Example usage for org.apache.solr.client.solrj SolrQuery set

List of usage examples for org.apache.solr.client.solrj SolrQuery set

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Introduction

In this page you can find the example usage for org.apache.solr.client.solrj SolrQuery set.

Prototype

public ModifiableSolrParams set(String name, String... val)

Source Link

Document

Replace any existing parameter with the given name.

Usage

From source file:uk.ac.ebi.phenotype.service.ObservationService.java

License:Apache License

public Map<String, List<DiscreteTimePoint>> getTimeSeriesMutantData(String parameter, List<String> genes,
        ArrayList<String> strains, String[] center, String[] sex) throws SolrServerException {

    Map<String, List<DiscreteTimePoint>> finalRes = new HashMap<String, List<DiscreteTimePoint>>(); // <allele_accession,
    // timeSeriesData>

    SolrQuery query = new SolrQuery().addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":experimental")
            .addFilterQuery(ObservationDTO.PARAMETER_STABLE_ID + ":" + parameter);

    String q = (strains.size() > 1) ? "(" + ObservationDTO.STRAIN_ACCESSION_ID + ":\""
            + StringUtils.join(strains.toArray(), "\" OR " + ObservationDTO.STRAIN_ACCESSION_ID + ":\"") + "\")"
            : ObservationDTO.STRAIN_ACCESSION_ID + ":\"" + strains.get(0) + "\"";

    if (genes != null && genes.size() > 0) {
        q += " AND (";
        q += (genes.size() > 1) ? ObservationDTO.GENE_ACCESSION_ID + ":\""
                + StringUtils.join(genes.toArray(), "\" OR " + ObservationDTO.GENE_ACCESSION_ID + ":\"") + "\""
                : ObservationDTO.GENE_ACCESSION_ID + ":\"" + genes.get(0) + "\"";
        q += ")";
    }/*from www . j  a v  a2s . co  m*/

    if (center != null && center.length > 0) {
        q += " AND (";
        q += (center.length > 1)
                ? ObservationDTO.PHENOTYPING_CENTER + ":\""
                        + StringUtils.join(center, "\" OR " + ObservationDTO.PHENOTYPING_CENTER + ":\"") + "\""
                : ObservationDTO.PHENOTYPING_CENTER + ":\"" + center[0] + "\"";
        q += ")";
    }

    if (sex != null && sex.length == 1) {
        q += " AND " + ObservationDTO.SEX + ":\"" + sex[0] + "\"";
    }

    query.setQuery(q);
    query.set("group.field", ObservationDTO.GENE_SYMBOL);
    query.set("group", true);
    query.set("fl", ObservationDTO.DATA_POINT + "," + ObservationDTO.DISCRETE_POINT);
    query.set("group.limit", 100000); // number of documents to be returned
    // per group
    query.set("group.sort", ObservationDTO.DISCRETE_POINT + " asc");
    query.setRows(10000);

    // System.out.println("+_+_+ " + solr.getBaseURL() + "/select?" +
    // query);
    List<Group> groups = solr.query(query).getGroupResponse().getValues().get(0).getValues();
    // for mutants it doesn't seem we need binning
    // groups are the alleles
    for (Group gr : groups) {
        SolrDocumentList resDocs = gr.getResult();
        DescriptiveStatistics stats = new DescriptiveStatistics();
        float discreteTime = (float) resDocs.get(0).getFieldValue(ObservationDTO.DISCRETE_POINT);
        ArrayList<DiscreteTimePoint> res = new ArrayList<DiscreteTimePoint>();
        for (int i = 0; i < resDocs.getNumFound(); i++) {
            SolrDocument doc = resDocs.get(i);
            stats.addValue((float) doc.getFieldValue(ObservationDTO.DATA_POINT));
            if (discreteTime != (float) doc.getFieldValue(ObservationDTO.DISCRETE_POINT)
                    || i == resDocs.getNumFound() - 1) { // we
                // are
                // at
                // the
                // end
                // of
                // the
                // document
                // list
                // add to list
                float discreteDataPoint = (float) stats.getMean();
                DiscreteTimePoint dp = new DiscreteTimePoint(discreteTime, discreteDataPoint,
                        new Float(stats.getStandardDeviation()));
                List<Float> errorPair = new ArrayList<>();
                Float lower = new Float(discreteDataPoint);
                Float higher = new Float(discreteDataPoint);
                errorPair.add(lower);
                errorPair.add(higher);
                dp.setErrorPair(errorPair);
                res.add(dp);
                // update discrete point
                discreteTime = Float.valueOf(doc.getFieldValue(ObservationDTO.DISCRETE_POINT).toString());
                // update stats
                stats = new DescriptiveStatistics();
            }
        }
        // add list
        finalRes.put(gr.getGroupValue(), res);
    }
    return finalRes;
}

