D-Net

{"type_source": "SVN", "goal": "package -U -T 4C source:jar", "url": "http://svn-public.driver.research-infrastructures.eu/driver/dnet40/modules/dnet-mapreduce-jobs/trunk/", "deploy_repository": "dnet4-snapshots", "version": "4", "mail": "sandro.labruzzo@isti.cnr.it,michele.artini@isti.cnr.it, claudio.atzori@isti.cnr.it, alessia.bardi@isti.cnr.it", "deploy_repository_url": "http://maven.research-infrastructures.eu/nexus/content/repositories/dnet4-snapshots", "name": "dnet-mapreduce-jobs"}

net.sf.saxon.TransformerFactoryImpl

^(Corpus Oral Dialectal \(COD\)\.).*$

^(Kiri Karl Morgensternile).*$

^(\[Eksliibris Aleksandr).*\]$

^(Kiri A\. de Vignolles).*$

^(2 kirja Karl Morgensternile).*$

^(Pirita kloostri idaosa arheoloogilised).*$

^(Kiri tundmatule).*$

^(Kiri Jenaer Allgemeine Literaturzeitung toimetusele).*$

^(Eksliibris Nikolai Birukovile).*$

^(Eksliibris Nikolai Issakovile).*$

^(\[Eksliibris Aleksandr).*$

^(WHP Cruise Summary Information of section).*$

^(Measurement of the top quark\-pair production cross section with ATLAS in pp collisions at).*$

^(Measurement of the spin\-dependent structure function).*

<oaf:$name$>

	$metadata:{$it$}$

  <rels>

    $rels:{$it$}$

  </rels>

  <children>

	$children:{$it$}$

  </children>

</oaf:$name$>

$inference:{$it$}$

<?xml version="1.0"?>

<record>

  <result xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">

    <header>

      <dri:objIdentifier>$id$</dri:objIdentifier>

      <dri:dateOfCollection>$dateofcollection$</dri:dateOfCollection>

      <dri:dateOfTransformation>$dateoftransformation$</dri:dateOfTransformation>

      <counters>

	  $counters:{$it$}$

	  </counters>

    </header>

    <metadata>

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

		    xmlns:oaf="http://namespace.openaire.eu/oaf" 

		    xsi:schemaLocation="http://namespace.openaire.eu/oaf $schemaLocation$">

		$it$

      </oaf:entity>

    </metadata>

  </result>

</record>

<result>

    <dri:objIdentifier>$objIdentifier$</dri:objIdentifier>

	$metadata:{$it$}$

</result>

<rel inferred="$inferred$" trust="$trust$" inferenceprovenance="$inferenceprovenance$" provenanceaction="$provenanceaction$">

  <to class="$class$" scheme="$scheme$" type="$type$">$objIdentifier$</to>

  $metadata:{$it$}$

</rel>

<$name$$if(hasId)$ objidentifier="$id$"$else$$endif$>

	$metadata:{$it$}$

</$name$>

<instance id="$instanceId$">

    $metadata:{$it$}$

	$webresources:{$it$}$

</instance>

<webresource>

  <url>$identifier$</url>

</webresource>

### Root Level ###

log4j.rootLogger=WARN, CONSOLE

### Configuration for the CONSOLE appender ###

log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender

log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout

log4j.appender.CONSOLE.layout.ConversionPattern=[%-5p] %d %c - %m%n

org.apache.cxf.Logger=org.apache.cxf.common.logging.Log4jLogger

### Application Level ###

log4j.logger.eu.dnetlib=INFO

log4j.logger.eu.dnetlib.pace=DEBUG

log4j.logger.eu.dnetlib.data.transform.OafEntityMerger=DEBUG

package eu.dnetlib.data.mapreduce;

import java.util.List;

public class OptionalConfig {

	private com.typesafe.config.Config config;

	public OptionalConfig(com.typesafe.config.Config config) {

		this.config = config;

	}

	protected Object safe(String path) {

		return config.hasPath(path) ? config.getAnyRef(path) : null;

	}

	public Integer getInt(String path) {

		return (Integer) safe(path);

	}

	public String getString(String path) {

		return (String) safe(path);

	}

	@SuppressWarnings("unchecked")

	public <T> List<T> getList(String path) {

		return (List<T>) safe(path);

	}	

	public Double getDouble(String path) {

		Object safe = safe(path);

		if (safe instanceof Integer) {

			return Double.parseDouble(safe.toString());

		}

		return (Double) safe;

	}

	public Object getObject(String path) {

		return safe(path);

	}

	public Boolean getBoolean(String path) {

		return (Boolean) safe(path);

	}

	public Boolean hasPath(String path) {

		return getConfig().hasPath(path);

	}

	public com.typesafe.config.Config getConfig() {

		return config;

	}

}

package eu.dnetlib.data.mapreduce.util;

import java.util.Collections;

import java.util.List;

import java.util.Map;

import java.util.Map.Entry;

import com.google.common.collect.Maps;

import org.apache.hadoop.hbase.util.Bytes;

import org.apache.hadoop.mapreduce.Mapper.Context;

import com.google.common.collect.Lists;

import com.google.protobuf.InvalidProtocolBufferException;

import eu.dnetlib.data.proto.OafProtos.Oaf;

import eu.dnetlib.data.transform.OafEntityMerger;

public class UpdateMerger {

	private static final String UPDATE_MERGER = "UPDATE_MERGE";

	private static final String N_MERGES = "N_MERGES";

	@SuppressWarnings("rawtypes")

	public static Oaf mergeBodyUpdates(final Context context, final Map<byte[], byte[]> map) throws InvalidProtocolBufferException {

		final Map<String, byte[]> stringMap = Maps.newHashMap();

		for(Entry<byte[], byte[]> e : map.entrySet()) {

			stringMap.put(Bytes.toString(e.getKey()), e.getValue());

		}

		return doMerge(context, stringMap);

	}

	public static Oaf mergeBodyUpdates(final Map<String, byte[]> map) throws InvalidProtocolBufferException {

		return doMerge(null, map);

	}

	private static Oaf doMerge(final Context context, final Map<String, byte[]> map)

			throws InvalidProtocolBufferException {

		final byte[] value = map.get(DedupUtils.BODY_S);

		if (value == null) return null;

		Oaf.Builder builder = Oaf.newBuilder(Oaf.parseFrom(value));

		final List<String> keys = Lists.newArrayList();

