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

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

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Introduction

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

Prototype

public SolrQuery setFacetMinCount(int cnt)

Source Link

Document

set facet minimum count

Usage

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  .jav  a2  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 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 {/*w ww . java2s  .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

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. j  av a  2 s .  c  o  m
    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  av a  2 s.com
    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  a2 s .  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;
}

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

License:Apache License

/**
 * @param mpTermName//from  ww  w. j  a va 2s .  c  o  m
 * @param resource
 * @return map <colony_id, occurences>
 */
public Map<String, Long> getAssociationsDistribution(String mpTermName, String resource) {

    String query = GenotypePhenotypeDTO.MP_TERM_NAME + ":\"" + mpTermName + "\"";
    if (resource != null) {
        query += " AND " + GenotypePhenotypeDTO.RESOURCE_NAME + ":" + resource;
    }

    SolrQuery q = new SolrQuery();
    q.setQuery(query);
    q.setFacet(true);
    q.setFacetMinCount(1);
    q.addFacetField(GenotypePhenotypeDTO.COLONY_ID);

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

    return null;
}

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

License:Apache License

public Set<String> getFertilityAssociatedMps() {

    SolrQuery q = new SolrQuery();
    q.setQuery(GenotypePhenotypeDTO.PARAMETER_STABLE_ID + ":*_FER_*");
    q.setFacet(true);//from   w  w w .j  a  v  a 2  s.com
    q.setFacetMinCount(1);
    q.addFacetField(GenotypePhenotypeDTO.MP_TERM_NAME);

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

    return null;
}

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 w w  w  . jav  a 2 s .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<>();

}

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

License:Apache License

/**
 *
 * @param mpId//from   w ww .  ja va  2 s . co m
 * @param filterOnAccessions list of marker accessions to restrict the results by e.g. for the hearing page we only want results for the 67 genes for the paper
 * @return
 * @throws JSONException
 */
public JSONArray getTopLevelPhenotypeIntersection(String mpId, Set<String> filterOnAccessions)
        throws JSONException {

    String pivot = GenotypePhenotypeDTO.MARKER_ACCESSION_ID + "," + GenotypePhenotypeDTO.MARKER_SYMBOL;
    SolrQuery query = new SolrQuery();
    query.setQuery(mpId == null ? "*:*"
            : GenotypePhenotypeDTO.MP_TERM_ID + ":\"" + mpId + "\" OR "
                    + GenotypePhenotypeDTO.INTERMEDIATE_MP_TERM_ID + ":\"" + mpId + "\" OR "
                    + GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID + ":\"" + mpId + "\"");
    query.setRows(0);
    query.setFacet(true);
    query.addFacetField(GenotypePhenotypeDTO.MARKER_ACCESSION_ID);
    query.setFacetLimit(-1);
    query.setFacetMinCount(1);
    query.add("facet.pivot", pivot);

    try {
        QueryResponse response = genotypePhenotypeCore.query(query);
        Map<String, Long> countByGene = getFacets(response).get(GenotypePhenotypeDTO.MARKER_ACCESSION_ID);
        Map<String, List<String>> geneAccSymbol = getFacetPivotResults(response, pivot);

        Set<String> jitter = new HashSet<>();
        JSONArray array = new JSONArray();
        for (String markerAcc : countByGene.keySet()) {
            JSONObject obj = new JSONObject();
            Double y = new Double(countByGene.get(markerAcc));
            Double x = (getDocumentCountByMgiGeneAccessionId().get(markerAcc) - y);
            obj = addJitter(x, y, jitter, obj);
            obj.accumulate("markerAcc", markerAcc);
            obj.accumulate("markerSymbol", geneAccSymbol.get(markerAcc).get(0));
            if (filterOnAccessions != null && filterOnAccessions.contains(markerAcc)) {
                array.put(obj);
            } else if (filterOnAccessions == null) {
                array.put(obj);
            }
        }

        return array;

    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }
    return null;
}

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

License:Apache License

public Map<String, Set<String>> getFacets(String anatomyId) throws SolrServerException, IOException {

    Map<String, Set<String>> res = new HashMap<>();
    SolrQuery query = new SolrQuery();
    query.setQuery(ImageDTO.PROCEDURE_NAME + ":*LacZ");

    if (anatomyId != null) {
        query.addFilterQuery("(" + ImageDTO.ANATOMY_ID + ":\"" + anatomyId + "\" OR "
                + ImageDTO.INTERMEDIATE_ANATOMY_ID + ":\"" + anatomyId + "\" OR "
                + ImageDTO.SELECTED_TOP_LEVEL_ANATOMY_ID + ":\"" + anatomyId + "\")");
    }/*from w  w  w  .  jav  a  2  s  .  c om*/
    query.addFilterQuery(ImageDTO.BIOLOGICAL_SAMPLE_GROUP + ":\"experimental\"")
            .addFilterQuery("(" + ImageDTO.PARAMETER_ASSOCIATION_VALUE + ":\"no expression\" OR "
                    + ObservationDTO.PARAMETER_ASSOCIATION_VALUE + ":\"expression\"" + ")"); // only have expressed and
    // not expressed ingnore
    // ambiguous and no tissue
    query.setFacet(true);
    query.setFacetLimit(-1);
    query.setFacetMinCount(1);
    query.addFacetField(ImageDTO.ANATOMY_TERM);
    query.addFacetField(ImageDTO.PHENOTYPING_CENTER);
    query.addFacetField(ImageDTO.PROCEDURE_NAME);
    query.addFacetField(ImageDTO.PARAMETER_ASSOCIATION_VALUE);
    QueryResponse response = impcImagesCore.query(query);

    for (FacetField facetField : response.getFacetFields()) {
        Set<String> filter = new TreeSet<>();
        for (Count facet : facetField.getValues()) {
            if (!facet.getName().equals("tissue not available") && !facet.getName().equals("ambiguous")) {
                filter.add(facet.getName());
            }
        }
        res.put(facetField.getName(), filter);

    }

    return res;
}