@galaxy-tool-util/tool-xml 1.11.0

package/dist/outputs.js

@@ -0,0 +1,165 @@
+import { parseDiscoverDatasets } from "@galaxy-tool-util/schema";
+import { stringAsBool, xmlText, xmlTextOrNull } from "./element.js";
+/**
+ * Port of ``XmlToolSource.parse_outputs`` + ``output_objects.from_tool_source``
+ * — turns an expanded ``<outputs>`` tree into the `ToolOutput` union from
+ * `@galaxy-tool-util/schema`. The `discover_datasets` translation reuses that
+ * package's shared descriptor parser (Galaxy shares `dataset_collection_description`
+ * across the XML and YAML paths too).
+ *
+ * Raw extraction: the collection-structure invariants Python's
+ * `ToolOutputCollectionStructure.__init__` raises on (e.g. both `type` and
+ * `type_source`) are not enforced here; those land with `ParsedTool` assembly.
+ */
+export function parseOutputs(root, profile) {
+    const outElem = root.findChild("outputs");
+    if (outElem === null)
+        return [];
+    // ``legacy_defaults = Version(parse_profile()) == Version("16.01")``.
+    const legacy = profile === "16.01";
+    const dataDict = new Map();
+    const collections = new Map();
+    const expressionDict = new Map();
+    // Pass 1 mirrors Python's initial ``for _ in out_elem.findall("data")``.
+    for (const dataEl of outElem.findChildren("data")) {
+        const out = parseOutputData(dataEl, legacy, profile);
+        dataDict.set(out.name, out);
+    }
+    // Main pass over direct children in document order.
+    for (const child of outElem.children) {
+        if (child.tag === "data") {
+            const out = parseOutputData(child, legacy, profile);
+            dataDict.set(out.name, out);
+        }
+        else if (child.tag === "collection") {
+            const coll = parseOutputCollection(child);
+            collections.set(coll.name, coll);
+        }
+        else if (child.tag === "output") {
+            const outputType = child.attrs.get("type");
+            if (outputType === "data") {
+                const out = parseOutputData(child, legacy, profile);
+                dataDict.set(out.name, out);
+            }
+            else if (outputType === "collection") {
+                // Python remaps collection_type/collection_type_source onto type/type_source.
+                // Note: this form is effectively unusable upstream — Python assigns
+                // `unicodify(None)` into an ElementTree attribute and raises TypeError
+                // when either is absent (and ValueError when both are set). We handle it
+                // gracefully instead of reproducing that breakage.
+                const coll = parseOutputCollection(child, {
+                    collectionType: child.attrs.get("collection_type") ?? null,
+                    collectionTypeSource: child.attrs.get("collection_type_source") ?? null,
+                });
+                collections.set(coll.name, coll);
+            }
+            else {
+                const expr = parseExpressionOutput(child);
+                expressionDict.set(expr.name, expr);
+            }
+        }
+        // Unknown tags are skipped (Python logs a warning).
+    }
+    // Final order: collections (document order), then data, then expression —
+    // Python builds `outputs` with collections during the loop, then
+    // `chain(data_dict.values(), expression_dict.values())`.
+    const outputs = new Map(collections);
+    for (const out of dataDict.values())
+        outputs.set(out.name, out);
+    for (const out of expressionDict.values())
+        outputs.set(out.name, out);
+    return [...outputs.values()];
+}
+function parseOutputData(el, legacy, profile) {
+    let format = el.attrs.get("format") ?? "data";
+    const autoFormat = stringAsBool(el.attrs.get("auto_format"));
+    if (autoFormat && format !== "data") {
+        throw new Error("Setting format and auto_format is not supported at this time.");
+    }
+    if (autoFormat)
+        format = "_sniff_";
+    let fromWorkDir = el.attrs.get("from_work_dir") ?? null;
+    // Pre-21.09 tools quoted from_work_dir without stripping; keep them working.
+    if (fromWorkDir && profileLt(profile, "21.09"))
+        fromWorkDir = fromWorkDir.trim();
+    return {
+        name: el.attrs.get("name") ?? "",
+        label: xmlTextOrNull(el, "label"),
+        hidden: stringAsBool(el.attrs.get("hidden")),
+        type: "data",
+        format,
+        format_source: el.attrs.get("format_source") ?? null,
+        metadata_source: el.attrs.get("metadata_source") ?? null,
+        discover_datasets: parseDataDiscover(el, legacy),
+        from_work_dir: fromWorkDir,
+        precreate_directory: stringAsBool(el.attrs.get("precreate_directory")),
+    };
+}
+function parseOutputCollection(el, override) {
+    const structure = {
+        collection_type: override ? override.collectionType : (el.attrs.get("type") ?? null),
+        collection_type_source: override
+            ? override.collectionTypeSource
+            : (el.attrs.get("type_source") ?? null),
+        collection_type_from_rules: el.attrs.get("type_from_rules") ?? null,
+        structured_like: el.attrs.get("structured_like") ?? null,
+        // <collection> discover_datasets are always parsed non-legacy.
+        discover_datasets: parseDataDiscover(el, false),
+    };
+    return {
+        name: el.attrs.get("name") ?? "",
+        // _parse_collection uses xml_text (default ""), unlike data's None default.
+        label: xmlText(el, "label"),
+        // Python's _parse_collection never reads a hidden attribute on collections.
+        hidden: false,
+        type: "collection",
+        ...structure,
+    };
+}
+const EXPRESSION_TYPES = new Set(["integer", "float", "boolean", "text"]);
+function parseExpressionOutput(el) {
+    const type = el.attrs.get("type");
+    if (type === undefined || !EXPRESSION_TYPES.has(type)) {
+        throw new Error(`Unknown output type encountered [${type ?? ""}]`);
+    }
+    return {
+        name: el.attrs.get("name") ?? "",
+        label: xmlTextOrNull(el, "label"),
+        hidden: stringAsBool(el.attrs.get("hidden")),
+        type,
+    };
+}
+/**
+ * Port of ``dataset_collector_descriptions_from_elem`` — collect the
+ * ``<discover_datasets>`` blocks (inheriting the element's ``format`` attribute
+ * when a block sets neither ``format`` nor ``ext``), or the single default
+ * collector when there are none and the tool is legacy (profile 16.01).
+ */
+function parseDataDiscover(el, legacy) {
+    const blocks = el.findChildren("discover_datasets");
+    if (blocks.length === 0 && legacy) {
+        return parseDiscoverDatasets([{}]) ?? [];
+    }
+    const defaultFormat = el.attrs.get("format");
+    const dicts = blocks.map((block) => {
+        const attrs = Object.fromEntries(block.attrs);
+        if (defaultFormat && !("format" in attrs) && !("ext" in attrs)) {
+            attrs.format = defaultFormat;
+        }
+        return attrs;
+    });
+    return parseDiscoverDatasets(dicts) ?? [];
+}
+/** ``Version(a) < Version(b)`` for dotted numeric tool profile strings. */
+function profileLt(a, b) {
+    const pa = a.split(".").map(Number);
+    const pb = b.split(".").map(Number);
+    for (let i = 0; i < Math.max(pa.length, pb.length); i++) {
+        const x = pa[i] ?? 0;
+        const y = pb[i] ?? 0;
+        if (x !== y)
+            return x < y;
+    }
+    return false;
+}
+//# sourceMappingURL=outputs.js.map

