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.ExpressionService.java

License:Apache License

private QueryResponse getEmbryoLaczImageFacetsForGene(String mgiAccession, String parameterStableId,
        String... fields) throws SolrServerException, IOException {
    //solrQuery.addFilterQuery(ImageDTO.PARAMETER_STABLE_ID + ":IMPC_ELZ_064_001" + " OR "
    //+ ImageDTO.PARAMETER_STABLE_ID + ":IMPC_ELZ_063_001");
    // e.g.//from  w w w . j  a  v a 2s . c  o  m
    // http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/impc_images/select?q=gene_accession_id:%22MGI:1920455%22&facet=true&facet.field=selected_top_level_ma_term&fq=(parameter_name:%22LacZ%20Images%20Section%22%20OR%20parameter_name:%22LacZ%20Images%20Wholemount%22)
    // for embryo data the fields would be like this
    // "parameter_name": "LacZ images section",
    // "procedure_name": "Embryo LacZ",

    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery(ImageDTO.GENE_ACCESSION_ID + ":\"" + mgiAccession + "\"");
    solrQuery.addFilterQuery(ImageDTO.PARAMETER_STABLE_ID + ":" + parameterStableId);// reduce
    // the number to image parameters only as we are talking about images not expression data here
    solrQuery.setFacetMinCount(1);
    solrQuery.setFacet(true);
    solrQuery.setFields(fields);
    solrQuery.addFacetField(ImageDTO.SELECTED_TOP_LEVEL_ANATOMY_TERM);
    solrQuery.setRows(Integer.MAX_VALUE);
    solrQuery.setSort(ObservationDTO.ID, SolrQuery.ORDER.asc);
    QueryResponse response = impcImagesCore.query(solrQuery);
    return response;
}

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

License:Apache License

/**
 * Method that checks the impc images and categorical obeservations for expression data which is either expressed or not expressed.
 * @param anatomyId/*from   ww w  .  j  ava  2  s .co m*/
 * @return
 * @throws SolrServerException, IOException
 */
public boolean expressionDataAvailable(String anatomyId) throws SolrServerException, IOException {
    boolean expressionData = false;
    SolrQuery query = getBasicExpressionQuery(anatomyId);
    query.setRows(0);
    QueryResponse response = experimentCore.query(query);
    if (response.getResults().getNumFound() > 0) {
        expressionData = true;
    }

    //check the impc images core
    if (this.impcImagesHasExpression(anatomyId)) {
        expressionData = true;
    }
    return expressionData;
}

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

License:Apache License

/**
 * Return all genes in the gene core matching latestPhenotypeStatus and
 * latestProductionCentre.//from w  w  w. ja v  a 2  s.  c o  m
 * 
 * @param latestPhenotypeStatus
 *            latest phenotype status (i.e. most advanced along the pipeline)
 * @param latestProductionCentre
 *            latest production centre (i.e. most advanced along the pipeline)
 * @return all genes in the gene core matching phenotypeStatus and
 *         productionCentre.
 * @throws SolrServerException, IOException
 */
public Set<String> getGenesByLatestPhenotypeStatusAndProductionCentre(String latestPhenotypeStatus,
        String latestProductionCentre) throws SolrServerException, IOException {
    SolrQuery solrQuery = new SolrQuery();
    String queryString = "(" + GeneDTO.LATEST_PHENOTYPE_STATUS + ":\"" + latestPhenotypeStatus + "\") AND ("
            + GeneDTO.LATEST_PRODUCTION_CENTRE + ":\"" + latestProductionCentre + "\")";
    solrQuery.setQuery(queryString);
    solrQuery.setRows(1000000);
    solrQuery.setFields(GeneDTO.MGI_ACCESSION_ID);
    QueryResponse rsp = null;
    rsp = geneCore.query(solrQuery);
    SolrDocumentList res = rsp.getResults();
    HashSet<String> allGenes = new HashSet<String>();
    for (SolrDocument doc : res) {
        allGenes.add((String) doc.getFieldValue(GeneDTO.MGI_ACCESSION_ID));
    }

    log.debug("getGenesByLatestPhenotypeStatusAndProductionCentre: solrQuery = " + queryString);
    return allGenes;
}

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

License:Apache License

/**
 * Return all genes in the gene core matching latestPhenotypeStatus and
 * latestPhenotypeCentre.//from  w  ww  . j ava  2s  .  co m
 * 
 * @param latestPhenotypeStatus
 *            latest phenotype status (i.e. most advanced along the pipeline)
 * @param latestPhenotypeCentre
 *            latest phenotype centre (i.e. most advanced along the pipeline)
 * @return all genes in the gene core matching phenotypeStatus and
 *         productionCentre.
 * @throws SolrServerException, IOException
 */
public Set<String> getGenesByLatestPhenotypeStatusAndPhenotypeCentre(String latestPhenotypeStatus,
        String latestPhenotypeCentre) throws SolrServerException, IOException {

    SolrQuery solrQuery = new SolrQuery();
    String queryString = "(" + GeneDTO.LATEST_PHENOTYPE_STATUS + ":\"" + latestPhenotypeStatus + "\") AND ("
            + GeneDTO.LATEST_PHENOTYPING_CENTRE + ":\"" + latestPhenotypeCentre + "\")";
    solrQuery.setQuery(queryString);
    solrQuery.setRows(1000000);
    solrQuery.setFields(GeneDTO.MGI_ACCESSION_ID);
    QueryResponse rsp = null;
    rsp = geneCore.query(solrQuery);
    SolrDocumentList res = rsp.getResults();
    HashSet<String> allGenes = new HashSet<String>();
    for (SolrDocument doc : res) {
        allGenes.add((String) doc.getFieldValue(GeneDTO.MGI_ACCESSION_ID));
    }

    log.debug("getGenesByLatestPhenotypeStatusAndPhenotypeCentre: solrQuery = " + queryString);
    return allGenes;
}

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

License:Apache License

/**
 * Return all gene MGI IDs from the gene core.
 * //  w w w .  j a v  a  2  s  . c o m
 * @return all genes from the gene core.
 * @throws SolrServerException, IOException
 */
public Set<String> getAllGenes() throws SolrServerException, IOException {

    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery(GeneDTO.MGI_ACCESSION_ID + ":*");
    solrQuery.setRows(1000000);
    solrQuery.setFields(GeneDTO.MGI_ACCESSION_ID);
    QueryResponse rsp = null;
    rsp = geneCore.query(solrQuery);
    SolrDocumentList res = rsp.getResults();
    HashSet<String> allGenes = new HashSet<String>();
    for (SolrDocument doc : res) {
        allGenes.add((String) doc.getFieldValue(GeneDTO.MGI_ACCESSION_ID));
    }
    return allGenes;
}

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

License:Apache License

/**
 * Return all genes from the gene core.//from  w  w w  .  ja  v a  2  s.  com
 *
 * @return all genes from the gene core.
 * @throws SolrServerException, IOException
 */
public List<GeneDTO> getAllGeneDTOs() throws SolrServerException, IOException {

    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery("*:*");
    solrQuery.setRows(Integer.MAX_VALUE);
    return geneCore.query(solrQuery).getBeans(GeneDTO.class);
}

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

License:Apache License

/**
 * Return all genes from the gene core whose MGI_ACCESSION_ID does not start
 * with 'MGI'.//from w w w.  j  a  v a 2s . c o  m
 * 
 * @return all genes from the gene core whose MGI_ACCESSION_ID does not
 *         start with 'MGI'.
 * @throws SolrServerException, IOException
 */
public Set<String> getAllNonConformingGenes() throws SolrServerException, IOException {

    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery("-" + GeneDTO.MGI_ACCESSION_ID + ":MGI*");
    solrQuery.setRows(1000000);
    solrQuery.setFields(GeneDTO.MGI_ACCESSION_ID);
    QueryResponse rsp = null;
    rsp = geneCore.query(solrQuery);
    SolrDocumentList res = rsp.getResults();
    HashSet<String> allGenes = new HashSet<String>();

    for (SolrDocument doc : res) {
        allGenes.add((String) doc.getFieldValue(GeneDTO.MGI_ACCESSION_ID));
    }

    return allGenes;
}

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

License:Apache License

public List<GeneDTO> getGenesWithEmbryoViewer() throws SolrServerException, IOException {

    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery(GeneDTO.EMBRYO_DATA_AVAILABLE + ":true");
    solrQuery.setRows(1000000);
    solrQuery.setFields(GeneDTO.MGI_ACCESSION_ID, GeneDTO.MARKER_SYMBOL);

    return geneCore.query(solrQuery).getBeans(GeneDTO.class);

}

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//from w  w  w  .  j  av  a2 s  .  c  o m
 * @return Returns SolrDocument because that;s what the method to produce the status icons gets.
 * @throws SolrServerException, IOException
 */
public List<SolrDocument> getProductionStatusForGeneSet(Set<String> geneIds, Set<String> humanGeneSymbols)
        throws SolrServerException, IOException {

    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery("*:*");
    if (geneIds != null) {
        solrQuery.setFilterQueries(
                GeneDTO.MGI_ACCESSION_ID + ":(" + StringUtils.join(geneIds, " OR ").replace(":", "\\:") + ")");
    }
    if (humanGeneSymbols != null) {
        solrQuery.setFilterQueries(
                GeneDTO.HUMAN_GENE_SYMBOL + ":(" + StringUtils.join(humanGeneSymbols, " OR ") + ")");
    }
    solrQuery.setRows(Integer.MAX_VALUE);

    solrQuery.setFields(GeneDTO.MGI_ACCESSION_ID, GeneDTO.HUMAN_GENE_SYMBOL, GeneDTO.MARKER_SYMBOL,
            GeneDTO.ALLELE_NAME, GeneDTO.MOUSE_STATUS, GeneDTO.LATEST_ES_CELL_STATUS,
            GeneDTO.LATEST_PHENOTYPE_STATUS, GeneDTO.LEGACY_PHENOTYPE_STATUS, GeneDTO.HAS_QC,
            GeneDTO.TOP_LEVEL_MP_TERM);

    QueryResponse rsp = geneCore.query(solrQuery, METHOD.POST);

    return rsp.getResults();
}

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

License:Apache License

/**
 * Get the mouse top level mp associations for gene (not allele) for geneHeatMap implementation for idg for each of 300 odd genes
 * @param geneIds// ww w.j  a  v  a2  s . c  o m
 * @return
 * @throws SolrServerException, IOException
 */
public Map<String, List<String>> getTopLevelMpForGeneSet(Set<String> geneIds)
        throws SolrServerException, IOException {

    Map<String, List<String>> geneToStatusMap = new HashMap<>();
    SolrQuery solrQuery = new SolrQuery();
    String query = "*:*";
    solrQuery.setQuery(query);
    solrQuery.setFilterQueries(
            GeneDTO.MGI_ACCESSION_ID + ":(" + StringUtils.join(geneIds, " OR ").replace(":", "\\:") + ")");
    solrQuery.setRows(100000);
    solrQuery.setFields(GeneDTO.MGI_ACCESSION_ID, GeneDTO.TOP_LEVEL_MP_ID);

    QueryResponse rsp = geneCore.query(solrQuery, METHOD.POST);

    SolrDocumentList res = rsp.getResults();
    for (SolrDocument doc : res) {
        String accession = (String) doc.getFieldValue(GeneDTO.MGI_ACCESSION_ID);//each doc should have an accession
        List<String> topLevelMpIds = Collections.emptyList();
        if (doc.containsKey(GeneDTO.TOP_LEVEL_MP_ID)) {
            topLevelMpIds = getListFromCollection(doc.getFieldValues(GeneDTO.TOP_LEVEL_MP_ID));
        }

        geneToStatusMap.put(accession, topLevelMpIds);
    }
    return geneToStatusMap;
}