Revision 49324
Added by Alessia Bardi over 6 years ago
| modules/dnet-parthenos-publisher/trunk/src/main/java/eu/dnetlib/parthenos/registry/GCubeResourceGenerator.java | ||
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package eu.dnetlib.parthenos.registry; |
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import java.io.IOException; |
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import java.io.StringWriter; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Set; |
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import com.fasterxml.jackson.core.JsonFactory; |
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import com.fasterxml.jackson.core.JsonGenerator; |
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import com.google.common.collect.Lists; |
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import com.google.common.collect.Maps; |
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import com.google.common.collect.Sets; |
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import eu.dnetlib.parthenos.CRM; |
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import eu.dnetlib.parthenos.CRMdig; |
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import eu.dnetlib.parthenos.CRMpe; |
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import org.apache.commons.io.IOUtils; |
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import org.apache.commons.lang3.StringUtils; |
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import org.apache.commons.logging.Log; |
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import org.apache.commons.logging.LogFactory; |
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import org.apache.jena.assembler.AssemblerHelp; |
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import org.apache.jena.assembler.exceptions.AmbiguousSpecificTypeException; |
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import org.apache.jena.ontology.OntModel; |
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import org.apache.jena.ontology.OntModelSpec; |
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import org.apache.jena.rdf.model.InfModel; |
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import org.apache.jena.rdf.model.ModelFactory; |
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import org.apache.jena.rdf.model.ResIterator; |
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import org.apache.jena.rdf.model.Resource; |
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import org.apache.jena.vocabulary.RDF; |
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import org.springframework.beans.factory.annotation.Autowired; |
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import org.springframework.stereotype.Component; |
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/** |
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* Created by Alessia Bardi on 26/09/2017. |
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* |
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* @author Alessia Bardi |
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*/ |
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@Component |
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public class GCubeResourceGenerator {
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private static final Log log = LogFactory.getLog(GCubeResourceGenerator.class); |
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private OntModel baseModel; |
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@Autowired |
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private FacetWriter facetWriter; |
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@Autowired |
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private RelWriter relWriter; |
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public GCubeResourceGenerator() {
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baseModel = ModelFactory.createOntologyModel(OntModelSpec.RDFS_MEM_TRANS_INF); |
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baseModel.read(CRMpe.RDFS_URL); |
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baseModel.read(CRM.RDFS_URL); |
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baseModel.read(CRMdig.RDFS_URL); |
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} |
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protected InfModel loadBaseModel(){
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return ModelFactory.createRDFSModel(baseModel); |
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} |
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/** |
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* Generates the Gcube ER instances (Entity [Resource/Facet] and Relation) as json strings to be registered from a given RDF record serialised in RDF/XML PLAIN format. |
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* @param rdfRecord RDF record in RDF/XML PLAIN format |
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* @return an Iterable of json strings or an empty Iterable if the record is blank |
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*/ |
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public Iterable<String> getGCubeER(final String rdfRecord) throws IOException {
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List<String> jsonResources = Lists.newArrayList(); |
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//This map contains the pair (rdf:about, registryUUID) registered so far, useful I guess to create relationships between resources/facets. |
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Map<String,String> resourceIdentifiers = Maps.newHashMap(); |
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if (StringUtils.isBlank(rdfRecord)) {
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log.warn("Got empty record");
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return Lists.newArrayList(); |
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} |
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InfModel model = loadBaseModel(); |
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model.read(IOUtils.toInputStream(rdfRecord, "UTF-8"), CRMpe.NS); |
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JsonFactory jsonFactory = new JsonFactory(); |
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Set<String> uriProcessed = Sets.newHashSet(); |
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//TODO: many things in common in the code below: re-factor it! |
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log.debug("Processing services");
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//let's start with services |
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ResIterator iter = model.listResourcesWithProperty(RDF.type, CRMpe.PE1_Service); |
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while (iter.hasNext()) {
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Resource res = iter.nextResource(); |
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String resourceURI = res.getURI(); |
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if (!uriProcessed.contains(resourceURI)) {
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log.debug("Processing "+resourceURI);
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Resource specificType = findSpecificType(res, CRMpe.PE1_Service); |
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StringWriter sw = new StringWriter(); |
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JsonGenerator jg = jsonFactory.createGenerator(sw); |
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jg.writeStartObject(); |
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//TODO: generate header with uuid for all type of entities, so we can also generate the rels. Need a map for uri --> uuid. |
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jg.writeStringField("@class", specificType.getLocalName());
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//******THE FACETS *******// |
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jg.writeArrayFieldStart("consistsOf");
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//list of facets |
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//TODO: write P1 identifier facet following the existing links (for all types) |
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facetWriter.writeIdentifierFacet(jg, resourceURI); |
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facetWriter.writeInfoFacet(jg, res); |
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facetWriter.writeEventFacet(jg); |
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facetWriter.writeRightsFacet(jg, res); |
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if(res.hasProperty(CRMpe.PP2_provided_by)){
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//TODO: shouldn't this be a rel to an actor? |
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Resource provider = res.getPropertyResourceValue(CRMpe.PP2_provided_by); |
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facetWriter.writeContactReferenceFacet(jg, provider); |
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} |
