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ontocast.onto.ontology_operations

merge_ontologies(onto1, onto2)

Merge two ontologies algorithmically.

This performs a union merge of the two ontology graphs, mapping contradictions. The result has both ontologies as parents. This is similar to a git merge: - Takes union of all triples from both ontologies - Detects contradictions (same subject-predicate with different objects) - Creates a new ontology with both parents - Sets created_at to merge time

Parameters:

Name Type Description Default
onto1 Ontology

First ontology to merge

 required
onto2 Ontology

Second ontology to merge

 required

Returns:

Name Type Description
Ontology Ontology

Merged ontology with both parents

Raises:

Type Description
ValueError

If ontologies have different IRIs
Source code in ontocast/onto/ontology_operations.py 
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def merge_ontologies(onto1: Ontology, onto2: Ontology) -> Ontology:
    """Merge two ontologies algorithmically.

    This performs a union merge of the two ontology graphs, mapping contradictions.
    The result has both ontologies as parents. This is similar to a git merge:
    - Takes union of all triples from both ontologies
    - Detects contradictions (same subject-predicate with different objects)
    - Creates a new ontology with both parents
    - Sets created_at to merge time

    Args:
        onto1: First ontology to merge
        onto2: Second ontology to merge

    Returns:
        Ontology: Merged ontology with both parents

    Raises:
        ValueError: If ontologies have different IRIs
    """
    # Validate that both ontologies have the same IRI
    if onto1.iri != onto2.iri:
        raise ValueError(
            f"Cannot merge ontologies with different IRIs: {onto1.iri} != {onto2.iri}"
        )

    # Ensure both ontologies have hashes
    if not onto1.hash:
        onto1._compute_and_set_hash()
    if not onto2.hash:
        onto2._compute_and_set_hash()

    if not onto1.hash or not onto2.hash:
        raise ValueError("Cannot merge ontologies without hashes")

    # Create merged graph (union) - use RDFGraph's __add__ operator
    merged_graph = onto1.graph + onto2.graph

    # Map contradictions (same subject-predicate with different objects)
    contradictions = _find_contradictions(onto1.graph, onto2.graph)
    if contradictions:
        logger.warning(f"Found {len(contradictions)} contradictions in merge")
        for (s, p), (obj1_set, obj2) in contradictions.items():
            logger.debug(f"Contradiction: {s} {p} -> {obj1_set} vs {obj2}")
            # For now, keep both objects (RDF allows multiple values)
            # In future LLM-based merge, this would be resolved intelligently

    # Create merged ontology
    # Note: sync_properties_to_graph() will remove existing versionInfo triples,
    # so we need to preserve them manually after creation
    merged_ontology = Ontology(
        graph=merged_graph,
        iri=onto1.iri,  # Use IRI from first ontology (should be same)
        title=onto1.title or onto2.title,
        description=onto1.description or onto2.description,
        ontology_id=onto1.ontology_id or onto2.ontology_id,
        version=onto1.version or onto2.version or "1.0.0",
        parent_hashes=[onto1.hash, onto2.hash],
        created_at=datetime.now(timezone.utc),
    )

    # Compute hash for merged ontology
    # Note: Hash excludes metadata (version, title, description, created_at, hash, parent_hash)
    # so it only reflects the actual ontology content (classes, properties, etc.)
    merged_ontology._compute_and_set_hash()

    logger.info(
        f"Merged ontologies {onto1.hash[:8]}... "
        f"and {onto2.hash[:8]}... "
        f"-> {merged_ontology.hash[:8] if merged_ontology.hash else 'None'}..."
    )

    return merged_ontology