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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.io.markup;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Stack;
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import java.util.UUID;
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import javax.xml.namespace.QName;
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import javax.xml.stream.Location;
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import javax.xml.stream.XMLEventReader;
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import javax.xml.stream.XMLStreamConstants;
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import javax.xml.stream.XMLStreamException;
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import javax.xml.stream.events.Attribute;
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import javax.xml.stream.events.Characters;
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import javax.xml.stream.events.EndElement;
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import javax.xml.stream.events.StartElement;
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import javax.xml.stream.events.XMLEvent;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.lang.WordUtils;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.service.IClassificationService;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.ext.geo.GeoServiceArea;
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import eu.etaxonomy.cdm.ext.geo.IEditGeoService;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.CdmImportBase.TermMatchMode;
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import eu.etaxonomy.cdm.io.common.events.IIoEvent;
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import eu.etaxonomy.cdm.io.common.events.IoProblemEvent;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PolytomousKey;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author a.mueller
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* @created 04.08.2008
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*/
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public abstract class MarkupImportBase {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(MarkupImportBase.class);
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//Base
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protected static final String ALTITUDE = "altitude";
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protected static final String ANNOTATION = "annotation";
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protected static final String BOLD = "bold";
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protected static final String BR = "br";
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protected static final String CITATION = "citation";
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protected static final String CLASS = "class";
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protected static final String COORDINATES = "coordinates";
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protected static final String DATES = "dates";
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protected static final String GATHERING = "gathering";
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protected static final String GENUS_ABBREVIATION = "genus abbreviation";
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protected static final String FOOTNOTE = "footnote";
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protected static final String FOOTNOTE_REF = "footnoteRef";
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protected static final String FULL_NAME = "fullName";
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protected static final String ITALICS = "italics";
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protected static final String NUM = "num";
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protected static final String NOTES = "notes";
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protected static final String PUBLICATION = "publication";
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protected static final String SPECIMEN_TYPE = "specimenType";
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protected static final String STATUS = "status";
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protected static final String SUB_HEADING = "subHeading";
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protected static final String TYPE = "type";
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protected static final String TYPE_STATUS = "typeStatus";
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protected static final boolean CREATE_NEW = true;
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protected static final boolean NO_IMAGE_GALLERY = false;
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protected static final boolean IMAGE_GALLERY = true;
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protected static final String ADDENDA = "addenda";
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protected static final String BIBLIOGRAPHY = "bibliography";
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protected static final String BIOGRAPHIES = "biographies";
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protected static final String CHAR = "char";
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protected static final String DEDICATION = "dedication";
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protected static final String DEFAULT_MEDIA_URL = "defaultMediaUrl";
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protected static final String DISTRIBUTION_LIST = "distributionList";
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protected static final String DISTRIBUTION_LOCALITY = "distributionLocality";
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protected static final String FEATURE = "feature";
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protected static final String FIGURE = "figure";
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protected static final String FIGURE_LEGEND = "figureLegend";
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protected static final String FIGURE_PART = "figurePart";
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protected static final String FIGURE_REF = "figureRef";
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protected static final String FIGURE_TITLE = "figureTitle";
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protected static final String FOOTNOTE_STRING = "footnoteString";
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protected static final String FREQUENCY = "frequency";
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protected static final String HEADING = "heading";
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protected static final String HABITAT = "habitat";
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protected static final String HABITAT_LIST = "habitatList";
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protected static final String IS_FREETEXT = "isFreetext";
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protected static final String ID = "id";
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protected static final String KEY = "key";
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protected static final String LIFE_CYCLE_PERIODS = "lifeCyclePeriods";
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protected static final String META_DATA = "metaData";
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protected static final String MODS = "mods";
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protected static final String NOMENCLATURE = "nomenclature";
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protected static final String QUOTE = "quote";
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protected static final String RANK = "rank";
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protected static final String REF = "ref";
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protected static final String REF_NUM = "refNum";
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protected static final String REFERENCE = "reference";
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protected static final String REFERENCES = "references";
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protected static final String SUB_CHAR = "subChar";
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protected static final String TAXON = "taxon";
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protected static final String TAXONTITLE = "taxontitle";
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protected static final String TAXONTYPE = "taxontype";
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protected static final String TEXT_SECTION = "textSection";
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protected static final String TREATMENT = "treatment";
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protected static final String SERIALS_ABBREVIATIONS = "serialsAbbreviations";
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protected static final String STRING = "string";
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protected static final String URL = "url";
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protected static final String VERNACULAR_NAMES = "vernacularNames";
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protected static final String WRITER = "writer";
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//Nomenclature
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protected static final String ACCEPTED = "accepted";
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protected static final String ACCEPTED_NAME = "acceptedName";
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protected static final String ALTERNATEPUBTITLE = "alternatepubtitle";
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protected static final String AUTHOR = "author";
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protected static final String DETAILS = "details";
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protected static final String EDITION = "edition";
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protected static final String EDITORS = "editors";
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protected static final String HOMONYM = "homonym";
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protected static final String HOMOTYPES = "homotypes";
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protected static final String INFRANK = "infrank";
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protected static final String INFRAUT = "infraut";
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protected static final String INFRPARAUT = "infrparaut";
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protected static final String ISSUE = "issue";
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protected static final String NAME = "name";
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protected static final String NAME_TYPE = "nameType";
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protected static final String NOM = "nom";
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protected static final String PAGES = "pages";
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protected static final String PARAUT = "paraut";
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protected static final String PUBFULLNAME = "pubfullname";
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protected static final String PUBNAME = "pubname";
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protected static final String PUBTITLE = "pubtitle";
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protected static final String PUBTYPE = "pubtype";
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protected static final String REF_PART = "refPart";
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protected static final String SYNONYM = "synonym";
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protected static final String USAGE = "usage";
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protected static final String VOLUME = "volume";
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protected static final String YEAR = "year";
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//keys
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protected static final String COUPLET = "couplet";
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protected static final String IS_SPOTCHARACTERS = "isSpotcharacters";
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protected static final String ONLY_NUMBERED_TAXA_EXIST = "onlyNumberedTaxaExist";
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protected static final String EXISTS = "exists";
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protected static final String KEYNOTES = "keynotes";
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protected static final String KEY_TITLE = "keyTitle";
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protected static final String QUESTION = "question";
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protected static final String TEXT = "text";
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protected static final String TO_COUPLET = "toCouplet";
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protected static final String TO_KEY = "toKey";
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protected static final String TO_TAXON = "toTaxon";
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protected MarkupDocumentImport docImport;
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private IEditGeoService editGeoService;
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public MarkupImportBase(MarkupDocumentImport docImport) {
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super();
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this.docImport = docImport;
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this.editGeoService = docImport.getEditGeoService();
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}
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private Stack<QName> unhandledElements = new Stack<QName>();
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private Stack<QName> handledElements = new Stack<QName>();
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protected <T extends CdmBase> void save(Collection<T> collection, MarkupImportState state) {
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if (state.isCheck() || collection.isEmpty()){
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return;
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}
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T example = collection.iterator().next();
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if (example.isInstanceOf(TaxonBase.class)){
