@galaxy-tool-util/schema 0.1.0 → 0.4.0
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/LICENSE +21 -0
- package/dist/index.d.ts +87 -3
- package/dist/index.d.ts.map +1 -1
- package/dist/index.js +62 -1
- package/dist/index.js.map +1 -1
- package/dist/schema/type-guards.d.ts +14 -0
- package/dist/schema/type-guards.d.ts.map +1 -0
- package/dist/schema/type-guards.js +25 -0
- package/dist/schema/type-guards.js.map +1 -0
- package/dist/test-format/cross-check/check.d.ts +18 -0
- package/dist/test-format/cross-check/check.d.ts.map +1 -0
- package/dist/test-format/cross-check/check.js +89 -0
- package/dist/test-format/cross-check/check.js.map +1 -0
- package/dist/test-format/cross-check/extract-format2.d.ts +13 -0
- package/dist/test-format/cross-check/extract-format2.d.ts.map +1 -0
- package/dist/test-format/cross-check/extract-format2.js +98 -0
- package/dist/test-format/cross-check/extract-format2.js.map +1 -0
- package/dist/test-format/cross-check/extract-native.d.ts +4 -0
- package/dist/test-format/cross-check/extract-native.d.ts.map +1 -0
- package/dist/test-format/cross-check/extract-native.js +89 -0
- package/dist/test-format/cross-check/extract-native.js.map +1 -0
- package/dist/test-format/cross-check/extract.d.ts +9 -0
- package/dist/test-format/cross-check/extract.d.ts.map +1 -0
- package/dist/test-format/cross-check/extract.js +16 -0
- package/dist/test-format/cross-check/extract.js.map +1 -0
- package/dist/test-format/cross-check/index.d.ts +7 -0
- package/dist/test-format/cross-check/index.d.ts.map +1 -0
- package/dist/test-format/cross-check/index.js +6 -0
- package/dist/test-format/cross-check/index.js.map +1 -0
- package/dist/test-format/cross-check/type-compat.d.ts +23 -0
- package/dist/test-format/cross-check/type-compat.d.ts.map +1 -0
- package/dist/test-format/cross-check/type-compat.js +48 -0
- package/dist/test-format/cross-check/type-compat.js.map +1 -0
- package/dist/test-format/cross-check/types.d.ts +23 -0
- package/dist/test-format/cross-check/types.d.ts.map +1 -0
- package/dist/test-format/cross-check/types.js +10 -0
- package/dist/test-format/cross-check/types.js.map +1 -0
- package/dist/test-format/index.d.ts +3 -0
- package/dist/test-format/index.d.ts.map +1 -0
- package/dist/test-format/index.js +3 -0
- package/dist/test-format/index.js.map +1 -0
- package/dist/test-format/tests.schema.generated.d.ts +5610 -0
- package/dist/test-format/tests.schema.generated.d.ts.map +1 -0
- package/dist/test-format/tests.schema.generated.js +6899 -0
- package/dist/test-format/tests.schema.generated.js.map +1 -0
- package/dist/test-format/validate.d.ts +20 -0
- package/dist/test-format/validate.d.ts.map +1 -0
- package/dist/test-format/validate.js +41 -0
- package/dist/test-format/validate.js.map +1 -0
- package/dist/tool-state-validator.d.ts +23 -0
- package/dist/tool-state-validator.d.ts.map +1 -0
- package/dist/tool-state-validator.js +59 -0
- package/dist/tool-state-validator.js.map +1 -0
- package/dist/workflow/clean.d.ts +56 -3
- package/dist/workflow/clean.d.ts.map +1 -1
- package/dist/workflow/clean.js +227 -27
- package/dist/workflow/clean.js.map +1 -1
- package/dist/workflow/coercions.d.ts +22 -0
- package/dist/workflow/coercions.d.ts.map +1 -0
- package/dist/workflow/coercions.js +67 -0
- package/dist/workflow/coercions.js.map +1 -0
- package/dist/workflow/index.d.ts +17 -4
- package/dist/workflow/index.d.ts.map +1 -1
- package/dist/workflow/index.js +18 -3
- package/dist/workflow/index.js.map +1 -1
- package/dist/workflow/lint-profiles.d.ts +27 -0
- package/dist/workflow/lint-profiles.d.ts.map +1 -0
- package/dist/workflow/lint-profiles.js +49 -0
- package/dist/workflow/lint-profiles.js.map +1 -0
- package/dist/workflow/lint-rules.d.ts +15 -0
