@galaxy-tool-util/schema 1.10.0 → 1.12.0

package/dist/user-tool-parse/inputs.js.map

@@ -1 +1 @@
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package/dist/user-tool-parse/outputs.d.ts

@@ -5,6 +5,7 @@
  * Produces the `ToolOutput` union from `../schema/parsed-tool.ts` (data /
  * collection / text / integer / float / boolean).
  */
-import type { ToolOutput } from "../schema/parsed-tool.js";
+import type { DatasetCollectionDescription, ToolOutput } from "../schema/parsed-tool.js";
 export declare function parseOutputs(raw: unknown): ToolOutput[];
+export declare function parseDiscoverDatasets(raw: unknown): DatasetCollectionDescription[] | null;
 //# sourceMappingURL=outputs.d.ts.map

package/dist/user-tool-parse/outputs.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"outputs.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/outputs.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAGV,UAAU,EAOX,MAAM,0BAA0B,CAAC;AAwBlC,wBAAgB,YAAY,CAAC,GAAG,EAAE,OAAO,GAAG,UAAU,EAAE,CAGvD"}
+{"version":3,"file":"outputs.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/outputs.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EACV,4BAA4B,EAE5B,UAAU,EAOX,MAAM,0BAA0B,CAAC;AAwBlC,wBAAgB,YAAY,CAAC,GAAG,EAAE,OAAO,GAAG,UAAU,EAAE,CAGvD;AAuFD,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,OAAO,GAAG,4BAA4B,EAAE,GAAG,IAAI,CAezF"}

package/dist/user-tool-parse/outputs.js

@@ -87,7 +87,7 @@ function parseOutputCollection(entry) {
         label: readNullableString(entry.label),
         hidden: readBool(entry.hidden, false),
         type: "collection",
-        structure: parseStructure(entry),
+        ...parseStructure(entry),
     };
 }
 function parseStructure(entry) {
@@ -109,7 +109,7 @@ function parseStructure(entry) {
         discover_datasets: discoverDatasets,
     };
 }
-function parseDiscoverDatasets(raw) {
+export function parseDiscoverDatasets(raw) {
     let list;
     if (raw === undefined || raw === null)
         return null;
@@ -135,7 +135,8 @@ function parseDiscoverDataset(entry) {
             ? "tool_provided_metadata"
             : "pattern";
     const base = {
-        format: readNullableString(entry.format ?? entry.ext),
+        // ext-first, matching Galaxy's DatasetCollectionDescription (ext, then format).
+        format: readNullableString(entry.ext ?? entry.format),
         visible: readBool(entry.visible, false),
         assign_primary_output: readBool(entry.assign_primary_output, false),
         directory: readNullableString(entry.directory),

package/dist/user-tool-parse/outputs.js.map

@@ -1 +1 @@
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package/dist/user-tool-parse/parse.d.ts

@@ -1,12 +1,27 @@
 /**
- * Inline GalaxyUserTool → ParsedTool conversion. Mirrors
+ * YAML tool → ParsedTool conversion. Mirrors
  * `galaxy.tool_util.model_factory.parse_tool(YamlToolSource(repr))` for the
  * fields surfaced on the TS `ParsedTool`. See `./inputs.ts` and `./outputs.ts`
  * for the parameter / output trees.
  */
 import type { ParsedTool } from "../schema/parsed-tool.js";
-export type InlineRepresentation = Record<string, unknown>;
+/** A decoded YAML tool document (`class: GalaxyTool` or `GalaxyUserTool`). */
+export type YamlToolRepresentation = Record<string, unknown>;
+/** The inline-tool API's `tool_representation` (always `class: GalaxyUserTool`). */
+export type InlineRepresentation = YamlToolRepresentation;
 export declare class InlineToolParseError extends Error {
 }
+/**
+ * Parse a decoded YAML tool document into a `ParsedTool`. Handles both the
+ * legacy `GalaxyTool` and the user-facing `GalaxyUserTool` classes — the input
+ * and output trees already cover the block/when-map inputs and map-form outputs
+ * the `GalaxyTool` format uses, so a single field layout serves both.
+ */
+export declare function parseYamlTool(repr: YamlToolRepresentation): ParsedTool;
+/**
+ * Parse an inline `GalaxyUserTool` representation. Enforces the `GalaxyUserTool`
+ * class the inline-tool API contract requires, then delegates to
+ * {@link parseYamlTool}.
+ */
 export declare function parseInlineTool(repr: InlineRepresentation): ParsedTool;
 //# sourceMappingURL=parse.d.ts.map

