Merge pull request #1563 from OpenRefine/jena-migrate
migrate from JRDF to JENA library
This commit is contained in:
Jacky
GitHub
commit
1a0d1fabd4
16
.classpath
16
.classpath
@ -17,7 +17,6 @@
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<classpathentry exported="true" kind="lib" path="main/webapp/WEB-INF/lib/clojure-1.5.1-slim.jar"/>
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<classpathentry exported="true" kind="lib" path="main/webapp/WEB-INF/lib/dom4j-1.6.1.jar"/>
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<classpathentry exported="true" kind="lib" path="main/webapp/WEB-INF/lib/jcl-over-slf4j-1.5.6.jar"/>
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<classpathentry exported="true" kind="lib" path="main/webapp/WEB-INF/lib/jrdf-0.5.6.jar" sourcepath="main/webapp/WEB-INF/lib-src/jrdf-0.5.6-sources.jar"/>
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<classpathentry exported="true" kind="lib" path="main/webapp/WEB-INF/lib/lessen-trunk-r8.jar"/>
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<classpathentry exported="true" kind="lib" path="main/webapp/WEB-INF/lib/log4j-1.2.15.jar"/>
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<classpathentry exported="true" kind="lib" path="main/webapp/WEB-INF/lib/marc4j-2.4.jar"/>
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@ -113,5 +112,20 @@
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/commons-beanutils-1.9.3.jar"/>
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<classpathentry kind="lib" path="extensions/gdata/module/MOD-INF/lib/google-auth-library-oauth2-http-0.9.0.jar"/>
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<classpathentry kind="lib" path="extensions/gdata/module/MOD-INF/lib/google-oauth-client-jetty-1.23.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-arq-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-base-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-cmds-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-core-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-dboe-base-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-dboe-index-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-dboe-trans-data-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-dboe-transaction-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-iri-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-rdfconnection-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-shaded-guava-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-tdb-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jena-tdb2-3.6.0.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/jsonld-java-0.11.1.jar"/>
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<classpathentry kind="lib" path="main/webapp/WEB-INF/lib/libthrift-0.10.0.jar"/>
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<classpathentry kind="output" path="main/webapp/WEB-INF/classes"/>
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</classpath>
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@ -33,10 +33,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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package com.google.refine.importers;
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import static org.jrdf.graph.AnyObjectNode.ANY_OBJECT_NODE;
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import static org.jrdf.graph.AnyPredicateNode.ANY_PREDICATE_NODE;
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import static org.jrdf.graph.AnySubjectNode.ANY_SUBJECT_NODE;
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import java.io.InputStream;
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import java.util.ArrayList;
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import java.util.LinkedHashMap;
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@ -44,10 +40,10 @@ import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import org.jrdf.graph.Graph;
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import org.jrdf.graph.Triple;
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import org.jrdf.parser.RdfReader;
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import org.jrdf.util.ClosableIterable;
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import org.apache.jena.rdf.model.Model;
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import org.apache.jena.rdf.model.ModelFactory;
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import org.apache.jena.rdf.model.Statement;
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import org.apache.jena.rdf.model.StmtIterator;
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import org.json.JSONObject;
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import com.google.refine.expr.ExpressionUtils;
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@ -60,13 +56,13 @@ import com.google.refine.model.Row;
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import com.google.refine.model.medadata.ProjectMetadata;
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public class RdfTripleImporter extends ImportingParserBase {
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private RdfReader rdfReader;
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private Mode mode;
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public enum Mode {
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RDFXML,
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NT,
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N3
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N3,
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TTL
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}
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public RdfTripleImporter() {
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@ -75,27 +71,25 @@ public class RdfTripleImporter extends ImportingParserBase {
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public RdfTripleImporter(Mode mode) {
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super(true);
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rdfReader = new RdfReader();
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this.mode = mode;
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}
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public void parseOneFile(Project project, ProjectMetadata metadata, ImportingJob job, String fileSource,
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InputStream input, int limit, JSONObject options, List<Exception> exceptions) {
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// create an empty model
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Model model = ModelFactory.createDefaultModel();
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@Override
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public void parseOneFile(Project project, ProjectMetadata metadata,
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ImportingJob job, String fileSource, InputStream input, int limit,
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JSONObject options, List<Exception> exceptions) {
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Graph graph;
