owltools.gaf.lego
Class MolecularModelJsonRenderer

java.lang.Object
  extended by owltools.gaf.lego.MolecularModelJsonRenderer

public class MolecularModelJsonRenderer
extends Object

A Renderer that takes a MolecularModel (an OWL ABox) and generates Map objects that can be translated to JSON using Gson. TODO - make this inherit from a generic renderer - use OWLAPI visitor? TODO - abstract some of this into a generic OWL to JSON-LD converter TODO - include inferred types

Author:
cjm

Nested Class Summary
static class MolecularModelJsonRenderer.KEY
          JSON-LD keywords for elements of different vocabularies: RDF OWL GO RO TODO: use a complex enum to generate IRIs for each
static class MolecularModelJsonRenderer.VAL
          merge with KEY?
 
Constructor Summary
MolecularModelJsonRenderer(OWLGraphWrapper graph)
           
MolecularModelJsonRenderer(org.semanticweb.owlapi.model.OWLOntology ontology)
           
 
Method Summary
static String getId(org.semanticweb.owlapi.model.IRI iri)
           
static String getId(org.semanticweb.owlapi.model.OWLNamedObject i, OWLGraphWrapper graph)
           
static org.semanticweb.owlapi.model.IRI getIRI(String id, OWLGraphWrapper graph)
          Inverse method to getId(org.semanticweb.owlapi.model.OWLNamedObject, owltools.graph.OWLGraphWrapper)
static List<Map<Object,Object>> renderEvidences(MolecularModelManager mmm)
           
 Map<Object,Object> renderIndividuals(Collection<org.semanticweb.owlapi.model.OWLNamedIndividual> individuals)
           
 Map<Object,Object> renderModel()
           
static List<Object> renderModelAnnotations(org.semanticweb.owlapi.model.OWLOntology ont)
           
 Map<Object,Object> renderObject(org.semanticweb.owlapi.model.OWLNamedIndividual i)
           
 Map<Object,Object> renderObject(org.semanticweb.owlapi.model.OWLObjectProperty p)
           
 Map<Object,Object> renderObject(org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom opa)
           
static List<Map<Object,Object>> renderRelations(MolecularModelManager mmm, Set<String> relevantRelations)
           
static String renderToJson(org.semanticweb.owlapi.model.OWLOntology ont)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MolecularModelJsonRenderer

public MolecularModelJsonRenderer(org.semanticweb.owlapi.model.OWLOntology ontology)
Parameters:
ontology -

MolecularModelJsonRenderer

public MolecularModelJsonRenderer(OWLGraphWrapper graph)
Parameters:
graph -
Method Detail

renderModel

public Map<Object,Object> renderModel()
Returns:
Map to be passed to Gson

renderModelAnnotations

public static List<Object> renderModelAnnotations(org.semanticweb.owlapi.model.OWLOntology ont)

renderIndividuals

public Map<Object,Object> renderIndividuals(Collection<org.semanticweb.owlapi.model.OWLNamedIndividual> individuals)

renderObject

public Map<Object,Object> renderObject(org.semanticweb.owlapi.model.OWLNamedIndividual i)
Parameters:
i -
Returns:
Map to be passed to Gson

renderObject

public Map<Object,Object> renderObject(org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom opa)
Parameters:
opa -
Returns:
Map to be passed to Gson

renderObject

public Map<Object,Object> renderObject(org.semanticweb.owlapi.model.OWLObjectProperty p)
Parameters:
p -
Returns:
Map to be passed to Gson

getId

public static String getId(org.semanticweb.owlapi.model.OWLNamedObject i,
                           OWLGraphWrapper graph)
Parameters:
i -
graph -
Returns:
id
See Also:
getIRI(java.lang.String, owltools.graph.OWLGraphWrapper)

getId

public static String getId(org.semanticweb.owlapi.model.IRI iri)
Parameters:
iri -
Returns:
id

getIRI

public static org.semanticweb.owlapi.model.IRI getIRI(String id,
                                                      OWLGraphWrapper graph)
Inverse method to getId(org.semanticweb.owlapi.model.OWLNamedObject, owltools.graph.OWLGraphWrapper)

Parameters:
id -
graph -
Returns:
IRI
See Also:
getId(org.semanticweb.owlapi.model.OWLNamedObject, owltools.graph.OWLGraphWrapper)

renderRelations

public static List<Map<Object,Object>> renderRelations(MolecularModelManager mmm,
                                                       Set<String> relevantRelations)
                                                throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

renderEvidences

public static List<Map<Object,Object>> renderEvidences(MolecularModelManager mmm)
                                                throws org.semanticweb.owlapi.model.OWLException,
                                                       IOException
Throws:
org.semanticweb.owlapi.model.OWLException
IOException

renderToJson

public static String renderToJson(org.semanticweb.owlapi.model.OWLOntology ont)


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