Metacat

        Map<String, SolrDoc> mergedDocuments;

            perfLog.log("RdfXmlSubprocess.process gets a dataset from tripe store service ", System.currentTimeMillis() - start);

            // read the annotation

            String indexDocId = indexDocument.getIdentifier();

            String name = indexDocId;

            //Check if the identifier is a valid URI and if not, make it one by prepending "http://"

            URI nameURI;

            String scheme = null;

            try {

                nameURI = new URI(indexDocId);

                scheme = nameURI.getScheme();

            } catch (URISyntaxException use) {

                // The identifier can't be parsed due to offending characters. It's not a URL

                name = "https://cn.dataone.org/cn/v1/resolve/"+indexDocId;

            }

            // The had no scheme prefix. It's not a URL

            if ((scheme == null) || (scheme.isEmpty())) {

                name = "https://cn.dataone.org/cn/v1/resolve/"+indexDocId;

            }

            long startOntModel = System.currentTimeMillis();

            boolean loaded = dataset.containsNamedModel(name);

            if (!loaded) {

                OntModel ontModel = ModelFactory.createOntologyModel();

                ontModel.read(is, name);

                dataset.addNamedModel(name, ontModel);

            }

            perfLog.log("RdfXmlSubprocess.process adds ont-model ", System.currentTimeMillis() - startOntModel);

            //dataset.getDefaultModel().add(ontModel);

            // process each field query

            Map<String, SolrDoc> documentsToIndex = new HashMap<String, SolrDoc>();

            long startField = System.currentTimeMillis();

            for (ISolrDataField field : this.fieldList) {

                long filed = System.currentTimeMillis();

                String q = null;

                if (field instanceof SparqlField) {

                    q = ((SparqlField) field).getQuery();

                    q = q.replaceAll("\\$GRAPH_NAME", name);

                    Query query = QueryFactory.create(q);

                    log.trace("Executing SPARQL query:\n" + query.toString());

                    QueryExecution qexec = QueryExecutionFactory.create(query, dataset);

                    ResultSet results = qexec.execSelect();

                    while (results.hasNext()) {

                        SolrDoc solrDoc = null;

                        QuerySolution solution = results.next();

                        log.trace(solution.toString());

                        // find the index document we are trying to augment with the annotation

                        if (solution.contains("pid")) {

                            String id = solution.getLiteral("pid").getString();

                            // TODO: check if anyone with permissions on the annotation document has write permission on the document we are annotating

                            boolean statementAuthorized = true;

                            if (!statementAuthorized) {

                                continue;

                            }

                            // otherwise carry on with the indexing

                            solrDoc = documentsToIndex.get(id);

                            if (solrDoc == null) {

                                solrDoc = new SolrDoc();

                                solrDoc.addField(new SolrElementField(SolrElementField.FIELD_ID, id));

                                documentsToIndex.put(id, solrDoc);

                            }

                        // add the field to the index document

                        if (solution.contains(field.getName())) {

                            String value = solution.get(field.getName()).toString();

                            SolrElementField f = new SolrElementField(field.getName(), value);

                            if (!solrDoc.hasFieldWithValue(f.getName(), f.getValue())) {

                                solrDoc.addField(f);

                            }

                perfLog.log("RdfXmlSubprocess.process process the field "+field.getName(), System.currentTimeMillis() - filed);

            perfLog.log("RdfXmlSubprocess.process process the fields total ", System.currentTimeMillis() - startField);

            // clean up the triple store

            //TDBFactory.release(dataset);

            // merge the existing index with the new[er] values

            long getStart = System.currentTimeMillis();

            Map<String, SolrDoc> existingDocuments = getSolrDocs(documentsToIndex.keySet());

            perfLog.log("RdfXmlSubprocess.process get existing solr docs ", System.currentTimeMillis() - getStart);

            mergedDocuments = mergeDocs(documentsToIndex, existingDocuments);

            mergedDocuments.put(indexDocument.getIdentifier(), indexDocument);

            perfLog.log("RdfXmlSubprocess.process() total take ", System.currentTimeMillis() - start);

        } finally {

            try {

                TripleStoreService.getInstance().destoryDataset(dataset);

            } catch (Exception e) {

                log.warn("A tdb directory can't be removed since "+e.getMessage(), e);

            }