package/dist/user-tool-parse/parse.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"parse.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/parse.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAmC,MAAM,0BAA0B,CAAC;AAK5F,8EAA8E;AAC9E,MAAM,MAAM,sBAAsB,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;AAE7D,oFAAoF;AACpF,MAAM,MAAM,oBAAoB,GAAG,sBAAsB,CAAC;AAE1D,qBAAa,oBAAqB,SAAQ,KAAK;CAAG;AAElD;;;;;GAKG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,sBAAsB,GAAG,UAAU,CAyBtE;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,oBAAoB,GAAG,UAAU,CAUtE"}

package/dist/user-tool-parse/parse.js

@@ -1,5 +1,5 @@
 /**
- * Inline GalaxyUserTool → ParsedTool conversion. Mirrors
+ * YAML tool → ParsedTool conversion. Mirrors
  * `galaxy.tool_util.model_factory.parse_tool(YamlToolSource(repr))` for the
  * fields surfaced on the TS `ParsedTool`. See `./inputs.ts` and `./outputs.ts`
  * for the parameter / output trees.
@@ -8,12 +8,15 @@ import { parseInputs } from "./inputs.js";
 import { parseOutputs } from "./outputs.js";
 export class InlineToolParseError extends Error {
 }
-export function parseInlineTool(repr) {
+/**
+ * Parse a decoded YAML tool document into a `ParsedTool`. Handles both the
+ * legacy `GalaxyTool` and the user-facing `GalaxyUserTool` classes — the input
+ * and output trees already cover the block/when-map inputs and map-form outputs
+ * the `GalaxyTool` format uses, so a single field layout serves both.
+ */
+export function parseYamlTool(repr) {
     if (!repr || typeof repr !== "object" || Array.isArray(repr)) {
-        throw new InlineToolParseError("inline tool representation must be an object");
-    }
-    if (repr.class !== "GalaxyUserTool") {
-        throw new InlineToolParseError(`inline tool representation must have class 'GalaxyUserTool' (got ${JSON.stringify(repr.class)})`);
+        throw new InlineToolParseError("tool representation must be an object");
     }
     const id = typeof repr.id === "string" ? repr.id : "";
     const version = repr.version == null ? null : String(repr.version);
@@ -35,6 +38,20 @@ export function parseInlineTool(repr) {
         help: parseHelp(repr.help),
     };
 }
+/**
+ * Parse an inline `GalaxyUserTool` representation. Enforces the `GalaxyUserTool`
+ * class the inline-tool API contract requires, then delegates to
+ * {@link parseYamlTool}.
+ */
+export function parseInlineTool(repr) {
+    if (!repr || typeof repr !== "object" || Array.isArray(repr)) {
+        throw new InlineToolParseError("inline tool representation must be an object");
+    }
+    if (repr.class !== "GalaxyUserTool") {
+        throw new InlineToolParseError(`inline tool representation must have class 'GalaxyUserTool' (got ${JSON.stringify(repr.class)})`);
+    }
+    return parseYamlTool(repr);
+}
 function parseStringList(raw) {
     if (!Array.isArray(raw))
         return [];

package/dist/user-tool-parse/parse.js.map

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package/dist/workflow/draft-checks.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/draft-checks.js

