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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.net.MalformedURLException;
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import java.util.ArrayList;
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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.HashSet;
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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.Set;
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import java.util.Stack;
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import java.util.UUID;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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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.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.Annotation;
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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.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Extension;
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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.MarkerType;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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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.Distribution;
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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.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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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.IdentifiableMediaEntity;
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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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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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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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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 DOUBTFUL = "doubtful";
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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 GATHERING_GROUP = "gatheringGroup";
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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 String UNKNOWN = "unknown";
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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 WRITER = "writer";
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protected static final String LOCALITY = "locality";
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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 NOMENCLATURAL_NOTES = "nomenclaturalNotes";
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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 PUBLOCATION = "publocation";
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protected static final String PUBLISHER = "publisher";
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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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//Feature
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protected static final String VERNACULAR_NAMES = "vernacularNames";
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protected static final String VERNACULAR_NAME = "vernacularName";
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protected static final String TRANSLATION = "translation";
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protected static final String LOCAL_LANGUAGE = "localLanguage";
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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 if (cdmBase.isInstanceOf(Reference.class)){
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docImport.getReferenceService().saveOrUpdate((Reference<?>)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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326
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result.put(attribute.getName().getLocalPart(), attribute);
|
|
327
|
}
|
|
328
|
return result;
|
|
329
|
}
|
|
330
|
|
|
331
|
/**
|
|
332
|
* Throws an unexpected attributes event if the event has any attributes.
|
|
333
|
* @param event
|
|
334
|
*/
|
|
335
|
protected void checkNoAttributes(Map<String, Attribute> attributes, XMLEvent event) {
|
|
336
|
String[] exceptions = new String[]{};
|
|
337
|
handleUnexpectedAttributes(event.getLocation(), attributes, 1, exceptions);
|
|
338
|
}
|
|
339
|
|
|
340
|
|
|
341
|
|
|
342
|
/**
|
|
343
|
* Throws an unexpected attributes event if the event has any attributes.
|
|
344
|
* @param event
|
|
345
|
*/
|
|
346
|
protected void checkNoAttributes(XMLEvent event) {
|
|
347
|
String[] exceptions = new String[]{};
|
|
348
|
checkNoAttributes(event, 1, exceptions);
|
|
349
|
}
|
|
350
|
|
|
351
|
/**
|
|
352
|
* Throws an unexpected attributes event if the event has any attributes except those mentioned in "exceptions".
|
|
353
|
* @param event
|
|
354
|
* @param exceptions
|
|
355
|
*/
|
|
356
|
protected void checkNoAttributes(XMLEvent event, int stackDepth, String... exceptions) {
|
|
357
|
if (! event.isStartElement()){
|
|
358
|
fireWarningEvent("Event is not an startElement. Can't check attributes", makeLocationStr(event.getLocation()), 1, 1);
|
|
359
|
return;
|
|
360
|
}
|
|
361
|
StartElement startElement = event.asStartElement();
|
|
362
|
Map<String, Attribute> attributes = getAttributes(startElement);
|
|
363
|
handleUnexpectedAttributes(startElement.getLocation(), attributes, stackDepth+1, exceptions);
|
|
364
|
}
|
|
365
|
|
|
366
|
|
|
367
|
/**
|
|
368
|
* Checks if the given attribute exists and has the given value.
|
|
369
|
* If yes, true is returned and the attribute is removed from the attributes map.
|
|
370
|
* Otherwise false is returned.
|
|
371
|
* @param attributes
|
|
372
|
* @param attrName
|
|
373
|
* @param value
|
|
374
|
* @return <code>true</code> if attribute has given value, <code>false</code> otherwise
|
|
375
|
*/
|
|
376
|
protected boolean checkAndRemoveAttributeValue( Map<String, Attribute> attributes, String attrName, String value) {
|
|
377
|
Attribute attr = attributes.get(attrName);
|
|
378
|
if (attr == null ||value == null ){
|
|
379
|
return false;
|
|
380
|
}else{
|
|
381
|
if (value.equals(attr.getValue())){
|
|
382
|
attributes.remove(attrName);
|
|
383
|
return true;
|
|
384
|
}else{
|
|
385
|
return false;
|
|
386
|
}
|
|
387
|
}
|
|
388
|
}
|
|
389
|
|
|
390
|
|
|
391
|
/**
|
|
392
|
* Returns the value of a given attribute name and removes the attribute from the attributes map.
|
|
393
|
* @param attributes
|
|
394
|
* @param attrName
|
|
395
|
* @return
|
|
396
|
*/
|
|
397
|
protected String getAndRemoveAttributeValue(Map<String, Attribute> attributes, String attrName) {
|
|
398
|
return getAndRemoveAttributeValue(null, attributes, attrName, false, 1);
|
|
399
|
}
|
|
400
|
|
|
401
|
/**
|
|
402
|
* Returns the value of a boolean attribute with the given name and removes the attribute from the attributes map.
|
|
403
|
* Returns <code>defaultValue</code> if the attribute does not exist. ALso returns <code>defaultValue</code> and throws a warning if the
|
|
404
|
* attribute has no boolean value (true, false).
|
|
405
|
* @param
|
|
406
|
* @param attributes the
|
|
407
|
* @param attrName the name of the attribute
|
|
408
|
* @param defaultValue the default value to return if attribute does not exist or can not be defined
|
|
409
|
* @return
|
|
410
|
*/
|
|
411
|
protected Boolean getAndRemoveBooleanAttributeValue(XMLEvent event, Map<String, Attribute> attributes, String attrName, Boolean defaultValue) {
|
|
412
|
String value = getAndRemoveAttributeValue(null, attributes, attrName, false, 1);
|
|
413
|
Boolean result = defaultValue;
|
|
414
|
if (value != null){
|
|
415
|
if (value.equalsIgnoreCase("true")){
|
|
416
|
result = true;
|
|
417
|
}else if (value.equalsIgnoreCase("false")){
|
|
418
|
result = false;
|
|
419
|
}else{
|
|
420
|
String message = "Boolean attribute has no boolean value ('true', 'false') but '%s'";
|
|
421
|
fireWarningEvent(String.format(message, value), makeLocationStr(event.getLocation()), 6, 1);
|
|
422
|
}
|
|
423
|
}
|
|
424
|
return result;
|
|
425
|
}
|
|
426
|
|
|
427
|
|
|
428
|
/**
|
|
429
|
* Returns the value of a given attribute name and returns the attribute from the attributes map.
|
|
430
|
* Fires a mandatory field is missing event if the attribute does not exist.
|
|
431
|
* @param xmlEvent
|
|
432
|
* @param attributes
|
|
433
|
* @param attrName
|
|
434
|
* @return
|
|
435
|
*/
|
|
436
|
protected String getAndRemoveRequiredAttributeValue(XMLEvent xmlEvent, Map<String, Attribute> attributes, String attrName) {
|
|
437
|
return getAndRemoveAttributeValue(xmlEvent, attributes, attrName, true, 1);
|
|
438
|
}
|
|
439
|
|
|
440
|
/**
|
|
441
|
* Returns the value of a given attribute name and returns the attribute from the attributes map.
|
|
442
|
* If required is <code>true</code> and the attribute does not exist a mandatory field is missing event is fired.
|
|
443
|
* @param xmlEvent
|
|
444
|
* @param attributes
|
|
445
|
* @param attrName
|
|
446
|
* @param isRequired
|
|
447
|
* @return
|
|
448
|
*/
|
|
449
|
private String getAndRemoveAttributeValue(XMLEvent xmlEvent, Map<String, Attribute> attributes, String attrName, boolean isRequired, int stackDepth) {
|
|
450
|
Attribute attr = attributes.get(attrName);
|
|
451
|
if (attr == null ){
|
|
452
|
if (isRequired){
|
|
453
|
fireMandatoryElementIsMissing(xmlEvent, attrName, 8, stackDepth+1);
|
|
454
|
}
|
|
455
|
return null;
|
|
456
|
}else{
|
|
457
|
attributes.remove(attrName);
|
|
458
|
return attr.getValue();
|
|
459
|
}
|
|
460
|
}
|
|
461
|
|
|
462
|
/**
|
|
463
|
* Fires an not yet implemented event if the given attribute exists in attributes.
|
|
464
|
* @param attributes
|
|
465
|
* @param attrName
|
|
466
|
*/
|
|
467
|
protected void handleNotYetImplementedAttribute(Map<String, Attribute> attributes, String attrName) {
|
|
468
|
Attribute attr = attributes.get(attrName);
|
|
469
|
if (attr != null){
|
|
470
|
attributes.remove(attrName);
|
|
471
|
QName qName = attr.getName();
|
|
472
|
fireNotYetImplementedAttribute(attr.getLocation(), qName, 1);
|
|
473
|
}
|
|
474
|
}
|
|
475
|
|
|
476
|
/**
|
|
477
|
* Fires an unhandled attributes event, if attributes exist in attributes map not covered by the exceptions.
|
|
478
|
* No event is fired if the unhandled elements stack is not empty.
|
|
479
|
* @param location
|
|
480
|
* @param attributes
|
|
481
|
* @param exceptions
|
|
482
|
*/
|
|
483
|
protected void handleUnexpectedAttributes(Location location,Map<String, Attribute> attributes, String... exceptions) {
|
|
484
|
handleUnexpectedAttributes(location, attributes, 1, exceptions);
|
|
485
|
}
|
|
486
|
|
|
487
|
/**
|
|
488
|
* see {@link #handleUnexpectedAttributes(Location, Map, String...)}
|
|
489
|
*
|
|
490
|
* @param location
|
|
491
|
* @param attributes
|
|
492
|
* @param stackDepth the stack trace depth
|
|
493
|
* @param exceptions
|
|
494
|
*/
|
|
495
|
private void handleUnexpectedAttributes(Location location,Map<String, Attribute> attributes, int stackDepth, String... exceptions) {
|
|
496
|
if (attributes.size() > 0){
|
|
497
|
if (this.unhandledElements.size() == 0 ){
|
|
498
|
boolean hasUnhandledAttributes = false;
|
|
499
|
for (String key : attributes.keySet()){
|
|
500
|
boolean isException = false;
|
|
501
|
for (String exception : exceptions){
|
|
502
|
if(key.equals(exception)){
|
|
503
|
isException = true;
|
|
504
|
}
|
|
505
|
}
|
|
506
|
if (!isException){
|
|
507
|
hasUnhandledAttributes = true;
|
|
508
|
}
|
|
509
|
}
|
|
510
|
if (hasUnhandledAttributes){
|
|
511
|
fireUnexpectedAttributes(location, attributes, stackDepth+1);
|
|
512
|
}
|
|
513
|
}
|
|
514
|
}
|
|
515
|
}
|
|
516
|
|
|
517
|
|
|
518
|
private void fireUnexpectedAttributes(Location location, Map<String, Attribute> attributes, int stackDepth) {
|
|
519
|
String attributesString = "";
|
|
520
|
for (String key : attributes.keySet()){
|
|
521
|
Attribute attribute = attributes.get(key);
|
|
522
|
attributesString = CdmUtils.concat(",", attributesString, attribute.getName().getLocalPart() + ":" + attribute.getValue());
|
|
523
|
}
|
|
524
|
String message = "Unexpected attributes: %s";
|
|
525
|
IoProblemEvent event = makeProblemEvent(location, String.format(message, attributesString), 1 , stackDepth +1 );
|
|
526
|
fire(event);
|
|
527
|
}
|
|
528
|
|
|
529
|
|
|
530
|
protected void fireUnexpectedAttributeValue(XMLEvent parentEvent, String attrName, String attrValue) {
|
|
531
|
String message = "Unexpected attribute value %s='%s'";
|
|
532
|
message = String.format(message, attrName, attrValue);
|
|
533
|
IoProblemEvent event = makeProblemEvent(parentEvent.getLocation(), message, 1 , 1 );
|
|
534
|
fire(event);
|
|
535
|
}
|
|
536
|
|
|
537
|
protected void handleNotYetImplementedAttributeValue(XMLEvent xmlEvent, String attrName, String attrValue) {
|
|
538
|
String message = "Attribute %s not yet implemented for value '%s'";
|
|
539
|
message = String.format(message, attrName, attrValue);
|
|
540
|
IIoEvent event = makeProblemEvent(xmlEvent.getLocation(), message, 1, 1 );
|
|
541
|
fire(event);
|
|
542
|
}
|
|
543
|
|
|
544
|
protected void fireNotYetImplementedAttribute(Location location, QName qName, int stackDepth) {
|
|
545
|
String message = "Attribute not yet implemented: %s";
|
|
546
|
IIoEvent event = makeProblemEvent(location, String.format(message, qName.getLocalPart()), 1, stackDepth+1 );
|
|
547
|
fire(event);
|
|
548
|
}
|
|
549
|
|
|
550
|
|
|
551
|
protected void fireUnexpectedEvent(XMLEvent xmlEvent, int stackDepth) {
|
|
552
|
Location location = xmlEvent.getLocation();
|
|
553
|
String message = "Unexpected event: %s";
|
|
554
|
IIoEvent event = makeProblemEvent(location, String.format(message, xmlEvent.toString()), 2, stackDepth +1);
|
|
555
|
fire(event);
|
|
556
|
}
|
|
557
|
|
|
558
|
protected void fireUnexpectedStartElement(Location location, StartElement startElement, int stackDepth) {
|
|
559
|
QName qName = startElement.getName();
|
|
560
|
String message = "Unexpected start element: %s";
|
|
561
|
IIoEvent event = makeProblemEvent(location, String.format(message, qName.getLocalPart()), 2, stackDepth +1);
|
|
562
|
fire(event);
|
|
563
|
}
|
|
564
|
|
|
565
|
|
|
566
|
protected void fireUnexpectedEndElement(Location location, EndElement endElement, int stackDepth) {
|
|
567
|
QName qName = endElement.getName();
|
|
568
|
String message = "Unexpected end element: %s";
|
|
569
|
IIoEvent event = makeProblemEvent(location, String.format(message, qName.getLocalPart()), 16, stackDepth+1);
|
|
570
|
fire(event);
|
|
571
|
}
|
|
572
|
|
|
573
|
protected void fireNotYetImplementedElement(Location location, QName qName, int stackDepth) {
|
|
574
|
String message = "Element not yet implemented: %s";
|
|
575
|
IIoEvent event = makeProblemEvent(location, String.format(message, qName.getLocalPart()), 1, stackDepth+1 );
|
|
576
|
fire(event);
|
|
577
|
}
|
|
578
|
|
|
579
|
protected void fireNotYetImplementedCharacters(Location location, Characters chars, int stackDepth) {
|
|
580
|
String message = "Characters not yet handled: %s";
|
|
581
|
IIoEvent event = makeProblemEvent(location, String.format(message, chars.getData()), 1, stackDepth+1 );
|
|
582
|
fire(event);
|
|
583
|
}
|
|
584
|
|
|
585
|
/**
|
|
586
|
* Creates a problem event.
