[VIVO-1031] Use streaming result set for co- visualisations
This commit is contained in:
grahamtriggs
parent
208f103629
commit
8fc40fcf98
2 changed files with 457 additions and 485 deletions
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@ -16,6 +16,8 @@ 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 edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
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import net.sf.jga.algorithms.Unique;
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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.jena.iri.IRI;
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@ -23,7 +25,6 @@ import org.apache.jena.iri.IRIFactory;
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import org.apache.jena.iri.Violation;
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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.query.Syntax;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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@ -58,10 +59,6 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
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private Log log;
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private UniqueIDGenerator nodeIDGenerator;
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private UniqueIDGenerator edgeIDGenerator;
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public CoAuthorshipQueryRunner(String egoURI,
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RDFService rdfService, Log log) {
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@ -69,18 +66,13 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
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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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this.edgeIDGenerator = new UniqueIDGenerator();
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}
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private CollaborationData createQueryResult(ResultSet resultSet) {
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private static class QueryResultConsumer extends ResultSetConsumer {
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Set<Collaborator> nodes = new HashSet<Collaborator>();
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Map<String, Activity> biboDocumentURLToVO = new HashMap<String, Activity>();
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Map<String, Set<Collaborator>> biboDocumentURLToCoAuthors =
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new HashMap<String, Set<Collaborator>>();
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Map<String, Set<Collaborator>> biboDocumentURLToCoAuthors = new HashMap<String, Set<Collaborator>>();
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Map<String, Collaborator> nodeURLToVO = new HashMap<String, Collaborator>();
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Map<String, Collaboration> edgeUniqueIdentifierToVO = new HashMap<String, Collaboration>();
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@ -88,13 +80,15 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
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Set<Collaboration> edges = new HashSet<Collaboration>();
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while (resultSet.hasNext()) {
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QuerySolution solution = resultSet.nextSolution();
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private UniqueIDGenerator nodeIDGenerator = new UniqueIDGenerator();
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private UniqueIDGenerator edgeIDGenerator = new UniqueIDGenerator();
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@Override
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protected void processQuerySolution(QuerySolution qs) {
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/*
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* We only want to create only ONE ego node.
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* */
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RDFNode egoAuthorURLNode = solution.get(QueryFieldLabels.AUTHOR_URL);
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RDFNode egoAuthorURLNode = qs.get(QueryFieldLabels.AUTHOR_URL);
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if (nodeURLToVO.containsKey(egoAuthorURLNode.toString())) {
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egoNode = nodeURLToVO.get(egoAuthorURLNode.toString());
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@ -105,19 +99,19 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
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nodes.add(egoNode);
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nodeURLToVO.put(egoAuthorURLNode.toString(), egoNode);
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RDFNode authorLabelNode = solution.get(QueryFieldLabels.AUTHOR_LABEL);
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RDFNode authorLabelNode = qs.get(QueryFieldLabels.AUTHOR_LABEL);
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if (authorLabelNode != null) {
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egoNode.setCollaboratorName(authorLabelNode.toString());
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}
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}
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RDFNode documentNode = solution.get(QueryFieldLabels.DOCUMENT_URL);
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RDFNode documentNode = qs.get(QueryFieldLabels.DOCUMENT_URL);
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Activity biboDocument;
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if (biboDocumentURLToVO.containsKey(documentNode.toString())) {
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biboDocument = biboDocumentURLToVO.get(documentNode.toString());
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} else {
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biboDocument = createDocumentVO(solution, documentNode.toString());
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biboDocument = createDocumentVO(qs, documentNode.toString());
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biboDocumentURLToVO.put(documentNode.toString(), biboDocument);
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}
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@ -128,14 +122,14 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
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* we do not want a co-author node or Collaboration if the publication has only one
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* author and that happens to be the ego.
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* */
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if (solution.get(QueryFieldLabels.AUTHOR_URL).toString().equalsIgnoreCase(
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solution.get(QueryFieldLabels.CO_AUTHOR_URL).toString())) {
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continue;
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if (qs.get(QueryFieldLabels.AUTHOR_URL).toString().equalsIgnoreCase(
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qs.get(QueryFieldLabels.CO_AUTHOR_URL).toString())) {
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return;
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}
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Collaborator coAuthorNode;
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RDFNode coAuthorURLNode = solution.get(QueryFieldLabels.CO_AUTHOR_URL);
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RDFNode coAuthorURLNode = qs.get(QueryFieldLabels.CO_AUTHOR_URL);
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if (nodeURLToVO.containsKey(coAuthorURLNode.toString())) {
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coAuthorNode = nodeURLToVO.get(coAuthorURLNode.toString());
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@ -146,7 +140,7 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
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nodes.add(coAuthorNode);
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nodeURLToVO.put(coAuthorURLNode.toString(), coAuthorNode);
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RDFNode coAuthorLabelNode = solution.get(QueryFieldLabels.CO_AUTHOR_LABEL);
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RDFNode coAuthorLabelNode = qs.get(QueryFieldLabels.CO_AUTHOR_LABEL);
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if (coAuthorLabelNode != null) {
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coAuthorNode.setCollaboratorName(coAuthorLabelNode.toString());
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}
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@ -158,11 +152,11 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
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if (biboDocumentURLToCoAuthors.containsKey(biboDocument.getActivityURI())) {
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coAuthorsForCurrentBiboDocument = biboDocumentURLToCoAuthors
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.get(biboDocument.getActivityURI());
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.get(biboDocument.getActivityURI());
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} else {
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coAuthorsForCurrentBiboDocument = new HashSet<Collaborator>();
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biboDocumentURLToCoAuthors.put(biboDocument.getActivityURI(),
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coAuthorsForCurrentBiboDocument);
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coAuthorsForCurrentBiboDocument);
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}
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coAuthorsForCurrentBiboDocument.add(coAuthorNode);
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@ -183,70 +177,173 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
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edges.add(egoCoAuthorEdge);
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edgeUniqueIdentifierToVO.put(
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getEdgeUniqueIdentifier(egoNode.getCollaboratorID(),
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coAuthorNode.getCollaboratorID()),
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coAuthorNode.getCollaboratorID()),
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egoCoAuthorEdge);
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}
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}
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@Override
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protected void endProcessing() {
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/*
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* This method takes out all the authors & edges between authors that belong to documents
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* that have more than 100 authors. We conjecture that these papers do not provide much
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* insight. However, we have left the documents be.
