Revision 50937
Added by Alessia Bardi about 6 years ago
| CatalogueRegistrator.java | ||
|---|---|---|
| 10 | 10 |
import com.fasterxml.jackson.core.JsonEncoding; |
| 11 | 11 |
import com.fasterxml.jackson.core.JsonFactory; |
| 12 | 12 |
import com.fasterxml.jackson.core.JsonGenerator; |
| 13 |
import com.google.common.collect.Lists; |
|
| 13 | 14 |
import eu.dnetlib.parthenos.CRM; |
| 14 | 15 |
import eu.dnetlib.parthenos.CRMdig; |
| 15 | 16 |
import eu.dnetlib.parthenos.CRMpe; |
| 16 | 17 |
import eu.dnetlib.parthenos.publisher.ParthenosPublisherException; |
| 17 | 18 |
import eu.dnetlib.parthenos.rdf.ResourceReader; |
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import org.apache.commons.io.IOUtils; |
|
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import org.apache.commons.lang3.StringUtils; |
| 20 | 20 |
import org.apache.commons.logging.Log; |
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import org.apache.commons.logging.LogFactory; |
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import org.apache.http.client.methods.HttpGet; |
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import org.apache.http.client.methods.HttpRequestBase; |
|
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import org.apache.http.client.utils.URIBuilder; |
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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.beans.factory.annotation.Value; |
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import org.springframework.http.*; |
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import org.springframework.stereotype.Component; |
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import org.springframework.web.client.RestTemplate; |
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import static eu.dnetlib.parthenos.CRM.*; |
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|
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/** |
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* Created by Alessia Bardi on 21/11/2017. |
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* |
| ... | ... | |
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public class CatalogueRegistrator {
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|
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private static final Log log = LogFactory.getLog(CatalogueRegistrator.class); |
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private OntModel baseModel; |
|
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|
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@Value("${gcube.catalogue.baseurl}")
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private String baseURL; |
| ... | ... | |
| 52 | 50 |
@Autowired |
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private ResourceReader resourceReader; |
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@PostConstruct |
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public void init(){
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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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@Autowired |
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private RestTemplate jrrRestTemplate; |
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public int register(final String rdfRecord, final String objIdentifier) throws ParthenosPublisherException, IOException {
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log.info("Catalogue --> Processing record " + objIdentifier);
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int registered = 0; |
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int total = 0; |
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InfModel model = loadBaseModel(); |
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model.read(IOUtils.toInputStream(rdfRecord, "UTF-8"), CRMpe.NS); |
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ResIterator activities = model.listSubjectsWithProperty(RDF.type, CRM.E7_Activity); |
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log.debug("Registering instances of E7_Activity");
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while (activities.hasNext()) {
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total++; |
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Resource activity = activities.nextResource(); |
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String resURI = activity.getURI(); |
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if(!resURI.startsWith("http")){
|
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//this is something George said: if it has no http URI, then it is not to be considered relevant by itself |
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log.info("E7_Activity "+resURI+" skipped: URI does not start with http");
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} |
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String resCatName = resURI.substring(resURI.lastIndexOf("/") + 1);
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String json = getJsonForActivity(activity, resCatName ); |
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registered += doRegister(json, objIdentifier, resCatName); |
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public String register(final Resource resource, final Resource type) throws IOException, ParthenosPublisherException {
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String resURI = resource.getURI(); |
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log.debug(String.format("Catalogue --> Processing resource : %s with type: %s", resURI, type.getLocalName()));
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String resCatName = resURI.substring(resURI.lastIndexOf("/") + 1);
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String json; |