package/dist/outputs.js.map

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package/dist/parse.d.ts

@@ -0,0 +1,17 @@
+import type { ParsedTool as ParsedToolType } from "@galaxy-tool-util/schema";
+import type { ImportResolver } from "./macros.js";
+import type { XmlToolSource } from "./tool-source.js";
+export declare function parsedToolFromSource(src: XmlToolSource): ParsedToolType;
+/** Parse XML tool text into a validated {@link ParsedToolType} (macros expanded via `importResolver`). */
+export declare function parseXmlTool(text: string, importResolver: ImportResolver): ParsedToolType;
+/** Load an XML tool file from disk and parse it into a validated {@link ParsedToolType}. */
+export declare function loadXmlTool(path: string): ParsedToolType;
+/**
+ * Load a tool file from disk and parse it into a validated {@link ParsedToolType},
+ * dispatching on extension like Galaxy's ``get_tool_source``: ``.yml`` is a YAML
+ * tool source, everything else is XML. CWL (``.cwl``/``.json``) is not supported.
+ */
+export declare function loadToolFile(path: string): ParsedToolType;
+/** Load a YAML tool file from disk and parse it into a validated {@link ParsedToolType}. */
+export declare function loadYamlTool(path: string): ParsedToolType;
+//# sourceMappingURL=parse.d.ts.map

