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.common.DataApiHandler.java

License:Apache License

/**
 * wrapper function of field facet query
 *
 * @param core SolrCore/*from   w ww.j  a  va2 s .co  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  .ja  v  a 2s. 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"));
    }//from   w w w  .  j  av  a 2 s  .  co 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.FASTAHelper.java

License:Apache License

public static String getFASTASequence(PortletRequest request, List<String> featureIds, String type)
        throws IOException {
    StringBuilder fasta = new StringBuilder();

    SolrQuery query = new SolrQuery("feature_id:(" + StringUtils.join(featureIds, " OR ") + ")");
    query.setFields(/*from ww w. j av  a2 s.  c o m*/
            "feature_id,patric_id,alt_locus_tag,refseq_locus_tag,annotation,gi,product,genome_id,genome_name,na_sequence,aa_sequence");
    query.setRows(featureIds.size());

    DataApiHandler dataApi = new DataApiHandler(request);
    LOGGER.trace("getFASTASequence: [{}] {}", SolrCore.FEATURE.getSolrCoreName(), query);
    String apiResponse = dataApi.solrQuery(SolrCore.FEATURE, query);
    Map resp = jsonReader.readValue(apiResponse);
    Map respBody = (Map) resp.get("response");

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

    for (GenomeFeature feature : features) {

        if (type.equals("dna") || type.equals("both")) {
            fasta.append(">");
            if (feature.getAnnotation().equals("PATRIC")) {
                if (feature.hasPatricId()) {
                    fasta.append(feature.getPatricId()).append("|");
                }
            } else if (feature.getAnnotation().equals("RefSeq")) {
                if (feature.getGi() > 0) {
                    fasta.append("gi|").append(feature.getGi()).append("|");
                }
            }

            if (feature.hasRefseqLocusTag()) {
                fasta.append(feature.getRefseqLocusTag()).append("|");
            }
            if (feature.hasAltLocusTag()) {
                fasta.append(feature.getAltLocusTag()).append("|");
            }
            if (feature.hasProduct()) {
                fasta.append("   ").append(feature.getProduct());
            }
            fasta.append("   [").append(feature.getGenomeName()).append(" | ").append(feature.getGenomeId())
                    .append("]");

            fasta.append("\n");
            if (feature.hasNaSequence()) {
                fasta.append(StringHelper.chunk_split(feature.getNaSequence(), 60, "\n"));
            }
        }

        if (type.equals("protein") || type.equals("both")) {
            fasta.append(">");
            if (feature.getAnnotation().equals("PATRIC")) {
                if (feature.hasPatricId()) {
                    fasta.append(feature.getPatricId()).append("|");
                }
            } else if (feature.getAnnotation().equals("RefSeq")) {
                if (feature.getGi() > 0) {
                    fasta.append("gi|").append(feature.getGi()).append("|");
                }
            }

            if (feature.hasRefseqLocusTag()) {
                fasta.append(feature.getRefseqLocusTag()).append("|");
            }
            if (feature.hasAltLocusTag()) {
                fasta.append(feature.getAltLocusTag()).append("|");
            }
            if (feature.hasProduct()) {
                fasta.append("   ").append(feature.getProduct());
            }
            fasta.append("   [").append(feature.getGenomeName()).append(" | ").append(feature.getGenomeId())
                    .append("]");

            fasta.append("\n");
            if (feature.hasAaSequence()) {
                fasta.append(StringHelper.chunk_split(feature.getAaSequence(), 60, "\n"));
            }
        }
    }

    return fasta.toString();
}

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);
    String experiment_id = "";

    //      try {
    //         QueryResponse qr = server.query(query);
    //         SolrDocumentList sdl = qr.getResults();
    ///* w ww.jav a2s  . co m*/
    //         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.CompareRegionViewer.java

License:Apache License

@SuppressWarnings("unchecked")
private void printTrackList(ResourceRequest request, ResourceResponse response) throws IOException {

