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package edu.ucsb.nceas.metacat.annotation;
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import java.io.InputStream;
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import java.io.StringWriter;
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import java.sql.PreparedStatement;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Vector;
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import org.apache.commons.io.IOUtils;
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import org.apache.log4j.Logger;
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import org.apache.wicket.protocol.http.mock.MockHttpServletRequest;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v1.Session;
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import org.dataone.service.types.v1.Subject;
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import org.ecoinformatics.datamanager.parser.Attribute;
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import org.ecoinformatics.datamanager.parser.DataPackage;
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import org.ecoinformatics.datamanager.parser.Entity;
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import org.ecoinformatics.datamanager.parser.Party;
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import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;
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import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser;
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import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
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import com.hp.hpl.jena.ontology.Individual;
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import com.hp.hpl.jena.ontology.ObjectProperty;
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import com.hp.hpl.jena.ontology.OntClass;
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import com.hp.hpl.jena.ontology.OntDocumentManager;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.Ontology;
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import com.hp.hpl.jena.query.Dataset;
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import com.hp.hpl.jena.query.Query;
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import com.hp.hpl.jena.query.QueryExecution;
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import com.hp.hpl.jena.query.QueryExecutionFactory;
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import com.hp.hpl.jena.query.QueryFactory;
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import com.hp.hpl.jena.query.QuerySolution;
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import com.hp.hpl.jena.query.ResultSet;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.Property;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.tdb.TDBFactory;
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import edu.ucsb.nceas.metacat.DBUtil;
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import edu.ucsb.nceas.metacat.DocumentImpl;
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import edu.ucsb.nceas.metacat.IdentifierManager;
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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
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import edu.ucsb.nceas.metacat.database.DBConnection;
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import edu.ucsb.nceas.metacat.database.DBConnectionPool;
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import edu.ucsb.nceas.metacat.dataone.MNodeService;
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import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.replication.ReplicationService;
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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import edu.ucsb.nceas.utilities.SortedProperties;
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public class DatapackageSummarizer {
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private static Logger logMetacat = Logger.getLogger(DatapackageSummarizer.class);
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public static String rdf = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
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public static String rdfs = "http://www.w3.org/2000/01/rdf-schema#";
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public static String owl = "http://www.w3.org/2002/07/owl#";
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public static String oboe = "http://ecoinformatics.org/oboe/oboe.1.0/oboe.owl#";
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public static String oboe_core = "http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#";
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public static String oboe_characteristics = "http://ecoinformatics.org/oboe/oboe.1.0/oboe-characteristics.owl#";
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public static String oboe_sbc = "http://ecoinformatics.org/oboe-ext/sbclter.1.0/oboe-sbclter.owl#";
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public static String oa = "http://www.w3.org/ns/oa#";
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public static String oa_source = "http://www.w3.org/ns/oa.rdf";
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public static String dcterms = "http://purl.org/dc/terms/";
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public static String dcterms_source = "http://dublincore.org/2012/06/14/dcterms.rdf";
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public static String foaf = "http://xmlns.com/foaf/0.1/";
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public static String foaf_source = "http://xmlns.com/foaf/spec/index.rdf";
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public static String prov = "http://www.w3.org/ns/prov#";
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public static String prov_source = "http://www.w3.org/ns/prov.owl";
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public static String cito = "http://purl.org/spar/cito/";
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public static String OBOE_SBC = "OBOE-SBC";
