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)

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Document

Replace any existing parameter with the given name.

Usage

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

public Map<String, Long> getColoniesNoMPHit(List<String> resourceName, ZygosityType zygosity)
        throws SolrServerException, IOException {

    Map<String, Long> res = new HashMap<>();
    SolrQuery q = new SolrQuery();

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

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

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

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

    logger.info(
            "Solr url for getColoniesNoMPHit " + SolrUtils.getBaseURL(statisticalResultCore) + "/select?" + q);
    QueryResponse response = statisticalResultCore.query(q);

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

    return res;
}

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

/**
 *
 * @param geneAccessionId//  w ww  . j av a  2 s .  c  om
 * @return Basic information for allele pages in an AllelePageDTO
 */
public AllelePageDTO getAllelesInfo(String geneAccessionId, List<String> alleleSymbol,
        List<String> phenotypingCenter, List<String> pipelineName, List<String> procedureStableId,
        List<String> procedureName, List<String> mpTermIds, ArrayList<String> resource) {

    AllelePageDTO dto = new AllelePageDTO();
    SolrQuery q = buildQuery(geneAccessionId, procedureName, alleleSymbol, phenotypingCenter, pipelineName,
            procedureStableId, resource, mpTermIds, null, null, null, null, null, null, null, null);

    q.addField(StatisticalResultDTO.MARKER_SYMBOL);
    q.addField(StatisticalResultDTO.MARKER_ACCESSION_ID);
    q.addFilterQuery(StatisticalResultDTO.P_VALUE + ":[* TO *]");
    q.setFacet(true);
    q.setFacetLimit(-1);
    q.setFacetMinCount(1);
    q.addFacetField(StatisticalResultDTO.PHENOTYPING_CENTER);
    q.addFacetField(StatisticalResultDTO.PIPELINE_NAME);
    q.addFacetField(StatisticalResultDTO.ALLELE_SYMBOL);
    q.setRows(1);

    String pivotFacet = StatisticalResultDTO.PROCEDURE_NAME + "," + StatisticalResultDTO.PARAMETER_STABLE_ID;
    q.set("facet.pivot", pivotFacet);
    q.set("facet.pivot.mincount", 1);

    try {
        QueryResponse res = statisticalResultCore.query(q);

        FacetField phenotypingCenters = res.getFacetField(StatisticalResultDTO.PHENOTYPING_CENTER);

        for (Count facet : phenotypingCenters.getValues()) {
            dto.addPhenotypingCenter(facet.getName());
        }

        FacetField alleles = statisticalResultCore.query(q).getFacetField(StatisticalResultDTO.ALLELE_SYMBOL);
        for (Count facet : alleles.getValues()) {
            dto.addAlleleSymbol(facet.getName());
        }

        FacetField pipelines = statisticalResultCore.query(q).getFacetField(StatisticalResultDTO.PIPELINE_NAME);
        for (Count facet : pipelines.getValues()) {
            dto.addPipelineName(facet.getName());
        }

        for (PivotField pivot : res.getFacetPivot().get(pivotFacet)) {
            if (pivot.getPivot() != null) {
                List<String> lst = new ArrayList<>();
                for (PivotField gene : pivot.getPivot()) {
                    lst.add(gene.getValue().toString());
                }
                dto.addParametersByProcedure(pivot.getValue().toString(), new ArrayList<>(lst));
                dto.addProcedureNames(pivot.getValue().toString());
            }
        }

        SolrDocument doc = res.getResults().get(0);
        dto.setGeneSymbol(doc.getFieldValue(StatisticalResultDTO.MARKER_SYMBOL).toString());
        dto.setGeneAccession(geneAccessionId);

    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }

    return dto;

}

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

public List<String> getCenters(String pipelineStableId, String observationType, String resource, String status)
        throws SolrServerException, IOException {

    List<String> res = new ArrayList<>();

