dist/trs/index.d.ts.map +1 -0
  30. package/dist/trs/index.js +64 -0
  31. package/dist/trs/index.js.map +1 -0
  32. package/dist/user-tool-parse/index.d.ts +4 -1
  33. package/dist/user-tool-parse/index.d.ts.map +1 -1
  34. package/dist/user-tool-parse/index.js +4 -1
  35. package/dist/user-tool-parse/index.js.map +1 -1
  36. package/dist/user-tool-parse/input-source.d.ts +105 -0
  37. package/dist/user-tool-parse/input-source.d.ts.map +1 -0
  38. package/dist/user-tool-parse/input-source.js +271 -0
  39. package/dist/user-tool-parse/input-source.js.map +1 -0
  40. package/dist/user-tool-parse/inputs.d.ts +15 -8
  41. package/dist/user-tool-parse/inputs.d.ts.map +1 -1
  42. package/dist/user-tool-parse/inputs.js +188 -295
  43. package/dist/user-tool-parse/inputs.js.map +1 -1
  44. package/dist/user-tool-parse/outputs.d.ts +2 -1
  45. package/dist/user-tool-parse/outputs.d.ts.map +1 -1
  46. package/dist/user-tool-parse/outputs.js +4 -3
  47. package/dist/user-tool-parse/outputs.js.map +1 -1
  48. package/dist/user-tool-parse/parse.d.ts +17 -2
  49. package/dist/user-tool-parse/parse.d.ts.map +1 -1
  50. package/dist/user-tool-parse/parse.js +23 -6
  51. package/dist/user-tool-parse/parse.js.map +1 -1
  52. package/dist/workflow/cytoscape.d.ts.map +1 -1
  53. package/dist/workflow/cytoscape.js +5 -3
  54. package/dist/workflow/cytoscape.js.map +1 -1
  55. package/dist/workflow/draft-checks.d.ts +2 -1
  56. package/dist/workflow/draft-checks.d.ts.map +1 -1
  57. package/dist/workflow/draft-checks.js +29 -5
  58. package/dist/workflow/draft-checks.js.map +1 -1
  59. package/dist/workflow/index.d.ts +1 -1
  60. package/dist/workflow/index.d.ts.map +1 -1
  61. package/dist/workflow/index.js +1 -1
  62. package/dist/workflow/index.js.map +1 -1
  63. package/dist/workflow/mermaid.d.ts +1 -1
  64. package/dist/workflow/mermaid.d.ts.map +1 -1
  65. package/dist/workflow/mermaid.js +5 -3
  66. package/dist/workflow/mermaid.js.map +1 -1
  67. package/dist/workflow/normalized/expanded.d.ts.map +1 -1
  68. package/dist/workflow/normalized/expanded.js +8 -2
  69. package/dist/workflow/normalized/expanded.js.map +1 -1
  70. package/dist/workflow/normalized/format2.d.ts +22 -1
  71. package/dist/workflow/normalized/format2.d.ts.map +1 -1
  72. package/dist/workflow/normalized/format2.js +26 -5
  73. package/dist/workflow/normalized/format2.js.map +1 -1
  74. package/dist/workflow/normalized/index.d.ts +1 -1
  75. package/dist/workflow/normalized/index.d.ts.map +1 -1
  76. package/dist/workflow/normalized/index.js +1 -1
  77. package/dist/workflow/normalized/index.js.map +1 -1
  78. package/dist/workflow/normalized/stateful-runner.d.ts +3 -1
  79. package/dist/workflow/normalized/stateful-runner.d.ts.map +1 -1
  80. package/dist/workflow/normalized/stateful-runner.js +1 -1
  81. package/dist/workflow/normalized/stateful-runner.js.map +1 -1
  82. package/dist/workflow/normalized/toFormat2.d.ts.map +1 -1
  83. package/dist/workflow/normalized/toFormat2.js +34 -11
  84. package/dist/workflow/normalized/toFormat2.js.map +1 -1
  85. package/dist/workflow/normalized/toFormat2Stateful.js +8 -10
  86. package/dist/workflow/normalized/toFormat2Stateful.js.map +1 -1
