@kgdiff/formats 0.0.0-stage → 0.1.0

package/dist/xml.js

@@ -0,0 +1,508 @@
+/**
+ * A small, non-validating XML 1.0 parser with namespaces and SAX-style callbacks, for RDF/XML.
+ *
+ * Supports what real RDF/XML files contain: the XML declaration, comments, processing
+ * instructions, CDATA sections, character references, the predefined entities and general
+ * entities declared in the internal DTD subset (`<!ENTITY owl "…">`, as older Protégé / OWL API
+ * versions write). External DTDs and entities are never loaded (referencing an external
+ * entity is an error), and entity expansion is capped, so a "billion laughs" document fails
+ * fast instead of exhausting memory. Linear in the input size; no recursion, so nesting depth
+ * is unlimited.
+ */
+import { lineAndColumn } from './shared.js';
+export const XML_NS = 'http://www.w3.org/XML/1998/namespace';
+const XMLNS_NS = 'http://www.w3.org/2000/xmlns/';
+/**
+ * A well-formedness (or, thrown by a handler, grammar) error at an offset of the parsed text.
+ * `parseXml` fills in the 1-based `line` before passing it on.
+ */
+export class XmlSyntaxError {
+    message;
+    offset;
+    line = 0;
+    constructor(message, offset) {
+        this.message = message;
+        this.offset = offset;
+    }
+}
+const NAME_START = 'A-Z_a-z\\u00C0-\\u00D6\\u00D8-\\u00F6\\u00F8-\\u02FF\\u0370-\\u037D\\u037F-\\u1FFF\\u200C\\u200D' +
+    '\\u2070-\\u218F\\u2C00-\\u2FEF\\u3001-\\uD7FF\\uF900-\\uFDCF\\uFDF0-\\uFFFD\\u{10000}-\\u{EFFFF}';
+const NAME_CHAR = `${NAME_START}\\-.0-9\\u00B7\\u0300-\\u036F\\u203F\\u2040`;
+const NC_NAME_SOURCE = `[${NAME_START}][${NAME_CHAR}]*`;
+/** XML namespaces `NCName` (a name without colons): rdf:ID and rdf:nodeID values. */
+export const NC_NAME = new RegExp(`^${NC_NAME_SOURCE}$`, 'u');
+/** A qualified name at a position (sticky): `local` or `prefix:local`. */
+const QNAME_AT = new RegExp(`(?:${NC_NAME_SOURCE}:)?${NC_NAME_SOURCE}`, 'uy');
+/** An XML `Name` at a position (DTD declarations may use colons freely). */
+const NAME_AT = new RegExp(`[:${NAME_START}][:${NAME_CHAR}]*`, 'uy');
+const ENTITY_NAME = new RegExp(`^[:${NAME_START}][:${NAME_CHAR}]*$`, 'u');
+const NOT_SPACE = /[^ \t\n\r]/;
+const GT = 0x3e;
+const SLASH = 0x2f;
+const BANG = 0x21;
+const QUESTION = 0x3f;
+/** Entity expansion budget: generous for real files, fatal for exponential blow-ups. */
+const MIN_EXPANSION_BUDGET = 4 * 1024 * 1024;
+const EXPANSION_FACTOR = 16;
+const PREDEFINED = {
+    lt: '<',
+    gt: '>',
+    amp: '&',
+    apos: "'",
+    quot: '"',
+};
+/**
+ * Parses an XML document, reporting elements, text, comments and processing instructions to
+ * `handler`. Line breaks are normalized to `\n` first (XML 1.0 §2.11). Throws `XmlSyntaxError`
+ * (with its line) on documents that are not namespace-well-formed, and passes on whatever
+ * the handler throws, filling in the line of handler-thrown `XmlSyntaxError`s too.
