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1. Improved logic in data response for temporal graphs.

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2. Fixed a performance problem with co-investigator network visualization.
This commit is contained in:
tankchintan 2011-08-10 23:02:42 +00:00
parent 88929f9cad
commit 40245b1a91
8 changed files with 269 additions and 467 deletions
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253
src/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java
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@ -1,253 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.visualization.persongrantcount;
import java.util.HashSet;
import java.util.Set;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import com.hp.hpl.jena.iri.IRI;
import com.hp.hpl.jena.iri.IRIFactory;
import com.hp.hpl.jena.iri.Violation;
import com.hp.hpl.jena.query.Dataset;
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.RDFNode;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryFieldLabels;
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Activity;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Individual;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
/**
* This query runner is used to execute Sparql query that will fetch all the grants for an
* individual.
* @author bkoniden
* Deepak Konidena
*
*/
public class PersonGrantCountQueryRunner implements QueryRunner<Set<Activity>> {
protected static final Syntax SYNTAX = Syntax.syntaxARQ;
private String personURI;
private Dataset dataset;
private Individual principalInvestigator;
public Individual getPrincipalInvestigator() {
return principalInvestigator;
}
private Log log;
private static final String SPARQL_QUERY_COMMON_SELECT_CLAUSE = ""
+ " SELECT (str(?PILabel) as ?PILabelLit) "
+ " (str(?Grant) as ?grantLit)"
+ " (str(?GrantLabel) as ?grantLabelLit)"
+ " (str(?startDateTimeValue) as ?grantStartDateLit) "
+ " (str(?endDateTimeValue) as ?grantEndDateLit) "
+ " (str(?startDateTimeValueForGrant) as ?grantStartDateForGrantLit) "
+ " (str(?endDateTimeValueForGrant) as ?grantEndDateForGrantLit) ";
private static final String SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME = ""
+ "OPTIONAL {"
+ " ?Role core:dateTimeInterval ?dateTimeIntervalValue . "
+ "?dateTimeIntervalValue core:start ?startDate . "
+ "?startDate core:dateTime ?startDateTimeValue . "
+ "OPTIONAL {"
+ "?dateTimeIntervalValue core:end ?endDate . "
+ "?endDate core:dateTime ?endDateTimeValue . "
+ "}"
+ "} . ";
private static final String SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME = ""
+ "OPTIONAL {"
+ " ?Grant core:dateTimeInterval ?dateTimeIntervalValueForGrant . "
+ "?dateTimeIntervalValueForGrant core:start ?startDateForGrant . "
+ "?startDateForGrant core:dateTime ?startDateTimeValueForGrant . "
+ "OPTIONAL {"
+ "?dateTimeIntervalValueForGrant core:end ?endDateForGrant . "
+ "?endDateForGrant core:dateTime ?endDateTimeValueForGrant . "
+ "}"
+ "}";
public PersonGrantCountQueryRunner(String personURI, Dataset dataset, Log log) {
this.personURI = personURI;
this.dataset = dataset;
this.log = log;
}
private Set<Activity> createJavaValueObjects(ResultSet resultSet) {
Set<Activity> grants = new HashSet<Activity>();
while (resultSet.hasNext()) {
QuerySolution solution = resultSet.nextSolution();
Activity grant = new Activity(solution.get(QueryFieldLabels.GRANT_URL).toString());
RDFNode grantLabelNode = solution.get(QueryFieldLabels.GRANT_LABEL);
if (grantLabelNode != null) {
