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

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

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Introduction

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

Prototype

public SolrQuery setQuery(String query)

Source Link

Usage

From source file:edu.vt.vbi.patric.common.DataApiHandler.java

License:Apache License

/**
 * wrapper function of field facet query
 *
 * @param core SolrCore/*from w  w w .ja  v  a  2 s  . c  o m*/
 * @param queryParam query condition
 * @param filterParam filter condition
 * @param facetFields comma separated list of fields
 */
public Map getFieldFacets(SolrCore core, String queryParam, String filterParam, String facetFields)
        throws IOException {
    Map<String, Object> res = new HashMap<>();
    SolrQuery query = new SolrQuery();

    query.setQuery(queryParam);
    if (filterParam != null) {
        query.addFilterQuery(filterParam);
    }
    query.setRows(0).setFacet(true).setFacetLimit(-1).setFacetMinCount(1)
            .setFacetSort(FacetParams.FACET_SORT_COUNT).set("json.nl", "map");
    query.addFacetField(facetFields.split(","));

    List<String> fields = Arrays.asList(facetFields.split(","));

    LOGGER.trace("getFieldFacets: [{}] {}", core.getSolrCoreName(), query.toString());
    String response = this.solrQuery(core, query);
    Map resp = jsonParser.readValue(response);
    Map facet_fields = (Map) ((Map) resp.get("facet_counts")).get("facet_fields");

    Map<String, Object> facets = new HashMap<>();
    for (String field : fields) {
        Map values = (Map) facet_fields.get(field);
        Map<String, Integer> facetValues = new LinkedHashMap<>();

        for (Map.Entry<String, Integer> entry : (Iterable<Map.Entry>) values.entrySet()) {
            facetValues.put(entry.getKey(), entry.getValue());
        }

        facets.put(field, facetValues);
    }

    res.put("total", ((Map) resp.get("response")).get("numFound"));
    res.put("facets", facets);

    return res;
}

From source file:edu.vt.vbi.patric.common.DataApiHandler.java

License:Apache License

/**
 * wrapper function of pivot facet query
 *
 * @param core SolrCore/*ww  w . j  a v a  2 s  . c  o m*/
 * @param queryParam query condition
 * @param filterParam filter condition
 * @param facetFields comma separated list of fields
 */

public Map getPivotFacets(SolrCore core, String queryParam, String filterParam, String facetFields)
        throws IOException {
    Map<String, Object> res = new HashMap<>();
    SolrQuery query = new SolrQuery();

    query.setQuery(queryParam);
    if (filterParam != null) {
        query.addFilterQuery(filterParam);
    }
    query.setRows(0).setFacet(true).setFacetLimit(-1).setFacetMinCount(1)
            .setFacetSort(FacetParams.FACET_SORT_INDEX);
    query.addFacetPivotField(facetFields);

    LOGGER.trace("getPivotFacets: [{}] {}", core.getSolrCoreName(), query.toString());
    String response = this.solrQuery(core, query);
    Map<String, Object> resp = jsonParser.readValue(response);
    Map facet_fields = (Map) ((Map) resp.get("facet_counts")).get("facet_pivot");
    List<Map> values = (List) facet_fields.get(facetFields);

    Map<String, Object> facet = new LinkedHashMap<>();

    for (Map value : values) {
        String localKey = value.get("value").toString();
        List<Map> localValues = (List) value.get("pivot");

        Map<String, Integer> pivotValues = new LinkedHashMap<>();
        for (Map local : localValues) {
            pivotValues.put(local.get("value").toString(), (Integer) local.get("count"));
        }
        facet.put(localKey, pivotValues);
    }

    res.put("total", ((Map) resp.get("response")).get("numFound"));
    res.put(facetFields, facet);

    return res;
}

From source file:edu.vt.vbi.patric.common.DataApiHandler.java

License:Apache License

public SolrQuery buildSolrQuery(Map<String, String> key, String sorts, String facets, int start, int end,
        boolean highlight) {

    SolrQuery query = new SolrQuery();
    SolrInterface solr = new SolrInterface();

