org.phenotips.data.indexing.internal.SolrPatientIndexer.java Source code

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Here is the source code for org.phenotips.data.indexing.internal.SolrPatientIndexer.java

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/*
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership.
 *
 * This is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2.1 of
 * the License, or (at your option) any later version.
 *
 * This software 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
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this software; if not, write to the Free
 * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
 * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
 */
package org.phenotips.data.indexing.internal;

import org.phenotips.data.Feature;
import org.phenotips.data.Patient;
import org.phenotips.data.PatientRepository;
import org.phenotips.data.indexing.PatientIndexer;
import org.phenotips.ontology.SolrCoreContainerHandler;

import org.xwiki.component.annotation.Component;
import org.xwiki.component.phase.Initializable;
import org.xwiki.component.phase.InitializationException;
import org.xwiki.query.Query;
import org.xwiki.query.QueryException;
import org.xwiki.query.QueryManager;

import java.io.IOException;
import java.util.List;

import javax.inject.Inject;
import javax.inject.Singleton;

import org.apache.solr.client.solrj.SolrServer;
import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.client.solrj.embedded.EmbeddedSolrServer;
import org.apache.solr.client.solrj.util.ClientUtils;
import org.apache.solr.common.SolrInputDocument;
import org.slf4j.Logger;

/**
 * Indexes patients in a local Solr core.
 *
 * @version $Id: 4316ab041afec59de4b8a3285d24e67f2b75b1cf $
 * @since 1.0M8
 */
@Component
@Singleton
public class SolrPatientIndexer implements PatientIndexer, Initializable {
    /** Logging helper object. */
    @Inject
    private Logger logger;

    @Inject
    private SolrCoreContainerHandler cores;

    /** The Solr server instance used. */
    private SolrServer server;

    /** Allows querying for patients. */
    @Inject
    private QueryManager qm;

    /** Provides access to patients. */
    @Inject
    private PatientRepository patientRepository;

    @Override
    public void initialize() throws InitializationException {
        this.server = new EmbeddedSolrServer(this.cores.getContainer(), "patients");
    }

    @Override
    public void index(Patient patient) {
        SolrInputDocument input = new SolrInputDocument();
        input.setField("document", patient.getDocument().toString());
        String reporter = "";
        if (patient.getReporter() != null) {
            reporter = patient.getReporter().toString();
        }
        input.setField("reporter", reporter);

        for (Feature phenotype : patient.getFeatures()) {
            input.addField((phenotype.isPresent() ? "" : "negative_") + phenotype.getType(), phenotype.getId());
        }
        try {
            this.server.add(input);
        } catch (SolrServerException ex) {
            this.logger.warn("Failed to perform Solr search: {}", ex.getMessage());
        } catch (IOException ex) {
            this.logger.warn("Error occurred while performing Solr search: {}", ex.getMessage());
        }
    }

    @Override
    public void delete(Patient patient) {
        try {
            this.server.deleteByQuery("document:" + ClientUtils.escapeQueryChars(patient.getDocument().toString()));
            this.server.commit();
        } catch (SolrServerException ex) {
            this.logger.warn("Failed to delete from Solr: {}", ex.getMessage());
        } catch (IOException ex) {
            this.logger.warn("Error occurred while deleting Solr documents: {}", ex.getMessage());
        }
    }

    @Override
    public void reindex() {
        try {
            List<String> patientDocs = this.qm
                    .createQuery("from doc.object(PhenoTips.PatientClass) as patient", Query.XWQL).execute();
            this.server.deleteByQuery("*:*");
            for (String patientDoc : patientDocs) {
                this.index(this.patientRepository.getPatientById(patientDoc));
            }
            this.server.commit();
        } catch (SolrServerException ex) {
            this.logger.warn("Failed to reindex patients: {}", ex.getMessage());
        } catch (IOException ex) {
            this.logger.warn("Error occurred while reindexing patients: {}", ex.getMessage());
        } catch (QueryException ex) {
            this.logger.warn("Failed to search patients for reindexing: {}", ex.getMessage());
        }
    }
}