D-Net

package eu.dnetlib.resolver;

import java.io.IOException;

import java.io.InputStream;

import java.util.Arrays;

import java.util.List;

import eu.dnetlib.data.transform.OntologyLoader;

import eu.dnetlib.dli.DLIUtils;

import eu.dnetlib.dli.resolver.NCBINParser;

import eu.dnetlib.dli.resolver.NCBINResolver;

import eu.dnetlib.dli.resolver.OpenAireParser;

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.ResolverSerializer;

import eu.dnetlib.enabling.locators.UniqueServiceLocator;

import eu.dnetlib.resolver.parser.DMFResolverParser;

import eu.dnetlib.resolver.parser.PMFResolverParser;

import eu.dnetlib.resolver.parser.ScholixResolverParser;

import eu.dnetlib.rmi.enabling.ISLookUpException;

import eu.dnetlib.rmi.enabling.ISLookUpService;

import org.apache.commons.io.IOUtils;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.junit.Assert;

import org.junit.Before;

import org.junit.Ignore;

import org.junit.Test;

import org.mockito.Mock;

import org.mockito.Mockito;

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

import static org.mockito.Mockito.when;

/**

 * Created by sandro on 9/12/16.

 */

//@RunWith(SpringJUnit4ClassRunner.class)

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

@Ignore

public class DLIParserTest {

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

	@Mock

	private DLIUtils dliUtilsInstance;

	@Mock

	private UniqueServiceLocator uniqueServiceLocator;

	@Mock

	private ISLookUpService isLookUpServiceMock;

	@Autowired

	private ResolverSerializer serializer;

	@Before

	public void initialize() throws ISLookUpException, IOException {

		final String query = "for $x in collection('/db/DRIVER/RepositoryServiceResources/RepositoryServiceResourceType') "

				+ "return concat($x//FIELD[./key='NamespacePrefix']/value/text(),'@--@',$x//FIELD[./key='DataSourceId']/value/text(),'@--@',$x//ENGLISH_NAME )";

		dliUtilsInstance = Mockito.mock(DLIUtils.class);

		uniqueServiceLocator = Mockito.mock(UniqueServiceLocator.class);

		isLookUpServiceMock = Mockito.mock(ISLookUpService.class);

		dliUtilsInstance.setServiceLocator(uniqueServiceLocator);

		DLIUtils.setInstance(dliUtilsInstance);

		when(dliUtilsInstance.getServiceLocator()).thenReturn(uniqueServiceLocator);

		when(uniqueServiceLocator.getService(ISLookUpService.class)).thenReturn(isLookUpServiceMock);

		List<String> resutlDS = Arrays.asList(

				"r3d100010255@--@dli_________::r3d100010255@--@icpsr",

				"datacite____@--@dli_________::datacite____@--@Datasets in Datacite",

                "r3d100010134@--@dli_________::r3d100010134@--@pangaea",

                "r3d100010527@--@dli_________::r3d100010527@--@European Nucleotide Archive"

		);

		when(isLookUpServiceMock.quickSearchProfile(query)).thenReturn(resutlDS);

		DLIUtils.ontologies = OntologyLoader.loadOntologiesFromCp();

	}

	@Test

	public void testDMFParser() throws IOException {

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

		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 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 {

		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.incomplete.toString()));

		Assert.assertNotNull(object.getRelations());

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

        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 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);

		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);

	}

}