Examples with BigdataSailRepositoryConnection com.bigdata.rdf.sail.BigdataSailRepositoryConnection used on opensource projects

Example 21 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphMolecularModelManager method dumpStoredModel.

/**
 * Save a model to disk.
 *
 * @throws OWLOntologyStorageException
 * @throws OWLOntologyCreationException
 * @throws IOException
 */
public void dumpStoredModel(IRI modelId, File folder) throws IOException {
    // preliminary checks for the target file
    String fileName = StringUtils.replaceOnce(modelId.toString(), modelIdPrefix, "") + ".ttl";
    File targetFile = new File(folder, fileName).getAbsoluteFile();
    if (targetFile.exists()) {
        if (targetFile.isFile() == false) {
            throw new IOException("For modelId: '" + modelId + "', the resulting path is not a file: " + targetFile.getAbsolutePath());
        }
        if (targetFile.canWrite() == false) {
            throw new IOException("For modelId: '" + modelId + "', Cannot write to the file: " + targetFile.getAbsolutePath());
        }
    } else {
        File targetFolder = targetFile.getParentFile();
        FileUtils.forceMkdir(targetFolder);
    }
    File tempFile = null;
    try {
        // create tempFile
        // TODO escape
        String prefix = modelId.toString();
        tempFile = File.createTempFile(prefix, ".ttl");
        try {
            BigdataSailRepositoryConnection connection = repo.getReadOnlyConnection();
            OutputStream out = new FileOutputStream(tempFile);
            try {
                // Workaround for order dependence of RDF reading by OWL API
                // Need to output ontology triple first until this bug is fixed:
                // https://github.com/owlcs/owlapi/issues/574
                ValueFactory factory = connection.getValueFactory();
                Statement ontologyDeclaration = factory.createStatement(factory.createURI(modelId.toString()), RDF.TYPE, OWL.ONTOLOGY);
                Rio.write(Collections.singleton(ontologyDeclaration), out, RDFFormat.TURTLE);
                // end workaround
                RDFWriter writer = Rio.createWriter(RDFFormat.TURTLE, out);
                connection.export(writer, new URIImpl(modelId.toString()));
                // copy temp file to the finalFile
                FileUtils.copyFile(tempFile, targetFile);
            } finally {
                out.close();
                connection.close();
            }
        } catch (RepositoryException e) {
            throw new IOException(e);
        } catch (RDFHandlerException e) {
            throw new IOException(e);
        }
    } finally {
        // delete temp file
        FileUtils.deleteQuietly(tempFile);
    }
}

Example 22 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphOntologyManager method getLabels.

public Map<String, String> getLabels(Set<String> entities) throws IOException {
    Map<String, String> uri_label = new HashMap<String, String>();
    String values = "VALUES ?entity {";
    for (String uri : entities) {
        values += "<" + uri + "> ";
    }
    values += "} . ";
    String query = "select ?entity ?label where { " + values + " ?entity rdfs:label ?label }";
    try {
        BigdataSailRepositoryConnection connection = go_lego_repo.getReadOnlyConnection();
        try {
            TupleQuery tupleQuery = connection.prepareTupleQuery(QueryLanguage.SPARQL, query);
            TupleQueryResult result = tupleQuery.evaluate();
            while (result.hasNext()) {
                BindingSet binding = result.next();
                Value v = binding.getValue("label");
                String label = v.stringValue();
                Value ev = binding.getValue("entity");
                String entity = ev.stringValue();
                uri_label.put(entity, label);
            }
        } catch (MalformedQueryException e) {
            throw new IOException(e);
        } catch (QueryEvaluationException e) {
            throw new IOException(e);
        } finally {
            connection.close();
        }
    } catch (RepositoryException e) {
        throw new IOException(e);
    }
    return uri_label;
}

Example 23 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphOntologyManager method getGenesByTaxid.

