ubic.gemma.web.controller.common.HomePageController.java Source code

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Here is the source code for ubic.gemma.web.controller.common.HomePageController.java

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/*
 * The Gemma project
 * 
 * Copyright (c) 2006 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.gemma.web.controller.common;

import org.apache.commons.lang3.StringUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.servlet.ModelAndView;
import ubic.gemma.model.genome.Taxon;
import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
import ubic.gemma.web.controller.WebConstants;

import java.util.*;
import java.util.Map.Entry;

/**
 * Responsible for display of the Gemma 2.0 home page. Based on original HomePageController.java
 * 
 * @author thea
 *
 */
@Controller
public class HomePageController {

    private static final class TaxonComparator implements Comparator<Map.Entry<Taxon, Long>> {
        @Override
        public int compare(Map.Entry<Taxon, Long> e1, Map.Entry<Taxon, Long> e2) {
            Long e1value = e1.getValue();
            Long e2value = e2.getValue();

            int cf = e1value.compareTo(e2value);
            if (cf == 0) {
                try {
                    String e1commonName = e1.getKey().getCommonName();
                    String e2commonName = e2.getKey().getCommonName();

                    cf = e1commonName.compareTo(e2commonName);
                } catch (Exception e) {
                    cf = 1;
                }
            }
            return cf;
        }
    }

    @Autowired
    private ExpressionExperimentService expressionExperimentService;

    private ModelAndView mav = new ModelAndView();

    private Taxon otherTaxa;

    public HomePageController() {
        otherTaxa = Taxon.Factory.newInstance();
        otherTaxa.setId(-1L);
        otherTaxa.setCommonName("Other");
        otherTaxa.setScientificName("Other");
        otherTaxa.setIsGenesUsable(false);
    }

    /**
     * For the show-off graph that shows number of data sets per taxon.
     */
    public void getCountsForTaxonPieChart() {

        Map<Taxon, Long> unsortedEEsPerTaxon = expressionExperimentService.getPerTaxonCount();

        /*
         * Sort taxa by count.
         */
        TreeSet<Map.Entry<Taxon, Long>> eesPerTaxonValueSorted = new TreeSet<Map.Entry<Taxon, Long>>(
                new TaxonComparator());

        eesPerTaxonValueSorted.addAll(unsortedEEsPerTaxon.entrySet());

        long expressionExperimentCount = expressionExperimentService.countAll();

        double groupBelow = 0.1; // if a taxon has less then this percent of total count, group into 'other'
        String googleData = encodeDataForGoogle(eesPerTaxonValueSorted.descendingSet(), expressionExperimentCount,
                groupBelow);

        List<String> googleLabelsColls = new ArrayList<String>();
        boolean grouped = false;
        List<String> others = new ArrayList<String>();

        for (Entry<Taxon, Long> entry : eesPerTaxonValueSorted.descendingSet()) {
            String tname = entry.getKey().getCommonName();
            if (StringUtils.isBlank(tname))
                tname = entry.getKey().getScientificName();

            if (entry.getValue() == 0)
                continue;

            if (groupIntoOther(entry.getValue(), expressionExperimentCount, groupBelow)) {
                grouped = true;
                others.add(tname);
            } else {
                googleLabelsColls.add(tname);
            }
        }

        if (grouped) {
            googleLabelsColls.add(StringUtils.abbreviate(StringUtils.join(others, ", "), 50));
        }

        String googleLabels = StringUtils.join(googleLabelsColls, '|');

        mav.addObject("googleData", googleData);
        mav.addObject("googleLabels", googleLabels);

    }

    @RequestMapping(WebConstants.HOME_PAGE)
    public ModelAndView showHomePage() {

        /*
         * Note that this needs to be fast. The queries involved almost always result in a O(1) cache hit. Don't add new
         * functionality here without considering that.
         */
        getCountsForTaxonPieChart();
        return mav;
    }

    private final static char[] simpleEncoding = new String(
            "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789").toCharArray();

    private String encodeDataForGoogle(Set<Entry<Taxon, Long>> eesPerTaxonValueSorted, long maxValue,
            double groupBelow) {

        // This function scales the submitted values so that
        // maxVal becomes the highest value.
        String chartData = "s:";
        int otherSum = 0;
        for (Entry<Taxon, Long> currentValue : eesPerTaxonValueSorted) {
            if (groupIntoOther(currentValue.getValue(), maxValue, groupBelow)) {
                otherSum += currentValue.getValue();
            } else {
                chartData += simpleEncoding[Math
                        .round((simpleEncoding.length - 1) * currentValue.getValue() / maxValue)];
            }
        }
        if (otherSum != 0) {
            chartData += simpleEncoding[Math.round((simpleEncoding.length - 1) * otherSum / maxValue)];
        }
        return chartData;
    }

    private boolean groupIntoOther(long value, long maxValue, double threshold) {
        double a = (new Double(value) / new Double(maxValue));
        return threshold > a;
    }
}