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.io.BufferedReader;

import java.io.IOException;

import java.io.InputStream;

import java.io.InputStreamReader;

import java.net.URISyntaxException;

import java.net.URL;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.UUID;

import org.apache.http.HttpResponse;

import org.apache.http.NameValuePair;

import org.apache.http.message.BasicNameValuePair;

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.URI;

import eu.etaxonomy.cdm.common.UriUtils;

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

import eu.etaxonomy.cdm.print.XMLHelper.EntityType;

/**

 * Implementation of an IXMLEntityFactory that is connected to a CDM Community

 * Server on a remote machine. API call will be executed by accessing the

 * servers REST API.

 *

 * @author n.hoffmann

 * @author l.morris

 * @since Apr 6, 2010

 */

public class RemoteXMLEntityFactory extends XmlEntityFactoryBase {

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

	private URL serviceUrl;

	private IProgressMonitor monitor;

	private static final List<NameValuePair> UNLIMITED_RESULTS = Arrays

			.asList(new NameValuePair[] { new BasicNameValuePair("start", "0"),

					new BasicNameValuePair("limit", "-1") });

	private static final String UUID = "{uuid}";

	private static final String CLASSIFICATIONS = "classification";

	private static final String CLASSIFICATION_CHILD_NODES = "classification/"

			+ UUID + "/childNodes/";

	private static final String TAXONNODE_CHILD_NODES = "taxonNode/" + UUID

			+ "/childNodes/";

	private static final String TAXONNODE = "taxonNode/" + UUID;

	private static final String TAXONNODE_TAXON = TAXONNODE + "/taxon";

	// private static final String TAXONNODES = TAXONNODE + "/taxon";

	private static final String TAXA_AND_NAMES = "taxon/findTaxaAndNames";

	private static final String TAXONNODES = "taxon/" + UUID + "/taxonNodes";

	// http://dev.e-taxonomy.eu/cdmserver/palmae/portal/taxon/d58c0b44-29f8-4071-aa49-32baa185296f/taxonNodes

	private static final String FEATURETREES = "featureTree";

	private static final String FEATURETREE = "featureTree/" + UUID;

	private static final String FEATURENODE = "featurenode/" + UUID;

	// private static final String FEATURENODE = "featureNode/" + UUID +

	// "/childNodes";

	private static final String FEATURENODE_FEATURE = FEATURENODE + "/feature";

	private static final String NAME_TYPE_DESIGNATIONS = "name/" + UUID

			+ "/typeDesignations";

	// TAXON_ACCEPTED should populate references but authorship is not always

	// populated so call the reference controller directly

	private static final String REFERENCES = "portal/reference/" + UUID;

	private static final String TAXON_ACCEPTED = "portal/taxon/" + UUID;

	private static final String TAXON_SYNONYMY = "portal/taxon/" + UUID

			+ "/synonymy";

	private static final String TAXON_DESCRIPTIONS = "portal/taxon/" + UUID

			+ "/descriptions";

	private static final String POLYTOMOUS_KEY = "dto/polytomousKey/linkedStyle?findByTaxonomicScope="

			+ UUID;

	// dto/polytomousKey/linkedStyle.json?findByTaxonomicScope=f820f533-06f2-4116-87e9-c9319c0c1cbf

	// images /portal/taxon/{uuid}

	private static final String TAXON_MEDIA = "portal/taxon/" + UUID + "/media";

	// http://test.e-taxonomy.eu/cdmserver/palmae/portal/media/bb49e8f0-49bc-41f7-9674-1cb36eb716fb

	/**

	 * Creates new instance of this factory and connects it to the given CDM

	 * Community Stores access point.

	 *

	 * Typically, there is no need to instantiate this class.

