@kgdiff/formats 0.0.0-stage → 0.2.0

package/dist/obo.js.map

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

@@ -0,0 +1,49 @@
+export declare const RDF_NS = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
+export declare const RDFS_NS = "http://www.w3.org/2000/01/rdf-schema#";
+export declare const OWL_NS = "http://www.w3.org/2002/07/owl#";
+export declare const XSD_NS = "http://www.w3.org/2001/XMLSchema#";
+export declare const SKOS_NS = "http://www.w3.org/2004/02/skos/core#";
+export declare const OBO_IN_OWL_NS = "http://www.geneontology.org/formats/oboInOwl#";
+export declare const OBO_PURL = "http://purl.obolibrary.org/obo/";
+/** Prefixes every parser knows without a declaration. */
+export declare const WELL_KNOWN_PREFIXES: Readonly<Record<string, string>>;
+/** `http://purl.obolibrary.org/obo/GO_0008150` → `GO:0008150`; `undefined` for other IRIs. */
+export declare function oboCurie(iri: string): string | undefined;
+/**
+ * Stable node id for an IRI: OBO PURLs become CURIEs, every other IRI stays whole so the same
+ * resource gets the same id whatever prefixes a file declares.
+ */
+export declare function nodeIdForIri(iri: string): string;
+/** Where a prefix came from. */
+export type PrefixSource = 'user' | 'well-known' | 'declared';
+/**
+ * Compiled prefix map. Compaction picks the longest matching namespace; when several prefixes
+ * share a namespace, explicit options beat well-known names, which beat file declarations,
+ * so `rdfs:` stays `rdfs:` even in a file that declares it under another name.
+ */
+export declare class PrefixTable {
+    /** Name → namespace, as reported in `ParseResult.prefixes` (sorted by name). */
+    readonly record: Readonly<Record<string, string>>;
+    private readonly entries;
+    /** Name → namespace for lookups (a Map: prefix names like `constructor` are ordinary). */
+    private readonly namespaces;
+    private readonly cache;
+    constructor(layers: readonly (readonly [PrefixSource, Readonly<Record<string, string>>])[]);
+    /** Compact form of `iri` (cached), or `iri` itself when no prefix applies. */
+    compact(iri: string): string;
+    /**
+     * Expands a CURIE with a known prefix (or an OBO-style `GO:0008150`) to a full IRI.
+     * Strings that already look like absolute IRIs are returned unchanged.
+     */
+    expand(value: string): string;
+    private compute;
+}
+/** Table for `compactIri`: well-known prefixes overlaid with `prefixes` (cached per object). */
+export declare function tableFor(prefixes?: Readonly<Record<string, string>>): PrefixTable;
+/**
+ * Readable form of a predicate or id, mirroring core's `predicateLabel`: the local part after
+ * the last `#`, `/` or `:`, with `_` turned into spaces. Opaque local parts (digits only) keep
+ * the whole compact form: `BFO:0000050` stays `BFO:0000050`.
+ */
+export declare function readableName(value: string): string;
+//# sourceMappingURL=prefixes.d.ts.map

package/dist/prefixes.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"prefixes.d.ts","sourceRoot":"","sources":["../src/prefixes.ts"],"names":[],"mappings":"AAMA,eAAO,MAAM,MAAM,gDAAgD,CAAC;AACpE,eAAO,MAAM,OAAO,0CAA0C,CAAC;AAC/D,eAAO,MAAM,MAAM,mCAAmC,CAAC;AACvD,eAAO,MAAM,MAAM,sCAAsC,CAAC;AAC1D,eAAO,MAAM,OAAO,yCAAyC,CAAC;AAC9D,eAAO,MAAM,aAAa,kDAAkD,CAAC;AAC7E,eAAO,MAAM,QAAQ,oCAAoC,CAAC;AAE1D,yDAAyD;AACzD,eAAO,MAAM,mBAAmB,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAa/D,CAAC;AAUH,8FAA8F;AAC9F,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAIxD;AAED;;;GAGG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAEhD;AAED,gCAAgC;AAChC,MAAM,MAAM,YAAY,GAAG,MAAM,GAAG,YAAY,GAAG,UAAU,CAAC;AAsB9D;;;;GAIG;AACH,qBAAa,WAAW;IACtB,gFAAgF;IAChF,QAAQ,CAAC,MAAM,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC;IAClD,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAmB;IAC3C,0FAA0F;IAC1F,OAAO,CAAC,QAAQ,CAAC,UAAU,CAA6B;IACxD,OAAO,CAAC,QAAQ,CAAC,KAAK,CAA6B;IAEnD,YAAY,MAAM,EAAE,SAAS,CAAC,SAAS,CAAC,YAAY,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,EAkCzF;IAED,8EAA8E;IAC9E,OAAO,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAO3B;IAED;;;OAGG;IACH,MAAM,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAU5B;IAED,OAAO,CAAC,OAAO;CAchB;AAKD,gGAAgG;AAChG,wBAAgB,QAAQ,CAAC,QAAQ,CAAC,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,GAAG,WAAW,CAWjF;AAED;;;;GAIG;AACH,wBAAgB,YAAY,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAKlD"}

package/dist/prefixes.js

@@ -0,0 +1,177 @@
+/**
+ * IRI compaction: well-known prefixes, declared prefixes and the OBO PURL rule
+ * (`http://purl.obolibrary.org/obo/GO_0008150` → `GO:0008150`).
+ */
+import { compareStrings, getOwn, setOwn } from './shared.js';
+export const RDF_NS = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
+export const RDFS_NS = 'http://www.w3.org/2000/01/rdf-schema#';
+export const OWL_NS = 'http://www.w3.org/2002/07/owl#';
+export const XSD_NS = 'http://www.w3.org/2001/XMLSchema#';
+export const SKOS_NS = 'http://www.w3.org/2004/02/skos/core#';
+export const OBO_IN_OWL_NS = 'http://www.geneontology.org/formats/oboInOwl#';
+export const OBO_PURL = 'http://purl.obolibrary.org/obo/';
+/** Prefixes every parser knows without a declaration. */
+export const WELL_KNOWN_PREFIXES = Object.freeze({
+    dc: 'http://purl.org/dc/elements/1.1/',
+    dcterms: 'http://purl.org/dc/terms/',
+    foaf: 'http://xmlns.com/foaf/0.1/',
+    obo: OBO_PURL,
+    oboInOwl: OBO_IN_OWL_NS,
+    owl: OWL_NS,
+    prov: 'http://www.w3.org/ns/prov#',
+    rdf: RDF_NS,
+    rdfs: RDFS_NS,
+    schema: 'https://schema.org/',
+    skos: SKOS_NS,
+    xsd: XSD_NS,
+});
+/** Namespaces that compact to a well-known prefix besides its canonical namespace. */
+const WELL_KNOWN_VARIANTS = [
+    ['schema', 'http://schema.org/'],
+];
+/** OBO Foundry id spaces: a letter followed by letters / digits, then `_` and a local id. */
+const OBO_LOCAL_ID = /^([A-Za-z][A-Za-z0-9]*)_([^\s/#?]+)$/;
+/** `http://purl.obolibrary.org/obo/GO_0008150` → `GO:0008150`; `undefined` for other IRIs. */
+export function oboCurie(iri) {
+    if (!iri.startsWith(OBO_PURL))
+        return undefined;
+    const match = OBO_LOCAL_ID.exec(iri.slice(OBO_PURL.length));
+    return match ? `${match[1]}:${match[2]}` : undefined;
+}
+/**
+ * Stable node id for an IRI: OBO PURLs become CURIEs, every other IRI stays whole so the same
+ * resource gets the same id whatever prefixes a file declares.
+ */
+export function nodeIdForIri(iri) {
+    return oboCurie(iri) ?? iri;
+}
+/** Preference when several names share one namespace (lower wins). */
+const SOURCE_PREFERENCE = {
+    user: 0,
+    'well-known': 1,
+    declared: 2,
+};
+/** Override order per name: well-known, then declared, then user. */
+const SOURCE_OVERRIDE = {
+    'well-known': 0,
+    declared: 1,
+    user: 2,
+};
+/**
+ * Compiled prefix map. Compaction picks the longest matching namespace; when several prefixes
+ * share a namespace, explicit options beat well-known names, which beat file declarations,
+ * so `rdfs:` stays `rdfs:` even in a file that declares it under another name.
+ */
+export class PrefixTable {
+    /** Name → namespace, as reported in `ParseResult.prefixes` (sorted by name). */
+    record;
+    entries;
+    /** Name → namespace for lookups (a Map: prefix names like `constructor` are ordinary). */
+    namespaces = new Map();
+    cache = new Map();
+    constructor(layers) {
+        // Name → namespace: declared names override well-known ones, user names override both.
+        const byName = new Map();
+        const ordered = [...layers].sort(([a], [b]) => SOURCE_OVERRIDE[a] - SOURCE_OVERRIDE[b]);
+        for (const [source, prefixes] of ordered) {
+            const preference = SOURCE_PREFERENCE[source];
+            for (const [prefix, namespace] of Object.entries(prefixes)) {
+                if (namespace)
+                    byName.set(prefix, { prefix, namespace, preference });
+            }
+        }
+        const record = {};
+        for (const name of [...byName.keys()].sort(compareStrings)) {
+            const entry = byName.get(name);
+            if (!entry)
+                continue;
+            setOwn(record, name, entry.namespace);
+            this.namespaces.set(name, entry.namespace);
+        }
+        this.record = record;
+        const entries = [...byName.values()];
+        for (const [prefix, namespace] of WELL_KNOWN_VARIANTS) {
+            if (byName.get(prefix)?.namespace === getOwn(WELL_KNOWN_PREFIXES, prefix)) {
+                entries.push({ prefix, namespace, preference: SOURCE_PREFERENCE['well-known'] });
+            }
+        }
+        // Longest namespace first; for equal namespaces the preferred name first.
+        this.entries = entries.sort((a, b) => b.namespace.length - a.namespace.length ||
+            compareStrings(a.namespace, b.namespace) ||
+            a.preference - b.preference ||
+            a.prefix.length - b.prefix.length ||
+            compareStrings(a.prefix, b.prefix));
+    }
+    /** Compact form of `iri` (cached), or `iri` itself when no prefix applies. */
+    compact(iri) {
+        let compact = this.cache.get(iri);
+        if (compact === undefined) {
+            compact = this.compute(iri);
+            this.cache.set(iri, compact);
+        }
+        return compact;
+    }
+    /**
+     * Expands a CURIE with a known prefix (or an OBO-style `GO:0008150`) to a full IRI.
+     * Strings that already look like absolute IRIs are returned unchanged.
+     */
+    expand(value) {
+        if (/^[a-z][a-z0-9+.-]*:\/\//i.test(value) || value.startsWith('urn:'))
+            return value;
+        const colon = value.indexOf(':');
+        if (colon < 0)
+            return value;
+        const namespace = this.namespaces.get(value.slice(0, colon));
+        if (namespace !== undefined)
+            return namespace + value.slice(colon + 1);
+        const prefix = value.slice(0, colon);
+        // Undeclared upper-case id spaces (`IAO:0100001`) follow the OBO PURL convention.
+        if (/^[A-Z][A-Za-z0-9]*$/.test(prefix))
+            return `${OBO_PURL}${prefix}_${value.slice(colon + 1)}`;
+        return value;
+    }
+    compute(iri) {
+        const obo = oboCurie(iri);
+        if (obo !== undefined) {
+            const idSpace = obo.slice(0, obo.indexOf(':'));
+            const declared = this.namespaces.get(idSpace);
+            // Respect a file that binds the id space to something else.
+            if (declared === undefined || declared === `${OBO_PURL}${idSpace}_`)
+                return obo;
+        }
+        for (const entry of this.entries) {
+            if (iri.startsWith(entry.namespace))
+                return `${entry.prefix}:${iri.slice(entry.namespace.length)}`;
+        }
+        return iri;
+    }
+}
+const defaultTable = new PrefixTable([['well-known', WELL_KNOWN_PREFIXES]]);
+const tables = new WeakMap();
+/** Table for `compactIri`: well-known prefixes overlaid with `prefixes` (cached per object). */
+export function tableFor(prefixes) {
+    if (!prefixes)
+        return defaultTable;
+    let table = tables.get(prefixes);
+    if (!table) {
+        table = new PrefixTable([
+            ['well-known', WELL_KNOWN_PREFIXES],
+            ['user', prefixes],
+        ]);
+        tables.set(prefixes, table);
+    }
+    return table;
+}
+/**
+ * Readable form of a predicate or id, mirroring core's `predicateLabel`: the local part after
+ * the last `#`, `/` or `:`, with `_` turned into spaces. Opaque local parts (digits only) keep
+ * the whole compact form: `BFO:0000050` stays `BFO:0000050`.
+ */
+export function readableName(value) {
+    const cut = Math.max(value.lastIndexOf('#'), value.lastIndexOf('/'), value.lastIndexOf(':'));
+    const local = value.slice(cut + 1);
+    if (local === '' || /^\d+$/.test(local))
+        return value;
+    return local.replace(/_/g, ' ');
+}
+//# sourceMappingURL=prefixes.js.map

package/dist/prefixes.js.map

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package/dist/rdf.d.ts

@@ -0,0 +1,46 @@
+/**
+ * RDF → `GraphInput`, following docs/architecture.md §"Formats: mapping conventions". Every
+ * RDF syntax produces quads first — Turtle, N-Triples, N-Quads and TriG through n3
+ * (`readN3`), RDF/XML through `rdfxml.ts`, JSON-LD through `jsonld.ts` — and `mapRdf` maps
+ * them all the same way, so one graph diffs identically in any syntax.
+ *
+ *  - Triples are a set: repeated triples count once, whatever the syntax.
+ *  - Node ids: OBO PURLs become CURIEs (`GO:0008150`), other IRIs stay whole; blank nodes get
+ *    content-hashed ids `_:b<hash>` (hash of their sorted outgoing triples, recursive,
+ *    cycle-safe), so ids are stable across files and parser runs.
+ *  - Labels: label predicates with language preference; the other label values become aliases.
+ *    Without a label a named node is labelled with its compact IRI.
+ *  - Identities (predicates, attr keys, types) are compacted with well-known and user prefixes
+ *    only by default (`RdfOptions.compactWith`), so they do not depend on file declarations.
+ *  - Literal-valued properties → attrs keyed by compact predicate (numbers / booleans typed,
+ *    language-tagged text as `"text@lang"`, multi-values as sorted arrays).
+ *  - IRI-valued properties → edges (compact predicate, readable label).
+ *  - `rdf:type` → types; `owl:deprecated` → deprecated; `IAO:0100001` → replacedBy.
+ *  - OWL: `C ⊑ ∃R.D` and `C ≡ A ⊓ ∃R.D` become edges; `owl:Ontology` becomes `meta`.
+ *  - Lists: literal lists become attr arrays; lists of resources become (unordered) edges.
+ *  - Statement annotations (`owl:Axiom`, `rdf:Statement`, RDF 1.2 `rdf:reifies`) are folded
+ *    into the attrs of the annotated edge (or of the node, for literal-valued statements),
+ *    unless `RdfOptions.foldAnnotations` is false.
+ */
+import type { GraphInput } from '@kgdiff/core';
+import type { Quad } from 'n3';
+import type { RdfOptions } from './index.js';
+import { type Warnings } from './shared.js';
+/** RDF syntaxes read by n3. */
+export type N3Format = 'turtle' | 'ntriples' | 'nquads' | 'trig';
+/** The quads of one RDF document and the prefixes it declares (for display only). */
+export interface RdfDocument {
+    readonly quads: readonly Quad[];
+    readonly prefixes: Readonly<Record<string, string>>;
+}
+export interface RdfParseOutput {
+    readonly graph: GraphInput;
+    readonly prefixes: Readonly<Record<string, string>>;
+    /** Labels the file gives the properties it uses, by compact predicate. */
+    readonly predicateLabels: Readonly<Record<string, string>>;
+}
+/** Reads Turtle-family text with n3. Throws `KgdiffError('invalid-input')` with the line on syntax errors. */
+export declare function readN3(text: string, format: N3Format, baseIRI: string | undefined): RdfDocument;
+/** Maps the quads of an RDF document (any syntax) to a `GraphInput`. */
+export declare function mapRdf(document: RdfDocument, options: RdfOptions | undefined, warnings: Warnings): RdfParseOutput;
+//# sourceMappingURL=rdf.d.ts.map

package/dist/rdf.d.ts.map

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