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

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

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Introduction

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

Prototype

public SolrQuery setFacetLimit(int lim)

Source Link

Document

set the facet limit

Usage

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

License:Apache License

public TreeMap<String, Long> getStatusCountByProductionCenter(String center, String statusField) {

    TreeMap<String, Long> res = new TreeMap<>(new ProductionStatusComparator());
    SolrQuery solrQuery = new SolrQuery();
    QueryResponse solrResponse;/*ww  w  .ja v a 2 s . c o m*/

    if (center != null) {
        String geneQuery = AlleleDTO.LATEST_PRODUCTION_CENTRE + ":\"" + center + "\"";
        solrQuery.setQuery(geneQuery);
    } else {
        solrQuery.setQuery("*:*");
    }

    solrQuery.setRows(1);
    solrQuery.setFacet(true);
    solrQuery.setFacetLimit(-1);
    try {
        solrQuery.addFacetField(statusField);
        solrResponse = alleleCore.query(solrQuery);
        for (Count c : solrResponse.getFacetField(statusField).getValues()) {
            // We don't want to show everything
            if (!c.getName().equals("")) {
                res.put(c.getName(), c.getCount());
            }
        }
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }
    return res;
}

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

License:Apache License

public Set<String> getFacets(String field) {
    SolrQuery solrQuery = new SolrQuery();
    QueryResponse solrResponse;//from   w ww .  j a  va  2  s .  c o  m
    Set<String> res = new HashSet<>();
    solrQuery.setQuery("*:*");
    solrQuery.setFacet(true);
    solrQuery.setFacetLimit(-1);
    solrQuery.addFacetField(field);

    logger.info(this.getClass().getEnclosingMethod() + "   " + SolrUtils.getBaseURL(alleleCore) + "/select?"
            + solrQuery);

    try {
        solrResponse = alleleCore.query(solrQuery);
        for (Count c : solrResponse.getFacetField(field).getValues()) {
            res.add(c.getName());
        }
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }
    return res;
}

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

License:Apache License

public Map<String, Set<String>> getFacets(String anatomyId) throws SolrServerException, IOException {
    Map<String, Set<String>> res = new HashMap<>();
    SolrQuery query = getBasicExpressionQuery(anatomyId); // only have expressed and
    // not expressed ingnore
    // ambiguous and no tissue
    //query.addFilterQuery("(" + ImageDTO.PARAMETER_ASSOCIATION_VALUE + ":\"no expression\" OR " + ImageDTO.PARAMETER_ASSOCIATION_VALUE
    //      + ":\"expression\"" + ")");
    query.setFacet(true);/*from www.  j ava2 s .com*/
    query.setFacetLimit(-1);
    query.setFacetMinCount(1);
    query.addFacetField(ObservationDTO.ANATOMY_TERM);
    query.addFacetField(ObservationDTO.PHENOTYPING_CENTER);
    query.addFacetField(ObservationDTO.PROCEDURE_NAME);
    query.addFacetField(ObservationDTO.CATEGORY);

    QueryResponse response = experimentCore.query(query);
    for (FacetField facetField : response.getFacetFields()) {
        Set<String> filter = new TreeSet<>();
        for (Count facet : facetField.getValues()) {
            filter.add(facet.getName());

        }

        res.put(facetField.getName(), filter);
    }

    return res;
}

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

License:Apache License

/**
 *
 * @param geneIds the input set of gene ids (e.g. idg genes)
 * @param statusField the status field/*from   w  ww .j a  va  2 s.  c  o m*/
 * @return Number of genes (from the provided list) in each status of interest.
 */
public HashMap<String, Long> getStatusCount(Set<String> geneIds, String statusField) {

    HashMap<String, Long> res = new HashMap<>();
    SolrQuery solrQuery = new SolrQuery();
    QueryResponse solrResponse;

    if (geneIds != null) {
        String geneQuery = GeneDTO.MGI_ACCESSION_ID + ":("
                + StringUtils.join(geneIds, " OR ").replace(":", "\\:") + ")";
        solrQuery.setQuery(geneQuery);
    } else {
        solrQuery.setQuery("*:*");
    }
    solrQuery.setRows(1);
    solrQuery.setFacet(true);
    solrQuery.setFacetLimit(-1);
    try {
        solrQuery.addFacetField(statusField);
        solrResponse = geneCore.query(solrQuery);
        for (Count c : solrResponse.getFacetField(statusField).getValues()) {
            res.put(c.getName(), c.getCount());
        }
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }

    return res;
}

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

License:Apache License

/**
 * @param zygosity - optional (pass null if not needed)
 * @return Map <String, Long> : <top_level_mp_name, number_of_annotations>
 * @author tudose/*from  w  w w. j a  v  a 2  s .com*/
 */
public TreeMap<String, Long> getDistributionOfAnnotationsByMPTopLevel(ZygosityType zygosity,
        String resourceName) {

    SolrQuery query = new SolrQuery();

    if (zygosity != null) {
        query.setQuery(GenotypePhenotypeDTO.ZYGOSITY + ":" + zygosity.getName());
    } else if (resourceName != null) {
        query.setFilterQueries(GenotypePhenotypeDTO.RESOURCE_NAME + ":" + resourceName);
    } else {
        query.setQuery("*:*");
    }

    query.setFacet(true);
    query.setFacetLimit(-1);
    query.setFacetMinCount(1);
    query.setRows(0);
    query.addFacetField(GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME);

    try {
        QueryResponse response = genotypePhenotypeCore.query(query);
        TreeMap<String, Long> res = new TreeMap<>();
        res.putAll(getFacets(response).get(GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME));
        return res;
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }
    return null;
}

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

License:Apache License

public PhenotypeFacetResult getMPByGeneAccessionAndFilter(String accId, List<String> topLevelMpTermName,
        List<String> resourceFullname) throws IOException, URISyntaxException, JSONException {

    String solrUrl = SolrUtils.getBaseURL(genotypePhenotypeCore) + "/select?";
    SolrQuery q = new SolrQuery();

    q.setQuery(GenotypePhenotypeDTO.MARKER_ACCESSION_ID + ":\"" + accId + "\"");
    q.setRows(10000000);/*  w w w.java  2  s.c om*/
    q.setFacet(true);
    q.setFacetMinCount(1);
    q.setFacetLimit(-1);
    q.addFacetField(GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME);
    //q.addFacetField(GenotypePhenotypeDTO.RESOURCE_FULLNAME);
    q.set("wt", "json");
    q.setSort(GenotypePhenotypeDTO.P_VALUE, ORDER.asc);

    if (topLevelMpTermName != null) {
        q.addFilterQuery(GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME + ":(\""
                + StringUtils.join(topLevelMpTermName, "\" OR \"") + "\")");
    }

    solrUrl += q;

    return createPhenotypeResultFromSolrResponse(solrUrl);
}

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

License:Apache License

public PhenotypeFacetResult getMPCallByMPAccessionAndFilter(String phenotype_id, List<String> procedureName,
        List<String> markerSymbol, List<String> mpTermName, Map<String, Synonym> synonyms)
        throws IOException, URISyntaxException, JSONException {

    String url = SolrUtils.getBaseURL(genotypePhenotypeCore) + "/select/?";
    SolrQuery q = new SolrQuery();

    q.setQuery("*:*");
    q.addFilterQuery("(" + GenotypePhenotypeDTO.MP_TERM_ID + ":\"" + phenotype_id + "\" OR "
            + GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID + ":\"" + phenotype_id + "\" OR "
            + GenotypePhenotypeDTO.INTERMEDIATE_MP_TERM_ID + ":\"" + phenotype_id + "\")");
    q.setRows(10000000);/*ww w. j a v a 2 s  .c o  m*/
    q.setFacet(true);
    q.setFacetMinCount(1);
    q.setFacetLimit(-1);
    q.addFacetField(GenotypePhenotypeDTO.PROCEDURE_NAME);
    q.addFacetField(GenotypePhenotypeDTO.MARKER_SYMBOL);
    q.addFacetField(GenotypePhenotypeDTO.MP_TERM_NAME);
    q.set("wt", "json");
    q.setSort(GenotypePhenotypeDTO.P_VALUE, ORDER.asc);

    q.setFields(GenotypePhenotypeDTO.MP_TERM_NAME, GenotypePhenotypeDTO.MP_TERM_ID,
            GenotypePhenotypeDTO.MPATH_TERM_NAME, GenotypePhenotypeDTO.MPATH_TERM_ID,
            GenotypePhenotypeDTO.EXTERNAL_ID, GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID,
            GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME, GenotypePhenotypeDTO.ALLELE_SYMBOL,
            GenotypePhenotypeDTO.PHENOTYPING_CENTER, GenotypePhenotypeDTO.ALLELE_ACCESSION_ID,
            GenotypePhenotypeDTO.MARKER_SYMBOL, GenotypePhenotypeDTO.MARKER_ACCESSION_ID,
            GenotypePhenotypeDTO.PHENOTYPING_CENTER, GenotypePhenotypeDTO.ZYGOSITY, GenotypePhenotypeDTO.SEX,
            GenotypePhenotypeDTO.LIFE_STAGE_NAME, GenotypePhenotypeDTO.RESOURCE_NAME,
            GenotypePhenotypeDTO.PARAMETER_STABLE_ID, GenotypePhenotypeDTO.PARAMETER_NAME,
            GenotypePhenotypeDTO.PIPELINE_STABLE_ID, GenotypePhenotypeDTO.PROJECT_NAME,
            GenotypePhenotypeDTO.PROJECT_EXTERNAL_ID, GenotypePhenotypeDTO.P_VALUE,
            GenotypePhenotypeDTO.EFFECT_SIZE, GenotypePhenotypeDTO.PROCEDURE_STABLE_ID,
            GenotypePhenotypeDTO.PROCEDURE_NAME, GenotypePhenotypeDTO.PIPELINE_NAME);

    if (procedureName != null) {
        q.addFilterQuery(GenotypePhenotypeDTO.PROCEDURE_NAME + ":(\""
                + StringUtils.join(procedureName, "\" OR \"") + "\")");
    }
    if (markerSymbol != null) {
        q.addFilterQuery(GenotypePhenotypeDTO.MARKER_SYMBOL + ":(\""
                + StringUtils.join(markerSymbol, "\" OR \"") + "\")");
    }
    if (mpTermName != null) {
        q.addFilterQuery(
                GenotypePhenotypeDTO.MP_TERM_NAME + ":(\"" + StringUtils.join(mpTermName, "\" OR \"") + "\")");
    }

    url += q;

    return createPhenotypeResultFromSolrResponse(url, synonyms);

}

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

License:Apache License

/**
 * Get a list of gene symbols for this phenotype
 * @param phenotype_id//w w  w .j a  v  a2 s  .co  m
 * @return
 * @throws IOException
 * @throws URISyntaxException
 * @throws SolrServerException
 */
public List<String> getGenesForMpId(String phenotype_id)
        throws IOException, URISyntaxException, SolrServerException {
    List<String> results = new ArrayList<>();
    String url = SolrUtils.getBaseURL(genotypePhenotypeCore) + "/select/?";
    SolrQuery q = new SolrQuery();

    q.setQuery("*:*");
    q.addFilterQuery("(" + GenotypePhenotypeDTO.MP_TERM_ID + ":\"" + phenotype_id + "\" OR "
            + GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID + ":\"" + phenotype_id + "\" OR "
            + GenotypePhenotypeDTO.INTERMEDIATE_MP_TERM_ID + ":\"" + phenotype_id + "\")");
    q.setRows(10000000);
    q.setFacet(true);
    q.setFacetMinCount(1);
    q.setFacetLimit(-1);
    //q.addFacetField(GenotypePhenotypeDTO.MARKER_ACCESSION_ID);
    q.addFacetField(GenotypePhenotypeDTO.MARKER_SYMBOL);
    // q.addFacetField(GenotypePhenotypeDTO.MP_TERM_NAME );
    q.set("wt", "json");
    q.setSort(GenotypePhenotypeDTO.P_VALUE, ORDER.asc);
    q.setFields(GenotypePhenotypeDTO.MARKER_SYMBOL);
    //               q.setFields(GenotypePhenotypeDTO.MP_TERM_NAME, GenotypePhenotypeDTO.MP_TERM_ID, GenotypePhenotypeDTO.MPATH_TERM_NAME, GenotypePhenotypeDTO.MPATH_TERM_ID, GenotypePhenotypeDTO.EXTERNAL_ID,
    //                     GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID, GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME, GenotypePhenotypeDTO.ALLELE_SYMBOL, 
    //                     GenotypePhenotypeDTO.PHENOTYPING_CENTER, GenotypePhenotypeDTO.ALLELE_ACCESSION_ID, GenotypePhenotypeDTO.MARKER_SYMBOL,
    //                     GenotypePhenotypeDTO.MARKER_ACCESSION_ID, GenotypePhenotypeDTO.PHENOTYPING_CENTER, GenotypePhenotypeDTO.ZYGOSITY, 
    //                     GenotypePhenotypeDTO.SEX, GenotypePhenotypeDTO.LIFE_STAGE_NAME, GenotypePhenotypeDTO.RESOURCE_NAME, GenotypePhenotypeDTO.PARAMETER_STABLE_ID, GenotypePhenotypeDTO.PARAMETER_NAME,
    //                     GenotypePhenotypeDTO.PIPELINE_STABLE_ID, GenotypePhenotypeDTO.PROJECT_NAME, GenotypePhenotypeDTO.PROJECT_EXTERNAL_ID,
    //                     GenotypePhenotypeDTO.P_VALUE, GenotypePhenotypeDTO.EFFECT_SIZE, GenotypePhenotypeDTO.PROCEDURE_STABLE_ID,
    //                     GenotypePhenotypeDTO.PROCEDURE_NAME, GenotypePhenotypeDTO.PIPELINE_NAME);

    QueryResponse response = genotypePhenotypeCore.query(q);
    for (Count facet : response.getFacetField(GenotypePhenotypeDTO.MARKER_SYMBOL).getValues()) {
        //System.out.println("facet="+facet.getName());
        results.add(facet.getName());
    }
    return results;
}

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

License:Apache License

/**
 * @author ilinca/*from   w  ww .  j  a  v  a2 s.  c  o  m*/
 * @since 2016/07/07
 * @return CSV string of facet values (mp,gene,colony,phenCenter,sex,zyg,param,pVal). At the moment of writing used to compare calls from EBI to DCC
 * @throws SolrServerException, IOException
 * @throws URISyntaxException 
 * @throws IOException 
 * @throws MalformedURLException 
 */
public String getTabbedCallSummary() throws MalformedURLException, IOException, URISyntaxException {
    //   http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/genotype-phenotype/select?q=resource_name:IMPC&facet=true&facet.mincount=1&facet.pivot=mp_term_name,marker_symbol,colony_id,phenotyping_center,sex,zygosity,parameter_stable_id,p_value&facet.limit=-1&facet.mincount=1&wt=xslt&tr=pivot.xsl

    SolrQuery q = new SolrQuery();
    q.setQuery(GenotypePhenotypeDTO.RESOURCE_NAME + ":IMPC");
    q.addFilterQuery("-" + GenotypePhenotypeDTO.ASSERTION_TYPE + ":manual");
    q.setFacet(true);
    q.setFacetLimit(-1).setFacetMinCount(1)
            .addFacetPivotField(GenotypePhenotypeDTO.MP_TERM_ID + "," + GenotypePhenotypeDTO.MARKER_SYMBOL + ","
                    + GenotypePhenotypeDTO.COLONY_ID + "," + GenotypePhenotypeDTO.PHENOTYPING_CENTER + ","
                    + GenotypePhenotypeDTO.SEX + "," + GenotypePhenotypeDTO.ZYGOSITY + ","
                    + GenotypePhenotypeDTO.PARAMETER_STABLE_ID + "," + GenotypePhenotypeDTO.P_VALUE);
    q.set("wt", "xslt").set("tr", "pivot.xsl");

    HttpProxy proxy = new HttpProxy();
    System.out.println("Solr ULR for getTabbedCallSummary " + SolrUtils.getBaseURL(genotypePhenotypeCore)
            + "/select?" + q);

    String content = proxy.getContent(new URL(SolrUtils.getBaseURL(genotypePhenotypeCore) + "/select?" + q));

    return content;
}

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

License:Apache License

Map<String, Long> getDocumentCountByMgiGeneAccessionId() {

    SolrQuery query = new SolrQuery();
    query.setQuery("*:*");
    query.setRows(0);/*from  ww  w . jav  a  2s . c o m*/
    query.setFacet(true);
    query.addFacetField(GenotypePhenotypeDTO.MARKER_ACCESSION_ID);
    query.setFacetLimit(-1);
    query.setFacetMinCount(1);

    try {
        return getFacets(genotypePhenotypeCore.query(query)).get(GenotypePhenotypeDTO.MARKER_ACCESSION_ID);
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }

    return new HashMap<>();

}