+ */
+export function parseXml(text, handler) {
+    const source = text.includes('\r') ? text.replace(/\r\n?/g, '\n') : text;
+    try {
+        new XmlParser(source, handler).parse();
+    }
+    catch (error) {
+        if (error instanceof XmlSyntaxError)
+            error.line = lineAndColumn(source, error.offset).line;
+        throw error;
+    }
+}
+export const isXmlSpace = (value) => !NOT_SPACE.test(value);
+class XmlParser {
+    text;
+    handler;
+    i = 0;
+    stack = [];
+    namespaces = new Map([['xml', XML_NS]]);
+    entities = new Map();
+    expansion = 0;
+    expansionBudget;
+    sawRoot = false;
+    sawDoctype = false;
+    constructor(text, handler) {
+        this.text = text;
+        this.handler = handler;
+        this.expansionBudget = Math.max(MIN_EXPANSION_BUDGET, EXPANSION_FACTOR * text.length);
+    }
+    parse() {
+        const { text } = this;
+        // Leading whitespace before the declaration is tolerated (strictly, it is an error).
+        const start = skipSpace(text, 0);
+        if (text.startsWith('<?xml', start) && /[ \t\n]/.test(text[start + 5] ?? '')) {
+            this.i = this.skipPast('?>', start, 'XML declaration');
+        }
+        while (this.i < text.length) {
+            const lt = text.indexOf('<', this.i);
+            const end = lt < 0 ? text.length : lt;
+            if (end > this.i)
+                this.characters(this.i, end);
+            if (lt < 0)
+                break;
+            this.i = lt;
+            const next = text.charCodeAt(lt + 1);
+            if (next === SLASH)
+                this.endTag();
+            else if (next === BANG)
+                this.markupDeclaration();
+            else if (next === QUESTION)
+                this.processingInstruction();
+            else
+                this.startTag();
+        }
+        const open = this.stack[this.stack.length - 1];
+        if (open)
+            throw new XmlSyntaxError(`Element <${open.qname}> is never closed`, open.offset);
+        if (!this.sawRoot)
+            throw new XmlSyntaxError('The document has no root element', text.length);
+    }
+    // ─── Markup ─────────────────────────────────────────────────────────────
+    startTag() {
+        const { text } = this;
+        const offset = this.i;
+        if (this.sawRoot && this.stack.length === 0) {
+            throw new XmlSyntaxError('Only one root element is allowed', offset);
+        }
+        const qname = this.qnameAt(offset + 1, 'an element name');
+        let i = offset + 1 + qname.length;
+        const raw = [];
+        let selfClosing = false;
+        for (;;) {
+            const at = skipSpace(text, i);
+            const c = text.charCodeAt(at);
+            if (c === GT) {
+                i = at + 1;
+                break;
+            }
+            if (c === SLASH && text.charCodeAt(at + 1) === GT) {
+                i = at + 2;
+                selfClosing = true;
+                break;
+            }
+            if (at >= text.length)
+                throw new XmlSyntaxError(`Unclosed tag <${qname}>`, offset);
+            if (at === i)
+                throw new XmlSyntaxError(`Expected whitespace, ">" or "/>" in <${qname}>`, at);
+            const name = this.qnameAt(at, 'an attribute name');
+            let j = skipSpace(text, at + name.length);
+            if (text[j] !== '=')
+                throw new XmlSyntaxError(`Expected "=" after attribute ${name}`, j);
+            j = skipSpace(text, j + 1);
+            const quote = text[j];
+            if (quote !== '"' && quote !== "'") {
+                throw new XmlSyntaxError(`Expected a quoted value for attribute ${name}`, j);
+            }
+            const close = text.indexOf(quote, j + 1);
+            if (close < 0)
+                throw new XmlSyntaxError(`Unterminated value of attribute ${name}`, j);
+            const value = text.slice(j + 1, close);
+            if (value.includes('<')) {
+                throw new XmlSyntaxError(`"<" is not allowed in the value of attribute ${name}`, j);
+            }
+            raw.push([name, value, at]);
+            i = close + 1;
+        }
+        this.i = i;
+        this.openElement(qname, raw, offset, selfClosing);
+    }
+    openElement(qname, raw, offset, selfClosing) {
+        const outer = this.namespaces;
+        let declarations;
+        const declared = [];
+        for (const [name, value, at] of raw) {
+            if (name !== 'xmlns' && !name.startsWith('xmlns:'))
+                continue;
+            const prefix = name === 'xmlns' ? '' : name.slice(6);
+            const uri = this.attributeValue(value, at);
+            checkNamespaceDeclaration(prefix, uri, at);
+            declarations ??= new Map(outer);
+            declarations.set(prefix, uri);
+            declared.push([prefix, uri]);
+        }
+        const scope = declarations ?? outer;
+        const element = splitName(qname, scope, offset, true);
+        const attributes = [];
+        const seen = raw.length > 1 ? new Set() : undefined;
+        for (const [name, value, at] of raw) {
+            if (seen) {
+                if (seen.has(name))
+                    throw new XmlSyntaxError(`Duplicate attribute ${name}`, at);
+                seen.add(name);
+            }
+            if (name === 'xmlns' || name.startsWith('xmlns:'))
+                continue;
+            const attribute = {
+                ...splitName(name, scope, at, false),
+                value: this.attributeValue(value, at),
+            };
+            // Two prefixes for one namespace still name the same attribute.
