@oml/cli 0.7.0

package/out/backend/reasoned-output.js

@@ -0,0 +1,568 @@
+// Copyright (c) 2026 Modelware. All rights reserved.
+import { isOntology, isVocabularyBundle, } from '@oml/language';
+import { createOwlOntologyQuads, OWL_ONTOLOGY_IRI, Oml2OwlMapper, owlOntologyPrefixes, } from '@oml/owl';
+import { checkConsistency } from '@oml/reasoner';
+import { URI } from 'langium';
+import { Parser, Writer } from 'n3';
+import * as fs from 'node:fs/promises';
+import * as path from 'node:path';
+import { VocabularyBundleClosureBuilder } from '../commands/closure.js';
+const SUPPORTED_RDF_FORMATS = new Map([
+    ['ttl', undefined],
+    ['trig', 'application/trig'],
+    ['nt', 'N-Triples'],
+    ['nq', 'N-Quads'],
+    ['n3', 'application/n3']
+]);
+const OWL_IMPORTS_IRI = 'http://www.w3.org/2002/07/owl#imports';
+const RDF_TYPE_IRI = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type';
+const SKIPPED_BUILT_IN_ONTOLOGIES = new Set([
+    'http://www.w3.org/2001/XMLSchema',
+    'http://www.w3.org/1999/02/22-rdf-syntax-ns',
+    'http://www.w3.org/2000/01/rdf-schema',
+    'http://www.w3.org/2002/07/owl',
+    'http://www.w3.org/2003/11/swrl',
+    'http://www.w3.org/2003/11/swrlb',
+]);
+export class OntologyInconsistencyError extends Error {
+    constructor(ontologyIri, result) {
+        super(formatConsistencyError(ontologyIri, result));
+        this.name = 'OntologyInconsistencyError';
+        this.ontologyIri = ontologyIri;
+        this.result = result;
+    }
+}
+export async function buildWorkspaceDocuments(services, workspaceRoot, validate = true) {
+    const documents = services.shared.workspace.LangiumDocuments;
+    const builder = services.shared.workspace.DocumentBuilder;
+    const omlUris = new Set();
+    for (const filePath of await findOmlFiles(workspaceRoot)) {
+        omlUris.add(URI.file(filePath).toString());
+    }
+    const docs = await Promise.all([...omlUris].sort().map((uri) => documents.getOrCreateDocument(URI.parse(uri))));
+    await builder.build(docs, { validation: validate });
+    return docs;
+}
+async function findOmlFiles(root) {
+    const entries = await fs.readdir(root, { withFileTypes: true });
+    const results = [];
+    for (const entry of entries) {
+        const fullPath = path.join(root, entry.name);
+        if (entry.isDirectory()) {
+            if (entry.name === 'node_modules' || entry.name.startsWith('.')) {
+                continue;
+            }
+            results.push(...await findOmlFiles(fullPath));
+            continue;
+        }
+        if (entry.isFile() && entry.name.toLowerCase().endsWith('.oml')) {
+            results.push(fullPath);
+        }
+    }
+    return results;
+}
+export async function writeCompiledWorkspace(services, workspaceRoot, outputRoot, format, pretty) {
+    const documents = await buildWorkspaceDocuments(services, workspaceRoot, true);
+    const entries = collectWorkspaceOntologyEntries(documents, outputRoot, format);
+    const ontologyByNamespace = new Map();
+    for (const entry of entries) {
+        ontologyByNamespace.set(entry.ontologyIri, entry.ontology);
+    }
+    const mapper = new Oml2OwlMapper();
+    const closureBuilder = new VocabularyBundleClosureBuilder(ontologyByNamespace);
+    const omlOntologyOutputFile = path.join(outputRoot, resolveOutputPathFromOntologyIriString(OWL_ONTOLOGY_IRI, format));
+    await fs.mkdir(path.dirname(omlOntologyOutputFile), { recursive: true });
+    await fs.writeFile(omlOntologyOutputFile, await serializeQuadsWithPrefixes(createOwlOntologyQuads(), owlOntologyPrefixes(), format, pretty), 'utf-8');