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Collection<TaxonBase> typedCollection = (Collection<TaxonBase>)collection;
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docImport.getTaxonService().saveOrUpdate(typedCollection);
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}else if (example.isInstanceOf(Classification.class)){
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Collection<Classification> typedCollection = (Collection<Classification>)collection;
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docImport.getClassificationService().saveOrUpdate(typedCollection);
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}else if (example.isInstanceOf(PolytomousKey.class)){
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Collection<PolytomousKey> typedCollection = (Collection<PolytomousKey>)collection;
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docImport.getPolytomousKeyService().saveOrUpdate(typedCollection);
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}else if (example.isInstanceOf(DefinedTermBase.class)){
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Collection<DefinedTermBase> typedCollection = (Collection<DefinedTermBase>)collection;
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getTermService().saveOrUpdate(typedCollection);
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}
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}
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//TODO move to service layer for all IdentifiableEntities
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protected void save(CdmBase cdmBase, MarkupImportState state) {
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if (state.isCheck()){
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return;
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}
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cdmBase = CdmBase.deproxy(cdmBase, CdmBase.class);
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if (cdmBase == null){
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String message = "Tried to save a null object.";
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fireWarningEvent(message, "--location ?? --", 6,1);
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} else if (cdmBase.isInstanceOf(TaxonBase.class)){
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docImport.getTaxonService().saveOrUpdate((TaxonBase<?>)cdmBase);
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}else if (cdmBase.isInstanceOf(Classification.class)){
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docImport.getClassificationService().saveOrUpdate((Classification)cdmBase);
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}else if (cdmBase.isInstanceOf(PolytomousKey.class)){
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docImport.getPolytomousKeyService().saveOrUpdate((PolytomousKey)cdmBase);
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}else if (cdmBase.isInstanceOf(DefinedTermBase.class)){
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docImport.getTermService().saveOrUpdate((DefinedTermBase<?>)cdmBase);
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}else if (cdmBase.isInstanceOf(Media.class)){
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docImport.getMediaService().saveOrUpdate((Media)cdmBase);
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}else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
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docImport.getOccurrenceService().saveOrUpdate((SpecimenOrObservationBase<?>)cdmBase);
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}else if (cdmBase.isInstanceOf(DescriptionElementBase.class)){
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docImport.getDescriptionService().saveDescriptionElement((DescriptionElementBase)cdmBase);
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}else{
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String message = "Unknown cdmBase type to save: " + cdmBase.getClass();
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fireWarningEvent(message, "Unknown location", 8);
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}
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//logger.warn("Saved " + cdmBase);
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}
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protected ITermService getTermService() {
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return docImport.getTermService();
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}
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protected IClassificationService getClassificationService() {
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return docImport.getClassificationService();
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}
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//*********************** Attribute methods *************************************/
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/**
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* Returns a map for all attributes of an start element
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* @param event
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* @return
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*/
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protected Map<String, Attribute> getAttributes(XMLEvent event) {
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Map<String, Attribute> result = new HashMap<String, Attribute>();
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if (!event.isStartElement()){
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fireWarningEvent("Event is not an startElement. Can't check attributes", makeLocationStr(event.getLocation()), 1, 1);
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return result;
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}
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StartElement element = event.asStartElement();
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Iterator<Attribute> attributes = element.getAttributes();
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while (attributes.hasNext()){
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Attribute attribute = attributes.next();
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//TODO namespaces
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result.put(attribute.getName().getLocalPart(), attribute);
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}
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return result;
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}
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/**
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* Throws an unexpected attributes event if the event has any attributes.
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* @param event
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*/
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protected void checkNoAttributes(Map<String, Attribute> attributes, XMLEvent event) {
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String[] exceptions = new String[]{};
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handleUnexpectedAttributes(event.getLocation(), attributes, 1, exceptions);
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}
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/**
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* Throws an unexpected attributes event if the event has any attributes.
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* @param event
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*/
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protected void checkNoAttributes(XMLEvent event) {
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String[] exceptions = new String[]{};
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checkNoAttributes(event, 1, exceptions);
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}
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/**
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* Throws an unexpected attributes event if the event has any attributes except those mentioned in "exceptions".
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* @param event
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* @param exceptions
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*/
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protected void checkNoAttributes(XMLEvent event, int stackDepth, String... exceptions) {
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if (! event.isStartElement()){
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fireWarningEvent("Event is not an startElement. Can't check attributes", makeLocationStr(event.getLocation()), 1, 1);
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return;
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}
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StartElement startElement = event.asStartElement();
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Map<String, Attribute> attributes = getAttributes(startElement);
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handleUnexpectedAttributes(startElement.getLocation(), attributes, stackDepth+1, exceptions);
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}
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/**
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* Checks if the given attribute exists and has the given value.
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* If yes, true is returned and the attribute is removed from the attributes map.
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* Otherwise false is returned.
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* @param attributes
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* @param attrName
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* @param value
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* @return <code>true</code> if attribute has given value, <code>false</code> otherwise
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*/
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protected boolean checkAndRemoveAttributeValue( Map<String, Attribute> attributes, String attrName, String value) {
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Attribute attr = attributes.get(attrName);
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if (attr == null ||value == null ){
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return false;
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}else{
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if (value.equals(attr.getValue())){
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attributes.remove(attrName);
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return true;
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}else{
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return false;
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}
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}
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}
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/**
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* Returns the value of a given attribute name and removes the attribute from the attributes map.
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* @param attributes
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* @param attrName
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* @return
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*/
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protected String getAndRemoveAttributeValue(Map<String, Attribute> attributes, String attrName) {
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return getAndRemoveAttributeValue(null, attributes, attrName, false, 1);
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}
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/**
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* Returns the value of a boolean attribute with the given name and removes the attribute from the attributes map.
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* Returns <code>defaultValue</code> if the attribute does not exist. ALso returns <code>defaultValue</code> and throws a warning if the
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* attribute has no boolean value (true, false).
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* @param
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* @param attributes the
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* @param attrName the name of the attribute
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* @param defaultValue the default value to return if attribute does not exist or can not be defined
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* @return
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*/
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protected Boolean getAndRemoveBooleanAttributeValue(XMLEvent event, Map<String, Attribute> attributes, String attrName, Boolean defaultValue) {
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String value = getAndRemoveAttributeValue(null, attributes, attrName, false, 1);
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Boolean result = defaultValue;
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if (value != null){
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if (value.equalsIgnoreCase("true")){
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result = true;
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}else if (value.equalsIgnoreCase("false")){
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result = false;
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}else{
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String message = "Boolean attribute has no boolean value ('true', 'false') but '%s'";
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386
|
fireWarningEvent(String.format(message, value), makeLocationStr(event.getLocation()), 6, 1);
|
387
|
}
|
388
|
}
|
389
|
return result;
|
390
|
}
|
391
|
|
392
|
|
393
|
/**
|
394
|
* Returns the value of a given attribute name and returns the attribute from the attributes map.
|
395
|
* Fires a mandatory field is missing event if the attribute does not exist.
|
396
|
* @param xmlEvent
|
397
|
* @param attributes
|
398
|
* @param attrName
|
399
|
* @return
|
400
|
*/
|
401
|
protected String getAndRemoveRequiredAttributeValue(XMLEvent xmlEvent, Map<String, Attribute> attributes, String attrName) {
|
402
|
return getAndRemoveAttributeValue(xmlEvent, attributes, attrName, true, 1);
|
403
|
}
|
404
|
|
405
|
/**
|
406
|
* Returns the value of a given attribute name and returns the attribute from the attributes map.
|
407
|
* If required is <code>true</code> and the attribute does not exist a mandatory field is missing event is fired.
