package eu.etaxonomy.cdm.io.markup;\r
\r
import java.net.MalformedURLException;\r
-import java.net.URISyntaxException;\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.LinkedList;\r
-import java.util.List;\r
-import java.util.Map;\r
import java.util.Queue;\r
-import java.util.Set;\r
import java.util.UUID;\r
\r
import javax.xml.stream.FactoryConfigurationError;\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.log4j.Logger;\r
import org.springframework.beans.factory.annotation.Autowired;\r
import org.springframework.security.access.PermissionEvaluator;\r
import org.springframework.security.authentication.AuthenticationManager;\r
import org.springframework.security.core.Authentication;\r
import org.springframework.stereotype.Component;\r
+import org.springframework.transaction.TransactionStatus;\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.IEditGeoService;\r
import eu.etaxonomy.cdm.io.common.ICdmIO;\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.io.common.XmlImportBase;\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.Figure;\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.DescriptionElementBase;\r
-import eu.etaxonomy.cdm.model.description.Distribution;\r
+import eu.etaxonomy.cdm.model.description.DescriptionBase;\r
import eu.etaxonomy.cdm.model.description.Feature;\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.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.media.IdentifiableMediaEntity;\r
+import eu.etaxonomy.cdm.model.location.NamedAreaType;\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.Specimen;\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
+/**\r
+ * @author pesiimport\r
+ *\r
+ */\r
@Component\r
-public class MarkupDocumentImport extends MarkupImportBase implements\r
- ICdmIO<MarkupImportState> {\r
- private static final String TO_COUPLET = "toCouplet";\r
-\r
- private static final String TO_TAXON = "toTaxon";\r
-\r
- private static final String TO_KEY = "toKey";\r
-\r
- private static final String TEXT = "text";\r
-\r
- private static final String QUESTION = "question";\r
-\r
- private static final String COUPLET = "couplet";\r
-\r
- private static final String KEYNOTES = "keynotes";\r
-\r
- private static final String KEY_TITLE = "keyTitle";\r
-\r
- private static final String IS_SPOTCHARACTERS = "isSpotcharacters";\r
-\r
- private static final String REF_NUM = "refNum";\r
-\r
- private static final String SERIALS_ABBREVIATIONS = "serialsAbbreviations";\r
-\r
- private static final String BIBLIOGRAPHY = "bibliography";\r
-\r
- private static final String HABITAT = "habitat";\r
-\r
- private static final String LIFE_CYCLE_PERIODS = "lifeCyclePeriods";\r
+public class MarkupDocumentImport extends XmlImportBase<MarkupImportConfigurator, MarkupImportState> implements ICdmIO<MarkupImportState> {\r
+ private static final Logger logger = Logger.getLogger(MarkupDocumentImport.class);\r
\r
- private static final String DISTRIBUTION_LOCALITY = "distributionLocality";\r
-\r
- private static final String REFERENCE = "reference";\r
-\r
- private static final Logger logger = Logger\r
- .getLogger(MarkupDocumentImport.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
- 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 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 = "collection";\r
- private static final String COLLECTION_TYPE_STATUS = "collectionTypeStatus";\r
- private static final String COLLECTOR = "collector";\r
- private static final String COORDINATES = "coordinates";\r
- private static final String DATES = "dates";\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 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 FULL_NAME = "fullName";\r
- private static final String FULL_TYPE = "fullType";\r
- private static final String HEADING = "heading";\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 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 NUM = "num";\r
- private static final String ORIGINAL_DETERMINATION = "originalDetermination";\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 RANK = "rank";\r
- private static final String REF = "ref";\r
- private static final String REF_PART = "refPart";\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 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 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
+ @Autowired\r
+ private IEditGeoService editGeoService;\r
+ \r
// TODO remove preliminary\r
@Autowired\r
private AuthenticationManager authenticationManager;\r
}\r
\r
@Override\r
- public void doInvoke(MarkupImportState state) {\r
- fireProgressEvent("Start import markup document",\r
- "Before start of document");\r
- fireWarningEvent("Test a warning", "At start", 17);\r
-\r
+ public void doInvoke(MarkupImportState state) { \r
+ fireProgressEvent("Start import markup document", "Before start of document");\r
+ \r
Queue<CdmBase> outputStream = new LinkedList<CdmBase>();\r
