@galaxy-tool-util/schema 0.1.0 → 0.2.0

package/dist/workflow/raw/native.effect.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"native.effect.d.ts","sourceRoot":"","sources":["../../../src/workflow/raw/native.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;;;;;;;;;GASG;AACH,eAAO,MAAM,oBAAoB,0HAQhC,CAAC;AACF,MAAM,MAAM,cAAc,GAAG,OAAO,oBAAoB,CAAC,IAAI,CAAC;AAE9D,eAAO,MAAM,gBAAgB;IAC3B,mGAAmG;;EAEnG,CAAC;AACH,MAAM,MAAM,UAAU,GAAG,OAAO,gBAAgB,CAAC,IAAI,CAAC;AAEtD;;GAEG;AACH,eAAO,MAAM,gBAAgB;IAC3B,wCAAwC;;IAExC,qBAAqB;;EAErB,CAAC;AACH,MAAM,MAAM,UAAU,GAAG,OAAO,gBAAgB,CAAC,IAAI,CAAC;AAEtD,eAAO,MAAM,kBAAkB;IAC7B,wCAAwC;;IAWxC,uBAAuB;;EAEvB,CAAC;AACH,MAAM,MAAM,YAAY,GAAG,OAAO,kBAAkB,CAAC,IAAI,CAAC;AAE1D,eAAO,MAAM,iBAAiB;IAC5B,8CAA8C;;QAjB9C,wCAAwC;;QAWxC,uBAAuB;;;QAnBvB,wCAAwC;;QAExC,qBAAqB;;;QAMrB,wCAAwC;;QAWxC,uBAAuB;;;QAnBvB,wCAAwC;;QAExC,qBAAqB;;;IA4CrB,sBAAsB;;EAEtB,CAAC;AACH,MAAM,MAAM,WAAW,GAAG,OAAO,iBAAiB,CAAC,IAAI,CAAC;AAExD;;GAEG;AACH,eAAO,MAAM,iBAAiB;IAE5B,4BAA4B;;IAE5B,qBAAqB;;QAlDrB,wCAAwC;;QAWxC,uBAAuB;;;QAnBvB,wCAAwC;;QAExC,qBAAqB;;;QAuBrB,8CAA8C;;YAjB9C,wCAAwC;;YAWxC,uBAAuB;;;YAnBvB,wCAAwC;;YAExC,qBAAqB;;;YAMrB,wCAAwC;;YAWxC,uBAAuB;;;YAnBvB,wCAAwC;;YAExC,qBAAqB;;;QA4CrB,sBAAsB;;;QAtCtB,wCAAwC;;QAWxC,uBAAuB;;;QAnBvB,wCAAwC;;QAExC,qBAAqB;;;QAuBrB,8CAA8C;;YAjB9C,wCAAwC;;YAWxC,uBAAuB;;;YAnBvB,wCAAwC;;YAExC,qBAAqB;;;YAMrB,wCAAwC;;YAWxC,uBAAuB;;;YAnBvB,wCAAwC;;YAExC,qBAAqB;;;QA4CrB,sBAAsB;;;;EA6BtB,CAAC;AACH,MAAM,MAAM,WAAW,GAAG,OAAO,iBAAiB,CAAC,IAAI,CAAC;AAExD,eAAO,MAAM,aAAa;IACxB,+CAA+C;;EAE/C,CAAC;AACH,MAAM,MAAM,OAAO,GAAG,OAAO,aAAa,CAAC,IAAI,CAAC;AAEhD,eAAO,MAAM,mBAAmB;IAC9B,+MAA+M;;EAE/M,CAAC;AACH,MAAM,MAAM,aAAa,GAAG,OAAO,mBAAmB,CAAC,IAAI,CAAC;AAE5D;;GAEG;AACH,eAAO,MAAM,kBAAkB;IAC7B,0FAA0F;;IAE1F,4FAA4F;;EAE5F,CAAC;AACH,MAAM,MAAM,YAAY,GAAG,OAAO,kBAAkB,CAAC,IAAI,CAAC;AAE1D,eAAO,MAAM,qBAAqB;;QAPhC,0FAA0F;;QAE1F,4FAA4F;;;EAO5F,CAAC;AACH,MAAM,MAAM,eAAe,GAAG,OAAO,qBAAqB,CAAC,IAAI,CAAC;AAEhE,eAAO,MAAM,wBAAwB;IACnC,sEAAsE;;IAEtE,0EAA0E;;IAE1E,uEAAuE;;IAEvE,sIAAsI;;EAEtI,CAAC;AACH,MAAM,MAAM,kBAAkB,GAAG,OAAO,wBAAwB,CAAC,IAAI,CAAC;AAEtE,eAAO,MAAM,oBAAoB;IAC/B,uJAAuJ;;IAEvJ,0FAA0F;;QAd1F,sEAAsE;;QAEtE,0EAA0E;;QAE1E,uEAAuE;;QAEvE,sIAAsI;;;IAUtI,qLAAqL;;EAErL,CAAC;AACH,MAAM,MAAM,cAAc,GAAG,OAAO,oBAAoB,CAAC,IAAI,CAAC;AAE9D;;;GAGG;AACH,eAAO,MAAM,qBAAqB;IAChC,mCAAmC;;IAEnC,gDAAgD;;EAEhD,CAAC;AACH,MAAM,MAAM,eAAe,GAAG,OAAO,qBAAqB,CAAC,IAAI,CAAC;AAEhE;;GAEG;AACH,eAAO,MAAM,sBAAsB;IACjC,0BAA0B;;IAE1B,sKAAsK;;EAEtK,CAAC;AACH,MAAM,MAAM,gBAAgB,GAAG,OAAO,sBAAsB,CAAC,IAAI,CAAC;AAElE;;;GAGG;AACH,eAAO,MAAM,0BAA0B;IACrC,uFAAuF;;IAEvF,8DAA8D;;IAE9D,qCAAqC;;EAErC,CAAC;AACH,MAAM,MAAM,oBAAoB,GAAG,OAAO,0BAA0B,CAAC,IAAI,CAAC;AAE1E;;;;;;GAMG;AACH,eAAO,MAAM,2BAA2B;IACtC,qDAAqD;;IAErD,sFAAsF;;IAEtF,sLAAsL;;EAEtL,CAAC;AACH,MAAM,MAAM,qBAAqB,GAAG,OAAO,2BAA2B,CAAC,IAAI,CAAC;AAE5E;;;;;;;;;GASG;AACH,eAAO,MAAM,yBAAyB;IACpC,+DAA+D;;IAE/D,8CAA8C;;IAE9C,+MAA+M;;EAI/M,CAAC;AACH,MAAM,MAAM,mBAAmB,GAAG,OAAO,yBAAyB,CAAC,IAAI,CAAC;AAExE;;GAEG;AACH,eAAO,MAAM,2BAA2B;IACtC,wBAAwB;;IAExB,6CAA6C;;IAE7C,+CAA+C;;IAE/C,6BAA6B;;EAE7B,CAAC;AACH,MAAM,MAAM,qBAAqB,GAAG,OAAO,2BAA2B,CAAC,IAAI,CAAC;AAE5E;;GAEG;AACH,eAAO,MAAM,+BAA+B;IAC1C,wBAAwB;;EAExB,CAAC;AACH,MAAM,MAAM,yBAAyB,GAAG,OAAO,+BAA+B,CAAC,IAAI,CAAC;AAEpF;;GAEG;AACH,eAAO,MAAM,4BAA4B;IACvC,2CAA2C;;EAE3C,CAAC;AACH,MAAM,MAAM,sBAAsB,GAAG,OAAO,4BAA4B,CAAC,IAAI,CAAC;AAE9E;;GAEG;AACH,eAAO,MAAM,+BAA+B;IAC1C,4EAA4E;;IAE5E,sBAAsB;;EAEtB,CAAC;AACH,MAAM,MAAM,yBAAyB,GAAG,OAAO,+BAA+B,CAAC,IAAI,CAAC;AAEpF;;GAEG;AACH,eAAO,MAAM,uBAAuB;IAClC,yDAAyD;;IAEzD,+DAA+D;;IAE/D,mCAAmC;;IAEnC,mDAAmD;;EAEnD,CAAC;AACH,MAAM,MAAM,iBAAiB,GAAG,OAAO,uBAAuB,CAAC,IAAI,CAAC;AAEpE;;GAEG;AACH,eAAO,MAAM,uBAAuB;IAElC,+BAA+B;;IAE/B,mEAAmE;;QA9DnE,wBAAwB;;QAExB,6CAA6C;;QAE7C,+CAA+C;;QAE/C,6BAA6B;;;;;;;EA0D7B,CAAC;AACH,MAAM,MAAM,iBAAiB,GAAG,OAAO,uBAAuB,CAAC,IAAI,CAAC;AAEpE;;GAEG;AACH,eAAO,MAAM,2BAA2B;IAEtC,mCAAmC;;IAEnC,uCAAuC;;QA3DvC,wBAAwB;;;;;;;EA6DxB,CAAC;AACH,MAAM,MAAM,qBAAqB,GAAG,OAAO,2BAA2B,CAAC,IAAI,CAAC;AAE5E;;GAEG;AACH,eAAO,MAAM,wBAAwB;IAEnC,gCAAgC;;IAEhC,qCAAqC;;QA9DrC,2CAA2C;;;IAgE3C,4CAA4C;;IAE5C,+CAA+C;;;;;;EAE/C,CAAC;AACH,MAAM,MAAM,kBAAkB,GAAG,OAAO,wBAAwB,CAAC,IAAI,CAAC;AAEtE;;GAEG;AACH,eAAO,MAAM,2BAA2B;IAEtC,mCAAmC;;IAEnC,sDAAsD;;QArEtD,4EAA4E;;QAE5E,sBAAsB;;;;;;;EAqEtB,CAAC;AACH,MAAM,MAAM,qBAAqB,GAAG,OAAO,2BAA2B,CAAC,IAAI,CAAC;AAE5E;;GAEG;AACH,eAAO,MAAM,kBAAkB;IAC7B,gJAAgJ;;EAEhJ,CAAC;AACH,MAAM,MAAM,YAAY,GAAG,OAAO,kBAAkB,CAAC,IAAI,CAAC;AAE1D;;;GAGG;AACH,eAAO,MAAM,uBAAuB;IAClC,+CAA+C;;IAE/C,oHAAoH;;IAEpH,8BAA8B;;IAE9B,uDAAuD;;IAEvD,iCAAiC;;IAEjC,mCAAmC;;IAEnC,kCAAkC;;IAElC,wBAAwB;;IAExB,kBAAkB;;EAElB,CAAC;AACH,MAAM,MAAM,iBAAiB,GAAG,OAAO,uBAAuB,CAAC,IAAI,CAAC;AAEpE;;;GAGG;AACH,eAAO,MAAM,yBAAyB;IAEpC,+CAA+C;;IAE/C,0BAA0B;;IAE1B,0BAA0B;;IAE1B,gDAAgD;;IAEhD,iDAAiD;;IAEjD,yBAAyB;;;;;;;;;;;EAEzB,CAAC;AACH,MAAM,MAAM,mBAAmB,GAAG,OAAO,yBAAyB,CAAC,IAAI,CAAC;AAExE;;;;;;;;GAQG;AACH,eAAO,MAAM,0BAA0B;IACrC,yDAAyD;;IAEzD,sHAAsH;;IAEtH,kEAAkE;;IAElE,gGAAgG;;IAEhG,+DAA+D;;EAE/D,CAAC;AACH,MAAM,MAAM,oBAAoB,GAAG,OAAO,0BAA0B,CAAC,I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package/dist/workflow/raw/native.effect.js

@@ -29,12 +29,6 @@ export const DocumentedSchema = Schema.Struct({
     /** A documentation string for this object, or an array of strings which should be concatenated. */
     doc: Schema.optional(Schema.Union(Schema.Null, Schema.String, Schema.Array(Schema.String))),
 });
-export const RecordSchemaSchema = Schema.Struct({
-    /** Defines the fields of the record. */
-    fields: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.suspend(() => RecordFieldSchema)))),
-    /** Must be `record` */
-    type: Schema.Literal("record"),
-});
 /**
  * Define an enumerated type.