		// we fetch all the body updates

		for (final String o : map.keySet()) {

			if (o.startsWith("update_")) {

				keys.add(o);

			}

		}

		if (!keys.isEmpty()) {

			// we merge all the sorted updates with the body

			Collections.sort(keys);

			for (final String k : keys) {

				final Oaf update = Oaf.parseFrom(map.get(k));

				// System.out.println("\n\nBODY: \n" + body.build().toString());

				// System.out.println("UPDATE: \n" + update.toString());

				builder.mergeFrom(update);

				// System.out.println("UDPATED BODY: \n" + body.build().toString() + "\n\n");

			}

			builder = OafEntityMerger.merge(builder);

			if (context != null) {

				context.getCounter(UPDATE_MERGER, N_MERGES).increment(keys.size());

			}

		}

		return builder.build();

	}

}

package eu.dnetlib.data.mapreduce.util;

import org.springframework.core.io.ClassPathResource;

import org.springframework.core.io.Resource;

public class TemplateResources {

	private Resource record = new ClassPathResource("/eu/dnetlib/data/mapreduce/util/record.st");

	private Resource instance = new ClassPathResource("/eu/dnetlib/data/mapreduce/util/instance.st");

	private Resource rel = new ClassPathResource("/eu/dnetlib/data/mapreduce/util/rel.st");

	private Resource webresource = new ClassPathResource("/eu/dnetlib/data/mapreduce/util/webresource.st");

	private Resource child = new ClassPathResource("/eu/dnetlib/data/mapreduce/util/child.st");

	private Resource tree = new ClassPathResource("/eu/dnetlib/data/mapreduce/util/tree.st");

	private Resource entity = new ClassPathResource("/eu/dnetlib/data/mapreduce/util/entity.st");

	public Resource getEntity() {

		return entity;

	}	

	public Resource getRecord() {

		return record;

	}

	public Resource getInstance() {

		return instance;

	}

	public Resource getRel() {

		return rel;

	}

	public Resource getWebresource() {

		return webresource;

	}

	public Resource getChild() {

		return child;

	}

	public Resource getTree() {

		return tree;

	}

}

package eu.dnetlib.data.mapreduce.util;

import java.io.StringReader;

import java.io.StringWriter;

import java.util.List;

import java.util.Map;

import java.util.Map.Entry;

import java.util.Set;

import javax.xml.transform.*;

import javax.xml.transform.dom.DOMSource;

import javax.xml.transform.stream.StreamResult;

import com.google.common.base.Joiner;

import com.google.common.base.Predicate;

import com.google.common.base.Splitter;

import com.google.common.collect.Lists;

import com.google.common.collect.Maps;

import com.google.common.collect.Sets;

import com.google.protobuf.Descriptors.EnumValueDescriptor;

import com.google.protobuf.Descriptors.FieldDescriptor;

import com.google.protobuf.GeneratedMessage;

import com.mycila.xmltool.XMLDoc;

import com.mycila.xmltool.XMLTag;

import eu.dnetlib.data.mapreduce.hbase.index.config.*;

import eu.dnetlib.data.proto.FieldTypeProtos.*;

import eu.dnetlib.data.proto.OafProtos.OafEntity;

import eu.dnetlib.data.proto.OafProtos.OafRel;

import eu.dnetlib.data.proto.PersonProtos.Person;

import eu.dnetlib.data.proto.ProjectProtos.Project;

import eu.dnetlib.data.proto.RelMetadataProtos.RelMetadata;

import eu.dnetlib.data.proto.ResultProtos.Result;

import eu.dnetlib.data.proto.ResultProtos.Result.Context;

import eu.dnetlib.data.proto.ResultProtos.Result.ExternalReference;

import eu.dnetlib.data.proto.ResultProtos.Result.Instance;

import eu.dnetlib.data.proto.ResultProtos.Result.Journal;

import eu.dnetlib.data.proto.TypeProtos.Type;

import eu.dnetlib.miscutils.functional.UnaryFunction;

import org.apache.commons.lang.StringUtils;

import org.dom4j.Document;

import org.dom4j.DocumentException;

import org.dom4j.Element;

import org.dom4j.Node;

import org.dom4j.io.SAXReader;

import static eu.dnetlib.miscutils.collections.MappedCollection.listMap;

public class XmlRecordFactory {

	// private static final Log log = LogFactory.getLog(XmlRecordFactory.class); // NOPMD by marko on 11/24/08 5:02 PM

	private final Map<String, Integer> relCounters = Maps.newHashMap();

	protected Set<String> specialDatasourceTypes = Sets.newHashSet("scholarcomminfra", "infospace", "pubsrepository::mock", "entityregistry");

	protected TemplateFactory templateFactory = new TemplateFactory();

	protected OafDecoder mainEntity = null;

	protected String key = null;

	protected List<OafDecoder> relations = Lists.newLinkedList();

	protected List<OafDecoder> children = Lists.newLinkedList();

	protected EntityConfigTable entityConfigTable;

	protected ContextMapper contextMapper;

	protected RelClasses relClasses;

	protected String schemaLocation;

	protected boolean entityDefaults;

	protected boolean relDefaults;

	protected boolean childDefaults;

	protected Set<String> contextes = Sets.newHashSet();

	protected List<String> extraInfo = Lists.newArrayList();

	protected Map<String, Integer> counters = Maps.newHashMap();

	protected Transformer transformer;

	public XmlRecordFactory(final EntityConfigTable entityConfigTable, final ContextMapper contextMapper, final RelClasses relClasses,

			final String schemaLocation, final boolean entityDefaults, final boolean relDefaults, final boolean childDefeaults)

			throws TransformerConfigurationException, TransformerFactoryConfigurationError {

		this.entityConfigTable = entityConfigTable;

		this.contextMapper = contextMapper;

		this.relClasses = relClasses;

		this.schemaLocation = schemaLocation;

		this.entityDefaults = entityDefaults;

		this.relDefaults = relDefaults;

		this.childDefaults = childDefeaults;

		transformer = TransformerFactory.newInstance().newTransformer();

		transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");

	}

	public static String removePrefix(final String s) {

		if (s.contains("|")) return StringUtils.substringAfter(s, "|");

		return s;

	}

	public static String escapeXml(final String value) {

		return value.replaceAll("&", "&amp;").replaceAll("<", "&lt;").replaceAll(">", "&gt;").replaceAll("\"", "&quot;").replaceAll("'", "&apos;");

	}

	public Map<String, Integer> getRelCounters() {

		return relCounters;

