edu.cmu.lti.oaqa.bioasq.document.retrieval.GoPubMedDocumentRetrievalExecutor.java Source code

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Here is the source code for edu.cmu.lti.oaqa.bioasq.document.retrieval.GoPubMedDocumentRetrievalExecutor.java

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/*
 * Open Advancement Question Answering (OAQA) Project Copyright 2016 Carnegie Mellon University
 *
 * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
 * in compliance with the License. You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software distributed under the License
 * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
 * or implied. See the License for the specific language governing permissions and limitations
 * under the License.
 */

package edu.cmu.lti.oaqa.bioasq.document.retrieval;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.PropertiesConfiguration;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;

import edu.cmu.lti.oaqa.baseqa.providers.query.QueryStringConstructor;
import edu.cmu.lti.oaqa.baseqa.util.UimaContextHelper;
import edu.cmu.lti.oaqa.bio.bioasq.services.GoPubMedService;
import edu.cmu.lti.oaqa.bioasq.util.BioASQUtil;
import edu.cmu.lti.oaqa.bioqa.providers.query.PubMedQueryStringConstructor;
import edu.cmu.lti.oaqa.type.retrieval.AbstractQuery;
import edu.cmu.lti.oaqa.type.retrieval.Document;
import edu.cmu.lti.oaqa.util.TypeUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * A {@link JCasAnnotator_ImplBase} that performs search using a query string, transformed from a
 * {@link AbstractQuery} by a {@link QueryStringConstructor} to retrieve relevant
 * {@link Document}s from {@link GoPubMedService}.
 *
 * @see edu.cmu.lti.oaqa.baseqa.document.retrieval.LuceneDocumentRetrievalExecutor
 *
 * @author <a href="mailto:ziy@cs.cmu.edu">Zi Yang</a> created on 11/3/14
 */
public class GoPubMedDocumentRetrievalExecutor extends JCasAnnotator_ImplBase {

    private GoPubMedService service;

    private int pages;

    private int hits;

    private QueryStringConstructor queryStringConstructor;

    private static final Logger LOG = LoggerFactory.getLogger(GoPubMedDocumentRetrievalExecutor.class);

    @Override
    public void initialize(UimaContext context) throws ResourceInitializationException {
        super.initialize(context);
        String conf = UimaContextHelper.getConfigParameterStringValue(context, "conf");
        PropertiesConfiguration gopubmedProperties = new PropertiesConfiguration();
        try {
            gopubmedProperties.load(getClass().getResourceAsStream(conf));
        } catch (ConfigurationException e) {
            throw new ResourceInitializationException(e);
        }
        service = new GoPubMedService(gopubmedProperties);
        pages = UimaContextHelper.getConfigParameterIntValue(context, "pages", 1);
        hits = UimaContextHelper.getConfigParameterIntValue(context, "hits", 100);
        queryStringConstructor = new PubMedQueryStringConstructor();
    }

    @Override
    public void process(JCas jcas) throws AnalysisEngineProcessException {
        Collection<AbstractQuery> aqueries = TypeUtil.getAbstractQueries(jcas);
        List<Document> documents = new ArrayList<>();
        Set<String> docIds = new HashSet<>();
        for (AbstractQuery aquery : aqueries) {
            try {
                String queryString = queryStringConstructor.construct(aquery);
                LOG.info("Search for query: {}", queryString);
                BioASQUtil.searchPubMed(service, jcas, queryString, pages, hits).stream()
                        .filter(doc -> !docIds.contains(doc.getDocId())).forEach(doc -> {
                            documents.add(doc);
                            docIds.add(doc.getDocId());
                        });
                LOG.info("Retrieved: {}", documents.size());
                if (documents.size() > 10) {
                    break;
                }
            } catch (IOException e) {
                throw new AnalysisEngineProcessException(e);
            }
        }
        documents.forEach(Document::addToIndexes);
    }
}