import org.apache.jena.rdf.model.Resource;
import org.apache.lucene.queryParser.QueryParser;
import org.bgbm.biovel.drf.client.ServiceProviderInfo;
-import org.bgbm.biovel.drf.query.IQueryClient;
-import org.bgbm.biovel.drf.query.SparqlClient;
import org.bgbm.biovel.drf.query.TinkerPopClient;
import org.bgbm.biovel.drf.store.Neo4jStore;
import org.bgbm.biovel.drf.store.Store;
-import org.bgbm.biovel.drf.store.TDBStore;
import org.bgbm.biovel.drf.tnr.msg.NameType;
import org.bgbm.biovel.drf.tnr.msg.Query;
import org.bgbm.biovel.drf.tnr.msg.Query.Request;
public static final String DOC_URL = "http://semantic.eea.europa.eu/documentation";
public static final String COPYRIGHT_URL = "http://www.eea.europa.eu/legal/eea-data-policy";
- private static final String SPARQL_ENDPOINT_URL = "http://semantic.eea.europa.eu/sparql";
- private static final boolean USE_REMOTE_SERVICE = false;
-
private static final String SPECIES_RDF_FILE_URL = "http://localhost/download/species.rdf.gz"; // http://eunis.eea.europa.eu/rdf/species.rdf.gz
private static final String LEGALREFS_RDF_FILE_URL = "http://localhost/download/legalrefs.rdf.gz"; // http://eunis.eea.europa.eu/rdf/legalrefs.rdf.gz
private static final String REFERENCES_RDF_FILE_URL = "http://localhost/download/references.rdf.gz"; // http://eunis.eea.europa.eu/rdf/references.rdf.gz
private static final boolean REFRESH_TDB = false;
- private static final Class<? extends IQueryClient> clientClass = TinkerPopClient.class;
-
- private static final int MAX_PAGING_LIMIT = 50;
-
public static final EnumSet<SearchMode> SEARCH_MODES = EnumSet.of(
SearchMode.scientificNameExact,
SearchMode.scientificNameLike,
@Override
public void initQueryClient() {
- if(SparqlClient.class.isAssignableFrom(clientClass)) {
- if(USE_REMOTE_SERVICE) {
- // use SPARQL end point
- //FIXME queryClient = new SparqlClient(SPARQL_ENDPOINT_URL);
- } else {
- TDBStore tripleStore;
- try {
- tripleStore = new TDBStore();
- } catch (Exception e1) {
- throw new RuntimeException("Creation of TripleStore failed", e1);
- }
- if(REFRESH_TDB) {
- updateStore(tripleStore);
- }
- //FIXME queryClient = new SparqlClient(tripleStore);
-
+ Neo4jStore neo4jStore;
+ try {
+ neo4jStore = new Neo4jStore();
+ } catch (Exception e1) {
+ throw new RuntimeException("Creation of Neo4jStore failed", e1);
}
- } else if(TinkerPopClient.class.isAssignableFrom(clientClass)) {
- if(USE_REMOTE_SERVICE) {
- throw new RuntimeException("USE_REMOTE_SERVICE not suported by QueryClient class "+ clientClass);
- } else {
- Neo4jStore neo4jStore;
- try {
- neo4jStore = new Neo4jStore();
- } catch (Exception e1) {
- throw new RuntimeException("Creation of Neo4jStore failed", e1);
- }
- if(REFRESH_TDB) {
- updateStore(neo4jStore);
- }
- queryClient = new TinkerPopClient(neo4jStore);
-
+ if(REFRESH_TDB) {
+ updateStore(neo4jStore);
}
-
- } else {
- throw new RuntimeException("Unsuported QueryClient class "+ clientClass);
- }
+ queryClient = new TinkerPopClient(neo4jStore);
}
/**
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
-import java.util.List;
import java.util.NoSuchElementException;
-import org.apache.jena.rdf.model.Model;
-import org.apache.jena.rdf.model.Property;
-import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.StmtIterator;
-import org.bgbm.biovel.drf.checklist.DRFChecklistException;
import org.bgbm.biovel.drf.checklist.EEA_BDC_Client.RdfSchema;
import org.bgbm.biovel.drf.store.Neo4jStore;
import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.index.AutoIndexer;
import org.neo4j.graphdb.index.IndexHits;
import org.openrdf.query.BindingSet;
-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.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;
/**
*/
public class TinkerPopClient implements IQueryClient {
- public static final String KIND = GraphSail.KIND;
-
- public static final String VALUE = GraphSail.VALUE;
-
- public static final Object URI = GraphSail.URI;
-
protected Logger logger = LoggerFactory.getLogger(TinkerPopClient.class);
- private final String baseUri = null;
