Revision 531fc7bc
Added by Andreas Müller almost 8 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfTaxonNameImport.java | ||
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import com.hp.hpl.jena.rdf.model.Model; |
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import com.hp.hpl.jena.rdf.model.ModelFactory; |
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import com.hp.hpl.jena.rdf.model.Property; |
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import com.hp.hpl.jena.rdf.model.RDFNode; |
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import com.hp.hpl.jena.rdf.model.ResIterator; |
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import com.hp.hpl.jena.rdf.model.Resource; |
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import com.hp.hpl.jena.rdf.model.Statement; |
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import com.hp.hpl.jena.rdf.model.StmtIterator; |
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import com.hp.hpl.jena.rdf.model.Property; |
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import eu.etaxonomy.cdm.common.XmlHelp; |
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import eu.etaxonomy.cdm.io.common.ICdmIO; |
| ... | ... | |
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Resource elTaxonName = root.getResource(taxonNameNamespace); |
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int i = 0; |
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TaxonNameBase name; |
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Property property = root.getProperty(taxonNameNamespace+"authorship"); |
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ResIterator iterator = root.listSubjectsWithProperty(property, (RDFNode) null); |
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String id ; |
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while (iterator.hasNext()){
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Resource resource = iterator.next(); |
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name = handleNameResource(resource, config); |
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id = resource.getNameSpace(); |
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taxonNameMap.put(id, name); |
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} |
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logger.info(i + " names handled"); |
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getNameService().save(taxonNameMap.objects()); |
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// makeNameSpecificData(nameMap); |
| ... | ... | |
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protected boolean isIgnore(TcsRdfImportState state){
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return ! state.getConfig().isDoTaxonNames(); |
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} |
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protected TaxonNameBase handleNameModel(Model model, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap, String uri){
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Resource nameAbout = model.getResource(uri); |
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TaxonNameBase result = handleNameResource(nameAbout, config); |
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taxonNameMap.put(uri, result); |
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return result; |
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} |
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private TaxonNameBase handleNameResource(Resource nameAbout, TcsRdfImportConfigurator config){
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String idNamespace = "TaxonName"; |
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StmtIterator stmts = nameAbout.listProperties(); |
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while(stmts.hasNext()){
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System.out.println(stmts.next().getPredicate().toString()); |
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} |
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Property prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"nomenclaturalCode"); |
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Statement stateNomenclaturalCode = nameAbout.getProperty(prop); |
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String strNomenclaturalCode = stateNomenclaturalCode.getObject().toString(); |
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//Rank |
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"rankString"); |
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String strRank = nameAbout.getProperty(prop).getString(); |
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try {
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Rank rank = TcsRdfTransformer.rankString2Rank(strRank); |
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NomenclaturalCode nomCode; |
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if (strNomenclaturalCode != null){
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| ... | ... | |
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}else{
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nomCode = NomenclaturalCode.ICNAFP; |
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} |
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TaxonNameBase<?,?> nameBase = nomCode.getNewTaxonNameInstance(rank); |
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Set<String> omitAttributes = null; |
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//makeStandardMapper(nameAbout, nameBase, omitAttributes, standardMappers); |
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"nameComplete"); |
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String strNameComplete = nameAbout.getProperty(prop).getString(); |
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nameBase.setTitleCache(strNameComplete, true); |
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prop = nameAbout.getModel().getProperty(config.getCommonNamespaceURIString()+"publishedIn"); |
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String strPublishedIn = nameAbout.getProperty(prop).getString(); |
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if (strPublishedIn != null && strPublishedIn != ""){
|
| ... | ... | |
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}catch(NullPointerException e){
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} |
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if (config.isPublishReferences()){
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((Reference<?>)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
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((Reference)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false)); |
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} |
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} |
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if (nameBase instanceof NonViralName){
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NonViralName<?> nonViralName = (NonViralName<?>)nameBase; |
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"genusPart"); |
| ... | ... | |
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"uninomial"); |
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strGenusPart = nameAbout.getProperty(prop).getString(); |
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} |
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nonViralName.setGenusOrUninomial(strGenusPart); |
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"infragenericEpithet"); |
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try{
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String strInfragenericEpithet = nameAbout.getProperty(prop).getString(); |
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nonViralName.setInfraGenericEpithet(strInfragenericEpithet); |
| 245 | 242 |
}catch(NullPointerException e){
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} |
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try {
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"specificEpithet"); |
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String strSpecificEpithet = nameAbout.getProperty(prop).getString(); |
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nonViralName.setSpecificEpithet(strSpecificEpithet); |
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}catch(NullPointerException e){
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} |
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try{
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"infraspecificEpithet"); |
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String strInfraspecificEpithet = nameAbout.getProperty(prop).getString(); |
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nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet); |
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}catch(NullPointerException e){
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} |
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//Authorships |
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//TODO |
| ... | ... | |
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<tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:2691-1" |
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tm:index="1" |
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tm:role="Combination Author"/> |
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<tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:8096-1"
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<tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:8096-1" |
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tm:index="1" |
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tm:role="Basionym Author"/> |
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</tm:Team> |
| ... | ... | |
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try{
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stateAutorTeamTeam = stateAuthorTeam.getProperty(prop); |
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}catch(Exception e){
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} |
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try{
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prop = stateAuthorTeam.getModel().getProperty(config.getTeamNamespaceURIString()+"name"); |
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stateAutorTeamName = stateAuthorTeam.getProperty(prop); |
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}catch(Exception e){
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} |
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try{
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prop = nameAbout.getModel().getProperty(config.getTeamNamespaceURIString()+"hasMember"); |
| ... | ... | |
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System.err.println(e.getMessage()); |
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} |
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} |
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nonViralName.setCombinationAuthorship(authorTeam); |
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//Annotations: |
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/* |
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* <tn:hasAnnotation> |
| ... | ... | |
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<tn:noteType rdf:resource="http://rs.tdwg.org/ontology/voc/TaxonName#replacementNameFor"/> |
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<tn:objectTaxonName rdf:resource="urn:lsid:ipni.org:names:151538-1"/> |
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</tn:NomenclaturalNote> |
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</tn:hasAnnotation>
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</tn:hasAnnotation> |
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*/ |
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/* |
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String strInfraspecificEpithet = nameAbout.getProperty(prop).getString(); |
| ... | ... | |
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//ImportHelper.setOriginalSource(nameBase, config.getSourceReference(), nameAbout, idNamespace); |
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//checkAdditionalContents(elTaxonName, standardMappers, operationalMappers, unclearMappers); |
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return nameBase; |
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}catch(Exception e){
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e.printStackTrace(); |
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return null; |
| ... | ... | |
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//name |
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String strNameComplete = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "nameComplete", rdfNamespace); |
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nameBase.setTitleCache(strNameComplete, true); |
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//Reference |
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//TODO |
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String tcsElementName = "publishedIn"; |
| ... | ... | |
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} |
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} |
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if (config.isPublishReferences()){
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((Reference<?>)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
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((Reference)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false)); |
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} |
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} |
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|
| ... | ... | |
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if (nameBase instanceof NonViralName){
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NonViralName<?> nonViralName = (NonViralName<?>)nameBase; |
| 439 | 436 |
String strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "genusPart", rdfNamespace); |
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//for names of rank genus the uninomial property should be used |
| 442 | 439 |
if (strGenusPart == null){
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strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "uninomial", rdfNamespace); |
| 444 | 441 |
} |
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nonViralName.setGenusOrUninomial(strGenusPart); |
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String strInfragenericEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infragenericEpithet", rdfNamespace); |
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nonViralName.setGenusOrUninomial(strInfragenericEpithet); |
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String strSpecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "specificEpithet", rdfNamespace); |
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nonViralName.setSpecificEpithet(strSpecificEpithet); |
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String strInfraspecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infraspecificEpithet", rdfNamespace); |
| 456 | 453 |
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet); |
| 457 | 454 |
//AuthorTeams |
| ... | ... | |
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} |
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return null;*/ |
| 509 | 506 |
} |
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protected TaxonNameBase handleNameElement(Element elTaxonName, Namespace rdfNamespace, Namespace taxonNameNamespace, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap){
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String idNamespace = "TaxonName"; |
| 513 | 510 |
Attribute about = elTaxonName.getAttribute("about", rdfNamespace);
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//create TaxonName element |
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String nameAbout = elTaxonName.getAttributeValue("about", rdfNamespace);
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if (nameAbout == null){
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nameAbout = XmlHelp.getChildAttributeValue(elTaxonName, "TaxonName", taxonNameNamespace, "about", rdfNamespace); |
| 521 | 518 |
} |
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String strRank = XmlHelp.getChildAttributeValue(elTaxonName, "rankString", taxonNameNamespace, "rankString", rdfNamespace); |
| 525 | 522 |
if (strRank == null){
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strRank = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "rankString", rdfNamespace); |
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} |
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if (strRank == null){
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strRank = XmlHelp.getChildAttributeValue(elTaxonName, "rank", taxonNameNamespace, "resource", rdfNamespace); |
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} |
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String strNomenclaturalCode = XmlHelp.getChildContentAttributeValue(elTaxonName, "TaxonName", taxonNameNamespace, "nomenclaturalCode", rdfNamespace); |
| 536 | 533 |
if (strNomenclaturalCode == null){
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strNomenclaturalCode = XmlHelp.getChildAttributeValue(elTaxonName, "nomenclaturalCode", taxonNameNamespace, "resource", rdfNamespace); |
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} |
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try {
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Rank rank = TcsRdfTransformer.rankString2Rank(strRank); |
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NomenclaturalCode nomCode; |
| 544 | 541 |
if (strNomenclaturalCode != null){
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| ... | ... | |
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}else{
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nomCode = NomenclaturalCode.ICNAFP; |
| 548 | 545 |
} |
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TaxonNameBase<?,?> nameBase = nomCode.getNewTaxonNameInstance(rank); |
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Set<String> omitAttributes = null; |
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//makeStandardMapper(elTaxonName, nameBase, omitAttributes, standardMappers); |
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//name |
| 556 | 553 |
String strNameComplete = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "nameComplete", rdfNamespace); |
| 557 | 554 |
nameBase.setTitleCache(strNameComplete, true); |
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//Reference |
| 560 | 557 |
//TODO |
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String tcsElementName = "publishedIn"; |
| ... | ... | |
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} |
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} |
| 583 | 580 |
if (config.isPublishReferences()){
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((Reference<?>)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
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((Reference)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false)); |
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} |
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} |
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|
| ... | ... | |
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if (nameBase instanceof NonViralName){
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| 614 | 611 |
NonViralName<?> nonViralName = (NonViralName<?>)nameBase; |
| 615 | 612 |
String strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "genusPart", rdfNamespace); |
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//for names of rank genus the uninomial property should be used |
| 618 | 615 |
if (strGenusPart == null){
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strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "uninomial", rdfNamespace); |
| 620 | 617 |
} |
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nonViralName.setGenusOrUninomial(strGenusPart); |
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String strInfragenericEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infragenericEpithet", rdfNamespace); |
| 624 | 621 |
nonViralName.setGenusOrUninomial(strInfragenericEpithet); |
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String strSpecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "specificEpithet", rdfNamespace); |
| 629 | 626 |
nonViralName.setSpecificEpithet(strSpecificEpithet); |
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String strInfraspecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infraspecificEpithet", rdfNamespace); |
| 632 | 629 |
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet); |
| 633 | 630 |
//AuthorTeams |
| ... | ... | |
| 688 | 685 |
Model model = ModelFactory.createDefaultModel(); |
| 689 | 686 |
try{
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model.read(is, null); |
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config.makeNamespaces(model); |
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String rdfNamespace = config.getRdfNamespaceURIString(); |
| 695 | 692 |
String taxonNameNamespace = config.getTnNamespaceURIString(); |
| 696 | 693 |
return handleNameModel(model, config, taxonNameMap, uri); |
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}catch(Exception e){
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logger.debug("The file was no valid rdf file");
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} |
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return null; |
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} |
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} |
Also available in: Unified diff
Remove generics from Reference in cdmlib (except for cdmlib-model) #5830