Merge branch 'maint-rel-1.6' of https://github.com/vivo-project/Vitro into maint-rel-1.6
This commit is contained in:
brianjlowe
commit
328abf20aa
4 changed files with 142 additions and 104 deletions
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@ -12,8 +12,10 @@ import edu.cornell.mannlib.vitro.webapp.beans.Individual;
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import edu.cornell.mannlib.vitro.webapp.search.IndexingException;
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import edu.cornell.mannlib.vitro.webapp.search.beans.IndexerIface;
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import edu.cornell.mannlib.vitro.webapp.search.solr.documentBuilding.IndividualToSolrDocument;
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import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
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class IndexWorkerThread extends Thread{
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class IndexWorkerThread extends VitroBackgroundThread{
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private static final Log log = LogFactory.getLog(IndexWorkerThread.class);
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protected final int threadNum;
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protected IndividualToSolrDocument individualToSolrDoc;
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@ -21,7 +23,6 @@ class IndexWorkerThread extends Thread{
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protected final Iterator<Individual> individualsToIndex;
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protected boolean stopRequested = false;
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private Log log = LogFactory.getLog(IndexWorkerThread.class);
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private static AtomicLong countCompleted= new AtomicLong();
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private static AtomicLong countToIndex= new AtomicLong();
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private static long starttime = 0;
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@ -38,6 +39,7 @@ class IndexWorkerThread extends Thread{
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}
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public void run(){
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setWorkLevel(WorkLevel.WORKING, "indexing " + individualsToIndex + " individuals");
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while( ! stopRequested ){
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@ -48,6 +50,8 @@ class IndexWorkerThread extends Thread{
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// done so shut this thread down.
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stopRequested = true;
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}
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setWorkLevel(WorkLevel.IDLE);
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log.debug("Worker number " + threadNum + " exiting.");
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}
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@ -82,8 +86,8 @@ class IndexWorkerThread extends Thread{
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}
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}
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}catch(Throwable th){
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//on tomcat shutdown odd exceptions get thrown and log can be null
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if( log != null && ! stopRequested )
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//on tomcat shutdown odd exceptions get thrown
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if( ! stopRequested )
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log.error("Exception during index building",th);
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}
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}
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@ -479,10 +479,10 @@ public class FakeApplicationOntologyService {
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@Override
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public Map<String, Object> getData(Map<String, Object> pageData) {
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Map<String, String[]> parms = new HashMap<String, String[]>();
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parms.put("uri", new String[] { individualUri });
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Map<String, Object> parms = new HashMap<>();
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parms.put("uri", individualUri);
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return doQuery(parms, getModel(ctx, vreq, null));
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return super.getData(parms);
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}
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}
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@ -29,8 +29,18 @@ import com.hp.hpl.jena.shared.Lock;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
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public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
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private final static Log log = LogFactory.getLog(SparqlQueryDataGetter.class);
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private static final String queryPropertyURI = "<" + DisplayVocabulary.QUERY + ">";
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private static final String saveToVarPropertyURI= "<" + DisplayVocabulary.SAVE_TO_VAR+ ">";
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private static final String queryModelPropertyURI= "<" + DisplayVocabulary.QUERY_MODEL+ ">";
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public static final String defaultVarNameForResults = "results";
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private static final String defaultTemplate = "menupage--defaultSparql.ftl";
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String dataGetterURI;
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String queryText;
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String saveToVar;
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@ -38,11 +48,6 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
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VitroRequest vreq;
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ServletContext context;
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final static Log log = LogFactory.getLog(SparqlQueryDataGetter.class);
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//default template
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private final static String defaultTemplate = "menupage--defaultSparql.ftl";
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/**
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* Constructor with display model and data getter URI that will be called by reflection.
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*/
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@ -50,20 +55,10 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
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this.configure(vreq, displayModel,dataGetterURI);
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}
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@Override
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public Map<String, Object> getData(Map<String, Object> pageData) {
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// Merge the pageData with the request parameters. PageData overrides
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Map<String, String[]> merged = new HashMap<String, String[]>();
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merged.putAll(vreq.getParameterMap());
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for (String key: pageData.keySet()) {
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merged.put(key, new String[] {String.valueOf(pageData.get(key))});
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}
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return doQuery( merged, getModel(context, vreq, modelURI));
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}
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/**
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* Configure this instance based on the URI and display model.