grant.setIndividualLabel(grantLabelNode.toString());
}
RDFNode grantStartDateNode = solution.get(QueryFieldLabels.ROLE_START_DATE);
if (grantStartDateNode != null) {
grant.setActivityDate(grantStartDateNode.toString());
} else {
grantStartDateNode = solution.get(QueryFieldLabels.GRANT_START_DATE);
if (grantStartDateNode != null) {
grant.setActivityDate(grantStartDateNode.toString());
}
}
//TODO: verify grant end date is used or not.
/*
RDFNode grantEndDateNode = solution.get(QueryFieldLabels.ROLE_END_DATE);
if(grantEndDateNode != null){
grant.setGrantEndDate(grantEndDateNode.toString());
}else {
grantEndDateNode = solution.get(QueryFieldLabels.GRANT_END_DATE);
if(grantEndDateNode != null){
grant.setGrantEndDate(grantEndDateNode.toString());
}
}
*/
/*
* Since we are getting grant count for just one PI at a time we need
* to create only one "Individual" instance. We test against the null for "PI" to
* make sure that it has not already been instantiated.
* */
RDFNode investigatorURINode = solution.get(QueryFieldLabels.PI_URL);
if (investigatorURINode != null && principalInvestigator == null) {
principalInvestigator = new Individual(investigatorURINode.toString());
RDFNode investigatorLabelNode = solution.get(QueryFieldLabels.PI_LABEL);
if (investigatorLabelNode != null) {
principalInvestigator.setIndividualLabel(investigatorLabelNode.toString());
}
}
grants.add(grant);
}
return grants;
}
private ResultSet executeQuery(String queryURI, Dataset dataset) {
QueryExecution queryExecution = null;
Query query = QueryFactory.create(getSparqlQuery(queryURI), SYNTAX);
queryExecution = QueryExecutionFactory.create(query, dataset);
return queryExecution.execSelect();
}
private String getSparqlQuery(String queryURI) {
String sparqlQuery = QueryConstants.getSparqlPrefixQuery()
+ SPARQL_QUERY_COMMON_SELECT_CLAUSE
+ "(str(<" + queryURI + ">) as ?PILit) "
+ "WHERE "
+ "{ "
+ "<" + queryURI + "> rdfs:label ?PILabel . "
+ "{ "
+ "<" + queryURI + "> core:hasCo-PrincipalInvestigatorRole ?Role . "
+ "?Role core:roleIn ?Grant . "
+ "?Grant rdfs:label ?GrantLabel . "
+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
+ "} "
+ "UNION "
+ "{ "
+ "<" + queryURI + "> core:hasPrincipalInvestigatorRole ?Role . "
+ "?Role core:roleIn ?Grant . "
+ "?Grant rdfs:label ?GrantLabel . "
+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
+ "} "
+ "UNION "
+ "{ "
+ "<" + queryURI + "> core:hasInvestigatorRole ?Role . "
+ "?Role core:roleIn ?Grant . "
+ "?Grant rdfs:label ?GrantLabel . "
+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_ROLE_DATE_TIME
+ SPARQL_QUERY_COMMON_OPTIONAL_BLOCK_FOR_GRANT_DATE_TIME
+ "} "
+ "} ";
log.debug("SPARQL query for person grant count -> \n" + sparqlQuery);
//System.out.println("SPARQL query for person grant count -> \n"+ sparqlQuery);
return sparqlQuery;
}
public Set<Activity> getQueryResult() throws MalformedQueryParametersException {
if (StringUtils.isNotBlank(this.personURI)) {
/*
* To test the validity of the URI submitted
*/
IRIFactory iriFactory = IRIFactory.jenaImplementation();
IRI iri = iriFactory.create(this.personURI);
if (iri.hasViolation(false)) {
String errorMsg = ((Violation) iri.violations(false).next()).getShortMessage();
log.error("Grant Count vis Query " + errorMsg);
throw new MalformedQueryParametersException(
"URI provided for an individual is malformed.");
}
} else {
throw new MalformedQueryParametersException("URL parameter is either null or empty.");
}
ResultSet resultSet = executeQuery(this.personURI, this.dataset);
return createJavaValueObjects(resultSet);
}
}

66
src/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountRequestHandler.java
View file

@ -5,10 +5,8 @@ package edu.cornell.mannlib.vitro.webapp.visualization.persongrantcount;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import com.hp.hpl.jena.query.Dataset;
@ -21,9 +19,9 @@ import edu.cornell.mannlib.vitro.webapp.controller.visualization.DataVisualizati
import edu.cornell.mannlib.vitro.webapp.controller.visualization.VisualizationFrameworkConstants;
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Activity;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Individual;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.SparklineData;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.SubEntity;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.SelectOnModelUtilities;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequestHandler;
@ -53,23 +51,21 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
String personURI = vitroRequest
.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
QueryRunner<Set<Activity>> queryManager =
new PersonGrantCountQueryRunner(personURI, dataset, log);
SubEntity person = new SubEntity(
personURI,
UtilityFunctions.getIndividualLabelFromDAO(vitroRequest, personURI));
Map<String, Activity> grantsToURI = SelectOnModelUtilities.getGrantsForPerson(dataset, person, false);
Set<Activity> piGrants = queryManager.getQueryResult();
/*
* Create a map from the year to number of grants. Use the Grant's
* parsedGrantYear to populate the data.
* */
Map<String, Integer> yearToGrantCount =
UtilityFunctions.getYearToActivityCount(piGrants);
UtilityFunctions.getYearToActivityCount(grantsToURI.values());
Individual investigator = ((PersonGrantCountQueryRunner) queryManager)
.getPrincipalInvestigator();
return prepareDataResponse(investigator,
piGrants,
return prepareDataResponse(person,
yearToGrantCount);
@ -96,17 +92,18 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
String visContainer = vitroRequest
.getParameter(VisualizationFrameworkConstants.VIS_CONTAINER_KEY);
QueryRunner<Set<Activity>> queryManager =
new PersonGrantCountQueryRunner(personURI, dataset, log);
Set<Activity> piGrants = queryManager.getQueryResult();
SubEntity person = new SubEntity(
personURI,
UtilityFunctions.getIndividualLabelFromDAO(vitroRequest, personURI));
Map<String, Activity> grantsToURI = SelectOnModelUtilities.getGrantsForPerson(dataset, person, false);
/*
* Create a map from the year to number of grants. Use the Grant's
* parsedGrantYear to populate the data.
* */
Map<String, Integer> yearToGrantCount =
UtilityFunctions.getYearToActivityCount(piGrants);
UtilityFunctions.getYearToActivityCount(grantsToURI.values());
boolean shouldVIVOrenderVis = yearToGrantCount.size() > 0 ? true : false;
@ -145,18 +142,19 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
String visContainer = vitroRequest
.getParameter(VisualizationFrameworkConstants.VIS_CONTAINER_KEY);
SubEntity person = new SubEntity(
personURI,
UtilityFunctions.getIndividualLabelFromDAO(vitroRequest, personURI));
QueryRunner<Set<Activity>> queryManager =
new PersonGrantCountQueryRunner(personURI, dataset, log);
Set<Activity> piGrants = queryManager.getQueryResult();
Map<String, Activity> grantsToURI = SelectOnModelUtilities.getGrantsForPerson(dataset, person, false);
/*
* Create a map from the year to number of grants. Use the Grant's
* parsedGrantYear to populate the data.
* */
Map<String, Integer> yearToGrantCount =
UtilityFunctions.getYearToActivityCount(piGrants);
UtilityFunctions.getYearToActivityCount(grantsToURI.values());
/*
* Computations required to generate HTML for the sparkline & related context.
@ -195,32 +193,14 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
* Provides response when csv file containing the grant count over the years
* is requested.
* @param investigator
* @param piGrants
* @param yearToGrantCount
* @return
*/
private Map<String, String> prepareDataResponse(
Individual investigator,
Set<Activity> piGrants,
SubEntity investigator,
Map<String, Integer> yearToGrantCount) {
String piName = null;
/*
* To protect against cases where there are no PI grants associated with the
* individual.
* */
if (piGrants.size() > 0) {
piName = investigator.getIndividualLabel();
}
/*
* To make sure that null/empty records for PI names do not cause any mischief.
* */
if (StringUtils.isBlank(piName)) {
piName = "no-principal-investigator";
}
String piName = investigator.getIndividualLabel();
String outputFileName = UtilityFunctions.slugify(piName)
+ "_grants-per-year" + ".csv";

43
src/edu/cornell/mannlib/vitro/webapp/visualization/personlevel/PersonLevelRequestHandler.java
View file

@ -4,7 +4,6 @@ package edu.cornell.mannlib.vitro.webapp.visualization.personlevel;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import org.apache.commons.logging.Log;
@ -23,14 +22,14 @@ import edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator.Co
import edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator.CoPIGrantCountQueryRunner;
import edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator.CoPIVisCodeGenerator;
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
import edu.cornell.mannlib.vitro.webapp.visualization.persongrantcount.PersonGrantCountQueryRunner;
import edu.cornell.mannlib.vitro.webapp.visualization.persongrantcount.PersonGrantCountVisCodeGenerator;
import edu.cornell.mannlib.vitro.webapp.visualization.personpubcount.PersonPublicationCountQueryRunner;
import edu.cornell.mannlib.vitro.webapp.visualization.personpubcount.PersonPublicationCountVisCodeGenerator;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Activity;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.SparklineData;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.SubEntity;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.ModelConstructor;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.SelectOnModelUtilities;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequestHandler;
@ -102,6 +101,8 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
if (VisualizationFrameworkConstants.COPI_VIS_MODE.equalsIgnoreCase(visMode)) {
ModelConstructor constructQueryRunner =
new CoPIGrantCountConstructQueryRunner(egoURI, dataset, log);
Model constructedModel = constructQueryRunner.getConstructedModel();
@ -109,23 +110,24 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
QueryRunner<CollaborationData> coPIQueryManager =
new CoPIGrantCountQueryRunner(egoURI, constructedModel, log);
QueryRunner<Set<Activity>> grantQueryManager =
new PersonGrantCountQueryRunner(egoURI, dataset, log);
CollaborationData coPIData = coPIQueryManager.getQueryResult();
/*
* grants over time sparkline
*/
Set<Activity> piGrants = grantQueryManager.getQueryResult();
/*
* Create a map from the year to number of grants. Use the Grant's
* parsedGrantYear to populate the data.
* */
Map<String, Integer> yearToGrantCount =
UtilityFunctions.getYearToActivityCount(piGrants);
SubEntity person = new SubEntity(egoURI,
UtilityFunctions
.getIndividualLabelFromDAO(vitroRequest, egoURI));
Map<String, Activity> grantsToURI = SelectOnModelUtilities.getGrantsForPerson(dataset, person, false);
/*
* Create a map from the year to number of grants. Use the Grant's
* parsedGrantYear to populate the data.
* */
Map<String, Integer> yearToGrantCount =
UtilityFunctions.getYearToActivityCount(grantsToURI.values());
PersonGrantCountVisCodeGenerator personGrantCountVisCodeGenerator =
new PersonGrantCountVisCodeGenerator(
@ -166,9 +168,6 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
QueryRunner<CollaborationData> coAuthorshipQueryManager =
new CoAuthorshipQueryRunner(egoURI, dataset, log);
QueryRunner<Set<Activity>> publicationQueryManager =
new PersonPublicationCountQueryRunner(egoURI, dataset, log);
CollaborationData coAuthorshipData = coAuthorshipQueryManager.getQueryResult();
/*
@ -176,14 +175,18 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
* sparklines. This will prepare all the data for the sparklines & other requested
* files.
* */
Set<Activity> authorDocuments = publicationQueryManager.getQueryResult();
SubEntity person = new SubEntity(egoURI,
UtilityFunctions
.getIndividualLabelFromDAO(vitroRequest, egoURI));
Map<String, Activity> publicationsToURI = SelectOnModelUtilities.getPublicationsForPerson(dataset, person, false);
/*
* Create a map from the year to number of publications. Use the BiboDocument's
* parsedPublicationYear to populate the data.
* */
Map<String, Integer> yearToPublicationCount =
UtilityFunctions.getYearToActivityCount(authorDocuments);
UtilityFunctions.getYearToActivityCount(publicationsToURI.values());
/*
* Computations required to generate HTML for the sparklines & related context.

2
src/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountRequestHandler.java
View file

@ -4,8 +4,8 @@ package edu.cornell.mannlib.vitro.webapp.visualization.personpubcount;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.Map.Entry;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;

54
src/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalGrantVisualizationRequestHandler.java
View file

@ -87,6 +87,8 @@ public class TemporalGrantVisualizationRequestHandler implements
String entityURI = vitroRequest
.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
VisConstants.DataVisMode currentDataMode = VisConstants.DataVisMode.CSV;
/*
* This will provide the data in json format mainly used for standalone temporal vis.
* */
@ -94,39 +96,27 @@ public class TemporalGrantVisualizationRequestHandler implements
.equalsIgnoreCase(vitroRequest
.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY))) {
if (StringUtils.isNotBlank(entityURI)) {
return getSubjectEntityAndGenerateDataResponse(
vitroRequest,
log,
dataset,
entityURI,
VisConstants.DataVisMode.JSON);
} else {
return getSubjectEntityAndGenerateDataResponse(
vitroRequest,
log,
dataset,
OrganizationUtilityFunctions
.getStaffProvidedOrComputedHighestLevelOrganization(
log,
dataset,
vitroRequest),
VisConstants.DataVisMode.JSON);
}
currentDataMode = VisConstants.DataVisMode.JSON;
} else {
/*
* This provides csv download files for the content in the tables.
* */
return getSubjectEntityAndGenerateDataResponse(
vitroRequest,
log,
dataset,
entityURI,
VisConstants.DataVisMode.CSV);
}
if (StringUtils.isBlank(entityURI)) {
entityURI = OrganizationUtilityFunctions
.getStaffProvidedOrComputedHighestLevelOrganization(
log,
dataset,
vitroRequest);
}
}
return getSubjectEntityAndGenerateDataResponse(
vitroRequest,
log,
dataset,
entityURI,
currentDataMode);
}
private Map<String, String> prepareDataErrorResponse() {

56
src/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalPublicationVisualizationRequestHandler.java
View file

@ -76,11 +76,6 @@ public class TemporalPublicationVisualizationRequestHandler implements
}
// System.out.println("current models in the system are");
// for (Map.Entry<String, Model> entry : ConstructedModelTracker.getAllModels().entrySet()) {
// System.out.println(entry.getKey() + " -> " + entry.getValue().size());
// }
//
return prepareStandaloneMarkupResponse(vitroRequest, entityURI);
}
@ -204,6 +199,8 @@ public class TemporalPublicationVisualizationRequestHandler implements
String entityURI = vitroRequest
.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
VisConstants.DataVisMode currentDataMode = VisConstants.DataVisMode.CSV;
/*
* This will provide the data in json format mainly used for standalone tmeporal vis.
* */
@ -211,41 +208,26 @@ public class TemporalPublicationVisualizationRequestHandler implements
.equalsIgnoreCase(vitroRequest.getParameter(
VisualizationFrameworkConstants.VIS_MODE_KEY))) {
if (StringUtils.isNotBlank(entityURI)) {
currentDataMode = VisConstants.DataVisMode.JSON;
if (StringUtils.isBlank(entityURI)) {
return getSubjectEntityAndGenerateDataResponse(
vitroRequest,
log,
dataset,
entityURI,
VisConstants.DataVisMode.JSON);
} else {
entityURI = OrganizationUtilityFunctions
.getStaffProvidedOrComputedHighestLevelOrganization(
log,
dataset,
vitroRequest);
return getSubjectEntityAndGenerateDataResponse(
vitroRequest,
log,
dataset,
OrganizationUtilityFunctions
.getStaffProvidedOrComputedHighestLevelOrganization(
log,
dataset,
vitroRequest),
VisConstants.DataVisMode.JSON);
}
}
} else {
/*
* This provides csv download files for the content in the tables.
* */
return getSubjectEntityAndGenerateDataResponse(
vitroRequest,
log,
dataset,
entityURI,
VisConstants.DataVisMode.CSV);
}
}
return getSubjectEntityAndGenerateDataResponse(
vitroRequest,
log,
dataset,
entityURI,
currentDataMode);
}

256
src/edu/cornell/mannlib/vitro/webapp/visualization/visutils/SelectOnModelUtilities.java
View file

@ -25,6 +25,8 @@ import edu.cornell.mannlib.vitro.webapp.visualization.modelconstructor.Organizat
import edu.cornell.mannlib.vitro.webapp.visualization.modelconstructor.OrganizationToPublicationsForSubOrganizationsModelConstructor;
import edu.cornell.mannlib.vitro.webapp.visualization.modelconstructor.PeopleToGrantsModelConstructor;
import edu.cornell.mannlib.vitro.webapp.visualization.modelconstructor.PeopleToPublicationsModelConstructor;
import edu.cornell.mannlib.vitro.webapp.visualization.modelconstructor.PersonToGrantsModelConstructor;
import edu.cornell.mannlib.vitro.webapp.visualization.modelconstructor.PersonToPublicationsModelConstructor;
import edu.cornell.mannlib.vitro.webapp.visualization.modelconstructor.SubOrganizationWithinModelConstructor;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Activity;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Entity;
@ -419,7 +421,8 @@ public class SelectOnModelUtilities {
private static void getPublicationForEntity(
ResultSet queryResult,
SubEntity subEntity, Map<String, Activity> allDocumentURIToVOs) {
SubEntity subEntity,
Map<String, Activity> allDocumentURIToVOs) {
Set<Activity> currentEntityPublications = new HashSet<Activity>();
@ -685,60 +688,137 @@ public class SelectOnModelUtilities {
dataset);
for (SubEntity person : people) {
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,
"",
peopleGrantsModel);
getGrantForEntity(personGrantsQuery.getQueryResult(), person, allGrantURIToVOs);
String lastCachedAtForEntity = getLastCachedAtDateTimeForEntityInModel(
person,
peopleGrantsModel);
person.setLastCachedAtDateTime(lastCachedAtForEntity);
updateGrantsForPerson(person, allGrantURIToVOs, peopleGrantsModel);
}
return allGrantURIToVOs;
}
/**
* This method side-effects person and the central grants map.
* @param person
* @param allGrantURIToVOs
* @param personGrantsModel
* @throws MalformedQueryParametersException
*/
private static void updateGrantsForPerson(SubEntity person,
Map<String, Activity> allGrantURIToVOs, Model personGrantsModel)
throws MalformedQueryParametersException {
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);
getGrantForEntity(personGrantsQuery.getQueryResult(), person, allGrantURIToVOs);
String lastCachedAtForEntity = getLastCachedAtDateTimeForEntityInModel(
person,
personGrantsModel);
person.setLastCachedAtDateTime(lastCachedAtForEntity);
}
public static Map<String, Activity> getGrantsForPerson(
Dataset dataset, SubEntity person, boolean doCache)
throws MalformedQueryParametersException {
Map<String, Activity> allGrantURIToVOs = new HashMap<String, Activity>();
Model personGrantsModel = null;
/*
* If we dont want to cache the results then create the model directly without
* using the ModelConstructorUtilities. Use case is the co-pi ego-centric
* visualization.
* */
if (doCache) {
personGrantsModel = ModelConstructorUtilities
.getOrConstructModel(
person.getIndividualURI(),
PersonToGrantsModelConstructor.MODEL_TYPE,
dataset);
} else {
ModelConstructor model = new PersonToGrantsModelConstructor(person.getIndividualURI(), dataset);
personGrantsModel = model.getConstructedModel();
}
updateGrantsForPerson(person, allGrantURIToVOs, personGrantsModel);
return allGrantURIToVOs;
}
public static Map<String, Activity> getPublicationsForPerson(
Dataset dataset, SubEntity person, boolean doCache)
throws MalformedQueryParametersException {
Map<String, Activity> allPublicationURIToVOs = new HashMap<String, Activity>();
Model personPublicationsModel = null;
/*
* If we dont want to cache the results then create the model directly without
* using the ModelConstructorUtilities. Use case is the co-author ego-centric
* visualization.
* */
if (doCache) {
personPublicationsModel = ModelConstructorUtilities
.getOrConstructModel(
person.getIndividualURI(),
PersonToPublicationsModelConstructor.MODEL_TYPE,
dataset);
} else {
ModelConstructor model = new PersonToPublicationsModelConstructor(person.getIndividualURI(), dataset);
personPublicationsModel = model.getConstructedModel();
}
updatePublicationsForPerson(person, allPublicationURIToVOs, personPublicationsModel);
return allPublicationURIToVOs;
}
public static Map<String, Activity> getPublicationsForAssociatedPeople(
Dataset dataset, Collection<SubEntity> people)
@ -753,40 +833,54 @@ public class SelectOnModelUtilities {
for (SubEntity person : people) {
// 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,
"",
peoplePublicationsModel);
getPublicationForEntity(personPublicationsQuery.getQueryResult(),
person,
allDocumentURIToVOs);
String lastCachedAtForEntity = getLastCachedAtDateTimeForEntityInModel(
person,
updatePublicationsForPerson(person, allDocumentURIToVOs,
peoplePublicationsModel);
person.setLastCachedAtDateTime(lastCachedAtForEntity);
}
return allDocumentURIToVOs;
}
/**
* This method side-effects the person and the central documents map.
* @param person
* @param allDocumentURIToVOs
* @param peoplePublicationsModel
* @throws MalformedQueryParametersException
*/
private static void updatePublicationsForPerson(SubEntity person,
Map<String, Activity> allDocumentURIToVOs,
Model peoplePublicationsModel)
throws MalformedQueryParametersException {
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,
"",
peoplePublicationsModel);
getPublicationForEntity(personPublicationsQuery.getQueryResult(),
person,
allDocumentURIToVOs);
String lastCachedAtForEntity = getLastCachedAtDateTimeForEntityInModel(
person,
peoplePublicationsModel);
person.setLastCachedAtDateTime(lastCachedAtForEntity);
}
public static Map<String, Activity> getPublicationsWithJournalForAssociatedPeople(
Dataset dataset, Collection<SubEntity> people)

6
src/edu/cornell/mannlib/vitro/webapp/visualization/visutils/UtilityFunctions.java
View file

@ -3,6 +3,7 @@
package edu.cornell.mannlib.vitro.webapp.visualization.visutils;
import java.io.IOException;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
@ -68,6 +69,11 @@ public class UtilityFunctions {
return yearToActivityCount;
}
public static Map<String, Integer> getYearToActivityCount(
Collection<Activity> activities) {
return getYearToActivityCount(new HashSet<Activity>(activities));
}
/**
* This method is used to return a mapping between activity year & all the collaborators
* that published with ego in that year.