D-Net

package eu.dnetlib.utils.ontologies;

import com.google.gson.Gson;

import org.apache.commons.lang3.StringUtils;

import org.junit.Assert;

import org.junit.Test;

import java.io.IOException;

import java.io.InputStream;

import static org.junit.Assert.*;

/**

 * Created by claudio on 12/12/2016.

 */

public class OntologyLoaderTest {

    private String basePath = "/eu/dnetlib/test/profiles/OntologyDSResources/OntologyDSResourceType/";

    @Test

    public void testLoadOntologyFromCp() {

        final InputStream i = getClass().getResourceAsStream(basePath + "result_result_relations.xml");

        Ontology o = OntologyLoader.loadOntologyFromCp(i);

        checkOntology(o);

        String supplement = o.inverseOf("isSupplementedBy");

        assertEquals(supplement, "isSupplementTo");

        String part = o.inverseOf("isPartOf");

        assertEquals(part, "hasPart");

    }

    @Test

    public void testLoadOntologiesFromCp() throws IOException {

        OntologyLoader.loadOntologiesFromCp().values().forEach(o -> checkOntology(o));

    }

    @Test

    public void testLoadOntologiesSerialization() throws IOException {

        final Ontologies o = OntologyLoader.loadOntologiesFromCp();

        assertNotNull(o);

        final String json = o.toJson(true);

        assertFalse(StringUtils.isBlank(json));

        assertFalse("{}".equals(json.trim()));

        //System.out.println(json);

        assertTrue(StringUtils.isNoneBlank(json));

        final Ontologies o1 = new Gson().fromJson(json, Ontologies.class);

        assertNotNull(o1);

        o1.entrySet().forEach(e -> checkOntology(e.getValue()));

    }

    private void checkOntology(Ontology o) {

        Assert.assertNotNull(o);

        Assert.assertTrue(StringUtils.isNotBlank(o.getCode()));

        Assert.assertTrue(StringUtils.isNotBlank(o.getDescription()));

        Assert.assertNotNull(o.getTerms().values());

        o.getTerms().values().forEach(it -> {

            Assert.assertTrue(StringUtils.isNotBlank(it.getCode()));

            Assert.assertTrue(StringUtils.isNotBlank(it.getEncoding()));

            Assert.assertTrue(StringUtils.isNotBlank(it.getEnglishName()));

            Assert.assertTrue(StringUtils.isNotBlank(it.getNativeName()));

            Assert.assertTrue(StringUtils.isNotBlank(it.getInverseCode()));

            Assert.assertNotNull(o.getTerms().get(it.getInverseCode()));

        });

    }

}

		case "software":

		case "other":

		if (relInfo.length != 3) {

package eu.dnetlib.msro.openaireplus.workflows.nodes;

import com.googlecode.sarasvati.Arc;

import com.googlecode.sarasvati.NodeToken;

import eu.dnetlib.msro.workflows.nodes.SimpleJobNode;

import eu.dnetlib.utils.ontologies.Ontologies;

import eu.dnetlib.utils.ontologies.OntologyLoader;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

public class FetchOntologiesJobNode extends SimpleJobNode {

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

    private String paramName;

    @Override

    protected String execute(NodeToken token) throws Exception {

        final Ontologies ontologies = OntologyLoader.loadOntologiesFromIS();

        log.info(String.format("loaded %s ontology profiles", ontologies.size()));

        token.getEnv().setAttribute(getParamName(), ontologies.toJson());

        return Arc.DEFAULT_ARC;

    }

    public String getParamName() {

        return paramName;

    }

    public void setParamName(String paramName) {

        this.paramName = paramName;

    }

}

import com.google.common.collect.Maps;

import com.google.gson.Gson;

import org.apache.commons.io.IOUtils;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.dom4j.Document;

import org.dom4j.DocumentException;

import org.dom4j.Element;

import org.dom4j.Node;

import org.dom4j.io.SAXReader;

import org.springframework.core.io.support.PathMatchingResourcePatternResolver;

import javax.annotation.PostConstruct;

import java.io.IOException;

import java.io.InputStream;

import java.io.StringReader;

import java.util.Arrays;

import java.util.List;

import java.util.Map;

import java.util.function.Function;

import java.util.stream.Collectors;

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

    private static final String PATTERN = "classpath*:/eu/dnetlib/test/profiles/OntologyDSResources/OntologyDSResourceType/*.xml";

    private static UniqueServiceLocator staticServiceLocator;

    @Autowired

    private UniqueServiceLocator serviceLocator;

    // <TERM code="merges" encoding="organizationOrganization_dedup_merges" english_name="merges" native_name="merges">

    public static String fetchInverse(final String relType) throws ISLookUpException {

        final String xquery = "let $x:= /RESOURCE_PROFILE["

                + " .//RESOURCE_TYPE/@value = 'OntologyDSResourceType' and "

                + " .//TERM/@encoding='" + relType + "']"

                + "let $y:= $x//TERM[./@encoding='" + relType + "']//RELATION[./@type='inverseOf']/@code/string() "

                + "return $x//TERM[./@code = $y]/@encoding/string()";

        return staticServiceLocator.getService(ISLookUpService.class).getResourceProfileByQuery(xquery);