    String contextType = request.getParameter("cType");
    String contextId = request.getParameter("cId");
    String pinFeatureSeedId = request.getParameter("feature"); // pin feature
    String windowSize = request.getParameter("window"); // window size

    int _numRegion = Integer.parseInt(request.getParameter("regions")); // number of genomes to compare
    int _numRegion_buffer = 10; // number of genomes to use as a buffer in case that PATRIC has no genome data,
    // which was retrieved from API
    String _key = "";

    DataApiHandler dataApi = new DataApiHandler(request);

    // if pin feature is not given, retrieve from the database based on na_feature_id
    if (pinFeatureSeedId == null
            && (contextType != null && contextType.equals("feature") && contextId != null)) {

        GenomeFeature feature = dataApi.getFeature(contextId);
        pinFeatureSeedId = feature.getPatricId();
    }/*w  ww  .j  a  v a2s.co  m*/

    if (pinFeatureSeedId != null && !pinFeatureSeedId.equals("") && windowSize != null) {
        CRResultSet crRS = null;

        try {
            SAPserver sapling = new SAPserver("http://servers.nmpdr.org/pseed/sapling/server.cgi");
            crRS = new CRResultSet(pinFeatureSeedId, sapling.compared_regions(pinFeatureSeedId,
                    _numRegion + _numRegion_buffer, Integer.parseInt(windowSize) / 2));

            long pk = (new Random()).nextLong();
            _key = "" + pk;

            Gson gson = new Gson();
            SessionHandler.getInstance().set(SessionHandler.PREFIX + pk, gson.toJson(crRS, CRResultSet.class));
            SessionHandler.getInstance().set(SessionHandler.PREFIX + "_windowsize" + pk, windowSize);

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

        JSONObject trackList = new JSONObject();
        JSONArray tracks = new JSONArray();
        JSONObject trStyle = new JSONObject();
        trStyle.put("className", "feature5");
        trStyle.put("showLabels", false);
        trStyle.put("label", "function( feature ) { return feature.get('patric_id'); }");
        JSONObject trHooks = new JSONObject();
        trHooks.put("modify",
                "function(track, feature, div) { div.style.backgroundColor = ['red','#1F497D','#938953','#4F81BD','#9BBB59','#806482','#4BACC6','#F79646'][feature.get('phase')];}");

        // query genome metadata
        SolrQuery query = new SolrQuery("genome_id:(" + StringUtils.join(crRS.getGenomeIds(), " OR ") + ")");
        query.setFields(
                "genome_id,genome_name,isolation_country,host_name,disease,collection_date,completion_date");
        query.setRows(_numRegion + _numRegion_buffer);

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

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

        int count_genomes = 1;
        if (crRS.getGenomeNames().size() > 0) {
            for (Integer idx : crRS.getTrackMap().keySet()) {
                if (count_genomes > _numRegion) {
                    break;
                }
                CRTrack crTrack = crRS.getTrackMap().get(idx);
                Genome currentGenome = null;
                for (Genome genome : patricGenomes) {
                    if (genome.getId().equals(crTrack.getGenomeID())) {
                        currentGenome = genome;
                    }
                }
                if (currentGenome != null) {
                    count_genomes++;
                    crRS.addToDefaultTracks(crTrack);
                    JSONObject tr = new JSONObject();
                    tr.put("style", trStyle);
                    tr.put("hooks", trHooks);
                    tr.put("type", "FeatureTrack");
                    tr.put("tooltip",
                            "<div style='line-height:1.7em'><b>{patric_id}</b> | {refseq_locus_tag} | {alt_locus_tag} | {gene}<br>{product}<br>{type}:{start}...{end} ({strand_str})<br> <i>Click for detail information</i></div>");
                    tr.put("urlTemplate",
                            "/portal/portal/patric/CompareRegionViewer/CRWindow?action=b&cacheability=PAGE&mode=getTrackInfo&key="
                                    + _key + "&rowId=" + crTrack.getRowID() + "&format=.json");
                    tr.put("key", crTrack.getGenomeName());
                    tr.put("label", "CR" + idx);
                    tr.put("dataKey", _key);
                    JSONObject metaData = new JSONObject();

