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.app.proibiosphere;

import java.awt.Dimension;

import java.io.BufferedReader;

import java.io.File;

import java.io.FileWriter;

import java.io.IOException;

import java.io.InputStream;

import java.io.InputStreamReader;

import java.net.MalformedURLException;

import java.net.URI;

import java.net.URISyntaxException;

import java.net.URL;

import java.util.ArrayList;

import java.util.Collections;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Scanner;

import javax.swing.JOptionPane;

import javax.swing.JScrollPane;

import javax.swing.JTextArea;

import javax.xml.parsers.DocumentBuilder;

import javax.xml.parsers.DocumentBuilderFactory;

import org.apache.log4j.Logger;

import org.w3c.dom.Document;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

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

import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;

import eu.etaxonomy.cdm.io.taxonx2013.TaxonXImportConfigurator;

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

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

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

public class TaxonXImportLauncher {

    private static final Logger log = Logger.getLogger(TaxonXImportLauncher.class);

    //    private static final Logger log = Logger.getLogger(CdmEntityDaoBase.class);

    //database validation status (create, update, validate ...)

    static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;

    static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_local();

    static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

    private static String askQuestion(String question){

        Scanner scan = new Scanner(System.in);

        System.out.println(question);

        String index = scan.nextLine();

        return index;

    }

    public static void main(String[] args) {

        String plaziUrl = "http://plazi.cs.umb.edu/GgServer/search?taxonomicName.isNomenclature=true&taxonomicName.exactMatch=true&indexName=0&subIndexName=taxonomicName&subIndexName=MODS&minSubResultSize=1&searchMode=index&resultFormat=xml&xsltUrl=http%3A%2F%2Fplazi.cs.umb.edu%2FGgServer%2FsrsWebPortalData%2FCdmSyncTreatmentList.xslt&taxonomicName.taxonomicName=";

        String plaziUrlDoc = "http://plazi.cs.umb.edu/GgServer/search?taxonomicName.isNomenclature=true&taxonomicName.exactMatch=true&indexName=0&subIndexName=taxonomicName&subIndexName=MODS&minSubResultSize=1&searchMode=index&resultFormat=xml&xsltUrl=http%3A%2F%2Fplazi.cs.umb.edu%2FGgServer%2FsrsWebPortalData%2FCdmSyncTreatmentList.xslt&MODS.ModsDocID=";

        //        String plaziUrl = "http://plazi.cs.umb.edu/GgServer/xslt/E01DD5BE427421156E0C0BAC56389E0D?xsltUrl=http%3A%2F%2Fplazi.cs.umb.edu%2FGgServer%2FsrsWebPortalData%2FLinkers%2FXmlDocumentLinkerData%2Fgg2taxonx.xsl";

        List<String> sourcesStr =  new ArrayList<String>();

        boolean plaziNotServer=false;

        Map<String,List<String>> documents = new HashMap<String,List<String>>();

//        plaziUrl=plaziUrl+"Chenopodium";

       plaziUrl=plaziUrlDoc+"0910-2878-5652";

        /*HOW TO HANDLE SECUNDUM REFERENCE*/

        boolean reuseSecundum = askIfReuseSecundum();

        Reference<?> secundum = null;

        if (!reuseSecundum) {

            secundum = askForSecundum();

        }

        String tnomenclature = "ICBN";

        URL plaziURL;

        try {

            plaziURL = new URL(plaziUrl);

            BufferedReader in = new BufferedReader(new InputStreamReader(plaziURL.openStream()));

            List<String> docList;

            String inputLine;

            String docID;

            String pageStart;

            String pageEnd;

            String taxon;

            String link;

            //TODO lastUpdate field

            if(!plaziNotServer){

                while ((inputLine = in.readLine()) != null) {

                    if (inputLine.startsWith("<treatment ")){

                        taxon = inputLine.split("taxon=\"")[1].split("\"")[0];

                        docID=inputLine.split("docId=\"")[1].split("\"")[0];

                        link=inputLine.split("link=\"")[1].split("\"")[0];

                        pageStart = inputLine.split("startPage=\"")[1].split("\"")[0];

                        pageEnd = inputLine.split("endPage=\"")[1].split("\"")[0];

                        docList = documents.get(docID);

                        if (docList == null) {

                            docList = new ArrayList<String>();

                        }

                        docList.add(pageStart+"---"+pageEnd+"---"+taxon+"---"+link);