    SolrQuery query = new SolrQuery().setQuery("*:*");
    query.set("facet", true);
    query.set("facet.field", StatisticalResultDTO.PHENOTYPING_CENTER);
    query.setRows(0);/*  ww  w .j  av  a2  s  .  c  o m*/
    query.set("facet.limit", -1);
    query.set("facet.mincount", 1);

    if (pipelineStableId != null) {
        query.addFilterQuery(StatisticalResultDTO.PIPELINE_STABLE_ID + ":" + pipelineStableId);
    }
    if (observationType != null) {
        query.addFilterQuery(StatisticalResultDTO.DATA_TYPE + ":" + observationType);
    }
    if (resource != null) {
        query.addFilterQuery(StatisticalResultDTO.RESOURCE_NAME + ":" + resource);
    }
    if (status != null) {
        query.addFilterQuery(StatisticalResultDTO.STATUS + ":" + status);
    }

    QueryResponse response = statisticalResultCore.query(query);

    for (Count facet : response.getFacetField(StatisticalResultDTO.PHENOTYPING_CENTER).getValues()) {
        res.add(facet.getName());
    }

    return res;
}

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

/**
 * @author tudose//from w  w  w.ja  v a  2  s .com
 * @since 2015/07/21
 * @return List<ProcedureBean>
 */
public List<ImpressBaseDTO> getProcedures(String pipelineStableId, String observationType, String resource,
        Integer minParameterNumber, List<String> proceduresToSkip, String status, boolean includeWilcoxon) {

    List<ImpressBaseDTO> procedures = new ArrayList<>();

    try {
        SolrQuery query = new SolrQuery().setQuery("*:*").addField(StatisticalResultDTO.PROCEDURE_ID)
                .addField(StatisticalResultDTO.PROCEDURE_NAME)
                .addField(StatisticalResultDTO.PROCEDURE_STABLE_ID);
        query.set("group", true);
        query.set("group.field", StatisticalResultDTO.PROCEDURE_NAME);
        query.setRows(10000);
        query.setSort(StatisticalResultDTO.DOCUMENT_ID, SolrQuery.ORDER.asc);
        query.set("group.limit", 1);
        if (!includeWilcoxon) {
            query.addFilterQuery("-" + StatisticalResultDTO.STATISTICAL_METHOD + ":Wilcoxon*");
        }
        if (pipelineStableId != null) {
            query.addFilterQuery(StatisticalResultDTO.PIPELINE_STABLE_ID + ":" + pipelineStableId);
        }
        if (observationType != null) {
            query.addFilterQuery(StatisticalResultDTO.DATA_TYPE + ":" + observationType);
        }
        if (resource != null) {
            query.addFilterQuery(StatisticalResultDTO.RESOURCE_NAME + ":" + resource);
        }
        if (status != null) {
            query.addFilterQuery(StatisticalResultDTO.STATUS + ":" + status);
        }
        String pivotField = StatisticalResultDTO.PROCEDURE_NAME + "," + StatisticalResultDTO.PARAMETER_NAME;

        if (minParameterNumber != null && minParameterNumber > 0) {

            query.setFacet(true);
            query.setFacetMinCount(1);
            query.set("facet.pivot.mincount", minParameterNumber);
            query.set("facet.pivot", pivotField);

        }

        QueryResponse response = statisticalResultCore.query(query);

        for (Group group : response.getGroupResponse().getValues().get(0).getValues()) {

            ImpressBaseDTO procedure = new ImpressBaseDTO(
                    Long.getLong(group.getResult().get(0).getFirstValue(StatisticalResultDTO.PROCEDURE_ID)
                            .toString()),
                    null,
                    group.getResult().get(0).getFirstValue(StatisticalResultDTO.PROCEDURE_STABLE_ID).toString(),
                    group.getResult().get(0).getFirstValue(StatisticalResultDTO.PROCEDURE_NAME).toString());
            procedures.add(procedure);
        }

        if (minParameterNumber != null && minParameterNumber > 0) {
            // get procedureList with more than minParameterNumber
            // remove from procedures the ones not in procedureList
            List<Map<String, String>> res = getFacetPivotResults(response, false);
            HashSet<String> proceduresWithMinCount = new HashSet<>();

            for (Map<String, String> pivot : res) {
                proceduresWithMinCount.addAll(pivot.values());
            }