\r
+ TransactionStatus tx = startTransaction();\r
// FIXME reset state\r
doAllTheOldOtherStuff(state);\r
\r
// StAX\r
XMLEventReader reader = getStaxReader(state);\r
state.setReader(reader);\r
+ \r
// start document\r
if (!validateStartOfDocument(reader)) {\r
state.setUnsuccessfull();\r
return;\r
}\r
\r
- // publication\r
- String elName = PUBLICATION;\r
- boolean hasPublication = false;\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
+ MarkupDocumentImportNoComponent x = new MarkupDocumentImportNoComponent(this);\r
+ x.doInvoke(state);\r
+ \r
+ commitTransaction(tx);\r
\r
// //SAX\r
// ImportHandlerBase handler= new PublicationHandler(this);\r
// parseSAX(state, handler);\r
\r
} catch (FactoryConfigurationError e1) {\r
- fireWarningEvent(\r
- "Some error occurred while setting up xml factory. Data can't be imported",\r
- "Start", 16);\r
+ fireWarningEvent("Some error occurred while setting up xml factory. Data can't be imported", "Start", 16);\r
state.setUnsuccessfull();\r
} catch (XMLStreamException e1) {\r
- fireWarningEvent(\r
- "An XMLStreamException occurred while parsing. Data can't be imported",\r
- "Start", 16);\r
+ fireWarningEvent("An XMLStreamException occurred while parsing. Data can't be imported", "Start", 16);\r
state.setUnsuccessfull();\r
- // } catch (ParserConfigurationException e) {\r
- // fireWarningEvent("A ParserConfigurationException occurred while parsing. Data can't be imported",\r
- // "Start", 16);\r
- // } catch (SAXException e) {\r
- // fireWarningEvent("A SAXException occurred while parsing. Data can't be imported",\r
- // "Start", 16);\r
- // } catch (IOException e) {\r
- // fireWarningEvent("An IO exception occurred while parsing. Data can't be imported",\r
- // "Start", 16);\r
-\r
}\r
\r
return;\r
\r
}\r
\r
- private void handlePublication(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent currentEvent, String elName)\r
- throws XMLStreamException {\r
-\r
- // attributes\r
- StartElement element = currentEvent.asStartElement();\r
- Map<String, Attribute> attributes = getAttributes(element);\r
- handleUnexpectedAttributes(element.getLocation(), attributes,\r
- "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,\r
- 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
-// 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);\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.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(),\r
- 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
+ * This comes from the old version, needs to be checked on need\r
+ * \r
* @param state\r
- * @return\r
*/\r
- private Classification makeTree(MarkupImportState state) {\r
- Classification result = state.getTree(null);\r
- if (result == null) {\r
- UUID uuid = state.getConfig().getClassificationUuid();\r
- if (uuid == null) {\r
- logger.warn("No classification uuid is defined");\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,\r
- 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
- \r
- makeKeyNodes(state, parentEvent);\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 {\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
- 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, 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)) {\r
- handleFigure(state, reader, next);\r
- } else if (isStartingElement(next, FOOTNOTE)) {\r
- FootnoteDataHolder footnote = handleFootnote(state, reader,\r
- 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
- private void makeKeyNodes(MarkupImportState state, XMLEvent event) {\r
- Taxon taxon = state.getCurrentTaxon();\r
- String num = state.getCurrentTaxonNum();\r
- \r
- String nameString = CdmBase.deproxy(taxon.getName(), NonViralName.class).getNameCache();\r
- \r
- //try to find matching lead nodes \r
- UnmatchedLeadsKey leadsKey = UnmatchedLeadsKey.NewInstance(num, nameString);\r
- Set<PolytomousKeyNode> matchingNodes = handleMatchingNodes(state, taxon, leadsKey);\r
- //same without using the num\r
- if (num != null){\r
- UnmatchedLeadsKey noNumLeadsKey = UnmatchedLeadsKey.NewInstance("", nameString);\r
- //TODO inform about differences\r
- handleMatchingNodes(state, taxon, noNumLeadsKey);\r
- }\r
- if (matchingNodes.isEmpty() && num != null){\r
- String message = "Taxon has num in taxontitle but no matching nodes exist: %s, Key: %s";\r
- message = String.format(message, num, leadsKey.toString());\r
- fireWarningEvent(message, event, 1);\r
- }\r
- \r
- }\r
- \r
- private Set<PolytomousKeyNode> handleMatchingNodes(MarkupImportState state, Taxon taxon, UnmatchedLeadsKey leadsKey) {\r
- Set<PolytomousKeyNode> matchingNodes = state.getUnmatchedLeads().getNodes(leadsKey);\r
- for (PolytomousKeyNode matchingNode : matchingNodes){\r
- state.getUnmatchedLeads().removeNode(leadsKey, matchingNode);\r
- matchingNode.setTaxon(taxon);\r
- state.getPolytomousKeyNodesToSave().add(matchingNode);\r
