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VIVO-452 Revise SparqlQueryDataGetter to use RDFService if possible.

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This commit is contained in:
j2blake 2013-11-04 15:02:15 -05:00
parent f75b1159e5
commit 2f78e09765
4 changed files with 142 additions and 104 deletions
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12
webapp/src/edu/cornell/mannlib/vitro/webapp/search/indexing/IndexWorkerThread.java
View file

@ -12,8 +12,10 @@ import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.search.IndexingException;
import edu.cornell.mannlib.vitro.webapp.search.beans.IndexerIface;
import edu.cornell.mannlib.vitro.webapp.search.solr.documentBuilding.IndividualToSolrDocument;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
class IndexWorkerThread extends Thread{
class IndexWorkerThread extends VitroBackgroundThread{
private static final Log log = LogFactory.getLog(IndexWorkerThread.class);
protected final int threadNum;
protected IndividualToSolrDocument individualToSolrDoc;
@ -21,7 +23,6 @@ class IndexWorkerThread extends Thread{
protected final Iterator<Individual> individualsToIndex;
protected boolean stopRequested = false;
private Log log = LogFactory.getLog(IndexWorkerThread.class);
private static AtomicLong countCompleted= new AtomicLong();
private static AtomicLong countToIndex= new AtomicLong();
private static long starttime = 0;
@ -38,6 +39,7 @@ class IndexWorkerThread extends Thread{
}
public void run(){
setWorkLevel(WorkLevel.WORKING, "indexing " + individualsToIndex + " individuals");
while( ! stopRequested ){
@ -48,6 +50,8 @@ class IndexWorkerThread extends Thread{
// done so shut this thread down.
stopRequested = true;
}
setWorkLevel(WorkLevel.IDLE);
log.debug("Worker number " + threadNum + " exiting.");
}
@ -82,8 +86,8 @@ class IndexWorkerThread extends Thread{
}
}
}catch(Throwable th){
//on tomcat shutdown odd exceptions get thrown and log can be null
if( log != null && ! stopRequested )
//on tomcat shutdown odd exceptions get thrown
if( ! stopRequested )
log.error("Exception during index building",th);
}
}

6
webapp/src/edu/cornell/mannlib/vitro/webapp/services/shortview/FakeApplicationOntologyService.java
View file

@ -479,10 +479,10 @@ public class FakeApplicationOntologyService {
@Override
public Map<String, Object> getData(Map<String, Object> pageData) {
Map<String, String[]> parms = new HashMap<String, String[]>();
parms.put("uri", new String[] { individualUri });
Map<String, Object> parms = new HashMap<>();
parms.put("uri", individualUri);
return doQuery(parms, getModel(ctx, vreq, null));
return super.getData(parms);
}
}

196
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/SparqlQueryDataGetter.java
View file