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private static boolean cacheInitialized;
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private static void initializeCache() {
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if (!cacheInitialized) {
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// cache the ontologies we use
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OntDocumentManager.getInstance().addModel(oboe, ModelFactory.createOntologyModel().read(oboe));
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OntDocumentManager.getInstance().addModel(oboe_sbc, ModelFactory.createOntologyModel().read(oboe_sbc));
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OntDocumentManager.getInstance().addModel(oa, ModelFactory.createOntologyModel().read(oa_source));
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OntDocumentManager.getInstance().addModel(dcterms, ModelFactory.createOntologyModel().read(dcterms_source));
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OntDocumentManager.getInstance().addModel(foaf, ModelFactory.createOntologyModel().read(foaf_source));
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OntDocumentManager.getInstance().addModel(prov, ModelFactory.createOntologyModel().read(prov));
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OntDocumentManager.getInstance().addModel(cito, ModelFactory.createOntologyModel().read(cito));
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cacheInitialized = true;
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}
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}
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public void indexEphemeralAnnotation(Identifier metadataPid) throws Exception {
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// generate an annotation for the metadata given
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String rdfContent = this.generateAnnotation(metadataPid);
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// load to triple store
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//Dataset dataset = TDBFactory.createDataset("./tbd");
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Dataset dataset = TDBFactory.createDataset();
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//Dataset dataset = DatasetFactory.createMem();
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// read the annotation into the triplestore
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InputStream source = IOUtils.toInputStream(rdfContent, "UTF-8");
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String name = "http://annotation/" + metadataPid.getValue();
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boolean loaded = dataset.containsNamedModel(name);
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if (loaded) {
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dataset.removeNamedModel(name);
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loaded = false;
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}
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OntModel ontModel = null;
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if (!loaded) {
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ontModel = ModelFactory.createOntologyModel();
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ontModel.read(source, name);
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dataset.addNamedModel(name, ontModel);
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}
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// query for fields to add to index
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Map<String, List<Object>> fields = new HashMap<String, List<Object>>();
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// TODO: look up the query to use (support multiple like in the indexing project)
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List<String> queries = new ArrayList<String>();
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queries.add("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
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+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> "
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+ "PREFIX owl: <http://www.w3.org/2002/07/owl#> "
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+ "PREFIX oboe-core: <http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#> "
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+ "PREFIX oa: <http://www.w3.org/ns/oa#> "
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+ "PREFIX dcterms: <http://purl.org/dc/terms/> "
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+ "SELECT ?standard_sm ?pid "
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+ "FROM <$GRAPH_NAME> "
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+ "WHERE { "
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+ " ?measurement rdf:type oboe-core:Measurement . "
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+ " ?measurement rdf:type ?restriction . "
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+ " ?restriction owl:onProperty oboe-core:usesStandard . "
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+ " ?restriction owl:allValuesFrom ?standard . "
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+ " ?standard rdfs:subClassOf+ ?standard_sm . "
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+ " ?standard_sm rdfs:subClassOf oboe-core:Standard . "
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+ " ?annotation oa:hasBody ?measurement . "
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+ " ?annotation oa:hasTarget ?target . "
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+ " ?target oa:hasSource ?metadata . "
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+ " ?metadata dcterms:identifier ?pid . "
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+ "}");
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queries.add("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
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+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> "