- package/dist/workflow/lint-rules.d.ts.map +1 -0
- package/dist/workflow/lint-rules.js +15 -0
- package/dist/workflow/lint-rules.js.map +1 -0
- package/dist/workflow/lint.d.ts +4 -18
- package/dist/workflow/lint.d.ts.map +1 -1
- package/dist/workflow/lint.js +9 -30
- package/dist/workflow/lint.js.map +1 -1
- package/dist/workflow/lint_profiles.yml +41 -0
- package/dist/workflow/linting.d.ts +54 -0
- package/dist/workflow/linting.d.ts.map +1 -0
- package/dist/workflow/linting.js +71 -0
- package/dist/workflow/linting.js.map +1 -0
- package/dist/workflow/normalized/index.d.ts +5 -2
- package/dist/workflow/normalized/index.d.ts.map +1 -1
- package/dist/workflow/normalized/index.js +2 -0
- package/dist/workflow/normalized/index.js.map +1 -1
- package/dist/workflow/normalized/stateful-runner.d.ts +82 -0
- package/dist/workflow/normalized/stateful-runner.d.ts.map +1 -0
- package/dist/workflow/normalized/stateful-runner.js +122 -0
- package/dist/workflow/normalized/stateful-runner.js.map +1 -0
- package/dist/workflow/normalized/toFormat2.d.ts +19 -1
- package/dist/workflow/normalized/toFormat2.d.ts.map +1 -1
- package/dist/workflow/normalized/toFormat2.js +47 -16
- package/dist/workflow/normalized/toFormat2.js.map +1 -1
- package/dist/workflow/normalized/toFormat2Stateful.d.ts +30 -0
- package/dist/workflow/normalized/toFormat2Stateful.d.ts.map +1 -0
- package/dist/workflow/normalized/toFormat2Stateful.js +58 -0
- package/dist/workflow/normalized/toFormat2Stateful.js.map +1 -0
- package/dist/workflow/normalized/toNative.d.ts +10 -1
- package/dist/workflow/normalized/toNative.d.ts.map +1 -1
- package/dist/workflow/normalized/toNative.js +24 -8
- package/dist/workflow/normalized/toNative.js.map +1 -1
- package/dist/workflow/normalized/toNativeStateful.d.ts +31 -0
- package/dist/workflow/normalized/toNativeStateful.d.ts.map +1 -0
- package/dist/workflow/normalized/toNativeStateful.js +55 -0
- package/dist/workflow/normalized/toNativeStateful.js.map +1 -0
- package/dist/workflow/param-navigation.d.ts +26 -0
- package/dist/workflow/param-navigation.d.ts.map +1 -0
- package/dist/workflow/param-navigation.js +60 -0
- package/dist/workflow/param-navigation.js.map +1 -0
- package/dist/workflow/precheck.d.ts +54 -0
- package/dist/workflow/precheck.d.ts.map +1 -0
- package/dist/workflow/precheck.js +91 -0
- package/dist/workflow/precheck.js.map +1 -0
- package/dist/workflow/raw/gxformat2.effect.d.ts +97 -97
- package/dist/workflow/raw/gxformat2.effect.d.ts.map +1 -1
- package/dist/workflow/raw/gxformat2.effect.js +98 -88
- package/dist/workflow/raw/gxformat2.effect.js.map +1 -1
- package/dist/workflow/raw/native.d.ts +2 -2
- package/dist/workflow/raw/native.d.ts.map +1 -1
- package/dist/workflow/raw/native.effect.d.ts +33 -33
- package/dist/workflow/raw/native.effect.d.ts.map +1 -1
- package/dist/workflow/raw/native.effect.js +42 -32
- package/dist/workflow/raw/native.effect.js.map +1 -1
- package/dist/workflow/report-models.d.ts +412 -0
- package/dist/workflow/report-models.d.ts.map +1 -0
- package/dist/workflow/report-models.js +342 -0
- package/dist/workflow/report-models.js.map +1 -0
- package/dist/workflow/roundtrip.d.ts +77 -0
- package/dist/workflow/roundtrip.d.ts.map +1 -0
- package/dist/workflow/roundtrip.js +597 -0
- package/dist/workflow/roundtrip.js.map +1 -0
- package/dist/workflow/runtime-markers.d.ts +20 -0
- package/dist/workflow/runtime-markers.d.ts.map +1 -0
- package/dist/workflow/runtime-markers.js +26 -0
- package/dist/workflow/runtime-markers.js.map +1 -0
- package/dist/workflow/schema-rules.d.ts +38 -0
- package/dist/workflow/schema-rules.d.ts.map +1 -0
- package/dist/workflow/schema-rules.js +28 -0
- package/dist/workflow/schema-rules.js.map +1 -0
- package/dist/workflow/schema_rules.yml +69 -0
