1. Fix for grants obtaining publication results
This commit is contained in:
cdtank
parent
81736350bb
commit
aee1d00801
1 changed files with 494 additions and 481 deletions
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@ -1,481 +1,494 @@
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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.freemarker.visutils;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import org.apache.commons.lang.StringUtils;
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import com.hp.hpl.jena.query.Dataset;
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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.Model;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryFieldLabels;
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import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants;
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import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.ModelConstructorUtilities;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.OrganizationAssociatedPeopleModelWithTypesConstructor;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.OrganizationModelWithTypesConstructor;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.OrganizationToGrantsForSubOrganizationsModelConstructor;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.OrganizationToPublicationsForSubOrganizationsModelConstructor;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.PersonToGrantsModelConstructor;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.PersonToPublicationsModelConstructor;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Activity;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Entity;
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import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubEntity;
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public class SelectOnModelUtilities {
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public static Entity getSubjectOrganizationHierarchy(Dataset dataset,
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String subjectEntityURI) throws MalformedQueryParametersException {
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Model organizationModel = ModelConstructorUtilities
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.getOrConstructModel(
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null,
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OrganizationModelWithTypesConstructor.MODEL_TYPE,
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dataset);
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Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
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fieldLabelToOutputFieldLabel.put("organizationLabel", QueryFieldLabels.ORGANIZATION_LABEL);
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fieldLabelToOutputFieldLabel.put("subOrganization", QueryFieldLabels.SUBORGANIZATION_URL);
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fieldLabelToOutputFieldLabel.put("subOrganizationLabel", QueryFieldLabels.SUBORGANIZATION_LABEL);
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fieldLabelToOutputFieldLabel.put("subOrganizationTypeLabel", QueryFieldLabels.SUBORGANIZATION_TYPE_LABEL);
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String whereClause = ""
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+ " <" + subjectEntityURI + "> rdfs:label ?organizationLabel . "
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+ " <" + subjectEntityURI + "> core:hasSubOrganization ?subOrganization . "
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+ " ?subOrganization rdfs:label ?subOrganizationLabel . "
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+ " ?subOrganization rdf:type ?subOrgType . "
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+ " ?subOrgType rdfs:label ?subOrganizationTypeLabel . ";
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QueryRunner<ResultSet> subOrganizationsWithTypesQuery =
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new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
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"",
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whereClause,
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"",
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organizationModel);
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return getEntityWithSubOrganizations(subjectEntityURI,
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subOrganizationsWithTypesQuery.getQueryResult());
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}
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private static Entity getEntityWithSubOrganizations(String subjectEntityURI, ResultSet queryResult) {
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Entity entity = new Entity(subjectEntityURI);
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Map<String, SubEntity> subOrganizationURIToVO = new HashMap<String, SubEntity>();
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while (queryResult.hasNext()) {
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QuerySolution solution = queryResult.nextSolution();
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if (StringUtils.isEmpty(entity.getEntityLabel())) {
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RDFNode organizationLabelNode = solution.get(QueryFieldLabels.ORGANIZATION_LABEL);
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if (organizationLabelNode != null) {
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entity.setIndividualLabel(organizationLabelNode.toString());
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}
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}
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RDFNode subOrganizationNode = solution.get(QueryFieldLabels.SUBORGANIZATION_URL);
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SubEntity subEntity;
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if (subOrganizationURIToVO.containsKey(subOrganizationNode.toString())) {
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subEntity = subOrganizationURIToVO.get(subOrganizationNode.toString());
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} else {
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subEntity = new SubEntity(subOrganizationNode.toString());