	}

	public RelClasses getRelClasses() {

		return relClasses;

	}

	public String getId() {

		return key;

	}

	public boolean isValid() {

		return mainEntity != null;

	}

	public void setMainEntity(final OafDecoder mainEntity) {

		this.mainEntity = mainEntity;

		this.key = mainEntity.decodeEntity().getId();

	}

	public void addRelation(final Type type, final OafDecoder rel) {

		addRelOrChild(type, relations, rel);

	}

	public void addChild(final Type type, final OafDecoder child) {

		addRelOrChild(type, children, child);

	}

	private void addRelOrChild(final Type type, final List<OafDecoder> list, final OafDecoder decoder) {

		final OafRel oafRel = decoder.getOafRel();

		final String rd = oafRel.getRelType().toString() + "_" + oafRel.getSubRelType() + "_" + relClasses.getInverse(oafRel.getRelClass());

		final LinkDescriptor ld = entityConfigTable.getDescriptor(type, new RelDescriptor(rd));

		if (getRelCounters().get(rd) == null) {

			getRelCounters().put(rd, 0);

		}

		if (ld == null) {

			list.add(decoder);

			return;

		}

		if (ld.getMax() < 0) {

			list.add(decoder);

			return;

		}

		if (getRelCounters().get(rd) < ld.getMax()) {

			getRelCounters().put(rd, getRelCounters().get(rd) + 1);

			list.add(decoder);

		}

	}

	public String build() {

		try {

			final OafEntityDecoder entity = mainEntity.decodeEntity();

			// log.info("building");

			// log.info("main: " + mainEntity);

			// log.info("rel:  " + relations);

			// log.info("chi:  " + children);

			// log.info("=============");

			final Type type = entity.getType();

			final List<String> metadata = decodeType(entity, null, entityDefaults, false);

			// rels has to be processed before the contexts because they enrich the contextMap with the funding info.

			final List<String> rels = listRelations();

			metadata.addAll(buildContexts(type));

			metadata.add(parseDataInfo(mainEntity));

			final String body = templateFactory.buildBody(type, metadata, rels, listChildren(), extraInfo);

			return templateFactory

					.buildRecord(type, key, entity.getDateOfCollection(), entity.getDateOfTransformation(), schemaLocation, body, countersAsXml());

		} catch (final Throwable e) {

			throw new RuntimeException(String.format("error building record '%s'", this.key), e);

		}

	}

	private String parseDataInfo(final OafDecoder decoder) {

		final DataInfo dataInfo = decoder.getOaf().getDataInfo();

		final StringBuilder sb = new StringBuilder();

		sb.append("<datainfo>");

		sb.append(asXmlElement("inferred", dataInfo.getInferred() + "", null, null));

		sb.append(asXmlElement("deletedbyinference", dataInfo.getDeletedbyinference() + "", null, null));

		sb.append(asXmlElement("trust", dataInfo.getTrust() + "", null, null));

		sb.append(asXmlElement("inferenceprovenance", dataInfo.getInferenceprovenance() + "", null, null));

		sb.append(asXmlElement("provenanceaction", null, dataInfo.getProvenanceaction(), null));

		sb.append("</datainfo>");

		return sb.toString();

	}

	private List<String> decodeType(final OafEntityDecoder decoder, final Set<String> filter, final boolean defaults, final boolean expandingRel) {

		final List<String> metadata = Lists.newArrayList();

		metadata.addAll(listFields(decoder.getMetadata(), filter, defaults, expandingRel));

		metadata.addAll(listFields(decoder.getOafEntity(), filter, defaults, expandingRel));

		if ((decoder.getEntity() instanceof Result) && !expandingRel) {

			metadata.add(asXmlElement("bestlicense", "", getBestLicense(), null));

			metadata.addAll(listFields(decoder.getEntity(), filter, defaults, expandingRel));

		}

		if ((decoder.getEntity() instanceof Person) && !expandingRel) {

			metadata.addAll(listFields(decoder.getEntity(), filter, defaults, expandingRel));

		}

		if ((decoder.getEntity() instanceof Project) && !expandingRel) {

			metadata.addAll(listFields(decoder.getEntity(), filter, defaults, expandingRel));

		}

		return metadata;

	}

	private Qualifier getBestLicense() {

		Qualifier bestLicense = getQualifier("UNKNOWN", "not available", "dnet:access_modes");

		final LicenseComparator lc = new LicenseComparator();

		for (final Instance instance : ((Result) mainEntity.decodeEntity().getEntity()).getInstanceList()) {

			if (lc.compare(bestLicense, instance.getLicence()) > 0) {

				bestLicense = instance.getLicence();

			}

		}

		return bestLicense;

	}

	public Qualifier getQualifier(final String classid, final String classname, final String schemename) {

		return Qualifier.newBuilder().setClassid(classid).setClassname(classname).setSchemeid(schemename).setSchemename(schemename).build();

	}

	private List<String> listRelations() {

		final List<String> rels = Lists.newArrayList();

		for (final OafDecoder decoder : this.relations) {

			final OafRel rel = decoder.getOafRel();

			final OafEntity cachedTarget = rel.getCachedTarget();

			final OafRelDecoder relDecoder = OafRelDecoder.decode(rel);

			// if (!relDecoder.getRelType().equals(RelType.personResult) || relDecoder.getRelTargetId().equals(key)) {

			if (relDecoder.getRelSourceId().equals(key) || relDecoder.getRelTargetId().equals(key)) {

				final List<String> metadata = Lists.newArrayList();

				final Type targetType = relDecoder.getTargetType(mainEntity.getEntity().getType());

				final Set<String> relFilter = entityConfigTable.getFilter(targetType, relDecoder.getRelDescriptor());

				metadata.addAll(listFields(relDecoder.getSubRel(), relFilter, false, true));

				String semanticclass = "";

				String semanticscheme = "";

				final RelDescriptor relDescriptor = relDecoder.getRelDescriptor();

				if ((cachedTarget != null) && cachedTarget.isInitialized()) {

					final Set<String> filter = entityConfigTable.getFilter(targetType, relDescriptor);

					metadata.addAll(decodeType(OafEntityDecoder.decode(cachedTarget), filter, relDefaults, true));

				}

				final RelMetadata relMetadata = relDecoder.getRelMetadata();

				// debug

				if (relMetadata == null) {

					// System.err.println(this);

					semanticclass = semanticscheme = "UNKNOWN";

