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

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

  1. HOME
  2. Java
  3. org.apache.solr
  4. org.apache.solr.client.solrj.*
  5. SolrQuery
  6. setFacetLimit

Introduction

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

Prototype

public SolrQuery setFacetLimit(int lim)

Source Link

Document

set the facet limit

Usage

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

License:Apache License

/**
 *
 * @param mpId//from w  w w.  j av  a  2 s  .com
 * @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.j  ava 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;
}

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

License:Apache License

public List<String[]> getLaczExpressionSpreadsheet(String imageCollectionLinkBase) {
    SolrQuery query = new SolrQuery();
    ArrayList<String[]> res = new ArrayList<>();
    String[] aux = new String[0];

    query.setQuery(ImageDTO.PROCEDURE_NAME + ":\"Adult LacZ\" AND " + ImageDTO.BIOLOGICAL_SAMPLE_GROUP
            + ":experimental");
    query.setRows(1000000);//  w  w w  .j  a  v  a 2  s. com
    query.addField(ImageDTO.GENE_SYMBOL);
    query.addField(ImageDTO.GENE_ACCESSION_ID);
    query.addField(ImageDTO.ALLELE_SYMBOL);
    query.addField(ImageDTO.COLONY_ID);
    query.addField(ImageDTO.BIOLOGICAL_SAMPLE_ID);
    query.addField(ImageDTO.ZYGOSITY);
    query.addField(ImageDTO.SEX);
    query.addField(ImageDTO.PARAMETER_ASSOCIATION_NAME);
    query.addField(ImageDTO.PARAMETER_STABLE_ID);
    query.addField(ImageDTO.PARAMETER_ASSOCIATION_VALUE);
    query.addField(ImageDTO.GENE_ACCESSION_ID);
    query.addField(ImageDTO.PHENOTYPING_CENTER);
    query.setFacet(true);
    query.setFacetLimit(100);
    query.addFacetField(ImageDTO.PARAMETER_ASSOCIATION_NAME);
    query.set("group", true);
    query.set("group.limit", 100000);
    query.set("group.field", ImageDTO.BIOLOGICAL_SAMPLE_ID);

    try {
        QueryResponse solrResult = impcImagesCore.query(query);
        ArrayList<String> allParameters = new ArrayList<>();
        List<String> header = new ArrayList<>();
        header.add("Gene Symbol");
        header.add("MGI Gene Id");
        header.add("Allele Symbol");
        header.add("Colony Id");
        header.add("Biological Sample Id");
        header.add("Zygosity");
        header.add("Sex");
        header.add("Phenotyping Centre");

        logger.info(SolrUtils.getBaseURL(impcImagesCore) + "/select?" + query);

        // Get facets as we need to turn them into columns
        for (Count facet : solrResult.getFacetField(ImageDTO.PARAMETER_ASSOCIATION_NAME).getValues()) {
            allParameters.add(facet.getName());
            header.add(facet.getName());
        }
        header.add("image_collection_link");
        res.add(header.toArray(aux));
        for (Group group : solrResult.getGroupResponse().getValues().get(0).getValues()) {

            List<String> row = new ArrayList<>();
            ArrayList<String> params = new ArrayList<>();
            ArrayList<String> paramValues = new ArrayList<>();
            String urlToImagePicker = imageCollectionLinkBase + "/imageComparator?acc=";

            for (SolrDocument doc : group.getResult()) {
                if (row.size() == 0) {
                    row.add(doc.getFieldValues(ImageDTO.GENE_SYMBOL).iterator().next().toString());
                    row.add(doc.getFieldValues(ImageDTO.GENE_ACCESSION_ID).iterator().next().toString());
                    urlToImagePicker += doc.getFieldValue(ImageDTO.GENE_ACCESSION_ID) + "&parameter_stable_id=";
                    urlToImagePicker += doc.getFieldValue(ImageDTO.PARAMETER_STABLE_ID);
                    if (doc.getFieldValue(ImageDTO.ALLELE_SYMBOL) != null) {
                        row.add(doc.getFieldValue(ImageDTO.ALLELE_SYMBOL).toString());
                    }
                    row.add(doc.getFieldValue(ImageDTO.COLONY_ID).toString());
                    row.add(doc.getFieldValue(ImageDTO.BIOLOGICAL_SAMPLE_ID).toString());
                    if (doc.getFieldValue(ImageDTO.ZYGOSITY) != null) {
                        row.add(doc.getFieldValue(ImageDTO.ZYGOSITY).toString());
                    }
                    row.add(doc.getFieldValue(ImageDTO.SEX).toString());
                    row.add(doc.getFieldValue(ImageDTO.PHENOTYPING_CENTER).toString());
                }

                if (doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_NAME) != null) {
                    for (int i = 0; i < doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_NAME).size(); i++) {
                        params.add(doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_NAME)
                                .toArray(new Object[0])[i].toString());