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subEntity.setEntityClass(VOConstants.EntityClassType.ORGANIZATION);
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subOrganizationURIToVO.put(subOrganizationNode.toString(), subEntity);
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RDFNode subOrganizationLabelNode = solution.get(QueryFieldLabels.SUBORGANIZATION_LABEL);
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if (subOrganizationLabelNode != null) {
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subEntity.setIndividualLabel(subOrganizationLabelNode.toString());
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}
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}
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RDFNode subOrganizationTypeLabelNode = solution.get(QueryFieldLabels.SUBORGANIZATION_TYPE_LABEL);
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if (subOrganizationTypeLabelNode != null) {
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subEntity.addEntityTypeLabel(subOrganizationTypeLabelNode.toString());
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}
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}
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entity.addSubEntitities(subOrganizationURIToVO.values());
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return entity;
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}
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public static Entity getSubjectOrganizationAssociatedPeople(Dataset dataset,
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String subjectEntityURI) throws MalformedQueryParametersException {
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Model associatedPeopleModel = ModelConstructorUtilities
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.getOrConstructModel(
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subjectEntityURI,
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OrganizationAssociatedPeopleModelWithTypesConstructor.MODEL_TYPE,
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dataset);
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Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
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fieldLabelToOutputFieldLabel.put("organizationLabel", QueryFieldLabels.ORGANIZATION_LABEL);
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fieldLabelToOutputFieldLabel.put("person", QueryFieldLabels.PERSON_URL);
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fieldLabelToOutputFieldLabel.put("personLabel", QueryFieldLabels.PERSON_LABEL);
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fieldLabelToOutputFieldLabel.put("personTypeLabel", QueryFieldLabels.PERSON_TYPE_LABEL);
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String whereClause = ""
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+ " <" + subjectEntityURI + "> rdfs:label ?organizationLabel . "
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+ " <" + subjectEntityURI + "> vivosocnet:hasPersonWithActivity ?person . "
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+ " ?person rdfs:label ?personLabel . "
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+ " ?person rdf:type ?personType . "
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+ " ?personType rdfs:label ?personTypeLabel . ";
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QueryRunner<ResultSet> associatedPeopleWithTypesQuery =
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new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
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"",
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whereClause,
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"",
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associatedPeopleModel);
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return getEntityWithAssociatedPeopleSubEntitities(subjectEntityURI, associatedPeopleWithTypesQuery.getQueryResult());
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}
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private static Entity getEntityWithAssociatedPeopleSubEntitities(
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String subjectEntityURI, ResultSet queryResult) {
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Entity entity = new Entity(subjectEntityURI);
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Map<String, SubEntity> associatedPeopleURIToVO = new HashMap<String, SubEntity>();
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while (queryResult.hasNext()) {
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QuerySolution solution = queryResult.nextSolution();
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if (StringUtils.isEmpty(entity.getEntityLabel())) {
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RDFNode organizationLabelNode = solution.get(QueryFieldLabels.ORGANIZATION_LABEL);
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if (organizationLabelNode != null) {
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entity.setIndividualLabel(organizationLabelNode.toString());
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}
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}
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RDFNode personNode = solution.get(QueryFieldLabels.PERSON_URL);
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SubEntity subEntity;
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if (associatedPeopleURIToVO.containsKey(personNode.toString())) {
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subEntity = associatedPeopleURIToVO.get(personNode.toString());
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} else {
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subEntity = new SubEntity(personNode.toString());
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subEntity.setEntityClass(VOConstants.EntityClassType.PERSON);
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associatedPeopleURIToVO.put(personNode.toString(), subEntity);
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RDFNode personLabelNode = solution.get(QueryFieldLabels.PERSON_LABEL);
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if (personLabelNode != null) {