From source file:uk.ac.ebi.phenotype.service.ObservationService.java

License:Apache License

public List<DiscreteTimePoint> getTimeSeriesControlData(String parameter, ArrayList<String> strains,
        String[] center, String[] sex) throws SolrServerException {

    ArrayList<DiscreteTimePoint> res = new ArrayList<DiscreteTimePoint>();
    SolrQuery query = new SolrQuery().addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":control")
            .addFilterQuery(ObservationDTO.PARAMETER_STABLE_ID + ":" + parameter);
    String q = (strains.size() > 1) ? "(" + ObservationDTO.STRAIN_ACCESSION_ID + ":\""
            + StringUtils.join(strains.toArray(), "\" OR " + ObservationDTO.STRAIN_ACCESSION_ID + ":\"") + "\")"
            : ObservationDTO.STRAIN_ACCESSION_ID + ":\"" + strains.get(0) + "\"";

    if (center != null && center.length > 0) {
        q += " AND (";
        q += (center.length > 1)//from ww w.j a va  2 s  .c  o m
                ? ObservationDTO.PHENOTYPING_CENTER + ":\""
                        + StringUtils.join(center, "\" OR " + ObservationDTO.PHENOTYPING_CENTER + ":\"") + "\""
                : ObservationDTO.PHENOTYPING_CENTER + ":\"" + center[0] + "\"";
        q += ")";
    }

    if (sex != null && sex.length == 1) {
        q += " AND " + ObservationDTO.SEX + ":\"" + sex[0] + "\"";
    }

    query.setQuery(q);
    query.set("group.field", ObservationDTO.DISCRETE_POINT);
    query.set("group", true);
    query.set("fl", ObservationDTO.DATA_POINT + "," + ObservationDTO.DISCRETE_POINT);
    query.set("group.limit", 100000); // number of documents to be returned
    // per group
    query.set("sort", ObservationDTO.DISCRETE_POINT + " asc");
    query.setRows(10000);

