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Revision 7413db32

Added by Andreas Kohlbecker over 8 years ago

ID 7413db324b2eaaf87e0de84ef7eb4d2410dafb0f
Parent 9e235ff9
Child 99b66a4f

implementing MatchingNameString and MatchingNameType

     import org.bgbm.biovel.drf.utils.Profiler;
     import org.bgbm.biovel.drf.utils.TnrMsgUtils;
     import org.neo4j.graphdb.Relationship;
     import org.openrdf.query.MalformedQueryException;
     import org.openrdf.query.QueryEvaluationException;
     import org.openrdf.query.QueryLanguage;
     import org.openrdf.query.TupleQuery;
     import org.openrdf.query.TupleQueryResult;
     import org.openrdf.repository.RepositoryException;
     import org.openrdf.repository.sail.SailRepositoryConnection;
     import com.tinkerpop.blueprints.Direction;
     import com.tinkerpop.blueprints.Graph;
     import com.tinkerpop.blueprints.Vertex;
     import com.tinkerpop.blueprints.impls.neo4j2.Neo4j2Graph;
     import com.tinkerpop.blueprints.impls.neo4j2.Neo4j2Vertex;
     import com.tinkerpop.blueprints.oupls.sail.GraphSail;
     import com.tinkerpop.gremlin.java.GremlinPipeline;
     import com.tinkerpop.pipes.PipeFunction;
     import com.tinkerpop.pipes.util.FastNoSuchElementException;
     import com.tinkerpop.pipes.util.structures.Table;
     public class EEA_BDC_Client extends AggregateChecklistClient<TinkerPopClient> {
-...
                 Query query = singleQueryFrom(tnrMsg);
                 boolean  TUPLEQUERY = false;
                 boolean Neo4jINDEX = true;
                 String filter;
                 String queryString = query.getRequest().getQueryString();
                 logger.debug("original queryString: "+ queryString);
                 queryString = QueryParser.escape(queryString);
                 queryString = queryString.replace(" ", "\\ ");
                 logger.debug("original queryString: "+ queryString);
                 PipeFunction<Vertex, Boolean> matchFilter;
                 if(query.getRequest().getSearchMode().equals(SearchMode.scientificNameLike.name())) {
                     filter = "(regex(?name, \"^" + queryString + "\"))";
                     matchFilter = queryClient.createStarttWithFilter(queryString);
                     // need to escape white space and add wildcard to the end
                     queryString += "*";
                 } else {
                     filter = "(?name = \"" + queryString + "\")";
                     matchFilter = queryClient.createEqualsFilter(queryString);
+                }
                 logger.debug("prepared queryString: "+ queryString);
                 if(TUPLEQUERY) {
                     StringBuilder sparql = prepareQueryString();
                     sparql.append(
                             "SELECT ?eunisurl \n"
                             + "WHERE {\n"
                             + "     ?eunisurl es:binomialName ?name . \n"
                             + "     FILTER " + filter  + " \n"
                             + "}"
                             );
                     Neo4j2Graph neo4jGraph = (Neo4j2Graph)queryClient.graph();
                     Vertex v = neo4jGraph.getVertex(2);
                     SailRepositoryConnection connection = null;
                     try {
                         Profiler profiler = Profiler.newCpuProfiler(true);
                         connection = queryClient.connection();
                         TupleQuery tquery = connection.prepareTupleQuery(QueryLanguage.SPARQL, sparql.toString());
                         TupleQueryResult tqresult = tquery.evaluate();
                         queryClient.showResults(tqresult);
                         profiler.end(System.err);
                     } catch (MalformedQueryException | RepositoryException | QueryEvaluationException e1) {
                         // TODO Auto-generated catch block
                         e1.printStackTrace();
                     } catch (Exception e1) {
                         // yourkit
                         e1.printStackTrace();
                     } finally {
                         try {
                             connection.close();
                         } catch (RepositoryException e1) {
                             // IGNORE //
+                        }
                         connection = null;
+                    }
+                }
                 GremlinPipeline<Graph, Vertex> pipe = null;
                 if(Neo4jINDEX) {
                     Profiler profiler = Profiler.newCpuProfiler(false);
                 Profiler profiler = Profiler.newCpuProfiler(false);
                     logger.debug("Neo4jINDEX");
                 logger.debug("Neo4jINDEX");
                     ArrayList<Vertex> hitVs = queryClient.vertexIndexQuery("value:" + queryString);
                     pipe = new GremlinPipeline<Graph, Vertex>(hitVs);
                 ArrayList<Vertex> hitVs = queryClient.vertexIndexQuery("value:" + queryString);
                 pipe = new GremlinPipeline<Graph, Vertex>(hitVs);
                     List<Vertex> vertices = new ArrayList<Vertex>();
                     pipe.in(RdfSchema.EUNIS_SPECIES.propertyURI("binomialName")).fill(vertices);
                 List<Vertex> vertices = new ArrayList<Vertex>();
                 pipe.in(RdfSchema.EUNIS_SPECIES.propertyURI("binomialName")).fill(vertices);
                     updateQueriesWithResponse(vertices, checklistInfo, query);
                     profiler.end(System.err);
+                }
                 updateQueriesWithResponse(vertices, null, null, checklistInfo, query);
                 profiler.end(System.err);
+            }
+        }
-...
                 Query query = singleQueryFrom(tnrMsg);
                 String queryString = query.getRequest().getQueryString();
                 logger.debug("original queryString: "+ queryString);
                 queryString = QueryParser.escape(queryString);
                 queryString = queryString.replace(" ", "\\ ");
                 logger.debug("original queryString: "+ queryString);
                 if(query.getRequest().getSearchMode().equals(SearchMode.vernacularNameLike.name())) {
                     queryString = "*" + queryString + "*";
+                }
-...
                 List<Vertex> vertices = new ArrayList<Vertex>();
                 pipe = new GremlinPipeline<Graph, Vertex>(hitVs);
                 pipe.in(RdfSchema.DWC.propertyURI("vernacularName")).fill(vertices);
                 Table table = new Table();
                 pipe.as("match").in(RdfSchema.DWC.propertyURI("vernacularName")).as("taxon").table(table).iterate();
                 updateQueriesWithResponse(vertices, checklistInfo, query);
                 updateQueriesWithResponse(
                         table.getColumn("taxon"), table.getColumn("match"),
                         NameType.VERNACULAR_NAME, checklistInfo, query);
                 profiler.end(System.err);
+            }
+        }
-...
                 queryString = QueryParser.escape(queryString);
                 ArrayList<Vertex> hitVs = queryClient.vertexIndexQuery("value:" + queryString);
                 if(hitVs.size() > 0) {
                     Response response = tnrResponseFromResource(hitVs.get(0), query.getRequest());
                     Response response = tnrResponseFromResource(hitVs.get(0), query.getRequest(), null, null);
                     query.getResponse().add(response);
                 } else if(hitVs.size() > 1) {
                     throw new DRFChecklistException("More than one node with the id '" + queryString + "' found");
-...
+            }
+        }
         private void updateQueriesWithResponse(List<Vertex> nodes, ServiceProviderInfo ci, Query query){
         private void updateQueriesWithResponse(List<Vertex> taxonNodes, List<Vertex> matchNodes, NameType matchType, ServiceProviderInfo ci, Query query){
             if (nodes == null) {
             if (taxonNodes == null) {
                 return;
+            }
             logger.debug("matching taxon nodes:");
             for (Vertex v : nodes) {
             int i = -1;
             for (Vertex v : taxonNodes) {
                 i++;
                 logger.debug("  " + v.toString());
                 printPropertyKeys(v, System.err);
                 if(v.getProperty("kind").equals("url")) {
                     logger.error("vertex of type 'url' expected, but was " + v.getProperty("type").equals("url"));
                     continue;
+                }
                 Response tnrResponse = tnrResponseFromResource(v, query.getRequest());
                 Vertex matchNode = null;
                 if(matchNodes != null) {
                     matchNode = matchNodes.get(i);
+                }
                 Response tnrResponse = tnrResponseFromResource(v, query.getRequest(), matchNode, matchType);
                 if(tnrResponse != null) {
                     query.getResponse().add(tnrResponse);
+                }
-...
          * @param model
          * @param taxonR
          * @param request
          * @param matchType
          * @param matchNode
          * @return
          */
         @SuppressWarnings("unused")
         private Response tnrResponseFromResource(Vertex taxonV, Request request) {
         private Response tnrResponseFromResource(Vertex taxonV, Request request, Vertex matchNode, NameType matchType) {
             Response tnrResponse = TnrMsgUtils.tnrResponseFor(getServiceProviderInfo());
-...
             String validName = queryClient.relatedVertexValue(taxonV, RdfSchema.EUNIS_SPECIES, "validName");
             boolean isAccepted = validName != null && validName.equals("true");
             boolean skipThis = false;
             logger.debug("processing " + (isAccepted ? "accepted taxon" : "synonym or other")  + " " + taxonV.getId());
             //
             if(matchNode != null) {
                 String matchingName = matchNode.getProperty(GraphSail.VALUE).toString();
                 tnrResponse.setMatchingNameString(matchingName);
                 tnrResponse.setMatchingNameType(matchType);
+            }
             // case when accepted name
             if(isAccepted) {
                 Taxon taxon = createTaxon(taxonV);
                 tnrResponse.setTaxon(taxon);
                 tnrResponse.setMatchingNameType(NameType.TAXON);
                 String matchingName = taxon.getTaxonName().getCanonicalName();
                 tnrResponse.setMatchingNameString(matchingName);
                 if(matchNode == null) {
                     tnrResponse.setMatchingNameType(NameType.TAXON);
                     String matchingName = taxon.getTaxonName().getCanonicalName();
                     tnrResponse.setMatchingNameString(matchingName);
+                }
+            }
             else {
-...
                     tnrResponse.setTaxon(taxon);
                 } else {
+                }
                 tnrResponse.setMatchingNameType(NameType.SYNONYM);
                 String matchingName = queryClient.relatedVertexValue(synonymV, RdfSchema.EUNIS_SPECIES, "binomialName");
                 tnrResponse.setMatchingNameString(matchingName);
                 if(matchNode == null) {
                     tnrResponse.setMatchingNameType(NameType.SYNONYM);
                     String matchingName = queryClient.relatedVertexValue(synonymV, RdfSchema.EUNIS_SPECIES, "binomialName");
                     tnrResponse.setMatchingNameString(matchingName);
+                }
+            }
             if(!skipThis && request.isAddSynonymy()) {
             if(request.isAddSynonymy()) {
                 createSynonyms(taxonV, tnrResponse);
+            }

     import static org.junit.Assert.assertEquals;
     import static org.junit.Assert.assertTrue;
     import org.bgbm.biovel.drf.tnr.msg.NameType;
     import org.bgbm.biovel.drf.tnr.msg.Response;
     import org.bgbm.biovel.drf.tnr.msg.TnrMsg;
     import org.bgbm.biovel.drf.utils.TnrMsgException;
-...
             String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg);
             System.out.println(outputXML);
             assertTrue(tnrMsg.getQuery().get(0).getResponse().size() > 0);
             tnrMsg.getQuery().get(0).getResponse().get(0).getTaxon().getTaxonName().getCanonicalName().equals("Cichorium intybus");
             Response response = tnrMsg.getQuery().get(0).getResponse().get(0);
             assertEquals("Cichorium intybus", response.getTaxon().getTaxonName().getCanonicalName());
             assertEquals("Wegwarte", response.getMatchingNameString());
             assertEquals(NameType.VERNACULAR_NAME, response.getMatchingNameType());
+        }
         @Test

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Revision 7413db32

Added by Andreas Kohlbecker over 8 years ago