package/dist/parse.d.ts.map

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package/dist/parse.js

@@ -0,0 +1,66 @@
+import { readFileSync } from "node:fs";
+import * as S from "effect/Schema";
+import * as yaml from "yaml";
+import { ParsedTool, parseYamlTool } from "@galaxy-tool-util/schema";
+import { loadXmlToolSource, xmlToolSourceFromString } from "./tool-source.js";
+/**
+ * Public XML tool-parsing entry — the TS mirror of Python's
+ * ``parse_tool(get_tool_source(path))``. Assembles the `ParsedTool` fields off
+ * an {@link XmlToolSource} and decodes them through the `ParsedTool` schema, so
+ * a non-tool root (`<toolbox>`, …) is rejected here exactly as Python's pydantic
+ * model rejects it (a missing `id`/`name` is not a valid `ParsedTool`).
+ */
+const decodeParsedTool = S.decodeUnknownSync(ParsedTool);
+export function parsedToolFromSource(src) {
+    return decodeParsedTool({
+        id: src.parseId(),
+        version: src.parseVersion(),
+        name: src.parseName(),
+        description: src.parseDescription() || null,
+        profile: src.parseProfile(),
+        license: src.parseLicense(),
+        edam_operations: src.parseEdamOperations(),
+        edam_topics: src.parseEdamTopics(),
+        xrefs: src.parseXrefs(),
+        citations: src.parseCitations(),
+        help: src.parseHelp(),
+        inputs: src.parseInputs(),
+        outputs: src.parseOutputs(),
+    });
+}
+/** Parse XML tool text into a validated {@link ParsedToolType} (macros expanded via `importResolver`). */
+export function parseXmlTool(text, importResolver) {
+    return parsedToolFromSource(xmlToolSourceFromString(text, importResolver));
+}
+/** Load an XML tool file from disk and parse it into a validated {@link ParsedToolType}. */
+export function loadXmlTool(path) {
+    return parsedToolFromSource(loadXmlToolSource(path));
+}
+/**
+ * Load a tool file from disk and parse it into a validated {@link ParsedToolType},
+ * dispatching on extension like Galaxy's ``get_tool_source``: ``.yml`` is a YAML
+ * tool source, everything else is XML. CWL (``.cwl``/``.json``) is not supported.
+ */
+export function loadToolFile(path) {
+    if (path.endsWith(".cwl") || path.endsWith(".json")) {
+        throw new Error(`CWL tools are not supported: ${path}`);
+    }
+    if (path.endsWith(".yml")) {
+        return loadYamlTool(path);
+    }
+    return loadXmlTool(path);
+}
+/** Load a YAML tool file from disk and parse it into a validated {@link ParsedToolType}. */
+export function loadYamlTool(path) {
+    const text = readFileSync(path, "utf-8");
+    const repr = yaml.parse(text);
+    // PyYAML renders a float version (`1.0`) as "1.0"; JS yaml collapses it to the
+    // number 1, so `String(version)` would yield "1". Recover the written token.
+    if (repr && typeof repr === "object" && typeof repr.version === "number") {
+        const node = yaml.parseDocument(text).get("version", true);
+        if (node && typeof node.source === "string")
+            repr.version = node.source;
+    }
+    return parseYamlTool(repr);
+}
+//# sourceMappingURL=parse.js.map

package/dist/parse.js.map

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package/dist/tool-source.d.ts