    }

    @PostConstruct

    public void init() {

        OntologyLoader.staticServiceLocator = serviceLocator;

    }

    public static Ontology loadOntologyFromCp(final InputStream profile) {

        return loadOntologyProfilefromPath(profile);

    }

    public static Ontologies loadOntologiesFromCp() throws IOException {

        final PathMatchingResourcePatternResolver resolver = new PathMatchingResourcePatternResolver();

        final List<InputStream> files = Arrays.asList(resolver.getResources(PATTERN)).stream().map(r -> {

            try {

                return r.getInputStream();

            } catch (IOException e) {

                throw new RuntimeException(e);

            }

        }).collect(Collectors.toList());

        return createOntologies(files);

    }

    public static Ontologies createOntologies(List<InputStream> files) {

        final Ontologies ontologies = new Ontologies();

        files.stream().map(

                s -> loadOntologyProfilefromPath(s))

                .collect(Collectors.toMap(Ontology::getCode, Function.identity()))

                .entrySet()

                .forEach(it -> ontologies.put(it.getKey(), it.getValue()));

        return ontologies;

    }

    public static Ontologies loadOntologiesFromIS() throws ISLookUpException {

        final ISLookUpService lookUpService = staticServiceLocator.getService(ISLookUpService.class);

        List<String> files = lookUpService.quickSearchProfile("for $x in collection('/db/DRIVER/OntologyDSResources/OntologyDSResourceType') return $x");

        final Ontologies ontologies = new Ontologies();

        files.stream().map

                (OntologyLoader::getOntologyFromProfile)

                .collect(Collectors.toMap(Ontology::getCode, Function.identity()))

                .entrySet()

                .forEach(it -> ontologies.put(it.getKey(), it.getValue()));

        return ontologies;

    }

    private static Ontology loadOntologyProfilefromPath(final InputStream profile) {

        final String profileXML;

        try {

            profileXML = IOUtils.toString(profile);

        } catch (IOException e) {

            log.error(e);

            return null;

        }

        return getOntologyFromProfile(profileXML);

    }

    private static Ontology getOntologyFromProfile(final String profile) {

        SAXReader saxReader = new SAXReader();

        Document doc = null;

        StringReader reader = new StringReader(profile);

        try {

            doc = saxReader.read(reader);

        } catch (DocumentException e) {

            e.printStackTrace();

            throw new RuntimeException(e);

        }

        return new Ontology()

                .setCode(doc.valueOf("//ONTOLOGY_NAME/@code"))

                .setDescription(doc.valueOf("//ONTOLOGY_DESCRIPTION/text()"))

                .setTerms(asTerms(doc.selectNodes("//TERMS/TERM")));

    }

    private static Map<String,OntologyTerm> asTerms(final List list) {

        final Map<String, OntologyTerm> terms = Maps.newHashMap();

        if (list != null) {

            list.forEach(o -> {

                final Element e = (Element) o;

                final OntologyTerm ot = OntologyTerm.newInstance()

                        .setCode(e.attributeValue("code"))

                        .setEncoding(e.attributeValue("encoding"))

                        .setEnglishName(e.attributeValue("english_name"))

                        .setNativeName(e.attributeValue("native_name"))

                        .setInverseCode(((Node) o).valueOf("./RELATIONS/RELATION[@type = 'inverseOf']/@code"));

                terms.put(ot.getCode(), ot);

            });

        }

        return terms;

    }

<RESOURCE_PROFILE>

	<HEADER>

		<RESOURCE_IDENTIFIER value="970c4826-cf6d-4dfe-850c-41e508d341fa_V29ya2Zsb3dEU1Jlc291cmNlcy9Xb3JrZmxvd0RTUmVzb3VyY2VUeXBl"/>

		<RESOURCE_TYPE value="WorkflowDSResourceType"/>

		<RESOURCE_KIND value="WorkflowDSResources"/>

		<RESOURCE_URI value=""/>

		<DATE_OF_CREATION value="2018-11-15T11:24:05+00:00"/>

	</HEADER>

	<BODY>

		<WORKFLOW_NAME>Import Organizations from DOIboost</WORKFLOW_NAME>

		<WORKFLOW_TYPE>Import InfoSpace</WORKFLOW_TYPE>

		<WORKFLOW_PRIORITY>30</WORKFLOW_PRIORITY>

		<CONFIGURATION start="manual">

			<NODE isStart="true" name="setOrgsOnly" type="SetEnvParameter">

				<DESCRIPTION>set the parameter to drive the import procedure behaviour so that it will import only organizations</DESCRIPTION>

				<PARAMETERS>

					<PARAM managedBy="system" name="parameterName" required="true" type="string">onlyOrganization</PARAM>

					<PARAM managedBy="user" name="parameterValue" required="false" type="string">true</PARAM>

				</PARAMETERS>

				<ARCS>

					<ARC to="importActionSet"/>

				</ARCS>

			</NODE>

			<NODE isStart="true" name="setInputPath" type="SetHdfsFile">

				<DESCRIPTION>set the hdfs output path</DESCRIPTION>

				<PARAMETERS>

					<PARAM managedBy="user" name="hdfsPath" required="true" type="string">/usr/dnet/data/doiboost</PARAM>