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subEntity.setIndividualLabel(personLabelNode.toString());
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}
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}
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RDFNode personTypeLabelNode = solution.get(QueryFieldLabels.PERSON_TYPE_LABEL);
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if (personTypeLabelNode != null) {
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subEntity.addEntityTypeLabel(personTypeLabelNode.toString());
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}
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}
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entity.addSubEntitities(associatedPeopleURIToVO.values());
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return entity;
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}
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public static Map<String, Activity> getPublicationsForAllSubOrganizations(
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Dataset dataset, Entity organizationEntity)
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throws MalformedQueryParametersException {
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Map<String, Activity> allDocumentURIToVOs = new HashMap<String, Activity>();
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for (SubEntity subOrganization : organizationEntity.getSubEntities()) {
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Model subOrganizationPublicationsModel = ModelConstructorUtilities
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.getOrConstructModel(
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subOrganization.getIndividualURI(),
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OrganizationToPublicationsForSubOrganizationsModelConstructor.MODEL_TYPE,
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dataset);
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System.out.println("getting publications for " + subOrganization.getIndividualLabel());
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Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
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fieldLabelToOutputFieldLabel.put("document", QueryFieldLabels.DOCUMENT_URL);
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fieldLabelToOutputFieldLabel.put("documentLabel", QueryFieldLabels.DOCUMENT_LABEL);
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fieldLabelToOutputFieldLabel.put("documentPublicationDate", QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
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String whereClause = ""
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+ " <" + subOrganization.getIndividualURI() + "> vivosocnet:hasPersonWithPublication ?document . "
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+ " ?document rdfs:label ?documentLabel . "
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+ " OPTIONAL { "
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+ " ?document core:dateTimeValue ?dateTimeValue . "
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+ " ?dateTimeValue core:dateTime ?documentPublicationDate } . ";
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QueryRunner<ResultSet> subOrganizationPublicationsQuery =
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new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
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"",
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whereClause,
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"",
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subOrganizationPublicationsModel);
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subOrganization.addActivities(getPublicationForEntity(
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subOrganizationPublicationsQuery.getQueryResult(),
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allDocumentURIToVOs));
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}
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return allDocumentURIToVOs;
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}
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private static Collection<Activity> getPublicationForEntity(
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ResultSet queryResult,
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Map<String, Activity> allDocumentURIToVOs) {
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Set<Activity> currentEntityPublications = new HashSet<Activity>();
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while (queryResult.hasNext()) {
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QuerySolution solution = queryResult.nextSolution();
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RDFNode documentNode = solution.get(QueryFieldLabels.DOCUMENT_URL);
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Activity biboDocument;
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if (allDocumentURIToVOs.containsKey(documentNode.toString())) {
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biboDocument = allDocumentURIToVOs.get(documentNode.toString());
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} else {
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biboDocument = new Activity(documentNode.toString());
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allDocumentURIToVOs.put(documentNode.toString(), biboDocument);
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RDFNode publicationDateNode = solution.get(QueryFieldLabels
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.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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}
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currentEntityPublications.add(biboDocument);
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}
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return currentEntityPublications;
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}
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private static Collection<Activity> getGrantForEntity(
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ResultSet queryResult,
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Map<String, Activity> allGrantURIToVO) {