    // Processing key map
    query.setQuery(StringHelper.stripQuoteAndParseSolrKeywordOperator(key.get("keyword")));

    if (key.containsKey("filter") && key.get("filter") != null) {
        query.addFilterQuery(key.get("filter"));
    }//w  ww . j a v a  2 s.c  o  m
    if (key.containsKey("filter2") && key.get("filter2") != null) {
        query.addFilterQuery(key.get("filter2"));
    }

    // use SolrJoin if possible
    if (key.containsKey("join")) {
        query.addFilterQuery(key.get("join"));
    }

    if (key.containsKey("fields") && !key.get("fields").equals("")) {
        query.addField(key.get("fields"));
    }

    // sort conditions
    if (sorts != null && !sorts.equals("") && !sorts.equals("[]")) {
        try {
            JSONArray sorter = (JSONArray) new JSONParser().parse(sorts);
            for (Object aSort : sorter) {
                JSONObject jsonSort = (JSONObject) aSort;
                query.addSort(SolrQuery.SortClause.create(jsonSort.get("property").toString(),
                        jsonSort.get("direction").toString().toLowerCase()));
            }
        } catch (ParseException e) {
            LOGGER.error(e.getMessage(), e);
        }
    }

    // facet conditions
    if (facets != null && !facets.equals("") && !facets.equals("{}")) {
        query.setFacet(true).setFacetMinCount(1).setFacetLimit(-1).setFacetSort(FacetParams.FACET_SORT_COUNT)
                .set("json.nl", "map");

        try {
            JSONObject facetConditions = (JSONObject) new JSONParser().parse(facets);

            if (facetConditions.containsKey("facet.sort")) {
                String facetSort = facetConditions.get("facet.sort").toString();
                if (facetSort.equals("index")) {
                    query.setFacetSort(FacetParams.FACET_SORT_INDEX);
                }
            }

            if (facetConditions.containsKey("field_facets")) {
                String[] fieldFacets = facetConditions.get("field_facets").toString().split(",");
                query.addFacetField(fieldFacets);
            }

            if (facetConditions.containsKey("date_range_facets")
                    && !facetConditions.get("date_range_facets").equals("")) {
                String[] dateRangeFacets = facetConditions.get("date_range_facets").toString().split(",");
                for (String field : dateRangeFacets) {
                    query.addDateRangeFacet(field, solr.getRangeStartDate(), solr.getRangeEndDate(),
                            solr.getRangeDate());
                }
            }
        } catch (ParseException e) {
            LOGGER.error(e.getMessage(), e);
        }
    }

    // start & end
    query.setStart(start); // setting starting index

    if (end == -1) {
        query.setRows(MAX_ROWS);
    } else {
        query.setRows(end);
    }

    // highlight
    if (highlight) {
        query.set("hl", "on").set("hl.fl", "*");
    }

    return query;
}

From source file:edu.vt.vbi.patric.common.FacetHelper.java

License:Apache License

private static JSONObject getSingleFacetsData(DataApiHandler dataApi, SolrCore core, String keyword,
        String single_facet, String[] facets, String fq) throws IOException, ParseException {

    SolrInterface solr = new SolrInterface();

    keyword = StringHelper.stripQuoteAndParseSolrKeywordOperator(keyword);

    int beginindex = keyword.indexOf(" AND (" + single_facet);
    int endindex = 0;

    StringBuffer s = new StringBuffer(keyword);

    if (beginindex < 0) {
        beginindex = keyword.indexOf("(" + single_facet);
        endindex = keyword.indexOf(") AND ", beginindex);
        if (endindex < 0) {
            endindex = keyword.indexOf("))", beginindex);

            // TODO: this cause java.lang.StringIndexOutOfBoundsException: String index out of range: -1
            // when Patric Libs keyword - (*) and endindex: 2
            LOGGER.debug("string:{}, beginIndex: {}, endIndex:{}", s, beginindex, endindex);
            if (endindex > 0) {
                s.delete(beginindex, endindex + 2);
            }/*  w  ww . j  a va  2  s  .  c  o m*/
        } else {
            s.delete(beginindex, endindex + 6);
        }
    } else {
        endindex = keyword.indexOf("))", beginindex);
        if (endindex == -1) {
            endindex = keyword.indexOf("])", beginindex);
        }
        s.delete(beginindex, endindex + 2);
    }
    if (s.length() == 0)
        s.append("(*)");

