Metacat

/**

 * This program is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 2 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program; if not, write to the Free Software

 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat.index.annotation;

import java.io.ByteArrayInputStream;

import java.io.ByteArrayOutputStream;

import java.io.IOException;

import java.io.InputStream;

import java.net.MalformedURLException;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Date;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.Set;

import javax.xml.parsers.ParserConfigurationException;

import javax.xml.transform.Result;

import javax.xml.transform.Source;

import javax.xml.transform.TransformerConfigurationException;

import javax.xml.transform.TransformerException;

import javax.xml.transform.TransformerFactory;

import javax.xml.transform.TransformerFactoryConfigurationError;

import javax.xml.transform.dom.DOMSource;

import javax.xml.transform.stream.StreamResult;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.apache.solr.client.solrj.SolrServer;

import org.apache.solr.client.solrj.SolrServerException;

import org.apache.solr.client.solrj.response.QueryResponse;

import org.apache.solr.common.SolrDocument;

import org.apache.solr.common.params.SolrParams;

import org.apache.solr.schema.IndexSchema;

import org.apache.solr.servlet.SolrRequestParsers;

import org.dataone.cn.indexer.convert.SolrDateConverter;

import org.dataone.cn.indexer.parser.AbstractDocumentSubprocessor;

import org.dataone.cn.indexer.parser.IDocumentSubprocessor;

import org.dataone.cn.indexer.parser.ISolrField;

import org.dataone.cn.indexer.solrhttp.SolrDoc;

import org.dataone.cn.indexer.solrhttp.SolrElementField;

import org.dataone.service.exceptions.NotFound;

import org.dataone.service.exceptions.UnsupportedType;

import org.dataone.service.types.v1.Permission;

import org.dataone.service.types.v1.Subject;

import org.dataone.service.types.v1.util.AccessUtil;

import org.dataone.service.types.v1.util.AuthUtils;

import org.dataone.service.util.DateTimeMarshaller;

import org.w3c.dom.Document;

import org.xml.sax.SAXException;

import com.hp.hpl.jena.ontology.OntModel;

import com.hp.hpl.jena.query.Dataset;

import com.hp.hpl.jena.query.Query;

import com.hp.hpl.jena.query.QueryExecution;

import com.hp.hpl.jena.query.QueryExecutionFactory;

import com.hp.hpl.jena.query.QueryFactory;

import com.hp.hpl.jena.query.QuerySolution;

import com.hp.hpl.jena.query.ResultSet;

import com.hp.hpl.jena.rdf.model.ModelFactory;

import com.hp.hpl.jena.tdb.TDBFactory;

import edu.ucsb.nceas.metacat.common.SolrServerFactory;

import edu.ucsb.nceas.metacat.common.query.SolrQueryServiceController;

import edu.ucsb.nceas.metacat.index.DistributedMapsFactory;

/**

 * A solr index parser for an RDF/XML file.

 * The solr doc of the RDF/XML object only has the system metadata information.

 * The solr docs of the science metadata doc and data file have the annotation information.

 */

public class RdfXmlSubprocessor extends AbstractDocumentSubprocessor implements IDocumentSubprocessor {

    private static final String QUERY ="q=id:";

    private static Log log = LogFactory.getLog(RdfXmlSubprocessor.class);

    private static SolrServer solrServer =  null;

    static {

        try {

            solrServer = SolrServerFactory.createSolrServer();

        } catch (Exception e) {

            log.error("RdfXmlSubprocessor - can't generate the SolrServer since - "+e.getMessage());

        }

    }

    @Override

    public Map<String, SolrDoc> processDocument(String identifier, Map<String, SolrDoc> docs, Document doc) throws Exception {

        SolrDoc resourceMapDoc = docs.get(identifier);

        List<SolrDoc> processedDocs = process(resourceMapDoc, doc);

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

        for (SolrDoc processedDoc : processedDocs) {

            processedDocsMap.put(processedDoc.getIdentifier(), processedDoc);

        }

        // make sure to merge any docs that are currently being processed

        Map<String, SolrDoc> mergedDocuments = mergeDocs(docs, processedDocsMap);

        return mergedDocuments;

    }

    private InputStream toInputStream(Document doc) throws TransformerConfigurationException, TransformerException, TransformerFactoryConfigurationError {

    	ByteArrayOutputStream outputStream = new ByteArrayOutputStream();

    	Source xmlSource = new DOMSource(doc);

    	Result outputTarget = new StreamResult(outputStream);

    	TransformerFactory.newInstance().newTransformer().transform(xmlSource, outputTarget);

    	InputStream is = new ByteArrayInputStream(outputStream.toByteArray());

    	return is;

    }

    private List<SolrDoc> process(SolrDoc indexDocument, Document rdfXmlDocument) throws Exception {

    	// get the triplestore dataset

		Dataset dataset = TripleStoreService.getInstance().getDataset();

    	// read the annotation

		InputStream source = toInputStream(rdfXmlDocument);

    	String name = indexDocument.getIdentifier();

    	boolean loaded = dataset.containsNamedModel(name);

		if (!loaded) {

			OntModel ontModel = ModelFactory.createOntologyModel();

			ontModel.read(source, name);

			dataset.addNamedModel(name, ontModel);

		}

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

		// process each field query

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

		for (ISolrField field: this.getFieldList()) {

			String q = null;

			if (field instanceof SparqlField) {

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

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

				Query query = QueryFactory.create(q);

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

				ResultSet results = qexec.execSelect();

				while (results.hasNext()) {

					SolrDoc solrDoc = null;

					QuerySolution solution = results.next();

					System.out.println(solution.toString());

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

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

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

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

						boolean statementAuthorized = false;

						try {

							HashMap<Subject, Set<Permission>> annotationPermissionMap = AccessUtil.getPermissionMap(DistributedMapsFactory.getSystemMetadata(name).getAccessPolicy());

							annotationPermissionMap.put(DistributedMapsFactory.getSystemMetadata(name).getRightsHolder(), new HashSet<Permission>(Arrays.asList(Permission.CHANGE_PERMISSION)));

							statementAuthorized = AuthUtils.isAuthorized(annotationPermissionMap.keySet(), Permission.WRITE, DistributedMapsFactory.getSystemMetadata(id));

						} catch (Exception e) {

							log.warn("Could not check for assertion permission on original pid: " + id, e);

						}

						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);

						}

					}

				}

			}

		}

		// clean up the triple store

		TDBFactory.release(dataset);

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

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

        Map<String, SolrDoc> mergedDocuments = mergeDocs(documentsToIndex, existingDocuments);

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

        return new ArrayList<SolrDoc>(mergedDocuments.values());

    }

    private Map<String, SolrDoc> getSolrDocs(Set<String> ids) throws Exception {

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

        if (ids != null) {

            for (String id : ids) {

            	SolrDoc doc = getSolrDoc(id);

                if (doc != null) {

                    list.put(id, doc);

                }

            }

        }

        return list;

    }

    private Map<String, SolrDoc> mergeDocs(Map<String, SolrDoc> pending, Map<String, SolrDoc> existing) throws Exception {

    	IndexSchema indexSchema = SolrQueryServiceController.getInstance().getSchema();

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

    	Iterator<String> pendingIter = pending.keySet().iterator();

    	while (pendingIter.hasNext()) {

    		String id = pendingIter.next();

    		SolrDoc pendingDoc = pending.get(id);

    		SolrDoc existingDoc = existing.get(id);

    		SolrDoc mergedDoc = new SolrDoc();

    		if (existingDoc != null) {

    			// merge the existing fields

    			for (SolrElementField field: existingDoc.getFieldList()) {

    				mergedDoc.addField(field);

    			}

    		}

    		// add the pending

    		for (SolrElementField field: pendingDoc.getFieldList()) {

    			if (field.getName().equals(SolrElementField.FIELD_ID) && mergedDoc.hasField(SolrElementField.FIELD_ID)) {

    				continue;

    			}

    			// don't transfer the copyTo fields, otherwise there are errors

				if (indexSchema.isCopyFieldTarget(indexSchema.getField(field.getName()))) {

					continue;

				}

				// only add if we don't already have it

				if (!mergedDoc.hasFieldWithValue(field.getName(), field.getValue())) {

					mergedDoc.addField(field);

				}	

			}

    		// include in results

			merged.put(id, mergedDoc);

    	}

    	return merged;

    }

	/*

	 * Get the SolrDoc for the specified id

	 */

	public static SolrDoc getSolrDoc(String id) throws SolrServerException, MalformedURLException, UnsupportedType, NotFound, ParserConfigurationException, IOException, SAXException {

		SolrDoc doc = null;

		if (solrServer != null) {

			String query = QUERY + "\"" + id + "\"";

			SolrParams solrParams = SolrRequestParsers.parseQueryString(query);

			QueryResponse qr = solrServer.query(solrParams);

			if (!qr.getResults().isEmpty()) {

				doc = new SolrDoc();

				SolrDocument orig = qr.getResults().get(0);

				IndexSchema indexSchema = SolrQueryServiceController.getInstance().getSchema();

				for (String fieldName : orig.getFieldNames()) {

					// don't transfer the copyTo fields, otherwise there are errors

					if (indexSchema.isCopyFieldTarget(indexSchema.getField(fieldName))) {

						continue;

					}

					for (Object value : orig.getFieldValues(fieldName)) {

						String stringValue = value.toString();

						// special handling for dates in ISO 8601

						if (value instanceof Date) {

							stringValue = DateTimeMarshaller.serializeDateToUTC((Date) value);

							SolrDateConverter converter = new SolrDateConverter();

							stringValue = converter.convert(stringValue);

						}

						SolrElementField field = new SolrElementField(fieldName, stringValue);

						log.debug("Adding field: " + fieldName);

						doc.addField(field);

					}

				}

			}

		}

		return doc;

	}

}