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Merge pull request #70 from julesjacobsen/57-loader_refactor
57 loader refactor
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237 changes: 237 additions & 0 deletions
237
owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/Ontology.java
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| package org.monarchinitiative.owlsim.io; | ||
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| import org.apache.commons.validator.routines.UrlValidator; | ||
| import org.apache.log4j.Logger; | ||
| import org.prefixcommons.CurieUtil; | ||
| import org.semanticweb.owlapi.apibinding.OWLManager; | ||
| import org.semanticweb.owlapi.model.*; | ||
| import org.semanticweb.owlapi.model.parameters.ChangeApplied; | ||
| import uk.ac.manchester.cs.owl.owlapi.concurrent.Concurrency; | ||
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| import java.io.*; | ||
| import java.nio.charset.Charset; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.util.Collection; | ||
| import java.util.Map; | ||
| import java.util.Objects; | ||
| import java.util.Set; | ||
| import java.util.zip.GZIPInputStream; | ||
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| /** | ||
| * OWL API wrapper to facilitate building OWLOntology objects to load into the {@link org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl} | ||
| * | ||
| * @author Jules Jacobsen <j.jacobsen@qmul.ac.uk> | ||
| */ | ||
| public class Ontology { | ||
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| private static final Logger logger = Logger.getLogger(Ontology.class); | ||
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| //OWLOntology is a mutable object | ||
| private final OntologySourceData sourceData; | ||
| private final CurieUtil curieUtil; | ||
| private final OWLOntology owlOntology; | ||
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| private final OWLOntologyManager ontologyManager; | ||
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| private Ontology(OntologySourceData sourceData, Concurrency concurrency) { | ||
| Objects.requireNonNull(sourceData, "Unable to create Ontology without data sources."); | ||
| this.sourceData = sourceData; | ||
| this.curieUtil = new CurieUtil(sourceData.getCuries()); | ||
| this.ontologyManager = createOntologyManager(concurrency); | ||
| this.owlOntology = createEmptyOntology(ontologyManager); | ||
| loadOwlOntology(); | ||
| } | ||
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| /** | ||
| * Loads an ontology using a concurrent OWLOntologyManager. | ||
| * | ||
| * @param sourceData | ||
| * @return An Ontology created from the source data provided. | ||
| */ | ||
| public static Ontology load(OntologySourceData sourceData) { | ||
| return new Ontology(sourceData, Concurrency.CONCURRENT); | ||
| } | ||
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| /** | ||
| * Loads an ontology using an OWLOntologyManager using the concurrency type specified. | ||
| * | ||
| * @param sourceData | ||
| * @param concurrency | ||
| * @return An Ontology created from the source data provided. | ||
| */ | ||
| public static Ontology load(OntologySourceData sourceData, Concurrency concurrency) { | ||
| return new Ontology(sourceData, useConcurrentIfNull(concurrency)); | ||
| } | ||
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| private static Concurrency useConcurrentIfNull(Concurrency concurrency) { | ||
| return concurrency == null ? Concurrency.CONCURRENT : concurrency; | ||
| } | ||
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| public OWLOntology getOwlOntology() { | ||
| return owlOntology; | ||
| } | ||
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| public OntologySourceData getSourceData() { | ||
| return sourceData; | ||
| } | ||
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| public CurieUtil getCurieUtil() { | ||
| return curieUtil; | ||
| } | ||
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| private void loadOwlOntology() { | ||
| //Order matters here - don't change it. | ||
| mergeOntologies(sourceData.getOntologies()); | ||
| mergeOntologies(sourceData.getDataOntologies()); | ||
| loadDataFromTsv(sourceData.getDataTsvs()); | ||
| loadDataFromPairwiseMappings(sourceData.getPairwiseMappings()); | ||
| logger.info("Ontology loaded"); | ||
| } | ||
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| private OWLOntologyManager createOntologyManager(Concurrency concurrencyType) { | ||
| if (concurrencyType == Concurrency.NON_CONCURRENT) { | ||
| logger.info("Using non-concurrent OWL ontology manager"); | ||
| return OWLManager.createOWLOntologyManager(); | ||
| } | ||
| logger.info("Using concurrent OWL ontology manager"); | ||
| return OWLManager.createConcurrentOWLOntologyManager(); | ||
| } | ||
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| private OWLOntology createEmptyOntology(OWLOntologyManager ontologyManager) { | ||
| try { | ||
| return ontologyManager.createOntology(); | ||
| } catch (OWLOntologyCreationException e) { | ||
| throw new OntologyLoadException(e); | ||
| } | ||
| } | ||
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| private OWLOntology mergeOntology(String uri) { | ||
| OWLOntology loadedOntology = loadOwlOntology(uri); | ||
| addAxioms(loadedOntology.getAxioms()); | ||
| return owlOntology; | ||
| } | ||
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| private OWLOntology mergeOntologies(Collection<String> uris) { | ||
| uris.forEach(uri -> mergeOntology(uri)); | ||
| return owlOntology; | ||
| } | ||
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| private ChangeApplied addAxiom(OWLAxiom axiom) { | ||
