@galaxy-tool-util/schema 1.1.0 → 1.5.0

package/dist/schema/parsed-tool.js

@@ -1,4 +1,5 @@
 import * as S from "effect/Schema";
+import * as JSONSchema from "effect/JSONSchema";
 /** Tool help content with format (rst, markdown, etc.) and rendered content. */
 export const HelpContent = S.Struct({
     format: S.String,
@@ -14,6 +15,75 @@ export const Citation = S.Struct({
     type: S.String,
     content: S.String,
 });
+export const DiscoverVia = S.Literal("pattern", "tool_provided_metadata");
+export const SortKey = S.Literal("filename", "name", "designation", "dbkey");
+export const SortComp = S.Literal("lexical", "numeric");
+const DatasetCollectionDescriptionBase = S.Struct({
+    discover_via: DiscoverVia,
+    format: S.NullOr(S.String),
+    visible: S.Boolean,
+    assign_primary_output: S.Boolean,
+    directory: S.NullOr(S.String),
+    recurse: S.Boolean,
+    match_relative_path: S.Boolean,
+});
+export const ToolProvidedMetadataDatasetCollection = S.Struct({
+    ...DatasetCollectionDescriptionBase.fields,
+    discover_via: S.Literal("tool_provided_metadata"),
+});
+export const FilePatternDatasetCollectionDescription = S.Struct({
+    ...DatasetCollectionDescriptionBase.fields,
+    discover_via: S.Literal("pattern"),
+    sort_key: SortKey,
+    sort_comp: SortComp,
+    sort_reverse: S.Boolean,
+    pattern: S.String,
+});
+export const DatasetCollectionDescription = S.Union(FilePatternDatasetCollectionDescription, ToolProvidedMetadataDatasetCollection);
+const ToolOutputBase = S.Struct({
+    name: S.String,
+    label: S.NullOr(S.String),
+    hidden: S.Boolean,
+});
+export const ToolOutputDataset = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("data"),
+    format: S.String,
+    format_source: S.NullOr(S.String),
+    metadata_source: S.NullOr(S.String),
+    discover_datasets: S.NullOr(S.Array(DatasetCollectionDescription)),
+    from_work_dir: S.NullOr(S.String),
+    precreate_directory: S.Boolean,
+});
+export const ToolOutputCollectionStructure = S.Struct({
+    collection_type: S.NullOr(S.String),
+    collection_type_source: S.NullOr(S.String),
+    collection_type_from_rules: S.NullOr(S.String),
+    structured_like: S.NullOr(S.String),
+    discover_datasets: S.NullOr(S.Array(DatasetCollectionDescription)),
+});
+export const ToolOutputCollection = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("collection"),
+    structure: ToolOutputCollectionStructure,
+});
+export const ToolOutputText = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("text"),
+});
+export const ToolOutputInteger = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("integer"),
+});
+export const ToolOutputFloat = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("float"),
+});
+export const ToolOutputBoolean = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("boolean"),
+});
+export const ToolOutput = S.Union(ToolOutputDataset, ToolOutputCollection, ToolOutputText, ToolOutputInteger, ToolOutputFloat, ToolOutputBoolean);
 /** Normalize empty string to null for description field. */
 const NullableDescription = S.transform(S.NullOr(S.String), S.NullOr(S.String), {
     decode: (val) => (val === "" ? null : val),
@@ -26,7 +96,7 @@ const NullableDescription = S.transform(S.NullOr(S.String), S.NullOr(S.String),
  * object-shaped guard here and supply the TS type via the generic parameter.
  * `ParsedTool` payloads come from Python's `model_dump()` — already trusted.
  */
-const ToolParameterModelSchema = S.declare((input) => typeof input === "object" && input !== null && !Array.isArray(input));
+const ToolParameterModelSchema = S.declare((input) => typeof input === "object" && input !== null && !Array.isArray(input)).annotations({ jsonSchema: { type: "object" } });
 /**
  * Effect Schema for parsed Galaxy tool metadata as returned by the ToolShed TRS API
  * or Galaxy's /api/tools/:id/parsed endpoint.
@@ -37,7 +107,7 @@ export const ParsedTool = S.Struct({
     name: S.String,
     description: NullableDescription,
     inputs: S.Array(ToolParameterModelSchema),
-    outputs: S.Array(S.Unknown),
+    outputs: S.Array(ToolOutput),
     citations: S.Array(Citation),
     license: S.NullOr(S.String),
     profile: S.NullOr(S.String),
@@ -46,4 +116,5 @@ export const ParsedTool = S.Struct({
     xrefs: S.Array(XrefDict),
     help: S.optional(S.Union(HelpContent, S.Null)),
 });
+export const parsedToolSchema = JSONSchema.make(ParsedTool, { target: "jsonSchema2020-12" });
 //# sourceMappingURL=parsed-tool.js.map

package/dist/schema/parsed-tool.js.map

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

@@ -0,0 +1,12 @@
+/**
+ * Parse a Galaxy inline `tool_representation` (class: `GalaxyUserTool`) into a
+ * `ParsedTool` — the same shape Galaxy's `/api/tools/:id/parsed` endpoint and
+ * ToolShed serve up. This is the TS port of Galaxy's
+ * `parse_tool(YamlToolSource(repr))` path; it covers the fields included in
+ * the TS `ParsedTool` schema (id/version/name/description, inputs, outputs,
+ * citations, license, profile, edam, xrefs, help). Stdio, requirements and
+ * containers are intentionally out of scope — they're not on the TS
+ * `ParsedTool` shape consumers depend on.
+ */
+export { parseInlineTool, type InlineRepresentation } from "./parse.js";
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,OAAO,EAAE,eAAe,EAAE,KAAK,oBAAoB,EAAE,MAAM,YAAY,CAAC"}

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

@@ -0,0 +1,12 @@
+/**
+ * Parse a Galaxy inline `tool_representation` (class: `GalaxyUserTool`) into a
+ * `ParsedTool` — the same shape Galaxy's `/api/tools/:id/parsed` endpoint and
+ * ToolShed serve up. This is the TS port of Galaxy's
+ * `parse_tool(YamlToolSource(repr))` path; it covers the fields included in
+ * the TS `ParsedTool` schema (id/version/name/description, inputs, outputs,
+ * citations, license, profile, edam, xrefs, help). Stdio, requirements and
+ * containers are intentionally out of scope — they're not on the TS
+ * `ParsedTool` shape consumers depend on.
+ */
+export { parseInlineTool } from "./parse.js";
+//# sourceMappingURL=index.js.map

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

@@ -0,0 +1 @@
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package/dist/user-tool-parse/inputs.d.ts

@@ -0,0 +1,13 @@
+/**
+ * Inline tool input parser. Mirrors
+ * `galaxy.tool_util.parameters.factory._from_input_source_galaxy`, normalized
+ * to the YAML pathway only (no XML). Produces the Galaxy `ToolParameterModel`
+ * union from `bundle-types.ts`. Validator handling is best-effort: we read
+ * `validators: [{type, ...}]` entries verbatim, mirroring
+ * `static_validators(parse_dict_validators(...))` once you've stripped the XML
+ * shorthand handling and the `in_range` synthesis from `min`/`max` (which is
+ * what Python does too).
+ */
+import type { ToolParameterModel } from "../schema/bundle-types.js";
+export declare function parseInputs(raw: unknown): ToolParameterModel[];
+//# sourceMappingURL=inputs.d.ts.map

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

@@ -0,0 +1 @@
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