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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.app.proibiosphere;
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import java.awt.Dimension;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.net.MalformedURLException;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Scanner;
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import javax.swing.JOptionPane;
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import javax.swing.JScrollPane;
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import javax.swing.JTextArea;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
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import eu.etaxonomy.cdm.io.taxonx2013.TaxonXImportConfigurator;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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public class TaxonXImportLauncher {
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private static final Logger log = Logger.getLogger(TaxonXImportLauncher.class);
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// private static final Logger log = Logger.getLogger(CdmEntityDaoBase.class);
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//database validation status (create, update, validate ...)
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
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// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_piB("piB_nephrolepis");
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_piB("guianas");
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
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private enum FilterType{MODS, TAXON};
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static String plaziUrlTaxName = "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%2Fresources%2FsrsWebPortalData%2FCdmSyncTreatmentList.xslt&taxonomicName.taxonomicName=";
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static String plaziUrlModsDoc = "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%2Fresources%2FsrsWebPortalData%2FCdmSyncTreatmentList.xslt&MODS.ModsDocID=";
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public static void main(String[] args) {
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String[] spiderModsList = new String[] {"zt03768p138","zt03750p196","zt03666p193","zt03664p068","zt03646p592","zt03507p056","zt03415p057","zt03383p038","zt03305p052","zt03228p068","zt03131p034","zt02963p068","zt02883p068","zt02814p018","zt02739p050","zt02730p043","zt02637p054","zt02593p127","zt02551p068","zt02534p036","zt02526p053","zt02427p035","zt02361p012","zt02267p068","zt02223p047","zt01826p058","zt01775p024","zt01744p040","zt01529p060","zt01004p028","zt00904","zt00872","zt00619","zt00109","DippenaarSchoeman1989Penestominae","Simon1902Cribellates","Simon1903Penestominae","Lehtinen1967CribellatePenestominae"};
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String[] taxonList = new String[] {"Campylopus"}; //{"Eupolybothrus","Polybothrus"}, Chenopodium, Lactarius, Campylopus, Nephrolepis, Comaroma (spiders)
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// /*ants Anochetus*/ String[] modsList = new String[] {"3924" /*, "3743", "4375", "6757", "6752", "3481", "21401_fisher_smith_plos_2008", "2592", "4096", "6877", "6192", "8071" */};
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// String[] modsList = new String[] {"21367", "21365", "8171", "6877", "21820", "3641", "6757"};
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// /*auch ants*/ debut="3743", "3628", "4022", "3994", "3603", "8070", "4001", "4071", "3948", "3481"};
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// suite: , };//,"3540555099"};
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// modsList = new String[] {"Zapparoli-1986-Eupolybothrus-fasciatus"};
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// taxonList = spiderModsList;
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FilterType filterType = FilterType.TAXON;
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NomenclaturalCode tnomenclature = NomenclaturalCode.ICNAFP;
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String defaultClassification= null;// "Nephrolepis";
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boolean alwaysUseDefaultClassification = false;
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boolean useOldUnparsedSynonymExtraction = false;
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Map<String,List<URI>>documentMap = new HashMap<String, List<URI>>();
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/*HOW TO HANDLE SECUNDUM REFERENCE*/
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boolean reuseSecundum = askIfReuseSecundum();
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Reference<?> secundum = null;
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if (!reuseSecundum) {
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secundum = askForSecundum();
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}
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loadTreatmentIfPresent(filterType,taxonList, documentMap);
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// loadTreatmentIfPresent(FilterType.MODS, modsList, documents,documentMap);
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CdmDefaultImport<TaxonXImportConfigurator> taxonImport = new CdmDefaultImport<TaxonXImportConfigurator>();
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ICdmDataSource destination = cdmDestination;
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TaxonXImportConfigurator config = prepareTaxonXImport(destination,reuseSecundum, secundum, tnomenclature, alwaysUseDefaultClassification);
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config.setUseOldUnparsedSynonymExtraction(useOldUnparsedSynonymExtraction);
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config.setImportClassificationName(defaultClassification);
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log.info("Start import from TaxonX Data");
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config.setLastImport(false);
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int j=0;
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for (String document : documentMap.keySet()){
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j++;
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if (doImportDocument(document, documentMap.get(document).size())){
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int i=0;
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for (URI source: documentMap.get(document)){
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System.out.println("START "+document+" "+i+" ("+(documentMap.get(document)).size()+"): "+source.getPath());
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i++;
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if (j==documentMap.keySet().size() && i==documentMap.get(document).size()) {
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config.setLastImport(true);
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}
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prepareReferenceAndSource(config,source);
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// taxonxImportConfigurator.setTaxonReference(null);
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taxonImport.invoke(config);
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log.info("End import from SpecimenData ("+ source.toString() + ")...");
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// //deduplicate
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// ICdmApplicationConfiguration app = taxonImport.getCdmAppController();