|
408
|
* @param xmlEvent
|
409
|
* @param attributes
|
410
|
* @param attrName
|
411
|
* @param isRequired
|
412
|
* @return
|
413
|
*/
|
414
|
private String getAndRemoveAttributeValue(XMLEvent xmlEvent, Map<String, Attribute> attributes, String attrName, boolean isRequired, int stackDepth) {
|
415
|
Attribute attr = attributes.get(attrName);
|
416
|
if (attr == null ){
|
417
|
if (isRequired){
|
418
|
fireMandatoryElementIsMissing(xmlEvent, attrName, 8, stackDepth+1);
|
419
|
}
|
420
|
return null;
|
421
|
}else{
|
422
|
attributes.remove(attrName);
|
423
|
return attr.getValue();
|
424
|
}
|
425
|
}
|
426
|
|
427
|
/**
|
428
|
* Fires an not yet implemented event if the given attribute exists in attributes.
|
429
|
* @param attributes
|
430
|
* @param attrName
|
431
|
*/
|
432
|
protected void handleNotYetImplementedAttribute(Map<String, Attribute> attributes, String attrName) {
|
433
|
Attribute attr = attributes.get(attrName);
|
434
|
if (attr != null){
|
435
|
attributes.remove(attrName);
|
436
|
QName qName = attr.getName();
|
437
|
fireNotYetImplementedAttribute(attr.getLocation(), qName, 1);
|
438
|
}
|
439
|
}
|
440
|
|
441
|
/**
|
442
|
* Fires an unhandled attributes event, if attributes exist in attributes map not covered by the exceptions.
|
443
|
* No event is fired if the unhandled elements stack is not empty.
|
444
|
* @param location
|
445
|
* @param attributes
|
446
|
* @param exceptions
|
447
|
*/
|
448
|
protected void handleUnexpectedAttributes(Location location,Map<String, Attribute> attributes, String... exceptions) {
|
449
|
handleUnexpectedAttributes(location, attributes, 1, exceptions);
|
450
|
}
|
451
|
|
452
|
/**
|
453
|
* see {@link #handleUnexpectedAttributes(Location, Map, String...)}
|
454
|
*
|
455
|
* @param location
|
456
|
* @param attributes
|
457
|
* @param stackDepth the stack trace depth
|
458
|
* @param exceptions
|
459
|
*/
|
460
|
private void handleUnexpectedAttributes(Location location,Map<String, Attribute> attributes, int stackDepth, String... exceptions) {
|
461
|
if (attributes.size() > 0){
|
462
|
if (this.unhandledElements.size() == 0 ){
|
463
|
boolean hasUnhandledAttributes = false;
|
464
|
for (String key : attributes.keySet()){
|
465
|
boolean isException = false;
|
466
|
for (String exception : exceptions){
|
467
|
if(key.equals(exception)){
|
468
|
isException = true;
|
469
|
}
|
470
|
}
|
471
|
if (!isException){
|
472
|
hasUnhandledAttributes = true;
|
473
|
}
|
474
|
}
|
475
|
if (hasUnhandledAttributes){
|
476
|
fireUnexpectedAttributes(location, attributes, stackDepth+1);
|
477
|
}
|
478
|
}
|
479
|
}
|
480
|
}
|
481
|
|
482
|
|
483
|
private void fireUnexpectedAttributes(Location location, Map<String, Attribute> attributes, int stackDepth) {
|
484
|
String attributesString = "";
|
485
|
for (String key : attributes.keySet()){
|
486
|
Attribute attribute = attributes.get(key);
|
487
|
attributesString = CdmUtils.concat(",", attributesString, attribute.getName().getLocalPart() + ":" + attribute.getValue());
|
488
|
}
|
489
|
String message = "Unexpected attributes: %s";
|
490
|
IoProblemEvent event = makeProblemEvent(location, String.format(message, attributesString), 1 , stackDepth +1 );
|
491
|
fire(event);
|
492
|
}
|
493
|
|
494
|
|
495
|
protected void fireUnexpectedAttributeValue(XMLEvent parentEvent, String attrName, String attrValue) {
|
496
|
String message = "Unexpected attribute value %s='%s'";
|
497
|
message = String.format(message, attrName, attrValue);
|
498
|
IoProblemEvent event = makeProblemEvent(parentEvent.getLocation(), message, 1 , 1 );
|
499
|
fire(event);
|
500
|
}
|
501
|
|
502
|
protected void handleNotYetImplementedAttributeValue(XMLEvent xmlEvent, String attrName, String attrValue) {
|
503
|
String message = "Attribute %s not yet implemented for value '%s'";
|
504
|
message = String.format(message, attrName, attrValue);
|
505
|
IIoEvent event = makeProblemEvent(xmlEvent.getLocation(), message, 1, 1 );
|
506
|
fire(event);
|
507
|
}
|
508
|
|
509
|
protected void fireNotYetImplementedAttribute(Location location, QName qName, int stackDepth) {
|
510
|
String message = "Attribute not yet implemented: %s";
|
511
|
IIoEvent event = makeProblemEvent(location, String.format(message, qName.getLocalPart()), 1, stackDepth+1 );
|
512
|
fire(event);
|
513
|
}
|
514
|
|
515
|
|
516
|
|
517
|
|
518
|
protected void fireUnexpectedEvent(XMLEvent xmlEvent, int stackDepth) {
|
519
|
Location location = xmlEvent.getLocation();
|
520
|
String message = "Unexpected event: %s";
|
521
|
IIoEvent event = makeProblemEvent(location, String.format(message, xmlEvent.toString()), 2, stackDepth +1);
|
522
|
fire(event);
|
523
|
}
|
524
|
|
525
|
protected void fireUnexpectedStartElement(Location location, StartElement startElement, int stackDepth) {
|
526
|
QName qName = startElement.getName();
|
527
|
String message = "Unexpected start element: %s";
|
528
|
IIoEvent event = makeProblemEvent(location, String.format(message, qName.getLocalPart()), 2, stackDepth +1);
|
529
|
fire(event);
|
530
|
}
|
531
|
|
532
|
|
533
|
protected void fireUnexpectedEndElement(Location location, EndElement endElement, int stackDepth) {
|
534
|
QName qName = endElement.getName();
|
535
|
String message = "Unexpected end element: %s";
|
536
|
IIoEvent event = makeProblemEvent(location, String.format(message, qName.getLocalPart()), 16, stackDepth+1);
|
537
|
fire(event);
|
538
|
}
|
539
|
|
540
|
protected void fireNotYetImplementedElement(Location location, QName qName, int stackDepth) {
|
541
|
String message = "Element not yet implemented: %s";
|
542
|
IIoEvent event = makeProblemEvent(location, String.format(message, qName.getLocalPart()), 1, stackDepth+1 );
|
543
|
fire(event);
|
544
|
}
|
545
|
|
546
|
protected void fireNotYetImplementedCharacters(Location location, Characters chars, int stackDepth) {
|
547
|
String message = "Characters not yet handled: %s";
|
548
|
IIoEvent event = makeProblemEvent(location, String.format(message, chars.getData()), 1, stackDepth+1 );
|
549
|
fire(event);
|
550
|
}
|
551
|
|
552
|
/**
|
553
|
* Creates a problem event.
|
554
|
* Be aware of the right depths of the stack trace !
