-/**\r
- * Copyright (C) 2009 EDIT\r
- * European Distributed Institute of Taxonomy\r
- * http://www.e-taxonomy.eu\r
- *\r
- * The contents of this file are subject to the Mozilla Public License Version 1.1\r
- * See LICENSE.TXT at the top of this package for the full license terms.\r
- */\r
-\r
-package eu.etaxonomy.cdm.io.markup;\r
-\r
-import java.net.MalformedURLException;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.Arrays;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
-import java.util.List;\r
-import java.util.Map;\r
-import java.util.Set;\r
-import java.util.UUID;\r
-import java.util.regex.Matcher;\r
-import java.util.regex.Pattern;\r
-\r
-import javax.xml.stream.Location;\r
-import javax.xml.stream.XMLEventReader;\r
-import javax.xml.stream.XMLStreamException;\r
-import javax.xml.stream.events.Attribute;\r
-import javax.xml.stream.events.StartElement;\r
-import javax.xml.stream.events.XMLEvent;\r
-\r
-import org.apache.commons.lang.StringUtils;\r
-import org.apache.commons.lang.WordUtils;\r
-import org.apache.log4j.Logger;\r
-\r
-import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;\r
-import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;\r
-import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeCacheStrategy;\r
-import eu.etaxonomy.cdm.common.CdmUtils;\r
-import eu.etaxonomy.cdm.ext.geo.GeoServiceArea;\r
-import eu.etaxonomy.cdm.ext.geo.IEditGeoService;\r
-import eu.etaxonomy.cdm.io.common.CdmImportBase;\r
-import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;\r
-import eu.etaxonomy.cdm.io.markup.UnmatchedLeads.UnmatchedLeadsKey;\r
-import eu.etaxonomy.cdm.model.agent.AgentBase;\r
-import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;\r
-import eu.etaxonomy.cdm.model.agent.Team;\r
-import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;\r
-import eu.etaxonomy.cdm.model.common.AnnotatableEntity;\r
-import eu.etaxonomy.cdm.model.common.Annotation;\r
-import eu.etaxonomy.cdm.model.common.AnnotationType;\r
-import eu.etaxonomy.cdm.model.common.CdmBase;\r
-import eu.etaxonomy.cdm.model.common.Extension;\r
-import eu.etaxonomy.cdm.model.common.ExtensionType;\r
-import eu.etaxonomy.cdm.model.common.Language;\r
-import eu.etaxonomy.cdm.model.common.TermVocabulary;\r
-import eu.etaxonomy.cdm.model.common.TimePeriod;\r
-import eu.etaxonomy.cdm.model.description.CommonTaxonName;\r
-import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
-import eu.etaxonomy.cdm.model.description.Distribution;\r
-import eu.etaxonomy.cdm.model.description.Feature;\r
-import eu.etaxonomy.cdm.model.description.IndividualsAssociation;\r
-import eu.etaxonomy.cdm.model.description.KeyStatement;\r
-import eu.etaxonomy.cdm.model.description.PolytomousKey;\r
-import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;\r
-import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;\r
-import eu.etaxonomy.cdm.model.description.PresenceTerm;\r
-import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
-import eu.etaxonomy.cdm.model.description.TextData;\r
-import eu.etaxonomy.cdm.model.location.NamedArea;\r
-import eu.etaxonomy.cdm.model.location.NamedAreaLevel;\r
-import eu.etaxonomy.cdm.model.location.NamedAreaType;\r
-import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;\r
-import eu.etaxonomy.cdm.model.media.Media;\r
-import eu.etaxonomy.cdm.model.name.CultivarPlantName;\r
-import eu.etaxonomy.cdm.model.name.HomotypicalGroup;\r
-import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;\r
-import eu.etaxonomy.cdm.model.name.NomenclaturalCode;\r
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;\r
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;\r
-import eu.etaxonomy.cdm.model.name.NonViralName;\r
-import eu.etaxonomy.cdm.model.name.Rank;\r
-import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
-import eu.etaxonomy.cdm.model.occurrence.Collection;\r
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;\r
-import eu.etaxonomy.cdm.model.occurrence.FieldObservation;\r
-import eu.etaxonomy.cdm.model.occurrence.Specimen;\r
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\r
-import eu.etaxonomy.cdm.model.reference.IArticle;\r
-import eu.etaxonomy.cdm.model.reference.IJournal;\r
-import eu.etaxonomy.cdm.model.reference.Reference;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceFactory;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceType;\r
-import eu.etaxonomy.cdm.model.taxon.Classification;\r
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;\r
-import eu.etaxonomy.cdm.model.taxon.Taxon;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonNode;\r
-import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;\r
-import eu.etaxonomy.cdm.strategy.parser.NameTypeParser;\r
-import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;\r
-import eu.etaxonomy.cdm.strategy.parser.SpecimenTypeParser;\r
-import eu.etaxonomy.cdm.strategy.parser.SpecimenTypeParser.TypeInfo;\r
-\r
-/**\r
- * @author a.mueller\r
- * \r
- */\r
-public class MarkupDocumentImportNoComponent extends MarkupImportBase {\r
- private static final Logger logger = Logger.getLogger(MarkupDocumentImportNoComponent.class);\r
-\r
- private static final boolean CREATE_NEW = true;\r
- private static final boolean IS_IMAGE_GALLERY = true;\r
- private static final boolean NO_IMAGE_GALLERY = false;\r
-\r
-\r
- private static final String ACCEPTED = "accepted";\r
- private static final String ACCEPTED_NAME = "acceptedName";\r
- private static final String ADDENDA = "addenda";\r
- private static final String ALTERNATEPUBTITLE = "alternatepubtitle";\r
- private static final String ALTERNATIVE_COLLECTION_TYPE_STATUS = "alternativeCollectionTypeStatus";\r
- private static final String ALTERNATIVE_COLLECTOR = "alternativeCollector";\r
- private static final String ALTERNATIVE_FIELD_NUM = "alternativeFieldNum";\r
- private static final String ALTITUDE = "altitude";\r
- private static final String ANNOTATION = "annotation";\r
- private static final String AUTHOR = "author";\r
- private static final String BIBLIOGRAPHY = "bibliography";\r
- private static final String BIOGRAPHIES = "biographies";\r
- private static final String BOLD = "bold";\r
- private static final String BR = "br";\r
- private static final String CHAR = "char";\r
- private static final String CITATION = "citation";\r
- private static final String COLLECTION_AND_TYPE = "collectionAndType";\r
- private static final String COLLECTION_TYPE_STATUS = "collectionTypeStatus";\r
- private static final String COLLECTOR = "collector";\r
- private static final String COLLECTION = "collection";\r
- private static final String COORDINATES = "coordinates";\r
- private static final String DATES = "dates";\r
- private static final String DEDICATION = "dedication";\r
- private static final String DEFAULT_MEDIA_URL = "defaultMediaUrl";\r
- private static final String DESTROYED = "destroyed";\r
- private static final String DETAILS = "details";\r
- private static final String DISTRIBUTION_LIST = "distributionList";\r
- private static final String DISTRIBUTION_LOCALITY = "distributionLocality";\r
- private static final String EDITION = "edition";\r
- private static final String EDITORS = "editors";\r
- private static final String FEATURE = "feature";\r
- private static final String FIGURE = "figure";\r
- private static final String FIGURE_LEGEND = "figureLegend";\r
- private static final String FIGURE_PART = "figurePart";\r
- private static final String FIGURE_REF = "figureRef";\r
- private static final String FIGURE_TITLE = "figureTitle";\r
- private static final String FOOTNOTE = "footnote";\r
- private static final String FOOTNOTE_REF = "footnoteRef";\r
- private static final String FOOTNOTE_STRING = "footnoteString";\r
- private static final String FIELD_NUM = "fieldNum";\r
- private static final String FREQUENCY = "frequency";\r
- private static final String FULL_NAME = "fullName";\r
- private static final String FULL_TYPE = "fullType";\r
- private static final String GATHERING = "gathering";\r
- private static final String HEADING = "heading";\r
- private static final String HABITAT = "habitat";\r
- private static final String HABITAT_LIST = "habitatList";\r
- private static final String HOMONYM = "homonym";\r
- private static final String HOMOTYPES = "homotypes";\r
- private static final String ID = "id";\r
- private static final String INFRANK = "infrank";\r
- private static final String INFRAUT = "infraut";\r
- private static final String INFRPARAUT = "infrparaut";\r
- private static final String ISSUE = "issue";\r
- private static final String ITALICS = "italics";\r
- private static final String KEY = "key";\r
- private static final String LIFE_CYCLE_PERIODS = "lifeCyclePeriods";\r
- private static final String LOCALITY = "locality";\r
- private static final String LOST = "lost";\r
- private static final String META_DATA = "metaData";\r
- private static final String NAME = "name";\r
- private static final String NAME_TYPE = "nameType";\r
- private static final String NOM = "nom";\r
- private static final String NOMENCLATURE = "nomenclature";\r
- private static final String NOT_FOUND = "notFound";\r
- private static final String NOT_SEEN = "notSeen";\r
- private static final String NOTES = "notes";\r
- private static final String ORIGINAL_DETERMINATION = "originalDetermination";\r
- private static final String PAGES = "pages";\r
- private static final String PARAUT = "paraut";\r
- private static final String PUBFULLNAME = "pubfullname";\r
- private static final String PUBLICATION = "publication";\r
- private static final String PUBNAME = "pubname";\r
- private static final String PUBTITLE = "pubtitle";\r
- private static final String PUBTYPE = "pubtype";\r
- private static final String QUOTE = "quote";\r
- private static final String RANK = "rank";\r
- private static final String REF = "ref";\r
- private static final String REF_NUM = "refNum";\r
- private static final String REF_PART = "refPart";\r
- private static final String REFERENCE = "reference";\r
- private static final String REFERENCES = "references";\r
- private static final String TAXON = "taxon";\r
- private static final String TAXONTITLE = "taxontitle";\r
- private static final String TAXONTYPE = "taxontype";\r
- private static final String TEXT_SECTION = "textSection";\r
- private static final String TYPE = "type";\r
- private static final String TYPE_STATUS = "typeStatus";\r
- private static final String TREATMENT = "treatment";\r
- private static final String SERIALS_ABBREVIATIONS = "serialsAbbreviations";\r
- private static final String SPECIMEN_TYPE = "specimenType";\r
- private static final String STATUS = "status";\r
- private static final String STRING = "string";\r
- private static final String SUB_HEADING = "subHeading";\r
- private static final String SUB_COLLECTION = "subCollection";\r
- private static final String SYNONYM = "synonym";\r
- private static final String UNKNOWN = "unknown";\r
- private static final String URL = "url";\r
- private static final String USAGE = "usage";\r
- private static final String VOLUME = "volume";\r
- private static final String WRITER = "writer";\r
- private static final String YEAR = "year";\r
-\r
- private NonViralNameParserImpl parser = new NonViralNameParserImpl();\r
-\r
- // TODO make part of state, but state is renewed when invoking the import a\r
- // second time\r
- private UnmatchedLeads unmatchedLeads;\r
-\r
-\r
- private IEditGeoService editGeoService;\r
- \r
- private MarkupKeyImport keyImport;\r
- \r
- public MarkupDocumentImportNoComponent(MarkupDocumentImport docImport) {\r
- super(docImport);\r
- this.editGeoService = docImport.getEditGeoService();\r
- keyImport = new MarkupKeyImport(docImport);\r
- }\r
-\r
- public void doInvoke(MarkupImportState state) throws XMLStreamException { \r
- XMLEventReader reader = state.getReader();\r
- \r
- // publication (= root element)\r
- String elName = PUBLICATION;\r
- boolean hasPublication = false;\r
- \r
- while (reader.hasNext()) {\r
- XMLEvent nextEvent = reader.nextEvent();\r
- if (isStartingElement(nextEvent, elName)) {\r
- handlePublication(state, reader, nextEvent, elName);\r
- hasPublication = true;\r
- } else if (nextEvent.isEndDocument()) {\r
- if (!hasPublication) {\r
- String message = "No publication root element found";\r
- fireWarningEvent(message, nextEvent, 8);\r
- }\r
- // done\r
- } else {\r
- fireSchemaConflictEventExpectedStartTag(elName, reader);\r
- }\r
- }\r
-\r
- \r
- return;\r
-\r
- }\r
-\r
- private void handlePublication(MarkupImportState state, XMLEventReader reader, XMLEvent currentEvent, String elName) throws XMLStreamException {\r
-\r
- // attributes\r
- StartElement element = currentEvent.asStartElement();\r
- Map<String, Attribute> attributes = getAttributes(element);\r
- String lang = getAndRemoveAttributeValue(attributes, "lang");\r
- if (lang != null){\r
- Language language = getTermService().getLanguageByIso(lang);\r
- state.setDefaultLanguage(language);\r
- }\r
- \r
- handleUnexpectedAttributes(element.getLocation(), attributes, "noNamespaceSchemaLocation");\r
-\r
- while (reader.hasNext()) {\r
- XMLEvent event = readNoWhitespace(reader);\r
- // TODO cardinality of alternative\r
- if (event.isEndElement()) {\r
- if (isEndingElement(event, elName)) {\r
- return;\r
- } else {\r
- if (isEndingElement(event, BIOGRAPHIES)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(event.asEndElement());\r
- } else if (isEndingElement(event, REFERENCES)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(event.asEndElement());\r
- } else if (isEndingElement(event, TEXT_SECTION)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(event.asEndElement());\r
- } else if (isEndingElement(event, ADDENDA)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(event.asEndElement());\r
- } else {\r
- handleUnexpectedElement(event);\r
- }\r
- }\r
- } else if (event.isStartElement()) {\r
- if (isStartingElement(event, META_DATA)) {\r
- handleMetaData(state, reader, event);\r
- } else if (isStartingElement(event, TREATMENT)) {\r
- handleTreatment(state, reader, event);\r
- } else if (isStartingElement(event, BIOGRAPHIES)) {\r
- handleNotYetImplementedElement(event);\r
- } else if (isStartingElement(event, REFERENCES)) {\r
- handleNotYetImplementedElement(event);\r
- } else if (isStartingElement(event, TEXT_SECTION)) {\r
- handleNotYetImplementedElement(event);\r
- } else if (isStartingElement(event, ADDENDA)) {\r
- handleNotYetImplementedElement(event);\r
- } else {\r
- handleUnexpectedStartElement(event);\r
- }\r
- } else {\r
- handleUnexpectedElement(event);\r
- }\r
- }\r
- throw new IllegalStateException("Publication has no ending element");\r
- }\r
-\r
- private void handleMetaData(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return;\r
- } else if (isStartingElement(next, DEFAULT_MEDIA_URL)) {\r
- String baseUrl = getCData(state, reader, next);\r
- try {\r
- new URL(baseUrl);\r
- state.setBaseMediaUrl(baseUrl);\r
- } catch (MalformedURLException e) {\r
- String message = "defaultMediaUrl '%s' is not a valid URL";\r
- message = String.format(message, baseUrl);\r
- fireWarningEvent(message, next, 8);\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("MetaData has no ending element");\r
-\r
- }\r
-\r
- private void handleTreatment(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
- Taxon lastTaxon = null;\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isStartingElement(next, TAXON)) {\r
- Taxon thisTaxon = handleTaxon(state, reader, next.asStartElement());\r
- doTaxonRelation(state, thisTaxon, lastTaxon, parentEvent.getLocation());\r
- lastTaxon = thisTaxon;\r
- // TODO for imports spanning multiple documents ?? Still needed?\r
- state.getConfig().setLastTaxonUuid(lastTaxon.getUuid());\r
- } else if (isMyEndingElement(next, parentEvent)) {\r
- Set<PolytomousKeyNode> keyNodesToSave = state.getPolytomousKeyNodesToSave();\r
- //better save the key then the nodes\r
- Set<PolytomousKey> keySet = new HashSet<PolytomousKey>();\r
- for (PolytomousKeyNode node : keyNodesToSave){\r
- PolytomousKey key = node.getKey();\r
- keySet.add(key);\r
- }\r
- save(keySet, state);\r
- //unmatched key leads\r
- UnmatchedLeads unmatched = state.getUnmatchedLeads();\r
- if (unmatched.size() > 0){\r
- String message = "The following key leads are unmatched: %s";\r
- message = String.format(message, state.getUnmatchedLeads().toString());\r
- fireWarningEvent(message, next, 6);\r
- }\r
-// save(keyNodesToSave, state);\r
-\r
- return;\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- return;\r
- }\r
-\r
- /**\r
- * @param taxon\r
- * @param lastTaxon\r
- */\r
- private void doTaxonRelation(MarkupImportState state, Taxon taxon,\r
- Taxon lastTaxon, Location dataLocation) {\r
-\r
- Classification tree = makeTree(state, dataLocation);\r
- if (lastTaxon == null) {\r
- tree.addChildTaxon(taxon, null, null, null);\r
- return;\r
- }\r
- Rank thisRank = taxon.getName().getRank();\r
- Rank lastRank = lastTaxon.getName().getRank();\r
- if (lastTaxon.getTaxonNodes().size() > 0) {\r
- TaxonNode lastNode = lastTaxon.getTaxonNodes().iterator().next();\r
- if (thisRank == null){\r
- String message = "rank is undefined for taxon '%s'. Can't create classification without rank.";\r
- message = String.format(message, taxon.getName().getTitleCache());\r
- fireWarningEvent(message, makeLocationStr(dataLocation), 6);\r
- }else if (thisRank.isLower(lastRank)) {\r
- lastNode.addChildTaxon(taxon, null, null, null);\r
- fillMissingEpithetsForTaxa(lastTaxon, taxon);\r
- } else if (thisRank.equals(lastRank)) {\r
- TaxonNode parent = lastNode.getParent();\r
- if (parent != null) {\r
- parent.addChildTaxon(taxon, null, null, null);\r
- fillMissingEpithetsForTaxa(parent.getTaxon(), taxon);\r
- } else {\r
- tree.addChildTaxon(taxon, null, null, null);\r
- }\r
- } else if (thisRank.isHigher(lastRank)) {\r
- doTaxonRelation(state, taxon, lastNode.getParent().getTaxon(), dataLocation);\r
- // TaxonNode parentNode = handleTaxonRelation(state, taxon,\r
- // lastNode.getParent().getTaxon());\r
- // parentNode.addChildTaxon(taxon, null, null, null);\r
- }\r
- } else {\r
-\r
- String message = "Last taxon has no node";\r
- fireWarningEvent(message, makeLocationStr(dataLocation), 6);\r
- }\r
- }\r
-\r
-\r
-\r
- /**\r
- * @param state\r
- * @param dataLocation \r
- * @return\r
- */\r
- private Classification makeTree(MarkupImportState state, Location dataLocation) {\r
- Classification result = state.getTree(null);\r
- if (result == null) {\r
- UUID uuid = state.getConfig().getClassificationUuid();\r
- if (uuid == null) {\r
- String message = "No classification uuid is defined";\r
- fireWarningEvent(message, makeLocationStr(dataLocation), 6);\r
- result = createNewClassification(state);\r
- } else {\r
- result = getClassificationService().find(uuid);\r
- if (result == null) {\r
- result = createNewClassification(state);\r
- result.setUuid(uuid);\r
- }\r
- }\r
- state.putTree(null, result);\r
- }\r
- save(result, state);\r
- return result;\r
- }\r
-\r
- private Classification createNewClassification(MarkupImportState state) {\r
- Classification result;\r
- result = Classification.NewInstance(state.getConfig().getClassificationTitle());\r
- state.putTree(null, result);\r
- return result;\r
- }\r
-\r
- private Taxon handleTaxon(MarkupImportState state, XMLEventReader reader, StartElement parentEvent) throws XMLStreamException {\r
- // TODO progress monitoring\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- Taxon taxon = createTaxonAndName(state, attributes);\r
- state.setCurrentTaxon(taxon);\r
-\r
- boolean hasTitle = false;\r
- boolean hasNomenclature = false;\r
- String taxonTitle = null;\r
-\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- checkMandatoryElement(hasTitle, parentEvent, TAXONTITLE);\r
- checkMandatoryElement(hasNomenclature, parentEvent, NOMENCLATURE);\r
- handleUnexpectedAttributes(parentEvent.getLocation(),attributes);\r
- if (taxon.getName().getRank() == null){\r
- String warning = "No rank exists for taxon " + taxon.getTitleCache();\r
- fireWarningEvent(warning, next, 12);\r
- }\r
- \r
- keyImport.makeKeyNodes(state, parentEvent, taxonTitle);\r
- state.setCurrentTaxon(null);\r
- state.setCurrentTaxonNum(null);\r
- save(taxon, state);\r
- return taxon;\r
- } else {\r
- if (isEndingElement(next, HEADING)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, TEXT_SECTION)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, REFERENCES)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, FIGURE_REF)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, HEADING)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, TAXONTITLE)) {\r
- taxonTitle = handleTaxonTitle(state, reader, next);\r
- hasTitle = true;\r
- } else if (isStartingElement(next, WRITER)) {\r
- makeKeyWriter(state, reader, taxon, taxonTitle, next);\r
- } else if (isStartingElement(next, TEXT_SECTION)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, KEY)) {\r
- keyImport.handleKey(state, reader, next);\r
- } else if (isStartingElement(next, NOMENCLATURE)) {\r
- handleNomenclature(state, reader, next);\r
- hasNomenclature = true;\r
- } else if (isStartingElement(next, FEATURE)) {\r
- handleFeature(state, reader, next);\r
- } else if (isStartingElement(next, NOTES)) {\r
- // TODO is this the correct way to handle notes?\r
- String note = handleNotes(state, reader, next);\r
-\r
- UUID notesUuid;\r
- try {\r
- notesUuid = state.getTransformer().getFeatureUuid(\r
- "notes");\r
- Feature feature = getFeature(state, notesUuid, "Notes",\r
- "Notes", "note", null);\r
- TextData textData = TextData.NewInstance(feature);\r
- textData.putText(Language.DEFAULT(), note);\r
- TaxonDescription description = getTaxonDescription(\r
- taxon, null, false, true);\r
- description.addElement(textData);\r
- } catch (UndefinedTransformerMethodException e) {\r
- String message = "getFeatureUuid method not yet implemented";\r
- fireWarningEvent(message, next, 8);\r
- }\r
- } else if (isStartingElement(next, REFERENCES)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, FIGURE_REF)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, FIGURE)) {\r
- handleFigure(state, reader, next);\r
- } else if (isStartingElement(next, FOOTNOTE)) {\r
- FootnoteDataHolder footnote = handleFootnote(state, reader, next);\r
- if (footnote.isRef()) {\r
- String message = "Ref footnote not implemented here";\r
- fireWarningEvent(message, next, 4);\r
- } else {\r
- registerGivenFootnote(state, footnote);\r
- }\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<Taxon> has no closing tag");\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param taxon\r
- * @param taxonTitle\r
- * @param next\r
- * @throws XMLStreamException\r
- */\r
- private void makeKeyWriter(MarkupImportState state, XMLEventReader reader, Taxon taxon, String taxonTitle, XMLEvent next) throws XMLStreamException {\r
- WriterDataHolder writer = handleWriter(state, reader, next);\r
- taxon.addExtension(writer.extension);\r
- // TODO what if taxonTitle comes later\r
- if (StringUtils.isNotBlank(taxonTitle)\r
- && writer.extension != null) {\r
- Reference<?> sec = ReferenceFactory.newBookSection();\r
- sec.setTitle(taxonTitle);\r
- TeamOrPersonBase<?> author = createAuthor(writer.writer);\r
- sec.setAuthorTeam(author);\r
- sec.setInReference(state.getConfig()\r
- .getSourceReference());\r
- taxon.setSec(sec);\r
- registerFootnotes(state, sec, writer.footnotes);\r
- } else {\r
- String message = "No taxontitle exists for writer";\r
- fireWarningEvent(message, next, 6);\r
- }\r
- }\r
-\r
- private String handleNotes(MarkupImportState state, XMLEventReader reader,\r
- XMLEvent parentEvent) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return text;\r
- } else if (next.isEndElement()) {\r
- if (isEndingElement(next, HEADING)) {\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, WRITER)) {\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, NUM)) {\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, HEADING)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, SUB_HEADING)) {\r
- String subheading = getCData(state, reader, next).trim();\r
- if (! isNoteHeading(subheading)) {\r
- fireNotYetImplementedElement(next.getLocation(), next.asStartElement().getName(), 0);\r
- }\r
- } else if (isStartingElement(next, WRITER)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, NUM)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, STRING)) {\r
- // TODO why multiple strings in schema?\r
- text = makeNotesString(state, reader, text, next);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<Notes> has no closing tag");\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param text\r
- * @param next\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private String makeNotesString(MarkupImportState state, XMLEventReader reader, String text, XMLEvent next) throws XMLStreamException {\r
- Map<String, String> stringMap = handleString(state, reader, next, null);\r
- if (stringMap.size() == 0){\r
- String message = "No text available in <notes>";\r
- fireWarningEvent(message, next, 4);\r
- }else if (stringMap.size() > 1){\r
- String message = "Subheadings not yet supported in <notes>";\r
- fireWarningEvent(message, next, 4);\r
- }else{\r
- String firstSubheading = stringMap.keySet().iterator().next();\r
- if ( firstSubheading != null && ! isNoteHeading (firstSubheading) ) {\r
- String message = "Subheadings not yet supported in <notes>";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- }\r
- for (String subheading : stringMap.keySet()){\r
- text += subheading;\r
- text += stringMap.get(subheading);\r
- }\r
- return text;\r
- }\r
-\r
- private boolean isNoteHeading(String heading) {\r
- String excludePattern = "(i?)(Notes?):?";\r
- return heading.matches(excludePattern);\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param attributes\r
- */\r
- private Taxon createTaxonAndName(MarkupImportState state,\r
- Map<String, Attribute> attributes) {\r
- NonViralName<?> name;\r
- Rank rank = null; //Rank.SPECIES(); // default\r
- boolean isCultivar = checkAndRemoveAttributeValue(attributes, CLASS, "cultivated");\r
- if (isCultivar) {\r
- name = CultivarPlantName.NewInstance(rank);\r
- } else {\r
- name = createNameByCode(state, rank);\r
- }\r
- Taxon taxon = Taxon.NewInstance(name, state.getConfig().getSourceReference());\r
- if (checkAndRemoveAttributeValue(attributes, CLASS, "dubious")) {\r
- taxon.setDoubtful(true);\r
- } else if (checkAndRemoveAttributeValue(attributes, CLASS, "excluded")) {\r
- taxon.setExcluded(true);\r
- }\r
- // TODO insufficient, new, expected\r
- handleNotYetImplementedAttribute(attributes, CLASS);\r
- // From old version\r
- // MarkerType markerType = getMarkerType(state, attrValue);\r
- // if (markerType == null){\r
- // logger.warn("Class attribute value for taxon not yet supported: " +\r
- // attrValue);\r
- // }else{\r
- // taxon.addMarker(Marker.NewInstance(markerType, true));\r
- // }\r
-\r
- // save(name, state);\r
- // save(taxon, state);\r
- return taxon;\r
- }\r
-\r
- private String handleTaxonTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- //attributes\r
- String text = "";\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String rankAttr = getAndRemoveAttributeValue(attributes, RANK);\r
- Rank rank = makeRank(state, rankAttr, false);\r
- String num = getAndRemoveAttributeValue(attributes, NUM);\r
- state.setCurrentTaxonNum(num);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- // TODO handle attributes\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- Taxon taxon = state.getCurrentTaxon();\r
- String titleText = null;\r
- if (checkMandatoryText(text, parentEvent)) {\r
- titleText = normalize(text);\r
- UUID uuidTitle = MarkupTransformer.uuidTaxonTitle;\r
- ExtensionType titleExtension = this.getExtensionType(state, uuidTitle, "Taxon Title ","taxon title", "title");\r
- taxon.addExtension(titleText, titleExtension);\r
- }\r
- taxon.getName().setRank(rank);\r
- // TODO check title exists\r
- return titleText;\r
- } else {\r
- if (isEndingElement(next, FOOTNOTE)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- state.setUnsuccessfull();\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, FOOTNOTE)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- state.setUnsuccessfull();\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
-\r
- } else {\r
- handleUnexpectedElement(next);\r
- state.setUnsuccessfull();\r
- }\r
- }\r
- return null;\r
-\r
- }\r
-\r
- private WriterDataHolder handleWriter(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- String text = "";\r
- checkNoAttributes(parentEvent);\r
- WriterDataHolder dataHolder = new WriterDataHolder();\r
- List<FootnoteDataHolder> footnotes = new ArrayList<FootnoteDataHolder>();\r
-\r
- // TODO handle attributes\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- text = CdmUtils.removeBrackets(text);\r
- if (checkMandatoryText(text, parentEvent)) {\r
- text = normalize(text);\r
- dataHolder.writer = text;\r
- dataHolder.footnotes = footnotes;\r
-\r
- // Extension\r
- UUID uuidWriterExtension = MarkupTransformer.uuidWriterExtension;\r
- ExtensionType writerExtensionType = this\r
- .getExtensionType(state, uuidWriterExtension,\r
- "Writer", "writer", "writer");\r
- Extension extension = Extension.NewInstance();\r
- extension.setType(writerExtensionType);\r
- extension.setValue(text);\r
- dataHolder.extension = extension;\r
-\r
- // Annotation\r
- UUID uuidWriterAnnotation = MarkupTransformer.uuidWriterAnnotation;\r
- AnnotationType writerAnnotationType = this.getAnnotationType(state, uuidWriterAnnotation, "Writer", "writer", "writer", null);\r
- Annotation annotation = Annotation.NewInstance(text, writerAnnotationType, Language.DEFAULT());\r
- dataHolder.annotation = annotation;\r
-\r
- return dataHolder;\r
- } else {\r
- return null;\r
- }\r
- } else if (isStartingElement(next, FOOTNOTE_REF)) {\r
- FootnoteDataHolder footNote = handleFootnoteRef(state, reader, next);\r
- if (footNote.isRef()) {\r
- footnotes.add(footNote);\r
- } else {\r
- logger.warn("Non ref footnotes not yet impelemnted");\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
-\r
- } else {\r
- handleUnexpectedElement(next);\r
- state.setUnsuccessfull();\r
- }\r
- }\r
- throw new IllegalStateException("<writer> has no end tag");\r
- }\r
-\r
- private void registerFootnotes(MarkupImportState state, AnnotatableEntity entity, List<FootnoteDataHolder> footnotes) {\r
- for (FootnoteDataHolder footNote : footnotes) {\r
- registerFootnoteDemand(state, entity, footNote);\r
- }\r
- }\r
-\r
- private void registerGivenFootnote(MarkupImportState state, FootnoteDataHolder footnote) {\r
- state.registerFootnote(footnote);\r
- Set<AnnotatableEntity> demands = state.getFootnoteDemands(footnote.id);\r
- if (demands != null) {\r
- for (AnnotatableEntity entity : demands) {\r
- attachFootnote(state, entity, footnote);\r
- }\r
- }\r
- }\r
-\r
- private void registerGivenFigure(MarkupImportState state, String id, Media figure) {\r
- state.registerFigure(id, figure);\r
- Set<AnnotatableEntity> demands = state.getFigureDemands(id);\r
- if (demands != null) {\r
- for (AnnotatableEntity entity : demands) {\r
- attachFigure(state, entity, figure);\r
- }\r
- }\r
- }\r
-\r
- private void registerFootnoteDemand(MarkupImportState state, AnnotatableEntity entity, FootnoteDataHolder footnote) {\r
- FootnoteDataHolder existingFootnote = state.getFootnote(footnote.ref);\r
- if (existingFootnote != null) {\r
- attachFootnote(state, entity, existingFootnote);\r
- } else {\r
- Set<AnnotatableEntity> demands = state.getFootnoteDemands(footnote.ref);\r
- if (demands == null) {\r
- demands = new HashSet<AnnotatableEntity>();\r
- state.putFootnoteDemands(footnote.ref, demands);\r
- }\r
- demands.add(entity);\r
- }\r
- }\r
-\r
- private void registerFigureDemand(MarkupImportState state, AnnotatableEntity entity, String figureRef) {\r
- Media existingFigure = state.getFigure(figureRef);\r
- if (existingFigure != null) {\r
- attachFigure(state, entity, existingFigure);\r
- } else {\r
- Set<AnnotatableEntity> demands = state.getFigureDemands(figureRef);\r
- if (demands == null) {\r
- demands = new HashSet<AnnotatableEntity>();\r
- state.putFigureDemands(figureRef, demands);\r
- }\r
- demands.add(entity);\r
- }\r
- }\r
-\r
- private void attachFootnote(MarkupImportState state, AnnotatableEntity entity, FootnoteDataHolder footnote) {\r
- AnnotationType annotationType = this.getAnnotationType(state, MarkupTransformer.uuidFootnote, "Footnote", "An e-flora footnote", "fn", null);\r
- Annotation annotation = Annotation.NewInstance(footnote.string,\r
- annotationType, Language.DEFAULT());\r
- // TODO transient objects\r
