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sandro.lab
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package eu.dnetlib.data.transform;
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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 com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.googlecode.protobuf.format.JsonFormat;
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import eu.dnetlib.data.graph.model.DNGFDecoder;
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import eu.dnetlib.data.graph.model.DNGFRowKeyDecoder;
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import eu.dnetlib.data.mapreduce.util.dao.HBaseTableDAO;
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import eu.dnetlib.data.proto.DNGFProtos.DNGF;
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import eu.dnetlib.data.proto.DliFieldTypeProtos;
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import eu.dnetlib.data.proto.DliProtos;
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import eu.dnetlib.data.proto.TypeProtos.Type;
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import eu.dnetlib.dli.proto.DNGFDLISummaryConverter;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.junit.Before;
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import org.junit.Test;
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import static eu.dnetlib.data.graph.utils.RelDescriptor.QUALIFIER_SEPARATOR;
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/**
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* Created by sandro on 2/13/17.
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*/
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public class DLIConvertertTest extends AbstractTransformerTest {
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private static final Log log = LogFactory.getLog(DLIConvertertTest.class);
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private Ontologies ontologies;
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@Before
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public void setUp() throws Exception {
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factory = new XsltRowTransformerFactory();
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ontologies = OntologyLoader.loadOntologiesFromCp();
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}
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@Test
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public void testLinkPangaeaDLI() throws Exception {
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final List<Row> rows = Lists.newArrayList();
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rows.addAll(asRows(loadFromTransformationProfile("dmfdli2hbase.xml"), load("record_dli_dmf.xml")));
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rows.addAll(asRows(loadFromTransformationProfile("dmfdli2hbase.xml"), load("record_dli_dmf2.xml")));
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rows.addAll(asRows(loadFromTransformationProfile("pmfdli2hbase.xml"), load("record_dli_pmf.xml")));
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printAll(mapAll(buildTable(rows)));
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}
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private void printAll(final Map<String, DNGFDLISummaryConverter> converters) {
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converters.forEach((id, converter) -> log.info(JsonFormat.printToString(converter.convert())));
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}
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private Map<String, DNGFDLISummaryConverter> mapAll(final Map<String, Map<String, Map<String, byte[]>>> table) throws Exception {
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final Map<String, DNGFDLISummaryConverter> builders = Maps.newHashMap();
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for (final Entry<String, Map<String, Map<String, byte[]>>> e : table.entrySet()) {
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map(builders, e.getKey(), e.getValue());
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}
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return builders;
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}
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private void map(final Map<String, DNGFDLISummaryConverter> converters, final String rowKey, final Map<String, Map<String, byte[]>> row) throws Exception {
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final Type type = DNGFRowKeyDecoder.decode(rowKey).getType();
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final Map<String, byte[]> familyMap = row.get("metadata");
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if (familyMap == null) return;
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final byte[] bodyB = familyMap.get(type.toString());
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if (bodyB != null) {
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ensureBuilder(converters, rowKey);
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final DNGF mainEntity = DNGFDecoder.decode(
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familyMap.get(type.toString()),
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DliFieldTypeProtos.completionStatus, DliProtos.completionStatus, DliProtos.resolvedfrom, DliProtos.typedIdentifier).getDNGF();
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converters.get(rowKey).setMainEntity(mainEntity);
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final Map<String, byte[]> rels = row.get("rels");
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rels.forEach((q, v) -> {
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final DNGF.Builder rel = DNGF.newBuilder(HBaseTableDAO.parseProto(v));
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rel.getRelBuilder().setCachedTarget(mainEntity.getEntity());
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final String source = rel.getRel().getSource();
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final Type sourceType = rel.getRel().getSourceType();
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rel.getRelBuilder().setSource(rel.getRel().getTarget());
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rel.getRelBuilder().setSourceType(rel.getRel().getTargetType());
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rel.getRelBuilder().setTarget(source);
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rel.getRelBuilder().setTargetType(sourceType);
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final Ontology o = ontologies.get(rel.getRel().getRelType().getSchemeid());
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final String inverse = o.inverseOf(rel.getRel().getRelType().getClassid());
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rel.getRelBuilder().getRelTypeBuilder().setClassid(inverse).setClassname(inverse);
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final String targetId = StringUtils.substringAfter(q, QUALIFIER_SEPARATOR);
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ensureBuilder(converters, targetId);
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converters.get(targetId).addRelation(rel.build());
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});
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}
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}
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private void ensureBuilder(final Map<String, DNGFDLISummaryConverter> builders, final String rowKey) {
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if (!builders.containsKey(rowKey)) {
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builders.put(rowKey, new DNGFDLISummaryConverter());
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}
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}
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}
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