|
555
|
* @param location
|
556
|
* @param message
|
557
|
* @param severity
|
558
|
* @return
|
559
|
*/
|
560
|
private IoProblemEvent makeProblemEvent(Location location, String message, int severity, int stackDepth) {
|
561
|
stackDepth++;
|
562
|
StackTraceElement[] stackTrace = new Exception().getStackTrace();
|
563
|
int lineNumber = stackTrace[stackDepth].getLineNumber();
|
564
|
String methodName = stackTrace[stackDepth].getMethodName();
|
565
|
String locationStr = makeLocationStr(location);
|
566
|
String className = stackTrace[stackDepth].getClassName();
|
567
|
Class<?> declaringClass;
|
568
|
try {
|
569
|
declaringClass = Class.forName(className);
|
570
|
} catch (ClassNotFoundException e) {
|
571
|
declaringClass = this.getClass();
|
572
|
}
|
573
|
IoProblemEvent event = IoProblemEvent.NewInstance(declaringClass, message,
|
574
|
locationStr, lineNumber, severity, methodName);
|
575
|
return event;
|
576
|
}
|
577
|
|
578
|
/**
|
579
|
* Creates a string from a location
|
580
|
* @param location
|
581
|
* @return
|
582
|
*/
|
583
|
protected String makeLocationStr(Location location) {
|
584
|
String locationStr = location == null ? " - no location - " : "l." + location.getLineNumber() + "/c."+ location.getColumnNumber();
|
585
|
return locationStr;
|
586
|
}
|
587
|
|
588
|
|
589
|
/**
|
590
|
* Fires an unexpected element event if the unhandled elements stack is empty.
|
591
|
* Otherwise adds the element to the stack.
|
592
|
* @param event
|
593
|
*/
|
594
|
protected void handleUnexpectedStartElement(XMLEvent event) {
|
595
|
handleUnexpectedStartElement(event, 1);
|
596
|
}
|
597
|
|
598
|
/**
|
599
|
* Fires an unexpected element event if the unhandled elements stack is empty.
|
600
|
* Otherwise adds the element to the stack.
|
601
|
* @param event
|
602
|
*/
|
603
|
protected void handleUnexpectedStartElement(XMLEvent event, int stackDepth) {
|
604
|
QName qName = event.asStartElement().getName();
|
605
|
if (! unhandledElements.empty()){
|
606
|
unhandledElements.push(qName);
|
607
|
}else{
|
608
|
fireUnexpectedStartElement(event.getLocation(), event.asStartElement(), stackDepth + 1);
|
609
|
}
|
610
|
}
|
611
|
|
612
|
|
613
|
protected void handleUnexpectedEndElement(EndElement event) {
|
614
|
handleUnexpectedEndElement(event, 1);
|
615
|
}
|
616
|
|
617
|
/**
|
618
|
* Fires an unexpected element event if the event is not the last on the stack.
|
619
|
* Otherwise removes last stack element.
|
620
|
* @param event
|
621
|
*/
|
622
|
protected void handleUnexpectedEndElement(EndElement event, int stackDepth) {
|
623
|
QName qName = event.asEndElement().getName();
|
624
|
if (!unhandledElements.isEmpty() && unhandledElements.peek().equals(qName)){
|
625
|
unhandledElements.pop();
|
626
|
}else{
|
627
|
fireUnexpectedEndElement(event.getLocation(), event.asEndElement(), stackDepth + 1);
|
628
|
}
|
629
|
}
|
630
|
|
631
|
/**
|
632
|
*
|
633
|
* @param endElement
|
634
|
*/
|
635
|
protected void popUnimplemented(EndElement endElement) {
|
636
|
QName qName = endElement.asEndElement().getName();
|
637
|
if (unhandledElements.peek().equals(qName)){
|
638
|
unhandledElements.pop();
|
639
|
}else{
|
640
|
String message = "End element is not last on stack: %s";
|
641
|
message = String.format(message, qName.getLocalPart());
|
642
|
IIoEvent event = makeProblemEvent(endElement.getLocation(), message, 16, 1);
|
643
|
fire(event);
|
644
|
}
|
645
|
|
646
|
}
|
647
|
|
648
|
|
649
|
/**
|
650
|
* Fires an unexpected element event if the unhandled element stack is empty.
|
651
|
* @param event
|
652
|
*/
|
653
|
protected void handleUnexpectedElement(XMLEvent event) {
|
654
|
if (event.isStartElement()){
|
655
|
handleUnexpectedStartElement(event);
|
656
|
}else if (event.isEndElement()){
|
657
|
handleUnexpectedEndElement(event.asEndElement());
|
658
|
}else if (event.getEventType() == XMLStreamConstants.COMMENT){
|
659
|
//do nothing
|
660
|
}else if (! unhandledElements.empty()){
|
661
|
//do nothing
|
662
|
}else{
|
663
|
fireUnexpectedEvent(event, 1);
|
664
|
}
|
665
|
}
|
666
|
|
667
|
/**
|
668
|
* Fires an not yet implemented event and adds the element name to the unhandled elements stack.
|
669
|
* @param event
|
670
|
*/
|
671
|
protected void handleNotYetImplementedCharacters(XMLEvent event) {
|
672
|
Characters chars = event.asCharacters();
|
673
|
fireNotYetImplementedCharacters(event.getLocation(), chars, 1);
|
674
|
}
|
675
|
|
676
|
/**
|
677
|
* Fires an not yet implemented event and adds the element name to the unhandled elements stack.
|
678
|
* @param event
|
679
|
*/
|
680
|
protected void handleNotYetImplementedElement(XMLEvent event) {
|
681
|
QName qName = event.asStartElement().getName();
|
682
|
boolean isTopLevel = unhandledElements.isEmpty();
|
683
|
unhandledElements.push(qName);
|
684
|
if (isTopLevel){
|
685
|
fireNotYetImplementedElement(event.getLocation(), qName, 1);
|
686
|
}
|
687
|
}
|
688
|
|
689
|
/**
|
690
|
* Checks if a mandatory text is not empty or null.
|
691
|
* Returns true if text is given.
|
692
|
* Fires an mandatory element is missing event otherwise and returns <code>null</code>.
|
693
|
* @param text
|
694
|
* @param parentEvent
|
695
|
* @return
|
696
|
*/
|
697
|
protected boolean checkMandatoryText(String text, XMLEvent parentEvent) {
|
698
|
if (! StringUtils.isNotBlank(text)){
|
699
|
fireMandatoryElementIsMissing(parentEvent, "CData", 4, 1);
|
700
|
return false;
|
701
|
}
|
702
|
return true;
|
703
|
}
|
704
|
|
705
|
/**
|
706
|
* Fires an mandatory element is missing event if exists is <code>false</code>.
|
707
|
* @param hasMandatory
|
708
|
* @param parentEvent
|
709
|
* @param string
|
710
|
*/
|
711
|
protected void checkMandatoryElement(boolean exists, StartElement parentEvent, String attrName) {
|
712
|
if (! exists){
|
713
|
fireMandatoryElementIsMissing(parentEvent, attrName, 5, 1);
|
714
|
}
|
715
|
}
|
716
|
|
717
|
|
718
|
/**
|
719
|
* Fires an element is missing event.
|
720
|
* @param xmlEvent
|
721
|
* @param string
|
722
|
* @param severity
|
723
|
* @param stackDepth
|
724
|
* @throws IllegalStateException if xmlEvent is not a StartElement and not an Attribute
|
725
|
*/
|
726
|
private void fireMandatoryElementIsMissing(XMLEvent xmlEvent, String missingEventName, int severity, int stackDepth) throws IllegalStateException{
|
727
|
Location location = xmlEvent.getLocation();
|
728
|
String typeName;
|
729
|
QName qName;
|
730
|
if (xmlEvent.isAttribute()){
|
731
|
Attribute attribute = ((Attribute)xmlEvent);
|
732
|
typeName = "attribute";
|
733
|
qName = attribute.getName();
|
734
|
}else if (xmlEvent.isStartElement()){
|
735
|
typeName = "element";
|
736
|
qName = xmlEvent.asStartElement().getName();
|
737
|
}else{
|
738
|
throw new IllegalStateException("mandatory element only allowed for attributes and start tags in " + makeLocationStr(location));
|
739
|
}
|
740
|
String message = "Mandatory %s '%s' is missing in %s";
|
741
|
message = String.format(message, typeName , missingEventName, qName.getLocalPart());
|
742
|
IIoEvent event = makeProblemEvent(location, message, severity, stackDepth +1);
|
743
|
fire(event);
|
744
|
}
|
745
|
|
746
|
|
747
|
|
748
|
|
749
|
/**
|
750
|
* Returns true if the "next" event is the ending tag for the "parent" event.