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facetWriter.writeDesignatedAccessPointFacet(jg, res); |
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jg.writeEndArray(); |
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// ******* RELATIONSHIPS ***** ??? or separately after we got the ids of everything?// |
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//jg.writeArrayFieldStart("isRelatedto");
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//jg.writeEndArray(); |
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jg.writeEndObject(); |
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jg.close(); |
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String json = sw.toString(); |
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log.debug(json); |
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jsonResources.add(json); |
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uriProcessed.add(resourceURI); |
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} else {
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log.debug(resourceURI+" already processed, now skipping it"); |
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} |
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} |
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log.debug("Processing digital objects (include dataset and software)");
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//and then the datasets |
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ResIterator iterDo = model.listResourcesWithProperty(RDF.type, CRMdig.D1_Digital_Object); |
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while (iterDo.hasNext()) {
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Resource res = iterDo.nextResource(); |
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String resourceURI = res.getURI(); |
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if (!uriProcessed.contains(resourceURI)) {
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log.debug("Processing " + resourceURI);
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Resource specificType = findSpecificType(res, CRMdig.D1_Digital_Object); |
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StringWriter sw = new StringWriter(); |
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JsonGenerator jg = jsonFactory.createGenerator(sw); |
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jg.writeStartObject(); |
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jg.writeStringField("@class", specificType.getLocalName());
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//******THE FACETS *******// |
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jg.writeArrayFieldStart("consistsOf");
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//list of facets |
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facetWriter.writeIdentifierFacet(jg, resourceURI); |
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facetWriter.writeInfoFacet(jg, res); |
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facetWriter.writeTemporalCoverageFacet(jg, res); |
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facetWriter.writeRightsFacet(jg, res); |
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jg.writeEndArray(); |
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jg.writeEndObject(); |
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jg.close(); |
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String json = sw.toString(); |
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log.debug(json); |
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jsonResources.add(json); |
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uriProcessed.add(resourceURI); |
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} else {
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log.debug(resourceURI + " already processed, now skipping it"); |
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} |
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} |
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log.debug("Processing actors");
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//and then the datasets |
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ResIterator iterActors = model.listResourcesWithProperty(RDF.type, CRM.E39_Actor); |
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while (iterActors.hasNext()) {
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Resource res = iterActors.nextResource(); |
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String resourceURI = res.getURI(); |
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if (!uriProcessed.contains(resourceURI)) {
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log.debug("Processing " + resourceURI);
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Resource specificType = findSpecificType(res, CRM.E39_Actor); |
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StringWriter sw = new StringWriter(); |
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JsonGenerator jg = jsonFactory.createGenerator(sw); |
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jg.writeStartObject(); |
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jg.writeStringField("@class", specificType.getLocalName());
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//******THE FACETS *******// |
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jg.writeArrayFieldStart("consistsOf");
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//list of facets |
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facetWriter.writeIdentifierFacet(jg, resourceURI); |
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facetWriter.writeContactReferenceFacet(jg, res); |
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jg.writeEndArray(); |
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jg.writeEndObject(); |
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jg.close(); |
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String json = sw.toString(); |
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log.debug(json); |
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jsonResources.add(json); |
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uriProcessed.add(resourceURI); |
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} else {
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log.debug(resourceURI + " already processed, now skipping it"); |
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} |
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} |
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log.debug("Processing software");
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ResIterator iterSw = model.listResourcesWithProperty(RDF.type, CRMdig.D14_Software); |
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while (iterSw.hasNext()) {
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Resource res = iterSw.nextResource(); |
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String resourceURI = res.getURI(); |
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if (!uriProcessed.contains(resourceURI)) {
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log.debug("Processing " + resourceURI);
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Resource specificType = findSpecificType(res, CRMdig.D14_Software); |
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StringWriter sw = new StringWriter(); |
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JsonGenerator jg = jsonFactory.createGenerator(sw); |
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jg.writeStartObject(); |
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jg.writeStringField("@class", specificType.getLocalName());
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//******THE FACETS *******// |
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jg.writeArrayFieldStart("consistsOf");
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//list of facets |
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facetWriter.writeIdentifierFacet(jg, resourceURI); |
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facetWriter.writeInfoFacet(jg, res); |
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jg.writeEndArray(); |
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jg.writeEndObject(); |
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jg.close(); |
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String json = sw.toString(); |
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log.debug(json); |
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jsonResources.add(json); |
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uriProcessed.add(resourceURI); |
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} else {
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log.debug(resourceURI + " already processed, now skipping it"); |
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} |
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} |
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log.debug("Processing projects");
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//and then the projects |
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ResIterator iterProjects = model.listResourcesWithProperty(RDF.type, CRMpe.PE35_Project); |