  87. package/dist/workflow/normalized/toNative.d.ts.map +1 -1
  88. package/dist/workflow/normalized/toNative.js +16 -26
  89. package/dist/workflow/normalized/toNative.js.map +1 -1
  90. package/dist/workflow/normalized/toNativeStateful.d.ts.map +1 -1
  91. package/dist/workflow/normalized/toNativeStateful.js +3 -10
  92. package/dist/workflow/normalized/toNativeStateful.js.map +1 -1
  93. package/dist/workflow/report-models.d.ts +1 -1
  94. package/dist/workflow/report-models.d.ts.map +1 -1
  95. package/dist/workflow/report-models.js +1 -0
  96. package/dist/workflow/report-models.js.map +1 -1
  97. package/dist/workflow/stateful-convert.d.ts.map +1 -1
  98. package/dist/workflow/stateful-convert.js +6 -0
  99. package/dist/workflow/stateful-convert.js.map +1 -1
  100. package/dist/workflow/stateful-validate.d.ts +12 -5
  101. package/dist/workflow/stateful-validate.d.ts.map +1 -1
  102. package/dist/workflow/stateful-validate.js +62 -24
  103. package/dist/workflow/stateful-validate.js.map +1 -1
  104. package/package.json +1 -1
package/dist/workflow/normalized/format2.js.map CHANGED
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package/dist/workflow/normalized/index.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, } from "./format2.js";
1
+ export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, type GalaxyUserToolStub, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, } from "./format2.js";
2
2
  export { normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, } from "./native.js";
3
3
  export { toFormat2, type ToFormat2Options, type Format2StateOverride } from "./toFormat2.js";
4
4
  export { toNative, type ToNativeOptions } from "./toNative.js";
package/dist/workflow/normalized/index.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/workflow/normalized/index.js CHANGED
@@ -1,4 +1,4 @@
1
- export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, } from "./format2.js";
1
+ export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, } from "./format2.js";
2
2
  export { normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, } from "./native.js";
3
3
  export { toFormat2 } from "./toFormat2.js";
4
4
  export { toNative } from "./toNative.js";
package/dist/workflow/normalized/index.js.map CHANGED
@@ -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,GAOlC,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,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"}
package/dist/workflow/normalized/stateful-runner.d.ts CHANGED
@@ -63,8 +63,10 @@ export interface StepRunnerConfig<Args, Result> {
63
63
  /**
64
64
  * Optional post-conversion validation on the converted result. Throw to
65
65
  * signal failure — classified as `post_validation`, result discarded.
66
+ * Receives the original `args` (the step) so validation can re-inject the
67
+ * connection markers that conversion strips out of the converted state.
66
68
  */
67
- postValidate?: (result: Result, inputs: ToolParameterModel[]) => void;
69
+ postValidate?: (result: Result, inputs: ToolParameterModel[], args: Args) => void;
68
70
  }
69
71
  /**
70
72
  * Build a per-step callback with status tracking and graceful fallback.