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Set<Activity> currentEntityGrants = new HashSet<Activity>();
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while (queryResult.hasNext()) {
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QuerySolution solution = queryResult.nextSolution();
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RDFNode grantNode = solution.get(QueryFieldLabels.GRANT_URL);
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Activity coreGrant;
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if (allGrantURIToVO.containsKey(grantNode.toString())) {
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coreGrant = allGrantURIToVO.get(grantNode.toString());
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} else {
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coreGrant = new Activity(grantNode.toString());
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allGrantURIToVO.put(grantNode.toString(), coreGrant);
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RDFNode grantStartDateNode = solution.get(QueryFieldLabels.ROLE_START_DATE);
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if (grantStartDateNode != null) {
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coreGrant.setActivityDate(grantStartDateNode.toString());
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} else {
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grantStartDateNode = solution
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.get(QueryFieldLabels.GRANT_START_DATE);
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if (grantStartDateNode != null) {
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coreGrant.setActivityDate(grantStartDateNode.toString());
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}
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}
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}
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currentEntityGrants.add(coreGrant);
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}
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return currentEntityGrants;
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}
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public static Map<String, Activity> getGrantsForAllSubOrganizations(
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Dataset dataset, Entity organizationEntity)
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throws MalformedQueryParametersException {
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Map<String, Activity> allGrantURIToVO = new HashMap<String, Activity>();
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for (SubEntity subOrganization : organizationEntity.getSubEntities()) {
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System.out.println("constructing grants for " + subOrganization.getIndividualLabel() + " :: " + subOrganization.getIndividualURI());
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Model subOrganizationGrantsModel = ModelConstructorUtilities
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.getOrConstructModel(
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subOrganization.getIndividualURI(),
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OrganizationToGrantsForSubOrganizationsModelConstructor.MODEL_TYPE,
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dataset);
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Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
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fieldLabelToOutputFieldLabel.put("grant", QueryFieldLabels.GRANT_URL);
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fieldLabelToOutputFieldLabel.put("grantLabel", QueryFieldLabels.GRANT_LABEL);
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fieldLabelToOutputFieldLabel.put("grantStartDate", QueryFieldLabels.GRANT_START_DATE);
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fieldLabelToOutputFieldLabel.put("roleStartDate", QueryFieldLabels.ROLE_START_DATE);
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String whereClause = ""
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+ "{"
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+ " <" + subOrganization.getIndividualURI() + "> vivosocnet:hasInvestigatorWithGrant ?grant . "
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+ " ?grant rdfs:label ?grantLabel . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
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+ "}"
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+ "UNION"
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+ "{"
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+ " <" + subOrganization.getIndividualURI() + "> vivosocnet:hasPIWithGrant ?grant . "
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+ " ?grant rdfs:label ?grantLabel . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
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+ "}"
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+ "UNION"
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+ "{"
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+ " <" + subOrganization.getIndividualURI() + "> vivosocnet:hascoPIWithGrant ?grant . "
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+ " ?grant rdfs:label ?grantLabel . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
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+ "}";
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QueryRunner<ResultSet> subOrganizationGrantsQuery =
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new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
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"",
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whereClause,
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"",
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subOrganizationGrantsModel);
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subOrganization.addActivities(getGrantForEntity(
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subOrganizationGrantsQuery.getQueryResult(),
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allGrantURIToVO));
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}
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return allGrantURIToVO;
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}