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*
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* This method side-effects "nodes" & "edges".
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* */
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removeLowQualityNodesAndEdges(nodes,
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biboDocumentURLToVO,
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biboDocumentURLToCoAuthors,
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edges);
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/*
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* We need to create edges between 2 co-authors. E.g. On a paper there were 3 authors
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* ego, A & B then we have already created edges like,
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* ego - A
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* ego - B
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* The below sub-routine will take care of,
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* A - B
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*
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* We are side-effecting "edges" here. The only reason to do this is because we are adding
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* edges en masse for all the co-authors on all the publications considered so far. The
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* other reason being we dont want to compare against 2 sets of edges (edges created before
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* & co-author edges created during the course of this method) when we are creating a new
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* Collaboration.
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* */
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createCoAuthorEdges(biboDocumentURLToVO,
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biboDocumentURLToCoAuthors,
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edges,
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edgeUniqueIdentifierToVO);
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}
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public CollaborationData getCollaborationData() {
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return new CoAuthorshipData(egoNode, nodes, edges);
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}
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private Activity createDocumentVO(QuerySolution solution, String documentURL) {
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Activity biboDocument = new Activity(documentURL);
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RDFNode publicationDateNode = solution.get(QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
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if (publicationDateNode != null) {
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biboDocument.setActivityDate(publicationDateNode.toString());
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}
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return biboDocument;
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}
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private String getEdgeUniqueIdentifier(int nodeID1, int nodeID2) {
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String separator = "*";
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if (nodeID1 < nodeID2) {
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return nodeID1 + separator + nodeID2;
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} else {
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return nodeID2 + separator + nodeID1;
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}
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}
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private void createCoAuthorEdges(
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Map<String, Activity> biboDocumentURLToVO,
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Map<String, Set<Collaborator>> biboDocumentURLToCoAuthors, Set<Collaboration> edges,
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Map<String, Collaboration> edgeUniqueIdentifierToVO) {
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for (Map.Entry<String, Set<Collaborator>> currentBiboDocumentEntry
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: biboDocumentURLToCoAuthors.entrySet()) {
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/*
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* If there was only one co-author (other than ego) then we dont have to create any
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* edges. so the below condition will take care of that.
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*
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* We are restricting edges between co-author if a particular document has more than
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* 100 co-authors. Our conjecture is that such edges do not provide any good insight
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* & causes unnecessary computations causing the server to time-out.
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* */
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if (currentBiboDocumentEntry.getValue().size() > 1
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&& currentBiboDocumentEntry.getValue().size()
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<= MAX_AUTHORS_PER_PAPER_ALLOWED) {
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/*
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* This method takes out all the authors & edges between authors that belong to documents
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* that have more than 100 authors. We conjecture that these papers do not provide much
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* insight. However, we have left the documents be.
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*
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* This method side-effects "nodes" & "edges".
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* */
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removeLowQualityNodesAndEdges(nodes,
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biboDocumentURLToVO,
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biboDocumentURLToCoAuthors,
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edges);
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Set<Collaboration> newlyAddedEdges = new HashSet<Collaboration>();
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/*
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* We need to create edges between 2 co-authors. E.g. On a paper there were 3 authors
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* ego, A & B then we have already created edges like,
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* ego - A
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* ego - B
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* The below sub-routine will take care of,
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* A - B
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*
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* We are side-effecting "edges" here. The only reason to do this is because we are adding
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* edges en masse for all the co-authors on all the publications considered so far. The
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* other reason being we dont want to compare against 2 sets of edges (edges created before
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* & co-author edges created during the course of this method) when we are creating a new
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* Collaboration.
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* */
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createCoAuthorEdges(biboDocumentURLToVO,
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biboDocumentURLToCoAuthors,
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edges,
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edgeUniqueIdentifierToVO);
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/*
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* In order to leverage the nested "for loop" for making edges between all the
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* co-authors we need to create a list out of the set first.
