-/**\r
-* Copyright (C) 2009 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-\r
-package eu.etaxonomy.cdm.io.tcsxml.in;\r
-\r
-import java.io.InputStream;\r
-import java.util.ArrayList;\r
-import java.util.HashSet;\r
-import java.util.List;\r
-import java.util.Map;\r
-import java.util.Set;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.jdom.Element;\r
-import org.jdom.Namespace;\r
-import org.springframework.beans.factory.annotation.Autowired;\r
-import org.springframework.stereotype.Component;\r
-\r
-import eu.etaxonomy.cdm.common.CdmUtils;\r
-import eu.etaxonomy.cdm.common.ResultWrapper;\r
-import eu.etaxonomy.cdm.common.XmlHelp;\r
-import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;\r
-import eu.etaxonomy.cdm.io.common.ICdmIO;\r
-import eu.etaxonomy.cdm.io.common.MapWrapper;\r
-import eu.etaxonomy.cdm.io.tcsrdf.TcsRdfImportConfigurator;\r
-import eu.etaxonomy.cdm.io.tcsrdf.TcsRdfTaxonNameImport;\r
-import eu.etaxonomy.cdm.io.tcsxml.TcsXmlTransformer;\r
-import eu.etaxonomy.cdm.model.common.CdmBase;\r
-import eu.etaxonomy.cdm.model.common.OriginalSourceType;\r
-import eu.etaxonomy.cdm.model.common.RelationshipTermBase;\r
-import eu.etaxonomy.cdm.model.description.CommonTaxonName;\r
-import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
-import eu.etaxonomy.cdm.model.name.TaxonName;\r
-import eu.etaxonomy.cdm.model.name.TaxonNameFactory;\r
-import eu.etaxonomy.cdm.model.reference.Reference;\r
-import eu.etaxonomy.cdm.model.taxon.Classification;\r
-import eu.etaxonomy.cdm.model.taxon.Synonym;\r
-import eu.etaxonomy.cdm.model.taxon.SynonymType;\r
-import eu.etaxonomy.cdm.model.taxon.Taxon;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonNode;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;\r
-import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;\r
-\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-@Component\r
-public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdmIO<TcsXmlImportState> {\r
- private static final long serialVersionUID = 6632990505515905663L;\r
-\r
- private static final Logger logger = Logger.getLogger(TcsXmlTaxonRelationsImport.class);\r
-\r
- private static int modCount = 30000;\r
-\r
- @Autowired\r
- private TcsRdfTaxonNameImport rdfNameImport;\r
- private TcsRdfImportConfigurator rdfConfig = TcsRdfImportConfigurator.NewInstance(null, null);\r
-\r
- public TcsXmlTaxonRelationsImport(){\r
- super();\r
-\r
- }\r
-\r
- @Override\r
- public boolean doCheck(TcsXmlImportState state){\r
- boolean result = true;\r
- logger.warn("Checking for TaxonRelations not yet implemented");\r
- logger.warn("Creation of homotypic relations is still problematic");\r
- //result &= checkArticlesWithoutJournal(bmiConfig);\r
- //result &= checkPartOfJournal(bmiConfig);\r
-\r
- return result;\r
- }\r
-\r
- @Override\r
- public void doInvoke(TcsXmlImportState state){\r
-\r
-\r
- logger.info("start make taxon relations ...");\r
- MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)state.getStore(ICdmIO.TAXON_STORE);\r
- MapWrapper<TaxonName> taxonNameMap = (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE);\r
- MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE);\r
-\r
- Set<TaxonBase> taxonStore = new HashSet<TaxonBase>();\r
-\r
- ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);\r
- String childName;\r
- boolean obligatory;\r
- String idNamespace = "TaxonRelation";\r
-\r
- TcsXmlImportConfigurator config = state.getConfig();\r
- Element elDataSet = super.getDataSetElement(config);\r
- Namespace tcsNamespace = config.getTcsXmlNamespace();\r
-\r
- childName = "TaxonConcepts";\r
- obligatory = false;\r
- Element elTaxonConcepts = XmlHelp.getSingleChildElement(success, elDataSet, childName, tcsNamespace, obligatory);\r
-\r
- childName = "TaxonConcept";\r
- List<Element> elTaxonConceptList = elTaxonConcepts == null ? new ArrayList<Element>() : elTaxonConcepts.getChildren(childName, tcsNamespace);\r
-\r
- int i = 0;\r
- int taxonRelCount = 0;\r
-\r
- //for each taxonConcept\r
- logger.info("NUmber of taxon concepts: " + elTaxonConceptList.size());\r
- for (Element elTaxonConcept : elTaxonConceptList){\r
- if ((i++ % modCount) == 0){ logger.info("Taxa handled: " + (i-1));}\r
- taxonRelCount += makeTaxonConcept(state, taxonMap, taxonStore, elTaxonConcept, tcsNamespace, success);\r
- }//elTaxonConcept\r
- logger.info("Taxa handled: " + taxonStore.size());\r
- //TaxonRelationshipAssertions\r
- taxonRelCount += makeTaxonRelationshipAssertion(state, taxonMap, referenceMap, taxonStore, elDataSet, tcsNamespace, success);\r
-\r
- logger.info("Taxa to save: " + taxonStore.size());\r
- getTaxonService().save(taxonStore);\r
-\r
- //do basionym relationships\r
- childName = "TaxonNames";\r
- obligatory = false;\r
- Element elTaxonNames = XmlHelp.getSingleChildElement(success, elDataSet, childName, tcsNamespace, obligatory);\r
-\r
- childName = "TaxonName";\r
- List<Element> elTaxonNameList = elTaxonNames == null ? new ArrayList<Element>() : elTaxonNames.getChildren(childName, tcsNamespace);\r
-\r
- logger.info("NUmber of taxon concepts: " + elTaxonNameList.size());\r
- for (Element elTaxonName : elTaxonNameList){\r
- if ((i++ % modCount) == 0){ logger.info("Taxa handled: " + (i-1));}\r
- taxonRelCount += makeBasionymRelations(state, taxonMap, taxonNameMap, taxonStore, elTaxonName, tcsNamespace, success);\r
- }//elTaxonConcept\r
- logger.info("Taxa handled: " + taxonStore.size());\r