|
751
|
* @param next end element to test, must not be null
|
752
|
* @param parentEvent start element to test
|
753
|
* @return true if the "next" event is the ending tag for the "parent" event.
|
754
|
* @throws XMLStreamException
|
755
|
*/
|
756
|
protected boolean isMyEndingElement(XMLEvent next, XMLEvent parentEvent) throws XMLStreamException {
|
757
|
if (! parentEvent.isStartElement()){
|
758
|
String message = "Parent event should be start tag";
|
759
|
fireWarningEvent(message, makeLocationStr(next.getLocation()), 6);
|
760
|
return false;
|
761
|
}
|
762
|
return isEndingElement(next, parentEvent.asStartElement().getName().getLocalPart());
|
763
|
}
|
764
|
|
765
|
/**
|
766
|
* Trims the text and removes turns all whitespaces into single empty space.
|
767
|
* @param text
|
768
|
* @return
|
769
|
*/
|
770
|
protected String normalize(String text) {
|
771
|
text = StringUtils.trimToEmpty(text);
|
772
|
text = text.replaceAll("\\s+", " ");
|
773
|
return text;
|
774
|
}
|
775
|
|
776
|
|
777
|
|
778
|
/**
|
779
|
* Removes whitespaces at beginning and end and makes the first letter
|
780
|
* a capital letter and all other letters small letters.
|
781
|
* @param value
|
782
|
* @return
|
783
|
*/
|
784
|
protected String toFirstCapital(String value) {
|
785
|
if (StringUtils.isBlank(value)){
|
786
|
return value;
|
787
|
}else{
|
788
|
String result = "";
|
789
|
value = value.trim();
|
790
|
result += value.trim().substring(0,1).toUpperCase();
|
791
|
if (value.length()>1){
|
792
|
result += value.substring(1).toLowerCase();
|
793
|
}
|
794
|
return result;
|
795
|
}
|
796
|
}
|
797
|
|
798
|
/**
|
799
|
* Currently not used.
|
800
|
* @param str
|
801
|
* @param allowedNumberOfCharacters
|
802
|
* @param onlyFirstCapital
|
803
|
* @return
|
804
|
*/
|
805
|
protected boolean isAbbreviation(String str, int allowedNumberOfCharacters, boolean onlyFirstCapital){
|
806
|
if (isBlank(str)){
|
807
|
return false;
|
808
|
}
|
809
|
str = str.trim();
|
810
|
if (! str.endsWith(".")){
|
811
|
return false;
|
812
|
}
|
813
|
str = str.substring(0, str.length() -1);
|
814
|
if (str.length() > allowedNumberOfCharacters){
|
815
|
return false;
|
816
|
}
|
817
|
final String re = "^\\p{javaUpperCase}\\p{javaLowerCase}*$";
|
818
|
if (str.matches(re)){
|
819
|
return true;
|
820
|
}else{
|
821
|
return false;
|
822
|
}
|
823
|
}
|
824
|
|
825
|
/**
|
826
|
* Checks if <code>abbrev</code> is the short form for the genus name (strGenusName).
|
827
|
* Usually this is the case if <code>abbrev</code> is the first letter (optional with ".")
|
828
|
* of strGenusName. But in older floras it may also be the first 2 or 3 letters (optional with dot).
|
829
|
* However, we allow only a maximum of 2 letters to be anambigous. In cases with 3 letters better
|
830
|
* change the original markup data.
|
831
|
* @param single
|
832
|
* @param strGenusName
|
833
|
* @return
|
834
|
*/
|
835
|
protected boolean isGenusAbbrev(String abbrev, String strGenusName) {
|
836
|
if (! abbrev.matches("[A-Z][a-z]?\\.?")) {
|
837
|
return false;
|
838
|
}else if (abbrev.length() == 0 || strGenusName == null || strGenusName.length() == 0){
|
839
|
return false;
|
840
|
}else{
|
841
|
abbrev = abbrev.replace(".", "");
|
842
|
return strGenusName.startsWith(abbrev);
|
843
|
// boolean result = true;
|
844
|
// for (int i = 0 ; i < abbrev.length(); i++){
|
845
|
// result &= ( abbrev.charAt(i) == strGenusName.charAt(i));
|
846
|
// }
|
847
|
// return result;
|
848
|
}
|
849
|
}
|
850
|
|
851
|
|
852
|
/**
|
853
|
* Checks if all words in the given string start with a capital letter but do not have any further capital letter.
|
854
|
* @param word the string to be checekd. Usually should be a single word.
|
855
|
* @return true if the above is the case, false otherwise
|
856
|
*/
|
857
|
protected boolean isFirstCapitalWord(String word) {
|
858
|
if (WordUtils.capitalizeFully(word).equals(word)){
|
859
|
return true;
|
860
|
}else if (WordUtils.capitalizeFully(word,new char[]{'-'}).equals(word)){
|
861
|
//for words like Le-Testui (which is a species epithet)
|
862
|
return true;
|
863
|
}else{
|
864
|
return false;
|
865
|
}
|
866
|
}
|
867
|
|
868
|
|
869
|
/**
|
870
|
* Read next event. Ignore whitespace events.
|
871
|
* @param reader
|
872
|
* @return
|
873
|
* @throws XMLStreamException
|
874
|
*/
|
875
|
protected XMLEvent readNoWhitespace(XMLEventReader reader) throws XMLStreamException {
|
876
|
XMLEvent event = reader.nextEvent();
|
877
|
while (event.isCharacters() && event.asCharacters().isWhiteSpace()){
|
878
|
event = reader.nextEvent();
|
879
|
}
|
880
|
return event;
|
881
|
}
|
882
|
|
883
|
/**
|
884
|
* Returns the REQUIRED "class" attribute for a given event and checks that it is the only attribute.
|
885
|
* @param parentEvent
|
886
|
* @return
|
887
|
*/
|
888
|
protected String getClassOnlyAttribute(XMLEvent parentEvent) {
|
889
|
return getClassOnlyAttribute(parentEvent, true);
|
890
|
}
|
891
|
|
892
|
|
893
|
/**
|
894
|
* Returns the "class" attribute for a given event and checks that it is the only attribute.
|
895
|
* @param parentEvent
|
896
|
* @return
|
897
|
*/
|
898
|
protected String getClassOnlyAttribute(XMLEvent parentEvent, boolean required) {
|
899
|
return getOnlyAttribute(parentEvent, CLASS, required);
|
900
|
}
|
901
|
|
902
|
/**
|
903
|
* Returns the value for the only attribute for a given event and checks that it is the only attribute.