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* */
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List<Collaborator> coAuthorNodes =
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new ArrayList<Collaborator>(currentBiboDocumentEntry.getValue());
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Collections.sort(coAuthorNodes, new CollaboratorComparator());
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return new CoAuthorshipData(egoNode, nodes, edges);
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}
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int numOfCoAuthors = coAuthorNodes.size();
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private void removeLowQualityNodesAndEdges(
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Set<Collaborator> nodes,
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Map<String, Activity> biboDocumentURLToVO,
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Map<String, Set<Collaborator>> biboDocumentURLToCoAuthors,
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Set<Collaboration> edges) {
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for (int ii = 0; ii < numOfCoAuthors - 1; ii++) {
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for (int jj = ii + 1; jj < numOfCoAuthors; jj++) {
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Set<Collaborator> nodesToBeRemoved = new HashSet<Collaborator>();
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for (Map.Entry<String, Set<Collaborator>> currentBiboDocumentEntry
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Collaborator coAuthor1 = coAuthorNodes.get(ii);
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Collaborator coAuthor2 = coAuthorNodes.get(jj);
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Collaboration coAuthor1_2Edge = getExistingEdge(coAuthor1,
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coAuthor2,
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edgeUniqueIdentifierToVO);
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Activity currentBiboDocument = biboDocumentURLToVO
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.get(currentBiboDocumentEntry
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.getKey());
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if (coAuthor1_2Edge != null) {
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coAuthor1_2Edge.addActivity(currentBiboDocument);
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} else {
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coAuthor1_2Edge = new Collaboration(coAuthor1,
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coAuthor2,
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currentBiboDocument,
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edgeIDGenerator);
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newlyAddedEdges.add(coAuthor1_2Edge);
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edgeUniqueIdentifierToVO.put(
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getEdgeUniqueIdentifier(coAuthor1.getCollaboratorID(),
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coAuthor2.getCollaboratorID()),
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coAuthor1_2Edge);
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}
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}
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}
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edges.addAll(newlyAddedEdges);
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}
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}
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}
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private Collaboration getExistingEdge(
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Collaborator collaboratingNode1,
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Collaborator collaboratingNode2,
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Map<String, Collaboration> edgeUniqueIdentifierToVO) {
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String edgeUniqueIdentifier = getEdgeUniqueIdentifier(
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collaboratingNode1.getCollaboratorID(),
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collaboratingNode2.getCollaboratorID());
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return edgeUniqueIdentifierToVO.get(edgeUniqueIdentifier);
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}
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private void removeLowQualityNodesAndEdges(
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Set<Collaborator> nodes,
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Map<String, Activity> biboDocumentURLToVO,
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Map<String, Set<Collaborator>> biboDocumentURLToCoAuthors,
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Set<Collaboration> edges) {
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Set<Collaborator> nodesToBeRemoved = new HashSet<Collaborator>();
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for (Map.Entry<String, Set<Collaborator>> currentBiboDocumentEntry
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: biboDocumentURLToCoAuthors.entrySet()) {
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if (currentBiboDocumentEntry.getValue().size() > MAX_AUTHORS_PER_PAPER_ALLOWED) {
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Activity currentBiboDocument = biboDocumentURLToVO
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.get(currentBiboDocumentEntry.getKey());
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.get(currentBiboDocumentEntry.getKey());
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Set<Collaboration> edgesToBeRemoved = new HashSet<Collaboration>();
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for (Collaboration currentEdge : edges) {
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Set<Activity> currentCollaboratorDocuments =
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currentEdge.getCollaborationActivities();
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currentEdge.getCollaborationActivities();
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if (currentCollaboratorDocuments.contains(currentBiboDocument)) {
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currentCollaboratorDocuments.remove(currentBiboDocument);
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@ -265,114 +362,11 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
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}
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}
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}
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}
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nodes.removeAll(nodesToBeRemoved);
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}
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private void createCoAuthorEdges(
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Map<String, Activity> biboDocumentURLToVO,
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Map<String, Set<Collaborator>> biboDocumentURLToCoAuthors, Set<Collaboration> edges,
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Map<String, Collaboration> edgeUniqueIdentifierToVO) {
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for (Map.Entry<String, Set<Collaborator>> currentBiboDocumentEntry
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: biboDocumentURLToCoAuthors.entrySet()) {
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/*
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* If there was only one co-author (other than ego) then we dont have to create any
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* edges. so the below condition will take care of that.
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*
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* We are restricting edges between co-author if a particular document has more than
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* 100 co-authors. Our conjecture is that such edges do not provide any good insight
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* & causes unnecessary computations causing the server to time-out.
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* */
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if (currentBiboDocumentEntry.getValue().size() > 1
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&& currentBiboDocumentEntry.getValue().size()
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<= MAX_AUTHORS_PER_PAPER_ALLOWED) {
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Set<Collaboration> newlyAddedEdges = new HashSet<Collaboration>();
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/*
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* In order to leverage the nested "for loop" for making edges between all the
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* co-authors we need to create a list out of the set first.