	 *

	 * @param monitor

	 */

	protected RemoteXMLEntityFactory(URL webserviceUrl, IProgressMonitor monitor) {

		this.serviceUrl = webserviceUrl;

		this.monitor = monitor;

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see eu.etaxonomy.printpublisher.IXMLEntityFactory#getClassifications()

	 */

	@Override

    public List<Element> getClassifications() {

		Element result = queryServiceWithParameters(CLASSIFICATIONS,

				UNLIMITED_RESULTS);

		return processElementList(result);

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see

	 * eu.etaxonomy.printpublisher.IXMLEntityFactory#getChildNodes(org.jdom.

	 * Element)

	 */

	@Override

    public List<Element> getChildNodes(Element treeNode) {

		EntityType entityType = XMLHelper.getEntityType(treeNode);

		Element result = null;

		if (EntityType.CLASSIFICATION.equals(entityType)) {

			result = queryService(treeNode, CLASSIFICATION_CHILD_NODES);

		} else if (EntityType.TAXON_NODE.equals(entityType)) {

			result = queryService(treeNode, TAXONNODE_CHILD_NODES);

		}

		return processElementList(result);

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see

	 * eu.etaxonomy.printpublisher.IXMLEntityFactory#getTaxonNode(java.util.

	 * UUID)

	 */

	@Override

    public Element getTaxonNode(UUID taxonNodeUuid) {

		return queryService(taxonNodeUuid, TAXONNODE);

	}

	/*

	 * Returns the taxonNode for a specific taxon name string.

	 */

	@Override

    public Element getTaxonNodesByName(String taxonName, String classification) {

		// 1-To find the uuid of a Taxon name:

		// http://dev.e-taxonomy.eu/cdmserver/palmae/taxon/findTaxaAndNames.json?doTaxa=1&matchMode=EXACT&query=Acrocomia

		// 2-Then get the taxonNodes for this name:

		// http://dev.e-taxonomy.eu/cdmserver/palmae/portal/taxon/d58c0b44-29f8-4071-aa49-32baa185296f/taxonNodes

		Element taxonNodes = null;

		List <NameValuePair> params = new ArrayList<NameValuePair>();

		params.add(new BasicNameValuePair("doTaxa", "1"));

		params.add(new BasicNameValuePair("matchMode", "EXACT"));

		params.add(new BasicNameValuePair("query", taxonName));

		if (classification != null) {

			List<Element> classifications = getClassifications();

			String classificationUuid = "";

			// String xPathString="//titleCache[.='" +

			// classification+"']/../uuid";

			for (Element element : classifications) {

				if (element.getChild("titleCache").getValue()

						.equals(classification)) {

					System.out.println(element.getChild("uuid").getValue());

					classificationUuid = element.getChild("uuid").getValue();

				}

			}

			params.add(new BasicNameValuePair("tree", classificationUuid));

		}

		Element element = queryServiceWithParameters(TAXA_AND_NAMES, params);

		Element taxonNodeString = null;

		UUID taxonNodeUuid = null;

		try {

			// TODO: we only get the first Taxon to match this name - we should

			// get all Taxons to match the name

			Element taxonUuid = (Element) XPath.selectSingleNode(element,

					"//records/e[1]");

			taxonNodes = queryService(taxonUuid, TAXONNODES);

			taxonNodeString = (Element) XPath.selectSingleNode(taxonNodes,

					"//PersistentSet/e[1]/uuid");

			String val = taxonNodeString.getValue();

			taxonNodeUuid = java.util.UUID.fromString(taxonNodeString

					.getValue());

		} catch (JDOMException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

		return getTaxonNode(taxonNodeUuid);

		// TODO: Should be return a set of taxonNodes if there is more than one

		// for the name

		// public List<Element> getTaxonNodesByName(String taxonName) {

		// return taxonNodes;

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see

	 * eu.etaxonomy.printpublisher.IXMLEntityFactory#getFeatureTree(java.util

	 * .UUID)

	 */

	@Override

    public Element getFeatureTree(UUID featureTreeUuid) {

		return queryService(featureTreeUuid, FEATURETREE);

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see eu.etaxonomy.printpublisher.IXMLEntityFactory#getFeatureTrees()

	 */

	@Override

    public List<Element> getFeatureTrees() {

		Element result = queryServiceWithParameters(FEATURETREES,

				UNLIMITED_RESULTS);

		return processElementList(result);

	}

	@Override

    public Element getTermNode(UUID featureNodeUuid) {

		Element result = queryService(featureNodeUuid, FEATURENODE);

		return result;

	}

	@Override

    public Element getFeatureForTermNode(UUID featureNodeUuid) {

		Element result = queryService(featureNodeUuid, FEATURENODE_FEATURE);

		return result;

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see

	 * eu.etaxonomy.printpublisher.IXMLEntityFactory#getTaxonFromTaxonNode(org

	 * .jdom.Element)

	 */

	@Override

    public Element getTaxonForTaxonNode(Element taxonNodeElement) {

		return queryService(taxonNodeElement, TAXONNODE_TAXON);

	}

	/*

	 *

	 */

	/*

	 * public List<Element> getReferences(Element taxonElement) throws

	 * JDOMException {

	 *

	 * //get the references from the taxonElement String referencePattern =

	 * "//name/nomenclaturalSource.citation";

	 *

	 * //but there could be many references Element referenceElement = (Element)

	 * XPath.selectSingleNode(taxonElement, referencePattern); //List<Element>

	 * descriptionElementElements = XPath.selectNodes(context, featurePattern +

	 * "/..");

	 *

	 * List<Element> elementList = null;

	 *

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

	 * taxonElement

	 *

	 * Element result = queryService(referenceElement, REFERENCES);

	 *

	 * elementList = new ArrayList<Element>();

	 *

	 * for(Object child : result.getChildren()){ if(child instanceof Element){

	 * Element childElement = (Element) ((Element)child).clone();

	 *

	 * childElement.detach();

	 *

	 * elementList.add(childElement); } } }

	 *

	 * return elementList; }

	 */

	@Override

    public List<Element> getReferences(Element referenceElement) {

		Element result = queryService(referenceElement, REFERENCES);

		List<Element> elementList = new ArrayList<Element>();

		for (Object child : result.getChildren()) {

			if (child instanceof Element) {

				Element childElement = (Element) ((Element) child).clone();

				childElement.detach();

				elementList.add(childElement);

			}

		}

		return elementList;

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see

	 * eu.etaxonomy.printpublisher.IXMLEntityFactory#getAcceptedTaxonElement

	 * (org.jdom.Element)

	 */

	@Override

    public Element getAcceptedTaxonElement(Element taxonElement) {

		Element result = queryService(taxonElement, TAXON_ACCEPTED);

		return result;

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see

	 * eu.etaxonomy.printpublisher.IXMLEntityFactory#getSynonymy(org.jdom.Element

	 * )

	 */

	@Override

    public List<Element> getSynonymy(Element taxonElement) {

		Element result = queryService(taxonElement, TAXON_SYNONYMY);

		List<Element> elementList = new ArrayList<Element>();

		for (Object child : result.getChildren()) {

			if (child instanceof Element) {

				Element childElement = (Element) ((Element) child).clone();

				childElement.detach();

				elementList.add(childElement);

			}

		}

		return elementList;

	}

	/*

	 *

	 */

	@Override

    public List<Element> getMedia(Element taxonElement) {

		List<NameValuePair> params = Arrays

				.asList(new NameValuePair[] {

						new BasicNameValuePair("includeTaxonDescriptions",

								"true"),

						new BasicNameValuePair("includeOccurrences", "false"),

						new BasicNameValuePair("includeTaxonNameDescriptions",

								"false") });

		UUID uuid = XMLHelper.getUuid(taxonElement);

		Element result = queryServiceWithParameters(

				TAXON_MEDIA.replace(UUID, uuid.toString()), params);

		// Element result = queryService(taxonElement, TAXON_MEDIA);

		List<Element> elementList = new ArrayList<Element>();

		for (Object child : result.getChildren()) {

			if (child instanceof Element) {

				Element childElement = (Element) ((Element) child).clone();

				childElement.detach();

				elementList.add(childElement);