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public static Map<String, Activity> getGrantForAssociatedPeople(
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Dataset dataset, Collection<SubEntity> people)
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throws MalformedQueryParametersException {
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Map<String, Activity> allGrantURIToVOs = new HashMap<String, Activity>();
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for (SubEntity person : people) {
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System.out.println("constructing grants for " + person.getIndividualLabel() + " :: " + person.getIndividualURI());
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Model personGrantsModel = ModelConstructorUtilities
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.getOrConstructModel(
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person.getIndividualURI(),
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PersonToGrantsModelConstructor.MODEL_TYPE,
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dataset);
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Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
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fieldLabelToOutputFieldLabel.put("grant", QueryFieldLabels.GRANT_URL);
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fieldLabelToOutputFieldLabel.put("grantLabel", QueryFieldLabels.GRANT_LABEL);
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fieldLabelToOutputFieldLabel.put("grantStartDate", QueryFieldLabels.GRANT_START_DATE);
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fieldLabelToOutputFieldLabel.put("roleStartDate", QueryFieldLabels.ROLE_START_DATE);
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String whereClause = ""
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+ "{"
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+ " <" + person.getIndividualURI() + "> vivosocnet:hasGrantAsAnInvestigator ?grant . "
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+ " ?grant rdfs:label ?grantLabel . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
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+ "}"
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+ "UNION"
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+ "{"
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+ " <" + person.getIndividualURI() + "> vivosocnet:hasGrantAsPI ?grant . "
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+ " ?grant rdfs:label ?grantLabel . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
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+ "}"
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+ "UNION"
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+ "{"
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+ " <" + person.getIndividualURI() + "> vivosocnet:hasGrantAsCoPI ?grant . "
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+ " ?grant rdfs:label ?grantLabel . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
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+ " OPTIONAL { "
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+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
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+ "}";
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QueryRunner<ResultSet> personGrantsQuery =
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new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
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"",
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whereClause,
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"",
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personGrantsModel);
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person.addActivities(getGrantForEntity(
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personGrantsQuery.getQueryResult(),
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allGrantURIToVOs));
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}
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return allGrantURIToVOs;
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}
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public static Map<String, Activity> getPublicationsForAssociatedPeople(
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Dataset dataset, Collection<SubEntity> people)
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throws MalformedQueryParametersException {
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Map<String, Activity> allDocumentURIToVOs = new HashMap<String, Activity>();
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for (SubEntity person : people) {
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Model personPublicationsModel = ModelConstructorUtilities
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.getOrConstructModel(
|
||||
person.getIndividualURI(),
|
||||
PersonToPublicationsModelConstructor.MODEL_TYPE,
|
||||
dataset);
|
||||
|
||||
System.out.println("getting publications for " + person.getIndividualLabel());
|
||||
|
||||
Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
|
||||
fieldLabelToOutputFieldLabel.put("document", QueryFieldLabels.DOCUMENT_URL);
|
||||
fieldLabelToOutputFieldLabel.put("documentLabel", QueryFieldLabels.DOCUMENT_LABEL);
|
||||
fieldLabelToOutputFieldLabel.put("documentPublicationDate", QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
|
||||
|
||||
String whereClause = ""
|
||||
+ " <" + person.getIndividualURI() + "> vivosocnet:hasPublication ?document . "
|
||||
+ " ?document rdfs:label ?documentLabel . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?document core:dateTimeValue ?dateTimeValue . "
|
||||
+ " ?dateTimeValue core:dateTime ?documentPublicationDate } . ";
|
||||
|
||||
QueryRunner<ResultSet> personPublicationsQuery =
|
||||
new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
|
||||
"",
|
||||
whereClause,
|
||||
"",
|
||||
personPublicationsModel);
|
||||
|
||||
person.addActivities(getPublicationForEntity(
|
||||
personPublicationsQuery.getQueryResult(),
|
||||
allDocumentURIToVOs));
|
||||
|
||||
}
|
||||
return allDocumentURIToVOs;
|
||||
}
|
||||
|
||||
}
|
||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils;
|
||||
|
||||
import java.util.Collection;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
|