    SolrQuery query = new SolrQuery();
    query.setQuery(s.toString());
    if (fq != null) {
        query.setFilterQueries(fq);
    }

    query.setStart(0).setRows(1).setFacet(true).setFacetMinCount(1).set("json.nl", "map");

    for (String facet : facets) {
        if (!facet.equals("completion_date") && !facet.equals("release_date")) {
            query.addFacetField(facet);
        } else {
            query.addDateRangeFacet(facet, solr.getRangeStartDate(), solr.getRangeEndDate(),
                    solr.getRangeDate());
        }
    }

    String apiResponse = dataApi.solrQuery(core, query);

    Map resp = jsonMapReader.readValue(apiResponse);
    Map respBody = (Map) resp.get("response");

    JSONObject ret = new JSONObject();
    ret.put("response", new JSONObject(respBody));
    ret.put("facets", FacetHelper.formatFacetTree((Map) resp.get("facet_counts")));

    return ret;
}

From source file:edu.vt.vbi.patric.common.SolrInterface.java

License:Apache License

public String getProteomicsTaxonIdFromFeatureId(String id) {
    SolrQuery query = new SolrQuery();
    query.setQuery("na_feature_id:" + id);
    query.setRows(1000000);/*from  w  ww .j ava  2s . c o  m*/
    String experiment_id = "";

    //      try {
    //         QueryResponse qr = server.query(query);
    //         SolrDocumentList sdl = qr.getResults();
    //
    //         for (SolrDocument d : sdl) {
    //            for (Entry<String, Object> el : d) {
    //               if (el.getKey().equals("experiment_id")) {
    //                  if (experiment_id.length() == 0)
    //                     experiment_id = el.getValue().toString();
    //                  else
    //                     experiment_id += "##" + el.getValue().toString();
    //               }
    //            }
    //         }
    //      }
    //      catch (SolrServerException e) {
    //         e.printStackTrace();
    //      }

    return experiment_id;
}

From source file:edu.vt.vbi.patric.portlets.CompPathwayTable.java

License:Apache License

@SuppressWarnings("unchecked")
private JSONObject processEcNumberTab(DataApiHandler dataApi, String pathwayClass, String pathwayId,
        String ecNumber, String annotation, String contextType, String contextId)
        throws PortletException, IOException {

    JSONObject jsonResult = new JSONObject();
    SolrQuery query = new SolrQuery("*:*");

    if (pathwayClass != null && !pathwayClass.equals("")) {
        query.addFilterQuery("pathway_class:" + pathwayClass);
    }//from w w w.  jav  a 2  s . c o  m

    if (pathwayId != null && !pathwayId.equals("")) {
        query.addFilterQuery("pathway_id:" + pathwayId);
    }

    if (ecNumber != null && !ecNumber.equals("")) {
        query.addFilterQuery("ec_number:" + ecNumber);
    }

    if (annotation != null && !annotation.equals("")) {
        query.addFilterQuery("annotation:" + annotation);
    }

    if (contextType.equals("genome")) {
        query.addFilterQuery(
                SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "genome_id:" + contextId));
    } else if (contextType.equals("taxon")) {
        query.addFilterQuery(
                SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "taxon_lineage_ids:" + contextId));
    }

    JSONArray items = new JSONArray();
    int count_total = 0;
    int count_unique = 0;

    try {
        Set<String> listPathwayIds = new HashSet<>();
        Set<String> listEcNumbers = new HashSet<>();

        // get pathway stat
        query.setRows(0).setFacet(true);
        query.add("json.facet",
                "{stat:{field:{field:pathway_ec,limit:-1,facet:{genome_count:\"unique(genome_id)\",gene_count:\"unique(feature_id)\",ec_count:\"unique(ec_number)\"}}}}");

        LOGGER.trace("[{}] {}", SolrCore.PATHWAY.getSolrCoreName(), query);