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* */
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List<Collaborator> coAuthorNodes =
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new ArrayList<Collaborator>(currentBiboDocumentEntry.getValue());
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Collections.sort(coAuthorNodes, new CollaboratorComparator());
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int numOfCoAuthors = coAuthorNodes.size();
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for (int ii = 0; ii < numOfCoAuthors - 1; ii++) {
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for (int jj = ii + 1; jj < numOfCoAuthors; jj++) {
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Collaborator coAuthor1 = coAuthorNodes.get(ii);
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Collaborator coAuthor2 = coAuthorNodes.get(jj);
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Collaboration coAuthor1_2Edge = getExistingEdge(coAuthor1,
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coAuthor2,
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edgeUniqueIdentifierToVO);
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Activity currentBiboDocument = biboDocumentURLToVO
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.get(currentBiboDocumentEntry
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.getKey());
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if (coAuthor1_2Edge != null) {
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coAuthor1_2Edge.addActivity(currentBiboDocument);
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} else {
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coAuthor1_2Edge = new Collaboration(coAuthor1,
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coAuthor2,
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currentBiboDocument,
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edgeIDGenerator);
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newlyAddedEdges.add(coAuthor1_2Edge);
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edgeUniqueIdentifierToVO.put(
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getEdgeUniqueIdentifier(coAuthor1.getCollaboratorID(),
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coAuthor2.getCollaboratorID()),
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coAuthor1_2Edge);
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}
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}
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}
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edges.addAll(newlyAddedEdges);
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}
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}
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}
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private Collaboration getExistingEdge(
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Collaborator collaboratingNode1,
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Collaborator collaboratingNode2,
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Map<String, Collaboration> edgeUniqueIdentifierToVO) {
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String edgeUniqueIdentifier = getEdgeUniqueIdentifier(
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collaboratingNode1.getCollaboratorID(),
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collaboratingNode2.getCollaboratorID());
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return edgeUniqueIdentifierToVO.get(edgeUniqueIdentifier);
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}
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private String getEdgeUniqueIdentifier(int nodeID1, int nodeID2) {
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String separator = "*";
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if (nodeID1 < nodeID2) {
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return nodeID1 + separator + nodeID2;
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} else {
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return nodeID2 + separator + nodeID1;
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nodes.removeAll(nodesToBeRemoved);
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}
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}
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private Activity createDocumentVO(QuerySolution solution, String documentURL) {
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|
||||
Activity biboDocument = new Activity(documentURL);
|
||||
|
||||
RDFNode publicationDateNode = solution.get(QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
|
||||
if (publicationDateNode != null) {
|
||||
biboDocument.setActivityDate(publicationDateNode.toString());
|
||||
}
|
||||
|
||||
return biboDocument;
|
||||
/* END QUERY RUNNER */
|
||||
}
|
||||
|
||||
private String generateEgoCoAuthorshipSparqlQuery(String queryURI) {
|
||||
|
|
@ -455,19 +449,13 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
|
|||
throw new MalformedQueryParametersException("URI parameter is either null or empty.");
|
||||
}
|
||||
|
||||
InputStream is = null;
|
||||
ResultSet rs = null;
|
||||
try {
|
||||
is = rdfService.sparqlSelectQuery(generateEgoCoAuthorshipSparqlQuery(this.egoURI), RDFService.ResultFormat.JSON);
|
||||
rs = ResultSetFactory.fromJSON(is);
|
||||
data = createQueryResult(rs);
|
||||
QueryResultConsumer consumer = new QueryResultConsumer();
|
||||
rdfService.sparqlSelectQuery(generateEgoCoAuthorshipSparqlQuery(this.egoURI), consumer);
|
||||
data = consumer.getCollaborationData();
|
||||
} catch (RDFServiceException e) {
|
||||
log.error("Unable to execute query", e);
|
||||
throw new RuntimeException(e);
|
||||
} finally {
|
||||
if (is != null) {
|
||||
try { is.close(); } catch (Throwable t) { }
|
||||
}
|
||||
}
|
||||
|
||||
CollaborationDataCacheEntry newEntry = new CollaborationDataCacheEntry();
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
|
||||
package edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator;
|
||||
|
||||
import java.io.InputStream;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collections;
|
||||
import java.util.Date;
|
||||
|
|
@ -13,9 +12,9 @@ import java.util.Map;
|
|||
import java.util.Set;
|
||||
import java.util.concurrent.ConcurrentHashMap;
|
||||
|
||||
import com.hp.hpl.jena.query.ResultSetFactory;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
|
||||
import org.apache.commons.lang.StringUtils;