||||
import org.apache.commons.lang.StringUtils;
|
||||
|
||||
import com.hp.hpl.jena.query.Dataset;
|
||||
import com.hp.hpl.jena.query.QuerySolution;
|
||||
import com.hp.hpl.jena.query.ResultSet;
|
||||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.RDFNode;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryFieldLabels;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.ModelConstructorUtilities;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.OrganizationAssociatedPeopleModelWithTypesConstructor;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.OrganizationModelWithTypesConstructor;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.OrganizationToGrantsForSubOrganizationsModelConstructor;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.OrganizationToPublicationsForSubOrganizationsModelConstructor;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.PersonToGrantsModelConstructor;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.PersonToPublicationsModelConstructor;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Activity;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Entity;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubEntity;
|
||||
|
||||
public class SelectOnModelUtilities {
|
||||
|
||||
public static Entity getSubjectOrganizationHierarchy(Dataset dataset,
|
||||
String subjectEntityURI) throws MalformedQueryParametersException {
|
||||
Model organizationModel = ModelConstructorUtilities
|
||||
.getOrConstructModel(
|
||||
null,
|
||||
OrganizationModelWithTypesConstructor.MODEL_TYPE,
|
||||
dataset);
|
||||
|
||||
Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
|
||||
fieldLabelToOutputFieldLabel.put("organizationLabel", QueryFieldLabels.ORGANIZATION_LABEL);
|
||||
fieldLabelToOutputFieldLabel.put("subOrganization", QueryFieldLabels.SUBORGANIZATION_URL);
|
||||
fieldLabelToOutputFieldLabel.put("subOrganizationLabel", QueryFieldLabels.SUBORGANIZATION_LABEL);
|
||||
fieldLabelToOutputFieldLabel.put("subOrganizationTypeLabel", QueryFieldLabels.SUBORGANIZATION_TYPE_LABEL);
|
||||
|
||||
String whereClause = ""
|
||||
+ " <" + subjectEntityURI + "> rdfs:label ?organizationLabel . "
|
||||
+ " <" + subjectEntityURI + "> core:hasSubOrganization ?subOrganization . "
|
||||
+ " ?subOrganization rdfs:label ?subOrganizationLabel . "
|
||||
+ " ?subOrganization rdf:type ?subOrgType . "
|
||||
+ " ?subOrgType rdfs:label ?subOrganizationTypeLabel . ";
|
||||
|
||||
QueryRunner<ResultSet> subOrganizationsWithTypesQuery =
|
||||
new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
|
||||
"",
|
||||
whereClause,
|
||||
"",
|
||||
organizationModel);
|
||||
|
||||
return getEntityWithSubOrganizations(subjectEntityURI,
|
||||
subOrganizationsWithTypesQuery.getQueryResult());
|
||||
}
|
||||
|
||||
private static Entity getEntityWithSubOrganizations(String subjectEntityURI, ResultSet queryResult) {
|
||||
|
||||
Entity entity = new Entity(subjectEntityURI);
|
||||
Map<String, SubEntity> subOrganizationURIToVO = new HashMap<String, SubEntity>();
|
||||
|
||||
while (queryResult.hasNext()) {
|
||||
|
||||
QuerySolution solution = queryResult.nextSolution();
|
||||
|
||||
if (StringUtils.isEmpty(entity.getEntityLabel())) {
|
||||
|
||||
RDFNode organizationLabelNode = solution.get(QueryFieldLabels.ORGANIZATION_LABEL);
|
||||
if (organizationLabelNode != null) {
|
||||
entity.setIndividualLabel(organizationLabelNode.toString());
|
||||
}
|
||||
}
|
||||
|
||||
RDFNode subOrganizationNode = solution.get(QueryFieldLabels.SUBORGANIZATION_URL);
|
||||
|
||||
SubEntity subEntity;
|
||||
|
||||
if (subOrganizationURIToVO.containsKey(subOrganizationNode.toString())) {
|
||||
|
||||
subEntity = subOrganizationURIToVO.get(subOrganizationNode.toString());
|
||||
|
||||
} else {
|
||||
|
||||
subEntity = new SubEntity(subOrganizationNode.toString());
|
||||
|
||||
subEntity.setEntityClass(VOConstants.EntityClassType.ORGANIZATION);
|
||||
|
||||
subOrganizationURIToVO.put(subOrganizationNode.toString(), subEntity);
|
||||
|
||||
RDFNode subOrganizationLabelNode = solution.get(QueryFieldLabels.SUBORGANIZATION_LABEL);
|
||||
if (subOrganizationLabelNode != null) {
|
||||
subEntity.setIndividualLabel(subOrganizationLabelNode.toString());
|
||||
}
|
||||
}
|
||||
|
||||
RDFNode subOrganizationTypeLabelNode = solution.get(QueryFieldLabels.SUBORGANIZATION_TYPE_LABEL);
|
||||
if (subOrganizationTypeLabelNode != null) {
|
||||
subEntity.addEntityTypeLabel(subOrganizationTypeLabelNode.toString());
|
||||
}
|
||||
}
|
||||
|
||||
entity.addSubEntitities(subOrganizationURIToVO.values());
|
||||
|
||||
return entity;
|
||||
}
|
||||
|
||||
public static Entity getSubjectOrganizationAssociatedPeople(Dataset dataset,
|
||||
String subjectEntityURI) throws MalformedQueryParametersException {
|
||||
Model associatedPeopleModel = ModelConstructorUtilities
|
||||
.getOrConstructModel(
|
||||
subjectEntityURI,
|
||||
OrganizationAssociatedPeopleModelWithTypesConstructor.MODEL_TYPE,
|
||||
dataset);
|
||||
|
||||
Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
|
||||
fieldLabelToOutputFieldLabel.put("organizationLabel", QueryFieldLabels.ORGANIZATION_LABEL);
|
||||
fieldLabelToOutputFieldLabel.put("person", QueryFieldLabels.PERSON_URL);
|
||||
fieldLabelToOutputFieldLabel.put("personLabel", QueryFieldLabels.PERSON_LABEL);
|
||||
fieldLabelToOutputFieldLabel.put("personTypeLabel", QueryFieldLabels.PERSON_TYPE_LABEL);
|
||||
|
||||
String whereClause = ""
|
||||
+ " <" + subjectEntityURI + "> rdfs:label ?organizationLabel . "
|
||||
+ " <" + subjectEntityURI + "> vivosocnet:hasPersonWithActivity ?person . "
|
||||
+ " ?person rdfs:label ?personLabel . "
|
||||
+ " ?person rdf:type ?personType . "
|
||||
+ " ?personType rdfs:label ?personTypeLabel . ";
|
||||
|
||||
QueryRunner<ResultSet> associatedPeopleWithTypesQuery =
|
||||
new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
|
||||
"",
|
||||
whereClause,
|
||||
"",
|
||||
associatedPeopleModel);
|
||||
|
||||
return getEntityWithAssociatedPeopleSubEntitities(subjectEntityURI, associatedPeopleWithTypesQuery.getQueryResult());
|
||||
}
|
||||
|
||||
private static Entity getEntityWithAssociatedPeopleSubEntitities(
|
||||
String subjectEntityURI, ResultSet queryResult) {
|
||||
|
||||
Entity entity = new Entity(subjectEntityURI);
|
||||
Map<String, SubEntity> associatedPeopleURIToVO = new HashMap<String, SubEntity>();
