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

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

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Introduction

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

Prototype

public SolrQuery setRows(Integer rows)

Source Link

Usage

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);
    }//ww w .  j  a va  2  s.  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);
    }/*  ww w  .jav a  2 s.com*/

    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"));
    }/*from   w w w.  j a  va 2s.c o m*/

    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();
}

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

License:Apache License

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

    response.setContentType("application/json");

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

    if (callType != null && callType.equals("savetopk")) {

        String cId = request.getParameter("cId");
        String cType = request.getParameter("cType");
        String map = request.getParameter("map");
        String algorithm = request.getParameter("algorithm");
        String ec_number = request.getParameter("ec_number");

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

        if (cId != null && !cId.equals("")) {
            key.put("genomeId", cId);
        }//from ww  w  . jav  a 2s .co m
        if (cType != null && !cType.equals("")) {
            key.put("cType", cType);
        }

        if (map != null && !map.equals("")) {
            key.put("map", map);
        }

        if (algorithm != null && !algorithm.equals("")) {
            key.put("algorithm", algorithm);
        }

        if (ec_number != null && !ec_number.equals("")) {
            key.put("ec_number", ec_number);
        }

        key.put("which", "download_from_heatmap_feature");

        long pk = (new Random()).nextLong();

        SessionHandler.getInstance().set(SessionHandler.PREFIX + pk, jsonWriter.writeValueAsString(key));

        PrintWriter writer = response.getWriter();
        writer.write("" + pk);
        writer.close();

    } else if (callType != null && callType.equals("show")) {

        JSONObject jsonResult = new JSONObject();
        JSONArray results = new JSONArray();
        String pk = request.getParameter("pk");
        Map<String, String> key = jsonReader
                .readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));

        DataApiHandler dataApi = new DataApiHandler(request);
        try {
            SolrQuery query = new SolrQuery("*:*");
            List<String> joinConditions = new ArrayList<>();

            if (key.containsKey("map")) {
                joinConditions.add("pathway_id:(" + key.get("map") + ")");
            }
            if (key.containsKey("algorithm")) {
                joinConditions.add("annotation:(" + key.get("algorithm") + ")");
            }
            if (key.containsKey("ec_number")) {
                joinConditions.add("ec_number:(" + key.get("ec_number").replaceAll(",", " OR ") + ")");
            }
            if (key.containsKey("genomeId")) {
                joinConditions.add("genome_id:(" + key.get("genomeId").replace(",", " OR ") + ")");
            }

            if (!joinConditions.isEmpty()) {
                query.addFilterQuery(SolrCore.PATHWAY.getSolrCoreJoin("feature_id", "feature_id",
                        StringUtils.join(joinConditions, " AND ")));
            }
            query.setRows(10000);

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

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

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

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

            for (GenomeFeature feature : features) {

                results.add(feature.toJSONObject());
            }

            jsonResult.put("total", numFound);
            jsonResult.put("results", results);
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }

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

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

License:Apache License

protected void doView(RenderRequest request, RenderResponse response) throws PortletException, IOException {
    response.setContentType("text/html");

    SiteHelper.setHtmlMetaElements(request, response, "Phylogeny");

    List<Integer> phylogenyOrderIds = Arrays.asList(2037, 1385, 80840, 213849, 51291, 186802, 91347, 186826,
            118969, 356, 766, 136, 72273, 135623);

    String contextType = request.getParameter("context_type");
    String contextId = request.getParameter("context_id");

    if (contextType != null && contextId != null) {

        DataApiHandler dataApi = new DataApiHandler(request);

        List<Map<String, Object>> orderList = new ArrayList<>();
        int taxonId = 0;

        try {/*  ww w. j av a  2s  .  c  o  m*/
            if (contextType.equals("genome")) {

                Genome genome = dataApi.getGenome(contextId);
                taxonId = genome.getTaxonId();
            } else {
                taxonId = Integer.parseInt(contextId);
            }

            // Step1. has Order in lineage?
            Taxonomy taxonomy = dataApi.getTaxonomy(taxonId);