|
|
587
|
* Be aware of the right depths of the stack trace !
|
|
588
|
* @param location
|
|
589
|
* @param message
|
|
590
|
* @param severity
|
|
591
|
* @return
|
|
592
|
*/
|
|
593
|
private IoProblemEvent makeProblemEvent(Location location, String message, int severity, int stackDepth) {
|
|
594
|
stackDepth++;
|
|
595
|
StackTraceElement[] stackTrace = new Exception().getStackTrace();
|
|
596
|
int lineNumber = stackTrace[stackDepth].getLineNumber();
|
|
597
|
String methodName = stackTrace[stackDepth].getMethodName();
|
|
598
|
String locationStr = makeLocationStr(location);
|
|
599
|
String className = stackTrace[stackDepth].getClassName();
|
|
600
|
Class<?> declaringClass;
|
|
601
|
try {
|
|
602
|
declaringClass = Class.forName(className);
|
|
603
|
} catch (ClassNotFoundException e) {
|
|
604
|
declaringClass = this.getClass();
|
|
605
|
}
|
|
606
|
IoProblemEvent event = IoProblemEvent.NewInstance(declaringClass, message,
|
|
607
|
locationStr, lineNumber, severity, methodName);
|
|
608
|
return event;
|
|
609
|
}
|
|
610
|
|
|
611
|
/**
|
|
612
|
* Creates a string from a location
|
|
613
|
* @param location
|
|
614
|
* @return
|
|
615
|
*/
|
|
616
|
protected String makeLocationStr(Location location) {
|
|
617
|
String locationStr = location == null ? " - no location - " : "l." + location.getLineNumber() + "/c."+ location.getColumnNumber();
|
|
618
|
return locationStr;
|
|
619
|
}
|
|
620
|
|
|
621
|
|
|
622
|
/**
|
|
623
|
* Fires an unexpected element event if the unhandled elements stack is empty.
|
|
624
|
* Otherwise adds the element to the stack.
|
|
625
|
* @param event
|
|
626
|
*/
|
|
627
|
protected void handleUnexpectedStartElement(XMLEvent event) {
|
|
628
|
handleUnexpectedStartElement(event, 1);
|
|
629
|
}
|
|
630
|
|
|
631
|
/**
|
|
632
|
* Fires an unexpected element event if the unhandled elements stack is empty.
|
|
633
|
* Otherwise adds the element to the stack.
|
|
634
|
* @param event
|
|
635
|
*/
|
|
636
|
protected void handleUnexpectedStartElement(XMLEvent event, int stackDepth) {
|
|
637
|
QName qName = event.asStartElement().getName();
|
|
638
|
if (! unhandledElements.empty()){
|
|
639
|
unhandledElements.push(qName);
|
|
640
|
}else{
|
|
641
|
fireUnexpectedStartElement(event.getLocation(), event.asStartElement(), stackDepth + 1);
|
|
642
|
}
|
|
643
|
}
|
|
644
|
|
|
645
|
|
|
646
|
protected void handleUnexpectedEndElement(EndElement event) {
|
|
647
|
handleUnexpectedEndElement(event, 1);
|
|
648
|
}
|
|
649
|
|
|
650
|
/**
|
|
651
|
* Fires an unexpected element event if the event is not the last on the stack.
|
|
652
|
* Otherwise removes last stack element.
|
|
653
|
* @param event
|
|
654
|
*/
|
|
655
|
protected void handleUnexpectedEndElement(EndElement event, int stackDepth) {
|
|
656
|
QName qName = event.asEndElement().getName();
|
|
657
|
if (!unhandledElements.isEmpty() && unhandledElements.peek().equals(qName)){
|
|
658
|
unhandledElements.pop();
|
|
659
|
}else{
|
|
660
|
fireUnexpectedEndElement(event.getLocation(), event.asEndElement(), stackDepth + 1);
|
|
661
|
}
|
|
662
|
}
|
|
663
|
|
|
664
|
/**
|
|
665
|
*
|
|
666
|
* @param endElement
|
|
667
|
*/
|
|
668
|
protected void popUnimplemented(EndElement endElement) {
|
|
669
|
QName qName = endElement.asEndElement().getName();
|
|
670
|
if (unhandledElements.peek().equals(qName)){
|
|
671
|
unhandledElements.pop();
|
|
672
|
}else{
|
|
673
|
String message = "End element is not last on stack: %s";
|
|
674
|
message = String.format(message, qName.getLocalPart());
|
|
675
|
IIoEvent event = makeProblemEvent(endElement.getLocation(), message, 16, 1);
|
|
676
|
fire(event);
|
|
677
|
}
|
|
678
|
|
|
679
|
}
|
|
680
|
|
|
681
|
|
|
682
|
/**
|
|
683
|
* Fires an unexpected element event if the unhandled element stack is empty.
|
|
684
|
* @param event
|
|
685
|
*/
|
|
686
|
protected void handleUnexpectedElement(XMLEvent event) {
|
|
687
|
if (event.isStartElement()){
|
|
688
|
handleUnexpectedStartElement(event, 2);
|
|
689
|
}else if (event.isEndElement()){
|
|
690
|
handleUnexpectedEndElement(event.asEndElement(), 2);
|
|
691
|
}else if (event.getEventType() == XMLStreamConstants.COMMENT){
|
|
692
|
//do nothing
|
|
693
|
}else if (! unhandledElements.empty()){
|
|
694
|
//do nothing
|
|
695
|
}else{
|
|
696
|
fireUnexpectedEvent(event, 1);
|
|
697
|
}
|
|
698
|
}
|
|
699
|
|
|
700
|
/**
|
|
701
|
* Fires an not yet implemented event and adds the element name to the unhandled elements stack.
|
|
702
|
* @param event
|
|
703
|
*/
|
|
704
|
protected void handleNotYetImplementedCharacters(XMLEvent event) {
|
|
705
|
Characters chars = event.asCharacters();
|
|
706
|
fireNotYetImplementedCharacters(event.getLocation(), chars, 1);
|
|
707
|
}
|
|
708
|
|
|
709
|
/**
|
|
710
|
* Fires an not yet implemented event and adds the element name to the unhandled elements stack.
|
|
711
|
* @param event
|
|
712
|
*/
|
|
713
|
protected void handleNotYetImplementedElement(XMLEvent event) {
|
|
714
|
QName qName = event.asStartElement().getName();
|
|
715
|
boolean isTopLevel = unhandledElements.isEmpty();
|
|
716
|
unhandledElements.push(qName);
|
|
717
|
if (isTopLevel){
|
|
718
|
fireNotYetImplementedElement(event.getLocation(), qName, 1);
|
|
719
|
}
|
|
720
|
}
|
|
721
|
|
|
722
|
/**
|
|
723
|
* Fires an not yet implemented event and adds the element name to the unhandled elements stack.
|
|
724
|
* @param event
|
|
725
|
*/
|
|
726
|
protected void handleIgnoreElement(XMLEvent event) {
|
|
727
|
QName qName = event.asStartElement().getName();
|
|
728
|
unhandledElements.push(qName);
|
|
729
|
}
|
|
730
|
|
|
731
|
protected void handleAmbigousManually(MarkupImportState state,
|
|
732
|
XMLEventReader reader, StartElement startElement) {
|
|
733
|
QName qName = startElement.getName();
|
|
734
|
unhandledElements.push(qName);
|
|
735
|
fireWarningEvent(
|
|
736
|
"Handle manually: " + qName.getLocalPart() + " is ambigous and should therefore be handled manually",
|
|
737
|
makeLocationStr(startElement.getLocation()), 2, 2);
|
|
738
|
}
|
|
739
|
|
|
740
|
/**
|
|
741
|
* Checks if a mandatory text is not empty or null.
|
|
742
|
* Returns true if text is given.
|
|
743
|
* Fires an mandatory element is missing event otherwise and returns <code>null</code>.
|
|
744
|
* @param text
|
|
745
|
* @param parentEvent
|
|
746
|
* @return
|
|
747
|
*/
|
|
748
|
protected boolean checkMandatoryText(String text, XMLEvent parentEvent) {
|
|
749
|
if (! StringUtils.isNotBlank(text)){
|
|
750
|
fireMandatoryElementIsMissing(parentEvent, "CData", 4, 1);
|
|
751
|
return false;
|
|
752
|
}
|
|
753
|
return true;
|
|
754
|
}
|
|
755
|
|
|
756
|
/**
|
|
757
|
* Fires an mandatory element is missing event if exists is <code>false</code>.
|
|
758
|
* @param hasMandatory
|
|
759
|
* @param parentEvent
|
|
760
|
* @param string
|
|
761
|
*/
|
|
762
|
protected void checkMandatoryElement(boolean exists, StartElement parentEvent, String attrName) {
|
|
763
|
if (! exists){
|
|
764
|
fireMandatoryElementIsMissing(parentEvent, attrName, 5, 1);
|
|
765
|
}
|
|
766
|
}
|
|
767
|
|
|
768
|
|
|
769
|
/**
|
|
770
|
* Fires an element is missing event.