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switch(type.getLocalName()){
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case "E7_Activity": |
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json = getJsonForActivity(resource, resCatName); |
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break; |
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case "E39_Actor": |
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json = getJsonForActor(resource, resCatName); |
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break; |
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case "E70_Thing": |
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json = getJsonForThing(resource, resCatName); |
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break; |
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//TODO: handle more tyopes, see JRRPublisher |
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default: |
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throw new IllegalArgumentException(String.format("Type "+type.getLocalName()+" not supported"));
|
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} |
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|
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ResIterator actors = model.listSubjectsWithProperty(RDF.type, CRM.E39_Actor); |
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log.debug("Registering instances of E39_Actor");
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while (actors.hasNext()) {
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total++; |
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Resource actor = actors.nextResource(); |
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String resURI = actor.getURI(); |
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if(!resURI.startsWith("http")){
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//this is something George said: if it has no http URI, then it is not to be considered relevant by itself |
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log.info("E39_Actor "+resURI+" skipped: URI does not start with http");
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} |
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String resCatName = resURI.substring(resURI.lastIndexOf("/") + 1);
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String json = getJsonForActor(actor, resCatName ); |
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registered += doRegister(json, objIdentifier, resCatName); |
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} |
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//TODO: nothing to do for E29 and Curation plan subclass? |
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//ResIterator procs = model.listResourcesWithProperty(RDF.type, CRM.E29_Design_or_Procedure); |
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|
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ResIterator things = model.listSubjectsWithProperty(RDF.type, CRM.E70_Thing); |
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log.debug("Registering instances of E70_Thing");
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while (things.hasNext()) {
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total++; |
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Resource thing = things.nextResource(); |
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String resURI = thing.getURI(); |
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if(!resURI.startsWith("http")){
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//this is something George said: if it has no http URI, then it is not to be considered relevant by itself |
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log.info("E70_Thing "+resURI+" skipped: URI does not start with http");
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} |
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String resCatName = resURI.substring(resURI.lastIndexOf("/") + 1);
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String json = getJsonForThing(thing, resCatName ); |
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registered += doRegister(json, objIdentifier, resCatName); |
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} |
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log.debug(String.format("Registering finished: %s/%s", registered, total));
|
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return registered; |
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String uuid = doRegister(json, resCatName); |
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log.debug(String.format("%s registered on the catalogue with uuid: %s", resURI, uuid));
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return uuid; |
|
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} |
| 120 | 80 |
|
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protected String getJsonForThing(final Resource res, final String resNameForCatalogue) throws IOException {
|
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JsonFactory jsonFactory = new JsonFactory(); |
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final ByteArrayOutputStream out = new ByteArrayOutputStream(); |
|
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BufferedOutputStream bos = new BufferedOutputStream(out); |
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JsonGenerator jg = jsonFactory.createGenerator(bos, JsonEncoding.UTF8); |
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jg.writeStartObject(); |
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writeCommonFields(jg, res, resNameForCatalogue); |
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jg.writeArrayFieldStart("extras");
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addExtra(jg, "system:type", CRM.E70_Thing.getLocalName()); |