            List<String> lineageRanks = taxonomy.getLineageRanks();

            if (lineageRanks.contains("order")) {
                List<Integer> lineageIds = taxonomy.getLineageIds();
                List<String> lineageNames = taxonomy.getLineageNames();

                int index = lineageRanks.indexOf("order");
                int orderTaxonId = lineageIds.get(index);

                if (phylogenyOrderIds.contains(orderTaxonId)) {
                    Map order = new HashMap();
                    order.put("name", lineageNames.get(index));
                    order.put("taxonId", lineageIds.get(index));

                    orderList.add(order);
                }
            }

            if (orderList.isEmpty()) {
                // no rank Order found in lineage, then,
                // Step2. has Order rank in descendants
                SolrQuery query = new SolrQuery(
                        "lineage_ids:" + taxonId + " AND taxon_rank:order AND taxon_id:("
                                + StringUtils.join(phylogenyOrderIds, " OR ") + ")");
                query.setFields("taxon_id,taxon_name,taxon_rank");
                query.setRows(100);

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

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

                List<Map> sdl = (List<Map>) respBody.get("docs");
                for (Map doc : sdl) {
                    if (doc.get("taxon_rank").equals("order")) {
                        Map node = new HashMap<>();
                        node.put("taxonId", doc.get("taxon_id"));
                        node.put("name", doc.get("taxon_name").toString());

                        orderList.add(node);
                    }
                }
            }
        } catch (MalformedURLException e) {
            LOGGER.error(e.getMessage(), e);
        }

        request.setAttribute("orderList", orderList);
        request.setAttribute("taxonId", taxonId);

        PortletRequestDispatcher prd = getPortletContext().getRequestDispatcher("/index.jsp");
        prd.include(request, response);
    }
}

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

License:Apache License

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

    String contextType = request.getParameter("context_type");
    String contextId = request.getParameter("context_id");
    String genomeFilter = request.getParameter("genome_filter");

    DataApiHandler dataApi = new DataApiHandler(request);

    if (contextType != null && contextId != null) {

        if (contextType.equals("genome")) {

            Genome genome = dataApi.getGenome(contextId);

            if (genome != null) {

                // check genome_amr data is available.
                SolrQuery query = new SolrQuery("genome_id:" + genome.getId());
                query.addSort("antibiotic", SolrQuery.ORDER.asc).addSort("resistant_phenotype",
                        SolrQuery.ORDER.asc);
                query.setRows(dataApi.MAX_ROWS);
                dataApi = new DataApiHandler(request);
                String apiResponse = dataApi.solrQuery(SolrCore.GENOME_AMR, query);

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

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

                request.setAttribute("genome", genome);
                request.setAttribute("amr", amr);

                response.setContentType("text/html");
                PortletRequestDispatcher prd = getPortletContext()
                        .getRequestDispatcher("/WEB-INF/jsp/overview/sequence_summary.jsp");
                prd.include(request, response);
            }/*from  w w  w.j  a  v a 2  s  .  c  o  m*/
        } else {
            // taxon level

            List<String> annotations = Arrays.asList("PATRIC", "RefSeq");

            for (String annotation : annotations) {

                String queryParam;

                switch (annotation) {
                case "PATRIC":
                    queryParam = "patric_cds:[1 TO *]";
                    break;
                case "RefSeq":
                    queryParam = "refseq_cds:[1 TO *]";
                    break;
                default:
                    queryParam = "*:*";
                    break;
                }

                if (genomeFilter != null && !genomeFilter.equals("")) {
                    queryParam += " AND (" + genomeFilter + ")";
                }

                Map counts = dataApi.getFieldFacets(SolrCore.GENOME, queryParam,
                        "taxon_lineage_ids:" + contextId, "genome_status");

                request.setAttribute(annotation, counts);
            }

            response.setContentType("text/html");
            PortletRequestDispatcher prd = getPortletContext()
                    .getRequestDispatcher("/WEB-INF/jsp/overview/sequence_summary.jsp");
            prd.include(request, response);
        }
    }
}

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

License:Apache License

public void serveResource(ResourceRequest request, ResourceResponse response)
        throws PortletException, IOException {
    int taxonId = Integer.parseInt(request.getParameter("taxonId"));
    String mode = request.getParameter("mode");

