import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.ResIterator;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
-import com.hp.hpl.jena.rdf.model.Property;
-
-
-
import eu.etaxonomy.cdm.common.XmlHelp;
import eu.etaxonomy.cdm.io.common.ICdmIO;
import eu.etaxonomy.cdm.model.common.Marker;
import eu.etaxonomy.cdm.model.common.MarkerType;
import eu.etaxonomy.cdm.model.common.TimePeriod;
+import eu.etaxonomy.cdm.model.name.INonViralName;
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
-import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
+import eu.etaxonomy.cdm.model.name.TaxonName;
import eu.etaxonomy.cdm.model.reference.IGeneric;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
/**
* @author a.mueller
* @created 29.05.2008
- * @version 1.0
*/
@Component
public class TcsRdfTaxonNameImport extends TcsRdfImportBase implements ICdmIO<TcsRdfImportState> {
- private static final Logger logger = Logger.getLogger(TcsRdfTaxonNameImport.class);
+ private static final long serialVersionUID = -2547422867292051979L;
+
+ private static final Logger logger = Logger.getLogger(TcsRdfTaxonNameImport.class);
private static int modCount = 5000;
@Override
protected void doInvoke(TcsRdfImportState state){
- MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)state.getStore(ICdmIO.TAXONNAME_STORE);
+ MapWrapper<TaxonName> taxonNameMap = (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE);
MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE);
MapWrapper<TeamOrPersonBase> authorMap = (MapWrapper<TeamOrPersonBase>)state.getStore(ICdmIO.TEAM_STORE);
Resource elTaxonName = root.getResource(taxonNameNamespace);
int i = 0;
-
- TaxonNameBase name;
+
+ TaxonName name;
Property property = root.getProperty(taxonNameNamespace+"authorship");
-
+
ResIterator iterator = root.listSubjectsWithProperty(property, (RDFNode) null);
String id ;
while (iterator.hasNext()){
-
+
Resource resource = iterator.next();
-
+
name = handleNameResource(resource, config);
id = resource.getNameSpace();
taxonNameMap.put(id, name);
}
-
+
logger.info(i + " names handled");
getNameService().save(taxonNameMap.objects());
// makeNameSpecificData(nameMap);
protected boolean isIgnore(TcsRdfImportState state){
return ! state.getConfig().isDoTaxonNames();
}
-
- protected TaxonNameBase handleNameModel(Model model, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap, String uri){
+
+ protected TaxonName handleNameModel(Model model, TcsRdfImportConfigurator config, MapWrapper<TaxonName> taxonNameMap, String uri){
Resource nameAbout = model.getResource(uri);
- TaxonNameBase result = handleNameResource(nameAbout, config);
+ TaxonName result = handleNameResource(nameAbout, config);
taxonNameMap.put(uri, result);
return result;
-
+
}
-
- private TaxonNameBase handleNameResource(Resource nameAbout, TcsRdfImportConfigurator config){
+
+ private TaxonName handleNameResource(Resource nameAbout, TcsRdfImportConfigurator config){
String idNamespace = "TaxonName";
-
- StmtIterator stmts = nameAbout.listProperties();
- while(stmts.hasNext()){
- System.out.println(stmts.next().getPredicate().toString());
- }
-
+
+// StmtIterator stmts = nameAbout.listProperties();
+// while(stmts.hasNext()){
+// System.out.println(stmts.next().getPredicate().toString());
+// }
+
Property prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"nomenclaturalCode");
Statement stateNomenclaturalCode = nameAbout.getProperty(prop);
String strNomenclaturalCode = stateNomenclaturalCode.getObject().toString();
//Rank
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"rankString");
String strRank = nameAbout.getProperty(prop).getString();
-
-
-
+
+
+
try {
-
+
Rank rank = TcsRdfTransformer.rankString2Rank(strRank);
NomenclaturalCode nomCode;
if (strNomenclaturalCode != null){
}else{
nomCode = NomenclaturalCode.ICNAFP;
}
-
- TaxonNameBase<?,?> nameBase = nomCode.getNewTaxonNameInstance(rank);
+
+ TaxonName nameBase = nomCode.getNewTaxonNameInstance(rank);
Set<String> omitAttributes = null;
//makeStandardMapper(nameAbout, nameBase, omitAttributes, standardMappers);
-
+
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"nameComplete");
String strNameComplete = nameAbout.getProperty(prop).getString();