package/dist/workflow/normalized/stateful-runner.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"stateful-runner.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/stateful-runner.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AAEH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,8BAA8B,CAAC;AAEvE,MAAM,MAAM,kBAAkB,GAAG,CAC/B,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,MAAM,GAAG,IAAI,KACvB,kBAAkB,EAAE,GAAG,SAAS,CAAC;AAEtC,MAAM,MAAM,0BAA0B,GAClC,cAAc,GACd,UAAU,GACV,gBAAgB,GAChB,YAAY,GACZ,iBAAiB,CAAC;AAEtB,MAAM,WAAW,oBAAoB;IACnC,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,SAAS,EAAE,OAAO,CAAC;IACnB,6EAA6E;IAC7E,YAAY,CAAC,EAAE,0BAA0B,CAAC;IAC1C,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,gBAAgB,CAAC,IAAI,EAAE,MAAM;IAC5C,sEAAsE;IACtE,kBAAkB,EAAE,kBAAkB,CAAC;IACvC,0DAA0D;IAC1D,MAAM,EAAE,oBAAoB,EAAE,CAAC;IAC/B,yEAAyE;IACzE,UAAU,EAAE,CAAC,IAAI,EAAE,IAAI,KAAK,OAAO,CAAC;IACpC,2DAA2D;IAC3D,UAAU,EAAE,CAAC,IAAI,EAAE,IAAI,KAAK;QAC1B,MAAM,EAAE,MAAM,CAAC;QACf,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;KAC7B,CAAC;IACF;;;;OAIG;IACH,QAAQ,CAAC,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE,kBAAkB,EAAE,KAAK,MAAM,EAAE,GAAG,IAAI,CAAC;IACzE;;;OAGG;IACH,WAAW,CAAC,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE,kBAAkB,EAAE,KAAK,IAAI,CAAC;IACjE,4EAA4E;IAC5E,OAAO,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE,kBAAkB,EAAE,KAAK,MAAM,CAAC;IAC9D;;;OAGG;IACH,YAAY,CAAC,EAAE,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,kBAAkB,EAAE,KAAK,IAAI,CAAC;CACvE;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,MAAM,EACnD,MAAM,EAAE,gBAAgB,CAAC,IAAI,EAAE,MAAM,CAAC,GACrC,CAAC,IAAI,EAAE,IAAI,KAAK,MAAM,GAAG,IAAI,CAiG/B"}
1
+ {"version":3,"file":"stateful-runner.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/stateful-runner.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AAEH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,8BAA8B,CAAC;AAEvE,MAAM,MAAM,kBAAkB,GAAG,CAC/B,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,MAAM,GAAG,IAAI,KACvB,kBAAkB,EAAE,GAAG,SAAS,CAAC;AAEtC,MAAM,MAAM,0BAA0B,GAClC,cAAc,GACd,UAAU,GACV,gBAAgB,GAChB,YAAY,GACZ,iBAAiB,CAAC;AAEtB,MAAM,WAAW,oBAAoB;IACnC,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,SAAS,EAAE,OAAO,CAAC;IACnB,6EAA6E;IAC7E,YAAY,CAAC,EAAE,0BAA0B,CAAC;IAC1C,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,gBAAgB,CAAC,IAAI,EAAE,MAAM;IAC5C,sEAAsE;IACtE,kBAAkB,EAAE,kBAAkB,CAAC;IACvC,0DAA0D;IAC1D,MAAM,EAAE,oBAAoB,EAAE,CAAC;IAC/B,yEAAyE;IACzE,UAAU,EAAE,CAAC,IAAI,EAAE,IAAI,KAAK,OAAO,CAAC;IACpC,2DAA2D;IAC3D,UAAU,EAAE,CAAC,IAAI,EAAE,IAAI,KAAK;QAC1B,MAAM,EAAE,MAAM,CAAC;QACf,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;KAC7B,CAAC;IACF;;;;OAIG;IACH,QAAQ,CAAC,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE,kBAAkB,EAAE,KAAK,MAAM,EAAE,GAAG,IAAI,CAAC;IACzE;;;OAGG;IACH,WAAW,CAAC,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE,kBAAkB,EAAE,KAAK,IAAI,CAAC;IACjE,4EAA4E;IAC5E,OAAO,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE,kBAAkB,EAAE,KAAK,MAAM,CAAC;IAC9D;;;;;OAKG;IACH,YAAY,CAAC,EAAE,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,kBAAkB,EAAE,EAAE,IAAI,EAAE,IAAI,KAAK,IAAI,CAAC;CACnF;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,MAAM,EACnD,MAAM,EAAE,gBAAgB,CAAC,IAAI,EAAE,MAAM,CAAC,GACrC,CAAC,IAAI,EAAE,IAAI,KAAK,MAAM,GAAG,IAAI,CAiG/B"}
package/dist/workflow/normalized/stateful-runner.js CHANGED
@@ -101,7 +101,7 @@ export function makeStepConversionRunner(config) {
