D-Net

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.Iterables;

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;

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

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;

	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;

	protected static Predicate<String> instanceFilter = new Predicate<String>() {

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

		@Override

		public boolean apply(final String s) {

			return instanceFieldFilter.contains(s);

		}

	};

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

			final String schemaLocation, final boolean entityDefaults, final boolean relDefaults, final boolean childDefeaults, final Set<String> otherDatasourceTypesUForUI)

			throws TransformerConfigurationException, TransformerFactoryConfigurationError {

		this.entityConfigTable = entityConfigTable;

		this.contextMapper = contextMapper;

		this.relClasses = relClasses;

		this.schemaLocation = schemaLocation;

		this.entityDefaults = entityDefaults;

		this.relDefaults = relDefaults;

		this.childDefaults = childDefeaults;

		this.specialDatasourceTypes = otherDatasourceTypesUForUI;

		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 Predicate<String> filter = entityConfigTable.getFilter(entity.getType());

			final List<String> metadata = decodeType(entity, filter, 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(entity.getType()));

			metadata.add(parseDataInfo(mainEntity));

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

			return templateFactory

					.buildRecord(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 Predicate<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 TypeProtos.Type targetType = relDecoder.getTargetType(mainEntity.getEntity().getType());

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

				metadata.addAll(listFields(relDecoder.getSubRel(), entityConfigTable.getIncludeFilter(targetType, relDecoder.getRelDescriptor()), false, true));

				String semanticclass = "";

				String semanticscheme = "";

				final RelDescriptor relDescriptor = relDecoder.getRelDescriptor();

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

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

					final OafEntityDecoder d = OafEntityDecoder.decode(cachedTarget);

					metadata.addAll(decodeType(d, entityConfigTable.getIncludeFilter(targetType, relDescriptor), relDefaults, true));

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

						for(Instance i : cachedTarget.getResult().getInstanceList()) {

							final List<String> fields = listFields(i, entityConfigTable.getIncludeFilter(targetType, relDecoder.getRelDescriptor()), false, true);

							metadata.addAll(fields);

						}

					}

				}

				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();

				}

				final String rd = relDescriptor.getSubRelType().toString();

				incrementCounter(rd);

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

				if (info.getInferred()) {

					incrementCounter(rd + "_inferred");

				} else if(StringUtils.startsWith(info.getProvenanceaction().getClassid(), "sysimport:crosswalk")) {

					incrementCounter(rd + "_collected");

				} else if(StringUtils.startsWith(info.getProvenanceaction().getClassid(), "user:")) {

					incrementCounter(rd + "_claimed");

				}

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

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

				rels.add(templateFactory.getRel(targetType, relId, Sets.newHashSet(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()) {

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

						listMap(instance.getUrlList(), identifier -> 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 Predicate<String> filter = entityConfigTable.getIncludeFilter(target.getType(), relDescriptor);

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

	}

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

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

		if (fields != null) {

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

			final Map<FieldDescriptor, Object> filtered = filterFields(fields, filter);

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

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

				seen.add(name);

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

			}

			if (defaults) {

				final Iterable<FieldDescriptor> unseen =

						Iterables.filter(fields.getDescriptorForType().getFields(), fd -> !seen.contains(fd.getName()) && filter.apply(fd.getName()));

				for(FieldDescriptor fd : unseen){

					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 ("dateofcollection".equals(fd.getName()) ||

			"dateoftransformation".equals(fd.getName()) ||

			"id".equals(fd.getName()) ||

				(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(Author.getDescriptor().equals(fd.getMessageType())) {

				final Author a = (Author) o;

				final StringBuilder sb = new StringBuilder("<creator rank=\"" + a.getRank() + "\"");

				if (a.hasName()) {

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

				}

				if (a.hasSurname()) {

					sb.append(" surname=\"" + escapeXml(a.getSurname()) + "\"");

				}

				sb.append(">" + escapeXml(a.getFullname()) + "</creator>");

				metadata.add(sb.toString());

			}

			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()) + "\" " + "ep=\"" + escapeXml(j.getEp()) + "\" " + "iss=\"" + escapeXml(j.getIss()) + "\" " + "sp=\""

						+ escapeXml(j.getSp()) + "\" " + "vol=\"" + escapeXml(j.getVol()) + "\">" + escapeXml(j.getName()) + "</journal>");

			}

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

				contextes.add(((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"));