					<PARAM managedBy="system" name="hdfsPathParam" required="true" type="string">inputPath</PARAM>

				</PARAMETERS>

				<ARCS>

					<ARC to="prepareActionSets"/>

				</ARCS>

			</NODE>

			<NODE name="prepareActionSets" type="PrepareActionSets">

				<DESCRIPTION>prepare action sets</DESCRIPTION>

				<PARAMETERS>

					<PARAM managedBy="system" name="sets" required="true" type="string">

						[

						{

						'set' : 'doiboost-organizations',

						'jobProperty' : 'export_action_set_doiboost-organizations',

						'enablingProperty' : 'active_doiboost-organizations',

						'enabled' : 'true'

						}

						]

					</PARAM>

				</PARAMETERS>

				<ARCS>

					<ARC to="extractOutputPath"/>

				</ARCS>

			</NODE>

			<NODE name="extractOutputPath" type="ExtractOutputPath">

				<DESCRIPTION>extract the hdfs output path generated in the previous node</DESCRIPTION>

				<PARAMETERS>

					<PARAM managedBy="system" name="hdfsOutputPathParam" required="true" type="string">outputPath</PARAM>

				</PARAMETERS>

				<ARCS>

					<ARC to="importActionSet"/>

				</ARCS>

			</NODE>

			<NODE isJoin="true" name="importActionSet" type="SubmitHadoopJob">

				<DESCRIPTION>IIS main</DESCRIPTION>

				<PARAMETERS>

					<PARAM managedBy="system" name="hadoopJob" required="true" type="string">importDOIBoostJob</PARAM>

					<PARAM managedBy="system" name="cluster" required="true" type="string">DM</PARAM>

					<PARAM managedBy="system" name="envParams" required="true" type="string">

						{

						'mapred.input.dir':'inputPath',

						'mapred.output.dir':'outputPath',

						'onlyOrganization' : 'onlyOrganization'

						}

					</PARAM>

					<PARAM managedBy="user" name="simulation" required="true" type="boolean">false</PARAM>

				</PARAMETERS>

				<ARCS>

					<ARC to="updateActionSets"/>

				</ARCS>

			</NODE>

			<NODE name="updateActionSets" type="UpdateActionSets">

				<DESCRIPTION>update action sets</DESCRIPTION>

				<PARAMETERS/>

				<ARCS>

					<ARC to="success"/>

				</ARCS>

			</NODE>

		</CONFIGURATION>

		<STATUS>

			<LAST_EXECUTION_ID>wf_20181026_140552_878</LAST_EXECUTION_ID>

			<LAST_EXECUTION_DATE>2018-10-26T14:21:47+00:00</LAST_EXECUTION_DATE>

			<LAST_EXECUTION_STATUS>SUCCESS</LAST_EXECUTION_STATUS>

			<LAST_EXECUTION_ERROR/>

		</STATUS>

	</BODY>

</RESOURCE_PROFILE>

<RESOURCE_PROFILE>

	<HEADER>

		<RESOURCE_IDENTIFIER value="e03f256e-1e4d-4b3d-9c07-91faf5d25208_V29ya2Zsb3dEU1Jlc291cmNlcy9Xb3JrZmxvd0RTUmVzb3VyY2VUeXBl"/>

		<RESOURCE_TYPE value="WorkflowDSResourceType"/>

		<RESOURCE_KIND value="WorkflowDSResources"/>

		<RESOURCE_URI value=""/>

		<DATE_OF_CREATION value="2018-10-26T14:04:42+00:00"/>

	</HEADER>

	<BODY>

		<WORKFLOW_NAME>Import DOIboost</WORKFLOW_NAME>

		<WORKFLOW_TYPE>Import InfoSpace</WORKFLOW_TYPE>

		<WORKFLOW_PRIORITY>30</WORKFLOW_PRIORITY>

		<CONFIGURATION start="manual">

			<NODE isStart="true" name="setInputPath" type="SetHdfsFile">

				<DESCRIPTION>set the hdfs output path</DESCRIPTION>

				<PARAMETERS>

					<PARAM managedBy="user" name="hdfsPath" required="true" type="string">/usr/dnet/data/doiboost</PARAM>

					<PARAM managedBy="system" name="hdfsPathParam" required="true" type="string">inputPath</PARAM>

				</PARAMETERS>

				<ARCS>

					<ARC to="prepareActionSets"/>

				</ARCS>

			</NODE>

			<NODE name="prepareActionSets" type="PrepareActionSets">

				<DESCRIPTION>prepare action sets</DESCRIPTION>

				<PARAMETERS>

					<PARAM managedBy="system" name="sets" required="true" type="string">

						[

						{

						'set' : 'doiboost',

						'jobProperty' : 'export_action_set_doiboost',

						'enablingProperty' : 'active_doiboost',

						'enabled' : 'true'

						}

						]

					</PARAM>

				</PARAMETERS>

				<ARCS>

					<ARC to="extractOutputPath"/>

				</ARCS>

			</NODE>

			<NODE name="extractOutputPath" type="ExtractOutputPath">

				<DESCRIPTION>extract the hdfs output path generated in the previous node</DESCRIPTION>

				<PARAMETERS>

					<PARAM managedBy="system" name="hdfsOutputPathParam" required="true" type="string">outputPath</PARAM>

				</PARAMETERS>

				<ARCS>

					<ARC to="importActionSet"/>

				</ARCS>

			</NODE>

			<NODE isJoin="true" name="importActionSet" type="SubmitHadoopJob">

				<DESCRIPTION>IIS main</DESCRIPTION>

				<PARAMETERS>

					<PARAM managedBy="system" name="hadoopJob" required="true" type="string">importDOIBoostJob</PARAM>

					<PARAM managedBy="system" name="cluster" required="true" type="string">DM</PARAM>

					<PARAM managedBy="system" name="envParams" required="true" type="string">

						{

						'mapred.input.dir':'inputPath',

						'mapred.output.dir':'outputPath'

						}

					</PARAM>

					<PARAM managedBy="user" name="simulation" required="true" type="boolean">false</PARAM>

				</PARAMETERS>

				<ARCS>

					<ARC to="updateActionSets"/>

				</ARCS>

			</NODE>

			<NODE name="updateActionSets" type="UpdateActionSets">

				<DESCRIPTION>update action sets</DESCRIPTION>

				<PARAMETERS/>

				<ARCS>

					<ARC to="success"/>

				</ARCS>

			</NODE>

		</CONFIGURATION>

		<STATUS>

			<LAST_EXECUTION_ID>wf_20181114_161523_453</LAST_EXECUTION_ID>

			<LAST_EXECUTION_DATE>2018-11-14T16:59:55+00:00</LAST_EXECUTION_DATE>

			<LAST_EXECUTION_STATUS>SUCCESS</LAST_EXECUTION_STATUS>

			<LAST_EXECUTION_ERROR/>

		</STATUS>

	</BODY>

</RESOURCE_PROFILE>

<?xml version="1.0" encoding="UTF-8"?>

<RESOURCE_PROFILE xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">

    <HEADER>

        <RESOURCE_IDENTIFIER value="f3b803df-d9a9-4b78-a867-a106b74a8584_V29ya2Zsb3dEU1Jlc291cmNlcy9Xb3JrZmxvd0RTUmVzb3VyY2VUeXBl"/>

        <RESOURCE_TYPE value="WorkflowDSResourceType"/>

        <RESOURCE_KIND value="WorkflowDSResources"/>

        <RESOURCE_URI value=""/>

        <DATE_OF_CREATION value="2006-05-04T18:13:51.0Z"/>

    </HEADER>

    <BODY>

        <WORKFLOW_NAME>Fix relationships</WORKFLOW_NAME>

        <WORKFLOW_TYPE>Data Provision</WORKFLOW_TYPE>

        <WORKFLOW_PRIORITY>30</WORKFLOW_PRIORITY>

        <CONFIGURATION start="manual">

            <NODE name="fetchOntologies" type="FetchOntologies" isStart="true">

                <DESCRIPTION/>

                <PARAMETERS>

                    <PARAM name="paramName" type="string" managedBy="system" required="true">ontologies</PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="waitConf"/>

                </ARCS>

            </NODE>

            <NODE name="hadoopConfig" type="SetClusterAndTable" isStart="true">

                <DESCRIPTION>Set table name</DESCRIPTION>

                <PARAMETERS>

                    <PARAM required="true" type="string" name="cluster" managedBy="system">DM</PARAM>

                    <PARAM required="true" type="string" name="tableParam" managedBy="system">tableName</PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="waitConf"/>

                </ARCS>

            </NODE>

            <NODE name="waitConf" isJoin="true">

                <DESCRIPTION/>

                <PARAMETERS/>

                <ARCS>

                    <ARC to="setRelOrganizationsParam"/>

                </ARCS>

            </NODE>

            <NODE name="setRelOrganizationsParam" type="SetEnvParameter">

                <DESCRIPTION>set sub-entity type for organizations</DESCRIPTION>

                <PARAMETERS>

                    <PARAM name="parameterName" type="string" managedBy="system" required="true">subentitytype</PARAM>

                    <PARAM name="parameterValue" type="string" managedBy="system" required="true">organization</PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="fixRelOrganizations"/>

                </ARCS>

            </NODE>

            <NODE name="fixRelOrganizations" type="SubmitHadoopJob">

                <DESCRIPTION>fix the relationships among deduped and non-deduped objects</DESCRIPTION>

                <PARAMETERS>

                    <PARAM required="true" type="string" name="hadoopJob" managedBy="system">dedupFixRelationsJob</PARAM>

                    <PARAM required="true" type="string" name="envParams" managedBy="system">

                        {

                        'cluster' : 'cluster',

                        'hbase.mapred.inputtable' : 'tableName',

                        'hbase.mapreduce.inputtable' : 'tableName',

                        'hbase.mapred.outputtable' : 'tableName',

                        'hbase.mapreduce.outputtable' : 'tableName'

                        'ontologies' : 'ontologies',

                        'subentitytype' : 'subentitytype'

                        }

                    </PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="setRelPublicationsParam"/>

                </ARCS>

            </NODE>

            <NODE name="setRelPublicationsParam" type="SetEnvParameter">

                <DESCRIPTION>set sub-entity type for organizations</DESCRIPTION>

                <PARAMETERS>

                    <PARAM name="parameterName" type="string" managedBy="system" required="true">subentitytype</PARAM>

                    <PARAM name="parameterValue" type="string" managedBy="system" required="true">publication</PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="fixRelPublications"/>

                </ARCS>

            </NODE>

            <NODE name="fixRelPublications" type="SubmitHadoopJob">

                <DESCRIPTION>fix the relationships among deduped and non-deduped objects</DESCRIPTION>

                <PARAMETERS>

                    <PARAM required="true" type="string" name="hadoopJob" managedBy="system">dedupFixRelationsJob</PARAM>

                    <PARAM required="true" type="string" name="envParams" managedBy="system">

                        {

                        'cluster' : 'cluster',

                        'hbase.mapred.inputtable' : 'tableName',

                        'hbase.mapreduce.inputtable' : 'tableName',

                        'hbase.mapred.outputtable' : 'tableName',

                        'hbase.mapreduce.outputtable' : 'tableName'

                        'ontologies' : 'ontologies',

                        'subentitytype' : 'subentitytype'

                        }

                    </PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="setRelDatasetsParam"/>

                </ARCS>

            </NODE>

            <NODE name="setRelDatasetsParam" type="SetEnvParameter">

                <DESCRIPTION>set sub-entity type for organizations</DESCRIPTION>

                <PARAMETERS>

                    <PARAM name="parameterName" type="string" managedBy="system" required="true">subentitytype</PARAM>

                    <PARAM name="parameterValue" type="string" managedBy="system" required="true">dataset</PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="fixRelDatasets"/>

                </ARCS>

            </NODE>

            <NODE name="fixRelDatasets" type="SubmitHadoopJob">

                <DESCRIPTION>fix the relationships among deduped and non-deduped objects</DESCRIPTION>

                <PARAMETERS>

                    <PARAM required="true" type="string" name="hadoopJob" managedBy="system">dedupFixRelationsJob</PARAM>

                    <PARAM required="true" type="string" name="envParams" managedBy="system">

                        {

                        'cluster' : 'cluster',

                        'hbase.mapred.inputtable' : 'tableName',

                        'hbase.mapreduce.inputtable' : 'tableName',

                        'hbase.mapred.outputtable' : 'tableName',

                        'hbase.mapreduce.outputtable' : 'tableName'

                        'ontologies' : 'ontologies',

                        'subentitytype' : 'subentitytype'

                        }

                    </PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="setRelSoftwaresParam"/>

                </ARCS>

            </NODE>

            <NODE name="setRelSoftwaresParam" type="SetEnvParameter">

                <DESCRIPTION>set sub-entity type for organizations</DESCRIPTION>

                <PARAMETERS>

                    <PARAM name="parameterName" type="string" managedBy="system" required="true">subentitytype</PARAM>

                    <PARAM name="parameterValue" type="string" managedBy="system" required="true">software</PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="fixRelSoftwares"/>

                </ARCS>

            </NODE>

            <NODE name="fixRelSoftwares" type="SubmitHadoopJob">

                <DESCRIPTION>fix the relationships among deduped and non-deduped objects</DESCRIPTION>

                <PARAMETERS>

                    <PARAM required="true" type="string" name="hadoopJob" managedBy="system">dedupFixRelationsJob</PARAM>

                    <PARAM required="true" type="string" name="envParams" managedBy="system">

                        {

                        'cluster' : 'cluster',

                        'hbase.mapred.inputtable' : 'tableName',

                        'hbase.mapreduce.inputtable' : 'tableName',

                        'hbase.mapred.outputtable' : 'tableName',

                        'hbase.mapreduce.outputtable' : 'tableName'

                        'ontologies' : 'ontologies',

                        'subentitytype' : 'subentitytype'

                        }

                    </PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="setRelOthersParam"/>

                </ARCS>

            </NODE>

            <NODE name="setRelOthersParam" type="SetEnvParameter">

                <DESCRIPTION>set sub-entity type for organizations</DESCRIPTION>

                <PARAMETERS>

                    <PARAM name="parameterName" type="string" managedBy="system" required="true">subentitytype</PARAM>

                    <PARAM name="parameterValue" type="string" managedBy="system" required="true">other</PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="fixRelOthers"/>

                </ARCS>

            </NODE>

            <NODE name="fixRelOthers" type="SubmitHadoopJob">

                <DESCRIPTION>fix the relationships among deduped and non-deduped objects</DESCRIPTION>

                <PARAMETERS>

                    <PARAM required="true" type="string" name="hadoopJob" managedBy="system">dedupFixRelationsJob</PARAM>

                    <PARAM required="true" type="string" name="envParams" managedBy="system">

                        {

                        'cluster' : 'cluster',

                        'hbase.mapred.inputtable' : 'tableName',

                        'hbase.mapreduce.inputtable' : 'tableName',

                        'hbase.mapred.outputtable' : 'tableName',

                        'hbase.mapreduce.outputtable' : 'tableName'

                        'ontologies' : 'ontologies',

                        'subentitytype' : 'subentitytype'

                        }

                    </PARAM>

                </PARAMETERS>

                <ARCS>

                    <ARC to="success"/>

                </ARCS>

            </NODE>

        </CONFIGURATION>

        <STATUS/>

    </BODY>

</RESOURCE_PROFILE>

<?xml version="1.0" encoding="UTF-8"?>

<xsl:stylesheet version="2.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">

    <xsl:output indent="yes"/>

    <xsl:template match="/">

        <fundings>

            <fundingtree>

                <funder>

                    <id>rpf_________::RPF</id>

                    <shortname>RPF</shortname>

                    <name>Research Promotion Foundation</name>

                    <originalname>Research Promotion Foundation</originalname>

                    <jurisdiction>CY</jurisdiction>

                </funder>

            </fundingtree>

        </fundings>

    </xsl:template>

</xsl:stylesheet>

    <bean id="wfNodeUpdateActionSets"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.actions.UpdateSetsJobNode"

          scope="prototype"/>

    <bean id="wfNodePrepareActionSets"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.actions.PrepareActionSetsJobNode"

          scope="prototype"/>

    <bean id="wfNodeCleanActionSetsProfile"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.actions.CleanActionSetsProfileJobNode"

          p:xupdate="${dnet.actionmanager.garbage.sets.xupdate}" scope="prototype"/>

    <bean id="wfNodeGarbageSets"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.actions.GarbageSetsJobNode"

          scope="prototype"/>

    <bean id="wfNodeGarbageSetsHDFS"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.actions.GarbageSetsHDFSJobNode"

          scope="prototype"/>

    <bean id="wfNodePromoteActionsHDFS"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.actions.PromoteActionsHDFSJobNode"

          scope="prototype"/>

    <bean id="wfNodePromoteActions"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.actions.PromoteActionsJobNode"

          scope="prototype"/>

    <bean id="wfNodePrepareCopyTable"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.hbase.PrepareCopyTableJobNode"

          scope="prototype"/>

    <bean id="wfNodeIncrementalTransformation"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.IncrementalTransformationJobNode"

          scope="prototype"/>

    <bean id="wfNodeIncrementalOperation"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.IncrementalOperationJobNode"

          scope="prototype"/>

    <bean id="wfNodeDecapsuleClaims"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.claims.DecapsuleClaimsJobNode"

          scope="prototype"/>

    <bean id="wfNodeOpenaireMdBuilder"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.OpenaireMdBuilderJobNode"

          p:xsltMappedResultSetFactory-ref="xsltResultSetFactory"

          p:mdBuilderTemplateXslt-ref="openaireMdBuilderTemplateXslt" scope="prototype"/>

    <bean id="openaireMdBuilderTemplateXslt"

          class="eu.dnetlib.springutils.stringtemplate.StringTemplateFactory"

          p:template="classpath:/eu/dnetlib/msro/openaireplus/workflows/repo-hi/xslt/openaireMdBuilder.xslt.st"

          scope="prototype"/>

    <bean id="wfNodeUpdateOpenaireMetaWfStatus"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.repohi.UpdateOpenaireMetaWfStatusJobNode"

          scope="prototype"/>

    <bean id="wfNodeDeleteOpenaireMetaWf"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.repobye.DeleteOpenaireMetaWfJobNode"

          scope="prototype"/>

    <bean id="wfNodeUpdateRepositoryProfiles"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.UpdateRepositoryProfilesJobNode"

          scope="prototype"/>

    <bean id="wfNodeUpdateOpenaireDb" class="eu.dnetlib.msro.workflows.nodes.db.UpdateDbJobNode"

          scope="prototype" p:processCountingResultSetFactory-ref="msroProcessCountingResultSetFactory"

          p:db="${dnet.openaire.db.name}"/>

    <bean id="wfNodeUpdateVocabularyEntries"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.UpdateVocabularyEntriesJobNode"

          scope="prototype"

          p:xquery="classpath:/eu/dnetlib/msro/openaireplus/workflows/db/vocabulary_entries.xquery"/>

    <bean id="wfNodeFindVocabularyEntries"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.FindVocabularyEntriesJobNode"

          scope="prototype"

          p:xquery="classpath:/eu/dnetlib/msro/openaireplus/workflows/db/vocabulary_entries.xquery"/>

    <!-- 	<bean id="wfNodeGetHBaseTableDescription" -->

    <!-- 		class="eu.dnetlib.msro.openaireplus.workflows.nodes.hbase.GetHBaseTableDescriptionJobNode" -->

    <!-- 		scope="prototype" /> -->

    <bean id="wfNodeImportFiles"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.objectStore.ImportFilesJobNode"

          scope="prototype" p:processCountingResultSetFactory-ref="msroProcessCountingResultSetFactory"

          p:iterableResultSetFactory-ref="iterableResultSetFactory"/>

    <bean id="wfNodeRetreiveInterfaceInfo"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.repohi.RetrieveInterfaceInfoJobNode"

          scope="prototype"/>

    <bean id="wfNodeObtainOpenaireDataSourceParams"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.ObtainOpenaireDataSourceParamsJobNode"

          scope="prototype"/>

    <bean id="wfNodeSetHdfsFile"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.SetHdfsFileJobNode"

          scope="prototype"/>

    <!-- <bean id="wfNodeMDStoreImportJob" -->

    <!-- class="eu.dnetlib.msro.openaireplus.workflows.nodes.hbase.HBaseMapReduceJobNode" -->