@@ -0,0 +1,42 @@
+import type { Citation, HelpContent, ToolOutput, ToolParameterModel, XrefDict } from "@galaxy-tool-util/schema";
+import type { XmlElement } from "./element.js";
+import { type ImportResolver } from "./macros.js";
+/**
+ * Port of the metadata-reading half of ``galaxy.tool_util.parser.xml.XmlToolSource``.
+ *
+ * Wraps an already-macro-expanded {@link XmlElement} tool tree and exposes the
+ * ``parse_*`` accessors that don't depend on the input-parameter tree (that
+ * lives behind the ``InputSource`` seam and is added later). Extraction is raw
+ * and does not yet apply the model-level validation/normalization Python's
+ * pydantic models run when the `ParsedTool` is assembled — e.g. citation
+ * `doi:`-prefix stripping, DOI/BibTeX shape checks, and the profile-gated skip
+ * of malformed citations. Those land with the `ParsedTool` assembly step.
+ */
+export declare class XmlToolSource {
+    static readonly language = "xml";
+    readonly root: XmlElement;
+    constructor(root: XmlElement);
+    parseId(): string | null;
+    parseVersion(): string | null;
+    parseName(): string | null;
+    parseToolType(): string | null;
+    parseDescription(): string;
+    parseProfile(): string;
+    parseLicense(): string | null;
+    parseEdamOperations(): string[];
+    parseEdamTopics(): string[];
+    private edamChildTexts;
+    parseXrefs(): XrefDict[];
+    parseCitations(): Citation[];
+    parseHelp(): HelpContent | null;
+    parseCommand(): string | null;
+    parseOutputs(): ToolOutput[];
+    parseInputs(): ToolParameterModel[];
+}
+/** Build an {@link XmlToolSource} from raw XML text with a caller-supplied import resolver. */
+export declare function xmlToolSourceFromString(text: string, importResolver: ImportResolver): XmlToolSource;
+/** Load a tool XML file from disk, expand its macros, and wrap it as an {@link XmlToolSource}. */
+export declare function loadXmlToolSource(path: string): XmlToolSource;
+/** Read raw XML text without resolving any ``<import>`` (throws if one is present). */
+export declare function xmlToolSourceFromStringNoImports(text: string): XmlToolSource;
+//# sourceMappingURL=tool-source.d.ts.map

