EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.tcsxml.in;

import static eu.etaxonomy.cdm.io.common.ImportHelper.OBLIGATORY;

import static eu.etaxonomy.cdm.io.common.ImportHelper.OVERWRITE;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import org.apache.log4j.Logger;

import org.jdom.Content;

import org.jdom.Element;

import org.jdom.Namespace;

import org.jdom.Text;

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

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.common.ResultWrapper;

import eu.etaxonomy.cdm.common.XmlHelp;

import eu.etaxonomy.cdm.ext.ipni.IpniService;

import eu.etaxonomy.cdm.io.common.CdmImportBase;

import eu.etaxonomy.cdm.io.common.ImportHelper;

import eu.etaxonomy.cdm.io.common.MapWrapper;

import eu.etaxonomy.cdm.io.tcsxml.CdmSingleAttributeXmlMapperBase;

import eu.etaxonomy.cdm.model.agent.Person;

import eu.etaxonomy.cdm.model.agent.Team;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.common.IdentifiableEntity;

import eu.etaxonomy.cdm.model.name.TaxonName;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.reference.ReferenceFactory;

import eu.etaxonomy.cdm.model.taxon.Synonym;

import eu.etaxonomy.cdm.model.taxon.Taxon;

/**

 * @author a.mueller

 * @since 04.08.2008

 */

public abstract class TcsXmlImportBase  extends CdmImportBase<TcsXmlImportConfigurator, TcsXmlImportState> {

    private static final long serialVersionUID = -2169244092211698392L;

    private static final Logger logger = Logger.getLogger(TcsXmlImportBase.class);

	protected static Namespace nsTcom = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/Common#");

	protected static Namespace nsTn = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/TaxonName#");

	protected static Namespace nsTgeo = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/GeographicRegion#");

	protected static Namespace nsTc = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/TaxonConcept#");

	protected static Namespace nsTpub = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/PublicationCitation#");

	protected static Namespace nsTpalm = Namespace.getNamespace("http://wp5.e-taxonomy.eu/import/palmae/common");

	@Autowired

	IpniService service;

	@Override

    protected abstract void doInvoke(TcsXmlImportState state);

//	@Override

//	protected boolean doInvoke(IImportConfigurator config,

//			Map<String, MapWrapper<? extends CdmBase>> stores){

//		TcsXmlImportState state = ((TcsXmlImportConfigurator)config).getState();

//		state.setConfig((TcsXmlImportConfigurator)config);

//		return doInvoke(state);

//	}

	protected boolean makeStandardMapper(Element parentElement, CdmBase ref, Set<String> omitAttributes, CdmSingleAttributeXmlMapperBase[] classMappers){

		if (omitAttributes == null){

			omitAttributes = new HashSet<>();

		}

		boolean result = true;

		for (CdmSingleAttributeXmlMapperBase mapper : classMappers){

			Object value = getValue(mapper, parentElement);

			//write to destination

			if (value != null){

				String destinationAttribute = mapper.getDestinationAttribute();

				if (! omitAttributes.contains(destinationAttribute)){

					result &= ImportHelper.addValue(value, ref, destinationAttribute, mapper.getTypeClass(), OVERWRITE, OBLIGATORY);

				}

			}

		}

		return true;

	}

	private Object getValue(CdmSingleAttributeXmlMapperBase mapper, Element parentElement){

		String sourceAttribute = mapper.getSourceAttribute();

		Namespace sourceNamespace = mapper.getSourceNamespace(parentElement);

		Element child = parentElement.getChild(sourceAttribute, sourceNamespace);

		if (child == null){

			return null;

		}

		if (child.getContentSize() > 1){

			logger.warn("Element is not String");

		}

		Object value = child.getTextTrim();

		return value;

	}

	protected boolean checkAdditionalContents(Element parentElement, CdmSingleAttributeXmlMapperBase[] classMappers, CdmSingleAttributeXmlMapperBase[] operationalMappers, CdmSingleAttributeXmlMapperBase[] unclearMappers){