- package/dist/workflow/serialize.d.ts +30 -0
- package/dist/workflow/serialize.d.ts.map +1 -0
- package/dist/workflow/serialize.js +37 -0
- package/dist/workflow/serialize.js.map +1 -0
- package/dist/workflow/stale-keys.d.ts +16 -0
- package/dist/workflow/stale-keys.d.ts.map +1 -0
- package/dist/workflow/stale-keys.js +43 -0
- package/dist/workflow/stale-keys.js.map +1 -0
- package/dist/workflow/state-merge.d.ts +15 -32
- package/dist/workflow/state-merge.d.ts.map +1 -1
- package/dist/workflow/state-merge.js +31 -225
- package/dist/workflow/state-merge.js.map +1 -1
- package/dist/workflow/stateful-convert.d.ts +47 -0
- package/dist/workflow/stateful-convert.d.ts.map +1 -0
- package/dist/workflow/stateful-convert.js +151 -0
- package/dist/workflow/stateful-convert.js.map +1 -0
- package/dist/workflow/stateful-validate.d.ts +67 -0
- package/dist/workflow/stateful-validate.d.ts.map +1 -0
- package/dist/workflow/stateful-validate.js +123 -0
- package/dist/workflow/stateful-validate.js.map +1 -0
- package/dist/workflow/strict-checks.d.ts +22 -0
- package/dist/workflow/strict-checks.d.ts.map +1 -0
- package/dist/workflow/strict-checks.js +95 -0
- package/dist/workflow/strict-checks.js.map +1 -0
- package/dist/workflow/tool-state-io.d.ts +14 -0
- package/dist/workflow/tool-state-io.d.ts.map +1 -0
- package/dist/workflow/tool-state-io.js +33 -0
- package/dist/workflow/tool-state-io.js.map +1 -0
- package/dist/workflow/validators.d.ts +34 -0
- package/dist/workflow/validators.d.ts.map +1 -0
- package/dist/workflow/validators.js +83 -0
- package/dist/workflow/validators.js.map +1 -0
- package/dist/workflow/walk-helpers.d.ts +29 -0
- package/dist/workflow/walk-helpers.d.ts.map +1 -0
- package/dist/workflow/walk-helpers.js +89 -0
- package/dist/workflow/walk-helpers.js.map +1 -0
- package/dist/workflow/walker.d.ts +55 -0
- package/dist/workflow/walker.d.ts.map +1 -0
- package/dist/workflow/walker.js +199 -0
- package/dist/workflow/walker.js.map +1 -0
- package/package.json +21 -16
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/**
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* Utility for navigating a ToolParameterModel tree by path segments.
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*
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* Used by LSP language servers to resolve completion and hover context
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* inside tool_state YAML, including conditional branch filtering.
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*/
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import { isConditionalParam, isRepeatParam, isSectionParam } from "../schema/type-guards.js";
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import { selectWhichWhen } from "./walk-helpers.js";
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/**
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* Navigate a tool parameter tree by path segments.
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*
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* - Sections: recurse into `parameters`
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* - Repeats: skip numeric path segments, recurse into `parameters`
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* - Conditionals: call selectWhichWhen(conditional, stateAtCurrentLevel),
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* fall back to all branches merged if no state provided or no match
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*
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* `state` is the full state dict at the top of the tree; the function
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* navigates it in parallel with the param tree to resolve nested conditionals.