    <!-- scope="prototype" p:hadoopJob-ref="mdStoreHdfsImportJob" -->

    <!-- p:targetTable="${hbase.mapred.datatable}" p:hFileOutput="${services.mapreduce.mdrecords.hdsf.hfile.output}" -->

    <!-- p:xslt="classpath:/eu/dnetlib/data/transform/dmf_2_hbase.xsl" /> -->

    <bean id="wfNodeFindSearchService"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.index.FindSearchServiceJobNode"

          scope="prototype"/>

    <bean id="wfNodeFindSearchServices"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.index.FindSearchServicesJobNode"

          scope="prototype"/>

    <bean id="wfNodeLoadContextsJob"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.LoadContextsJobNode"

          scope="prototype"/>

    <bean id="wfNodeLoadEntityLinksJob"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.LoadEntityLinksJobNode"

          scope="prototype"/>

    <bean id="wfNodePrepareIndexJob"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.index.PrepareIndexDataJobNode"

          scope="prototype" p:hbaseTable="${hbase.mapred.datatable}"/>

    <bean id="wfNodePrepareStatsParams"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.PrepareStatsParamJobNode"

          scope="prototype"/>

    <bean id="wfNodePrepareLodParams"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.PrepareLodParamJobNode"

          scope="prototype"/>

    <bean id="wfNodeFinalizeIndexFeeding"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.index.FinalizeIndexJobNode"

          scope="prototype"/>

    <bean id="wfNodeSwitchIndexes"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.index.SwitchIndexesJobNode"

          scope="prototype"/>

    <bean id="wfNodeSwitchSearchService"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.index.SwitchSearchServiceJobNode"

          scope="prototype"/>

    <!-- DEDUP -->

    <!-- 	<bean id="wfNodeConfigureOfflineDataLoad" -->

    <!-- 		class="eu.dnetlib.msro.openaireplus.workflows.nodes.dedup.ConfigureOfflineDataLoadJobNode" -->

    <!-- 		scope="prototype" />		 -->

    <!-- 	<bean id="wfNodeDefineHBaseDedupSchema" -->

    <!-- 		class="eu.dnetlib.msro.openaireplus.workflows.nodes.dedup.DefineHBaseDedupSchemaJobNode" -->

    <!-- 		scope="prototype" /> -->

    <!-- / DEDUP -->

    <bean id="wfNodePrepareIisMainParamsV2"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.PrepareIISMainParamsV2JobNode"

          scope="prototype" p:xqueryMdStoreService="${dnet.openaire.iis.mdstore.endpoint.xquery}"

          p:xqueryDatasetStore="${dnet.openaire.iis.mdstore.dataset.xquery}"

          p:xqueryObjectStores="${dnet.openaire.iis.objecstores.xquery}"

          p:xqueryObjectStoreService="${dnet.openaire.iis.objecstore.endpoint.xquery}"

          p:xqueryIsLookupService="${dnet.openaire.iis.islookup.endpoint.xquery}"/>

    <bean id="wfNodePreparePreprocessParamsV2"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.PrepareIISPreprocessingParamsV2JobNode"

          scope="prototype" p:xqueryDatabaseService="${dnet.openaire.iis.dbservice.endpoint.xquery}"

          p:xqueryMdStoreService="${dnet.openaire.iis.mdstore.endpoint.xquery}"

          p:xqueryObjectStoreService="${dnet.openaire.iis.objecstore.endpoint.xquery}"

          p:xqueryDatasetStore="${dnet.openaire.iis.mdstore.dataset.xquery}"

          p:xqueryWosMDStore="${dnet.openaire.iis.mdstore.wos.xquery}"

          p:xqueryDataciteObjectStore="${dnet.openaire.iis.objecstores.dataset.xquery}"

          p:xqueryWosObjectStore="${dnet.openaire.iis.objecstores.wos.xquery}"

          p:xqueryIsLookupService="${dnet.openaire.iis.islookup.endpoint.xquery}"/>

    <bean id="wfNodeIISCacheBuilder"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.IISCacheBuilderJobNode"

          scope="prototype" p:xqueryObjectStoreService="${dnet.openaire.iis.objecstore.endpoint.xquery}"/>