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+ "PREFIX owl: <http://www.w3.org/2002/07/owl#> "
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+ "PREFIX oboe-core: <http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#> "
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+ "PREFIX oa: <http://www.w3.org/ns/oa#> "
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+ "PREFIX dcterms: <http://purl.org/dc/terms/> "
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+ "SELECT ?characteristic_sm ?pid "
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+ "FROM <$GRAPH_NAME>"
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+ "WHERE { "
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+ " ?measurement rdf:type oboe-core:Measurement . "
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+ " ?measurement rdf:type ?restriction . "
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+ " ?restriction owl:onProperty oboe-core:ofCharacteristic . "
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+ " ?restriction owl:allValuesFrom ?characteristic . "
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+ " ?characteristic rdfs:subClassOf+ ?characteristic_sm . "
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+ " ?characteristic_sm rdfs:subClassOf oboe-core:Characteristic . "
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+ " ?annotation oa:hasBody ?measurement . "
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+ " ?annotation oa:hasTarget ?target . "
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+ " ?target oa:hasSource ?metadata . "
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+ " ?metadata dcterms:identifier ?pid . "
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+ "}");
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for (String q: queries) {
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q = q.replaceAll("\\$GRAPH_NAME", name);
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Query query = QueryFactory.create(q);
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QueryExecution qexec = QueryExecutionFactory.create(query, dataset);
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ResultSet results = qexec.execSelect();
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while (results.hasNext()) {
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QuerySolution solution = results.next();
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System.out.println(solution.toString());
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// find the index document we are trying to augment with the annotation
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if (solution.contains("pid")) {
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String id = solution.getLiteral("pid").getString();
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if (!id.equals(metadataPid.getValue())) {
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// skip any solution that does not annotate the given pid
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continue;
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}
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}
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// loop through the solution variables, add an index value for each
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Iterator<String> varNameIter = solution.varNames();
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while (varNameIter.hasNext()) {
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String key = varNameIter.next();
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if (key.equals("pid")) {
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// don't include the id
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continue;
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}
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String value = solution.get(key).toString();
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List<Object> values = fields.get(key);
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if (values == null) {
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values = new ArrayList<Object>();
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}
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values.add(value);
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fields.put(key, values);
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}
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}
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}
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// remove the graph to save storage
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// ontModel.removeAll();
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// ontModel.commit();
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// ontModel.close();
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dataset.removeNamedModel(name);
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// clean up the triple store
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TDBFactory.release(dataset);
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// add to index
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MetacatSolrIndex.getInstance().submit(metadataPid, null, fields, true);
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}
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/**
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* Generate annotation for given metadata identifier
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* @param metadataPid
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*/
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public String generateAnnotation(Identifier metadataPid) throws Exception {
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DataPackage dataPackage = this.getDataPackage(metadataPid);
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OntModel m = ModelFactory.createOntologyModel();
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Ontology ont = m.createOntology("http://annotation/" + metadataPid.getValue());
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// TODO: import the ontologies we use
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initializeCache();
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ont.addImport(m.createResource(oboe));
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m.addSubModel(OntDocumentManager.getInstance().getModel(oboe));
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ont.addImport(m.createResource(oboe_sbc));
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m.addSubModel(OntDocumentManager.getInstance().getModel(oboe_sbc));
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ont.addImport(m.createResource(oa));
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m.addSubModel(OntDocumentManager.getInstance().getModel(oa));
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ont.addImport(m.createResource(dcterms));
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m.addSubModel(OntDocumentManager.getInstance().getModel(dcterms));
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ont.addImport(m.createResource(foaf));
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m.addSubModel(OntDocumentManager.getInstance().getModel(foaf));
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ont.addImport(m.createResource(prov));
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//m.addSubModel(ModelFactory.createOntologyModel().read(prov_source));
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ont.addImport(m.createResource(cito));
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// properties
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ObjectProperty hasBodyProperty = m.getObjectProperty(oa + "hasBody");
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ObjectProperty hasTargetProperty = m.getObjectProperty(oa + "hasTarget");
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ObjectProperty hasSourceProperty = m.getObjectProperty(oa + "hasSource");
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ObjectProperty hasSelectorProperty = m.getObjectProperty(oa + "hasSelector");
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ObjectProperty annotatedByProperty = m.getObjectProperty(oa + "annotatedBy");
|
| 264 |
|
|
Property identifierProperty = m.getProperty(dcterms + "identifier");
|
| 265 |
8710
|
leinfelder
|
Property conformsToProperty = m.getProperty(dcterms + "conformsTo");
|
| 266 |
8718
|
leinfelder
|
Property wasAttributedTo = m.getProperty(prov + "wasAttributedTo");
|
| 267 |
8702
|
leinfelder
|
Property nameProperty = m.getProperty(foaf + "name");
|
| 268 |
8710
|
leinfelder
|
Property rdfValue = m.getProperty(rdf + "value");
|
| 269 |
8702
|
leinfelder
|
|
| 270 |
|
|
ObjectProperty ofCharacteristic = m.getObjectProperty(oboe_core + "ofCharacteristic");
|
| 271 |
|
|
ObjectProperty usesStandard = m.getObjectProperty(oboe_core + "usesStandard");
|
| 272 |
8743
|
leinfelder
|
ObjectProperty ofEntity = m.getObjectProperty(oboe_core + "ofEntity");
|
| 273 |
|
|
ObjectProperty hasMeasurement = m.getObjectProperty(oboe_core + "hasMeasurement");
|
| 274 |
8702
|
leinfelder
|
|
| 275 |
|
|
// classes
|
| 276 |
8743
|
leinfelder
|
OntClass entityClass = m.getOntClass(oboe_core + "Entity");
|
| 277 |
|
|
OntClass observationClass = m.getOntClass(oboe_core + "Observation");
|
| 278 |
8702
|
leinfelder
|
OntClass measurementClass = m.getOntClass(oboe_core + "Measurement");
|
| 279 |
|
|
OntClass characteristicClass = m.getOntClass(oboe_core + "Characteristic");
|
| 280 |
|
|
OntClass standardClass = m.getOntClass(oboe_core + "Standard");
|
| 281 |
|
|
|
| 282 |
|
|
Resource annotationClass = m.getOntClass(oa + "Annotation");
|
| 283 |
|
|
Resource specificResourceClass = m.getOntClass(oa + "SpecificResource");
|
| 284 |
8710
|
leinfelder
|
Resource fragmentSelectorClass = m.getOntClass(oa + "FragmentSelector");
|
| 285 |
8743
|
leinfelder
|
Resource provEntityClass = m.getResource(prov + "Entity");
|
| 286 |
8702
|
leinfelder
|
Resource personClass = m.getResource(prov + "Person");
|
| 287 |
8718
|
leinfelder
|
|
| 288 |
8702
|
leinfelder
|
// these apply to every attribute annotation
|
| 289 |
8743
|
leinfelder
|
Individual meta1 = m.createIndividual(ont.getURI() + "#meta", provEntityClass);
|
| 290 |
8702
|
leinfelder
|
meta1.addProperty(identifierProperty, metadataPid.getValue());
|
| 291 |
|
|
|
| 292 |
8718
|
leinfelder
|
// decide who should be credited with the package
|
| 293 |
|
|
Individual p1 = null;
|
| 294 |
8716
|
leinfelder
|
|
| 295 |
8718
|
leinfelder
|
// look up creators from the EML metadata
|
| 296 |
8788
|
leinfelder
|
List<Party> creators = dataPackage.getCreators();
|
| 297 |
8716
|
leinfelder
|
//creators = Arrays.asList("Matthew Jones");
|
| 298 |
8718
|
leinfelder
|
if (creators != null && creators.size() > 0) {
|
| 299 |
|
|
// use an orcid if we can find one from their system
|
| 300 |
8788
|
leinfelder
|
String orcidUri = OrcidService.lookupOrcid(creators.get(0).getOrganization(), creators.get(0).getSurName(), creators.get(0).getGivenNames(), null);
|
| 301 |
8718
|
leinfelder
|
if (orcidUri != null) {
|
| 302 |
|
|
p1 = m.createIndividual(orcidUri, personClass);
|
| 303 |
|
|
p1.addProperty(identifierProperty, orcidUri);
|
| 304 |
|
|
} else {
|
| 305 |
|
|
p1 = m.createIndividual(ont.getURI() + "#person", personClass);
|
| 306 |
|
|
}
|
| 307 |
|
|
// include the name we have in the metadata
|
| 308 |
8788
|
leinfelder
|
if (creators.get(0).getSurName() != null) {
|
| 309 |
|
|
p1.addProperty(nameProperty, creators.get(0).getSurName());
|
| 310 |
|
|
} else if (creators.get(0).getOrganization() != null) {
|
| 311 |
|
|
p1.addProperty(nameProperty, creators.get(0).getOrganization());
|
| 312 |
|
|
}
|
| 313 |
8716
|
leinfelder
|
}
|
| 314 |
|
|
|
| 315 |
8718
|
leinfelder
|
// attribute the package to this creator if we have one
|
| 316 |
|
|
if (p1 != null) {
|
| 317 |
|
|
meta1.addProperty(wasAttributedTo, p1);
|
| 318 |
|
|
}
|
| 319 |
|
|
|
| 320 |
8702
|
leinfelder
|
// loop through the tables and attributes
|
| 321 |
8714
|
leinfelder
|
int entityCount = 1;
|
| 322 |
8702
|
leinfelder
|
Entity[] entities = dataPackage.getEntityList();
|
| 323 |
8724
|
leinfelder
|
if (entities != null) {
|
| 324 |
|
|
for (Entity entity: entities) {
|
| 325 |
|
|
String entityName = entity.getName();
|
| 326 |
8743