			}

		}

		return elementList;

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see

	 * eu.etaxonomy.printpublisher.IXMLEntityFactory#getTypeDesignations(org

	 * .jdom.Element)

	 */

	@Override

    public List<Element> getTypeDesignations(Element nameElement) {

		Element result = queryService(nameElement, NAME_TYPE_DESIGNATIONS);

		return processElementList(result);

	}

	/*

	 * (non-Javadoc)

	 *

	 * @see

	 * eu.etaxonomy.printpublisher.IXMLEntityFactory#getDescriptions(org.jdom

	 * .Element)

	 */

	@Override

    public Element getDescriptions(Element taxonElement) {

		Element result = queryService(taxonElement, TAXON_DESCRIPTIONS);

		return result;

	}

	/**

	 * Queries the service with the uuid of the given element

	 *

	 * @param element

	 * @param restRequest

	 * @return

	 */

	private Element queryService(Element element, String restRequest) {

		UUID uuid = XMLHelper.getUuid(element);

		return queryService(uuid, restRequest);

	}

	/**

	 * Queries the service with the given uuid

	 *

	 * @param uuid

	 * @param restRequest

	 * @return

	 */

	private Element queryService(UUID uuid, String restRequest) {

		String request = restRequest.replace(UUID, uuid.toString());

		return queryServiceWithParameters(request, null);

	}

	/**

	 *

	 * @param restRequest

	 * @return

	 * @throws URISyntaxException

	 */

	private Element queryServiceWithParameters(String restRequest,

			List<NameValuePair> queryParameters) {

		try {

			URI newUri = UriUtils.createUri(serviceUrl, restRequest,

					queryParameters, null);

			Map<String, String> requestHeaders = new HashMap<String, String>();

			requestHeaders.put("Accept", "application/xml");

			// requestHeaders.put("Accept", "application/json");

			requestHeaders.put("Accept-Charset", "UTF-8");

			HttpResponse response = UriUtils

					.getResponse(newUri, requestHeaders);

			logger.info("Firing request for URI: " + newUri);

			if (UriUtils.isOk(response)) {

				// get the content at the resource

				InputStream content = UriUtils.getContent(response);

				// specify encoding in the reader

				BufferedReader in = new BufferedReader(new InputStreamReader(

						content, "UTF-8"));

				// build the jdom document

				Document document = builder.build(in);

				// Document document = builder.build(content);

				return document.getRootElement();

			} else {

				monitor.warning(UriUtils.getStatus(response));

				logger.error(UriUtils.getStatus(response));

			}

		} catch (IOException e) {

			monitor.warning("No content for request: " + restRequest, e);

			logger.error("No content for request: " + restRequest);

		} catch (JDOMException e) {

			monitor.warning("Error building the document.", e);

			logger.error("Error building the document.", e);

		} catch (URISyntaxException e) {

			monitor.warning("Error building URI", e);

			logger.error("Error building URI", e);

		}

		// error

		return null;

	}

	/**

	 * The access point of a CDM Community Server

	 *

	 * @return the serviceUrl

	 */

	public URL getServiceUrl() {

		return serviceUrl;

	}

	/**

	 * The CDM Community Servers access point

	 *

	 * @param serviceUrl

	 */

	public void setServiceUrl(URL serviceUrl) {

		this.serviceUrl = serviceUrl;

	}

	// dto/polytomousKey/linkedStyle.json?findByTaxonomicScope=f820f533-06f2-4116-87e9-c9319c0c1cbf

	/*

	 * (non-Javadoc) TODO: Implement this method.

	 *

	 * @see

	 * eu.etaxonomy.cdm.print.IXMLEntityFactory#getPolytomousKey(org.jdom.Element

	 * )

	 */

	@Override

	// public List<Element> getPolytomousKey(Element taxonElement) {

	public Element getPolytomousKey(Element taxonElement) {

		Element result = queryService(taxonElement, POLYTOMOUS_KEY);

		return result;

		// TODO Auto-generated method stub

		// return null;

	}

}