		List<Content> additionalContentList = new ArrayList<Content>();

		List<Content> contentList = parentElement.getContent();

		List<CdmSingleAttributeXmlMapperBase> mapperList = new ArrayList<CdmSingleAttributeXmlMapperBase>();

		mapperList.addAll(Arrays.asList(classMappers));

		mapperList.addAll(Arrays.asList(operationalMappers));

		mapperList.addAll(Arrays.asList(unclearMappers));

		for(Content content: contentList){

			boolean contentExists = false;

			if (content instanceof Element){

				for (CdmSingleAttributeXmlMapperBase mapper : mapperList){

					if (mapper.mapsSource(content, parentElement)){

						contentExists = true;

						break;

					}

				}

			}else if (content instanceof Text){

				//empty Text

				if (((Text)content).getTextNormalize().equals("")){

					contentExists = true;

				}else{

					//

				}

			}

			if (contentExists == false){

				additionalContentList.add(content);

			}

		}

		for (Content additionalContent : additionalContentList){

			logger.warn("Additional content: " +  additionalContent);

		}

		return (additionalContentList.size() == 0);

	}

	protected Element getDataSetElement(TcsXmlImportConfigurator tcsConfig){

		Element root = tcsConfig.getSourceRoot();

		if (! "DataSet".equals(root.getName())){

			logger.error("Root element is not 'DataSet'");

			return null;

		}

		if (tcsConfig.getTcsXmlNamespace() == null){

			logger.error("No namespace defined for tcs");

			return null;

		}

		if (! tcsConfig.getTcsXmlNamespace().equals(root.getNamespace())){

			logger.error("Wrong namespace for element 'DataSet'");

			return null;

		}

		//TODO prevent multiple elements

		return root;

	}

//	static public boolean checkFirstTwoFunctionElements(List<Object> objList){

//		if (! (objList.get(0) instanceof TcsXmlImportConfigurator)){

//			logger.error("first method object has wrong type. Must be " + TcsXmlImportConfigurator.class.getSimpleName() + " but is " + (objList.get(0) == null ? "null": objList.get(0).getClass().getSimpleName()));

//			return false;

//		}

//		if (! (objList.get(1) == null) && ! (objList.get(1) instanceof Element)){

//			logger.error("first method object has wrong type. Must be " + Element.class.getSimpleName() + " but is " + (objList.get(1) == null ? "null": objList.get(1).getClass().getSimpleName()));

//			return false;

//		}

//		return true;

//	}

	protected boolean testAdditionalElements(Element parentElement, List<String> excludeList){

		boolean result = true;

		List<Element> list = parentElement.getChildren();

		for (Element element : list){

			if (! excludeList.contains(element.getName())){

				logger.warn("Unknown element (" + element.getName() + ") in parent element (" + parentElement.getName() + ")");

				result = false;

			}

		}

		return result;

	}

	protected <T extends IdentifiableEntity> T makeReferenceType(Element element, Class<? extends T> clazz, MapWrapper<? extends T> objectMap, ResultWrapper<Boolean> success){

		T result = null;

		String linkType = element.getAttributeValue("linkType");

		String ref = element.getAttributeValue("ref");

		if (ref != null){

			if (ref.matches("urn:lsid:ipni.org:.*:*")){

				ref = ref.substring(0,ref.lastIndexOf(":"));

			}

		}

		if(ref == null && linkType == null){

			result = getInstance(clazz);

			if (result != null){

				String title = element.getTextNormalize();

				result.setTitleCache(title, true);

			}

		}else if (linkType == null || linkType.equals("local")){

			//TODO

			result = objectMap.get(ref);

			if (result == null){

				result = getInstance(clazz);

				if (result != null){

					String title = element.getTextNormalize();

					result.setTitleCache(title, true);

