ubic.pubmedgate.resolve.focusedAnalysis.TopRegions.java Source code

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Here is the source code for ubic.pubmedgate.resolve.focusedAnalysis.TopRegions.java

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/*
 * The WhiteText project
 * 
 * Copyright (c) 2012 University of British Columbia
 * 
 * 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 ubic.pubmedgate.resolve.focusedAnalysis;

import java.io.FileInputStream;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import ubic.BAMSandAllen.JenaUtil;
import ubic.BAMSandAllen.Util;
import ubic.basecode.dataStructure.params.ParamKeeper;
import ubic.pubmedgate.Config;
import ubic.pubmedgate.resolve.EvaluationRDFModel;
import ubic.pubmedgate.resolve.SpeciesCounter;

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

public class TopRegions {
    protected static Log log = LogFactory.getLog(TopRegions.class);

    /**
     * @param args
     */
    public static void main(String[] args) throws Exception {
        // iterate and dump out regions - use Excel to sort and present
        ParamKeeper keeper = new ParamKeeper();

        boolean allComp = true;
        // if training then check for accepted
        Model modelLoad;
        String fileProperty;
        boolean reason = true;
        EvaluationRDFModel allCompModel = null;

        if (allComp) {
            modelLoad = ModelFactory.createDefaultModel();
            fileProperty = "resolve.Lexicon.resolution.RDF.allComp";
            modelLoad.read(new FileInputStream(Config.config.getString(fileProperty)), null);
            allCompModel = new EvaluationRDFModel(modelLoad, reason);
        }

        fileProperty = "resolve.Lexicon.resolution.RDF";
        modelLoad = ModelFactory.createDefaultModel();
        modelLoad.read(new FileInputStream(Config.config.getString(fileProperty)), null);

        EvaluationRDFModel model = new EvaluationRDFModel(modelLoad, reason);

        Set<Resource> commonSpeciesMentions = new HashSet<Resource>();
        Set<Resource> commonAllSpeciesMentions = new HashSet<Resource>();
        Set<String> commonSpecies = SpeciesCounter.getCommonSpeciesLinStrings();

        for (String common : commonSpecies) {
            common = common.substring(common.lastIndexOf(":") + 1);
            Set<Resource> mentionsForSpecies = model.getMentionsForSpecies(common);
            commonSpeciesMentions.addAll(mentionsForSpecies);
            if (allComp)
                commonAllSpeciesMentions.addAll(allCompModel.getMentionsForSpecies(common));
        }

        int count = 0;
        for (Resource concept : model.getConcepts()) {
            Map<String, String> line = new HashMap<String, String>();
            line.put("conceptURI", concept.getURI());
            line.put("conceptLabel", "\"" + JenaUtil.getLabel(concept) + "\"");

            Set<Resource> terms = model.getTermsFromConcepts(concept);
            line.put("terms", terms.size() + "");

            Set<Resource> mentions = model.getMentionsFromTerms(terms);
            line.put("unique mentions", mentions.size() + "");

            line.put("mentionFrequency", model.sumMentionFrequencies(mentions) + "");

            Set<Resource> commonMentions = (Set<Resource>) Util.intersect(commonSpeciesMentions, mentions);
            line.put("unique Common Mentions", commonMentions.size() + "");
            line.put("Common mentionFrequency", model.sumMentionFrequencies(commonMentions) + "");

            Set<Resource> rejectMentions = new HashSet<Resource>();
            Set<Resource> spec2genMentions = new HashSet<Resource>();
            for (Resource mention : mentions) {
                if (model.rejected(mention, concept)) {
                    rejectMentions.add(mention);
                }
                if (model.specToGen(mention, concept)) {
                    spec2genMentions.add(mention);
                }
            }
            line.put("Rejected Mentions", rejectMentions.size() + "");
            line.put("Spec2Gen Mentions", spec2genMentions.size() + "");
            String baseURI = concept.getURI();
            baseURI = baseURI.substring(0, baseURI.lastIndexOf('#'));
            line.put("Base URI", baseURI);

            Set<String> termStrings = new HashSet<String>();
            for (Resource term : terms) {
                termStrings.add(JenaUtil.getLabel(term));
            }
            line.put("terms", termStrings.toString());
            line.put("termCount", termStrings.size() + "");

            if (allComp) {
                Set<Resource> allMentions = allCompModel.getMentionsFromTerms(terms);

                line.put("unique allCompMentions", allMentions.size() + "");
                line.put("allCompMentions frequency", model.sumMentionFrequencies(allMentions) + "");

                Set<Resource> commonMentionsAll = (Set<Resource>) Util.intersect(commonAllSpeciesMentions,
                        allMentions);

                line.put("unique allComp Common Mentions", commonMentionsAll.size() + "");
                line.put("frequency allComp Common Mentions",
                        allCompModel.sumMentionFrequencies(commonMentionsAll) + "");
            }

            keeper.addParamInstance(line);
            if (count++ % 100 == 0) {
                log.info(count);
                //                if (count > 100) break;
            }

        }

        keeper.writeExcel(Config.config.getString("whitetext.resolve.results.folder") + "TopRegions.xls");

    }
}