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try {
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switch (mode) {
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case NT:
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graph = rdfReader.parseNTriples(input);
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model.read(input, null, "NT");
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break;
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case N3:
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graph = rdfReader.parseN3(input);
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case TTL:
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model.read(input, null, "TTL");
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break;
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case RDFXML:
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graph = rdfReader.parseRdfXml(input);
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model.read(input, null);
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break;
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default:
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throw new IllegalArgumentException("Unknown parsing mode");
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@ -105,62 +99,62 @@ public class RdfTripleImporter extends ImportingParserBase {
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return;
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}
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ClosableIterable<Triple> triples = graph.find(ANY_SUBJECT_NODE, ANY_PREDICATE_NODE, ANY_OBJECT_NODE);
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try {
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Map<String, List<Row>> subjectToRows = new LinkedHashMap<String, List<Row>>();
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Column subjectColumn = new Column(project.columnModel.allocateNewCellIndex(), "subject");
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project.columnModel.addColumn(0, subjectColumn, false);
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project.columnModel.setKeyColumnIndex(0);
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StmtIterator triples = model.listStatements();
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for (Triple triple : triples) {
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String subject = triple.getSubject().toString();
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String predicate = triple.getPredicate().toString();
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String object = triple.getObject().toString();
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try {
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Map<String, List<Row>> subjectToRows = new LinkedHashMap<String, List<Row>>();
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Column subjectColumn = new Column(project.columnModel.allocateNewCellIndex(), "subject");
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project.columnModel.addColumn(0, subjectColumn, false);
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project.columnModel.setKeyColumnIndex(0);
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Column column = project.columnModel.getColumnByName(predicate);
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if (column == null) {
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column = new Column(project.columnModel.allocateNewCellIndex(), predicate);
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project.columnModel.addColumn(-1, column, true);
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}
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while (triples.hasNext()) {
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Statement triple = triples.nextStatement();
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String subject = triple.getSubject().toString();
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String predicate = triple.getPredicate().toString();
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String object = triple.getObject().toString();
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int cellIndex = column.getCellIndex();
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if (subjectToRows.containsKey(subject)) {
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List<Row> rows = subjectToRows.get(subject);
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for (Row row : rows) {
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if (!ExpressionUtils.isNonBlankData(row.getCellValue(cellIndex))) {
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row.setCell(cellIndex, new Cell(object, null));
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object = null;
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break;
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}
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}
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Column column = project.columnModel.getColumnByName(predicate);
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if (column == null) {
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column = new Column(project.columnModel.allocateNewCellIndex(), predicate);
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project.columnModel.addColumn(-1, column, true);
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}
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if (object != null) {
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Row row = new Row(project.columnModel.getMaxCellIndex() + 1);
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rows.add(row);
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int cellIndex = column.getCellIndex();
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if (subjectToRows.containsKey(subject)) {
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List<Row> rows = subjectToRows.get(subject);
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for (Row row : rows) {
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if (!ExpressionUtils.isNonBlankData(row.getCellValue(cellIndex))) {
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row.setCell(cellIndex, new Cell(object, null));
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object = null;
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break;
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}
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}
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row.setCell(cellIndex, new Cell(object, null));
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}
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} else {
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List<Row> rows = new ArrayList<Row>();
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subjectToRows.put(subject, rows);
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if (object != null) {
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Row row = new Row(project.columnModel.getMaxCellIndex() + 1);