				}

			}

		}else if(linkType.equals("external")){

			logger.warn("External link types not yet implemented");

		}else if(linkType.equals("other")){

			logger.warn("Other link types not yet implemented");

		}else{

			logger.warn("Unknown link type or missing ref");

		}

		if (result == null){

			success.setValue(false);

		}

		return result;

	}

	protected Reference makeAccordingTo(Element elAccordingTo, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){

		Reference result = null;

		if (elAccordingTo != null){

			String childName = "AccordingToDetailed";

			boolean obligatory = false;

			Element elAccordingToDetailed = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);

			childName = "Simple";

			obligatory = true;

			Element elSimple = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);

			if (elAccordingToDetailed != null){

				result = makeAccordingToDetailed(elAccordingToDetailed, referenceMap, success);

			}else{

				result = ReferenceFactory.newGeneric();

				String title = elSimple.getTextNormalize();

				result.setTitleCache(title, true);

			}

		}

		return result;

	}

	private Reference makeAccordingToDetailed(Element elAccordingToDetailed, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){

		Reference result = null;

		Namespace tcsNamespace = elAccordingToDetailed.getNamespace();

		if (elAccordingToDetailed != null){

			//AuthorTeam

			String childName = "AuthorTeam";

			boolean obligatory = false;

			Element elAuthorTeam = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);

			makeAccordingToAuthorTeam(elAuthorTeam, success);

			//PublishedIn

			childName = "PublishedIn";

			obligatory = false;

			Element elPublishedIn = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);

			result = makeReferenceType(elPublishedIn, Reference.class, referenceMap, success);

			//MicroReference

			childName = "MicroReference";

			obligatory = false;

			Element elMicroReference = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);

			if (elMicroReference != null){

				String microReference = elMicroReference.getTextNormalize();

				if (CdmUtils.Nz(microReference).equals("")){

					//TODO

					logger.warn("MicroReference not yet implemented for AccordingToDetailed");

				}

			}

		}

		return result;

	}

	private Team makeAccordingToAuthorTeam(Element elAuthorTeam, ResultWrapper<Boolean> succes){

		Team result = null;

		if (elAuthorTeam != null){

			//TODO

			logger.warn("AuthorTeam not yet implemented for AccordingToDetailed");

		}

		return result;

	}

	protected void testNoMoreElements(){

		//TODO

		//logger.info("testNoMoreElements Not yet implemented");

	}

	@SuppressWarnings("unchecked")

	protected TeamOrPersonBase<?> makeNameCitation(Element elNameCitation, MapWrapper<Person> authorMap, ResultWrapper<Boolean> success){

		TeamOrPersonBase<?> result = null;

		String childName;

		boolean obligatory;

		if (elNameCitation != null){

			Namespace ns = elNameCitation.getNamespace();

			childName = "Authors";

			obligatory = false;

			Element elAuthors = XmlHelp.getSingleChildElement(success, elNameCitation, childName, ns, obligatory);

			testNoMoreElements();

			if (elAuthors != null){

				childName = "AgentName";

				List<Element> elAgentList = elAuthors.getChildren(childName, ns);

				Team team = Team.NewInstance();

				result = team;

				if (elAgentList.size() > 1){

					for(Element elAgent : elAgentList){

						Person teamMember = makeAgent(elAgent, ns, authorMap, success);

						team.addTeamMember(teamMember);

					}

				}else if(elAgentList.size() == 1){

					result = makeAgent(elAgentList.get(0), ns, authorMap, success);

				}

			}else{

				childName = "Simple";

				obligatory = true;

				Element elSimple = XmlHelp.getSingleChildElement(success, elNameCitation, childName, ns, obligatory);

				String simple = (elSimple == null)? "" : elSimple.getTextNormalize();

				result = Team.NewInstance();

				result.setNomenclaturalTitle(simple);

			}

		}

		return result;

	}

	private Person makeAgent(Element elAgentName, Namespace ns, MapWrapper<Person> agentMap, ResultWrapper<Boolean> success){

		Person result = null;

		if (elAgentName != null){

			String authorTitle = elAgentName.getTextNormalize();

			result = Person.NewTitledInstance(authorTitle);

			Class<? extends Person> clazz = Person.class;

			result = makeReferenceType(elAgentName, clazz, agentMap, success);

			return result;

		}else{

			return null;

		}

	}

	protected Integer getIntegerYear(String year){

		try {

			Integer result = Integer.valueOf(year);

			return result;

		} catch (NumberFormatException e) {

			logger.warn("Year string could not be parsed. Set = 9999 instead");

			return 9999;

		}

	}

	protected String removeVersionOfRef(String ref){

		if (ref != null && ref.matches("urn:lsid:ipni.org:.*:.*:.*")){

			return ref = ref.substring(0,ref.lastIndexOf(":"));

		} else {

			return ref;

		}

	}

	protected void makeTypification(TaxonName name, Element elTypifiacation, ResultWrapper<Boolean> success){

		if (elTypifiacation != null){

			//logger.warn("makeTypification not yet implemented");

			//success.setValue(false);

		}

	}

	protected void makePublicationStatus(TaxonName name, Element elPublicationStatus, ResultWrapper<Boolean> success){

		//Status

		if (elPublicationStatus != null){

			String pubStat = elPublicationStatus.getAttributeValue("Note");

		}

	}

	protected void makeProviderLink(TaxonName name, Element elProviderLink, ResultWrapper<Boolean> success){

		if (elProviderLink != null){

			//logger.warn("makeProviderLink not yet implemented");

			//success.setValue(false);

		}

	}

	protected void makeProviderSpecificData(TaxonName name, Element elProviderSpecificData, ResultWrapper<Boolean> success, TcsXmlImportState state){

		if (elProviderSpecificData != null){

			Namespace ns = elProviderSpecificData.getNamespace();

			String childName = "ipniData";

			boolean obligatory = true;

			List<Element> elIpniData = elProviderSpecificData.getChildren();

			Element el =  elIpniData.get(0);

			childName = "citationType";

			ns = el.getNamespace();

			Element elCitationType = XmlHelp.getSingleChildElement(success, el, childName, ns, obligatory);

			childName = "referenceRemarks";

			Element elReferenceRemarks = XmlHelp.getSingleChildElement(success, el, childName, ns, obligatory);

			childName = "suppressed";

			Element elSuppressed = XmlHelp.getSingleChildElement(success, el, childName, ns, obligatory);

			childName = "score";

			Element elScore = XmlHelp.getSingleChildElement(success, el, childName, ns, obligatory);

			childName = "nomenclaturalSynonym";

			Element elNomenclaturalSynonym = XmlHelp.getSingleChildElement(success, el, childName, ns, obligatory);

			 ns = elProviderSpecificData.getNamespace();

			childName = "RelatedName";

			Element elRelatedName = XmlHelp.getSingleChildElement(success, elNomenclaturalSynonym, childName, ns, obligatory);

			//create homotypic synonym

			if (elRelatedName != null){

    			String id =elRelatedName.getAttributeValue("ref");

    			System.out.println(removeVersionOfRef(id));

    			if (name.getTaxa().iterator().hasNext()){

    			    Taxon taxon = name.getTaxa().iterator().next();

    			    //if taxon already exist

    			    taxon.addHomotypicSynonym((Synonym)state.getStore(TAXON_STORE).get(removeVersionOfRef(id)));

    			    //otherwise add to a map for homotypic synonyms

    			}

			}

		}

	}

	@Override

    protected boolean isIgnore(TcsXmlImportState state){

		return ! state.getConfig().isDoTaxonNames();

	}

	protected static final Reference unknownSec(){

		Reference result = ReferenceFactory.newGeneric();

		result.setTitleCache("UNKNOWN", true);

		return result;

	}

}