@@ -10,7 +10,7 @@
  */
 import { Either, ParseResult, Schema } from "effect";
 import { GalaxyWorkflowDraftSchema } from "./raw/gxformat2-draft.effect.js";
-import { rawStepRenderIdentity } from "./normalized/labels.js";
+import { rawStepRenderIdentity, resolveSourceReference } from "./normalized/labels.js";
 export const TODO_SENTINEL_PATTERN = /^TODO(_[a-zA-Z0-9_]+)?$/;
 // Heuristic for TODO-shaped strings — flags malformed sentinels (TODO-foo,
 // TODOfoo, TODO_) that the canonical pattern misses. Mixed-case suffixes
@@ -128,11 +128,12 @@ function walkDraftSteps(workflow, prefix, todos, planFields) {
     // reach this workflow (i.e. the outer step's path); inner outputs collect
     // at that prefix. For the outermost call `prefix` is [], so outer outputs
     // collect at path [].
+    const stepLabels = collectStepLabels(workflow.steps);
     for (const [label, output] of iterateOutputs(workflow.outputs)) {
         const ref = readOutputSource(output);
         if (ref == null)
             continue;
-        const [, port] = splitSourceRef(ref);
+        const [, port] = splitSourceRef(ref, stepLabels);
         if (port != null && isTodoSentinel(port)) {
             todos.push({
                 path: prefix,
@@ -212,11 +213,25 @@ function readOutputSource(output) {
     const src = output.outputSource ?? output.source;
     return typeof src === "string" ? src : null;
 }
-function splitSourceRef(ref) {
+function collectStepLabels(steps) {
+    const labels = new Set();
+    for (const [label] of iterateSteps(steps))
+        labels.add(label);
+    return labels;
+}
+/**
+ * Parse a source ref into `[label, port]`. A slash-less ref that names a step
+ * is gxformat2 shorthand for `<step>/output` (matching `resolveSourceReference`
+ * on the concrete path and `checkEdgeRef`); anything else is a workflow-input
+ * ref, reported port-less (`null`) so callers can treat it as a non-step edge.
+ */
+function splitSourceRef(ref, stepLabels) {
     const slash = ref.indexOf("/");
-    if (slash < 0)
-        return [ref, null];
-    return [ref.slice(0, slash), ref.slice(slash + 1)];
+    if (slash >= 0)
+        return [ref.slice(0, slash), ref.slice(slash + 1)];
+    if (stepLabels.has(ref))
+        return [ref, "output"];
+    return [ref, null];
 }
 function* iterateStepOutIds(out) {
     if (Array.isArray(out)) {
@@ -334,6 +349,9 @@ function walkDraftValidation(workflow, prefix, topologyErrors, semanticErrors, w
     }
     // Workflow outputs: labels must be concrete; outputSource resolves.
     const stepIndex = buildStepIndex(workflow.steps);
+    // The label universe every edge ref resolves against — built once per level
+    // and shared by the output and step-input edge checks below.
+    const knownLabels = new Set([...inputLabels, ...stepIndex.keys()]);
     for (const [label, output] of iterateMapOrArrayLabeled(workflow.outputs)) {
         if (isTodoSentinel(label)) {
             topologyErrors.push({
@@ -346,7 +364,7 @@ function walkDraftValidation(workflow, prefix, topologyErrors, semanticErrors, w
         }
         const ref = readOutputSource(output);
         if (ref != null) {
-            checkEdgeRef(ref, prefix, `workflow output "${label}"`, stepIndex, inputLabels, topologyErrors, semanticErrors);
+            checkEdgeRef(ref, prefix, `workflow output "${label}"`, stepIndex, inputLabels, knownLabels, topologyErrors, semanticErrors);
         }
     }
     // Steps: labels, types, edge refs, sentinel-form on every TODO-shaped string.
@@ -387,7 +405,7 @@ function walkDraftValidation(workflow, prefix, topologyErrors, semanticErrors, w
         // Step input edges.
         for (const [inKey, inValue] of iterateStepInputEntries(step.in)) {
             for (const ref of extractSourceRefs(inValue)) {
-                checkEdgeRef(ref, stepPath, `step input "${inKey}"`, stepIndex, inputLabels, topologyErrors, semanticErrors);
+                checkEdgeRef(ref, stepPath, `step input "${inKey}"`, stepIndex, inputLabels, knownLabels, topologyErrors, semanticErrors);
             }
         }
         // _plan_* on a fully-resolved tool step is a contract violation: planning
@@ -445,34 +463,36 @@ function buildStepIndex(steps) {
     }
     return index;
 }
-function checkEdgeRef(ref, path, context, stepIndex, inputLabels, topologyErrors, semanticErrors) {
+function checkEdgeRef(ref, path, context, stepIndex, inputLabels, knownLabels, topologyErrors, semanticErrors) {
     checkTodoLike(ref, path, `${context} source "${ref}"`, semanticErrors);
-    const slash = ref.indexOf("/");
-    if (slash < 0) {
-        if (!inputLabels.has(ref)) {
+    // Parse via the shared resolver so draft-validate agrees with the concrete
+    // conversion path on what a source string means. A bare ref that names a
+    // step is gxformat2 shorthand for `<step>/output`; the resolver returns
+    // `[step, "output"]`, and matching known labels longest-first also handles