public Set<String> getGenesByTaxid(String ncbi_tax_id) throws IOException {
    Set<String> genes = new HashSet<String>();
    try {
        BigdataSailRepositoryConnection connection = go_lego_repo.getReadOnlyConnection();
        try {
            String query = "select ?gene   \n" + "where { \n" + "  ?gene rdfs:subClassOf ?taxon_restriction .\n" + "  ?taxon_restriction owl:onProperty <http://purl.obolibrary.org/obo/RO_0002162> .\n" + "  ?taxon_restriction owl:someValuesFrom <http://purl.obolibrary.org/obo/NCBITaxon_" + ncbi_tax_id + "> \n" + "}";
            TupleQuery tupleQuery = connection.prepareTupleQuery(QueryLanguage.SPARQL, query);
            TupleQueryResult result = tupleQuery.evaluate();
            while (result.hasNext()) {
                BindingSet binding = result.next();
                Value v = binding.getValue("gene");
                // ignore anonymous sub classes
                if (v instanceof URI) {
                    String gene = binding.getValue("gene").stringValue();
                    genes.add(gene);
                }
            }
        } catch (MalformedQueryException e) {
            throw new IOException(e);
        } catch (QueryEvaluationException e) {
            throw new IOException(e);
        } finally {
            connection.close();
        }
    } catch (RepositoryException e) {
        throw new IOException(e);
    }
    return genes;
}

Example 24 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphOntologyManager method loadRepositoryFromOWLFile.

public void loadRepositoryFromOWLFile(File file, String iri, boolean reset) throws OWLOntologyCreationException, RepositoryException, IOException, RDFParseException, RDFHandlerException {
    synchronized (go_lego_repo) {
        final BigdataSailRepositoryConnection connection = go_lego_repo.getUnisolatedConnection();
        try {
            connection.begin();
            try {
                URI graph = new URIImpl(iri);
                if (reset) {
                    connection.clear(graph);
                }
                if (file.getName().endsWith(".ttl")) {
                    connection.add(file, "", RDFFormat.TURTLE, graph);
                } else if (file.getName().endsWith(".owl")) {
                    connection.add(file, "", RDFFormat.RDFXML, graph);
                }
                connection.commit();
            } catch (Exception e) {
                connection.rollback();
                throw e;
            }
        } finally {
            connection.close();
        }
    }
}

Example 25 with BigdataSailRepositoryConnection

use of com.bigdata.rdf.sail.BigdataSailRepositoryConnection in project minerva by geneontology.

the class BlazegraphOntologyManager method buildClassDepthMap.

public Map<String, Integer> buildClassDepthMap(String root_term) throws IOException {
    Map<String, Integer> class_depth = new HashMap<String, Integer>();
    try {
        BigdataSailRepositoryConnection connection = go_lego_repo.getReadOnlyConnection();
        try {
            String query = "PREFIX owl: <http://www.w3.org/2002/07/owl#> " + "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " + "SELECT ?class (count(?mid) as ?depth) " + "WHERE { " + "?class rdfs:subClassOf* ?mid . " + "values ?root_term {<" + root_term + ">} . " + "  ?mid rdfs:subClassOf* ?root_term ." + "filter ( ?class != ?mid )}" + "group by ?class " + " order by ?depth";
            TupleQuery tupleQuery = connection.prepareTupleQuery(QueryLanguage.SPARQL, query);
            TupleQueryResult result = tupleQuery.evaluate();
            while (result.hasNext()) {
                BindingSet binding = result.next();
                Value v = binding.getValue("depth");
                Integer depth = Integer.parseInt(v.stringValue());
                String c = binding.getValue("class").stringValue();
                Integer k = class_depth.get(c);
                if ((k == null) || (depth < k)) {
                    class_depth.put(c, depth);
                }
            }
        } catch (MalformedQueryException e) {
            throw new IOException(e);
        } catch (QueryEvaluationException e) {
            throw new IOException(e);
        } finally {
            connection.close();
        }
    } catch (RepositoryException e) {
        throw new IOException(e);
    }
    return class_depth;
}