    DataApiHandler dataApi = new DataApiHandler(request);
    JSONArray tree;/*w  w  w.  j  a  v a2  s  .c  o  m*/
    response.setContentType("application/json");

    switch (mode) {
    case "txtree":
        tree = OrganismTreeBuilder.buildGenomeTree(dataApi, taxonId);
        tree.writeJSONString(response.getWriter());
        break;
    case "azlist":
        tree = OrganismTreeBuilder.buildGenomeList(dataApi, taxonId);
        tree.writeJSONString(response.getWriter());
        break;
    case "tgm":
        tree = OrganismTreeBuilder.buildTaxonGenomeMapping(dataApi, taxonId);
        tree.writeJSONString(response.getWriter());
        break;
    case "search":
        String searchOn = request.getParameter("searchon");
        String keyword = request.getParameter("query");

        tree = new JSONArray();
        SolrQuery query = new SolrQuery();
        if (searchOn.equals("txtree")) {
            query.setQuery("taxon_name:" + keyword + " AND genomes:[1 TO *] AND lineage_ids:" + taxonId);
            query.setRows(10000).addField("taxon_name,taxon_id");

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

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

            for (Taxonomy taxon : taxonomyList) {
                JSONObject item = new JSONObject();
                item.put("display_name", taxon.getTaxonName());
                item.put("taxon_id", taxon.getId());

                tree.add(item);
            }
        } else {
            // searchOn is "azlist"
            query.setQuery("genome_name:" + keyword + " AND taxon_lineage_ids:" + taxonId);
            query.setRows(10000).addField("genome_name,genome_id");

            String apiResponse = dataApi.solrQuery(SolrCore.TAXONOMY, 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) {
                JSONObject item = new JSONObject();
                item.put("display_name", genome.getGenomeName());
                item.put("genome_id", genome.getId());

                tree.add(item);
            }
        }

        JSONObject result = new JSONObject();
        result.put("genomeList", tree);
        result.put("keyword", keyword);
        result.put("totalCount", tree.size());

        result.writeJSONString(response.getWriter());
        break;
    default:
        tree = new JSONArray();
        tree.writeJSONString(response.getWriter());
        break;
    }
}

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

License:Apache License

protected void doView(RenderRequest request, RenderResponse response) throws PortletException, IOException {
    response.setContentType("text/html");
    response.setTitle("TB");

    int mtbTaxon = 77643;
    DataApiHandler dataApi = new DataApiHandler(request);

    Map<Integer, Integer> genomes = new HashMap<>();
    int cntExperiments = -1;

    // getting genome count
    {/*from  w w  w .java  2  s  .c  o  m*/
        SolrQuery query = new SolrQuery("taxon_id:(1773 OR 77643)");
        query.setRows(2).addField("taxon_id,genomes");

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

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

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

        for (Taxonomy taxonomy : taxonomyList) {
            genomes.put(taxonomy.getId(), taxonomy.getGenomeCount());
        }
    }

    // getting expression data count
    {
        SolrQuery query = new SolrQuery("*:*");
        query.setRows(0).addFilterQuery(
                SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_ids", "taxon_lineage_ids:1763"));

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

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

        cntExperiments = (Integer) respBody.get("numFound");
    }
    request.setAttribute("genomes", genomes);
    request.setAttribute("cntExperiments", cntExperiments);
    request.setAttribute("mtbTaxon", mtbTaxon);

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

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

License:Apache License

private JSONObject getEnrichmentPathway(ResourceRequest request, List<String> featureIDs) throws IOException {

    DataApiHandler dataApi = new DataApiHandler(request);

    // 1. get Pathway ID, Pathway Name & genomeID
    //solr/pathway/select?q=feature_id:(PATRIC.83332.12.NC_000962.CDS.34.1524.fwd)&fl=pathway_name,pathway_id,gid

    Map<String, JSONObject> pathwayMap = new LinkedHashMap<>();
    Set<String> listFeatureID = new HashSet<>();
    Set<String> listGenomeID = new HashSet<>();
    Set<String> listPathwayID = new HashSet<>();

    SolrQuery query = new SolrQuery("feature_id:(" + StringUtils.join(featureIDs, " OR ") + ")");
    int queryRows = Math.max(dataApi.MAX_ROWS, (featureIDs.size() * 2));
    query.addField("pathway_name,pathway_id,genome_id,feature_id").setRows(queryRows);