|
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//specific class |
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addExtra(jg,"instance of", resourceReader.findSpecificType(res, CRM.E70_Thing).getLocalName()); |
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if(res.getURI().startsWith("http://parthenos.d4science.org")) {
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addExtra(jg,"Parthenos URL", res.getURI()); |
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} |
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//TODO: things include digital objects, software, datasets, schema. Guess we should know what to add here. |
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jg.writeEndArray(); |
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|
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jg.writeEndObject(); |
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jg.close(); |
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return out.toString("UTF-8");
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} |
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|
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protected void addExtra(final JsonGenerator jg, final String key, final String value) throws IOException {
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jg.writeStartObject(); |
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jg.writeStringField("key", key );
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jg.writeStringField("value", value);
|
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jg.writeEndObject(); |
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} |
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|
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protected void writeCommonFields(final JsonGenerator jg, final Resource res, final String resNameForCatalogue) throws IOException {
|
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//end of URI |
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jg.writeStringField("name", resNameForCatalogue);
|
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//default license |
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jg.writeStringField("license_id", "notspecified");
|
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String title = resourceReader.getTitle(res); |
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if(StringUtils.isBlank(title)) |
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title = resNameForCatalogue; |
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jg.writeStringField("title", title);
|
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//description |
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jg.writeStringField("notes", resourceReader.getDescription(res));
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} |
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|
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protected String getJsonForActor(final Resource res, final String resNameForCatalogue) throws IOException {
|
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JsonFactory jsonFactory = new JsonFactory(); |
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final ByteArrayOutputStream out = new ByteArrayOutputStream(); |
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BufferedOutputStream bos = new BufferedOutputStream(out); |
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JsonGenerator jg = jsonFactory.createGenerator(bos, JsonEncoding.UTF8); |
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jg.writeStartObject(); |
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writeCommonFields(jg, res, resNameForCatalogue); |
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|
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jg.writeArrayFieldStart("extras");
|
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addExtra(jg,"system:type", CRM.E39_Actor.getLocalName()); |
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//specific class |
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addExtra(jg,"instance of", resourceReader.findSpecificType(res, CRM.E39_Actor).getLocalName()); |
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if(res.getURI().startsWith("http://parthenos.d4science.org"))
|
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addExtra(jg,"Parthenos URL", res.getURI()); |
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jg.writeEndArray(); |
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|
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jg.writeEndObject(); |
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jg.close(); |
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return out.toString("UTF-8");
|
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} |
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|
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| 185 | 82 |
protected String getJsonForActivity(final Resource res, final String resNameForCatalogue) throws IOException {
|
| 186 | 83 |
JsonFactory jsonFactory = new JsonFactory(); |
| 187 | 84 |
final ByteArrayOutputStream out = new ByteArrayOutputStream(); |
| ... | ... | |
| 195 | 92 |
//the names of all superclasses of the entity |
| 196 | 93 |
jg.writeArrayFieldStart("tags");
|
| 197 | 94 |
Iterator<String> classNames = resourceReader.getRDFClassNames(res); |
| 198 |
while(classNames.hasNext()) {
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while (classNames.hasNext()) {
|
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| 199 | 96 |
jg.writeStartObject(); |
| 200 | 97 |
jg.writeStringField("name", classNames.next());
|
| 201 | 98 |
jg.writeEndObject(); |
| ... | ... | |
| 213 | 110 |
jg.writeEndArray(); |
| 214 | 111 |
|
| 215 | 112 |
jg.writeArrayFieldStart("extras");
|
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addExtra(jg,"system:type", CRM.E7_Activity.getLocalName());
|
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addExtra(jg, "system:type", E7_Activity.getLocalName());
|
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| 217 | 114 |
//specific class |
| 218 |
addExtra(jg,"instance of", resourceReader.findSpecificType(res, CRM.E7_Activity).getLocalName());
|
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if(res.getURI().startsWith("http://parthenos.d4science.org"))
|
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addExtra(jg,"Parthenos URL", res.getURI()); |
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addExtra(jg,"competence", res.getURI()); |
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addExtra(jg, "instance of", resourceReader.findSpecificType(res, E7_Activity).getLocalName());
|
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if (res.getURI().startsWith("http://parthenos.d4science.org"))
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addExtra(jg, "Parthenos URL", res.getURI());
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addExtra(jg, "competence", res.getURI());
|
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| 222 | 119 |
//TODO: from which linked E39_Actors? Should be the same as for groups above |
| 223 |
addExtra(jg,"provided by", ""); |
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addExtra(jg, "provided by", "");
|
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| 224 | 121 |
//TODO: get begin/end of operation from PP42_has_declarative_time |
| 225 |
addExtra(jg,"declared begin/end of operation", ""); |
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addExtra(jg, "declared begin/end of operation", "");
|
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| 226 | 123 |
//TODO: where to get it? |
| 227 |
addExtra(jg,"last confirmation", ""); |
|
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addExtra(jg, "last confirmation", "");
|
|
| 228 | 125 |
//TODO: where to get it? |
| 229 |
addExtra(jg,"date of registration", ""); |
|
| 230 |
addExtra(jg,"availability", resourceReader.getAvailability(res)); |
|
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addExtra(jg,"condition of use", resourceReader.getConditionOfUse(res)); |
|
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addExtra(jg, "date of registration", "");
|
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addExtra(jg, "availability", resourceReader.getAvailability(res));
|
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| 128 |
addExtra(jg, "condition of use", resourceReader.getConditionOfUse(res));
|
|
| 232 | 129 |
//TODO: where to get the contact person |
| 233 | 130 |
//Resource contactPerson = null; |
| 234 | 131 |
//jg.writeStringField("contact person", resourceReader.getTitle(contactPerson));
|
| 235 | 132 |
//TODO: where to get it? |
| 236 |
addExtra(jg,"activity type", ""); |
|
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addExtra(jg, "activity type", "");
|
|
| 237 | 134 |
// can't add multiple fields with same name, hence skipping |
| 238 | 135 |
//jg.writeStringField("hosts", "");
|
| 239 | 136 |
//TODO: where to get it? |
| 240 |
addExtra(jg,"online access point", ""); |
|
| 137 |
addExtra(jg, "online access point", "");
|
|
| 241 | 138 |
//TODO: where to get it? |
| 242 |
addExtra(jg,"authorization", ""); |
|
| 139 |
addExtra(jg, "authorization", "");
|
|
| 243 | 140 |
//TODO: where to get it? |
| 244 |
addExtra(jg,"protocol", ""); |
|
| 141 |
addExtra(jg, "protocol", "");
|
|
| 245 | 142 |
//can't add multiple fields with same name, hence skipping |
| 246 | 143 |
//addExtra(jg,"curates", ""); |
| 247 | 144 |
//TODO: where to get it? |
| 248 |
addExtra(jg,"runs on request", ""); |
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| 145 |
addExtra(jg, "runs on request", "");
|
|
| 249 | 146 |
//TODO: where to get it? |
| 250 |
addExtra(jg,"delivers on request", ""); |
|
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addExtra(jg, "delivers on request", "");
|
|
| 251 | 148 |
jg.writeEndArray(); //end extras |
| 252 | 149 |
|
| 253 | 150 |
jg.writeEndObject(); |
| 254 | 151 |
jg.close(); |
| 255 | 152 |
return out.toString("UTF-8");
|
| 256 | 153 |
} |
| 154 |
protected String getJsonForActor(final Resource res, final String resNameForCatalogue) throws IOException {
|
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| 155 |
JsonFactory jsonFactory = new JsonFactory(); |
|
| 156 |
final ByteArrayOutputStream out = new ByteArrayOutputStream(); |
|
| 157 |
BufferedOutputStream bos = new BufferedOutputStream(out); |
|
| 158 |
JsonGenerator jg = jsonFactory.createGenerator(bos, JsonEncoding.UTF8); |
|
| 159 |
jg.writeStartObject(); |
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| 160 |
writeCommonFields(jg, res, resNameForCatalogue); |
|
| 257 | 161 |
|
| 162 |
jg.writeArrayFieldStart("extras");
|
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| 163 |
addExtra(jg, "system:type", E39_Actor.getLocalName()); |
|
| 164 |
//specific class |
|
| 165 |
addExtra(jg, "instance of", resourceReader.findSpecificType(res, E39_Actor).getLocalName()); |
|
| 166 |
if (res.getURI().startsWith("http://parthenos.d4science.org"))
|
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| 167 |
addExtra(jg, "Parthenos URL", res.getURI()); |
|
| 168 |
jg.writeEndArray(); |
|
| 258 | 169 |
|
| 259 |
private int doRegister(final String json, final String objIdentifier, final String catName) throws ParthenosPublisherException {
|
|
| 260 |
//TODO: implement me |
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| 261 |
log.debug(String.format("Catalogue --> Registering %s (from %s) : %s", catName, objIdentifier, json));
|
|
| 262 |
//if resCatName is already registered --> delete it and then saves it again |
|
| 263 |
try {
|