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*/
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export function findParamAtPath(params, path, state) {
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if (path.length === 0)
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return { param: undefined, availableParams: params };
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const [head, ...tail] = path;
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// Skip numeric segments (repeat instance indices)
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if (typeof head === "number")
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return findParamAtPath(params, tail, state);
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const match = params.find((p) => p.name === head);
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if (!match)
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return { param: undefined, availableParams: params };
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if (tail.length === 0)
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return { param: match, availableParams: params };
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if (isSectionParam(match)) {
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return findParamAtPath(match.parameters, tail, _getSubState(state, head));
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}
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if (isRepeatParam(match)) {
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return findParamAtPath(match.parameters, tail, _getSubState(state, head));
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}
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if (isConditionalParam(match)) {
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const conditionalState = _getSubState(state, head);
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// Only filter to a specific branch when the discriminator key is
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// explicitly present in state. If state is absent OR the discriminator
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// key hasn't been set yet, merge all branches so completions/hover
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// aren't artificially restricted to a default branch the user may not
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// have chosen.
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const discriminatorSet = conditionalState !== undefined && match.test_parameter.name in conditionalState;
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const activeWhen = discriminatorSet ? selectWhichWhen(match, conditionalState) : null;
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const branchParams = activeWhen
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? activeWhen.parameters
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: match.whens.flatMap((w) => w.parameters);
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return findParamAtPath([match.test_parameter, ...branchParams], tail, conditionalState);
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}
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return { param: undefined, availableParams: params };
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}
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function _getSubState(state, key) {
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const val = state?.[key];
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return val && typeof val === "object" && !Array.isArray(val)
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? val
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: undefined;
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}
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//# sourceMappingURL=param-navigation.js.map
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/**
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* Precheck native workflow steps for stateful conversion compatibility.
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*
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* Checks whether a step's tool_state can be walked by the schema-aware
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* stateful converter, or whether it has issues (legacy replacement params,
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* legacy parameter encoding) that require falling back to schema-free
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* passthrough.
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*
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* Usage: called per-step by the stateful runner before conversion. A
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* failing precheck short-circuits `convert` and pushes a structured
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* `failureClass: "precheck"` status entry.
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*
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* Tool lookup is callback-shaped (`ToolInputsResolver`) matching the rest
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* of the stateful conversion pipeline — the caller owns tool loading and
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* version disambiguation.
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*/
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import type { NormalizedNativeWorkflow, NormalizedNativeStep } from "./normalized/native.js";
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import type { ToolInputsResolver } from "./normalized/stateful-runner.js";
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import type { ToolParameterModel } from "../schema/bundle-types.js";
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export interface StepPrecheckResult {
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stepId: string;
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toolId?: string;
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canProcess: boolean;
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skipReasons: string[];
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}
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export interface PrecheckResult {
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canProcess: boolean;
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skipReasons: string[];
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stepResults: StepPrecheckResult[];
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}
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/**
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* Precheck a single tool step's tool_state against its parameter inputs.
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*
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* Returns `canProcess: true` with empty reasons if the step is clean or
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* or legacy parameter encoding is detected.
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*
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export declare function precheckNativeWorkflow(workflow: NormalizedNativeWorkflow, resolver: ToolInputsResolver | null): PrecheckResult;
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{"version":3,"file":"precheck.d.ts","sourceRoot":"","sources":["../../src/workflow/precheck.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,KAAK,EAAE,wBAAwB,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AAC7F,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,iCAAiC,CAAC;AAC1E,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAIpE,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,OAAO,CAAC;IACpB,WAAW,EAAE,MAAM,EAAE,CAAC;CACvB;AAED,MAAM,WAAW,cAAc;IAC7B,UAAU,EAAE,OAAO,CAAC;IACpB,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,WAAW,EAAE,kBAAkB,EAAE,CAAC;CACnC;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,kBAAkB,CAChC,IAAI,EAAE,oBAAoB,EAC1B,MAAM,EAAE,kBAAkB,EAAE,GAAG,SAAS,GACvC,kBAAkB,CA8BpB;AAED;;;;;;;;;GASG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,wBAAwB,EAClC,QAAQ,EAAE,kBAAkB,GAAG,IAAI,GAClC,cAAc,CA0BhB"}
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/**
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* Precheck native workflow steps for stateful conversion compatibility.
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*
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* Checks whether a step's tool_state can be walked by the schema-aware
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* stateful converter, or whether it has issues (legacy replacement params,
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* legacy parameter encoding) that require falling back to schema-free
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* passthrough.