  */
@@ -44,9 +38,21 @@ export const EnumSchemaSchema = Schema.Struct({
     /** Must be `enum` */
     type: Schema.Literal("enum"),
 });
+export const RecordSchemaSchema = Schema.Struct({
+    /** Defines the fields of the record. */
+    fields: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.suspend(() => RecordFieldSchema).annotations({
+        identifier: "RecordFieldSchema",
+    })))),
+    /** Must be `record` */
+    type: Schema.Literal("record"),
+});
 export const ArraySchemaSchema = Schema.Struct({
     /** Defines the type of the array elements. */
-    items: Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema), Schema.String, Schema.Array(Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema), Schema.String))),
+    items: Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema).annotations({
+        identifier: "ArraySchemaSchema",
+    }), Schema.String, Schema.Array(Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema).annotations({
+        identifier: "ArraySchemaSchema",
+    }), Schema.String))),
     /** Must be `array` */
     type: Schema.Literal("array"),
 });
@@ -255,27 +261,6 @@ export const NativeFreehandCommentSchema = Schema.Struct({
     /** Freehand content data: ``line``, ``thickness``. */
     data: Schema.optional(Schema.Union(Schema.Null, NativeFreehandCommentDataSchema)),
 });
-/**
- * Provenance tracking for workflows imported from external sources.
-Contains either a direct URL or TRS (Tool Registry Service) metadata,
-depending on how the workflow was imported.
-
-For URL imports, only ``url`` is set. For TRS imports (Dockstore,
-WorkflowHub), ``trs_tool_id``, ``trs_version_id``, and ``trs_url``
-are set, with ``trs_server`` optionally identifying the server.
- */
-export const NativeSourceMetadataSchema = Schema.Struct({
-    /** URL from which the workflow was directly imported. */
-    url: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** Tool identifier in the Tool Registry Service (e.g. ``"#workflow/github.com/user/repo/workflow"`` or ``"109"``). */
-    trs_tool_id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** Version identifier in the TRS (e.g. ``"master"``, ``"5"``). */
-    trs_version_id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** TRS server name (e.g. ``"dockstore"``, ``"workflowhub"``). Optional even for TRS imports. */
-    trs_server: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** Complete TRS API endpoint URL for this workflow version. */
-    trs_url: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-});
 /**
  * Workflow invocation report template.
  */
@@ -326,6 +311,27 @@ export const NativeCreatorPersonSchema = Schema.Struct({
     /** Job title or role. */
     jobTitle: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
 });
+/**
+ * Provenance tracking for workflows imported from external sources.
+Contains either a direct URL or TRS (Tool Registry Service) metadata,
+depending on how the workflow was imported.
+
+For URL imports, only ``url`` is set. For TRS imports (Dockstore,
+WorkflowHub), ``trs_tool_id``, ``trs_version_id``, and ``trs_url``
+are set, with ``trs_server`` optionally identifying the server.
+ */
+export const NativeSourceMetadataSchema = Schema.Struct({
+    /** URL from which the workflow was directly imported. */
+    url: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** Tool identifier in the Tool Registry Service (e.g. ``"#workflow/github.com/user/repo/workflow"`` or ``"109"``). */
+    trs_tool_id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** Version identifier in the TRS (e.g. ``"master"``, ``"5"``). */
+    trs_version_id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** TRS server name (e.g. ``"dockstore"``, ``"workflowhub"``). Optional even for TRS imports. */
+    trs_server: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** Complete TRS API endpoint URL for this workflow version. */
+    trs_url: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+});
 /**
  * An organization that created or contributed to the workflow.
 Corresponds to a `schema.org Organization <https://schema.org/Organization>`_.