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rows.add(row);
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Row row = new Row(project.columnModel.getMaxCellIndex() + 1);
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rows.add(row);
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row.setCell(cellIndex, new Cell(object, null));
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}
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} else {
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List<Row> rows = new ArrayList<Row>();
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subjectToRows.put(subject, rows);
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row.setCell(subjectColumn.getCellIndex(), new Cell(subject, null));
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row.setCell(cellIndex, new Cell(object, null));
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}
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}
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Row row = new Row(project.columnModel.getMaxCellIndex() + 1);
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rows.add(row);
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for (Entry<String, List<Row>> entry : subjectToRows.entrySet()) {
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project.rows.addAll(entry.getValue());
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}
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} catch (ModelException e) {
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exceptions.add(e);
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} finally {
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triples.iterator().close();
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}
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row.setCell(subjectColumn.getCellIndex(), new Cell(subject, null));
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row.setCell(cellIndex, new Cell(object, null));
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}
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}
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super.parseOneFile(project, metadata, job, fileSource, input, limit, options, exceptions);
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for (Entry<String, List<Row>> entry : subjectToRows.entrySet()) {
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project.rows.addAll(entry.getValue());
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}
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} catch (ModelException e) {
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exceptions.add(e);
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}
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super.parseOneFile(project, metadata, job, fileSource, input, limit, options, exceptions);
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}
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}
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@ -106,7 +106,7 @@ public class RdfTripleImporterTests extends ImporterTest {
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//row0
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Assert.assertEquals(project.rows.get(0).cells.size(), 2);
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Assert.assertEquals(project.rows.get(0).cells.get(0).value, "http://rdf.freebase.com/ns/en.bob_dylan");
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Assert.assertEquals(project.rows.get(0).cells.get(1).value, "http://rdf.freebase.com/ns/en.blood_on_the_tracks");
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Assert.assertEquals(project.rows.get(0).cells.get(1).value, "http://rdf.freebase.com/ns/en.bringing_it_all_back_home");
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//row1
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Assert.assertEquals(project.rows.get(1).cells.size(), 2);
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@ -118,7 +118,7 @@ public class RdfTripleImporterTests extends ImporterTest {
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//row2
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Assert.assertEquals(project.rows.get(2).cells.size(), 2);
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Assert.assertNull(project.rows.get(2).cells.get(0));
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Assert.assertEquals(project.rows.get(2).cells.get(1).value, "http://rdf.freebase.com/ns/en.bringing_it_all_back_home");
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Assert.assertEquals(project.rows.get(2).cells.get(1).value, "http://rdf.freebase.com/ns/en.blood_on_the_tracks");
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Assert.assertEquals(project.recordModel.getRowDependency(2).cellDependencies[1].rowIndex, 0);
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Assert.assertEquals(project.recordModel.getRowDependency(2).cellDependencies[1].cellIndex, 0);
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}
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@ -143,23 +143,23 @@ public class RdfTripleImporterTests extends ImporterTest {
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//row0
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Assert.assertEquals(project.rows.get(0).cells.size(), 3);
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Assert.assertEquals(project.rows.get(0).cells.get(0).value, "http://rdf.freebase.com/ns/en.bob_dylan");
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Assert.assertEquals(project.rows.get(0).cells.get(1).value, "http://rdf.freebase.com/ns/en.blood_on_the_tracks");
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Assert.assertEquals(project.rows.get(0).cells.get(1).value, "http://rdf.freebase.com/ns/en.bringing_it_all_back_home");
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Assert.assertEquals(project.rows.get(0).cells.get(2).value, "http://rdf.freebase.com/ns/en.folk_rock");
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//row1
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Assert.assertEquals(project.rows.get(1).cells.size(), 2);
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Assert.assertNull(project.rows.get(1).cells.get(0));
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Assert.assertEquals(project.rows.get(1).cells.get(1).value, "http://rdf.freebase.com/ns/en.bringing_it_all_back_home");
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Assert.assertEquals(project.rows.get(1).cells.get(1).value, "http://rdf.freebase.com/ns/en.blood_on_the_tracks");
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Assert.assertEquals(project.recordModel.getRowDependency(1).cellDependencies[1].rowIndex, 0);
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Assert.assertEquals(project.recordModel.getRowDependency(1).cellDependencies[1].cellIndex, 0);
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}
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@Test
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public void canParseTripleWithValue() throws UnsupportedEncodingException {