|
leinfelder
|
|
| 327 |
|
|
Individual o1 = m.createIndividual(ont.getURI() + "#observation" + entityCount, observationClass);
|
| 328 |
|
|
Resource entityConcept = lookupEntity(entityClass, entity);
|
| 329 |
|
|
if (entityConcept != null) {
|
| 330 |
|
|
AllValuesFromRestriction avfr = m.createAllValuesFromRestriction(null, ofEntity, entityConcept);
|
| 331 |
|
|
o1.addOntClass(avfr);
|
| 332 |
|
|
}
|
| 333 |
|
|
|
| 334 |
8724
|
leinfelder
|
logMetacat.debug("Entity name: " + entityName);
|
| 335 |
|
|
Attribute[] attributes = entity.getAttributeList().getAttributes();
|
| 336 |
|
|
int attributeCount = 1;
|
| 337 |
|
|
if (attributes != null) {
|
| 338 |
|
|
for (Attribute attribute: attributes) {
|
| 339 |
|
|
|
| 340 |
|
|
// for naming the individuals uniquely
|
| 341 |
|
|
String cnt = entityCount + "_" + attributeCount;
|
| 342 |
|
|
|
| 343 |
|
|
String attributeName = attribute.getName();
|
| 344 |
|
|
String attributeLabel = attribute.getLabel();
|
| 345 |
|
|
String attributeDefinition = attribute.getDefinition();
|
| 346 |
|
|
String attributeType = attribute.getAttributeType();
|
| 347 |
|
|
String attributeScale = attribute.getMeasurementScale();
|
| 348 |
|
|
String attributeUnitType = attribute.getUnitType();
|
| 349 |
|
|
String attributeUnit = attribute.getUnit();
|
| 350 |
|
|
String attributeDomain = attribute.getDomain().getClass().getSimpleName();
|
| 351 |
|
|
|
| 352 |
|
|
logMetacat.debug("Attribute name: " + attributeName);
|
| 353 |
|
|
logMetacat.debug("Attribute label: " + attributeLabel);
|
| 354 |
|
|
logMetacat.debug("Attribute definition: " + attributeDefinition);
|
| 355 |
|
|
logMetacat.debug("Attribute type: " + attributeType);
|
| 356 |
|
|
logMetacat.debug("Attribute scale: " + attributeScale);
|
| 357 |
|
|
logMetacat.debug("Attribute unit type: " + attributeUnitType);
|
| 358 |
|
|
logMetacat.debug("Attribute unit: " + attributeUnit);
|
| 359 |
|
|
logMetacat.debug("Attribute domain: " + attributeDomain);
|
| 360 |
8702
|
leinfelder
|
|
| 361 |
8724
|
leinfelder
|
// look up the characteristic or standard subclasses
|
| 362 |
|
|
Resource standard = this.lookupStandard(standardClass, attribute);
|
| 363 |
|
|
Resource characteristic = this.lookupCharacteristic(characteristicClass, attribute);
|
| 364 |
|
|
|
| 365 |
|
|
if (standard != null || characteristic != null) {
|
| 366 |
|
|
|
| 367 |
|
|
// instances
|
| 368 |
|
|
Individual m1 = m.createIndividual(ont.getURI() + "#measurement" + cnt, measurementClass);
|
| 369 |
|
|
Individual a1 = m.createIndividual(ont.getURI() + "#annotation" + cnt, annotationClass);
|
| 370 |
|
|
Individual t1 = m.createIndividual(ont.getURI() + "#target" + cnt, specificResourceClass);
|
| 371 |
8910
|
leinfelder
|
String xpointer = "xpointer(/eml/dataSet/dataTable[" + entityCount + "]/attributeList/attribute[" + attributeCount + "])";
|
| 372 |
8724
|
leinfelder
|
Individual s1 = m.createIndividual(ont.getURI() + "#" + xpointer, fragmentSelectorClass);
|
| 373 |
|
|
s1.addLiteral(rdfValue, xpointer);
|
| 374 |
8910
|
leinfelder
|
s1.addProperty(conformsToProperty, "http://tools.ietf.org/rfc/rfc3023");
|
| 375 |
|
|
//s1.addProperty(conformsToProperty, "http://www.w3.org/TR/xptr/");
|
| 376 |
|
|
|
| 377 |
8724
|
leinfelder
|
|
| 378 |
|
|
// statements about the annotation
|
| 379 |
|
|
a1.addProperty(hasBodyProperty, m1);
|
| 380 |
|
|
a1.addProperty(hasTargetProperty, t1);
|
| 381 |
|
|
t1.addProperty(hasSourceProperty, meta1);
|
| 382 |
|
|
t1.addProperty(hasSelectorProperty, s1);
|
| 383 |
|
|
//a1.addProperty(annotatedByProperty, p1);
|
| 384 |
|
|
|
| 385 |
|
|
// describe the measurement in terms of restrictions
|
| 386 |
|
|
if (standard != null) {
|
| 387 |
|
|
AllValuesFromRestriction avfr = m.createAllValuesFromRestriction(null, usesStandard, standard);
|
| 388 |
|
|
m1.addOntClass(avfr);
|
| 389 |
|
|
}
|
| 390 |
|
|
if (characteristic != null) {
|
| 391 |
|
|
AllValuesFromRestriction avfr = m.createAllValuesFromRestriction(null, ofCharacteristic, characteristic);
|
| 392 |
|
|
m1.addOntClass(avfr);
|
| 393 |
|
|
}
|
| 394 |
8743
|
leinfelder
|
|
| 395 |
|
|
// attach to the observation
|
| 396 |
|
|
// TODO: evaluate whether the measurement can apply to the given observed entity
|
| 397 |
|
|
o1.addProperty(hasMeasurement, m1);
|
| 398 |
8724
|
leinfelder
|
}
|
| 399 |
|
|
attributeCount++;
|
| 400 |
|
|
|
| 401 |
8702
|
leinfelder
|
}
|
| 402 |
|
|
}
|
| 403 |
8724
|
leinfelder
|
entityCount++;
|
| 404 |
8714
|
leinfelder
|
}
|
| 405 |
8702
|
leinfelder
|
}
|
| 406 |
|
|
|
| 407 |
|
|
StringWriter sw = new StringWriter();
|
| 408 |
|
|
// only write the base model
|
| 409 |
|
|
//m.write(sw, "RDF/XML-ABBREV");
|
| 410 |
|
|
m.write(sw, null);
|
| 411 |
|
|
|
| 412 |
|
|
return sw.toString();
|
| 413 |
|
|
|
| 414 |
|
|
}
|
| 415 |
|
|
|
| 416 |
|
|
private Resource lookupStandard(OntClass standardClass, Attribute attribute) {
|
| 417 |
|
|
// what's our unit?
|
| 418 |
|
|
String unit = attribute.getUnit().toLowerCase();
|
| 419 |
8763
|
leinfelder
|
|
| 420 |
|
|
/*
|
| 421 |
|
|
boolean found = false;
|
| 422 |
8710
|
leinfelder
|
List<String> tokens = Arrays.asList(unit.split(" "));
|
| 423 |
8702
|
leinfelder
|
ExtendedIterator iter = standardClass.listSubClasses(false);
|
| 424 |
|
|
while (iter.hasNext()) {
|
| 425 |
|
|
OntClass subclass = (OntClass) iter.next();
|
| 426 |
|
|
String subclassName = subclass.getLocalName().toLowerCase();
|
| 427 |
|
|
logMetacat.debug("subclass: " + subclassName);
|
| 428 |
8710
|
leinfelder
|
if (tokens.contains(subclassName)) {
|
| 429 |
8702
|
leinfelder
|
found = true;
|
| 430 |
|
|
}
|
| 431 |
|
|
if (subclass.hasLabel(unit, null)) {
|
| 432 |
|
|
found = true;
|
| 433 |
|
|
}
|
| 434 |
|
|
if (found) {
|
| 435 |
|
|
return subclass;
|
| 436 |
|
|
}
|
| 437 |
|
|
}
|
| 438 |
8763
|
leinfelder
|
*/
|
| 439 |
|
|
|
| 440 |
8711
|
leinfelder
|
// try to look it up if we got this far
|
| 441 |
8717
|
leinfelder
|
return BioPortalService.lookupAnnotationClass(standardClass, unit, OBOE_SBC);
|
| 442 |
8702
|
leinfelder
|
}
|
| 443 |
|
|
|
| 444 |
|
|
private Resource lookupCharacteristic(OntClass characteristicClass, Attribute attribute) {
|
| 445 |
8763
|
leinfelder
|
// what are we looking for?