|
|
771
|
* @param xmlEvent
|
|
772
|
* @param string
|
|
773
|
* @param severity
|
|
774
|
* @param stackDepth
|
|
775
|
* @throws IllegalStateException if xmlEvent is not a StartElement and not an Attribute
|
|
776
|
*/
|
|
777
|
private void fireMandatoryElementIsMissing(XMLEvent xmlEvent, String missingEventName, int severity, int stackDepth) throws IllegalStateException{
|
|
778
|
Location location = xmlEvent.getLocation();
|
|
779
|
String typeName;
|
|
780
|
QName qName;
|
|
781
|
if (xmlEvent.isAttribute()){
|
|
782
|
Attribute attribute = ((Attribute)xmlEvent);
|
|
783
|
typeName = "attribute";
|
|
784
|
qName = attribute.getName();
|
|
785
|
}else if (xmlEvent.isStartElement()){
|
|
786
|
typeName = "element";
|
|
787
|
qName = xmlEvent.asStartElement().getName();
|
|
788
|
}else{
|
|
789
|
throw new IllegalStateException("mandatory element only allowed for attributes and start tags in " + makeLocationStr(location));
|
|
790
|
}
|
|
791
|
String message = "Mandatory %s '%s' is missing in %s";
|
|
792
|
message = String.format(message, typeName , missingEventName, qName.getLocalPart());
|
|
793
|
IIoEvent event = makeProblemEvent(location, message, severity, stackDepth +1);
|
|
794
|
fire(event);
|
|
795
|
}
|
|
796
|
|
|
797
|
|
|
798
|
|
|
799
|
|
|
800
|
/**
|
|
801
|
* Returns true if the "next" event is the ending tag for the "parent" event.
|
|
802
|
* @param next end element to test, must not be null
|
|
803
|
* @param parentEvent start element to test
|
|
804
|
* @return true if the "next" event is the ending tag for the "parent" event.
|
|
805
|
* @throws XMLStreamException
|
|
806
|
*/
|
|
807
|
protected boolean isMyEndingElement(XMLEvent next, XMLEvent parentEvent) throws XMLStreamException {
|
|
808
|
if (! parentEvent.isStartElement()){
|
|
809
|
String message = "Parent event should be start tag";
|
|
810
|
fireWarningEvent(message, makeLocationStr(next.getLocation()), 6);
|
|
811
|
return false;
|
|
812
|
}
|
|
813
|
return isEndingElement(next, parentEvent.asStartElement().getName().getLocalPart());
|
|
814
|
}
|
|
815
|
|
|
816
|
/**
|
|
817
|
* Trims the text and removes turns all whitespaces into single empty space.
|
|
818
|
* @param text
|
|
819
|
* @return
|
|
820
|
*/
|
|
821
|
protected String normalize(String text) {
|
|
822
|
text = StringUtils.trimToEmpty(text);
|
|
823
|
text = text.replaceAll("\\s+", " ");
|
|
824
|
return text;
|
|
825
|
}
|
|
826
|
|
|
827
|
|
|
828
|
|
|
829
|
/**
|
|
830
|
* Removes whitespaces at beginning and end and makes the first letter
|
|
831
|
* a capital letter and all other letters small letters.
|
|
832
|
* @param value
|
|
833
|
* @return
|
|
834
|
*/
|
|
835
|
protected String toFirstCapital(String value) {
|
|
836
|
if (StringUtils.isBlank(value)){
|
|
837
|
return value;
|
|
838
|
}else{
|
|
839
|
String result = "";
|
|
840
|
value = value.trim();
|
|
841
|
result += value.trim().substring(0,1).toUpperCase();
|
|
842
|
if (value.length()>1){
|
|
843
|
result += value.substring(1).toLowerCase();
|
|
844
|
}
|
|
845
|
return result;
|
|
846
|
}
|
|
847
|
}
|
|
848
|
|
|
849
|
/**
|
|
850
|
* Currently not used.
|
|
851
|
* @param str
|
|
852
|
* @param allowedNumberOfCharacters
|
|
853
|
* @param onlyFirstCapital
|
|
854
|
* @return
|
|
855
|
*/
|
|
856
|
protected boolean isAbbreviation(String str, int allowedNumberOfCharacters, boolean onlyFirstCapital){
|
|
857
|
if (isBlank(str)){
|
|
858
|
return false;
|
|
859
|
}
|
|
860
|
str = str.trim();
|
|
861
|
if (! str.endsWith(".")){
|
|
862
|
return false;
|
|
863
|
}
|
|
864
|
str = str.substring(0, str.length() -1);
|
|
865
|
if (str.length() > allowedNumberOfCharacters){
|
|
866
|
return false;
|
|
867
|
}
|
|
868
|
final String re = "^\\p{javaUpperCase}\\p{javaLowerCase}*$";
|
|
869
|
if (str.matches(re)){
|
|
870
|
return true;
|
|
871
|
}else{
|
|
872
|
return false;
|
|
873
|
}
|
|
874
|
}
|
|
875
|
|
|
876
|
/**
|
|
877
|
* Checks if <code>abbrev</code> is the short form for the genus name (strGenusName).
|
|
878
|
* Usually this is the case if <code>abbrev</code> is the first letter (optional with ".")
|
|
879
|
* of strGenusName. But in older floras it may also be the first 2 or 3 letters (optional with dot).
|
|
880
|
* However, we allow only a maximum of 2 letters to be anambigous. In cases with 3 letters better
|
|
881
|
* change the original markup data.
|
|
882
|
* @param single
|
|
883
|
* @param strGenusName
|
|
884
|
* @return
|
|
885
|
*/
|
|
886
|
protected boolean isGenusAbbrev(String abbrev, String strGenusName) {
|
|
887
|
if (! abbrev.matches("[A-Z][a-z]?\\.?")) {
|
|
888
|
return false;
|
|
889
|
}else if (abbrev.length() == 0 || strGenusName == null || strGenusName.length() == 0){
|
|
890
|
return false;
|
|
891
|
}else{
|
|
892
|
abbrev = abbrev.replace(".", "");
|
|
893
|
return strGenusName.startsWith(abbrev);
|
|
894
|
// boolean result = true;
|
|
895
|
// for (int i = 0 ; i < abbrev.length(); i++){
|
|
896
|
// result &= ( abbrev.charAt(i) == strGenusName.charAt(i));
|
|
897
|
// }
|
|
898
|
// return result;
|
|
899
|
}
|
|
900
|
}
|
|
901
|
|
|
902
|
|
|
903
|
/**
|
|
904
|
* Checks if all words in the given string start with a capital letter but do not have any further capital letter.
|
|
905
|
* @param word the string to be checekd. Usually should be a single word.
|
|
906
|
* @return true if the above is the case, false otherwise
|
|
907
|
*/
|
|
908
|
protected boolean isFirstCapitalWord(String word) {
|
|
909
|
if (WordUtils.capitalizeFully(word).equals(word)){
|
|
910
|
return true;
|
|
911
|
}else if (WordUtils.capitalizeFully(word,new char[]{'-'}).equals(word)){
|
|
912
|
//for words like Le-Testui (which is a species epithet)
|
|
913
|
return true;
|
|
914
|
}else{
|
|
915
|
return false;
|
|
916
|
}
|
|
917
|
}
|
|
918
|
|
|
919
|
|
|
920
|
/**
|
|
921
|
* Read next event. Ignore whitespace events.
|
|
922
|
* @param reader
|
|
923
|
* @return
|
|
924
|
* @throws XMLStreamException
|
|
925
|
*/
|
|
926
|
protected XMLEvent readNoWhitespace(XMLEventReader reader) throws XMLStreamException {
|
|
927
|
XMLEvent event = reader.nextEvent();
|
|
928
|
while (!unhandledElements.isEmpty()){
|
|
929
|
if (event.isStartElement()){
|
|
930
|
handleNotYetImplementedElement(event);
|
|
931
|
}else if (event.isEndElement()){
|
|
932
|
popUnimplemented(event.asEndElement());
|
|
933
|
}
|
|
934
|
event = reader.nextEvent();
|
|
935
|
}
|
|
936
|
while (event.isCharacters() && event.asCharacters().isWhiteSpace()){
|
|
937
|
event = reader.nextEvent();
|
|
938
|
}
|
|
939
|
return event;
|
|
940
|
}
|
|
941
|
|
|
942
|
/**
|
|
943
|
* Returns the REQUIRED "class" attribute for a given event and checks that it is the only attribute.
|
|
944
|
* @param parentEvent
|
|
945
|
* @return
|
|
946
|
*/
|
|
947
|
protected String getClassOnlyAttribute(XMLEvent parentEvent) {
|
|
948
|
return getClassOnlyAttribute(parentEvent, true);
|
|
949
|
}
|
|
950
|
|
|
951
|
|
|
952
|
/**
|
|
953
|
* Returns the "class" attribute for a given event and checks that it is the only attribute.
|
|
954
|
* @param parentEvent
|
|
955
|
* @return
|
|
956
|
*/
|
|
957
|
protected String getClassOnlyAttribute(XMLEvent parentEvent, boolean required) {
|
|
958
|
return getOnlyAttribute(parentEvent, CLASS, required);
|
|
959
|
}
|
|
960
|
|
|
961
|
/**
|
|
962
|
* Returns the value for the only attribute for a given event and checks that it is the only attribute.
|
|
963
|
* @param parentEvent
|
|
964
|
* @return
|
|
965
|
*/
|
|
966
|
protected String getOnlyAttribute(XMLEvent parentEvent, String attrName, boolean required) {
|
|
967
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
968
|
String classValue =getAndRemoveAttributeValue(parentEvent, attributes, attrName, required, 1);
|
|
969
|
checkNoAttributes(attributes, parentEvent);
|
|
970
|
return classValue;
|
|
971
|
}
|
|
972
|
|
|
973
|
|
|
974
|
protected void fireWarningEvent(String message, String locationStr, Integer severity, Integer depth) {
|
|
975
|
docImport.fireWarningEvent(message, locationStr, severity, depth);
|
|
976
|
}
|
|
977
|
|
|
978
|
protected void fireWarningEvent(String message, XMLEvent event, Integer severity) {
|
|
979
|
docImport.fireWarningEvent(message, makeLocationStr(event.getLocation()), severity, 1);
|
|
980
|
}
|
|
981
|
|
|
982
|
protected void fireSchemaConflictEventExpectedStartTag(String elName, XMLEventReader reader) throws XMLStreamException {
|
|
983
|
docImport.fireSchemaConflictEventExpectedStartTag(elName, reader);
|
|
984
|
}
|
|
985
|
|
|
986
|
|
|
987
|
protected void fireWarningEvent(String message, String locationStr, int severity) {
|
|
988
|
docImport.fireWarningEvent(message, locationStr, severity, 1);
|
|
989
|
}
|
|
990
|
|
|
991
|
protected void fire(IIoEvent event) {
|
|
992
|
docImport.fire(event);
|
|
993
|
}
|
|
994
|
|
|
995
|
protected boolean isNotBlank(String str){
|
|
996
|
return StringUtils.isNotBlank(str);
|
|
997
|
}
|
|
998
|
|
|
999
|
protected boolean isBlank(String str){
|
|
1000
|
return StringUtils.isBlank(str);
|
|
1001
|
}
|
|
1002
|
|
|
1003
|
protected TaxonDescription getTaxonDescription(Taxon taxon, Reference<?> ref, boolean isImageGallery, boolean createNewIfNotExists) {
|
|
1004
|
return docImport.getTaxonDescription(taxon, isImageGallery, createNewIfNotExists);
|
|
1005
|
}
|
|
1006
|
|
|
1007
|
|
|
1008
|
/**
|
|
1009
|
* Returns the default language defined in the state. If no default language is defined in the state,
|
|
1010
|
* the CDM default language is returned.