    // System.out.println("+_+_+ " + solr.getBaseURL() + "/select?" +
    // query);
    List<Group> groups = solr.query(query).getGroupResponse().getValues().get(0).getValues();
    boolean rounding = false;
    // decide if binning is needed i.e. is the increment points are too
    // scattered, as for calorimetry
    if (groups.size() > 30) { // arbitrary value, just piced it because it
        // seems reasonable for the size of our
        // graphs
        if (Float.valueOf(groups.get(groups.size() - 1).getGroupValue())
                - Float.valueOf(groups.get(0).getGroupValue()) <= 30) { // then
            // rounding
            // will
            // be
            // enough
            rounding = true;
        }
    }
    if (rounding) {
        int bin = Math.round(Float.valueOf(groups.get(0).getGroupValue()));
        for (Group gr : groups) {
            int discreteTime = Math.round(Float.valueOf(gr.getGroupValue()));
            // for calormetry ignore what's before -5 and after 16
            if (parameter.startsWith("IMPC_CAL") || parameter.startsWith("ESLIM_003_001")
                    || parameter.startsWith("M-G-P_003_001")) {
                if (discreteTime < -5) {
                    continue;
                } else if (discreteTime > 16) {
                    break;
                }
            }
            float sum = 0;
            SolrDocumentList resDocs = gr.getResult();
            DescriptiveStatistics stats = new DescriptiveStatistics();
            for (SolrDocument doc : resDocs) {
                sum += (float) doc.getFieldValue(ObservationDTO.DATA_POINT);
                stats.addValue((float) doc.getFieldValue(ObservationDTO.DATA_POINT));
            }
            if (bin < discreteTime || groups.indexOf(gr) == groups.size() - 1) { // finished
                // the
                // groups
                // of
                // filled
                // the
                // bin
                float discreteDataPoint = sum / resDocs.getNumFound();
                DiscreteTimePoint dp = new DiscreteTimePoint((float) discreteTime, discreteDataPoint,
                        new Float(stats.getStandardDeviation()));
                List<Float> errorPair = new ArrayList<>();
                double std = stats.getStandardDeviation();
                Float lower = new Float(discreteDataPoint - std);
                Float higher = new Float(discreteDataPoint + std);
                errorPair.add(lower);
                errorPair.add(higher);
                dp.setErrorPair(errorPair);
                res.add(dp);
                bin = discreteTime;
            }
        }
    } else {
        for (Group gr : groups) {
            Float discreteTime = Float.valueOf(gr.getGroupValue());
            float sum = 0;
            SolrDocumentList resDocs = gr.getResult();
            DescriptiveStatistics stats = new DescriptiveStatistics();
            for (SolrDocument doc : resDocs) {
                sum += (float) doc.getFieldValue(ObservationDTO.DATA_POINT);
                stats.addValue((float) doc.getFieldValue(ObservationDTO.DATA_POINT));
            }
            float discreteDataPoint = sum / resDocs.getNumFound();
            DiscreteTimePoint dp = new DiscreteTimePoint(discreteTime, discreteDataPoint,
                    new Float(stats.getStandardDeviation()));
            List<Float> errorPair = new ArrayList<>();
            double std = stats.getStandardDeviation();
            Float lower = new Float(discreteDataPoint - std);
            Float higher = new Float(discreteDataPoint + std);
            errorPair.add(lower);
            errorPair.add(higher);
            dp.setErrorPair(errorPair);
            res.add(dp);
        }
    }
    return res;
}

From source file:uk.ac.ebi.phenotype.service.ObservationService.java

License:Apache License

/**
 *
 * @param p/*from   w  ww.  j  a v  a  2  s  .com*/
 * @param genes
 * @param strains
 * @param biologicalSample
 * @return list of centers and sexes for the given parameters
 * @throws SolrServerException
 */
public Set<String> getCenters(Parameter p, List<String> genes, ArrayList<String> strains,
        String biologicalSample) throws SolrServerException {

    Set<String> centers = new HashSet<String>();
    SolrQuery query = new SolrQuery()
            .addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":" + biologicalSample)
            .addFilterQuery(ObservationDTO.PARAMETER_STABLE_ID + ":" + p.getStableId());
    String q = (strains.size() > 1) ? "(" + ObservationDTO.STRAIN_ACCESSION_ID + ":\""
            + StringUtils.join(strains.toArray(), "\" OR " + ObservationDTO.STRAIN_ACCESSION_ID + ":\"") + "\")"
            : ObservationDTO.STRAIN_ACCESSION_ID + ":\"" + strains.get(0) + "\"";
    String fq = "";
    if (genes != null && genes.size() > 0) {
        fq += " (";
        fq += (genes.size() > 1) ? ObservationDTO.GENE_ACCESSION_ID + ":\""
                + StringUtils.join(genes.toArray(), "\" OR " + ObservationDTO.GENE_ACCESSION_ID + ":\"") + "\""
                : ObservationDTO.GENE_ACCESSION_ID + ":\"" + genes.get(0) + "\"";
        fq += ")";
    }
    query.addFilterQuery(fq);
    query.setQuery(q);
    query.setRows(100000000);
    query.setFields(ObservationDTO.GENE_ACCESSION_ID, ObservationDTO.DATA_POINT);
    query.set("group", true);
    query.set("group.field", ObservationDTO.PHENOTYPING_CENTER);