            List<ImpressBaseDTO> proceduresToReturn = new ArrayList<>();

            for (ImpressBaseDTO proc : procedures) {
                if (proceduresWithMinCount.contains(proc.getName())) {
                    if (proceduresToSkip != null && !proceduresToSkip.contains(proc.getStableId())
                            || proceduresToSkip == null) {
                        proceduresToReturn.add(proc);
                    }
                }
            }
            procedures = proceduresToReturn;

        }

    } catch (SolrServerException | IOException | IndexOutOfBoundsException e) {
        e.printStackTrace();
    }

    return procedures;
}

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

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

    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  w  ww  .  ja va2s  .  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.setSort(StatisticalResultDTO.DOCUMENT_ID, SolrQuery.ORDER.asc);
    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 = statisticalResultCore.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);
    List<String> mutantGenes = new ArrayList<>();
    List<String> controlGenes = new ArrayList<>();
    List<String> mutantGeneAcc = new ArrayList<>();
    List<String> controlGeneAcc = new ArrayList<>();
    List<Double> upperBounds = new ArrayList<>();
    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
        List<Double> controlM = new ArrayList<>();
        List<Double> phenMutants = new ArrayList<>();

        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));
            }
        }

        // 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;
}

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

public Map<String, List<String>> getDistributionOfLinesByMPTopLevel(List<String> resourceName,
        Float pValueThreshold)//from  w w w .ja v a  2 s  .c o  m
        throws SolrServerException, IOException, InterruptedException, ExecutionException {

    Map<String, List<String>> res = new ConcurrentHashMap<>(); //<parameter, <genes>>
    String pivotFacet = StatisticalResultDTO.TOP_LEVEL_MP_TERM_NAME + "," + StatisticalResultDTO.COLONY_ID;
    SolrQuery q = new SolrQuery();

    if (resourceName != null) {
        q.setQuery(StatisticalResultDTO.RESOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + StatisticalResultDTO.RESOURCE_NAME + ":"));
    } else {
        q.setQuery("*:*");
    }

    if (pValueThreshold != null) {
        q.setFilterQueries(StatisticalResultDTO.P_VALUE + ":[0 TO " + pValueThreshold + "]");
    }

    q.set("facet.pivot", pivotFacet);
    q.setFacet(true);
    q.setFacetMinCount(1);
    q.setRows(1);
    q.set("facet.limit", -1);

    logger.info("Solr url for getDistributionOfLinesByMPTopLevel " + SolrUtils.getBaseURL(statisticalResultCore)
            + "/select?" + q);
    QueryResponse response = statisticalResultCore.query(q);

    for (PivotField pivot : response.getFacetPivot().get(pivotFacet)) {
        if (pivot.getPivot() != null) {
            List<String> colonies = new ArrayList<>();
            for (PivotField colony : pivot.getPivot()) {
                colonies.add(colony.getValue().toString());
            }
            res.put(pivot.getValue().toString(), new ArrayList<String>(colonies));
        }
    }

    return res;
}

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

public Map<String, List<String>> getDistributionOfGenesByMPTopLevel(List<String> resourceName,
        Float pValueThreshold)/*from www. ja  v a  2 s. co m*/
        throws SolrServerException, IOException, InterruptedException, ExecutionException {

    Map<String, List<String>> res = new ConcurrentHashMap<>(); //<parameter, <genes>>
    String pivotFacet = StatisticalResultDTO.TOP_LEVEL_MP_TERM_NAME + ","
            + StatisticalResultDTO.MARKER_ACCESSION_ID;
    SolrQuery q = new SolrQuery();

    if (resourceName != null) {
        q.setQuery(StatisticalResultDTO.RESOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + StatisticalResultDTO.RESOURCE_NAME + ":"));
    } else {
        q.setQuery("*:*");
    }

    if (pValueThreshold != null) {
        q.setFilterQueries(StatisticalResultDTO.P_VALUE + ":[0 TO " + pValueThreshold + "]");
    }

    q.set("facet.pivot", pivotFacet);
    q.setFacet(true);
    q.setRows(1);
    q.set("facet.limit", -1);

    logger.info("Solr url for getDistributionOfGenesByMPTopLevel " + SolrUtils.getBaseURL(statisticalResultCore)
            + "/select?" + q);
    QueryResponse response = statisticalResultCore.query(q);

    for (PivotField pivot : response.getFacetPivot().get(pivotFacet)) {
        if (pivot.getPivot() != null) {
            List<String> genes = new ArrayList<>();
            for (PivotField gene : pivot.getPivot()) {
                genes.add(gene.getValue().toString());
            }
            res.put(pivot.getValue().toString(), new ArrayList<String>(genes));
        }
    }

    return res;
}

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

public PhenotypeFacetResult getPhenotypeFacetResultByPhenotypingCenterAndPipeline(String phenotypingCenter,
        String pipelineStableId) throws IOException, URISyntaxException, JSONException {

    SolrQuery query = new SolrQuery();
    query.setQuery(StatisticalResultDTO.PHENOTYPING_CENTER + ":\"" + phenotypingCenter);
    query.addFilterQuery(StatisticalResultDTO.PIPELINE_STABLE_ID + ":" + pipelineStableId);
    query.setFacet(true);/*ww  w  . j a  v a 2 s  . c  om*/
    query.addFacetField(StatisticalResultDTO.RESOURCE_FULLNAME);
    query.addFacetField(StatisticalResultDTO.PROCEDURE_NAME);
    query.addFacetField(StatisticalResultDTO.MARKER_SYMBOL);
    query.addFacetField(StatisticalResultDTO.MP_TERM_NAME);
    query.setSort(StatisticalResultDTO.P_VALUE, SolrQuery.ORDER.asc);
    query.setRows(10000000);
    query.set("wt", "json");
    query.set("version", "2.2");

    String solrUrl = SolrUtils.getBaseURL(statisticalResultCore) + "/select?" + query;
    return createPhenotypeResultFromSolrResponse(solrUrl);
}

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

public HashMap<String, GeneRowForHeatMap> getSecondaryProjectMapForGeneList(Set<String> geneAccessions,
        List<BasicBean> topLevelMps) throws IOException, SolrServerException {

    HashMap<String, GeneRowForHeatMap> geneRowMap = new HashMap<>(); // <geneAcc, row>

    SolrQuery q = new SolrQuery()
            .setQuery(geneAccessions.stream().collect(
                    Collectors.joining("\" OR \"", StatisticalResultDTO.MARKER_ACCESSION_ID + ":(\"", "\")")))
            .addField(StatisticalResultDTO.PROCEDURE_STABLE_ID)
            .addField(StatisticalResultDTO.MARKER_ACCESSION_ID)
            .addField(StatisticalResultDTO.TOP_LEVEL_MP_TERM_NAME).addField(StatisticalResultDTO.MP_TERM_NAME)
            .addField(StatisticalResultDTO.MARKER_SYMBOL).addField(StatisticalResultDTO.STATUS)
            .addField(StatisticalResultDTO.SIGNIFICANT).setRows(Integer.MAX_VALUE)
            .setSort(StatisticalResultDTO.DOCUMENT_ID, SolrQuery.ORDER.asc);

    q.addFilterQuery(StatisticalResultDTO.MP_TERM_ID + ":*"); // Ignore MPATH or other types of associations
    q.add("group", "true");
    q.add("group.field", StatisticalResultDTO.MARKER_ACCESSION_ID);
    q.set("group.limit", Integer.MAX_VALUE);

    GroupCommand groups = statisticalResultCore.query(q, SolrRequest.METHOD.POST).getGroupResponse().getValues()
            .get(0);//from  w  w  w .  ja  v  a  2s.c  o  m

    for (Group group : groups.getValues()) {
        // Each group contains data for a different gene
        String geneAcc = group.getGroupValue();
        SolrDocumentList docs = group.getResult();
        GeneRowForHeatMap row = new GeneRowForHeatMap(geneAcc,
                docs.get(0).getFieldValue(StatisticalResultDTO.MARKER_SYMBOL).toString(), topLevelMps); // Fill row with default values for all mp top levels

        for (SolrDocument doc : docs) {
            List<String> currentTopLevelMps = (ArrayList<String>) doc
                    .get(StatisticalResultDTO.TOP_LEVEL_MP_TERM_NAME);

            // The current top level might be null, because the actual term is already a top level,
            // check the associated mp term to see, and add it if it's already top-level
            if (currentTopLevelMps == null) {
                if (topLevelMps.stream().anyMatch(x -> x.getName()
                        .equals(doc.getFieldValue(StatisticalResultDTO.MP_TERM_NAME).toString()))) {
                    currentTopLevelMps = new ArrayList<>();
                    currentTopLevelMps.add(doc.getFieldValue(StatisticalResultDTO.MP_TERM_NAME).toString());
                }
            }

            // The term might have been annotated to "mammalian phenotype" which doesn't have an icon in the grid.  Skip it
            if (currentTopLevelMps != null) {
                for (String mp : currentTopLevelMps) {
                    HeatMapCell cell = row.getXAxisToCellMap().containsKey(mp) ? row.getXAxisToCellMap().get(mp)
                            : new HeatMapCell(mp, HeatMapCell.THREE_I_NO_DATA);
                    if (doc.getFieldValue(StatisticalResultDTO.SIGNIFICANT) != null
                            && doc.getFieldValue(StatisticalResultDTO.SIGNIFICANT).toString()
                                    .equalsIgnoreCase("true")) {
                        cell.addStatus(HeatMapCell.THREE_I_DEVIANCE_SIGNIFICANT);
                    } else if (doc.getFieldValue(StatisticalResultDTO.STATUS).toString().equals("Success")) {
                        cell.addStatus(HeatMapCell.THREE_I_DATA_ANALYSED_NOT_SIGNIFICANT);
                    } else {
                        cell.addStatus(HeatMapCell.THREE_I_COULD_NOT_ANALYSE);
                    }

                    row.add(cell);
                }
            }
        }
        geneRowMap.put(geneAcc, row);
    }

    return geneRowMap;
}

From source file:org.mousephenotype.cda.solr.service.StatisticalResultService.java

License:Apache License

public Map<String, List<String>> getParametersToProcedureMap(String alleleAccession, String geneAccession,
        String resourceName, String phenotypingCenter, String pipelineSrableId, String procedure)
        throws SolrServerException, IOException {

    Map<String, List<String>> res = new ConcurrentHashMap<>(); //<parameter, <genes>>

    SolrQuery q = new SolrQuery().setQuery("*:*");
    q.add("fl", StatisticalResultDTO.PARAMETER_NAME + "," + StatisticalResultDTO.PARAMETER_STABLE_ID);

    if (resourceName != null) {
        q.addFilterQuery(StatisticalResultDTO.RESOURCE_NAME + ":\"" + resourceName + "\"");
    }/*from   w  w w .  ja v  a2s .  co  m*/
    if (phenotypingCenter != null) {
        q.addFilterQuery(StatisticalResultDTO.PHENOTYPING_CENTER + ":\"" + phenotypingCenter + "\"");
    }
    if (pipelineSrableId != null) {
        q.addFilterQuery(StatisticalResultDTO.PIPELINE_STABLE_ID + ":\"" + pipelineSrableId + "\"");
    }
    String pivotFacet = StatisticalResultDTO.PROCEDURE_NAME + "," + StatisticalResultDTO.PARAMETER_STABLE_ID;
    q.set("facet.pivot", pivotFacet);
    q.setFacet(true);
    q.setRows(1);
    q.set("facet.limit", -1);

    logger.info("Solr url for getParametersToProcedureMap " + SolrUtils.getBaseURL(statisticalResultCore)
            + "/select?" + q);
    QueryResponse response = statisticalResultCore.query(q);

    for (PivotField pivot : response.getFacetPivot().get(pivotFacet)) {
        if (pivot.getPivot() != null) {
            List<String> lst = new ArrayList<>();
            for (PivotField gene : pivot.getPivot()) {
                lst.add(gene.getValue().toString());
            }
            res.put(pivot.getValue().toString(), new ArrayList<String>(lst));
        }
    }

    return res;
}