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

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

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Introduction

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

Prototype

public SolrQuery setFields(String... fields)

Source Link

Usage

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

License:Apache License

private QueryResponse getAdultLaczImageFacetsForGene(String mgiAccession, String parameterStableId,
        String... fields) throws SolrServerException, IOException {

    //solrQuery.addFilterQuery(ImageDTO.PARAMETER_NAME + ":\"LacZ Images Section\" OR " + ImageDTO.PARAMETER_NAME
    //      + ":\"LacZ Images Wholemount\"");// reduce the number to image
    // e.g./*from   w w w.  j a  va2  s  .  com*/
    // 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 + "\"");
    if (!StringUtils.isEmpty(parameterStableId)) {
        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);
    QueryResponse response = impcImagesCore.query(solrQuery);
    return response;
}

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

License:Apache License

public List<Count> getLaczCategoricalParametersForGene(String mgiAccession, String... fields)
        throws SolrServerException, IOException {
    // e.g./*from  w  w w.j a  va  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.PROCEDURE_NAME + ":\"Adult LacZ\"");
    solrQuery.addFilterQuery("-" + ImageDTO.PARAMETER_NAME + ":\"LacZ Images Section\"");
    solrQuery.addFilterQuery("-" + ImageDTO.PARAMETER_NAME + ":\"LacZ Images Wholemount\"");
    solrQuery.addFilterQuery(ObservationDTO.CATEGORY + ":\"expression\"");
    // only look for expresssion at the moment as that is all the anatamogram can  display
    solrQuery.setFacetMinCount(1);
    solrQuery.setFacet(true);
    solrQuery.setFields(fields);
    solrQuery.addFacetField(ImageDTO.PARAMETER_STABLE_ID);
    solrQuery.setRows(0);
    QueryResponse response = experimentCore.query(solrQuery);
    List<FacetField> categoryParameterFields = response.getFacetFields();

    return categoryParameterFields.get(0).getValues();
}

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 www .j a v  a2 s  .  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.GeneService.java

License:Apache License

/**
 * Return all genes in the gene core matching latestPhenotypeStatus and
 * latestProductionCentre./*from   w w  w . ja va  2 s.co 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 www.j a v a 2 s.c o 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.
 * //from w w w. ja  va2  s.  c  om
 * @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 whose MGI_ACCESSION_ID does not start
 * with 'MGI'.//from w ww  .ja  v a 2  s .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 GeneDTO getGeneById(String mgiId, String... fields) throws SolrServerException, IOException {

    SolrQuery solrQuery = new SolrQuery().setQuery(GeneDTO.MGI_ACCESSION_ID + ":\"" + mgiId + "\"").setRows(1);
    if (fields != null) {
        solrQuery.setFields(fields);
    }/*w w w  .jav a  2s  . c o m*/

    QueryResponse rsp = geneCore.query(solrQuery);
    if (rsp.getResults().getNumFound() > 0) {
        return rsp.getBeans(GeneDTO.class).get(0);
    }
    return null;
}

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

License:Apache License

/**
 * Return a list of gene DTOs cooresponding to the
 * @param mgiIds//from   w ww.  jav a  2 s.  c  om
 * @param fields (Optional) list of fields
 * @return
 * @throws SolrServerException
 * @throws IOException
 */
public List<GeneDTO> getGenesByMgiIds(List<String> mgiIds, String... fields)
        throws SolrServerException, IOException {

    if (mgiIds == null)
        return new ArrayList<>();
    List<String> quotedMgiIds = mgiIds.stream().map(x -> String.format("\"%s\"", x))
            .collect(Collectors.toList());

    SolrQuery query = new SolrQuery()
            .setQuery(GeneDTO.MGI_ACCESSION_ID + ":(" + StringUtils.join(quotedMgiIds, ",") + ")")
            .setRows(mgiIds.size());

    if (fields != null) {
        query.setFields(fields);
    }

    QueryResponse response = geneCore.query(query, METHOD.POST);

    List<GeneDTO> genes = new ArrayList<>();
    if (response.getResults().getNumFound() > 0) {
        genes = response.getBeans(GeneDTO.class);
    }

    return genes;
}

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

License:Apache License

/**
 * Returns a set of MARKER_ACCESSION_ID strings of all genes that have
 * phenotype associations./*from   w  w  w . j a v a2 s  . c  o  m*/
 *
 * @return a set of MARKER_ACCESSION_ID strings of all genes that have
 * phenotype associations.
 * @throws SolrServerException, IOException
 */
public Set<String> getAllGenesWithPhenotypeAssociations() throws SolrServerException, IOException {

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