|
||||
|
||||
while (queryResult.hasNext()) {
|
||||
|
||||
QuerySolution solution = queryResult.nextSolution();
|
||||
|
||||
if (StringUtils.isEmpty(entity.getEntityLabel())) {
|
||||
|
||||
RDFNode organizationLabelNode = solution.get(QueryFieldLabels.ORGANIZATION_LABEL);
|
||||
if (organizationLabelNode != null) {
|
||||
entity.setIndividualLabel(organizationLabelNode.toString());
|
||||
}
|
||||
}
|
||||
|
||||
RDFNode personNode = solution.get(QueryFieldLabels.PERSON_URL);
|
||||
|
||||
SubEntity subEntity;
|
||||
|
||||
if (associatedPeopleURIToVO.containsKey(personNode.toString())) {
|
||||
|
||||
subEntity = associatedPeopleURIToVO.get(personNode.toString());
|
||||
|
||||
} else {
|
||||
|
||||
subEntity = new SubEntity(personNode.toString());
|
||||
subEntity.setEntityClass(VOConstants.EntityClassType.PERSON);
|
||||
associatedPeopleURIToVO.put(personNode.toString(), subEntity);
|
||||
|
||||
RDFNode personLabelNode = solution.get(QueryFieldLabels.PERSON_LABEL);
|
||||
if (personLabelNode != null) {
|
||||
subEntity.setIndividualLabel(personLabelNode.toString());
|
||||
}
|
||||
}
|
||||
|
||||
RDFNode personTypeLabelNode = solution.get(QueryFieldLabels.PERSON_TYPE_LABEL);
|
||||
if (personTypeLabelNode != null) {
|
||||
subEntity.addEntityTypeLabel(personTypeLabelNode.toString());
|
||||
}
|
||||
}
|
||||
|
||||
entity.addSubEntitities(associatedPeopleURIToVO.values());
|
||||
return entity;
|
||||
}
|
||||
|
||||
public static Map<String, Activity> getPublicationsForAllSubOrganizations(
|
||||
Dataset dataset, Entity organizationEntity)
|
||||
throws MalformedQueryParametersException {
|
||||
Map<String, Activity> allDocumentURIToVOs = new HashMap<String, Activity>();
|
||||
|
||||
for (SubEntity subOrganization : organizationEntity.getSubEntities()) {
|
||||
|
||||
Model subOrganizationPublicationsModel = ModelConstructorUtilities
|
||||
.getOrConstructModel(
|
||||
subOrganization.getIndividualURI(),
|
||||
OrganizationToPublicationsForSubOrganizationsModelConstructor.MODEL_TYPE,
|
||||
dataset);
|
||||
|
||||
System.out.println("getting publications for " + subOrganization.getIndividualLabel());
|
||||
|
||||
Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
|
||||
fieldLabelToOutputFieldLabel.put("document", QueryFieldLabels.DOCUMENT_URL);
|
||||
fieldLabelToOutputFieldLabel.put("documentLabel", QueryFieldLabels.DOCUMENT_LABEL);
|
||||
fieldLabelToOutputFieldLabel.put("documentPublicationDate", QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
|
||||
fieldLabelToOutputFieldLabel.put("lastCachedDateTime", QueryFieldLabels.LAST_CACHED_AT_DATETIME);
|
||||
|
||||
String whereClause = ""
|
||||
+ " <" + subOrganization.getIndividualURI() + "> vivosocnet:hasPersonWithPublication ?document . "
|
||||
+ " <" + subOrganization.getIndividualURI() + "> vivosocnet:lastCachedAt ?lastCachedDateTime . "
|
||||
+ " ?document rdfs:label ?documentLabel . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?document core:dateTimeValue ?dateTimeValue . "
|
||||
+ " ?dateTimeValue core:dateTime ?documentPublicationDate } . ";
|
||||
|
||||
QueryRunner<ResultSet> subOrganizationPublicationsQuery =
|
||||
new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
|
||||
"",
|
||||
whereClause,
|
||||
"",
|
||||
subOrganizationPublicationsModel);
|
||||
|
||||
subOrganization.addActivities(getPublicationForEntity(
|
||||
subOrganizationPublicationsQuery.getQueryResult(),
|
||||
allDocumentURIToVOs));
|
||||
|
||||
}
|
||||
return allDocumentURIToVOs;
|
||||
}
|
||||
|
||||
private static Collection<Activity> getPublicationForEntity(
|
||||
ResultSet queryResult,
|
||||
Map<String, Activity> allDocumentURIToVOs) {
|
||||
|
||||
Set<Activity> currentEntityPublications = new HashSet<Activity>();
|
||||
|
||||
while (queryResult.hasNext()) {
|
||||
|
||||
QuerySolution solution = queryResult.nextSolution();
|
||||
|
||||
RDFNode documentNode = solution.get(QueryFieldLabels.DOCUMENT_URL);
|
||||
Activity biboDocument;
|
||||
|
||||
if (allDocumentURIToVOs.containsKey(documentNode.toString())) {
|
||||
biboDocument = allDocumentURIToVOs.get(documentNode.toString());
|
||||
|
||||
} else {
|
||||
|
||||
biboDocument = new Activity(documentNode.toString());
|
||||
allDocumentURIToVOs.put(documentNode.toString(), biboDocument);
|
||||
|
||||
RDFNode publicationDateNode = solution.get(QueryFieldLabels
|
||||
.DOCUMENT_PUBLICATION_DATE);
|
||||
if (publicationDateNode != null) {
|
||||
biboDocument.setActivityDate(publicationDateNode.toString());
|
||||
}
|
||||
}
|
||||
|
||||
currentEntityPublications.add(biboDocument);
|
||||
|
||||
}
|
||||
|
||||
return currentEntityPublications;
|
||||
}
|
||||
|
||||
|
||||
private static Collection<Activity> getGrantForEntity(
|
||||
ResultSet queryResult,
|
||||
Map<String, Activity> allGrantURIToVO) {
|
||||
|
||||
Set<Activity> currentEntityGrants = new HashSet<Activity>();
|
||||
|
||||
while (queryResult.hasNext()) {
|
||||
|
||||
QuerySolution solution = queryResult.nextSolution();
|
||||
|
||||
RDFNode grantNode = solution.get(QueryFieldLabels.GRANT_URL);
|
||||
Activity coreGrant;
|
||||
|
||||
if (allGrantURIToVO.containsKey(grantNode.toString())) {
|
||||
coreGrant = allGrantURIToVO.get(grantNode.toString());
|
||||
|
||||
} else {
|
||||
|
||||
coreGrant = new Activity(grantNode.toString());
|
||||
allGrantURIToVO.put(grantNode.toString(), coreGrant);
|
||||
|
||||
RDFNode grantStartDateNode = solution.get(QueryFieldLabels.ROLE_START_DATE);
|
||||
|
||||
if (grantStartDateNode != null) {
|
||||
coreGrant.setActivityDate(grantStartDateNode.toString());
|
||||
} else {
|
||||
grantStartDateNode = solution
|
||||
.get(QueryFieldLabels.GRANT_START_DATE);
|
||||
if (grantStartDateNode != null) {
|
||||
coreGrant.setActivityDate(grantStartDateNode.toString());
|
||||
}
|
||||
}
|
||||
}
|
||||
currentEntityGrants.add(coreGrant);
|
||||
}
|
||||
return currentEntityGrants;
|
||||
}
|
||||
|
||||
public static Map<String, Activity> getGrantsForAllSubOrganizations(
|
||||
Dataset dataset, Entity organizationEntity)
|
||||
throws MalformedQueryParametersException {
|
||||
Map<String, Activity> allGrantURIToVO = new HashMap<String, Activity>();
|
||||
|
||||
for (SubEntity subOrganization : organizationEntity.getSubEntities()) {
|
||||
|
||||
System.out.println("constructing grants for " + subOrganization.getIndividualLabel() + " :: " + subOrganization.getIndividualURI());
|
||||
|
||||
Model subOrganizationGrantsModel = ModelConstructorUtilities
|
||||
.getOrConstructModel(
|
||||
subOrganization.getIndividualURI(),
|
||||
OrganizationToGrantsForSubOrganizationsModelConstructor.MODEL_TYPE,
|
||||
dataset);
|
||||
|
||||
Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
|
||||
fieldLabelToOutputFieldLabel.put("grant", QueryFieldLabels.GRANT_URL);
|
||||
fieldLabelToOutputFieldLabel.put("grantLabel", QueryFieldLabels.GRANT_LABEL);
|
||||
fieldLabelToOutputFieldLabel.put("grantStartDate", QueryFieldLabels.GRANT_START_DATE);
|
||||
fieldLabelToOutputFieldLabel.put("roleStartDate", QueryFieldLabels.ROLE_START_DATE);
|
||||
|
||||
String whereClause = ""
|
||||
+ "{"
|
||||
+ " <" + subOrganization.getIndividualURI() + "> vivosocnet:hasInvestigatorWithGrant ?grant . "
|
||||
+ " ?grant rdfs:label ?grantLabel . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
|
||||
+ "}"
|
||||
+ "UNION"
|
||||
+ "{"
|
||||
+ " <" + subOrganization.getIndividualURI() + "> vivosocnet:hasPIWithGrant ?grant . "
|
||||
+ " ?grant rdfs:label ?grantLabel . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
|
||||
+ "}"
|
||||
+ "UNION"
|
||||
+ "{"
|
||||
+ " <" + subOrganization.getIndividualURI() + "> vivosocnet:hascoPIWithGrant ?grant . "
|
||||
+ " ?grant rdfs:label ?grantLabel . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
|
||||
+ "}";
|
||||
|
||||
QueryRunner<ResultSet> subOrganizationGrantsQuery =
|
||||
new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
|
||||
"",
|
||||
whereClause,
|
||||
"",
|
||||
subOrganizationGrantsModel);
|
||||
|
||||
subOrganization.addActivities(getGrantForEntity(
|
||||
subOrganizationGrantsQuery.getQueryResult(),
|
||||
allGrantURIToVO));
|
||||
|
||||
}
|
||||
return allGrantURIToVO;
|
||||
}
|
||||
|
||||
public static Map<String, Activity> getGrantsForAssociatedPeople(
|
||||
Dataset dataset, Collection<SubEntity> people)
|
||||
throws MalformedQueryParametersException {
|
||||
Map<String, Activity> allGrantURIToVOs = new HashMap<String, Activity>();
|
||||
|
||||
System.out.println("peopel for grants under consideration are ");
|
||||
for (SubEntity person : people) {
|
||||
System.out.println(person.getIndividualURI() + " -- " + person.getIndividualLabel());
|
||||
}
|
||||
|
||||
for (SubEntity person : people) {
|
||||
|
||||
System.out.println("constructing grants for " + person.getIndividualLabel() + " :: " + person.getIndividualURI());
|
||||
|
||||
long before = System.currentTimeMillis();
|
||||
|
||||
Model personGrantsModel = ModelConstructorUtilities
|
||||
.getOrConstructModel(
|
||||
person.getIndividualURI(),
|
||||
PersonToGrantsModelConstructor.MODEL_TYPE,
|
||||
dataset);
|
||||
|
||||
System.out.print("\t construct took " + (System.currentTimeMillis() - before));
|
||||
|
||||
before = System.currentTimeMillis();
|
||||
|
||||
Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
|
||||
fieldLabelToOutputFieldLabel.put("grant", QueryFieldLabels.GRANT_URL);
|
||||
fieldLabelToOutputFieldLabel.put("grantLabel", QueryFieldLabels.GRANT_LABEL);
|
||||
fieldLabelToOutputFieldLabel.put("grantStartDate", QueryFieldLabels.GRANT_START_DATE);
|
||||
fieldLabelToOutputFieldLabel.put("roleStartDate", QueryFieldLabels.ROLE_START_DATE);
|
||||
|
||||
String whereClause = ""
|
||||
+ "{"
|
||||
+ " <" + person.getIndividualURI() + "> vivosocnet:hasGrantAsAnInvestigator ?grant . "
|
||||
+ " ?grant rdfs:label ?grantLabel . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
|
||||
+ "}"
|
||||
+ "UNION"
|
||||
+ "{"
|
||||
+ " <" + person.getIndividualURI() + "> vivosocnet:hasGrantAsPI ?grant . "
|
||||
+ " ?grant rdfs:label ?grantLabel . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
|
||||
+ "}"
|
||||
+ "UNION"
|
||||
+ "{"
|
||||
+ " <" + person.getIndividualURI() + "> vivosocnet:hasGrantAsCoPI ?grant . "
|
||||
+ " ?grant rdfs:label ?grantLabel . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnGrant ?grantStartDate } . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?grant vivosocnet:startDateTimeOnRole ?roleStartDate } . "
|
||||
+ "}";
|
||||
|
||||
QueryRunner<ResultSet> personGrantsQuery =
|
||||
new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
|
||||
"",
|
||||
whereClause,
|
||||
"",
|
||||
personGrantsModel);
|
||||
|
||||
person.addActivities(getGrantForEntity(
|
||||
personGrantsQuery.getQueryResult(),
|
||||
allGrantURIToVOs));
|
||||
|
||||
System.out.println("\t || select took " + (System.currentTimeMillis() - before));
|
||||
|
||||
}
|
||||
return allGrantURIToVOs;
|
||||
}
|
||||
|
||||
public static Map<String, Activity> getPublicationsForAssociatedPeople(
|
||||
Dataset dataset, Collection<SubEntity> people)
|
||||
throws MalformedQueryParametersException {
|
||||
Map<String, Activity> allDocumentURIToVOs = new HashMap<String, Activity>();
|
||||
|
||||
for (SubEntity person : people) {
|
||||
|
||||
Model personPublicationsModel = ModelConstructorUtilities
|
||||
.getOrConstructModel(
|
||||
person.getIndividualURI(),
|
||||
PersonToPublicationsModelConstructor.MODEL_TYPE,
|
||||
dataset);
|
||||
|
||||
System.out.println("getting publications for " + person.getIndividualLabel());
|
||||
|
||||
Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
|
||||
fieldLabelToOutputFieldLabel.put("document", QueryFieldLabels.DOCUMENT_URL);
|
||||
fieldLabelToOutputFieldLabel.put("documentLabel", QueryFieldLabels.DOCUMENT_LABEL);
|
||||
fieldLabelToOutputFieldLabel.put("documentPublicationDate", QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
|
||||
|
||||
String whereClause = ""
|
||||
+ " <" + person.getIndividualURI() + "> vivosocnet:hasPublication ?document . "
|
||||
+ " ?document rdfs:label ?documentLabel . "
|
||||
+ " OPTIONAL { "
|
||||
+ " ?document core:dateTimeValue ?dateTimeValue . "
|
||||
+ " ?dateTimeValue core:dateTime ?documentPublicationDate } . ";
|
||||
|
||||
QueryRunner<ResultSet> personPublicationsQuery =
|
||||
new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
|
||||
"",
|
||||
whereClause,
|
||||
"",
|
||||
personPublicationsModel);
|
||||
|
||||
person.addActivities(getPublicationForEntity(
|
||||
personPublicationsQuery.getQueryResult(),
|
||||
allDocumentURIToVOs));
|
||||
}
|
||||
return allDocumentURIToVOs;
|
||||
}
|
||||
}
|
||||
Loading…
Add table
Reference in a new issue