|
|
1011
|
* @param state
|
|
1012
|
* @return
|
|
1013
|
*/
|
|
1014
|
protected Language getDefaultLanguage(MarkupImportState state) {
|
|
1015
|
Language result = state.getDefaultLanguage();
|
|
1016
|
if (result == null){
|
|
1017
|
result = Language.DEFAULT();
|
|
1018
|
}
|
|
1019
|
return result;
|
|
1020
|
}
|
|
1021
|
|
|
1022
|
|
|
1023
|
//*********************** FROM XML IMPORT BASE ****************************************
|
|
1024
|
protected boolean isEndingElement(XMLEvent event, String elName) throws XMLStreamException {
|
|
1025
|
return docImport.isEndingElement(event, elName);
|
|
1026
|
}
|
|
1027
|
|
|
1028
|
protected boolean isStartingElement(XMLEvent event, String elName) throws XMLStreamException {
|
|
1029
|
return docImport.isStartingElement(event, elName);
|
|
1030
|
}
|
|
1031
|
|
|
1032
|
|
|
1033
|
protected void fillMissingEpithetsForTaxa(Taxon parentTaxon, Taxon childTaxon) {
|
|
1034
|
docImport.fillMissingEpithetsForTaxa(parentTaxon, childTaxon);
|
|
1035
|
}
|
|
1036
|
|
|
1037
|
protected Feature getFeature(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<Feature> voc){
|
|
1038
|
return docImport.getFeature(state, uuid, label, text, labelAbbrev, voc);
|
|
1039
|
}
|
|
1040
|
|
|
1041
|
protected ExtensionType getExtensionType(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev){
|
|
1042
|
return docImport.getExtensionType(state, uuid, label, text, labelAbbrev);
|
|
1043
|
}
|
|
1044
|
|
|
1045
|
protected DefinedTerm getIdentifierType(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<DefinedTerm> voc){
|
|
1046
|
return docImport.getIdentifierType(state, uuid, label, text, labelAbbrev, voc);
|
|
1047
|
}
|
|
1048
|
|
|
1049
|
protected AnnotationType getAnnotationType(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<AnnotationType> voc){
|
|
1050
|
return docImport.getAnnotationType(state, uuid, label, text, labelAbbrev, voc);
|
|
1051
|
}
|
|
1052
|
|
|
1053
|
protected MarkerType getMarkerType(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<MarkerType> voc){
|
|
1054
|
return docImport.getMarkerType(state, uuid, label, text, labelAbbrev, voc);
|
|
1055
|
}
|
|
1056
|
|
|
1057
|
protected NamedAreaLevel getNamedAreaLevel(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<NamedAreaLevel> voc){
|
|
1058
|
return docImport.getNamedAreaLevel(state, uuid, label, text, labelAbbrev, voc);
|
|
1059
|
}
|
|
1060
|
|
|
1061
|
protected NamedArea getNamedArea(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level, TermVocabulary voc, TermMatchMode matchMode){
|
|
1062
|
return docImport.getNamedArea(state, uuid, label, text, labelAbbrev, areaType, level, voc, matchMode);
|
|
1063
|
}
|
|
1064
|
|
|
1065
|
protected Language getLanguage(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<?> voc){
|
|
1066
|
return docImport.getLanguage(state, uuid, label, text, labelAbbrev, voc);
|
|
1067
|
}
|
|
1068
|
|
|
1069
|
// *************************************** Concrete methods **********************************************/
|
|
1070
|
|
|
1071
|
|
|
1072
|
/**
|
|
1073
|
* @param state
|
|
1074
|
* @param classValue
|
|
1075
|
* @param byAbbrev
|
|
1076
|
* @return
|
|
1077
|
*/
|
|
1078
|
protected Rank makeRank(MarkupImportState state, String value, boolean byAbbrev) {
|
|
1079
|
Rank rank = null;
|
|
1080
|
if (StringUtils.isBlank(value)) {
|
|
1081
|
return null;
|
|
1082
|
}
|
|
1083
|
try {
|
|
1084
|
boolean useUnknown = true;
|
|
1085
|
NomenclaturalCode nc = makeNomenclaturalCode(state);
|
|
1086
|
if (value.equals(GENUS_ABBREVIATION)){
|
|
1087
|
rank = Rank.GENUS();
|
|
1088
|
}else if (byAbbrev) {
|
|
1089
|
rank = Rank.getRankByIdInVoc(value, nc, useUnknown);
|
|
1090
|
} else {
|
|
1091
|
rank = Rank.getRankByEnglishName(value, nc, useUnknown);
|
|
1092
|
}
|
|
1093
|
if (rank.equals(Rank.UNKNOWN_RANK())) {
|
|
1094
|
rank = null;
|
|
1095
|
}
|
|
1096
|
if (rank == null && "sous-genre".equalsIgnoreCase(value)){
|
|
1097
|
rank = Rank.SUBGENUS();
|
|
1098
|
}
|
|
1099
|
} catch (UnknownCdmTypeException e) {
|
|
1100
|
// doNothing
|
|
1101
|
}
|
|
1102
|
return rank;
|
|
1103
|
}
|
|
1104
|
|
|
1105
|
|
|
1106
|
|
|
1107
|
protected TeamOrPersonBase<?> createAuthor(String authorTitle) {
|
|
1108
|
// TODO atomize and also use by name creation
|
|
1109
|
TeamOrPersonBase<?> result = Team.NewTitledInstance(authorTitle, authorTitle);
|
|
1110
|
return result;
|
|
1111
|
}
|
|
1112
|
|
|
1113
|
protected String getAndRemoveMapKey(Map<String, String> map, String key) {
|
|
1114
|
String result = map.get(key);
|
|
1115
|
map.remove(key);
|
|
1116
|
if (result != null) {
|
|
1117
|
result = normalize(result);
|
|
1118
|
}
|
|
1119
|
return StringUtils.stripToNull(result);
|
|
1120
|
}
|
|
1121
|
|
|
1122
|
|
|
1123
|
/**
|
|
1124
|
* Creates a {@link NonViralName} object depending on the defined {@link NomenclaturalCode}
|
|
1125
|
* and the given parameters.
|
|
1126
|
* @param state
|
|
1127
|
* @param rank
|
|
1128
|
* @return
|
|
1129
|
*/
|
|
1130
|
protected NonViralName<?> createNameByCode(MarkupImportState state, Rank rank) {
|
|
1131
|
NonViralName<?> name;
|
|
1132
|
NomenclaturalCode nc = makeNomenclaturalCode(state);
|
|
1133
|
name = (NonViralName<?>) nc.getNewTaxonNameInstance(rank);
|
|
1134
|
return name;
|
|
1135
|
}
|
|
1136
|
|
|
1137
|
protected void handleFullName(MarkupImportState state, XMLEventReader reader,
|
|
1138
|
NonViralName<?> name, XMLEvent next) throws XMLStreamException {
|
|
1139
|
String fullNameStr;
|
|
1140
|
Map<String, Attribute> attrs = getAttributes(next);
|
|
1141
|
String rankStr = getAndRemoveRequiredAttributeValue(next,
|
|
1142
|
attrs, "rank");
|
|
1143
|
Rank rank = makeRank(state, rankStr, false);
|
|
1144
|
name.setRank(rank);
|
|
1145
|
if (rank == null) {
|
|
1146
|
String message = "Rank was computed as null. This must not be.";
|
|
1147
|
fireWarningEvent(message, next, 6);
|
|
1148
|
name.setRank(Rank.UNKNOWN_RANK());
|
|
1149
|
}
|
|
1150
|
if (!attrs.isEmpty()) {
|
|
1151
|
handleUnexpectedAttributes(next.getLocation(), attrs);
|
|
1152
|
}
|
|
1153
|
// next = readNoWhitespace(reader);
|
|
1154
|
fullNameStr = getCData(state, reader, next, false);
|
|
1155
|
NonViralNameParserImpl.NewInstance().parseFullName(name, fullNameStr, rank, false);
|
|
1156
|
// name.setTitleCache(fullNameStr, true);
|
|
1157
|
}
|
|
1158
|
|
|
1159
|
|
|
1160
|
/**
|
|
1161
|
* Returns the {@link NomenclaturalCode} for this import. Default is {@link NomenclaturalCode#ICBN} if
|
|
1162
|
* no code is defined.
|
|
1163
|
* @param state
|
|
1164
|
* @return
|
|
1165
|
*/
|
|
1166
|
protected NomenclaturalCode makeNomenclaturalCode(MarkupImportState state) {
|
|
1167
|
NomenclaturalCode nc = state.getConfig().getNomenclaturalCode();
|
|
1168
|
if (nc == null) {
|
|
1169
|
nc = NomenclaturalCode.ICNAFP; // default;
|
|
1170
|
}
|
|
1171
|
return nc;
|
|
1172
|
}
|
|
1173
|
|
|
1174
|
|
|
1175
|
/**
|
|
1176
|
* @param state
|
|
1177
|
* @param levelString
|
|
1178
|
* @param next
|
|
1179
|
* @return
|
|
1180
|
*/
|
|
1181
|
protected NamedAreaLevel makeNamedAreaLevel(MarkupImportState state, String levelString, XMLEvent next) {
|
|
1182
|
NamedAreaLevel level;
|
|
1183
|
try {
|
|
1184
|
level = state.getTransformer().getNamedAreaLevelByKey(levelString);
|
|
1185
|
if (level == null) {
|
|
1186
|
UUID levelUuid = state.getTransformer().getNamedAreaLevelUuid(levelString);
|
|
1187
|
if (levelUuid == null) {
|
|
1188
|
String message = "Unknown distribution locality class (named area level): %s. Create new level instead.";
|
|
1189
|
message = String.format(message, levelString);
|
|
1190
|
fireWarningEvent(message, next, 6);
|
|
1191
|
}
|
|
1192
|
level = getNamedAreaLevel(state, levelUuid, levelString, levelString, levelString, null);
|
|
1193
|
}
|
|
1194
|
} catch (UndefinedTransformerMethodException e) {
|
|
1195
|
throw new RuntimeException(e);
|
|
1196
|
}
|
|
1197
|
return level;
|
|
1198
|
}
|
|
1199
|
|
|
1200
|
|
|
1201
|
/**
|
|
1202
|
* @param state
|
|
1203
|
* @param areaName
|
|
1204
|
* @param level
|
|
1205
|
* @return
|
|
1206
|
*/
|
|
1207
|
protected NamedArea makeArea(MarkupImportState state, String areaName, NamedAreaLevel level) {
|
|
1208
|
|
|
1209
|
//TODO FM vocabulary
|
|
1210
|
TermVocabulary<NamedArea> voc = null;
|
|
1211
|
NamedAreaType areaType = null;
|
|
1212
|
|
|
1213
|
NamedArea area = null;
|
|
1214
|
try {
|
|
1215
|
area = state.getTransformer().getNamedAreaByKey(areaName);
|
|
1216
|
} catch (UndefinedTransformerMethodException e) {
|
|
1217
|
throw new RuntimeException(e);
|
|
1218
|
}
|
|
1219
|
if (area == null){
|
|
1220
|
boolean isNewInState = false;
|
|
1221
|
UUID uuid = state.getAreaUuid(areaName);
|
|
1222
|
if (uuid == null){
|
|
1223
|
isNewInState = true;
|
|
1224
|
|
|
1225
|
|
|
1226
|
try {
|
|
1227
|
uuid = state.getTransformer().getNamedAreaUuid(areaName);
|
|
1228
|
} catch (UndefinedTransformerMethodException e) {
|
|
1229
|
throw new RuntimeException(e);
|
|
1230
|
}
|
|
1231
|
}
|
|
1232
|
|
|
1233
|
CdmImportBase.TermMatchMode matchMode = CdmImportBase.TermMatchMode.UUID_LABEL;
|
|
1234
|
area = getNamedArea(state, uuid, areaName, areaName, areaName, areaType, level, voc, matchMode);
|
|
1235
|
if (isNewInState){
|
|
1236
|
state.putAreaUuid(areaName, area.getUuid());
|
|
1237
|
|
|
1238
|
//TODO just for testing -> make generic and move to better place
|
|
1239
|
String geoServiceLayer="vmap0_as_bnd_political_boundary_a";
|
|
1240
|
String layerFieldName ="nam";
|
|
1241
|
|
|
1242
|
if ("Bangka".equals(areaName)){
|
|
1243
|
String areaValue = "PULAU BANGKA#SUMATERA SELATAN";
|
|
1244
|
GeoServiceArea geoServiceArea = new GeoServiceArea();
|
|
1245
|
geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);
|
|
1246
|
this.editGeoService.setMapping(area, geoServiceArea);
|
|
1247
|
// save(area, state);
|
|
1248
|
}
|
|
1249
|
if ("Luzon".equals(areaName)){
|
|
1250
|
GeoServiceArea geoServiceArea = new GeoServiceArea();
|
|
1251
|
|
|
1252
|
List<String> list = Arrays.asList("HERMANA MAYOR ISLAND#CENTRAL LUZON",
|
|
1253
|
"HERMANA MENOR ISLAND#CENTRAL LUZON",
|
|
1254
|
"CENTRAL LUZON");
|
|
1255
|
for (String areaValue : list){
|
|
1256
|
geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);
|
|
1257
|
}
|
|
1258
|
|
|
1259
|
this.editGeoService.setMapping(area, geoServiceArea);
|
|
1260
|
// save(area, state);
|
|
1261
|
}
|
|
1262
|
if ("Mindanao".equals(areaName)){
|
|
1263
|
GeoServiceArea geoServiceArea = new GeoServiceArea();
|
|
1264
|
|
|
1265
|
List<String> list = Arrays.asList("NORTHERN MINDANAO",
|
|
1266
|
"SOUTHERN MINDANAO",
|
|
1267
|
"WESTERN MINDANAO");
|
|
1268
|
//TODO to be continued
|
|
1269
|
for (String areaValue : list){
|
|
1270
|
geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);
|
|
1271
|
}
|
|
1272
|
|
|
1273
|
this.editGeoService.setMapping(area, geoServiceArea);
|
|
1274
|
// save(area, state);
|
|
1275
|
}
|
|
1276
|
if ("Palawan".equals(areaName)){
|
|
1277
|
GeoServiceArea geoServiceArea = new GeoServiceArea();
|
|
1278
|
|
|
1279
|
List<String> list = Arrays.asList("PALAWAN#SOUTHERN TAGALOG");
|
|
1280
|
for (String areaValue : list){
|
|
1281
|
geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);
|
|
1282
|
}
|
|
1283
|
|
|
1284
|
this.editGeoService.setMapping(area, geoServiceArea);
|
|
1285
|
// save(area, state);
|
|
1286
|
}
|
|
1287
|
|
|
1288
|
}
|
|
1289
|
}
|
|
1290
|
return area;
|
|
1291
|
}
|
|
1292
|
|
|
1293
|
|
|
1294
|
|
|
1295
|
/**
|
|
1296
|
* Reads character data. Any element other than character data or the ending
|
|
1297
|
* tag will fire an unexpected element event.