101
101
  }
102
102
  if (postValidate) {
103
103
  try {
104
- postValidate(result, inputs);
104
+ postValidate(result, inputs, args);
105
105
  }
106
106
  catch (err) {
107
107
  status.push({
package/dist/workflow/normalized/stateful-runner.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"stateful-runner.js","sourceRoot":"","sources":["../../../src/workflow/normalized/stateful-runner.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AA2DH;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,wBAAwB,CACtC,MAAsC;IAEtC,MAAM,EACJ,kBAAkB,EAClB,MAAM,EACN,UAAU,EACV,UAAU,EACV,QAAQ,EACR,WAAW,EACX,OAAO,EACP,YAAY,GACb,GAAG,MAAM,CAAC;IAEX,OAAO,CAAC,IAAI,EAAE,EAAE;QACd,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC;YAAE,OAAO,IAAI,CAAC;QACnC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,IAAI,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAC;QAChE,MAAM,MAAM,GAAG,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,kBAAkB,CAAC,MAAM,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;QAEpF,IAAI,MAAM,IAAI,IAAI,EAAE,CAAC;YACnB,MAAM,CAAC,IAAI,CAAC;gBACV,MAAM;gBACN,MAAM;gBACN,WAAW;gBACX,SAAS,EAAE,KAAK;gBAChB,YAAY,EAAE,cAAc;gBAC5B,KAAK,EACH,MAAM,IAAI,IAAI;oBACZ,CAAC,CAAC,qBAAqB;oBACvB,CAAC,CAAC,sBAAsB,MAAM,GAAG,WAAW,CAAC,CAAC,CAAC,IAAI,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE;aAC5E,CAAC,CAAC;YACH,OAAO,IAAI,CAAC;QACd,CAAC;QAED,IAAI,QAAQ,EAAE,CAAC;YACb,MAAM,OAAO,GAAG,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;YACvC,IAAI,OAAO,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAClC,MAAM,CAAC,IAAI,CAAC;oBACV,MAAM;oBACN,MAAM;oBACN,WAAW;oBACX,SAAS,EAAE,KAAK;oBAChB,YAAY,EAAE,UAAU;oBACxB,KAAK,EAAE,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC;iBAC1B,CAAC,CAAC;gBACH,OAAO,IAAI,CAAC;YACd,CAAC;QACH,CAAC;QAED,IAAI,WAAW,EAAE,CAAC;YAChB,IAAI,CAAC;gBACH,WAAW,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;YAC5B,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,MAAM,CAAC,IAAI,CAAC;oBACV,MAAM;oBACN,MAAM;oBACN,WAAW;oBACX,SAAS,EAAE,KAAK;oBAChB,YAAY,EAAE,gBAAgB;oBAC9B,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;iBACxD,CAAC,CAAC;gBACH,OAAO,IAAI,CAAC;YACd,CAAC;QACH,CAAC;QAED,IAAI,MAAc,CAAC;QACnB,IAAI,CAAC;YACH,MAAM,GAAG,OAAO,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QACjC,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,MAAM,CAAC,IAAI,CAAC;gBACV,MAAM;gBACN,MAAM;gBACN,WAAW;gBACX,SAAS,EAAE,KAAK;gBAChB,YAAY,EAAE,YAAY;gBAC1B,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;aACxD,CAAC,CAAC;YACH,OAAO,IAAI,CAAC;QACd,CAAC;QAED,IAAI,YAAY,EAAE,CAAC;YACjB,IAAI,CAAC;gBACH,YAAY,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;YAC/B,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,MAAM,CAAC,IAAI,CAAC;oBACV,MAAM;oBACN,MAAM;oBACN,WAAW;oBACX,SAAS,EAAE,KAAK;oBAChB,YAAY,EAAE,iBAAiB;oBAC/B,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;iBACxD,CAAC,CAAC;gBACH,OAAO,IAAI,CAAC;YACd,CAAC;QACH,CAAC;QAED,MAAM,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QAC9D,OAAO,MAAM,CAAC;IAChB,CAAC,CAAC;AACJ,CAAC"}
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package/dist/workflow/normalized/toFormat2.d.ts.map CHANGED
@@ -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;AAUtB;;;;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;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"}
package/dist/workflow/normalized/toFormat2.js CHANGED
@@ -4,6 +4,7 @@
4
4
  * Port of gxformat2/normalized/_conversion.py to_format2 + helpers.