        String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY, query);
        Map resp = jsonReader.readValue(apiResponse);
        List<Map> buckets = (List<Map>) ((Map) ((Map) resp.get("facets")).get("stat")).get("buckets");

        Map<String, Map> mapStat = new HashMap<>();
        for (Map value : buckets) {

            if (!value.get("genome_count").toString().equals("0")) {
                mapStat.put(value.get("val").toString(), value);

                String[] pathway_ec = value.get("val").toString().split("_");
                listPathwayIds.add(pathway_ec[0]);
                listEcNumbers.add(pathway_ec[1]);
            }
        }

        // get pathway list
        SolrQuery pathwayQuery = new SolrQuery("*:*");
        if (!listPathwayIds.isEmpty()) {
            pathwayQuery.setQuery("pathway_id:(" + StringUtils.join(listPathwayIds, " OR ") + ")");

            pathwayQuery.setFields("pathway_id,pathway_name,pathway_class,ec_number,ec_description");
            pathwayQuery.setRows(Math.max(dataApi.MAX_ROWS, listPathwayIds.size()));

            LOGGER.trace("[{}] {}", SolrCore.PATHWAY_REF.getSolrCoreName(), pathwayQuery);

            apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, pathwayQuery);
            resp = jsonReader.readValue(apiResponse);
            Map respBody = (Map) resp.get("response");

            List<Map> sdl = (List<Map>) respBody.get("docs");

            for (Map doc : sdl) {
                String aPathwayId = doc.get("pathway_id").toString();
                String aEcNumber = doc.get("ec_number").toString();
                Map stat = mapStat.get(aPathwayId + "_" + aEcNumber);

                if (stat != null && !stat.get("genome_count").toString().equals("0")) {
                    JSONObject item = new JSONObject();
                    item.put("pathway_id", aPathwayId);
                    item.put("pathway_name", doc.get("pathway_name"));
                    item.put("pathway_class", doc.get("pathway_class"));

                    float genome_count = Float.parseFloat(stat.get("genome_count").toString());
                    float gene_count = Float.parseFloat(stat.get("gene_count").toString());

                    item.put("ec_name", doc.get("ec_description"));
                    item.put("ec_number", doc.get("ec_number"));
                    item.put("gene_count", gene_count);
                    item.put("genome_count", genome_count);
                    item.put("algorithm", annotation);

                    items.add(item);
                }
            }
            count_total = items.size();
            count_unique = listEcNumbers.size();
        }
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    // Wrapping jsonResult
    jsonResult.put("total", count_total);
    jsonResult.put("results", items);
    jsonResult.put("unique", count_unique);

    return jsonResult;
}

From source file:edu.vt.vbi.patric.portlets.Downloads.java

License:Apache License

public void serveResource(ResourceRequest request, ResourceResponse response)
        throws PortletException, IOException {

    String mode = request.getParameter("mode");

    if (mode.equals("getGenomeCount")) {

        String taxonId = request.getParameter("taxonId");
        String dataSource = request.getParameter("data_source");

        DataApiHandler dataApi = new DataApiHandler(request);

        SolrQuery query = new SolrQuery();

        if (taxonId != null) {
            query.setQuery("taxon_lineage_ids:" + taxonId);
        } else {//from  w  ww .j a v a 2 s.  c o m
            query.setQuery("*:*");
        }

        if (dataSource != null) {
            String[] sources = dataSource.split(",");
            List<String> conditions = new ArrayList<>();

            for (String source : sources) {
                switch (source) {
                case ".PATRIC":
                    conditions.add("patric_cds:[1 TO *]");
                    break;
                case ".RefSeq":
                    conditions.add("refseq_cds:[1 TO *]");
                    break;
                }
            }

            query.setFilterQueries(StringUtils.join(conditions, " OR "));
        }
        query.setRows(0);

        LOGGER.debug("[{}] {}", SolrCore.GENOME, query.toString());
        String apiResponse = dataApi.solrQuery(SolrCore.GENOME, query);

        Map resp = jsonReader.readValue(apiResponse);
        Map respBody = (Map) resp.get("response");

        int numFound = (Integer) respBody.get("numFound");

        response.getWriter().write("" + numFound);
    } else if (mode.equals("download")) {

