D-Net

package eu.dnetlib.resolver;

import com.googlecode.protobuf.format.JsonFormat;

import eu.dnetlib.data.collector.plugins.datacite.DataciteParser;

import eu.dnetlib.data.proto.dli.ScholixObjectProtos;

import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions;

import eu.dnetlib.dli.DLIUtils;

import eu.dnetlib.dli.resolver.*;

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

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

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

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

import eu.dnetlib.dli.resolver.model.serializer.DLIResolverSerializer;

import eu.dnetlib.pid.resolver.AbstractPIDResolver;

import eu.dnetlib.resolver.parser.DMFResolverParser;

import eu.dnetlib.resolver.parser.PMFResolverParser;

import eu.dnetlib.resolver.parser.ScholixResolverParser;

import org.apache.commons.io.IOUtils;

import org.apache.commons.lang3.StringUtils;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.junit.Assert;

import org.junit.Ignore;

import org.junit.Test;

import org.springframework.beans.factory.annotation.Autowired;

import java.io.IOException;

import java.io.InputStream;

import java.net.URISyntaxException;

import java.net.URL;

import java.time.LocalDateTime;

import java.util.Arrays;

/**

 * Created by sandro on 9/12/16.

 */

//@RunWith(SpringJUnit4ClassRunner.class)

//@ContextConfiguration(classes = { ConfigurationTestConfig.class})

@Ignore

public class DLIParserTest extends  DLIAbstractTest{

	private static final Log log = LogFactory.getLog(DLIParserTest.class);

	@Autowired

    private DLIResolverSerializer serializer;

	@Test

	public void testDMFParser() throws IOException {

		final InputStream resourceAsStream = getClass().getResourceAsStream("/eu/dnetlib/dli/transform/huge.xml");

		String str = IOUtils.toString(resourceAsStream);

		DMFResolverParser parser = new DMFResolverParser();

        DLIResolvedObject object = parser.parseObject(str);

        Assert.assertNotNull(object);

		Assert.assertNotNull(object.getTitles());

		Assert.assertNotNull(object.getDescription());

		Assert.assertNotNull(object.getType());

		System.out.println(object);

//		object.setTitles(Arrays.asList("TITOLO 1", "TITOLO 2"));

//		Assert.assertEquals(CompletionStatus.complete.toString(), object.getCompletionStatus());

//        DLIResolvedObject nullObject = parser.parseObject(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputRecordScholix.xml")));

//        Assert.assertNull(nullObject);

//		nullObject = parser.parseObject(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputPMFRecord.xml")));

//		Assert.assertNull(nullObject);

	}

	@Test

    public void testDOI(){

	    final String url="https://ssl.fao.org/glisapi/v1/pgrfas?doi=5gg0w";

	    DLIUtils.isValidDoi(url);

    }

	@Test

	public void testResolvedDate() throws IOException {

		final InputStream resourceAsStream = getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputPMF.xml");

		String str = IOUtils.toString(resourceAsStream);

		PMFResolverParser parser = new PMFResolverParser();

        DLIResolvedObject object = parser.parseObject(str);

        Assert.assertNotNull(object.getResolvedDate());

	}

	@Test

	public void testDataciteParser() throws Exception {

		final InputStream resourceAsStream = getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputRecordOpenaire.xml");

		String str = IOUtils.toString(resourceAsStream);

		DMFResolverParser parser = new DMFResolverParser();

        DLIResolvedObject object = parser.parseObject(str);

        System.out.println(object.getType());

		object.getRelations().forEach(it -> System.out.println(it.getTargetPID()));

		Assert.assertTrue(object.getCompletionStatus().equals("complete"));

		System.out.println("object = " + object);

		final String replacingXML = serializer.serializeReplacingXML(str, object);

		log.debug(replacingXML);

	}

	@Test

	public void testScholixParser() throws IOException, URISyntaxException {

		final InputStream resourceAsStream = getClass().getResourceAsStream("/eu/dnetlib/dli/parser/ieda.xml");

		String str = IOUtils.toString(resourceAsStream);