5
5
  */
6
6
  import { normalizedNative } from "./native.js";
7
+ import { isGalaxyUserToolRun } from "./format2.js";
7
8
  import { flattenCommentData } from "./comments.js";
8
9
  import { UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, isUnlabeled, Labels } from "./labels.js";
9
10
  // Effect schemas produce deeply-readonly types. We build plain objects
@@ -123,6 +124,23 @@ function _buildInputParam(step) {
123
124
  }
124
125
  }
125
126
  }
127
+ if (inputType === "int" || inputType === "float") {
128
+ const validators = ts.validators;
129
+ if (Array.isArray(validators)) {
130
+ for (const validator of validators) {
131
+ if (validator &&
132
+ typeof validator === "object" &&
133
+ validator.type === "in_range" &&
134
+ !validator.negate) {
135
+ if (typeof validator.min === "number")
136
+ result.min = validator.min;
137
+ if (typeof validator.max === "number")
138
+ result.max = validator.max;
139
+ break;
140
+ }
141
+ }
142
+ }
143
+ }
126
144
  if (step.annotation)
127
145
  result.doc = step.annotation;
128
146
  if (step.position)
@@ -152,9 +170,7 @@ function _buildFormat2Step(step, labelMap, options) {
152
170
  return _buildToolFormat2Step(step, labelMap, options);
153
171
  }
154
172
  function _buildToolFormat2Step(step, labelMap, options) {
155
- // User-defined tool: tool_representation with class GalaxyUserTool
156
- const toolRep = step.tool_representation;
157
- if (toolRep && toolRep.class === "GalaxyUserTool") {
173
+ if (isGalaxyUserToolRun(step.tool_representation)) {
158
174
  return _buildUserToolFormat2Step(step, labelMap);
159
175
  }
160
176
  const inList = _buildFormat2StepInputs(step, labelMap);
@@ -176,13 +192,7 @@ function _buildToolFormat2Step(step, labelMap, options) {
176
192
  }
177
193
  }
178
194
  else {
179
- // Default: copy tool_state, strip bookkeeping keys
180
- const ts = { ...step.tool_state };
181
- delete ts.__page__;
182
- delete ts.__rerun_remap_job_id__;
183
- if (Object.keys(ts).length > 0) {
184
- toolState = ts;
185
- }
195
+ toolState = _passthroughToolState(step);
186
196
  }
187
197
  const { stepId, displayLabel } = _resolveStepIdentity(step, labelMap);
188
198
  return {
@@ -202,6 +212,15 @@ function _buildToolFormat2Step(step, labelMap, options) {
202
212
  errors: step.errors ?? undefined,
203
213
  };
204
214
  }
215
+ /** Default: copy tool_state verbatim, minus bookkeeping keys; null when nothing is left. */
216
+ function _passthroughToolState(step) {
217
+ const ts = { ...step.tool_state };
218
+ delete ts.__page__;
219
+ delete ts.__rerun_remap_job_id__;
220
+ return Object.keys(ts).length > 0 ? ts : null;
221
+ }
222
+ // The stateful encoder resolves tools by tool_id, which a user-defined tool
223
+ // step doesn't have, so its tool_state always passes through verbatim.
205
224
  function _buildUserToolFormat2Step(step, labelMap) {
206
225
  const inList = _buildFormat2StepInputs(step, labelMap);
207
226
  const outList = _buildFormat2StepOutputs(step);
@@ -213,7 +232,11 @@ function _buildUserToolFormat2Step(step, labelMap) {
213
232
  run: step.tool_representation,
214
233
  in: inList,
215
234
  out: outList,
235
+ tool_state: _passthroughToolState(step),
216
236
  position: step.position,
237
+ when: step.when ?? undefined,
238
+ uuid: step.uuid ?? undefined,
239
+ errors: step.errors ?? undefined,
217
240
  };
218
241
  }
219
242
  function _buildSubworkflowFormat2Step(step, labelMap, options) {
@@ -393,7 +416,7 @@ function _replaceAnonymousOutputReferences(outputParams, fmt2Steps) {
393
416
  const runsByLabel = new Map();
394
417
  for (const step of fmt2Steps) {
395
418
  const label = step.label ?? step.id;
396
- if (step.run && typeof step.run === "object") {
419
+ if (step.run && typeof step.run === "object" && !isGalaxyUserToolRun(step.run)) {
397
420
  runsByLabel.set(String(label), step.run);
398
421
  }
399
422
  }
package/dist/workflow/normalized/toFormat2.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/workflow/normalized/toFormat2Stateful.js CHANGED
@@ -36,20 +36,18 @@ export function toFormat2Stateful(raw, toolInputsResolver) {
36
36
  toolVersion: step.tool_version ?? null,
37
37
  }),
38
38
  precheck: (step, inputs) => precheckNativeStep(step, inputs).skipReasons,
39
- preValidate: (step, inputs) => {
40
- const connections = {};
41
- for (const [key, val] of Object.entries(step.input_connections)) {
42
- connections[key] = val;
43
- }
44
- validateNativeStepState(inputs, step.tool_state, connections);
45
- },
39
+ preValidate: (step, inputs) => validateNativeStepState(inputs, step.tool_state, step.input_connections),
46
40
  convert: (step, inputs) => {
47
41
  const result = convertStateToFormat2(step, inputs);
48
42
  return { state: result.state, in: result.in };
49
43
  },
50
- postValidate: (result, inputs) => {
51
- validateFormat2StepState(inputs, result.state);
52
- },
44
+ postValidate: (result, inputs, step) => validateFormat2StepState(inputs, result.state, {
45
+ ...step.input_connections,
46
+ // Required RuntimeValue markers are lifted into synthetic `in`
47
+ // entries by convertStateToFormat2. They satisfy linked requiredness
48
+ // just like ordinary workflow connections.
49
+ ...result.in,
50
+ }),
53
51
  });
54
52
  const options = { stateEncodeToFormat2 };
55
53
  const workflow = toFormat2(raw, options);
package/dist/workflow/normalized/toFormat2Stateful.js.map CHANGED
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package/dist/workflow/normalized/toNative.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"toNative.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toNative.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,wBAAwB,EAAwB,MAAM,aAAa,CAAC;AAClF,OAAO,KAAK,EAEV,qBAAqB,EAGtB,MAAM,cAAc,CAAC;AA2FtB,MAAM,WAAW,eAAe;IAC9B;;;;OAIG;IACH,mBAAmB,CAAC,EAAE,CACpB,IAAI,EAAE,qBAAqB,EAC3B,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CACrC;AAED;;GAEG;AACH,wBAAgB,QAAQ,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,wBAAwB,CAS1F"}
package/dist/workflow/normalized/toNative.js CHANGED
@@ -3,7 +3,7 @@
3
3
  *
4
4
  * Port of gxformat2/normalized/_conversion.py to_native + helpers.
5
5
  */
6
- import { normalizedFormat2 } from "./format2.js";
6
+ import { isGalaxyUserToolRun, normalizedFormat2 } from "./format2.js";
7
7
  import { unflattenCommentData } from "./comments.js";
8
8
  import { isUnlabeled, resolveSourceReference } from "./labels.js";
9
9
  function _uuid() {
@@ -81,23 +81,14 @@ const POST_JOB_ACTIONS = {
81
81
  * Convert a Format2 workflow to normalized native Galaxy format.
82
82
  */
83
83
  export function toNative(raw, options) {
84
- let wf;
85
- if (_isNormalizedFormat2(raw)) {
86
- wf = raw;
87
- }
88
- else {
89
- wf = normalizedFormat2(raw);
90
- }
84
+ // Normalize unconditionally: `normalizedFormat2` is idempotent, and no
85
+ // top-level shape check can tell an already-normalized workflow from a raw
86
+ // one with list-form `inputs`/`steps` but dict-form `in`/`out` on its steps.
87
+ const wf = normalizedFormat2(raw);
91
88
  const ctx = new ConversionContext(options);
92
89
  _registerLabels(wf, ctx);
93
90
  return _buildNativeWorkflow(wf, ctx);
94
91
  }
95
- function _isNormalizedFormat2(raw) {
96
- if (raw == null || typeof raw !== "object")
97
- return false;
98
- const obj = raw;
99
- return obj.class === "GalaxyWorkflow" && Array.isArray(obj.inputs) && Array.isArray(obj.steps);
100
- }
101
92
  function _registerLabels(wf, ctx) {
102
93
  for (let i = 0; i < wf.inputs.length; i++) {
103
94
  const inp = wf.inputs[i];
@@ -201,6 +192,13 @@ function _buildInputStep(inp, orderIndex) {
201
192
  toolState.collection_type = inp.collection_type;
202
193
  if (inp.default != null)
203
194
  toolState.default = inp.default;
195
+ if (stepType === "parameter_input" &&
196
+ ["integer", "int", "float"].includes(typeStr) &&
197
+ (inp.min != null || inp.max != null)) {
198
+ toolState.validators = [
199
+ { type: "in_range", min: inp.min ?? null, max: inp.max ?? null, negate: false },
200
+ ];
201
+ }
204
202
  // Copy extra fields
205
203
  for (const key of [
206
204
  "restrictions",
@@ -255,10 +253,7 @@ function _buildStep(step, orderIndex, ctx) {
255
253
  function _resolveStepType(step) {
256
254
  if (step.run != null) {
257
255
  if (typeof step.run === "object") {
258
- const runObj = step.run;
259
- if (runObj.class === "GalaxyUserTool")
260
- return "tool";
261
- return "subworkflow";
256
+ return isGalaxyUserToolRun(step.run) ? "tool" : "subworkflow";
262
257
  }
263
258
  if (typeof step.run === "string")
264
259
  return "subworkflow";
@@ -267,14 +262,9 @@ function _resolveStepType(step) {
267
262
  return STEP_TYPE_ALIASES[rawType] ?? rawType;
268
263
  }
269
264
  function _buildToolStep(step, orderIndex, ctx) {
270
- // Detect GalaxyUserTool in run field
271
- let toolRepresentation;
272
- if (step.run && typeof step.run === "object") {
273
- const runObj = step.run;
274
- if (runObj.class === "GalaxyUserTool") {
275
- toolRepresentation = runObj;
276
- }
277
- }
265
+ const toolRepresentation = isGalaxyUserToolRun(step.run)
266
+ ? step.run
267
+ : undefined;
278
268
  const toolState = { __page__: 0 };
279
269
  const connect = _extractConnections(step);
280
270
  const runtimeInputs = step.runtime_inputs ?? [];
package/dist/workflow/normalized/toNative.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/workflow/normalized/toNativeStateful.d.ts.map CHANGED
@@ -1 +1 @@
1
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