        String genomeId = request.getParameter("genomeId");
        String taxonId = request.getParameter("taxonId");
        String fileTypes = request.getParameter("finalfiletype");
        String annotations = request.getParameter("finalalgorithm");

        Logger LOGGER = LoggerFactory.getLogger(CreateZip.class);

        List<String> genomeIdList = new LinkedList<>();

        DataApiHandler dataApi = new DataApiHandler(request);

        SolrQuery query = new SolrQuery("*:*");

        if (genomeId != null && !genomeId.equals("")) {
            query.addFilterQuery("genome_id:(" + genomeId.replaceAll(",", " OR ") + ")");
        }
        if (taxonId != null && !taxonId.equals("")) {
            query.addFilterQuery("taxon_lineage_ids:" + taxonId);
        }
        query.setRows(dataApi.MAX_ROWS).addField("genome_id");

        LOGGER.debug("[{}] {}", SolrCore.GENOME, query.toString());

        String apiResponse = dataApi.solrQuery(SolrCore.GENOME, query);
        Map resp = jsonReader.readValue(apiResponse);
        Map respBody = (Map) resp.get("response");

        List<Genome> genomeList = dataApi.bindDocuments((List<Map>) respBody.get("docs"), Genome.class);

        for (Genome genome : genomeList) {
            genomeIdList.add(genome.getId());
        }

        CreateZip zip = new CreateZip();
        byte[] bytes = zip.ZipIt(genomeIdList, Arrays.asList(annotations.split(",")),
                Arrays.asList(fileTypes.split(",")));

        if (bytes.length > 0) {
            response.setContentType("application/octetstream");
            response.setProperty("Cache-Control", "cache");
            response.setProperty("Content-Disposition", "attachment; filename=\"patric_downloads.zip\"");
            response.setContentLength(bytes.length);
            response.getPortletOutputStream().write(bytes);
        } else {
            response.getWriter().write("Sorry. The requested file(s) are not available.");
        }
    }
}

From source file:edu.vt.vbi.patric.portlets.ExperimentListPortlet.java

License:Apache License

@Override
protected void doView(RenderRequest request, RenderResponse response) throws PortletException, IOException {

    response.setContentType("text/html");

    SiteHelper.setHtmlMetaElements(request, response, "Experiment List");
    response.setTitle("Experiment List");

    String cType = request.getParameter("context_type");
    String cId = request.getParameter("context_id");

    if (cType != null && cId != null) {

        String kw = (request.getParameter("keyword") != null) ? request.getParameter("keyword") : "";
        if (kw != null && (kw.startsWith("/") || kw.startsWith("#"))) {
            kw = "";
        }//  ww  w  . j  av  a 2 s.  c o  m

        String keyword = "(*)";
        String filter;
        String eid;

        if (cType.equals("taxon") && cId.equals("2")) {
            filter = "*";
            eid = "";
        } else {
            DataApiHandler dataApi = new DataApiHandler(request);
            List<String> items = new ArrayList<>();

            SolrQuery query = new SolrQuery();

            if (cType.equals("taxon")) {
                query.setQuery("*:*");
                query.setFilterQueries(
                        SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_ids", "taxon_lineage_ids:" + cId));
            } else if (cType.equals("genome")) {
                query = new SolrQuery("genome_ids:" + cId);
            }

            query.setRows(10000).setFields("eid");
            String apiResponse = dataApi.solrQuery(SolrCore.TRANSCRIPTOMICS_EXPERIMENT, query);

            Map resp = jsonReader.readValue(apiResponse);
            Map respBody = (Map) resp.get("response");
            List<Map> sdl = (List<Map>) respBody.get("docs");

            for (Map doc : sdl) {
                items.add(doc.get("eid").toString());
            }

            if (items.size() > 0) {
                eid = StringUtils.join(items, "##");
            } else {
                eid = "0";
            }
            filter = eid;
        }

        request.setAttribute("keyword", keyword);
        request.setAttribute("kw", kw);
        request.setAttribute("eid", eid);
        request.setAttribute("filter", filter);