				} else {

					semanticclass = relClasses.getInverse(relMetadata.getSemantics().getClassname());

					semanticscheme = relMetadata.getSemantics().getSchemename();

				}

				incrementCounter(relDescriptor.getSubRelType().toString());

				final LinkDescriptor ld = entityConfigTable.getDescriptor(relDecoder.getTargetType(mainEntity.getEntity().getType()), relDescriptor);

				final String relId = (ld != null) && !ld.isSymmetric() ? relDecoder.getRelTargetId() : relDecoder.getRelSourceId();

				final DataInfo info = decoder.getOaf().getDataInfo();

				rels.add(templateFactory.getRel(targetType, relId, metadata, semanticclass, semanticscheme, info.getInferred(), info.getTrust(),

						info.getInferenceprovenance(), info.getProvenanceaction().getClassid()));

			}

		}

		return rels;

	}

	// //////////////////////////////////

	private List<String> listChildren() {

		final List<String> children = Lists.newArrayList();

		for (final OafDecoder decoder : this.children) {

			final OafEntity cachedTarget = decoder.getOafRel().getCachedTarget();

			addChildren(children, cachedTarget, decoder.getRelDescriptor());

		}

		final OafEntityDecoder entity = mainEntity.decodeEntity();

		if (entity.getType().equals(Type.result)) {

			for (final Instance instance : ((Result) entity.getEntity()).getInstanceList()) {

				final Set<String> instanceFieldFilter = Sets.newHashSet("instancetype", "hostedby", "licence");

				children.add(templateFactory.getInstance(instance.getHostedby().getKey(), listFields(instance, instanceFieldFilter, false, false),

						listMap(instance.getUrlList(), new UnaryFunction<String, String>() {

							@Override

							public String evaluate(final String identifier) {

								return templateFactory.getWebResource(identifier);

							}

						})));

			}

			for (final ExternalReference er : ((Result) entity.getEntity()).getExternalReferenceList()) {

				// Set<String> filters = entityConfigTable.getFilter(Type.result, RelType.resultResult);

				final List<String> fields = listFields(er, null, false, false);

				children.add(templateFactory.getChild("externalreference", null, fields));

			}

		}

		return children;

	}

	private void addChildren(final List<String> children, final OafEntity target, final RelDescriptor relDescriptor) {

		final OafEntityDecoder decoder = OafEntityDecoder.decode(target);

		incrementCounter(relDescriptor.getSubRelType().toString());

		final Set<String> filters = entityConfigTable.getFilter(target.getType(), relDescriptor);

		children.add(templateFactory.getChild(decoder.getType().toString(), decoder.getId(), listFields(decoder.getMetadata(), filters, childDefaults, false)));

	}

	private List<String> listFields(final GeneratedMessage fields, final Set<String> filter, final boolean defaults, final boolean expandingRel) {

		final List<String> metadata = Lists.newArrayList();

		if (fields != null) {

			final Set<String> seen = Sets.newHashSet();

			for (final Entry<FieldDescriptor, Object> e : filterFields(fields, filter)) {

				// final String name = getFieldName(e.getKey().getName());

				final String name = e.getKey().getName();

				seen.add(name);

				addFieldValue(metadata, e.getKey(), e.getValue(), expandingRel);

			}

			if (defaults) {

				for (final FieldDescriptor fd : fields.getDescriptorForType().getFields()) {

					if (!seen.contains(fd.getName())) {

						addFieldValue(metadata, fd, getDefault(fd), expandingRel);

					}

				}

			}

		}

		return metadata;

	}

	private Object getDefault(final FieldDescriptor fd) {

		switch (fd.getType()) {

		case BOOL:

			return false;

		case BYTES:

			return "".getBytes();

		case MESSAGE: {

			if (Qualifier.getDescriptor().equals(fd.getMessageType())) return defaultQualifier();

			if (StructuredProperty.getDescriptor().equals(fd.getMessageType()))

				return StructuredProperty.newBuilder().setValue("").setQualifier(defaultQualifier()).build();

			if (KeyValue.getDescriptor().equals(fd.getMessageType())) return KeyValue.newBuilder().setKey("").setValue("").build();

			if (StringField.getDescriptor().equals(fd.getMessageType())) return StringField.newBuilder().setValue("").build();

			if (BoolField.getDescriptor().equals(fd.getMessageType())) return BoolField.newBuilder().buildPartial();

			return null;

		}

		case SFIXED32:

		case SFIXED64:

		case SINT32:

		case SINT64:

		case INT32:

		case INT64:

		case DOUBLE:

		case FIXED32:

		case FIXED64:

		case FLOAT:

			return 0;

		case STRING:

			return "";

		default:

			return null;

		}

	}

	private Qualifier defaultQualifier() {

		return Qualifier.newBuilder().setClassid("").setClassname("").setSchemeid("").setSchemename("").build();

	}

	@SuppressWarnings("unchecked")

	private void addFieldValue(final List<String> metadata, final FieldDescriptor fd, final Object value, final boolean expandingRel) {

		if (fd.getName().equals("dateofcollection") || fd.getName().equals("id") || /* fd.getName().equals("url") || */(value == null)) return;

		if (fd.getName().equals("datasourcetype")) {

			final String classid = ((Qualifier) value).getClassid();

			final Qualifier.Builder q = Qualifier.newBuilder((Qualifier) value);

			if (specialDatasourceTypes.contains(classid)) {

				q.setClassid("other").setClassname("other");

			}

			metadata.add(asXmlElement("datasourcetypeui", "", q.build(), null));

		}

		if (fd.isRepeated() && (value instanceof List<?>)) {

			for (final Object o : (List<Object>) value) {

				guessType(metadata, fd, o, expandingRel);

			}

		} else {

			guessType(metadata, fd, value, expandingRel);

		}

	}

	private void guessType(final List<String> metadata, final FieldDescriptor fd, final Object o, final boolean expandingRel) {

		if (fd.getType().equals(FieldDescriptor.Type.MESSAGE)) {

			if (Qualifier.getDescriptor().equals(fd.getMessageType())) {

				final Qualifier qualifier = (Qualifier) o;

				metadata.add(asXmlElement(fd.getName(), "", qualifier, null));