                    if (currentGenome.getIsolationCountry() != null) {
                        metaData.put("Isolation Country", currentGenome.getIsolationCountry());
                    }
                    if (currentGenome.getHostName() != null) {
                        metaData.put("Host Name", currentGenome.getHostName());
                    }
                    if (currentGenome.getDisease() != null) {
                        metaData.put("Disease", currentGenome.getDisease());
                    }
                    if (currentGenome.getCollectionDate() != null) {
                        metaData.put("Collection Date", currentGenome.getCollectionDate());
                    }
                    if (currentGenome.getCompletionDate() != null) {
                        metaData.put("Completion Date", currentGenome.getCompletionDate());
                    }

                    tr.put("metadata", metaData);
                    tracks.add(tr);
                }
            }
        }
        trackList.put("tracks", tracks);

        JSONObject facetedTL = new JSONObject();
        JSONArray dpColumns = new JSONArray();
        dpColumns.addAll(Arrays.asList("key", "Isolation Country", "Host Name", "Disease", "Collection Date",
                "Completion Date"));
        facetedTL.put("displayColumns", dpColumns);
        facetedTL.put("type", "Faceted");
        facetedTL.put("escapeHTMLInData", false);
        trackList.put("trackSelector", facetedTL);
        trackList.put("defaultTracks", crRS.getDefaultTracks());

        response.setContentType("application/json");
        trackList.writeJSONString(response.getWriter());
        response.getWriter().close();
    } else {
        response.getWriter().write("{}");
    }
}

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

License:Apache License

/**
 * Retrieves features that can be mapped by PSEED peg ID. This is used for CompareRegionViewer to map
 * features each other.//from  ww  w .ja  v  a  2  s . c o  m
 *
 * @param IDs IDs
 * @return list of features (na_feature_id, pseed_id, source_id, start, end, strand, na_length, aa_length, product, genome_name, accession)
 */
private Map<String, GenomeFeature> getPSeedMapping(ResourceRequest request, String IDs) throws IOException {

    Map<String, GenomeFeature> result = new HashMap<>();

    DataApiHandler dataApi = new DataApiHandler(request);

    SolrQuery query = new SolrQuery("patric_id:(" + IDs + ")");
    query.setFields(
            "feature_id,patric_id,alt_locus_tag,start,end,strand,feature_type,product,gene,refseq_locus_tag,genome_name,accession");
    query.setRows(1000);

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

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

    for (GenomeFeature feature : features) {
        result.put(feature.getPatricId(), feature);
    }
    return result;
}

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

License:Apache License

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

    SiteHelper.setHtmlMetaElements(request, response, "Comparative Pathway Map");

    DataApiHandler dataApi = new DataApiHandler(request);

    String pk = request.getParameter("param_key") != null ? request.getParameter("param_key") : "";
    String dm = request.getParameter("display_mode") != null ? request.getParameter("display_mode") : "";
    String cType = request.getParameter("context_type") != null ? request.getParameter("context_type") : "";
    String map = request.getParameter("map") != null ? request.getParameter("map") : "";
    String algorithm = request.getParameter("algorithm") != null ? request.getParameter("algorithm") : "";
    String cId = request.getParameter("context_id") != null ? request.getParameter("context_id") : "";
    String ec_number = request.getParameter("ec_number") != null ? request.getParameter("ec_number") : "";
    String feature_id = request.getParameter("feature_id") != null ? request.getParameter("feature_id") : "";
    String ec_names = "";
    int occurrences = 0;
    String genomeId = "";
    String taxonId = "";
    String pathway_name = "";
    String pathway_class = "";
    String definition = "";

    int patricGenomeCount = 0;
    int brc1GenomeCount = 0;
    int refseqGenomeCount = 0;

    // get attributes
    try {//from   w w  w .j  a  v  a 2 s  .c  o m
        SolrQuery query = new SolrQuery("pathway_id:" + map);
        query.setFields("pathway_name,pathway_class,ec_description");