-\r
-\r
- taxonStore = null;\r
- logger.info("end make taxon relations ...");\r
- if (!success.getValue()){\r
- state.setUnsuccessfull();\r
- }\r
- return;\r
- }\r
-\r
- private int makeBasionymRelations(TcsXmlImportState state,\r
- MapWrapper<TaxonBase> taxonMap, MapWrapper<TaxonName> taxonNameMap, Set<TaxonBase> taxonStore,\r
- Element elTaxonName, Namespace tcsNamespace,\r
- ResultWrapper<Boolean> success) {\r
-\r
- /*\r
- * <tcs:Basionym>\r
- <tcs:RelatedName ref="urn:lsid:ipni.org:names:50000063-1">Caryophyllaceae</tcs:RelatedName>\r
- </tcs:Basionym>\r
- */\r
-\r
-\r
- String childName = "Basionym";\r
- boolean obligatory = false;\r
- Element elBasionymRelationships = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);\r
- if (elBasionymRelationships != null){\r
- childName = "RelatedName";\r
- obligatory = false;\r
- Element elBasionym = XmlHelp.getSingleChildElement(success, elBasionymRelationships, childName, tcsNamespace, obligatory);\r
-\r
- String id = elTaxonName.getAttributeValue("id");\r
- TaxonName name = taxonNameMap.get(removeVersionOfRef(id));\r
-\r
- TaxonBase taxonBase = (TaxonBase)name.getTaxonBases().iterator().next();\r
-\r
- String ref = elBasionym.getAttributeValue("ref");\r
- TaxonName basionymName = taxonNameMap.get(removeVersionOfRef(ref));\r
-\r
- if (basionymName != null){\r
- basionymName = HibernateProxyHelper.deproxy(basionymName, TaxonName.class);\r
- TaxonBase basionym;\r
- if (basionymName.getTaxonBases().isEmpty()){\r
- basionym = Synonym.NewInstance(basionymName, null);\r
- }else{\r
- basionym = (TaxonBase)basionymName.getTaxonBases().iterator().next();\r
- }\r
- //Synonym basionymSyn;\r
- if (basionym instanceof Taxon){\r
-\r
- if (!(taxonBase instanceof Synonym)){\r
- logger.debug("The taxon " + basionymName.getTitleCache() + " is used in a concept and can not be a synonym " + name.getTitleCache() + "but will be added as basionym for the homotypical group");\r
- name.addBasionym(basionymName);\r
- //basionymName.getHomotypicalGroup().addTypifiedName(name);\r
- } else if (taxonBase instanceof Synonym){\r
- Synonym synonym = (Synonym) taxonBase;\r
- ((Taxon)basionym).addSynonym(synonym, SynonymType.HOMOTYPIC_SYNONYM_OF());\r
- basionym.getHomotypicGroup().setGroupBasionym(basionymName);\r
- taxonStore.add(basionym);\r
- }\r
- }else{\r
- if (taxonBase instanceof Taxon){\r
- Synonym synonym = (Synonym) basionym;\r
- ((Taxon)taxonBase).addSynonym(synonym, SynonymType.HOMOTYPIC_SYNONYM_OF());\r
- taxonBase.getHomotypicGroup().setGroupBasionym(basionymName);\r
- taxonStore.add(taxonBase);\r
- } else{\r
- Taxon acc = ((Synonym)taxonBase).getAcceptedTaxon();\r
- if (acc != null){\r
- acc.addHomotypicSynonym((Synonym)basionym);\r
- basionymName.getHomotypicalGroup().setGroupBasionym(basionymName);\r
- }\r
- }\r
- }\r
-\r
-\r
- } else{\r
- basionymName = TaxonNameFactory.NewNonViralInstance(name.getRank());\r
- childName = "RelatedName";\r
- obligatory = true;\r
- Element elName = XmlHelp.getSingleChildElement(success, elBasionym, childName, tcsNamespace, obligatory);\r
- String strName = (elName == null)? "" : elName.getTextNormalize();\r
- basionymName.setTitleCache(strName, false);\r
- Synonym basionymSyn = Synonym.NewInstance(basionymName, unknownSec());\r
- if (taxonBase instanceof Taxon){\r
- Taxon taxon = (Taxon)taxonBase;\r
- taxon.addSynonym(basionymSyn, SynonymType.HOMOTYPIC_SYNONYM_OF());\r
- taxon.getHomotypicGroup().setGroupBasionym(basionymName);\r
- taxonStore.add(taxon);\r
- } else{\r
- Synonym syn = (Synonym) taxonBase;\r
- if (syn.getAcceptedTaxon() != null){\r
- Taxon accTaxon = syn.getAcceptedTaxon();\r
- accTaxon.addSynonym(basionymSyn, SynonymType.HOMOTYPIC_SYNONYM_OF());\r
- accTaxon.getHomotypicGroup().setGroupBasionym(basionymName);\r
- taxonStore.add(accTaxon);\r
- }\r
- }\r
- }\r
- }\r
- return 1;\r
- }\r
-\r
- private int makeTaxonConcept(TcsXmlImportState state, MapWrapper<TaxonBase> taxonMap, Set<TaxonBase> taxonStore, Element elTaxonConcept, Namespace tcsNamespace, ResultWrapper<Boolean> success){\r
- int taxonRelCount = 0;\r
-\r
- String childName = "TaxonRelationships";\r
- boolean obligatory = false;\r
- Element elTaxonRelationships = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);\r
-\r
- if (elTaxonRelationships != null){\r
- //Relationships\r
- String tcsElementName = "TaxonRelationship";\r
- List<Element> elTaxonRelationshipList = elTaxonRelationships.getChildren(tcsElementName, tcsNamespace);\r
- logger.info("Number of taxonrelationships: " + elTaxonRelationshipList.size());\r
- for (Element elTaxonRelationship: elTaxonRelationshipList){\r
-\r
- taxonRelCount++;\r
- logger.debug("TaxonRelationship "+ taxonRelCount);\r
-\r
- String strId = elTaxonConcept.getAttributeValue("id");\r
- //TODO\r
-// String strConceptType = elTaxonConcept.getAttributeValue("type"); //original, revision, incomplete, aggregate, nominal\r
-// String strPrimary = elTaxonConcept.getAttributeValue("primary"); //If primary='true' the concept is the first level response to a query. If 'false' the concept may be a secondary concept linked directly or indirectly to the definition of a primary concept.\r
-// String strForm = elTaxonConcept.getAttributeValue("form"); //anamorph, teleomorph, hybrid\r
-\r
- TaxonBase fromTaxon = taxonMap.get(removeVersionOfRef(strId));\r
- makeRelationshipType(state, elTaxonRelationship, taxonMap, taxonStore, fromTaxon, success);\r
-\r