+    for (const entry of entries) {
+        const mappedQuads = entry.ontology ? mapper.toQuads(entry.ontology) : [];
+        const closureQuads = isVocabularyBundle(entry.ontology)
+            ? closureBuilder.buildClosureQuads(entry.ontology)
+            : [];
+        const quads = filterBuiltInImportQuads([...mappedQuads, ...closureQuads]);
+        await fs.mkdir(path.dirname(entry.compiledPath), { recursive: true });
+        await fs.writeFile(entry.compiledPath, await serializeQuads(quads, entry.ontology, format, pretty), 'utf-8');
+    }
+    return entries;
+}
+export function collectWorkspaceOntologyEntries(documents, outputRoot, format) {
+    const ontologies = documents
+        .map((document) => ({
+        modelUri: document.uri.toString(),
+        root: document.parseResult.value,
+    }))
+        .filter((entry) => isOntology(entry.root));
+    return ontologies
+        .map(({ modelUri, root }) => {
+        const ontologyIri = normalizeNamespace(root.namespace)?.replace(/[\/#]+$/, '');
+        if (!ontologyIri || SKIPPED_BUILT_IN_ONTOLOGIES.has(ontologyIri)) {
+            return undefined;
+        }
+        const compiledPath = path.join(outputRoot, resolveOutputPathFromOntologyIriString(ontologyIri, format));
+        return {
+            modelUri,
+            ontology: root,
+            ontologyIri,
+            imports: extractImportedModelUris(root),
+            compiledPath,
+            entailmentPath: compiledPath.replace(new RegExp(`\\.${format}$`, 'i'), `__entailments.${format}`),
+        };
+    })
+        .filter((entry) => Boolean(entry));
+}
+export async function reasonWorkspaceOntologies(entries, options) {
+    const orderedEntries = topologicallyOrder(entries);
+    let entailmentsWritten = 0;
+    for (const entry of orderedEntries) {
+        const result = await checkConsistency({
+            input: entry.compiledPath,
+            inputRoot: options.outputRoot,
+            explanations: options.explanations,
+            uniqueNamesAssumption: options.uniqueNamesAssumption,
+            checkOnly: options.checkOnly,
+            profile: options.profile,
+            timeout: 120000,
+        });
+        if (!result.consistent) {
+            throw new OntologyInconsistencyError(entry.ontologyIri, result);
+        }
+        if (!options.checkOnly) {
+            // await normalizeEntailmentOutput(entry, entailmentKeysByModelUri, options.format, options.pretty);
+            entailmentsWritten += 1;
+            continue;
+        }
+    }
+    return {
+        ontologiesReasoned: orderedEntries.length,
+        entailmentsWritten: options.checkOnly ? 0 : entailmentsWritten,
+    };
+}
+export async function loadPreparedDatasetFromOutput(workspaceRoot, outputRoot, format) {
+    const aliasBySuffix = await buildOmlAliasIndex(workspaceRoot);
+    const assertedFiles = await findRdfFiles(outputRoot, format);
+    const rawModels = [];
+    const modelUriByOntologyIri = new Map();
+    for (const assertedFile of assertedFiles) {
+        if (assertedFile.endsWith(`__entailments.${format}`)) {
+            continue;
+        }
+        const assertedQuads = await readRequiredRdfQuads(assertedFile);
+        const ontologyIri = ontologyIriFromQuads(assertedQuads);
+        if (!ontologyIri) {
+            continue;
+        }
+        const canonicalModelUri = ontologyIri;
+        modelUriByOntologyIri.set(ontologyIri, canonicalModelUri);
+        const relativeStem = relativeOntologyStem(outputRoot, assertedFile, format);