                        documents.put(docID,docList);

                    }

                }

            }

            for (String docId:documents.keySet()){

                in = new BufferedReader(new InputStreamReader(new URL(plaziUrlDoc+docId).openStream()));

                while ((inputLine = in.readLine()) != null) {

                    if (inputLine.startsWith("<treatment ")){

                        taxon = inputLine.split("taxon=\"")[1].split("\"")[0];

                        docID=inputLine.split("docId=\"")[1].split("\"")[0];

                        link=inputLine.split("link=\"")[1].split("\"")[0];

                        pageStart = inputLine.split("startPage=\"")[1].split("\"")[0];

                        pageEnd = inputLine.split("endPage=\"")[1].split("\"")[0];

                        docList = documents.get(docID);

                        if (docList == null) {

                            docList = new ArrayList<String>();

                        }

                        docList.add(pageStart+"---"+pageEnd+"---"+taxon+"---"+link);

                        documents.put(docID,docList);

                    }

                }

            }

            if(plaziNotServer) {

                sourcesStr.add(plaziUrl);

            }

            in.close();

        } catch (MalformedURLException e1) {

            // TODO Auto-generated catch block

            e1.printStackTrace();

        } catch (IOException e) {

            // TODO Auto-generated catch block

            e.printStackTrace();

        }

        //        System.exit(0);

        //        sourcesStr.add("/home/pkelbert/Documents/Proibiosphere/ChenopodiumXML/1362148061170_Chenopodium_K_hn_U_1993_tx.xml");

        for (String docId : documents.keySet()){

            /*remove documents bad quality*/

            log.info(docId);

//            if (!docId.equalsIgnoreCase("3891-7797-6564")){

                            log.info("document "+docId);

                List<String> treatments = new ArrayList<String>(new HashSet<String>(documents.get(docId)));

                Map<Integer, List<String>> startPages = new HashMap<Integer, List<String>>();

                for (String treatment:treatments) {

                    List<String>tmplist = startPages.get(Integer.valueOf(treatment.split("---")[0]));

                    if (tmplist == null) {

                        tmplist = new ArrayList<String>();

                    }

                    tmplist.add(treatment.split("---")[3]);

                    startPages.put(Integer.valueOf(treatment.split("---")[0]),tmplist);

                }

                List<Integer> pages = new ArrayList<Integer>();

                pages.addAll(startPages.keySet());

                Collections.sort(pages);

                //            log.info(pages);

                log.info("Document "+docId+" should have "+treatments.size()+" treatments");

                int cnt=0;

                for (String source:treatments){

                    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();

                    DocumentBuilder builder;

                    URL url;

                    try {

                        builder = factory.newDocumentBuilder();

                        url = new URL(source.split("---")[3]);

                        Object o = url.getContent();

                        InputStream is = (InputStream) o;

                        Document document = builder.parse(is);

                        cnt++;

                    }catch(Exception e){

                        //  e.printStackTrace();

                        log.warn(e);

                    }

                }

                log.info("Document "+docId+" has "+cnt+" treatments available");

                if(treatments.size() != cnt)

                {

                    File file = new File("/home/pkelbert/Bureau/urlTaxonXToDoLater.txt");

                    FileWriter writer;

                    try {

                        writer = new FileWriter(file ,true);

                        writer.write(docId+"\n");

                        writer.flush();

                        writer.close();

                    } catch (IOException e1) {

                        // TODO Auto-generated catch block

                        e1.printStackTrace();

                    }

                }

                else{

                    for (int page:pages) {

                        for (String treatment: startPages.get(page)) {

                            sourcesStr.add(treatment);

                        }

                    }

                }

//            }

        }

        log.info("NB SOURCES : "+sourcesStr.size());

//        sourcesStr = new ArrayList<String>();

//        sourcesStr.add("http://plazi.cs.umb.edu/exist/rest/db/taxonx_docs/cdmSync/4E7390346C05780D32283CCF6F5E4431_tx.xml");

        List<URI> sources = new ArrayList<URI>();

        for (String src: sourcesStr){

            URI uri;

            try {

                uri = new URL(src).toURI();

                sources.add(new URI(uri.toString()));

            } catch (MalformedURLException e1) {

                // TODO Auto-generated catch block

                e1.printStackTrace();

            } catch (URISyntaxException e1) {

                // TODO Auto-generated catch block

                e1.printStackTrace();

