Revision 2e0a90f1
Added by Patrick Plitzner over 5 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/descriptive/owl/in/StructureTreeOwlImport.java | ||
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import java.util.ArrayList; |
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import java.util.Collection; |
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import java.util.HashSet; |
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import java.util.List; |
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import java.util.Set; |
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import java.util.UUID; |
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|
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import org.springframework.stereotype.Component; |
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|
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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.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 eu.etaxonomy.cdm.common.CdmUtils; |
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
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import eu.etaxonomy.cdm.io.common.CdmImportBase; |
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import eu.etaxonomy.cdm.io.descriptive.owl.OwlConstants; |
|
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import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.description.Feature; |
| ... | ... | |
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|
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private static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(StructureTreeOwlImport.class); |
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private Property propHasSubStructure; |
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private Property propHasRepresentation; |
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private Property propHasRootNode; |
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private Property propUuid; |
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private Property propUri; |
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private Property propLabel; |
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private Property propLabelAbbrev; |
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private Property propLanguage; |
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private Property propLanguageUuid; |
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private Property propIsA; |
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private Property propType; |
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private Property propDescription; |
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|
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@Override |
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protected boolean doCheck(StructureTreeOwlImportState state) {
|
| ... | ... | |
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public void doInvoke(StructureTreeOwlImportState state) {
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URI source = state.getConfig().getSource(); |
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Model model = ModelFactory.createDefaultModel(); |
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propHasSubStructure = model.createProperty(OwlConstants.PROPERTY_HAS_SUBSTRUCTURE); |
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propHasRepresentation = model.createProperty(OwlConstants.PROPERTY_HAS_REPRESENTATION); |
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propHasRootNode = model.createProperty(OwlConstants.PROPERTY_HAS_ROOT_NODE); |
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propUuid = model.createProperty(OwlConstants.PROPERTY_UUID); |
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propUri = model.createProperty(OwlConstants.PROPERTY_URI); |
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propLabel = model.createProperty(OwlConstants.PROPERTY_LABEL); |
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propLabelAbbrev = model.createProperty(OwlConstants.PROPERTY_LABEL_ABBREV); |
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propLanguage = model.createProperty(OwlConstants.PROPERTY_LANGUAGE); |
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propLanguageUuid = model.createProperty(OwlConstants.PROPERTY_LANGUAGE_UUID); |
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propIsA = model.createProperty(OwlConstants.PROPERTY_IS_A); |
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propType = model.createProperty(OwlConstants.PROPERTY_TYPE); |
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propDescription = model.createProperty(OwlConstants.PROPERTY_DESCRIPTION); |
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model.read(source.toString()); |
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List<FeatureTree> featureTrees = new ArrayList<>(); |
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state.getModel().read(source.toString()); |
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//get all trees |
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ResIterator iterator = model.listResourcesWithProperty(propHasRootNode);
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ResIterator iterator = state.getModel().listResourcesWithProperty(StructureTreeOwlImportState.propHasRootNode);
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while(iterator.hasNext()){
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Resource tree = iterator.next(); |
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String type = tree.getProperty(propType).getString(); |
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String type = tree.getProperty(StructureTreeOwlImportState.propType).getString();
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FeatureTree featureTree = FeatureTree.NewInstance(TermType.getByKey(type)); |
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featureTree.setTitleCache(tree.getProperty(propLabel).getString(), true); |
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Resource rootNode = tree.getProperty(propHasRootNode).getResource(); |
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rootNode.listProperties(propHasSubStructure).forEachRemaining(prop->createNode(featureTree.getRoot(), prop, featureTree.getTitleCache(), model, state)); |
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featureTree.setTitleCache(tree.getProperty(StructureTreeOwlImportState.propLabel).getString(), true); |
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featureTrees.add(featureTree); |
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Resource rootNode = tree.getProperty(StructureTreeOwlImportState.propHasRootNode).getResource(); |
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rootNode.listProperties(StructureTreeOwlImportState.propHasSubStructure).forEachRemaining(prop->createNode(featureTree.getRoot(), prop, featureTree.getTitleCache(), state.getModel(), state)); |
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|
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getFeatureTreeService().save(featureTree); |
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} |
| ... | ... | |
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private void createNode(FeatureNode parent, Statement nodeStatement, String treeLabel, Model model, StructureTreeOwlImportState state) {
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Resource nodeResource = model.createResource(nodeStatement.getObject().toString()); |
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TermType termType = TermType.getByKey(nodeResource.getProperty(propType).getString()); |
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String uriString = nodeResource.hasProperty(propUri)?nodeResource.getProperty(propUri).toString():null; |
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Collection<TermDto> dtos = new ArrayList<>(); |
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// check representations if term already exists
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// import representations
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Set<Representation> representations = new HashSet<>(); |
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nodeResource.listProperties(propHasRepresentation).forEachRemaining(r->representations.add(createRepresentation(r, model))); |
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nodeResource.listProperties(StructureTreeOwlImportState.propHasRepresentation).forEachRemaining(r->representations.add(createRepresentation(r, model)));
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if(representations.isEmpty()){
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logger.error("No representations found for term: "+nodeResource.getProperty(propUuid));
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logger.error("No representations found for term: "+nodeResource.getProperty(StructureTreeOwlImportState.propUuid));
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return; |
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} |
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DefinedTermBase term = null; |
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String termLabel = null; |
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for (Representation representation : representations) {
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termLabel = representation.getLabel(); |
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if(uriString!=null){
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URI uri = URI.create(uriString); |
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dtos = getTermService().findByUriAsDto(uri, termLabel, termType); |
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} |
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else{
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dtos = getTermService().findByTitleAsDto(termLabel, termType); |
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} |
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if(dtos.size()>1){
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logger.warn("More than one term was found for: "+termLabel+"\nUsing the first one found");
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} |
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if(dtos.size()>=1){
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term = getTermService().load(dtos.iterator().next().getUuid()); |
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} |
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if(term!=null){
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break; |
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} |
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} |
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DefinedTermBase term = getTermService().load(dtos.iterator().next().getUuid()); |
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if(term==null){
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TermType termType = TermType.getByKey(nodeResource.getProperty(StructureTreeOwlImportState.propType).getString()); |
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// create new term |
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if(termType.equals(TermType.Feature)){
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term = Feature.NewInstance(); |
| ... | ... | |
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term.addRepresentation(representation); |
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} |
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} |
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IdentifiableSource importSource = IdentifiableSource.NewDataImportInstance(termLabel); |
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String uriString = nodeResource.hasProperty(StructureTreeOwlImportState.propUri)?nodeResource.getProperty(StructureTreeOwlImportState.propUri).toString():null; |
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if(CdmUtils.isNotBlank(uriString)){
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term.setUri(URI.create(uriString)); |
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} |
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IdentifiableSource importSource = IdentifiableSource.NewDataImportInstance("Import of term tree "+treeLabel);
|
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importSource.setCitation(state.getConfig().getSourceReference()); |
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term.addSource(importSource); |
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getTermService().save(term); |
| ... | ... | |
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|
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FeatureNode<?> childNode = parent.addChild(term); |
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nodeResource.listProperties(propHasSubStructure).forEachRemaining(prop->createNode(childNode, prop, treeLabel, model, state)); |
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nodeResource.listProperties(StructureTreeOwlImportState.propHasSubStructure).forEachRemaining(prop->createNode(childNode, prop, treeLabel, model, state));
|
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} |
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private Representation createRepresentation(Statement repr, Model model) {
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Resource repsentationResource = model.createResource(repr.getObject().toString()); |
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String languageLabel = repsentationResource.getProperty(propLanguage).getString(); |
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UUID languageUuid = UUID.fromString(repsentationResource.getProperty(propLanguageUuid).getString()); |
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String languageLabel = repsentationResource.getProperty(StructureTreeOwlImportState.propLanguage).getString();
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UUID languageUuid = UUID.fromString(repsentationResource.getProperty(StructureTreeOwlImportState.propLanguageUuid).getString());
|
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DefinedTermBase termBase = getTermService().load(languageUuid); |
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Language language = null; |
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if(termBase.isInstanceOf(Language.class)){
|
| ... | ... | |
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language = Language.getDefaultLanguage(); |
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} |
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String abbreviatedLabel = repsentationResource.hasProperty(propLabelAbbrev)?repsentationResource.getProperty(propLabelAbbrev).toString():null;
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String label = repsentationResource.getProperty(propLabel).getString(); |
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String description = repsentationResource.hasProperty(propDescription)?repsentationResource.getProperty(propDescription).getString():null;
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String abbreviatedLabel = repsentationResource.hasProperty(StructureTreeOwlImportState.propLabelAbbrev)?repsentationResource.getProperty(StructureTreeOwlImportState.propLabelAbbrev).toString():null;
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String label = repsentationResource.getProperty(StructureTreeOwlImportState.propLabel).getString();
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String description = repsentationResource.hasProperty(StructureTreeOwlImportState.propDescription)?repsentationResource.getProperty(StructureTreeOwlImportState.propDescription).getString():null;
|
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Representation representation = Representation.NewInstance(description, label, abbreviatedLabel, language); |
| 200 | 150 |
|
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return representation; |
Also available in: Unified diff
ref #8248 Move rdf model to import state