@@ -384,12 +390,16 @@ export const NativeGalaxyWorkflowSchema = Schema.Struct({
     /** Step dictionary keyed by string integers (``"0"``, ``"1"``, ...). Values are NativeStep objects. Steps are processed in sorted numeric order during import. */
     steps: Schema.optional(Schema.Union(Schema.Record({
         key: Schema.String,
-        value: Schema.suspend(() => NativeStepSchema),
+        value: Schema.suspend(() => NativeStepSchema).annotations({
+            identifier: "NativeStepSchema",
+        }),
     }), Schema.Null)),
     /** Map of locally-defined subworkflow dicts, used during format conversion. */
     subworkflows: Schema.optional(Schema.Union(Schema.Record({
         key: Schema.String,
-        value: Schema.suspend(() => NativeGalaxyWorkflowSchema),
+        value: Schema.suspend(() => NativeGalaxyWorkflowSchema).annotations({
+            identifier: "NativeGalaxyWorkflowSchema",
+        }),
     }), Schema.Null)),
 });
 /**
@@ -447,7 +457,9 @@ export const NativeStepSchema = Schema.Struct({
     /** Post-job actions applied to outputs after tool execution. Keys are compound strings of the form ``{ActionType}{OutputName}``. Values are NativePostJobAction objects. */
     post_job_actions: Schema.optional(Schema.Union(Schema.Record({ key: Schema.String, value: NativePostJobActionSchema }), Schema.Null)),
     /** Embedded subworkflow definition. A complete native workflow document (with ``a_galaxy_workflow``, ``format-version``, ``steps``, etc.) nested inside this step. */
-    subworkflow: Schema.optional(Schema.Union(NativeGalaxyWorkflowSchema, Schema.Null)),
+    subworkflow: Schema.optional(Schema.Union(Schema.suspend(() => NativeGalaxyWorkflowSchema).annotations({
+        identifier: "NativeGalaxyWorkflowSchema",
+    }), Schema.Null)),
     /** Embedded tool definition for user-defined (dynamic) tools. Present when the step uses a ``GalaxyUserTool`` instead of a registered tool. Contains the full tool definition including ``class: GalaxyU... */
     tool_representation: Schema.optional(Schema.Union(Schema.Record({ key: Schema.String, value: Schema.Unknown }), Schema.Null)),
     /** Default values for step inputs. Keys are parameter names, values are objects with a ``default`` key. */

package/dist/workflow/raw/native.effect.js.map

@@ -1 +1 @@
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package/dist/workflow/roundtrip.d.ts

@@ -0,0 +1,54 @@
+import type { StepConversionStatus, ToolInputsResolver } from "./normalized/stateful-runner.js";
+export type RoundtripFailureClass = "conversion_error" | "reimport_error" | "roundtrip_mismatch"
+/** Subworkflow ref was an external URL/TRS string — inline steps not available for diff. */
+ | "subworkflow_external_ref";
+export type DiffSeverity = "error" | "benign";
+export type BenignArtifactKind = "type_coercion" | "multi_select_normalized" | "all_null_section_omitted" | "empty_container_omitted" | "connection_only_section_omitted" | "bookkeeping_stripped"
+/**
+ * Runtime-leak key (`__workflow_invocation_uuid__` or `*|__identifier__`)
+ * dropped or appeared during roundtrip. Walker drops these silently during
+ * stateful conversion; mirrors Galaxy's `RUNTIME_LEAK` classification.
+ */
+ | "runtime_leak_stripped";
+export interface StepDiff {
+    path: string;
+    severity: DiffSeverity;
+    kind?: BenignArtifactKind;
+    message: string;
+}
+export interface StepRoundtripResult {
+    stepId: string;
+    toolId?: string;
+    success: boolean;
+    failureClass?: RoundtripFailureClass;
+    error?: string;
+    diffs: StepDiff[];
+    /**
+     * Nesting depth inside subworkflows. 0 = top-level, 1 = inside one
+     * subworkflow, etc. Used by CLI reporters to indent nested results.
+     * `stepId` is prefixed with parent ids using `.` (e.g. `3.1.0`).
+     */
+    depth: number;
+}
+export interface RoundtripResult {
+    workflowName?: string;
+    stepResults: StepRoundtripResult[];
+    /** Per-step forward (native→format2) status from stateful conversion. */
+    forwardSteps: StepConversionStatus[];
+    /** Per-step reverse (format2→native) status from stateful conversion. */
+    reverseSteps: StepConversionStatus[];
+    /** No error-severity diffs and no step failures (benign diffs allowed). */
+    success: boolean;
+    /** No diffs at all (clean roundtrip). */
+    clean: boolean;
+}
+/**
+ * Roundtrip a native workflow through format2 and back, diffing each
+ * tool step's `tool_state`. Benign diffs (type coercion, connection
+ * moves, stale-key stripping) are reported but don't count as failures.
+ *
+ * Returns `success=true` iff no error-severity diffs and no conversion
+ * failures. `clean=true` iff there are zero diffs of any severity.
+ */
+export declare function roundtripValidate(nativeRaw: unknown, toolInputsResolver: ToolInputsResolver): RoundtripResult;
+//# sourceMappingURL=roundtrip.d.ts.map

package/dist/workflow/roundtrip.d.ts.map

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