			}

			if (StructuredProperty.getDescriptor().equals(fd.getMessageType())) {

				final StructuredProperty sp = (StructuredProperty) o;

				metadata.add(asXmlElement(fd.getName(), sp.getValue(), sp.getQualifier(), sp.hasDataInfo() ? sp.getDataInfo() : null));

				if (!expandingRel && fd.getName().equals("pid")) {

					if (sp.getQualifier().getClassid().equalsIgnoreCase("doi")) {

						incrementCounter("doi");

					}

				}

			}

			if (KeyValue.getDescriptor().equals(fd.getMessageType())) {

				final KeyValue kv = (KeyValue) o;

				metadata.add("<" + fd.getName() + " name=\"" + escapeXml(kv.getValue()) + "\" id=\"" + escapeXml(removePrefix(kv.getKey())) + "\"/>");

			}

			if (StringField.getDescriptor().equals(fd.getMessageType())) {

				final String fieldName = fd.getName();

				if (fieldName.equals("fundingtree")) {

					final String xmlTree = o instanceof StringField ? ((StringField) o).getValue() : o.toString();

					if (expandingRel) {

						metadata.add(getRelFundingTree(xmlTree));

						fillContextMap(xmlTree);

					} else {

						metadata.add(xmlTree);

					}

				} else {

					final StringField sf = (StringField) o;

					final StringBuilder sb = new StringBuilder("<" + fd.getName());

					if (sf.hasDataInfo()) {

						final DataInfo dataInfo = sf.getDataInfo();

						dataInfoAsAttributes(sb, dataInfo);

					}

					sb.append(">" + escapeXml(sf.getValue()) + "</" + fd.getName() + ">");

					metadata.add(sb.toString());

				}

			}

			if (BoolField.getDescriptor().equals(fd.getMessageType())) {

				final BoolField bf = (BoolField) o;

				final StringBuilder sb = new StringBuilder("<" + fd.getName());

				if (bf.hasDataInfo()) {

					final DataInfo dataInfo = bf.getDataInfo();

					dataInfoAsAttributes(sb, dataInfo);

				}

				sb.append(">" + (bf.hasValue() ? bf.getValue() : "") + "</" + fd.getName() + ">");

				metadata.add(sb.toString());

			}

			if (Journal.getDescriptor().equals(fd.getMessageType()) && (o != null)) {

				final Journal j = (Journal) o;

				metadata.add("<journal " + "issn=\"" + escapeXml(j.getIssnPrinted()) + "\" " + "eissn=\"" + escapeXml(j.getIssnOnline()) + "\" " + "lissn=\""

						+ escapeXml(j.getIssnLinking()) + "\">" + escapeXml(j.getName()) + "</journal>");

			}

			if (Context.getDescriptor().equals(fd.getMessageType()) && (o != null)) {

				contextes.add(((Result.Context) o).getId());

			}

			if (ExtraInfo.getDescriptor().equals(fd.getMessageType()) && (o != null)) {

				final ExtraInfo e = (ExtraInfo) o;

				final StringBuilder sb = new StringBuilder("<" + fd.getName() + " ");

				sb.append("name=\"" + e.getName() + "\" ");

				sb.append("typology=\"" + e.getTypology() + "\" ");

				sb.append("provenance=\"" + e.getProvenance() + "\" ");

				sb.append("trust=\"" + e.getTrust() + "\"");

				sb.append(">");

				sb.append(e.getValue());

				sb.append("</" + fd.getName() + ">");

				extraInfo.add(sb.toString());

			}

		} else if (fd.getType().equals(FieldDescriptor.Type.ENUM)) {

			if (fd.getFullName().equals("eu.dnetlib.data.proto.OafEntity.type")) return;

			metadata.add(asXmlElement(fd.getName(), ((EnumValueDescriptor) o).getName(), null, null));

		} else {

			metadata.add(asXmlElement(fd.getName(), o.toString(), null, null));

		}

	}

	private StringBuilder dataInfoAsAttributes(final StringBuilder sb, final DataInfo dataInfo) {

		sb.append(" inferred=\"" + dataInfo.getInferred() + "\"");

		sb.append(" inferenceprovenance=\"" + dataInfo.getInferenceprovenance() + "\"");

		sb.append(" provenanceaction=\"" + dataInfo.getProvenanceaction().getClassid() + "\"");

		sb.append(" trust=\"" + dataInfo.getTrust() + "\" ");

		return sb;

	}

	private List<String> buildContexts(final Type type) {

		final List<String> res = Lists.newArrayList();

		if ((contextMapper != null) && !contextMapper.isEmpty() && type.equals(Type.result)) {

			XMLTag document = XMLDoc.newDocument(true).addRoot("contextRoot");

			for (final String context : contextes) {

				String id = "";

				for (final String token : Splitter.on("::").split(context)) {

					id += token;

					final ContextDef def = contextMapper.get(id);

					if (def == null) throw new IllegalStateException(String.format("cannot find context for id '%s'", id));

					if (def.getName().equals("context")) {

						final String xpath = "//context/@id='" + def.getId() + "'";

						if (!document.gotoRoot().rawXpathBoolean(xpath, new Object())) {

							document = addContextDef(document.gotoRoot(), def);

						}

					}

					if (def.getName().equals("category")) {

						final String rootId = StringUtils.substringBefore(def.getId(), "::");

						document = addContextDef(document.gotoRoot().gotoTag("//context[./@id='" + rootId + "']", new Object()), def);

					}

					if (def.getName().equals("concept")) {

						document = addContextDef(document, def).gotoParent();

					}

					id += "::";

				}

			}

			for (final org.w3c.dom.Element x : document.gotoRoot().getChildElement()) {

				try {

					res.add(asStringElement(x));

				} catch (final TransformerException e) {

					throw new RuntimeException(e);

				}

			}

		}

		return res;

	}

	private XMLTag addContextDef(final XMLTag tag, final ContextDef def) {

		tag.addTag(def.getName()).addAttribute("id", def.getId()).addAttribute("label", def.getLabel());

		if ((def.getType() != null) && !def.getType().isEmpty()) {

			tag.addAttribute("type", def.getType());

		}

		return tag;

	}

	private String asStringElement(final org.w3c.dom.Element element) throws TransformerException {

		final StringWriter buffer = new StringWriter();

		transformer.transform(new DOMSource(element), new StreamResult(buffer));

		return buffer.toString();

	}

	@SuppressWarnings("unchecked")

	private String getRelFundingTree(final String xmlTree) {

		String funding = "<funding>";

		try {

			final Document ftree = new SAXReader().read(new StringReader(xmlTree));

			funding = "<funding>";

