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

Introduction

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

Prototype

public SolrQuery setFacet(boolean b) 

Source Link

Document

enable/disable faceting.

Usage

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

License:Apache License

/**
 * @author tudose/*from  w  w w  .ja v a  2 s.  co  m*/
 * @since 2015/09/25
 * @return List< [(Procedure, parameter, observationNumber)]>
 */
public List<String[]> getProcedureParameterList() {

    List<String[]> result = new ArrayList<>();
    SolrQuery q = new SolrQuery();

    q.setQuery("*:*");
    q.setFacet(true);
    q.setFacetLimit(-1);
    q.setRows(0);

    String pivotFacet = ImpressDTO.PROCEDURE_STABLE_ID + "," + ImpressDTO.PARAMETER_STABLE_ID;
    q.set("facet.pivot", pivotFacet);

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

        for (PivotField pivot : res.getFacetPivot().get(pivotFacet)) {
            if (pivot.getPivot() != null) {
                for (PivotField parameter : pivot.getPivot()) {
                    String[] row = { pivot.getValue().toString(), parameter.getValue().toString() };
                    result.add(row);
                }
            }
        }

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

    return result;
}

---

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

License:Apache License

public List<String> getGenesWithMoreProcedures(int n, List<String> resourceName)
        throws SolrServerException, IOException, InterruptedException, ExecutionException {

    List<String> genes = new ArrayList<>();
    SolrQuery q = new SolrQuery();

    if (resourceName != null) {
        q.setQuery(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    } else {/*from w  w w.  j a  va2  s  .co  m*/
        q.setQuery("*:*");
    }

    String geneProcedurePivot = ObservationDTO.GENE_SYMBOL + "," + ObservationDTO.PROCEDURE_NAME;

    q.add("facet.pivot", geneProcedurePivot);

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

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

    for (PivotField pivot : response.getFacetPivot().get(geneProcedurePivot)) {
        if (pivot.getPivot() != null) {
            if (pivot.getPivot().size() >= n) {
                genes.add(pivot.getValue().toString());
            }
        }
    }

    return genes;
}

---

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

License:Apache License

/**
 * Returns a map of categories, faceted by the given pivot, indexed by category, comprising # Genes and Gene Symbols
 *
 * @param resources//  www . j  a  v a2  s  .  c  o m
 * @param parameterStableIds A list of parameter_stable_id values (e.g. IMPC_VIA_001_001)
 * @param pivot              A comma-separated string of solr fields to pivot the facet by (e.g. category,gene_symbol)
 * @return a map of categories, faceted by the given pivot, indexed by category, comprising # Genes and Gene Symbols
 * @throws SolrServerException, IOException
 */
public List<Map<String, String>> getCategories(List<String> resources, List<String> parameterStableIds,
        String pivot) throws SolrServerException, IOException {

    SolrQuery query = new SolrQuery();

    if ((resources != null) && (!resources.isEmpty())) {
        query.setFilterQueries(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resources, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    }
    if ((parameterStableIds != null) && (!parameterStableIds.isEmpty())) {
        query.setQuery(ObservationDTO.PARAMETER_STABLE_ID + ":"
                + StringUtils.join(parameterStableIds, " OR " + ObservationDTO.PARAMETER_STABLE_ID + ":"));
    }
    query.setRows(0);
    query.setFacet(true);
    query.setFacetMinCount(1);
    query.setFacetLimit(-1);
    query.set("facet.pivot", pivot);

    logger.info("getCategories Url: " + SolrUtils.getBaseURL(experimentCore) + "/select?" + query);

    return getFacetPivotResults(experimentCore.query(query), false);
}

---

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

License:Apache License

public Map<String, Set<String>> getColoniesByPhenotypingCenter(List<String> resourceName, ZygosityType zygosity)
        throws SolrServerException, IOException, InterruptedException {

    Map<String, Set<String>> res = new HashMap<>();
    SolrQuery q = new SolrQuery();
    String pivotFacet = ObservationDTO.PHENOTYPING_CENTER + "," + ObservationDTO.COLONY_ID;
    NamedList<List<PivotField>> response;

    if (resourceName != null) {
        q.setQuery(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    } else {/*from  w w  w  . j a v a2s.co m*/
        q.setQuery("*:*");
    }

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

    q.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":experimental");
    q.addFacetPivotField(pivotFacet);
    q.setFacet(true);
    q.setFacetLimit(-1);
    q.setFacetMinCount(1);
    q.setRows(0);

    try {
        response = experimentCore.query(q).getFacetPivot();
        for (PivotField genePivot : response.get(pivotFacet)) {
            if (genePivot.getPivot() != null) {
                String center = genePivot.getValue().toString();
                HashSet<String> colonies = new HashSet<>();
                for (PivotField f : genePivot.getPivot()) {
                    colonies.add(f.getValue().toString());
                }
                res.put(center, colonies);
            }
        }
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }
    return res;
}

---

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

License:Apache License

public Set<String> getAllGeneIdsByResource(List<String> resourceName, boolean experimentalOnly) {

