Revision 484431ef
Added by Katja Luther over 12 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupDocumentImport.java | ||
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/** |
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* Copyright (C) 2009 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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* Copyright (C) 2009 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.net.URL; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.HashMap; |
| 14 | 17 |
import java.util.HashSet; |
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import java.util.LinkedList; |
| ... | ... | |
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import java.util.regex.Pattern; |
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|
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import javax.xml.stream.FactoryConfigurationError; |
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import javax.xml.stream.Location; |
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import javax.xml.stream.XMLEventReader; |
| 26 | 30 |
import javax.xml.stream.XMLStreamException; |
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import javax.xml.stream.events.Attribute; |
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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.CharUtils; |
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import org.apache.commons.lang.StringUtils; |
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import org.apache.log4j.Logger; |
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import org.jdom.Attribute; |
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import org.jdom.Element; |
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import org.springframework.beans.factory.annotation.Autowired; |
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import org.springframework.security.access.PermissionEvaluator; |
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import org.springframework.security.authentication.AuthenticationManager; |
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import org.springframework.security.core.Authentication; |
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import org.springframework.stereotype.Component; |
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import org.springframework.transaction.TransactionStatus; |
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType; |
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeCacheStrategy; |
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import eu.etaxonomy.cdm.common.CdmUtils; |
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import eu.etaxonomy.cdm.common.ResultWrapper;
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import eu.etaxonomy.cdm.common.XmlHelp;
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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.ICdmIO; |
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
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import eu.etaxonomy.cdm.io.markup.UnmatchedLeads.UnmatchedLeadsKey; |
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import eu.etaxonomy.cdm.model.agent.Person; |
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import eu.etaxonomy.cdm.model.agent.AgentBase; |
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import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor; |
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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.Credit;
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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.ISourceable; |
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.Marker; |
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import eu.etaxonomy.cdm.model.common.MarkerType; |
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import eu.etaxonomy.cdm.model.common.TermVocabulary; |
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import eu.etaxonomy.cdm.model.common.TimePeriod; |
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import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
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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.KeyStatement; |
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import eu.etaxonomy.cdm.model.description.PolytomousKey; |
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import eu.etaxonomy.cdm.model.description.PolytomousKeyNode; |
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase; |
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import eu.etaxonomy.cdm.model.description.PresenceTerm; |
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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.name.BotanicalName; |
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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.CultivarPlantName; |
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup; |
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import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation; |
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
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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.name.SpecimenTypeDesignation; |
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
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import eu.etaxonomy.cdm.model.occurrence.Collection; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase; |
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import eu.etaxonomy.cdm.model.occurrence.FieldObservation; |
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import eu.etaxonomy.cdm.model.occurrence.Specimen; |
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import eu.etaxonomy.cdm.model.reference.IBook;
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import eu.etaxonomy.cdm.model.reference.IArticle;
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import eu.etaxonomy.cdm.model.reference.IJournal; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| ... | ... | |
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import eu.etaxonomy.cdm.model.taxon.Classification; |
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
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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.model.taxon.TaxonNode; |
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
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import eu.etaxonomy.cdm.strategy.parser.NameTypeParser; |
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
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import eu.etaxonomy.cdm.strategy.parser.SpecimenTypeParser; |
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import eu.etaxonomy.cdm.strategy.parser.SpecimenTypeParser.TypeInfo; |
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/** |
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* @author a.mueller |
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* |
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*
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*/ |
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@Component |
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public class MarkupDocumentImport extends MarkupImportBase implements ICdmIO<MarkupImportState> {
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private static final Logger logger = Logger.getLogger(MarkupDocumentImport.class); |
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private static int modCount = 30000; |
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private static final boolean CREATE_NEW = true; |
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private static final boolean IS_IMAGE_GALLERY = true; |
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private static final boolean NO_IMAGE_GALLERY = false; |
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private static final String ACCEPTED = "accepted"; |
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private static final String ACCEPTED_NAME = "acceptedName"; |
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private static final String ADDENDA = "addenda"; |
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private static final String ALTERNATEPUBTITLE = "alternatepubtitle"; |
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private static final String ALTERNATIVE_COLLECTION_TYPE_STATUS = "alternativeCollectionTypeStatus"; |
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private static final String ALTERNATIVE_COLLECTOR = "alternativeCollector"; |
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private static final String ALTERNATIVE_FIELD_NUM = "alternativeFieldNum"; |
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private static final String ALTITUDE = "altitude"; |
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private static final String ANNOTATION = "annotation"; |
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private static final String AUTHOR = "author"; |
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private static final String BIBLIOGRAPHY = "bibliography"; |
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private static final String BIOGRAPHIES = "biographies"; |
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private static final String BOLD = "bold"; |
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private static final String BR = "br"; |
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private static final String CHAR = "char"; |
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private static final String CITATION = "citation"; |
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private static final String COLLECTION_TYPE_STATUS = "collectionTypeStatus"; |
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private static final String COLLECTOR = "collector"; |
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private static final String COORDINATES = "coordinates"; |
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private static final String COUPLET = "couplet"; |
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private static final String DATES = "dates"; |
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private static final String DEDICATION = "dedication"; |
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private static final String DEFAULT_MEDIA_URL = "defaultMediaUrl"; |
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private static final String DESTROYED = "destroyed"; |
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private static final String DETAILS = "details"; |
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private static final String DISTRIBUTION_LIST = "distributionList"; |
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private static final String DISTRIBUTION_LOCALITY = "distributionLocality"; |