+            const key = `{${attribute.uri}}${attribute.local}`;
+            if (seen && attribute.prefix !== '') {
+                if (seen.has(key))
+                    throw new XmlSyntaxError(`Duplicate attribute ${key}`, at);
+                seen.add(key);
+            }
+            attributes.push(attribute);
+        }
+        this.sawRoot = true;
+        this.handler.startElement({ ...element, attributes, namespaces: declared, offset });
+        if (selfClosing)
+            this.handler.endElement(offset);
+        else {
+            this.stack.push({ qname, offset, outer });
+            this.namespaces = scope;
+        }
+    }
+    endTag() {
+        const { text } = this;
+        const offset = this.i;
+        const qname = this.qnameAt(offset + 2, 'an element name');
+        const close = skipSpace(text, offset + 2 + qname.length);
+        if (text.charCodeAt(close) !== GT)
+            throw new XmlSyntaxError(`Expected ">" after </${qname}`, close);
+        const open = this.stack.pop();
+        if (!open)
+            throw new XmlSyntaxError(`Unexpected end tag </${qname}>`, offset);
+        if (open.qname !== qname) {
+            throw new XmlSyntaxError(`Expected </${open.qname}>, found </${qname}>`, offset);
+        }
+        this.namespaces = open.outer;
+        this.i = close + 1;
+        this.handler.endElement(offset);
+    }
+    markupDeclaration() {
+        const { text } = this;
+        const offset = this.i;
+        if (text.startsWith('<!--', offset)) {
+            this.i = this.skipPast('-->', offset + 4, 'comment');
+            if (this.stack.length > 0)
+                this.handler.comment(text.slice(offset + 4, this.i - 3), offset);
+        }
+        else if (text.startsWith('<![CDATA[', offset)) {
+            if (this.stack.length === 0) {
+                throw new XmlSyntaxError('CDATA sections are only allowed inside the root element', offset);
+            }
+            const end = text.indexOf(']]>', offset + 9);
+            if (end < 0)
+                throw new XmlSyntaxError('Unterminated CDATA section', offset);
+            if (end > offset + 9)
+                this.handler.text(text.slice(offset + 9, end), offset);
+            this.i = end + 3;
+        }
+        else if (text.startsWith('<!DOCTYPE', offset)) {
+            if (this.sawRoot || this.sawDoctype) {
+                throw new XmlSyntaxError('A DOCTYPE is only allowed once, before the root element', offset);
+            }
+            this.sawDoctype = true;
+            this.i = this.doctype(offset + 9);
+        }
+        else {
+            throw new XmlSyntaxError('Unexpected "<!"', offset);
+        }
+    }
+    processingInstruction() {
+        const offset = this.i;
+        const target = this.nameAt(offset + 2, 'a processing instruction target');
+        if (target.toLowerCase() === 'xml') {
+            throw new XmlSyntaxError('The XML declaration is only allowed at the very start', offset);
+        }
+        const end = this.text.indexOf('?>', offset + 2 + target.length);
+        if (end < 0)
+            throw new XmlSyntaxError('Unterminated processing instruction', offset);
+        if (this.stack.length > 0) {
+            const data = this.text.slice(offset + 2 + target.length, end).replace(/^[ \t\n]+/, '');