+    // labels that contain a slash.
+    const [label, port] = resolveSourceReference(ref, knownLabels);
+    // Consult steps before inputs so a label shared by both resolves the same way
+    // the concrete conversion path does: `_registerLabels` registers inputs first
+    // then steps into one map, so a step overwrites a colliding input and wins.
+    const entry = stepIndex.get(label);
+    if (entry != null) {
+        if (!entry.outPorts.has(port)) {
             topologyErrors.push({
                 path,
-                message: `${context} source "${ref}" does not match any declared workflow input`,
+                message: `${context} source "${ref}" references unknown port "${port}" on step "${label}"`,
             });
         }
         return;
     }
-    const stepLabel = ref.slice(0, slash);
-    const port = ref.slice(slash + 1);
-    const entry = stepIndex.get(stepLabel);
-    if (entry == null) {
-        topologyErrors.push({
-            path,
-            message: `${context} source "${ref}" references unknown step "${stepLabel}"`,
-        });
+    if (inputLabels.has(label)) {
         return;
     }
-    if (!entry.outPorts.has(port)) {
-        topologyErrors.push({
-            path,
-            message: `${context} source "${ref}" references unknown port "${port}" on step "${stepLabel}"`,
-        });
-    }
+    // An explicit `<step>/<port>` ref names a step; a bare ref could have meant
+    // either an input or a step — keep each message accurate to the input.
+    const message = ref.includes("/")
+        ? `${context} source "${ref}" references unknown step "${label}"`
+        : `${context} source "${ref}" does not match any declared workflow input or step`;
+    topologyErrors.push({ path, message });
 }
 function* iterateStepInputEntries(input) {
     if (Array.isArray(input)) {
@@ -539,7 +559,7 @@ export function nextDraftStep(workflow) {
 }
 function nextDraftStepIn(workflow, prefix) {
     const ordered = topoOrderedSteps(workflow.steps);
-    const outputRefs = collectOutputRefs(workflow.outputs);
+    const outputRefs = collectOutputRefs(workflow.outputs, collectStepLabels(workflow.steps));
     for (const [label, step] of ordered) {
         if (!isRecord(step))
             continue;
@@ -585,10 +605,9 @@ function topoOrderedSteps(steps) {
         const seen = new Set();
         for (const [, inValue] of iterateStepInputEntries(step.in)) {
             for (const ref of extractSourceRefs(inValue)) {
-                const slash = ref.indexOf("/");
-                if (slash < 0)
-                    continue;
-                const depLabel = ref.slice(0, slash);
+                const [depLabel, port] = splitSourceRef(ref, stepLabels);
+                if (port == null)
+                    continue; // workflow-input ref — not a step edge
                 if (depLabel !== label && stepLabels.has(depLabel)) {
                     seen.add(depLabel);
                 }
@@ -625,13 +644,13 @@ function topoOrderedSteps(steps) {
     }
     return ordered;
 }
-function collectOutputRefs(outputs) {
+function collectOutputRefs(outputs, stepLabels) {
     const byStepPort = new Map();
     for (const [label, output] of iterateOutputs(outputs)) {
         const ref = readOutputSource(output);
         if (ref == null)
             continue;
-        const [stepLabel, port] = splitSourceRef(ref);
+        const [stepLabel, port] = splitSourceRef(ref, stepLabels);
         if (port == null)
             continue;
         let perPort = byStepPort.get(stepLabel);
@@ -883,7 +902,7 @@ function checkStepCascade(step, prefix, drops, livePorts, stepLabels) {
         let anyAlive = false;
         const localDeps = [];
         for (const ref of refs) {
-            const [refStep, refPort] = splitSourceRef(ref);
+            const [refStep, refPort] = splitSourceRef(ref, stepLabels);
             if (refPort == null) {
                 // Workflow input ref — always alive (workflow inputs are preserved verbatim).
                 anyAlive = true;
@@ -992,7 +1011,9 @@ function computeInputRewrites(step, stepPath, drops, livePorts) {
     return out;
 }
 function refIsDead(ref, drops, livePorts) {
-    const [refStep, refPort] = splitSourceRef(ref);
+    // livePorts is keyed by every step label at this level (dropped steps get an
+    // empty set), so it doubles as the step-label universe for splitSourceRef.
+    const [refStep, refPort] = splitSourceRef(ref, livePorts);
     if (refPort == null)
         return false;
     if (drops.has(refStep))
@@ -1175,7 +1196,7 @@ function trimOutputsContainer(outputs, drops, livePorts, prefix) {
             return true;
         if (!refIsDead(ref, drops, livePorts))
             return true;
-        const [refStep] = splitSourceRef(ref);
+        const [refStep] = splitSourceRef(ref, livePorts);
         const drop = drops.get(refStep);
         const reason = drop != null
             ? { kind: "cascade", depends_on: [drop.path] }