			// String _id = "";

			funding += getFunderElement(ftree);

			for (final Object o : Lists.reverse(ftree.selectNodes("//fundingtree//*[starts-with(local-name(),'funding_level_')]"))) {

				final Element e = (Element) o;

				final String _id = e.valueOf("./id");

				funding += "<" + e.getName() + " name=\"" + escapeXml(e.valueOf("./name")) + "\">" + escapeXml(_id) + "</" + e.getName() + ">";

				// _id += "::";

			}

		} catch (final DocumentException e) {

			throw new IllegalArgumentException("unable to parse funding tree: " + xmlTree + "\n" + e.getMessage());

		} finally {

			funding += "</funding>";

		}

		return funding;

	}

	private String getFunderElement(final Document ftree) {

		final String funderId = ftree.valueOf("//fundingtree/funder/id/text()");

		final String funderShortName = ftree.valueOf("//fundingtree/funder/shortname/text()");

		final String funderName = ftree.valueOf("//fundingtree/funder/name/text()");

		final String funderJurisdiction = ftree.valueOf("//fundingtree/funder/jurisdiction/text()");

		return "<funder id=\"" + escapeXml(funderId) + "\" shortname=\"" + escapeXml(funderShortName) + "\" name=\"" + escapeXml(funderName)

				+ "\" jurisdiction=\"" + escapeXml(funderJurisdiction) + "\" />";

	}

	private void fillContextMap(final String xmlTree) {

		Document fundingPath;

		try {

			fundingPath = new SAXReader().read(new StringReader(xmlTree));

		} catch (final DocumentException e) {

			throw new RuntimeException(e);

		}

		try {

			final Node funder = fundingPath.selectSingleNode("//funder");

			if (funder != null) {

				final String funderShortName = funder.valueOf("./shortname");

				contextes.add(funderShortName);

				contextMapper.put(funderShortName, new ContextDef(funderShortName, funder.valueOf("./name"), "context", "funding"));

				final Node level0 = fundingPath.selectSingleNode("//funding_level_0");

				if (level0 != null) {

					final String level0Id = Joiner.on("::").join(funderShortName, level0.valueOf("./name"));

					contextMapper.put(level0Id, new ContextDef(level0Id, level0.valueOf("./description"), "category", ""));

					final Node level1 = fundingPath.selectSingleNode("//funding_level_1");

					if (level1 == null) {

						contextes.add(level0Id);

					} else {

						final String level1Id = Joiner.on("::").join(level0Id, level1.valueOf("./name"));

						contextMapper.put(level1Id, new ContextDef(level1Id, level1.valueOf("./description"), "concept", ""));

						final Node level2 = fundingPath.selectSingleNode("//funding_level_2");

						if (level2 == null) {

							contextes.add(level1Id);

						} else {

							final String level2Id = Joiner.on("::").join(level1Id, level2.valueOf("./name"));

							contextMapper.put(level2Id, new ContextDef(level2Id, level2.valueOf("./description"), "concept", ""));

							contextes.add(level2Id);

						}

					}

				}

			}

		} catch (final NullPointerException e) {

			throw new IllegalArgumentException("malformed funding path: " + xmlTree, e);

		}

	}

	private String asXmlElement(final String name, final String value, final Qualifier q, final DataInfo dataInfo) {

		StringBuilder sb = new StringBuilder();

		sb.append("<");

		sb.append(name);

		if (q != null) {

			sb.append(getAttributes(q));

		}

		if (dataInfo != null) {

			sb = dataInfoAsAttributes(sb, dataInfo);

		}

		if ((value == null) || value.isEmpty()) {

			sb.append("/>");

			return sb.toString();

			// return "<" + name + getAttributes(q) + "/>";

		}

		sb.append(">");

		// sb.append(escapeXml(Normalizer.normalize(value, Normalizer.Form.NFD)));

		sb.append(escapeXml(value));

		sb.append("</");

		sb.append(name);

		sb.append(">");

		return sb.toString();

		// return "<" + name + getAttributes(q) + ">" + escapeXml(value) + "</" + name + ">";

	}

	private String getAttributes(final Qualifier q) {

		if (q == null) return "";

		final StringBuilder sb = new StringBuilder();

		for (final Entry<FieldDescriptor, Object> e : q.getAllFields().entrySet()) {

			// sb.append(" " + e.getKey().getName() + "=\"" + escapeXml(e.getValue().toString()) + "\"");

			sb.append(" ");

			sb.append(e.getKey().getName());

			sb.append("=\"");

			sb.append(escapeXml(e.getValue().toString()));

			sb.append("\"");

		}

		return sb.toString();

	}

	private Set<Entry<FieldDescriptor, Object>> filterFields(final GeneratedMessage fields, final Set<String> filter) {

		if (filter != null) {

			final Predicate<FieldDescriptor> p = new Predicate<FieldDescriptor>() {

				@Override

				public boolean apply(final FieldDescriptor descriptor) {

					if (fields == null) return false;

					final String name = descriptor.getName();

					return filter.contains(name);

				}

			};

			final Map<FieldDescriptor, Object> filtered = Maps.filterKeys(fields.getAllFields(), p);

			// log.info(

			// "filtered " + type.toString() + ": " + toString(filterEntries.keySet()) + "\n" +

			// "builder  " + fields.getDescriptorForType().getFullName() + ": " + toString(fields.getAllFields().keySet()));

			return filtered.entrySet();

		}

		return fields.getAllFields().entrySet();

	}

	private List<String> countersAsXml() {

		final List<String> out = Lists.newArrayList();

		for (final Entry<String, Integer> e : counters.entrySet()) {

			out.add(String.format("<counter_%s value=\"%s\"/>", e.getKey(), e.getValue()));

		}

		return out;

	}

	private void incrementCounter(final String type) {

		if (!counters.containsKey(type)) {

			counters.put(type, 1);

		} else {

			counters.put(type, counters.get(type) + 1);

		}

	}

	@Override

	public String toString() {

		final StringBuilder sb = new StringBuilder();

		sb.append("################################################\n");

		sb.append("ID: ").append(key).append("\n");

		if (mainEntity != null) {

			sb.append("MAIN ENTITY:\n").append(mainEntity.getEntity().toString() + "\n");

		}

		if (relations != null) {

			sb.append("\nRELATIONS:\n");

			for (final OafDecoder decoder : relations) {

				sb.append(decoder.getOafRel().toString() + "\n");