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private static final String EDITION = "edition"; |
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private static final String EDITORS = "editors"; |
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private static final String FEATURE = "feature"; |
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private static final String FIGURE = "figure"; |
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private static final String FIGURE_LEGEND = "figureLegend"; |
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private static final String FIGURE_PART = "figurePart"; |
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private static final String FIGURE_REF = "figureRef"; |
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private static final String FIGURE_TITLE = "figureTitle"; |
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private static final String FOOTNOTE = "footnote"; |
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private static final String FOOTNOTE_REF = "footnoteRef"; |
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private static final String FOOTNOTE_STRING = "footnoteString"; |
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private static final String FIELD_NUM = "fieldNum"; |
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private static final String FREQUENCY = "frequency"; |
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private static final String FULL_NAME = "fullName"; |
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private static final String FULL_TYPE = "fullType"; |
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private static final String GATHERING = "gathering"; |
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private static final String HEADING = "heading"; |
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private static final String HABITAT = "habitat"; |
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private static final String HABITAT_LIST = "habitatList"; |
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private static final String HOMONYM = "homonym"; |
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private static final String HOMOTYPES = "homotypes"; |
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private static final String ID = "id"; |
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private static final String INFRANK = "infrank"; |
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private static final String INFRAUT = "infraut"; |
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private static final String INFRPARAUT = "infrparaut"; |
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private static final String IS_SPOTCHARACTERS = "isSpotcharacters"; |
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private static final String ISSUE = "issue"; |
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private static final String ITALICS = "italics"; |
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private static final String KEY = "key"; |
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private static final String KEY_TITLE = "keyTitle"; |
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private static final String KEYNOTES = "keynotes"; |
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private static final String LIFE_CYCLE_PERIODS = "lifeCyclePeriods"; |
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private static final String LOCALITY = "locality"; |
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private static final String LOST = "lost"; |
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private static final String META_DATA = "metaData"; |
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private static final String NAME = "name"; |
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private static final String NAME_TYPE = "nameType"; |
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private static final String NOM = "nom"; |
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private static final String NOMENCLATURE = "nomenclature"; |
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private static final String NOT_FOUND = "notFound"; |
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private static final String NOT_SEEN = "notSeen"; |
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private static final String NOTES = "notes"; |
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private static final String NUM = "num"; |
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private static final String ORIGINAL_DETERMINATION = "originalDetermination"; |
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private static final String PARAUT = "paraut"; |
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private static final String PUBFULLNAME = "pubfullname"; |
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private static final String PUBLICATION = "publication"; |
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private static final String PUBNAME = "pubname"; |
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private static final String PUBTITLE = "pubtitle"; |
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private static final String PUBTYPE = "pubtype"; |
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private static final String QUESTION = "question"; |
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private static final String QUOTE = "quote"; |
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private static final String RANK = "rank"; |
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private static final String REF = "ref"; |
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private static final String REF_NUM = "refNum"; |
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private static final String REF_PART = "refPart"; |
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private static final String REFERENCE = "reference"; |
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private static final String REFERENCES = "references"; |
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private static final String TAXON = "taxon"; |
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private static final String TAXONTITLE = "taxontitle"; |
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private static final String TAXONTYPE = "taxontype"; |
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private static final String TEXT = "text"; |
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private static final String TEXT_SECTION = "textSection"; |
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private static final String TO_COUPLET = "toCouplet"; |
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private static final String TO_KEY = "toKey"; |
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private static final String TO_TAXON = "toTaxon"; |
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private static final String TYPE = "type"; |
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private static final String TYPE_STATUS = "typeStatus"; |
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private static final String TREATMENT = "treatment"; |
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private static final String SERIALS_ABBREVIATIONS = "serialsAbbreviations"; |
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private static final String SPECIMEN_TYPE = "specimenType"; |
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private static final String STATUS = "status"; |
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private static final String STRING = "string"; |
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private static final String SUB_HEADING = "subHeading"; |
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private static final String SUB_COLLECTION = "subCollection"; |
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private static final String SYNONYM = "synonym"; |
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private static final String UNKNOWN = "unknown"; |
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private static final String URL = "url"; |
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private static final String USAGE = "usage"; |
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private static final String VOLUME = "volume"; |
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private static final String WRITER = "writer"; |
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private static final String YEAR = "year"; |
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private NonViralNameParserImpl parser = new NonViralNameParserImpl(); |
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//TODO make part of state, but state is renewed when invoking the import a second time |
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// TODO make part of state, but state is renewed when invoking the import a |
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// second time |
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private UnmatchedLeads unmatchedLeads; |
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@Autowired |
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private IEditGeoService editGeoService; |
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public MarkupDocumentImport(){
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// TODO remove preliminary |
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@Autowired |
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private AuthenticationManager authenticationManager; |
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private Authentication authentication; |
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private PermissionEvaluator permissionEvaluator; |
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public MarkupDocumentImport() {
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super(); |
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System.out.println("TODO remove preliminary authentication");
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// UsernamePasswordAuthenticationToken token = new |
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// UsernamePasswordAuthenticationToken("admin", "0000");
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// authentication = authenticationManager.authenticate(token); |
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// SecurityContext context = SecurityContextHolder.getContext(); |
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// context.setAuthentication(authentication); |
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// permissionEvaluator = new CdmPermissionEvaluator(); |
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} |
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@Override |
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public boolean doCheck(MarkupImportState state){
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public boolean doCheck(MarkupImportState state) {
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state.setCheck(true); |
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boolean result = doInvoke(state);
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doInvoke(state); |
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state.setCheck(false); |
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return result;
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return state.isSuccess();
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} |
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@Override |
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public boolean doInvoke(MarkupImportState state){
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public void doInvoke(MarkupImportState state) {
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fireProgressEvent("Start import markup document", "Before start of document");
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fireWarningEvent("Test a warning", "At start", 17);
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boolean success = false; |
|
| 123 | 270 |
|
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Queue<CdmBase> outputStream = new LinkedList<CdmBase>(); |
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//FIXME reset state |
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|
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TransactionStatus tx = startTransaction(); |
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// FIXME reset state |
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doAllTheOldOtherStuff(state); |
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//START |
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// START
|
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try {
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//StAX |
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XMLEventReader reader = getStaxReader(state);
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// StAX
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XMLEventReader reader = getStaxReader(state); |
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state.setReader(reader); |
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//start document |
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if (! validateStartOfDocument(reader)){
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return false; |
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// start document |
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if (!validateStartOfDocument(reader)) {
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state.setUnsuccessfull(); |
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return; |
|
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} |
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|
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// publication |
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String elName = PUBLICATION; |
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boolean hasPublication = false; |
|
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|
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//publication |
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String elName = "publication"; |
|
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while (reader.hasNext()) {
|
| 142 |
if (isStartingElement(reader, elName)){
|
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success &= handlePublication(reader, elName); |
|
| 144 |
}else{
|
|
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XMLEvent nextEvent = reader.nextEvent(); |
|
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if (isStartingElement(nextEvent, elName)) {
|
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handlePublication(state, reader, nextEvent, elName); |
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hasPublication = true; |
|
| 297 |
} else if (nextEvent.isEndDocument()) {
|
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if (!hasPublication) {
|
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String message = "No publication root element found"; |
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fireWarningEvent(message, nextEvent, 8); |
|
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} |
|
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// done |
|
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} else {
|
|
| 145 | 304 |
fireSchemaConflictEventExpectedStartTag(elName, reader); |
| 146 | 305 |
} |
| 147 | 306 |
} |
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|
|
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// //SAX |
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// ImportHandlerBase handler= new PublicationHandler(this); |
|
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// parseSAX(state, handler); |
|
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|
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| 307 |
commitTransaction(tx); |
|
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|
|
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// //SAX |
|
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// ImportHandlerBase handler= new PublicationHandler(this); |
|
| 311 |
// parseSAX(state, handler); |
|
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|
|
| 153 | 313 |
} catch (FactoryConfigurationError e1) {
|
| 154 |
// TODO Auto-generated catch block |
|
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fireWarningEvent("Some error occurred while setting up xml factory. Data can't be imported", "Start", 16);
|
| 156 |
success = false;
|
|
| 315 |
state.setUnsuccessfull();
|
|
| 157 | 316 |
} catch (XMLStreamException e1) {
|
| 158 |
// TODO Auto-generated catch block |
|
| 159 | 317 |
fireWarningEvent("An XMLStreamException occurred while parsing. Data can't be imported", "Start", 16);
|
| 160 |
success = false; |
|
| 161 |
// } catch (ParserConfigurationException e) {
|
|
| 162 |
// fireWarningEvent("A ParserConfigurationException occurred while parsing. Data can't be imported", "Start", 16);
|
|
| 163 |
// } catch (SAXException e) {
|
|
| 164 |
// fireWarningEvent("A SAXException occurred while parsing. Data can't be imported", "Start", 16);
|
|
| 165 |
// } catch (IOException e) {
|
|
| 166 |
// fireWarningEvent("An IO exception occurred while parsing. Data can't be imported", "Start", 16);
|
|
| 318 |
state.setUnsuccessfull(); |
|
| 319 |
// } catch (ParserConfigurationException e) {
|
|
| 320 |
// fireWarningEvent("A ParserConfigurationException occurred while parsing. Data can't be imported",
|
|
| 321 |
// "Start", 16); |
|
| 322 |
// } catch (SAXException e) {
|
|
| 323 |
// fireWarningEvent("A SAXException occurred while parsing. Data can't be imported",
|
|
| 324 |
// "Start", 16); |
|
| 325 |
// } catch (IOException e) {
|
|
| 326 |
// fireWarningEvent("An IO exception occurred while parsing. Data can't be imported",
|
|
| 327 |
// "Start", 16); |
|
| 167 | 328 |
|
| 168 | 329 |
} |
| 169 | 330 |
|
| 170 |
|
|
| 171 |
return success; |
|
| 172 |
|
|
| 173 |
} |
|
| 174 |
|
|
| 175 |
|
|
| 176 |
private boolean handlePublication(XMLEventReader reader, String elName) throws XMLStreamException {
|
|
| 177 |
boolean success = true; |
|
| 178 |
XMLEvent event = reader.nextEvent(); |
|
| 179 |
if (isEndingElement(event, elName)){
|
|
| 180 |
//TODO cardinality of alternative |
|
| 181 |
return success; |
|
| 182 |
}else if(isStartingElement(event, "metaData")){
|
|
| 183 |
|
|
| 184 |
}else if(isStartingElement(event, "treatment")){
|
|
| 185 |
|
|
| 186 |
}else if(isStartingElement(event, "biographies")){
|
|
| 187 |
|
|
| 188 |
}else if(isStartingElement(event, "references")){
|
|
| 189 |
|
|
| 190 |
}else if(isStartingElement(event, "metaData")){
|
|
| 191 |
|
|
| 192 |
}else if(isStartingElement(event, "metaData")){
|
|
| 193 |
|
|
| 194 |
}else if(isStartingElement(event, "metaData")){
|
|
| 195 |
|
|
| 196 |
} |
|
| 197 |
return success; |
|
| 198 |
} |
|
| 199 |
|
|
| 331 |
return; |
|
| 200 | 332 |
|
| 201 |
|
|
| 202 |
/** |
|
| 203 |
* This comes from the old version, needs to be checked on need |
|
| 204 |
* @param state |
|
| 205 |
*/ |
|
| 206 |
private void doAllTheOldOtherStuff(MarkupImportState state) {
|
|
| 207 |
state.putTree(null, null); |
|
| 208 |
if (unmatchedLeads == null){
|
|
| 209 |
unmatchedLeads = UnmatchedLeads.NewInstance(); |
|
| 210 |
} |
|
| 211 |
state.setUnmatchedLeads(unmatchedLeads); |
|
| 212 |
|
|
| 213 |
// TransactionStatus tx = startTransaction(); |
|
| 214 |
unmatchedLeads.saveToSession(getPolytomousKeyNodeService()); |
|
| 215 |
|
|
| 216 |
|
|
| 217 |
//TODO generally do not store the reference object in the config |
|
| 218 |
Reference sourceReference = state.getConfig().getSourceReference(); |
|
| 219 |
getReferenceService().saveOrUpdate(sourceReference); |
|
| 220 | 333 |
} |
| 221 | 334 |
|
| 335 |
private void handlePublication(MarkupImportState state, |
|
| 336 |
XMLEventReader reader, XMLEvent currentEvent, String elName) |
|
| 337 |
throws XMLStreamException {
|
|
| 222 | 338 |
|
| 223 |
private boolean doInvoke_old(MarkupImportState state){
|
|
| 224 |
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>(); |
|
| 225 |
ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true); |
|
| 226 |
|
|
| 227 |
// Element elbody= getBodyElement(state.getConfig()); |
|
| 228 |
Element elbody = null; |
|
| 229 |
List<Element> elTaxonList = elbody.getChildren(); |
|
| 230 |
|
|
| 231 |
int i = 0; |
|
| 232 |
|
|
| 233 |
Set<String> unhandledTitleClassess = new HashSet<String>(); |
|
| 234 |
Set<String> unhandledNomeclatureChildren = new HashSet<String>(); |
|
| 235 |
Set<String> unhandledDescriptionChildren = new HashSet<String>(); |
|
| 236 |
|
|
| 237 |
Taxon lastTaxon = getLastTaxon(state); |
|
| 238 |
|
|
| 239 |
//for each taxon |
|
| 240 |
for (Element elTaxon : elTaxonList){
|
|
| 339 |
// attributes |
|
| 340 |
StartElement element = currentEvent.asStartElement(); |
|
| 341 |
Map<String, Attribute> attributes = getAttributes(element); |
|
| 342 |
handleUnexpectedAttributes(element.getLocation(), attributes, |
|
| 343 |
"noNamespaceSchemaLocation"); |
|
| 344 |
|
|
| 345 |
while (reader.hasNext()) {
|
|
| 346 |
XMLEvent event = readNoWhitespace(reader); |
|
| 347 |
// TODO cardinality of alternative |
|
| 348 |
if (event.isEndElement()) {
|
|
| 349 |
if (isEndingElement(event, elName)) {
|
|
| 350 |
return; |
|
| 351 |
} else {
|
|
| 352 |
if (isEndingElement(event, BIOGRAPHIES)) {
|
|
| 353 |
// NOT YET IMPLEMENTED |
|
| 354 |
popUnimplemented(event.asEndElement()); |
|
| 355 |
} else if (isEndingElement(event, REFERENCES)) {
|
|
| 356 |
// NOT YET IMPLEMENTED |
|
| 357 |
popUnimplemented(event.asEndElement()); |
|
| 358 |
} else if (isEndingElement(event, TEXT_SECTION)) {
|
|
| 359 |
// NOT YET IMPLEMENTED |
|
| 360 |
popUnimplemented(event.asEndElement()); |
|
| 361 |
} else if (isEndingElement(event, ADDENDA)) {
|
|
| 362 |
// NOT YET IMPLEMENTED |
|
| 363 |
popUnimplemented(event.asEndElement()); |
|
| 364 |
} else {
|
|
| 365 |
handleUnexpectedElement(event); |
|
| 366 |
} |
|
| 367 |
} |
|
| 368 |
} else if (event.isStartElement()) {
|
|
| 369 |
if (isStartingElement(event, META_DATA)) {
|
|
| 370 |
handleMetaData(state, reader, event); |
|
| 371 |
} else if (isStartingElement(event, TREATMENT)) {
|
|
| 372 |
handleTreatment(state, reader, event); |
|
| 373 |
} else if (isStartingElement(event, BIOGRAPHIES)) {
|
|
| 374 |
handleNotYetImplementedElement(event); |
|
| 375 |
} else if (isStartingElement(event, REFERENCES)) {
|
|
| 376 |
handleNotYetImplementedElement(event); |
|
| 377 |
} else if (isStartingElement(event, TEXT_SECTION)) {
|
|
| 378 |
handleNotYetImplementedElement(event); |
|
| 379 |
} else if (isStartingElement(event, ADDENDA)) {
|
|
| 380 |
handleNotYetImplementedElement(event); |
|
| 381 |
} else {
|
|
| 382 |
handleUnexpectedStartElement(event); |
|
| 383 |
} |
|
| 384 |
} else {
|
|
| 385 |
handleUnexpectedElement(event); |
|
| 386 |
} |
|
| 387 |
} |
|
| 388 |
throw new IllegalStateException("Publication has no ending element");
|
|
| 389 |
} |
|
| 390 |
|
|
| 391 |
private void handleMetaData(MarkupImportState state, XMLEventReader reader, |
|
| 392 |
XMLEvent parentEvent) throws XMLStreamException {
|
|
| 393 |
checkNoAttributes(parentEvent); |
|
| 394 |
|
|
| 395 |
while (reader.hasNext()) {
|
|
| 396 |
XMLEvent next = readNoWhitespace(reader); |
|
| 397 |
if (isMyEndingElement(next, parentEvent)) {
|
|
| 398 |
return; |
|
| 399 |
} else if (isStartingElement(next, DEFAULT_MEDIA_URL)) {
|
|
| 400 |
String baseUrl = getCData(state, reader, next); |
|
| 241 | 401 |
try {
|
| 242 |
if ((i++ % modCount) == 0 && i > 1){ logger.info("Taxa handled: " + (i-1));}
|
|
| 243 |
if (! elTaxon.getName().equalsIgnoreCase("taxon")){
|
|
| 244 |
logger.warn("body has element other than 'taxon'");
|
|
| 402 |
new URL(baseUrl); |
|
| 403 |
state.setBaseMediaUrl(baseUrl); |
|
| 404 |
} catch (MalformedURLException e) {
|
|
| 405 |
String message = "defaultMediaUrl '%s' is not a valid URL"; |
|
| 406 |
message = String.format(message, baseUrl); |
|
| 407 |
fireWarningEvent(message, next, 8); |
|
| 245 | 408 |
} |
| 246 |
|
|
| 247 |
BotanicalName botanicalName = BotanicalName.NewInstance(Rank.SPECIES()); |
|
| 248 |
Taxon taxon = Taxon.NewInstance(botanicalName, state.getConfig().getSourceReference()); |
|
| 249 |
|
|
| 250 |
handleTaxonAttributes(elTaxon, taxon, state); |
|
| 251 |
|
|
| 252 |
|
|
| 253 |
List<Element> children = elTaxon.getChildren(); |
|
| 254 |
handleTaxonElement(state, unhandledTitleClassess, unhandledNomeclatureChildren, unhandledDescriptionChildren, taxon, children); |
|
| 255 |
handleTaxonRelation(state, taxon, lastTaxon); |
|
| 256 |
lastTaxon = taxon; |
|
| 257 |
taxaToSave.add(taxon); |
|
| 258 |
state.getConfig().setLastTaxonUuid(lastTaxon.getUuid()); |
|
| 259 |
|
|
| 260 |
} catch (Exception e) {
|
|
| 261 |
logger.warn("Exception occurred in Sapindacea taxon import: " + e);
|
|
| 262 |
e.printStackTrace(); |
|
| 409 |
} else {
|
|
| 410 |
handleUnexpectedElement(next); |
|
| 263 | 411 |
} |
| 264 |
|
|
| 265 | 412 |
} |
| 266 |
|
|
| 267 |
System.out.println(state.getUnmatchedLeads().toString()); |
|
| 268 |
logger.warn("There are taxa with attributes 'excluded' and 'dubious'");
|
|
| 269 |
|
|
| 270 |
logger.info("Children for nomenclature are: " + unhandledNomeclatureChildren);
|
|
| 271 |
logger.info("Children for description are: " + unhandledDescriptionChildren);
|
|
| 272 |
logger.info("Children for homotypes are: " + unhandledHomotypeChildren);
|
|
| 273 |
logger.info("Children for nom are: " + unhandledNomChildren);
|
|
| 274 |
|
|
| 275 |
|
|
| 276 |
//invokeRelations(source, cdmApp, deleteAll, taxonMap, referenceMap); |
|
| 277 |
logger.info(i + " taxa handled. Saving ..."); |
|
| 278 |
getTaxonService().saveOrUpdate(taxaToSave); |
|
| 279 |
getFeatureTreeService().saveOrUpdateFeatureNodesAll(state.getFeatureNodesToSave()); |
|
| 280 |
state.getFeatureNodesToSave().clear(); |
|
| 281 |
// commitTransaction(tx); |
|
| 282 |
|
|
| 283 |
logger.info("end makeTaxa ...");
|
|
| 284 |
logger.info("start makeKey ...");
|
|
| 285 |
// invokeDoKey(state); |
|
| 286 |
logger.info("end makeKey ...");
|
|
| 287 |
|
|
| 288 |
return success.getValue(); |
|
| 289 |
} |
|
| 290 |
|
|
| 291 |
|
|
| 413 |
throw new IllegalStateException("MetaData has no ending element");
|
|
| 292 | 414 |
|
| 415 |
} |
|
| 293 | 416 |
|
| 294 |
private void handleTaxonAttributes(Element elTaxon, Taxon taxon, MarkupImportState state) {
|
|
| 295 |
List<Attribute> attrList = elTaxon.getAttributes(); |
|
| 296 |
for (Attribute attr : attrList){
|
|
| 297 |
String attrName = attr.getName(); |
|
| 298 |
String attrValue = attr.getValue(); |
|
| 299 |
if ("class".equals(attrName)){
|
|
| 300 |
if (attrValue.equalsIgnoreCase("dubious") || attrValue.equalsIgnoreCase("DUBIOUS GENUS") || attrValue.equalsIgnoreCase("DOUBTFUL SPECIES") ){
|
|
| 301 |
taxon.setDoubtful(true); |
|
| 302 |
}else{
|
|
| 303 |
MarkerType markerType = getMarkerType(state, attrValue); |
|
| 304 |
if (markerType == null){
|
|
| 305 |
logger.warn("Class attribute value for taxon not yet supported: " + attrValue);
|
|
| 306 |
}else{
|
|
| 307 |
taxon.addMarker(Marker.NewInstance(markerType, true)); |
|
| 417 |
private void handleTreatment(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 418 |
checkNoAttributes(parentEvent); |
|
| 419 |
Taxon lastTaxon = null; |
|
| 420 |
while (reader.hasNext()) {
|
|
| 421 |
XMLEvent next = readNoWhitespace(reader); |
|
| 422 |
if (isStartingElement(next, TAXON)) {
|
|
| 423 |
Taxon thisTaxon = handleTaxon(state, reader, next.asStartElement()); |
|
| 424 |
doTaxonRelation(state, thisTaxon, lastTaxon, parentEvent.getLocation()); |
|
| 425 |
lastTaxon = thisTaxon; |
|
| 426 |
// TODO for imports spanning multiple documents ?? Still needed? |
|
| 427 |
state.getConfig().setLastTaxonUuid(lastTaxon.getUuid()); |
|
| 428 |
} else if (isMyEndingElement(next, parentEvent)) {
|
|
| 429 |
Set<PolytomousKeyNode> keyNodesToSave = state.getPolytomousKeyNodesToSave(); |
|
| 430 |
//better save the key then the nodes |
|
| 431 |
Set<PolytomousKey> keySet = new HashSet<PolytomousKey>(); |
|
| 432 |
for (PolytomousKeyNode node : keyNodesToSave){
|
|
| 433 |
PolytomousKey key = node.getKey(); |
|
| 434 |
keySet.add(key); |
|
| 308 | 435 |
} |
| 436 |
save(keySet, state); |
|
| 437 |
//unmatched key leads |
|
| 438 |
UnmatchedLeads unmatched = state.getUnmatchedLeads(); |
|
| 439 |
if (unmatched.size() > 0){
|
|
| 440 |
String message = "The following key leads are unmatched: %s"; |
|
| 441 |
message = String.format(message, state.getUnmatchedLeads().toString()); |
|
| 442 |
fireWarningEvent(message, next, 6); |
|
| 309 | 443 |
} |
| 310 |
}else if ("num".equals(attrName)){
|
|
| 311 |
logger.warn("num not yet supported");
|
|
| 312 |
}else{
|
|
| 313 |
logger.warn("Attribute " + attrName + " not yet supported for element taxon");
|
|
| 444 |
// save(keyNodesToSave, state); |
|
| 445 |
|
|
| 446 |
return; |
|
| 447 |
} else {
|
|
| 448 |
handleUnexpectedElement(next); |
|
| 314 | 449 |
} |
| 315 | 450 |
} |
| 316 |
|
|
| 451 |
return; |
|
| 317 | 452 |
} |
| 318 | 453 |
|
| 454 |
/** |
|
| 455 |
* @param taxon |
|
| 456 |
* @param lastTaxon |
|
| 457 |
*/ |
|
| 458 |
private void doTaxonRelation(MarkupImportState state, Taxon taxon, |
|
| 459 |
Taxon lastTaxon, Location dataLocation) {
|
|
| 319 | 460 |
|
| 320 |
private Taxon getLastTaxon(MarkupImportState state) {
|
|
| 321 |
if (state.getConfig().getLastTaxonUuid() == null){
|
|
| 322 |
return null; |
|
| 323 |
}else{
|
|
| 324 |
return (Taxon)getTaxonService().find(state.getConfig().getLastTaxonUuid()); |
|
| 325 |
} |
|
| 326 |
} |
|
| 327 |
|
|
| 328 |
|
|
| 329 |
// private void invokeDoKey(SapindaceaeImportState state) {
|
|
| 330 |
// TransactionStatus tx = startTransaction(); |
|
| 331 |
// |
|
| 332 |
// Set<FeatureNode> nodesToSave = new HashSet<FeatureNode>(); |
|
| 333 |
// ITaxonService taxonService = getTaxonService(); |
|
| 334 |
// ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true); |
|
| 335 |
// |
|
| 336 |
// Element elbody= getBodyElement(state.getConfig()); |
|
| 337 |
// List<Element> elTaxonList = elbody.getChildren(); |
|
| 338 |
// |
|
| 339 |
// int i = 0; |
|
| 340 |
// |
|
| 341 |
// //for each taxon |
|
| 342 |
// for (Element elTaxon : elTaxonList){
|
|
| 343 |
// if ((i++ % modCount) == 0 && i > 1){ logger.info("Taxa handled: " + (i-1));}
|
|
| 344 |
// if (! elTaxon.getName().equalsIgnoreCase("taxon")){
|
|
| 345 |
// continue; |
|
| 346 |
// } |
|
| 347 |
// |
|
| 348 |
// List<Element> children = elTaxon.getChildren("key");
|
|
| 349 |
// for (Element element : children){
|
|
| 350 |
// handleKeys(state, element, null); |
|
| 351 |
// } |
|
| 352 |
// nodesToSave.add(taxon); |
|
| 353 |
// |
|
| 354 |
// } |
|
| 355 |
// |
|
| 356 |
// } |
|
| 461 |
Classification tree = makeTree(state, dataLocation); |
|
| 462 |
if (lastTaxon == null) {
|
|
| 463 |
tree.addChildTaxon(taxon, null, null, null); |
|
| 464 |
return; |
|
| 465 |
} |
|
| 466 |
Rank thisRank = taxon.getName().getRank(); |
|
| 467 |
Rank lastRank = lastTaxon.getName().getRank(); |
|
| 468 |
if (lastTaxon.getTaxonNodes().size() > 0) {
|
|
| 469 |
TaxonNode lastNode = lastTaxon.getTaxonNodes().iterator().next(); |
|
| 470 |
if (thisRank.isLower(lastRank)) {
|
|
| 471 |
lastNode.addChildTaxon(taxon, null, null, null); |
|
| 472 |
fillMissingEpithetsForTaxa(lastTaxon, taxon); |
|
| 473 |
} else if (thisRank.equals(lastRank)) {
|
|
| 474 |
TaxonNode parent = lastNode.getParent(); |
|
| 475 |
if (parent != null) {
|
|
| 476 |
parent.addChildTaxon(taxon, null, null, null); |
|
| 477 |
fillMissingEpithetsForTaxa(parent.getTaxon(), taxon); |
|
| 478 |
} else {
|
|
| 479 |
tree.addChildTaxon(taxon, null, null, null); |
|
| 480 |
} |
|
| 481 |
} else if (thisRank.isHigher(lastRank)) {
|
|
| 482 |
doTaxonRelation(state, taxon, lastNode.getParent().getTaxon(), |
|
| 483 |
dataLocation); |
|
| 484 |
// TaxonNode parentNode = handleTaxonRelation(state, taxon, |
|
| 485 |
// lastNode.getParent().getTaxon()); |
|
| 486 |
// parentNode.addChildTaxon(taxon, null, null, null); |
|
| 487 |
} |
|
| 488 |
} else {
|
|
| 357 | 489 |
|
| 490 |
String message = "Last taxon has no node"; |
|
| 491 |
fireWarningEvent(message, makeLocationStr(dataLocation), 6); |
|
| 492 |
} |
|
| 493 |
} |
|
| 358 | 494 |
|
| 359 |
// body/taxon/* |
|
| 360 |
private void handleTaxonElement(MarkupImportState state, Set<String> unhandledTitleClassess, Set<String> unhandledNomeclatureChildren, Set<String> unhandledDescriptionChildren, Taxon taxon, List<Element> children) {