|
| 446 |
8702
|
leinfelder
|
String label = attribute.getLabel().toLowerCase();
|
| 447 |
8763
|
leinfelder
|
String definition = attribute.getDefinition();
|
| 448 |
|
|
String text = label + " " + definition;
|
| 449 |
8710
|
leinfelder
|
|
| 450 |
8763
|
leinfelder
|
/*
|
| 451 |
|
|
// find something that matches
|
| 452 |
8702
|
leinfelder
|
boolean found = false;
|
| 453 |
8763
|
leinfelder
|
List<String> tokens = Arrays.asList(label.split(" "));
|
| 454 |
8702
|
leinfelder
|
ExtendedIterator iter = characteristicClass.listSubClasses();
|
| 455 |
|
|
while (iter.hasNext()) {
|
| 456 |
|
|
OntClass subclass = (OntClass) iter.next();
|
| 457 |
|
|
String subclassName = subclass.getLocalName().toLowerCase();
|
| 458 |
|
|
logMetacat.debug("subclass: " + subclassName);
|
| 459 |
8710
|
leinfelder
|
if (tokens.contains(subclassName)) {
|
| 460 |
8702
|
leinfelder
|
found = true;
|
| 461 |
|
|
}
|
| 462 |
|
|
if (subclass.hasLabel(label, null)) {
|
| 463 |
|
|
found = true;
|
| 464 |
|
|
}
|
| 465 |
|
|
if (found) {
|
| 466 |
|
|
return subclass;
|
| 467 |
|
|
}
|
| 468 |
|
|
}
|
| 469 |
8763
|
leinfelder
|
*/
|
| 470 |
8711
|
leinfelder
|
|
| 471 |
8763
|
leinfelder
|
// try to look it up from the service
|
| 472 |
|
|
return BioPortalService.lookupAnnotationClass(characteristicClass, text, OBOE_SBC);
|
| 473 |
8711
|
leinfelder
|
|
| 474 |
|
|
}
|
| 475 |
|
|
|
| 476 |
8743
|
leinfelder
|
private Resource lookupEntity(OntClass entityClass, Entity entity) {
|
| 477 |
|
|
// what's our description like?
|
| 478 |
|
|
String name = entity.getName();
|
| 479 |
|
|
String definition = entity.getDefinition();
|
| 480 |
|
|
|
| 481 |
|
|
// try to look it up if we got this far
|
| 482 |
|
|
return BioPortalService.lookupAnnotationClass(entityClass, definition, OBOE_SBC);
|
| 483 |
|
|
|
| 484 |
|
|
}
|
| 485 |
|
|
|
| 486 |
8702
|
leinfelder
|
private DataPackage getDataPackage(Identifier pid) throws Exception {
|
| 487 |
|
|
// for using the MN API as the MN itself
|
| 488 |
|
|
MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);
|
| 489 |
|
|
Session session = new Session();
|
| 490 |
|
|
Subject subject = MNodeService.getInstance(request).getCapabilities().getSubject(0);
|
| 491 |
|
|
session.setSubject(subject);
|
| 492 |
|
|
InputStream emlStream = MNodeService.getInstance(request).get(session, pid);
|
| 493 |
|
|
|
| 494 |
|
|
// parse the metadata
|
| 495 |
|
|
DataPackageParserInterface parser = new Eml200DataPackageParser();
|
| 496 |
|
|
parser.parse(emlStream);
|
| 497 |
|
|
DataPackage dataPackage = parser.getDataPackage();
|
| 498 |
|
|
return dataPackage;
|
| 499 |
|
|
}
|
| 500 |
|
|
|
| 501 |
|
|
private void summarize(List<Identifier> identifiers) throws SQLException {
|
| 502 |
|
|
|
| 503 |
8646
|
leinfelder
|
DBConnection dbconn = null;
|
| 504 |
9463
|
tao
|
int serialNumber = -1;
|
| 505 |
|
|
PreparedStatement dropStatement = null;
|
| 506 |
|
|
PreparedStatement createStatement = null;
|
| 507 |
|
|
PreparedStatement insertStatement = null;
|
| 508 |
8646
|
leinfelder
|
try {
|
| 509 |
|
|
dbconn = DBConnectionPool.getDBConnection("DatapackageSummarizer.summarize");
|
| 510 |
9463
|
tao
|
serialNumber = dbconn.getCheckOutSerialNumber();
|
| 511 |
|
|
dropStatement = dbconn.prepareStatement("DROP TABLE IF EXISTS entity_summary");
|
| 512 |
8646
|
leinfelder
|
dropStatement.execute();
|
| 513 |
|
|
|
| 514 |
9463
|
tao
|
createStatement = dbconn.prepareStatement(
|
| 515 |
8646
|
leinfelder
|
"CREATE TABLE entity_summary (" +
|
| 516 |
|
|
"guid text, " +
|
| 517 |
|
|
"title text, " +
|
| 518 |
|
|
"entity text," +
|
| 519 |
|
|
"attributeName text," +
|
| 520 |
|
|
"attributeLabel text," +
|
| 521 |
|
|
"attributeDefinition text," +
|
| 522 |
|
|
"attributeType text," +
|
| 523 |
|
|
"attributeScale text," +
|
| 524 |
|
|