- entity.addAnnotation(annotation);\r
- save(entity, state);\r
- }\r
-\r
- private void attachFigure(MarkupImportState state,\r
- AnnotatableEntity entity, Media figure) {\r
- // IdentifiableEntity<?> toSave;\r
- if (entity.isInstanceOf(TextData.class)) {\r
- TextData deb = CdmBase.deproxy(entity, TextData.class);\r
- deb.addMedia(figure);\r
- // toSave = ((TaxonDescription)deb.getInDescription()).getTaxon();\r
- } else if (entity.isInstanceOf(IdentifiableMediaEntity.class)) {\r
- IdentifiableMediaEntity<?> ime = CdmBase.deproxy(entity,\r
- IdentifiableMediaEntity.class);\r
- ime.addMedia(figure);\r
- // toSave = ime;\r
- } else {\r
- String message = "Unsupported entity to attach media: %s";\r
- message = String.format(message, entity.getClass().getName());\r
- // toSave = null;\r
- }\r
- save(entity, state);\r
- }\r
-\r
- private void handleFigure(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- // FigureDataHolder result = new FigureDataHolder();\r
-\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String id = getAndRemoveAttributeValue(attributes, ID);\r
- String type = getAndRemoveAttributeValue(attributes, TYPE);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- String urlString = null;\r
- String legendString = null;\r
- String titleString = null;\r
- String numString = null;\r
- String text = null;\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- makeFigure(state, id, type, urlString, legendString, titleString, numString, next);\r
- return;\r
- } else if (isStartingElement(next, FIGURE_LEGEND)) {\r
- // TODO same as figurestring ?\r
- legendString = handleFootnoteString(state, reader, next);\r
- } else if (isStartingElement(next, FIGURE_TITLE)) {\r
- titleString = getCData(state, reader, next);\r
- } else if (isStartingElement(next, URL)) {\r
- String localUrl = getCData(state, reader, next);\r
- urlString = CdmUtils.Nz(state.getBaseMediaUrl()) + localUrl;\r
- } else if (isStartingElement(next, NUM)) {\r
- numString = getCData(state, reader, next);\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- fireUnexpectedEvent(next, 0);\r
- }\r
- }\r
- throw new IllegalStateException("<figure> has no end tag");\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param id\r
- * @param type\r
- * @param urlString\r
- * @param legendString\r
- * @param titleString\r
- * @param numString\r
- * @param next\r
- */\r
- private void makeFigure(MarkupImportState state, String id, String type, String urlString, \r
- String legendString, String titleString, String numString, XMLEvent next) {\r
- Media media = null;\r
- boolean isFigure = false;\r
- try {\r
- //TODO maybe everything is a figure as it is all taken from a book\r
- if ("lineart".equals(type)) {\r
- isFigure = true;\r
-// media = Figure.NewInstance(url.toURI(), null, null, null);\r
- } else if (type == null || "photo".equals(type)\r
- || "signature".equals(type)\r
- || "others".equals(type)) {\r
- } else {\r
- String message = "Unknown figure type '%s'";\r
- message = String.format(message, type);\r
- fireWarningEvent(message, next, 2);\r
- }\r
- media = docImport.getImageMedia(urlString, docImport.getReadMediaData(), isFigure);\r
- \r
- if (media != null){\r
- // title\r
- if (StringUtils.isNotBlank(titleString)) {\r
- media.putTitle(Language.DEFAULT(), titleString);\r
- }\r
- // legend\r
- if (StringUtils.isNotBlank(legendString)) {\r
- media.addDescription(legendString, Language.DEFAULT());\r
- }\r
- if (StringUtils.isNotBlank(numString)) {\r
- // TODO use concrete source (e.g. DAPHNIPHYLLACEAE in FM\r
- // vol.13)\r
- Reference<?> citation = state.getConfig().getSourceReference();\r
- media.addSource(numString, "num", citation, null);\r
- // TODO name used in source if available\r
- }\r
- // TODO which citation\r
- if (StringUtils.isNotBlank(id)) {\r
- media.addSource(id, null, state.getConfig().getSourceReference(), null);\r
- } else {\r
- String message = "Figure id should never be empty or null";\r
- fireWarningEvent(message, next, 6);\r
- }\r
- \r
- // text\r
- // do nothing\r
-\r
- }\r
- } catch (MalformedURLException e) {\r
- String message = "Media uri has incorrect syntax: %s";\r
- message = String.format(message, urlString);\r
- fireWarningEvent(message, next, 4);\r
-// } catch (URISyntaxException e) {\r
-// String message = "Media uri has incorrect syntax: %s";\r
-// message = String.format(message, urlString);\r
-// fireWarningEvent(message, next, 4);\r
- }\r
-\r
- registerGivenFigure(state, id, media);\r
- }\r
-\r
- private FigureDataHolder handleFigureRef(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- throws XMLStreamException {\r
- FigureDataHolder result = new FigureDataHolder();\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- result.ref = getAndRemoveAttributeValue(attributes, REF);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- // text is not handled, needed only for debugging purposes\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return result;\r
- } else if (isStartingElement(next, NUM)) {\r
- String num = getCData(state, reader, next);\r
- result.num = num; // num is not handled during import\r
- } else if (isStartingElement(next, FIGURE_PART)) {\r
- result.figurePart = getCData(state, reader, next);\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- fireUnexpectedEvent(next, 0);\r
- }\r
- }\r
- throw new IllegalStateException("<figureRef> has no end tag");\r
- }\r
-\r
- private FootnoteDataHolder handleFootnote(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- FootnoteDataHolder result = new FootnoteDataHolder();\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- result.id = getAndRemoveAttributeValue(attributes, ID);\r
- // result.ref = getAndRemoveAttributeValue(attributes, REF);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isStartingElement(next, FOOTNOTE_STRING)) {\r
- String string = handleFootnoteString(state, reader, next);\r
- result.string = string;\r
- } else if (isMyEndingElement(next, parentEvent)) {\r
- return result;\r
- } else {\r
- fireUnexpectedEvent(next, 0);\r
- }\r
- }\r
- return result;\r
- }\r
-\r
- private FootnoteDataHolder handleFootnoteRef(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- throws XMLStreamException {\r
- FootnoteDataHolder result = new FootnoteDataHolder();\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- result.ref = getAndRemoveAttributeValue(attributes, REF);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- // text is not handled, needed only for debugging purposes\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- // if (isStartingElement(next, FOOTNOTE_STRING)){\r
- // String string = handleFootnoteString(state, reader, next);\r
- // result.string = string;\r
- // }else\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return result;\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
-\r
- } else {\r
- fireUnexpectedEvent(next, 0);\r
- }\r
- }\r
- return result;\r
- }\r
-\r
- private void handleNomenclature(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isStartingElement(next, HOMOTYPES)) {\r
- handleHomotypes(state, reader, next.asStartElement());\r
- } else if (isMyEndingElement(next, parentEvent)) {\r
- return;\r
- } else {\r
- fireSchemaConflictEventExpectedStartTag(HOMOTYPES, reader);\r
- state.setUnsuccessfull();\r
- }\r
- }\r
- return;\r
- }\r
-\r
- private String handleFootnoteString(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- boolean isTextMode = true;\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return text;\r
- } else if (next.isEndElement()) {\r
- if (isEndingElement(next, FULL_NAME)) {\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, BR)) {\r
- isTextMode = true;\r
- } else if (isHtml(next)) {\r
- text += getXmlTag(next);\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, FULL_NAME)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, GATHERING)) {\r
- text += handleInLineGathering(state, reader, next);\r
- } else if (isStartingElement(next, REFERENCES)) {\r
- text += " " + handleInLineReferences(state, reader, next)+ " ";\r
- } else if (isStartingElement(next, BR)) {\r
- text += "<br/>";\r
- isTextMode = false;\r
- } else if (isHtml(next)) {\r
- text += getXmlTag(next);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- if (!isTextMode) {\r
- String message = "footnoteString is not in text mode";\r
- fireWarningEvent(message, next, 6);\r
- } else {\r
- text += next.asCharacters().getData().trim(); \r
- // getCData(state, reader, next); does not work as we have inner tags like <references>\r
- }\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("<footnoteString> has no closing tag");\r
-\r
- }\r
-\r
- private String handleInLineGathering(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(DerivedUnitType.DerivedUnit.FieldObservation);\r
- handleGathering(state, reader, parentEvent, facade);\r
- FieldObservation fieldObservation = facade.innerFieldObservation();\r
- String result = "<cdm:specimen uuid='%s'>%s</specimen>";\r
- result = String.format(result, fieldObservation.getUuid(), fieldObservation.getTitleCache());\r
- save(fieldObservation, state);\r
- return result; \r
- }\r
-\r
- private String handleInLineReferences(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- boolean hasReference = false;\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- checkMandatoryElement(hasReference, parentEvent.asStartElement(), REFERENCE);\r
- return text;\r
- } else if (isStartingElement(next, REFERENCE)) {\r
- text += handleInLineReference(state, reader, next);\r
- hasReference = true;\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<References> has no closing tag");\r
- }\r
-\r
- private String handleInLineReference(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {\r
- Reference<?> reference = handleReference(state, reader, parentEvent);\r
- String result = "<cdm:ref uuid='%s'>%s</ref>";\r
- result = String.format(result, reference.getUuid(), reference.getTitleCache());\r
- save(reference, state);\r
- return result;\r
- }\r
-\r
- private Reference<?> handleReference(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- boolean hasRefPart = false;\r
- Map<String, String> refMap = new HashMap<String, String>();\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- checkMandatoryElement(hasRefPart, parentEvent.asStartElement(),\r
- REF_PART);\r
- Reference<?> reference = createReference(state, refMap, next);\r
- return reference;\r
- } else if (isStartingElement(next, REF_PART)) {\r
- handleRefPart(state, reader, next, refMap);\r
- hasRefPart = true;\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- // TODO handle missing end element\r
- throw new IllegalStateException("<Reference> has no closing tag");\r
- }\r
-\r
- private void handleHomotypes(MarkupImportState state, XMLEventReader reader, StartElement parentEvent)\r
- throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- HomotypicalGroup homotypicalGroup = null;\r
-\r
- boolean hasNom = false;\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- checkMandatoryElement(hasNom, parentEvent, NOM);\r
- return;\r
- } else {\r
- if (isEndingElement(next, NAME_TYPE)) {\r
- state.setNameType(false);\r
- } else if (isEndingElement(next, NOTES)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, NOM)) {\r
- NonViralName<?> name = handleNom(state, reader, next, homotypicalGroup);\r
- homotypicalGroup = name.getHomotypicalGroup();\r
- hasNom = true;\r
- } else if (isStartingElement(next, NAME_TYPE)) {\r
- state.setNameType(true);\r
- handleNameType(state, reader, next, homotypicalGroup);\r
- } else if (isStartingElement(next, SPECIMEN_TYPE)) {\r
- handleSpecimenType(state, reader, next, homotypicalGroup);\r
- } else if (isStartingElement(next, NOTES)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- // TODO handle missing end element\r
- throw new IllegalStateException("Homotypes has no closing tag");\r
-\r
- }\r
-\r
- private void handleNameType(MarkupImportState state, XMLEventReader reader,\r
- XMLEvent parentEvent, HomotypicalGroup homotypicalGroup)\r
- throws XMLStreamException {\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String typeStatus = getAndRemoveAttributeValue(attributes, TYPE_STATUS);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- NameTypeDesignationStatus status;\r
- try {\r
- status = NameTypeParser.parseNameTypeStatus(typeStatus);\r
- } catch (UnknownCdmTypeException e) {\r
- String message = "Type status could not be recognized: %s";\r
- message = String.format(message, typeStatus);\r
- fireWarningEvent(message, parentEvent, 4);\r
- status = null;\r
- }\r
-\r
- boolean hasNom = false;\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- checkMandatoryElement(hasNom, parentEvent.asStartElement(),\r
- NOM);\r
- state.setNameType(false);\r
- return;\r
- } else {\r
- if (isEndingElement(next, ACCEPTED_NAME)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, NOM)) {\r
- // TODO should we check if the type is always a species, is\r
- // this a rule?\r
- NonViralName<?> speciesName = handleNom(state, reader,\r
- next, null);\r
- for (TaxonNameBase<?, ?> name : homotypicalGroup\r
- .getTypifiedNames()) {\r
- name.addNameTypeDesignation(speciesName, null, null,\r
- null, status, false, false, false, false);\r
- }\r
- hasNom = true;\r
- } else if (isStartingElement(next, ACCEPTED_NAME)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- // TODO handle missing end element\r
- throw new IllegalStateException("Homotypes has no closing tag");\r
-\r
- }\r
-\r
- private void handleSpecimenType(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent,\r
- HomotypicalGroup homotypicalGroup) throws XMLStreamException {\r
- // attributes\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String typeStatus = getAndRemoveAttributeValue(attributes, TYPE_STATUS);\r
- String notSeen = getAndRemoveAttributeValue(attributes, NOT_SEEN);\r
- String unknown = getAndRemoveAttributeValue(attributes, UNKNOWN);\r
- String notFound = getAndRemoveAttributeValue(attributes, NOT_FOUND);\r
- String destroyed = getAndRemoveAttributeValue(attributes, DESTROYED);\r
- String lost = getAndRemoveAttributeValue(attributes, LOST);\r
- checkNoAttributes(attributes, parentEvent);\r
- if (StringUtils.isNotEmpty(typeStatus)) {\r
- // TODO\r
- // currently not needed\r
- } else if (StringUtils.isNotEmpty(notSeen)) {\r
- handleNotYetImplementedAttribute(attributes, NOT_SEEN);\r
- } else if (StringUtils.isNotEmpty(unknown)) {\r
- handleNotYetImplementedAttribute(attributes, UNKNOWN);\r
- } else if (StringUtils.isNotEmpty(notFound)) {\r
- handleNotYetImplementedAttribute(attributes, NOT_FOUND);\r
- } else if (StringUtils.isNotEmpty(destroyed)) {\r
- handleNotYetImplementedAttribute(attributes, DESTROYED);\r
- } else if (StringUtils.isNotEmpty(lost)) {\r
- handleNotYetImplementedAttribute(attributes, LOST);\r
- }\r
-\r
- NonViralName<?> firstName = null;\r
- Set<TaxonNameBase> names = homotypicalGroup.getTypifiedNames();\r
- if (names.isEmpty()) {\r
- String message = "There is no name in a homotypical group. Can't create the specimen type";\r
- fireWarningEvent(message, parentEvent, 8);\r
- } else {\r
- firstName = CdmBase.deproxy(names.iterator().next(),NonViralName.class);\r
- }\r
-\r
- DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(DerivedUnitType.Specimen);\r
- String text = "";\r
- // elements\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- makeSpecimenType(state, facade, text, firstName, parentEvent);\r
- return;\r
- } else {\r
- if (isEndingElement(next, FULL_TYPE)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, TYPE_STATUS)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, ORIGINAL_DETERMINATION)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, SPECIMEN_TYPE)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, COLLECTION_AND_TYPE)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, CITATION)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, NOTES)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, ANNOTATION)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, FULL_TYPE)) {\r
- handleNotYetImplementedElement(next);\r
- // homotypicalGroup = handleNom(state, reader, next, taxon,\r
- // homotypicalGroup);\r
- } else if (isStartingElement(next, TYPE_STATUS)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, GATHERING)) {\r
- handleGathering(state, reader, next, facade);\r
- } else if (isStartingElement(next, ORIGINAL_DETERMINATION)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, SPECIMEN_TYPE)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, COLLECTION_AND_TYPE)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, CITATION)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, NOTES)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, ANNOTATION)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- // TODO handle missing end element\r
- throw new IllegalStateException("Specimen type has no closing tag"); \r
- }\r
-\r
- private void makeSpecimenType(MarkupImportState state, DerivedUnitFacade facade, String text, \r
- NonViralName name, XMLEvent parentEvent) {\r
- text = text.trim();\r
- // remove brackets\r
- if (text.matches("^\\(.*\\)\\.?$")) {\r
- text = text.replaceAll("\\.", "");\r
- text = text.substring(1, text.length() - 1);\r
- }\r
- String[] split = text.split("[;,]");\r
- for (String str : split) {\r
- str = str.trim();\r
- boolean addToAllNamesInGroup = true;\r
- TypeInfo typeInfo = makeSpecimenTypeTypeInfo(str, parentEvent);\r
- SpecimenTypeDesignationStatus typeStatus = typeInfo.status;\r
- Collection collection = createCollection(typeInfo.collectionString);\r
-\r
- // TODO improve cache strategy handling\r
- DerivedUnitBase typeSpecimen = facade.addDuplicate(collection,\r
- null, null, null, null);\r
- typeSpecimen.setCacheStrategy(new DerivedUnitFacadeCacheStrategy());\r
- name.addSpecimenTypeDesignation((Specimen) typeSpecimen, typeStatus, null, null, null, false, addToAllNamesInGroup);\r
- }\r
- }\r
-\r
- private Collection createCollection(String code) {\r
- // TODO deduplicate\r
- // TODO code <-> name\r
- Collection result = Collection.NewInstance();\r
- result.setCode(code);\r
- return result;\r
- }\r
-\r
- private TypeInfo makeSpecimenTypeTypeInfo(String originalString, XMLEvent event) {\r
- TypeInfo result = new TypeInfo();\r
- String[] split = originalString.split("\\s+");\r
- for (String str : split) {\r
- if (str.matches(SpecimenTypeParser.typeTypePattern)) {\r
- SpecimenTypeDesignationStatus status;\r
- try {\r
- status = SpecimenTypeParser.parseSpecimenTypeStatus(str);\r
- } catch (UnknownCdmTypeException e) {\r
- String message = "Specimen type status '%s' not recognized by parser";\r
- message = String.format(message, str);\r
- fireWarningEvent(message, event, 4);\r
- status = null;\r
- }\r
- result.status = status;\r
- } else if (str.matches(SpecimenTypeParser.collectionPattern)) {\r
- result.collectionString = str;\r
- } else {\r
- String message = "Type part '%s' could not be recognized";\r
- message = String.format(message, str);\r
- fireWarningEvent(message, event, 2);\r
- }\r
- }\r
-\r
- return result;\r
- }\r
-\r
- \r
- private void handleGathering(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent , DerivedUnitFacade facade) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
- boolean hasCollector = false;\r
- boolean hasFieldNum = false;\r
-\r
- // elements\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- checkMandatoryElement(hasCollector,parentEvent.asStartElement(), COLLECTOR);\r
- checkMandatoryElement(hasFieldNum,parentEvent.asStartElement(), FIELD_NUM);\r
- return;\r
- } else {\r
- if (isEndingElement(next, ALTERNATIVE_COLLECTOR)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, ALTERNATIVE_FIELD_NUM)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, COLLECTION_TYPE_STATUS)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, COLLECTION_AND_TYPE)) {\r
- // NOT YET IMPLEMENTED , does this make sense here? \r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next,\r
- ALTERNATIVE_COLLECTION_TYPE_STATUS)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, SUB_COLLECTION)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, COLLECTION)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, DATES)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, NOTES)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, COLLECTOR)) {\r
- hasCollector = true;\r
- String collectorStr = getCData(state, reader, next);\r
- AgentBase<?> collector = createCollector(collectorStr);\r
- facade.setCollector(collector);\r
- } else if (isStartingElement(next, ALTERNATIVE_COLLECTOR)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, FIELD_NUM)) {\r
- hasFieldNum = true;\r
- String fieldNumStr = getCData(state, reader, next);\r
- facade.setFieldNumber(fieldNumStr);\r
- } else if (isStartingElement(next, ALTERNATIVE_FIELD_NUM)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, COLLECTION_TYPE_STATUS)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, COLLECTION_AND_TYPE)) { //does this make sense here?\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, ALTERNATIVE_COLLECTION_TYPE_STATUS)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, SUB_COLLECTION)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, COLLECTION)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, LOCALITY)) {\r
- handleLocality(state, reader, next, facade);\r
- } else if (isStartingElement(next, DATES)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, NOTES)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- // TODO handle missing end element\r
- throw new IllegalStateException("Collection has no closing tag");\r
-\r
- }\r
-\r
- private void handleLocality(MarkupImportState state, XMLEventReader reader,XMLEvent parentEvent, DerivedUnitFacade facade)throws XMLStreamException {\r
- String classValue = getClassOnlyAttribute(parentEvent);\r
- boolean isLocality = false;\r
- NamedAreaLevel areaLevel = null;\r
- if ("locality".equalsIgnoreCase(classValue)) {\r
- isLocality = true;\r
- } else {\r
- areaLevel = makeNamedAreaLevel(state, classValue, parentEvent);\r
- }\r
-\r
- String text = "";\r
- // elements\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- if (StringUtils.isNotBlank(text)) {\r
- text = normalize(text);\r
- if (isLocality) {\r
- facade.setLocality(text);\r
- } else {\r
- text = CdmUtils.removeTrailingDot(text);\r
- NamedArea area = makeArea(state, text, areaLevel);\r
- facade.addCollectingArea(area);\r
- }\r
- }\r
- // TODO\r
- return;\r
- } else {\r
- if (isEndingElement(next, ALTITUDE)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, COORDINATES)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, ANNOTATION)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, ALTITUDE)) {\r
- handleNotYetImplementedElement(next);\r
- // homotypicalGroup = handleNom(state, reader, next, taxon,\r
- // homotypicalGroup);\r
- } else if (isStartingElement(next, COORDINATES)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, ANNOTATION)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<SpecimenType> has no closing tag"); \r
- }\r
-\r
-// private NamedArea createArea(String text, NamedAreaLevel areaLevel, MarkupImportState state) {\r
-// NamedArea area = NamedArea.NewInstance(text, text, null);\r
-// area.setLevel(areaLevel);\r
-// save(area, state);\r
-// return area;\r
-// }\r
-\r
- private AgentBase<?> createCollector(String collectorStr) {\r
- return createAuthor(collectorStr);\r
- }\r
-\r
- /**\r
- * Creates the name defined by a nom tag. Adds it to the given homotypical\r
- * group (if not null).\r
- * \r
- * @param state\r
- * @param reader\r
- * @param parentEvent\r
- * @param homotypicalGroup\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private NonViralName<?> handleNom(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent,\r
- HomotypicalGroup homotypicalGroup) throws XMLStreamException {\r
- boolean isSynonym = false;\r
- boolean isNameType = state.isNameType();\r
- // attributes\r
- String classValue = getClassOnlyAttribute(parentEvent);\r
- NonViralName<?> name;\r
- if (!isNameType && ACCEPTED.equalsIgnoreCase(classValue)) {\r
- isSynonym = false;\r
- name = createName(state, homotypicalGroup, isSynonym);\r
- } else if (!isNameType && SYNONYM.equalsIgnoreCase(classValue)) {\r
- isSynonym = true;\r
- name = createName(state, homotypicalGroup, isSynonym);\r
- } else if (isNameType && NAME_TYPE.equalsIgnoreCase(classValue)) {\r
- // TODO do we need to define the rank here?\r
- name = createNameByCode(state, null);\r
- } else {\r
- fireUnexpectedAttributeValue(parentEvent, CLASS, classValue);\r
- name = createNameByCode(state, null);\r
- }\r
-\r
- Map<String, String> nameMap = new HashMap<String, String>();\r
-\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- // fill the name with all data gathered\r
- fillName(state, nameMap, name, next);\r
- return name;\r
- } else {\r
- if (isEndingElement(next, FULL_NAME)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, HOMONYM)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, NOTES)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, ANNOTATION)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, FULL_NAME)) {\r
- handleNotYetImplementedElement(next);\r
- // homotypicalGroup = handleNom(state, reader, next, taxon,\r
- // homotypicalGroup);\r
- } else if (isStartingElement(next, NUM)) {\r
- String num = getCData(state, reader, next);\r
- num = num.replace(".", "");\r
- num = num.replace(")", "");\r
- if (StringUtils.isNotBlank(num)){\r
- if (state.getCurrentTaxonNum() != null && ! state.getCurrentTaxonNum().equals(num) ){\r
- String message = "Taxontitle num and homotypes/nom/num differ ( %s <-> %s ). I use the later one.";\r
- message = String.format(message, state.getCurrentTaxonNum(), num);\r
- fireWarningEvent(message, next, 4);\r
- }\r
- state.setCurrentTaxonNum(num);\r
- }\r
- } else if (isStartingElement(next, NAME)) {\r
- handleName(state, reader, next, nameMap);\r
- } else if (isStartingElement(next, CITATION)) {\r
- handleCitation(state, reader, next, name);\r
- } else if (isStartingElement(next, HOMONYM)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, NOTES)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, ANNOTATION)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- // TODO handle missing end element\r
- throw new IllegalStateException("Nom has no closing tag");\r
-\r
- }\r
-\r
- private void fillName(MarkupImportState state, Map<String, String> nameMap,\r
- NonViralName<?> name, XMLEvent event) {\r
-\r
- // Ranks: family, subfamily, tribus, genus, subgenus, section,\r
- // subsection, species, subspecies, variety, subvariety, forma\r
- // infrank, paraut, author, infrparaut, infraut, status, notes\r
-\r
- String infrank = getAndRemoveMapKey(nameMap, INFRANK);\r
- String authorStr = getAndRemoveMapKey(nameMap, AUTHOR);\r
- String paraut = getAndRemoveMapKey(nameMap, PARAUT);\r
-\r
- String infrParAut = getAndRemoveMapKey(nameMap, INFRPARAUT);\r
- String infrAut = getAndRemoveMapKey(nameMap, INFRAUT);\r
-\r
- String statusStr = getAndRemoveMapKey(nameMap, STATUS);\r
- String notes = getAndRemoveMapKey(nameMap, NOTES);\r
-\r
- makeRankDecision(state, nameMap, name, event, infrank);\r
-\r
- // test consistency of rank and authors\r
- testRankAuthorConsistency(name, event, authorStr, paraut, infrParAut,infrAut);\r
-\r
- // authors\r
- makeNomenclaturalAuthors(name, event, authorStr, paraut, infrParAut,infrAut);\r
-\r
- // status\r
- // TODO handle pro parte, pro syn. etc.\r
- if (StringUtils.isNotBlank(statusStr)) {\r
- String proPartePattern = "(pro parte|p.p.)";\r
- if (statusStr.matches(proPartePattern)) {\r
- state.setProParte(true);\r
- }\r
- try {\r
- // TODO handle trim earlier\r
- statusStr = statusStr.trim();\r
- NomenclaturalStatusType nomStatusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(statusStr);\r
- name.addStatus(NomenclaturalStatus.NewInstance(nomStatusType));\r
- } catch (UnknownCdmTypeException e) {\r
- String message = "Status '%s' could not be recognized";\r
- message = String.format(message, statusStr);\r
- fireWarningEvent(message, event, 4);\r
- }\r
- }\r
-\r
- // notes\r
- if (StringUtils.isNotBlank(notes)) {\r
- handleNotYetImplementedAttributeValue(event, CLASS, NOTES);\r
- }\r
-\r
- return;\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param nameMap\r
- * @param name\r
- * @param event\r
- * @param infrankStr\r
- */\r
- private void makeRankDecision(MarkupImportState state, Map<String, String> nameMap, \r
- NonViralName<?> name, XMLEvent event, String infrankStr) {\r
- // TODO ranks\r
- for (String key : nameMap.keySet()) {\r
- Rank rank = makeRank(state, key, false);\r
- if (rank == null) {\r
- handleNotYetImplementedAttributeValue(event, CLASS, key);\r
- } else {\r
- if (name.getRank() == null || rank.isLower(name.getRank())) {\r
- name.setRank(rank);\r
- }\r
- String value = nameMap.get(key);\r
- if (rank.isSupraGeneric() || rank.isGenus()) {\r
- name.setGenusOrUninomial(toFirstCapital(value));\r
- } else if (rank.isInfraGeneric()) {\r
- name.setInfraGenericEpithet(toFirstCapital(value));\r
- } else if (rank.isSpecies()) {\r
- if (isFirstCapitalWord(value)){ //capital letters are allowed for species epithet in case of person names (e.g. Manilkara Welwitschii Engl.\r
- name.setSpecificEpithet(value);\r
- }else{\r
- name.setSpecificEpithet(value.toLowerCase());\r
- }\r
- } else if (rank.isInfraSpecific()) {\r
- name.setInfraSpecificEpithet(value.toLowerCase());\r
- } else {\r
- String message = "Invalid rank '%s'. Can't decide which epithet to fill with '%s'";\r
- message = String.format(message, rank.getTitleCache(),value);\r
- fireWarningEvent(message, event, 4);\r
- }\r
- }\r
-\r
- }\r
- // handle given infrank marker\r
- if (StringUtils.isNotBlank(infrankStr)) {\r
- Rank infRank = makeRank(state, infrankStr, true);\r
-\r
- if (infRank == null) {\r
- String message = "Infrank '%s' rank not recognized";\r
- message = String.format(message, infrankStr);\r
- fireWarningEvent(message, event, 4);\r
- } else {\r
- if (name.getRank() == null) {\r
- name.setRank(infRank);\r
- } else if (infRank.isLower(name.getRank())) {\r
- String message = "InfRank '%s' is lower than existing rank ";\r
- message = String.format(message, infrankStr);\r
- fireWarningEvent(message, event, 2);\r
- name.setRank(infRank);\r
- } else if (infRank.equals(name.getRank())) {\r
- // nothing\r
- } else {\r
- String message = "InfRank '%s' is higher than existing rank ";\r
- message = String.format(message, infrankStr);\r
- fireWarningEvent(message, event, 2);\r
- }\r
- }\r
- }\r
- }\r
-\r
- private String toFirstCapital(String value) {\r
- if (StringUtils.isBlank(value)){\r
- return value;\r
- }else{\r
- String result = "";\r
- value = value.trim();\r
- result += value.trim().substring(0,1).toUpperCase();\r
- if (value.length()>1){\r
- result += value.substring(1).toLowerCase();\r
- }\r
- return result;\r
- }\r
- }\r
-\r
- /**\r
- * @param name\r
- * @param event\r
- * @param authorStr\r
- * @param paraut\r
- * @param infrParAut\r
- * @param infrAut\r
- */\r
- private void makeNomenclaturalAuthors(NonViralName name, XMLEvent event,\r
- String authorStr, String paraut, String infrParAut, String infrAut) {\r
- if (name.getRank() != null && name.getRank().isInfraSpecific()) {\r
- if (StringUtils.isNotBlank(infrAut)) {\r
- INomenclaturalAuthor[] authorAndEx = authorAndEx(infrAut, event);\r
- name.setCombinationAuthorTeam(authorAndEx[0]);\r
- name.setExCombinationAuthorTeam(authorAndEx[1]);\r
- }\r
- if (StringUtils.isNotBlank(infrParAut)) {\r
- INomenclaturalAuthor[] authorAndEx = authorAndEx(infrParAut, event);\r
- name.setBasionymAuthorTeam(authorAndEx[0]);\r
- name.setExBasionymAuthorTeam(authorAndEx[1]);\r
- }\r
- } else {\r
- if (name.getRank() == null){\r
- String message = "No rank defined. Check correct usage of authors!";\r
- fireWarningEvent(message, event, 4);\r
- if (isNotBlank(infrParAut) || isNotBlank(infrAut)){\r
- authorStr = infrAut;\r
- paraut = infrParAut;\r
- }\r
- }\r
- if (StringUtils.isNotBlank(authorStr)) {\r
- INomenclaturalAuthor[] authorAndEx = authorAndEx(authorStr, event);\r
- name.setCombinationAuthorTeam(authorAndEx[0]);\r
- name.setExCombinationAuthorTeam(authorAndEx[1]);\r
- }\r
- if (StringUtils.isNotBlank(paraut)) {\r
- INomenclaturalAuthor[] authorAndEx = authorAndEx(paraut, event);\r
- name.setBasionymAuthorTeam(authorAndEx[0]);\r
- name.setExBasionymAuthorTeam(authorAndEx[1]);\r
- }\r
- }\r
- }\r
-\r
- private TeamOrPersonBase[] authorAndEx(String authorAndEx, XMLEvent xmlEvent) {\r
- authorAndEx = authorAndEx.trim();\r
- TeamOrPersonBase[] result = new TeamOrPersonBase[2];\r
-\r
- String[] split = authorAndEx.split("\\sex\\s");\r
- if (split.length > 2) {\r
- String message = "There is more then 1 ' ex ' in author string. Can't separate author and ex-author";\r
- fireWarningEvent(message, xmlEvent, 4);\r
- result[0] = createAuthor(authorAndEx);\r
- } else if (split.length == 2) {\r
- result[0] = createAuthor(split[1]);\r
- result[1] = createAuthor(split[0]);\r
- } else {\r
- result[0] = createAuthor(split[0]);\r
- }\r
- return result;\r
- }\r
-\r
- /**\r
- * Tests if the names rank is consistent with the given author strings.\r
- * @param name\r
- * @param event\r
- * @param authorStr\r
- * @param paraut\r
- * @param infrParAut\r
- * @param infrAut\r
- */\r
- private void testRankAuthorConsistency(NonViralName name, XMLEvent event, \r
- String authorStr, String paraut, String infrParAut, String infrAut) {\r
- if (name.getRank() == null){\r
- return;\r
- }\r
- if (name.getRank().isInfraSpecific()) {\r
- if (StringUtils.isBlank(infrParAut)\r
- && StringUtils.isBlank(infrAut) //was isNotBlank before 29.5.2012\r
- && (StringUtils.isNotBlank(paraut) || StringUtils.isNotBlank(authorStr)) \r
- && ! name.isAutonym()) {\r
- String message = "Rank is infraspecicific but has only specific or higher author(s)";\r
- fireWarningEvent(message, event, 4);\r
- }\r
- } else {\r
- // is not infraspecific\r
- if (StringUtils.isNotBlank(infrParAut) || StringUtils.isNotBlank(infrAut)) {\r
- String message = "Rank is not infraspecicific but name has infra author(s)";\r
- fireWarningEvent(message, event, 4);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * Returns the (empty) name with the correct homotypical group depending on\r
- * the taxon status. Throws NPE if no currentTaxon is set in state.\r
- * \r
- * @param state\r
- * @param homotypicalGroup\r
- * @param isSynonym\r
- * @return\r
- */\r
- private NonViralName<?> createName(MarkupImportState state,\r
- HomotypicalGroup homotypicalGroup, boolean isSynonym) {\r
- NonViralName<?> name;\r
- Taxon taxon = state.getCurrentTaxon();\r
- if (isSynonym) {\r
- Rank defaultRank = Rank.SPECIES(); // can be any\r
- name = createNameByCode(state, defaultRank);\r
- if (homotypicalGroup != null) {\r
- name.setHomotypicalGroup(homotypicalGroup);\r
- }\r
- SynonymRelationshipType synonymType = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();\r
- if (taxon.getHomotypicGroup().equals(homotypicalGroup)) {\r
- synonymType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();\r
- }\r
- taxon.addSynonymName(name, synonymType);\r
- } else {\r
- name = CdmBase.deproxy(taxon.getName(), NonViralName.class);\r
- }\r
- return name;\r
- }\r
-\r
- private void handleName(MarkupImportState state, XMLEventReader reader, \r
- XMLEvent parentEvent, Map<String, String> nameMap)\r
- throws XMLStreamException {\r
- String classValue = getClassOnlyAttribute(parentEvent);\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- nameMap.put(classValue, text);\r
- return;\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, ANNOTATION)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("name has no closing tag");\r
-\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param classValue\r
- * @param byAbbrev\r
- * @return\r
- */\r
- private Rank makeRank(MarkupImportState state, String value,\r
- boolean byAbbrev) {\r
- Rank rank = null;\r
- if (StringUtils.isBlank(value)) {\r
- return null;\r
- }\r
- try {\r
- boolean useUnknown = true;\r
- NomenclaturalCode nc = makeNomenclaturalCode(state);\r
- if (byAbbrev) {\r
- rank = Rank.getRankByAbbreviation(value, nc, useUnknown);\r
- } else {\r
- rank = Rank.getRankByEnglishName(value, nc, useUnknown);\r
- }\r
- if (rank.equals(Rank.UNKNOWN_RANK())) {\r
- rank = null;\r
- }\r
- } catch (UnknownCdmTypeException e) {\r
- // doNothing\r
- }\r
- return rank;\r
- }\r
-\r
- // public void handleNameNotRank(MarkupImportState state, XMLEventReader\r
- // reader, XMLEvent parentEvent, String classValue, NonViralName name)\r
- // throws XMLStreamException {\r
- // if (ACCEPTED.equalsIgnoreCase(classValue)){\r
- // }else if (SYNONYM.equalsIgnoreCase(classValue)){\r
- // }else{\r
- // //TODO Not yet implemented\r
- // handleNotYetImplementedAttributeValue(parentEvent, CLASS, classValue);\r
- // }\r
- // }\r
-\r
- private void handleCitation(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, NonViralName name) throws XMLStreamException {\r
- String classValue = getClassOnlyAttribute(parentEvent);\r
-\r
- state.setCitation(true);\r
- boolean hasRefPart = false;\r
- Map<String, String> refMap = new HashMap<String, String>();\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- checkMandatoryElement(hasRefPart, parentEvent.asStartElement(),\r
- REF_PART);\r
- Reference<?> reference = createReference(state, refMap, next);\r
- String microReference = refMap.get(DETAILS);\r
- doCitation(state, name, classValue, reference, microReference,\r
- parentEvent);\r
- state.setCitation(false);\r
- return;\r
- } else if (isStartingElement(next, REF_PART)) {\r
- handleRefPart(state, reader, next, refMap);\r
- hasRefPart = true;\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("Citation has no closing tag");\r
-\r
- }\r
-\r
- private void handleRefPart(MarkupImportState state, XMLEventReader reader,XMLEvent parentEvent, Map<String, String> refMap) throws XMLStreamException {\r
- String classValue = getClassOnlyAttribute(parentEvent);\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- refMap.put(classValue, text);\r
- return;\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, ANNOTATION)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, ITALICS)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, BOLD)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("RefPart has no closing tag");\r
-\r
- }\r
-\r
- private Reference<?> createReference(MarkupImportState state, Map<String, String> refMap, XMLEvent parentEvent) {\r
- // TODO\r
- Reference<?> reference;\r
-\r
- String type = getAndRemoveMapKey(refMap, PUBTYPE);\r
- String authorStr = getAndRemoveMapKey(refMap, AUTHOR);\r
- String titleStr = getAndRemoveMapKey(refMap, PUBTITLE);\r
- String titleCache = getAndRemoveMapKey(refMap, PUBFULLNAME);\r
- String volume = getAndRemoveMapKey(refMap, VOLUME);\r
- String edition = getAndRemoveMapKey(refMap, EDITION);\r
- String editors = getAndRemoveMapKey(refMap, EDITORS);\r
- String year = getAndRemoveMapKey(refMap, YEAR);\r
- String pubName = getAndRemoveMapKey(refMap, PUBNAME);\r
- String pages = getAndRemoveMapKey(refMap, PAGES);\r
-\r
- if (state.isCitation()) {\r
- if (volume != null || "journal".equalsIgnoreCase(type)) {\r
- IArticle article = ReferenceFactory.newArticle();\r
- if (pubName != null) {\r
- IJournal journal = ReferenceFactory.newJournal();\r
- journal.setTitle(pubName);\r
- article.setInJournal(journal);\r
- }\r
- reference = (Reference<?>) article;\r
-\r
- } else {\r
- // TODO\r
- if (pubName != null){\r
- reference = ReferenceFactory.newBookSection();\r
- }else{\r
- reference = ReferenceFactory.newBook();\r
- }\r
- }\r
- // TODO use existing author from name or before\r
- TeamOrPersonBase<?> author = createAuthor(authorStr);\r
- reference.setAuthorTeam(author);\r
-\r
- reference.setTitle(titleStr);\r
- if (StringUtils.isNotBlank(titleCache)) {\r
- reference.setTitleCache(titleCache, true);\r
- }\r
- reference.setEdition(edition);\r
- reference.setEditor(editors);\r
-\r
- if (pubName != null) {\r
- Reference<?> inReference;\r
- if (reference.getType().equals(ReferenceType.Article)) {\r
- inReference = ReferenceFactory.newJournal();\r
- } else {\r
- inReference = ReferenceFactory.newGeneric();\r
- }\r
- inReference.setTitle(pubName);\r
- reference.setInReference(inReference);\r
- }\r
-\r
- \r
- } else { //no citation\r
- if (volume != null || "journal".equalsIgnoreCase(type)) {\r
- IArticle article = ReferenceFactory.newArticle();\r
- if (pubName != null) {\r
- IJournal journal = ReferenceFactory.newJournal();\r
- journal.setTitle(pubName);\r
- article.setInJournal(journal);\r
- }\r
- reference = (Reference<?>) article;\r
-\r
- } else {\r
- Reference<?> bookOrPartOf = ReferenceFactory.newGeneric();\r
- reference = bookOrPartOf;\r
- }\r
-\r
- // TODO type\r
- TeamOrPersonBase<?> author = createAuthor(authorStr);\r
- reference.setAuthorTeam(author);\r
-\r
- reference.setTitle(titleStr);\r
- if (StringUtils.isNotBlank(titleCache)) {\r
- reference.setTitleCache(titleCache, true);\r
- }\r
- reference.setEdition(edition);\r
- reference.setEditor(editors);\r
-\r
- if (pubName != null) {\r
- Reference<?> inReference;\r
- if (reference.getType().equals(ReferenceType.Article)) {\r
- inReference = ReferenceFactory.newJournal();\r
- } else {\r
- inReference = ReferenceFactory.newGeneric();\r
- }\r
- inReference.setTitle(pubName);\r
- reference.setInReference(inReference);\r
- }\r
- }\r
- reference.setVolume(volume);\r
- reference.setDatePublished(TimePeriod.parseString(year));\r
- //TODO check if this is handled correctly in FM markup\r
- reference.setPages(pages);\r
-\r
- // TODO\r
- String[] unhandledList = new String[]{ALTERNATEPUBTITLE, ISSUE, NOTES, STATUS};\r
- for (String unhandled : unhandledList){\r
- String value = getAndRemoveMapKey(refMap, unhandled);\r
- if (isNotBlank(value)){\r
- this.handleNotYetImplementedAttributeValue(parentEvent, CLASS, unhandled);\r
- }\r
- }\r
- \r
- for (String key : refMap.keySet()) {\r
- if (!DETAILS.equalsIgnoreCase(key)) {\r
- this.fireUnexpectedAttributeValue(parentEvent, CLASS, key);\r
- }\r
- }\r
-\r
- return reference;\r
- }\r
-\r
- private TeamOrPersonBase createAuthor(String authorTitle) {\r
- // TODO atomize and also use by name creation\r
- TeamOrPersonBase result = Team.NewTitledInstance(authorTitle,\r
- authorTitle);\r
- return result;\r
- }\r
-\r
- private String getAndRemoveMapKey(Map<String, String> map, String key) {\r
- String result = map.get(key);\r
- map.remove(key);\r
- if (result != null) {\r
- result = normalize(result);\r
- }\r
- return StringUtils.stripToNull(result);\r
- }\r
-\r
- private void doCitation(MarkupImportState state, NonViralName name,\r
- String classValue, Reference reference, String microCitation,\r
- XMLEvent parentEvent) {\r
- if (PUBLICATION.equalsIgnoreCase(classValue)) {\r
- name.setNomenclaturalReference(reference);\r
- name.setNomenclaturalMicroReference(microCitation);\r
- } else if (USAGE.equalsIgnoreCase(classValue)) {\r
- Taxon taxon = state.getCurrentTaxon();\r
- TaxonDescription td = getTaxonDescription(taxon, state\r
- .getConfig().getSourceReference(), false, true);\r
- TextData citation = TextData.NewInstance(Feature.CITATION());\r
- // TODO name used in source\r
- citation.addSource(null, null, reference, microCitation);\r
- td.addElement(citation);\r
- } else if (TYPE.equalsIgnoreCase(classValue)) {\r
- handleNotYetImplementedAttributeValue(parentEvent, CLASS,\r
- classValue);\r
- } else {\r
- // TODO Not yet implemented\r
- handleNotYetImplementedAttributeValue(parentEvent, CLASS,\r
- classValue);\r
- }\r
- }\r
-\r
- private void handleFeature(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- String classValue = getClassOnlyAttribute(parentEvent);\r
- Feature feature = makeFeature(classValue, state, parentEvent);\r
- Taxon taxon = state.getCurrentTaxon();\r
- TaxonDescription taxonDescription = getTaxonDescription(taxon, state.getConfig().getSourceReference(), NO_IMAGE_GALLERY, CREATE_NEW);\r
- // TextData figureHolderTextData = null; //for use with one TextData for\r
- // all figure only\r
-\r
- boolean isDescription = feature.equals(Feature.DESCRIPTION());\r
- DescriptionElementBase lastDescriptionElement = null;\r
- \r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return;\r
- } else if (isEndingElement(next, DISTRIBUTION_LIST) || isEndingElement(next, HABITAT_LIST)) { \r
- // only handle list elements\r
- } else if (isStartingElement(next, HEADING)) {\r
- makeFeatureHeading(state, reader, classValue, feature, next);\r
- } else if (isStartingElement(next, WRITER)) {\r
- makeFeatureWriter(state, reader, feature, taxon, next);\r
-// } else if (isStartingElement(next, DISTRIBUTION_LOCALITY)) {\r
-// if (!feature.equals(Feature.DISTRIBUTION())) {\r
-// String message = "Distribution locality only allowed for feature of type 'distribution'";\r
-// fireWarningEvent(message, next, 4);\r
-// }\r
-// handleDistributionLocality(state, reader, next);\r
- } else if (isStartingElement(next, DISTRIBUTION_LIST) || isStartingElement(next, HABITAT_LIST)) {\r
- // only handle single list elements\r
- } else if (isStartingElement(next, HABITAT)) {\r
- if (!(feature.equals(Feature.HABITAT())\r
- || feature.equals(Feature.HABITAT_ECOLOGY()) \r
- || feature.equals(Feature.ECOLOGY()))) {\r
- String message = "Habitat only allowed for feature of type 'habitat','habitat ecology' or 'ecology'";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- handleHabitat(state, reader, next);\r
- } else if (isStartingElement(next, CHAR)) {\r
- TextData textData = handleChar(state, reader, next);\r
- taxonDescription.addElement(textData);\r
- } else if (isStartingElement(next, STRING)) {\r
- lastDescriptionElement = makeFeatureString(state, reader,feature, taxonDescription, lastDescriptionElement,next);\r
- } else if (isStartingElement(next, FIGURE_REF)) {\r
- lastDescriptionElement = makeFeatureFigureRef(state, reader, taxonDescription, isDescription, lastDescriptionElement, next);\r
- } else if (isStartingElement(next, REFERENCES)) {\r
- // TODO details/microcitation ??\r
-\r
- List<Reference<?>> refs = handleReferences(state, reader, next);\r
- if (!refs.isEmpty()) {\r
- // TODO\r
- Reference<?> descriptionRef = state.getConfig().getSourceReference();\r
- TaxonDescription description = getTaxonDescription(taxon, descriptionRef, false, true);\r
- TextData featurePlaceholder = docImport.getFeaturePlaceholder(state, description, feature, true);\r
- for (Reference<?> citation : refs) {\r
- featurePlaceholder.addSource(null, null, citation, null);\r
- }\r
- } else {\r
- String message = "No reference found in references";\r
- fireWarningEvent(message, next, 6);\r
- }\r
- } else if (isStartingElement(next, NUM)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, NUM)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<Feature> has no closing tag");\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param taxonDescription\r
- * @param isDescription\r
- * @param lastDescriptionElement\r
- * @param next\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private DescriptionElementBase makeFeatureFigureRef(MarkupImportState state, XMLEventReader reader,TaxonDescription taxonDescription, \r
- boolean isDescription, DescriptionElementBase lastDescriptionElement, XMLEvent next)throws XMLStreamException {\r
- FigureDataHolder figureHolder = handleFigureRef(state, reader, next);\r
- Feature figureFeature = getFeature(state,MarkupTransformer.uuidFigures, "Figures", "Figures", "Fig.",null);\r
- if (isDescription) {\r
- TextData figureHolderTextData = null;\r
- // if (figureHolderTextData == null){\r
- figureHolderTextData = TextData.NewInstance(figureFeature);\r
- if (StringUtils.isNotBlank(figureHolder.num)) {\r
- String annotationText = "<num>" + figureHolder.num.trim()\r
- + "</num>";\r
- Annotation annotation = Annotation.NewInstance(annotationText,\r
- AnnotationType.TECHNICAL(), Language.DEFAULT());\r
- figureHolderTextData.addAnnotation(annotation);\r
- }\r
- if (StringUtils.isNotBlank(figureHolder.figurePart)) {\r
- String annotationText = "<figurePart>"+ figureHolder.figurePart.trim() + "</figurePart>";\r
- Annotation annotation = Annotation.NewInstance(annotationText,AnnotationType.EDITORIAL(), Language.DEFAULT());\r
- figureHolderTextData.addAnnotation(annotation);\r
- }\r
- // if (StringUtils.isNotBlank(figureText)){\r
- // figureHolderTextData.putText(Language.DEFAULT(), figureText);\r
- // }\r
- taxonDescription.addElement(figureHolderTextData);\r
- // }\r
- registerFigureDemand(state, figureHolderTextData, figureHolder.ref);\r
- } else {\r
- if (lastDescriptionElement == null) {\r
- String message = "No description element created yet that can be referred by figure. Create new TextData instead";\r
- fireWarningEvent(message, next, 4);\r
- lastDescriptionElement = TextData.NewInstance(figureFeature);\r
- taxonDescription.addElement(lastDescriptionElement);\r
- }\r
- registerFigureDemand(state, lastDescriptionElement,\r
- figureHolder.ref);\r
- }\r
- return lastDescriptionElement;\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param feature\r
- * @param taxonDescription\r
- * @param lastDescriptionElement\r
- * @param distributionList \r
- * @param next\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private DescriptionElementBase makeFeatureString(MarkupImportState state,XMLEventReader reader, Feature feature, \r
- TaxonDescription taxonDescription, DescriptionElementBase lastDescriptionElement, XMLEvent next) throws XMLStreamException {\r
- //for specimen only\r
- if (feature.equals(Feature.SPECIMEN()) || feature.equals(Feature.MATERIALS_EXAMINED())){\r
- \r
- List<DescriptionElementBase> specimens = handleMaterialsExamined(state, reader, next);\r
- for (DescriptionElementBase specimen : specimens){\r
- taxonDescription.addElement(specimen);\r
- lastDescriptionElement = specimen;\r
- }\r
- return lastDescriptionElement;\r
- }\r
- \r
- //others\r
- Map<String, String> subheadingMap = handleString(state, reader, next, feature);\r
- for (String subheading : subheadingMap.keySet()) {\r
- Feature subheadingFeature = feature;\r
- if (StringUtils.isNotBlank(subheading) && subheadingMap.size() > 1) {\r
- subheadingFeature = makeFeature(subheading, state, next);\r
- }\r
- if (feature.equals(Feature.COMMON_NAME())){\r
- List<DescriptionElementBase> commonNames = makeVernacular(state, subheading, subheadingMap.get(subheading));\r
- for (DescriptionElementBase commonName : commonNames){\r
- taxonDescription.addElement(commonName);\r
- lastDescriptionElement = commonName;\r
- }\r
- }else {\r
- TextData textData = TextData.NewInstance(subheadingFeature);\r
- textData.putText(Language.DEFAULT(), subheadingMap.get(subheading));\r
- taxonDescription.addElement(textData);\r
- lastDescriptionElement = textData;\r
- // TODO how to handle figures when these data are split in\r
- // subheadings\r
- }\r
- }\r
- return lastDescriptionElement;\r
- }\r
-\r
- private List<DescriptionElementBase> makeVernacular(MarkupImportState state, String subheading, String commonNameString) throws XMLStreamException {\r
- List<DescriptionElementBase> result = new ArrayList<DescriptionElementBase>();\r
- String[] splits = commonNameString.split(",");\r
- for (String split : splits){\r
- split = split.trim();\r
- if (! split.matches(".*\\(.*\\)\\.?")){\r
- fireWarningEvent("Common name string '"+split+"' does not match given pattern", state.getReader().peek(), 4);\r
- }\r
- \r
- String name = split.replaceAll("\\(.*\\)", "").replace(".", "").trim();\r
- String languageStr = split.replaceFirst(".*\\(", "").replaceAll("\\)\\.?", "").trim();\r
- \r
- Language language = null;\r
- if (StringUtils.isNotBlank(languageStr)){\r
- try {\r
- UUID langUuid = state.getTransformer().getLanguageUuid(languageStr);\r
- TermVocabulary<?> voc = null;\r
- language = getLanguage(state, langUuid, languageStr, languageStr, null, voc);\r
- if (language == null){\r
- logger.warn("Language " + languageStr + " not recognized by transformer");\r
- }\r
- } catch (UndefinedTransformerMethodException e) {\r
- throw new RuntimeException(e);\r
- }\r
- }\r
- NamedArea area = null;\r
- CommonTaxonName commonTaxonName = CommonTaxonName.NewInstance(name, language, area);\r
- result.add(commonTaxonName);\r
- }\r
- \r
- return result;\r
- }\r
- \r
- private List<DescriptionElementBase> handleMaterialsExamined(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- List<DescriptionElementBase> result = new ArrayList<DescriptionElementBase>();\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- if (result.isEmpty()){\r
- fireWarningEvent("Materials examined created empty Individual Associations list", parentEvent, 4);\r
- }\r
- return result;\r
- } else if (isStartingElement(next, SUB_HEADING)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, BR)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, GATHERING)) {\r
- DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(DerivedUnitType.DerivedUnit.DerivedUnit);\r
- handleGathering(state, reader, next, facade);\r
- SpecimenOrObservationBase<?> specimen;\r
- if (facade.innerDerivedUnit() != null){\r
- specimen = facade.innerDerivedUnit();\r
- }else{\r
- specimen = facade.innerFieldObservation();\r
- }\r
- IndividualsAssociation individualsAssociation = IndividualsAssociation.NewInstance();\r
- individualsAssociation.setAssociatedSpecimenOrObservation(specimen);\r
- result.add(individualsAssociation);\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<String> has no closing tag");\r
- \r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param feature\r
- * @param taxon\r
- * @param next\r
- * @throws XMLStreamException\r
- */\r
- private void makeFeatureWriter(MarkupImportState state,XMLEventReader reader, Feature feature, Taxon taxon, XMLEvent next) throws XMLStreamException {\r
- WriterDataHolder writer = handleWriter(state, reader, next);\r
- if (isNotBlank(writer.writer)) {\r
- // TODO\r
- Reference<?> ref = state.getConfig().getSourceReference();\r
- TaxonDescription description = getTaxonDescription(taxon, ref,\r
- false, true);\r
- TextData featurePlaceholder = docImport.getFeaturePlaceholder(state,\r
- description, feature, true);\r
- featurePlaceholder.addAnnotation(writer.annotation);\r
- registerFootnotes(state, featurePlaceholder, writer.footnotes);\r
- } else {\r
- String message = "Writer element is empty";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param classValue\r
- * @param feature\r
- * @param next\r
- * @throws XMLStreamException\r
- */\r
- private void makeFeatureHeading(MarkupImportState state, XMLEventReader reader, String classValue, Feature feature, XMLEvent next) throws XMLStreamException {\r
- String heading = handleHeading(state, reader, next);\r
- if (StringUtils.isNotBlank(heading)) {\r
- if (!heading.equalsIgnoreCase(classValue)) {\r
- try {\r
- if (!feature.equals(state.getTransformer().getFeatureByKey(\r
- heading))) {\r
- UUID headerFeatureUuid = state.getTransformer()\r
- .getFeatureUuid(heading);\r
- if (!feature.getUuid().equals(headerFeatureUuid)) {\r
- String message = "Feature heading '%s' differs from feature class '%s' and can not be transformed to feature";\r
- message = String.format(message, heading,\r
- classValue);\r
- fireWarningEvent(message, next, 1);\r
- }\r
- }\r
- } catch (UndefinedTransformerMethodException e) {\r
- throw new RuntimeException(e);\r
- }\r
- } else {\r
- // do nothing\r
- }\r
- }\r
- }\r
-\r
- private List<Reference<?>> handleReferences(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- // attributes\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String bibliography = getAndRemoveAttributeValue(attributes,\r
- BIBLIOGRAPHY);\r
- String serialsAbbreviations = getAndRemoveAttributeValue(attributes,\r
- SERIALS_ABBREVIATIONS);\r
- if (isNotBlank(bibliography) || isNotBlank(serialsAbbreviations)) {\r
- String message = "Attributes not yet implemented for <references>";\r
- fireWarningEvent(message, parentEvent, 4);\r
- }\r
-\r
- List<Reference<?>> result = new ArrayList<Reference<?>>();\r
-\r
- // elements\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return result;\r
- } else {\r
- if (isEndingElement(next, HEADING)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, WRITER)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, FOOTNOTE)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, STRING)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, REF_NUM)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, HEADING)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, SUB_HEADING)) {\r
- String subheading = getCData(state, reader, next).trim();\r
- String excludePattern = "(i?)(References?|Literature):?";\r
- if (!subheading.matches(excludePattern)) {\r
- fireNotYetImplementedElement(next.getLocation(), next.asStartElement().getName(), 0);\r
- }\r
- } else if (isStartingElement(next, WRITER)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, FOOTNOTE)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, STRING)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, REF_NUM)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, REFERENCE)) {\r
- Reference<?> ref = handleReference(state, reader, next);\r
- result.add(ref);\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<References> has no closing tag");\r
- }\r
-\r
- private void handleHabitat(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
- Taxon taxon = state.getCurrentTaxon();\r
- // TODO which ref to take?\r
- Reference<?> ref = state.getConfig().getSourceReference();\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- TaxonDescription description = getTaxonDescription(taxon, ref,\r
- false, true);\r
- UUID uuidExtractedHabitat = MarkupTransformer.uuidExtractedHabitat;\r
- Feature feature = getFeature(\r
- state,\r
- uuidExtractedHabitat,\r
- "Extracted Habitat",\r
- "An structured habitat that was extracted from a habitat text",\r
- "extr. habit.", null);\r
- TextData habitat = TextData.NewInstance(feature);\r
- habitat.putText(Language.DEFAULT(), text);\r
- description.addElement(habitat);\r
-\r
- return;\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, ALTITUDE)) {\r
- text = text.trim() + getTaggedCData(state, reader, next);\r
- } else if (isStartingElement(next, LIFE_CYCLE_PERIODS)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<Habitat> has no closing tag");\r
- }\r
-\r
- private String getTaggedCData(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- String text = getXmlTag(parentEvent);\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- text += getXmlTag(next);\r
- return text;\r
- } else if (next.isStartElement()) {\r
- text += getTaggedCData(state, reader, next);\r
- } else if (next.isEndElement()) {\r
- text += getTaggedCData(state, reader, next);\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("Some tag has no closing tag");\r
- }\r
-\r
- private String handleDistributionLocality(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String classValue = getAndRemoveRequiredAttributeValue(parentEvent, attributes, CLASS);\r
- String statusValue =getAndRemoveAttributeValue(attributes, STATUS);\r
- String frequencyValue =getAndRemoveAttributeValue(attributes, FREQUENCY);\r
- \r
-\r
- Taxon taxon = state.getCurrentTaxon();\r
- // TODO which ref to take?\r
- Reference<?> ref = state.getConfig().getSourceReference();\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- if (StringUtils.isNotBlank(text)) {\r
- String label = CdmUtils.removeTrailingDot(normalize(text));\r
- TaxonDescription description = getTaxonDescription(taxon, ref, false, true);\r
- NamedAreaLevel level = makeNamedAreaLevel(state,classValue, next);\r
- \r
- //status\r
- PresenceAbsenceTermBase<?> status = null;\r
- if (isNotBlank(statusValue)){\r
- try {\r
- status = state.getTransformer().getPresenceTermByKey(statusValue);\r
- if (status == null){\r
- //TODO\r
- String message = "The status '%s' could not be transformed to an CDM status";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- } catch (UndefinedTransformerMethodException e) {\r
- throw new RuntimeException(e);\r
- }\r
- }else{\r
- status = PresenceTerm.PRESENT();\r
- }\r
- //frequency\r
- if (isNotBlank(frequencyValue)){\r
- String message = "The frequency attribute is currently not yet available in CDM";\r
- fireWarningEvent(message, parentEvent, 6);\r
- }\r
- \r
- NamedArea higherArea = null;\r
- List<NamedArea> areas = new ArrayList<NamedArea>(); \r
- \r
- String patSingleArea = "([^,\\(]{3,})";\r
- String patSeparator = "(,|\\sand\\s)";\r
- String hierarchiePattern = String.format("%s\\((%s(%s%s)*)\\)",patSingleArea, patSingleArea, patSeparator, patSingleArea);\r
- Pattern patHierarchie = Pattern.compile(hierarchiePattern, Pattern.CASE_INSENSITIVE);\r
- Matcher matcher = patHierarchie.matcher(label); \r
- if (matcher.matches()){\r
- String higherAreaStr = matcher.group(1).trim();\r
- higherArea = makeArea(state, higherAreaStr, level);\r
- String[] innerAreas = matcher.group(2).split(patSeparator);\r
- for (String innerArea : innerAreas){\r
- if (isNotBlank(innerArea)){\r
- NamedArea singleArea = makeArea(state, innerArea.trim(), level);\r
- areas.add(singleArea);\r
- NamedArea partOf = singleArea.getPartOf();\r
-// if (partOf == null){\r
-// singleArea.setPartOf(higherArea);\r
-// }\r
- }\r
- }\r
- }else{\r
- NamedArea singleArea = makeArea(state, label, level);\r
- areas.add(singleArea);\r
- }\r
- \r
- for (NamedArea area : areas){\r
- //create distribution\r
- Distribution distribution = Distribution.NewInstance(area,status);\r
- description.addElement(distribution);\r
- }\r
- } else {\r
- String message = "Empty distribution locality";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- return text;\r
- } else if (isStartingElement(next, COORDINATES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, COORDINATES)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<DistributionLocality> has no closing tag");\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param areaName\r
- * @param level\r
- * @return \r
- */\r
- private NamedArea makeArea(MarkupImportState state, String areaName, NamedAreaLevel level) {\r
- \r
- \r
- //TODO FM vocabulary\r
- TermVocabulary<NamedArea> voc = null; \r
- NamedAreaType areaType = null;\r
- \r
- NamedArea area = null;\r
- try {\r
- area = state.getTransformer().getNamedAreaByKey(areaName);\r
- } catch (UndefinedTransformerMethodException e) {\r
- throw new RuntimeException(e);\r
- }\r
- if (area == null){\r
- boolean isNewInState = false;\r
- UUID uuid = state.getAreaUuid(areaName);\r
- if (uuid == null){\r
- isNewInState = true;\r
- \r
- \r
- try {\r
- uuid = state.getTransformer().getNamedAreaUuid(areaName);\r
- } catch (UndefinedTransformerMethodException e) {\r
- throw new RuntimeException(e);\r
- }\r
- }\r
- \r
- CdmImportBase.TermMatchMode matchMode = CdmImportBase.TermMatchMode.UUID_LABEL;\r
- area = getNamedArea(state, uuid, areaName, areaName, areaName, areaType, level, voc, matchMode);\r
- if (isNewInState){\r
- state.putAreaUuid(areaName, area.getUuid());\r
- \r
- //TODO just for testing -> make generic and move to better place\r
- String geoServiceLayer="vmap0_as_bnd_political_boundary_a";\r
- String layerFieldName ="nam";\r
- \r
- if ("Bangka".equals(areaName)){\r
- String areaValue = "PULAU BANGKA#SUMATERA SELATAN";\r
- GeoServiceArea geoServiceArea = new GeoServiceArea();\r
- geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);\r
- this.editGeoService.setMapping(area, geoServiceArea);\r
-// save(area, state);\r
- }\r
- if ("Luzon".equals(areaName)){\r
- GeoServiceArea geoServiceArea = new GeoServiceArea();\r
- \r
- List<String> list = Arrays.asList("HERMANA MAYOR ISLAND#CENTRAL LUZON",\r
- "HERMANA MENOR ISLAND#CENTRAL LUZON",\r
- "CENTRAL LUZON");\r
- for (String areaValue : list){\r
- geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);\r
- }\r
- \r
- this.editGeoService.setMapping(area, geoServiceArea);\r
-// save(area, state);\r
- }\r
- if ("Mindanao".equals(areaName)){\r
- GeoServiceArea geoServiceArea = new GeoServiceArea();\r
- \r
- List<String> list = Arrays.asList("NORTHERN MINDANAO",\r
- "SOUTHERN MINDANAO",\r
- "WESTERN MINDANAO");\r
- //TODO to be continued\r
- for (String areaValue : list){\r
- geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);\r
- }\r
- \r
- this.editGeoService.setMapping(area, geoServiceArea);\r
-// save(area, state);\r
- }\r
- if ("Palawan".equals(areaName)){\r
- GeoServiceArea geoServiceArea = new GeoServiceArea();\r
- \r
- List<String> list = Arrays.asList("PALAWAN#SOUTHERN TAGALOG");\r
- for (String areaValue : list){\r
- geoServiceArea.add(geoServiceLayer, layerFieldName, areaValue);\r
- }\r
- \r
- this.editGeoService.setMapping(area, geoServiceArea);\r
-// save(area, state);\r
- }\r
- \r
-\r
- }\r
- }\r
- return area;\r
- }\r
- \r
-\r
- /**\r
- * @param state\r
- * @param levelString\r
- * @param next\r
- * @return\r
- */\r
- private NamedAreaLevel makeNamedAreaLevel(MarkupImportState state,\r
- String levelString, XMLEvent next) {\r
- NamedAreaLevel level;\r
- try {\r
- level = state.getTransformer().getNamedAreaLevelByKey(levelString);\r
- if (level == null) {\r
- UUID levelUuid = state.getTransformer().getNamedAreaLevelUuid(levelString);\r
- if (levelUuid == null) {\r
- String message = "Unknown distribution locality class (named area level): %s. Create new level instead.";\r
- message = String.format(message, levelString);\r
- fireWarningEvent(message, next, 6);\r
- }\r
- level = getNamedAreaLevel(state, levelUuid, levelString, levelString, levelString, null);\r
- }\r
- } catch (UndefinedTransformerMethodException e) {\r
- throw new RuntimeException(e);\r
- }\r
- return level;\r
- }\r
-\r
- private String handleHeading(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return text;\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, FOOTNOTE)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("<String> has no closing tag");\r
-\r
- }\r
-\r
- /**\r
- * Handle string\r
- * @param state\r
- * @param reader\r
- * @param parentEvent\r
- * @param feature only needed for distributionLocalities\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private Map<String, String> handleString(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, Feature feature)throws XMLStreamException {\r
- // attributes\r
- String classValue = getClassOnlyAttribute(parentEvent, false);\r
- if (StringUtils.isNotBlank(classValue)) {\r
- String message = "class attribute for <string> not yet implemented";\r
- fireWarningEvent(message, parentEvent, 2);\r
- }\r
-\r
- // subheadings\r
- Map<String, String> subHeadingMap = new HashMap<String, String>();\r
- String currentSubheading = null;\r
-\r
- boolean isTextMode = true;\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- putCurrentSubheading(subHeadingMap, currentSubheading, text);\r
- return subHeadingMap;\r
- } else if (isStartingElement(next, BR)) {\r
- text += "<br/>";\r
- isTextMode = false;\r
- } else if (isEndingElement(next, BR)) {\r
- isTextMode = true;\r
- } else if (isHtml(next)) {\r
- text += getXmlTag(next);\r
- } else if (isStartingElement(next, SUB_HEADING)) {\r
- text = putCurrentSubheading(subHeadingMap,currentSubheading, text);\r
- // TODO footnotes\r
- currentSubheading = getCData(state, reader, next).trim();\r
- } else if (isStartingElement(next, DISTRIBUTION_LOCALITY)) {\r
- if (feature != null && !feature.equals(Feature.DISTRIBUTION())) {\r
- String message = "Distribution locality only allowed for feature of type 'distribution'";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- text += handleDistributionLocality(state, reader, next);\r
- } else if (next.isCharacters()) {\r
- if (!isTextMode) {\r
- String message = "String is not in text mode";\r
- fireWarningEvent(message, next, 6);\r
- } else {\r
- text += next.asCharacters().getData();\r
- }\r
- } else if (isStartingElement(next, HEADING)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, HEADING)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, QUOTE)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, QUOTE)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, DEDICATION)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, DEDICATION)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, TAXONTYPE)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, TAXONTYPE)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FULL_NAME)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FULL_NAME)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- }else if (isStartingElement(next, REFERENCES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, REFERENCES)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, GATHERING)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, GATHERING)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, ANNOTATION)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, ANNOTATION)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, HABITAT)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, HABITAT)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FIGURE_REF)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FIGURE_REF)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FIGURE)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FIGURE)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FOOTNOTE_REF)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FOOTNOTE_REF)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FOOTNOTE)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FOOTNOTE)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, WRITER)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, WRITER)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, DATES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, DATES)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<String> has no closing tag");\r
- }\r
-\r
- /**\r
- * @param subHeadingMap\r
- * @param currentSubheading\r
- * @param text\r
- * @return\r
- */\r
- private String putCurrentSubheading(Map<String, String> subHeadingMap, String currentSubheading, String text) {\r
- if (StringUtils.isNotBlank(text)) {\r
- text = removeStartingMinus(text);\r
- subHeadingMap.put(currentSubheading, text.trim());\r
- }\r
- return "";\r
- }\r
-\r
- private String removeStartingMinus(String string) {\r
- string = replaceStart(string, "-");\r
- string = replaceStart(string, "\u002d");\r
- string = replaceStart(string, "\u2013");\r
- string = replaceStart(string, "\u2014");\r
- string = replaceStart(string, "--");\r
- return string;\r
- }\r
- \r
- /**\r
- * @param value\r
- * @param replacementString\r
- */\r
- private String replaceStart(String value, String replacementString) {\r
- if (value.startsWith(replacementString) ){\r
- value = value.substring(replacementString.length()).trim();\r
- }\r
- while (value.startsWith("-") || value.startsWith("\u2014") ){\r
- value = value.substring("-".length()).trim();\r
- }\r
- return value;\r
- }\r
- \r
- private String getXmlTag(XMLEvent event) {\r
- String result;\r
- if (event.isStartElement()) {\r
- result = "<" + event.asStartElement().getName().getLocalPart()\r
- + ">";\r
- } else if (event.isEndElement()) {\r
- result = "</" + event.asEndElement().getName().getLocalPart() + ">";\r
- } else {\r
- String message = "Only start or end elements are allowed as Html tags";\r
- throw new IllegalStateException(message);\r
- }\r
- return result;\r
- }\r
-\r
- protected static final List<String> htmlList = Arrays.asList("sub", "sup",\r
- "ol", "ul", "li", "i", "b", "table", "br","tr","td");\r
-\r
- private boolean isHtml(XMLEvent event) {\r
- if (event.isStartElement()) {\r
- String tag = event.asStartElement().getName().getLocalPart();\r
- return htmlList.contains(tag);\r
- } else if (event.isEndElement()) {\r
- String tag = event.asEndElement().getName().getLocalPart();\r
- return htmlList.contains(tag);\r
- } else {\r
- return false;\r
- }\r
-\r
- }\r
-\r
- private TextData handleChar(MarkupImportState state, XMLEventReader reader,\r
- XMLEvent parentEvent) throws XMLStreamException {\r
- String classValue = getClassOnlyAttribute(parentEvent);\r
- Feature feature = makeFeature(classValue, state, parentEvent);\r
-\r
- boolean isTextMode = true;\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- TextData textData = TextData.NewInstance(feature);\r
- textData.putText(Language.DEFAULT(), text);\r
- return textData;\r
- } else if (isStartingElement(next, FIGURE_REF)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FIGURE_REF)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FOOTNOTE_REF)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FOOTNOTE_REF)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement()); \r
- } else if (isStartingElement(next, BR)) {\r
- text += "<br/>";\r
- isTextMode = false;\r
- } else if (isEndingElement(next, BR)) {\r
- isTextMode = true;\r
- } else if (isHtml(next)) {\r
- text += getXmlTag(next);\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, ANNOTATION)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, ITALICS)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, BOLD)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, FIGURE)) {\r
- handleFigure(state, reader, next);\r
- } else if (isStartingElement(next, FOOTNOTE)) {\r
- FootnoteDataHolder footnote = handleFootnote(state, reader, next);\r
- if (footnote.isRef()) {\r
- String message = "Ref footnote not implemented here";\r
- fireWarningEvent(message, next, 4);\r
- } else {\r
- registerGivenFootnote(state, footnote);\r
- }\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- if (!isTextMode) {\r
- String message = "String is not in text mode";\r
- fireWarningEvent(message, next, 6);\r
- } else {\r
- text += next.asCharacters().getData();\r
- }\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("RefPart has no closing tag");\r
- }\r
-\r
- /**\r
- * @param classValue\r
- * @param state\r
- * @param parentEvent\r
- * @return\r
- * @throws UndefinedTransformerMethodException\r
- */\r
- private Feature makeFeature(String classValue, MarkupImportState state, XMLEvent parentEvent) {\r
- UUID uuid;\r
- try {\r
- Feature feature = state.getTransformer().getFeatureByKey(classValue);\r
- if (feature != null) {\r
- return feature;\r
- }\r
- uuid = state.getTransformer().getFeatureUuid(classValue);\r
- if (uuid == null) {\r
- // TODO\r
- String message = "Uuid is not defined for '%s'";\r
- message = String.format(message, classValue);\r
- fireWarningEvent(message, parentEvent, 8);\r
- }\r
- String featureText = StringUtils.capitalize(classValue);\r
-\r
- // TODO eFlora vocabulary\r
- TermVocabulary<Feature> voc = null;\r
- feature = getFeature(state, uuid, featureText, featureText, classValue, voc);\r
- if (feature == null) {\r
- throw new NullPointerException(classValue + " not recognized as a feature");\r
- }\r
- return feature;\r
- } catch (Exception e) {\r
- String message = "Could not create feature for %s: %s";\r
- message = String.format(message, classValue, e.getMessage());\r
- fireWarningEvent(message, parentEvent, 4);\r
- return Feature.UNKNOWN();\r
- }\r
- }\r
-\r
-\r
-\r
-}\r
+/**
+ * Copyright (C) 2009 EDIT
+ * European Distributed Institute of Taxonomy
+ * http://www.e-taxonomy.eu
+ *
+ * The contents of this file are subject to the Mozilla Public License Version 1.1
+ * See LICENSE.TXT at the top of this package for the full license terms.
+ */
+
+package eu.etaxonomy.cdm.io.markup;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+
+import javax.xml.stream.Location;
+import javax.xml.stream.XMLEventReader;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.events.Attribute;
+import javax.xml.stream.events.StartElement;
+import javax.xml.stream.events.XMLEvent;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.log4j.Logger;
+
+import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
+import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
+import eu.etaxonomy.cdm.model.common.ExtensionType;
+import eu.etaxonomy.cdm.model.common.Language;
+import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.description.PolytomousKey;
+import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.description.TextData;
+import eu.etaxonomy.cdm.model.name.INonViralName;
+import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
+import eu.etaxonomy.cdm.model.taxon.Classification;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+
+
+/**
+ * @author a.mueller
+ *
+ */
+public class MarkupDocumentImportNoComponent extends MarkupImportBase {
+ @SuppressWarnings("unused")
+ private static final Logger logger = Logger.getLogger(MarkupDocumentImportNoComponent.class);
+
+ private final MarkupKeyImport keyImport;
+
+ private final MarkupModsImport modsImport;
+ private final MarkupSpecimenImport specimenImport;
+ private final MarkupNomenclatureImport nomenclatureImport;
+
+ public MarkupDocumentImportNoComponent(MarkupDocumentImport docImport) {
+ super(docImport);
+ this.keyImport = new MarkupKeyImport(docImport);
+ this.specimenImport = new MarkupSpecimenImport(docImport);
+ this.nomenclatureImport = new MarkupNomenclatureImport(docImport, specimenImport);
+ this.modsImport = new MarkupModsImport(docImport);
+ this.featureImport = new MarkupFeatureImport(docImport, specimenImport, nomenclatureImport, keyImport);
+ }
+
+ public void doInvoke(MarkupImportState state) throws XMLStreamException {
+ XMLEventReader reader = state.getReader();
+
+ // publication (= root element)
+ String elName = PUBLICATION;
+ boolean hasPublication = false;
+
+ while (reader.hasNext()) {
+ XMLEvent nextEvent = reader.nextEvent();
+ if (isStartingElement(nextEvent, elName)) {
+ handlePublication(state, reader, nextEvent, elName);
+ hasPublication = true;
+ } else if (nextEvent.isEndDocument()) {
+ if (!hasPublication) {
+ String message = "No publication root element found";
+ fireWarningEvent(message, nextEvent, 8);
+ }
+ // done
+ } else {
+ fireSchemaConflictEventExpectedStartTag(elName, reader);
+ }
+ }
+
+
+ return;
+
+ }
+
+ private void handlePublication(MarkupImportState state, XMLEventReader reader, XMLEvent currentEvent, String elName) throws XMLStreamException {
+
+ // attributes
+ StartElement element = currentEvent.asStartElement();
+ Map<String, Attribute> attributes = getAttributes(element);
+ String lang = getAndRemoveAttributeValue(attributes, "lang");
+ if (lang != null){
+ Language language = getTermService().getLanguageByIso(lang);
+ state.setDefaultLanguage(language);
+ }
+
+ handleUnexpectedAttributes(element.getLocation(), attributes, "noNamespaceSchemaLocation");
+
+ while (reader.hasNext()) {
+ XMLEvent event = readNoWhitespace(reader);
+ // TODO cardinality of alternative
+ if (isEndingElement(event, elName)) {
+ return;
+ } else if (event.isStartElement()) {
+ if (isStartingElement(event, META_DATA)) {
+ handleMetaData(state, reader, event);
+ } else if (isStartingElement(event, TREATMENT)) {
+ handleTreatment(state, reader, event);
+ } else if (isStartingElement(event, BIOGRAPHIES)) {
+ handleNotYetImplementedElement(event);
+ } else if (isStartingElement(event, REFERENCES)) {
+ handleNotYetImplementedElement(event);
+ } else if (isStartingElement(event, TEXT_SECTION)) {
+ handleNotYetImplementedElement(event);
+ } else if (isStartingElement(event, ADDENDA)) {
+ handleNotYetImplementedElement(event);
+ } else {
+ handleUnexpectedStartElement(event);
+ }
+ } else {
+ handleUnexpectedElement(event);
+ }
+ }
+ throw new IllegalStateException("Publication has no ending element");
+ }
+
+ private void handleMetaData(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
+ checkNoAttributes(parentEvent);
+
+ while (reader.hasNext()) {
+ XMLEvent next = readNoWhitespace(reader);
+ if (isMyEndingElement(next, parentEvent)) {
+ return;
+ } else if (isStartingElement(next, DEFAULT_MEDIA_URL)) {
+ String baseUrl = getCData(state, reader, next);
+ try {
+ new URL(baseUrl);
+ state.setBaseMediaUrl(baseUrl);
+ } catch (MalformedURLException e) {
+ String message = "defaultMediaUrl '%s' is not a valid URL";
+ message = String.format(message, baseUrl);
+ fireWarningEvent(message, next, 8);
+ }
+ } else if (isStartingElement(next, MODS)){
+ modsImport.handleMods(state, reader, next);
+ } else {
+ handleUnexpectedElement(next);
+ }
+ }
+ throw new IllegalStateException("MetaData has no ending element");
+
+ }
+
+ private void handleTreatment(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
+ checkNoAttributes(parentEvent);
+ Taxon lastTaxon = null;
+ while (reader.hasNext()) {
+ XMLEvent next = readNoWhitespace(reader);
+ if (isMyEndingElement(next, parentEvent)) {
+ Set<PolytomousKeyNode> keyNodesToSave = state.getPolytomousKeyNodesToSave();
+ //better save the key then the nodes
+ Set<PolytomousKey> keySet = new HashSet<PolytomousKey>();
+ for (PolytomousKeyNode node : keyNodesToSave){
+ PolytomousKey key = node.getKey();
+ keySet.add(key);
+ }
+ save(keySet, state);
+ //unmatched key leads
+ UnmatchedLeads unmatched = state.getUnmatchedLeads();
+ if (unmatched.size() > 0){
+ String message = "The following %d key leads are unmatched: %s";
+ message = String.format(message, unmatched.size(), state.getUnmatchedLeads().toString());
+ fireWarningEvent(message, next, 6);
+ }
+// save(keyNodesToSave, state);
+
+ return;
+ } else if (isStartingElement(next, TAXON)) {
+ state.setCurrentTaxonExcluded(false);
+ Taxon thisTaxon = handleTaxon(state, reader, next.asStartElement());
+ doTaxonRelation(state, thisTaxon, lastTaxon, parentEvent.getLocation());
+ if (state.isTaxonInClassification() == true){
+ lastTaxon = thisTaxon;
+ // TODO for imports spanning multiple documents ?? Still needed?
+ state.getConfig().setLastTaxonUuid(lastTaxon.getUuid());
+ }
+ } else if (isStartingElement(next, ADDENDA)) {
+ handleNotYetImplementedElement(next);
+ } else {
+ handleUnexpectedElement(next);
+ }
+ }
+ return;
+ }
+
+ /**
+ * @param taxon
+ * @param lastTaxon
+ */
+ private TaxonNode doTaxonRelation(MarkupImportState state, Taxon taxon, Taxon lastTaxon, Location dataLocation) {
+
+ if (state.isTaxonInClassification() == false){
+ return null;
+ }
+
+ boolean excluded = state.isCurrentTaxonExcluded();
+ TaxonNode node;
+ Classification tree = makeTree(state, dataLocation);
+ if (lastTaxon == null) {
+ node = tree.addChildTaxon(taxon, null, null);
+ node.setExcluded(excluded);
+ return node;
+ }
+ Rank thisRank = taxon.getName().getRank();
+ Rank lastRank = lastTaxon.getName().getRank();
+ if (lastRank == null){
+ String message = "Last rank was null. Can't create tree correctly";
+ fireWarningEvent(message, makeLocationStr(dataLocation), 12);
+ }
+ if (!lastTaxon.getTaxonNodes().isEmpty()) {
+ TaxonNode lastNode = lastTaxon.getTaxonNodes().iterator().next();
+ if (thisRank == null){
+ String message = "Rank is undefined for taxon '%s'. Can't create classification without rank.";
+ message = String.format(message, taxon.getName().getTitleCache());
+ fireWarningEvent(message, makeLocationStr(dataLocation), 6);
+ node = null;
+ }else if (thisRank.isLower(lastRank)) {
+ node = null;
+ node = lastNode.addChildTaxon(taxon, null, null);
+ fillMissingEpithetsForTaxa(lastTaxon, taxon);
+ } else if (thisRank.equals(lastRank)) {
+ TaxonNode parent = lastNode.getParent();
+ if (parent != null && parent.getTaxon() != null) {
+ node = parent.addChildTaxon(taxon, null, null);
+ fillMissingEpithetsForTaxa(parent.getTaxon(), taxon);
+ } else {
+ node = tree.addChildTaxon(taxon, null, null);
+ }
+ } else if (thisRank.isHigher(lastRank)) {
+ TaxonNode parent = lastNode.getParent();
+ if (parent != null){
+ node = doTaxonRelation(state, taxon, parent.getTaxon(), dataLocation);
+ }else{
+ String warning = "No parent available for lastNode. Classification can not be build correctly. Maybe the rank was missing for the lastNode";
+ fireWarningEvent(warning, makeLocationStr(dataLocation), 16);
+ //TODO what to do in this case (haven't spend time to think about yet
+ node = null;
+ }
+
+ // TaxonNode parentNode = handleTaxonRelation(state, taxon,
+ // lastNode.getParent().getTaxon());
+ // parentNode.addChildTaxon(taxon, null, null, null);
+ }else{
+ fireWarningEvent("Unhandled case", makeLocationStr(dataLocation), 8);
+ node = null;
+ }
+ } else {
+ String message = "Last taxon has no node";
+ fireWarningEvent(message, makeLocationStr(dataLocation), 6);
+ node = null;
+ }
+ if (excluded){
+ if (node != null){
+ node.setExcluded(excluded);
+ }else{
+ fireWarningEvent("Taxon is excluded but no taxon node can be created", makeLocationStr(dataLocation), 4);
+ }
+ }
+ return node;
+ }
+
+
+
+ /**
+ * @param state
+ * @param dataLocation
+ * @return
+ */
+ private Classification makeTree(MarkupImportState state, Location dataLocation) {
+ Classification result = state.getTree(null);
+ if (result == null) {
+ UUID uuid = state.getConfig().getClassificationUuid();
+ if (uuid == null) {
+ String message = "No classification uuid is defined";
+ fireWarningEvent(message, makeLocationStr(dataLocation), 6);
+ result = createNewClassification(state);
+ } else {
+ result = getClassificationService().find(uuid);
+ if (result == null) {
+ result = createNewClassification(state);
+ result.setUuid(uuid);
+ }
+ }
+ state.putTree(null, result);
+ }
+ save(result, state);
+ return result;
+ }
+
+ private Classification createNewClassification(MarkupImportState state) {
+ Classification result = Classification.NewInstance(state.getConfig().getClassificationName(), getDefaultLanguage(state));
+ state.putTree(null, result);
+ return result;
+ }
+
+ private Taxon handleTaxon(MarkupImportState state, XMLEventReader reader, StartElement parentEvent) throws XMLStreamException {
+ // TODO progress monitoring
+ Map<String, Attribute> attributes = getAttributes(parentEvent);
+ Taxon taxon = createTaxonAndName(state, attributes, parentEvent);
+ state.setCurrentTaxon(taxon);
+ state.addNewFeatureSorterLists(taxon.getUuid().toString());
+
+ boolean hasTitle = false;
+ boolean hasNomenclature = false;
+ String taxonTitle = null;
+
+ Reference sourceReference = state.getConfig().getSourceReference();
+ while (reader.hasNext()) {
+ XMLEvent next = readNoWhitespace(reader);
+ if (isMyEndingElement(next, parentEvent)) {
+// checkMandatoryElement(hasTitle, parentEvent, TAXONTITLE);
+ checkMandatoryElement(hasNomenclature, parentEvent, NOMENCLATURE);
+ boolean inClassification = getAndRemoveBooleanAttributeValue(next, attributes, "inClassification", true);
+ state.setTaxonInClassification(inClassification);
+ handleUnexpectedAttributes(parentEvent.getLocation(),attributes);
+ if (taxon.getName().getRank() == null){
+ String warning = "No rank exists for taxon " + taxon.getTitleCache();
+ fireWarningEvent(warning, next, 12);
+ taxon.getName().setRank(Rank.UNKNOWN_RANK());
+ }
+ //hybrid
+ if (state.isTaxonIsHybrid() && !taxon.getName().isHybrid()){
+ fireWarningEvent("Taxon is hybrid but name is not a hybrid name", next, 4);
+ }
+ state.setTaxonIsHybrid(false);
+
+ keyImport.makeKeyNodes(state, parentEvent, taxonTitle);
+ state.setCurrentTaxon(null);
+ state.setCurrentTaxonNum(null);
+ if (taxon.getName().getRank().isHigher(Rank.GENUS())){
+ state.setLatestGenusEpithet(null);
+ }else{
+ state.setLatestGenusEpithet(taxon.getName().getGenusOrUninomial());
+ }
+ save(taxon, state);
+ return taxon;
+ } else if (next.isStartElement()) {
+ if (isStartingElement(next, HEADING)) {
+ handleNotYetImplementedElement(next);
+ } else if (isStartingElement(next, TAXONTITLE)) {
+ taxonTitle = handleTaxonTitle(state, reader, next);
+ hasTitle = true;
+ } else if (isStartingElement(next, WRITER)) {
+ makeKeyWriter(state, reader, taxon, taxonTitle, next);
+ } else if (isStartingElement(next, TEXT_SECTION)) {
+ handleNotYetImplementedElement(next);
+ } else if (isStartingElement(next, KEY)) {
+ keyImport.handleKey(state, reader, next);
+ } else if (isStartingElement(next, NOMENCLATURE)) {
+ nomenclatureImport.handleNomenclature(state, reader, next);
+ hasNomenclature = true;
+ } else if (isStartingElement(next, FEATURE)) {
+ featureImport.handleFeature(state, reader, next);
+ } else if (isStartingElement(next, NOTES)) {
+ // TODO is this the correct way to handle notes?
+ String note = handleNotes(state, reader, next);
+
+ UUID notesUuid;
+ try {
+ notesUuid = state.getTransformer().getFeatureUuid("notes");
+ Feature feature = getFeature(state, notesUuid, "Notes", "Notes", "note", null);
+ TextData textData = TextData.NewInstance(feature);
+ textData.addPrimaryTaxonomicSource(sourceReference);
+ textData.putText(getDefaultLanguage(state), note);
+ TaxonDescription description = getDefaultTaxonDescription(taxon, false, true, sourceReference);
+ description.addElement(textData);
+ } catch (UndefinedTransformerMethodException e) {
+ String message = "getFeatureUuid method not yet implemented";
+ fireWarningEvent(message, next, 8);
+ }
+ } else if (isStartingElement(next, REFERENCES)) {
+ handleNotYetImplementedElement(next);
+ } else if (isStartingElement(next, FIGURE_REF)) {
+ TaxonDescription desc = getTaxonDescription(taxon, sourceReference, IMAGE_GALLERY, CREATE_NEW);
+ TextData textData;
+ if (desc.getElements().isEmpty()){
+ textData = TextData.NewInstance(Feature.IMAGE());
+ textData.addPrimaryTaxonomicSource(sourceReference);
+ desc.addElement(textData);
+ }
+ textData = (TextData)desc.getElements().iterator().next();
+ featureImport.makeFeatureFigureRef(state, reader, desc, false, textData, sourceReference, next);
+ } else if (isStartingElement(next, FIGURE)) {
+ handleFigure(state, reader, next, specimenImport, nomenclatureImport);
+ } else if (isStartingElement(next, FOOTNOTE)) {
+ FootnoteDataHolder footnote = handleFootnote(state, reader, next, specimenImport, nomenclatureImport);
+ if (footnote.isRef()) {
+ String message = "Ref footnote not implemented here";
+ fireWarningEvent(message, next, 4);
+ } else {
+ registerGivenFootnote(state, footnote);
+ }
+ } else {
+ handleUnexpectedStartElement(next);
+ }
+ } else {
+ handleUnexpectedElement(next);
+ }
+ }
+ throw new IllegalStateException("<Taxon> has no closing tag");
+ }
+
+ /**
+ * @param state
+ * @param reader
+ * @param taxon
+ * @param taxonTitle
+ * @param next
+ * @throws XMLStreamException
+ */
+ private void makeKeyWriter(MarkupImportState state, XMLEventReader reader, Taxon taxon, String taxonTitle, XMLEvent next) throws XMLStreamException {
+ WriterDataHolder writer = handleWriter(state, reader, next);
+ if (state.getConfig().isHandleWriterManually()){
+ fireWarningEvent("<Writer> is expected to be handled manually", next, 1);
+ }else{
+ taxon.addExtension(writer.extension);
+ // TODO what if taxonTitle comes later
+ taxonTitle = taxonTitle != null ? taxonTitle : taxon.getName() == null ? null : taxon.getName().getNameCache();
+ if (writer.extension != null) {
+ if (StringUtils.isBlank(taxonTitle)){
+ fireWarningEvent("No taxon title defined for writer. Please add sec.title manually.", next, 6);
+ taxonTitle = null;
+ }
+ Reference sec = ReferenceFactory.newBookSection();
+ sec.setTitle(taxonTitle);
+ TeamOrPersonBase<?> author = createAuthor(state, writer.writer);
+ sec.setAuthorship(author);
+ sec.setInReference(state.getConfig().getSourceReference());
+ taxon.setSec(sec);
+ registerFootnotes(state, sec, writer.footnotes);
+ } else {
+ String message = "There is no writer extension defined";
+ fireWarningEvent(message, next, 6);
+ }
+ }
+ }
+
+ private String handleNotes(MarkupImportState state, XMLEventReader reader,
+ XMLEvent parentEvent) throws XMLStreamException {
+ checkNoAttributes(parentEvent);
+
+ String text = "";
+ while (reader.hasNext()) {
+ XMLEvent next = readNoWhitespace(reader);
+ if (isMyEndingElement(next, parentEvent)) {
+ return text;
+ } else if (next.isStartElement()) {
+ if (isStartingElement(next, HEADING)) {
+ handleNotYetImplementedElement(next);
+ } else if (isStartingElement(next, SUB_HEADING)) {
+ String subheading = getCData(state, reader, next).trim();
+ if (! isNoteHeading(subheading)) {
+ fireNotYetImplementedElement(next.getLocation(), next.asStartElement().getName(), 0);
+ }
+ } else if (isStartingElement(next, WRITER)) {
+ handleNotYetImplementedElement(next);
+ } else if (isStartingElement(next, NUM)) {
+ handleNotYetImplementedElement(next);
+ } else if (isStartingElement(next, STRING)) {
+ // TODO why multiple strings in schema?
+ text = makeNotesString(state, reader, text, next);
+ } else {
+ handleUnexpectedStartElement(next.asStartElement());
+ }
+ } else {
+ handleUnexpectedElement(next);
+ }
+ }
+ throw new IllegalStateException("<Notes> has no closing tag");
+ }
+
+ /**
+ * @param state
+ * @param reader
+ * @param text
+ * @param next
+ * @return
+ * @throws XMLStreamException
+ */
+ private String makeNotesString(MarkupImportState state, XMLEventReader reader, String text, XMLEvent next) throws XMLStreamException {
+ Map<String, SubheadingResult> stringMap = handleString(state, reader, next, null);
+ if (stringMap.size() == 0){
+ String message = "No text available in <notes>";
+ fireWarningEvent(message, next, 4);
+ }else if (stringMap.size() > 1){
+ String message = "Subheadings not yet supported in <notes>";
+ fireWarningEvent(message, next, 4);
+ }else{
+ String firstSubheading = stringMap.keySet().iterator().next();
+ if ( firstSubheading != null && ! isNoteHeading (firstSubheading) ) {
+ String message = "Subheadings not yet supported in <notes>";
+ fireWarningEvent(message, next, 4);
+ }
+ }
+ for (String subheading : stringMap.keySet()){
+ text += subheading;
+ text += stringMap.get(subheading);
+ }
+ return text;
+ }
+
+ private boolean isNoteHeading(String heading) {
+ String excludePattern = "(i?)(Notes?):?";
+ return heading.matches(excludePattern);
+ }
+
+ /**
+ * @param state
+ * @param attributes
+ * @param event
+ */
+ private Taxon createTaxonAndName(MarkupImportState state,
+ Map<String, Attribute> attributes, StartElement event) {
+ INonViralName name;
+ Rank rank = null; //Rank.SPECIES(); // default
+ boolean isCultivar = checkAndRemoveAttributeValue(attributes, CLASS, "cultivated");
+
+ if (isCultivar) {
+ name = TaxonNameFactory.NewCultivarInstance(rank);
+ } else {
+ name = createNameByCode(state, rank);
+ }
+ Taxon taxon = Taxon.NewInstance(name, state.getConfig().getSourceReference());
+ if (checkAndRemoveAttributeValue(attributes, CLASS, "dubious")) {
+ taxon.setDoubtful(true);
+ } else if (checkAndRemoveAttributeValue(attributes, CLASS, "excluded")) {
+ state.setCurrentTaxonExcluded(true);
+ }
+ state.setTaxonIsHybrid(checkAndRemoveAttributeValue(attributes, CLASS, "hybrid"));
+
+ // TODO insufficient, new, expected
+ handleNotYetImplementedAttribute(attributes, CLASS, event);
+ // From old version
+ // MarkerType markerType = getMarkerType(state, attrValue);
+ // if (markerType == null){
+ // logger.warn("Class attribute value for taxon not yet supported: " +
+ // attrValue);
+ // }else{
+ // taxon.addMarker(Marker.NewInstance(markerType, true));
+ // }
+
+ // save(name, state);
+ // save(taxon, state);
+ return taxon;
+ }
+
+ private String handleTaxonTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
+ //attributes
+ String text = "";
+ Map<String, Attribute> attributes = getAttributes(parentEvent);
+ String rankAttr = getAndRemoveAttributeValue(attributes, RANK);
+ Rank rank = makeRank(state, rankAttr, false);
+ String num = getAndRemoveAttributeValue(attributes, NUM);
+ state.setCurrentTaxonNum(num);
+ checkNoAttributes(attributes, parentEvent);
+
+ // TODO handle attributes
+ while (reader.hasNext()) {
+ XMLEvent next = readNoWhitespace(reader);
+ if (next.isEndElement()) {
+ if (isMyEndingElement(next, parentEvent)) {
+ Taxon taxon = state.getCurrentTaxon();
+ String titleText = null;
+ if (state.getConfig().isDoExtensionForTaxonTitle() && checkMandatoryText(text, parentEvent)) {
+ titleText = normalize(text);
+ UUID uuidTitle = MarkupTransformer.uuidTaxonTitle;
+ ExtensionType titleExtension = this.getExtensionType(state, uuidTitle, "Taxon Title ","taxon title", "title");
+ taxon.addExtension(titleText, titleExtension);
+ }
+ taxon.getName().setRank(rank);
+ // TODO check title exists
+ return titleText;
+ } else {
+ if (isEndingElement(next, FOOTNOTE)) {
+ // NOT YET IMPLEMENTED
+ popUnimplemented(next.asEndElement());
+ } else {
+ handleUnexpectedEndElement(next.asEndElement());
+ state.setUnsuccessfull();
+ }
+ }
+ } else if (next.isStartElement()) {
+ if (isStartingElement(next, FOOTNOTE)) {
+ handleNotYetImplementedElement(next);
+ }else if (isStartingElement(next, FOOTNOTE_REF)) {
+ handleNotYetImplementedElement(next);
+ } else {
+ handleUnexpectedStartElement(next);
+ state.setUnsuccessfull();
+ }
+ } else if (next.isCharacters()) {
+ text += next.asCharacters().getData();
+
+ } else {
+ handleUnexpectedElement(next);
+ state.setUnsuccessfull();
+ }
+ }
+ return null;
+
+ }
+
+
+}
BGBM BDI Projects / cdmlib.git / blobdiff