			}

		}

		if (children != null) {

			sb.append("\nCHILDREN:\n");

			for (final OafDecoder decoder : children) {

				sb.append(decoder.getOafRel().toString() + "\n");

			}

		}

		return sb.toString();

	}

}

package eu.dnetlib.data.mapreduce.util;

import org.apache.hadoop.hbase.io.ImmutableBytesWritable;

import com.google.common.base.Function;

import com.google.protobuf.InvalidProtocolBufferException;

import eu.dnetlib.data.proto.OafProtos.Oaf;

import eu.dnetlib.data.transform.OafUtils;

public class OafHbaseUtils extends OafUtils {

	public static OafDecoder decode(final ImmutableBytesWritable oaf) {

		return new OafDecoder(oaf.copyBytes());

	}

	public static Function<ImmutableBytesWritable, OafDecoder> decoder() {

		return new Function<ImmutableBytesWritable, OafDecoder>() {

			@Override

			public OafDecoder apply(final ImmutableBytesWritable input) {

				return OafDecoder.decode(input.copyBytes());

			}

		};

	}

	public static Function<ImmutableBytesWritable, Oaf> oafDecoder() {

		return new Function<ImmutableBytesWritable, Oaf>() {

			@Override

			public Oaf apply(final ImmutableBytesWritable input) {

				return parse(input);

			}

		};

	}

	public static Oaf parse(final ImmutableBytesWritable input) {

		try {

			return Oaf.parseFrom(input.copyBytes());

		} catch (final InvalidProtocolBufferException e) {

			throw new IllegalArgumentException(e);

		}

	}

}

package eu.dnetlib.data.mapreduce.util;

import java.util.Comparator;

import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;

public class LicenseComparator implements Comparator<Qualifier> {

	@Override

	public int compare(Qualifier left, Qualifier right) {

		if (left == null && right == null) return 0;

		if (left == null) return 1;

		if (right == null) return -1;

		String lClass = left.getClassid();

		String rClass = right.getClassid();

		if (lClass.equals(rClass)) return 0;

		if (lClass.equals("OPEN")) return -1;

		if (rClass.equals("OPEN")) return 1;

		if (lClass.equals("6MONTHS")) return -1;

		if (rClass.equals("6MONTHS")) return 1;

		if (lClass.equals("12MONTHS")) return -1;

		if (rClass.equals("12MONTHS")) return 1;

		if (lClass.equals("EMBARGO")) return -1;

		if (rClass.equals("EMBARGO")) return 1;

		if (lClass.equals("RESTRICTED")) return -1;

		if (rClass.equals("RESTRICTED")) return 1;

		if (lClass.equals("CLOSED")) return -1;

		if (rClass.equals("CLOSED")) return 1;

		if (lClass.equals("UNKNOWN")) return -1;

		if (rClass.equals("UNKNOWN")) return 1;

		// Else (but unlikely), lexicographical ordering will do.

		return Float.compare(Float.parseFloat(lClass), Float.parseFloat(rClass));

	}

}

package eu.dnetlib.data.mapreduce.util;

import com.google.common.base.Predicate;

import eu.dnetlib.data.proto.OafProtos.Oaf;

import eu.dnetlib.data.proto.OafProtos.OafRel;

import eu.dnetlib.data.proto.RelTypeProtos.RelType;

public class PersonResultFilter implements Predicate<Oaf> {

	private String key;

	public PersonResultFilter(String key) {

		this.key = key;

	}

	@Override

	public boolean apply(Oaf oaf) {

		final OafRel oafRel = oaf.getRel();

		if (RelType.personResult.equals(oafRel.getRelType())) {

			return !key.contains(oafRel.getSource().replaceAll("^.*\\:\\:", ""));

		}

		return true;

	}

}

package eu.dnetlib.data.mapreduce.util;

import java.nio.ByteBuffer;

import eu.dnetlib.data.proto.DedupDissimilarityProtos.DedupDissimilarity;

import eu.dnetlib.data.proto.DedupDissimilarityProtos.DedupDissimilarity.RelName;

import org.apache.hadoop.hbase.io.ImmutableBytesWritable;

import org.apache.hadoop.hbase.util.Bytes;

import eu.dnetlib.data.proto.DedupProtos.Dedup;

import eu.dnetlib.data.proto.DedupSimilarityProtos.DedupSimilarity;

import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;

import eu.dnetlib.data.proto.OafProtos.OafRel;

import eu.dnetlib.data.proto.OafProtos.OafRel.Builder;

import eu.dnetlib.data.proto.OrganizationOrganizationProtos.OrganizationOrganization;

import eu.dnetlib.data.proto.PersonPersonProtos.PersonPerson;

import eu.dnetlib.data.proto.RelMetadataProtos.RelMetadata;

import eu.dnetlib.data.proto.RelTypeProtos.RelType;

import eu.dnetlib.data.proto.RelTypeProtos.SubRelType;

import eu.dnetlib.data.proto.ResultResultProtos.ResultResult;

import eu.dnetlib.data.proto.TypeProtos.Type;

import eu.dnetlib.pace.config.DedupConfig;

public class DedupUtils {

	public static final String CF_SEPARATOR = "_";

	public static final String ROOT = "dedup_wf";

	public static final String BODY_S = "body";

	public static final byte[] BODY_B = Bytes.toBytes(BODY_S);

	public static String dedupPrefix(final String dedupRun) {

		return "|" + ROOT + "_" + dedupRun + "::";

	}

	public static String newId(final String id, final String dedupRun) {

		if ((dedupRun == null) || (dedupRun.length() != 3)) throw new IllegalArgumentException("wrong dedupRun param");

		return id.replaceFirst("\\|.*\\:\\:", dedupPrefix(dedupRun));

	}

	public static byte[] newIdBytes(final String s, final String dedupRun) {

		return newId(s, dedupRun).getBytes();

	}

	public static byte[] newIdBytes(final ByteBuffer b, final String dedupRun) {

		return newId(new String(b.array()), dedupRun).getBytes();

	}

	public static boolean isRoot(final String s) {

		return s.contains(ROOT);

	}

	public static boolean isRoot(final ImmutableBytesWritable s) {

		return isRoot(s.copyBytes());

	}

	public static boolean isRoot(final byte[] s) {

		return isRoot(new String(s));

	}

	public static String getDedupCF_merges(final Type type) {

		return getRelType(type) + CF_SEPARATOR + SubRelType.dedup + CF_SEPARATOR + Dedup.RelName.merges;

