edu.cmu.lti.oaqa.bio.index.medline.annotated.query.SimpleQueryApp.java Source code

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Here is the source code for edu.cmu.lti.oaqa.bio.index.medline.annotated.query.SimpleQueryApp.java

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/*
 *  Copyright 2015 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.bio.index.medline.annotated.query;

import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.util.*;

import org.apache.commons.cli.*;
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.SolrDocumentList;

import com.google.common.base.Joiner;

/**
 * 
 * A simple query application that transforms Pubmed-like keyword[field] constructs
 * into SOLR-annographix queries, all query parts are connected using 
 * the default operator.
 * 
 * @author Leonid Boytsov
 *
 */
public class SimpleQueryApp {
    static void Usage(String err) {
        System.err.println("Error: " + err);
        System.err.println("Usage: " + "-u <Target Server URI> " + "-n <Max # of results> ");
        System.exit(1);
    }

    public static void main(String[] args) {
        Options options = new Options();

        options.addOption("u", null, true, "Solr URI");
        options.addOption("n", null, true, "Max # of results");

        CommandLineParser parser = new org.apache.commons.cli.GnuParser();

        try {
            CommandLine cmd = parser.parse(options, args);
            String solrURI = null;

            solrURI = cmd.getOptionValue("u");
            if (solrURI == null) {
                Usage("Specify Solr URI");
            }

            SolrServerWrapper solr = new SolrServerWrapper(solrURI);

            int numRet = 10;

            if (cmd.hasOption("n")) {
                numRet = Integer.parseInt(cmd.getOptionValue("n"));
            }

            List<String> fieldList = new ArrayList<String>();
            fieldList.add(UtilConstMedline.ID_FIELD);
            fieldList.add(UtilConstMedline.SCORE_FIELD);
            fieldList.add(UtilConstMedline.ARTICLE_TITLE_FIELD);
            fieldList.add(UtilConstMedline.ENTITIES_DESC_FIELD);
            fieldList.add(UtilConstMedline.ABSTRACT_TEXT_FIELD);

            BufferedReader sysInReader = new BufferedReader(new InputStreamReader(System.in));
            Joiner commaJoiner = Joiner.on(',');

            while (true) {
                System.out.println("Input query: ");
                String query = sysInReader.readLine();
                if (null == query)
                    break;

                QueryTransformer qt = new QueryTransformer(query);

                String tranQuery = qt.getQuery();

                System.out.println("Translated query:");
                System.out.println(tranQuery);
                System.out.println("=========================");

                SolrDocumentList res = solr.runQuery(tranQuery, fieldList, numRet);

                System.out.println("Found " + res.getNumFound() + " entries");

                for (SolrDocument doc : res) {
                    String id = (String) doc.getFieldValue(UtilConstMedline.ID_FIELD);
                    float score = (Float) doc.getFieldValue(UtilConstMedline.SCORE_FIELD);
                    String title = (String) doc.getFieldValue(UtilConstMedline.ARTICLE_TITLE_FIELD);
                    String titleAbstract = (String) doc.getFieldValue(UtilConstMedline.ABSTRACT_TEXT_FIELD);

                    System.out.println(score + " PMID=" + id + " " + titleAbstract);

                    String entityDesc = (String) doc.getFieldValue(UtilConstMedline.ENTITIES_DESC_FIELD);
                    System.out.println("Entities:");
                    for (EntityEntry e : EntityEntry.parseEntityDesc(entityDesc)) {
                        System.out.println(String.format("[%d %d] concept=%s concept_ids=%s", e.mStart, e.mEnd,
                                e.mConcept, commaJoiner.join(e.mConceptIds)));
                    }
                }
            }

            solr.close();

        } catch (ParseException e) {
            Usage("Cannot parse arguments");
        } catch (Exception e) {
            System.err.println("Terminating due to an exception: " + e);
            System.exit(1);
        }
    }
}