-
- private Neo4jStore tripleStore = null;
+ private Neo4jStore graphStore = null;
/**
- * @param tripleStore
+ * @param store
*/
- public TinkerPopClient(Neo4jStore tripleStore) {
- this.tripleStore = tripleStore;
- }
-
- public GremlinPipeline<Graph, Graph> newPipe() {
- GremlinPipeline<Graph, Object> pipe = new GremlinPipeline<Graph, Object>();
- return pipe.start(graph());
+ public TinkerPopClient(Neo4jStore store) {
+ this.graphStore = store;
}
public Graph graph() {
- return tripleStore.graph();
- }
-
- /**
- * @param sparql
- * @return
- * @throws MalformedQueryException
- * @throws RepositoryException
- * @throws QueryEvaluationException
- *
- * @deprecated directly use connection() and do not forget to close is after
- * doing the query. See
- * {@link org.openrdf.repository.sail.SailRepository#getConnection()}
- */
- @Deprecated
- public TupleQueryResult execute(String sparql) throws MalformedQueryException, RepositoryException,
- QueryEvaluationException {
- TupleQuery query = connection().prepareTupleQuery(QueryLanguage.SPARQL, sparql);
- TupleQueryResult result = query.evaluate();
- return result;
+ return graphStore.graph();
}
/**
* @throws RepositoryException
*/
public SailRepositoryConnection connection() throws RepositoryException {
- SailRepositoryConnection connection = tripleStore.getSailRepo().getConnection();
+ SailRepositoryConnection connection = graphStore.getSailRepo().getConnection();
return connection;
}
- public PipeFunction<Vertex, Boolean> createRegexMatchFilter(final String regex) {
- return new PipeFunction<Vertex, Boolean>() {
-
- @Override
- public Boolean compute(Vertex v) {
- return v.toString().matches(regex);
- }
- };
- }
-
- public PipeFunction<Vertex, Boolean> createEqualsFilter(final String string) {
- return new PipeFunction<Vertex, Boolean>() {
-
- @Override
- public Boolean compute(Vertex v) {
- return v.toString().equals(string);
- }
- };
- }
-
- public PipeFunction<Vertex, Boolean> createStarttWithFilter(final String string) {
- return new PipeFunction<Vertex, Boolean>() {
-
- @Override
- public Boolean compute(Vertex v) {
- return v.toString().startsWith(string);
- }
- };
- }
-
- public Model describe(String queryString) throws DRFChecklistException, QueryEvaluationException {
-
- // directly execute SPARQL queries in Gremlin over Sail-based graphs
- // using the method SailGraph.executeSparql().
-
- TupleQuery qe = executionFor(queryString);
- TupleQueryResult result = qe.evaluate();
- System.err.println(result.toString());
-
- if (result != null && logger.isDebugEnabled()) {
- StringBuilder msg = new StringBuilder();
- msg.append("subjects in response:\n");
- int i = 1;
- try {
- for (; result.hasNext(); ++i) {
- BindingSet res = result.next();
- msg.append(" " + i + ": " + res.toString() + "\n");
- }
- } catch (QueryEvaluationException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- logger.debug(msg.toString());
- }
-
- return null; // FIXME result;
- }
-
- /**
- * @param queryString
- * @return
- */
- private TupleQuery executionFor(String queryString) {
-
- if (baseUri != null) {
- // see
- // https://github.com/tinkerpop/blueprints/wiki/Sail-Implementation
- // FIXME
- throw new RuntimeException("Mode unsupported");
- // Graph graph = new SparqlRepositorySailGraph(baseUri);
- // return QueryExecutionFactory.sparqlService(baseUri, query);
- }
- if (tripleStore != null) {
- // local TDB Store
- try {
- SailRepositoryConnection connection = connection();
- return connection.prepareTupleQuery(QueryLanguage.SPARQL, queryString);
- } catch (MalformedQueryException | RepositoryException e) {
- // TODO Auto-generated catch block
- logger.error("Error while perparing query", e);
- }
-
- }
-
- return null;
- }
-
- /**
- * @param subject
- * @param nameSpace
- * @param localName
- * @return
- */
- public RDFNode asSingleObject(Resource subject, RdfSchema nameSpace, String localName) {
- RDFNode node = null;
- StmtIterator propertyIt = null;
- Resource _subject = subject;
- try {
-
- Model _model = _subject.getModel();
- Property property = _model.getProperty(nameSpace.schemaUri(), localName);
- propertyIt = _subject.listProperties(property);
-
- boolean propertyInGraph = propertyIt.hasNext();
- if (!propertyInGraph) {
- _subject = getFromUri(subject.getURI());
- propertyIt = _subject.listProperties(property);
- }
-
- node = propertyIt.next().getObject();
- } catch (NoSuchElementException e) {
- if (logger.isTraceEnabled()) {
- logger.debug(_subject.getURI() + " " + nameSpace + ":" + localName + " not found in current graph");
- printProperties(_subject);
- }
- }
- return node;
- }
-
- /**
- * @param subject
- * @param nameSpace
- * @param localName
- * @return
- */
- public StmtIterator listProperties(Resource subject, RdfSchema nameSpace, String localName) {
- RDFNode node = null;
- StmtIterator propertyIt = null;
- Resource _subject = subject;
- try {
-
- Model _model = _subject.getModel();
- Property property = _model.getProperty(nameSpace.schemaUri(), localName);
- propertyIt = _subject.listProperties(property);
-
- boolean propertyInGraph = propertyIt.hasNext();
- if (!propertyInGraph) {
- _subject = getFromUri(subject.getURI());
- propertyIt = _subject.listProperties(property);
- }
-
- } catch (NoSuchElementException e) {
- if (logger.isTraceEnabled()) {
- logger.debug(_subject.getURI() + " " + nameSpace + ":" + localName + " not found in current graph");
- printProperties(_subject);
- }
- }
- return propertyIt;
- }
-
- public List<RDFNode> listObjects(Resource subject, RdfSchema nameSpace, String localName) {
-
- List<RDFNode> list = new ArrayList<RDFNode>();
- StmtIterator it = listProperties(subject, nameSpace, localName);
- while (it.hasNext()) {
- list.add(it.next().getObject());
- }
- return list;
- }
-
/**
* @param subject
* @param nameSpace
return txt;
}
- //
-
/**
* @param subject
* @param nameSpace
* @param localName
* @return
*/
- public Resource objectAsResource(Resource subject, RdfSchema nameSpace, String localName) {
- Resource resource = null;
- RDFNode node = asSingleObject(subject, nameSpace, localName);
- if (node != null) {
- node.isResource();
- resource = node.asResource();
- }
- return resource;
- }
-
- /**
- * @param subject
- * @param nameSpace
- * @param localName
- * @return
- * @deprecated unused
- */
- @Deprecated
- public URI relatedVertexURI(GremlinPipeline<Graph, Vertex> pipe, RdfSchema nameSpace, String localName) {
- URI uri = null;
- String edgeLabel = nameSpace.propertyURI(localName);
- try {
- Vertex v = pipe.outE(1, edgeLabel).inV().next();
- if (v.getProperty(GraphSail.KIND).equals(GraphSail.URI)) {
- uri = (URI) v.getProperty(GraphSail.VALUE);
- } else {
- logger.warn("target vertex of '" + edgeLabel + "' is not an URI");
- }
- } catch (FastNoSuchElementException e) {
- logger.warn("edge with '" + edgeLabel + "' not found");
- }
-
- return uri;
- }
-
- /**
- * @param subject
- * @param nameSpace
- * @param localName
- * @return
- * @deprecated possibly broken
- */
- @Deprecated
public URI relatedVertexURI(Vertex v, RdfSchema nameSpace, String localName) {
URI uri = null;
- String edgeLabel = nameSpace.propertyURI(localName);
try {
if (v.getProperty(GraphSail.KIND).equals(GraphSail.URI)) {
uri = new URI(v.getProperty(GraphSail.VALUE).toString());
} else {
- logger.warn("target vertex of '" + edgeLabel + "' is not an URI");
+ logger.warn("vertex of '" + v.toString() + "' is not an URI");
}
- } catch (NoSuchElementException e) {
- logger.warn("edge with '" + edgeLabel + "' not found");
} catch (URISyntaxException e) {
logger.error("Invalid URI id in " + v, e);
}
}
}
- /**
- * @param matchedResourceURI
- * @return
- * @throws DRFChecklistException
- */
- public Resource getFromUri(URI matchedResourceURI) {
- return getFromUri(matchedResourceURI.toString());
- }
-
- public Resource getFromUri(String uri) {
-
- // not needed
- return null;
-
- }
-
public void showResults(TupleQueryResult result) throws QueryEvaluationException {
int i = 0;
while (result.hasNext()) {
BGBM BDI Projects / utis-core.git / commitdiff