	}

	public static String getDedupCF_merges(final String type) {

		return getDedupCF_merges(Type.valueOf(type));

	}

	public static byte[] getDedupCF_mergesBytes(final Type type) {

		return Bytes.toBytes(getDedupCF_merges(type));

	}

	public static byte[] getDedupCF_mergesBytes(final String type) {

		return getDedupCF_mergesBytes(Type.valueOf(type));

	}

	public static String getDedupCF_mergedIn(final Type type) {

		return getRelType(type) + CF_SEPARATOR + SubRelType.dedup + CF_SEPARATOR + Dedup.RelName.isMergedIn;

	}

	public static String getDedupCF_mergedIn(final String type) {

		return getDedupCF_mergedIn(Type.valueOf(type));

	}

	public static byte[] getDedupCF_mergedInBytes(final Type type) {

		return Bytes.toBytes(getDedupCF_mergedIn(type));

	}

	public static byte[] getDedupCF_mergedInBytes(final String type) {

		return getDedupCF_mergedInBytes(Type.valueOf(type));

	}

	public static String getSimilarityCF(final Type type) {

		return getRelType(type) + CF_SEPARATOR + SubRelType.dedupSimilarity + CF_SEPARATOR + DedupSimilarity.RelName.isSimilarTo;

	}

	public static String getSimilarityCF(final String type) {

		return getSimilarityCF(Type.valueOf(type));

	}

	public static byte[] getSimilarityCFBytes(final Type type) {

		return Bytes.toBytes(getSimilarityCF(type));

	}

	public static byte[] getSimilarityCFBytes(final String type) {

		return getSimilarityCFBytes(Type.valueOf(type));

	}

	public static String getRelTypeString(final Type type) {

		return getRelType(type).toString();

	}

	public static byte[] getDissimilarityCFBytes(final Type type) {

		return Bytes.toBytes(getDissimilarityCF(type));

	}

	public static String getDissimilarityCF(final Type type) {

		return getRelType(type) + CF_SEPARATOR + SubRelType.dedupDissimilarity + CF_SEPARATOR + DedupDissimilarity.RelName.isDissimilarFrom;

	}

	public static RelType getRelType(final Type type) {

		switch (type) {

		case organization:

			return RelType.organizationOrganization;

		case person:

			return RelType.personPerson;

		case result:

			return RelType.resultResult;

		default:

			throw new IllegalArgumentException("Deduplication not supported for entity type: " + type);

		}

	}

	public static ColumnFamily decodeCF(final byte[] b) {

		final String[] s = new String(b).split(CF_SEPARATOR);

		return new DedupUtils().getCF(RelType.valueOf(s[0]), SubRelType.valueOf(s[1]));

	}

	private ColumnFamily getCF(final RelType relType, final SubRelType subRelType) {

		return new ColumnFamily(relType, subRelType);

	}

	public static OafRel.Builder getDedup(final DedupConfig dedupConf, final String from, final String to, final Dedup.RelName relClass) {

		final Type type = Type.valueOf(dedupConf.getWf().getEntityType());

		final RelType relType = DedupUtils.getRelType(type);

		final Builder oafRel =

				OafRel.newBuilder().setRelType(relType).setSubRelType(SubRelType.dedup).setRelClass(relClass.toString()).setChild(false)

						.setSource(new String(from)).setTarget(new String(to));

		switch (type) {

		case organization:

			oafRel.setOrganizationOrganization(OrganizationOrganization.newBuilder().setDedup(

					DedupUtils.dedup(relClass, "dnet:organization_organization_relations")));

			break;

		case person:

			oafRel.setPersonPerson(PersonPerson.newBuilder().setDedup(DedupUtils.dedup(relClass, "dnet:person_person_relations")));

			break;

		case result:

			oafRel.setResultResult(ResultResult.newBuilder().setDedup(DedupUtils.dedup(relClass, "dnet:result_result_relations")));

			break;

		default:

			throw new IllegalArgumentException("Deduplication not supported for entity type: " + dedupConf.getWf().getEntityType());

		}

		return oafRel;

	}

	private static Dedup.Builder dedup(final Dedup.RelName relClass, final String scheme) {

		return Dedup.newBuilder().setRelMetadata(

				RelMetadata.newBuilder().setSemantics(

						Qualifier.newBuilder().setClassid(relClass.toString()).setClassname(relClass.toString()).setSchemeid(scheme).setSchemename(scheme)));

	}

	class ColumnFamily {

		private final RelType relType;

		private final SubRelType subRelType;

		public ColumnFamily(final RelType relType, final SubRelType subRelType) {

			this.relType = relType;

			this.subRelType = subRelType;

		}

		@Override

		public String toString() {

			return getRelType() + CF_SEPARATOR + getSubRelType();

		}

		public RelType getRelType() {

			return relType;

		}

		public SubRelType getSubRelType() {

			return subRelType;

		}

	}

}

package eu.dnetlib.data.mapreduce.util;

import java.io.IOException;

import java.io.StringWriter;

import java.util.List;

import eu.dnetlib.data.proto.TypeProtos.Type;

import org.antlr.stringtemplate.StringTemplate;

import org.apache.commons.io.IOUtils;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.springframework.core.io.Resource;

public class TemplateFactory {

	private static final Log log = LogFactory.getLog(TemplateFactory.class); // NOPMD by marko on 11/24/08 5:02 PM

	protected TemplateResources resources = new TemplateResources();

	public String buildBody(final Type type, final List<String> metadata, final List<String> rels, final List<String> children, final List<String> inference) {

		StringTemplate body = getTemplate(resources.getEntity());

		body.setAttribute("name", type.toString());

		body.setAttribute("metadata", metadata);

		body.setAttribute("rels", rels);

		body.setAttribute("children", children);

		body.setAttribute("inference", inference);

		return body.toString();

	}

	public String getChild(final String name, final String id, final List<String> metadata) {

		StringTemplate child = getTemplate(resources.getChild());

		child.setAttribute("name", name);

		child.setAttribute("hasId", !(id == null));

		child.setAttribute("id", id != null ? XmlRecordFactory.escapeXml(XmlRecordFactory.removePrefix(id)) : "");

		child.setAttribute("metadata", metadata);

		String string = child.toString();

		return string;

	}

	public String buildRecord(final Type type,

			final String objIdentifier,

			final String dateOfCollection,

			final String dateOfTransformation,

			final String schemaLocation,

			final String body,

			final List<String> counters) {