        PortletRequestDispatcher prd = getPortletContext()
                .getRequestDispatcher("/WEB-INF/jsp/experiment/list.jsp");
        prd.include(request, response);
    }
}

From source file:edu.vt.vbi.patric.portlets.GenomeBrowser.java

License:Apache License

private void printRefSeqInfo(ResourceRequest request, ResourceResponse response) throws IOException {

    String contextType = request.getParameter("cType");
    String contextId = request.getParameter("cId");

    DataApiHandler dataApi = new DataApiHandler(request);
    SolrQuery query = new SolrQuery();

    if (contextType.equals("genome")) {
        query.setQuery("genome_id:" + contextId);
    } else if (contextType.equals("feature")) {
        query.setQuery(SolrCore.FEATURE.getSolrCoreJoin("genome_id", "genome_id", "feature_id:" + contextId));
    }/* w ww  .  j a va  2  s.  c o  m*/
    query.setRows(dataApi.MAX_ROWS).addSort("accession", SolrQuery.ORDER.asc);

    JSONArray jsonResult = new JSONArray();

    LOGGER.trace("[{}] {}", SolrCore.SEQUENCE.getSolrCoreName(), query.toString());
    String apiResponse = dataApi.solrQuery(SolrCore.SEQUENCE, query);
    Map resp = jsonReader.readValue(apiResponse);
    Map respBody = (Map) resp.get("response");

    List<GenomeSequence> sequences = dataApi.bindDocuments((List<Map>) respBody.get("docs"),
            GenomeSequence.class);

    for (GenomeSequence sequence : sequences) {

        JSONObject seq = new JSONObject();
        seq.put("length", sequence.getLength());
        seq.put("name", sequence.getAccession());
        seq.put("accn", sequence.getAccession());
        //         seq.put("sid", sequence.getId());
        seq.put("sid", sequence.getGenomeId());
        seq.put("start", 0);
        seq.put("end", sequence.getLength());
        seq.put("seqDir", "");
        seq.put("seqChunkSize", sequence.getLength());

        jsonResult.add(seq);
    }

    // TODO: remove this when data API limit is removed
    int i = 1;
    while (sequences.size() == 25000) {
        query.setStart(25000 * i);

        apiResponse = dataApi.solrQuery(SolrCore.SEQUENCE, query);
        resp = jsonReader.readValue(apiResponse);
        respBody = (Map) resp.get("response");

        sequences = dataApi.bindDocuments((List<Map>) respBody.get("docs"), GenomeSequence.class);

        for (GenomeSequence sequence : sequences) {

            JSONObject seq = new JSONObject();
            seq.put("length", sequence.getLength());
            seq.put("name", sequence.getAccession());
            seq.put("accn", sequence.getAccession());
            seq.put("sid", sequence.getGenomeId());
            seq.put("start", 0);
            seq.put("end", sequence.getLength());
            seq.put("seqDir", "");
            seq.put("seqChunkSize", sequence.getLength());

            jsonResult.add(seq);
        }
        i++;
    }

    response.setContentType("application/json");
    jsonResult.writeJSONString(response.getWriter());
    response.getWriter().close();
}

From source file:edu.vt.vbi.patric.portlets.PathwayFinder.java

License:Apache License

@SuppressWarnings("unchecked")
private JSONObject processPathwayTab(DataApiHandler dataApi, String pathwayId, String ecNumber,
        String annotation, String taxonId, String genomeId, String keyword)
        throws PortletException, IOException {

    JSONObject jsonResult = new JSONObject();
    SolrQuery query = new SolrQuery("*:*");

    if (pathwayId != null && !pathwayId.equals("")) {
        query.addFilterQuery("pathway_id:" + pathwayId);
    }//from   w w  w  .j  a  v  a  2  s .  co m

    if (ecNumber != null && !ecNumber.equals("")) {
        query.addFilterQuery("ec_number:" + ecNumber);
    }

    if (annotation != null && !annotation.equals("") && !annotation.equalsIgnoreCase("ALL")) {
        query.addFilterQuery("annotation:" + annotation);
    }

    if (taxonId != null && !taxonId.equals("")) {
        query.addFilterQuery(
                SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "taxon_lineage_ids:" + taxonId));
    }

    if (genomeId != null && !genomeId.equals("")) {
        query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id",
                "genome_id:(" + genomeId.replaceAll(",", " OR ") + ")"));
    }

    if (keyword != null && !keyword.equals("")) {
        query.setQuery(keyword);
    }