nameBase.setTitleCache(strNameComplete, true);
-
+
prop = nameAbout.getModel().getProperty(config.getCommonNamespaceURIString()+"publishedIn");
String strPublishedIn = nameAbout.getProperty(prop).getString();
if (strPublishedIn != null && strPublishedIn != ""){
}catch(NullPointerException e){
}
if (config.isPublishReferences()){
- ((Reference<?>)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
+ ((Reference)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
}
}
-
- if (nameBase instanceof NonViralName){
- NonViralName<?> nonViralName = (NonViralName<?>)nameBase;
+
+ if (nameBase.isNonViral()){
+ INonViralName nonViralName = nameBase;
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"genusPart");
String strGenusPart;
try{
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"uninomial");
strGenusPart = nameAbout.getProperty(prop).getString();
}
-
+
nonViralName.setGenusOrUninomial(strGenusPart);
-
+
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"infragenericEpithet");
try{
String strInfragenericEpithet = nameAbout.getProperty(prop).getString();
nonViralName.setInfraGenericEpithet(strInfragenericEpithet);
}catch(NullPointerException e){
-
+
}
try {
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"specificEpithet");
String strSpecificEpithet = nameAbout.getProperty(prop).getString();
nonViralName.setSpecificEpithet(strSpecificEpithet);
}catch(NullPointerException e){
-
+
}
try{
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"infraspecificEpithet");
String strInfraspecificEpithet = nameAbout.getProperty(prop).getString();
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet);
}catch(NullPointerException e){
-
+
}
//Authorships
//TODO
<tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:2691-1"
tm:index="1"
tm:role="Combination Author"/>
- <tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:8096-1"
+ <tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:8096-1"
tm:index="1"
tm:role="Basionym Author"/>
</tm:Team>
try{
stateAutorTeamTeam = stateAuthorTeam.getProperty(prop);
}catch(Exception e){
-
+
}
try{
prop = stateAuthorTeam.getModel().getProperty(config.getTeamNamespaceURIString()+"name");
stateAutorTeamName = stateAuthorTeam.getProperty(prop);
}catch(Exception e){
-
+
}
try{
prop = nameAbout.getModel().getProperty(config.getTeamNamespaceURIString()+"hasMember");
System.err.println(e.getMessage());
}
}
-
-
-
+
+
+
nonViralName.setCombinationAuthorship(authorTeam);
-
+
//Annotations:
/*
* <tn:hasAnnotation>
<tn:noteType rdf:resource="http://rs.tdwg.org/ontology/voc/TaxonName#replacementNameFor"/>
<tn:objectTaxonName rdf:resource="urn:lsid:ipni.org:names:151538-1"/>
</tn:NomenclaturalNote>
- </tn:hasAnnotation>
+ </tn:hasAnnotation>
*/
/*
String strInfraspecificEpithet = nameAbout.getProperty(prop).getString();
//ImportHelper.setOriginalSource(nameBase, config.getSourceReference(), nameAbout, idNamespace);
//checkAdditionalContents(elTaxonName, standardMappers, operationalMappers, unclearMappers);
-
+
return nameBase;
-
+
}catch(Exception e){
e.printStackTrace();
return null;
//name
String strNameComplete = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "nameComplete", rdfNamespace);
nameBase.setTitleCache(strNameComplete, true);
-
+
//Reference
//TODO
String tcsElementName = "publishedIn";
}
}
if (config.isPublishReferences()){
- ((Reference<?>)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
+ ((Reference)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
}
}
}
if (nameBase instanceof NonViralName){
- NonViralName<?> nonViralName = (NonViralName<?>)nameBase;
+ INonViralName nonViralName = nameBase;
String strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "genusPart", rdfNamespace);
-
+
//for names of rank genus the uninomial property should be used
if (strGenusPart == null){
strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "uninomial", rdfNamespace);
}
nonViralName.setGenusOrUninomial(strGenusPart);
-
+
String strInfragenericEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infragenericEpithet", rdfNamespace);
nonViralName.setGenusOrUninomial(strInfragenericEpithet);
-
-
-
+
+
+
String strSpecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "specificEpithet", rdfNamespace);
nonViralName.setSpecificEpithet(strSpecificEpithet);
-
+
String strInfraspecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infraspecificEpithet", rdfNamespace);
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet);
//AuthorTeams
}
return null;*/
}
-
- protected TaxonNameBase handleNameElement(Element elTaxonName, Namespace rdfNamespace, Namespace taxonNameNamespace, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap){
+
+ protected TaxonName handleNameElement(Element elTaxonName, Namespace rdfNamespace, Namespace taxonNameNamespace, TcsRdfImportConfigurator config, MapWrapper<TaxonName> taxonNameMap){
String idNamespace = "TaxonName";
Attribute about = elTaxonName.getAttribute("about", rdfNamespace);
-
+
//create TaxonName element
-
-
+
+
String nameAbout = elTaxonName.getAttributeValue("about", rdfNamespace);
if (nameAbout == null){
nameAbout = XmlHelp.getChildAttributeValue(elTaxonName, "TaxonName", taxonNameNamespace, "about", rdfNamespace);
}
-
-
+
+
String strRank = XmlHelp.getChildAttributeValue(elTaxonName, "rankString", taxonNameNamespace, "rankString", rdfNamespace);
if (strRank == null){
strRank = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "rankString", rdfNamespace);
-
+
}
-
+
if (strRank == null){
strRank = XmlHelp.getChildAttributeValue(elTaxonName, "rank", taxonNameNamespace, "resource", rdfNamespace);
-
+
}
-
+
String strNomenclaturalCode = XmlHelp.getChildContentAttributeValue(elTaxonName, "TaxonName", taxonNameNamespace, "nomenclaturalCode", rdfNamespace);
if (strNomenclaturalCode == null){
strNomenclaturalCode = XmlHelp.getChildAttributeValue(elTaxonName, "nomenclaturalCode", taxonNameNamespace, "resource", rdfNamespace);
-
+
}
try {
-
+
Rank rank = TcsRdfTransformer.rankString2Rank(strRank);
NomenclaturalCode nomCode;
if (strNomenclaturalCode != null){
}else{
nomCode = NomenclaturalCode.ICNAFP;
}
-
- TaxonNameBase<?,?> nameBase = nomCode.getNewTaxonNameInstance(rank);
+
+ TaxonName nameBase = nomCode.getNewTaxonNameInstance(rank);
Set<String> omitAttributes = null;
//makeStandardMapper(elTaxonName, nameBase, omitAttributes, standardMappers);
-
+
//name
String strNameComplete = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "nameComplete", rdfNamespace);
nameBase.setTitleCache(strNameComplete, true);
-
+
//Reference
//TODO
String tcsElementName = "publishedIn";
}
}
if (config.isPublishReferences()){
- ((Reference<?>)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
+ ((Reference)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
}
}
}
if (nameBase instanceof NonViralName){
- NonViralName<?> nonViralName = (NonViralName<?>)nameBase;
+ INonViralName nonViralName = nameBase;
String strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "genusPart", rdfNamespace);
-
+
//for names of rank genus the uninomial property should be used
if (strGenusPart == null){
strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "uninomial", rdfNamespace);
}
nonViralName.setGenusOrUninomial(strGenusPart);
-
+
String strInfragenericEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infragenericEpithet", rdfNamespace);
nonViralName.setGenusOrUninomial(strInfragenericEpithet);
-
-
-
+
+
+
String strSpecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "specificEpithet", rdfNamespace);
nonViralName.setSpecificEpithet(strSpecificEpithet);
-
+
String strInfraspecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infraspecificEpithet", rdfNamespace);
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet);
//AuthorTeams
return null;
}
- public TaxonNameBase handleRdfElementFromStream(InputStream is, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap, String uri){
+ public TaxonName handleRdfElementFromStream(InputStream is, TcsRdfImportConfigurator config, MapWrapper<TaxonName> taxonNameMap, String uri){
Model model = ModelFactory.createDefaultModel();
try{
model.read(is, null);
-
+
config.makeNamespaces(model);
-
+
String rdfNamespace = config.getRdfNamespaceURIString();
String taxonNameNamespace = config.getTnNamespaceURIString();
return handleNameModel(model, config, taxonNameMap, uri);
-
-
+
+
}catch(Exception e){
logger.debug("The file was no valid rdf file");
}
-
-
-
+
+
+
return null;
}
-
+
}
BGBM BDI Projects / cdmlib.git / blobdiff