            }

        }

        log.info("Start import from  TaxonX Data");

        ICdmDataSource destination = cdmDestination;

        TaxonXImportConfigurator taxonxImportConfigurator = TaxonXImportConfigurator.NewInstance(destination);

        //        taxonxImportConfigurator.setClassificationName(taxonxImportConfigurator.getSourceReferenceTitle());

        taxonxImportConfigurator.setCheck(check);

        taxonxImportConfigurator.setDbSchemaValidation(hbm2dll);

        taxonxImportConfigurator.setDoAutomaticParsing(true);

        // invoke import

        CdmDefaultImport<TaxonXImportConfigurator> taxonImport = new CdmDefaultImport<TaxonXImportConfigurator>();

        taxonxImportConfigurator.setKeepOriginalSecundum(reuseSecundum);

        if (!reuseSecundum) {

            taxonxImportConfigurator.setSecundum(secundum);

        }

//        taxonxImportConfigurator.setDoMatchTaxa(true);

//        taxonxImportConfigurator.setReUseTaxon(true);

        for (URI source:sources){

            log.info("START : "+source.getPath());

            taxonxImportConfigurator.setSource(source);

            Reference<?> reference = ReferenceFactory.newGeneric();

            //            String tref = askQuestion("Import source? (ie Plazi document ID)");

            String tref="PLAZI - "+source.getPath().split("/")[source.getPath().split("/").length-1];

            reference.setTitleCache(tref,true);

            reference.setTitle(tref);

            reference.generateTitle();

            taxonxImportConfigurator.setSourceReference(reference);

            taxonxImportConfigurator.setSourceRef(reference);

            //            String tnomenclature = askQuestion("ICBN or ICZN ?");

            if (tnomenclature.equalsIgnoreCase("ICBN")) {

                taxonxImportConfigurator.setNomenclaturalCode(NomenclaturalCode.ICNAFP);

                //                taxonxImportConfigurator.setClassificationName("Chenopodiaceae");

            }

            if(tnomenclature.equalsIgnoreCase("ICZN")){

                taxonxImportConfigurator.setNomenclaturalCode(NomenclaturalCode.ICZN);

                //                taxonxImportConfigurator.setClassificationName("Ants");

            }

            //   taxonxImportConfigurator.setTaxonReference(null);

            //            log.info("INVOKE");

            taxonImport.invoke(taxonxImportConfigurator);

            log.info("End import from SpecimenData ("+ source.toString() + ")...");

            //          //deduplicate

            //            ICdmApplicationConfiguration app = taxonImport.getCdmAppController();

            //            int count = app.getAgentService().deduplicate(Person.class, null, null);

            //            logger.warn("Deduplicated " + count + " persons.");

            //            count = app.getReferenceService().deduplicate(Reference.class, null, null);

            //            logger.warn("Deduplicated " + count + " references.");

        }

    }

    /**

     * @return

     */

    private static boolean askIfReuseSecundum() {

            //        logger.info("getFullReference for "+ name);

            JTextArea textArea = new JTextArea("Reuse the secundum present in the current classification? " +

            		"\n Click Yes to reuse it, click No or Cancel to create a new one.");

            JScrollPane scrollPane = new JScrollPane(textArea);

            textArea.setLineWrap(true);

            textArea.setWrapStyleWord(true);

            scrollPane.setPreferredSize( new Dimension( 700, 100 ) );

            //        JFrame frame = new JFrame("I have a question");

            //        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

            int s = JOptionPane.showConfirmDialog(null, scrollPane);

           if (s==0) {

            return true;

        } else {

            return false;

        }

    }

    /**

     * @return

     */

    private static Reference<?> askForSecundum() {

            //        logger.info("getFullReference for "+ name);

            JTextArea textArea = new JTextArea("Enter the secundum name");

            JScrollPane scrollPane = new JScrollPane(textArea);

            textArea.setLineWrap(true);

            textArea.setWrapStyleWord(true);

            scrollPane.setPreferredSize( new Dimension( 700, 100 ) );

            //        JFrame frame = new JFrame("I have a question");

            //        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

            String s = (String) JOptionPane.showInputDialog(

                    null,

                    scrollPane,

                    "",

                    JOptionPane.PLAIN_MESSAGE,

                    null,

                    null,

                    null);

            Reference<?> ref = ReferenceFactory.newGeneric();

            ref.setTitle(s);

            return ref;

    }

}