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String sampleRdf = "<http://rdf.freebase.com/ns/en.bob_dylan> <http://rdf.freebase.com/ns/common.topic.alias> \"Robert Zimmerman\"@en.";
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String sampleRdf = "<http://rdf.freebase.com/ns/en.bob_dylan> <http://rdf.freebase.com/ns/common.topic.alias>\"Robert Zimmerman\"@en.";
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InputStream input = new ByteArrayInputStream(sampleRdf.getBytes("UTF-8"));
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SUT = new RdfTripleImporter(RdfTripleImporter.Mode.NT);
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SUT = new RdfTripleImporter(RdfTripleImporter.Mode.N3);
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parseOneFile(SUT, input);
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Assert.assertEquals(project.columnModel.columns.size(), 2);
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@ -168,10 +168,11 @@ public class RdfTripleImporterTests extends ImporterTest {
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Assert.assertEquals(project.rows.size(), 1);
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Assert.assertEquals(project.rows.get(0).cells.size(), 2);
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Assert.assertEquals(project.rows.get(0).cells.get(0).value, "http://rdf.freebase.com/ns/en.bob_dylan");
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Assert.assertEquals(project.rows.get(0).cells.get(1).value, "\"Robert Zimmerman\"@en");
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} @Test
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Assert.assertEquals(project.rows.get(0).cells.get(1).value, "Robert Zimmerman@en");
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}
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public void parseRdfXml() throws UnsupportedEncodingException {
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@Test
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public void canParseRdfXml() throws UnsupportedEncodingException {
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// From W3C spec http://www.w3.org/TR/REC-rdf-syntax/#example8
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String sampleRdf = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n"
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+ "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n"
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@ -200,10 +201,37 @@ public class RdfTripleImporterTests extends ImporterTest {
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Assert.assertEquals(project.rows.size(), 5);
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Assert.assertEquals(project.rows.get(0).cells.size(), 2);
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Assert.assertEquals(project.rows.get(0).cells.get(0).value, "http://www.w3.org/TR/rdf-syntax-grammar");
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Assert.assertEquals(project.rows.get(0).cells.get(1).value, "\"RDF/XML Syntax Specification (Revised)\"");
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Assert.assertEquals(project.rows.get(0).cells.get(1).value, "RDF/XML Syntax Specification (Revised)@en-US");
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Assert.assertEquals(project.rows.get(3).cells.size(), 3);
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Assert.assertEquals(project.rows.get(3).cells.get(0).value, "http://example.org/buecher/baum");
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Assert.assertEquals(project.rows.get(3).cells.get(1).value, "\"Der Baum\"@de");
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Assert.assertEquals(project.rows.get(3).cells.get(2).value, "\"Das Buch ist außergewöhnlich\"@de");
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Assert.assertEquals(project.rows.get(3).cells.get(1).value, "The Tree@en");
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Assert.assertEquals(project.rows.get(3).cells.get(2).value, "Das Buch ist außergewöhnlich@de");
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}
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@Test
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public void canParseN3() throws UnsupportedEncodingException {
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String sampleRdf = "@prefix p: <http://www.example.org/personal_details#> .\n" +
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"@prefix m: <http://www.example.org/meeting_organization#> .\n\n" +
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"<http://www.example.org/people#fred>\n" +
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"p:GivenName \"Fred\";\n" +
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"p:hasEmail <mailto:fred@example.com>;\n" +
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"m:attending <http://meetings.example.com/cal#m1> .\n";
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InputStream input = new ByteArrayInputStream(sampleRdf.getBytes("UTF-8"));
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SUT = new RdfTripleImporter(RdfTripleImporter.Mode.N3);
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parseOneFile(SUT, input);
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Assert.assertEquals(project.columnModel.columns.size(), 4);
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Assert.assertEquals(project.columnModel.columns.get(0).getName(), "subject");
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Assert.assertEquals(project.columnModel.columns.get(1).getName(), "http://www.example.org/meeting_organization#attending");
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Assert.assertEquals(project.columnModel.columns.get(2).getName(), "http://www.example.org/personal_details#hasEmail");
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Assert.assertEquals(project.columnModel.columns.get(3).getName(), "http://www.example.org/personal_details#GivenName");
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Assert.assertEquals(project.rows.size(), 1);
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Assert.assertEquals(project.rows.get(0).cells.size(), 4);
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Assert.assertEquals(project.rows.get(0).cells.get(0).value, "http://www.example.org/people#fred");
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Assert.assertEquals(project.rows.get(0).cells.get(1).value, "http://meetings.example.com/cal#m1");
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Assert.assertEquals(project.rows.get(0).cells.get(2).value, "mailto:fred@example.com");
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Assert.assertEquals(project.rows.get(0).cells.get(3).value, "Fred");
|
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}
|
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}
|
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|
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BIN
main/webapp/WEB-INF/lib/jena-arq-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-arq-3.6.0.jar
Normal file
Binary file not shown.
BIN
main/webapp/WEB-INF/lib/jena-base-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-base-3.6.0.jar
Normal file
Binary file not shown.
BIN
main/webapp/WEB-INF/lib/jena-cmds-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-cmds-3.6.0.jar
Normal file
Binary file not shown.
BIN
main/webapp/WEB-INF/lib/jena-core-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-core-3.6.0.jar
Normal file
Binary file not shown.
BIN
main/webapp/WEB-INF/lib/jena-dboe-base-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-dboe-base-3.6.0.jar
Normal file
Binary file not shown.
BIN
main/webapp/WEB-INF/lib/jena-dboe-index-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-dboe-index-3.6.0.jar
Normal file
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BIN
main/webapp/WEB-INF/lib/jena-dboe-trans-data-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-dboe-trans-data-3.6.0.jar
Normal file
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BIN
main/webapp/WEB-INF/lib/jena-dboe-transaction-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-dboe-transaction-3.6.0.jar
Normal file
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BIN
main/webapp/WEB-INF/lib/jena-iri-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-iri-3.6.0.jar
Normal file
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BIN
main/webapp/WEB-INF/lib/jena-rdfconnection-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-rdfconnection-3.6.0.jar
Normal file
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BIN
main/webapp/WEB-INF/lib/jena-shaded-guava-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-shaded-guava-3.6.0.jar
Normal file
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BIN
main/webapp/WEB-INF/lib/jena-tdb-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-tdb-3.6.0.jar
Normal file
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BIN
main/webapp/WEB-INF/lib/jena-tdb2-3.6.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jena-tdb2-3.6.0.jar
Normal file
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BIN
main/webapp/WEB-INF/lib/jsonld-java-0.11.1.jar
Normal file
BIN
main/webapp/WEB-INF/lib/jsonld-java-0.11.1.jar
Normal file
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BIN
main/webapp/WEB-INF/lib/libthrift-0.10.0.jar
Normal file
BIN
main/webapp/WEB-INF/lib/libthrift-0.10.0.jar
Normal file
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@ -210,7 +210,8 @@ function registerImporting() {
|
||||
IM.registerFormat("text/line-based/fixed-width", "Fixed-width field text files", "FixedWidthParserUI",
|
||||
new Packages.com.google.refine.importers.FixedWidthImporter());
|
||||
|
||||
IM.registerFormat("text/rdf+n3", "RDF/N3 files", "RdfTriplesParserUI", new Packages.com.google.refine.importers.RdfTripleImporter());
|
||||
IM.registerFormat("text/rdf+n3", "RDF/N3 files", "RdfTriplesParserUI",
|
||||
new Packages.com.google.refine.importers.RdfTripleImporter(Packages.com.google.refine.importers.RdfTripleImporter.Mode.N3));
|
||||
|
||||
IM.registerFormat("text/xml", "XML files", "XmlParserUI", new Packages.com.google.refine.importers.XmlImporter());
|
||||
IM.registerFormat("binary/text/xml/xls/xlsx", "Excel files", "ExcelParserUI", new Packages.com.google.refine.importers.ExcelImporter());
|
||||
|
||||
Loading…
Reference in New Issue
Block a user