|
|
1298
|
*
|
|
1299
|
* @see #getCData(MarkupImportState, XMLEventReader, XMLEvent, boolean)
|
|
1300
|
* @param state
|
|
1301
|
* @param reader
|
|
1302
|
* @param next
|
|
1303
|
* @return
|
|
1304
|
* @throws XMLStreamException
|
|
1305
|
*/
|
|
1306
|
protected String getCData(MarkupImportState state, XMLEventReader reader, XMLEvent next) throws XMLStreamException {
|
|
1307
|
return getCData(state, reader, next, true);
|
|
1308
|
}
|
|
1309
|
|
|
1310
|
/**
|
|
1311
|
* Reads character data. Any element other than character data or the ending
|
|
1312
|
* tag will fire an unexpected element event.
|
|
1313
|
*
|
|
1314
|
* @param state
|
|
1315
|
* @param reader
|
|
1316
|
* @param next
|
|
1317
|
* @param inlineMarkup map for inline markup, this is used for e.g. the locality markup within a subheading
|
|
1318
|
* The map will be filled by the markup element name as key. The value may be a String, a CdmBase or any other object.
|
|
1319
|
* If null any markup text will be neglected but a warning will be fired if they exist.
|
|
1320
|
* @param removeInlineMarkupText if true the markedup text will be removed from the returned String
|
|
1321
|
* @param checkAttributes
|
|
1322
|
* @return
|
|
1323
|
* @throws XMLStreamException
|
|
1324
|
*/
|
|
1325
|
protected String getCData(MarkupImportState state, XMLEventReader reader, XMLEvent parent, /*Map<String, Object> inlineMarkup, *boolean removeInlineMarkupText,*/ boolean checkAttributes) throws XMLStreamException {
|
|
1326
|
if (checkAttributes){
|
|
1327
|
checkNoAttributes(parent);
|
|
1328
|
}
|
|
1329
|
|
|
1330
|
String text = "";
|
|
1331
|
while (reader.hasNext()) {
|
|
1332
|
XMLEvent next = readNoWhitespace(reader);
|
|
1333
|
if (isMyEndingElement(next, parent)) {
|
|
1334
|
return text;
|
|
1335
|
} else if (next.isCharacters()) {
|
|
1336
|
text += next.asCharacters().getData();
|
|
1337
|
} else if (isStartingElement(next, FOOTNOTE_REF)){
|
|
1338
|
handleNotYetImplementedElement(next);
|
|
1339
|
// } else if (isStartingElement(next, LOCALITY)){
|
|
1340
|
// handleCDataLocality(state, reader, parent);
|
|
1341
|
} else {
|
|
1342
|
handleUnexpectedElement(next);
|
|
1343
|
}
|
|
1344
|
}
|
|
1345
|
throw new IllegalStateException("Event has no closing tag");
|
|
1346
|
|
|
1347
|
}
|
|
1348
|
|
|
1349
|
// private void handleCDataLocality(MarkupImportState state, XMLEventReader reader, XMLEvent parent) {
|
|
1350
|
// checkAndRemoveAttributeValue(attributes, attrName, value)
|
|
1351
|
//
|
|
1352
|
// }
|
|
1353
|
|
|
1354
|
|
|
1355
|
|
|
1356
|
/**
|
|
1357
|
* For it returns a pure CData annotation string. This behaviour may change in future. More complex annotations
|
|
1358
|
* should be handled differently.
|
|
1359
|
* @param state
|
|
1360
|
* @param reader
|
|
1361
|
* @param parentEvent
|
|
1362
|
* @return
|
|
1363
|
* @throws XMLStreamException
|
|
1364
|
*/
|
|
1365
|
protected String handleSimpleAnnotation(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
1366
|
String annotation = getCData(state, reader, parentEvent);
|
|
1367
|
return annotation;
|
|
1368
|
}
|
|
1369
|
|
|
1370
|
/**
|
|
1371
|
* True if text is single "." oder "," or ";" or ":"
|
|
1372
|
* @param text
|
|
1373
|
* @return
|
|
1374
|
*/
|
|
1375
|
protected boolean isPunctuation(String text) {
|
|
1376
|
return text == null ? false : text.trim().matches("^[\\.,;:]$");
|
|
1377
|
}
|
|
1378
|
|
|
1379
|
|
|
1380
|
/**
|
|
1381
|
* Text indicating that type information is following but no information about the type of the type
|
|
1382
|
* @param text
|
|
1383
|
* @return
|
|
1384
|
*/
|
|
1385
|
protected boolean charIsSimpleType(String text) {
|
|
1386
|
return text.matches("(?i)Type:");
|
|
1387
|
}
|
|
1388
|
|
|
1389
|
protected String getXmlTag(XMLEvent event) {
|
|
1390
|
String result;
|
|
1391
|
if (event.isStartElement()) {
|
|
1392
|
result = "<" + event.asStartElement().getName().getLocalPart()
|
|
1393
|
+ ">";
|
|
1394
|
} else if (event.isEndElement()) {
|
|
1395
|
result = "</" + event.asEndElement().getName().getLocalPart() + ">";
|
|
1396
|
} else {
|
|
1397
|
String message = "Only start or end elements are allowed as Html tags";
|
|
1398
|
throw new IllegalStateException(message);
|
|
1399
|
}
|
|
1400
|
return result;
|
|
1401
|
}
|
|
1402
|
|
|
1403
|
protected WriterDataHolder handleWriter(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
1404
|
String text = "";
|
|
1405
|
checkNoAttributes(parentEvent);
|
|
1406
|
WriterDataHolder dataHolder = new WriterDataHolder();
|
|
1407
|
List<FootnoteDataHolder> footnotes = new ArrayList<FootnoteDataHolder>();
|
|
1408
|
|
|
1409
|
// TODO handle attributes
|
|
1410
|
while (reader.hasNext()) {
|
|
1411
|
XMLEvent next = readNoWhitespace(reader);
|
|
1412
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1413
|
text = CdmUtils.removeBrackets(text);
|
|
1414
|
if (checkMandatoryText(text, parentEvent)) {
|
|
1415
|
text = normalize(text);
|
|
1416
|
dataHolder.writer = text;
|
|
1417
|
dataHolder.footnotes = footnotes;
|
|
1418
|
|
|
1419
|
// Extension
|
|
1420
|
UUID uuidWriterExtension = MarkupTransformer.uuidWriterExtension;
|
|
1421
|
ExtensionType writerExtensionType =
|
|
1422
|
this.getExtensionType(state, uuidWriterExtension,"Writer", "writer", "writer");
|
|
1423
|
Extension extension = Extension.NewInstance();
|
|
1424
|
extension.setType(writerExtensionType);
|
|
1425
|
extension.setValue(text);
|
|
1426
|
dataHolder.extension = extension;
|
|
1427
|
|
|
1428
|
// Annotation
|
|
1429
|
UUID uuidWriterAnnotation = MarkupTransformer.uuidWriterAnnotation;
|
|
1430
|
AnnotationType writerAnnotationType = this.getAnnotationType(state, uuidWriterAnnotation, "Writer", "writer", "writer", null);
|
|
1431
|
Annotation annotation = Annotation.NewInstance(text, writerAnnotationType, getDefaultLanguage(state));
|
|
1432
|
dataHolder.annotation = annotation;
|
|
1433
|
|
|
1434
|
return dataHolder;
|
|
1435
|
} else {
|
|
1436
|
return null;
|
|
1437
|
}
|
|
1438
|
} else if (isStartingElement(next, FOOTNOTE_REF)) {
|
|
1439
|
FootnoteDataHolder footNote = handleFootnoteRef(state, reader, next);
|
|
1440
|
if (footNote.isRef()) {
|
|
1441
|
footnotes.add(footNote);
|
|
1442
|
} else {
|
|
1443
|
logger.warn("Non ref footnotes not yet impelemnted");
|
|
1444
|
}
|
|
1445
|
} else if (next.isCharacters()) {
|
|
1446
|
text += next.asCharacters().getData();
|
|
1447
|
|
|
1448
|
} else {
|
|
1449
|
handleUnexpectedElement(next);
|
|
1450
|
state.setUnsuccessfull();
|
|
1451
|
}
|
|
1452
|
}
|
|
1453
|
throw new IllegalStateException("<writer> has no end tag");
|
|
1454
|
}
|
|
1455
|
|
|
1456
|
|
|
1457
|
protected void registerFootnotes(MarkupImportState state, AnnotatableEntity entity, List<FootnoteDataHolder> footnotes) {
|
|
1458
|
for (FootnoteDataHolder footNote : footnotes) {
|
|
1459
|
registerFootnoteDemand(state, entity, footNote);
|
|
1460
|
}
|
|
1461
|
}
|
|
1462
|
|
|
1463
|
|
|
1464
|
private void registerFootnoteDemand(MarkupImportState state, AnnotatableEntity entity, FootnoteDataHolder footnote) {
|
|
1465
|
FootnoteDataHolder existingFootnote = state.getFootnote(footnote.ref);
|
|
1466
|
if (existingFootnote != null) {
|
|
1467
|
attachFootnote(state, entity, existingFootnote);
|
|
1468
|
} else {
|
|
1469
|
Set<AnnotatableEntity> demands = state.getFootnoteDemands(footnote.ref);
|
|
1470
|
if (demands == null) {
|
|
1471
|
demands = new HashSet<AnnotatableEntity>();
|
|
1472
|
state.putFootnoteDemands(footnote.ref, demands);
|
|
1473
|
}
|
|
1474
|
demands.add(entity);
|
|
1475
|
}
|
|
1476
|
}
|
|
1477
|
|
|
1478
|
|
|
1479
|
protected void attachFootnote(MarkupImportState state, AnnotatableEntity entity, FootnoteDataHolder footnote) {
|
|
1480
|
AnnotationType annotationType = this.getAnnotationType(state, MarkupTransformer.uuidFootnote, "Footnote", "An e-flora footnote", "fn", null);
|
|
1481
|
Annotation annotation = Annotation.NewInstance(footnote.string, annotationType, getDefaultLanguage(state));
|
|
1482
|
// TODO transient objects
|
|
1483
|
entity.addAnnotation(annotation);
|
|
1484
|
save(entity, state);
|
|
1485
|
}
|
|
1486
|
|
|
1487
|
|
|
1488
|
protected void attachFigure(MarkupImportState state, XMLEvent next, AnnotatableEntity entity, Media figure) {
|
|
1489
|
// IdentifiableEntity<?> toSave;
|
|
1490
|
if (entity.isInstanceOf(TextData.class)) {
|
|
1491
|
TextData deb = CdmBase.deproxy(entity, TextData.class);
|
|
1492
|
deb.addMedia(figure);
|
|
1493
|
// toSave = ((TaxonDescription)deb.getInDescription()).getTaxon();
|
|
1494
|
} else if (entity.isInstanceOf(SpecimenOrObservationBase.class)) {
|
|
1495
|
String message = "figures for specimen should be handled as Textdata";
|
|
1496
|
fireWarningEvent(message, next, 4);
|
|
1497
|
// toSave = ime;
|
|
1498
|
} else if (entity.isInstanceOf(IdentifiableMediaEntity.class)) {
|
|
1499
|
IdentifiableMediaEntity<?> ime = CdmBase.deproxy(entity, IdentifiableMediaEntity.class);
|
|
1500
|
ime.addMedia(figure);
|
|
1501
|
// toSave = ime;
|
|
1502
|
} else {
|
|
1503
|
String message = "Unsupported entity to attach media: %s";
|
|
1504
|
message = String.format(message, entity.getClass().getName());
|
|
1505
|
// toSave = null;
|
|
1506
|
}
|
|
1507
|
save(entity, state);
|
|
1508
|
}
|
|
1509
|
|
|
1510
|
|
|
1511
|
protected void registerGivenFootnote(MarkupImportState state, FootnoteDataHolder footnote) {
|
|
1512
|
state.registerFootnote(footnote);
|
|
1513
|
Set<AnnotatableEntity> demands = state.getFootnoteDemands(footnote.id);
|
|
1514
|
if (demands != null) {
|
|
1515
|
for (AnnotatableEntity entity : demands) {
|
|
1516
|
attachFootnote(state, entity, footnote);
|
|
1517
|
}
|
|
1518
|
}
|
|
1519
|
}
|
|
1520
|
|
|
1521
|
|
|
1522
|
protected FootnoteDataHolder handleFootnote(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent,
|
|
1523
|
MarkupSpecimenImport specimenImport, MarkupNomenclatureImport nomenclatureImport) throws XMLStreamException {
|
|
1524
|
FootnoteDataHolder result = new FootnoteDataHolder();
|
|
1525
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
1526
|
result.id = getAndRemoveAttributeValue(attributes, ID);
|
|
1527
|
// result.ref = getAndRemoveAttributeValue(attributes, REF);
|
|
1528
|
checkNoAttributes(attributes, parentEvent);
|
|
1529
|
|
|
1530
|
while (reader.hasNext()) {
|
|
1531
|
XMLEvent next = readNoWhitespace(reader);
|
|
1532
|
if (isStartingElement(next, FOOTNOTE_STRING)) {
|
|
1533
|
String string = handleFootnoteString(state, reader, next, specimenImport, nomenclatureImport);
|
|
1534
|
result.string = string;
|
|
1535
|
} else if (isMyEndingElement(next, parentEvent)) {
|
|
1536
|
return result;
|
|
1537
|
} else {
|
|
1538
|
fireUnexpectedEvent(next, 0);
|
|
1539
|
}
|
|
1540
|
}
|
|
1541
|
return result;
|
|
1542
|
}
|
|
1543
|
|
|
1544
|
|
|
1545
|
protected Media handleFigure(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent,
|
|
1546
|
MarkupSpecimenImport specimenImport, MarkupNomenclatureImport nomenclatureImport) throws XMLStreamException {
|
|
1547
|
// FigureDataHolder result = new FigureDataHolder();
|
|
1548
|
|
|
1549
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
1550
|
String id = getAndRemoveAttributeValue(attributes, ID);
|
|
1551
|
String type = getAndRemoveAttributeValue(attributes, TYPE);
|
|
1552
|
String urlAttr = getAndRemoveAttributeValue(attributes, URL);
|
|
1553
|
checkNoAttributes(attributes, parentEvent);
|
|
1554
|
|
|
1555
|
String urlString = null;
|
|
1556
|
String legendString = null;
|
|
1557
|
String titleString = null;
|
|
1558
|
String numString = null;
|
|
1559
|
String text = null;
|
|
1560
|
if (isNotBlank(urlAttr)){
|
|
1561
|
urlString = CdmUtils.Nz(state.getBaseMediaUrl()) + urlAttr;
|
|
1562
|
}
|
|
1563
|
while (reader.hasNext()) {
|
|
1564
|
XMLEvent next = readNoWhitespace(reader);
|
|
1565
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1566
|
if (isNotBlank(text)){
|
|
1567
|
fireWarningEvent("Text not yet handled for figures: " + text, next, 4);
|
|
1568
|
}
|
|
1569
|
Media media = makeFigure(state, id, type, urlString, legendString, titleString, numString, next);
|
|
1570
|
return media;
|
|
1571
|
} else if (isStartingElement(next, FIGURE_LEGEND)) {
|
|
1572
|
// TODO same as figure string ?
|
|
1573
|
legendString = handleFootnoteString(state, reader, next, specimenImport, nomenclatureImport);
|
|
1574
|
} else if (isStartingElement(next, FIGURE_TITLE)) {
|
|
1575
|
titleString = getCData(state, reader, next);
|
|
1576
|
} else if (isStartingElement(next, URL)) {
|
|
1577
|
String localUrl = getCData(state, reader, next);
|
|
1578
|
String url = CdmUtils.Nz(state.getBaseMediaUrl()) + localUrl;
|
|
1579
|
if (isBlank(urlString)){
|
|
1580
|
urlString = url;
|
|
1581
|
}
|
|
1582
|
if (! url.equals(urlString)){
|
|
1583
|
String message = "URL attribute and URL element differ. Attribute: %s, Element: %s";
|
|
1584
|
fireWarningEvent(String.format(message, urlString, url), next, 2);
|
|
1585
|
}
|
|
1586
|
} else if (isStartingElement(next, NUM)) {
|
|
1587
|
numString = getCData(state, reader, next);
|
|
1588
|
} else if (next.isCharacters()) {
|
|
1589
|
text += CdmUtils.concat("", text, next.asCharacters().getData());
|
|
1590
|
} else {
|
|
1591
|
fireUnexpectedEvent(next, 0);
|
|
1592
|
}
|
|
1593
|
}
|
|
1594
|
throw new IllegalStateException("<figure> has no end tag");
|
|
1595
|
}
|
|
1596
|
|
|
1597
|
|
|
1598
|
/**
|
|
1599
|
* @param state
|
|
1600
|
* @param id
|
|
1601
|
* @param type
|
|
1602
|
* @param urlString
|
|
1603
|
* @param legendString
|
|
1604
|
* @param titleString
|
|
1605
|
* @param numString
|
|
1606
|
* @param next
|
|
1607
|
*/
|
|
1608
|
private Media makeFigure(MarkupImportState state, String id, String type, String urlString,
|
|
1609
|
String legendString, String titleString, String numString, XMLEvent next) {
|
|
1610
|
Media media = null;
|
|
1611
|
// boolean isFigure = false; //no difference between figure and media since v3.3
|
|
1612
|
try {
|
|
1613
|
//TODO maybe everything is a figure as it is all taken from a book
|
|
1614
|
if ("lineart".equals(type)) {
|
|
1615
|
// isFigure = true;
|
|
1616
|
// media = Figure.NewInstance(url.toURI(), null, null, null);
|
|
1617
|
} else if (type == null || "photo".equals(type)
|
|
1618
|
|| "signature".equals(type)
|
|
1619
|
|| "others".equals(type)) {
|
|
1620
|
//TODO
|
|
1621
|
} else {
|
|
1622
|
String message = "Unknown figure type '%s'";
|
|
1623
|
message = String.format(message, type);
|
|
1624
|
fireWarningEvent(message, next, 2);
|
|
1625
|
}
|
|
1626
|
media = docImport.getImageMedia(urlString, docImport.getReadMediaData());
|
|
1627
|
|
|
1628
|
if (media != null){
|
|
1629
|
// title
|
|
1630
|
if (StringUtils.isNotBlank(titleString)) {
|
|
1631
|
media.putTitle(getDefaultLanguage(state), titleString);
|
|
1632
|
}
|
|
1633
|
// legend
|
|
1634
|
if (StringUtils.isNotBlank(legendString)) {
|
|
1635
|
media.putDescription(getDefaultLanguage(state), legendString);
|
|
1636
|
}
|
|
1637
|
if (StringUtils.isNotBlank(numString)) {
|
|
1638
|
// TODO use concrete source (e.g. DAPHNIPHYLLACEAE in FM
|
|
1639
|
// vol.13)
|
|
1640
|
Reference<?> citation = state.getConfig().getSourceReference();
|
|
1641
|
media.addSource(OriginalSourceType.Import, numString, "num", citation, null);
|
|
1642
|
// TODO name used in source if available
|
|
1643
|
}
|
|
1644
|
// TODO which citation
|
|
1645
|
if (StringUtils.isNotBlank(id)) {
|
|
1646
|
media.addSource(OriginalSourceType.Import, id, null, state.getConfig().getSourceReference(), null);
|
|
1647
|
} else {
|
|
1648
|
String message = "Figure id should never be empty or null";
|
|
1649
|
fireWarningEvent(message, next, 6);
|
|
1650
|
}
|
|
1651
|
|
|
1652
|
// text
|
|
1653
|
// do nothing
|
|
1654
|
registerGivenFigure(state, next, id, media);
|
|
1655
|
|
|
1656
|
}else{
|
|
1657
|
String message = "No media found: ";
|
|
1658
|
fireWarningEvent(message, next, 4);
|
|
1659
|
}
|
|
1660
|
} catch (MalformedURLException e) {
|
|
1661
|
String message = "Media uri has incorrect syntax: %s";
|
|
1662
|
message = String.format(message, urlString);
|
|
1663
|
fireWarningEvent(message, next, 4);
|
|
1664
|
// } catch (URISyntaxException e) {
|
|
1665
|
// String message = "Media uri has incorrect syntax: %s";
|
|
1666
|
// message = String.format(message, urlString);
|
|
1667
|
// fireWarningEvent(message, next, 4);
|
|
1668
|
}
|
|
1669
|
|
|
1670
|
return media;
|
|
1671
|
}
|
|
1672
|
|
|
1673
|
|
|
1674
|
private void registerGivenFigure(MarkupImportState state, XMLEvent next, String id, Media figure) {
|
|
1675
|
state.registerFigure(id, figure);
|
|
1676
|
Set<AnnotatableEntity> demands = state.getFigureDemands(id);
|
|
1677
|
if (demands != null) {
|
|
1678
|
for (AnnotatableEntity entity : demands) {
|
|
1679
|
attachFigure(state, next, entity, figure);
|
|
1680
|
}
|
|
1681
|
}
|
|
1682
|
save(figure, state);
|
|
1683
|
}
|
|
1684
|
|
|
1685
|
|
|
1686
|
private FootnoteDataHolder handleFootnoteRef(MarkupImportState state,
|
|
1687
|
XMLEventReader reader, XMLEvent parentEvent)
|
|
1688
|
throws XMLStreamException {
|
|
1689
|
FootnoteDataHolder result = new FootnoteDataHolder();
|
|
1690
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
1691
|
result.ref = getAndRemoveAttributeValue(attributes, REF);
|
|
1692
|
checkNoAttributes(attributes, parentEvent);
|
|
1693
|
|
|
1694
|
// text is not handled, needed only for debugging purposes
|
|
1695
|
String text = "";
|
|
1696
|
while (reader.hasNext()) {
|
|
1697
|
XMLEvent next = readNoWhitespace(reader);
|
|
1698
|
// if (isStartingElement(next, FOOTNOTE_STRING)){
|
|
1699
|
// String string = handleFootnoteString(state, reader, next);
|
|
1700
|
// result.string = string;
|
|
1701
|
// }else
|
|
1702
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1703
|
if (StringUtils.isNotBlank(text)){
|
|
1704
|
fireWarningEvent("text is not empty but not handled during import", parentEvent, 4);
|
|
1705
|
}
|
|
1706
|
return result;
|
|
1707
|
} else if (next.isCharacters() && unhandledElements.isEmpty()) {
|
|
1708
|
text += next.asCharacters().getData();
|
|
1709
|
} else if (isStartingElement(next, NUM)) {
|
|
1710
|
//ignore numbering of footnotes as they are numbered differently in the CDM
|
|
1711
|
handleIgnoreElement(next);
|
|
1712
|
} else {
|
|
1713
|
handleUnexpectedElement(next);
|
|
1714
|
}
|
|
1715
|
}
|
|
1716
|
return result;
|
|
1717
|
}
|
|
1718
|
|
|
1719
|
|
|
1720
|
|
|
1721
|
private String handleFootnoteString(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, MarkupSpecimenImport specimenImport, MarkupNomenclatureImport nomenclatureImport) throws XMLStreamException {
|
|
1722
|
boolean isTextMode = true;
|
|
1723
|
String text = "";
|
|
1724
|
while (reader.hasNext()) {
|
|
1725
|
XMLEvent next = readNoWhitespace(reader);
|
|
1726
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1727
|
return text;
|
|
1728
|
} else if (next.isEndElement()) {
|
|
1729
|
if (isEndingElement(next, FULL_NAME)) {
|
|
1730
|
popUnimplemented(next.asEndElement());
|
|
1731
|
} else if (isEndingElement(next, BR)) {
|
|
1732
|
isTextMode = true;
|
|
1733
|
} else if (isHtml(next)) {
|
|
1734
|
text += getXmlTag(next);
|
|
1735
|
} else {
|
|
1736
|
handleUnexpectedEndElement(next.asEndElement());
|
|
1737
|
}
|
|
1738
|
} else if (next.isStartElement()) {
|
|
1739
|
if (isStartingElement(next, FULL_NAME)) {
|
|
1740
|
handleNotYetImplementedElement(next);
|
|
1741
|
} else if (isStartingElement(next, GATHERING)) {
|
|
1742
|
text += specimenImport.handleInLineGathering(state, reader, next);
|
|
1743
|
} else if (isStartingElement(next, REFERENCES)) {
|
|
1744
|
text += " " + handleInLineReferences(state, reader, next, nomenclatureImport)+ " ";
|
|
1745
|
} else if (isStartingElement(next, BR)) {
|
|
1746
|
text += "<br/>";
|
|
1747
|
isTextMode = false;
|
|
1748
|
} else if (isStartingElement(next, NOMENCLATURE)) {
|
|
1749
|
handleNotYetImplementedElement(next);
|
|
1750
|
} else if (isHtml(next)) {
|
|
1751
|
text += getXmlTag(next);
|
|
1752
|
} else {
|
|
1753
|
handleUnexpectedStartElement(next.asStartElement());
|
|
1754
|
}
|
|
1755
|
} else if (next.isCharacters()) {
|
|
1756
|
if (!isTextMode) {
|
|
1757
|
String message = "footnoteString is not in text mode";
|
|
1758
|
fireWarningEvent(message, next, 6);
|
|
1759
|
} else {
|
|
1760
|
text += next.asCharacters().getData().trim();
|
|
1761
|
// getCData(state, reader, next); does not work as we have inner tags like <references>
|
|
1762
|
}
|
|
1763
|
} else {
|
|
1764
|
handleUnexpectedEndElement(next.asEndElement());
|
|
1765
|
}
|
|
1766
|
}
|
|
1767
|
throw new IllegalStateException("<footnoteString> has no closing tag");
|
|
1768
|
|
|
1769
|
}
|
|
1770
|
|
|
1771
|
private static final List<String> htmlList = Arrays.asList("sub", "sup",
|
|
1772
|
"ol", "ul", "li", "i", "b", "table", "br","tr","td");
|
|
1773
|
|
|
1774
|
protected boolean isHtml(XMLEvent event) {
|
|
1775
|
if (event.isStartElement()) {
|
|
1776
|
String tag = event.asStartElement().getName().getLocalPart();
|
|
1777
|
return htmlList.contains(tag);
|
|
1778
|
} else if (event.isEndElement()) {
|
|
1779
|
String tag = event.asEndElement().getName().getLocalPart();
|
|
1780
|
return htmlList.contains(tag);
|
|
1781
|
} else {
|
|
1782
|
return false;
|
|
1783
|
}
|
|
1784
|
|
|
1785
|
}
|
|
1786
|
|
|
1787
|
|
|
1788
|
private String handleInLineReferences(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent, MarkupNomenclatureImport nomenclatureImport) throws XMLStreamException {
|
|
1789
|
checkNoAttributes(parentEvent);
|
|
1790
|
|
|
1791
|
boolean hasReference = false;
|
|
1792
|
String text = "";
|
|
1793
|
while (reader.hasNext()) {
|
|
1794
|
XMLEvent next = readNoWhitespace(reader);
|
|
1795
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1796
|
checkMandatoryElement(hasReference, parentEvent.asStartElement(), REFERENCE);
|
|
1797
|
return text;
|
|
1798
|
} else if (isStartingElement(next, REFERENCE)) {
|
|
1799
|
text += handleInLineReference(state, reader, next, nomenclatureImport);
|
|
1800
|
hasReference = true;
|
|
1801
|
} else {
|
|
1802
|
handleUnexpectedElement(next);
|
|
1803
|
}
|
|
1804
|
}
|
|
1805
|
throw new IllegalStateException("<References> has no closing tag");
|
|
1806
|
}
|
|
1807
|
|
|
1808
|
private String handleInLineReference(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent, MarkupNomenclatureImport nomenclatureImport)throws XMLStreamException {
|
|
1809
|
Reference<?> reference = nomenclatureImport.handleReference(state, reader, parentEvent);
|
|
1810
|
String result = "<cdm:ref uuid='%s'>%s</ref>";
|
|
1811
|
result = String.format(result, reference.getUuid(), reference.getTitleCache());
|
|
1812
|
save(reference, state);
|
|
1813
|
return result;
|
|
1814
|
}
|
|
1815
|
|
|
1816
|
|
|
1817
|
/**
|
|
1818
|
* Handle string
|
|
1819
|
* @param state
|
|
1820
|
* @param reader
|
|
1821
|
* @param parentEvent
|
|
1822
|
* @param feature only needed for distributionLocalities
|
|
1823
|
* @return
|
|
1824
|
* @throws XMLStreamException
|
|
1825
|
*/
|
|
1826
|
protected Map<String, String> handleString(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, Feature feature)throws XMLStreamException {
|
|
1827
|
// attributes
|
|
1828
|
String classValue = getClassOnlyAttribute(parentEvent, false);
|
|
1829
|
if (StringUtils.isNotBlank(classValue)) {
|
|
1830
|
String message = "class attribute for <string> not yet implemented";
|
|
1831
|
fireWarningEvent(message, parentEvent, 2);
|
|
1832
|
}
|
|
1833
|
|
|
1834
|
// subheadings
|
|
1835
|
Map<String, String> subHeadingMap = new HashMap<String, String>();
|
|
1836
|
String currentSubheading = null;
|
|
1837
|
|
|
1838
|
boolean isTextMode = true;
|
|
1839
|
String text = "";
|
|
1840
|
while (reader.hasNext()) {
|
|
1841
|
XMLEvent next = readNoWhitespace(reader);
|
|
1842
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1843
|
putCurrentSubheading(subHeadingMap, currentSubheading, text);
|
|
1844
|
return subHeadingMap;
|
|
1845
|
} else if (isStartingElement(next, BR)) {
|
|
1846
|
text += "<br/>";
|
|
1847
|
isTextMode = false;
|
|
1848
|
} else if (isEndingElement(next, BR)) {
|
|
1849
|
isTextMode = true;
|
|
1850
|
} else if (isHtml(next)) {
|
|
1851
|
text += getXmlTag(next);
|
|
1852
|
} else if (isStartingElement(next, SUB_HEADING)) {
|
|
1853
|
text = putCurrentSubheading(subHeadingMap,currentSubheading, text);
|
|
1854
|
// TODO footnotes
|
|
1855
|
currentSubheading = getCData(state, reader, next).trim();
|
|
1856
|
} else if (isStartingElement(next, DISTRIBUTION_LOCALITY)) {
|
|
1857
|
if (feature != null && !feature.equals(Feature.DISTRIBUTION())) {
|
|
1858
|
String message = "Distribution locality only allowed for feature of type 'distribution'";
|
|
1859
|
fireWarningEvent(message, next, 4);
|
|
1860
|
}
|
|
1861
|
text += handleDistributionLocality(state, reader, next);
|
|
1862
|
} else if (next.isCharacters()) {
|
|
1863
|
if (! isTextMode) {
|
|
1864
|
String message = "String is not in text mode";
|
|
1865
|
fireWarningEvent(message, next, 6);
|
|
1866
|
} else {
|
|
1867
|
text += next.asCharacters().getData();
|
|
1868
|
}
|
|
1869
|
} else if (isStartingElement(next, HEADING)) {
|
|
1870
|
//TODO
|
|
1871
|
handleNotYetImplementedElement(next);
|
|
1872
|
} else if (isStartingElement(next, VERNACULAR_NAMES)) {
|
|
1873
|
//TODO
|
|
1874
|
handleNotYetImplementedElement(next);
|
|
1875
|
} else if (isStartingElement(next, QUOTE)) {
|
|
1876
|
//TODO
|
|
1877
|
handleNotYetImplementedElement(next);
|
|
1878
|
} else if (isStartingElement(next, DEDICATION)) {
|
|
1879
|
//TODO
|
|
1880
|
handleNotYetImplementedElement(next);
|
|
1881
|
} else if (isStartingElement(next, TAXONTYPE)) {
|
|
1882
|
//TODO
|
|
1883
|
handleNotYetImplementedElement(next);
|
|
1884
|
} else if (isStartingElement(next, FULL_NAME)) {
|
|
1885
|
//TODO
|
|
1886
|
handleNotYetImplementedElement(next);
|
|
1887
|
}else if (isStartingElement(next, REFERENCES)) {
|
|
1888
|
//TODO
|
|
1889
|
handleNotYetImplementedElement(next);
|
|
1890
|
} else if (isStartingElement(next, GATHERING)) {
|
|
1891
|
//TODO
|
|
1892
|
handleNotYetImplementedElement(next);
|
|
1893
|
} else if (isStartingElement(next, ANNOTATION)) {
|
|
1894
|
//TODO //TODO test handleSimpleAnnotation
|
|
1895
|
handleNotYetImplementedElement(next);
|
|
1896
|
} else if (isStartingElement(next, HABITAT)) {
|
|
1897
|
//TODO
|
|
1898
|
handleNotYetImplementedElement(next);
|
|
1899
|
} else if (isStartingElement(next, FIGURE_REF)) {
|
|
1900
|
//TODO
|
|
1901
|
handleNotYetImplementedElement(next);
|
|
1902
|
} else if (isStartingElement(next, FIGURE)) {
|
|
1903
|
//TODO
|
|
1904
|
handleNotYetImplementedElement(next);
|
|
1905
|
} else if (isStartingElement(next, FOOTNOTE_REF)) {
|
|
1906
|
//TODO
|
|
1907
|
handleNotYetImplementedElement(next);
|
|
1908
|
} else if (isStartingElement(next, FOOTNOTE)) {
|
|
1909
|
//TODO
|
|
1910
|
handleNotYetImplementedElement(next);
|
|
1911
|
} else if (isStartingElement(next, WRITER)) {
|
|
1912
|
//TODO
|
|
1913
|
handleNotYetImplementedElement(next);
|
|
1914
|
} else if (isStartingElement(next, DATES)) {
|
|
1915
|
//TODO
|
|
1916
|
handleNotYetImplementedElement(next);
|
|
1917
|
} else {
|
|
1918
|
handleUnexpectedElement(next);
|
|
1919
|
}
|
|
1920
|
}
|
|
1921
|
throw new IllegalStateException("<String> has no closing tag");
|
|
1922
|
}
|
|
1923
|
|
|
1924
|
|
|
1925
|
/**
|
|
1926
|
* @param subHeadingMap
|
|
1927
|
* @param currentSubheading
|
|
1928
|
* @param text
|
|
1929
|
* @return
|
|
1930
|
*/
|
|
1931
|
private String putCurrentSubheading(Map<String, String> subHeadingMap, String currentSubheading, String text) {
|
|
1932
|
if (StringUtils.isNotBlank(text)) {
|
|
1933
|
text = removeStartingMinus(text);
|
|
1934
|
subHeadingMap.put(currentSubheading, text.trim());
|
|
1935
|
}
|
|
1936
|
return "";
|
|
1937
|
}
|
|
1938
|
|
|
1939
|
private String removeStartingMinus(String string) {
|
|
1940
|
string = replaceStart(string, "-");
|
|
1941
|
string = replaceStart(string, "\u002d");
|
|
1942
|
string = replaceStart(string, "\u2013");
|
|
1943
|
string = replaceStart(string, "\u2014");
|
|
1944
|
string = replaceStart(string, "--");
|
|
1945
|
return string;
|
|
1946
|
}
|
|
1947
|
|
|
1948
|
|
|
1949
|
/**
|
|
1950
|
* @param value
|
|
1951
|
* @param replacementString
|
|
1952
|
*/
|
|
1953
|
private String replaceStart(String value, String replacementString) {
|
|
1954
|
if (value.startsWith(replacementString) ){
|
|
1955
|
value = value.substring(replacementString.length()).trim();
|
|
1956
|
}
|
|
1957
|
while (value.startsWith("-") || value.startsWith("\u2014") ){
|
|
1958
|
value = value.substring("-".length()).trim();
|
|
1959
|
}
|
|
1960
|
return value;
|
|
1961
|
}
|
|
1962
|
|
|
1963
|
|
|
1964
|
private String handleDistributionLocality(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {
|
|
1965
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
1966
|
String classValue = getAndRemoveRequiredAttributeValue(parentEvent, attributes, CLASS);
|
|
1967
|
String statusValue =getAndRemoveAttributeValue(attributes, STATUS);
|
|
1968
|
String frequencyValue =getAndRemoveAttributeValue(attributes, FREQUENCY);
|
|
1969
|
|
|
1970
|
|
|
1971
|
Taxon taxon = state.getCurrentTaxon();
|
|
1972
|
// TODO which ref to take?
|
|
1973
|
Reference<?> ref = state.getConfig().getSourceReference();
|
|
1974
|
|
|
1975
|
String text = "";
|
|
1976
|
while (reader.hasNext()) {
|
|
1977
|
XMLEvent next = readNoWhitespace(reader);
|
|
1978
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1979
|
if (StringUtils.isNotBlank(text)) {
|
|
1980
|
String label = CdmUtils.removeTrailingDot(normalize(text));
|
|
1981
|
TaxonDescription description = getTaxonDescription(taxon, ref, false, true);
|
|
1982
|
NamedAreaLevel level = makeNamedAreaLevel(state,classValue, next);
|
|
1983
|
|
|
1984
|
//status
|
|
1985
|
PresenceAbsenceTerm status = null;
|
|
1986
|
if (isNotBlank(statusValue)){
|
|
1987
|
try {
|
|
1988
|
status = state.getTransformer().getPresenceTermByKey(statusValue);
|
|
1989
|
if (status == null){
|
|
1990
|
//TODO
|
|
1991
|
String message = "The presence/absence status '%s' could not be transformed to an CDM status";
|
|
1992
|
fireWarningEvent(String.format(message, statusValue), next, 4);
|
|
1993
|
}
|
|
1994
|
} catch (UndefinedTransformerMethodException e) {
|
|
1995
|
throw new RuntimeException(e);
|
|
1996
|
}
|
|
1997
|
}else{
|
|
1998
|
status = PresenceAbsenceTerm.PRESENT();
|
|
1999
|
}
|
|
2000
|
//frequency
|
|
2001
|
if (isNotBlank(frequencyValue)){
|
|
2002
|
String message = "The frequency attribute is currently not yet available in CDM";
|
|
2003
|
fireWarningEvent(message, parentEvent, 6);
|
|
2004
|
}
|
|
2005
|
|
|
2006
|
NamedArea higherArea = null;
|
|
2007
|
List<NamedArea> areas = new ArrayList<NamedArea>();
|
|
2008
|
|
|
2009
|
String patSingleArea = "([^,\\(]{3,})";
|
|
2010
|
String patSeparator = "(,|\\sand\\s)";
|
|
2011
|
String hierarchiePattern = String.format("%s\\((%s(%s%s)*)\\)",patSingleArea, patSingleArea, patSeparator, patSingleArea);
|
|
2012
|
Pattern patHierarchie = Pattern.compile(hierarchiePattern, Pattern.CASE_INSENSITIVE);
|
|
2013
|
Matcher matcher = patHierarchie.matcher(label);
|
|
2014
|
if (matcher.matches()){
|
|
2015
|
String higherAreaStr = matcher.group(1).trim();
|
|
2016
|
higherArea = makeArea(state, higherAreaStr, level);
|
|
2017
|
String[] innerAreas = matcher.group(2).split(patSeparator);
|
|
2018
|
for (String innerArea : innerAreas){
|
|
2019
|
if (isNotBlank(innerArea)){
|
|
2020
|
NamedArea singleArea = makeArea(state, innerArea.trim(), level);
|
|
2021
|
areas.add(singleArea);
|
|
2022
|
NamedArea partOf = singleArea.getPartOf();
|
|
2023
|
// if (partOf == null){
|
|
2024
|
// singleArea.setPartOf(higherArea);
|
|
2025
|
// }
|
|
2026
|
}
|
|
2027
|
}
|
|
2028
|
}else{
|
|
2029
|
NamedArea singleArea = makeArea(state, label, level);
|
|
2030
|
areas.add(singleArea);
|
|
2031
|
}
|
|
2032
|
|
|
2033
|
for (NamedArea area : areas){
|
|
2034
|
//create distribution
|
|
2035
|
Distribution distribution = Distribution.NewInstance(area,status);
|
|
2036
|
description.addElement(distribution);
|
|
2037
|
}
|
|
2038
|
} else {
|
|
2039
|
String message = "Empty distribution locality";
|
|
2040
|
fireWarningEvent(message, next, 4);
|
|
2041
|
}
|
|
2042
|
return text;
|
|
2043
|
} else if (isStartingElement(next, COORDINATES)) {
|
|
2044
|
//TODO
|
|
2045
|
handleNotYetImplementedElement(next);
|
|
2046
|
} else if (isEndingElement(next, COORDINATES)) {
|
|
2047
|
//TODO
|
|
2048
|
popUnimplemented(next.asEndElement());
|
|
2049
|
} else if (next.isCharacters()) {
|
|
2050
|
text += next.asCharacters().getData();
|
|
2051
|
} else {
|
|
2052
|
handleUnexpectedElement(next);
|
|
2053
|
}
|
|
2054
|
}
|
|
2055
|
throw new IllegalStateException("<DistributionLocality> has no closing tag");
|
|
2056
|
}
|
|
2057
|
|
|
2058
|
|
|
2059
|
//********************************************** OLD *************************************
|
|
2060
|
|
|
2061
|
// protected boolean testAdditionalElements(Element parentElement, List<String> excludeList){
|
|
2062
|
// boolean result = true;
|
|
2063
|
// List<Element> list = parentElement.getChildren();
|
|
2064
|
// for (Element element : list){
|
|
2065
|
// if (! excludeList.contains(element.getName())){
|
|
2066
|
// logger.warn("Unknown element (" + element.getName() + ") in parent element (" + parentElement.getName() + ")");
|
|
2067
|
// result = false;
|
|
2068
|
// }
|
|
2069
|
// }
|
|
2070
|
// return result;
|
|
2071
|
// }
|
|
2072
|
//
|
|
2073
|
//
|
|
2074
|
// protected <T extends IdentifiableEntity> T makeReferenceType(Element element, Class<? extends T> clazz, MapWrapper<? extends T> objectMap, ResultWrapper<Boolean> success){
|
|
2075
|
// T result = null;
|
|
2076
|
// String linkType = element.getAttributeValue("linkType");
|
|
2077
|
// String ref = element.getAttributeValue("ref");
|
|
2078
|
// if(ref == null && linkType == null){
|
|
2079
|
// result = getInstance(clazz);
|
|
2080
|
// if (result != null){
|
|
2081
|
// String title = element.getTextNormalize();
|
|
2082
|
// result.setTitleCache(title, true);
|
|
2083
|
// }
|
|
2084
|
// }else if (linkType == null || linkType.equals("local")){
|
|
2085
|
// //TODO
|
|
2086
|
// result = objectMap.get(ref);
|
|
2087
|
// if (result == null){
|
|
2088
|
// logger.warn("Object (ref = " + ref + ")could not be found in WrapperMap");
|
|
2089
|
// }
|
|
2090
|
// }else if(linkType.equals("external")){
|
|
2091
|
// logger.warn("External link types not yet implemented");
|
|
2092
|
// }else if(linkType.equals("other")){
|
|
2093
|
// logger.warn("Other link types not yet implemented");
|
|
2094
|
// }else{
|
|
2095
|
// logger.warn("Unknown link type or missing ref");
|
|
2096
|
// }
|
|
2097
|
// if (result == null){
|
|
2098
|
// success.setValue(false);
|
|
2099
|
// }
|
|
2100
|
// return result;
|
|
2101
|
// }
|
|
2102
|
//
|
|
2103
|
//
|
|
2104
|
// protected Reference makeAccordingTo(Element elAccordingTo, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){
|
|
2105
|
// Reference result = null;
|
|
2106
|
// if (elAccordingTo != null){
|
|
2107
|
// String childName = "AccordingToDetailed";
|
|
2108
|
// boolean obligatory = false;
|
|
2109
|
// Element elAccordingToDetailed = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
|
|
2110
|
//
|
|
2111
|
// childName = "Simple";
|
|
2112
|
// obligatory = true;
|
|
2113
|
// Element elSimple = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
|
|
2114
|
//
|
|
2115
|
// if (elAccordingToDetailed != null){
|
|
2116
|
// result = makeAccordingToDetailed(elAccordingToDetailed, referenceMap, success);
|
|
2117
|
// }else{
|
|
2118
|
// result = ReferenceFactory.newGeneric();
|
|
2119
|
// String title = elSimple.getTextNormalize();
|
|
2120
|
// result.setTitleCache(title, true);
|
|
2121
|
// }
|
|
2122
|
// }
|
|
2123
|
// return result;
|
|
2124
|
// }
|
|
2125
|
//
|
|
2126
|
//
|
|
2127
|
// private Reference makeAccordingToDetailed(Element elAccordingToDetailed, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){
|
|
2128
|
// Reference result = null;
|
|
2129
|
// Namespace tcsNamespace = elAccordingToDetailed.getNamespace();
|
|
2130
|
// if (elAccordingToDetailed != null){
|
|
2131
|
// //AuthorTeam
|
|
2132
|
// String childName = "AuthorTeam";
|
|
2133
|
// boolean obligatory = false;
|
|
2134
|
// Element elAuthorTeam = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
|
|
2135
|
// makeAccordingToAuthorTeam(elAuthorTeam, success);
|
|
2136
|
//
|
|
2137
|
// //PublishedIn
|
|
2138
|
// childName = "PublishedIn";
|
|
2139
|
// obligatory = false;
|
|
2140
|
// Element elPublishedIn = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
|
|
2141
|
// result = makeReferenceType(elPublishedIn, Reference.class, referenceMap, success);
|
|
2142
|
//
|
|
2143
|
// //MicroReference
|
|
2144
|
// childName = "MicroReference";
|
|
2145
|
// obligatory = false;
|
|
2146
|
// Element elMicroReference = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
|
|
2147
|
// String microReference = elMicroReference.getTextNormalize();
|
|
2148
|
// if (CdmUtils.Nz(microReference).equals("")){
|
|
2149
|
// //TODO
|
|
2150
|
// logger.warn("MicroReference not yet implemented for AccordingToDetailed");
|
|
2151
|
// }
|
|
2152
|
// }
|
|
2153
|
// return result;
|
|
2154
|
// }
|
|
2155
|
//
|
|
2156
|
// private Team makeAccordingToAuthorTeam(Element elAuthorTeam, ResultWrapper<Boolean> succes){
|
|
2157
|
// Team result = null;
|
|
2158
|
// if (elAuthorTeam != null){
|
|
2159
|
// //TODO
|
|
2160
|
// logger.warn("AuthorTeam not yet implemented for AccordingToDetailed");
|
|
2161
|
// }
|
|
2162
|
// return result;
|
|
2163
|
// }
|
|
2164
|
|
|
2165
|
|
|
2166
|
|
|
2167
|
}
|