+            this.handler.processingInstruction(target, data, offset);
+        }
+        this.i = end + 2;
+    }
+    characters(start, end) {
+        const raw = this.text.slice(start, end);
+        if (this.stack.length === 0) {
+            if (!isXmlSpace(raw)) {
+                throw new XmlSyntaxError(this.sawRoot ? 'Text after the root element' : 'Text before the root element', start + raw.search(NOT_SPACE));
+            }
+            return;
+        }
+        this.handler.text(raw.includes('&') ? this.resolve(raw, start, false) : raw, start);
+    }
+    // ─── DTD ────────────────────────────────────────────────────────────────
+    /** Skips `<!DOCTYPE …>`, reading entity declarations from the internal subset. */
+    doctype(start) {
+        const { text } = this;
+        let i = start;
+        for (;;) {
+            const c = text[i];
+            if (c === undefined)
+                throw new XmlSyntaxError('Unterminated DOCTYPE', start);
+            if (c === '"' || c === "'")
+                i = this.skipPast(c, i + 1, 'DOCTYPE literal');
+            else if (c === '[')
+                i = this.internalSubset(i + 1);
+            else if (c === '>')
+                return i + 1;
+            else
+                i++;
+        }
+    }
+    internalSubset(start) {
+        const { text } = this;
+        let i = start;
+        for (;;) {
+            i = skipSpace(text, i);
+            if (i >= text.length)
+                throw new XmlSyntaxError('Unterminated DTD internal subset', start);
+            if (text[i] === ']')
+                return i + 1;
+            if (text.startsWith('<!--', i))
+                i = this.skipPast('-->', i + 4, 'comment');
+            else if (text.startsWith('<?', i))
+                i = this.skipPast('?>', i + 2, 'processing instruction');
+            else if (text.startsWith('<!ENTITY', i))
+                i = this.entityDeclaration(i);
+            else if (text.startsWith('<!', i))
+                i = this.skipDeclaration(i);
+            else if (text[i] === '%')
+                i = this.skipPast(';', i + 1, 'parameter entity reference');
+            else
+                throw new XmlSyntaxError('Unexpected content in the DTD internal subset', i);
+        }
+    }
+    /** `<!ENTITY name "value">`, `<!ENTITY name SYSTEM "uri">`, `<!ENTITY % name …>`. */
+    entityDeclaration(start) {
+        const { text } = this;
+        let i = skipSpace(text, start + 8);
+        const parameter = text[i] === '%';
+        if (parameter)
+            i = skipSpace(text, i + 1);
+        const name = this.nameAt(i, 'an entity name');
+        i = skipSpace(text, i + name.length);
+        const quote = text[i];
+        // Without a quoted value it is SYSTEM / PUBLIC: an external entity, never fetched.
+        let entity = { value: '', external: true };
+        if (quote === '"' || quote === "'") {
+            const close = text.indexOf(quote, i + 1);
+            if (close < 0)
+                throw new XmlSyntaxError(`Unterminated value of entity ${name}`, i);
+            entity = { value: this.characterReferences(text.slice(i + 1, close), i), external: false };
+        }
+        // The first declaration of an entity is binding (XML 1.0 §4.2).
+        if (!parameter && !this.entities.has(name))
+            this.entities.set(name, entity);
+        return this.skipDeclaration(start);
+    }
+    /** Skips a markup declaration up to its closing `>`, honouring quoted literals. */
+    skipDeclaration(start) {
+        const { text } = this;
+        let i = start + 2;
+        for (;;) {
+            const c = text[i];
+            if (c === undefined)
+                throw new XmlSyntaxError('Unterminated DTD declaration', start);
+            if (c === '"' || c === "'")
+                i = this.skipPast(c, i + 1, 'DTD literal');
+            else if (c === '>')
+                return i + 1;
+            else
+                i++;
+        }
+    }
+    // ─── References ─────────────────────────────────────────────────────────
+    /** Attribute value normalization (XML 1.0 §3.3.3, CDATA attributes). */
+    attributeValue(raw, offset) {
+        const spaced = /[\t\n]/.test(raw) ? raw.replace(/[\t\n]/g, ' ') : raw;
+        return spaced.includes('&') ? this.resolve(spaced, offset, true) : spaced;
+    }
+    /** Resolves character and entity references in content or an attribute value. */
+    resolve(raw, offset, inAttribute) {
+        let out = '';
+        let last = 0;
+        for (let amp = raw.indexOf('&'); amp >= 0; amp = raw.indexOf('&', last)) {
+            const semicolon = raw.indexOf(';', amp + 1);
+            if (semicolon < 0)
+                throw new XmlSyntaxError('Unterminated "&" reference', offset + amp);
+            const name = raw.slice(amp + 1, semicolon);
+            out += raw.slice(last, amp);
+            if (name.startsWith('#'))
+                out += characterReference(name, offset + amp);
+            else {
+                const replacement = getPredefined(name) ?? this.entity(name, offset + amp, inAttribute);
+                out += replacement;
+            }
+            last = semicolon + 1;
+        }
+        return out + raw.slice(last);
+    }
+    entity(name, offset, inAttribute) {
+        if (!ENTITY_NAME.test(name))
+            throw new XmlSyntaxError(`Invalid reference "&${name};"`, offset);
+        const entity = this.entities.get(name);
+        if (!entity)
+            throw new XmlSyntaxError(`Undeclared entity "&${name};"`, offset);
+        if (entity.external) {
+            throw new XmlSyntaxError(`External entity "&${name};" is not loaded (external resources are never fetched)`, offset);
+        }
+        if (entity.expanded === undefined) {
+            if (entity.expanding)
+                throw new XmlSyntaxError(`Entity "&${name};" refers to itself`, offset);
+            entity.expanding = true;
+            // Memoized without attribute normalization, which applies per use.
+            entity.expanded = entity.value.includes('&')
+                ? this.resolve(entity.value, offset, false)
+                : entity.value;
+            entity.expanding = false;
+        }
+        const value = entity.expanded;
+        if (value.includes('<')) {
+            throw new XmlSyntaxError(`Entity "&${name};" contains markup, which is not supported`, offset);
+        }
+        this.expansion += value.length;
+        if (this.expansion > this.expansionBudget) {
+            throw new XmlSyntaxError('Entity expansion exceeds the size limit', offset);
+        }
+        return inAttribute && /[\t\n]/.test(value) ? value.replace(/[\t\n]/g, ' ') : value;
+    }
+    /** Character references in an entity value are resolved when it is declared (§4.5). */
+    characterReferences(value, offset) {
+        return value.includes('&#')
+            ? value.replace(/&(#[^;]*);/g, (_match, name) => characterReference(name, offset))
+            : value;
+    }
+    // ─── Scanning helpers ───────────────────────────────────────────────────
+    qnameAt(at, what) {
+        QNAME_AT.lastIndex = at;
+        const match = QNAME_AT.exec(this.text);
+        if (!match)
+            throw new XmlSyntaxError(`Expected ${what}`, at);
+        return match[0];
+    }
+    nameAt(at, what) {
+        NAME_AT.lastIndex = at;
+        const match = NAME_AT.exec(this.text);
+        if (!match)
+            throw new XmlSyntaxError(`Expected ${what}`, at);
+        return match[0];
+    }
+    /** Index just past the next `terminator` at or after `from`. */
+    skipPast(terminator, from, what) {
+        const end = this.text.indexOf(terminator, from);
+        if (end < 0)
+            throw new XmlSyntaxError(`Unterminated ${what}`, from);
+        return end + terminator.length;
+    }
+}
+function skipSpace(text, from) {
+    let i = from;
+    for (;;) {
+        const c = text.charCodeAt(i);
+        if (c === 0x20 || c === 0x0a || c === 0x09 || c === 0x0d)
+            i++;
+        else
+            return i;
+    }
+}
+function getPredefined(name) {
+    return Object.hasOwn(PREDEFINED, name) ? PREDEFINED[name] : undefined;
+}
+const isXmlChar = (c) => c === 0x9 ||
+    c === 0xa ||
+    c === 0xd ||
+    (c >= 0x20 && c <= 0xd7ff) ||
+    (c >= 0xe000 && c <= 0xfffd) ||
+    (c >= 0x10000 && c <= 0x10ffff);
+/** `#65` / `#x41` → `A`. */
+function characterReference(name, offset) {
+    const hex = name[1] === 'x';
+    const digits = name.slice(hex ? 2 : 1);
+    const code = (hex ? /^[0-9a-fA-F]+$/ : /^[0-9]+$/).test(digits)
+        ? Number.parseInt(digits, hex ? 16 : 10)
+        : Number.NaN;
+    if (!isXmlChar(code)) {
+        throw new XmlSyntaxError(`Invalid character reference "&${name};"`, offset);
+    }
+    return String.fromCodePoint(code);
+}
+function checkNamespaceDeclaration(prefix, uri, offset) {
+    const fail = (message) => new XmlSyntaxError(message, offset);
+    if (prefix === 'xmlns')
+        throw fail('The xmlns prefix cannot be declared');
+    if (prefix === 'xml' && uri !== XML_NS)
+        throw fail('The xml prefix cannot be rebound');
+    if (prefix !== 'xml' && uri === XML_NS)
+        throw fail(`Prefix "${prefix}" cannot be bound to the XML namespace`);
+    if (uri === XMLNS_NS)
+        throw fail('The xmlns namespace cannot be bound');
+    if (prefix !== '' && uri === '')
+        throw fail(`Prefix "${prefix}" cannot be undeclared`);
+}
+/** Resolves a qualified name; unprefixed attributes are in no namespace. */
+function splitName(qname, scope, offset, isElement) {
+    const colon = qname.indexOf(':');
+    if (colon < 0)
+        return { prefix: '', local: qname, uri: isElement ? (scope.get('') ?? '') : '' };
+    const prefix = qname.slice(0, colon);
+    const uri = scope.get(prefix);
+    if (uri === undefined)
+        throw new XmlSyntaxError(`Undeclared namespace prefix "${prefix}"`, offset);
+    return { prefix, local: qname.slice(colon + 1), uri };
+}
+//# sourceMappingURL=xml.js.map

package/dist/xml.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,58 @@
 {
   "name": "@kgdiff/formats",
-  "version": "0.0.0-stage",
-  "stub": true,
-  "description": "Temporary package placeholder for staged publishing"
+  "version": "0.1.0",
+  "description": "Parsers that turn RDF (Turtle, N-Triples, N-Quads, TriG, RDF/XML, JSON-LD), OBO and common JSON graph shapes into kgdiff graphs.",
+  "keywords": [
+    "kgdiff",
+    "rdf",
+    "turtle",
+    "rdf-xml",
+    "owl",
+    "json-ld",
+    "obo",
+    "parser"
+  ],
+  "homepage": "https://github.com/iiwish/kgdiff/tree/main/packages/formats#readme",
+  "bugs": {
+    "url": "https://github.com/iiwish/kgdiff/issues"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/iiwish/kgdiff.git",
+    "directory": "packages/formats"
+  },
+  "license": "MIT",
+  "author": "iiwish",
+  "type": "module",
+  "sideEffects": false,
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "default": "./dist/index.js"
+    }
+  },
+  "files": [
+    "dist",
+    "src",
+    "!src/**/*.test.ts"
+  ],
+  "engines": {
+    "node": ">=22"
+  },
+  "publishConfig": {
+    "access": "public",
+    "registry": "https://registry.npmjs.org/"
+  },
+  "dependencies": {
+    "@kgdiff/core": "0.1.0",
+    "n3": "2.13.12"
+  },
+  "devDependencies": {
+    "@types/n3": "1.26.6"
+  },
+  "scripts": {
+    "build": "tsc -p tsconfig.build.json",
+    "typecheck": "tsc -p tsconfig.json",
+    "test": "vitest run"
+  }
 }