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
|
|
@ -23,14 +22,8 @@ import org.apache.jena.iri.IRI;
|
|||
import org.apache.jena.iri.IRIFactory;
|
||||
import org.apache.jena.iri.Violation;
|
||||
|
||||
import com.hp.hpl.jena.query.Query;
|
||||
import com.hp.hpl.jena.query.QueryExecution;
|
||||
import com.hp.hpl.jena.query.QueryExecutionFactory;
|
||||
import com.hp.hpl.jena.query.QueryFactory;
|
||||
import com.hp.hpl.jena.query.QuerySolution;
|
||||
import com.hp.hpl.jena.query.ResultSet;
|
||||
import com.hp.hpl.jena.query.Syntax;
|
||||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.RDFNode;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CoInvestigationData;
|
||||
|
|
@ -60,10 +53,6 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
|
||||
private Log log = LogFactory.getLog(CoPIGrantCountQueryRunner.class.getName());
|
||||
|
||||
private UniqueIDGenerator nodeIDGenerator;
|
||||
|
||||
private UniqueIDGenerator edgeIDGenerator;
|
||||
|
||||
private long before, after;
|
||||
|
||||
private static final String SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME = ""
|
||||
|
|
@ -95,9 +84,6 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
this.egoURI = egoURI;
|
||||
this.rdfService = rdfService;
|
||||
// this.log = log;
|
||||
|
||||
this.nodeIDGenerator = new UniqueIDGenerator();
|
||||
this.edgeIDGenerator = new UniqueIDGenerator();
|
||||
}
|
||||
|
||||
private String generateEgoCoPIquery(String queryURI) {
|
||||
|
|
@ -294,19 +280,13 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
|
||||
before = System.currentTimeMillis();
|
||||
|
||||
InputStream is = null;
|
||||
ResultSet rs = null;
|
||||
try {
|
||||
is = rdfService.sparqlSelectQuery(generateEgoCoPIquery(this.egoURI), RDFService.ResultFormat.JSON);
|
||||
rs = ResultSetFactory.fromJSON(is);
|
||||
data = createQueryResult(rs);
|
||||
QueryResultConsumer consumer = new QueryResultConsumer();
|
||||
rdfService.sparqlSelectQuery(generateEgoCoPIquery(this.egoURI), consumer);
|
||||
data = consumer.getData();
|
||||
} catch (RDFServiceException e) {
|
||||
log.error("Unable to execute query", e);
|
||||
throw new RuntimeException(e);
|
||||
} finally {
|
||||
if (is != null) {
|
||||
try { is.close(); } catch (Throwable t) { }
|
||||
}
|
||||
}
|
||||
after = System.currentTimeMillis();
|
||||
|
||||
|
|
@ -356,34 +336,7 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
private Collaboration getExistingEdge(
|
||||
Collaborator collaboratingNode1,
|
||||
Collaborator collaboratingNode2,
|
||||
Map<String, Collaboration> edgeUniqueIdentifierToVO) {
|
||||
|
||||
String edgeUniqueIdentifier = getEdgeUniqueIdentifier(
|
||||
collaboratingNode1.getCollaboratorID(),
|
||||
collaboratingNode2.getCollaboratorID());
|
||||
|
||||
return edgeUniqueIdentifierToVO.get(edgeUniqueIdentifier);
|
||||
|
||||
}
|
||||
|
||||
private String getEdgeUniqueIdentifier(int nodeID1, int nodeID2) {
|
||||
|
||||
String separator = "*";
|
||||
|
||||
if (nodeID1 < nodeID2) {
|
||||
return nodeID1 + separator + nodeID2;
|
||||
} else {
|
||||
return nodeID2 + separator + nodeID1;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private CollaborationData createQueryResult(ResultSet resultSet) {
|
||||
|
||||
private static class QueryResultConsumer extends ResultSetConsumer {
|
||||
Set<Collaborator> nodes = new HashSet<Collaborator>();
|
||||
|
||||
Map<String, Activity> grantURLToVO = new HashMap<String, Activity>();
|
||||
|
|
@ -395,111 +348,116 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
|
||||
Set<Collaboration> edges = new HashSet<Collaboration>();
|
||||
|
||||
before = System.currentTimeMillis();
|
||||
private UniqueIDGenerator nodeIDGenerator = new UniqueIDGenerator();
|
||||
private UniqueIDGenerator edgeIDGenerator = new UniqueIDGenerator();
|
||||
|
||||
while (resultSet.hasNext()) {
|
||||
QuerySolution solution = resultSet.nextSolution();
|
||||
private Log log = LogFactory.getLog(CoPIGrantCountQueryRunner.class.getName());
|
||||
|
||||
@Override
|
||||
protected void processQuerySolution(QuerySolution qs) {
|
||||
/*
|
||||
* We only want to create only ONE ego node.
|
||||
* */
|
||||
RDFNode egoPIURLNode = solution.get(QueryFieldLabels.PI_URL);
|
||||
if (nodeURLToVO.containsKey(egoPIURLNode.toString())) {
|
||||
RDFNode egoPIURLNode = qs.get(QueryFieldLabels.PI_URL);
|
||||
if (nodeURLToVO.containsKey(egoPIURLNode.toString())) {
|
||||
|
||||
egoNode = nodeURLToVO.get(egoPIURLNode.toString());
|
||||
egoNode = nodeURLToVO.get(egoPIURLNode.toString());
|
||||
|
||||
} else {
|
||||
} else {
|
||||
|
||||
egoNode = new Collaborator(egoPIURLNode.toString(), nodeIDGenerator);
|
||||
nodes.add(egoNode);
|
||||
nodeURLToVO.put(egoPIURLNode.toString(), egoNode);
|
||||
egoNode = new Collaborator(egoPIURLNode.toString(), nodeIDGenerator);
|
||||
nodes.add(egoNode);
|
||||
nodeURLToVO.put(egoPIURLNode.toString(), egoNode);
|
||||
|
||||
|
||||
RDFNode authorLabelNode = solution.get(QueryFieldLabels.PI_LABEL);
|
||||
if (authorLabelNode != null) {
|
||||
egoNode.setCollaboratorName(authorLabelNode.toString());
|
||||
}
|
||||
RDFNode authorLabelNode = qs.get(QueryFieldLabels.PI_LABEL);
|
||||
if (authorLabelNode != null) {
|
||||
egoNode.setCollaboratorName(authorLabelNode.toString());
|
||||
}
|
||||
log.debug("PI: " + egoNode.getIndividualLabel());
|
||||
}
|
||||
log.debug("PI: " + egoNode.getIndividualLabel());
|
||||
|
||||
RDFNode grantNode = solution.get(QueryFieldLabels.GRANT_URL);
|
||||
Activity grant;
|
||||
RDFNode grantNode = qs.get(QueryFieldLabels.GRANT_URL);
|
||||
Activity grant;
|
||||
|
||||
if (grantURLToVO.containsKey(grantNode.toString())) {
|
||||
grant = grantURLToVO.get(grantNode.toString());
|
||||
} else {
|
||||
grant = createGrantVO(solution, grantNode.toString());
|
||||
grantURLToVO.put(grantNode.toString(), grant);
|
||||
}
|
||||
if (grantURLToVO.containsKey(grantNode.toString())) {
|
||||
grant = grantURLToVO.get(grantNode.toString());
|
||||
} else {
|
||||
grant = createGrantVO(qs, grantNode.toString());
|
||||
grantURLToVO.put(grantNode.toString(), grant);
|
||||
}
|
||||
|
||||
egoNode.addActivity(grant);
|
||||
log.debug("Adding grant: " + grant.getIndividualLabel());
|
||||
egoNode.addActivity(grant);
|
||||
log.debug("Adding grant: " + grant.getIndividualLabel());
|
||||
|
||||
/*
|
||||
* After some discussion we concluded that for the purpose of this visualization
|
||||
* we do not want a co-pi node or edge if the grant has only one
|
||||
* pi and that happens to be the ego.