|
904
|
* @param parentEvent
|
905
|
* @return
|
906
|
*/
|
907
|
protected String getOnlyAttribute(XMLEvent parentEvent, String attrName, boolean required) {
|
908
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
909
|
String classValue =getAndRemoveAttributeValue(parentEvent, attributes, attrName, required, 1);
|
910
|
checkNoAttributes(attributes, parentEvent);
|
911
|
return classValue;
|
912
|
}
|
913
|
|
914
|
|
915
|
protected void fireWarningEvent(String message, String locationStr, Integer severity, Integer depth) {
|
916
|
docImport.fireWarningEvent(message, locationStr, severity, depth);
|
917
|
}
|
918
|
|
919
|
protected void fireWarningEvent(String message, XMLEvent event, Integer severity) {
|
920
|
docImport.fireWarningEvent(message, makeLocationStr(event.getLocation()), severity, 1);
|
921
|
}
|
922
|
|
923
|
protected void fireSchemaConflictEventExpectedStartTag(String elName, XMLEventReader reader) throws XMLStreamException {
|
924
|
docImport.fireSchemaConflictEventExpectedStartTag(elName, reader);
|
925
|
}
|
926
|
|
927
|
|
928
|
protected void fireWarningEvent(String message, String locationStr, int severity) {
|
929
|
docImport.fireWarningEvent(message, locationStr, severity, 1);
|
930
|
}
|
931
|
|
932
|
protected void fire(IIoEvent event) {
|
933
|
docImport.fire(event);
|
934
|
}
|
935
|
|
936
|
protected boolean isNotBlank(String str){
|
937
|
return StringUtils.isNotBlank(str);
|
938
|
}
|
939
|
|
940
|
protected boolean isBlank(String str){
|
941
|
return StringUtils.isBlank(str);
|
942
|
}
|
943
|
|
944
|
public TaxonDescription getTaxonDescription(Taxon taxon, Reference<?> ref, boolean isImageGallery, boolean createNewIfNotExists) {
|
945
|
return docImport.getTaxonDescription(taxon, isImageGallery, createNewIfNotExists);
|
946
|
}
|
947
|
|
948
|
|
949
|
/**
|
950
|
* Returns the default language defined in the state. If no default language is defined in the state,
|
951
|
* the CDM default language is returned.
|
952
|
* @param state
|
953
|
* @return
|
954
|
*/
|
955
|
protected Language getDefaultLanguage(MarkupImportState state) {
|
956
|
Language result = state.getDefaultLanguage();
|
957
|
if (result == null){
|
958
|
result = Language.DEFAULT();
|
959
|
}
|
960
|
return result;
|
961
|
}
|
962
|
|
963
|
|
964
|
//*********************** FROM XML IMPORT BASE ****************************************
|
965
|
protected boolean isEndingElement(XMLEvent event, String elName) throws XMLStreamException {
|
966
|
return docImport.isEndingElement(event, elName);
|
967
|
}
|
968
|
|
969
|
protected boolean isStartingElement(XMLEvent event, String elName) throws XMLStreamException {
|
970
|
return docImport.isStartingElement(event, elName);
|
971
|
}
|
972
|
|
973
|
|
974
|
protected void fillMissingEpithetsForTaxa(Taxon parentTaxon, Taxon childTaxon) {
|
975
|
docImport.fillMissingEpithetsForTaxa(parentTaxon, childTaxon);
|
976
|
}
|
977
|
|
978
|
protected Feature getFeature(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<Feature> voc){
|
979
|
return docImport.getFeature(state, uuid, label, text, labelAbbrev, voc);
|
980
|
}
|
981
|
|
982
|
protected ExtensionType getExtensionType(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev){
|
983
|
return docImport.getExtensionType(state, uuid, label, text, labelAbbrev);
|
984
|
}
|
985
|
|
986
|
protected AnnotationType getAnnotationType(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<AnnotationType> voc){
|
987
|
return docImport.getAnnotationType(state, uuid, label, text, labelAbbrev, voc);
|
988
|
}
|
989
|
|
990
|
protected NamedAreaLevel getNamedAreaLevel(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<NamedAreaLevel> voc){
|
991
|
return docImport.getNamedAreaLevel(state, uuid, label, text, labelAbbrev, voc);
|
992
|
}
|
993
|
|
994
|
protected NamedArea getNamedArea(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level, TermVocabulary voc, TermMatchMode matchMode){
|
995
|
return docImport.getNamedArea(state, uuid, label, text, labelAbbrev, areaType, level, voc, matchMode);
|
996
|
}
|
997
|
|
998
|
protected Language getLanguage(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<?> voc){
|
999
|
return docImport.getLanguage(state, uuid, label, text, labelAbbrev, voc);
|
1000
|
}
|
1001
|
|
1002
|
// *************************************** Concrete methods **********************************************/
|
1003
|
|
1004
|
|
1005
|
/**
|
1006
|
* @param state
|
1007
|
* @param classValue
|
1008
|
* @param byAbbrev
|
1009
|
* @return
|
1010
|
*/
|
1011
|
protected Rank makeRank(MarkupImportState state, String value, boolean byAbbrev) {
|
1012
|
Rank rank = null;
|
1013
|
if (StringUtils.isBlank(value)) {
|
1014
|
return null;
|
1015
|
}
|
1016
|
try {
|
1017
|
boolean useUnknown = true;
|
1018
|
NomenclaturalCode nc = makeNomenclaturalCode(state);
|
1019
|
if (value.equals(GENUS_ABBREVIATION)){
|
1020
|
rank = Rank.GENUS();
|
1021
|
}else if (byAbbrev) {
|
1022
|
rank = Rank.getRankByAbbreviation(value, nc, useUnknown);
|
1023
|
} else {
|
1024
|
rank = Rank.getRankByEnglishName(value, nc, useUnknown);
|
1025
|
}
|
1026
|
if (rank.equals(Rank.UNKNOWN_RANK())) {
|
1027
|
rank = null;
|
1028
|
}
|
1029
|
} catch (UnknownCdmTypeException e) {
|
1030
|
// doNothing
|
1031
|
}
|
1032
|
return rank;
|
1033
|
}
|
1034
|
|
1035
|
|
1036
|
|
1037
|
protected TeamOrPersonBase<?> createAuthor(String authorTitle) {
|
1038
|
// TODO atomize and also use by name creation
|
1039
|
TeamOrPersonBase<?> result = Team.NewTitledInstance(authorTitle, authorTitle);
|
1040
|
return result;
|
1041
|
}
|
1042
|
|
1043
|
protected String getAndRemoveMapKey(Map<String, String> map, String key) {
|
1044
|
String result = map.get(key);
|
1045
|
map.remove(key);
|
1046
|
if (result != null) {
|
1047
|
result = normalize(result);
|
1048
|
}
|
1049
|
return StringUtils.stripToNull(result);
|
1050
|
}
|
1051
|
|
1052
|
|
1053
|
/**
|
1054
|
* Creates a {@link NonViralName} object depending on the defined {@link NomenclaturalCode}
|
1055
|
* and the given parameters.
|
1056
|
* @param state
|
1057
|
* @param rank
|
1058
|
* @return
|
1059
|
*/
|
1060
|
protected NonViralName<?> createNameByCode(MarkupImportState state, Rank rank) {
|
1061
|
NonViralName<?> name;
|
1062
|
NomenclaturalCode nc = makeNomenclaturalCode(state);
|
1063
|
name = (NonViralName<?>) nc.getNewTaxonNameInstance(rank);
|
1064
|
return name;
|
1065
|
}
|
1066
|
|
1067
|
|
1068
|
/**
|
1069
|
* Returns the {@link NomenclaturalCode} for this import. Default is {@link NomenclaturalCode#ICBN} if
|
1070
|
* no code is defined.