package/dist/tool-source.d.ts.map

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package/dist/tool-source.js

@@ -0,0 +1,124 @@
+import { parseXmlToTree, xmlText } from "./element.js";
+import { expandMacros } from "./macros.js";
+import { loadTool } from "./loader.js";
+import { parseInputs } from "./inputs.js";
+import { parseOutputs } from "./outputs.js";
+/**
+ * Port of the metadata-reading half of ``galaxy.tool_util.parser.xml.XmlToolSource``.
+ *
+ * Wraps an already-macro-expanded {@link XmlElement} tool tree and exposes the
+ * ``parse_*`` accessors that don't depend on the input-parameter tree (that
+ * lives behind the ``InputSource`` seam and is added later). Extraction is raw
+ * and does not yet apply the model-level validation/normalization Python's
+ * pydantic models run when the `ParsedTool` is assembled — e.g. citation
+ * `doi:`-prefix stripping, DOI/BibTeX shape checks, and the profile-gated skip
+ * of malformed citations. Those land with the `ParsedTool` assembly step.
+ */
+export class XmlToolSource {
+    static language = "xml";
+    root;
+    constructor(root) {
+        this.root = root;
+    }
+    parseId() {
+        return this.root.attrs.get("id") ?? null;
+    }
+    parseVersion() {
+        return this.root.attrs.get("version") ?? null;
+    }
+    parseName() {
+        return this.root.attrs.get("name") || this.parseId();
+    }
+    parseToolType() {
+        return this.root.attrs.get("tool_type") ?? null;
+    }
+    parseDescription() {
+        return xmlText(this.root, "description");
+    }
+    parseProfile() {
+        // XML default differs from YAML's — pre-16.04 behaviour is the classic default.
+        return this.root.attrs.get("profile") ?? "16.01";
+    }
+    parseLicense() {
+        return this.root.attrs.get("license") ?? null;
+    }
+    parseEdamOperations() {
+        return this.edamChildTexts("edam_operations", "edam_operation");
+    }
+    parseEdamTopics() {
+        return this.edamChildTexts("edam_topics", "edam_topic");
+    }
+    edamChildTexts(containerTag, itemTag) {
+        const container = this.root.findChild(containerTag);
+        if (container === null)
+            return [];
+        return container.findChildren(itemTag).map((el) => el.text);
+    }
+    parseXrefs() {
+        const xrefs = this.root.findChild("xrefs");
+        if (xrefs === null)
+            return [];
+        const out = [];
+        for (const xref of xrefs.findChildren("xref")) {
+            const type = xref.attrs.get("type");
+            // Mirror the `if xref.get("type") and xref.text` guard.
+            if (type && xref.text) {
+                out.push({ value: xref.text.trim(), type });
+            }
+        }
+        return out;
+    }
+    parseCitations() {
+        const citationsEl = this.root.findChild("citations");
+        if (citationsEl === null)
+            return [];
+        const out = [];
+        for (const child of citationsEl.children) {
+            // `parse_citation_elem` ignores non-<citation> children.
+            if (child.tag !== "citation")
+                continue;
+            const content = child.text.trim();
+            // Raw extraction: skip empty content (Python's model asserts it) but do
+            // NOT yet apply DOI/BibTeX shape validation, `doi:` normalization, or the
+            // profile-gated skip of malformed citations — a `type`-less or malformed
+            // citation is passed through here rather than dropped. See class docstring.
+            if (!content)
+                continue;
+            const type = child.attrs.get("type") ?? "";
+            out.push({ type, content });
+        }
+        return out;
+    }
+    parseHelp() {
+        const helpEl = this.root.findChild("help");
+        if (helpEl === null)
+            return null;
+        const format = helpEl.attrs.get("format") ?? "restructuredtext";
+        return { format, content: helpEl.text || "" };
+    }
+    parseCommand() {
+        const commandEl = this.root.findChild("command");
+        return (commandEl && commandEl.text) || null;
+    }
+    parseOutputs() {
+        return parseOutputs(this.root, this.parseProfile());
+    }
+    parseInputs() {
+        return parseInputs(this.root);
+    }
+}
+/** Build an {@link XmlToolSource} from raw XML text with a caller-supplied import resolver. */
+export function xmlToolSourceFromString(text, importResolver) {
+    return new XmlToolSource(expandMacros(parseXmlToTree(text), importResolver));
+}
+/** Load a tool XML file from disk, expand its macros, and wrap it as an {@link XmlToolSource}. */
+export function loadXmlToolSource(path) {
+    return new XmlToolSource(loadTool(path));
+}
+/** Read raw XML text without resolving any ``<import>`` (throws if one is present). */
+export function xmlToolSourceFromStringNoImports(text) {
+    return xmlToolSourceFromString(text, (relPath) => {
+        throw new Error(`<import> not supported without a resolver: ${relPath}`);
+    });
+}
+//# sourceMappingURL=tool-source.js.map

package/dist/tool-source.js.map

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package/package.json

@@ -0,0 +1,53 @@
+{
+  "name": "@galaxy-tool-util/tool-xml",
+  "version": "1.11.0",
+  "description": "XML tool-source layer for Galaxy tools \u2014 macro expansion (port of galaxy.util.xml_macros) and XML parsing into ParsedTool",
+  "type": "module",
+  "sideEffects": false,
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js"
+    },
+    "./package.json": "./package.json"
+  },
+  "files": [
+    "dist",
+    "README.md",
+    "LICENSE"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/jmchilton/galaxy-tool-util-ts",
+    "directory": "packages/tool-xml"
+  },
+  "publishConfig": {
+    "access": "public",
+    "provenance": false
+  },
+  "keywords": [
+    "galaxy",
+    "tool",
+    "xml",
+    "macros"
+  ],
+  "license": "MIT",
+  "dependencies": {
+    "fast-xml-parser": "^5.10.1",
+    "yaml": "^2.8.3",
+    "@galaxy-tool-util/schema": "1.12.0"
+  },
+  "devDependencies": {
+    "@types/node": "^25.5.0",
+    "effect": "^3.21.0"
+  },
+  "scripts": {
+    "build": "tsc",
+    "typecheck": "tsc --noEmit",
+    "test": "tsc --noEmit && vitest run",
+    "test:watch": "vitest",
+    "lint": "eslint src/ test/",
+    "format": "prettier --check 'src/**/*.ts' 'test/**/*.ts'",
+    "format-fix": "prettier --write 'src/**/*.ts' 'test/**/*.ts'"
+  }
+}