"attributeUnitType text," +
|
| 525 |
|
|
"attributeUnit text," +
|
| 526 |
|
|
"attributeDomain text" +
|
| 527 |
|
|
")");
|
| 528 |
|
|
createStatement.execute();
|
| 529 |
|
|
|
| 530 |
9463
|
tao
|
insertStatement = dbconn.prepareStatement(
|
| 531 |
8646
|
leinfelder
|
"INSERT INTO entity_summary " +
|
| 532 |
|
|
"VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)");
|
| 533 |
|
|
|
| 534 |
|
|
for (Identifier pid: identifiers) {
|
| 535 |
|
|
|
| 536 |
|
|
logMetacat.debug("Parsing pid: " + pid.getValue());
|
| 537 |
|
|
|
| 538 |
|
|
try {
|
| 539 |
|
|
|
| 540 |
8702
|
leinfelder
|
// get the package
|
| 541 |
|
|
DataPackage dataPackage = this.getDataPackage(pid);
|
| 542 |
8646
|
leinfelder
|
String title = dataPackage.getTitle();
|
| 543 |
|
|
logMetacat.debug("Title: " + title);
|
| 544 |
|
|
|
| 545 |
|
|
Entity[] entities = dataPackage.getEntityList();
|
| 546 |
|
|
if (entities != null) {
|
| 547 |
|
|
for (Entity entity: entities) {
|
| 548 |
|
|
String entityName = entity.getName();
|
| 549 |
|
|
logMetacat.debug("Entity name: " + entityName);
|
| 550 |
|
|
Attribute[] attributes = entity.getAttributeList().getAttributes();
|
| 551 |
|
|
for (Attribute attribute: attributes) {
|
| 552 |
|
|
String attributeName = attribute.getName();
|
| 553 |
|
|
String attributeLabel = attribute.getLabel();
|
| 554 |
|
|
String attributeDefinition = attribute.getDefinition();
|
| 555 |
|
|
String attributeType = attribute.getAttributeType();
|
| 556 |
|
|
String attributeScale = attribute.getMeasurementScale();
|
| 557 |
|
|
String attributeUnitType = attribute.getUnitType();
|
| 558 |
|
|
String attributeUnit = attribute.getUnit();
|
| 559 |
|
|
String attributeDomain = attribute.getDomain().getClass().getSimpleName();
|
| 560 |
|
|
|
| 561 |
|
|
logMetacat.debug("Attribute name: " + attributeName);
|
| 562 |
|
|
logMetacat.debug("Attribute label: " + attributeLabel);
|
| 563 |
|
|
logMetacat.debug("Attribute definition: " + attributeDefinition);
|
| 564 |
|
|
logMetacat.debug("Attribute type: " + attributeType);
|
| 565 |
|
|
logMetacat.debug("Attribute scale: " + attributeScale);
|
| 566 |
|
|
logMetacat.debug("Attribute unit type: " + attributeUnitType);
|
| 567 |
|
|
logMetacat.debug("Attribute unit: " + attributeUnit);
|
| 568 |
|
|
logMetacat.debug("Attribute domain: " + attributeDomain);
|
| 569 |
|
|
|
| 570 |
|
|
// set the values for this attribute
|
| 571 |
|
|
insertStatement.setString(1, pid.getValue());
|
| 572 |
|
|
insertStatement.setString(2, title);
|
| 573 |
|
|
insertStatement.setString(3, entityName);
|
| 574 |
|
|
insertStatement.setString(4, attributeName);
|
| 575 |
|
|
insertStatement.setString(5, attributeLabel);
|
| 576 |
|
|
insertStatement.setString(6, attributeDefinition);
|
| 577 |
|
|
insertStatement.setString(7, attributeType);
|
| 578 |
|
|
insertStatement.setString(8, attributeScale);
|
| 579 |
|
|
insertStatement.setString(9, attributeUnitType);
|
| 580 |
|
|
insertStatement.setString(10, attributeUnit);
|
| 581 |
|
|
insertStatement.setString(11, attributeDomain);
|
| 582 |
|
|
insertStatement.execute();
|
| 583 |
|
|
|
| 584 |
|
|
}
|
| 585 |
|
|
}
|
| 586 |
|
|
}
|
| 587 |
|
|
|
| 588 |
|
|
} catch (Exception e) {
|
| 589 |
|
|
logMetacat.warn("error parsing metadata for: " + pid.getValue(), e);
|
| 590 |
|
|
}
|
| 591 |
|
|
}
|
| 592 |
|
|
} catch (SQLException sqle) {
|
| 593 |
|
|
// just throw it
|
| 594 |
|
|
throw sqle;
|
| 595 |
|
|
} finally {
|
| 596 |
9463
|
tao
|
try {
|
| 597 |
|
|
if(dropStatement != null) {
|
| 598 |
|
|
dropStatement.close();
|
| 599 |
|
|
}
|
| 600 |
|
|
if(createStatement != null) {
|
| 601 |
|
|
createStatement.close();
|
| 602 |
|
|
}
|
| 603 |
|
|
if(insertStatement != null) {
|
| 604 |
|
|
insertStatement.close();
|
| 605 |
|
|
}
|
| 606 |
|
|
} catch (Exception e) {
|
| 607 |
|
|