|
1071
|
* @param state
|
1072
|
* @return
|
1073
|
*/
|
1074
|
protected NomenclaturalCode makeNomenclaturalCode(MarkupImportState state) {
|
1075
|
NomenclaturalCode nc = state.getConfig().getNomenclaturalCode();
|
1076
|
if (nc == null) {
|
1077
|
nc = NomenclaturalCode.ICBN; // default;
|
1078
|
}
|
1079
|
return nc;
|
1080
|
}
|
1081
|
|
1082
|
|
1083
|
/**
|
1084
|
* @param state
|
1085
|
* @param levelString
|
1086
|
* @param next
|
1087
|
* @return
|
1088
|
*/
|
1089
|
protected NamedAreaLevel makeNamedAreaLevel(MarkupImportState state, String levelString, XMLEvent next) {
|
1090
|
NamedAreaLevel level;
|
1091
|
try {
|
1092
|
level = state.getTransformer().getNamedAreaLevelByKey(levelString);
|
1093
|
if (level == null) {
|
1094
|
UUID levelUuid = state.getTransformer().getNamedAreaLevelUuid(levelString);
|
1095
|
if (levelUuid == null) {
|
1096
|
String message = "Unknown distribution locality class (named area level): %s. Create new level instead.";
|
1097
|
message = String.format(message, levelString);
|
1098
|
fireWarningEvent(message, next, 6);
|
1099
|
}
|
1100
|
level = getNamedAreaLevel(state, levelUuid, levelString, levelString, levelString, null);
|
1101
|
}
|
1102
|
} catch (UndefinedTransformerMethodException e) {
|
1103
|
throw new RuntimeException(e);
|
1104
|
}
|
1105
|
return level;
|
1106
|
}
|
1107
|
|
1108
|
|
1109
|
/**
|
1110
|
* @param state
|
1111
|
* @param areaName
|
1112
|
* @param level
|
1113
|
* @return
|
1114
|
*/
|
1115
|
protected NamedArea makeArea(MarkupImportState state, String areaName, NamedAreaLevel level) {
|
1116
|
|
1117
|
//TODO FM vocabulary
|
1118
|
TermVocabulary<NamedArea> voc = null;
|
1119
|
NamedAreaType areaType = null;
|
1120
|
|
1121
|
NamedArea area = null;
|
1122
|
try {
|
1123
|
area = state.getTransformer().getNamedAreaByKey(areaName);
|
1124
|
} catch (UndefinedTransformerMethodException e) {
|
1125
|
throw new RuntimeException(e);
|
1126
|
}
|
1127
|
if (area == null){
|
1128
|
boolean isNewInState = false;
|
1129
|
UUID uuid = state.getAreaUuid(areaName);
|
1130
|
if (uuid == null){
|
1131
|
isNewInState = true;
|
1132
|
|
1133
|
|
1134
|
try {
|
1135
|
uuid = state.getTransformer().getNamedAreaUuid(areaName);
|
1136
|
} catch (UndefinedTransformerMethodException e) {
|
1137
|
throw new RuntimeException(e);
|
1138
|
}
|
1139
|
}
|
1140
|
|
1141
|
CdmImportBase.TermMatchMode matchMode = CdmImportBase.TermMatchMode.UUID_LABEL;
|
1142
|
area = getNamedArea(state, uuid, areaName, areaName, areaName, areaType, level, voc, matchMode);
|
1143
|
if (isNewInState){
|
1144
|
state.putAreaUuid(areaName, area.getUuid());
|
1145
|
|
1146
|
//TODO just for testing -> make generic and move to better place
|
1147
|
String geoServiceLayer="vmap0_as_bnd_political_boundary_a";
|
1148
|
String layerFieldName ="nam";
|
1149
|
|
1150
|
if ("Bangka".equals(areaName)){
|
1151
|
String areaValue = "PULAU BANGKA#SUMATERA SELATAN";
|
1152
|
GeoServiceArea geoServiceArea = new GeoServiceArea();
|
1153
|
geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);
|
1154
|
this.editGeoService.setMapping(area, geoServiceArea);
|
1155
|
// save(area, state);
|
1156
|
}
|
1157
|
if ("Luzon".equals(areaName)){
|
1158
|
GeoServiceArea geoServiceArea = new GeoServiceArea();
|
1159
|
|
1160
|
List<String> list = Arrays.asList("HERMANA MAYOR ISLAND#CENTRAL LUZON",
|
1161
|
"HERMANA MENOR ISLAND#CENTRAL LUZON",
|
1162
|
"CENTRAL LUZON");
|
1163
|
for (String areaValue : list){
|
1164
|
geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);
|
1165
|
}
|
1166
|
|
1167
|
this.editGeoService.setMapping(area, geoServiceArea);
|
1168
|
// save(area, state);
|
1169
|
}
|
1170
|
if ("Mindanao".equals(areaName)){
|
1171
|
GeoServiceArea geoServiceArea = new GeoServiceArea();
|
1172
|
|
1173
|
List<String> list = Arrays.asList("NORTHERN MINDANAO",
|
1174
|
"SOUTHERN MINDANAO",
|
1175
|
"WESTERN MINDANAO");
|
1176
|
//TODO to be continued
|
1177
|
for (String areaValue : list){
|
1178
|
geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);
|
1179
|
}
|
1180
|
|
1181
|
this.editGeoService.setMapping(area, geoServiceArea);
|
1182
|
// save(area, state);
|
1183
|
}
|
1184
|
if ("Palawan".equals(areaName)){
|
1185
|
GeoServiceArea geoServiceArea = new GeoServiceArea();
|
1186
|
|
1187
|
List<String> list = Arrays.asList("PALAWAN#SOUTHERN TAGALOG");
|
1188
|
for (String areaValue : list){
|
1189
|
geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);
|
1190
|
}
|
1191
|
|
1192
|
this.editGeoService.setMapping(area, geoServiceArea);
|
1193
|
// save(area, state);
|
1194
|
}
|
1195
|
|
1196
|
}
|
1197
|
}
|
1198
|
return area;
|
1199
|
}
|
1200
|
|
1201
|
|
1202
|
|
1203
|
/**
|
1204
|
* Reads character data. Any element other than character data or the ending
|
1205
|
* tag will fire an unexpected element event.
|
1206
|
*
|
1207
|
* @see #getCData(MarkupImportState, XMLEventReader, XMLEvent, boolean)
|
1208
|
* @param state
|
1209
|
* @param reader
|
1210
|
* @param next
|
1211
|
* @return
|
1212
|
* @throws XMLStreamException
|
1213
|
*/
|
1214
|
protected String getCData(MarkupImportState state, XMLEventReader reader, XMLEvent next) throws XMLStreamException {
|
1215
|
return getCData(state, reader, next, true);
|
1216
|
}
|
1217
|
|
1218
|
/**
|
1219
|
* Reads character data. Any element other than character data or the ending
|
1220
|
* tag will fire an unexpected element event.
|
1221
|
*
|
1222
|
* @param state
|
1223
|
* @param reader
|
1224
|
* @param next
|
1225
|
* @param inlineMarkup map for inline markup, this is used for e.g. the locality markup within a subheading
|
1226
|
* The map will be filled by the markup element name as key. The value may be a String, a CdmBase or any other object.
|
1227
|
* If null any markup text will be neglected but a warning will be fired if they exist.