|
||||
* */
|
||||
if (solution.get(QueryFieldLabels.PI_URL).toString().equalsIgnoreCase(
|
||||
solution.get(QueryFieldLabels.CO_PI_URL).toString())) {
|
||||
continue;
|
||||
if (qs.get(QueryFieldLabels.PI_URL).toString().equalsIgnoreCase(
|
||||
qs.get(QueryFieldLabels.CO_PI_URL).toString())) {
|
||||
return;
|
||||
}
|
||||
|
||||
Collaborator coPINode;
|
||||
|
||||
RDFNode coPIURLNode = qs.get(QueryFieldLabels.CO_PI_URL);
|
||||
if (nodeURLToVO.containsKey(coPIURLNode.toString())) {
|
||||
|
||||
coPINode = nodeURLToVO.get(coPIURLNode.toString());
|
||||
|
||||
} else {
|
||||
|
||||
coPINode = new Collaborator(coPIURLNode.toString(), nodeIDGenerator);
|
||||
nodes.add(coPINode);
|
||||
nodeURLToVO.put(coPIURLNode.toString(), coPINode);
|
||||
|
||||
RDFNode coPILabelNode = qs.get(QueryFieldLabels.CO_PI_LABEL);
|
||||
if (coPILabelNode != null) {
|
||||
coPINode.setCollaboratorName(coPILabelNode.toString());
|
||||
}
|
||||
}
|
||||
|
||||
Collaborator coPINode;
|
||||
log.debug("Adding CO-PI: "+ coPINode.getIndividualLabel());
|
||||
coPINode.addActivity(grant);
|
||||
|
||||
RDFNode coPIURLNode = solution.get(QueryFieldLabels.CO_PI_URL);
|
||||
if (nodeURLToVO.containsKey(coPIURLNode.toString())) {
|
||||
Set<Collaborator> coPIsForCurrentGrant;
|
||||
|
||||
coPINode = nodeURLToVO.get(coPIURLNode.toString());
|
||||
if (grantURLToCoPIs.containsKey(grant.getActivityURI())) {
|
||||
coPIsForCurrentGrant = grantURLToCoPIs.get(grant.getActivityURI());
|
||||
} else {
|
||||
coPIsForCurrentGrant = new HashSet<Collaborator>();
|
||||
grantURLToCoPIs.put(grant.getActivityURI(),
|
||||
coPIsForCurrentGrant);
|
||||
}
|
||||
|
||||
} else {
|
||||
coPIsForCurrentGrant.add(coPINode);
|
||||
log.debug("Co-PI for current grant : " + coPINode.getIndividualLabel());
|
||||
|
||||
coPINode = new Collaborator(coPIURLNode.toString(), nodeIDGenerator);
|
||||
nodes.add(coPINode);
|
||||
nodeURLToVO.put(coPIURLNode.toString(), coPINode);
|
||||
|
||||
RDFNode coPILabelNode = solution.get(QueryFieldLabels.CO_PI_LABEL);
|
||||
if (coPILabelNode != null) {
|
||||
coPINode.setCollaboratorName(coPILabelNode.toString());
|
||||
}
|
||||
}
|
||||
|
||||
log.debug("Adding CO-PI: "+ coPINode.getIndividualLabel());
|
||||
coPINode.addActivity(grant);
|
||||
|
||||
Set<Collaborator> coPIsForCurrentGrant;
|
||||
|
||||
if (grantURLToCoPIs.containsKey(grant.getActivityURI())) {
|
||||
coPIsForCurrentGrant = grantURLToCoPIs.get(grant.getActivityURI());
|
||||
} else {
|
||||
coPIsForCurrentGrant = new HashSet<Collaborator>();
|
||||
grantURLToCoPIs.put(grant.getActivityURI(),
|
||||
coPIsForCurrentGrant);
|
||||
}
|
||||
|
||||
coPIsForCurrentGrant.add(coPINode);
|
||||
log.debug("Co-PI for current grant : " + coPINode.getIndividualLabel());
|
||||
|
||||
Collaboration egoCoPIEdge =
|
||||
getExistingEdge(egoNode, coPINode, edgeUniqueIdentifierToVO);
|
||||
Collaboration egoCoPIEdge =
|
||||
getExistingEdge(egoNode, coPINode, edgeUniqueIdentifierToVO);
|
||||
/*
|
||||
* If "egoCoPIEdge" is null it means that no edge exists in between the egoNode
|
||||
* & current coPINode. Else create a new edge, add it to the edges set & add
|
||||
* the collaborator grant to it.
|
||||
* */
|
||||
if (egoCoPIEdge != null) {
|
||||
egoCoPIEdge.addActivity(grant);
|
||||
} else {
|
||||
egoCoPIEdge = new Collaboration(egoNode, coPINode, grant, edgeIDGenerator);
|
||||
edges.add(egoCoPIEdge);
|
||||
edgeUniqueIdentifierToVO.put(
|
||||
getEdgeUniqueIdentifier(egoNode.getCollaboratorID(),
|
||||
coPINode.getCollaboratorID()),
|
||||
egoCoPIEdge);
|
||||
}
|
||||
|
||||
if (egoCoPIEdge != null) {
|
||||
egoCoPIEdge.addActivity(grant);
|
||||
} else {
|
||||
egoCoPIEdge = new Collaboration(egoNode, coPINode, grant, edgeIDGenerator);
|
||||
edges.add(egoCoPIEdge);
|
||||
edgeUniqueIdentifierToVO.put(
|
||||
getEdgeUniqueIdentifier(egoNode.getCollaboratorID(),
|
||||
coPINode.getCollaboratorID()),
|
||||
egoCoPIEdge);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
protected void endProcessing() {
|
||||
super.endProcessing();
|
||||
/*
|
||||
* This method takes out all the PIs & edges between PIs that belong to grants
|
||||
* that have more than 100 PIs. We conjecture that these grants do not provide much
|
||||
|
|
@ -507,9 +465,9 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
* This method side-effects "nodes" & "edges".
