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.GenotypePhenotypeService.java

License:Apache License

/**
 * @param mpTermName//  ww w .java  2  s  .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);
    q.setFacetMinCount(1);//from www .j av  a2s  . co  m
    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

/**
 * @author ilinca//from   ww  w  . j  a  va  2s.co m
 * @since 2016/07/07
 * @return CSV string of facet values (mp,gene,colony,phenCenter,sex,zyg,param,pVal). At the moment of writing used to compare calls from EBI to DCC
 * @throws SolrServerException, IOException
 * @throws URISyntaxException 
 * @throws IOException 
 * @throws MalformedURLException 
 */
public String getTabbedCallSummary() throws MalformedURLException, IOException, URISyntaxException {
    //   http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/genotype-phenotype/select?q=resource_name:IMPC&facet=true&facet.mincount=1&facet.pivot=mp_term_name,marker_symbol,colony_id,phenotyping_center,sex,zygosity,parameter_stable_id,p_value&facet.limit=-1&facet.mincount=1&wt=xslt&tr=pivot.xsl

    SolrQuery q = new SolrQuery();
    q.setQuery(GenotypePhenotypeDTO.RESOURCE_NAME + ":IMPC");
    q.addFilterQuery("-" + GenotypePhenotypeDTO.ASSERTION_TYPE + ":manual");
    q.setFacet(true);
    q.setFacetLimit(-1).setFacetMinCount(1)
            .addFacetPivotField(GenotypePhenotypeDTO.MP_TERM_ID + "," + GenotypePhenotypeDTO.MARKER_SYMBOL + ","
                    + GenotypePhenotypeDTO.COLONY_ID + "," + GenotypePhenotypeDTO.PHENOTYPING_CENTER + ","
                    + GenotypePhenotypeDTO.SEX + "," + GenotypePhenotypeDTO.ZYGOSITY + ","
                    + GenotypePhenotypeDTO.PARAMETER_STABLE_ID + "," + GenotypePhenotypeDTO.P_VALUE);
    q.set("wt", "xslt").set("tr", "pivot.xsl");

    HttpProxy proxy = new HttpProxy();
    System.out.println("Solr ULR for getTabbedCallSummary " + SolrUtils.getBaseURL(genotypePhenotypeCore)
            + "/select?" + q);

    String content = proxy.getContent(new URL(SolrUtils.getBaseURL(genotypePhenotypeCore) + "/select?" + q));

    return content;
}

---

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 . ja  v  a 2 s  .  c om*/
    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 w  w  . j av a  2  s .  c o  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 . j a  v a  2 s  .co m*/
    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 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);// w  w w.j  av a2  s  . com
    solrQuery.setFacet(true);
    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 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);//from www.ja  v a  2 s  .c om
    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

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

    // e.g.//from   w  w  w .j  a  v  a2s  .  c o m
    // 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//from w w w .j a va2  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;

}

---

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