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*
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* Usage: called per-step by the stateful runner before conversion. A
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* failing precheck short-circuits `convert` and pushes a structured
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* `failureClass: "precheck"` status entry.
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*
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* version disambiguation.
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*/
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import { scanForReplacements } from "./replacement-scan.js";
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import { scanToolState } from "./legacy-encoding.js";
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/**
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export function precheckNativeStep(step, inputs) {
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const stepId = String(step.id ?? "");
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const reasons = [];
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}
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if (scanForReplacements(inputs, step.tool_state) === "yes") {
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reasons.push("legacy replacement parameter (${...}) in typed field");
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}
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// Legacy parameter encoding (string-encoded containers)
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const encodingResult = scanToolState(inputs, step.tool_state);
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const details = encodingResult.hits.map((h) => `${h.parameterName}: ${h.detail}`).join("; ");
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}
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return {
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stepId,
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toolId,
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skipReasons: reasons,
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};
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}
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/**
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*
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|
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* verdict (`canProcess` = all steps passed) plus per-step details, so
|
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* callers can still do per-step stateful conversion for clean steps.
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*
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* Passing `null` as the resolver is allowed and means "no tool inputs
|
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* available" — every step will pass (conversion-time fallback still runs).
|
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*/
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export function precheckNativeWorkflow(workflow, resolver) {
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for (const [key, step] of Object.entries(workflow.steps)) {
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const inputs = resolver != null && step.tool_id != null
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? resolver(step.tool_id, step.tool_version ?? null)
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: undefined;
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const stepResult = precheckNativeStep(step, inputs);
|
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if (stepResult.stepId === "") {
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|
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}
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}
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}
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}
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return {
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skipReasons: workflowReasons,
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stepResults,
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};
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}
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{"version":3,"file":"precheck.js","sourceRoot":"","sources":["../../src/workflow/precheck.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAKH,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAerD;;;;;;;;;;GAUG;AACH,MAAM,UAAU,kBAAkB,CAChC,IAA0B,EAC1B,MAAwC;IAExC,MAAM,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC;IACrC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,IAAI,SAAS,CAAC;IACzC,MAAM,OAAO,GAAa,EAAE,CAAC;IAE7B,IAAI,IAAI,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;QACzB,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,WAAW,EAAE,EAAE,EAAE,CAAC;IAC/D,CAAC;IACD,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,IAAI,IAAI,EAAE,CAAC;QACrC,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,WAAW,EAAE,EAAE,EAAE,CAAC;IAC/D,CAAC;IAED,yDAAyD;IACzD,IAAI,mBAAmB,CAAC,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,KAAK,KAAK,EAAE,CAAC;QAC3D,OAAO,CAAC,IAAI,CAAC,sDAAsD,CAAC,CAAC;IACvE,CAAC;IAED,wDAAwD;IACxD,MAAM,cAAc,GAAG,aAAa,CAAC,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;IAC9D,IAAI,cAAc,CAAC,cAAc,KAAK,KAAK,EAAE,CAAC;QAC5C,MAAM,OAAO,GAAG,cAAc,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,aAAa,KAAK,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAC7F,OAAO,CAAC,IAAI,CAAC,uCAAuC,OAAO,GAAG,CAAC,CAAC;IAClE,CAAC;IAED,OAAO;QACL,MAAM;QACN,MAAM;QACN,UAAU,EAAE,OAAO,CAAC,MAAM,KAAK,CAAC;QAChC,WAAW,EAAE,OAAO;KACrB,CAAC;AACJ,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,sBAAsB,CACpC,QAAkC,EAClC,QAAmC;IAEnC,MAAM,WAAW,GAAyB,EAAE,CAAC;IAC7C,MAAM,eAAe,GAAa,EAAE,CAAC;IAErC,KAAK,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;QACzD,MAAM,MAAM,GACV,QAAQ,IAAI,IAAI,IAAI,IAAI,CAAC,OAAO,IAAI,IAAI;YACtC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,CAAC,YAAY,IAAI,IAAI,CAAC;YACnD,CAAC,CAAC,SAAS,CAAC;QAChB,MAAM,UAAU,GAAG,kBAAkB,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QACpD,IAAI,UAAU,CAAC,MAAM,KAAK,EAAE,EAAE,CAAC;YAC7B,UAAU,CAAC,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,EAAE,IAAI,GAAG,CAAC,CAAC;QAC7C,CAAC;QACD,WAAW,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;QAC7B,IAAI,CAAC,UAAU,CAAC,UAAU,EAAE,CAAC;YAC3B,KAAK,MAAM,MAAM,IAAI,UAAU,CAAC,WAAW,EAAE,CAAC;gBAC5C,eAAe,CAAC,IAAI,CAAC,QAAQ,UAAU,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC,CAAC;YAC/D,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO;QACL,UAAU,EAAE,eAAe,CAAC,MAAM,KAAK,CAAC;QACxC,WAAW,EAAE,eAAe;QAC5B,WAAW;KACZ,CAAC;AACJ,CAAC"}
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export type RecordSchema = typeof RecordSchemaSchema.Type;
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/** Defines the type of the array elements. */
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|
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@@ -204,25 +204,6 @@ export declare const OutputParameterSchema: Schema.Struct<{
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/**
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connected to one parameter defined in the workflow that
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will provide the value of the output parameter. It is legal to
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connect a WorkflowInputParameter to a WorkflowOutputParameter.
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*/
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/** A short, human-readable label of this object. */
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label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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/** A documentation string for this object, or an array of strings which should be concatenated. */
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doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
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/** Specifies workflow parameter that supply the value of to the output parameter. */
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outputSource: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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/** Specify valid types of data that may be assigned to this parameter. */
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type: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>]>>;
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}>;
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|
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export type WorkflowOutputParameter = typeof WorkflowOutputParameterSchema.Type;
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|
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*/
|
|
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|
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|
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|
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248
|
}>;
|
|
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249
|
export type WorkflowInputParameter = typeof WorkflowInputParameterSchema.Type;
|
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|
+
/**
|
|
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|
+
* Describe an output parameter of a workflow. The parameter must be
|
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|
+
connected to one parameter defined in the workflow that
|
|
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|
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will provide the value of the output parameter. It is legal to
|
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|
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|
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|
+
*/
|
|
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|
+
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|
|
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|
+
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|
|
258
|
+
id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
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|
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/** A short, human-readable label of this object. */
|
|
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|
+
label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
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|
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/** A documentation string for this object, or an array of strings which should be concatenated. */
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|
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|
+
doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
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|
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|
+
/** Specifies workflow parameter that supply the value of to the output parameter. */
|
|
264
|
+
outputSource: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
265
|
+
/** Specify valid types of data that may be assigned to this parameter. */
|
|
266
|
+
type: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>]>>;
|
|
267
|
+
}>;
|
|
268
|
+
export type WorkflowOutputParameter = typeof WorkflowOutputParameterSchema.Type;
|
|
269
269
|
/**
|
|
270
270
|
* The base executable type in CWL is the `Process` object defined by the
|
|
271
271
|
document. Note that the `Process` object is abstract and cannot be
|
|
@@ -386,43 +386,6 @@ export declare const ReferencesToolSchema: Schema.Struct<{
|
|
|
386
386
|
tool_version: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
387
387
|
}>;
|
|
388
388
|
export type ReferencesTool = typeof ReferencesToolSchema.Type;
|
|
389
|
-
/**
|
|
390
|
-
* Associate an output parameter of the underlying process with a workflow
|
|
391
|
-
parameter. The workflow parameter (given in the `id` field) be may be used
|
|
392
|
-
as a `source` to connect with input parameters of other workflow steps, or
|
|
393
|
-
with an output parameter of the process.
|
|
394
|
-
|
|
395
|
-
A unique identifier for this workflow output parameter. This is
|
|
396
|
-
the identifier to use in the `source` field of `WorkflowStepInput`
|
|
397
|
-
to connect the output value to downstream parameters.
|
|
398
|
-
*/
|
|
399
|
-
export declare const WorkflowStepOutputSchema: Schema.Struct<{
|
|
400
|
-
add_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
|
|
401
|
-
change_datatype: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
402
|
-
delete_intermediate_datasets: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
|
|
403
|
-
hide: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
|
|
404
|
-
remove_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
|
|
405
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-
rename: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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set_columns: Schema.optional<Schema.Union<[Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
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id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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}>;
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export type WorkflowStepOutput = typeof WorkflowStepOutputSchema.Type;
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export declare const SinkSchema: Schema.Struct<{
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/** Specifies one or more workflow parameters that will provide input to the underlying step parameter. */
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source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
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}>;
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export type Sink = typeof SinkSchema.Type;
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/**
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* TODO:
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*/
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export declare const WorkflowStepInputSchema: Schema.Struct<{
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/** The default value for this parameter to use if either there is no `source` field, or the value produced by the `source` is `null`. The default must be applied prior to scattering or evaluating `va... */
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default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
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label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
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id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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}>;
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export type WorkflowStepInput = typeof WorkflowStepInputSchema.Type;
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/**
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* Definition of an invocation report for this workflow. Currently the only
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field is 'markdown'.
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@@ -446,40 +409,6 @@ export declare const BaseCommentSchema: Schema.Struct<{
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label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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}>;
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411
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export type BaseComment = typeof BaseCommentSchema.Type;
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/**
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* A plain text annotation in the workflow editor.
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*/
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export declare const TextCommentSchema: Schema.Struct<{
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/** Comment type (``text``). */
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type: Schema.Literal<["text"]>;
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455
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/** The text content. */
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456
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-
text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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457
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-
/** Whether the text is displayed in bold. */
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bold: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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459
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/** Whether the text is displayed in italic. */
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460
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italic: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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461
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/** Font size of the text. */
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462
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text_size: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
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463
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-
position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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464
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-
size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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465
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-
color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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466
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-
label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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467
|
-
}>;
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468
|
-
export type TextComment = typeof TextCommentSchema.Type;
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|
469
|
-
/**
|
|
470
|
-
* A Markdown-rendered annotation in the workflow editor.
|
|
471
|
-
*/
|
|
472
|
-
export declare const MarkdownCommentSchema: Schema.Struct<{
|
|
473
|
-
/** Comment type (``markdown``). */
|
|
474
|
-
type: Schema.Literal<["markdown"]>;
|
|
475
|
-
/** Markdown content. */
|
|
476
|
-
text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
477
|
-
position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
|
|
478
|
-
size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
|
|
479
|
-
color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
480
|
-
label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
481
|
-
}>;
|
|
482
|
-
export type MarkdownComment = typeof MarkdownCommentSchema.Type;
|
|
483
412
|
/**
|
|
484
413
|
* A freehand drawn line on the editor canvas.
|
|
485
414
|
*/
|
|
@@ -549,6 +478,26 @@ export declare const CreatorPersonSchema: Schema.Struct<{
|
|
|
549
478
|
faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
550
479
|
}>;
|
|
551
480
|
export type CreatorPerson = typeof CreatorPersonSchema.Type;
|
|
481
|
+
/**
|
|
482
|
+
* A plain text annotation in the workflow editor.
|
|
483
|
+
*/
|
|
484
|
+
export declare const TextCommentSchema: Schema.Struct<{
|
|
485
|
+
/** Comment type (``text``). */
|
|
486
|
+
type: Schema.Literal<["text"]>;
|
|
487
|
+
/** The text content. */
|
|
488
|
+
text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
489
|
+
/** Whether the text is displayed in bold. */
|
|
490
|
+
bold: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
|
|
491
|
+
/** Whether the text is displayed in italic. */
|
|
492
|
+
italic: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
|
|
493
|
+
/** Font size of the text. */
|
|
494
|
+
text_size: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
|
|
495
|
+
position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
|
|
496
|
+
size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
|
|
497
|
+
color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
498
|
+
label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
499
|
+
}>;
|
|
500
|
+
export type TextComment = typeof TextCommentSchema.Type;
|
|
552
501
|
/**
|
|
553
502
|
* A rectangular grouping box that visually contains steps and other comments.
|
|
554
503
|
*/
|
|
@@ -567,6 +516,20 @@ export declare const FrameCommentSchema: Schema.Struct<{
|
|
|
567
516
|
label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
568
517
|
}>;
|
|
569
518
|
export type FrameComment = typeof FrameCommentSchema.Type;
|
|
519
|
+
/**
|
|
520
|
+
* A Markdown-rendered annotation in the workflow editor.
