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.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.  ja va  2 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.ExpressionService.java

License:Apache License

/**
 * @author ilinca//www  .j a  va 2  s  . c  o  m
 * @since 2016/07/08
 * @param anatomyId
 * @return List of gene ids with positive expression in given anatomy term. 
 * @throws SolrServerException, IOException
 */
public List<String> getGenesWithExpression(String anatomyId) throws SolrServerException, IOException {

    List<String> geneIds = new ArrayList<>();
    SolrQuery q = new SolrQuery();
    q.setQuery(ObservationDTO.CATEGORY + ":\"expression\"")
            .addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":\"experimental\"");
    if (anatomyId != null) {
        q.setFilterQueries(ObservationDTO.ANATOMY_ID + ":\"" + anatomyId + "\" OR "
                + ObservationDTO.TOP_LEVEL_ANATOMY_ID + ":\"" + anatomyId + "\" OR "
                + ObservationDTO.INTERMEDIATE_ANATOMY_ID + ":\"" + anatomyId + "\"");
    }
    q.setFacet(true).setFacetMinCount(1).setFacetLimit(-1).addFacetField(ObservationDTO.GENE_ACCESSION_ID);

    for (Count value : experimentCore.query(q).getFacetFields().get(0).getValues()) {
        geneIds.add(value.getName());
    }
    return geneIds;

}

---

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);
    query.setFacetLimit(-1);//from w  w  w.ja  v  a 2  s. co m
    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//  w w  w  .j  av  a  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  va  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 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 w w w .j  a va  2  s.c  o  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  a2s. c  om*/

    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;

}

---

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);//from  w  ww . j av a  2s  .  com
    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);//from   ww w . j av a2s .  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.ja  v  a 2s  .  com
 * @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;
}

---

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