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

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

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Introduction

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

Prototype

public SolrQuery setFields(String... fields)

Source Link

Usage

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

License:Apache License

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

    SiteHelper.setHtmlMetaElements(request, response, "Feature Overview");

    response.setContentType("text/html");
    String cType = request.getParameter("context_type");
    String cId = request.getParameter("context_id");

    if (cType != null && cId != null && cType.equals("feature")) {

        DataApiHandler dataApi = new DataApiHandler(request);
        GenomeFeature feature = dataApi.getPATRICFeature(cId);

        if (feature != null) {
            List<GenomeFeature> listReleateFeatures;
            List<String> listUniprotkbAccessions = null;
            List<Map<String, String>> listUniprotIds = null;
            String refseqLink = null;
            String refseqLocusTag = null;
            Map<String, String> virulenceFactor = null;

            SolrQuery query = new SolrQuery("pos_group:" + feature.getPosGroupInQuote());
            query.setSort("annotation_sort", SolrQuery.ORDER.asc);

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

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

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

            // build listUniprotkbAccessions based on GI number
            if (feature.getGi() > 0) {
                query = new SolrQuery("id_value:(" + feature.getGi() + ")");
                query.addFilterQuery("id_type:GI").setRows(dataApi.MAX_ROWS);

                apiResponse = dataApi.solrQuery(SolrCore.ID_REF, query);

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

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

                if (uniprotList.size() > 0) {
                    listUniprotkbAccessions = new ArrayList<>();
                }//www.j a v  a2 s . c o  m

                for (Map doc : uniprotList) {
                    listUniprotkbAccessions.add(doc.get("uniprotkb_accession").toString());
                }
            }

            if (listUniprotkbAccessions != null) {
                query = new SolrQuery(
                        "uniprotkb_accession:(" + StringUtils.join(listUniprotkbAccessions, " OR ") + ")");
                query.setFields("uniprotkb_accession,id_type,id_value");
                query.setRows(1000);

                apiResponse = dataApi.solrQuery(SolrCore.ID_REF, query);

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

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

                if (!sdl.isEmpty()) {
                    listUniprotIds = new ArrayList<>();
                }

                for (Map doc : sdl) {
                    Map<String, String> uniprot = new HashMap<>();

                    uniprot.put("Accession", doc.get("uniprotkb_accession").toString());
                    uniprot.put("idType", doc.get("id_type").toString());
                    uniprot.put("idValue", doc.get("id_value").toString());

                    listUniprotIds.add(uniprot);
                }
            }

            if (feature.getAnnotation().equals("PATRIC")) {

                if (feature.hasGeneId()) {
                    refseqLink = SiteHelper.getExternalLinks("ncbi_gene").replace("&", "&amp;")
                            + feature.getGeneId();
                }
                refseqLocusTag = feature.getRefseqLocusTag();
            } else if (feature.getAnnotation().equals("RefSeq")) {
                refseqLocusTag = feature.getAltLocusTag();
            }

            query = new SolrQuery("(locus_tag:" + feature.getAltLocusTag()
                    + (feature.hasRefseqLocusTag() ? " OR locus_tag: " + feature.getRefseqLocusTag() : "")
                    + ")");
            query.setFilterQueries("source:PATRIC_VF");
            query.setFields("source,source_id");

            apiResponse = dataApi.solrQuery(SolrCore.SPECIALTY_GENE, query);

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

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

            for (Map doc : sdl) {
                virulenceFactor = new HashMap<>();

                virulenceFactor.put("source", doc.get("source").toString());
                virulenceFactor.put("sourceId", doc.get("source_id").toString());
            }

            request.setAttribute("feature", feature);
            request.setAttribute("listReleateFeatures", listReleateFeatures);
            request.setAttribute("listUniprotkbAccessions", listUniprotkbAccessions);
            request.setAttribute("listUniprotIds", listUniprotIds);
            request.setAttribute("refseqLink", refseqLink);
            request.setAttribute("refseqLocusTag", refseqLocusTag);
            request.setAttribute("virulenceFactor", virulenceFactor);

            PortletRequestDispatcher prd = getPortletContext()
                    .getRequestDispatcher("/WEB-INF/jsp/overview/feature_properties.jsp");
            prd.include(request, response);
        } else {
            PrintWriter writer = response.getWriter();
            writer.write(" ");
            writer.close();
        }
    } else {
        PrintWriter writer = response.getWriter();
        writer.write("<p>Invalid Parameter - missing context information</p>");
        writer.close();
    }
}

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

License:Apache License

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

    String sequenceId = request.getParameter("sequence_id");

    DataApiHandler dataApi = new DataApiHandler(request);
    String SequenceString = null;
    SolrQuery query = new SolrQuery("sequence_id:" + sequenceId);
    query.setFields("sequence");