|
|
| 361 |
AnnotatableEntity lastEntity = null; |
|
| 362 |
for (Element element : children){
|
|
| 363 |
String elName = element.getName(); |
|
| 364 |
|
|
| 365 |
if (elName.equalsIgnoreCase("title")){
|
|
| 366 |
handleTitle(state, element, taxon, unhandledTitleClassess); |
|
| 367 |
lastEntity = null; |
|
| 368 |
}else if(elName.equalsIgnoreCase("nomenclature")){
|
|
| 369 |
handleNomenclature(state, element, taxon, unhandledNomeclatureChildren); |
|
| 370 |
lastEntity = null; |
|
| 371 |
}else if(elName.equalsIgnoreCase("description")){
|
|
| 372 |
handleDescription(state, element, taxon, unhandledDescriptionChildren); |
|
| 373 |
lastEntity = null; |
|
| 374 |
}else if(elName.equalsIgnoreCase("habitatecology")){
|
|
| 375 |
lastEntity = handleEcology(state, element, taxon); |
|
| 376 |
}else if(elName.equalsIgnoreCase("distribution")){
|
|
| 377 |
lastEntity = handleDistribution(state, element, taxon); |
|
| 378 |
}else if(elName.equalsIgnoreCase("uses")){
|
|
| 379 |
lastEntity = handleUses(state, element, taxon); |
|
| 380 |
}else if(elName.equalsIgnoreCase("notes")){
|
|
| 381 |
lastEntity = handleTaxonNotes(state, element, taxon); |
|
| 382 |
}else if(elName.equalsIgnoreCase("chromosomes")){
|
|
| 383 |
lastEntity = handleChromosomes(state, element, taxon); |
|
| 384 |
}else if(elName.equalsIgnoreCase("vernacularnames")){
|
|
| 385 |
handleVernaculars(state, element, taxon); |
|
| 386 |
}else if(elName.equalsIgnoreCase("key")){
|
|
| 387 |
lastEntity = handleKeys(state, element, taxon); |
|
| 388 |
}else if(elName.equalsIgnoreCase("references")){
|
|
| 389 |
handleReferences(state, element, taxon, lastEntity); |
|
| 390 |
lastEntity = null; |
|
| 391 |
}else if(elName.equalsIgnoreCase("taxon")){
|
|
| 392 |
logger.warn("A taxon should not be part of a taxon");
|
|
| 393 |
}else if(elName.equalsIgnoreCase("homotypes")){
|
|
| 394 |
logger.warn("Homotypes should be included in the nomenclature flag but is child of taxon [XPath: body/taxon/homotypes]");
|
|
| 395 |
}else{
|
|
| 396 |
logger.warn("Unexpected child for taxon: " + elName);
|
|
| 495 |
/** |
|
| 496 |
* @param state |
|
| 497 |
* @param dataLocation |
|
| 498 |
* @return |
|
| 499 |
*/ |
|
| 500 |
private Classification makeTree(MarkupImportState state, Location dataLocation) {
|
|
| 501 |
Classification result = state.getTree(null); |
|
| 502 |
if (result == null) {
|
|
| 503 |
UUID uuid = state.getConfig().getClassificationUuid(); |
|
| 504 |
if (uuid == null) {
|
|
| 505 |
String message = "No classification uuid is defined"; |
|
| 506 |
fireWarningEvent(message, makeLocationStr(dataLocation), 6); |
|
| 507 |
result = createNewClassification(state); |
|
| 508 |
} else {
|
|
| 509 |
result = getClassificationService().find(uuid); |
|
| 510 |
if (result == null) {
|
|
| 511 |
result = createNewClassification(state); |
|
| 512 |
result.setUuid(uuid); |
|
| 397 | 513 |
} |
| 398 | 514 |
} |
| 515 |
state.putTree(null, result); |
|
| 399 | 516 |
} |
| 400 |
|
|
| 401 |
|
|
| 402 |
private void handleVernaculars(MarkupImportState state, Element elVernacular, Taxon taxon) {
|
|
| 403 |
verifyNoAttribute(elVernacular); |
|
| 404 |
verifyNoChildren(elVernacular, false); |
|
| 405 |
String value = elVernacular.getTextNormalize(); |
|
| 406 |
Feature feature = Feature.COMMON_NAME(); |
|
| 407 |
value = replaceStart(value, "Noms vernaculaires"); |
|
| 408 |
String[] dialects = value.split(";");
|
|
| 409 |
for (String singleDialect : dialects){
|
|
| 410 |
handleSingleDialect(taxon, singleDialect, feature, state); |
|
| 517 |
save(result, state); |
|
| 518 |
return result; |
|
| 411 | 519 |
} |
| 412 |
return; |
|
| 520 |
|
|
| 521 |
private Classification createNewClassification(MarkupImportState state) {
|
|
| 522 |
Classification result; |
|
| 523 |
result = Classification.NewInstance(state.getConfig().getClassificationTitle()); |
|
| 524 |
state.putTree(null, result); |
|
| 525 |
return result; |
|
| 413 | 526 |
} |
| 414 | 527 |
|
| 528 |
private Taxon handleTaxon(MarkupImportState state, XMLEventReader reader, StartElement parentEvent) throws XMLStreamException {
|
|
| 529 |
// TODO progress monitoring |
|
| 530 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
|
| 531 |
Taxon taxon = createTaxonAndName(state, attributes); |
|
| 532 |
state.setCurrentTaxon(taxon); |
|
| 415 | 533 |
|
| 416 |
private void handleSingleDialect(Taxon taxon, String singleDialect, Feature feature, MarkupImportState state) {
|
|
| 417 |
singleDialect = singleDialect.trim(); |
|
| 418 |
TaxonDescription description = getDescription(taxon); |
|
| 419 |
String reDialect = "\\(dial\\.\\s.*\\)"; |
|
| 420 |
// String reDialect = "\\(.*\\)"; |
|
| 421 |
Pattern patDialect = Pattern.compile(reDialect); |
|
| 422 |
Matcher matcher = patDialect.matcher(singleDialect); |
|
| 423 |
if (matcher.find()){
|
|
| 424 |
String dialect = singleDialect.substring(matcher.start(), matcher.end()); |
|
| 425 |
dialect = dialect.replace("(dial. ", "").replace(")", "");
|
|
| 534 |
boolean hasTitle = false; |
|
| 535 |
boolean hasNomenclature = false; |
|
| 536 |
String taxonTitle = null; |
|
| 537 |
|
|
| 538 |
while (reader.hasNext()) {
|
|
| 539 |
XMLEvent next = readNoWhitespace(reader); |
|
| 540 |
if (next.isEndElement()) {
|
|
| 541 |
if (isMyEndingElement(next, parentEvent)) {
|
|
| 542 |
checkMandatoryElement(hasTitle, parentEvent, TAXONTITLE); |
|
| 543 |
checkMandatoryElement(hasNomenclature, parentEvent, NOMENCLATURE); |
|
| 544 |
handleUnexpectedAttributes(parentEvent.getLocation(),attributes); |
|
| 426 | 545 |
|
| 427 |
Language language = null; |
|
| 546 |
makeKeyNodes(state, parentEvent, taxonTitle); |
|
| 547 |
state.setCurrentTaxon(null); |
|
| 548 |
state.setCurrentTaxonNum(null); |
|
| 549 |
save(taxon, state); |
|
| 550 |
return taxon; |
|
| 551 |
} else {
|
|
| 552 |
if (isEndingElement(next, HEADING)) {
|
|
| 553 |
// NOT YET IMPLEMENTED |
|
| 554 |
popUnimplemented(next.asEndElement()); |
|
| 555 |
} else if (isEndingElement(next, TEXT_SECTION)) {
|
|
| 556 |
// NOT YET IMPLEMENTED |
|
| 557 |
popUnimplemented(next.asEndElement()); |
|
| 558 |
} else if (isEndingElement(next, REFERENCES)) {
|
|
| 559 |
// NOT YET IMPLEMENTED |
|
| 560 |
popUnimplemented(next.asEndElement()); |
|
| 561 |
} else {
|
|
| 562 |
handleUnexpectedEndElement(next.asEndElement()); |
|
| 563 |
} |
|
| 564 |
} |
|
| 565 |
} else if (next.isStartElement()) {
|
|
| 566 |
if (isStartingElement(next, HEADING)) {
|
|
| 567 |
handleNotYetImplementedElement(next); |
|
| 568 |
} else if (isStartingElement(next, TAXONTITLE)) {
|
|
| 569 |
taxonTitle = handleTaxonTitle(state, reader, next); |
|
| 570 |
hasTitle = true; |
|
| 571 |
} else if (isStartingElement(next, WRITER)) {
|
|
| 572 |
makeKeyWriter(state, reader, taxon, taxonTitle, next); |
|
| 573 |
} else if (isStartingElement(next, TEXT_SECTION)) {
|
|
| 574 |
handleNotYetImplementedElement(next); |
|
| 575 |
} else if (isStartingElement(next, KEY)) {
|
|
| 576 |
handleKey(state, reader, next); |
|
| 577 |
} else if (isStartingElement(next, NOMENCLATURE)) {
|
|
| 578 |
handleNomenclature(state, reader, next); |
|
| 579 |
hasNomenclature = true; |
|
| 580 |
} else if (isStartingElement(next, FEATURE)) {
|
|
| 581 |
handleFeature(state, reader, next); |
|
| 582 |
} else if (isStartingElement(next, NOTES)) {
|
|
| 583 |
// TODO is this the correct way to handle notes? |
|
| 584 |
String note = handleNotes(state, reader, next); |
|
| 585 |
|
|
| 586 |
UUID notesUuid; |
|
| 428 | 587 |
try {
|
| 429 |
language = this.getLanguage(state, state.getTransformer().getLanguageUuid(dialect), dialect, dialect, dialect); |
|
| 588 |
notesUuid = state.getTransformer().getFeatureUuid( |
|
| 589 |
"notes"); |
|
| 590 |
Feature feature = getFeature(state, notesUuid, "Notes", |
|
| 591 |
"Notes", "note", null); |
|
| 592 |
TextData textData = TextData.NewInstance(feature); |
|
| 593 |
textData.putText(Language.DEFAULT(), note); |
|
| 594 |
TaxonDescription description = getTaxonDescription( |
|
| 595 |
taxon, false, true); |
|
| 596 |
description.addElement(textData); |
|
| 430 | 597 |
} catch (UndefinedTransformerMethodException e) {
|
| 431 |
logger.error(e.getMessage()); |
|
| 598 |
String message = "getFeatureUuid method not yet implemented"; |
|
| 599 |
fireWarningEvent(message, next, 8); |
|
| 432 | 600 |
} |
| 433 |
|
|
| 434 |
String commonNames = singleDialect.substring(0, matcher.start()); |
|
| 435 |
String[] splitNames = commonNames.split(",");
|
|
| 436 |
for (String commonNameString : splitNames){
|
|
| 437 |
commonNameString = commonNameString.trim(); |
|
| 438 |
CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, language); |
|
| 439 |
description.addElement(commonName); |
|
| 601 |
} else if (isStartingElement(next, REFERENCES)) {
|
|
| 602 |
handleNotYetImplementedElement(next); |
|
| 603 |
} else if (isStartingElement(next, FIGURE)) {
|
|
| 604 |
handleFigure(state, reader, next); |
|
| 605 |
} else if (isStartingElement(next, FOOTNOTE)) {
|
|
| 606 |
FootnoteDataHolder footnote = handleFootnote(state, reader, |
|
| 607 |
next); |
|
| 608 |
if (footnote.isRef()) {
|
|
| 609 |
String message = "Ref footnote not implemented here"; |
|
| 610 |
fireWarningEvent(message, next, 4); |
|
| 611 |
} else {
|
|
| 612 |
registerGivenFootnote(state, footnote); |
|
| 440 | 613 |
} |
| 441 |
}else{
|
|
| 442 |
logger.warn("No dialect match: " + singleDialect);
|
|
| 614 |
} else {
|
|
| 615 |
handleUnexpectedStartElement(next);
|
|
| 443 | 616 |
} |
| 617 |
} else {
|
|
| 618 |
handleUnexpectedElement(next); |
|
| 444 | 619 |
} |
| 445 |
|
|
| 446 |
|
|
| 447 |
private void handleReferences(MarkupImportState state, Element elReferences, Taxon taxon, AnnotatableEntity lastEntity) {
|
|
| 448 |
verifyNoAttribute(elReferences); |
|
| 449 |
verifyNoChildren(elReferences, true); |
|
| 450 |
String refString = elReferences.getTextNormalize(); |
|
| 451 |
if (lastEntity == null){
|
|
| 452 |
logger.warn("No last entity defined: " + refString);
|
|
| 453 |
return; |
|
| 454 | 620 |
} |
| 455 |
|
|
| 456 |
Annotation annotation = Annotation.NewInstance(refString, AnnotationType.EDITORIAL(), Language.DEFAULT()); |
|
| 457 |
lastEntity.addAnnotation(annotation); |
|
| 621 |
throw new IllegalStateException("<Taxon> has no closing tag");
|
|
| 458 | 622 |
} |
| 459 | 623 |
|
| 460 |
|
|
| 461 |
private PolytomousKey handleKeys(MarkupImportState state, Element elKey, Taxon taxon) {
|
|
| 462 |
UnmatchedLeads openKeys = state.getUnmatchedLeads(); |
|
| 463 |
|
|
| 464 |
//title |
|
| 465 |
String title = makeKeyTitle(elKey); |
|
| 466 |
|
|
| 467 |
//key |
|
| 468 |
PolytomousKey key = PolytomousKey.NewTitledInstance(title); |
|
| 624 |
private void makeKeyNodes(MarkupImportState state, XMLEvent event, String taxonTitle) {
|
|
| 625 |
Taxon taxon = state.getCurrentTaxon(); |
|
| 626 |
String num = state.getCurrentTaxonNum(); |
|
| 469 | 627 |
|
| 470 |
//TODO add covered taxa etc.
|
|
| 471 |
verifyNoAttribute(elKey);
|
|
| 628 |
String nameString = CdmBase.deproxy(taxon.getName(), NonViralName.class).getNameCache();
|
|
| 629 |
// String nameString = taxonTitle;
|
|
| 472 | 630 |
|
| 473 |
//notes |
|
| 474 |
makeKeyNotes(elKey, key); |
|
| 631 |
//try to find matching lead nodes |
|
| 632 |
UnmatchedLeadsKey leadsKey = UnmatchedLeadsKey.NewInstance(num, nameString); |
|
| 633 |
Set<PolytomousKeyNode> matchingNodes = handleMatchingNodes(state, taxon, leadsKey); |
|
| 475 | 634 |
|
| 476 |
//keycouplets |
|
| 477 |
List<Element> keychoices = new ArrayList<Element>(); |
|
| 478 |
keychoices.addAll(elKey.getChildren("keycouplet"));
|
|
| 479 |
keychoices.addAll(elKey.getChildren("keychoice"));
|
|
| 480 |
|
|
| 481 |
|
|
| 482 |
for (Element elKeychoice : keychoices){
|
|
| 483 |
handleKeyChoices(state, openKeys, key, elKeychoice, taxon); |
|
| 484 |
elKey.removeContent(elKeychoice); |
|
| 635 |
if (num != null){//same without using the num
|
|
| 636 |
UnmatchedLeadsKey noNumLeadsKey = UnmatchedLeadsKey.NewInstance("", nameString);
|
|
| 637 |
Set<PolytomousKeyNode> noNumMatchingNodes = handleMatchingNodes(state, taxon, noNumLeadsKey); |
|
| 638 |
if(noNumMatchingNodes.size() > 0){
|
|
| 639 |
String message ="Taxon matches additional key node when not considering <num> attribute in taxontitle. This may be correct but may also indicate an error."; |
|
| 640 |
fireWarningEvent(message, event, 1); |
|
| 641 |
} |
|
| 485 | 642 |
} |
| 486 |
|
|
| 487 |
// |
|
| 488 |
verifyNoChildren(elKey); |
|
| 489 |
logger.info("Unmatched leads after key handling:" + openKeys.toString());
|
|
| 490 |
|
|
| 491 |
|
|
| 492 |
if (state.getConfig().isDoPrintKeys()){
|
|
| 493 |
key.print(System.err); |
|
| 643 |
//report missing match, if num exists |
|
| 644 |
if (matchingNodes.isEmpty() && num != null){
|
|
| 645 |
String message = "Taxon has <num> attribute in taxontitle but no matching key nodes exist: %s, Key: %s"; |
|
| 646 |
message = String.format(message, num, leadsKey.toString()); |
|
| 647 |
fireWarningEvent(message, event, 1); |
|
| 494 | 648 |
} |
| 495 |
getPolytomousKeyService().save(key); |
|
| 496 |
return key; |
|
| 497 |
} |
|
| 498 |
|
|
| 499 |
|
|
| 500 |
/** |
|
| 501 |
* @param state |
|
| 502 |
* @param elKey |
|
| 503 |
* @param openKeys |
|
| 504 |
* @param key |
|
| 505 |
* @param elKeychoice |
|
| 506 |
* @param taxon |
|
| 507 |
*/ |
|
| 508 |
private void handleKeyChoices(MarkupImportState state, UnmatchedLeads openKeys, PolytomousKey key, Element elKeychoice, Taxon taxon) {
|
|
| 509 |
|
|
| 510 |
//char Attribute |
|
| 511 |
//TODO it's still unclear if char is a feature and needs to be a new attribute |
|
| 512 |
//or if it is handled as question. Therefore both cases are handled but feature |
|
| 513 |
//is finally not yet set |
|
| 514 |
KeyStatement question = handleKeychoiceChar(state, elKeychoice); |
|
| 515 |
Feature feature = handleKeychoiceCharAsFeature(state, elKeychoice); |
|
| 516 | 649 |
|
| 517 |
//lead |
|
| 518 |
List<PolytomousKeyNode> childNodes = handleKeychoiceLeads(state, key, elKeychoice, taxon, question, feature); |
|
| 519 |
|
|
| 520 |
//num -> match with unmatched leads |
|
| 521 |
handleKeychoiceNum(openKeys, key, elKeychoice, childNodes); |
|
| 522 |
|
|
| 523 |
//others |
|
| 524 |
verifyNoAttribute(elKeychoice); |
|
| 525 | 650 |
} |
| 526 |
|
|
| 527 |
|
|
| 528 |
/** |
|
| 529 |
* @param openKeys |
|
| 530 |
* @param key |
|
| 531 |
* @param elKeychoice |
|
| 532 |
* @param childNodes |
|
| 533 |
*/ |
|
| 534 |
private void handleKeychoiceNum(UnmatchedLeads openKeys, PolytomousKey key, Element elKeychoice, List<PolytomousKeyNode> childNodes) {
|
|
| 535 |
Attribute numAttr = elKeychoice.getAttribute("num");
|
|
| 536 |
String num = CdmUtils.removeTrailingDot(numAttr == null? "":numAttr.getValue()); |
|
| 537 |
UnmatchedLeadsKey okk = UnmatchedLeadsKey.NewInstance(key, num); |
|
| 538 |
Set<PolytomousKeyNode> matchingNodes = openKeys.getNodes(okk); |
|
| 651 |
|
|
| 652 |
private Set<PolytomousKeyNode> handleMatchingNodes(MarkupImportState state, Taxon taxon, UnmatchedLeadsKey leadsKey) {
|
|
| 653 |
Set<PolytomousKeyNode> matchingNodes = state.getUnmatchedLeads().getNodes(leadsKey); |
|
| 539 | 654 |
for (PolytomousKeyNode matchingNode : matchingNodes){
|
| 540 |
for (PolytomousKeyNode childNode : childNodes){
|
|
| 541 |
matchingNode.addChild(childNode); |
|
| 542 |
} |
|
| 543 |
openKeys.removeNode(okk, matchingNode); |
|
| 544 |
} |
|
| 545 |
if (matchingNodes.isEmpty()){
|
|
| 546 |
for (PolytomousKeyNode childNode : childNodes){
|
|
| 547 |
key.getRoot().addChild(childNode); |
|
| 548 |
} |
|
| 655 |
state.getUnmatchedLeads().removeNode(leadsKey, matchingNode); |
|
| 656 |
matchingNode.setTaxon(taxon); |
|
| 657 |
state.getPolytomousKeyNodesToSave().add(matchingNode); |
|
| 549 | 658 |
} |
| 550 |
|
|
| 551 |
elKeychoice.removeAttribute("num");
|
|
| 659 |
return matchingNodes; |
|
| 552 | 660 |
} |
| 553 | 661 |
|
| 662 |
private void handleKey(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 663 |
// attributes |
|
| 664 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
|
| 665 |
String isSpotcharacters = getAndRemoveAttributeValue(attributes, IS_SPOTCHARACTERS); |
|
| 666 |
if (isNotBlank(isSpotcharacters) ) {
|
|
| 667 |
//TODO isSpotcharacters |
|
| 668 |
String message = "Attribute isSpotcharacters not yet implemented for <key>"; |
|
| 669 |
fireWarningEvent(message, parentEvent, 4); |
|
| 670 |
} |
|
| 671 |
|
|
| 672 |
PolytomousKey key = PolytomousKey.NewInstance(); |
|
| 673 |
key.addTaxonomicScope(state.getCurrentTaxon()); |
|
| 674 |
state.setCurrentKey(key); |
|
| 675 |
|
|
| 676 |
boolean isFirstCouplet = true; |
|
| 677 |
while (reader.hasNext()) {
|
|
| 678 |
XMLEvent next = readNoWhitespace(reader); |
|
| 679 |
if (isMyEndingElement(next, parentEvent)) {
|
|
| 680 |
save(key, state); |
|
| 681 |
state.setCurrentKey(null); |
|
| 682 |
return; |
|
| 683 |
} else if (isEndingElement(next, KEYNOTES)){
|
|
| 684 |
popUnimplemented(next.asEndElement()); |
|
| 685 |
} else if (isStartingElement(next, KEY_TITLE)) {
|
|
| 686 |
handleKeyTitle(state, reader, next); |
|
| 687 |
} else if (isStartingElement(next, KEYNOTES)) {
|
|
| 688 |
//TODO |
|
| 689 |
handleNotYetImplementedElement(next); |
|
| 690 |
} else if (isStartingElement(next, COUPLET)) {
|
|
| 691 |
PolytomousKeyNode node = null; |
|
| 692 |
if (isFirstCouplet){
|
|
| 693 |
node = key.getRoot(); |
|
| 694 |
isFirstCouplet = false; |
|
| 695 |
} |
|
| 696 |
handleCouplet(state, reader, next, node); |
|
| 697 |
} else {
|
|
| 698 |
handleUnexpectedElement(next); |
|
| 699 |
} |
|
| 700 |
} |
|
| 701 |
throw new IllegalStateException("<key> has no closing tag");
|
|
| 702 |
} |
|
| 554 | 703 |
|
| 555 | 704 |
/** |
| 556 | 705 |
* @param state |
| 706 |
* @param reader |
|
| 557 | 707 |
* @param key |
| 558 |
* @param elKeychoice |
|
| 559 |
* @param taxon |
|
| 560 |
* @param feature |
|
| 561 |
* @return |
|
| 708 |
* @param next |
|
| 709 |
* @throws XMLStreamException |
|
| 562 | 710 |
*/ |
| 563 |
private List<PolytomousKeyNode> handleKeychoiceLeads( MarkupImportState state, PolytomousKey key, Element elKeychoice, Taxon taxon, KeyStatement question, Feature feature) {
|
|
| 564 |
List<PolytomousKeyNode> childNodes = new ArrayList<PolytomousKeyNode>();
|
|
| 565 |
List<Element> leads = elKeychoice.getChildren("lead");
|
|
| 566 |
for(Element elLead : leads){
|
|
| 567 |
PolytomousKeyNode childNode = handleLead(state, key, elLead, taxon, question, feature); |
|
| 568 |
childNodes.add(childNode);
|
|
| 569 |
}
|
|
| 570 |
return childNodes;
|
|
| 711 |
private void handleKeyTitle(MarkupImportState state, XMLEventReader reader, XMLEvent next) throws XMLStreamException {
|
|
| 712 |
PolytomousKey key = state.getCurrentKey();
|
|
| 713 |
String keyTitle = getCData(state, reader, next);
|
|
| 714 |
String standardTitles = "(?i)(Key\\sto\\sthe\\s(genera|species|varieties|forms))";
|
|
| 715 |
|
|
| 716 |
if (isNotBlank(keyTitle) ){
|
|
| 717 |
if (!state.getConfig().isReplaceStandardKeyTitles() || ! keyTitle.matches(standardTitles)){
|
|
| 718 |
key.setTitleCache(keyTitle, true);
|
|
| 571 | 719 |
} |
| 572 |
|
|
| 573 |
|
|
| 574 |
/** |
|
| 575 |
* @param state |
|
| 576 |
* @param elKeychoice |
|
| 577 |
* @return |
|
| 578 |
*/ |
|
| 579 |
private KeyStatement handleKeychoiceChar(MarkupImportState state, Element elKeychoice) {
|
|
| 580 |
KeyStatement statement = null; |
|
| 581 |
Attribute charAttr = elKeychoice.getAttribute("char");
|
|
| 582 |
if (charAttr != null){
|
|
| 583 |
String charStr = charAttr.getValue(); |
|
| 584 |
if (StringUtils.isNotBlank(charStr)){
|
|
| 585 |
statement = KeyStatement.NewInstance(charStr); |
|
| 586 | 720 |
} |
| 587 |
elKeychoice.removeAttribute("char");
|
|
| 588 |
} |
|
| 589 |
return statement; |
|
| 590 |
} |
|
| 591 |
|
|
| 592 |
/** |
|
| 593 |
* @param state |
|
| 594 |
* @param elKeychoice |
|
| 595 |
* @return |
|
| 596 |
*/ |
|
| 597 |
private Feature handleKeychoiceCharAsFeature(MarkupImportState state, Element elKeychoice) {
|
|
| 598 |
Feature feature = null; |
|
| 599 |
Attribute charAttr = elKeychoice.getAttribute("char");
|
|
| 600 |
if (charAttr != null){
|
|
| 601 |
String charStr = charAttr.getValue(); |
|
| 602 |
feature = getFeature(charStr, state); |
|
| 603 |
elKeychoice.removeAttribute("char");
|
|
| 604 | 721 |
} |
| 605 |
return feature; |
|
| 606 |
} |
|
| 607 |
|
|
| 608 | 722 |
|
| 609 |
private PolytomousKeyNode handleLead(MarkupImportState state, PolytomousKey key, Element elLead, Taxon taxon, KeyStatement question, Feature feature) {
|
|
| 610 |
PolytomousKeyNode node = PolytomousKeyNode.NewInstance(); |
|
| 611 |
//TODO the char attribute in the keychoice is more a feature than a question |
|
| 612 |
//needs to be discussed on model side |
|
| 613 |
node.setQuestion(question); |
|
| 614 |
// node.setFeature(feature); |
|
| 615 |
|
|
| 616 |
//text |
|
| 617 |
String text = handleLeadText(elLead, node); |
|
| 618 |
|
|
| 619 |
//num |
|
| 620 |
handleLeadNum(elLead, text); |
|
| 723 |
private void handleCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode parentNode) throws XMLStreamException {
|
|
| 724 |
String num = getOnlyAttribute(parentEvent, NUM, true); |
|
| 725 |
List<PolytomousKeyNode> childList = new ArrayList<PolytomousKeyNode>(); |
|
| 621 | 726 |
|
| 622 |
//goto |
|
| 623 |
handleLeadGoto(state, key, elLead, taxon, node); |
|
| 624 |
|
|
| 625 |
//others |
|
| 626 |
verifyNoAttribute(elLead); |
|
| 627 |
|
|
| 628 |
return node; |
|
| 727 |
while (reader.hasNext()) {
|
|
| 728 |
XMLEvent next = readNoWhitespace(reader); |
|
| 729 |
if (isMyEndingElement(next, parentEvent)) {
|
|
| 730 |
completeCouplet(state, parentEvent, parentNode, num, childList); |
|
| 731 |
return; |
|
| 732 |
} else if (isStartingElement(next, QUESTION)) {
|
|
| 733 |
handleQuestion(state, reader, next, childList); |
|
| 734 |
} else if (isStartingElement(next, KEYNOTES)) {
|
|
| 735 |
//TODO |
|
| 736 |
handleNotYetImplementedElement(next); |
|
| 737 |
} else if (isEndingElement(next, KEYNOTES)) {
|
|
| 738 |
//TODO |
|
| 739 |
popUnimplemented(next.asEndElement()); |
|
| 740 |
} else {
|
|
| 741 |
handleUnexpectedElement(next); |
|
| 629 | 742 |
} |
| 630 |
|
|
| 631 |
|
|
| 632 |
/** |
|
| 633 |
* @param elLead |
|
| 634 |
* @param node |
|
| 635 |
* @return |
|
| 636 |
*/ |
|
| 637 |
private String handleLeadText(Element elLead, PolytomousKeyNode node) {
|
|
| 638 |
String text = elLead.getAttributeValue("text").trim();
|
|
| 639 |
if (StringUtils.isBlank(text)){
|
|
| 640 |
logger.warn("Empty text in lead");
|
|
| 641 |
} |
|
| 642 |
elLead.removeAttribute("text");
|
|
| 643 |
KeyStatement statement = KeyStatement.NewInstance(text); |
|
| 644 |
node.setStatement(statement); |
|
| 645 |
return text; |
|
| 743 |
} |
|
| 744 |
throw new IllegalStateException("<couplet> has no closing tag");
|
|
| 646 | 745 |
} |
| 647 | 746 |
|
| 648 |
|
|
| 649 | 747 |
/** |
| 650 | 748 |
* @param state |
| 651 |
* @param key
|
|
| 652 |
* @param elLead
|
|
| 653 |
* @param taxon
|
|
| 654 |
* @param node
|
|
| 749 |
* @param parentEvent
|
|
| 750 |
* @param parentNode
|
|
| 751 |
* @param num
|
|
| 752 |
* @param childList
|
|
| 655 | 753 |
*/ |
| 656 |
private void handleLeadGoto(MarkupImportState state, PolytomousKey key, Element elLead, Taxon taxon, PolytomousKeyNode node) {
|
|
| 657 |
Attribute gotoAttr = elLead.getAttribute("goto");
|
|
| 658 |
if (gotoAttr != null){
|
|
| 659 |
String strGoto = gotoAttr.getValue().trim(); |
|
| 660 |
//create key |
|
| 661 |
UnmatchedLeadsKey gotoKey = null; |
|
| 662 |
if (isInternalNode(strGoto)){
|
|
| 663 |
gotoKey = UnmatchedLeadsKey.NewInstance(key, strGoto); |
|
| 664 |
}else{
|
|
| 665 |
String taxonKey = makeTaxonKey(strGoto, taxon); |
|
| 666 |
gotoKey = UnmatchedLeadsKey.NewInstance(taxonKey); |
|
| 667 |
} |
|
| 668 |
// |
|
| 669 |
UnmatchedLeads openKeys = state.getUnmatchedLeads(); |
|
| 670 |
if (gotoKey.isInnerLead()){
|
|
| 671 |
Set<PolytomousKeyNode> existingNodes = openKeys.getNodes(gotoKey); |
|
| 672 |
for (PolytomousKeyNode existingNode : existingNodes){
|
|
| 673 |
node.addChild(existingNode); |
|
| 674 |
} |
|
| 754 |
private void completeCouplet(MarkupImportState state, XMLEvent parentEvent, |
|
| 755 |
PolytomousKeyNode parentNode, String num, |
|
| 756 |
List<PolytomousKeyNode> childList) {
|
|
| 757 |
if (parentNode != null){
|
|
| 758 |
for (PolytomousKeyNode childNode : childList){
|
|
| 759 |
parentNode.addChild(childNode); |
|
| 675 | 760 |
} |
| 676 |
openKeys.addKey(gotoKey, node); |
|
| 677 |
//remove attribute (need for consistency check) |
|
| 678 |
elLead.removeAttribute("goto");
|
|
| 679 |
}else{
|
|
| 680 |
logger.warn("lead has no goto attribute");
|
|
| 761 |
}else if (isNotBlank(num)){
|
|
| 762 |
UnmatchedLeadsKey unmatchedKey = UnmatchedLeadsKey.NewInstance(state.getCurrentKey(), num); |
|
| 763 |
Set<PolytomousKeyNode> nodes = state.getUnmatchedLeads().getNodes(unmatchedKey); |
|
| 764 |
for(PolytomousKeyNode nodeToMatch: nodes){
|
|
| 765 |
for (PolytomousKeyNode childNode : childList){
|
|
| 766 |
nodeToMatch.addChild(childNode); |
|
| 681 | 767 |
} |
| 768 |
state.getUnmatchedLeads().removeNode(unmatchedKey, nodeToMatch); |
|
| 682 | 769 |
} |
| 683 |
|
|
| 684 |
|
|
| 685 |
/** |
|
| 686 |
* @param elLead |
|
| 687 |
* @param text |
|
| 688 |
*/ |
|
| 689 |
private void handleLeadNum(Element elLead, String text) {
|
|
| 690 |
Attribute numAttr = elLead.getAttribute("num");
|
|
| 691 |
if (numAttr != null){
|
|
| 692 |
//TODO num |
|
| 693 |
String num = numAttr.getValue(); |
|
| 694 |
elLead.removeAttribute("num");
|
|
| 695 | 770 |
}else{
|
| 696 |
logger.info("Keychoice has no num attribute: " + text);
|
|
| 771 |
String message = "Parent num could not be matched. Please check if num (%s) is correct"; |
|
| 772 |
message = String.format(message, num); |
|
| 773 |
fireWarningEvent(message, parentEvent, 6); |
|
| 697 | 774 |
} |
| 698 | 775 |
} |
| 699 | 776 |
|
| 777 |
private void handleQuestion(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, List<PolytomousKeyNode> nodesList) throws XMLStreamException {
|
|
| 778 |
// attributes |
|
| 779 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
|
| 780 |
//needed only for data lineage |
|
| 781 |
String questionNum = getAndRemoveRequiredAttributeValue(parentEvent, attributes, NUM); |
|
| 782 |
|
|
| 783 |
PolytomousKeyNode myNode = PolytomousKeyNode.NewInstance(); |
|
| 784 |
myNode.setKey(state.getCurrentKey()); //to avoid NPE while computing num in PolytomousKeyNode in case this node is not matched correctly with a parent |
|
| 785 |
nodesList.add(myNode); |
|
| 786 |
|
|
| 787 |
while (reader.hasNext()) {
|
|
| 788 |
XMLEvent next = readNoWhitespace(reader); |
|
| 789 |
if (isMyEndingElement(next, parentEvent)) {
|
|
| 790 |
return; |
|
| 791 |
} else if (isStartingElement(next, TEXT)) {
|
|
| 792 |
String text = getCData(state, reader, next); |
|
| 793 |
KeyStatement statement = KeyStatement.NewInstance(text); |
|
| 794 |
myNode.setStatement(statement); |
|
| 795 |
} else if (isStartingElement(next, COUPLET)) {
|
|
| 796 |
//TODO test |
|
| 797 |
handleCouplet(state, reader, next, myNode); |
|
| 798 |
} else if (isStartingElement(next, TO_COUPLET)) {
|
|
| 799 |
handleToCouplet(state, reader, next, myNode); |
|
| 800 |
} else if (isStartingElement(next, TO_TAXON)) {
|
|
| 801 |
handleToTaxon(state, reader, next, myNode); |
|
| 802 |
|
|
| 803 |
} else if (isStartingElement(next, TO_KEY)) {
|
|
| 804 |
//TODO |
|
| 805 |
handleNotYetImplementedElement(next); |
|
| 806 |
} else if (isEndingElement(next, TO_KEY)){
|
|
| 807 |
//TODO |
|
| 808 |
popUnimplemented(next.asEndElement()); |
|
| 809 |
} else if (isStartingElement(next, KEYNOTES)) {
|
|
| 810 |
//TODO |
|
| 811 |
handleNotYetImplementedElement(next); |
|
| 812 |
} else if (isEndingElement(next, KEYNOTES)){
|
|
| 813 |
//TODO |
|
| 814 |
popUnimplemented(next.asEndElement()); |
|
| 815 |
} else {
|
|
| 816 |
handleUnexpectedElement(next); |
|
| 817 |
} |
|
| 818 |
} |
|
| 819 |
throw new IllegalStateException("<question> has no closing tag");
|
|
| 820 |
} |
|
| 821 |
|
|
| 822 |
private void handleToCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent next, PolytomousKeyNode node) throws XMLStreamException {
|
|
| 823 |
String num = getOnlyAttribute(next, NUM, true); |
|
| 824 |
String cData = getCData(state, reader, next, false); |
|
| 825 |
if (isNotBlank(cData) && ! cData.equals(num)){
|
|
| 826 |
String message = "CData ('%s') not handled in <toCouplet>";
|
|
| 827 |
message = String.format(message, cData); |
|
| 828 |
fireWarningEvent(message, next, 4); |
|
| 829 |
} |
|
| 830 |
UnmatchedLeadsKey unmatched = UnmatchedLeadsKey.NewInstance(state.getCurrentKey(), num); |
|
| 831 |
state.getUnmatchedLeads().addKey(unmatched, node); |
|
| 832 |
} |
|
| 700 | 833 |
|
| 834 |
private void handleToTaxon(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode node) throws XMLStreamException {
|
|
| 835 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
|
| 836 |
String num = getAndRemoveAttributeValue(attributes, NUM); |
|
| 837 |
String taxonStr = getCData(state, reader, parentEvent, false); |
|
| 838 |
//TODO ? |
|
| 839 |
taxonStr = makeTaxonKey(taxonStr, state.getCurrentTaxon()); |
|
| 840 |
UnmatchedLeadsKey unmatched = UnmatchedLeadsKey.NewInstance(num, taxonStr); |
|
| 841 |
state.getUnmatchedLeads().addKey(unmatched, node); |
|
| 842 |
return; |
|
| 843 |
} |
|
| 844 |
|
|
| 701 | 845 |
private String makeTaxonKey(String strGoto, Taxon taxon) {
|
| 702 | 846 |
String result = ""; |
| 703 | 847 |
if (strGoto == null){
|
| 704 | 848 |
return ""; |
| 705 | 849 |
} |
| 706 |
String strGenusName = CdmBase.deproxy(taxon.getName(), NonViralName.class).getGenusOrUninomial(); |
|
| 850 |
|
|
| 851 |
NonViralName<?> name = CdmBase.deproxy(taxon.getName(), NonViralName.class); |
|
| 852 |
String strGenusName = name.getGenusOrUninomial(); |
|
| 853 |
|
|
| 854 |
|
|
| 707 | 855 |
strGoto = strGoto.replaceAll("\\([^\\(\\)]*\\)", ""); //replace all brackets
|
| 708 | 856 |
strGoto = strGoto.replaceAll("\\s+", " "); //replace multiple whitespaces by exactly one whitespace
|
| 709 | 857 |
|
| ... | ... | |
| 714 | 862 |
if (isGenusAbbrev(single, strGenusName)){
|
| 715 | 863 |
split[i] = strGenusName; |
| 716 | 864 |
} |
| 717 |
// if (isInfraSpecificMarker(single)){
|
|
| 718 |
// String strSpeciesName = CdmBase.deproxy(taxon.getName(), NonViralName.class).getSpecificEpithet(); |
|
| 719 |
// split[i] = strGenusName + " " + strSpeciesName + " "; |
|
| 720 |
// } |
|
| 865 |
if (isInfraSpecificMarker(single)){
|
|
| 866 |
String strSpeciesEpi = name.getSpecificEpithet(); |
|
| 867 |
if (isBlank(result)){
|
|
| 868 |
result += strGenusName + " " + strSpeciesEpi; |
|
| 869 |
} |
|
| 870 |
} |
|
| 721 | 871 |
result = (result + " " + split[i]).trim(); |
| 722 | 872 |
} |
| 723 | 873 |
return result; |
| 724 | 874 |
} |
| 725 |
|
|
| 875 |
|
|
| 726 | 876 |
|
| 727 | 877 |
private boolean isInfraSpecificMarker(String single) {
|
| 728 | 878 |
try {
|
| 729 | 879 |
if (Rank.getRankByAbbreviation(single).isInfraSpecific()){
|
| 730 | 880 |
return true; |
| 881 |
}else{
|
|
| 882 |
return false; |
|
| 731 | 883 |
} |
| 732 | 884 |
} catch (UnknownCdmTypeException e) {
|
| 733 | 885 |
return false; |
| 734 | 886 |
} |
| 735 |
return false; |
|
| 736 | 887 |
} |
| 737 |
|
|
| 738 |
|
|
| 888 |
|
|
| 739 | 889 |
private boolean isGenusAbbrev(String single, String strGenusName) {
|
| 740 | 890 |
if (! single.matches("[A-Z]\\.?")) {
|
| 741 | 891 |
return false; |
| ... | ... | |
| 746 | 896 |
} |
| 747 | 897 |
} |
| 748 | 898 |
|
| 749 |
|
|
| 750 |
private boolean isInternalNode(String strGoto) {
|
|
| 751 |
return CdmUtils.isNumeric(strGoto); |
|
| 752 |
} |
|
| 753 |
|
|
| 754 |
|
|
| 755 |
private void makeKeyNotes(Element keyElement, PolytomousKey key) {
|
|
| 756 |
Element elNotes = keyElement.getChild("notes");
|
|
| 757 |
if (elNotes != null){
|
|
| 758 |
keyElement.removeContent(elNotes); |
|
| 759 |
String notes = elNotes.getTextNormalize(); |
|
| 760 |
if (StringUtils.isNotBlank(notes)){
|
|
| 761 |
key.addAnnotation(Annotation.NewInstance(notes, AnnotationType.EDITORIAL(), Language.DEFAULT())); |
|
| 899 |
/** |
|
| 900 |
* @param state |
|
| 901 |
* @param reader |
|
| 902 |
* @param taxon |
|
| 903 |
* @param taxonTitle |
|
| 904 |
* @param next |
|
| 905 |
* @throws XMLStreamException |
|
| 906 |
*/ |
|
| 907 |
private void makeKeyWriter(MarkupImportState state, XMLEventReader reader, Taxon taxon, String taxonTitle, XMLEvent next) throws XMLStreamException {
|
|
| 908 |
WriterDataHolder writer = handleWriter(state, reader, next); |
|
| 909 |
taxon.addExtension(writer.extension); |
|
| 910 |
// TODO what if taxonTitle comes later |
|
| 911 |
if (StringUtils.isNotBlank(taxonTitle) |
|
| 912 |
&& writer.extension != null) {
|
|
| 913 |
Reference<?> sec = ReferenceFactory.newBookSection(); |
|
| 914 |
sec.setTitle(taxonTitle); |
|
| 915 |
TeamOrPersonBase<?> author = createAuthor(writer.writer); |
|
| 916 |
sec.setAuthorTeam(author); |
|
| 917 |
sec.setInReference(state.getConfig() |
|
| 918 |
.getSourceReference()); |
|
| 919 |
taxon.setSec(sec); |
|
| 920 |
registerFootnotes(state, sec, writer.footnotes); |
|
| 921 |
} else {
|
|
| 922 |
String message = "No taxontitle exists for writer"; |
|
| 923 |
fireWarningEvent(message, next, 6); |
|
| 924 |
} |
|
| 925 |
} |
|
| 926 |
|
|
| 927 |
private String handleNotes(MarkupImportState state, XMLEventReader reader, |
|
| 928 |
XMLEvent parentEvent) throws XMLStreamException {
|
|
| 929 |
checkNoAttributes(parentEvent); |
|
| 930 |
|
|
| 931 |
String text = ""; |
|
| 932 |
while (reader.hasNext()) {
|
|
| 933 |
XMLEvent next = readNoWhitespace(reader); |
|
| 934 |
if (isMyEndingElement(next, parentEvent)) {
|
|
| 935 |
return text; |
|
| 936 |
} else if (next.isEndElement()) {
|
|
| 937 |
if (isEndingElement(next, HEADING)) {
|
|
| 938 |
popUnimplemented(next.asEndElement()); |
|
| 939 |
} else if (isEndingElement(next, WRITER)) {
|
|
| 940 |
popUnimplemented(next.asEndElement()); |
|
| 941 |
} else if (isEndingElement(next, NUM)) {
|
|
| 942 |
popUnimplemented(next.asEndElement()); |
|
| 943 |
} else {
|
|
| 944 |
handleUnexpectedEndElement(next.asEndElement()); |
|
| 945 |
} |
|
| 946 |
} else if (next.isStartElement()) {
|
|
| 947 |
if (isStartingElement(next, HEADING)) {
|
|
| 948 |
handleNotYetImplementedElement(next); |
|
| 949 |
} else if (isStartingElement(next, SUB_HEADING)) {
|
|
| 950 |
String subheading = getCData(state, reader, next).trim(); |
|
| 951 |
if (! isNoteHeading(subheading)) {
|
|
Also available in: Unified diff
trunk merged into branch