    SolrQuery q = new SolrQuery();
    q.setFacet(true);
    q.setFacetMinCount(1);//from   www . j  a va 2 s  .  c  o  m
    q.setFacetLimit(-1);
    q.setRows(0);
    q.addFacetField(ObservationDTO.GENE_ACCESSION_ID);
    if (resourceName != null) {
        q.setQuery(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    } else {
        q.setQuery("*:*");
    }

    if (experimentalOnly) {
        q.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":experimental");
    }

    logger.info("Solr URL getAllGeneIdsByResource " + SolrUtils.getBaseURL(experimentCore) + "/select?" + q);
    try {
        return getFacets(experimentCore.query(q)).get(ObservationDTO.GENE_ACCESSION_ID).keySet();
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }

    return null;
}

---

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

License:Apache License

public Set<String> getAllColonyIdsByResource(List<String> resourceName, boolean experimentalOnly) {

    SolrQuery q = new SolrQuery();
    q.setFacet(true);
    q.setFacetMinCount(1);/*from   w w w. j a  va  2  s.c o m*/
    q.setFacetLimit(-1);
    q.setRows(0);
    q.addFacetField(ObservationDTO.COLONY_ID);

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

    if (experimentalOnly) {
        q.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":experimental");
    }

    logger.info("Solr URL getAllColonyIdsByResource " + SolrUtils.getBaseURL(experimentCore) + "/select?" + q);
    try {
        return getFacets(experimentCore.query(q)).get(ObservationDTO.COLONY_ID).keySet();
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }

    return null;
}

---

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

License:Apache License

public NamedList<List<PivotField>> getHistopathGeneParameterNameCategoryPivots()
        throws SolrServerException, IOException {

    //http://ves-hx-d1.ebi.ac.uk:8986/solr/experiment/select?q=*:*&rows=0&sort=id+asc&fq=parameter_stable_id:*HIS*&facet=true&facet.pivot=gene_symbol,category&facet.limit=-1
    //we need the significance score only can't filter based on a parameter ids as all different for each anatomy but can do search for "Significance score " in parameter_name string
    SolrQuery q = new SolrQuery().setQuery("*:*").setRows(0)//we don't care about the observations themselfs so don't return them only which anatomy has significant Histopath data on which genes.
            .setSort(ObservationDTO.ID, SolrQuery.ORDER.asc)
            //.setFields(fields)
            .addFilterQuery("parameter_stable_id:*HIS*").addFilterQuery("parameter_name:*Significance*");//.addFilterQuery("gene_symbol:Prkab1");
    //.addFilterQuery("category:Significant");
    //.addFilterQuery("category:Significant");//otherwise query takes too long
    q.setFacet(true);
    String pivotFacet = ObservationDTO.GENE_SYMBOL + "," + ObservationDTO.PARAMETER_NAME + ","
            + ObservationDTO.CATEGORY;/*from w  w  w.  j  a va  2  s.  c  om*/

    q.add("facet.pivot", pivotFacet);
    q.setFacetLimit(-1);
    System.out.println("solr query in getObservationByProcedureNameAndGene=" + q);
    return experimentCore.query(q).getFacetPivot();
}

---

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

License:Apache License

public Set<String> getChartPivots(String baseUrl, String acc, ParameterDTO parameter,
        List<String> pipelineStableIds, List<String> zyList, List<String> phenotypingCentersList,
        List<String> strainsParams, List<String> metaDataGroup, List<String> alleleAccession)
        throws IOException, SolrServerException, URISyntaxException {

    SolrQuery query = new SolrQuery();
    query.setQuery("*:*");
    if (acc != null) {
        query.addFilterQuery("gene_accession_id" + ":\"" + acc + "\"");
    }//from   w  w  w .ja  v a  2  s. co  m
    if (parameter != null) {
        query.addFilterQuery(StatisticalResultDTO.PARAMETER_STABLE_ID + ":" + parameter.getStableId());
    }
    if (pipelineStableIds != null && pipelineStableIds.size() > 0) {
        query.addFilterQuery(pipelineStableIds.stream()
                .collect(Collectors.joining(" OR ", StatisticalResultDTO.PIPELINE_STABLE_ID + ":(", ")")));
    }
    if (zyList != null && zyList.size() > 0) {
        query.addFilterQuery(
                zyList.stream().collect(Collectors.joining(" OR ", StatisticalResultDTO.ZYGOSITY + ":(", ")")));
    }
    if (phenotypingCentersList != null && phenotypingCentersList.size() > 0) {
        query.addFilterQuery(phenotypingCentersList.stream().collect(
                Collectors.joining("\" OR \"", StatisticalResultDTO.PHENOTYPING_CENTER + ":(\"", "\")")));
    }
    if (strainsParams != null && strainsParams.size() > 0) {
        query.addFilterQuery(strainsParams.stream().collect(
                Collectors.joining("\" OR \"", StatisticalResultDTO.STRAIN_ACCESSION_ID + ":(\"", "\")")));
    }
    if (metaDataGroup != null && metaDataGroup.size() > 0) {
        query.addFilterQuery(metaDataGroup.stream()
                .collect(Collectors.joining("\" OR \"", StatisticalResultDTO.METADATA_GROUP + ":(\"", "\")")));
    }
    if (alleleAccession != null && alleleAccession.size() > 0) {
        query.addFilterQuery(alleleAccession.stream().collect(
                Collectors.joining("\" OR \"", StatisticalResultDTO.ALLELE_ACCESSION_ID + ":(\"", "\")")));
    }
    query.setFacet(true);

    // If you add/change order of pivots, make sure you do the same in the for loops below
    String pivotFacet = StatisticalResultDTO.PIPELINE_STABLE_ID + "," + StatisticalResultDTO.ZYGOSITY + ","
            + StatisticalResultDTO.PHENOTYPING_CENTER + "," + StatisticalResultDTO.STRAIN_ACCESSION_ID + ","
            + StatisticalResultDTO.ALLELE_ACCESSION_ID;
    if (metaDataGroup != null && metaDataGroup.size() > 0) {
        pivotFacet += "," + StatisticalResultDTO.METADATA_GROUP;

    }
    query.add("facet.pivot", pivotFacet);

    query.setFacetLimit(-1);

    Set<String> resultParametersForCharts = new HashSet<>();
    NamedList<List<PivotField>> facetPivot = experimentCore.query(query).getFacetPivot();
    for (PivotField pivot : facetPivot.get(pivotFacet)) {
        getParametersForChartFromPivot(pivot, baseUrl, resultParametersForCharts);
    }
    return resultParametersForCharts;
}

---

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

License:Apache License

public Set<String> getChartPivots(String baseUrl, String acc, String parameterStableId,
        List<String> pipelineStableIds, List<String> zyList, List<String> phenotypingCentersList,
        List<String> strainsParams, List<String> metaDataGroup, List<String> alleleAccession)
        throws IOException, SolrServerException, URISyntaxException {

    SolrQuery query = new SolrQuery();
    query.setQuery("*:*");
    if (acc != null) {
        query.addFilterQuery(StatisticalResultDTO.MARKER_ACCESSION_ID + ":\"" + acc + "\"");
    }//from  w  w  w .ja  va 2 s  .com
    if ((parameterStableId != null) && (!parameterStableId.trim().isEmpty())) {
        query.addFilterQuery(StatisticalResultDTO.PARAMETER_STABLE_ID + ":" + parameterStableId);
    }
    if (pipelineStableIds != null & pipelineStableIds.size() > 0) {
        query.addFilterQuery(pipelineStableIds.stream()
                .collect(Collectors.joining(" OR ", StatisticalResultDTO.PIPELINE_STABLE_ID + ":(", ")")));
    }
    if (zyList != null && zyList.size() > 0) {
        query.addFilterQuery(
                zyList.stream().collect(Collectors.joining(" OR ", StatisticalResultDTO.ZYGOSITY + ":(", ")")));
    }
    if (phenotypingCentersList != null && phenotypingCentersList.size() > 0) {
        query.addFilterQuery(phenotypingCentersList.stream().collect(
                Collectors.joining("\" OR \"", StatisticalResultDTO.PHENOTYPING_CENTER + ":(\"", "\")")));
    }
    if (strainsParams != null && strainsParams.size() > 0) {
        query.addFilterQuery(strainsParams.stream().collect(
                Collectors.joining("\" OR \"", StatisticalResultDTO.STRAIN_ACCESSION_ID + ":(\"", "\")")));
    }
    if (metaDataGroup != null && metaDataGroup.size() > 0) {
        query.addFilterQuery(metaDataGroup.stream()
                .collect(Collectors.joining("\" OR \"", StatisticalResultDTO.METADATA_GROUP + ":(\"", "\")")));
    }
    if (alleleAccession != null && alleleAccession.size() > 0) {
        query.addFilterQuery(alleleAccession.stream().collect(
                Collectors.joining("\" OR \"", StatisticalResultDTO.ALLELE_ACCESSION_ID + ":(\"", "\")")));
    }
    query.setFacet(true);

    // If you add/change order of pivots, make sure you do the same in the for loops below
    String pivotFacet = StatisticalResultDTO.PIPELINE_STABLE_ID + "," + StatisticalResultDTO.ZYGOSITY + ","
            + StatisticalResultDTO.PHENOTYPING_CENTER + "," + StatisticalResultDTO.STRAIN_ACCESSION_ID + ","
            + StatisticalResultDTO.ALLELE_ACCESSION_ID;
    //pivot needs to have metadata_group irrespective of if it's included in filter or not as we want seperate experiments based on the metadata
    pivotFacet += "," + StatisticalResultDTO.METADATA_GROUP;

    //}
    query.add("facet.pivot", pivotFacet);

    query.setFacetLimit(-1);

    Set<String> resultParametersForCharts = new HashSet<>();
    System.out.println("SR facet pivot query=" + query);
    NamedList<List<PivotField>> facetPivot = statisticalResultCore.query(query).getFacetPivot();
    for (PivotField pivot : facetPivot.get(pivotFacet)) {
        getParametersForChartFromPivot(pivot, baseUrl, resultParametersForCharts);
    }

    return resultParametersForCharts;
}

---

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  w w  w  . ja  v a 2 s  .  co 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;
}

---

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