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.print;

import java.util.ArrayList;

import java.util.List;

import java.util.Locale;

import java.util.UUID;

import org.apache.logging.log4j.LogManager;

import org.apache.logging.log4j.Logger;

import org.jdom.Document;

import org.jdom.Element;

import org.jdom.JDOMException;

import org.jdom.xpath.XPath;

import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;

import eu.etaxonomy.cdm.print.out.IPublishOutputModule;

/**

 * Retrieves all necessary data from an {@link IXMLEntityFactory}.

 *

 * @author n.hoffmann

 * @since Apr 8, 2010

 * @version 1.0

 */

public class XMLHarvester {

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

	private IXMLEntityFactory factory;

	private PublishConfigurator configurator;

	private List<SimplifiedFeatureNode> simplifiedFeatureTree;

	private IProgressMonitor progressMonitor;

	/**

	 *

	 * @param configurator

	 */

	public XMLHarvester(PublishConfigurator configurator){

		this.configurator = configurator;

		this.progressMonitor = configurator.getProgressMonitor();

		this.factory = configurator.getFactory();

		Element featureTreeElement = factory.getFeatureTree(configurator.getFeatureTreeUuid());

		createSimplifiedFeatureTree(featureTreeElement);

	}

	private void createSimplifiedFeatureTree(Element featureTreeElement) {

		Element root = featureTreeElement.getChild("root");

		Element realRoot = factory.getTermNode(XMLHelper.getUuid(root));

		progressMonitor.subTask("Generating simplified Feature Tree.");

		simplifiedFeatureTree = featureTreeRecursive(realRoot);

		progressMonitor.worked(1);

		logger.info("Simplified FeeatureTree created");

	}

	private List<SimplifiedFeatureNode> featureTreeRecursive(Element featureNode){

		List<SimplifiedFeatureNode> result = new ArrayList<SimplifiedFeatureNode>();

		if(featureNode != null){

			Element children = featureNode.getChild("children");

			if (children != null){

				List<Element> childFeatureNodes = children.getChildren();

				for(Element childNode : childFeatureNodes){

					UUID uuid = XMLHelper.getUuid(childNode);

					Element featureNodeElement = factory.getTermNode(uuid);

					Element featureElement = factory.getFeatureForTermNode(uuid);

					try {

						Element featureTitleCache = (Element) XPath.selectSingleNode(featureElement, "//Feature/titleCache");

						logger.info("The featureNode uuid is " + uuid);

						logger.info("The feature element name is " + featureTitleCache.getValue());

						logger.info("The feature title cache text french is " + featureTitleCache.getText().toLowerCase(Locale.FRENCH));

						logger.info("The feature title cache value french is " + featureTitleCache.getValue().toLowerCase(Locale.FRENCH));

						featureTitleCache.setText(featureTitleCache.getText().toLowerCase(Locale.FRENCH));

					} catch (JDOMException e) {

						// TODO Auto-generated catch block

						e.printStackTrace();

					}

					////We set it to French here but this isn't the correct place the Feature/titleCache

					featureElement.setName(featureElement.getName().toLowerCase(Locale.FRENCH));

					SimplifiedFeatureNode simplifiedFeatureNode = new SimplifiedFeatureNode(featureElement, featureTreeRecursive(featureNodeElement));

					result.add(simplifiedFeatureNode);

				}

			}

		}

		return result;

	}

	private class SimplifiedFeatureNode{

		private Element featureElement;

		private List<SimplifiedFeatureNode> children;

		public SimplifiedFeatureNode(Element featureElement, List<SimplifiedFeatureNode> children){

			this.featureElement = featureElement;

			this.children = children;

		}

		/**

		 * @return the uuid

		 */

		public Element getFeatureElement() {

			return featureElement;

		}

		/**

		 * @return the children

		 */

		public List<SimplifiedFeatureNode> getChildren() {

			return children;

		}

	}

	/**

	 * Commences harvesting the given {@link List} of taxonNodeElements

	 *

	 * @param taxonNodeElements

	 * @return a {@link Document} containing the necessary XML needed by the {@link IPublishOutputModule IPublishOutputModules}

	 */

	public Document harvest(List<Element> taxonNodeElements){

		Element root = new Element(IXMLElements.ROOT);

		for(Element taxonNodeElement : taxonNodeElements){

			logger.warn("Adding taxonNodeElement " + taxonNodeElement.getChildText("uuid"));

			//temporarily filter c15e12c1-6118-4929-aed0-b0cc90f5ab22 as it's causing a lazyInitializationException

			if (!taxonNodeElement.getChildText("uuid").equals("c15e12c1-6118-4929-aed0-b0cc90f5ab22")) {

			taxonNodeElement.detach();

			populateTreeNodeContainer(taxonNodeElement);

			root.addContent(taxonNodeElement);

			}

		}

		Document result = new Document();

		result.addContent(root);

		cleanDateFields(result);

		return result;

	}

	/**

	 * FIXME

	 * This is a hack to circumvent problems with the serialized version of

	 * datePublished objects. Remove this once this was fixed in the library

	 * @param element the context

	 */

	@Deprecated

	private void cleanDateFields(Object context) {

		String path = "//datePublished/start";

		try {

			List<Element> nodes = XPath.selectNodes(context, path);

			for(Element node : nodes){

				String textWithRubbish = node.getText() ;

				if (textWithRubbish.length() > 5) {

				String cleanedText = textWithRubbish.substring(0, 4);

				node.setText(cleanedText);

				}

				/*else {

					Element parentOfParent = (Element) node.getParent().getParent().getParent();

					if (parentOfParent.getName().equals("inReference")) {

					List<Element> parentNodes = XPath.selectNodes(parentOfParent, "//nomenclaturalReference/titleCache");

					for(Element parentNode : parentNodes){

					logger.error("Problem with date for node  with titleCache: " + parentNode.getText());

					}

					}

				}*/

				/*Element parent = (Element) node.getParent().getParent();

				if(parent.getName().equals("citation")){

					Element parent2 = (Element) parent.getParent();

					parent2.setAttribute("sort", cleanedText);

				}*/

			}

		} catch (Exception e) {

			logger.error("Error trying to clean date published field", e);

		}

	}

	/**

	 * Get all additional content that is not included in taxon node initialization

	 *

	 * @param container

	 */

	private void populateTreeNodeContainer(Element taxonNodeElement){

		// get the taxon from the generic service to have the uuid for further processing

		Element taxonElement = factory.getTaxonForTaxonNode(taxonNodeElement);

		progressMonitor.subTask("Gathering data for taxon: " + XMLHelper.getTitleCache(taxonElement));

		// get initialized accepted taxon

		// TODO right now we are getting that from the portal service but should consider to use the generic service

		// as the portal service is more likely to change

		Element fullTaxonElement = factory.getAcceptedTaxonElement(taxonElement);

		//populateTypeDesignations(fullTaxonElement);

		// get descriptions

		if(configurator.isDoDescriptions()){

			populateDescriptions(fullTaxonElement);

		}

		// get polytomous key

		if(configurator.isDoPolytomousKey()){

			populatePolytomousKey(fullTaxonElement);

		}

		// get synonym

		if(configurator.isDoSynonymy()){

			populateSynonyms(fullTaxonElement);

		}

		// get media

		if(configurator.isDoImages()){

			populateImages(fullTaxonElement);

		}

		// add taxon element to the node element

		XMLHelper.addContent(fullTaxonElement, taxonNodeElement);

		// get taxonomically included taxa

		if(configurator.isDoPublishEntireBranches()){

			populateChildren(taxonNodeElement);

		}

		try {

			populateReferences(fullTaxonElement);

		} catch (JDOMException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

		populateTypeDesignations(fullTaxonElement);

		progressMonitor.worked(1);

	}

	// the name isn't populated in the taxonNode http://dev.e-taxonomy.eu/cdmserver/flora_central_africa/taxonNode/de808dae-e50a-42f2-a4da-bd12f2c2faaf/taxon.json

	// but can get the name from http://dev.e-taxonomy.eu/cdmserver/flora_central_africa/portal/taxon/8f6d5498-1f4b-420f-a1ae-3f0ed9406bb1.json

	private void populateTypeDesignations(Element fullTaxonElement) {

		Element nameElement = fullTaxonElement.getChild("name");

		Element uuidElement = fullTaxonElement.getChild("uuid");

		List<Element> typeDesignations = factory.getTypeDesignations(nameElement);

		nameElement.removeChild("typeDesignations");

		for(Element typeDesignation: typeDesignations){

			XMLHelper.addContent(typeDesignation, "typeDesignations", nameElement);

		}

	}

	private void populateReferences(Element fullTaxonElement) throws JDOMException {

		//get the references from the taxonElement

		//String referencePattern = "//name/nomenclaturalReference";

		String referencePattern = "/Taxon/name/nomenclaturalSource/citation";

		//but there could be many references

		Element referenceElement = (Element) XPath.selectSingleNode(fullTaxonElement, referencePattern); //Mon 1st july do we get the /Taxon/name/nomenclaturalSource/citation from the taxon node - is this working

		//List<Element> descriptionElementElements = XPath.selectNodes(context, featurePattern + "/..");

		List<Element> elementList = null;

		if(referenceElement != null){  //the referencePattern was found in the taxonElement

			List<Element> refs = factory.getReferences(referenceElement);//getReferences

			fullTaxonElement.removeChild("nomenclaturalSource");//remove the references  ;TODO after #6851 do we need to handle nomenclaturalSource.citation somehow?

			for(Element ref: refs){

				XMLHelper.addContent(ref, "nomenclaturalSource", fullTaxonElement);   //TODO after #6851 do we need to handle nomenclaturalSource.citation somehow?

			}

		}

	}

	/**

	 * Populates all child nodes of the given taxonNodeElement

	 *

	 * @param container

	 */

	private void populateChildren(Element taxonNodeElement){

		logger.info("populating branch");

		List<Element> childNodeElements = factory.getChildNodes(taxonNodeElement);

		for(Element childNodeElement : childNodeElements){

			populateTreeNodeContainer(childNodeElement);

			XMLHelper.addContent(childNodeElement, "childNodes", taxonNodeElement);

		}

	}

	private void populatePolytomousKey(Element taxonElement){

		logger.info("populating Polytomous key");

		logger.info("populating Polytomous key taxonElement " + XMLHelper.getUuid(taxonElement) + " name " + XMLHelper.getTitleCache(taxonElement));

		//List<Element> polytomousKey = factory.getPolytomousKey(taxonElement);

		Element polytomousKey = factory.getPolytomousKey(taxonElement);

		XMLHelper.addContent(polytomousKey, "key", taxonElement);

		/*for(Element keyRow : polytomousKey){

			XMLHelper.addContent(keyRow, "key", taxonElement);

		}*/

	}

	/**

	 * Retrieves descriptions for the given taxonElement and adds them to a SimplifiedFeatureNode

	 *

	 * @param taxonElement

	 */

	private void populateDescriptions(Element taxonElement){

		taxonElement.removeChild("descriptions");

		Element rawDescriptions = factory.getDescriptions(taxonElement);

		Element featureTitleCache;

		try {

			//featureTitleCache = (Element) XPath.selectSingleNode(rawDescriptions, "//feature/representation_L10n");

			List descs = XPath.selectNodes(rawDescriptions, "//feature/representation_L10n");

			for(Object des : descs){

				logger.info("The descriptions //feature/representation_L10n is " + ((Element) des).getValue());

			}

		} catch (JDOMException e1) {

			// TODO Auto-generated catch block

			e1.printStackTrace();

		}

		//logger.setLevel(Level.DEBUG);

		logger.debug("The taxonElement is " + XMLHelper.getUuid(taxonElement) + " name " + XMLHelper.getTitleCache(taxonElement));

		Element descriptionsElement = new Element("descriptions");

		Element featuresElement = new Element("features");

		for(SimplifiedFeatureNode simplifiedFeatureNode : simplifiedFeatureTree){

			try {

				processFeatureNode(simplifiedFeatureNode, rawDescriptions, featuresElement);

				//UUID featureUuid = XMLHelper.getUuid(simplifiedFeatureNode.getFeatureElement());

				//String featureTitleCache = XMLHelper.getTitleCache(simplifiedFeatureNode.getFeatureElement());

				//logger.debug(" The feature uuid is " + featureUuid + " and name is " + featureTitleCache);

			} catch (JDOMException e) {

				logger.error(e);

			}

		}

		XMLHelper.addContent(featuresElement, descriptionsElement);

		XMLHelper.addContent(descriptionsElement, taxonElement);

	}

	private void processFeatureNode(SimplifiedFeatureNode featureNode, Object context, Element parentFeatureElement)  throws JDOMException{

		// gets the feature elements with the current feature uuid

		UUID featureUuid = XMLHelper.getUuid(featureNode.getFeatureElement());

		String featurePatternold = "//feature[contains(uuid,'" + featureUuid + "')]";

		//String featurePattern = "/ArrayList[1]/e[1]/elements[1]/e[1]/feature/uuid[.='" + featureUuid + "']";

		//Xpath is now more specific so that only the feature associated with a particular Taxon and not the

		//Taxon's parent or children are selected.

		//Alternative would be to ensure the context object only contains descriptions for the Taxon element of interest

		//Need to look at the taxonPortalController.doGetDescriptions to change this

		String featurePattern = "/ArrayList[1]/e/elements/e/feature[contains(uuid,'" + featureUuid + "')]";

		Element feature = (Element) XPath.selectSingleNode(context, featurePattern);

		if(feature != null){  //the featurePattern was found in the raw descriptions data

			List<Element> descriptionElementElements = XPath.selectNodes(context, featurePattern + "/..");

			logger.debug("No of desc elements " +  descriptionElementElements.size() + " featureUUID " + featureUuid + " feature type is " + XMLHelper.getTitleCache(featureNode.getFeatureElement()));

			// add matching description elements as children to this feature element

			for(Element descriptionElementElement : descriptionElementElements){

				descriptionElementElement.removeChild("feature");

				descriptionElementElement.setName("descriptionelement");

				XMLHelper.addContent(descriptionElementElement, "descriptionelements", feature);

			}

			XMLHelper.addContent(feature, parentFeatureElement);

		}else if(featureNode.getChildren().size() > 0){

			Element featureElement = featureNode.getFeatureElement();

			Element featureElementClone = (Element) featureElement.clone();

			feature = (Element) featureElementClone.detach();

			XMLHelper.addContent(feature, parentFeatureElement);

		}

		// recurse into children

		for(SimplifiedFeatureNode childFeatureNode : featureNode.getChildren()){

			logger.debug("No of featureNode children " + featureNode.getChildren().size());//always 10

			UUID childFeatureUuid = XMLHelper.getUuid(childFeatureNode.getFeatureElement());

			String childFeatureTitleCache = XMLHelper.getTitleCache(childFeatureNode.getFeatureElement());

			logger.debug(" The feature is " + childFeatureUuid + " name " + childFeatureTitleCache);

			//9 features in each simplifiedFeatureNode but some of the feature elements are null for a particular featureTitleCache,

			//e.g. Ecology, Description - Description has child features

			//creates the second level features i.e. descriptions/features/feature/feature for the description

			processFeatureNode(childFeatureNode, context, feature);

		}

	}

	/*private Element processDescriptionsRecursive(Object context, SimplifiedFeatureNode simplifiedFeatureNode) throws JDOMException{

		// gets the feature elements with the current uuid

		String featurePattern = "//feature[contains(uuid,'" + simplifiedFeatureNode.getUuid() + "')]";

		Element feature = (Element) XPath.selectSingleNode(context, featurePattern);

		if(feature != null){

			// recurse into children

			for(SimplifiedFeatureNode childFeatureNode : simplifiedFeatureNode.getChildren()){

				Element childFeatureWithElements = processDescriptionsRecursive(context, childFeatureNode);

				XMLHelper.addContent(childFeatureWithElements, "features", feature);

			}

			// get the parents of all feature elements with the current uuid

			List<Element> descriptionElementElements = XPath.selectNodes(context, featurePattern + "/..");

			// add matching description elements as children to this feature element

			for(Element descriptionElementElement : descriptionElementElements){

				descriptionElementElement.removeChild("feature");

				descriptionElementElement.setName("descriptionelement");

				XMLHelper.addContent(descriptionElementElement, "descriptionelements", feature);

			}

		}

		return feature;

	}*/

	/**

	 * Retrieves the synonymy for the given taxonElement

	 *

	 * @param taxonElement

	 */

	private void populateSynonyms(Element taxonElement){

		List<Element> synonymy = factory.getSynonymy(taxonElement);

		for(Element synonymyNode : synonymy){

			List<Element> children = synonymyNode.getChildren("e");

			for(Element child : children){

				List<Element> children2 = child.getChildren("e");

				for(Element child2 : children2){

					if (child2.getChild("name") != null) {

						populateTypeDesignations(child2);// pass in the name of the synonym from synonymy/e/e/name

						//populateImages(child2);

						}

				}

			}

			XMLHelper.addContent(synonymyNode, "synonymy", taxonElement);

		}

	}

	/**

	 *

	 * @param taxonElement

	 */

	private void populateImages(Element taxonElement){

		factory.getMedia(taxonElement);

		logger.warn("Populating images");

		//Element nameElement = fullTaxonElement.getChild("name");

		//Element uuidElement = fullTaxonElement.getChild("uuid");

		List<Element> mediaElements = factory.getMedia(taxonElement);

		//nameElement.removeChild("typeDesignations");

		for(Element media: mediaElements){

			XMLHelper.addContent(media, "media", taxonElement);

		}

	}

}