    JSONArray items = new JSONArray();
    int count_total = 0;
    int count_unique = 0;

    try {
        Set<String> listPathwayIds = new HashSet<>();
        Map<String, JSONObject> uniquePathways = new HashMap<>();

        // get pathway stat
        query.setRows(0).setFacet(true);
        query.add("json.facet",
                "{stat:{field:{field:pathway_id,limit:-1,facet:{genome_count:\"unique(genome_id)\",gene_count:\"unique(feature_id)\",ec_count:\"unique(ec_number)\",genome_ec:\"unique(genome_ec)\"}}}}");

        LOGGER.trace("processPathwayTab: [{}] {}", SolrCore.PATHWAY.getSolrCoreName(), query);

        String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY, query);

        Map resp = jsonReader.readValue(apiResponse);
        List<Map> buckets = (List<Map>) ((Map) ((Map) resp.get("facets")).get("stat")).get("buckets");

        Map<String, Map> mapStat = new HashMap<>();
        for (Map value : buckets) {
            mapStat.put(value.get("val").toString(), value);
            listPathwayIds.add(value.get("val").toString());
        }

        if (!listPathwayIds.isEmpty()) {
            // get pathway list
            SolrQuery pathwayQuery = new SolrQuery(
                    "pathway_id:(" + StringUtils.join(listPathwayIds, " OR ") + ")");
            pathwayQuery.setFields("pathway_id,pathway_name,pathway_class");
            pathwayQuery.setRows(Math.max(dataApi.MAX_ROWS, listPathwayIds.size()));

            LOGGER.trace("processPathwayTab: [{}] {}", SolrCore.PATHWAY_REF.getSolrCoreName(), pathwayQuery);

            apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, pathwayQuery);
            resp = jsonReader.readValue(apiResponse);
            Map respBody = (Map) resp.get("response");

            List<Map> sdl = (List<Map>) respBody.get("docs");

            for (Map doc : sdl) {
                String aPathwayId = doc.get("pathway_id").toString();
                Map stat = mapStat.get(aPathwayId);

                if (!uniquePathways.containsKey(aPathwayId)
                        && !stat.get("genome_count").toString().equals("0")) {
                    JSONObject item = new JSONObject();
                    item.put("pathway_id", aPathwayId);
                    item.put("pathway_name", doc.get("pathway_name"));
                    item.put("pathway_class", doc.get("pathway_class"));

                    float genome_ec = Float.parseFloat(stat.get("genome_ec").toString());
                    float genome_count = Float.parseFloat(stat.get("genome_count").toString());
                    float ec_count = Float.parseFloat(stat.get("ec_count").toString());
                    float gene_count = Float.parseFloat(stat.get("gene_count").toString());

                    float ec_cons = 0;
                    float gene_cons = 0;
                    if (genome_count > 0 && ec_count > 0) {
                        ec_cons = genome_ec / genome_count / ec_count * 100;
                        gene_cons = gene_count / genome_count / ec_count;
                    }

                    item.put("ec_cons", ec_cons);
                    item.put("ec_count", ec_count);
                    item.put("gene_cons", gene_cons);
                    item.put("gene_count", gene_count);
                    item.put("genome_count", genome_count);
                    item.put("algorithm", annotation);

                    uniquePathways.put(aPathwayId, item);
                }
            }

            for (Map.Entry<String, JSONObject> pathway : uniquePathways.entrySet()) {
                items.add(pathway.getValue());
            }
            count_total = uniquePathways.entrySet().size();
            count_unique = count_total;
        }
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    // Wrapping jsonResult
    try {
        jsonResult.put("total", count_total);
        jsonResult.put("results", items);
        jsonResult.put("unique", count_unique);
    } catch (Exception ex) {
        LOGGER.error(ex.getMessage(), ex);
    }

    return jsonResult;
}