- if (fromTaxon instanceof Taxon){\r
- makeHomotypicSynonymRelations((Taxon)fromTaxon);\r
- }\r
- }// end Relationship\r
- }\r
- return taxonRelCount;\r
- }\r
-\r
- private int makeTaxonRelationshipAssertion(\r
- TcsXmlImportState state,\r
- MapWrapper<TaxonBase> taxonMap,\r
- MapWrapper<Reference> referenceMap,\r
- Set<TaxonBase> taxonStore,\r
- Element elDataSet,\r
- Namespace tcsNamespace,\r
- ResultWrapper<Boolean> success){\r
-\r
- int i = 0;\r
- String childName = "TaxonRelationshipAssertions";\r
- boolean obligatory = false;\r
- Element elTaxonRelationshipAssertions = XmlHelp.getSingleChildElement(success, elDataSet, childName, tcsNamespace, obligatory);\r
- if(elTaxonRelationshipAssertions == null){\r
- return 0;\r
- }\r
-\r
- childName = "TaxonRelationshipAssertion";\r
- List<Element> elTaxonRelationshipAssertionList = elTaxonRelationshipAssertions.getChildren(childName, tcsNamespace);\r
- //for each taxon relationship assertion\r
- for (Element elTaxonRelationshipAssertion : elTaxonRelationshipAssertionList){\r
- if ((i++ % modCount) == 0){ logger.info("TaxonRelationshipAssertions handled: " + (i-1));}\r
- String strId = elTaxonRelationshipAssertion.getAttributeValue("id");\r
- //TODO id\r
-\r
- childName = "AccordingTo";\r
- obligatory = true;\r
- Element elAccordingTo = XmlHelp.getSingleChildElement(success, elTaxonRelationshipAssertion, childName, tcsNamespace, obligatory);\r
- Reference ref = makeAccordingTo(elAccordingTo, referenceMap, success);\r
-\r
- childName = "FromTaxonConcept";\r
- obligatory = true;\r
- Element elFromTaxonConcept = XmlHelp.getSingleChildElement(success, elTaxonRelationshipAssertion, childName, tcsNamespace, obligatory);\r
-\r
- Class<? extends TaxonBase> clazz = Taxon.class;\r
- //TODO if synonym\r
- TaxonBase fromTaxon = makeReferenceType(elFromTaxonConcept, clazz, taxonMap, success);\r
-\r
- makeRelationshipType(state, elTaxonRelationshipAssertion, taxonMap, taxonStore, fromTaxon, success);\r
- }//elTaxonRelationshipAssertion\r
-\r
- return i;\r
- }\r
-\r
-\r
- /**\r
- * Handles the TCS RelationshipType element.\r
- * @param tcsConfig\r
- * @param elRelationship\r
- * @param taxonMap\r
- * @param taxonStore\r
- * @param fromTaxon\r
- * @param success\r
- */\r
- private void makeRelationshipType(\r
- TcsXmlImportState state\r
- , Element elRelationship\r
- , MapWrapper<TaxonBase> taxonMap\r
- , Set<TaxonBase> taxonStore\r
- , TaxonBase fromTaxon\r
- , ResultWrapper<Boolean> success\r
- ){\r
-\r
- if (elRelationship == null){\r
- success.setValue(false);\r
- }\r
- String strRelType = elRelationship.getAttributeValue("type");\r
-\r
-\r
- try {\r
- ResultWrapper<Boolean> isInverse = new ResultWrapper<Boolean>();\r
- isInverse.setValue(false);\r
- if ("has vernacular".equalsIgnoreCase(strRelType)){\r
- handleVernacular(success, state, elRelationship, fromTaxon);\r
- }else{\r
- RelationshipTermBase<?> relType = TcsXmlTransformer.tcsRelationshipType2Relationship(strRelType, isInverse);\r
-\r
- //toTaxon (should be part of relationshipType)\r
- boolean isSynonym = (relType instanceof SynonymType);\r
- TaxonBase toTaxon = getToTaxon(elRelationship, taxonMap, state.getMissingConceptLSIDs(), isSynonym, success, state);\r
-\r
- if (toTaxon != null && fromTaxon != null){\r
- //exchange taxa if relationship is inverse\r
- if (isInverse.getValue() == true ){\r
- TaxonBase tmp = toTaxon;\r
- toTaxon = fromTaxon;\r
- fromTaxon = tmp;\r
- }\r
-\r
- //Create relationship\r
- if (! (toTaxon instanceof Taxon)){\r
- logger.warn("TaxonBase toTaxon is not of Type 'Taxon'. Relationship is not added.");\r
- success.setValue(false);\r
- }else{\r
- Taxon taxonTo = (Taxon)toTaxon;\r
- if (relType instanceof SynonymType){\r
- SynonymType synRelType = (SynonymType)relType;\r
- if (! (fromTaxon instanceof Synonym )){\r
- logger.warn("TaxonBase fromTaxon is not of Type 'Synonym'. Relationship is not added.");\r
- success.setValue(false);\r
- }else{\r
- Synonym synonym = (Synonym)fromTaxon;\r
- TaxonName synName = synonym.getName();\r
- TaxonName accName = taxonTo.getName();\r
- if (synName != null && accName != null && synName.isHomotypic(accName)\r
- && ( synRelType.equals(SynonymType.SYNONYM_OF()))){\r
- synRelType = SynonymType.HOMOTYPIC_SYNONYM_OF();\r
- }\r
- if (! relationExists(taxonTo, synonym, synRelType)){\r
- taxonTo.addSynonym(synonym, synRelType);\r
- }else{\r
- //TODO citation, microReference\r
- //TODO different synRelTypes -> warning\r
- success.setValue(false);\r
- }\r
- }\r
- }else if (relType instanceof TaxonRelationshipType){\r
- Reference citation = null;\r
- String microReference = null;\r
- makeTaxonRelationship(state, (TaxonRelationshipType)relType, fromTaxon, taxonTo, citation, microReference, success);\r
- }else{\r
- logger.warn("Unknown Relationshiptype");\r
- success.setValue(false);\r
- }\r
- taxonStore.add(toTaxon);\r
- }\r
- }else{\r
- if (toTaxon == null){\r
- // logger.warn("toTaxon (" + /*strToTaxon + */ ") could not be found in taxonMap. Relationship of type " + strRelType + " was not added to CDM");\r
- }\r
- if (fromTaxon == null){\r
- // logger.warn("fromTaxon (" + /*strTaxonAbout + */") could not be found in taxonMap. Relationship was not added to CDM");\r
- }\r
- success.setValue(false);\r
- }\r
- }\r
- } catch (UnknownCdmTypeException e) {\r
- //TODO\r
- logger.warn("relationshipType " + strRelType + " not yet implemented");\r
- success.setValue(false);\r
- }\r
- return;\r
- }\r
-\r