                        if (doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_VALUE) != null) {
                            paramValues.add(doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_VALUE)
                                    .toArray(new Object[0])[i].toString());
                        } else {
                            paramValues.add(Constants.NO_INFORMATION_AVAILABLE);
                        }
                    }
                }
            }

            for (String tissue : allParameters) {
                if (params.contains(tissue)) {
                    row.add(paramValues.get(params.indexOf(tissue)));
                } else {
                    row.add("");
                }
            }
            row.add(urlToImagePicker);
            res.add(row.toArray(aux));
        }

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

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

License:Apache License

/**
 *
 * @param acc/*w  w w  .  j av  a2 s  .c om*/
 * @return a map containing the mp and colony_id combinations so that if we have these then we show an image link on the phenotype table on the gene page. Each row in table could have a different colony_id as well as mp id
 * @throws SolrServerException, IOException
 */

public Map<String, Set<String>> getImagePropertiesThatHaveMp(String acc)
        throws SolrServerException, IOException {
    //http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/impc_images/select?q=gene_accession_id:%22MGI:1913955%22&fq=mp_id:*&facet=true&facet.mincount=1&facet.limit=-1&facet.field=colony_id&facet.field=mp_id&facet.field=mp_term&rows=0
    Map<String, Set<String>> mpToColony = new HashMap<>();
    SolrQuery query = new SolrQuery();

    query.setQuery(ImageDTO.GENE_ACCESSION_ID + ":\"" + acc + "\"").setRows(100000000);
    query.addFilterQuery(ImageDTO.MP_ID_TERM + ":*");
    query.setFacet(true);
    query.setFacetLimit(-1);
    query.setFacetMinCount(1);

    String pivotFacet = ImageDTO.MP_ID_TERM + "," + ImageDTO.COLONY_ID;
    query.set("facet.pivot", pivotFacet);
    query.addFacetField(ObservationDTO.COLONY_ID);
    logger.debug("solr query for images properties for mp = " + query);
    QueryResponse response = impcImagesCore.query(query);
    for (PivotField pivot : response.getFacetPivot().get(pivotFacet)) {
        if (pivot.getPivot() != null) {
            //logger.info("pivot="+pivot.getValue());
            String mpIdAndName = pivot.getValue().toString();
            //logger.info("mpIdAndName" +mpIdAndName);
            String mpId = "";
            Set<String> colonIds = new TreeSet<>();
            if (mpIdAndName.contains("_")) {
                mpId = (mpIdAndName.split("_")[0]);
            }
            for (PivotField mp : pivot.getPivot()) {

                //logger.info("adding mp="+pivot.getValue()+" adding value="+mp.getValue());
                String colonyId = mp.getValue().toString();
                colonIds.add(colonyId);
            }
            mpToColony.put(mpId, colonIds);
        }

    }
    return mpToColony;

}

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

License:Apache License

/**
 * @author tudose/*from  ww  w.j  a  v a2s. c o  m*/
 * @since 2015/09/25
 * @return List< [(Procedure, parameter, observationNumber)]>
 */
public List<String[]> getProcedureParameterList() {

    List<String[]> result = new ArrayList<>();
    SolrQuery q = new SolrQuery();

    q.setQuery("*:*");
    q.setFacet(true);
    q.setFacetLimit(-1);
    q.setRows(0);

    String pivotFacet = ImpressDTO.PROCEDURE_STABLE_ID + "," + ImpressDTO.PARAMETER_STABLE_ID;
    q.set("facet.pivot", pivotFacet);

    try {
        QueryResponse res = pipelineCore.query(q);

        for (PivotField pivot : res.getFacetPivot().get(pivotFacet)) {
            if (pivot.getPivot() != null) {
                for (PivotField parameter : pivot.getPivot()) {
                    String[] row = { pivot.getValue().toString(), parameter.getValue().toString() };
                    result.add(row);
                }
            }
        }

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

    return result;
}

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

License:Apache License

/**
 * Returns a map of categories, faceted by the given pivot, indexed by category, comprising # Genes and Gene Symbols
 *
 * @param resources/*w ww  .j a v a 2 s  .co  m*/
 * @param parameterStableIds A list of parameter_stable_id values (e.g. IMPC_VIA_001_001)
 * @param pivot              A comma-separated string of solr fields to pivot the facet by (e.g. category,gene_symbol)
 * @return a map of categories, faceted by the given pivot, indexed by category, comprising # Genes and Gene Symbols
 * @throws SolrServerException, IOException
 */
public List<Map<String, String>> getCategories(List<String> resources, List<String> parameterStableIds,
        String pivot) throws SolrServerException, IOException {

    SolrQuery query = new SolrQuery();

    if ((resources != null) && (!resources.isEmpty())) {
        query.setFilterQueries(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resources, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    }
    if ((parameterStableIds != null) && (!parameterStableIds.isEmpty())) {
        query.setQuery(ObservationDTO.PARAMETER_STABLE_ID + ":"
                + StringUtils.join(parameterStableIds, " OR " + ObservationDTO.PARAMETER_STABLE_ID + ":"));
    }
    query.setRows(0);
    query.setFacet(true);
    query.setFacetMinCount(1);
    query.setFacetLimit(-1);
    query.set("facet.pivot", pivot);

    logger.info("getCategories Url: " + SolrUtils.getBaseURL(experimentCore) + "/select?" + query);

    return getFacetPivotResults(experimentCore.query(query), false);
}

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

License:Apache License

public Map<String, Set<String>> getColoniesByPhenotypingCenter(List<String> resourceName, ZygosityType zygosity)
        throws SolrServerException, IOException, InterruptedException {

    Map<String, Set<String>> res = new HashMap<>();
    SolrQuery q = new SolrQuery();
    String pivotFacet = ObservationDTO.PHENOTYPING_CENTER + "," + ObservationDTO.COLONY_ID;
    NamedList<List<PivotField>> response;

    if (resourceName != null) {
        q.setQuery(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    } else {//from  w w w .j  av  a 2 s  . c om
        q.setQuery("*:*");
    }

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

    q.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":experimental");
    q.addFacetPivotField(pivotFacet);
    q.setFacet(true);
    q.setFacetLimit(-1);
    q.setFacetMinCount(1);
    q.setRows(0);

    try {
        response = experimentCore.query(q).getFacetPivot();
        for (PivotField genePivot : response.get(pivotFacet)) {
            if (genePivot.getPivot() != null) {
                String center = genePivot.getValue().toString();
                HashSet<String> colonies = new HashSet<>();
                for (PivotField f : genePivot.getPivot()) {
                    colonies.add(f.getValue().toString());
                }
                res.put(center, colonies);
            }
        }
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }
    return res;
}

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

License:Apache License

/**
 * Returns a collection of biological sample ids for all mice matching the PROCEDURE_STABLE_ID.
 *
 * @param procedureStableId the procedure stable id (e.g. "IMPC_CAL_*" or "IMPC_IPG_*")
 *
 * @return a collection of biological sample ids for all mice matching the PROCEDURE_STABLE_ID
 *
 * @throws SolrServerException, IOException
 *//* w w  w.  ja  v a2s .co  m*/
public Collection<String> getMetabolismReportBiologicalSampleIds(String procedureStableId)
        throws SolrServerException, IOException {
    SolrQuery query = new SolrQuery();

    query.setQuery(String.format("%s:%s", ObservationDTO.PROCEDURE_STABLE_ID, procedureStableId));
    query.setRows(0);
    query.setFacetMinCount(1);
    query.setFacetLimit(100000);
    query.addFacetField(ObservationDTO.BIOLOGICAL_SAMPLE_ID);

    logger.info(SolrUtils.getBaseURL(experimentCore) + "/select?" + query);

    return getFacets(experimentCore.query(query)).get(ObservationDTO.BIOLOGICAL_SAMPLE_ID).keySet();
}

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

License:Apache License

public Set<String> getAllGeneIdsByResource(List<String> resourceName, boolean experimentalOnly) {

    SolrQuery q = new SolrQuery();
    q.setFacet(true);//from  w ww.j  a v a2  s  .c o m
    q.setFacetMinCount(1);
    q.setFacetLimit(-1);
    q.setRows(0);
    q.addFacetField(ObservationDTO.GENE_ACCESSION_ID);
    if (resourceName != null) {
        q.setQuery(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    } else {
        q.setQuery("*:*");
    }

    if (experimentalOnly) {
        q.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":experimental");
    }

    logger.info("Solr URL getAllGeneIdsByResource " + SolrUtils.getBaseURL(experimentCore) + "/select?" + q);
    try {
        return getFacets(experimentCore.query(q)).get(ObservationDTO.GENE_ACCESSION_ID).keySet();
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }

    return null;
}

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

License:Apache License

public Set<String> getAllColonyIdsByResource(List<String> resourceName, boolean experimentalOnly) {

    SolrQuery q = new SolrQuery();
    q.setFacet(true);/*w  w w .  j a  v  a  2s .c  om*/
    q.setFacetMinCount(1);
    q.setFacetLimit(-1);
    q.setRows(0);
    q.addFacetField(ObservationDTO.COLONY_ID);

    if (resourceName != null) {
        q.setQuery(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    } else {
        q.setQuery("*:*");
    }

    if (experimentalOnly) {
        q.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":experimental");
    }

    logger.info("Solr URL getAllColonyIdsByResource " + SolrUtils.getBaseURL(experimentCore) + "/select?" + q);
    try {
        return getFacets(experimentCore.query(q)).get(ObservationDTO.COLONY_ID).keySet();
    } catch (SolrServerException | IOException e) {
        e.printStackTrace();
    }

    return null;
}