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*/
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@SuppressWarnings("hiding")
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protected void configure(VitroRequest vreq, Model displayModel, String dataGetterURI) {
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if( vreq == null )
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throw new IllegalArgumentException("VitroRequest may not be null.");
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@ -79,7 +74,6 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
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QuerySolutionMap initBindings = new QuerySolutionMap();
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initBindings.add("dataGetterURI", ResourceFactory.createResource(this.dataGetterURI));
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int count = 0;
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Query dataGetterConfigurationQuery = QueryFactory.create(dataGetterQuery) ;
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displayModel.enterCriticalSection(Lock.READ);
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try{
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@ -88,7 +82,6 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
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ResultSet res = qexec.execSelect();
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try{
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while( res.hasNext() ){
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count++;
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QuerySolution soln = res.next();
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//query is NOT OPTIONAL
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@ -121,52 +114,116 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
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}
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/**
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* Do the query and return a result. This is in its own method
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* to make testing easy.
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* Query to get the definition of the SparqlDataGetter for a given URI.
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*/
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protected Map<String, Object> doQuery(Map<String, String[]>parameterMap, Model queryModel){
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private static final String dataGetterQuery =
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"PREFIX display: <" + DisplayVocabulary.DISPLAY_NS +"> \n" +
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"SELECT ?query ?saveToVar ?queryModel WHERE { \n" +
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" ?dataGetterURI "+queryPropertyURI+" ?query . \n" +
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" OPTIONAL{ ?dataGetterURI "+saveToVarPropertyURI+" ?saveToVar } \n " +
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" OPTIONAL{ ?dataGetterURI "+queryModelPropertyURI+" ?queryModel } \n" +
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"}";
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if( this.queryText == null ){
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log.error("no SPARQL query defined for page " + this.dataGetterURI);
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@Override
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public Map<String, Object> getData(Map<String, Object> pageData) {
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Map<String, String> merged = mergeParameters(vreq.getParameterMap(), pageData);
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String boundQueryText = bindParameters(queryText, merged);
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if (modelURI != null) {
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return doQueryOnModel(boundQueryText, getModel(context, vreq, modelURI));
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} else {
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return doQueryOnRDFService(boundQueryText);
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}
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}
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/** Merge the pageData with the request parameters. PageData overrides. */
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private Map<String, String> mergeParameters(
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Map<String, String[]> parameterMap, Map<String, Object> pageData) {
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Map<String, String> merged = new HashMap<>();
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for (String key: parameterMap.keySet()) {
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merged.put(key, parameterMap.get(key)[0]);
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}
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for (String key: pageData.keySet()) {
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merged.put(key, String.valueOf(pageData.get(key)));
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}
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return merged;
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}
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/**
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* InitialBindings don't always work, and besides, RDFService doesn't accept
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* them. So do a text-based substitution.
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*
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* This assumes that every parameter is a URI. What if we want to substitute
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* a string value?
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*/
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private String bindParameters(String text, Map<String, String> merged) {
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String bound = text;
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for (String key : merged.keySet()) {
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bound.replace('?' + key, '<' + merged.get(key) + '>');
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}
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log.debug("query after binding parameters: " + bound);
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return bound;
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}
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/**
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* Do the query and return a result. This is in its own method, with
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* protected access, to make testing easy.
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*/
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protected Map<String, Object> doQueryOnRDFService(String q) {
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log.debug("Going to RDFService with " + q);
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ResultSet results = QueryUtils.getQueryResults(q, vreq);
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return assembleMap(parseResults(results));
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}
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/**
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* Do the query and return a result. This is in its own method, with
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* protected access, to make testing easy.
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*/
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protected Map<String, Object> doQueryOnModel(String q, Model queryModel){
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log.debug("Going to model " + modelURI + " with " + q);
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if (q == null) {
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return Collections.emptyMap();
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}
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//this may throw a SPARQL syntax error
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Query query = QueryFactory.create( this.queryText );
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//build query bindings
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QuerySolutionMap initialBindings = createBindings( parameterMap);
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//execute query
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List<Map<String,String>> results = executeQuery( query, queryModel, initialBindings);
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//put results in page data, what key to use for results?
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Map<String, Object> rmap = new HashMap<String,Object>();
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//also store the variable name within which results will be returned
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rmap.put("variableName", this.saveToVar);
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rmap.put(this.saveToVar, results);
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//This will be overridden at page level in display model if template specified there
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rmap.put("bodyTemplate", defaultTemplate);
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return rmap;
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Query query = makeQuery(q);
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if (query == null) {
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return Collections.emptyMap();
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}
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private List<Map<String, String>> executeQuery(Query query, Model model,
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QuerySolutionMap initialBindings) {
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return assembleMap(executeQuery( query, queryModel));
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}
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List<Map<String,String>> rows = new ArrayList<Map<String,String>>();
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private Query makeQuery(String q) {
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try {
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return QueryFactory.create(q);
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} catch (Exception e) {
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log.error("Failed to build a query from ''", e);
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return null;
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}
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}
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private List<Map<String, String>> executeQuery(Query query, Model model) {
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model.enterCriticalSection(Lock.READ);
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try{
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QueryExecution qexec= QueryExecutionFactory.create(query, model,initialBindings );
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QueryExecution qexec= QueryExecutionFactory.create(query, model );
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ResultSet results = qexec.execSelect();
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try{
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return parseResults(results);
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}finally{ qexec.close(); }
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}finally{ model.leaveCriticalSection(); }
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}
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/**
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* Converts a ResultSet into a List of Maps.
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*/
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private List<Map<String, String>> parseResults(ResultSet results) {
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List<Map<String,String>> rows = new ArrayList<Map<String,String>>();
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while (results.hasNext()) {
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QuerySolution soln = results.nextSolution();
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rows.add( toRow( soln ) );
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}
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}finally{ qexec.close(); }
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}finally{ model.leaveCriticalSection(); }
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return rows;
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}
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@ -186,8 +243,8 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
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private String toCell(RDFNode rdfNode) {
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if( rdfNode == null){
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return "";
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}else if( rdfNode.canAs( Literal.class )){
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return ((Literal)rdfNode.as(Literal.class)).getLexicalForm();
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}else if( rdfNode.isLiteral() ){
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return rdfNode.asLiteral().getLexicalForm();
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}else if( rdfNode.isResource() ){
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Resource resource = (Resource)rdfNode;
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if( ! resource.isAnon() ){
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@ -200,40 +257,17 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
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}
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}
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private Map<String, Object> assembleMap(List<Map<String, String>> results) {
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Map<String, Object> rmap = new HashMap<String,Object>();
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//put results in page data
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rmap.put(this.saveToVar, results);
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//also store the variable name within which results will be returned
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rmap.put("variableName", this.saveToVar);
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//This will be overridden at page level in display model if template specified there
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rmap.put("bodyTemplate", defaultTemplate);
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private QuerySolutionMap createBindings(Map<String, String[]>parameterMap) {
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QuerySolutionMap initBindings = new QuerySolutionMap();
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//could have bindings from HTTP parameters
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for( String var : parameterMap.keySet() ) {
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String[] values = parameterMap.get(var);
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if( values != null && values.length == 1 ){
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//what do do when we don't want a Resource?
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initBindings.add(var, ResourceFactory.createResource(values[0]) );
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}else if( values.length > 1){
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log.error("more than 1 http parameter for " + var);
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}
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}
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return initBindings;
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return rmap;
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}
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private static final String queryPropertyURI = "<" + DisplayVocabulary.QUERY + ">";
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private static final String saveToVarPropertyURI= "<" + DisplayVocabulary.SAVE_TO_VAR+ ">";
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private static final String queryModelPropertyURI= "<" + DisplayVocabulary.QUERY_MODEL+ ">";
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public static final String defaultVarNameForResults = "results";
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/**
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* Query to get the definition of the SparqlDataGetter for a given URI.
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*/
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private static final String dataGetterQuery =
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"PREFIX display: <" + DisplayVocabulary.DISPLAY_NS +"> \n" +
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"SELECT ?query ?saveToVar ?queryModel WHERE { \n" +
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" ?dataGetterURI "+queryPropertyURI+" ?query . \n" +
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" OPTIONAL{ ?dataGetterURI "+saveToVarPropertyURI+" ?saveToVar } \n " +
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" OPTIONAL{ ?dataGetterURI "+queryModelPropertyURI+" ?queryModel } \n" +
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"}";
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}
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@ -67,9 +67,9 @@ public class SparqlQueryDataGetterTest extends AbstractTestClass{
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String bobURI = "http://example.com/p/bob";
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dataModel.add(ResourceFactory.createResource(bobURI), RDF.type, ResourceFactory.createResource("http://xmlns.com/foaf/0.1/Person"));
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Map<String, String[]> params = Collections.emptyMap();
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Map<String, String> params = Collections.emptyMap();
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Map<String,Object> mapOut = sdg.doQuery(params, dataModel);
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Map<String,Object> mapOut = sdg.doQueryOnModel(sdg.queryText, dataModel);
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Assert.assertNotNull(mapOut);
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Assert.assertTrue("should contain key people" , mapOut.containsKey("people"));
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