- private void handleVernacular(ResultWrapper<Boolean> success, TcsXmlImportState state, Element elRelationship, TaxonBase taxonBase) {\r
- if (! taxonBase.isInstanceOf(Taxon.class)){\r
- logger.warn("From Taxon is not of type Taxon but of type " + taxonBase.getClass().getSimpleName());\r
- success.setValue(false);\r
- return;\r
- }else{\r
- Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);\r
- Map<String, CommonTaxonName> commonNameMap = state.getCommonNameMap();\r
- CommonTaxonName commonTaxonName = getCommonName(elRelationship, commonNameMap, success);\r
- TaxonDescription description = getDescription(taxon);\r
- description.addElement(commonTaxonName);\r
- }\r
- }\r
-\r
- private TaxonDescription getDescription(Taxon taxon) {\r
- if (taxon.getDescriptions().isEmpty()){\r
- return TaxonDescription.NewInstance(taxon);\r
- }else{\r
- //TODO only if the description represents this TCS file\r
- return taxon.getDescriptions().iterator().next();\r
- }\r
- }\r
-\r
- private CommonTaxonName getCommonName(Element elTaxonRelationship, Map<String, CommonTaxonName> commonNameMap, ResultWrapper<Boolean> success){\r
- CommonTaxonName result = null;\r
- if (elTaxonRelationship == null || commonNameMap == null){\r
- success.setValue(false);\r
- }else{\r
- String childName = "ToTaxonConcept";\r
- boolean obligatory = true;\r
- Element elToTaxonConcept = XmlHelp.getSingleChildElement(success, elTaxonRelationship, childName, elTaxonRelationship.getNamespace(), obligatory);\r
-\r
- String linkType = elToTaxonConcept.getAttributeValue("linkType");\r
- if (linkType == null || linkType.equals("local")){\r
- String ref = elToTaxonConcept.getAttributeValue("ref");\r
- if (ref != null){\r
- result = commonNameMap.get(ref);\r
- }else{\r
- logger.warn("Non ref not yet implemented for vernacular name relationship");\r
- }\r
- }else{\r
- logger.warn("External link types for vernacular name not yet implemented");\r
- }\r
- }\r
- return result;\r
- }\r
-\r
- private void makeTaxonRelationship(TcsXmlImportState state, TaxonRelationshipType relType, TaxonBase fromTaxon, Taxon taxonTo, Reference citation, String microReference, ResultWrapper<Boolean> success){\r
- TaxonRelationshipType taxRelType = relType;\r
- if (! (fromTaxon instanceof Taxon )){\r
- logger.warn("TaxonBase fromTaxon " + /*strTaxonAbout +*/ "is not of Type 'Taxon'. Relationship is not added.");\r
- success.setValue(false);\r
- }else{\r
- Taxon taxonFrom = (Taxon)fromTaxon;\r
- if (relType.equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())){\r
- makeTaxonomicallyIncluded(state, taxonTo, taxonFrom, citation, microReference);\r
- }else{\r
- taxonFrom.addTaxonRelation(taxonTo, taxRelType, citation, microReference);\r
- }\r
- }\r
- }\r
-\r
- private boolean makeTaxonomicallyIncluded(TcsXmlImportState state, Taxon toTaxon, Taxon fromTaxon, Reference citation, String microCitation){\r
- Reference sec = toTaxon.getSec();\r
- Classification tree = state.getTree(sec);\r
- if (tree == null){\r
- tree = makeTree(state, sec);\r
- }\r
- TaxonNode childNode = tree.addParentChild(toTaxon, fromTaxon, citation, microCitation);\r
- return (childNode != null);\r
- }\r
-\r
-\r
- @SuppressWarnings("rawtypes")\r
- private TaxonBase getToTaxon(Element elTaxonRelationship, MapWrapper<TaxonBase> map, List<String> missingNameID,boolean isSynonym, ResultWrapper<Boolean> success, TcsXmlImportState state){\r
- TaxonBase result = null;\r
- if (elTaxonRelationship == null || map == null){\r
- success.setValue(false);\r
- }else{\r
- String childName = "ToTaxonConcept";\r
- boolean obligatory = true;\r
- Element elToTaxonConcept = XmlHelp.getSingleChildElement(success, elTaxonRelationship, childName, elTaxonRelationship.getNamespace(), obligatory);\r
-\r
-\r
- String linkType = elToTaxonConcept.getAttributeValue("linkType");\r
- if (linkType == null || linkType.equals("local")){\r
- String ref = elToTaxonConcept.getAttributeValue("ref");\r
- if (ref != null){\r
- result = map.get(ref);\r
- if (result == null && state.getConfig().isDoGetMissingNames()){\r
-\r
-\r
- String[] split= ref.split(":");\r
- String id = split[split.length-1];\r
- logger.info("get name for id " + id);\r
- if (missingNameID.contains(id)){\r
- return null;\r
- }\r
- InputStream nameStream = service.getNamesById(id);\r
-\r
-\r
- try{\r
- String nameUri = "urn:lsid:ipni.org:names:"+ id;\r
- TaxonName name = rdfNameImport.handleRdfElementFromStream(nameStream, rdfConfig, (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE), nameUri);\r
- if (name != null){\r
- if (name.getTaxa().isEmpty()){\r
-\r
- result = Taxon.NewInstance(name, null);\r
- }else{\r
- result = (TaxonBase)name.getTaxa().iterator().next();\r
- }\r
- name.addSource(OriginalSourceType.Import, ref, "TaxonConcept", null, null);\r
- result.addSource(OriginalSourceType.Import, ref, "TaxonConcept", null, null);\r
-\r
- map.put(removeVersionOfRef(ref), result);\r
- } else{\r
- missingNameID.add(id);\r
- }\r
- }catch(Exception e){\r
- logger.debug(e.getMessage());\r
- e.printStackTrace();\r
- }\r
- }\r
- }else{\r
- String title = elToTaxonConcept.getTextNormalize();\r
- //TODO synonym?\r
- TaxonName taxonName = TaxonNameFactory.NewNonViralInstance(null);\r
- taxonName.setTitleCache(title, true);\r
- logger.warn("Free text related taxon seems to be bug in TCS");\r
- if (isSynonym){\r
- result = Synonym.NewInstance(taxonName, TcsXmlTaxonImport.unknownSec());\r
- }else{\r
- result = Taxon.NewInstance(taxonName, TcsXmlTaxonImport.unknownSec());\r
- }\r
- result.setTitleCache(title, true);\r
- }\r
- }else{\r
- logger.warn("External link types for synonym not yet implemented");\r
- }\r
- }\r
- return result;\r
- }\r
-\r
- private boolean relationExists(Taxon taxonTo, Synonym synonym, SynonymType synRelType){\r
- if (synonym == null || taxonTo == null\r
- || !taxonTo.equals(synonym.getAcceptedTaxon())){\r
- return false;\r
- }else{\r
- return CdmUtils.nullSafeEqual(synonym.getType(),synRelType);\r
- }\r
- }\r
-\r
- private boolean makeHomotypicSynonymRelations(Taxon aboutTaxon){\r
- TaxonName aboutName = aboutTaxon.getName();\r
- if (aboutName != null){\r
- Set<TaxonName> typifiedNames = aboutName.getHomotypicalGroup().getTypifiedNames();\r
- for (TaxonName<?,?> typifiedName : typifiedNames){\r
- //TODO check if name is part of this tcs file\r
- if (typifiedName.equals(aboutName)){\r
- continue;\r
- }\r
- Set<Synonym> syns = typifiedName.getSynonyms();\r
- for(Synonym syn:syns){\r
- aboutTaxon.addSynonym(syn, SynonymType.HOMOTYPIC_SYNONYM_OF());\r
- }\r
- }\r
- }\r
- return true;\r
- }\r
-\r
- @Override\r
- protected boolean isIgnore(TcsXmlImportState state){\r
- return ! state.getConfig().isDoRelTaxa();\r
- }\r
-}\r
+/**
+* Copyright (C) 2009 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+
+package eu.etaxonomy.cdm.io.tcsxml.in;
+
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.jdom.Element;
+import org.jdom.Namespace;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import eu.etaxonomy.cdm.common.CdmUtils;
+import eu.etaxonomy.cdm.common.ResultWrapper;
+import eu.etaxonomy.cdm.common.XmlHelp;
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
+import eu.etaxonomy.cdm.io.common.ICdmIO;
+import eu.etaxonomy.cdm.io.common.MapWrapper;
+import eu.etaxonomy.cdm.io.tcsrdf.TcsRdfImportConfigurator;
+import eu.etaxonomy.cdm.io.tcsrdf.TcsRdfTaxonNameImport;
+import eu.etaxonomy.cdm.io.tcsxml.TcsXmlTransformer;
+import eu.etaxonomy.cdm.model.common.CdmBase;
+import eu.etaxonomy.cdm.model.common.IRelationshipType;
+import eu.etaxonomy.cdm.model.description.CommonTaxonName;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.name.TaxonName;
+import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
+import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.taxon.Classification;
+import eu.etaxonomy.cdm.model.taxon.Synonym;
+import eu.etaxonomy.cdm.model.taxon.SynonymType;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
+import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
+
+
+/**
+ * @author a.mueller
+ *
+ */
+@Component
+public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdmIO<TcsXmlImportState> {
+ private static final long serialVersionUID = 6632990505515905663L;
+
+ private static final Logger logger = LogManager.getLogger(TcsXmlTaxonRelationsImport.class);
+
+ private static int modCount = 30000;
+
+ @Autowired
+ private TcsRdfTaxonNameImport rdfNameImport;
+ private TcsRdfImportConfigurator rdfConfig = TcsRdfImportConfigurator.NewInstance(null, null);
+
+ public TcsXmlTaxonRelationsImport(){
+ super();
+
+ }
+
+ @Override
+ public boolean doCheck(TcsXmlImportState state){
+ boolean result = true;
+ logger.warn("Checking for TaxonRelations not yet implemented");
+ logger.warn("Creation of homotypic relations is still problematic");
+ //result &= checkArticlesWithoutJournal(bmiConfig);
+ //result &= checkPartOfJournal(bmiConfig);
+
+ return result;
+ }
+
+ @Override
+ public void doInvoke(TcsXmlImportState state){
+
+
+ logger.info("start make taxon relations ...");
+ MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)state.getStore(ICdmIO.TAXON_STORE);
+ MapWrapper<TaxonName> taxonNameMap = (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE);
+ MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE);
+
+ Set<TaxonBase> taxonStore = new HashSet<TaxonBase>();
+
+ ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);
+ String childName;
+ boolean obligatory;
+ String idNamespace = "TaxonRelationDTO";
+
+ TcsXmlImportConfigurator config = state.getConfig();
+ Element elDataSet = super.getDataSetElement(config);
+ Namespace tcsNamespace = config.getTcsXmlNamespace();
+
+ childName = "TaxonConcepts";
+ obligatory = false;
+ Element elTaxonConcepts = XmlHelp.getSingleChildElement(success, elDataSet, childName, tcsNamespace, obligatory);
+
+ childName = "TaxonConcept";
+ List<Element> elTaxonConceptList = elTaxonConcepts == null ? new ArrayList<Element>() : elTaxonConcepts.getChildren(childName, tcsNamespace);
+
+ int i = 0;
+ int taxonRelCount = 0;
+
+ //for each taxonConcept
+ logger.info("NUmber of taxon concepts: " + elTaxonConceptList.size());
+ for (Element elTaxonConcept : elTaxonConceptList){
+ if ((i++ % modCount) == 0){ logger.info("Taxa handled: " + (i-1));}
+ taxonRelCount += makeTaxonConcept(state, taxonMap, taxonStore, elTaxonConcept, tcsNamespace, success);
+ }//elTaxonConcept
+ logger.info("Taxa handled: " + taxonStore.size());
+ //TaxonRelationshipAssertions
+ taxonRelCount += makeTaxonRelationshipAssertion(state, taxonMap, referenceMap, taxonStore, elDataSet, tcsNamespace, success);
+
+ logger.info("Taxa to save: " + taxonStore.size());
+ getTaxonService().save(taxonStore);
+
+ //do basionym relationships
+ childName = "TaxonNames";
+ obligatory = false;
+ Element elTaxonNames = XmlHelp.getSingleChildElement(success, elDataSet, childName, tcsNamespace, obligatory);
+
+ childName = "TaxonName";
+ List<Element> elTaxonNameList = elTaxonNames == null ? new ArrayList<Element>() : elTaxonNames.getChildren(childName, tcsNamespace);
+
+ logger.info("NUmber of taxon concepts: " + elTaxonNameList.size());
+ for (Element elTaxonName : elTaxonNameList){
+ if ((i++ % modCount) == 0){ logger.info("Taxa handled: " + (i-1));}
+ taxonRelCount += makeBasionymRelations(state, taxonMap, taxonNameMap, taxonStore, elTaxonName, tcsNamespace, success);
+ }//elTaxonConcept
+ logger.info("Taxa handled: " + taxonStore.size());
+
+
+ taxonStore = null;
+ logger.info("end make taxon relations ...");
+ if (!success.getValue()){
+ state.setUnsuccessfull();
+ }
+ return;
+ }
+
+ private int makeBasionymRelations(TcsXmlImportState state,
+ MapWrapper<TaxonBase> taxonMap, MapWrapper<TaxonName> taxonNameMap, Set<TaxonBase> taxonStore,
+ Element elTaxonName, Namespace tcsNamespace,
+ ResultWrapper<Boolean> success) {
+
+ /*
+ * <tcs:Basionym>
+ <tcs:RelatedName ref="urn:lsid:ipni.org:names:50000063-1">Caryophyllaceae</tcs:RelatedName>
+ </tcs:Basionym>
+ */
+
+
+ String childName = "Basionym";
+ boolean obligatory = false;
+ Element elBasionymRelationships = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
+ if (elBasionymRelationships != null){
+ childName = "RelatedName";
+ obligatory = false;
+ Element elBasionym = XmlHelp.getSingleChildElement(success, elBasionymRelationships, childName, tcsNamespace, obligatory);
+
+ String id = elTaxonName.getAttributeValue("id");
+ TaxonName name = taxonNameMap.get(removeVersionOfRef(id));
+
+ TaxonBase taxonBase = name.getTaxonBases().iterator().next();
+
+ String ref = elBasionym.getAttributeValue("ref");
+ TaxonName basionymName = taxonNameMap.get(removeVersionOfRef(ref));
+
+ if (basionymName != null){
+ basionymName = HibernateProxyHelper.deproxy(basionymName, TaxonName.class);
+ TaxonBase basionym;
+ if (basionymName.getTaxonBases().isEmpty()){
+ basionym = Synonym.NewInstance(basionymName, null);
+ }else{
+ basionym = basionymName.getTaxonBases().iterator().next();
+ }
+ //Synonym basionymSyn;
+ if (basionym instanceof Taxon){
+
+ if (!(taxonBase instanceof Synonym)){
+ logger.debug("The taxon " + basionymName.getTitleCache() + " is used in a concept and can not be a synonym " + name.getTitleCache() + "but will be added as basionym for the homotypical group");
+ name.addBasionym(basionymName);
+ //basionymName.getHomotypicalGroup().addTypifiedName(name);
+ } else if (taxonBase instanceof Synonym){
+ Synonym synonym = (Synonym) taxonBase;
+ ((Taxon)basionym).addSynonym(synonym, SynonymType.HOMOTYPIC_SYNONYM_OF);
+ basionym.getHomotypicGroup().setGroupBasionym(basionymName);
+ taxonStore.add(basionym);
+ }
+ }else{
+ if (taxonBase instanceof Taxon){
+ Synonym synonym = (Synonym) basionym;
+ ((Taxon)taxonBase).addSynonym(synonym, SynonymType.HOMOTYPIC_SYNONYM_OF);
+ taxonBase.getHomotypicGroup().setGroupBasionym(basionymName);
+ taxonStore.add(taxonBase);
+ } else{
+ Taxon acc = ((Synonym)taxonBase).getAcceptedTaxon();
+ if (acc != null){
+ acc.addHomotypicSynonym((Synonym)basionym);
+ basionymName.getHomotypicalGroup().setGroupBasionym(basionymName);
+ }
+ }
+ }
+
+
+ } else{
+ basionymName = TaxonNameFactory.NewNonViralInstance(name.getRank());
+ childName = "RelatedName";
+ obligatory = true;
+ Element elName = XmlHelp.getSingleChildElement(success, elBasionym, childName, tcsNamespace, obligatory);
+ String strName = (elName == null)? "" : elName.getTextNormalize();
+ basionymName.setTitleCache(strName, false);
+ Synonym basionymSyn = Synonym.NewInstance(basionymName, unknownSec());
+ if (taxonBase instanceof Taxon){
+ Taxon taxon = (Taxon)taxonBase;
+ taxon.addSynonym(basionymSyn, SynonymType.HOMOTYPIC_SYNONYM_OF);
+ taxon.getHomotypicGroup().setGroupBasionym(basionymName);
+ taxonStore.add(taxon);
+ } else{
+ Synonym syn = (Synonym) taxonBase;
+ if (syn.getAcceptedTaxon() != null){
+ Taxon accTaxon = syn.getAcceptedTaxon();
+ accTaxon.addSynonym(basionymSyn, SynonymType.HOMOTYPIC_SYNONYM_OF);
+ accTaxon.getHomotypicGroup().setGroupBasionym(basionymName);
+ taxonStore.add(accTaxon);
+ }
+ }
+ }
+ }
+ return 1;
+ }
+
+ private int makeTaxonConcept(TcsXmlImportState state, MapWrapper<TaxonBase> taxonMap, Set<TaxonBase> taxonStore, Element elTaxonConcept, Namespace tcsNamespace, ResultWrapper<Boolean> success){
+ int taxonRelCount = 0;
+
+ String childName = "TaxonRelationships";
+ boolean obligatory = false;
+ Element elTaxonRelationships = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);
+
+ if (elTaxonRelationships != null){
+ //Relationships
+ String tcsElementName = "TaxonRelationship";
+ List<Element> elTaxonRelationshipList = elTaxonRelationships.getChildren(tcsElementName, tcsNamespace);
+ logger.info("Number of taxonrelationships: " + elTaxonRelationshipList.size());
+ for (Element elTaxonRelationship: elTaxonRelationshipList){
+
+ taxonRelCount++;
+ logger.debug("TaxonRelationship "+ taxonRelCount);
+
+ String strId = elTaxonConcept.getAttributeValue("id");
+ //TODO
+// String strConceptType = elTaxonConcept.getAttributeValue("type"); //original, revision, incomplete, aggregate, nominal
+// String strPrimary = elTaxonConcept.getAttributeValue("primary"); //If primary='true' the concept is the first level response to a query. If 'false' the concept may be a secondary concept linked directly or indirectly to the definition of a primary concept.