    LOGGER.trace("Enrichment 1/3: [{}] {}", SolrCore.PATHWAY.getSolrCoreName(), query);

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

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

    for (Map doc : pathwayList) {
        JSONObject pw = new JSONObject();
        pw.put("pathway_id", doc.get("pathway_id"));
        pw.put("pathway_name", doc.get("pathway_name"));
        pathwayMap.put(doc.get("pathway_id").toString(), pw);

        // LOGGER.debug("{}", pw.toJSONString());
        listFeatureID.add(doc.get("feature_id").toString());
        listGenomeID.add(doc.get("genome_id").toString());
        listPathwayID.add(doc.get("pathway_id").toString());
    }//from www .j  ava  2 s.co m

    // 2. get pathway ID & Ocnt
    //solr/pathway/select?q=feature_id:(PATRIC.83332.12.NC_000962.CDS.34.1524.fwd)&rows=0&facet=true
    // &json.facet={stat:{field:{field:pathway_id,limit:-1,facet:{gene_count:"unique(feature_id)"}}}}
    query = new SolrQuery("feature_id:(" + StringUtils.join(featureIDs, " OR ") + ")");
    query.setRows(0).setFacet(true);
    query.add("json.facet",
            "{stat:{field:{field:pathway_id,limit:-1,facet:{gene_count:\"unique(feature_id)\"}}}}");

    LOGGER.trace("Enrichment 2/3: [{}] {}", SolrCore.PATHWAY.getSolrCoreName(),
            URLDecoder.decode(query.toString(), "UTF-8"));

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

    resp = jsonReader.readValue(apiResponse);
    Map facets = (Map) resp.get("facets");
    if ((Integer) facets.get("count") > 0) {
        Map stat = (Map) facets.get("stat");
        List<Map> buckets = (List) stat.get("buckets");

        for (Map value : buckets) {
            String aPathwayId = value.get("val").toString();

            if (pathwayMap.containsKey(aPathwayId)) {
                pathwayMap.get(aPathwayId).put("ocnt", value.get("gene_count"));
            }
        }
    }

    // 3. with genomeID, get pathway ID & Ecnt
    //solr/pathway/select?q=genome_id:83332.12 AND pathway_id:(00230 OR 00240)&fq=annotation:PATRIC&rows=0&facet=true //&facet.mincount=1&facet.limit=-1
    // &json.facet={stat:{field:{field:pathway_id,limit:-1,facet:{gene_count:"unique(feature_id)"}}}}
    if (!listGenomeID.isEmpty() && !listPathwayID.isEmpty()) {
        query = new SolrQuery("genome_id:(" + StringUtils.join(listGenomeID, " OR ") + ") AND pathway_id:("
                + StringUtils.join(listPathwayID, " OR ") + ")");
        query.setRows(0).setFacet(true).addFilterQuery("annotation:PATRIC");
        query.add("json.facet",
                "{stat:{field:{field:pathway_id,limit:-1,facet:{gene_count:\"unique(feature_id)\"}}}}");

        LOGGER.trace("Enrichment 3/3: {}", query.toString());

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

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

        for (Map value : buckets) {
            pathwayMap.get(value.get("val").toString()).put("ecnt", value.get("gene_count"));
        }
    }

    // 4. Merge hash and calculate percentage on the fly
    JSONObject jsonResult = new JSONObject();
    JSONArray results = new JSONArray();
    for (JSONObject item : pathwayMap.values()) {
        if (item.get("ecnt") != null && item.get("ocnt") != null) {
            float ecnt = Float.parseFloat(item.get("ecnt").toString());
            float ocnt = Float.parseFloat(item.get("ocnt").toString());
            float percentage = ocnt / ecnt * 100;
            item.put("percentage", (int) percentage);
            results.add(item);
        }
    }
    jsonResult.put("results", results);
    jsonResult.put("total", results.size());
    jsonResult.put("featureRequested", featureIDs.size());
    jsonResult.put("featureFound", listFeatureID.size());

    return jsonResult;
}

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

License:Apache License

public void serveResource(ResourceRequest request, ResourceResponse response)
        throws PortletException, IOException {
    String callType = request.getParameter("callType");

    if (callType != null) {
        switch (callType) {
        case "saveParams": {

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

            Map<String, String> key = new HashMap<>();
            key.put("keyword", "locus_tag:(" + keyword + ") OR refseq_locus_tag:(" + keyword + ") ");
            key.put("fields", "pid");

            SolrQuery query = dataApi.buildSolrQuery(key, null, null, 0, -1, false);

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

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

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

            Set<String> sampleIds = new HashSet<>();

            for (Map doc : sdl) {
                sampleIds.add(doc.get("pid").toString());
            }/*from  w ww  . ja  v  a  2s .  c  o  m*/

            String sId = StringUtils.join(sampleIds, ",");

            key = new HashMap();
            if (!keyword.equals("")) {
                key.put("keyword", keyword);
            }

            response.setContentType("text/html");
            PrintWriter writer = response.getWriter();

            if (!sId.equals("")) {
                key.put("sampleId", sId);
                long pk = (new Random()).nextLong();

                SessionHandler.getInstance().set(SessionHandler.PREFIX + pk,
                        jsonWriter.writeValueAsString(key));

                writer.write("" + pk);
            } else {
                writer.write("");
            }
            writer.close();

            break;
        }
        case "getTables": {

            String expId = request.getParameter("expId");
            String sampleId = request.getParameter("sampleId");
            String wsExperimentId = request.getParameter("wsExperimentId");
            String wsSampleId = request.getParameter("wsSampleId");
            String keyword = request.getParameter("keyword");
            DataApiHandler dataApi = new DataApiHandler(request);

            JSONArray sample = new JSONArray();

            if ((sampleId != null && !sampleId.equals("")) || (expId != null && !expId.equals(""))) {

                String query_keyword = "";

                if (expId != null && !expId.equals("")) {
                    query_keyword += "eid:(" + expId.replaceAll(",", " OR ") + ")";
                }

                if (sampleId != null && !sampleId.equals("")) {
                    if (query_keyword.length() > 0) {
                        query_keyword += " AND ";
                    }
                    query_keyword += "pid:(" + sampleId.replaceAll(",", " OR ") + ")";
                }

                Map<String, String> key = new HashMap<>();
                key.put("keyword", query_keyword);
                key.put("fields", "pid,expname,expmean,timepoint,mutant,strain,condition");

                SolrQuery query = dataApi.buildSolrQuery(key, null, null, 0, -1, false);

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

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

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

                for (final Map doc : sdl) {
                    final JSONObject item = new JSONObject(doc);
                    sample.add(item);
                }
            }

            // Read from JSON if collection parameter is there
            ExpressionDataCollection parser = null;
            if (wsExperimentId != null && !wsExperimentId.equals("")) {
                String token = getAuthorizationToken(request);

                parser = new ExpressionDataCollection(wsExperimentId, token);
                parser.read(ExpressionDataCollection.CONTENT_SAMPLE);
                if (wsSampleId != null && !wsSampleId.equals("")) {
                    parser.filter(wsSampleId, ExpressionDataCollection.CONTENT_SAMPLE);
                }
                // Append samples from collection to samples from DB
                sample = parser.append(sample, ExpressionDataCollection.CONTENT_SAMPLE);
            }

            String sampleList = "";
            sampleList += ((JSONObject) sample.get(0)).get("pid");

            for (int i = 1; i < sample.size(); i++) {
                sampleList += "," + ((JSONObject) sample.get(i)).get("pid");
            }

            JSONObject jsonResult = new JSONObject();
            jsonResult.put(ExpressionDataCollection.CONTENT_SAMPLE + "Total", sample.size());
            jsonResult.put(ExpressionDataCollection.CONTENT_SAMPLE, sample);
            JSONArray expression = new JSONArray();

            if ((sampleId != null && !sampleId.equals("")) || (expId != null && !expId.equals(""))) {

                String query_keyword = "";

                if (keyword != null && !keyword.equals("")) {
                    query_keyword += "(alt_locus_tag:(" + keyword + ") OR refseq_locus_tag:(" + keyword + ")) ";
                }

                if (expId != null && !expId.equals("")) {
                    if (query_keyword.length() > 0) {
                        query_keyword += " AND ";
                    }
                    query_keyword += "eid:(" + expId.replaceAll(",", " OR ") + ")";
                }

                if (sampleId != null && !sampleId.equals("")) {
                    if (query_keyword.length() > 0) {
                        query_keyword += " AND ";
                    }
                    query_keyword += "pid:(" + sampleId.replaceAll(",", " OR ") + ")";
                }