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while (iterProjects.hasNext()) {
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Resource res = iterProjects.nextResource(); |
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String resourceURI = res.getURI(); |
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if (!uriProcessed.contains(resourceURI)) {
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log.debug("Processing " + resourceURI);
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Resource specificType = findSpecificType(res, CRMpe.PE35_Project); |
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StringWriter sw = new StringWriter(); |
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JsonGenerator jg = jsonFactory.createGenerator(sw); |
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jg.writeStartObject(); |
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jg.writeStringField("@class", specificType.getLocalName());
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//******THE FACETS *******// |
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jg.writeArrayFieldStart("consistsOf");
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//list of facets |
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facetWriter.writeIdentifierFacet(jg, resourceURI); |
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facetWriter.writeInfoFacet(jg, res); |
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jg.writeEndArray(); |
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jg.writeEndObject(); |
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jg.close(); |
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String json = sw.toString(); |
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log.debug(json); |
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jsonResources.add(json); |
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uriProcessed.add(resourceURI); |
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} else {
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log.debug(resourceURI + " already processed, now skipping it"); |
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} |
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} |
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return jsonResources; |
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} |
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/** |
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* Finds the most specific type of res. |
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* @param res Resource you want to find the most specific type |
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* @param fallbackType Resource representing the type to return if there is no type or if we get AmbiguousSpecificTypeException |
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* @return Resource: the most specific type, if any. fallbackType otherwise |
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*/ |
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protected Resource findSpecificType(final Resource res, final Resource fallbackType){
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Resource specType = fallbackType; |
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try{
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specType = AssemblerHelp.findSpecificType(res, fallbackType); |
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}catch(AmbiguousSpecificTypeException e){
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log.warn(res.getURI()+": "+e.getMessage()); |
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} |
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return specType; |
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} |
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public FacetWriter getFacetWriter() {
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return facetWriter; |
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} |
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public void setFacetWriter(final FacetWriter facetWriter) {
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this.facetWriter = facetWriter; |
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} |
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} |
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| modules/dnet-parthenos-publisher/trunk/test/main/java/eu/dnetlib/parthenos/registry/FacetWriterTest.java | ||
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*/ |
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@Test |
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public void testWriteContactReferenceFacet() throws Exception {
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GCubeResourceGenerator generator = new GCubeResourceGenerator();
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GCubeResourceRegistrator generator = new GCubeResourceRegistrator();
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JsonFactory jsonFactory = new JsonFactory(); |
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StringWriter sw = new StringWriter(); |
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JsonGenerator jg = jsonFactory.createGenerator(sw); |
| modules/dnet-parthenos-publisher/trunk/test/main/java/eu/dnetlib/parthenos/registry/RelWriterTest.java | ||
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package eu.dnetlib.parthenos.registry; |
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import java.io.IOException; |
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import com.fasterxml.jackson.core.JsonFactory; |
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import org.junit.Test; |
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/** |
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* Created by Alessia Bardi on 06/10/2017. |
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* |
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* @author Alessia Bardi |
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*/ |
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public class RelWriterTest {
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private RelWriter relWriter = new RelWriter(); |
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@Test |
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public void test() throws IOException {
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String rel = relWriter.writeRelationship(new JsonFactory(), "theType", "uuid1", "typeSource", "uuid2", "typeTarget"); |
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System.out.println(rel); |
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} |
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} |
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| modules/dnet-parthenos-publisher/trunk/test/main/java/eu/dnetlib/parthenos/registry/GCubeResourceGeneratorTest.java | ||
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private static String recordPath = "eu/dnetlib/parthenos/registry/sample1.rdf"; |
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private static String baseURI = "http://parthenos.d4science.org/CRMext/CRMpe.rdfs/"; |
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private static GCubeResourceGenerator generator = new GCubeResourceGenerator();
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private static GCubeResourceRegistrator generator = new GCubeResourceRegistrator();
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private static InfModel baseModel; |
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static{
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| ... | ... | |
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@Test |
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public void testLoadBaseModel() {
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GCubeResourceGenerator generator1 = new GCubeResourceGenerator();
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GCubeResourceRegistrator generator1 = new GCubeResourceRegistrator();
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InfModel model = generator1.loadBaseModel(); |
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//let's snapshot to a normal model to write all statements |
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Model snapshot = ModelFactory.createDefaultModel(); |
| modules/dnet-parthenos-publisher/trunk/dnet-parthenos-publisher.iml | ||
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| 96 | 96 |
<orderEntry type="library" name="Maven: org.codehaus.woodstox:woodstox-core-asl:4.4.1" level="project" /> |
| 97 | 97 |
<orderEntry type="library" name="Maven: org.noggit:noggit:0.6" level="project" /> |
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<orderEntry type="library" name="Maven: org.slf4j:jcl-over-slf4j:1.7.25" level="project" /> |
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<orderEntry type="module" module-name="parthenos-entities" />
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<orderEntry type="library" name="Maven: org.gcube.information-system:parthenos-entities:0.0.1-SNAPSHOT" level="project" />
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<orderEntry type="library" name="Maven: org.gcube.information-system:information-system-model:1.6.0-SNAPSHOT" level="project" /> |
| 101 | 101 |
<orderEntry type="library" name="Maven: org.gcube.information-system:gcube-resources:1.6.0-SNAPSHOT" level="project" /> |
| 102 | 102 |
<orderEntry type="library" name="Maven: com.fasterxml.jackson.core:jackson-annotations:2.8.0" level="project" /> |
| 103 | 103 |
<orderEntry type="library" name="Maven: com.fasterxml.jackson.core:jackson-core:2.8.9" level="project" /> |
| 104 |
<orderEntry type="module" module-name="resource-registry-publisher" />
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<orderEntry type="library" name="Maven: org.gcube.information-system:resource-registry-publisher:1.5.0-SNAPSHOT" level="project" />
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| 105 | 105 |
<orderEntry type="library" name="Maven: org.gcube.common:authorization-client:2.0.1-4.6.1-134803" level="project" /> |
| 106 | 106 |
<orderEntry type="library" name="Maven: org.gcube.common:common-authorization:2.0.2-4.6.1-144378" level="project" /> |
| 107 | 107 |
<orderEntry type="library" name="Maven: org.gcube.core:common-configuration-scanner:1.0.0-4.6.1-144261" level="project" /> |
| ... | ... | |
| 111 | 111 |
<orderEntry type="library" name="Maven: org.gcube.resources.discovery:discovery-client:1.0.1-4.6.1-125857" level="project" /> |
| 112 | 112 |
<orderEntry type="library" name="Maven: org.gcube.resources:common-gcore-resources:1.3.3-4.6.1-144114" level="project" /> |
| 113 | 113 |
<orderEntry type="library" name="Maven: org.gcube.core:common-gcore-stubs:1.2.2-4.6.1-132342" level="project" /> |
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<orderEntry type="library" name="Maven: org.gcube.information-system:resource-registry-api:1.6.0-SNAPSHOT" level="project" />
|
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<orderEntry type="library" name="Maven: org.gcube.information-system:resource-registry-api:1.7.0-SNAPSHOT" level="project" />
|
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| 115 | 115 |
<orderEntry type="library" name="Maven: org.gcube.information-system:resource-registry-client:1.5.0-SNAPSHOT" level="project" /> |
| 116 | 116 |
</component> |
| 117 | 117 |
</module> |
| modules/dnet-parthenos-publisher/trunk/src/main/java/eu/dnetlib/parthenos/registry/FacetWriter.java | ||
|---|---|---|
| 5 | 5 |
import com.fasterxml.jackson.core.JsonGenerator; |
| 6 | 6 |
import eu.dnetlib.parthenos.CRM; |
| 7 | 7 |
import eu.dnetlib.parthenos.CRMpe; |
| 8 |
import org.apache.commons.lang3.StringUtils; |
|
| 8 | 9 |
import org.apache.jena.rdf.model.Resource; |
| 9 | 10 |
import org.apache.jena.rdf.model.Statement; |
| 10 | 11 |
import org.apache.jena.rdf.model.StmtIterator; |
| 11 | 12 |
import org.apache.jena.vocabulary.RDF; |
| 12 | 13 |
import org.apache.jena.vocabulary.RDFS; |
| 13 |
import org.gcube.informationsystem.model.entity.facet.IdentifierFacet.IdentificationType; |
|
| 14 | 14 |
import org.springframework.stereotype.Component; |
| 15 | 15 |
|
| 16 | 16 |
/** |
| ... | ... | |
| 21 | 21 |
@Component |
| 22 | 22 |
public class FacetWriter {
|
| 23 | 23 |
|
| 24 |
public void writeP1Facet(final JsonGenerator jg, final String value, final IdentificationType type) throws IOException {
|
|
| 24 |
//final IdentificationType type |
|
| 25 |
public void writeP1Facet(final JsonGenerator jg, final String value) throws IOException {
|
|
| 25 | 26 |
jg.writeStartObject(); |
| 26 | 27 |
jg.writeStringField("@class", "P1_is_identified_by");
|
| 27 | 28 |
jg.writeObjectFieldStart("target");
|
| 28 | 29 |
jg.writeStringField("@class", "IdentifierFacet");
|
| 29 | 30 |
jg.writeStringField("value", value);
|
| 30 |
jg.writeStringField("type", type.name());
|
|
| 31 |
//jg.writeStringField("type", type.name());
|
|
| 31 | 32 |
jg.writeEndObject(); |
| 32 | 33 |
jg.writeEndObject(); |
| 33 | 34 |
} |
| ... | ... | |
| 38 | 39 |
jg.writeObjectFieldStart("target");
|
| 39 | 40 |
jg.writeStringField("@class", "IdentifierFacet");
|
| 40 | 41 |
jg.writeStringField("value", identifier);
|
| 41 |
jg.writeStringField("type", IdentificationType.URI.name());
|
|
| 42 |
//jg.writeStringField("type", IdentificationType.URI.name());
|
|
| 42 | 43 |
jg.writeEndObject(); |
| 43 | 44 |
jg.writeEndObject(); |
| 44 | 45 |
} |
| 45 | 46 |
|
| 47 |
public void writeP1Facets(final JsonGenerator jg, final Resource res) throws IOException {
|
|
| 48 |
if(res.hasProperty(CRM.P1_is_identified_by)){
|
|
| 49 |
StmtIterator idRelsIt = res.listProperties(CRM.P1_is_identified_by); |
|
| 50 |
while(idRelsIt.hasNext()){
|
|
| 51 |
Resource target = idRelsIt.nextStatement().getResource(); |
|
| 52 |
String label = getLabelFromRDFResource(target); |
|
| 53 |
if(StringUtils.isNotBlank(label)) {
|
|
| 54 |
writeP1Facet(jg, label); |
|
| 55 |
} |
|
| 56 |
} |
|
| 57 |
} |
|
| 58 |
} |
|
| 59 |
|
|
| 46 | 60 |
public void writeInfoFacet(final JsonGenerator jg, final Resource res) throws IOException {
|
| 47 | 61 |
jg.writeStartObject(); |
| 62 |
jg.writeStringField("@class", "consistsOf");
|
|
| 63 |
jg.writeObjectFieldStart("target");
|
|
| 48 | 64 |
jg.writeStringField("@class", "PE_Info_Facet");
|
| 49 |
jg.writeObjectFieldStart("target");
|
|
| 50 | 65 |
jg.writeStringField("title", getTitleFromRDFResource(res));
|
| 51 | 66 |
jg.writeStringField("description", getDescriptionFromRDFResource(res));
|
| 52 | 67 |
//new object comp + field value + schema="noSchema" |
| 53 |
jg.writeStringField("competence", getCompetenceFromRDFResource(res));
|
|
| 68 |
String competence = getCompetenceFromRDFResource(res); |
|
| 69 |
if(StringUtils.isNotBlank(competence)) {
|
|
| 70 |
writeValueSchema(jg, "competence", competence, "noSchema"); |
|
| 71 |
} |
|
| 54 | 72 |
//TODO: uncomment this when George adds the rel to the model, see method getAvailabilityFromRDFResource below |
| 55 |
//jg.writeStringField("availability", getAvailabilityFromRDFResource(res));
|
|
| 73 |
//String availability = getAvailabilityFromRDFResource(res); |
|
| 74 |
// if(StringUtils.isNotBlank(availability)) {
|
|
| 75 |
// writeValueSchema(jg, "availability", availability, "noSchema"); |
|
| 76 |
// } |
|
| 56 | 77 |
jg.writeEndObject(); |
| 57 | 78 |
jg.writeEndObject(); |
| 58 | 79 |
} |
| 59 | 80 |
|
| 81 |
protected void writeValueSchema(final JsonGenerator jg, final String fieldName, final String value, final String schema) throws IOException {
|
|
| 82 |
jg.writeObjectFieldStart(fieldName); |
|
| 83 |
jg.writeStringField("value", value);
|
|
| 84 |
jg.writeStringField("schema", schema);
|
|
| 85 |
jg.writeEndObject(); |
|
| 86 |
} |
|
| 87 |
|
|
| 60 | 88 |
public void writeEventFacet(final JsonGenerator jg) {
|
| 61 | 89 |
//TODO: implement me. get begin/end of operation from PP42_has_declarative_time |
| 62 | 90 |
} |
| modules/dnet-parthenos-publisher/trunk/src/main/java/eu/dnetlib/parthenos/registry/RegistryClientFactory.java | ||
|---|---|---|
| 35 | 35 |
@Autowired |
| 36 | 36 |
private SaxonHelper saxonHelper; |
| 37 | 37 |
@Autowired |
| 38 |
private GCubeResourceGenerator resourceGenerator;
|
|
| 38 |
private GCubeResourceRegistrator resourceGenerator;
|
|
| 39 | 39 |
|
| 40 | 40 |
public RegistryClient getRegistryClient() throws ParthenosPublisherException {
|
| 41 | 41 |
log.debug("Creating RegistryClient for "+registryBaseURL);
|
| ... | ... | |
| 101 | 101 |
this.defaultBaseURI = defaultBaseURI; |
| 102 | 102 |
} |
| 103 | 103 |
|
| 104 |
public GCubeResourceGenerator getResourceGenerator() {
|
|
| 104 |
public GCubeResourceRegistrator getResourceGenerator() {
|
|
| 105 | 105 |
return resourceGenerator; |
| 106 | 106 |
} |
| 107 | 107 |
|
| 108 |
public void setResourceGenerator(final GCubeResourceGenerator resourceGenerator) {
|
|
| 108 |
public void setResourceGenerator(final GCubeResourceRegistrator resourceGenerator) {
|
|
| 109 | 109 |
this.resourceGenerator = resourceGenerator; |
| 110 | 110 |
} |
| 111 | 111 |
} |
| modules/dnet-parthenos-publisher/trunk/src/main/java/eu/dnetlib/parthenos/registry/RelWriter.java | ||
|---|---|---|
| 1 | 1 |
package eu.dnetlib.parthenos.registry; |
| 2 | 2 |
|
| 3 |
import java.io.IOException; |
|
| 4 |
import java.io.StringWriter; |
|
| 5 |
|
|
| 6 |
import com.fasterxml.jackson.core.JsonFactory; |
|
| 7 |
import com.fasterxml.jackson.core.JsonGenerator; |
|
| 3 | 8 |
import org.springframework.stereotype.Component; |
| 4 | 9 |
|
| 5 | 10 |
/** |
| ... | ... | |
| 10 | 15 |
@Component |
| 11 | 16 |
public class RelWriter {
|
| 12 | 17 |
|
| 18 |
protected String writeRelationship(final JsonFactory jsonFactory, final String relType, final String sourceUUID, final String sourceType, final String targetUUID, final String targetType) |
|
| 19 |
throws IOException {
|
|
| 20 |
StringWriter sw = new StringWriter(); |
|
| 21 |
JsonGenerator jg = jsonFactory.createGenerator(sw); |
|
| 22 |
jg.writeStartObject(); |
|
| 23 |
jg.writeStringField("@class", relType);
|
|
| 24 |
jg.writeObjectFieldStart("source");
|
|
| 25 |
jg.writeObjectFieldStart("header");
|
|
| 26 |
jg.writeStringField("uuid", sourceUUID);
|
|
| 27 |
jg.writeEndObject(); |
|
| 28 |
jg.writeStringField("@class", sourceType);
|
|
| 29 |
jg.writeEndObject(); |
|
| 30 |
jg.writeObjectFieldStart("target");
|
|
| 31 |
jg.writeObjectFieldStart("header");
|
|
| 32 |
jg.writeStringField("uuid", targetUUID);
|
|
| 33 |
jg.writeEndObject(); |
|
| 34 |
jg.writeStringField("@class", targetType);
|
|
| 35 |
jg.writeEndObject(); |
|
| 36 |
jg.close(); |
|
| 37 |
return sw.toString(); |
|
| 38 |
} |
|
| 13 | 39 |
} |
| modules/dnet-parthenos-publisher/trunk/src/main/java/eu/dnetlib/parthenos/registry/GCubeResourceRegistrator.java | ||
|---|---|---|
| 1 |
package eu.dnetlib.parthenos.registry; |
|
| 2 |
|
|
| 3 |
import java.io.IOException; |
|
| 4 |
import java.io.StringWriter; |
|
| 5 |
import java.util.Map; |
|
| 6 |
import java.util.Set; |
|
| 7 |
import java.util.UUID; |
|
| 8 |
|
|
| 9 |
import com.fasterxml.jackson.core.JsonFactory; |
|
| 10 |
import com.fasterxml.jackson.core.JsonGenerator; |
|
| 11 |
import com.google.common.collect.Maps; |
|
| 12 |
import com.google.common.collect.Sets; |
|
| 13 |
import eu.dnetlib.parthenos.CRM; |
|
| 14 |
import eu.dnetlib.parthenos.CRMdig; |
|
| 15 |
import eu.dnetlib.parthenos.CRMpe; |
|
| 16 |
import eu.dnetlib.parthenos.publisher.ParthenosPublisherException; |
|
| 17 |
import org.apache.commons.io.IOUtils; |
|
| 18 |
import org.apache.commons.lang3.StringUtils; |
|
| 19 |
import org.apache.commons.logging.Log; |
|
| 20 |
import org.apache.commons.logging.LogFactory; |
|
| 21 |
import org.apache.jena.assembler.AssemblerHelp; |
|
| 22 |
import org.apache.jena.assembler.exceptions.AmbiguousSpecificTypeException; |
|
| 23 |
import org.apache.jena.ontology.OntModel; |
|
| 24 |
import org.apache.jena.ontology.OntModelSpec; |
|
| 25 |
import org.apache.jena.rdf.model.*; |
|
| 26 |
import org.apache.jena.vocabulary.RDF; |
|
| 27 |
import org.gcube.informationsystem.resourceregistry.api.exceptions.ResourceRegistryException; |
|
| 28 |
import org.gcube.informationsystem.resourceregistry.client.ResourceRegistryClient; |
|
| 29 |
import org.gcube.informationsystem.resourceregistry.client.ResourceRegistryClientFactory; |
|
| 30 |
import org.gcube.informationsystem.resourceregistry.publisher.ResourceRegistryPublisher; |
|
| 31 |
import org.gcube.informationsystem.resourceregistry.publisher.ResourceRegistryPublisherFactory; |
|
| 32 |
import org.springframework.beans.factory.annotation.Autowired; |
|
| 33 |
import org.springframework.stereotype.Component; |
|
| 34 |
|
|
| 35 |
/** |
|
| 36 |
* Created by Alessia Bardi on 26/09/2017. |
|
| 37 |
* |
|
| 38 |
* @author Alessia Bardi |
|
| 39 |
*/ |
|
| 40 |
@Component |
|
| 41 |
public class GCubeResourceRegistrator {
|
|
| 42 |
|
|
| 43 |
private static final Log log = LogFactory.getLog(GCubeResourceRegistrator.class); |
|
| 44 |
|
|
| 45 |
private OntModel baseModel; |
|
| 46 |
|
|
| 47 |
@Autowired |
|
| 48 |
private FacetWriter facetWriter; |
|
| 49 |
@Autowired |
|
| 50 |
private RelWriter relWriter; |
|
| 51 |
|
|
| 52 |
private ResourceRegistryPublisher resourceRegistryPublisher; |
|
| 53 |
private ResourceRegistryClient resourceRegistryClient; |
|
| 54 |
|
|
| 55 |
public GCubeResourceRegistrator() {
|
|
| 56 |
this.resourceRegistryPublisher = ResourceRegistryPublisherFactory.create(); |
|
| 57 |
this.resourceRegistryClient = ResourceRegistryClientFactory.create(); |
|
| 58 |
baseModel = ModelFactory.createOntologyModel(OntModelSpec.RDFS_MEM_TRANS_INF); |
|
| 59 |
baseModel.read(CRMpe.RDFS_URL); |
|
| 60 |
baseModel.read(CRM.RDFS_URL); |
|
| 61 |
baseModel.read(CRMdig.RDFS_URL); |
|
| 62 |
} |
|
| 63 |
|
|
| 64 |
public int unregister(final String datasourceApi){
|
|
| 65 |
//TODO: implement me |
|
| 66 |
return -1; |
|
| 67 |
} |
|
| 68 |
|
|
| 69 |
/** |
|
| 70 |
* Registers resources and relationships into the Parthenos Registry |
|
| 71 |
* |
|
| 72 |
* @param rdfRecord RDF record in RDF/XML PLAIN format |
|
| 73 |
*/ |
|
| 74 |
public void register(final String rdfRecord, final String objIdentifier) throws IOException, ResourceRegistryException, ParthenosPublisherException {
|
|
| 75 |
if (StringUtils.isBlank(rdfRecord)) {
|
|
| 76 |
log.warn("Got empty record "+objIdentifier);
|
|
| 77 |
} else {
|
|
| 78 |
InfModel model = loadBaseModel(); |
|
| 79 |
model.read(IOUtils.toInputStream(rdfRecord, "UTF-8"), CRMpe.NS); |
|
| 80 |
|
|
| 81 |
JsonFactory jsonFactory = new JsonFactory(); |
|
| 82 |
Set<String> uriProcessed = Sets.newHashSet(); |
|
| 83 |
/* Maps URI to ParthenosRegistryResource (with uuids) */ |
|
| 84 |
Map<String, ParthenosRegistryResource> idMap = Maps.newHashMap(); |
|
| 85 |
|
|
| 86 |
/* Resource */ |
|
| 87 |
int registeredServices = processServices(model, uriProcessed, jsonFactory, idMap); |
|
| 88 |
int registeredDigitalObjects = processDigitalObjects(model, uriProcessed, jsonFactory, idMap); |
|
| 89 |
int registeredActors = processActors(model, uriProcessed, jsonFactory, idMap); |
|
| 90 |
int registeredProjects = processProjects(model, uriProcessed, jsonFactory, idMap); |
|
| 91 |
|
|
| 92 |
int total = registeredActors+registeredDigitalObjects+registeredProjects+registeredServices; |
|
| 93 |
log.debug(String.format("Registered %d resources from record with objIdentifier %s", total, objIdentifier));
|
|
| 94 |
|
|
| 95 |
/* Relationships */ |
|
| 96 |
int relTotal = 0; |
|
| 97 |
for(String uri : uriProcessed){
|
|
| 98 |
relTotal += processRelationships(model, uri, idMap); |
|
| 99 |
} |
|
| 100 |
log.debug(String.format("Registered %d relationships from record with objIdentifier %s", relTotal, objIdentifier));
|
|
| 101 |
} |
|
| 102 |
} |
|
| 103 |
|
|
| 104 |
private int processRelationships(final InfModel model, final String uri, final Map<String, ParthenosRegistryResource> idMap) |
|
| 105 |
throws IOException, ResourceRegistryException, ParthenosPublisherException {
|
|
| 106 |
Resource subject = model.getResource(uri); |
|
| 107 |
String uuid = idMap.get(uri).getUuid(); |
|
| 108 |
JsonFactory jsonFactory = new JsonFactory(); |
|
| 109 |
int relCount = 0; |
|
| 110 |
|
|
| 111 |
if(subject.hasProperty(RDF.type, CRMpe.PE1_Service)){
|
|
| 112 |
StmtIterator itOfferedBy = subject.listProperties(CRMpe.PP1i_is_currently_offered_by); |
|
| 113 |
while(itOfferedBy.hasNext()){
|
|
| 114 |
Resource project = itOfferedBy.nextStatement().getResource(); |
|
| 115 |
ParthenosRegistryResource source = idMap.get(uri); |
|
| 116 |
ParthenosRegistryResource projectRes = idMap.get(project.getURI()); |
|
| 117 |
String relJson = relWriter.writeRelationship(jsonFactory, "PP1_currently_offers", projectRes.getUuid(), projectRes.getType(), source.getUuid(), source.getType()); |
|
| 118 |
this.resourceRegistryPublisher.createIsRelatedTo("PP1_currently_offers", relJson);
|
|
| 119 |
relCount++; |
|
| 120 |
} |
|
| 121 |
StmtIterator itProvidedBy = subject.listProperties(CRMpe.PP2_provided_by); |
|
| 122 |
while(itProvidedBy.hasNext()){
|
|
| 123 |
Resource provider = itProvidedBy.nextStatement().getResource(); |
|
| 124 |
ParthenosRegistryResource prr = idMap.get(uri); |
|
| 125 |
ParthenosRegistryResource providerRes = idMap.get(provider.getURI()); |
|
| 126 |
String relJson = relWriter.writeRelationship(jsonFactory, "PP2_provided_by", prr.getUuid(), prr.getType(), providerRes.getUuid(), providerRes.getType()); |
|
| 127 |
this.resourceRegistryPublisher.createIsRelatedTo("PP2_provided_by", relJson);
|
|
| 128 |
relCount++; |
|
| 129 |
//TODO: IsRelatedTo the contact person of the provider. Interpret '"Follow path of service ‘Provided by’ and switch E39 for E21: E21- >p76->E51"" |
|
| 130 |
} |
|
| 131 |
relCount += registerRelationship(CRMpe.PP45_has_competency, subject, idMap, jsonFactory); |
|
| 132 |
relCount += registerRelationship(CRMpe.PP4_hosts_object, subject, idMap, jsonFactory); |
|
| 133 |
relCount += registerRelationship(CRMpe.PP31_uses_curation_plan, subject, idMap, jsonFactory); |
|
| 134 |
relCount += registerRelationship(CRMpe.PP32_curates, subject, idMap, jsonFactory); |
|
| 135 |
relCount += registerRelationship(CRMpe.PP6_hosts_digital_object, subject, idMap, jsonFactory); |
|
| 136 |
relCount += registerRelationship(CRMpe.PP7_hosts_software_object, subject, idMap, jsonFactory); |
|
| 137 |
relCount += registerRelationship(CRMpe.PP8_hosts_dataset, subject, idMap, jsonFactory); |
|
| 138 |
relCount += registerRelationship(CRMpe.PP29_uses_access_protocol, subject, idMap, jsonFactory); |
|
| 139 |
relCount += registerRelationship(CRMpe.PP47_has_protocol_type, subject, idMap, jsonFactory); |
|
| 140 |
relCount += registerRelationship(CRMpe.PP48_uses_protocol_parameter, subject, idMap, jsonFactory); |
|
| 141 |
relCount += registerRelationship(CRMpe.PP46_brokers_access_to, subject, idMap, jsonFactory); |
|
| 142 |
relCount += registerRelationship(CRMpe.PP11_curates_volatile_digital_object, subject, idMap, jsonFactory); |
|
| 143 |
relCount += registerRelationship(CRMpe.PP12_curates_volatile_software, subject, idMap, jsonFactory); |
|
| 144 |
relCount += registerRelationship(CRMpe.PP13_curates_volatile_dataset, subject, idMap, jsonFactory); |
|
| 145 |
relCount += registerRelationship(CRMpe.PP15_delivers_on_request, subject, idMap, jsonFactory); |
|
| 146 |
relCount += registerRelationship(CRMpe.PP46_brokers_access_to, subject, idMap, jsonFactory); |
|
| 147 |
} |
|
| 148 |
if(subject.hasProperty(RDF.type, CRMpe.PE18_Dataset)){
|
|
| 149 |
StmtIterator itPartOf = subject.listProperties(CRMpe.PP23i_is_dataset_part_of); |
|
| 150 |
while(itPartOf.hasNext()){
|
|
| 151 |
Resource obj = itPartOf.nextStatement().getResource(); |
|
| 152 |
ParthenosRegistryResource prr = idMap.get(uri); |
|
| 153 |
ParthenosRegistryResource objres = idMap.get(obj.getURI()); |
|
| 154 |
String relJson = relWriter.writeRelationship(jsonFactory, "PP23_has_dataset_part", objres.getUuid(), objres.getType(), prr.getUuid(), prr.getType()); |
|
| 155 |
this.resourceRegistryPublisher.createIsRelatedTo("PP23_has_dataset_part", relJson);
|
|
| 156 |
relCount++; |
|
| 157 |
} |
|
| 158 |
//TODO: this is in the registry model but I am not sure what's going to happen... |
|
| 159 |
StmtIterator itIsAbout = subject.listProperties(CRM.P129_is_about); |
|
| 160 |
while(itIsAbout.hasNext()){
|
|
| 161 |
Resource obj = itIsAbout.nextStatement().getResource(); |
|
| 162 |
if(obj.hasProperty(RDF.type, CRM.E55_Type)) {
|
|
| 163 |
ParthenosRegistryResource prr = idMap.get(uri); |
|
| 164 |
ParthenosRegistryResource objres = idMap.get(obj.getURI()); |
|
| 165 |
String relJson = relWriter.writeRelationship(jsonFactory, "P129_is_about", prr.getUuid(), prr.getType(), objres.getUuid(), objres.getType()); |
|
| 166 |
this.resourceRegistryPublisher.createIsRelatedTo("P129_is_about", relJson);
|
|
| 167 |
relCount++; |
|
| 168 |
} |
|
| 169 |
} |
|
| 170 |
} |
|
| 171 |
if(subject.hasProperty(RDF.type, CRMpe.PE19_Persistent_Digital_Object)){
|
|
| 172 |
relCount += registerRelationship(CRMpe.PP16_has_persistent_digital_object_part, subject, idMap, jsonFactory); |
|
| 173 |
} |
|
| 174 |
if(subject.hasProperty(RDF.type, CRMpe.PE20_Volatile_Digital_Object)){
|
|
| 175 |
relCount += registerRelationship(CRMpe.PP17_has_snapshot, subject, idMap, jsonFactory); |
|
| 176 |
relCount += registerRelationship(CRMpe.PP18_has_digital_object_part, subject, idMap, jsonFactory); |
|
| 177 |
} |
|
| 178 |
if(subject.hasProperty(RDF.type, CRMpe.PE21_Persistent_Software)){
|
|
| 179 |
relCount += registerRelationship(CRMpe.PP19_has_persistent_software_part, subject, idMap, jsonFactory); |
|
| 180 |
} |
|
| 181 |
if(subject.hasProperty(RDF.type, CRMpe.PE22_Persistent_Dataset)){
|
|
| 182 |
relCount += registerRelationship(CRMpe.PP20_has_persistent_dataset_part, subject, idMap, jsonFactory); |
|
| 183 |
relCount += registerRelationship(CRMpe.PP39_is_metadata_for, subject, idMap, jsonFactory); |
|
| 184 |
} |
|
| 185 |
if(subject.hasProperty(RDF.type, CRMpe.PE23_Volatile_Software)){
|
|
| 186 |
relCount += registerRelationship(CRMpe.PP21_has_software_part, subject, idMap, jsonFactory); |
|
| 187 |
relCount += registerRelationship(CRMpe.PP22_has_release, subject, idMap, jsonFactory); |
|
| 188 |
} |
|
| 189 |
if(subject.hasProperty(RDF.type, CRMpe.PE24_Volatile_Dataset)){
|
|
| 190 |
relCount += registerRelationship(CRMpe.PP23_has_dataset_part, subject, idMap, jsonFactory); |
|
| 191 |
relCount += registerRelationship(CRMpe.PP24_has_dataset_snapshot, subject, idMap, jsonFactory); |
|
| 192 |
relCount += registerRelationship(CRMpe.PP41_is_index_of, subject, idMap, jsonFactory); |
|
| 193 |
} |
|
| 194 |
if(subject.hasProperty(RDF.type, CRMpe.PE26_RI_Project)){
|
|
| 195 |
relCount += registerRelationship(CRMpe.PP25_has_maintaining_RI, subject, idMap, jsonFactory); |
|
| 196 |
} |
|
| 197 |
if(subject.hasProperty(RDF.type, CRMpe.PE35_Project)){
|
|
| 198 |
relCount += registerRelationship(CRMpe.PP43_supported_project_activity, subject, idMap, jsonFactory); |
|
| 199 |
relCount += registerRelationship(CRMpe.PP44_has_maintaining_team, subject, idMap, jsonFactory); |
|
| 200 |
} |
|
| 201 |
log.debug(String.format("Registered %d relationships for uri %s, uuid %s", relCount, uri, uuid));
|
|
| 202 |
return relCount; |
|
| 203 |
} |
|
| 204 |
|
|
| 205 |
protected int registerRelationship(final Property rel, final Resource subject, final Map<String,ParthenosRegistryResource> idMap, final JsonFactory jsonFactory) |
|
| 206 |
throws IOException, ResourceRegistryException, ParthenosPublisherException {
|
|
| 207 |
int relCount = 0; |
|
| 208 |
StmtIterator it = subject.listProperties(rel); |
|
| 209 |
while(it.hasNext()){
|
|
| 210 |
Resource obj = it.nextStatement().getResource(); |
|
| 211 |
if(obj == null) throw new ParthenosPublisherException(String.format("No target resource available for %s --> %s", subject.getURI(), rel.getURI()));
|
|
| 212 |
ParthenosRegistryResource source = idMap.get(subject.getURI()); |
|
| 213 |
ParthenosRegistryResource target = idMap.get(obj.getURI()); |
|
| 214 |
String relJson = relWriter.writeRelationship(jsonFactory, rel.getLocalName(), source.getUuid(), source.getType(), target.getUuid(), target.getType()); |
|
| 215 |
this.resourceRegistryPublisher.createIsRelatedTo(rel.getLocalName(), relJson); |
|
| 216 |
relCount++; |
|
| 217 |
} |
|
| 218 |
return relCount; |
|
| 219 |
} |
|
| 220 |
|
|
| 221 |
|
|
| 222 |
protected InfModel loadBaseModel() {
|
|
| 223 |
return ModelFactory.createRDFSModel(baseModel); |
|
| 224 |
} |
|
| 225 |
|
|
| 226 |
protected int processServices(final InfModel model, final Set<String> uriProcessed, final JsonFactory jsonFactory, final Map<String, ParthenosRegistryResource> idMap) |
|
| 227 |
throws IOException, ResourceRegistryException {
|
|
| 228 |
log.debug("Processing services");
|
|
| 229 |
int count = 0; |
|
| 230 |
int total = 0; |
|
| 231 |
ResIterator iter = model.listResourcesWithProperty(RDF.type, CRMpe.PE1_Service); |
|
| 232 |
while (iter.hasNext()) {
|
|
| 233 |
total++; |
|
| 234 |
Resource res = iter.nextResource(); |
|
| 235 |
String resourceURI = res.getURI(); |
|
| 236 |
if (!uriProcessed.contains(resourceURI)) {
|
|
| 237 |
ParthenosRegistryResource prr = processService(res, jsonFactory, idMap); |
|
| 238 |
this.resourceRegistryPublisher.createResource(prr.getType(), prr.getJson()); |
|
| 239 |
uriProcessed.add(resourceURI); |
|
| 240 |
idMap.put(resourceURI, prr); |
|
| 241 |
count++; |
|
| 242 |
} else {
|
|
| 243 |
log.debug(resourceURI + " already processed, now skipping it"); |
|
| 244 |
} |
|
| 245 |
} |
|
| 246 |
log.debug(String.format("Registered %d/%d services", count, total));
|
|
| 247 |
return count; |
|
| 248 |
|
|
| 249 |
} |
|
| 250 |
|
|
| 251 |
private ParthenosRegistryResource processService(final Resource res, final JsonFactory jsonFactory, final Map<String, ParthenosRegistryResource> idMap) throws IOException {
|
|
| 252 |
log.debug("Processing " + res.getURI());
|
|
| 253 |
|
|
| 254 |
StringWriter sw = new StringWriter(); |
|
| 255 |
JsonGenerator jg = jsonFactory.createGenerator(sw); |
|
| 256 |
jg.writeStartObject(); |
|
| 257 |
String specificType = findSpecificType(res, CRMpe.PE1_Service).getLocalName(); |
|
| 258 |
String uuid = writeCommon(res, specificType, jg, idMap); |
|
| 259 |
//******THE FACETS *******// |
|
| 260 |
jg.writeArrayFieldStart("consistsOf");
|
|
| 261 |
//list of facets |
|
| 262 |
writeCommonFacets(res, jg); |
|
| 263 |
facetWriter.writeEventFacet(jg); |
|
| 264 |
facetWriter.writeRightsFacet(jg, res); |
|
| 265 |
if (res.hasProperty(CRMpe.PP2_provided_by)) {
|
|
| 266 |
//TODO: shouldn't this be a rel to an actor? |
|
| 267 |
Resource provider = res.getPropertyResourceValue(CRMpe.PP2_provided_by); |
|
| 268 |
facetWriter.writeContactReferenceFacet(jg, provider); |
|
| 269 |
} |
|
| 270 |
facetWriter.writeDesignatedAccessPointFacet(jg, res); |
|
| 271 |
jg.writeEndArray(); |
|
| 272 |
jg.writeEndObject(); |
|
| 273 |
jg.close(); |
|
| 274 |
String json = sw.toString(); |
|
| 275 |
log.debug(json); |
|
| 276 |
return new ParthenosRegistryResource().setJson(json).setType(specificType).setUuid(uuid); |
|
| 277 |
} |
|
| 278 |
|
|
| 279 |
/** |
|
| 280 |
* Write the common properties: header, class for all resources |
|
| 281 |
* |
|
| 282 |
* @param resource input Resource. |
|
| 283 |
* @param className name of the class for the registry |
|
| 284 |
* @param jg JsonGenerator to write with. |
|
| 285 |
* @param idMap map of the already assigned UUID |
|
| 286 |
* @return the uuid of the resource |
|
| 287 |
*/ |
|
| 288 |
protected String writeCommon(final Resource resource, final String className, final JsonGenerator jg, final Map<String, ParthenosRegistryResource> idMap) throws IOException {
|
|
| 289 |
String uuid; |
|
| 290 |
if (idMap.containsKey(resource.getURI())) {
|
|
| 291 |
uuid = idMap.get(resource.getURI()).getUuid(); |
|
| 292 |
} else {
|
|
| 293 |
uuid = UUID.randomUUID().toString(); |
|
| 294 |
idMap.put(resource.getURI(), new ParthenosRegistryResource().setUuid(uuid)); |
|
| 295 |
} |
|
| 296 |
jg.writeStartObject(); |
|
| 297 |
jg.writeObjectFieldStart("header");
|
|
| 298 |
jg.writeStringField("uuid", uuid);
|
|
| 299 |
jg.writeEndObject(); |
|
| 300 |
jg.writeStringField("@class", className);
|
|
| 301 |
return uuid; |
|
| 302 |
} |
|
| 303 |
|
|
| 304 |
/** |
|
| 305 |
* Write the common facets: identifier and info facets |
|
| 306 |
* |
|
| 307 |
* @param res |
|
| 308 |
* @param jg |
|
| 309 |
*/ |
|
| 310 |
protected void writeCommonFacets(final Resource res, final JsonGenerator jg) throws IOException {
|
|
| 311 |
facetWriter.writeIdentifierFacet(jg, res.getURI()); |
|
| 312 |
facetWriter.writeP1Facets(jg, res); |
|
| 313 |
facetWriter.writeInfoFacet(jg, res); |
|
| 314 |
} |
|
| 315 |
|
|
| 316 |
protected int processDigitalObjects(final InfModel model, final Set<String> uriProcessed, final JsonFactory jsonFactory, final Map<String, ParthenosRegistryResource> idMap) |
|
| 317 |
throws IOException, ResourceRegistryException {
|
|
| 318 |
log.debug("Processing digital objects (include dataset and software)");
|
|
| 319 |
int count = 0; |
|
| 320 |
int total = 0; |
|
| 321 |
ResIterator iterDo = model.listResourcesWithProperty(RDF.type, CRMdig.D1_Digital_Object); |
|
| 322 |
while (iterDo.hasNext()) {
|
|
| 323 |
total++; |
|
| 324 |
Resource res = iterDo.nextResource(); |
|
| 325 |
String resourceURI = res.getURI(); |
|
| 326 |
if (!uriProcessed.contains(resourceURI)) {
|
|
| 327 |
ParthenosRegistryResource prr = processDigitalObject(res, jsonFactory, idMap); |
|
| 328 |
this.resourceRegistryPublisher.createResource(prr.getType(), prr.getJson()); |
|
| 329 |
uriProcessed.add(resourceURI); |
|
| 330 |
idMap.put(resourceURI, prr); |
|
| 331 |
count++; |
|
| 332 |
} else {
|
|
| 333 |
log.debug(resourceURI + " already processed, now skipping it"); |
|
| 334 |
} |
|
| 335 |
} |
|
| 336 |
log.debug(String.format("Registered %d/%d digital objects", count, total));
|
|
| 337 |
return count; |
|
| 338 |
} |
|
| 339 |
|
|
| 340 |
protected ParthenosRegistryResource processDigitalObject(final Resource res, final JsonFactory jsonFactory, final Map<String, ParthenosRegistryResource> idMap) |
|
| 341 |
throws IOException {
|
|
| 342 |
log.debug("Processing " + res.getURI());
|
|
| 343 |
String specificType = findSpecificType(res, CRMdig.D1_Digital_Object).getLocalName(); |
|
| 344 |
StringWriter sw = new StringWriter(); |
|
| 345 |
JsonGenerator jg = jsonFactory.createGenerator(sw); |
|
| 346 |
jg.writeStartObject(); |
|
| 347 |
|
|
| 348 |
String uuid = writeCommon(res, specificType, jg, idMap); |
|
| 349 |
//******THE FACETS *******// |
|
| 350 |
jg.writeArrayFieldStart("consistsOf");
|
|
| 351 |
//list of facets |
|
| 352 |
writeCommonFacets(res, jg); |
|
| 353 |
facetWriter.writeTemporalCoverageFacet(jg, res); |
|
| 354 |
facetWriter.writeRightsFacet(jg, res); |
|
| 355 |
|
|
| 356 |
jg.writeEndArray(); |
|
| 357 |
jg.writeEndObject(); |
|
| 358 |
jg.close(); |
|
| 359 |
String json = sw.toString(); |
|
| 360 |
log.debug(json); |
|
| 361 |
return new ParthenosRegistryResource().setUuid(uuid).setType(specificType).setJson(json); |
|
| 362 |
} |
|
| 363 |
|
|
| 364 |
protected int processActors(final InfModel model, Set<String> uriProcessed, final JsonFactory jsonFactory, final Map<String, ParthenosRegistryResource> idMap) |
|
| 365 |
throws IOException {
|
|
| 366 |
log.debug("Processing actors");
|
|
| 367 |
int count = 0; |
|
| 368 |
int total = 0; |
|
| 369 |
ResIterator iterActors = model.listResourcesWithProperty(RDF.type, CRM.E39_Actor); |
|
| 370 |
while (iterActors.hasNext()) {
|
|
| 371 |
total++; |
|
| 372 |
Resource res = iterActors.nextResource(); |
|
| 373 |
String resourceURI = res.getURI(); |
|
| 374 |
if (!uriProcessed.contains(resourceURI)) {
|
|
| 375 |
ParthenosRegistryResource prr = processActor(res, jsonFactory, idMap); |
|
| 376 |
uriProcessed.add(resourceURI); |
|
| 377 |
idMap.put(resourceURI, prr); |
|
| 378 |
count++; |
|
| 379 |
|
|
| 380 |
} else {
|
|
| 381 |
log.debug(resourceURI + " already processed, now skipping it"); |
|
| 382 |
} |
|
| 383 |
} |
|
| 384 |
log.debug(String.format("Registered %d/%d actors", count, total));
|
|
| 385 |
return count; |
|
| 386 |
} |
|
| 387 |
|
|
| 388 |
protected ParthenosRegistryResource processActor(final Resource r, final JsonFactory jsonFactory, final Map<String, ParthenosRegistryResource> idMap) throws IOException {
|
|
| 389 |
log.debug("Processing " + r.getURI());
|
|
| 390 |
String specificType = findSpecificType(r, CRM.E39_Actor).getLocalName(); |
|
| 391 |
StringWriter sw = new StringWriter(); |
|
| 392 |
JsonGenerator jg = jsonFactory.createGenerator(sw); |
|
| 393 |
jg.writeStartObject(); |
|
| 394 |
|
|
| 395 |
String uuid = writeCommon(r, specificType, jg, idMap); |
|
| 396 |
//******THE FACETS *******// |
|
| 397 |
jg.writeArrayFieldStart("consistsOf");
|
|
| 398 |
//list of facets |
|
| 399 |
writeCommonFacets(r, jg); |
|
| 400 |
facetWriter.writeContactReferenceFacet(jg, r); |
|
| 401 |
|
|
| 402 |
jg.writeEndArray(); |
|
| 403 |
jg.writeEndObject(); |
|
| 404 |
jg.close(); |
|
| 405 |
String json = sw.toString(); |
|
| 406 |
log.debug(json); |
|
| 407 |
return new ParthenosRegistryResource().setJson(json).setType(specificType).setUuid(uuid); |
|
| 408 |
} |
|
| 409 |
|
|
| 410 |
protected int processProjects(final InfModel model, Set<String> uriProcessed, final JsonFactory jsonFactory, final Map<String, ParthenosRegistryResource> idMap) |
|
| 411 |
throws IOException, ResourceRegistryException {
|
|
| 412 |
log.debug("Processing projects");
|
|
| 413 |
int count = 0; |
|
| 414 |
int total = 0; |
|
| 415 |
ResIterator iterProjects = model.listResourcesWithProperty(RDF.type, CRMpe.PE35_Project); |
|
| 416 |
while (iterProjects.hasNext()) {
|
|
| 417 |
total++; |
|
| 418 |
Resource res = iterProjects.nextResource(); |
|
| 419 |
String resourceURI = res.getURI(); |
|
| 420 |
if (!uriProcessed.contains(resourceURI)) {
|
|
| 421 |
ParthenosRegistryResource prr = processProject(res, jsonFactory, idMap); |
|
| 422 |
this.resourceRegistryPublisher.createResource(prr.getType(), prr.getJson()); |
|
| 423 |
uriProcessed.add(resourceURI); |
|
| 424 |
idMap.put(resourceURI, prr); |
|
| 425 |
count++; |
|
| 426 |
} else {
|
|
| 427 |
log.debug(resourceURI + " already processed, now skipping it"); |
|
| 428 |
} |
|
| 429 |
} |
|
| 430 |
log.debug(String.format("Registered %d/%d projects", count, total));
|
|
| 431 |
return count; |
|
| 432 |
} |
|
| 433 |
|
|
| 434 |
protected ParthenosRegistryResource processProject(final Resource res, final JsonFactory jsonFactory, final Map<String, ParthenosRegistryResource> idMap) throws IOException {
|
|
| 435 |
log.debug("Processing " + res.getURI());
|
|
| 436 |
String specificType = findSpecificType(res, CRMpe.PE35_Project).getLocalName(); |
|
| 437 |
StringWriter sw = new StringWriter(); |
|
| 438 |
JsonGenerator jg = jsonFactory.createGenerator(sw); |
|
| 439 |
jg.writeStartObject(); |
|
| 440 |
|
|
| 441 |
String uuid = writeCommon(res, specificType, jg, idMap); |
|
| 442 |
jg.writeArrayFieldStart("consistsOf");
|
|
| 443 |
writeCommonFacets(res, jg); |
|
| 444 |
|
|
| 445 |
jg.writeEndArray(); |
|
| 446 |
jg.writeEndObject(); |
|
| 447 |
jg.close(); |
|
| 448 |
String json = sw.toString(); |
|
| 449 |
log.debug(json); |
|
| 450 |
return new ParthenosRegistryResource().setJson(json).setType(specificType).setUuid(uuid); |
|
| 451 |
} |
|
| 452 |
|
|
| 453 |
/** |
|
| 454 |
* Finds the most specific type of res. |
|
| 455 |
* |
|
| 456 |
* @param res Resource you want to find the most specific type |
|
| 457 |
* @param fallbackType Resource representing the type to return if there is no type or if we get AmbiguousSpecificTypeException |
|
| 458 |
* @return Resource: the most specific type, if any. fallbackType otherwise |
|
| 459 |
*/ |
|
| 460 |
protected Resource findSpecificType(final Resource res, final Resource fallbackType) {
|
|
| 461 |
Resource specType = fallbackType; |
|
| 462 |
try {
|
|
| 463 |
specType = AssemblerHelp.findSpecificType(res, fallbackType); |
|
| 464 |
} catch (AmbiguousSpecificTypeException e) {
|
|
| 465 |
log.warn(res.getURI() + ": " + e.getMessage()); |
|
| 466 |
} |
|
| 467 |
return specType; |
|
| 468 |
} |
|
| 469 |
|
|
| 470 |
public FacetWriter getFacetWriter() {
|
|
| 471 |
return facetWriter; |
|
| 472 |
} |
|
| 473 |
|
|
| 474 |
public void setFacetWriter(final FacetWriter facetWriter) {
|
|
| 475 |
this.facetWriter = facetWriter; |
|
| 476 |
} |
|
| 477 |
} |
|
| modules/dnet-parthenos-publisher/trunk/src/main/java/eu/dnetlib/parthenos/registry/ParthenosRegistryResource.java | ||
|---|---|---|
| 1 |
package eu.dnetlib.parthenos.registry; |
|
| 2 |
|
|
| 3 |
/** |
|
| 4 |
* Created by Alessia Bardi on 06/10/2017. |
|
| 5 |
* |
|
| 6 |
* @author Alessia Bardi |
|
| 7 |
*/ |
|
| 8 |
public class ParthenosRegistryResource {
|
|
| 9 |
|
|
| 10 |
private String uuid; |
|
| 11 |
private String type; |
|
| 12 |
private String json; |
|
| 13 |
|
|
| 14 |
public String getUuid() {
|
|
| 15 |
return uuid; |
|
| 16 |
} |
|
| 17 |
|
|
| 18 |
public ParthenosRegistryResource setUuid(final String uuid) {
|
|
| 19 |
this.uuid = uuid; |
|
| 20 |
return this; |
|
| 21 |
} |
|
| 22 |
|
|
| 23 |
public String getType() {
|
|
| 24 |
return type; |
|
| 25 |
} |
|
| 26 |
|
|
| 27 |
public ParthenosRegistryResource setType(final String type) {
|
|
| 28 |
this.type = type; |
|
| 29 |
return this; |
|
| 30 |
} |
|
| 31 |
|
|
| 32 |
public String getJson() {
|
|
| 33 |
return json; |
|
| 34 |
} |
|
| 35 |
|
|
| 36 |
public ParthenosRegistryResource setJson(final String json) {
|
|
| 37 |
this.json = json; |
|
| 38 |
return this; |
|
| 39 |
} |
|
| 40 |
} |
|
| modules/dnet-parthenos-publisher/trunk/src/main/java/eu/dnetlib/parthenos/registry/RegistryClient.java | ||
|---|---|---|
| 29 | 29 |
private static final String DRI_NAMESPACE_URI = "http://www.driver-repository.eu/namespace/dri"; |
| 30 | 30 |
private static final String RDF_NAMESPACE_URI = "http://www.w3.org/1999/02/22-rdf-syntax-ns#"; |
| 31 | 31 |
|
| 32 |
private GCubeResourceGenerator resourceGenerator;
|
|
| 32 |
private GCubeResourceRegistrator gCubeResourceRegistrator;
|
|
| 33 | 33 |
private SaxonHelper saxonHelper; |
| 34 | 34 |
private XPathSelector xpathSelectorObjIdentifier; |
| 35 |
private XPathSelector xpathSelectorCollectionDate; |
|
| 36 |
private XPathSelector xpathSelectorTransformationDate; |
|
| 37 |
private XPathSelector xpathSelectorDatasourceName; |
|
| 38 |
private XPathSelector xpathSelectorDatasourceApi; |
|
| 35 |
// private XPathSelector xpathSelectorCollectionDate;
|
|
| 36 |
// private XPathSelector xpathSelectorTransformationDate;
|
|
| 37 |
// private XPathSelector xpathSelectorDatasourceName;
|
|
| 38 |
// private XPathSelector xpathSelectorDatasourceApi;
|
|
| 39 | 39 |
private XPathSelector xpathSelectorRDF; |
| 40 | 40 |
|
| 41 | 41 |
private ResourceRegistryPublisher resourceRegistryPublisher; |
| ... | ... | |
| 43 | 43 |
private String registryBaseURL; |
| 44 | 44 |
private String defaultBaseURI; |
| 45 | 45 |
|
| 46 |
protected RegistryClient(final String registryBaseURL, final SaxonHelper saxonHelper, final String defaultBaseURI, final GCubeResourceGenerator resourceGenerator) |
|
| 46 |
protected RegistryClient(final String registryBaseURL, |
|
| 47 |
final SaxonHelper saxonHelper, |
|
| 48 |
final String defaultBaseURI, |
|
| 49 |
final GCubeResourceRegistrator gCubeResourceRegistrator) |
|
| 47 | 50 |
throws ParthenosPublisherException {
|
| 48 | 51 |
this.registryBaseURL = registryBaseURL; |
| 49 | 52 |
this.saxonHelper = saxonHelper; |
| 50 | 53 |
this.defaultBaseURI = defaultBaseURI; |
| 51 | 54 |
this.resourceRegistryPublisher = ResourceRegistryPublisherFactory.create(); |
| 52 | 55 |
this.resourceRegistryClient = ResourceRegistryClientFactory.create(); |
| 53 |
this.resourceGenerator = resourceGenerator;
|
|
| 56 |
this.gCubeResourceRegistrator = gCubeResourceRegistrator;
|
|
| 54 | 57 |
try {
|
| 55 | 58 |
prepareXpathSelectors(); |
| 56 |
}catch(SaxonApiException e){
|
|
| 59 |
} catch (SaxonApiException e) {
|
|
| 57 | 60 |
throw new ParthenosPublisherException(e); |
| 58 | 61 |
} |
| 59 | 62 |
} |
| 60 | 63 |
|
| 61 |
public int register(final String record) throws ParthenosPublisherException{
|
|
| 64 |
public int unregister(final String datasourceInterface) {
|
|
| 65 |
return gCubeResourceRegistrator.unregister(datasourceInterface); |
|
| 66 |
} |
|
| 67 |
|
|
| 68 |
public void register(final String record) throws ParthenosPublisherException {
|
|
| 62 | 69 |
try {
|
| 63 | 70 |
if (StringUtils.isBlank(record)) {
|
| 64 | 71 |
log.warn("Got empty record");
|
| 65 |
return 0; |
|
| 66 | 72 |
} |
| 67 | 73 |
String objIdentifier = extractFromRecord(record, xpathSelectorObjIdentifier); |
| 68 | 74 |
if (StringUtils.isBlank(objIdentifier)) {
|
| 69 | 75 |
log.warn("Got record with no objIdentifier -- skipping");
|
| 70 |
return 0; |
|
| 71 | 76 |
} |
| 72 |
//TODO: get the json strings to register |
|
| 73 |
Iterable<String> resources = resourceGenerator.getGCubeER(record); |
|
| 74 |
for(String res : resources){
|
|
| 75 |
//resourceRegistryPublisher. |
|
| 76 |
} |
|
| 77 |
return 0; |
|
| 78 |
}catch(Throwable e){
|
|
| 77 |
String recordRDF = extractFromRecord(record, xpathSelectorRDF); |
|
| 78 |
gCubeResourceRegistrator.register(recordRDF, objIdentifier); |
|
| 79 |
} catch (Throwable e) {
|
|
| 79 | 80 |
log.error(e.getMessage()); |
| 80 | 81 |
throw new ParthenosPublisherException(e); |
| 81 | 82 |
} |
| 82 | 83 |
} |
| 83 | 84 |
|
| 84 |
|
|
| 85 | 85 |
private void prepareXpathSelectors() throws SaxonApiException {
|
| 86 | 86 |
Map<String, String> namespaces = Maps.newHashMap(); |
| 87 | 87 |
namespaces.put("oai", OAI_NAMESPACE_URI);
|
| 88 | 88 |
namespaces.put("dri", DRI_NAMESPACE_URI);
|
| 89 | 89 |
namespaces.put("rdf", RDF_NAMESPACE_URI);
|
| 90 | 90 |
xpathSelectorObjIdentifier = this.saxonHelper.help().prepareXPathSelector("//oai:header/dri:objIdentifier/text()", namespaces);
|
| 91 |
xpathSelectorCollectionDate = this.saxonHelper.help().prepareXPathSelector("//oai:header/dri:dateOfCollection/text()", namespaces);
|
|
| 92 |
xpathSelectorTransformationDate = this.saxonHelper.help().prepareXPathSelector("//oai:header/dri:dateOfTransformation/text()", namespaces);
|
|
| 93 |
xpathSelectorDatasourceName = this.saxonHelper.help().prepareXPathSelector("//oai:header/dri:datasourcename/text()", namespaces);
|
|
| 94 |
xpathSelectorDatasourceApi = this.saxonHelper.help().prepareXPathSelector("//oai:header/dri:datasourceapi/text()", namespaces);
|
|
| 91 |
//xpathSelectorCollectionDate = this.saxonHelper.help().prepareXPathSelector("//oai:header/dri:dateOfCollection/text()", namespaces);
|
|
| 92 |
//xpathSelectorTransformationDate = this.saxonHelper.help().prepareXPathSelector("//oai:header/dri:dateOfTransformation/text()", namespaces);
|
|
| 93 |
//xpathSelectorDatasourceName = this.saxonHelper.help().prepareXPathSelector("//oai:header/dri:datasourcename/text()", namespaces);
|
|
| 94 |
//xpathSelectorDatasourceApi = this.saxonHelper.help().prepareXPathSelector("//oai:header/dri:datasourceapi/text()", namespaces);
|
|
| 95 | 95 |
xpathSelectorRDF = this.saxonHelper.help().prepareXPathSelector("//oai:metadata/rdf:RDF", namespaces);
|
| 96 | 96 |
} |
| 97 | 97 |
|
| ... | ... | |
| 103 | 103 |
} |
| 104 | 104 |
} |
| 105 | 105 |
|
| 106 |
|
|
| 107 | 106 |
public void setSaxonHelper(final SaxonHelper saxonHelper) {
|
| 108 | 107 |
this.saxonHelper = saxonHelper; |
| 109 | 108 |
} |
| ... | ... | |
| 128 | 127 |
return defaultBaseURI; |
| 129 | 128 |
} |
| 130 | 129 |
|
| 131 |
public GCubeResourceGenerator getResourceGenerator() {
|
|
| 132 |
return resourceGenerator;
|
|
| 130 |
public GCubeResourceRegistrator getgCubeResourceRegistrator() {
|
|
| 131 |
return gCubeResourceRegistrator;
|
|
| 133 | 132 |
} |
| 134 | 133 |
|
| 135 |
public void setResourceGenerator(final GCubeResourceGenerator resourceGenerator) {
|
|
| 136 |
this.resourceGenerator = resourceGenerator;
|
|
| 134 |
public void setgCubeResourceRegistrator(final GCubeResourceRegistrator gCubeResourceRegistrator) {
|
|
| 135 |
this.gCubeResourceRegistrator = gCubeResourceRegistrator;
|
|
| 137 | 136 |
} |
| 138 | 137 |
|
| 139 | 138 |
public ResourceRegistryPublisher getResourceRegistryPublisher() {
|
| modules/dnet-parthenos-publisher/trunk/src/main/java/eu/dnetlib/parthenos/publisher/ParthenosPublisherHelper.java | ||
|---|---|---|
| 64 | 64 |
virtuosoClient.feed(record); |
| 65 | 65 |
} |
| 66 | 66 |
|
| 67 |
private long unpublishVirtuoso(final String datasourceInterface) throws ParthenosPublisherException {
|
|
| 68 |
log.debug("Unublishing from virtuoso "+datasourceInterface);
|
|
| 69 |
VirtuosoClient virtuosoClient = this.virtuosoClientFactory.getVirtuosoClient(); |
|
| 70 |
return virtuosoClient.drop(datasourceInterface); |
|
| 71 |
} |
|
| 72 |
|
|
| 67 | 73 |
private void publishJRR(final String record) throws ParthenosPublisherException {
|
| 68 | 74 |
log.debug("Publishing on Registry");
|
| 69 | 75 |
RegistryClient registryClient = this.registryClientFactory.getRegistryClient(); |
| 70 | 76 |
registryClient.register(record); |
| 71 | 77 |
} |
| 72 | 78 |
|
| 73 |
private long unpublishVirtuoso(final String datasourceInterface) throws ParthenosPublisherException {
|
|
| 74 |
log.debug("Unublishing from virtuoso "+datasourceInterface);
|
|
| 75 |
VirtuosoClient virtuosoClient = this.virtuosoClientFactory.getVirtuosoClient();
|
|
| 76 |
return virtuosoClient.drop(datasourceInterface);
|
|
| 79 |
private int unpublishJRR(final String datasourceInterface) throws ParthenosPublisherException {
|
|
| 80 |
log.debug("Unublishing from registry "+datasourceInterface);
|
|
| 81 |
RegistryClient registryClient = this.registryClientFactory.getRegistryClient();
|
|
| 82 |
return registryClient.unregister(datasourceInterface);
|
|
| 77 | 83 |
} |
| 78 | 84 |
|
| 79 | 85 |
|
| modules/dnet-parthenos-publisher/trunk/pom.xml | ||
|---|---|---|
| 159 | 159 |
<dependency> |
| 160 | 160 |
<groupId>org.gcube.information-system</groupId> |
| 161 | 161 |
<artifactId>parthenos-entities</artifactId> |
| 162 |
<version>LATEST</version>
|
|
| 162 |
<version>0.0.1-SNAPSHOT</version>
|
|
| 163 | 163 |
</dependency> |
| 164 | 164 |
<dependency> |
| 165 | 165 |
<groupId>org.gcube.information-system</groupId> |
| 166 | 166 |
<artifactId>resource-registry-publisher</artifactId> |
| 167 |
<version>LATEST</version>
|
|
| 167 |
<version>1.5.0-SNAPSHOT</version>
|
|
| 168 | 168 |
</dependency> |
| 169 | 169 |
<dependency> |
| 170 | 170 |
<groupId>org.gcube.information-system</groupId> |
| 171 | 171 |
<artifactId>resource-registry-client</artifactId> |
| 172 |
<version>LATEST</version>
|
|
| 172 |
<version>1.5.0-SNAPSHOT</version>
|
|
| 173 | 173 |
</dependency> |
| 174 | 174 |
<dependency> |
| 175 | 175 |
<groupId>org.gcube.common</groupId> |
| 176 | 176 |
<artifactId>authorization-client</artifactId> |
| 177 | 177 |
<version>LATEST</version> |
| 178 | 178 |
</dependency> |
| 179 |
<dependency> |
|
| 180 |
<groupId>org.gcube.information-system</groupId> |
|
| 181 |
<artifactId>resource-registry-api</artifactId> |
|
| 182 |
<version>RELEASE</version> |
|
| 183 |
</dependency> |
|
| 179 | 184 |
</dependencies> |
| 180 | 185 |
|
| 181 | 186 |
<build> |
Also available in: Unified diff
feeding the registry with resources and relationships