+        const aliases = [canonicalModelUri, ...resolveAliasesForStem(relativeStem, aliasBySuffix)];
+        const entailedQuads = await readOptionalRdfQuads(assertedFile.replace(new RegExp(`\\.${format}$`, 'i'), `__entailments.${format}`));
+        rawModels.push({
+            modelUri: canonicalModelUri,
+            aliases,
+            importedOntologyIris: importedOntologyIris(assertedQuads),
+            assertedQuads,
+            entailedQuads,
+        });
+    }
+    return rawModels.map((model) => ({
+        modelUri: model.modelUri,
+        aliases: model.aliases,
+        imports: model.importedOntologyIris
+            .map((ontologyIri) => modelUriByOntologyIri.get(ontologyIri) ?? ontologyIri)
+            .filter((uri) => uri !== model.modelUri),
+        assertedQuads: model.assertedQuads,
+        entailedQuads: model.entailedQuads,
+        validationWarnings: [],
+    }));
+}
+export function normalizeFormatExtension(value) {
+    const normalized = (value ?? 'ttl').trim().toLowerCase().replace(/^\./, '');
+    if (!SUPPORTED_RDF_FORMATS.has(normalized)) {
+        throw new Error(`Unsupported RDF format '${value ?? ''}'. Supported formats: ttl, trig, nt, nq, n3.`);
+    }
+    return normalized;
+}
+function extractImportedModelUris(ontology) {
+    const imports = (ontology.ownedImports ?? [])
+        .map((ownedImport) => ownedImport.imported?.ref?.$document?.uri?.toString())
+        .filter((modelUri) => Boolean(modelUri));
+    return [...new Set(imports)].sort();
+}
+function topologicallyOrder(entries) {
+    const entryByModelUri = new Map(entries.map((entry) => [entry.modelUri, entry]));
+    const ordered = [];
+    const visiting = new Set();
+    const visited = new Set();
+    const visit = (modelUri) => {
+        if (visited.has(modelUri) || visiting.has(modelUri)) {
+            return;
+        }
+        const entry = entryByModelUri.get(modelUri);
+        if (!entry) {
+            return;
+        }
+        visiting.add(modelUri);
+        for (const importedModelUri of entry.imports) {
+            visit(importedModelUri);
+        }
+        visiting.delete(modelUri);
+        visited.add(modelUri);
+        ordered.push(entry);
+    };
+    for (const entry of [...entries].sort((left, right) => left.ontologyIri.localeCompare(right.ontologyIri))) {
+        visit(entry.modelUri);
+    }
+    return ordered;
+}
+function formatConsistencyError(ontologyIri, result) {
+    return JSON.stringify({
+        ontologyIri,
+        ...result,
+    }, null, 2);
+}
+async function readRequiredRdfQuads(filePath) {
+    const source = await fs.readFile(filePath, 'utf-8');
+    const parser = new Parser({ format: formatFromExtension(path.extname(filePath)) });
+    return parser.parse(source);
+}
+// async function normalizeEntailmentOutput(
+//     entry: WorkspaceOntologyEntry,
+//     entailmentKeysByModelUri: Map<string, Set<string>>,
+//     format: string,
+//     pretty: boolean
+// ): Promise<void> {
+//     const entailedQuads = await readOptionalRdfQuads(entry.entailmentPath);
+//     const inheritedKeys = new Set<string>();
+//     for (const importedModelUri of entry.imports) {
+//         const inherited = entailmentKeysByModelUri.get(importedModelUri);
+//         if (!inherited) {
+//             continue;
+//         }
+//         for (const key of inherited) {
+//             inheritedKeys.add(key);
+//         }
+//     }
+//     const emittedKeys = new Set<string>();
+//     const normalizedEntailments = entailedQuads.filter((quad) => {
+//         const key = quadIdentityKey(quad);
+//         if (inheritedKeys.has(key) || emittedKeys.has(key)) {
+//             return false;
+//         }
+//         emittedKeys.add(key);
+//         return true;
+//     });
+//     await fs.writeFile(entry.entailmentPath, await serializeQuads(normalizedEntailments, entry.ontology, format, pretty), 'utf-8');
+//     entailmentKeysByModelUri.set(entry.modelUri, emittedKeys);
+// }
+async function buildOmlAliasIndex(workspaceRoot) {
+    const index = new Map();
+    for (const filePath of await findOmlFiles(workspaceRoot)) {
+        const suffix = omlSuffixKey(filePath);
+        if (!suffix) {
+            continue;
+        }
+        const uri = URI.file(filePath).toString();
+        const existing = index.get(suffix) ?? [];
+        existing.push(uri);
+        index.set(suffix, existing);
+    }
+    return index;
+}
+async function findRdfFiles(root, format) {
+    const entries = await fs.readdir(root, { withFileTypes: true });
+    const results = [];
+    for (const entry of entries) {
+        const fullPath = path.join(root, entry.name);
+        if (entry.isDirectory()) {
+            results.push(...await findRdfFiles(fullPath, format));
+            continue;
+        }
+        if (entry.isFile() && entry.name.toLowerCase().endsWith(`.${format.toLowerCase()}`)) {
+            results.push(fullPath);
+        }
+    }
+    return results.sort();
+}
+function resolveAliasesForStem(relativeStem, aliasBySuffix) {
+    return [...new Set(aliasBySuffix.get(relativeStem.replace(/\\/g, '/')) ?? [])];
+}
+// function quadIdentityKey(quad: Quad): string {
+//     return `${quad.subject.id}|${quad.predicate.id}|${quad.object.id}`;
+// }
+function relativeOntologyStem(outputRoot, assertedFile, format) {
+    const relative = path.relative(outputRoot, assertedFile).split(path.sep).join('/');
+    return relative.replace(new RegExp(`\\.${format}$`, 'i'), '');
+}
+function omlSuffixKey(filePath) {
+    const normalized = filePath.split(path.sep).join('/');
+    const marker = '/oml/';
+    const index = normalized.lastIndexOf(marker);
+    if (index < 0) {
+        return undefined;
+    }
+    return normalized.slice(index + marker.length).replace(/\.oml$/i, '');
+}
+function ontologyIriFromQuads(quads) {
+    const namespace = quads.find((q) => q.predicate.value === 'http://opencaesar.io/oml#namespace' && q.object.termType === 'NamedNode')?.object.value;
+    return namespace?.replace(/[\/#]+$/, '');
+}
+async function readOptionalRdfQuads(filePath) {
+    try {
+        return await readRequiredRdfQuads(filePath);
+    }
+    catch (error) {
+        const code = error.code;
+        if (code === 'ENOENT') {
+            return [];
+        }
+        throw error;
+    }
+}
+async function serializeQuads(quads, ontology, format, pretty) {
+    return serializeQuadsWithPrefixes(quads, collectPrefixes(quads, ontology), format, pretty);
+}
+async function serializeQuadsWithPrefixes(quads, prefixes, format = 'ttl', pretty = false) {
+    const writer = new Writer({
+        format: SUPPORTED_RDF_FORMATS.get(format),
+        prefixes
+    });
+    writer.addQuads(orderQuadsForSerialization(quads));
+    const serialized = await new Promise((resolve, reject) => {
+        writer.end((error, result) => {
+            if (error) {
+                reject(error);
+                return;
+            }
+            resolve(result);
+        });
+    });
+    return pretty ? prettyPrintRdf(serialized, format) : serialized;
+}
+function collectPrefixes(quads, ontology) {
+    const prefixes = {};
+    const ownPrefix = ontology.prefix;
+    const ownNamespace = normalizeNamespace(ontology.namespace);
+    if (ownPrefix && ownNamespace) {
+        prefixes[ownPrefix] = ownNamespace;
+    }
+    for (const { prefix, namespace } of Object.values(BUILT_IN_PREFIXES)) {
+        if (!(prefix in prefixes)) {
+            prefixes[prefix] = namespace;
+        }
+    }
+    const importedPrefixByIri = new Map();
+    for (const ownedImport of ontology.ownedImports ?? []) {
+        const imported = ownedImport.imported?.ref;
+        const prefix = ownedImport.prefix ?? imported?.prefix;
+        const namespace = normalizeNamespace(imported?.namespace);
+        if (prefix && namespace) {
+            importedPrefixByIri.set(namespace.replace(/[\/#]+$/, ''), prefix);
+        }
+    }
+    for (const importedOntologyIri of importedOntologyIris(quads)) {
+        const prefix = importedPrefixByIri.get(importedOntologyIri) ?? BUILT_IN_PREFIXES[importedOntologyIri]?.prefix;
+        const namespace = BUILT_IN_PREFIXES[importedOntologyIri]?.namespace;
+        if (prefix && namespace && !(prefix in prefixes)) {
+            prefixes[prefix] = namespace;
+        }
+    }
+    addPrefixesUsedByQuads(prefixes, quads);
+    return prefixes;
+}
+function addPrefixesUsedByQuads(prefixes, quads) {
+    const usedNamespaces = new Set();
+    for (const quad of quads) {
+        collectTermNamespace(quad.subject, usedNamespaces);
+        collectTermNamespace(quad.predicate, usedNamespaces);
+        collectTermNamespace(quad.object, usedNamespaces);
+        collectTermNamespace(quad.graph, usedNamespaces);
+    }
+    const taken = new Set(Object.keys(prefixes));
+    for (const namespace of [...usedNamespaces].sort()) {
+        if (Object.values(prefixes).includes(namespace)) {
+            continue;
+        }
+        const prefix = allocatePrefix(namespace, taken);
+        prefixes[prefix] = namespace;
+        taken.add(prefix);
+    }
+}
+function collectTermNamespace(term, namespaces) {
+    if (term.termType === 'NamedNode') {
+        const namespace = namespaceOfIri(term.value);
+        if (namespace) {
+            namespaces.add(namespace);
+        }
+        return;
+    }
+    if (term.termType === 'Literal') {
+        const namespace = namespaceOfIri(term.datatype.value);
+        if (namespace) {
+            namespaces.add(namespace);
+        }
+    }
+}
+function namespaceOfIri(iri) {
+    const hashIndex = iri.lastIndexOf('#');
+    if (hashIndex >= 0) {
+        return iri.slice(0, hashIndex + 1);
+    }
+    const slashIndex = iri.lastIndexOf('/');
+    if (slashIndex >= 0) {
+        return iri.slice(0, slashIndex + 1);
+    }
+    return undefined;
+}
+function allocatePrefix(namespace, taken) {
+    const base = suggestPrefix(namespace);
+    if (!taken.has(base)) {
+        return base;
+    }
+    let counter = 1;
+    while (taken.has(`${base}${counter}`)) {
+        counter += 1;
+    }
+    return `${base}${counter}`;
+}
+function suggestPrefix(namespace) {
+    try {
+        const url = new URL(namespace);
+        const candidates = [
+            ...url.pathname.split('/').filter(Boolean).reverse(),
+            ...url.hostname.split('.').filter(Boolean).reverse(),
+        ];
+        for (const candidate of candidates) {
+            const normalized = candidate
+                .replace(/[^A-Za-z0-9_-]/g, '')
+                .replace(/^[^A-Za-z_]+/, '')
+                .toLowerCase();
+            if (normalized) {
+                return normalized;
+            }
+        }
+    }
+    catch {
+        // Fall through to the generic prefix.
+    }
+    return 'ns';
+}
+function importedOntologyIris(quads) {
+    const imported = new Set();
+    for (const quad of quads) {
+        if (quad.predicate.value !== OWL_IMPORTS_IRI || quad.object.termType !== 'NamedNode') {
+            continue;
+        }
+        imported.add(quad.object.value.replace(/[\/#]+$/, ''));
+    }
+    return [...imported];
+}
+function filterBuiltInImportQuads(quads) {
+    return quads.filter((quad) => {
+        if (quad.predicate.value !== OWL_IMPORTS_IRI || quad.object.termType !== 'NamedNode') {
+            return true;
+        }
+        return !SKIPPED_BUILT_IN_ONTOLOGIES.has(quad.object.value.replace(/[\/#]+$/, ''));
+    });
+}
+export function resolveOutputPathFromOntologyIriString(ontologyIri, format) {
+    const iri = new URL(ontologyIri);
+    const rawPath = iri.pathname.replace(/\/+$/, '');
+    const pathSegments = rawPath.split('/').filter(Boolean);
+    const fileStem = pathSegments.at(-1) || 'index';
+    const directorySegments = iri.host
+        ? [iri.host, ...pathSegments.slice(0, -1)]
+        : pathSegments.slice(0, -1);
+    return path.join(...directorySegments, `${fileStem}.${format}`);
+}
+export function normalizeNamespace(value) {
+    return value?.replace(/^<|>$/g, '');
+}
+function formatFromExtension(extension) {
+    switch (extension.toLowerCase()) {
+        case '.trig':
+            return 'application/trig';
+        case '.nt':
+            return 'N-Triples';
+        case '.nq':
+            return 'N-Quads';
+        case '.n3':
+            return 'application/n3';
+        default:
+            return undefined;
+    }
+}
+function orderQuadsForSerialization(quads) {
+    return [...quads].sort((left, right) => {
+        const graph = compareTerm(left.graph, right.graph);
+        if (graph !== 0) {
+            return graph;
+        }
+        const subject = compareTerm(left.subject, right.subject);
+        if (subject !== 0) {
+            return subject;
+        }
+        const predicate = comparePredicate(left.predicate.value, right.predicate.value);
+        if (predicate !== 0) {
+            return predicate;
+        }
+        return compareTerm(left.object, right.object);
+    });
+}
+function comparePredicate(left, right) {
+    if (left === right) {
+        return 0;
+    }
+    if (left === RDF_TYPE_IRI) {
+        return -1;
+    }
+    if (right === RDF_TYPE_IRI) {
+        return 1;
+    }
+    return left.localeCompare(right);
+}
+function compareTerm(left, right) {
+    if (left.termType !== right.termType) {
+        return left.termType.localeCompare(right.termType);
+    }
+    if (left.termType === 'Literal' && right.termType === 'Literal') {
+        const value = left.value.localeCompare(right.value);
+        if (value !== 0) {
+            return value;
+        }
+        const language = left.language.localeCompare(right.language);
+        if (language !== 0) {
+            return language;
+        }
+        return left.datatype.value.localeCompare(right.datatype.value);
+    }
+    return left.value.localeCompare(right.value);
+}
+function prettyPrintRdf(serialized, format) {
+    if (format !== 'ttl' && format !== 'trig' && format !== 'n3') {
+        return serialized;
+    }
+    return serialized.replace(/\.\n(?=(?:<|_:[^\s]+|[A-Za-z][A-Za-z0-9_-]*:))/g, '.\n\n');
+}
+const BUILT_IN_PREFIXES = {
+    [OWL_ONTOLOGY_IRI]: { prefix: 'oml', namespace: owlOntologyPrefixes().oml },
+    'http://www.w3.org/1999/02/22-rdf-syntax-ns': {
+        prefix: 'rdf',
+        namespace: 'http://www.w3.org/1999/02/22-rdf-syntax-ns#',
+    },
+    'http://www.w3.org/2000/01/rdf-schema': {
+        prefix: 'rdfs',
+        namespace: 'http://www.w3.org/2000/01/rdf-schema#',
+    },
+    'http://www.w3.org/2002/07/owl': {
+        prefix: 'owl',
+        namespace: 'http://www.w3.org/2002/07/owl#',
+    },
+    'http://www.w3.org/2001/XMLSchema': {
+        prefix: 'xsd',
+        namespace: 'http://www.w3.org/2001/XMLSchema#',
+    },
+    'http://www.w3.org/2003/11/swrl': {
+        prefix: 'swrl',
+        namespace: 'http://www.w3.org/2003/11/swrl#',
+    },
+};
+//# sourceMappingURL=reasoned-output.js.map

package/out/backend/reasoned-output.js.map

@@ -0,0 +1 @@
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package/out/cli.d.ts

@@ -0,0 +1 @@
+export declare function runCli(argv?: string[]): Promise<void>;