D-Net

package eu.dnetlib.dli.resolver;

import com.google.common.collect.Lists;

import com.ximpleware.AutoPilot;

import com.ximpleware.VTDGen;

import com.ximpleware.VTDNav;

import eu.dnetlib.data.transform.VtdUtilityParser;

import eu.dnetlib.dli.resolver.model.*;

import eu.dnetlib.pid.resolver.model.ObjectType;

import eu.dnetlib.pid.resolver.model.SubjectType;

import java.util.Arrays;

import java.util.List;

/**

 * Created by sandro on 3/6/17.

 */

public class ENAParser {

    private static String ENA_NS_PREFIX = "r3d100010527";

    public DLIResolvedObject parser(final String record, final String pid, final String pidType) throws Exception {

        final VTDGen vg = new VTDGen();

        vg.setDoc(record.getBytes());

        vg.parse(true);

        final VTDNav vn = vg.getNav();

        final AutoPilot ap = new AutoPilot(vn);

        final DLIResolvedObject result = new DLIResolvedObject();

        List<VtdUtilityParser.Node> textValuesWithAttributes = VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//ROOT/entry", Arrays.asList("taxonomicDivision", "moleculeType", "firstPublic"));

        if (textValuesWithAttributes != null && !textValuesWithAttributes.isEmpty()) {

            result.setType(ObjectType.dataset);

            final VtdUtilityParser.Node firstNode = textValuesWithAttributes.get(0);

            result.setDate(firstNode.getAttributes().get("firstPublic"));

            final String moleculeType = firstNode.getAttributes().get("moleculeType");

            final String taxonomicDivision = firstNode.getAttributes().get("taxonomicDivision");

            result.setSubjects(Arrays.asList(new SubjectType("moleculeType", moleculeType), new SubjectType("taxonomicDivision", taxonomicDivision)));

        } else return null;

        result.setTitles(Arrays.asList(VtdUtilityParser.getSingleValue(ap, vn, "//ROOT/entry/description")));

        result.setPid(pid);

        result.setPidType(pidType);

        result.setCompletionStatus(CompletionStatus.complete.toString());

        final DLIObjectProvenance provenance = new DLIObjectProvenance();

        provenance.setCompletionStatus(CompletionStatus.complete.toString());

        provenance.setProvisionMode(ObjectProvisionMode.resolved.toString());

        DLIPIDResolver.setDatasourceProvenance(provenance, ENA_NS_PREFIX);

        result.setDatasourceProvenance(Lists.newArrayList(provenance));

        return result;

    }

}