|
|
521
|
+
*/
|
|
522
|
+
export declare const MarkdownCommentSchema: Schema.Struct<{
|
|
523
|
+
/** Comment type (``markdown``). */
|
|
524
|
+
type: Schema.Literal<["markdown"]>;
|
|
525
|
+
/** Markdown content. */
|
|
526
|
+
text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
527
|
+
position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
|
|
528
|
+
size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
|
|
529
|
+
color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
530
|
+
label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
531
|
+
}>;
|
|
532
|
+
export type MarkdownComment = typeof MarkdownCommentSchema.Type;
|
|
570
533
|
/**
|
|
571
534
|
* An organization that created or contributed to the workflow.
|
|
572
535
|
Corresponds to a `schema.org Organization <https://schema.org/Organization>`_.
|
|
@@ -825,6 +788,43 @@ export declare const GalaxyWorkflowSchema: Schema.Struct<{
|
|
|
825
788
|
}>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
|
|
826
789
|
}>;
|
|
827
790
|
export type GalaxyWorkflow = typeof GalaxyWorkflowSchema.Type;
|
|
791
|
+
/**
|
|
792
|
+
* Associate an output parameter of the underlying process with a workflow
|
|
793
|
+
parameter. The workflow parameter (given in the `id` field) be may be used
|
|
794
|
+
as a `source` to connect with input parameters of other workflow steps, or
|
|
795
|
+
with an output parameter of the process.
|
|
796
|
+
|
|
797
|
+
A unique identifier for this workflow output parameter. This is
|
|
798
|
+
the identifier to use in the `source` field of `WorkflowStepInput`
|
|
799
|
+
to connect the output value to downstream parameters.
|
|
800
|
+
*/
|
|
801
|
+
export declare const WorkflowStepOutputSchema: Schema.Struct<{
|
|
802
|
+
add_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
|
|
803
|
+
change_datatype: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
804
|
+
delete_intermediate_datasets: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
|
|
805
|
+
hide: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
|
|
806
|
+
remove_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
|
|
807
|
+
rename: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
808
|
+
set_columns: Schema.optional<Schema.Union<[Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
|
|
809
|
+
id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
810
|
+
}>;
|
|
811
|
+
export type WorkflowStepOutput = typeof WorkflowStepOutputSchema.Type;
|
|
812
|
+
export declare const SinkSchema: Schema.Struct<{
|
|
813
|
+
/** Specifies one or more workflow parameters that will provide input to the underlying step parameter. */
|
|
814
|
+
source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
|
|
815
|
+
}>;
|
|
816
|
+
export type Sink = typeof SinkSchema.Type;
|
|
817
|
+
/**
|
|
818
|
+
* TODO:
|
|
819
|
+
*/
|
|
820
|
+
export declare const WorkflowStepInputSchema: Schema.Struct<{
|
|
821
|
+
/** The default value for this parameter to use if either there is no `source` field, or the value produced by the `source` is `null`. The default must be applied prior to scattering or evaluating `va... */
|
|
822
|
+
default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
|
|
823
|
+
label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
824
|
+
source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
|
|
825
|
+
id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
|
|
826
|
+
}>;
|
|
827
|
+
export type WorkflowStepInput = typeof WorkflowStepInputSchema.Type;
|
|
828
828
|
/**
|
|
829
829
|
* This represents a non-input step a Galaxy Workflow.
|
|
830
830
|
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gxformat2.effect.d.ts","sourceRoot":"","sources":["../../../src/workflow/raw/gxformat2.effect.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAEhC;;;;;;;;;;;;GAYG;AACH,eAAO,MAAM,mBAAmB,iFAQ/B,CAAC;AACF,MAAM,MAAM,aAAa,GAAG,OAAO,mBAAmB,CAAC,IAAI,CAAC;AAE5D;;;;;;;GAOG;AACH,eAAO,MAAM,gBAAgB,kIAa5B,CAAC;AACF,MAAM,MAAM,UAAU,GAAG,OAAO,gBAAgB,CAAC,IAAI,CAAC;AAEtD;;;;;;;;GAQG;AACH,eAAO,MAAM,sBAAsB,gEAA+D,CAAC;AACnG,MAAM,MAAM,gBAAgB,GAAG,OAAO,sBAAsB,CAAC,IAAI,CAAC;AAElE,eAAO,MAAM,gBAAgB;IAC3B,mGAAmG;;EAEnG,CAAC;AACH,MAAM,MAAM,UAAU,GAAG,OAAO,gBAAgB,CAAC,IAAI,CAAC;AAEtD
|
|
1
|
+
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