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

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

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

        if (!sdl.isEmpty()) {
            Map doc = sdl.get(0);

            definition = doc.get("ec_description").toString();
            pathway_name = doc.get("pathway_name").toString();
            pathway_class = doc.get("pathway_class").toString();
        }
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    try {
        if (cType != null && cType.equals("taxon")) {
            taxonId = cId;
        } else if (cType != null && cType.equals("genome")) {
            genomeId = cId;
        }

        if (pk != null && !pk.isEmpty()) {
            Map<String, String> key = jsonReader
                    .readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));

            if (key != null && key.containsKey("genomeId") && !key.get("genomeId").equals("")) {
                genomeId = key.get("genomeId");
            } else if (key != null && key.containsKey("taxonId") && !key.get("taxonId").equals("")) {
                taxonId = key.get("taxonId");
            }
            if (key != null && key.containsKey("feature_id") && !key.get("feature_id").equals("")) {
                feature_id = key.get("feature_id");
            }
        }

        SolrQuery query = new SolrQuery("*:*");
        query.setRows(dataApi.MAX_ROWS);
        if (!genomeId.equals("")) {
            if (genomeId.contains(",")) {
                query.addFilterQuery("genome_id:(" + StringUtils.join(genomeId.split(","), " OR ") + ")");
                query.setRows(genomeId.split(",").length);
            } else {
                query.addFilterQuery("genome_id:" + genomeId);
            }
        }
        if (!taxonId.equals("")) {
            query.addFilterQuery("taxon_lineage_ids:" + taxonId);
        }

        LOGGER.debug("counting features: {}", query.toString());

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

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

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

        for (Genome genome : genomes) {
            if (genome.hasPatricCds()) {
                patricGenomeCount++;
            }
            //            if (doc.get("brc1_cds") != null && !doc.get("brc1_cds").toString().equals("0")) {
            //               brc1GenomeCount++;
            //            }
            if (genome.hasRefseqCds()) {
                refseqGenomeCount++;
            }
        }
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    // TODO: implement with solr
    if (dm != null && dm.equals("ec")) {

        SolrQuery query = new SolrQuery("ec_number:(" + ec_number + ") AND pathway_id:(" + map + ")");

        LOGGER.debug("[{}]:{}", SolrCore.PATHWAY_REF.getSolrCoreName(), query);

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

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

        List<Map> sdl = (List<Map>) respBody.get("docs");
        for (Map doc : sdl) {
            ec_names = (String) doc.get("ec_description");
            occurrences = (Integer) doc.get("occurrence");
        }
    } else if (dm != null && dm.equals("feature")) {

        // q=pathway_id:00051&fq={!join%20from=ec_number%20to=ec_number%20fromIndex=pathway}feature_id:PATRIC.235.14.JMSA01000002.CDS.537.665.fwd+AND+pathway_id:00051
        SolrQuery query = new SolrQuery("pathway_id:" + map);
        query.addFilterQuery(SolrCore.PATHWAY.getSolrCoreJoin("ec_number", "ec_number",
                "feature_id:(" + feature_id + ") AND pathway_id:(" + map + ")"));

        LOGGER.debug("[{}]:{}", SolrCore.PATHWAY_REF.getSolrCoreName(), query);

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

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

        List<Map> sdl = (List<Map>) respBody.get("docs");
        for (Map doc : sdl) {
            ec_number = (String) doc.get("ec_number");
            ec_names = (String) doc.get("ec_description");
            occurrences = (Integer) doc.get("occurrence");
        }
    }

    /////
    request.setAttribute("cType", cType);
    request.setAttribute("cId", cId);
    request.setAttribute("taxonId", taxonId);
    request.setAttribute("genomeId", genomeId);
    request.setAttribute("algorithm", algorithm);
    request.setAttribute("map", map);
    request.setAttribute("dm", dm);
    request.setAttribute("pk", pk);
    request.setAttribute("feature_id", feature_id);

    request.setAttribute("ec_number", ec_number);
    request.setAttribute("ec_names", ec_names);
    request.setAttribute("occurrences", occurrences);

    request.setAttribute("taxongenomecount_patric", patricGenomeCount);
    request.setAttribute("taxongenomecount_brc1", brc1GenomeCount);
    request.setAttribute("taxongenomecount_refseq", refseqGenomeCount);

    request.setAttribute("definition", definition);
    request.setAttribute("pathway_name", pathway_name);
    request.setAttribute("pathway_class", pathway_class);