		ScholixResolverParser parser = new ScholixResolverParser();

        DLIResolvedObject object = parser.parseObject(str);

        final ScholixObjectProtos.Scholix.Builder scholix = ScholixObjectProtos.Scholix.newBuilder();

        scholix.addLinkproviderBuilder()

                .setName(object.getDatasourceProvenance().get(0).getDatasource())

                .addIdentifiersBuilder()

                .setIdentifier(object.getDatasourceProvenance().get(0).getDatasourceId())

                .setSchema("dnetIdentifier");

        scholix.setRelationship(ScholixObjectProtos.ScholixRelationship.newBuilder()

                .setName(object.getRelations().get(0).getRelationSemantics())

                .setInverse(object.getRelations().get(0).getInverseRelation())

                .setSchema("datacite")

                .build());

        final CrossRefParserJSON parserJSON = new CrossRefParserJSON();

        DLIResolvedObject dli_source = parserJSON.parseRecord(IOUtils.toString(new URL("https://api.crossref.org/works/10.1002/2016JG003630").openStream()));

        DLIResolvedObject dli_target = DataciteResolver.parseResponse(AbstractPIDResolver.requestURL("http://search.datacite.org/api?wt=json&q=doi:10.6073/pasta/6038bd9745347610df8a51c92ca0e452"));

        final ScholixObjectProtos.ScholixResource source = generateResource(dli_source);

        final ScholixObjectProtos.ScholixResource target = generateResource(dli_target);

        scholix.setSource(source);

        scholix.setTarget(target);

        scholix.setPublicationDate(LocalDateTime.now().toString());

        System.out.println(JsonFormat.printToString(scholix.build()));

        System.out.println(generateIdentifier(dli_source, dli_target));

	}

    private String generateIdentifier(final DLIResolvedObject source, DLIResolvedObject target) {

        return AbstractDNetXsltFunctions.md5(String.format("%s::%s", source.getPid().toLowerCase().trim(), target.getPid().toLowerCase().trim()));

    }

    private ScholixObjectProtos.ScholixResource generateResource(DLIResolvedObject result) {

        final ScholixObjectProtos.ScholixResource.Builder builder = ScholixObjectProtos.ScholixResource.newBuilder();

        if (result.getDatasourceProvenance() != null)

            result.getDatasourceProvenance().forEach(

                    objectProvenance -> {

                        builder.addCollectedFrom(ScholixObjectProtos.ScholixCollectedFrom.newBuilder()

                                .setProvisionMode(((DLIObjectProvenance) objectProvenance).getProvisionMode())

                                .setCompletionStatus(((DLIObjectProvenance) objectProvenance).getCompletionStatus())

                                .setProvider(ScholixObjectProtos.ScholixEntityId.newBuilder()

                                        .setName(objectProvenance.getDatasource())

                                        .addIdentifiers(ScholixObjectProtos.ScholixIdentifier.newBuilder().setIdentifier(objectProvenance.getDatasourceId())

                                                .setSchema("dnetIdentifier").build())

                                        .build()));

                        if (StringUtils.isNotEmpty(((DLIObjectProvenance) objectProvenance).getPublisher())) {

                            builder.addPublisher(ScholixObjectProtos.ScholixEntityId.newBuilder()

                                    .setName(((DLIObjectProvenance) objectProvenance).getPublisher())

                                    .build());

                        }

                    });

        builder.addIdentifier(ScholixObjectProtos.ScholixIdentifier.newBuilder().

                setIdentifier(result.getPid())

                .setSchema(result.getPidType())

                .build());

        builder.setObjectType(result.getType().toString());

        if (result.getTitles() != null && result.getTitles().size() > 0)

            builder.setTitle(result.getTitles().get(0));

        if (result.getAuthors() != null)

            result.getAuthors().forEach(author -> builder.addCreator(

                    ScholixObjectProtos.ScholixEntityId.newBuilder()

                            .setName(author)

                            .build()));

        if (StringUtils.isNotBlank(result.getDate())) {

            builder.setPublicationDate(result.getDate());