|
1228
|
* @param removeInlineMarkupText if true the markedup text will be removed from the returned String
|
1229
|
* @param checkAttributes
|
1230
|
* @return
|
1231
|
* @throws XMLStreamException
|
1232
|
*/
|
1233
|
protected String getCData(MarkupImportState state, XMLEventReader reader, XMLEvent parent, /*Map<String, Object> inlineMarkup, *boolean removeInlineMarkupText,*/ boolean checkAttributes) throws XMLStreamException {
|
1234
|
if (checkAttributes){
|
1235
|
checkNoAttributes(parent);
|
1236
|
}
|
1237
|
|
1238
|
String text = "";
|
1239
|
while (reader.hasNext()) {
|
1240
|
XMLEvent next = readNoWhitespace(reader);
|
1241
|
if (isMyEndingElement(next, parent)) {
|
1242
|
return text;
|
1243
|
} else if (next.isCharacters()) {
|
1244
|
text += next.asCharacters().getData();
|
1245
|
} else if (isStartingElement(next, FOOTNOTE_REF)){
|
1246
|
handleNotYetImplementedElement(next);
|
1247
|
// } else if (isStartingElement(next, LOCALITY)){
|
1248
|
// handleCDataLocality(state, reader, parent);
|
1249
|
} else {
|
1250
|
handleUnexpectedElement(next);
|
1251
|
}
|
1252
|
}
|
1253
|
throw new IllegalStateException("Event has no closing tag");
|
1254
|
|
1255
|
}
|
1256
|
|
1257
|
// private void handleCDataLocality(MarkupImportState state, XMLEventReader reader, XMLEvent parent) {
|
1258
|
// checkAndRemoveAttributeValue(attributes, attrName, value)
|
1259
|
//
|
1260
|
// }
|
1261
|
|
1262
|
|
1263
|
|
1264
|
/**
|
1265
|
* For it returns a pure CData annotation string. This behaviour may change in future. More complex annotations
|
1266
|
* should be handled differently.
|
1267
|
* @param state
|
1268
|
* @param reader
|
1269
|
* @param parentEvent
|
1270
|
* @return
|
1271
|
* @throws XMLStreamException
|
1272
|
*/
|
1273
|
protected String handleSimpleAnnotation(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
1274
|
String annotation = getCData(state, reader, parentEvent);
|
1275
|
return annotation;
|
1276
|
}
|
1277
|
|
1278
|
/**
|
1279
|
* True if text is single "." oder "," or ";" or ":"
|
1280
|
* @param text
|
1281
|
* @return
|
1282
|
*/
|
1283
|
protected boolean isPunctuation(String text) {
|
1284
|
return text == null ? false : text.trim().matches("^[\\.,;:]$");
|
1285
|
}
|
1286
|
|
1287
|
|
1288
|
|
1289
|
//********************************************** OLD *************************************
|
1290
|
|
1291
|
// protected boolean testAdditionalElements(Element parentElement, List<String> excludeList){
|
1292
|
// boolean result = true;
|
1293
|
// List<Element> list = parentElement.getChildren();
|
1294
|
// for (Element element : list){
|
1295
|
// if (! excludeList.contains(element.getName())){
|
1296
|
// logger.warn("Unknown element (" + element.getName() + ") in parent element (" + parentElement.getName() + ")");
|
1297
|
// result = false;
|
1298
|
// }
|
1299
|
// }
|
1300
|
// return result;
|
1301
|
// }
|
1302
|
//
|
1303
|
//
|
1304
|
// protected <T extends IdentifiableEntity> T makeReferenceType(Element element, Class<? extends T> clazz, MapWrapper<? extends T> objectMap, ResultWrapper<Boolean> success){
|
1305
|
// T result = null;
|
1306
|
// String linkType = element.getAttributeValue("linkType");
|
1307
|
// String ref = element.getAttributeValue("ref");
|
1308
|
// if(ref == null && linkType == null){
|
1309
|
// result = getInstance(clazz);
|
1310
|
// if (result != null){
|
1311
|
// String title = element.getTextNormalize();
|
1312
|
// result.setTitleCache(title, true);
|
1313
|
// }
|
1314
|
// }else if (linkType == null || linkType.equals("local")){
|
1315
|
// //TODO
|
1316
|
// result = objectMap.get(ref);
|
1317
|
// if (result == null){
|
1318
|
// logger.warn("Object (ref = " + ref + ")could not be found in WrapperMap");
|
1319
|
// }
|
1320
|
// }else if(linkType.equals("external")){
|
1321
|
// logger.warn("External link types not yet implemented");
|
1322
|
// }else if(linkType.equals("other")){
|
1323
|
// logger.warn("Other link types not yet implemented");
|
1324
|
// }else{
|
1325
|
// logger.warn("Unknown link type or missing ref");
|
1326
|
// }
|
1327
|
// if (result == null){
|
1328
|
// success.setValue(false);
|
1329
|
// }
|
1330
|
// return result;
|
1331
|
// }
|
1332
|
//
|
1333
|
//
|
1334
|
// protected Reference makeAccordingTo(Element elAccordingTo, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){
|
1335
|
// Reference result = null;
|
1336
|
// if (elAccordingTo != null){
|
1337
|
// String childName = "AccordingToDetailed";
|
1338
|
// boolean obligatory = false;
|
1339
|
// Element elAccordingToDetailed = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
|
1340
|
//
|
1341
|
// childName = "Simple";
|
1342
|
// obligatory = true;
|
1343
|
// Element elSimple = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
|
1344
|
//
|
1345
|
// if (elAccordingToDetailed != null){
|
1346
|
// result = makeAccordingToDetailed(elAccordingToDetailed, referenceMap, success);
|
1347
|
// }else{
|
1348
|
// result = ReferenceFactory.newGeneric();
|
1349
|
// String title = elSimple.getTextNormalize();
|
1350
|
// result.setTitleCache(title, true);
|
1351
|
// }
|
1352
|
// }
|
1353
|
// return result;
|
1354
|
// }
|
1355
|
//
|
1356
|
//
|
1357
|
// private Reference makeAccordingToDetailed(Element elAccordingToDetailed, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){
|
1358
|
// Reference result = null;
|
1359
|
// Namespace tcsNamespace = elAccordingToDetailed.getNamespace();
|
1360
|
// if (elAccordingToDetailed != null){
|
1361
|
// //AuthorTeam
|
1362
|
// String childName = "AuthorTeam";
|
1363
|
// boolean obligatory = false;
|
1364
|
// Element elAuthorTeam = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
|
1365
|
// makeAccordingToAuthorTeam(elAuthorTeam, success);
|
1366
|
//
|
1367
|
// //PublishedIn
|
1368
|
// childName = "PublishedIn";
|
1369
|
// obligatory = false;
|
1370
|
// Element elPublishedIn = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
|
1371
|
// result = makeReferenceType(elPublishedIn, Reference.class, referenceMap, success);
|
1372
|
//
|
1373
|
// //MicroReference
|
1374
|
// childName = "MicroReference";
|
1375
|
// obligatory = false;
|
1376
|
// Element elMicroReference = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
|
1377
|
// String microReference = elMicroReference.getTextNormalize();
|
1378
|
// if (CdmUtils.Nz(microReference).equals("")){
|
1379
|
// //TODO
|
1380
|
// logger.warn("MicroReference not yet implemented for AccordingToDetailed");
|
1381
|
// }
|
1382
|
// }
|
1383
|
// return result;
|
1384
|
// }
|
1385
|
//
|
1386
|
// private Team makeAccordingToAuthorTeam(Element elAuthorTeam, ResultWrapper<Boolean> succes){
|
1387
|
// Team result = null;
|
1388
|
// if (elAuthorTeam != null){
|
1389
|
// //TODO
|
1390
|
// logger.warn("AuthorTeam not yet implemented for AccordingToDetailed");
|
1391
|
// }
|
1392
|
// return result;
|
1393
|
// }
|
1394
|
|
1395
|
|
1396
|
|
1397
|
}
|