    List<Group> groups = solr.query(query, METHOD.POST).getGroupResponse().getValues().get(0).getValues();
    for (Group gr : groups) {
        centers.add((String) gr.getGroupValue());
    }

    System.out.println("CENTERS ::: " + centers);
    return centers;
}

From source file:uk.ac.ebi.phenotype.service.ObservationService.java

License:Apache License

public double getMeanPValue(Parameter p, ArrayList<String> strains, String biologicalSample, String[] center,
        SexType sex) throws SolrServerException {

    System.out.println("GETTING THE MEAN");
    SolrQuery query = new SolrQuery()
            .addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":" + biologicalSample)
            .addFilterQuery(ObservationDTO.PARAMETER_STABLE_ID + ":" + p.getStableId());
    String q = (strains.size() > 1) ? "(" + ObservationDTO.STRAIN_ACCESSION_ID + ":\""
            + StringUtils.join(strains.toArray(), "\" OR " + ObservationDTO.STRAIN_ACCESSION_ID + ":\"") + "\")"
            : ObservationDTO.STRAIN_ACCESSION_ID + ":\"" + strains.get(0) + "\"";
    double mean = 0;

    if (center != null && center.length > 0) {
        q += " AND (";
        q += (center.length > 1)//from w w  w . java 2s . com
                ? ObservationDTO.PHENOTYPING_CENTER + ":\""
                        + StringUtils.join(center, "\" OR " + ObservationDTO.PHENOTYPING_CENTER + ":\"") + "\""
                : ObservationDTO.PHENOTYPING_CENTER + ":\"" + center[0] + "\"";
        q += ")";
    }

    if (sex != null) {
        q += " AND " + ObservationDTO.SEX + ":\"" + sex.getName() + "\"";
    }

    query.setQuery(q);
    query.setRows(0);
    query.set("stats", true);
    query.set("stats.field", ObservationDTO.DATA_POINT);
    query.set("omitHeader", true);
    query.set("wt", "json");

    try {
        JSONObject response = JSONRestUtil.getResults(solr.getBaseURL() + "/select?" + query);
        mean = response.getJSONObject("stats").getJSONObject("stats_fields").getJSONObject("data_point")
                .getDouble("mean");
    } catch (JSONException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    } catch (URISyntaxException e) {
        e.printStackTrace();
    }

    return mean;
}

From source file:uk.ac.ebi.phenotype.service.ObservationService.java

License:Apache License

public CategoricalSet getCategories(Parameter parameter, ArrayList<String> genes, String biologicalSampleGroup,
        ArrayList<String> strains, String[] center, String[] sex) throws SolrServerException, SQLException {

    CategoricalSet resSet = new CategoricalSet();
    resSet.setName(biologicalSampleGroup);
    SolrQuery query = new SolrQuery()
            .addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":" + biologicalSampleGroup)
            .addFilterQuery(ObservationDTO.PARAMETER_STABLE_ID + ":" + parameter.getStableId());

    String q = (strains.size() > 1) ? "(" + ObservationDTO.STRAIN_ACCESSION_ID + ":\""
            + StringUtils.join(strains.toArray(), "\" OR " + ObservationDTO.STRAIN_ACCESSION_ID + ":\"") + "\")"
            : ObservationDTO.STRAIN_ACCESSION_ID + ":\"" + strains.get(0) + "\"";

    if (genes != null && genes.size() > 0) {
        q += " AND (";
        q += (genes.size() > 1) ? ObservationDTO.GENE_ACCESSION_ID + ":\""
                + StringUtils.join(genes.toArray(), "\" OR " + ObservationDTO.GENE_ACCESSION_ID + ":\"") + "\""
                : ObservationDTO.GENE_ACCESSION_ID + ":\"" + genes.get(0) + "\"";
        q += ")";
    }/*from   ww  w  . jav a  2  s .  c o  m*/

    if (center != null && center.length > 0) {
        q += " AND (";
        q += (center.length > 1)
                ? ObservationDTO.PHENOTYPING_CENTER + ":\""
                        + StringUtils.join(center, "\" OR " + ObservationDTO.PHENOTYPING_CENTER + ":\"") + "\""
                : ObservationDTO.PHENOTYPING_CENTER + ":\"" + center[0] + "\"";
        q += ")";
    }

    if (sex != null && sex.length == 1) {
        q += " AND " + ObservationDTO.SEX + ":\"" + sex[0] + "\"";
    }

    query.setQuery(q);
    query.set("group.field", ObservationDTO.CATEGORY);
    query.set("group", true);
    query.setRows(100);

    List<String> categories = new ArrayList<String>();
    List<Group> groups = solr.query(query).getGroupResponse().getValues().get(0).getValues();
    for (Group gr : groups) {
        categories.add((String) gr.getGroupValue());
        CategoricalDataObject catObj = new CategoricalDataObject();
        catObj.setCount((long) gr.getResult().getNumFound());
        String catLabel = parameterDAO.getCategoryDescription(parameter.getId(), gr.getGroupValue());
        catObj.setCategory(catLabel);
        resSet.add(catObj);
    }
    return resSet;
}

From source file:uk.ac.ebi.phenotype.service.ObservationService.java

License:Apache License

public ObservationType getObservationTypeForParameterStableId(String paramStableId) throws SolrServerException {

    SolrQuery q = new SolrQuery().setQuery(ObservationDTO.PARAMETER_STABLE_ID + ":" + paramStableId);
    q.set("rows", 1);
    QueryResponse response = solr.query(q);
    String type = (String) response.getResults().get(0).getFieldValue(ObservationDTO.OBSERVATION_TYPE);

    if (type.equalsIgnoreCase(ObservationType.unidimensional.toString())) {
        return ObservationType.unidimensional;
    }/*  w w  w .  j a v  a 2 s .co m*/

    if (type.equalsIgnoreCase(ObservationType.categorical.toString())) {
        return ObservationType.categorical;
    }

    if (type.equalsIgnoreCase(ObservationType.time_series.toString())) {
        return ObservationType.time_series;
    }

    if (type.equalsIgnoreCase(ObservationType.image_record.toString())) {
        return ObservationType.image_record;
    }

    if (type.equalsIgnoreCase(ObservationType.metadata.toString())) {
        return ObservationType.metadata;
    }

    if (type.equalsIgnoreCase(ObservationType.multidimensional.toString())) {
        return ObservationType.multidimensional;
    }

    if (type.equalsIgnoreCase(ObservationType.text.toString())) {
        return ObservationType.text;
    }

    return null;
}

From source file:uk.ac.ebi.phenotype.service.ObservationService.java

License:Apache License

public Set<String> getTestedGenes(String sex, List<String> parameters) throws SolrServerException {

    HashSet<String> genes = new HashSet<String>();
    int i = 0;//from   w  w w .j a va2 s . c o m
    while (i < parameters.size()) {
        // Add no more than 10 params at the time so the url doesn't get too
        // long
        String parameter = parameters.get(i++);
        String query = "(" + ObservationDTO.PARAMETER_STABLE_ID + ":" + parameter;
        while (i % 15 != 0 && i < parameters.size()) {
            parameter = parameters.get(i++);
            query += " OR " + ObservationDTO.PARAMETER_STABLE_ID + ":" + parameter;
        }
        query += ")";

        SolrQuery q = new SolrQuery().setQuery(query).addField(ObservationDTO.GENE_ACCESSION_ID)
                .setFilterQueries(
                        ObservationDTO.STRAIN_ACCESSION_ID + ":\""
                                + StringUtils.join(OverviewChartsController.OVERVIEW_STRAINS,
                                        "\" OR " + ObservationDTO.STRAIN_ACCESSION_ID + ":\"")
                                + "\"")
                .setRows(-1);
        q.set("group.field", ObservationDTO.GENE_ACCESSION_ID);
        q.set("group", true);
        if (sex != null) {
            q.addFilterQuery(ObservationDTO.SEX + ":" + sex);
        }
        List<Group> groups = solr.query(q).getGroupResponse().getValues().get(0).getValues();
        for (Group gr : groups) {
            genes.add((String) gr.getGroupValue());
        }
    }
    return genes;
}

From source file:uk.ac.ebi.phenotype.service.ObservationService.java

License:Apache License

/**
 * Returns a list of <code>count</code> parameter stable ids matching <code>observationType</code>.
 * //from  www .j  a  va  2 s.  co  m
 * @param observationType desired observation type
 * @param count the number of parameter stable ids to return
 * 
 * @return a list of <code>count</code> parameter stable ids matching <code>observationType</code>.
 * @throws SolrServerException
 */
public List<String> getParameterStableIdsByObservationType(ObservationType observationType, int count)
        throws SolrServerException {
    List<String> retVal = new ArrayList();

    if (count < 1)
        return retVal;

    SolrQuery query = new SolrQuery();
    // http://ves-ebi-d0:8090/mi/impc/dev/solr/experiment/select?q=observation_type%3Acategorical&rows=12&wt=json&indent=true&facet=true&facet.field=parameter_stable_id
    query.setQuery("observation_type:" + observationType.name())
            .addFacetField(ObservationDTO.PARAMETER_STABLE_ID).setFacetMinCount(1).setFacet(true).setRows(count)
            .set("facet.limit", count);

    QueryResponse response = solr.query(query);
    for (Count facet : response.getFacetField(ObservationDTO.PARAMETER_STABLE_ID).getValues()) {
        retVal.add(facet.getName());
    }

    return retVal;
}

From source file:uk.ac.ebi.phenotype.service.StatisticalResultService.java

License:Apache License

public Map<String, Long> getColoniesNoMPHit(ArrayList<String> resourceName, ZygosityType zygosity)
        throws SolrServerException {
    Map<String, Long> res = new HashMap<>();
    Long time = System.currentTimeMillis();
    SolrQuery q = new SolrQuery();

    if (resourceName != null) {
        q.setQuery(GenotypePhenotypeDTO.RESOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + GenotypePhenotypeDTO.RESOURCE_NAME + ":"));
    } else {/*from w  w  w  . ja  v  a  2 s .c  o  m*/
        q.setQuery("*:*");
    }

    if (zygosity != null) {
        q.addFilterQuery(GenotypePhenotypeDTO.ZYGOSITY + ":" + zygosity.name());
    }

    q.addFilterQuery(GenotypePhenotypeDTO.P_VALUE + ":[" + this.P_VALUE_THRESHOLD + " TO 1]");

    q.addFacetField(StatisticalResultDTO.COLONY_ID);
    q.setFacetMinCount(1);
    q.setFacet(true);
    q.setRows(1);
    q.set("facet.limit", -1);

    System.out.println("Solr url for getColoniesNoMPHit " + solr.getBaseURL() + "/select?" + q);
    QueryResponse response = solr.query(q);

    for (Count facet : response.getFacetField(StatisticalResultDTO.COLONY_ID).getValues()) {
        String value = facet.getName();
        long count = facet.getCount();
        res.put(value, count);
    }

    System.out.println("Done in " + (System.currentTimeMillis() - time));
    return res;

}

From source file:uk.ac.ebi.phenotype.service.StatisticalResultService.java

License:Apache License

public StackedBarsData getUnidimensionalData(Parameter p, List<String> genes, ArrayList<String> strains,
        String biologicalSample, String[] center, String[] sex) throws SolrServerException {

    String urlParams = "";
    SolrQuery query = new SolrQuery()
            .addFilterQuery(StatisticalResultDTO.PARAMETER_STABLE_ID + ":" + p.getStableId());
    String q = "*:*";
    query.addFilterQuery((strains.size() > 1)
            ? "(" + StatisticalResultDTO.STRAIN_ACCESSION_ID + ":\""
                    + StringUtils.join(strains.toArray(),
                            "\" OR " + StatisticalResultDTO.STRAIN_ACCESSION_ID + ":\"")
                    + "\")"
            : StatisticalResultDTO.STRAIN_ACCESSION_ID + ":\"" + strains.get(0) + "\"");
    if (strains.size() > 0) {
        urlParams += "&strain=" + StringUtils.join(strains.toArray(), "&strain=");
    }/*from www  .j  a va 2 s  .c  o m*/

    if (center != null && center.length > 0) {
        query.addFilterQuery(
                "(" + ((center.length > 1)
                        ? StatisticalResultDTO.PHENOTYPING_CENTER + ":\""
                                + StringUtils.join(center,
                                        "\" OR " + StatisticalResultDTO.PHENOTYPING_CENTER + ":\"")
                                + "\""
                        : StatisticalResultDTO.PHENOTYPING_CENTER + ":\"" + center[0] + "\"") + ")");
        urlParams += "&phenotyping_center=" + StringUtils.join(center, "&phenotyping_center=");
    }

    if (sex != null && sex.length == 1) {
        if (sex[0].equalsIgnoreCase("male")) {
            query.addFilterQuery(StatisticalResultDTO.MALE_CONTROL_COUNT + ":[4 TO 100000]");
            query.addFilterQuery(StatisticalResultDTO.MALE_MUTANT_COUNT + ":[4 TO 100000]");
        } else {
            query.addFilterQuery(StatisticalResultDTO.FEMALE_CONTROL_COUNT + ":[4 TO 100000]");
            query.addFilterQuery(StatisticalResultDTO.FEMALE_MUTANT_COUNT + ":[4 TO 100000]");
        }
    }

    query.setQuery(q);
    query.addFilterQuery("(" + StatisticalResultDTO.FEMALE_CONTROL_COUNT + ":[4 TO 100000] OR "
            + StatisticalResultDTO.MALE_CONTROL_COUNT + ":[4 TO 100000])");
    query.setRows(10000000);
    query.setFields(StatisticalResultDTO.MARKER_ACCESSION_ID, StatisticalResultDTO.FEMALE_CONTROL_MEAN,
            StatisticalResultDTO.MARKER_SYMBOL, StatisticalResultDTO.FEMALE_MUTANT_MEAN,
            StatisticalResultDTO.MALE_CONTROL_MEAN, StatisticalResultDTO.MALE_MUTANT_MEAN,
            StatisticalResultDTO.FEMALE_CONTROL_COUNT, StatisticalResultDTO.FEMALE_MUTANT_COUNT,
            StatisticalResultDTO.MALE_CONTROL_COUNT, StatisticalResultDTO.MALE_MUTANT_COUNT);
    query.set("group", true);
    query.set("group.field", StatisticalResultDTO.COLONY_ID);
    query.set("group.limit", 1);

    List<Group> groups = solr.query(query).getGroupResponse().getValues().get(0).getValues();
    double[] meansArray = new double[groups.size()];
    String[] genesArray = new String[groups.size()];
    String[] geneSymbolArray = new String[groups.size()];
    int size = 0;

    for (Group gr : groups) {

        SolrDocumentList resDocs = gr.getResult();
        String sexToDisplay = null;
        OverviewRatio overviewRatio = new OverviewRatio();

        for (SolrDocument doc : resDocs) {
            sexToDisplay = getSexToDisplay(sex, sexToDisplay, doc);
            overviewRatio.add(doc);
        }

        if (sexToDisplay != null) {
            Double ratio = overviewRatio.getPlotRatio(sexToDisplay);
            if (ratio != null) {
                genesArray[size] = (String) resDocs.get(0).get(StatisticalResultDTO.MARKER_ACCESSION_ID);
                geneSymbolArray[size] = (String) resDocs.get(0).get(StatisticalResultDTO.MARKER_SYMBOL);
                meansArray[size] = ratio;
                size++;
            }
        }
    }

    // we do the binning for all the data but fill the bins after that to
    // keep tract of phenotype associations
    int binCount = Math.min((int) Math.floor((double) groups.size() / 2), 20);
    ArrayList<String> mutantGenes = new ArrayList<String>();
    ArrayList<String> controlGenes = new ArrayList<String>();
    ArrayList<String> mutantGeneAcc = new ArrayList<String>();
    ArrayList<String> controlGeneAcc = new ArrayList<String>();
    ArrayList<Double> upperBounds = new ArrayList<Double>();
    EmpiricalDistribution distribution = new EmpiricalDistribution(binCount);
    if (size > 0) {
        distribution.load(ArrayUtils.subarray(meansArray, 0, size - 1));
        for (double bound : distribution.getUpperBounds()) {
            upperBounds.add(bound);
        }
        // we we need to distribute the control mutants and the
        // phenotype-mutants in the bins
        ArrayList<Double> controlM = new ArrayList<Double>();
        ArrayList<Double> phenMutants = new ArrayList<Double>();

        for (int j = 0; j < upperBounds.size(); j++) {
            controlM.add((double) 0);
            phenMutants.add((double) 0);
            controlGenes.add("");
            mutantGenes.add("");
            controlGeneAcc.add("");
            mutantGeneAcc.add("");
        }

        for (int j = 0; j < size; j++) {
            // find out the proper bin
            int binIndex = getBin(upperBounds, meansArray[j]);
            if (genes.contains(genesArray[j])) {
                phenMutants.set(binIndex, 1 + phenMutants.get(binIndex));
                String genesString = mutantGenes.get(binIndex);
                if (!genesString.contains(geneSymbolArray[j])) {
                    if (genesString.equals("")) {
                        mutantGenes.set(binIndex, geneSymbolArray[j]);
                        mutantGeneAcc.set(binIndex, "accession=" + genesArray[j]);
                    } else {
                        mutantGenes.set(binIndex, genesString + ", " + geneSymbolArray[j]);
                        mutantGeneAcc.set(binIndex,
                                mutantGeneAcc.get(binIndex) + "&accession=" + genesArray[j]);
                    }
                }
            } else { // treat as control because they don't have this phenotype association
                String genesString = controlGenes.get(binIndex);
                if (!genesString.contains(geneSymbolArray[j])) {
                    if (genesString.equalsIgnoreCase("")) {
                        controlGenes.set(binIndex, geneSymbolArray[j]);
                        controlGeneAcc.set(binIndex, "accession=" + genesArray[j]);
                    } else {
                        controlGenes.set(binIndex, genesString + ", " + geneSymbolArray[j]);
                        controlGeneAcc.set(binIndex,
                                controlGeneAcc.get(binIndex) + "&accession=" + genesArray[j]);
                    }
                }
                controlM.set(binIndex, 1 + controlM.get(binIndex));
            }
        }
        // System.out.println(" Mutants list " + phenMutants);

        // add the rest of parameters to the graph urls
        for (int t = 0; t < controlGeneAcc.size(); t++) {
            controlGeneAcc.set(t, controlGeneAcc.get(t) + urlParams);
            mutantGeneAcc.set(t, mutantGeneAcc.get(t) + urlParams);
        }

        StackedBarsData data = new StackedBarsData();
        data.setUpperBounds(upperBounds);
        data.setControlGenes(controlGenes);
        data.setControlMutatns(controlM);
        data.setMutantGenes(mutantGenes);
        data.setPhenMutants(phenMutants);
        data.setControlGeneAccesionIds(controlGeneAcc);
        data.setMutantGeneAccesionIds(mutantGeneAcc);
        return data;
    }

    return null;
}