|
||||
* */
|
||||
removeLowQualityNodesAndEdges(nodes,
|
||||
grantURLToVO,
|
||||
grantURLToCoPIs,
|
||||
edges);
|
||||
grantURLToVO,
|
||||
grantURLToCoPIs,
|
||||
edges);
|
||||
/*
|
||||
* We need to create edges between 2 co-PIs. E.g. On a grant there were 3 PI
|
||||
* ego, A & B then we have already created edges like,
|
||||
|
|
@ -525,23 +483,22 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
* a new edge.
|
||||
* */
|
||||
createCoPIEdges(grantURLToVO,
|
||||
grantURLToCoPIs,
|
||||
edges,
|
||||
edgeUniqueIdentifierToVO);
|
||||
grantURLToCoPIs,
|
||||
edges,
|
||||
edgeUniqueIdentifierToVO);
|
||||
}
|
||||
|
||||
after = System.currentTimeMillis();
|
||||
log.debug("Time taken to iterate through the ResultSet of SELECT queries is in ms: "
|
||||
+ (after - before));
|
||||
|
||||
public CollaborationData getData() {
|
||||
return new CoInvestigationData(egoNode, nodes, edges);
|
||||
}
|
||||
}
|
||||
|
||||
private void createCoPIEdges(Map<String, Activity> grantURLToVO,
|
||||
Map<String, Set<Collaborator>> grantURLToCoPIs, Set<Collaboration> edges,
|
||||
Map<String, Collaboration> edgeUniqueIdentifierToVO) {
|
||||
private void createCoPIEdges(Map<String, Activity> grantURLToVO,
|
||||
Map<String, Set<Collaborator>> grantURLToCoPIs, Set<Collaboration> edges,
|
||||
Map<String, Collaboration> edgeUniqueIdentifierToVO) {
|
||||
|
||||
for (Map.Entry<String, Set<Collaborator>> currentGrantEntry
|
||||
: grantURLToCoPIs.entrySet()) {
|
||||
for (Map.Entry<String, Set<Collaborator>> currentGrantEntry
|
||||
: grantURLToCoPIs.entrySet()) {
|
||||
|
||||
/*
|
||||
* If there was only one co-PI (other than ego) then we dont have to create any
|
||||
|
|
@ -551,60 +508,60 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
* 100 co-PIs. Our conjecture is that such edges do not provide any good insight
|
||||
* & causes unnecessary computations causing the server to time-out.
|
||||
* */
|
||||
if (currentGrantEntry.getValue().size() > 1
|
||||
&& currentGrantEntry.getValue().size()
|
||||
if (currentGrantEntry.getValue().size() > 1
|
||||
&& currentGrantEntry.getValue().size()
|
||||
<= MAX_PI_PER_GRANT_ALLOWED) {
|
||||
|
||||
Set<Collaboration> newlyAddedEdges = new HashSet<Collaboration>();
|
||||
Set<Collaboration> newlyAddedEdges = new HashSet<Collaboration>();
|
||||
|
||||
/*
|
||||
* In order to leverage the nested "for loop" for making edges between all the
|
||||
* co-PIs we need to create a list out of the set first.
|
||||
* */
|
||||
List<Collaborator> coPINodes =
|
||||
new ArrayList<Collaborator>(currentGrantEntry.getValue());
|
||||
Collections.sort(coPINodes, new CollaboratorComparator());
|
||||
List<Collaborator> coPINodes =
|
||||
new ArrayList<Collaborator>(currentGrantEntry.getValue());
|
||||
Collections.sort(coPINodes, new CollaboratorComparator());
|
||||
|
||||
int numOfCoPIs = coPINodes.size();
|
||||
int numOfCoPIs = coPINodes.size();
|
||||
|
||||
for (int ii = 0; ii < numOfCoPIs - 1; ii++) {
|
||||
for (int jj = ii + 1; jj < numOfCoPIs; jj++) {
|
||||
for (int ii = 0; ii < numOfCoPIs - 1; ii++) {
|
||||
for (int jj = ii + 1; jj < numOfCoPIs; jj++) {
|
||||
|
||||
Collaborator coPI1 = coPINodes.get(ii);
|
||||
Collaborator coPI2 = coPINodes.get(jj);
|
||||
Collaborator coPI1 = coPINodes.get(ii);
|
||||
Collaborator coPI2 = coPINodes.get(jj);
|
||||
|
||||
Collaboration coPI1_2Edge = getExistingEdge(coPI1,
|
||||
coPI2,
|
||||
edgeUniqueIdentifierToVO);
|
||||
Collaboration coPI1_2Edge = getExistingEdge(coPI1,
|
||||
coPI2,
|
||||
edgeUniqueIdentifierToVO);
|
||||
|
||||
Activity currentGrant = grantURLToVO.get(currentGrantEntry.getKey());
|
||||
Activity currentGrant = grantURLToVO.get(currentGrantEntry.getKey());
|
||||
|
||||
if (coPI1_2Edge != null) {
|
||||
coPI1_2Edge.addActivity(currentGrant);
|
||||
} else {
|
||||
coPI1_2Edge = new Collaboration(coPI1,
|
||||
coPI2,
|
||||
currentGrant,
|
||||
edgeIDGenerator);
|
||||
newlyAddedEdges.add(coPI1_2Edge);
|
||||
edgeUniqueIdentifierToVO.put(
|
||||
getEdgeUniqueIdentifier(coPI1.getCollaboratorID(),
|
||||
coPI2.getCollaboratorID()),
|
||||
coPI1_2Edge);
|
||||
if (coPI1_2Edge != null) {
|
||||
coPI1_2Edge.addActivity(currentGrant);
|
||||
} else {
|
||||