    <bean id="wfNodeDownloadFromMetadataOpenaire"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.objectStore.DownloadFromMetadataOpenaire"

          scope="prototype"/>

    <bean id="wfNodePatchHostedBy"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.hostedby.PatchHostedByJobNode"

          scope="prototype" p:mappedResultSetFactory-ref="mappedResultSetFactory"

          p:resultSetClientFactory-ref="resultSetClientFactory"/>

    <bean id="wfNodeFindHostedBy"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.hostedby.FindHostedByJobNode"

          scope="prototype" p:mappedResultSetFactory-ref="mappedResultSetFactory"

          p:resultSetClientFactory-ref="resultSetClientFactory"/>

    <bean id="wfNodeUpsertHostedByApis"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.hostedby.UpsertHostedByApisJobNode"

          scope="prototype"/>

    <bean id="wfNodeSplitDatasetRecord"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.datacite.SplitDatasetRecord"

          p:resultSetClientFactory-ref="resultSetClientFactory" scope="prototype"/>

    <bean id="wfNodeCollectDatasetsByJournal"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.datacite.CollectDatasetsByJournalJobNode"

          p:resultSetClientFactory-ref="resultSetClientFactory" scope="prototype"/>

    <!-- Stats -->

    <bean id="wfNodeFindStatsService"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.stats.FindStatsServiceJobNode"

          scope="prototype"/>

    <bean id="wfNodePromoteShadowStats"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.stats.PromoteShadowStatsJobNode"

          scope="prototype"/>

    <bean id="wfNodeRefreshShadowCache"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.stats.RefreshShadowCacheJobNode"

          scope="prototype"/>

    <bean id="wfNodeValidateShadowStats"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.stats.ValidateShadowStatsJobNode"

          scope="prototype"/>

    <bean id="wfNodeBackupStatsCache"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.stats.BackupStatsCacheJobNode"

          scope="prototype"/>

    <bean id="wfNodeRestoreStatsCache"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.stats.RestoreStatsCacheJobNode"

          scope="prototype"/>

    <bean id="wfNodePromoteShadowCacheStats"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.stats.PromoteShadowCacheStatsJobNode"

          scope="prototype"/>

    <bean id="wfNodeMigrateStatsCache"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.stats.MigrateStatsCacheJobNode"

          scope="prototype"/>

    <bean id="wfNodeRunMDStorePlugin"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.RunMDStorePluginJobNode"

          scope="prototype"/>

    <!-- Contexts -->

    <bean id="wfNodeProcessContexts"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.contexts.ProcessContextsJobNode"

          scope="prototype"/>

    <bean id="wfNodePrepareContextDbEntries"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.contexts.PrepareContextDbEntriesJobNode"

          scope="prototype"/>

    <bean id="wfNodeSaveContextProfile"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.contexts.SaveContextProfileJobNode"

          scope="prototype"/>

    <bean id="wfNodeCheckHDFSCounts"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.CheckHDFSCountJobNode"

          scope="prototype"/>

    <!-- Data Flow Monitoring -->

    <bean id="wfNodeTriggerPrepublicMonitoringScenario"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.dataFlowMonitoring.TriggerPrepublicMonitoringScenarioJobNode"

          scope="prototype"/>

    <bean id="wfNodeTriggerIndexMonitoringScenario"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.dataFlowMonitoring.TriggerIndexMonitoringScenarioJobNode"

          scope="prototype"/>

    <bean id="wfNodeFeedMissingClaims"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.index.FeedMissingClaimsJobNode"

          p:queue-ref="recentResultsQueue" p:oafToIndexRecordFactory-ref="apiOafToIndexRecordFactory"

          scope="prototype"/>

    <bean id="wfNodePrepareHostedbyUpdateSQL"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.hostedby.PrepareHostedbyUpdateSQL"

          scope="prototype"/>

    <bean id="wfNodeVREPost"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.vre.VREPostJobNode"

          scope="prototype"/>

    <bean id="wfNodeGenerateFETContext"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.contexts.GenerateFETH2020ContextJobNode"

          scope="prototype"/>

    <bean id="listActionManagerSetsValues" lazy-init="true"

          class="eu.dnetlib.functionality.modular.ui.workflows.values.ListActionManagerSetsValues"

          p:name="actionSets"/>

    <bean id="wfNodeApplyClaimRels"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.claims.ApplyClaimRelsJobNode"

          scope="prototype"/>

    <bean id="wfNodeApplyClaimUpdates"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.claims.ApplyClaimUpdatesJobNode"

          scope="prototype"/>

    <bean id="wfNodeFilterManagedDatasources"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.FilterManagedDatasourcesJobNode"

          scope="prototype"/>

    <bean id="wfNodeLoadBulkTaggingConfiguration"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.bulktag.LoadBulkTaggingConfigurationJobNode"

          p:xquery="${dnet.openaire.bulktag.xquery}"

          scope="prototype"/>

    <!-- Consistency nodes -->

    <bean id="wfNodeFixRepoMdstoreSizes"

    <bean id="wfNodeVerifyMdStoreSizes"

    <bean id="wfNodeFindInvalidRepoProfiles"

    <bean id="wfNodeFindInvalidMetaWorkflows"

    <bean id="wfNodeFindInvalidWorkflows"

    <bean id="wfNodeFindInvalidStores"

    <bean id="wfNodeFetchOntologies"

          class="eu.dnetlib.msro.openaireplus.workflows.nodes.FetchOntologiesJobNode"

          scope="prototype"/>

		<version>1.0.0</version>

			<version>[6.2.21-solr75]</version>

			<version>[2.3.2-solr75]</version>

			<version>[1.6.1-solr75]</version>

			<version>[2.1.6-solr75]</version>