    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) {
        SequenceString = sequence.getSequence();
    }/*  w w w  .ja  va  2 s  .c om*/

    response.getWriter().println(SequenceString);
}

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

License:Apache License

private Map processGlobalSearchFeature(ResourceRequest request) throws IOException {

    DataApiHandler dataApi = new DataApiHandler(request);
    String keyword = request.getParameter("keyword");
    String need = request.getParameter("need");

    SolrQuery query = new SolrQuery(StringHelper.stripQuoteAndParseSolrKeywordOperator(keyword));
    if (need.equals("search")) {
        query.setRows(3).set("hl", "on").set("hl.fl", "*");
    } else {// w ww  .  java 2s .c  om
        query.setRows(dataApi.MAX_ROWS);
    }

    query.setFields(StringUtils.join(DownloadHelper.getFieldsForFeatures(), ","));
    query.addFilterQuery("!feature_type:source");
    query.addFilterQuery("!annotation:BRC1");

    LOGGER.trace("processGlobalSearch: [{}] {}", SolrCore.FEATURE.getSolrCoreName(), query);
    String apiResponse = dataApi.solrQuery(SolrCore.FEATURE, query);

    Map resp = jsonReader.readValue(apiResponse);

    return resp;
}

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

License:Apache License

private Map processGlobalSearchGenome(ResourceRequest request) throws IOException {

    DataApiHandler dataApi = new DataApiHandler(request);
    String keyword = request.getParameter("keyword");
    String need = request.getParameter("need");

    SolrQuery query = new SolrQuery(StringHelper.stripQuoteAndParseSolrKeywordOperator(keyword));
    if (need.equals("search")) {
        query.setRows(3).set("hl", "on").set("hl.fl", "*");
    } else {//from   www .  java  2 s .  com
        query.setRows(dataApi.MAX_ROWS);
    }

    query.setFields(StringUtils.join(DownloadHelper.getFieldsForGenomes(), ","));

    LOGGER.trace("processGlobalSearch: [{}] {}", SolrCore.GENOME.getSolrCoreName(), query);
    String apiResponse = dataApi.solrQuery(SolrCore.GENOME, query);

    Map resp = jsonReader.readValue(apiResponse);

    return resp;
}

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

License:Apache License

private Map processGlobalSearchTaxonomy(ResourceRequest request) throws IOException {

    DataApiHandler dataApi = new DataApiHandler(request);
    String keyword = request.getParameter("keyword");
    String need = request.getParameter("need");

    SolrQuery query = new SolrQuery(StringHelper.stripQuoteAndParseSolrKeywordOperator(keyword));
    if (need.equals("search")) {
        query.setRows(3).set("hl", "on").set("hl.fl", "*");
    } else {//from  ww  w .j  ava2s .c  o m
        query.setRows(dataApi.MAX_ROWS);
    }

    query.setFields("taxon_id,taxon_name,taxon_rank,genomes");

    LOGGER.trace("processGlobalSearch: [{}] {}", SolrCore.TAXONOMY.getSolrCoreName(), query);
    String apiResponse = dataApi.solrQuery(SolrCore.TAXONOMY, query);

    Map resp = jsonReader.readValue(apiResponse);

    return resp;
}

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

License:Apache License

private Map processGlobalSearchExperiment(ResourceRequest request) throws IOException {

    DataApiHandler dataApi = new DataApiHandler(request);
    String keyword = request.getParameter("keyword");
    String need = request.getParameter("need");

    SolrQuery query = new SolrQuery(StringHelper.stripQuoteAndParseSolrKeywordOperator(keyword));
    if (need.equals("search")) {
        query.setRows(3).set("hl", "on").set("hl.fl", "*");
    } else {/* ww w . j a  v  a2s  .co m*/
        query.setRows(dataApi.MAX_ROWS);
    }

    query.setFields("eid,accession,title,description,organism,strain,mutant,timeseries,condition");

    LOGGER.trace("processGlobalSearch: [{}] {}", SolrCore.TRANSCRIPTOMICS_EXPERIMENT.getSolrCoreName(), query);
    String apiResponse = dataApi.solrQuery(SolrCore.TRANSCRIPTOMICS_EXPERIMENT, query);

    Map resp = jsonReader.readValue(apiResponse);

    return resp;
}

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  ww.  j  a  v  a2  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;
}

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

License:Apache License

@SuppressWarnings("unchecked")
private JSONObject processEcNumberTab(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 ww .  j a  v  a 2s  .co  m*/

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

    if (annotation != null && !annotation.equals("")) {
        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<>();
        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("processEcNumberTab: [{}] {}", 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(1000000, listPathwayIds.size()));

            LOGGER.trace("processEcNumberTab: [{}] {}", 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
    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;
}