+// String strForm = elTaxonConcept.getAttributeValue("form"); //anamorph, teleomorph, hybrid
+
+ TaxonBase fromTaxon = taxonMap.get(removeVersionOfRef(strId));
+ makeRelationshipType(state, elTaxonRelationship, taxonMap, taxonStore, fromTaxon, success);
+
+ if (fromTaxon instanceof Taxon){
+ makeHomotypicSynonymRelations((Taxon)fromTaxon);
+ }
+ }// end Relationship
+ }
+ return taxonRelCount;
+ }
+
+ private int makeTaxonRelationshipAssertion(
+ TcsXmlImportState state,
+ MapWrapper<TaxonBase> taxonMap,
+ MapWrapper<Reference> referenceMap,
+ Set<TaxonBase> taxonStore,
+ Element elDataSet,
+ Namespace tcsNamespace,
+ ResultWrapper<Boolean> success){
+
+ int i = 0;
+ String childName = "TaxonRelationshipAssertions";
+ boolean obligatory = false;
+ Element elTaxonRelationshipAssertions = XmlHelp.getSingleChildElement(success, elDataSet, childName, tcsNamespace, obligatory);
+ if(elTaxonRelationshipAssertions == null){
+ return 0;
+ }
+
+ childName = "TaxonRelationshipAssertion";
+ List<Element> elTaxonRelationshipAssertionList = elTaxonRelationshipAssertions.getChildren(childName, tcsNamespace);
+ //for each taxon relationship assertion
+ for (Element elTaxonRelationshipAssertion : elTaxonRelationshipAssertionList){
+ if ((i++ % modCount) == 0){ logger.info("TaxonRelationshipAssertions handled: " + (i-1));}
+ String strId = elTaxonRelationshipAssertion.getAttributeValue("id");
+ //TODO id
+
+ childName = "AccordingTo";
+ obligatory = true;
+ Element elAccordingTo = XmlHelp.getSingleChildElement(success, elTaxonRelationshipAssertion, childName, tcsNamespace, obligatory);
+ Reference ref = makeAccordingTo(elAccordingTo, referenceMap, success);
+
+ childName = "FromTaxonConcept";
+ obligatory = true;
+ Element elFromTaxonConcept = XmlHelp.getSingleChildElement(success, elTaxonRelationshipAssertion, childName, tcsNamespace, obligatory);
+
+ Class<? extends TaxonBase> clazz = Taxon.class;
+ //TODO if synonym
+ TaxonBase fromTaxon = makeReferenceType(elFromTaxonConcept, clazz, taxonMap, success);
+
+ makeRelationshipType(state, elTaxonRelationshipAssertion, taxonMap, taxonStore, fromTaxon, success);
+ }//elTaxonRelationshipAssertion
+
+ return i;
+ }
+
+
+ /**
+ * Handles the TCS RelationshipType element.
+ * @param tcsConfig
+ * @param elRelationship
+ * @param taxonMap
+ * @param taxonStore
+ * @param fromTaxon
+ * @param success
+ */
+ private void makeRelationshipType(
+ TcsXmlImportState state
+ , Element elRelationship
+ , MapWrapper<TaxonBase> taxonMap
+ , Set<TaxonBase> taxonStore
+ , TaxonBase fromTaxon
+ , ResultWrapper<Boolean> success
+ ){
+
+ if (elRelationship == null){
+ success.setValue(false);
+ }
+ String strRelType = elRelationship.getAttributeValue("type");
+
+
+ try {
+ ResultWrapper<Boolean> isInverse = new ResultWrapper<Boolean>();
+ isInverse.setValue(false);
+ if ("has vernacular".equalsIgnoreCase(strRelType)){
+ handleVernacular(success, state, elRelationship, fromTaxon);
+ }else{
+ IRelationshipType relType = TcsXmlTransformer.tcsRelationshipType2Relationship(strRelType, isInverse);
+
+ //toTaxon (should be part of relationshipType)
+ boolean isSynonym = (relType instanceof SynonymType);
+ TaxonBase toTaxon = getToTaxon(elRelationship, taxonMap, state.getMissingConceptLSIDs(), isSynonym, success, state);
+
+ if (toTaxon != null && fromTaxon != null){
+ //exchange taxa if relationship is inverse
+ if (isInverse.getValue() == true ){
+ TaxonBase tmp = toTaxon;
+ toTaxon = fromTaxon;
+ fromTaxon = tmp;
+ }
+
+ //Create relationship
+ if (! (toTaxon instanceof Taxon)){
+ logger.warn("TaxonBase toTaxon is not of Type 'Taxon'. Relationship is not added.");
+ success.setValue(false);
+ }else{
+ Taxon taxonTo = (Taxon)toTaxon;
+ if (relType instanceof SynonymType){
+ SynonymType synRelType = (SynonymType)relType;
+ if (! (fromTaxon instanceof Synonym )){
+ logger.warn("TaxonBase fromTaxon is not of Type 'Synonym'. Relationship is not added.");
+ success.setValue(false);
+ }else{
+ Synonym synonym = (Synonym)fromTaxon;
+ TaxonName synName = synonym.getName();
+ TaxonName accName = taxonTo.getName();
+ if (synName != null && accName != null && synName.isHomotypic(accName)
+ && ( synRelType.equals(SynonymType.SYNONYM_OF))){
+ synRelType = SynonymType.HOMOTYPIC_SYNONYM_OF;
+ }
+ if (! relationExists(taxonTo, synonym, synRelType)){
+ taxonTo.addSynonym(synonym, synRelType);
+ }else{
+ //TODO citation, microReference
+ //TODO different synRelTypes -> warning
+ success.setValue(false);
+ }
+ }
+ }else if (relType instanceof TaxonRelationshipType){
+ Reference citation = null;
+ String microReference = null;
+ makeTaxonRelationship(state, (TaxonRelationshipType)relType, fromTaxon, taxonTo, citation, microReference, success);
+ }else{
+ logger.warn("Unknown Relationshiptype");
+ success.setValue(false);
+ }
+ taxonStore.add(toTaxon);
+ }
+ }else{
+ if (toTaxon == null){
+ // logger.warn("toTaxon (" + /*strToTaxon + */ ") could not be found in taxonMap. Relationship of type " + strRelType + " was not added to CDM");
+ }
+ if (fromTaxon == null){
+ // logger.warn("fromTaxon (" + /*strTaxonAbout + */") could not be found in taxonMap. Relationship was not added to CDM");
+ }
+ success.setValue(false);
+ }
+ }
+ } catch (UnknownCdmTypeException e) {
+ //TODO
+ logger.warn("relationshipType " + strRelType + " not yet implemented");
+ success.setValue(false);
+ }
+ return;
+ }
+
+ private void handleVernacular(ResultWrapper<Boolean> success, TcsXmlImportState state, Element elRelationship, TaxonBase taxonBase) {
+ if (! taxonBase.isInstanceOf(Taxon.class)){
+ logger.warn("From Taxon is not of type Taxon but of type " + taxonBase.getClass().getSimpleName());
+ success.setValue(false);
+ return;
+ }else{
+ Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
+ Map<String, CommonTaxonName> commonNameMap = state.getCommonNameMap();