| return ontologyManager.addAxiom(owlOntology, axiom); | ||
| } | ||
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| private ChangeApplied addAxioms(Set<OWLAxiom> axioms) { | ||
| return ontologyManager.addAxioms(owlOntology, axioms); | ||
| } | ||
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| private OWLOntology loadOwlOntology(String uri) { | ||
| UrlValidator urlValidator = UrlValidator.getInstance(); | ||
| if (urlValidator.isValid(uri)) { | ||
| return loadRemoteOntology(IRI.create(uri)); | ||
| } else if (uri.endsWith(".gz")) { | ||
| return loadGzippedOntology(Paths.get(uri)); | ||
| } else { | ||
| return loadOwlOntologyFromDocument(Paths.get(uri)); | ||
| } | ||
| } | ||
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| private OWLOntology loadRemoteOntology(IRI iri) { | ||
| return loadOwlOntology(iri); | ||
| } | ||
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| private OWLOntology loadGzippedOntology(Path path) { | ||
| logger.info("Loading gzipped ontology from " + path); | ||
| try (InputStream is = new GZIPInputStream(new FileInputStream(path.toFile()))) { | ||
| return loadOwlOntologyFromDocument(is); | ||
| } catch (IOException e) { | ||
| throw new OntologyLoadException(e); | ||
| } | ||
| } | ||
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| private OWLOntology loadOwlOntology(IRI iri) { | ||
| try { | ||
| logger.info("Loading ontology from IRI" + iri.getShortForm()); | ||
| return ontologyManager.loadOntology(iri); | ||
| } catch (OWLOntologyCreationException e) { | ||
| throw new OntologyLoadException(e); | ||
| } | ||
| } | ||
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| private OWLOntology loadDataFromTsv(Collection<String> paths) { | ||
| paths.forEach(this::loadDataFromTsv); | ||
| return owlOntology; | ||
| } | ||
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| private OWLOntology loadDataFromTsv(String path) { | ||
| if (path.endsWith(".gz")) { | ||
| return loadDataFromTsvGzip(path); | ||
| } | ||
| Path file = Paths.get(path); | ||
| logger.info("Reading tsv data from " + path); | ||
| try { | ||
| Files.lines(file).forEach(line -> loadLineIntoDataOntology(line)); | ||
| } catch (IOException e) { | ||
| throw new OntologyLoadException(e); | ||
| } | ||
| return owlOntology; | ||
| } | ||
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| private OWLOntology loadDataFromTsvGzip(String path) { | ||
| Path file = Paths.get(path); | ||
| logger.info("Reading gzipped tsv data from " + file); | ||
| try (GZIPInputStream gis = new GZIPInputStream(new FileInputStream(file.toFile())); | ||
| BufferedReader bf = new BufferedReader(new InputStreamReader(gis, Charset.forName("UTF-8"))) | ||
| ) { | ||
| bf.lines().forEach(line -> loadLineIntoDataOntology(line)); | ||
| } catch (IOException e) { | ||
| throw new OntologyLoadException(e); | ||
| } | ||
| return owlOntology; | ||
| } | ||
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| private void loadDataFromPairwiseMappings(Map<String, String> pairwiseMappings) { | ||
| pairwiseMappings.forEach(this::addInstanceOf); | ||
| } | ||
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| private void loadLineIntoDataOntology(String line) { | ||
| String[] vals = line.split("\t", 2); | ||
| String[] terms = vals[1].split(";"); | ||
| for (String t : terms) { | ||
| addInstanceOf(vals[0], t); | ||
| } | ||
| } | ||
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| private void addInstanceOf(String individual, String ontologyClass) { | ||
| // logger.info("Adding axiom " + individual + ": " + ontologyClass); | ||
| OWLDataFactory owlDataFactory = ontologyManager.getOWLDataFactory(); | ||
| OWLClass owlClass = owlDataFactory.getOWLClass(toIri(ontologyClass)); | ||
| OWLNamedIndividual owlNamedIndividual = owlDataFactory.getOWLNamedIndividual(toIri(individual)); | ||
| OWLClassAssertionAxiom axiom = owlDataFactory.getOWLClassAssertionAxiom(owlClass, owlNamedIndividual); | ||
| addAxiom(axiom); | ||
| } | ||
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| private IRI toIri(String id) { | ||
| return IRI.create(curieUtil.getIri(id).orElse(id)); | ||
| } | ||
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| private OWLOntology loadOwlOntologyFromDocument(Path path) { | ||
| try { | ||
| logger.info("Loading ontology from document " + path); | ||
| return ontologyManager.loadOntologyFromOntologyDocument(path.toFile()); | ||
| } catch (OWLOntologyCreationException e) { | ||
| throw new OntologyLoadException(e); | ||
| } | ||
| } | ||
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| private OWLOntology loadOwlOntologyFromDocument(InputStream is) { | ||
| try { | ||
| return ontologyManager.loadOntologyFromOntologyDocument(is); | ||
| } catch (OWLOntologyCreationException e) { | ||
| logger.error("Unable to create ontology" + e); | ||
| throw new OntologyLoadException(e); | ||
| } | ||
| } | ||
| } | ||
|
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14 changes: 14 additions & 0 deletions
14
owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologyLoadException.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| package org.monarchinitiative.owlsim.io; | ||
|
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| /** | ||
| * @author Jules Jacobsen <j.jacobsen@qmul.ac.uk> | ||
| */ | ||
| class OntologyLoadException extends RuntimeException { | ||
|
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| OntologyLoadException(String message) { | ||
| super(message); | ||
| } | ||
|
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| OntologyLoadException(Exception e) { | ||
| } | ||
| } |
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