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

License:Apache License

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

    LOGGER.debug("pathwayId:{}, ecNumber:{}, annotation:{}, taxonId:{}, genomeId:{}, keyword:{}", pathwayId,
            ecNumber, annotation, taxonId, genomeId, keyword);

    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  2s .c o  m*/

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

    if (annotation != null && !annotation.equals("")) {
        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> listFeatureIds = new HashSet<>();

        query.setFields("pathway_id,pathway_name,feature_id,ec_number,ec_description");
        query.setRows(dataApi.MAX_ROWS);

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

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

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

        Map<String, Map> mapStat = new HashMap<>();
        for (Map doc : sdl) {

            mapStat.put(doc.get("feature_id").toString(), doc);
            listFeatureIds.add(doc.get("feature_id").toString());
        }

        // get pathway list
        if (!listFeatureIds.isEmpty()) {
            SolrQuery featureQuery = new SolrQuery(
                    "feature_id:(" + StringUtils.join(listFeatureIds, " OR ") + ")");
            featureQuery.setFields(
                    "genome_name,genome_id,accession,alt_locus_tag,refseq_locus_tag,patric_id,feature_id,gene,product");
            featureQuery.setRows(Math.max(dataApi.MAX_ROWS, listFeatureIds.size()));

            LOGGER.trace("processGeneTab: [{}] {}", SolrCore.FEATURE.getSolrCoreName(), featureQuery);

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

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

            for (GenomeFeature feature : features) {
                String featureId = feature.getId();
                Map stat = mapStat.get(featureId);

                JSONObject item = new JSONObject();
                item.put("genome_name", feature.getGenomeName());
                item.put("genome_id", feature.getGenomeId());
                item.put("accession", feature.getAccession());
                item.put("feature_id", feature.getId());
                item.put("alt_locus_tag", feature.getAltLocusTag());
                item.put("refseq_locus_tag", feature.getRefseqLocusTag());
                item.put("algorithm", annotation);
                item.put("patric_id", feature.getPatricId());
                item.put("gene", feature.getGene());
                item.put("product", feature.getProduct());

                item.put("ec_name", stat.get("ec_description"));
                item.put("ec_number", stat.get("ec_number"));
                item.put("pathway_id", stat.get("pathway_id"));
                item.put("pathway_name", stat.get("pathway_name"));

                items.add(item);
            }
            count_total = items.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;
}

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

License:Apache License

@SuppressWarnings("unchecked")
public void serveResource(ResourceRequest request, ResourceResponse response)
        throws PortletException, IOException {

    response.setContentType("application/json");

    HashMap<String, String> key = new HashMap<>();

    if (request.getParameter("id") != null) {
        key.put("feature_id", request.getParameter("id"));
    }//  w  w w . ja  v  a 2  s. c om

    DataApiHandler dataApi = new DataApiHandler(request);

    int count_total = 0;
    JSONArray results = new JSONArray();
    List<String> pathwayKeys = new ArrayList<>();
    Map<String, Integer> mapOccurrence = new HashMap<>();
    try {
        SolrQuery query = new SolrQuery("feature_id:" + request.getParameter("id"));
        query.setRows(dataApi.MAX_ROWS);

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

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

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

        for (Map doc : sdl) {
            String pathwayKey = "(pathway_id:" + doc.get("pathway_id").toString() + " AND ec_number:"
                    + doc.get("ec_number").toString() + ")";

            pathwayKeys.add(pathwayKey);
        }

        SolrQuery queryRef = new SolrQuery(StringUtils.join(pathwayKeys, " OR "));
        queryRef.setFields("pathway_id,ec_number,occurrence");
        queryRef.setRows(pathwayKeys.size());

        apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, queryRef);

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

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

        for (Map doc : refList) {
            mapOccurrence.put(doc.get("pathway_id") + "_" + doc.get("ec_number"),
                    (Integer) doc.get("occurrence"));
        }

        for (Map doc : sdl) {
            JSONObject item = new JSONObject();
            item.put("pathway_id", doc.get("pathway_id"));
            item.put("feature_id", doc.get("feature_id"));
            item.put("pathway_name", doc.get("pathway_name"));
            item.put("pathway_class", doc.get("pathway_class"));
            item.put("algorithm", doc.get("annotation"));
            item.put("ec_number", doc.get("ec_number"));
            item.put("ec_name", doc.get("ec_description"));
            item.put("taxon_id", doc.get("taxon_id"));
            item.put("genome_id", doc.get("genome_id"));

            item.put("occurrence", mapOccurrence.get(doc.get("pathway_id") + "_" + doc.get("ec_number")));

            results.add(item);
        }
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    JSONObject jsonResult = new JSONObject();

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

    PrintWriter writer = response.getWriter();
    jsonResult.writeJSONString(writer);
    writer.close();
}