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.GenomeBrowser.java

License:Apache License

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

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

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

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

    JSONArray jsonResult = new JSONArray();

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

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

    for (GenomeSequence sequence : sequences) {

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

        jsonResult.add(seq);
    }

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

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

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

        for (GenomeSequence sequence : sequences) {

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

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

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

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

License:Apache License

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

    String accession = request.getParameter("accession");
    String annotation = request.getParameter("annotation");
    String genomeId = request.getParameter("genomeId");
    //      LOGGER.debug("printTrackInfo: {}", request.getParameterMap().toString());

    if (accession != null && annotation != null) {
        DataApiHandler dataApi = new DataApiHandler(request);

        JSONArray ncList = new JSONArray();
        List<Integer> histogram = this.getFeatureCountHistogram(request);
        Integer sum = 0;//from w w w.  j  a  v a2 s  .  c  o  m
        for (Integer hist : histogram) {
            sum += hist;
        }
        double avgCount = sum.doubleValue() / histogram.size();

        SolrQuery query = new SolrQuery("genome_id:" + genomeId + " AND accession:" + accession
                + " AND annotation:" + annotation + " AND !(feature_type:source)");
        query.setRows(dataApi.MAX_ROWS);
        query.addSort("start", SolrQuery.ORDER.asc);

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

            JSONArray alist = new JSONArray();

            alist.addAll(Arrays.asList(0, (f.getStart() - 1), f.getStart(), f.getEnd(),
                    (f.getStrand().equals("+") ? 1 : -1), f.getStrand(),

                    f.getId(), f.hasPatricId() ? f.getPatricId() : "",
                    f.hasRefseqLocusTag() ? f.getRefseqLocusTag() : "",
                    f.hasAltLocusTag() ? f.getAltLocusTag() : "", annotation, f.getFeatureType(),
                    f.hasProduct() ? f.getProduct() : "",

                    f.hasGene() ? f.getGene() : "",
                    (f.getFeatureType().equals("CDS") ? 0 : (f.getFeatureType().contains("RNA") ? 1 : 2))));

            ncList.add(alist);
        }

        //         {
        //            "featureCount": <%=features_count %>,
        //            "formatVersion": 1,
        //            "histograms": {
        //               "meta": [{
        //                  "arrayParams": {
        //                     "chunkSize": 10000,
        //                     "length": <%=hist.size()%>,
        //                     "urlTemplate": "Hist.json.jsp?accession=<%=_accession%>&algorithm=<%=_algorithm%>&chunk={Chunk}&format=.json"
        //                  },
        //                  "basesPerBin": "10000"
        //               }],
        //               "stats": [{
        //                  "basesPerBin": "10000",
        //                  "max": <%=(hist.isEmpty())?"0":Collections.max(hist)%>,
        //                  "mean": <%=hist_avg%>
        //               }]
        //            },
        //            "intervals": {
        //               "classes": [{
        //                  "attributes": [
        //                     "Start", "Start_str", "End", "Strand", "strand_str",
        //                     "id", "locus_tag", "source", "type", "product",
        //                     "gene", "refseq", "phase"],
        //                  "isArrayAttr": {}
        //               }],
        //               "count": <%=features_count %>,
        //               "lazyClass": 5,
        //               "maxEnd": 20000,
        //               "minStart": 1,
        //               "nclist": [<%=nclist.toString() %>],
        //               "urlTemplate": "lf-{Chunk}.json"
        //            }
        //         }
        JSONObject track = new JSONObject();
        track.put("featureCount", features.size());
        track.put("formatVersion", 1);
        // histogram
        JSONObject histograms = new JSONObject();
        // meta
        JSONArray meta = new JSONArray();
        JSONObject aMeta = new JSONObject();
        // arrayParams
        JSONObject arrayParams = new JSONObject();
        arrayParams.put("chunkSize", 10000);
        arrayParams.put("length", histogram.size());
        arrayParams.put("urlTemplate",
                "/portal/portal/patric/GenomeBrowser/GBWindow?action=b&cacheability=PAGE&mode=getHistogram&accession="
                        + accession + "&annotation=" + annotation + "&chunk={Chunk}");
        aMeta.put("arrayParams", arrayParams);
        aMeta.put("basesPerBin", 10000);
        meta.add(aMeta);
        // stats
        JSONArray stats = new JSONArray();
        JSONObject aStat = new JSONObject();
        aStat.put("basesPerBin", 10000);
        aStat.put("max", (histogram.isEmpty() ? 0 : Collections.max(histogram)));
        aStat.put("mean", avgCount);
        stats.add(aStat);