                Map<String, String> key = new HashMap<>();
                key.put("keyword", query_keyword);
                key.put("fields", "pid,refseq_locus_tag,feature_id,log_ratio,z_score");

                SolrQuery query = dataApi.buildSolrQuery(key, null, null, 0, -1, false);

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

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

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

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

                for (final Map doc : sdl) {
                    final JSONObject item = new JSONObject(doc);
                    expression.add(item);
                }

                // TODO: re-implement when data API removes limit 25k records
                int start = 0;
                int fetchedSize = sdl.size();
                while (fetchedSize == 25000) {
                    start += 25000;
                    query.setStart(start);

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

                    final String apiResponseSub = dataApi.solrQuery(SolrCore.TRANSCRIPTOMICS_GENE, query);
                    final Map respSub = jsonReader.readValue(apiResponseSub);
                    final Map respBodySub = (Map) respSub.get("response");

                    sdl = (List<Map>) respBodySub.get("docs");
                    fetchedSize = sdl.size();

                    for (final Map doc : sdl) {
                        final JSONObject item = new JSONObject(doc);
                        expression.add(item);
                    }
                }
            }

            if (wsExperimentId != null && !wsExperimentId.equals("")) {

                parser.read(ExpressionDataCollection.CONTENT_EXPRESSION);
                if (wsSampleId != null && !wsSampleId.equals(""))
                    parser.filter(wsSampleId, ExpressionDataCollection.CONTENT_EXPRESSION);

                // Append expression from collection to expression from DB
                expression = parser.append(expression, ExpressionDataCollection.CONTENT_EXPRESSION);
            }

            JSONArray stats = getExperimentStats(dataApi, expression, sampleList, sample);
            jsonResult.put(ExpressionDataCollection.CONTENT_EXPRESSION + "Total", stats.size());
            jsonResult.put(ExpressionDataCollection.CONTENT_EXPRESSION, stats);

            response.setContentType("application/json");
            PrintWriter writer = response.getWriter();
            jsonResult.writeJSONString(writer);
            writer.close();

            break;
        }
        case "doClustering": {

            String data = request.getParameter("data");
            String g = request.getParameter("g");
            String e = request.getParameter("e");
            String m = request.getParameter("m");
            String ge = request.getParameter("ge");
            String pk = request.getParameter("pk");
            String action = request.getParameter("action");

            String folder = "/tmp/";
            String filename = folder + "tmp_" + pk + ".txt";
            String output_filename = folder + "cluster_tmp_" + pk;
            try {

                PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(filename, true)));
                out.write(data);
                out.close();

            } catch (Exception es) {
                LOGGER.error(es.getMessage(), es);
            }

            response.setContentType("text/html");
            PrintWriter writer = response.getWriter();
            if (action.equals("Run"))
                writer.write(doCLustering(filename, output_filename, g, e, m, ge).toString());

            writer.close();

            break;
        }
        case "saveState": {

            String keyType = request.getParameter("keyType");
            String pageAt = request.getParameter("pageAt");
            String sampleFilter = request.getParameter("sampleFilter");
            String regex = request.getParameter("regex");
            String regexGN = request.getParameter("regexGN");
            String upFold = request.getParameter("upFold");
            String downFold = request.getParameter("downFold");
            String upZscore = request.getParameter("upZscore");
            String downZscore = request.getParameter("downZscore");
            String significantGenes = request.getParameter("significantGenes");
            String ClusterColumnOrder = request.getParameter("ClusterColumnOrder");
            String ClusterRowOrder = request.getParameter("ClusterRowOrder");
            String heatmapState = request.getParameter("heatmapState");
            String heatmapAxis = request.getParameter("heatmapAxis");
            String colorScheme = request.getParameter("colorScheme");
            String filterOffset = request.getParameter("filterOffset");

            Map<String, String> key = new HashMap<>();
            key.put("sampleFilter", (sampleFilter == null) ? "" : sampleFilter);
            key.put("pageAt", (pageAt == null) ? "" : pageAt);
            key.put("regex", (regex == null) ? "" : regex);
            key.put("regexGN", (regexGN == null) ? "" : regexGN);
            key.put("upFold", (upFold == null) ? "" : upFold);
            key.put("downFold", (downFold == null) ? "" : downFold);
            key.put("upZscore", (upZscore == null) ? "" : upZscore);
            key.put("downZscore", (downZscore == null) ? "" : downZscore);
            key.put("significantGenes", (significantGenes == null) ? "" : significantGenes);
            key.put("ClusterRowOrder", (ClusterRowOrder == null) ? "" : ClusterRowOrder);
            key.put("ClusterColumnOrder", (ClusterColumnOrder == null) ? "" : ClusterColumnOrder);
            key.put("heatmapState", (heatmapState == null) ? "" : heatmapState);
            key.put("heatmapAxis", (heatmapAxis == null) ? "" : heatmapAxis);
            key.put("colorScheme", (colorScheme == null) ? "" : colorScheme);
            key.put("filterOffset", (filterOffset == null) ? "" : filterOffset);

            long pk = (new Random()).nextLong();
            SessionHandler.getInstance().set(SessionHandler.PREFIX + pk, jsonWriter.writeValueAsString(key));

            response.setContentType("text/html");
            PrintWriter writer = response.getWriter();
            writer.write("" + pk);
            writer.close();

            break;
        }
        case "getState": {

            String keyType = request.getParameter("keyType");
            String pk = request.getParameter("random");

            if ((pk != null) && (keyType != null)) {
                JSONArray results = new JSONArray();
                JSONObject a = new JSONObject();
                Map<String, String> key = jsonReader
                        .readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));
                if (key != null) {
                    a.put("sampleFilter", key.get("sampleFilter"));
                    a.put("pageAt", key.get("pageAt"));
                    a.put("regex", key.get("regex"));
                    a.put("regexGN", key.get("regexGN"));
                    a.put("upFold", key.get("upFold"));
                    a.put("downFold", key.get("downFold"));
                    a.put("upZscore", key.get("upZscore"));
                    a.put("downZscore", key.get("downZscore"));
                    a.put("significantGenes", key.get("significantGenes"));
                    a.put("ClusterRowOrder", key.get("ClusterRowOrder"));
                    a.put("ClusterColumnOrder", key.get("ClusterColumnOrder"));
                    a.put("heatmapState", key.get("heatmapState"));
                    a.put("heatmapAxis", key.get("heatmapAxis"));
                    a.put("colorScheme", key.get("colorScheme"));
                    a.put("filterOffset", key.get("filterOffset"));
                }
                results.add(a);
                response.setContentType("application/json");
                PrintWriter writer = response.getWriter();
                results.writeJSONString(writer);
                writer.close();
            }
            break;
        }
        case "downloadFeatures": {
            String featureIds = request.getParameter("featureIds");
            String fileFormat = request.getParameter("fileFormat");
            String fileName = "Table_Gene";

            List<String> tableHeader = DownloadHelper.getHeaderForFeatures();
            List<String> tableField = DownloadHelper.getFieldsForFeatures();
            JSONArray tableSource = new JSONArray();

            DataApiHandler dataApi = new DataApiHandler(request);

            SolrQuery query = new SolrQuery("feature_id:(" + featureIds.replaceAll(",", " OR ") + ")");
            query.setFields(StringUtils.join(DownloadHelper.getFieldsForFeatures(), ","));
            query.setRows(dataApi.MAX_ROWS);

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

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

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

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

            for (final GenomeFeature feature : features) {
                tableSource.add(feature.toJSONObject());
            }

            final ExcelHelper excel = new ExcelHelper("xssf", tableHeader, tableField, tableSource);
            excel.buildSpreadsheet();

            if (fileFormat.equalsIgnoreCase("xlsx")) {
                response.setContentType("application/octetstream");
                response.addProperty("Content-Disposition",
                        "attachment; filename=\"" + fileName + "." + fileFormat + "\"");

                excel.writeSpreadsheettoBrowser(response.getPortletOutputStream());
            } else {
                response.setContentType("application/octetstream");
                response.addProperty("Content-Disposition",
                        "attachment; filename=\"" + fileName + "." + fileFormat + "\"");

                response.getWriter().write(excel.writeToTextFile());
            }
        }
        }
    }
}