        }

        String tp = null;

        switch (result.getType()) {

            case dataset:

                tp = "60";

                break;

            case unknown:

                tp = "70";

                break;

            case publication:

                tp = "50";

                break;

        }

        builder.setDnetIdentifier(tp + "|dnet________::" + result.getIdentifier());

        return builder.build();

    }

	@Test

	public void testScholixCompleteParser() throws IOException {

		final InputStream resourceAsStream = getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputRecordScholix.xml");

		String str = IOUtils.toString(resourceAsStream);

		ScholixResolverParser parser = new ScholixResolverParser();

        DLIResolvedObject object = parser.parseObject(str);

		log.debug("object = " + object);

		Assert.assertNotNull(object);

		log.debug("object.getCompletionStatus() = " + object.getCompletionStatus());

//		Assert.assertTrue(object.getCompletionStatus().equals(CompletionStatus.complete.toString()));

//

//		Assert.assertNotNull(object.getDate());

//		Assert.assertNotNull(object.getTitles());

//		Assert.assertTrue(object.getTitles().size() == 1);

//

//		Assert.assertNotNull(object.getDatasourceProvenance());

//		Assert.assertTrue(object.getDatasourceProvenance().size() == 1);

//		Assert.assertNotNull(object.getDatasourceProvenance().get(0).getPublisher());

//		Assert.assertNotNull(object.getDatasourceProvenance().get(0).getPublisherId());

//

//

//		Assert.assertNotNull(object.getRelations());

//

//		Assert.assertTrue(object.getRelations().size() == 1);

//

//		Assert.assertNotNull(object.getRelations().get(0).getTargetPID().getId());

//		Assert.assertNotNull(object.getRelations().get(0).getTargetPID().getType());

//

//

//		DLIResolvedObject nullObject = parser.parseObject(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputRecordDMF.xml")));

//		Assert.assertNull(nullObject);

//		nullObject = parser.parseObject(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputPMFRecord.xml")));

//		Assert.assertNull(nullObject);

	}

	@Test

	public void testPMFParser() throws Exception {

		final InputStream resource = getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputPMF.xml");

		String xml = IOUtils.toString(resource);

		PMFResolverParser parser = new PMFResolverParser();

        final DLIResolvedObject resolvedObject = parser.parseObject(xml);

        Assert.assertNotNull(resolvedObject);

        Assert.assertNotNull(resolvedObject.getPidType());

		log.debug("resolvedObject = " + resolvedObject);

		Assert.assertNotNull(resolvedObject.getRelations());

		resolvedObject.getRelations().forEach(it -> Assert.assertNotNull(it));

        DLIResolvedObject nullObject = parser.parseObject(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputRecordScholix.xml")));

        Assert.assertNull(nullObject);

		nullObject = parser.parseObject(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputRecordDMF.xml")));

		Assert.assertNull(nullObject);

	}

	@Test

	public void testOpenAIREParser() throws Exception {

		final InputStream resource = getClass().getResourceAsStream("/eu/dnetlib/dli/parser/InputRecordOpenaire.xml");

		final String record = IOUtils.toString(resource);

		final OpenAireParser parser = new OpenAireParser();

        final DLIResolvedObject object = parser.parseObject(record);

        object.setPid("od_______908::ff0270cae25acd9367ef26a53ee5e4a3");

		object.setPidType("openaire");

        final DLIObjectProvenance provenance = new DLIObjectProvenance();

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

		provenance.setDatasourceId("dli::r3d100010778");

		provenance.setDatasource("NCBI Nucleotide");

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

		object.setDatasourceProvenance(Arrays.asList(provenance));

		log.debug(object);

	}

	@Test

	public void testProteinParser() throws IOException {

		final NCBINResolver resolver = new NCBINResolver();

		resolver.setNCBINParser(new NCBINParser());

        final DLIResolvedObject p02768 = resolver.resolve("U36380", "protein");

		log.debug(p02768.getDescription());

		Assert.assertNotNull(p02768);

		Assert.assertNotNull(p02768.getDescription());

		log.debug("p02768 = " + p02768);

	}

}