[VIVO-1031] Convert Co-Investigator graph to RDFService
This commit is contained in:
grahamtriggs
parent
d5b3058f44
commit
2519914833
4 changed files with 65 additions and 197 deletions
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@ -1,9 +1,13 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator;
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import java.io.InputStream;
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import java.util.HashSet;
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import java.util.Set;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
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import org.apache.commons.lang.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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@ -30,7 +34,7 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
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private String egoURI;
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private Dataset dataset;
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private RDFService rdfService;
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private long before, after;
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@ -42,10 +46,9 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
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+ "?Grant rdf:type core:Grant ."
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+ "?Grant core:relates ?RelatedRole . ";
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public CoPIGrantCountConstructQueryRunner(String egoURI, Dataset dataset,
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Log log) {
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public CoPIGrantCountConstructQueryRunner(String egoURI, RDFService rdfService, Log log) {
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this.egoURI = egoURI;
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this.dataset = dataset;
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this.rdfService = rdfService;
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// this.log = log;
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}
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@ -220,38 +223,29 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
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return sparqlQuery;
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}
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private Model executeQuery(Set<String> constructQueries, Dataset dataset) {
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private Model executeQuery(Set<String> constructQueries, RDFService rdfService) {
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Model constructedModel = ModelFactory.createDefaultModel();
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for (String queryString : constructQueries) {
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before = System.currentTimeMillis();
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log.debug("CONSTRUCT query string : " + queryString);
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Query query = null;
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InputStream is = null;
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try {
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query = QueryFactory.create(
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QueryConstants.getSparqlPrefixQuery() + queryString,
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SYNTAX);
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} catch (Throwable th) {
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log.error("Could not create CONSTRUCT SPARQL query for query "
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+ "string. " + th.getMessage());
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log.error(queryString);
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}
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QueryExecution qe = QueryExecutionFactory.create(query, dataset);
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try {
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qe.execConstruct(constructedModel);
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is = rdfService.sparqlConstructQuery(QueryConstants.getSparqlPrefixQuery() + queryString, RDFService.ModelSerializationFormat.N3);
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constructedModel.read(is, null, RDFServiceUtils.getSerializationFormatString(RDFService.ModelSerializationFormat.N3));
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} catch (RDFServiceException e) {
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log.error("Unable to execute query", e);
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throw new RuntimeException(e);
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} finally {
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qe.close();
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if (is != null) {
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try { is.close(); } catch (Throwable t) { }
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}
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}
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after = System.currentTimeMillis();
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log.debug("Time taken to execute the CONSTRUCT query is in milliseconds: "
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+ (after - before));
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log.debug("Time taken to execute the CONSTRUCT query is in milliseconds: " + (after - before));
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}
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@ -282,7 +276,7 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
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populateConstructQueries(constructQueries);
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Model model = executeQuery(constructQueries, this.dataset);
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Model model = executeQuery(constructQueries, this.rdfService);
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return model;
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@ -2,6 +2,7 @@
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package edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator;
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import java.io.InputStream;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Date;
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@ -12,6 +13,9 @@ import java.util.Map;
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import java.util.Set;
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import java.util.concurrent.ConcurrentHashMap;
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import com.hp.hpl.jena.query.ResultSetFactory;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
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import org.apache.commons.lang.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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@ -52,7 +56,7 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
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private String egoURI;
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private Model dataSource;
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private RDFService rdfService;
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private Log log = LogFactory.getLog(CoPIGrantCountQueryRunner.class.getName());
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@ -86,10 +90,10 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
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public CoPIGrantCountQueryRunner(String egoURI,
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Model dataSource, Log log) {
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RDFService rdfService, Log log) {
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this.egoURI = egoURI;
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this.dataSource = dataSource;
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this.rdfService = rdfService;
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// this.log = log;
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this.nodeIDGenerator = new UniqueIDGenerator();
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@ -114,276 +118,134 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
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+ "{ "
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+ "<" + queryURI + "> rdfs:label ?PILabel . "
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+ "{ "
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+ "<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
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+ "?Role rdf:type core:CoPrincipalInvestigatorRole . "
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+ "?Role core:relatedBy ?Grant . "
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+ "?Grant rdf:type core:Grant . "
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+ "?Grant core:relates ?RelatedRole . "
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+ "?RelatedRole rdf:type core:PrincipalInvestigatorRole . "
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+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . "
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+ "?CoPI rdf:type foaf:Person . "
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+ "?CoPI rdfs:label ?CoPILabel . "
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
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+ "} "
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+ "UNION "
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+ "{ "
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+ "<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
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+ "?Role rdf:type core:CoPrincipalInvestigatorRole . "
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+ "?Role core:relatedBy ?Grant . "
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+ "?Grant rdf:type core:Grant . "
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+ "?Grant core:relates ?RelatedRole . "
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+ "?RelatedRole rdf:type core:InvestigatorRole . "
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+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . "
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+ "?CoPI rdf:type foaf:Person . "
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+ "?CoPI rdfs:label ?CoPILabel . "
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
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+ "} "
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+ "UNION "
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+ "{ "
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+ "<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
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+ "?Role rdf:type core:CoPrincipalInvestigatorRole . "
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+ "?Role core:relatedBy ?Grant . "
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+ "?Grant rdf:type core:Grant . "
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+ "?Grant core:relates ?RelatedRole . "
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+ "?RelatedRole rdf:type core:CoPrincipalInvestigatorRole . "
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+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . "
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+ "?CoPI rdf:type foaf:Person . "
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+ "?CoPI rdfs:label ?CoPILabel . "
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
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+ "} "
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+ "UNION "
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+ "{ "
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+ "<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
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+ "?Role rdf:type core:PrincipalInvestigatorRole . "
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+ "?Role core:relatedBy ?Grant . "
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+ "?Grant rdf:type core:Grant . "
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+ "?Grant core:relates ?RelatedRole . "
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+ "?RelatedRole rdf:type core:PrincipalInvestigatorRole . "
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+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . "
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+ "?CoPI rdf:type foaf:Person . "
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+ "?CoPI rdfs:label ?CoPILabel . "
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
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+ "} "
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+ "UNION "
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+ "{ "
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+ "<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
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+ "?Role rdf:type core:PrincipalInvestigatorRole . "
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+ "?Role core:relatedBy ?Grant . "
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+ "?Grant rdf:type core:Grant . "
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+ "?Grant core:relates ?RelatedRole . "
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+ "?RelatedRole rdf:type core:InvestigatorRole . "
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+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . "
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+ "?CoPI rdf:type foaf:Person . "
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+ "?CoPI rdfs:label ?CoPILabel . "
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
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+ "} "
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+ "UNION "
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+ "{ "
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+ "<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
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+ "?Role rdf:type core:PrincipalInvestigatorRole . "
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+ "?Role core:relatedBy ?Grant . "
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+ "?Grant rdf:type core:Grant . "
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+ "?Grant core:relates ?RelatedRole . "
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+ "?RelatedRole rdf:type core:CoPrincipalInvestigatorRole . "
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+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . "
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+ "?CoPI rdf:type foaf:Person . "
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+ "?CoPI rdfs:label ?CoPILabel . "
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
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+ "} "
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+ "UNION "
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+ "{ "
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+ "<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
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+ "?Role rdf:type core:InvestigatorRole . "
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+ "?Role core:relatedBy ?Grant . "
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+ "?Grant rdf:type core:Grant . "
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+ "?Grant core:relates ?RelatedRole . "
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+ "?RelatedRole rdf:type core:InvestigatorRole . "
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+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . "
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+ "?CoPI rdf:type foaf:Person . "
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+ "?CoPI rdfs:label ?CoPILabel . "
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
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+ "} "
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+ "UNION "
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+ "{ "
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+ "<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
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+ "?Role rdf:type core:InvestigatorRole . "
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+ "?Role core:relatedBy ?Grant . "
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+ "?Grant rdf:type core:Grant . "
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+ "?Grant core:relates ?RelatedRole . "
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+ "?RelatedRole rdf:type core:CoPrincipalInvestigatorRole . "
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+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . "
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+ "?CoPI rdf:type foaf:Person . "
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+ "?CoPI rdfs:label ?CoPILabel . "
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
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+ "} "
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+ "UNION "
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+ "{ "
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+ "<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
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+ "?Role rdf:type core:InvestigatorRole . "
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+ "?Role core:relatedBy ?Grant . "
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+ "?Grant rdf:type core:Grant . "
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+ "?Grant core:relates ?RelatedRole . "
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+ "?RelatedRole rdf:type core:PrincipalInvestigatorRole . "
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+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . "
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+ "?CoPI rdf:type foaf:Person . "
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+ "?CoPI rdfs:label ?CoPILabel . "
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
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+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
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+ "} "
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+ "} ";
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return sparqlQuery;
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}
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private ResultSet executeQuery(String queryText, Model dataSource) {
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QueryExecution queryExecution = null;
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Query query = QueryFactory.create(queryText, SYNTAX);
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queryExecution = QueryExecutionFactory.create(query, dataSource);
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return queryExecution.execSelect();
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}
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public CollaborationData getQueryResult()
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throws MalformedQueryParametersException {
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@ -431,13 +293,25 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
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}
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before = System.currentTimeMillis();
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ResultSet resultSet = executeQuery(generateEgoCoPIquery(this.egoURI), this.dataSource);
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InputStream is = null;
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ResultSet rs = null;
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try {
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is = rdfService.sparqlSelectQuery(generateEgoCoPIquery(this.egoURI), RDFService.ResultFormat.JSON);
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rs = ResultSetFactory.fromJSON(is);
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data = createQueryResult(rs);
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} catch (RDFServiceException e) {
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log.error("Unable to execute query", e);
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throw new RuntimeException(e);
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} finally {
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if (is != null) {
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try { is.close(); } catch (Throwable t) { }
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}
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}
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after = System.currentTimeMillis();
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log.debug("Time taken to execute the SELECT queries is in milliseconds: " + (after - before));
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data = createQueryResult(resultSet);
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CollaborationDataCacheEntry newEntry = new CollaborationDataCacheEntry();
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newEntry.uri = this.egoURI;
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@ -54,11 +54,11 @@ public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler
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String visMode = vitroRequest.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY);
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ModelConstructor constructQueryRunner =
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new CoPIGrantCountConstructQueryRunner(egoURI, dataset, log);
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new CoPIGrantCountConstructQueryRunner(egoURI, vitroRequest.getRDFService(), log);
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Model constructedModel = constructQueryRunner.getConstructedModel();
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QueryRunner<CollaborationData> queryManager =
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new CoPIGrantCountQueryRunner(egoURI, constructedModel, log);
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new CoPIGrantCountQueryRunner(egoURI, vitroRequest.getRDFService(), log);
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CollaborationData investigatorNodesAndEdges = queryManager.getQueryResult();
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@ -104,11 +104,11 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
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ModelConstructor constructQueryRunner =
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new CoPIGrantCountConstructQueryRunner(egoURI, dataset, log);
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new CoPIGrantCountConstructQueryRunner(egoURI, vitroRequest.getRDFService(), log);
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Model constructedModel = constructQueryRunner.getConstructedModel();
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QueryRunner<CollaborationData> coPIQueryManager =
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new CoPIGrantCountQueryRunner(egoURI, constructedModel, log);
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new CoPIGrantCountQueryRunner(egoURI, vitroRequest.getRDFService(), log);
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CollaborationData coPIData = coPIQueryManager.getQueryResult();
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