coPI1_2Edge = new Collaboration(coPI1,
|
||||
coPI2,
|
||||
currentGrant,
|
||||
edgeIDGenerator);
|
||||
newlyAddedEdges.add(coPI1_2Edge);
|
||||
edgeUniqueIdentifierToVO.put(
|
||||
getEdgeUniqueIdentifier(coPI1.getCollaboratorID(),
|
||||
coPI2.getCollaboratorID()),
|
||||
coPI1_2Edge);
|
||||
}
|
||||
}
|
||||
}
|
||||
edges.addAll(newlyAddedEdges);
|
||||
}
|
||||
}
|
||||
edges.addAll(newlyAddedEdges);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private void removeLowQualityNodesAndEdges(Set<Collaborator> nodes,
|
||||
Map<String, Activity> grantURLToVO,
|
||||
Map<String, Set<Collaborator>> grantURLToCoPIs, Set<Collaboration> edges) {
|
||||
private void removeLowQualityNodesAndEdges(Set<Collaborator> nodes,
|
||||
Map<String, Activity> grantURLToVO,
|
||||
Map<String, Set<Collaborator>> grantURLToCoPIs, Set<Collaboration> edges) {
|
||||
|
||||
Set<Collaborator> nodesToBeRemoved = new HashSet<Collaborator>();
|
||||
for (Map.Entry<String, Set<Collaborator>> currentGrantEntry
|
||||
Set<Collaborator> nodesToBeRemoved = new HashSet<Collaborator>();
|
||||
for (Map.Entry<String, Set<Collaborator>> currentGrantEntry
|
||||
: grantURLToCoPIs.entrySet()) {
|
||||
|
||||
if (currentGrantEntry.getValue().size() > MAX_PI_PER_GRANT_ALLOWED) {
|
||||
|
|
@ -615,7 +572,7 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
|
||||
for (Collaboration currentEdge : edges) {
|
||||
Set<Activity> currentCollaboratorGrants =
|
||||
currentEdge.getCollaborationActivities();
|
||||
currentEdge.getCollaborationActivities();
|
||||
|
||||
if (currentCollaboratorGrants.contains(currentGrant)) {
|
||||
currentCollaboratorGrants.remove(currentGrant);
|
||||
|
|
@ -634,14 +591,14 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
nodes.removeAll(nodesToBeRemoved);
|
||||
|
||||
}
|
||||
nodes.removeAll(nodesToBeRemoved);
|
||||
|
||||
}
|
||||
private Activity createGrantVO(QuerySolution solution, String grantURL) {
|
||||
|
||||
private Activity createGrantVO(QuerySolution solution, String grantURL) {
|
||||
|
||||
Activity grant = new Activity(grantURL);
|
||||
Activity grant = new Activity(grantURL);
|
||||
|
||||
// RDFNode grantLabelNode = solution.get(QueryFieldLabels.GRANT_LABEL);
|
||||
// if (grantLabelNode != null) {
|
||||
|
|
@ -649,17 +606,17 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
// }
|
||||
|
||||
|
||||
RDFNode grantStartYear = solution.get(QueryFieldLabels.ROLE_START_DATE);
|
||||
if (grantStartYear != null) {
|
||||
grant.setActivityDate(grantStartYear.toString());
|
||||
} else {
|
||||
grantStartYear = solution.get(QueryFieldLabels.GRANT_START_DATE);
|
||||
RDFNode grantStartYear = solution.get(QueryFieldLabels.ROLE_START_DATE);
|
||||
if (grantStartYear != null) {
|
||||
grant.setActivityDate(grantStartYear.toString());
|
||||
} else {
|
||||
grantStartYear = solution.get(QueryFieldLabels.GRANT_START_DATE);
|
||||
if (grantStartYear != null) {
|
||||
grant.setActivityDate(grantStartYear.toString());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
//TODO: Verify that grant end date is not required.
|
||||
//TODO: Verify that grant end date is not required.
|
||||
/*
|
||||
RDFNode grantEndDate = solution.get(QueryFieldLabels.ROLE_END_DATE);
|
||||
if (grantEndDate != null) {
|
||||
|
|
@ -672,6 +629,33 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
|
|||
}
|
||||
*/
|
||||
|
||||
return grant;
|
||||
return grant;
|
||||
}
|
||||
|
||||
private Collaboration getExistingEdge(
|
||||
Collaborator collaboratingNode1,
|
||||
Collaborator collaboratingNode2,
|
||||
Map<String, Collaboration> edgeUniqueIdentifierToVO) {
|
||||
|
||||
String edgeUniqueIdentifier = getEdgeUniqueIdentifier(
|
||||
collaboratingNode1.getCollaboratorID(),
|
||||
collaboratingNode2.getCollaboratorID());
|
||||
|
||||
return edgeUniqueIdentifierToVO.get(edgeUniqueIdentifier);
|
||||
|
||||
}
|
||||
|
||||
private String getEdgeUniqueIdentifier(int nodeID1, int nodeID2) {
|
||||
|
||||
String separator = "*";
|
||||
|
||||
if (nodeID1 < nodeID2) {
|
||||
return nodeID1 + separator + nodeID2;
|
||||
} else {
|
||||
return nodeID2 + separator + nodeID1;
|
||||
}
|
||||
|
||||
}
|
||||
/** END QUERY RESULT CONSUMER **/
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue