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fix: support rdf:Description typed-node syntax in RDF import (Brick) #96

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fix: support rdf:Description typed-node syntax in RDF import (Brick) #96

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95 changes: 95 additions & 0 deletions src/lib/rdf/parser.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -407,4 +407,99 @@ describe('parseRDF', () => {
expect(ontology.entityTypes[0].name).toBe('Widget');
});
});

describe('rdf:Description typed-node syntax (#85)', () => {
// Serializers like Python's rdflib (used by Brick and many published
// ontologies) declare resources as <rdf:Description> with an rdf:type
// child instead of typed elements like <owl:Class>.
const descriptionRdf = `<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:owl="http://www.w3.org/2002/07/owl#">

<rdf:Description rdf:about="http://example.org/desc/">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Ontology"/>
<rdfs:label>Description Ontology</rdfs:label>
<rdfs:comment>Serialized via rdf:Description</rdfs:comment>
</rdf:Description>

<rdf:Description rdf:about="http://example.org/desc/Building">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
<rdfs:label>Building</rdfs:label>
<rdfs:comment>A building</rdfs:comment>
</rdf:Description>

<rdf:Description rdf:about="http://example.org/desc/Sensor">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
<rdfs:label>Sensor</rdfs:label>
</rdf:Description>

<rdf:Description rdf:about="http://example.org/desc/building_name">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
<rdfs:label>name</rdfs:label>
<rdfs:domain rdf:resource="http://example.org/desc/Building"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</rdf:Description>

<rdf:Description rdf:about="http://example.org/desc/hasSensor">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
<rdfs:label>hasSensor</rdfs:label>
<rdfs:domain rdf:resource="http://example.org/desc/Building"/>
<rdfs:range rdf:resource="http://example.org/desc/Sensor"/>
</rdf:Description>

</rdf:RDF>`;

it('extracts ontology metadata from rdf:Description elements', () => {
const { ontology } = parseRDF(descriptionRdf);
expect(ontology.name).toBe('Description Ontology');
expect(ontology.description).toBe('Serialized via rdf:Description');
});

it('extracts classes declared via rdf:type', () => {
const { ontology } = parseRDF(descriptionRdf);
expect(ontology.entityTypes).toHaveLength(2);
const names = ontology.entityTypes.map((e) => e.name);
expect(names).toContain('Building');
expect(names).toContain('Sensor');
});

it('extracts datatype properties declared via rdf:type', () => {
const { ontology } = parseRDF(descriptionRdf);
const building = ontology.entityTypes.find((e) => e.name === 'Building');
expect(building?.properties).toHaveLength(1);
expect(building?.properties[0]).toMatchObject({ name: 'name', type: 'string' });
});

it('extracts object properties declared via rdf:type', () => {
const { ontology } = parseRDF(descriptionRdf);
expect(ontology.relationships).toHaveLength(1);
expect(ontology.relationships[0]).toMatchObject({ from: 'building', to: 'sensor' });
});

it('does not duplicate entities when typed elements and descriptions coexist', () => {
const mixed = descriptionRdf.replace(
'</rdf:RDF>',
`<owl:Class rdf:about="http://example.org/desc/Building">
<rdfs:label>Building</rdfs:label>
</owl:Class></rdf:RDF>`
);
const { ontology } = parseRDF(mixed);
expect(ontology.entityTypes).toHaveLength(2);
});
});

describe('Turtle input detection (#85)', () => {
it('gives an actionable error for Turtle content', () => {
const ttl = `@prefix brick: <https://brickschema.org/schema/Brick#> .\n@prefix owl: <http://www.w3.org/2002/07/owl#> .\n\nbrick:Building a owl:Class .`;
expect(() => parseRDF(ttl)).toThrow(RDFParseError);
expect(() => parseRDF(ttl)).toThrow(/Turtle/);
});

it('still reports malformed XML for non-Turtle garbage', () => {
expect(() => parseRDF('this is not xml at all')).toThrow(RDFParseError);
expect(() => parseRDF('this is not xml at all')).toThrow(/Malformed XML|No ontology metadata/);
});
});
});
60 changes: 54 additions & 6 deletions src/lib/rdf/parser.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -125,6 +125,41 @@ const RDF_NS = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
const RDFS_NS = 'http://www.w3.org/2000/01/rdf-schema#';
const OWL_NS = 'http://www.w3.org/2002/07/owl#';

/**
* Collect all elements declaring a resource of the given type, supporting both
* RDF/XML syntaxes:
*
* 1. Typed node elements: `<owl:Class rdf:about="...">`
* 2. rdf:Description elements: `<rdf:Description rdf:about="...">`
* ` <rdf:type rdf:resource=".../owl#Class"/>`
*
* Many serializers (e.g. Python's rdflib, used by Brick and other published
* ontologies) emit only the second form, which we previously ignored (#85).
*/
function getTypedElements(root: Element, namespace: string, localName: string): Element[] {
const results: Element[] = Array.from(root.getElementsByTagNameNS(namespace, localName));
const typeUri = namespace + localName;

// Snapshot the live collection: indexed access on live collections is
// expensive in some DOM implementations (quadratic in jsdom).
const descEls = Array.from(root.getElementsByTagNameNS(RDF_NS, 'Description'));
for (let i = 0; i < descEls.length; i++) {
const el = descEls[i];
for (let j = 0; j < el.children.length; j++) {
const child = el.children[j];
const childLocal = child.localName || child.tagName.split(':').pop();
if (childLocal !== 'type') continue;
const resource =
child.getAttribute('rdf:resource') || child.getAttributeNS(RDF_NS, 'resource');
if (resource === typeUri) {
results.push(el);
break;
}
}
}
return results;
}

interface ParsedDatatypeProperty {
about: string;
label: string;
Expand All @@ -143,6 +178,15 @@ interface ParsedDatatypeProperty {
* Parse an RDF/XML (OWL) string into an Ontology and optional DataBindings.
*/
export function parseRDF(rdfXml: string): { ontology: Ontology; bindings: DataBinding[] } {
// Give Turtle input a clear, actionable error instead of an XML parse error.
const sniff = rdfXml.trimStart();
if (!sniff.startsWith('<') && /^(@prefix|@base|PREFIX\s|BASE\s)/m.test(sniff)) {
throw new RDFParseError(
'This file appears to be Turtle (.ttl), which is not supported yet. ' +
'Please convert it to RDF/XML first (for example with Apache Jena "riot" or an online RDF converter).'
);
}

const parser = new DOMParser();
const doc = parser.parseFromString(rdfXml, 'application/xml');

Expand All @@ -158,15 +202,15 @@ export function parseRDF(rdfXml: string): { ontology: Ontology; bindings: DataBi
let ontologyName = '';
let ontologyDescription = '';

const ontologyEls = root.getElementsByTagNameNS(OWL_NS, 'Ontology');
const ontologyEls = getTypedElements(root, OWL_NS, 'Ontology');
if (ontologyEls.length > 0) {
const ontEl = ontologyEls[0];
ontologyName = getChildText(ontEl, 'label', RDFS_NS) || '';
ontologyDescription = getChildText(ontEl, 'comment', RDFS_NS) || '';
}

// --- Extract OWL Classes → EntityTypes ---
const classEls = root.getElementsByTagNameNS(OWL_NS, 'Class');
const classEls = getTypedElements(root, OWL_NS, 'Class');
const entityMap = new Map<string, EntityType>();

for (let i = 0; i < classEls.length; i++) {
Expand All @@ -192,7 +236,7 @@ export function parseRDF(rdfXml: string): { ontology: Ontology; bindings: DataBi
}

// --- Extract DatatypeProperties → Properties + Relationship Attributes ---
const dtPropEls = root.getElementsByTagNameNS(OWL_NS, 'DatatypeProperty');
const dtPropEls = getTypedElements(root, OWL_NS, 'DatatypeProperty');
const parsedDtProps: ParsedDatatypeProperty[] = [];

for (let i = 0; i < dtPropEls.length; i++) {
Expand Down Expand Up @@ -268,7 +312,7 @@ export function parseRDF(rdfXml: string): { ontology: Ontology; bindings: DataBi
}

// --- Extract ObjectProperties → Relationships ---
const objPropEls = root.getElementsByTagNameNS(OWL_NS, 'ObjectProperty');
const objPropEls = getTypedElements(root, OWL_NS, 'ObjectProperty');
const relationships: Relationship[] = [];

for (let i = 0; i < objPropEls.length; i++) {
Expand Down Expand Up @@ -323,8 +367,12 @@ export function parseRDF(rdfXml: string): { ontology: Ontology; bindings: DataBi

// --- Extract DataBindings ---
const bindings: DataBinding[] = [];
// Look for ont:DataBinding elements (they use the ontology namespace)
const allElements = root.getElementsByTagName('*');
// Look for ont:DataBinding elements (they use the ontology namespace).
// Use a static snapshot instead of the live getElementsByTagName('*')
// collection: repeated indexed access on live collections is quadratic in
// some DOM implementations, which made importing large ontologies
// (e.g. Brick, ~500k elements) pathologically slow.
const allElements = root.querySelectorAll('*');
for (let i = 0; i < allElements.length; i++) {
const el = allElements[i];
const localName = el.localName || el.tagName.split(':').pop();
Expand Down