logMetacat.warn("couldn't close the prepared statement "+e.getMessage());
|
| 608 |
|
|
} finally {
|
| 609 |
|
|
if (dbconn != null) {
|
| 610 |
|
|
DBConnectionPool.returnDBConnection(dbconn, serialNumber);
|
| 611 |
|
|
//dbconn.close();
|
| 612 |
|
|
}
|
| 613 |
|
|
}
|
| 614 |
|
|
|
| 615 |
8646
|
leinfelder
|
}
|
| 616 |
|
|
}
|
| 617 |
|
|
|
| 618 |
|
|
public static void main(String[] args) throws Exception {
|
| 619 |
|
|
// set up the properties based on the test/deployed configuration of the workspace
|
| 620 |
8702
|
leinfelder
|
SortedProperties testProperties = new SortedProperties("test/test.properties");
|
| 621 |
|
|
testProperties.load();
|
| 622 |
|
|
String metacatContextDir = testProperties.getProperty("metacat.contextDir");
|
| 623 |
|
|
PropertyService.getInstance(metacatContextDir + "/WEB-INF");
|
| 624 |
|
|
|
| 625 |
|
|
testGenerate();
|
| 626 |
|
|
// testSummary();
|
| 627 |
|
|
System.exit(0);
|
| 628 |
|
|
}
|
| 629 |
|
|
|
| 630 |
|
|
public static void testGenerate() throws Exception {
|
| 631 |
|
|
Identifier metadataPid = new Identifier();
|
| 632 |
8743
|
leinfelder
|
metadataPid.setValue("tao.1.4");
|
| 633 |
8702
|
leinfelder
|
DatapackageSummarizer ds = new DatapackageSummarizer();
|
| 634 |
|
|
String rdfString = ds.generateAnnotation(metadataPid);
|
| 635 |
|
|
logMetacat.info("RDF annotation: \n" + rdfString);
|
| 636 |
8646
|
leinfelder
|
|
| 637 |
8702
|
leinfelder
|
}
|
| 638 |
|
|
|
| 639 |
|
|
public static void testSummary() throws Exception {
|
| 640 |
|
|
|
| 641 |
8646
|
leinfelder
|
// summarize the packages
|
| 642 |
|
|
DatapackageSummarizer ds = new DatapackageSummarizer();
|
| 643 |
|
|
List<Identifier> identifiers = new ArrayList<Identifier>();
|
| 644 |
8689
|
leinfelder
|
Map<Integer, String> serverCodes = ReplicationService.getServerCodes();
|
| 645 |
|
|
|
| 646 |
|
|
// select the metadata ids we want to summarize
|
| 647 |
|
|
boolean includeReplicas = true;
|
| 648 |
|
|
Iterator<Integer> codeIter = Arrays.asList(new Integer[] {1}).iterator();
|
| 649 |
|
|
if (includeReplicas ) {
|
| 650 |
|
|
codeIter = serverCodes.keySet().iterator();
|
| 651 |
|
|
}
|
| 652 |
8646
|
leinfelder
|
|
| 653 |
8689
|
leinfelder
|
Vector<String> idList = new Vector<String>();
|
| 654 |
|
|
while (codeIter.hasNext()) {
|
| 655 |
|
|
int serverLocation = codeIter.next();
|
| 656 |
|
|
Vector<String> idList0 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_0_0NAMESPACE, false, serverLocation);
|
| 657 |
|
|
Vector<String> idList1 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_0_1NAMESPACE, false, serverLocation);
|
| 658 |
|
|
Vector<String> idList2 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_1_0NAMESPACE, false, serverLocation);
|
| 659 |
|
|
Vector<String> idList3 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_1_1NAMESPACE, false, serverLocation);
|
| 660 |
|
|
|
| 661 |
|
|
idList.addAll(idList0);
|
| 662 |
|
|
idList.addAll(idList1);
|
| 663 |
|
|
idList.addAll(idList2);
|
| 664 |
|
|
idList.addAll(idList3);
|
| 665 |
8646
|
leinfelder
|
|
| 666 |
8689
|
leinfelder
|
}
|
| 667 |
|
|
|
| 668 |
|
|
// go through all the identifiers now
|
| 669 |
8646
|
leinfelder
|
for (String localId : idList) {
|
| 670 |
|
|
try {
|
| 671 |
|
|
String guid = IdentifierManager.getInstance().getGUID(
|
| 672 |
|
|
DocumentUtil.getDocIdFromAccessionNumber(localId),
|
| 673 |
|
|
DocumentUtil.getRevisionFromAccessionNumber(localId));
|
| 674 |
|
|
Identifier pid = new Identifier();
|
| 675 |
|
|
pid.setValue(guid);
|
| 676 |
|
|
identifiers.add(pid);
|
| 677 |
|
|
} catch (McdbDocNotFoundException nfe) {
|
| 678 |
|
|
// just skip it
|
| 679 |
|
|
continue;
|
| 680 |
|
|
}
|
| 681 |
|
|
}
|
| 682 |
|
|
ds.summarize(identifiers);
|
| 683 |
|
|
System.exit(0);
|
| 684 |
|
|
}
|
| 685 |
|
|
|
| 686 |
|
|
}
|