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| 264 |
URI uri = new URIBuilder(getBaseURL()).build(); |
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| 265 |
HttpGet req = new HttpGet(uri); |
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| 266 |
setHeaders(req); |
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| 267 |
System.out.println(req.getURI()); |
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| 268 |
return 0; |
|
| 269 |
}catch(Throwable t){
|
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| 270 |
throw new ParthenosPublisherException(t); |
|
| 170 |
jg.writeEndObject(); |
|
| 171 |
jg.close(); |
|
| 172 |
return out.toString("UTF-8");
|
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| 173 |
} |
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| 174 |
protected String getJsonForThing(final Resource res, final String resNameForCatalogue) throws IOException {
|
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| 175 |
JsonFactory jsonFactory = new JsonFactory(); |
|
| 176 |
final ByteArrayOutputStream out = new ByteArrayOutputStream(); |
|
| 177 |
BufferedOutputStream bos = new BufferedOutputStream(out); |
|
| 178 |
JsonGenerator jg = jsonFactory.createGenerator(bos, JsonEncoding.UTF8); |
|
| 179 |
jg.writeStartObject(); |
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| 180 |
writeCommonFields(jg, res, resNameForCatalogue); |
|
| 181 |
|
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| 182 |
jg.writeArrayFieldStart("extras");
|
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| 183 |
addExtra(jg, "system:type", E70_Thing.getLocalName()); |
|
| 184 |
//specific class |
|
| 185 |
addExtra(jg, "instance of", resourceReader.findSpecificType(res, E70_Thing).getLocalName()); |
|
| 186 |
if (res.getURI().startsWith("http://parthenos.d4science.org")) {
|
|
| 187 |
addExtra(jg, "Parthenos URL", res.getURI()); |
|
| 271 | 188 |
} |
| 189 |
//TODO: things include digital objects, software, datasets, schema. Guess we should know what to add here. |
|
| 190 |
jg.writeEndArray(); |
|
| 191 |
|
|
| 192 |
jg.writeEndObject(); |
|
| 193 |
jg.close(); |
|
| 194 |
return out.toString("UTF-8");
|
|
| 272 | 195 |
} |
| 273 | 196 |
|
| 274 |
private void setHeaders(final HttpRequestBase req){
|
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| 275 |
req.setHeader("Content-type", "application/json");
|
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| 276 |
req.setHeader("Accept","application/json");
|
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| 277 |
req.setHeader("gcube-token", getApplicationToken() );
|
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| 197 |
protected void addExtra(final JsonGenerator jg, final String key, final String value) throws IOException {
|
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| 198 |
jg.writeStartObject(); |
|
| 199 |
jg.writeStringField("key", key);
|
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| 200 |
jg.writeStringField("value", value);
|
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| 201 |
jg.writeEndObject(); |
|
| 278 | 202 |
} |
| 279 | 203 |
|
| 280 |
protected InfModel loadBaseModel() {
|
|
| 281 |
return ModelFactory.createRDFSModel(baseModel); |
|
| 204 |
protected void writeCommonFields(final JsonGenerator jg, final Resource res, final String resNameForCatalogue) throws IOException {
|
|
| 205 |
//end of URI |
|
| 206 |
jg.writeStringField("name", resNameForCatalogue);
|
|
| 207 |
//default license |
|
| 208 |
jg.writeStringField("license_id", "notspecified");
|
|
| 209 |
String title = resourceReader.getTitle(res); |
|
| 210 |
if (StringUtils.isBlank(title)) |
|
| 211 |
title = resNameForCatalogue; |
|
| 212 |
jg.writeStringField("title", title);
|
|
| 213 |
//description |
|
| 214 |
jg.writeStringField("notes", resourceReader.getDescription(res));
|
|
| 282 | 215 |
} |
| 283 | 216 |
|
| 284 |
public OntModel getBaseModel() {
|
|
| 285 |
return baseModel; |
|
| 217 |
/** |
|
| 218 |
* @param json |
|
| 219 |
* @param resCatName |
|
| 220 |
* @return the uuid assigned by the catalogue to the registered resource |
|
| 221 |
* @throws ParthenosPublisherException |
|
| 222 |
*/ |
|
| 223 |
private String doRegister(final String json, final String resCatName) throws ParthenosPublisherException {
|
|
| 224 |
//TODO: implement me |
|
| 225 |
log.debug(String.format("Catalogue --> Registering %s : %s", resCatName, json));
|
|
| 226 |
//if resCatName is already registered --> delete it and then saves it again |
|
| 227 |
HttpEntity<String> entity = new HttpEntity<String>(json, getHeaders()); |
|
| 228 |
try {
|
|
| 229 |
URI uri = new URIBuilder(getBaseURL()).addParameter("gcube-token", getApplicationToken()).build();
|
|
| 230 |
ResponseEntity<String> res = jrrRestTemplate.<String>exchange(uri, HttpMethod.POST, entity, String.class); |
|
| 231 |
//TODO: I guess response is a json, need to check the format, parse it to get the uuid of the registered resource |
|
| 232 |
String uuid = res.getBody(); |
|
| 233 |
return uuid; |
|
| 234 |
} catch (Throwable t) {
|
|
| 235 |
throw new ParthenosPublisherException(t); |
|
| 236 |
} |
|
| 286 | 237 |
} |
| 287 | 238 |
|
| 288 |
public void setBaseModel(final OntModel baseModel) {
|
|
| 289 |
this.baseModel = baseModel; |
|
| 239 |
private HttpHeaders getHeaders() {
|
|
| 240 |
HttpHeaders headers = new HttpHeaders(); |
|
| 241 |
headers.setContentType(MediaType.APPLICATION_JSON); |
|
| 242 |
headers.setAccept(Lists.newArrayList(MediaType.APPLICATION_JSON)); |
|
| 243 |
//headers.set("gcube-token", getApplicationToken() );
|
|
| 244 |
return headers; |
|
| 290 | 245 |
} |
| 291 | 246 |
|
| 247 |
|
|
| 292 | 248 |
public String getBaseURL() {
|
| 293 | 249 |
return baseURL; |
| 294 | 250 |
} |
Also available in: Unified diff
Refactoring and deprecation for registration on catalogue and registry