@galaxy-tool-util/tool-xml 1.11.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2025 John Chilton
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# @galaxy-tool-util/tool-xml
+
+XML tool-source layer for Galaxy tools. Holds the XML-specific parsing weight
+(an XML parser dependency) out of the browser-safe `@galaxy-tool-util/schema`
+package.
+
+Currently ships a port of Galaxy's macro expander,
+`lib/galaxy/util/xml_macros.py`: the XML-only, pre-parse transform that expands
+`<macros>` — `<token>` substitution (including nested tokens and cycle
+detection), `<xml>`/`<macro>` templates via `<expand>`, `<import>` of external
+macro files, named/unnamed `yield`, and macro token parameters — mutating an
+`XmlElement` tree in place.
+
+```ts
+import { loadTool, canonicalize } from "@galaxy-tool-util/tool-xml";
+
+const expanded = loadTool("tool.xml"); // reads + expands macros
+```
+
+`parseXmlToTree(text)` parses XML into a mutable `XmlElement` tree;
+`expandMacros(root, importResolver)` expands it (filesystem-agnostic);
+`loadTool(path)` is the filesystem-backed convenience that resolves `<import>`
+paths relative to the tool file. `canonicalize(el)` reduces a tree to a
+whitespace-normalized shape for structural comparison.
+
+Behavior is verified against golden macro-expansion fixtures synced from Galaxy
+(`test/fixtures/macro-expansion/cases/`), compared structurally rather than
+byte-for-byte so the port need not reproduce Galaxy's XML serializer.
+
+On top of the expander, `XmlToolSource` ports the parse accessors from Galaxy's
+`galaxy.tool_util.parser.xml.XmlToolSource` that don't need the input-parameter
+tree — the tool metadata (id, version, name, description, profile, license,
+edam operations/topics, xrefs, citations, help, command) and the `<outputs>`
+tree (`parseOutputs()` → the `ToolOutput` union: data / collection / expression
+outputs, with `discover_datasets`):
+
+```ts
+import { loadXmlToolSource } from "@galaxy-tool-util/tool-xml";
+
+const src = loadXmlToolSource("tool.xml");
+src.parseId(); // "cat1"
+src.parseCitations(); // [{ type: "doi", content: "..." }]
+src.parseOutputs(); // [{ type: "data", name: "out1", format: "bam", ... }]
+```
+
+Extraction is raw — the model-level validation Galaxy's pydantic models run
+when the `ParsedTool` is assembled is not applied yet. `parseCitations` passes
+`doi:`-prefixed or malformed citations through rather than normalizing/dropping
+them (DOI/BibTeX shape checks, profile-gated skips), and `parseOutputs` does not
+enforce the collection-structure invariants (e.g. both `type` and `type_source`
+set) that Galaxy raises on.
+
+Assembling these (plus inputs, behind the `InputSource` seam) into a full
+`ParsedTool`, with that validation, is the remaining work; see the repository's
+tool-parsing issue.

package/dist/element.d.ts

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+/**
+ * A minimal, mutable XML element tree modeled on Python's
+ * ``xml.etree.ElementTree.Element`` — enough to faithfully port
+ * ``galaxy.util.xml_macros`` (macro expansion) and to compare expanded trees
+ * structurally against golden fixtures.
+ *
+ * ``text`` mirrors ElementTree's ``.text``: the character data immediately
+ * following the start tag and preceding the first child element. Trailing /
+ * inter-element ("tail") text is not modeled — it is whitespace-only in tool
+ * XML and is normalized away by {@link canonicalize}.
+ */
+export declare class XmlElement {
+    tag: string;
+    /** Attributes in document order. */
+    attrs: Map<string, string>;
+    /** Leading text content (ElementTree ``.text``); "" when absent. */
+    text: string;
+    children: XmlElement[];
+    parent: XmlElement | null;
+    constructor(tag: string);
+    /** Deep copy with a detached parent (mirrors ``copy.deepcopy``). */
+    clone(): XmlElement;
+    /** Remove all children, attributes and text (mirrors ``Element.clear``). */
+    clear(): void;
+    /** First direct child with the given tag, or null (mirrors ``find(tag)``). */
+    findChild(tag: string): XmlElement | null;
+    /** Direct children with the given tag (mirrors ``findall(tag)``). */
+    findChildren(tag: string): XmlElement[];
+    /**
+     * First descendant (excluding self) matching ``tag`` in document order —
+     * mirrors ``Element.find(".//tag")``.
+     */
+    findFirstDescendant(tag: string): XmlElement | null;
+    /**
+     * All descendants (excluding self) matching ``tag`` (and optional predicate)
+     * in document order — mirrors ``Element.findall(".//tag")``.
+     */
+    findAllDescendants(tag: string, predicate?: (el: XmlElement) => boolean): XmlElement[];
+}
+/** Parse XML text into an {@link XmlElement} tree, returning the root element. */
+export declare function parseXmlToTree(text: string): XmlElement;
+export interface CanonicalElement {
+    tag: string;
+    text: string;
+    attrs: Record<string, string>;
+    children: CanonicalElement[];
+}
+/**
+ * Reduce an element tree to a whitespace-normalized, serializer-independent
+ * shape for structural comparison: tag, trimmed text, attributes (compared
+ * order-insensitively), and ordered children.
+ */
+export declare function canonicalize(el: XmlElement): CanonicalElement;
+/**
+ * Attribute-first text lookup — tries ``root``'s ``name`` attribute, then the
+ * ``<name>`` child element's text with line breaks collapsed
+ * (``"".join(splitlines())``) and the result trimmed; ``null`` if neither is
+ * present. The shared core of ``galaxy.util.xml_text``.
+ */
+export declare function xmlTextOrNull(root: XmlElement, name: string): string | null;
+/** Port of ``galaxy.util.xml_text`` — {@link xmlTextOrNull} with a string default. */
+export declare function xmlText(root: XmlElement, name: string, defaultValue?: string): string;
+/**
+ * Port of ``galaxy.util.string_as_bool`` — truthy for ``true``/``yes``/``on``/``1``
+ * (case-insensitive), false otherwise (including ``undefined``/empty string).
+ */
+export declare function stringAsBool(value: string | undefined): boolean;
+/**
+ * Insert deep copies of ``targets`` where ``query`` sits among its parent's
+ * children, then remove ``query`` — port of ``xml_macros._xml_replace``.
+ */
+export declare function xmlReplace(query: XmlElement, targets: XmlElement[]): void;
+//# sourceMappingURL=element.d.ts.map

package/dist/element.d.ts.map

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package/dist/element.js

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+import { XMLParser } from "fast-xml-parser";
+/**
+ * A minimal, mutable XML element tree modeled on Python's
+ * ``xml.etree.ElementTree.Element`` — enough to faithfully port
+ * ``galaxy.util.xml_macros`` (macro expansion) and to compare expanded trees
+ * structurally against golden fixtures.
+ *
+ * ``text`` mirrors ElementTree's ``.text``: the character data immediately
+ * following the start tag and preceding the first child element. Trailing /
+ * inter-element ("tail") text is not modeled — it is whitespace-only in tool
+ * XML and is normalized away by {@link canonicalize}.
+ */
+export class XmlElement {
+    tag;
+    /** Attributes in document order. */
+    attrs;
+    /** Leading text content (ElementTree ``.text``); "" when absent. */
+    text;
+    children;
+    parent;
+    constructor(tag) {
+        this.tag = tag;
+        this.attrs = new Map();
+        this.text = "";
+        this.children = [];
+        this.parent = null;
+    }
+    /** Deep copy with a detached parent (mirrors ``copy.deepcopy``). */
+    clone() {
+        const copy = new XmlElement(this.tag);
+        copy.attrs = new Map(this.attrs);
+        copy.text = this.text;
+        for (const child of this.children) {
+            const childCopy = child.clone();
+            childCopy.parent = copy;
+            copy.children.push(childCopy);
+        }
+        return copy;
+    }
+    /** Remove all children, attributes and text (mirrors ``Element.clear``). */
+    clear() {
+        this.attrs = new Map();
+        this.text = "";
+        this.children = [];
+    }
+    /** First direct child with the given tag, or null (mirrors ``find(tag)``). */
+    findChild(tag) {
+        for (const child of this.children) {
+            if (child.tag === tag)
+                return child;
+        }
+        return null;
+    }
+    /** Direct children with the given tag (mirrors ``findall(tag)``). */
+    findChildren(tag) {
+        return this.children.filter((c) => c.tag === tag);
+    }
+    /**
+     * First descendant (excluding self) matching ``tag`` in document order —
+     * mirrors ``Element.find(".//tag")``.
+     */
+    findFirstDescendant(tag) {
+        for (const child of this.children) {
+            if (child.tag === tag)
+                return child;
+            const found = child.findFirstDescendant(tag);
+            if (found)
+                return found;
+        }
+        return null;
+    }
+    /**
+     * All descendants (excluding self) matching ``tag`` (and optional predicate)
+     * in document order — mirrors ``Element.findall(".//tag")``.
+     */
+    findAllDescendants(tag, predicate) {
+        const out = [];
+        const walk = (el) => {
+            for (const child of el.children) {
+                if (child.tag === tag && (!predicate || predicate(child)))
+                    out.push(child);
+                walk(child);
+            }
+        };
+        walk(this);
+        return out;
+    }
+}
+// ---------------------------------------------------------------------------
+// Parsing (fast-xml-parser preserveOrder tree → XmlElement)
+// ---------------------------------------------------------------------------
+const PARSER = new XMLParser({
+    preserveOrder: true,
+    ignoreAttributes: false,
+    attributeNamePrefix: "",
+    attributesGroupName: ":@",
+    parseTagValue: false,
+    parseAttributeValue: false,
+    trimValues: false,
+    processEntities: true,
+    cdataPropName: "#cdata",
+    // No commentPropName → comments are dropped (matches remove_comments=True).
+});
+/** Text carried by a preserveOrder "#text"/"#cdata" node, else null. */
+function nodeText(node) {
+    if ("#text" in node)
+        return String(node["#text"]);
+    if ("#cdata" in node) {
+        const parts = node["#cdata"];
+        return parts.map((p) => ("#text" in p ? String(p["#text"]) : "")).join("");
+    }
+    return null;
+}
+/** Tag name of a preserveOrder element node (the non-special, non-attrs key). */
+function nodeTag(node) {
+    for (const key of Object.keys(node)) {
+        // Skip attribute group, text/cdata specials, and the "?xml"/PI declaration.
+        if (key === ":@" || key.startsWith("#") || key.startsWith("?"))
+            continue;
+        return key;
+    }
+    return null;
+}
+function buildElement(node) {
+    const tag = nodeTag(node);
+    if (tag === null)
+        return null;
+    const el = new XmlElement(tag);
+    const rawAttrs = node[":@"];
+    if (rawAttrs) {
+        for (const [k, v] of Object.entries(rawAttrs))
+            el.attrs.set(k, String(v));
+    }
+    const childNodes = node[tag] ?? [];
+    let sawElement = false;
+    for (const child of childNodes) {
+        const text = nodeText(child);
+        if (text !== null) {
+            // Leading text only (before the first child element); tails are dropped.
+            if (!sawElement)
+                el.text += text;
+            continue;
+        }
+        const childEl = buildElement(child);
+        if (childEl) {
+            childEl.parent = el;
+            el.children.push(childEl);
+            sawElement = true;
+        }
+    }
+    return el;
+}
+/** Parse XML text into an {@link XmlElement} tree, returning the root element. */
+export function parseXmlToTree(text) {
+    const parsed = PARSER.parse(text);
+    for (const node of parsed) {
+        const el = buildElement(node);
+        if (el)
+            return el;
+    }
+    throw new Error("No root element found in XML input.");
+}
+/**
+ * Reduce an element tree to a whitespace-normalized, serializer-independent
+ * shape for structural comparison: tag, trimmed text, attributes (compared
+ * order-insensitively), and ordered children.
+ */
+export function canonicalize(el) {
+    return {
+        tag: el.tag,
+        text: el.text.trim(),
+        attrs: Object.fromEntries(el.attrs),
+        children: el.children.map(canonicalize),
+    };
+}
+/**
+ * Attribute-first text lookup — tries ``root``'s ``name`` attribute, then the
+ * ``<name>`` child element's text with line breaks collapsed
+ * (``"".join(splitlines())``) and the result trimmed; ``null`` if neither is
+ * present. The shared core of ``galaxy.util.xml_text``.
+ */
+export function xmlTextOrNull(root, name) {
+    const attr = root.attrs.get(name);
+    if (attr)
+        return attr;
+    const elem = root.findChild(name);
+    if (elem !== null && elem.text) {
+        return elem.text
+            .split(/\r\n|\r|\n/)
+            .join("")
+            .trim();
+    }
+    return null;
+}
+/** Port of ``galaxy.util.xml_text`` — {@link xmlTextOrNull} with a string default. */
+export function xmlText(root, name, defaultValue = "") {
+    return xmlTextOrNull(root, name) ?? defaultValue;
+}
+/**
+ * Port of ``galaxy.util.string_as_bool`` — truthy for ``true``/``yes``/``on``/``1``
+ * (case-insensitive), false otherwise (including ``undefined``/empty string).
+ */
+export function stringAsBool(value) {
+    if (value === undefined)
+        return false;
+    return ["true", "yes", "on", "1"].includes(value.toLowerCase());
+}
+/**
+ * Insert deep copies of ``targets`` where ``query`` sits among its parent's
+ * children, then remove ``query`` — port of ``xml_macros._xml_replace``.
+ */
+export function xmlReplace(query, targets) {
+    const parent = query.parent;
+    if (parent === null)
+        throw new Error("xmlReplace: element has no parent");
+    const index = parent.children.indexOf(query);
+    if (index < 0)
+        throw new Error("xmlReplace: element not found in parent");
+    const clones = targets.map((t) => {
+        const c = t.clone();
+        c.parent = parent;
+        return c;
+    });
+    parent.children.splice(index, 1, ...clones);
+}
+//# sourceMappingURL=element.js.map

package/dist/element.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,8 @@
+export { XmlElement, parseXmlToTree, canonicalize, xmlReplace, type CanonicalElement, } from "./element.js";
+export { expandMacros, XmlMacroDef, type ImportResolver } from "./macros.js";
+export { loadTool } from "./loader.js";
+export { XmlToolSource, loadXmlToolSource, xmlToolSourceFromString, xmlToolSourceFromStringNoImports, } from "./tool-source.js";
+export { parseOutputs } from "./outputs.js";
+export { parseInputs, XmlPageSource, XmlInputSource } from "./inputs.js";
+export { parseXmlTool, loadXmlTool, loadYamlTool, loadToolFile, parsedToolFromSource, } from "./parse.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/index.js

@@ -0,0 +1,8 @@
+export { XmlElement, parseXmlToTree, canonicalize, xmlReplace, } from "./element.js";
+export { expandMacros, XmlMacroDef } from "./macros.js";
+export { loadTool } from "./loader.js";
+export { XmlToolSource, loadXmlToolSource, xmlToolSourceFromString, xmlToolSourceFromStringNoImports, } from "./tool-source.js";
+export { parseOutputs } from "./outputs.js";
+export { parseInputs, XmlPageSource, XmlInputSource } from "./inputs.js";
+export { parseXmlTool, loadXmlTool, loadYamlTool, loadToolFile, parsedToolFromSource, } from "./parse.js";
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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

@@ -0,0 +1,48 @@
+import type { DrillDownOption, InputSource, InputType, LabelValue, PageSource, ToolParameterModel, ValidatorModel } from "@galaxy-tool-util/schema";
+import type { XmlElement } from "./element.js";
+/**
+ * XML-backed `InputSource` / `PageSource` — the TS port of Galaxy's
+ * `parser.xml.XmlInputSource` / `XmlPageSource`. It adapts an `<inputs>` tree
+ * (already macro-expanded) onto the seam consumed by the shared parameter-model
+ * factory in `@galaxy-tool-util/schema`, so XML and the inline/YAML dict path
+ * build the same `ToolParameterModel` union.
+ *
+ * Coercion here is XML-native: attribute reads default to string, booleans go
+ * through `string_as_bool`, and `parse_static_options` deduplicates `<option>`
+ * children by `value` (mirroring the Python source). Dynamic-option detection
+ * nulls a select's / drill-down's options but the option source itself is not
+ * modeled. Accessors the factory does not consume yet (conversion tuples,
+ * sanitizers) are stubbed to their empty forms and grow with the feature slices
+ * that need them.
+ */
+/** Port of `XmlToolSource.parse_inputs` entry — `<inputs>` tree → models. */
+export declare function parseInputs(root: XmlElement): ToolParameterModel[];
+/** Port of `parser.xml.XmlPageSource`. */
+export declare class XmlPageSource implements PageSource {
+    private readonly parentElem;
+    constructor(parentElem: XmlElement);
+    parseInputSources(): InputSource[];
+}
+/** Port of `parser.xml.XmlInputSource`. */
+export declare class XmlInputSource implements InputSource {
+    private readonly inputElem;
+    constructor(inputElem: XmlElement);
+    get(key: string, defaultValue?: unknown): unknown;
+    getBool(key: string, defaultValue: boolean): boolean;
+    parseInputType(): InputType;
+    parseName(): string;
+    parseLabel(): string | null;
+    parseHelp(): string | null;
+    parseOptional(defaultValue?: boolean): boolean;
+    parseExtensions(): string[];
+    hasDynamicOptions(): boolean;
+    parseStaticOptions(): LabelValue[] | null;
+    hasDrillDownDynamicOptions(): boolean;
+    parseDrillDownStaticOptions(): DrillDownOption[] | null;
+    parseValidators(): ValidatorModel[];
+    parseNestedInputsSource(): PageSource;
+    parseTestInputSource(): InputSource;
+    parseWhenInputSources(): Array<[unknown, PageSource]>;
+    parseDefault(): unknown;
+}
+//# sourceMappingURL=inputs.d.ts.map

package/dist/inputs.d.ts.map

@@ -0,0 +1 @@
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