+ CommonTaxonName commonTaxonName = getCommonName(elRelationship, commonNameMap, success);
+ TaxonDescription description = getDescription(taxon);
+ description.addElement(commonTaxonName);
+ }
+ }
+
+ private TaxonDescription getDescription(Taxon taxon) {
+ if (taxon.getDescriptions().isEmpty()){
+ return TaxonDescription.NewInstance(taxon);
+ }else{
+ //TODO only if the description represents this TCS file
+ return taxon.getDescriptions().iterator().next();
+ }
+ }
+
+ private CommonTaxonName getCommonName(Element elTaxonRelationship, Map<String, CommonTaxonName> commonNameMap, ResultWrapper<Boolean> success){
+ CommonTaxonName result = null;
+ if (elTaxonRelationship == null || commonNameMap == null){
+ success.setValue(false);
+ }else{
+ String childName = "ToTaxonConcept";
+ boolean obligatory = true;
+ Element elToTaxonConcept = XmlHelp.getSingleChildElement(success, elTaxonRelationship, childName, elTaxonRelationship.getNamespace(), obligatory);
+
+ String linkType = elToTaxonConcept.getAttributeValue("linkType");
+ if (linkType == null || linkType.equals("local")){
+ String ref = elToTaxonConcept.getAttributeValue("ref");
+ if (ref != null){
+ result = commonNameMap.get(ref);
+ }else{
+ logger.warn("Non ref not yet implemented for vernacular name relationship");
+ }
+ }else{
+ logger.warn("External link types for vernacular name not yet implemented");
+ }
+ }
+ return result;
+ }
+
+ private void makeTaxonRelationship(TcsXmlImportState state, TaxonRelationshipType relType, TaxonBase fromTaxon, Taxon taxonTo, Reference citation, String microReference, ResultWrapper<Boolean> success){
+ TaxonRelationshipType taxRelType = relType;
+ if (! (fromTaxon instanceof Taxon )){
+ logger.warn("TaxonBase fromTaxon " + /*strTaxonAbout +*/ "is not of Type 'Taxon'. Relationship is not added.");
+ success.setValue(false);
+ }else{
+ Taxon taxonFrom = (Taxon)fromTaxon;
+ if (relType.equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())){
+ makeTaxonomicallyIncluded(state, taxonTo, taxonFrom, citation, microReference);
+ }else{
+ taxonFrom.addTaxonRelation(taxonTo, taxRelType, citation, microReference);
+ }
+ }
+ }
+
+ private boolean makeTaxonomicallyIncluded(TcsXmlImportState state, Taxon toTaxon, Taxon fromTaxon, Reference citation, String microCitation){
+ Reference sec = toTaxon.getSec();
+ Classification tree = state.getTree(sec);
+ if (tree == null){
+ tree = makeTree(state, sec);
+ }
+ TaxonNode childNode = tree.addParentChild(toTaxon, fromTaxon, citation, microCitation);
+ return (childNode != null);
+ }
+
+
+ @SuppressWarnings("rawtypes")
+ private TaxonBase getToTaxon(Element elTaxonRelationship, MapWrapper<TaxonBase> map, List<String> missingNameID,boolean isSynonym, ResultWrapper<Boolean> success, TcsXmlImportState state){
+ TaxonBase result = null;
+ if (elTaxonRelationship == null || map == null){
+ success.setValue(false);
+ }else{
+ String childName = "ToTaxonConcept";
+ boolean obligatory = true;
+ Element elToTaxonConcept = XmlHelp.getSingleChildElement(success, elTaxonRelationship, childName, elTaxonRelationship.getNamespace(), obligatory);
+
+
+ String linkType = elToTaxonConcept.getAttributeValue("linkType");
+ if (linkType == null || linkType.equals("local")){
+ String ref = elToTaxonConcept.getAttributeValue("ref");
+ if (ref != null){
+ result = map.get(ref);
+ if (result == null && state.getConfig().isDoGetMissingNames()){
+
+
+ String[] split= ref.split(":");
+ String id = split[split.length-1];
+ logger.info("get name for id " + id);
+ if (missingNameID.contains(id)){
+ return null;
+ }
+ InputStream nameStream = service.getNamesById(id);
+
+
+ try{
+ String nameUri = "urn:lsid:ipni.org:names:"+ id;
+ TaxonName name = rdfNameImport.handleRdfElementFromStream(nameStream, rdfConfig, (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE), nameUri);
+ if (name != null){
+ if (name.getTaxa().isEmpty()){
+
+ result = Taxon.NewInstance(name, null);
+ }else{
+ result = name.getTaxa().iterator().next();
+ }
+ name.addSource(OriginalSourceType.Import, ref, "TaxonConcept", null, null);
+ result.addSource(OriginalSourceType.Import, ref, "TaxonConcept", null, null);
+
+ map.put(removeVersionOfRef(ref), result);
+ } else{
+ missingNameID.add(id);
+ }
+ }catch(Exception e){
+ logger.debug(e.getMessage());
+ e.printStackTrace();
+ }
+ }
+ }else{
+ String title = elToTaxonConcept.getTextNormalize();
+ //TODO synonym?
+ TaxonName taxonName = TaxonNameFactory.NewNonViralInstance(null);
+ taxonName.setTitleCache(title, true);
+ logger.warn("Free text related taxon seems to be bug in TCS");
+ if (isSynonym){
+ result = Synonym.NewInstance(taxonName, TcsXmlTaxonImport.unknownSec());
+ }else{
+ result = Taxon.NewInstance(taxonName, TcsXmlTaxonImport.unknownSec());
+ }
+ result.setTitleCache(title, true);
+ }
+ }else{
+ logger.warn("External link types for synonym not yet implemented");
+ }
+ }
+ return result;
+ }
+
+ private boolean relationExists(Taxon taxonTo, Synonym synonym, SynonymType synRelType){
+ if (synonym == null || taxonTo == null
+ || !taxonTo.equals(synonym.getAcceptedTaxon())){
+ return false;
+ }else{
+ return CdmUtils.nullSafeEqual(synonym.getType(),synRelType);
+ }
+ }
+
+ private boolean makeHomotypicSynonymRelations(Taxon aboutTaxon){
+ TaxonName aboutName = aboutTaxon.getName();
+ if (aboutName != null){
+ Set<TaxonName> typifiedNames = aboutName.getHomotypicalGroup().getTypifiedNames();
+ for (TaxonName typifiedName : typifiedNames){
+ //TODO check if name is part of this tcs file
+ if (typifiedName.equals(aboutName)){
+ continue;
+ }
+ Set<Synonym> syns = typifiedName.getSynonyms();
+ for(Synonym syn:syns){
+ aboutTaxon.addSynonym(syn, SynonymType.HOMOTYPIC_SYNONYM_OF);
+ }
+ }
+ }
+ return true;
+ }
+
+ @Override
+ protected boolean isIgnore(TcsXmlImportState state){
+ return ! state.getConfig().isDoRelTaxa();
+ }
+}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff