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

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.ImageService.java

License:Apache License

public QueryResponse getProcedureFacetsForGeneByProcedure(String mgiAccession, String experimentOrControl)
        throws SolrServerException, IOException {

    // Map<String, ResponseWrapper<ImageDTO>> map=new HashMap<String,
    // ResponseWrapper<ImageDTO>>();
    // String queryString = "q=gene_accession_id:\"" + mgiAccession +
    // "\"&fq=" + ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":" +
    // experimentOrControl+"&facet=true&facet.field=procedure_name&facet.mincount=1";
    // log.debug("queryString in ImageService getFacets=" + queryString);

    // make a facet request first to get the procedures and then reuturn
    // make requests for each procedure
    // http://wwwdev.ebi.ac.uk/mi/impc/dev/solr/impc_images/select?q=gene_accession_id:%22MGI:2384986%22&&fq=biological_sample_group:experimental&facet=true&facet.field=procedure_name
    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery(ImageDTO.GENE_ACCESSION_ID + ":\"" + mgiAccession + "\"");
    solrQuery.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":" + experimentOrControl);
    solrQuery.setFacetMinCount(1);
    solrQuery.setFacet(true);//from  w  w w.  ja  v a2  s  . c om
    solrQuery.addFacetField("procedure_name");
    // solrQuery.setRows(0);
    QueryResponse response = impcImagesCore.query(solrQuery);
    return response;
}

---

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

License:Apache License

public QueryResponse getParameterFacetsForGeneByProcedure(String acc, String procedureName,
        String controlOrExperimental) throws SolrServerException, IOException {

    // e.g./*from  w w  w . jav a 2s.  com*/
    // http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/impc_images/query?q=gene_accession_id:%22MGI:2384986%22&fq=biological_sample_group:experimental&fq=procedure_name:X-ray&facet=true&facet.field=parameter_stable_id
    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery("gene_accession_id:\"" + acc + "\"");
    solrQuery.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":" + controlOrExperimental);
    solrQuery.setFacetMinCount(1);
    solrQuery.setFacet(true);
    solrQuery.addFilterQuery(ObservationDTO.PROCEDURE_NAME + ":\"" + procedureName + "\"");
    solrQuery.addFacetField(ObservationDTO.PARAMETER_STABLE_ID);
    // solrQuery.setRows(0);
    QueryResponse response = impcImagesCore.query(solrQuery);
    return response;

}

---

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

License:Apache License

/**
 *
 * @param acc//w w  w .  j a  va 2 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.ObservationService.java

License:Apache License

public List<String> getGenesWithMoreProcedures(int n, List<String> resourceName)
        throws SolrServerException, IOException, InterruptedException, ExecutionException {

    List<String> genes = new ArrayList<>();
    SolrQuery q = new SolrQuery();

    if (resourceName != null) {
        q.setQuery(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    } else {/*from w  w  w.j ava2s. com*/
        q.setQuery("*:*");
    }

    String geneProcedurePivot = ObservationDTO.GENE_SYMBOL + "," + ObservationDTO.PROCEDURE_NAME;

    q.add("facet.pivot", geneProcedurePivot);

    q.setFacet(true);
    q.setRows(1);
    q.setFacetMinCount(1);
    q.set("facet.limit", -1);

    logger.info("Solr url for getOverviewGenesWithMoreProceduresThan " + SolrUtils.getBaseURL(experimentCore)
            + "/select?" + q);
    QueryResponse response = experimentCore.query(q);

    for (PivotField pivot : response.getFacetPivot().get(geneProcedurePivot)) {
        if (pivot.getPivot() != null) {
            if (pivot.getPivot().size() >= n) {
                genes.add(pivot.getValue().toString());
            }
        }
    }

    return genes;
}

---

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/*from   w  w w.j  ava 2s .  c o  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   www.jav a  2s  . c o  m
        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.  j  av  a2  s  . c o  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 w  w. j av  a  2s.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);//from w w w .  j  ava  2  s. co m
    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;
}

---

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

License:Apache License

public Map<String, Long> getColoniesNoMPHit(List<String> resourceName, ZygosityType zygosity)
        throws SolrServerException, IOException {

    Map<String, Long> res = new HashMap<>();
    SolrQuery q = new SolrQuery();

    if (resourceName != null) {
        q.setQuery(GenotypePhenotypeDTO.RESOURCE_NAME + ":"
                + StringUtils.join(resourceName, " OR " + GenotypePhenotypeDTO.RESOURCE_NAME + ":"));
    } else {/* w ww.jav a  2 s.  c o m*/
        q.setQuery("*:*");
    }

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

    q.addFilterQuery(
            GenotypePhenotypeDTO.P_VALUE + ":[" + StatisticalResultService.P_VALUE_THRESHOLD + " TO 1]");

    q.addFacetField(StatisticalResultDTO.COLONY_ID);
    q.setFacetMinCount(1);
    q.setFacet(true);
    q.setRows(1);
    q.set("facet.limit", -1);

    logger.info(
            "Solr url for getColoniesNoMPHit " + SolrUtils.getBaseURL(statisticalResultCore) + "/select?" + q);
    QueryResponse response = statisticalResultCore.query(q);

    for (Count facet : response.getFacetField(StatisticalResultDTO.COLONY_ID).getValues()) {
        res.put(facet.getName(), facet.getCount());
    }

    return res;
}

---

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