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

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

License:Apache License

private void processEcTable(ResourceRequest request, ResourceResponse response) throws IOException {
    String genomeId = request.getParameter("genomeId");
    String taxonId = request.getParameter("taxonId");
    String cType = request.getParameter("cType");
    String map = request.getParameter("map");
    String algorithm = request.getParameter("algorithm");
    String pk = request.getParameter("pk");

    Map<String, String> key = null;
    if (pk != null && !pk.isEmpty()) {
        key = jsonReader.readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));
    }/*from w  w  w .  java  2  s. com*/

    int count_total = 0;
    JSONArray results = new JSONArray();
    try {
        Set<String> ecNumbers = new HashSet<>();

        DataApiHandler dataApi = new DataApiHandler(request);

        SolrQuery query = new SolrQuery("pathway_id:" + map + " AND annotation:" + algorithm);
        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 (key != null && key.containsKey("genomeId") && !key.get("genomeId").equals("")) {
            query.addFilterQuery("genome_id:(" + key.get("genomeId").replaceAll(",", " OR ") + ")");
        }

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

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

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

        if (numFound > 0) {
            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 (Integer.parseInt(value.get("gene_count").toString()) > 0) {
                    mapStat.put(value.get("val").toString(), value);
                    ecNumbers.add(value.get("val").toString());
                }
            }

            if (!ecNumbers.isEmpty()) {
                query = new SolrQuery(
                        "pathway_id:" + map + " AND ec_number:(" + StringUtils.join(ecNumbers, " OR ") + ")");
                query.setRows(ecNumbers.size()).setFields("ec_number,ec_description,occurrence");
                query.addSort("ec_number", SolrQuery.ORDER.asc);

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

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

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

                    JSONObject item = new JSONObject();
                    item.put("algorithm", algorithm);
                    item.put("ec_name", doc.get("ec_description"));
                    item.put("ec_number", ecNumber);
                    item.put("occurrence", doc.get("occurrence"));
                    item.put("gene_count", stat.get("gene_count"));
                    item.put("genome_count", stat.get("genome_count"));

                    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.CompPathwayMap.java

License:Apache License

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

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

    DataApiHandler dataApi = new DataApiHandler(request);
    JSONObject ret = new JSONObject();
    JSONObject val = new JSONObject();
    try {//from w ww . j ava 2s .  com
        val = (JSONObject) (new JSONParser()).parse(request.getParameter("val").toString());
    } catch (ParseException e) {
        LOGGER.error(e.getMessage(), e);
    }

    String need = val.get("need").toString();
    String genomeId = null, taxonId = null, map = null, pk = null;
    if (val.containsKey("genomeId") && val.get("genomeId") != null && !val.get("genomeId").equals("")) {
        genomeId = val.get("genomeId").toString();
    }

    if (val.containsKey("taxonId") && val.get("taxonId") != null && !val.get("taxonId").equals("")) {
        taxonId = val.get("taxonId").toString();
    }

    if (val.containsKey("map") && val.get("map") != null && !val.get("map").equals("")) {
        map = val.get("map").toString();
    }

    if (val.containsKey("pk") && val.get("pk") != null && !val.get("pk").equals("")) {
        pk = val.get("pk").toString();
    }

    if (need.equals("all")) {
        if (genomeId != null) {
            key.put("genomeId", genomeId);
        }
        if (taxonId != null) {
            key.put("taxonId", taxonId);
        }
        if (map != null) {
            key.put("map", map);
        }

        Map<String, String> sessKey = null;
        if (pk != null && !pk.isEmpty()) {
            sessKey = jsonReader.readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));
            if (sessKey != null && sessKey.containsKey("genomeId") && !sessKey.get("genomeId").equals("")) {
                genomeId = sessKey.get("genomeId");
            }
        }