        histograms.put("meta", meta);
        histograms.put("stats", stats);

        // intervals
        JSONObject intervals = new JSONObject();
        // classes
        JSONArray classes = new JSONArray();
        JSONObject aClass = new JSONObject();
        JSONArray attributes = new JSONArray();
        attributes.addAll(Arrays.asList("Start", "Start_str", "End", "Strand", "strand_str", "id", "patric_id",
                "refseq_locus_tag", "alt_locus_tag", "source", "type", "product", "gene", "phase"));

        aClass.put("attributes", attributes);
        aClass.put("isArrayAttr", new JSONObject());
        classes.add(aClass);
        intervals.put("classes", classes);
        intervals.put("count", features.size());
        intervals.put("lazyClass", 5);
        intervals.put("maxEnd", 20000);
        intervals.put("minStart", 1);
        intervals.put("nclist", ncList);
        intervals.put("urlTemplate", "lf-{Chunk}.json");

        track.put("histograms", histograms);
        track.put("intervals", intervals);

        // print track info
        response.setContentType("application/json");
        track.writeJSONString(response.getWriter());
    }
}

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

License:Apache License

private List<Integer> getFeatureCountHistogram(ResourceRequest request) throws IOException {

    String accession = request.getParameter("accession");
    String annotation = request.getParameter("annotation");
    String genomeId = request.getParameter("genomeId");

    SolrQuery query = new SolrQuery("accession:" + accession + " AND genome_id:" + genomeId);
    query.setFilterQueries("annotation:" + annotation + " AND !(feature_type:source)");
    query.setRows(0);
    query.setFacet(true);//from ww  w .  ja  v a 2  s  . co m
    query.setFacetMinCount(1);
    query.addNumericRangeFacet("start", 0, 10000000, 10000);

    List<Integer> results = new ArrayList<>();
    DataApiHandler dataApi = new DataApiHandler(request);

    LOGGER.trace("[{}] {}", SolrCore.FEATURE.getSolrCoreName(), query.toString());
    String apiResponse = dataApi.solrQuery(SolrCore.FEATURE, query);
    Map resp = jsonReader.readValue(apiResponse);
    Map facetCounts = (Map) resp.get("facet_counts");
    Map facetRanges = (Map) facetCounts.get("facet_ranges");
    List counts = (List) ((Map) facetRanges.get("start")).get("counts");

    for (int i = 0; i < counts.size(); i = i + 2) {
        int value = (Integer) counts.get(i + 1);
        results.add(value);
    }

    return results;
}

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

License:Apache License

private Map processGlobalSearchFeature(ResourceRequest request) throws IOException {

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

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

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

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

    Map resp = jsonReader.readValue(apiResponse);

    return resp;
}

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

License:Apache License

private Map processGlobalSearchGenome(ResourceRequest request) throws IOException {

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

    SolrQuery query = new SolrQuery(StringHelper.stripQuoteAndParseSolrKeywordOperator(keyword));
    if (need.equals("search")) {
        query.setRows(3).set("hl", "on").set("hl.fl", "*");
    } else {/*from w w  w .j  av  a  2s .  c o m*/
        query.setRows(dataApi.MAX_ROWS);
    }

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

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

    Map resp = jsonReader.readValue(apiResponse);

    return resp;
}

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

License:Apache License

private Map processGlobalSearchTaxonomy(ResourceRequest request) throws IOException {

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

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

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

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

    Map resp = jsonReader.readValue(apiResponse);

    return resp;
}

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

License:Apache License

private Map processGlobalSearchExperiment(ResourceRequest request) throws IOException {

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

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

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

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

    Map resp = jsonReader.readValue(apiResponse);

    return resp;
}

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

License:Apache License

@SuppressWarnings("unchecked")
private JSONObject processIDMapping(DataApiHandler dataApi, String fromId, String fromIdGroup, String toId,
        String toIdGroup, String keyword) throws IOException {

    JSONArray results = new JSONArray();
    int total;/*from w w  w .j  a v  a2s  .  c  om*/

    if (fromIdGroup.equals("PATRIC")) {
        if (toIdGroup.equals("PATRIC")) { // from PATRIC to PATRIC

            // query to GenomeFeature
            try {
                SolrQuery query = new SolrQuery(fromId + ":(" + keyword + ")");
                query.addFilterQuery("annotation:PATRIC").setRows(10000);

                if (toId.equals("gene_id") || toId.equals("gi")) {
                    query.addFilterQuery(toId + ":[1 TO *]");
                }

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

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

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

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

                for (GenomeFeature feature : featureList) {
                    results.add(feature.toJSONObject());
                }
            } catch (IOException e) {
                LOGGER.error(e.getMessage(), e);
            }

            total = results.size();
        } else { // from PATRIC to Other

            Set<Long> giList = new HashSet<>();
            Map<String, String> accessionGiMap = new LinkedHashMap<>();
            List<Map<Long, String>> giTargetList = new LinkedList<>();
            List<GenomeFeature> featureList = new ArrayList<>();

            // Query GenomeFeature, get GInumbers
            try {
                SolrQuery query = new SolrQuery(fromId + ":(" + keyword + ")");
                query.setRows(10000);
                LOGGER.trace("PATRIC TO Other 1/3: [{}] {}", SolrCore.FEATURE.getSolrCoreName(), query);

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

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

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

                for (GenomeFeature feature : featureList) {
                    giList.add(feature.getGi());
                }
            } catch (IOException e) {
                LOGGER.error(e.getMessage(), e);
            }

            // get UniprotKBAccessions wigh GI
            try {
                SolrQuery query = new SolrQuery("id_value:(" + StringUtils.join(giList, " OR ") + ")");
                query.addFilterQuery("id_type:GI").setRows(10000);

                LOGGER.trace("PATRIC TO Other 2/3: [{}] {}", SolrCore.ID_REF.getSolrCoreName(),
                        query.toString());

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

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

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

                for (Map doc : uniprotList) {

                    accessionGiMap.put(doc.get("uniprotkb_accession").toString(),
                            doc.get("id_value").toString());
                }
            } catch (IOException e) {
                LOGGER.error(e.getMessage(), e);
            }
            LOGGER.trace("accessionGiMap:{}", accessionGiMap);

            if (!accessionGiMap.isEmpty()) {
                // get Target Value
                try {
                    SolrQuery query = new SolrQuery(
                            "uniprotkb_accession:(" + StringUtils.join(accessionGiMap.keySet(), " OR ") + ")");
                    if (toId.equals("UniProtKB-Accession")) {
                        query.addFilterQuery("id_type:GI");
                    } else {
                        query.addFilterQuery("id_type:(" + toId + ")");
                    }
                    query.setRows(accessionGiMap.size());

                    LOGGER.trace("PATRIC TO Other 3/3: [{}] {}", SolrCore.ID_REF.getSolrCoreName(),
                            query.toString());

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

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

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

                    for (Map doc : targets) {
                        String accession = doc.get("uniprotkb_accession").toString();
                        String target = doc.get("id_value").toString();

                        Long targetGi = Long.parseLong(accessionGiMap.get(accession));

                        Map<Long, String> giTarget = new HashMap<>();
                        if (toId.equals("UniProtKB-Accession")) {
                            giTarget.put(targetGi, accession);
                        } else {
                            giTarget.put(targetGi, target);
                        }
                        giTargetList.add(giTarget);
                    }
                } catch (IOException e) {
                    LOGGER.error(e.getMessage(), e);
                }

                LOGGER.trace("giTargetList:{}", giTargetList);

                // query to GenomeFeature
                for (GenomeFeature feature : featureList) {
                    for (Map<Long, String> targetMap : giTargetList) {
                        if (targetMap.containsKey(feature.getGi())) {
                            JSONObject item = feature.toJSONObject();
                            item.put("target", targetMap.get(feature.getGi()));

                            results.add(item);
                        }
                    }
                }
            }

            total = results.size();
        }
    } else { // from Other to PATRIC (patric_id)

        Map<String, String> accessionTargetMap = new LinkedHashMap<>();
        Set<Long> giList = new HashSet<>();
        List<Map<Long, String>> giTargetList = new LinkedList<>();

        if (fromId.equals("UniProtKB-Accession")) {
            // we have treat this as a special case, since UniProtKB-Accession is stored in a separate field, named 'uniprotkb_accession'
            for (String accession : keyword.split(" OR ")) {
                accessionTargetMap.put(accession, accession);
            }
        } else {
            try {
                SolrQuery query = new SolrQuery("id_value:(" + keyword + ")");
                query.addFilterQuery("id_type:" + fromId).setRows(10000)
                        .addField("uniprotkb_accession,id_value");

                LOGGER.trace("Other to PATRIC 1/3: [{}] {}", SolrCore.ID_REF.getSolrCoreName(),
                        query.toString());

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

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

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

                for (Map doc : accessions) {
                    accessionTargetMap.put(doc.get("uniprotkb_accession").toString(),
                            doc.get("id_value").toString());
                }
            } catch (IOException e) {
                LOGGER.error(e.getMessage(), e);
            }
        }

        if (!accessionTargetMap.isEmpty()) {
            try {
                SolrQuery query = new SolrQuery(
                        "uniprotkb_accession:(" + StringUtils.join(accessionTargetMap.keySet(), " OR ") + ")");
                query.addFilterQuery("id_type:GI").setRows(10000);

                LOGGER.trace("Other to PATRIC 2/3: [{}] {}", SolrCore.ID_REF.getSolrCoreName(),
                        query.toString());

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

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

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

                for (Map doc : accessions) {
                    Long targetGi = Long.parseLong(doc.get("id_value").toString());
                    String accession = doc.get("uniprotkb_accession").toString();
                    String target = accessionTargetMap.get(accession);

                    giList.add(targetGi);

                    Map<Long, String> targetMap = new HashMap<>();
                    targetMap.put(targetGi, target);
                    giTargetList.add(targetMap);
                }
            } catch (IOException e) {
                LOGGER.error(e.getMessage(), e);
            }
        }

        LOGGER.trace("giTargetList:{}", giTargetList);
        if (!giList.isEmpty()) {
            try {
                SolrQuery query = new SolrQuery("gi:(" + StringUtils.join(giList, " OR ") + ")");
                query.addFilterQuery("annotation:PATRIC").setRows(10000);

                LOGGER.trace("Other to PATRIC 3/3: [{}] {}", SolrCore.FEATURE.getSolrCoreName(),
                        query.toString());

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

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

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

                for (GenomeFeature feature : featureList) {
                    for (Map<Long, String> targetMap : giTargetList) {
                        if (targetMap.containsKey(feature.getGi())) {
                            JSONObject item = feature.toJSONObject();
                            item.put("target", targetMap.get(feature.getGi()));

                            results.add(item);
                        }
                    }
                }

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

        total = results.size();
    }

    JSONObject jsonResult = new JSONObject();
    jsonResult.put("total", total);
    jsonResult.put("results", results);

    return jsonResult;
}

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

License:Apache License

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

    SiteHelper.setHtmlMetaElements(request, response, "3D Structure");

    response.setContentType("text/html");
    String pdbID = request.getParameter("pdb_id");

    if (pdbID != null) {

        String chainID = request.getParameter("chain_id");

        String _context_path = request.getContextPath();
        String _codebase = _context_path + "/jmol";
        String _datafile = "https://" + request.getServerName() + _context_path + "/jsp/readPDB.jsp?pdbID="
                + pdbID;//from   w w w. j a v a2 s .  c  om

        String urlNCBIStructure = "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure&cmd=DetailsSearch&term=";
        String urlPDB = "http://www.pdb.org/pdb/explore/explore.do?structureId=";
        String urlSSGCID = "http://www.ssgcid.org/";
        String urlCSGID = "http://www.csgid.org/";

        String nameSSGCID = "Seattle Structural Genomics Center for Infectious Disease";
        String nameCSGID = "Center for Structural Genomics of Infectious Diseases";

        PDBInterface api = new PDBInterface();
        Map<String, String> description = api.getDescription(pdbID);

        if (description != null) {

            DataApiHandler dataApi = new DataApiHandler(request);
            List<GenomeFeature> features = new ArrayList<>();
            List<String> targetIDs = new ArrayList<>();

            // 1. read associated features for given PDB ID
            // 1.1 read uniprotkb_accession
            List<String> uniprotKbAccessions = new ArrayList<>();
            SolrQuery query = new SolrQuery("id_type:PDB AND id_value:" + pdbID);

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

            Map resp = jsonReader.readValue(apiResponse);
            Map respBody = (Map<String, Object>) resp.get("response");

            int numFound = (Integer) respBody.get("numFound");
            if (numFound > 0) {
                List<Map> records = (List<Map>) respBody.get("docs");
                for (Map item : records) {
                    uniprotKbAccessions.add(item.get("uniprotkb_accession").toString());
                }
            }

            // 1.2 read features with uniprotkb_accession
            if (!uniprotKbAccessions.isEmpty()) {
                query = new SolrQuery(
                        "uniprotkb_accession:(" + StringUtils.join(uniprotKbAccessions, " OR ") + ")");

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

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

            // 2. retrieve structural meta data
            if (!uniprotKbAccessions.isEmpty()) {
                List<String> ids = new ArrayList<>();
                for (String uniprotkbAccession : uniprotKbAccessions) {
                    ids.add("\"UniProt:" + uniprotkbAccession + "\"");
                }

                query = new SolrQuery("gene_symbol_collection:(" + StringUtils.join(ids, " OR ") + ")");
                query.setRows(uniprotKbAccessions.size());

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

                List<Map> sdl = (List<Map>) respBody.get("docs");
                for (Map doc : sdl) {
                    targetIDs.add(doc.get("target_id").toString());
                }
            }

            //
            request.setAttribute("pdbID", pdbID);
            request.setAttribute("chainID", chainID);
            request.setAttribute("_codebase", _codebase);
            request.setAttribute("_datafile", _datafile);
            request.setAttribute("urlNCBIStructure", urlNCBIStructure);
            request.setAttribute("urlPDB", urlPDB);
            request.setAttribute("urlSSGCID", urlSSGCID);
            request.setAttribute("urlCSGID", urlCSGID);
            request.setAttribute("nameSSGCID", nameSSGCID);
            request.setAttribute("nameCSGID", nameCSGID);
            request.setAttribute("description", description); // Map<String, String>
            request.setAttribute("features", features); // List<GenomeFeature>
            request.setAttribute("targetIDs", targetIDs); // List<String>

            PortletRequestDispatcher prd = getPortletContext().getRequestDispatcher("/WEB-INF/jsp/jmol.jsp");
            prd.include(request, response);
        } else {
            PrintWriter writer = response.getWriter();
            writer.write("No data available.");
            writer.close();
        }
    } else {
        PrintWriter writer = response.getWriter();
        writer.write("Invalid Parameter - missing context information");
        writer.close();
    }
}

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

License:Apache License

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

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

    if (pathwayId != null && !pathwayId.equals("")) {
        query.addFilterQuery("pathway_id:" + pathwayId);
    }/*from  w ww .  java 2 s . c om*/

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

                    uniquePathways.put(aPathwayId, item);
                }
            }

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

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

    return jsonResult;
}