Examples with MalformedQueryException org.openrdf.query.MalformedQueryException used on opensource projects

Example 16 with MalformedQueryException

use of org.openrdf.query.MalformedQueryException in project minerva by geneontology.

the class ReplaceObsoleteReferencesCommand method run.

public static void run(String ontologyIRI, String catalogPath, String journalFilePath) throws FatalReplaceObsoleteReferencesError {
    if (journalFilePath == null) {
        throw new FatalReplaceObsoleteReferencesError("No journal file was configured.");
    }
    if (ontologyIRI == null) {
        throw new FatalReplaceObsoleteReferencesError("No ontology IRI was configured.");
    }
    final OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    if (catalogPath != null) {
        try {
            manager.getIRIMappers().set(new CatalogXmlIRIMapper(catalogPath));
        } catch (IOException e) {
            throw new FatalReplaceObsoleteReferencesError("Could not load catalog file from " + catalogPath, e);
        }
    }
    final OWLOntology tbox;
    try {
        tbox = manager.loadOntology(IRI.create(ontologyIRI));
    } catch (OWLOntologyCreationException e) {
        throw new FatalReplaceObsoleteReferencesError("Could not load tbox ontology from " + ontologyIRI, e);
    }
    Properties properties = new Properties();
    try {
        properties.load(CommandLineInterface.class.getResourceAsStream("/org/geneontology/minerva/blazegraph.properties"));
    } catch (IOException e) {
        throw new FatalReplaceObsoleteReferencesError("Could not read blazegraph properties resource from jar file.");
    }
    properties.setProperty(com.bigdata.journal.Options.FILE, journalFilePath);
    BigdataSail sail = new BigdataSail(properties);
    BigdataSailRepository repository = new BigdataSailRepository(sail);
    try {
        repository.initialize();
    } catch (RepositoryException e) {
        throw new FatalReplaceObsoleteReferencesError("Could not initialize SAIL repository for database.", e);
    }
    BlazegraphMutationCounter counter = new BlazegraphMutationCounter();
    String replacements = createReplacementsValuesList(tbox);
    String sparqlUpdate = updateTemplate.replace("%%%values%%%", replacements);
    String complementsSparqlUpdate = complementsUpdateTemplate.replace("%%%values%%%", replacements);
    LOGGER.debug("Will apply SPARQL update:\n" + sparqlUpdate);
    try {
        applySPARQLUpdate(repository, sparqlUpdate, Optional.of(counter));
        applySPARQLUpdate(repository, complementsSparqlUpdate, Optional.of(counter));
        int changes = counter.mutationCount();
        LOGGER.info("Successfully applied database updates to replace obsolete terms: " + changes + " changes");
    } catch (RepositoryException | UpdateExecutionException | MalformedQueryException e) {
        throw new FatalReplaceObsoleteReferencesError("Failed to apply SPARQL update.", e);
    }
}