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

        // getting coordinates
        try {
            JSONArray listCoordinates = new JSONArray();

            for (String annotation : annotations) {
                Set<String> ecNumbers = new HashSet<String>();

                // step1. genome_count, feature_count
                // pathway/select?q=pathway_id:00053+AND+annotation:PATRIC&fq={!join+from=genome_id+to=genome_id+fromIndex=genome}taxon_lineage_ids:83332+AND+genome_status:(complete+OR+wgs)
                // &rows=0&facet=true&json.facet={stat:{field:{field:ec_number,limit:-1,facet:{genome_count:"unique(genome_id)",gene_count:"unique(feature_id)"}}}}

                SolrQuery query = new SolrQuery("pathway_id:" + map + " AND annotation:" + annotation);
                if (taxonId != null) {
                    query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id",
                            "taxon_lineage_ids:" + taxonId));
                }
                if (genomeId != null) {
                    query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id",
                            "genome_id:(" + genomeId.replaceAll(",", " OR ") + ")"));
                }
                query.setRows(0).setFacet(true);

                query.add("json.facet",
                        "{stat:{field:{field:ec_number,limit:-1,facet:{genome_count:\"unique(genome_id)\",gene_count:\"unique(feature_id)\"}}}}");

                LOGGER.debug("step 1. [{}] {}", SolrCore.PATHWAY.getSolrCoreName(), query);

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

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

                if (numFound > 0) {
                    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 (Integer.parseInt(value.get("count").toString()) > 0) {
                            mapStat.put(value.get("val").toString(), value);
                            ecNumbers.add(value.get("val").toString());
                        }
                    }

                    // step2. coordinates, occurrence
                    // pathway_ref/select?q=pathway_id:00010+AND+map_type:enzyme%+AND+ec_number:("1.2.1.3"+OR+"1.1.1.1")&fl=ec_number,ec_description,map_location,occurrence

                    if (!ecNumbers.isEmpty()) {
                        query = new SolrQuery("pathway_id:" + map + " AND map_type:enzyme AND ec_number:("
                                + StringUtils.join(ecNumbers, " OR ") + ")");
                        query.setFields("ec_number,ec_description,map_location,occurrence");
                        query.setRows(dataApi.MAX_ROWS);

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

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

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

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

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

                            if (!stat.get("gene_count").toString().equals("0")) {

                                List<String> locations = (List<String>) doc.get("map_location");
                                for (String location : locations) {

                                    JSONObject coordinate = new JSONObject();
                                    coordinate.put("algorithm", annotation);
                                    coordinate.put("description", doc.get("ec_description"));
                                    coordinate.put("ec_number", ecNumber);
                                    coordinate.put("genome_count", stat.get("genome_count"));

                                    String[] loc = location.split(",");
                                    coordinate.put("x", loc[0]);
                                    coordinate.put("y", loc[1]);

                                    listCoordinates.add(coordinate);
                                }
                            }
                        }
                    }
                }
            }

            ret.put("genome_x_y", listCoordinates);
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }

        // get pathways
        try {

            SolrQuery query = new SolrQuery("annotation:(" + StringUtils.join(annotations, " OR ") + ")");
            if (taxonId != null) {
                query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id",
                        "taxon_lineage_ids:" + taxonId));
            }
            if (genomeId != null) {
                query.addFilterQuery("genome_id:(" + genomeId.replaceAll(",", " OR ") + ")");
            }
            query.setFields("pathway_id,pathway_name,annotation").setRows(dataApi.MAX_ROWS);

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

            JSONArray listEnzymes = new JSONArray();
            Set<String> hash = new HashSet<>();

            for (Map doc : sdl) {
                // TODO: need to improve this using solr
                String hashKey = doc.get("pathway_id").toString() + ":" + doc.get("annotation").toString();

                if (!hash.contains(hashKey)) {

                    hash.add(hashKey);

                    JSONObject enzyme = new JSONObject();
                    enzyme.put("algorithm", doc.get("annotation"));
                    enzyme.put("map_id", doc.get("pathway_id"));
                    enzyme.put("map_name", doc.get("pathway_name"));

                    listEnzymes.add(enzyme);
                }
            }

            ret.put("genome_pathway_x_y", listEnzymes);
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }

        // map_ids_in_map
        try {
            SolrQuery query = new SolrQuery("pathway_id:" + map + " AND map_type:path");
            query.setFields("ec_number,ec_description,map_location").setRows(dataApi.MAX_ROWS);

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

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

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

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

            JSONArray listCoordinates = new JSONArray();
            for (Map doc : sdl) {
                List<String> locations = (List<String>) doc.get("map_location");
                for (String location : locations) {

                    JSONObject coordinate = new JSONObject();
                    coordinate.put("source_id", doc.get("ec_number"));

                    String[] loc = location.split(",");
                    coordinate.put("x", loc[0]);
                    coordinate.put("y", loc[1]);
                    coordinate.put("width", loc[2]);
                    coordinate.put("height", loc[3]);

                    listCoordinates.add(coordinate);
                }
            }

            ret.put("map_ids_in_map", listCoordinates);
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }

        // all coordinates
        try {
            SolrQuery query = new SolrQuery("pathway_id:" + map + " AND map_type:enzyme");
            query.setFields("ec_number,ec_description,map_location").setRows(dataApi.MAX_ROWS);

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

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

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

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

            JSONArray listCoordinates = new JSONArray();
            for (Map doc : sdl) {
                List<String> locations = (List<String>) doc.get("map_location");
                for (String location : locations) {

                    JSONObject coordinate = new JSONObject();
                    coordinate.put("ec", doc.get("ec_number"));
                    coordinate.put("description", doc.get("ec_description"));

                    String[] loc = location.split(",");
                    coordinate.put("x", loc[0]);
                    coordinate.put("y", loc[1]);

                    listCoordinates.add(coordinate);
                }
            }

            ret.put("all_coordinates", listCoordinates);
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }

    } else {
        // need: feature_id or ec_number
        JSONArray coordinates = new JSONArray();

        if (need.equals("ec_number")) {
            try {
                SolrQuery query = new SolrQuery("*:*");
                if (map != null) {
                    query.addFilterQuery("pathway_id:(" + map + ")");
                }

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

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

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

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

                for (Map doc : sdl) {
                    List<String> locations = (List<String>) doc.get("map_location");

                    for (String loc : locations) {
                        JSONObject coordinate = new JSONObject();
                        coordinate.put("ec_number", doc.get("ec_number"));
                        String[] xy = loc.split(",");
                        coordinate.put("x", xy[0]);
                        coordinate.put("y", xy[1]);

                        coordinates.add(coordinate);
                    }
                }
            } catch (IOException e) {
                LOGGER.error(e.getMessage(), e);
            }
        } else {
            // feature
            String featureIds = null;
            if (val.containsKey("value") && val.get("value") != null && !val.get("value").equals("")) {
                featureIds = val.get("value").toString();
            }

            try {
                SolrQuery query = new SolrQuery("*:*");
                if (map != null) {
                    query.addFilterQuery("pathway_id:(" + map + ")");
                }
                if (featureIds != null) {
                    query.addFilterQuery(SolrCore.PATHWAY.getSolrCoreJoin("ec_number", "ec_number",
                            "feature_id:(" + featureIds.replaceAll(",", " OR ") + ")"));
                }

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

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

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

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

                for (Map doc : sdl) {
                    List<String> locations = (List<String>) doc.get("map_location");

                    for (String loc : locations) {
                        JSONObject coordinate = new JSONObject();
                        coordinate.put("ec_number", doc.get("ec_number"));
                        String[] xy = loc.split(",");
                        coordinate.put("x", xy[0]);
                        coordinate.put("y", xy[1]);

                        coordinates.add(coordinate);
                    }
                }
            } catch (IOException e) {
                LOGGER.error(e.getMessage(), e);
            }
        }

        ret.put("coordinates", coordinates);
    }

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