@ -29,8 +29,18 @@ import com.hp.hpl.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
private final static Log log = LogFactory.getLog(SparqlQueryDataGetter.class);
private static final String queryPropertyURI = "<" + DisplayVocabulary.QUERY + ">";
private static final String saveToVarPropertyURI= "<" + DisplayVocabulary.SAVE_TO_VAR+ ">";
private static final String queryModelPropertyURI= "<" + DisplayVocabulary.QUERY_MODEL+ ">";
public static final String defaultVarNameForResults = "results";
private static final String defaultTemplate = "menupage--defaultSparql.ftl";
String dataGetterURI;
String queryText;
String saveToVar;
@ -38,11 +48,6 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
VitroRequest vreq;
ServletContext context;
final static Log log = LogFactory.getLog(SparqlQueryDataGetter.class);
//default template
private final static String defaultTemplate = "menupage--defaultSparql.ftl";
/**
* Constructor with display model and data getter URI that will be called by reflection.
*/
@ -50,20 +55,10 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
this.configure(vreq, displayModel,dataGetterURI);
}
@Override
public Map<String, Object> getData(Map<String, Object> pageData) {
// Merge the pageData with the request parameters. PageData overrides
Map<String, String[]> merged = new HashMap<String, String[]>();
merged.putAll(vreq.getParameterMap());
for (String key: pageData.keySet()) {
merged.put(key, new String[] {String.valueOf(pageData.get(key))});
}
return doQuery( merged, getModel(context, vreq, modelURI));
}
/**
* Configure this instance based on the URI and display model.
*/
@SuppressWarnings("hiding")
protected void configure(VitroRequest vreq, Model displayModel, String dataGetterURI) {
if( vreq == null )
throw new IllegalArgumentException("VitroRequest may not be null.");
@ -79,7 +74,6 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
QuerySolutionMap initBindings = new QuerySolutionMap();
initBindings.add("dataGetterURI", ResourceFactory.createResource(this.dataGetterURI));
int count = 0;
Query dataGetterConfigurationQuery = QueryFactory.create(dataGetterQuery) ;
displayModel.enterCriticalSection(Lock.READ);
try{
@ -88,7 +82,6 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
ResultSet res = qexec.execSelect();
try{
while( res.hasNext() ){
count++;
QuerySolution soln = res.next();
//query is NOT OPTIONAL
@ -121,52 +114,116 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
}
/**
* Do the query and return a result. This is in its own method
* to make testing easy.
* Query to get the definition of the SparqlDataGetter for a given URI.
*/
protected Map<String, Object> doQuery(Map<String, String[]>parameterMap, Model queryModel){
private static final String dataGetterQuery =
"PREFIX display: <" + DisplayVocabulary.DISPLAY_NS +"> \n" +
"SELECT ?query ?saveToVar ?queryModel WHERE { \n" +
" ?dataGetterURI "+queryPropertyURI+" ?query . \n" +
" OPTIONAL{ ?dataGetterURI "+saveToVarPropertyURI+" ?saveToVar } \n " +
" OPTIONAL{ ?dataGetterURI "+queryModelPropertyURI+" ?queryModel } \n" +
"}";
if( this.queryText == null ){
log.error("no SPARQL query defined for page " + this.dataGetterURI);
@Override
public Map<String, Object> getData(Map<String, Object> pageData) {
Map<String, String> merged = mergeParameters(vreq.getParameterMap(), pageData);
String boundQueryText = bindParameters(queryText, merged);
if (modelURI != null) {
return doQueryOnModel(boundQueryText, getModel(context, vreq, modelURI));
} else {
return doQueryOnRDFService(boundQueryText);
}
}
/** Merge the pageData with the request parameters. PageData overrides. */
private Map<String, String> mergeParameters(
Map<String, String[]> parameterMap, Map<String, Object> pageData) {
Map<String, String> merged = new HashMap<>();
for (String key: parameterMap.keySet()) {
merged.put(key, parameterMap.get(key)[0]);
}
for (String key: pageData.keySet()) {
merged.put(key, String.valueOf(pageData.get(key)));
}
return merged;
}
/**
* InitialBindings don't always work, and besides, RDFService doesn't accept
* them. So do a text-based substitution.
*
* This assumes that every parameter is a URI. What if we want to substitute
* a string value?
*/
private String bindParameters(String text, Map<String, String> merged) {
String bound = text;
for (String key : merged.keySet()) {
bound.replace('?' + key, '<' + merged.get(key) + '>');
}
log.debug("query after binding parameters: " + bound);
return bound;
}
/**
* Do the query and return a result. This is in its own method, with
* protected access, to make testing easy.
*/
protected Map<String, Object> doQueryOnRDFService(String q) {
log.debug("Going to RDFService with " + q);
ResultSet results = QueryUtils.getQueryResults(q, vreq);
return assembleMap(parseResults(results));
}
/**
* Do the query and return a result. This is in its own method, with
* protected access, to make testing easy.
*/
protected Map<String, Object> doQueryOnModel(String q, Model queryModel){
log.debug("Going to model " + modelURI + " with " + q);
if (q == null) {
return Collections.emptyMap();
}
//this may throw a SPARQL syntax error
Query query = QueryFactory.create( this.queryText );
//build query bindings
QuerySolutionMap initialBindings = createBindings( parameterMap);
//execute query
List<Map<String,String>> results = executeQuery( query, queryModel, initialBindings);
//put results in page data, what key to use for results?
Map<String, Object> rmap = new HashMap<String,Object>();
//also store the variable name within which results will be returned
rmap.put("variableName", this.saveToVar);
rmap.put(this.saveToVar, results);
//This will be overridden at page level in display model if template specified there
rmap.put("bodyTemplate", defaultTemplate);
return rmap;
Query query = makeQuery(q);
if (query == null) {
return Collections.emptyMap();
}
private List<Map<String, String>> executeQuery(Query query, Model model,
QuerySolutionMap initialBindings) {
return assembleMap(executeQuery( query, queryModel));
}
List<Map<String,String>> rows = new ArrayList<Map<String,String>>();
private Query makeQuery(String q) {
try {
return QueryFactory.create(q);
} catch (Exception e) {
log.error("Failed to build a query from ''", e);
return null;
}
}
private List<Map<String, String>> executeQuery(Query query, Model model) {
model.enterCriticalSection(Lock.READ);
try{
QueryExecution qexec= QueryExecutionFactory.create(query, model,initialBindings );
QueryExecution qexec= QueryExecutionFactory.create(query, model );
ResultSet results = qexec.execSelect();
try{
return parseResults(results);
}finally{ qexec.close(); }
}finally{ model.leaveCriticalSection(); }
}
/**
* Converts a ResultSet into a List of Maps.
*/
private List<Map<String, String>> parseResults(ResultSet results) {
List<Map<String,String>> rows = new ArrayList<Map<String,String>>();
while (results.hasNext()) {
QuerySolution soln = results.nextSolution();
rows.add( toRow( soln ) );
}
}finally{ qexec.close(); }
}finally{ model.leaveCriticalSection(); }
return rows;
}
@ -186,8 +243,8 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
private String toCell(RDFNode rdfNode) {
if( rdfNode == null){
return "";
}else if( rdfNode.canAs( Literal.class )){
return ((Literal)rdfNode.as(Literal.class)).getLexicalForm();
}else if( rdfNode.isLiteral() ){
return rdfNode.asLiteral().getLexicalForm();
}else if( rdfNode.isResource() ){
Resource resource = (Resource)rdfNode;
if( ! resource.isAnon() ){
@ -200,40 +257,17 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
}
}
private Map<String, Object> assembleMap(List<Map<String, String>> results) {
Map<String, Object> rmap = new HashMap<String,Object>();
//put results in page data
rmap.put(this.saveToVar, results);
//also store the variable name within which results will be returned
rmap.put("variableName", this.saveToVar);
//This will be overridden at page level in display model if template specified there
rmap.put("bodyTemplate", defaultTemplate);
private QuerySolutionMap createBindings(Map<String, String[]>parameterMap) {
QuerySolutionMap initBindings = new QuerySolutionMap();
//could have bindings from HTTP parameters
for( String var : parameterMap.keySet() ) {
String[] values = parameterMap.get(var);
if( values != null && values.length == 1 ){
//what do do when we don't want a Resource?
initBindings.add(var, ResourceFactory.createResource(values[0]) );
}else if( values.length > 1){
log.error("more than 1 http parameter for " + var);
}
}
return initBindings;
return rmap;
}
private static final String queryPropertyURI = "<" + DisplayVocabulary.QUERY + ">";
private static final String saveToVarPropertyURI= "<" + DisplayVocabulary.SAVE_TO_VAR+ ">";
private static final String queryModelPropertyURI= "<" + DisplayVocabulary.QUERY_MODEL+ ">";
public static final String defaultVarNameForResults = "results";
/**
* Query to get the definition of the SparqlDataGetter for a given URI.
*/
private static final String dataGetterQuery =
"PREFIX display: <" + DisplayVocabulary.DISPLAY_NS +"> \n" +
"SELECT ?query ?saveToVar ?queryModel WHERE { \n" +
" ?dataGetterURI "+queryPropertyURI+" ?query . \n" +
" OPTIONAL{ ?dataGetterURI "+saveToVarPropertyURI+" ?saveToVar } \n " +
" OPTIONAL{ ?dataGetterURI "+queryModelPropertyURI+" ?queryModel } \n" +
"}";
}

4
webapp/test/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/SparqlQueryDataGetterTest.java
View file

@ -67,9 +67,9 @@ public class SparqlQueryDataGetterTest extends AbstractTestClass{
String bobURI = "http://example.com/p/bob";
dataModel.add(ResourceFactory.createResource(bobURI), RDF.type, ResourceFactory.createResource("http://xmlns.com/foaf/0.1/Person"));
Map<String, String[]> params = Collections.emptyMap();
Map<String, String> params = Collections.emptyMap();
Map<String,Object> mapOut = sdg.doQuery(params, dataModel);
Map<String,Object> mapOut = sdg.doQueryOnModel(sdg.queryText, dataModel);
Assert.assertNotNull(mapOut);
Assert.assertTrue("should contain key people" , mapOut.containsKey("people"));