+ private void doAllTheOldOtherStuff(MarkupImportState state) {\r
+ state.putTree(null, null);\r
+ if (unmatchedLeads == null) {\r
+ unmatchedLeads = UnmatchedLeads.NewInstance();\r
}\r
- return matchingNodes;\r
- }\r
+ state.setUnmatchedLeads(unmatchedLeads);\r
\r
- private void handleKey(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- // attributes\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String isSpotcharacters = getAndRemoveAttributeValue(attributes, IS_SPOTCHARACTERS);\r
- if (isNotBlank(isSpotcharacters) ) {\r
- //TODO isSpotcharacters\r
- String message = "isSpotcharacters not yet implemented for <key>";\r
- fireWarningEvent(message, parentEvent, 4);\r
- }\r
- \r
- PolytomousKey key = PolytomousKey.NewInstance();\r
- key.addTaxonomicScope(state.getCurrentTaxon());\r
- state.setCurrentKey(key);\r
- \r
- boolean isFirstCouplet = true;\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- save(key, state);\r
- state.setCurrentKey(null);\r
- return;\r
- } else if (isEndingElement(next, KEYNOTES)){\r
- popUnimplemented(next.asEndElement());\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, KEY_TITLE)) {\r
- handleKeyTitle(state, reader, next);\r
- } else if (isStartingElement(next, KEYNOTES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, COUPLET)) {\r
- PolytomousKeyNode node = null;\r
- if (isFirstCouplet){\r
- node = key.getRoot();\r
- isFirstCouplet = false;\r
- }\r
- handleCouplet(state, reader, next, node);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<key> has no closing tag");\r
- \r
+ // TransactionStatus tx = startTransaction();\r
+ unmatchedLeads.saveToSession(getPolytomousKeyNodeService());\r
\r
+ // TODO generally do not store the reference object in the config\r
+ Reference<?> sourceReference = state.getConfig().getSourceReference();\r
+ getReferenceService().saveOrUpdate(sourceReference);\r
}\r
\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param key\r
- * @param next\r
- * @throws XMLStreamException\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common\r
+ * .IImportConfigurator)\r
*/\r
- private void handleKeyTitle(MarkupImportState state, XMLEventReader reader, XMLEvent next) throws XMLStreamException {\r
- PolytomousKey key = state.getCurrentKey();\r
- String keyTitle = getCData(state, reader, next);\r
- String standardTitles = "(?i)(Key\\sto\\sthe\\s(genera|species|varieties|forms))";\r
- \r
- if (isNotBlank(keyTitle) ){\r
- if (!state.getConfig().isReplaceStandardKeyTitles() || ! keyTitle.matches(standardTitles)){\r
- key.setTitleCache(keyTitle, true);\r
- }\r
- }\r
+ protected boolean isIgnore(MarkupImportState state) {\r
+ return !state.getConfig().isDoTaxa();\r
}\r
+ \r
\r
- private void handleCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode parentNode) throws XMLStreamException {\r
- String num = getOnlyAttribute(parentEvent, NUM, true);\r
- List<PolytomousKeyNode> childList = new ArrayList<PolytomousKeyNode>(); \r
- \r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- completeCouplet(state, parentEvent, parentNode, num, childList);\r
- return;\r
- } else if (isEndingElement(next, KEYNOTES)){\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, QUESTION)) {\r
- handleQuestion(state, reader, next, childList);\r
- } else if (isStartingElement(next, KEYNOTES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<couplet> has no closing tag");\r
- }\r
+// ************************* OPEN AFTER REFACTORING ****************************************/ \r
\r
- /**\r
- * @param state\r
- * @param parentEvent\r
- * @param parentNode\r
- * @param num\r
- * @param childList\r
+ \r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.common.CdmIoBase#fireWarningEvent(java.lang.String, java.lang.String, java.lang.Integer)\r
*/\r
- private void completeCouplet(MarkupImportState state, XMLEvent parentEvent,\r
- PolytomousKeyNode parentNode, String num,\r
- List<PolytomousKeyNode> childList) {\r
- if (parentNode != null){\r
- for (PolytomousKeyNode childNode : childList){\r
- parentNode.addChild(childNode);\r
- }\r
- }else if (isNotBlank(num)){\r
- UnmatchedLeadsKey unmatchedKey = UnmatchedLeadsKey.NewInstance(state.getCurrentKey(), num);\r
- Set<PolytomousKeyNode> nodes = state.getUnmatchedLeads().getNodes(unmatchedKey);\r
- for(PolytomousKeyNode nodeToMatch: nodes){\r
- for (PolytomousKeyNode childNode : childList){\r
- nodeToMatch.addChild(childNode);\r
- }\r
- state.getUnmatchedLeads().removeNode(unmatchedKey, nodeToMatch);\r
- }\r
- }else{\r
- String message = "Parent num could not be matched. Please check if num (%s) is correct";\r
- message = String.format(message, num);\r
- fireWarningEvent(message, parentEvent, 6);\r
- }\r
- }\r
-\r
- private void handleQuestion(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, List<PolytomousKeyNode> nodesList) throws XMLStreamException {\r
- // attributes\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- //needed only for data lineage\r
- String questionNum = getAndRemoveRequiredAttributeValue(parentEvent, attributes, NUM);\r
- \r
- PolytomousKeyNode myNode = PolytomousKeyNode.NewInstance();\r
- myNode.setKey(state.getCurrentKey()); //to avoid NPE while computing num in PolytomousKeyNode in case this node is not matched correctly with a parent\r
- nodesList.add(myNode);\r
- \r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return;\r
- } else if (isEndingElement(next, TO_KEY)){\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, KEYNOTES)){\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- \r
- } else if (isStartingElement(next, TEXT)) {\r
- String text = getCData(state, reader, next);\r
- KeyStatement statement = KeyStatement.NewInstance(text);\r
- myNode.setStatement(statement);\r
- } else if (isStartingElement(next, COUPLET)) {\r
- //TODO test\r
- handleCouplet(state, reader, next, myNode);\r
- } else if (isStartingElement(next, TO_COUPLET)) {\r
- handleToCouplet(state, reader, next, myNode);\r
- } else if (isStartingElement(next, TO_TAXON)) {\r
- handleToTaxon(state, reader, next, myNode);\r
- } else if (isStartingElement(next, TO_KEY)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, KEYNOTES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<question> has no closing tag");\r
- }\r
-\r
- private void handleToCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent next, PolytomousKeyNode node) throws XMLStreamException {\r
- String num = getOnlyAttribute(next, NUM, true);\r
- String cData = getCData(state, reader, next, false);\r
- if (isNotBlank(cData)){\r
- String message = "CData ('%s') not handled";\r
- message = String.format(message, cData);\r
- fireWarningEvent(message, next, 4);\r
- }\r
- UnmatchedLeadsKey unmatched = UnmatchedLeadsKey.NewInstance(state.getCurrentKey(), num);\r
- state.getUnmatchedLeads().addKey(unmatched, node);\r
- }\r
-\r
- private void handleToTaxon(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode node) throws XMLStreamException {\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String num = getAndRemoveAttributeValue(attributes, NUM);\r
- String taxonStr = getCData(state, reader, parentEvent, false);\r
- //TODO ?\r
- taxonStr = makeTaxonKey(taxonStr, state.getCurrentTaxon());\r
- UnmatchedLeadsKey unmatched = UnmatchedLeadsKey.NewInstance(num, taxonStr);\r
- state.getUnmatchedLeads().addKey(unmatched, node);\r
- return;\r
+ public void fireWarningEvent(String message, String dataLocation, Integer severity) {\r
+ super.fireWarningEvent(message, dataLocation, severity, 1);\r
}\r
\r
- private String makeTaxonKey(String strGoto, Taxon taxon) {\r
- String result = "";\r
- if (strGoto == null){\r
- return "";\r
- }\r
- String strGenusName = CdmBase.deproxy(taxon.getName(), NonViralName.class).getGenusOrUninomial();\r
- strGoto = strGoto.replaceAll("\\([^\\(\\)]*\\)", ""); //replace all brackets\r
- strGoto = strGoto.replaceAll("\\s+", " "); //replace multiple whitespaces by exactly one whitespace\r
- \r
- strGoto = strGoto.trim(); \r
- String[] split = strGoto.split("\\s");\r
- for (int i = 0; i<split.length; i++){\r
- String single = split[i];\r
- if (isGenusAbbrev(single, strGenusName)){\r
- split[i] = strGenusName;\r
- }\r
-// if (isInfraSpecificMarker(single)){\r
-// String strSpeciesName = CdmBase.deproxy(taxon.getName(), NonViralName.class).getSpecificEpithet();\r
-// split[i] = strGenusName + " " + strSpeciesName + " ";\r
-// }\r
- result = (result + " " + split[i]).trim();\r
- }\r
- return result;\r
+ public void fireWarningEvent(String message, String dataLocation, Integer severity, int stackDepth) {\r
+ super.fireWarningEvent(message, dataLocation, severity, stackDepth + 1);\r
}\r
\r
- private boolean isGenusAbbrev(String single, String strGenusName) {\r
- if (! single.matches("[A-Z]\\.?")) {\r
- return false;\r
- }else if (single.length() == 0 || strGenusName == null || strGenusName.length() == 0){\r
- return false; \r
- }else{\r
- return single.charAt(0) == strGenusName.charAt(0);\r
- }\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);\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
+ public void fireSchemaConflictEventExpectedStartTag(String elName, XMLEventReader reader) throws XMLStreamException {\r
+ super.fireSchemaConflictEventExpectedStartTag(elName, reader);\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 = Rank.SPECIES(); // default\r
- boolean isCultivar = checkAndRemoveAttributeValue(attributes, CLASS,\r
- "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()\r
- .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
- /**\r
- * @param state\r
- * @param rank\r
- * @return\r
- */\r
- private NonViralName<?> createNameByCode(MarkupImportState state, Rank rank) {\r
- NonViralName<?> name;\r
- NomenclaturalCode nc = makeNomenclaturalCode(state);\r
- name = (NonViralName<?>) nc.getNewTaxonNameInstance(rank);\r
- return name;\r
- }\r
-\r
- /**\r
- * @param state\r
- * @return\r
- */\r
- private NomenclaturalCode makeNomenclaturalCode(MarkupImportState state) {\r
- NomenclaturalCode nc = state.getConfig().getNomenclaturalCode();\r
- if (nc == null) {\r
- nc = NomenclaturalCode.ICBN; // default;\r
- }\r
- return nc;\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,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- 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 (next.isEndElement()) {\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\r
- .getAnnotationType(state, uuidWriterAnnotation,\r
- "Writer", "writer", "writer", null);\r
- Annotation annotation = Annotation.NewInstance(text,\r
- writerAnnotationType, Language.DEFAULT());\r
- dataHolder.annotation = annotation;\r
-\r
- return dataHolder;\r
- } else {\r
- return null;\r
- }\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_REF)) {\r
- FootnoteDataHolder footNote = handleFootnoteRef(state,\r
- reader, next);\r
- if (footNote.isRef()) {\r
- footnotes.add(footNote);\r
- } else {\r
- logger.warn("Non ref footnotes not yet impelemnted");\r
- }\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
+// ************************* END Events ************************************************************\r
+ \r
+ \r
+ public boolean isStartingElement(XMLEvent event, String elName) throws XMLStreamException {\r
+ return super.isStartingElement(event, elName);\r
}\r
\r
- private void registerFootnotes(MarkupImportState state,\r
- AnnotatableEntity entity, List<FootnoteDataHolder> footnotes) {\r
- for (FootnoteDataHolder footNote : footnotes) {\r
- registerFootnoteDemand(state, entity, footNote);\r
- }\r
+ public boolean isEndingElement(XMLEvent event, String elName) throws XMLStreamException {\r
+ return super.isEndingElement(event, elName);\r
+ } \r
+ \r
+ public void fillMissingEpithetsForTaxa(Taxon parentTaxon, Taxon childTaxon) {\r
+ super.fillMissingEpithetsForTaxa(parentTaxon, childTaxon);\r
}\r
-\r
- private void registerGivenFootnote(MarkupImportState state,\r
- 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
+ public Feature getFeature(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<Feature> voc){\r
+ return super.getFeature(state, uuid, label, text, labelAbbrev, voc);\r
}\r
-\r
- private void registerGivenFigure(MarkupImportState state, String id,\r
- 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
+ public ExtensionType getExtensionType(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev){\r
+ return super.getExtensionType(state, uuid, label, text, labelAbbrev);\r
}\r
-\r
- private void registerFootnoteDemand(MarkupImportState state,\r
- 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\r
- .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
+ public AnnotationType getAnnotationType(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<AnnotationType> voc){\r
+ return super.getAnnotationType(state, uuid, label, text, labelAbbrev, voc);\r
}\r
-\r
- private void registerFigureDemand(MarkupImportState state,\r
- 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
+ public TextData getFeaturePlaceholder(MarkupImportState state, DescriptionBase<?> description, Feature feature, boolean createIfNotExists) {\r
+ return super.getFeaturePlaceholder(state, description, feature, createIfNotExists);\r
}\r
-\r
- private void attachFootnote(MarkupImportState state,\r
- AnnotatableEntity entity, FootnoteDataHolder footnote) {\r
- AnnotationType annotationType = this.getAnnotationType(state,\r
- MarkupTransformer.uuidFootnote, "Footnote",\r
- "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
+ public NamedAreaLevel getNamedAreaLevel(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<NamedAreaLevel> voc){\r
+ return super.getNamedAreaLevel(state, uuid, label, text, labelAbbrev, voc);\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
+ public NamedArea getNamedArea(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level, TermVocabulary voc, TermMatchMode matchMode){\r
+ return super.getNamedArea(state, uuid, label, text, labelAbbrev, areaType, level, voc, matchMode);\r
}\r
-\r
- private void handleFigure(MarkupImportState state, XMLEventReader reader,\r
- 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,\r
- 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
+ public Language getLanguage(MarkupImportState state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary voc){\r
+ return super.getLanguage(state, uuid, label, text, labelAbbrev, voc);\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,\r
- String urlString, String legendString, String titleString,\r
- String numString, XMLEvent next) {\r
- Media media = null;\r
- try {\r
- URL url = new URL(urlString);\r
- if ("lineart".equals(type)) {\r
- media = Figure.NewInstance(url.toURI(), null, null,\r
- null);\r
- } else if (type == null || "photo".equals(type)\r
- || "signature".equals(type)\r
- || "others".equals(type)) {\r
- media = Media.NewInstance(url.toURI(), null, null, null);\r
- } else {\r
- String message = "Unknown figure type '%s'";\r
- message = String.format(message, type);\r
- // TODO location\r
- fireWarningEvent(message, "-", 2);\r
- media = Media.NewInstance(url.toURI(), null, null, null);\r
- }\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()\r
- .getSourceReference(), null);\r
- } else {\r
- String message = "Figure id should never be empty or null";\r
- fireWarningEvent(message, next, 6);\r
- }\r
- // text\r
- // do nothing\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
+ public boolean getReadMediaData(){\r
+ return this.READ_MEDIA_DATA;\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
+ public Media getImageMedia(String uriString, boolean readMediaData, boolean isFigure) throws MalformedURLException {\r
+ return super.getImageMedia(uriString, readMediaData, isFigure);\r
}\r
\r
- private FootnoteDataHolder handleFootnote(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- 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
+ public IEditGeoService getEditGeoService() {\r
+ return editGeoService;\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,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- 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, COLLECTION)) {\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, COLLECTION)) {\r
- handleNotYetImplementedElement(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(); // getCData(state,\r
- // reader,\r
- // next);\r
- // does not\r
- // work as\r
- // we have\r
- // inner\r
- // tags like\r
- // <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 handleInLineReferences(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- 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,\r
- 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
- // TODO handle missing end element\r
- throw new IllegalStateException("<References> has no closing tag");\r
- }\r
-\r
- private String handleInLineReference(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- throws XMLStreamException {\r
- Reference<?> reference = handleReference(state, reader, parentEvent);\r
- String result = "<ref uuid='%s'>%s</ref>";\r
- result = String.format(result, reference.getUuid(),\r
- reference.getTitleCache());\r
- return result;\r
- }\r
-\r
- private Reference<?> handleReference(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- 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,\r
- 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,\r
- 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,\r
- 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(),\r
- NonViralName.class);\r
- }\r
-\r
- DerivedUnitFacade facade = DerivedUnitFacade\r
- .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,\r
- 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, 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, COLLECTION)) {\r
- handleCollection(state, reader, next, homotypicalGroup,\r
- 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, 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,\r
- DerivedUnitFacade facade, String text, NonViralName name,\r
- 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,\r
- 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 handleCollection(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, HomotypicalGroup homotypicalGroup, DerivedUnitFacade facade)\r
- 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,\r
- parentEvent.asStartElement(), COLLECTOR);\r
- checkMandatoryElement(hasFieldNum,\r
- 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,\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, 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,\r
- ALTERNATIVE_COLLECTION_TYPE_STATUS)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, SUB_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,\r
- XMLEvent parentEvent, DerivedUnitFacade facade)\r
- 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 (StringUtils.isNotBlank(text)) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- if (isLocality) {\r
- facade.setLocality(text);\r
- } else {\r
- NamedArea area = createArea(text, areaLevel, state);\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
- // TODO handle missing end element\r
- throw new IllegalStateException("Specimen type has no closing tag"); // TODO\r
- // Auto-generated\r
- // method\r
- // stub\r
-\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
- private String getCData(MarkupImportState state, XMLEventReader reader, XMLEvent next) throws XMLStreamException {\r
- return getCData(state, reader, next, true);\r
- }\r
- \r
- /**\r
- * Reads character data. Any element other than character data or the ending\r
- * tag will fire an unexpected element event.\r
- * \r
- * @param state\r
- * @param reader\r
- * @param next\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private String getCData(MarkupImportState state, XMLEventReader reader, XMLEvent next,boolean checkAttributes) throws XMLStreamException {\r
- if (checkAttributes){\r
- checkNoAttributes(next);\r
- }\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent myNext = readNoWhitespace(reader);\r
- if (isMyEndingElement(myNext, next)) {\r
- return text;\r
- } else if (myNext.isCharacters()) {\r
- text += myNext.asCharacters().getData();\r
- } else {\r
- handleUnexpectedElement(myNext);\r
- }\r
- }\r
- throw new IllegalStateException("Event has no closing tag");\r
-\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,\r
- 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, NUM)) {\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
- handleNotYetImplementedElement(next);\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,\r
- infrAut);\r
-\r
- // authors\r
- makeNomenclaturalAuthors(name, event, authorStr, paraut, infrParAut,\r
- 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\r
- .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,\r
- Map<String, String> nameMap, NonViralName<?> name, XMLEvent event,\r
- 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(value);\r
- } else if (rank.isInfraGeneric()) {\r
- name.setInfraGenericEpithet(value);\r
- } else if (rank.isSpecies()) {\r
- name.setSpecificEpithet(value);\r
- } else if (rank.isInfraSpecific()) {\r
- name.setInfraSpecificEpithet(value);\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
- /**\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().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,\r
- event);\r
- name.setBasionymAuthorTeam(authorAndEx[0]);\r
- name.setExBasionymAuthorTeam(authorAndEx[1]);\r
- }\r
- } else {\r
- if (StringUtils.isNotBlank(authorStr)) {\r
- INomenclaturalAuthor[] authorAndEx = authorAndEx(authorStr,\r
- 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
- * @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().isInfraSpecific()) {\r
- if (StringUtils.isBlank(infrParAut)\r
- && StringUtils.isNotBlank(infrAut)\r
- && (StringUtils.isNotBlank(paraut) || StringUtils\r
- .isNotBlank(authorStr))) {\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)\r
- || 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\r
- .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,\r
- 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,\r
- XMLEvent parentEvent, Map<String, String> refMap)\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
- 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,\r
- 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
-\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
- Reference bookOrPartOf = ReferenceFactory.newGeneric();\r
- reference = bookOrPartOf;\r
- }\r
- // TODO use existing author from name or before\r
- TeamOrPersonBase author = createAuthor(authorStr);\r
- reference.setAuthorTeam(author);\r
-\r
- } else {\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
-\r
- // TODO\r
- // ALTERNATEPUBTITLE\r
- // ISSUE\r
- // NOTES\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 = this.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,\r
- 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\r
- .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
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return;\r
- } else {\r
- if (isEndingElement(next, DISTRIBUTION_LIST)\r
- || isEndingElement(next, HABITAT_LIST)) {\r
- // only handle list elements\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- 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)\r
- || 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()) || feature\r
- .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 = 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 {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- // TODO handle missing end element\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(\r
- MarkupImportState state, XMLEventReader reader,\r
- TaxonDescription taxonDescription, boolean isDescription,\r
- DescriptionElementBase lastDescriptionElement, XMLEvent next)\r
- throws XMLStreamException {\r
- FigureDataHolder figureHolder = handleFigureRef(state, reader, next);\r
- Feature figureFeature = getFeature(state,\r
- MarkupTransformer.uuidFigures, "Figures", "Figures", "Fig.",\r
- 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>"\r
- + figureHolder.figurePart.trim() + "</figurePart>";\r
- Annotation annotation = Annotation.NewInstance(annotationText,\r
- 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 next\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private DescriptionElementBase makeFeatureString(MarkupImportState state,XMLEventReader reader, Feature feature,\r
- TaxonDescription taxonDescription, DescriptionElementBase lastDescriptionElement, XMLEvent next)\r
- throws XMLStreamException {\r
- Map<String, String> subheadingMap = handleString(state, reader, next);\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
- TextData textData = TextData.NewInstance(subheadingFeature);\r
- textData.putText(Language.DEFAULT(), subheadingMap.get(subheading));\r
- taxonDescription.addElement(textData);\r
- // TODO how to handle figures when these data are split in\r
- // subheadings\r
- lastDescriptionElement = textData;\r
- }\r
- return lastDescriptionElement;\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,\r
- XMLEventReader reader, Feature feature, Taxon taxon, XMLEvent next)\r
- 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 = 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,\r
- XMLEventReader reader, String classValue, Feature feature,\r
- 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)\r
- 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,\r
- 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,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- 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
-\r
- private void handleDistributionLocality(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- throws XMLStreamException {\r
- String classValue = getClassOnlyAttribute(parentEvent);\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
- TaxonDescription description = getTaxonDescription(taxon,\r
- ref, false, true);\r
- NamedAreaLevel level = makeNamedAreaLevel(state,\r
- classValue, next);\r
- NamedArea area = createArea(text, level, state);\r
-\r
- PresenceAbsenceTermBase<?> status = null;\r
- Distribution distribution = Distribution.NewInstance(area,\r
- status);\r
- description.addElement(distribution);\r
- } else {\r
- String message = "Empty distribution locality";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- return;\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, COORDINATES)) {\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(\r
- "<DistributionLocality> has no closing tag");\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(\r
- 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,\r
- 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,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- 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
- private Map<String, String> handleString(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- 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 (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, COLLECTION)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, COLLECTION)) {\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 {\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
\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");\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
- 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 (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
- * @param classValue\r
- * @param state\r
- * @param parentEvent\r
- * @return\r
- * @throws UndefinedTransformerMethodException\r
- */\r
- private Feature makeFeature(String classValue, MarkupImportState state,\r
- XMLEvent parentEvent) {\r
- UUID uuid;\r
- try {\r
- Feature feature = state.getTransformer()\r
- .getFeatureByKey(classValue);\r
- if (feature != null) {\r
- return feature;\r
- }\r
- uuid = state.getTransformer().getFeatureUuid(classValue);\r
- if (uuid == null) {\r
- // TODO\r
- logger.warn("Uuid is null for " + classValue);\r
- }\r
- String featureText = StringUtils.capitalize(classValue);\r
-\r
- // TODO eFlora vocabulary\r
- TermVocabulary<Feature> voc = null;\r
- feature = getFeature(state, uuid, featureText, featureText,\r
- classValue, voc);\r
- if (feature == null) {\r
- throw new NullPointerException(classValue\r
- + " 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
- * This comes from the old version, needs to be checked on need\r
- * \r
- * @param state\r
- */\r
- private void doAllTheOldOtherStuff(MarkupImportState state) {\r
- state.putTree(null, null);\r
- if (unmatchedLeads == null) {\r
- unmatchedLeads = UnmatchedLeads.NewInstance();\r
- }\r
- state.setUnmatchedLeads(unmatchedLeads);\r
-\r
- // TransactionStatus tx = startTransaction();\r
- unmatchedLeads.saveToSession(getPolytomousKeyNodeService());\r
-\r
- // TODO generally do not store the reference object in the config\r
- Reference sourceReference = state.getConfig().getSourceReference();\r
- getReferenceService().saveOrUpdate(sourceReference);\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see\r
- * eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common\r
- * .IImportConfigurator)\r
- */\r
- protected boolean isIgnore(MarkupImportState state) {\r
- return !state.getConfig().isDoTaxa();\r
- }\r
-\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff