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

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

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Introduction

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

Prototype

public SolrQuery setRows(Integer rows)

Source Link

Usage

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

License:Apache License

/**
 * Get the mouse production status for gene (not allele) for geneHeatMap implementation for idg for each of 300 odd genes
 * @param geneIds/* w  w  w.  j a  v a 2s. co  m*/
 * @return
 * @throws SolrServerException, IOException
 */
public Map<String, GeneDTO> getHumanOrthologsForGeneSet(Set<String> geneIds)
        throws SolrServerException, IOException {

    Map<String, GeneDTO> geneToHumanOrthologMap = new HashMap<>();

    SolrQuery solrQuery = new SolrQuery();

    solrQuery.setQuery("*:*");
    solrQuery.setFilterQueries(
            GeneDTO.MGI_ACCESSION_ID + ":(" + StringUtils.join(geneIds, " OR ").replace(":", "\\:") + ")");
    solrQuery.setRows(100000);
    solrQuery.setFields(GeneDTO.MGI_ACCESSION_ID, GeneDTO.HUMAN_GENE_SYMBOL, GeneDTO.DISEASE_ID,
            GeneDTO.LATEST_PHENOTYPE_STATUS);
    log.info("server query is: {}", solrQuery.toString());
    QueryResponse rsp = geneCore.query(solrQuery);

    List<GeneDTO> genes = rsp.getBeans(GeneDTO.class);
    for (GeneDTO gene : genes) {
        geneToHumanOrthologMap.put(gene.getMgiAccessionId(), gene);
    }

    return geneToHumanOrthologMap;
}

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

License:Apache License

public List<GeneDTO> getGenesSymbolsBy(String mpId) throws IOException, SolrServerException {

    if (mpId == null) {
        return null;
    }//w  ww .j  a  v  a 2s. c  om

    SolrQuery query = new SolrQuery();
    query.setQuery(
            "(" + GeneDTO.MP_ID + ":\"" + mpId + "\" OR " + GeneDTO.TOP_LEVEL_MP_ID + ":\"" + mpId + "\")");
    query.setRows(Integer.MAX_VALUE);
    query.setFields(GeneDTO.MARKER_SYMBOL, GeneDTO.MGI_ACCESSION_ID, GeneDTO.HUMAN_GENE_SYMBOL, GeneDTO.MP_ID,
            GeneDTO.MP_TERM);

    QueryResponse rsp = geneCore.query(query);

    return rsp.getBeans(GeneDTO.class);

}

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 w  w.  j  a v  a  2s  . co 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.GeneService.java

License:Apache License

/**
 * Get the mouse project status for a set of genes (not alleles) for table implementation for cmg
 *
 * @param geneId//from  w w  w . j  a va2s . com
 * @return
 * @throws SolrServerException, IOException
 */
public String getLatestProjectStatusForGeneSet(String geneId) throws SolrServerException, IOException {
    String latestProjectStatus = "";
    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery("*:*");
    solrQuery.setFilterQueries(GeneDTO.MGI_ACCESSION_ID + ":(" + geneId.replace(":", "\\:") + ")");
    solrQuery.setRows(100000);
    solrQuery.setFields(GeneDTO.MGI_ACCESSION_ID, GeneDTO.LATEST_PROJECT_STATUS);
    log.info("server query is: {}", solrQuery.toString());
    QueryResponse rsp = geneCore.query(solrQuery);
    List<GeneDTO> genes = rsp.getBeans(GeneDTO.class);
    for (GeneDTO gene : genes) {
        latestProjectStatus = gene.getLatestProjectStatus();
    }

    return latestProjectStatus;
}

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// w w  w  . j  a  v  a  2s. c om
 */
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 long getNumberOfDocuments(List<String> resourceName) throws SolrServerException, IOException {

    SolrQuery query = new SolrQuery();
    query.setRows(0);
    if (resourceName != null) {
        query.setQuery(GenotypePhenotypeDTO.RESOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + GenotypePhenotypeDTO.RESOURCE_NAME + ":"));
    } else {/*from   ww w  .  ja v a  2  s.  c o  m*/
        query.setQuery("*:*");
    }

    return genotypePhenotypeCore.query(query).getResults().getNumFound();
}

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

License:Apache License

/**
 * @since 2016/07/04/*from  w  w  w .  j  av a  2  s  . c om*/
 * @author ilinca
 * @param anatomyId
 * @return
 * @throws SolrServerException, IOException
 */
public List<GenotypePhenotypeDTO> getPhenotypesForAnatomy(String anatomyId)
        throws SolrServerException, IOException {

    SolrQuery query = new SolrQuery();
    query.setRows(Integer.MAX_VALUE);
    query.setQuery(GenotypePhenotypeDTO.ANATOMY_TERM_ID + ":\"" + anatomyId + "\" OR "
            + GenotypePhenotypeDTO.INTERMEDIATE_ANATOMY_TERM_ID + ":\"" + anatomyId + "\" OR "
            + GenotypePhenotypeDTO.TOP_LEVEL_ANATOMY_TERM_ID + ":\"" + anatomyId + "\"");

    query.setFields(GenotypePhenotypeDTO.MP_TERM_ID, GenotypePhenotypeDTO.MP_TERM_NAME,
            GenotypePhenotypeDTO.P_VALUE, GenotypePhenotypeDTO.MARKER_ACCESSION_ID,
            GenotypePhenotypeDTO.MARKER_SYMBOL, GenotypePhenotypeDTO.SEX, GenotypePhenotypeDTO.ZYGOSITY);

    return genotypePhenotypeCore.query(query).getBeans(GenotypePhenotypeDTO.class);

}

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

License:Apache License

public Map<String, Long> getHitsDistributionBySomethingNoIds(String fieldToDistributeBy,
        List<String> resourceName, ZygosityType zygosity, int facetMincount, Double maxPValue)
        throws SolrServerException, IOException, InterruptedException, ExecutionException {

    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   ww  w.j  a v  a2 s  .co m*/
        q.setQuery("*:*");
    }

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

    if (maxPValue != null) {
        q.addFilterQuery(GenotypePhenotypeDTO.P_VALUE + ":[0 TO " + maxPValue + "]");
    }

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

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

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

    logger.info("Done in " + (System.currentTimeMillis() - time));
    return res;

}

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

License:Apache License

private List<String[]> getHitsDistributionBySomething(String field, List<String> resourceName)
        throws SolrServerException, IOException, InterruptedException, ExecutionException {

    List<String[]> res = new ArrayList<>();
    Long time = System.currentTimeMillis();
    String pivotFacet = "";
    SolrQuery q = new SolrQuery();

    if (field.equals(GenotypePhenotypeDTO.PARAMETER_STABLE_ID)) {
        pivotFacet = GenotypePhenotypeDTO.PARAMETER_STABLE_ID + "," + StatisticalResultDTO.PARAMETER_NAME;
    } else if (field.equals(GenotypePhenotypeDTO.PROCEDURE_STABLE_ID)) {
        pivotFacet = GenotypePhenotypeDTO.PROCEDURE_STABLE_ID + "," + StatisticalResultDTO.PROCEDURE_NAME;
    }/*from w  w  w .j a  v a  2 s .  c  o m*/

    if (resourceName != null) {
        q.setQuery(GenotypePhenotypeDTO.RESOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + GenotypePhenotypeDTO.RESOURCE_NAME + ":"));
    } else {
        q.setQuery("*:*");
    }
    q.set("facet.pivot", pivotFacet);
    q.setFacet(true);
    q.setRows(1);
    q.set("facet.limit", -1);

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

    for (PivotField pivot : response.getFacetPivot().get(pivotFacet)) {
        if (pivot.getPivot() != null) {
            String id = pivot.getValue().toString();
            String name = pivot.getPivot().get(0).getValue().toString();
            int count = pivot.getPivot().get(0).getCount();
            String[] row = { id, name, Integer.toString(count) };
            res.add(row);
        }
    }

    logger.info("Done in " + (System.currentTimeMillis() - time));
    return res;

}