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// int count = app.getAgentService().deduplicate(Person.class, null, null);
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// logger.warn("Deduplicated " + count + " persons.");
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// count = app.getReferenceService().deduplicate(Reference.class, null, null);
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// logger.warn("Deduplicated " + count + " references.");
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}
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}
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}
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}
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private static String askQuestion(String question){
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Scanner scan = new Scanner(System.in);
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System.out.println(question);
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String index = scan.nextLine();
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return index;
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}
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/**
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* @param taxonxImportConfigurator
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* @param source
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*
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*/
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private static void prepareReferenceAndSource(TaxonXImportConfigurator taxonxImportConfigurator, URI source) {
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Reference<?> reference = ReferenceFactory.newGeneric();
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// String tref = askQuestion("Import source? (ie Plazi document ID)");
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String tref="PLAZI - "+source.getPath().split("/")[source.getPath().split("/").length-1];
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reference.setTitleCache(tref,true);
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reference.setTitle(tref);
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taxonxImportConfigurator.setSourceReference(reference);
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TaxonXImportConfigurator.setSourceRef(reference);
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Reference<?> referenceUrl = ReferenceFactory.newWebPage();
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referenceUrl.setTitleCache(source.toString(), true);
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referenceUrl.setTitle(source.toString());
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reference.setUri(source);
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referenceUrl.generateTitle();
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taxonxImportConfigurator.addOriginalSource(referenceUrl);
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taxonxImportConfigurator.setSource(source);
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}
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/**
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* @param destination
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* @param reuseSecundum
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* @param secundum
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* @param tnomenclature
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* @param alwaysUseDefaultClassification
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* @return
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*/
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private static TaxonXImportConfigurator prepareTaxonXImport(ICdmDataSource destination, boolean reuseSecundum, Reference<?> secundum, NomenclaturalCode tnomenclature, boolean alwaysUseDefaultClassification) {
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TaxonXImportConfigurator taxonxImportConfigurator = TaxonXImportConfigurator.NewInstance(destination);
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//taxonxImportConfigurator.setClassificationName(taxonxImportConfigurator.getSourceReferenceTitle());
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taxonxImportConfigurator.setCheck(check);
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taxonxImportConfigurator.setDbSchemaValidation(hbm2dll);
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taxonxImportConfigurator.setDoAutomaticParsing(true);
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taxonxImportConfigurator.setInteractWithUser(true);
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taxonxImportConfigurator.setNomenclaturalCode(tnomenclature);
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taxonxImportConfigurator.setAlwaysUseDefaultClassification(alwaysUseDefaultClassification);
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taxonxImportConfigurator.setKeepOriginalSecundum(reuseSecundum);
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if (!reuseSecundum) {
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taxonxImportConfigurator.setSecundum(secundum);
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}
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//taxonxImportConfigurator.setDoMatchTaxa(true);
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// taxonxImportConfigurator.setReUseTaxon(true);
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return taxonxImportConfigurator;
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}
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/**
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* @param filterType
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* @param modsList
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* @param documents
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* @param documentMap
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* @return
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*/
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private static Map<String, List<URI>> loadTreatmentIfPresent(FilterType filterType, String[] filterList, Map<String, List<URI>> documentMap) {
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Map<String, List<String>> docs = new HashMap<String, List<String>>();
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try {
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List<String> docList;
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String inputLine;
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String urlstr="";
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Map<String,List<String>> documents = fillDocumentMap(filterType, filterList, urlstr);
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// checkTreatmentAvailable(documents, docs);
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docs = documents;
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} catch (Exception e1) {
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e1.printStackTrace();
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}
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//System.out.println(documents);
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for (String docId : docs.keySet()){
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List<String> treatments = new ArrayList<String>(new HashSet<String>(docs.get(docId)));
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Map<Integer, List<String>> startPages = new HashMap<Integer, List<String>>();
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for (String treatment:treatments) {
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List<String>tmplist = startPages.get(Integer.valueOf(treatment.split("---")[0]));
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if (tmplist == null) {
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tmplist = new ArrayList<String>();
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}
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tmplist.add(treatment.split("---")[3]);
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startPages.put(Integer.valueOf(treatment.split("---")[0]),tmplist);
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}
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List<Integer> pages = new ArrayList<Integer>();
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pages.addAll(startPages.keySet());
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Collections.sort(pages);
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// log.info(pages);
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log.info("Document "+docId+" should have "+treatments.size()+" treatments");
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List<URI> uritmp = documentMap.get(docId);
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if (uritmp == null) {
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uritmp = new ArrayList<URI>();
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}
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for (int page:pages) {
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for (String treatment: startPages.get(page)) {
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try {
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uritmp.add(new URL(treatment).toURI());
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} catch (MalformedURLException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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} catch (URISyntaxException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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}
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}
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documentMap.put(docId, uritmp);
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}
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return documentMap;
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}
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private static void checkTreatmentAvailable(Map<String, List<String>> documents, Map<String, List<String>> docs)
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throws IOException, MalformedURLException {
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List<String> docList;
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String inputLine;
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for (String docId:documents.keySet()){
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URL url = new URL(plaziUrlModsDoc+docId);
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BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
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while ((inputLine = in.readLine()) != null) {
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if (inputLine.startsWith("<treatment ")){
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String taxon = inputLine.split("taxon=\"")[1].split("\"")[0];
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String docID=inputLine.split("docId=\"")[1].split("\"")[0];
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String link=inputLine.split("link=\"")[1].split("\"")[0];
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String pageStart = inputLine.split("startPage=\"")[1].split("\"")[0];
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String pageEnd = inputLine.split("endPage=\"")[1].split("\"")[0];
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docList = documents.get(docID);
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if (docList == null) {
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docList = new ArrayList<String>();
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}
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docList.add(pageStart+"---" + pageEnd + "---" + taxon + "---"+link);
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docs.put(docID,docList);
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}
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}
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}
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}
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private static Map<String, List<String>> fillDocumentMap(FilterType filterType,
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String[] filterList, String urlstr)
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throws MalformedURLException, IOException {
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Map<String, List<String>> documents = new HashMap<String, List<String>>();
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List<String> docList;
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String inputLine;
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for(String filter : filterList){
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// plaziUrl=plaziUrl+"Eupolybothrus";
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if (filterType == FilterType.MODS) {
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urlstr=plaziUrlModsDoc + filter;
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}else if (filterType == FilterType.TAXON) {
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urlstr=plaziUrlTaxName + filter;
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}
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log.info("URLstr: " + urlstr);
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URL plaziURL = new URL(urlstr);
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BufferedReader in = new BufferedReader(new InputStreamReader(plaziURL.openStream()));
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321
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//TODO lastUpdate field
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// if(!plaziNotServer){
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while ((inputLine = in.readLine()) != null) {
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System.out.println(inputLine);
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if (inputLine.startsWith("<treatment ")){
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String taxon = inputLine.split("taxon=\"")[1].split("\"")[0];
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String docID=inputLine.split("docId=\"")[1].split("\"")[0];
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329
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System.out.println("docID: "+docID);
|
|
330
|
|
|
331
|
String link=inputLine.split("link=\"")[1].split("\"")[0];
|
|
332
|
String pageStart = inputLine.split("startPage=\"")[1].split("\"")[0];
|
|
333
|
String pageEnd = inputLine.split("endPage=\"")[1].split("\"")[0];
|
|
334
|
docList = documents.get(docID);
|
|
335
|
if (docList == null) {
|
|
336
|
docList = new ArrayList<String>();
|
|
337
|
}
|
|
338
|
docList.add(pageStart+"---" + pageEnd + "---"+taxon+"---"+link);
|
|
339
|
documents.put(docID,docList);
|
|
340
|
}
|
|
341
|
}
|
|
342
|
}
|
|
343
|
System.out.println("documents created");
|
|
344
|
|
|
345
|
return documents;
|
|
346
|
}
|
|
347
|
|
|
348
|
/**
|
|
349
|
* @param document
|
|
350
|
* @return
|
|
351
|
*/
|
|
352
|
private static boolean doImportDocument(String document, int nbtreatments) {
|
|
353
|
|
|
354
|
if (nbtreatments>400) {
|
|
355
|
return false;
|
|
356
|
}
|
|
357
|
if (document.equalsIgnoreCase("1314-2828-2")) { //this is a mix of several publications..
|
|
358
|
return false;
|
|
359
|
}
|
|
360
|
if (document.equalsIgnoreCase("21367")) { //600treatments for ants..
|
|
361
|
return false;
|
|
362
|
}
|
|
363
|
if (document.equalsIgnoreCase("1314-2828-1")) { //900treatments for eupoly..
|
|
364
|
return false;
|
|
365
|
}
|
|
366
|
return true;
|
|
367
|
/*
|
|
368
|
// List<String> docDone = Arrays.asList(new String[]{"3540555099", "0910-2878-5652", "5012-9059-4108",
|
|
369
|
// "3784-0748-2261","3-201-00728-5", "FloNuttDuWin1838", "FlNordica_chenop","2580-1363-7530",
|
|
370
|
// "1842460692","5161-7797-8064","FlCaboVerde_Chen","2819-9661-8339","2626-3794-9273"});//,
|
|
371
|
// // "8776-7797-8303"});
|
|
372
|
// if (docDone.contains(document)) {
|
|
373
|
// return false;
|
|
374
|
// }
|
|
375
|
|
|
376
|
JTextArea textArea = new JTextArea("Should this document be imported ("+nbtreatments+")? \n'"+document+"'");
|
|
377
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
378
|
textArea.setLineWrap(true);
|
|
379
|
textArea.setWrapStyleWord(true);
|
|
380
|
scrollPane.setPreferredSize( new Dimension( 700, 70 ) );
|
|
381
|
|
|
382
|
// JFrame frame = new JFrame("I have a question");
|
|
383
|
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
|
|
384
|
int s = JOptionPane.showConfirmDialog(null, scrollPane);
|
|
385
|
if (s==0) {
|
|
386
|
return true;
|
|
387
|
} else {
|
|
388
|
return false;
|
|
389
|
}
|
|
390
|
*/
|
|
391
|
}
|
|
392
|
|
|
393
|
/**
|
|
394
|
* @return
|
|
395
|
*/
|
|
396
|
private static boolean askIfReuseSecundum() {
|
|
397
|
// logger.info("getFullReference for "+ name);
|
|
398
|
JTextArea textArea = new JTextArea("Reuse the secundum present in the current classification? " +
|
|
399
|
"\n Click Yes to reuse it, click No or Cancel to create a new one.\nA default secundum will be created if needed.");
|
|
400
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
401
|
textArea.setLineWrap(true);
|
|
402
|
textArea.setWrapStyleWord(true);
|
|
403
|
scrollPane.setPreferredSize( new Dimension( 700, 70 ) );
|
|
404
|
|
|
405
|
// JFrame frame = new JFrame("I have a question");
|
|
406
|
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
|
|
407
|
int s = JOptionPane.showConfirmDialog(null, scrollPane);
|
|
408
|
if (s==0) {
|
|
409
|
return true;
|
|
410
|
} else {
|
|
411
|
return false;
|
|
412
|
}
|
|
413
|
}
|
|
414
|
|
|
415
|
/**
|
|
416
|
* @return
|
|
417
|
*/
|
|
418
|
private static Reference<?> askForSecundum() {
|
|
419
|
// logger.info("getFullReference for "+ name);
|
|
420
|
JTextArea textArea = new JTextArea("Enter the secundum name");
|
|
421
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
422
|
textArea.setLineWrap(true);
|
|
423
|
textArea.setWrapStyleWord(true);
|
|
424
|
scrollPane.setPreferredSize( new Dimension( 700, 100 ) );
|
|
425
|
|
|
426
|
// JFrame frame = new JFrame("I have a question");
|
|
427
|
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
|
|
428
|
String s = (String) JOptionPane.showInputDialog(
|
|
429
|
null,
|
|
430
|
scrollPane,
|
|
431
|
"",
|
|
432
|
JOptionPane.PLAIN_MESSAGE,
|
|
433
|
null,
|
|
434
|
null,
|
|
435
|
null);
|
|
436
|
Reference<?> ref = ReferenceFactory.newGeneric();
|
|
437
|
ref.setTitle(s);
|
|
438
|
return ref;
|
|
439
|
}
|
|
440
|
|
|
441
|
|
|
442
|
}
|