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

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

  1. HOME
  2. Java
  3. org.apache.solr
  4. org.apache.solr.client.solrj.*
  5. SolrQuery
  6. SolrQuery

Introduction

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

Prototype

public SolrQuery(String q)

Source Link

Document

Create a new SolrQuery

Usage

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

License:Apache License

private JSONObject getPathwayECDist() {
    JSONObject jsonData;/*w  ww . java  2 s  . c  o m*/
    JSONArray series = new JSONArray();

    for (Integer txId : GENUS_TAXON_IDS) {
        int total = 0;
        List<Integer> distribution = new LinkedList<>();

        // {stat:{field:{field:pathway_id,limit:-1,facet:{ec_count:"unique(ec_number)",genome_count:"unique(genome_id)",genome_ec_count:"unique(genome_ec)"}}}}
        try {
            SolrQuery query = new SolrQuery("annotation:PATRIC");
            query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id",
                    "genome_status:(Complete OR WGS) AND taxon_lineage_ids:" + txId));
            query.setRows(0).setFacet(true).set("json.facet",
                    "{stat:{field:{field:pathway_id,limit:-1,facet:{ec_count:\"unique(ec_number)\",genome_count:\"unique(genome_id)\",genome_ec_count:\"unique(genome_ec)\"}}}}");

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

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

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

            int bin1 = 0, bin2 = 0, bin3 = 0, bin4 = 0, bin5 = 0;

            for (Map bucket : buckets) {

                double ec_count = ((Integer) bucket.get("ec_count")).doubleValue();
                double genome_count = ((Integer) bucket.get("genome_count")).doubleValue();
                double genome_ec_count = ((Integer) bucket.get("genome_ec_count")).doubleValue();

                long bin = Math.round(genome_ec_count / genome_count / ec_count * 100);

                //               LOGGER.trace("calculating conservation, ec:{}, genome:{}, genome_ec:{}, bin:{}", ec_count, genome_count, genome_ec_count, bin);
                if (bin < 20) {
                    bin5++;
                } else if (bin >= 20 && bin < 40) {
                    bin4++;
                } else if (bin >= 40 && bin < 60) {
                    bin3++;
                } else if (bin >= 60 && bin < 80) {
                    bin2++;
                } else if (bin >= 80) {
                    bin1++;
                }
                total++;
            }
            distribution.addAll(Arrays.asList(bin1, bin2, bin3, bin4, bin5));
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }

        Taxonomy taxonomy = dataApi.getTaxonomy(txId);

        JSONObject item = new JSONObject();
        item.put("pathogen", taxonomy.getTaxonName());
        item.put("total", total);
        item.put("dist", distribution);

        series.add(item);
    }

    jsonData = new JSONObject();
    jsonData.put("chart_title", "Pathway Conservation in Pathogenic Bacteria");
    jsonData.put("chart_desc",
            "The graph below shows conservation of metabolic pathways across percentage of total genomes in each pathogenic genus.");
    jsonData.put("data", series);

    return jsonData;
}

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

License:Apache License

private Map<String, Integer> getFIGFamStat(int taxonId) {
    Map<String, Integer> stat = new HashMap<>();

    try {/*from   w  w  w .j a v a  2 s.c om*/
        final String filterCondition = SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id",
                "taxon_lineage_ids:" + taxonId);

        Map response = dataApi.getFieldFacets(SolrCore.FEATURE, "feature_type:CDS AND annotation:PATRIC",
                filterCondition, "figfam_id");
        Map figfamFacets = (Map) ((Map) response.get("facets")).get("figfam_id");
        int total = figfamFacets.size();

        response = dataApi.getFieldFacets(SolrCore.FEATURE, "product:(hypothetical AND protein)",
                filterCondition, "figfam_id");
        Map hypotheticalFacets = (Map) ((Map) response.get("facets")).get("figfam_id");
        int hypothetical = hypotheticalFacets.size();

        stat.put("total", total);
        stat.put("hypothetical", hypothetical);
        stat.put("functional", (total - hypothetical));

        // counting core vs accessary
        int countCore = 0;
        SolrQuery query = new SolrQuery("*:*").addFilterQuery(filterCondition).setRows(0).setFacet(true);
        query.set("json.facet",
                "{stat:{field:{field:figfam_id,limit:-1,allBuckets:true,facet:{genome_count:\"unique(genome_id)\"}}}}");

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

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

        Map resp = jsonReader.readValue(apiResponse);
        Map facets = (Map) resp.get("facets");
        Map allBuckets = (Map) ((Map) facets.get("stat")).get("allBuckets");

        double genomeCount = ((Integer) allBuckets.get("genome_count")).doubleValue();
        double cutoff = 0.95 * genomeCount;

        List<Map> buckets = (List) ((Map) facets.get("stat")).get("buckets");

        for (Map bucket : buckets) {
            if (((Integer) bucket.get("genome_count")).doubleValue() > cutoff) {
                countCore++;
            }
        }
        stat.put("core", countCore);
        stat.put("accessory", (total - countCore));
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    return stat;
}

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

License:Apache License

private JSONArray getFIGFamConservationDistribution(int taxonId) {
    JSONArray dist = new JSONArray();

    try {/*  w  w w .  j  a  v a  2 s. c o m*/
        Map<Integer, List<String>> distMap = new LinkedHashMap<>();

        SolrQuery query = new SolrQuery("*:*");
        query.addFilterQuery("feature_type:CDS AND annotation:PATRIC");
        query.addFilterQuery(
                SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "taxon_lineage_ids:" + taxonId));
        query.setRows(0).setFacet(true).set("json.facet",
                "{stat:{field:{field:figfam_id,limit:-1,allBuckets:true,facet:{genome_count:\"unique(genome_id)\"}}}}");

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

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

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

        Map allBuckets = (Map) ((Map) facets.get("stat")).get("allBuckets");
        double totalGenomeCount = ((Integer) allBuckets.get("genome_count")).doubleValue();

        List<Map> buckets = (List<Map>) ((Map) facets.get("stat")).get("buckets");

        for (Map bucket : buckets) {
            String figfamID = (String) bucket.get("val");
            double genomeCount = ((Integer) bucket.get("genome_count")).doubleValue();
            int groupHash = ((Double) Math.ceil(genomeCount / totalGenomeCount * 10.0d)).intValue();

            //            LOGGER.trace("group hashing.. {}:{}/{} -> {}", figfamID, genomeCount, totalGenomeCount, groupHash);
            if (distMap.get(groupHash) == null) {
                distMap.put(groupHash, new LinkedList<String>());
            }
            distMap.get(groupHash).add(figfamID);
        }

        for (int i = 1; i <= 10; i++) {
            JSONObject item = new JSONObject();
            if (distMap.get(i) != null && !distMap.get(i).isEmpty()) {
                item.put("x", (i) + "0%");
                item.put("y", distMap.get(i).size());
            } else {
                item.put("x", (i) + "0%");
                item.put("y", 0);
            }
            dist.add(item);
        }
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    return dist;
}

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 w  ww  .  j a  v a  2  s  .  com
            "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.OrganismTreeBuilder.java

License:Apache License

/**
 * Builds an array of nodes for Genome List view
 * // w  w w .j av  a 2  s.  c o m
 * @param taxonId root taxon ID
 * @return json array of feed for Genome List
 */
public static JSONArray buildGenomeList(DataApiHandler dataApi, int taxonId) throws IOException {

    JSONArray treeJSON = new JSONArray();

    SolrQuery query = new SolrQuery("taxon_lineage_ids:" + taxonId);
    query.addField("taxon_id,genome_id,genome_name").setRows(1000000);
    query.addSort("genome_name", SolrQuery.ORDER.asc);
    LOGGER.trace("buildGenomeList:{}", query.toString());

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

    List<Genome> genomeList = dataApi.bindDocuments((List<Map>) respBody.get("docs"), Genome.class);
    Set<TaxonomyGenomeNode> children = new LinkedHashSet<>();

    for (Genome genome : genomeList) {
        TaxonomyGenomeNode node = new TaxonomyGenomeNode(genome);
        node.setParentId("0");

        children.add(node);
    }

    TaxonomyGenomeNode rootTaxonomyGenomeNode = new TaxonomyGenomeNode();
    Taxonomy rootTaxonomy = dataApi.getTaxonomy(taxonId);
    rootTaxonomyGenomeNode.setName(rootTaxonomy.getTaxonName() + " (" + rootTaxonomy.getGenomeCount() + ")");
    rootTaxonomyGenomeNode.setTaxonId(rootTaxonomy.getId());
    rootTaxonomyGenomeNode.setId("0");

    rootTaxonomyGenomeNode.setChildren(children);
    treeJSON.add(rootTaxonomyGenomeNode.getJSONObject());

    return treeJSON;
}

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

License:Apache License

/**
 * Build an array of nodes for Taxonomy Tree view
 * /*from  www.  ja v  a 2  s . c  o  m*/
 * @param taxonId root taxon ID
 * @return json array of feed for Taxonomy Tree
 */
public static JSONArray buildGenomeTree(DataApiHandler dataApi, int taxonId) throws IOException {
    JSONArray treeJSON = new JSONArray();

    SolrQuery query = new SolrQuery("lineage_ids:" + taxonId + " AND genomes:[1 TO *]");
    query.addField("taxon_id,taxon_rank,taxon_name,genomes,lineage_ids").setRows(1000000);
    query.addSort("lineage", SolrQuery.ORDER.asc);
    LOGGER.trace("buildGenomeTree:{}", query.toString());

    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);

    Map<Integer, Taxonomy> taxonomyMap = new HashMap<>();

    // 1 populate map for detail info
    for (Taxonomy tx : taxonomyList) {
        taxonomyMap.put(tx.getId(), tx);
    }

    // 2 add to rawData array
    List<List<TaxonomyTreeNode>> rawData = new ArrayList<>();
    for (Taxonomy tx : taxonomyList) {
        List<Integer> lineage = tx.getLineageIds();
        List<Integer> descendantIds = lineage;
        if (lineage.indexOf(taxonId) > 0) {
            descendantIds = lineage.subList(lineage.indexOf(taxonId), lineage.size());
        }

        List<TaxonomyTreeNode> descendant = new LinkedList<>();
        for (Integer txId : descendantIds) {
            if (taxonomyMap.containsKey(txId)) {
                descendant.add(new TaxonomyTreeNode(taxonomyMap.get(txId)));
            }
        }
        rawData.add(descendant);
    }

    // 3 build a tree
    TaxonomyTreeNode wrapper = new TaxonomyTreeNode();
    TaxonomyTreeNode current = wrapper;
    for (List<TaxonomyTreeNode> tree : rawData) {
        TaxonomyTreeNode root = current;

        int parentId = taxonId;
        for (TaxonomyTreeNode node : tree) {
            node.setParentId(parentId);
            current = current.child(node);
            parentId = node.getTaxonId();
        }

        current = root;
    }

    TaxonomyTreeNode root = wrapper.getFirstChild();
    treeJSON.add(root.getJSONObject());

    return treeJSON;
}

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

License:Apache License

/**
 * Build a taxonomy-genome map.//from   w  w w. j av  a  2 s  .c  om
 * @param taxonId root taxon ID
 * @return json array of mapping {ncbi_taxon_id,genome_info_id}
 */
public static JSONArray buildTaxonGenomeMapping(DataApiHandler dataApi, int taxonId) throws IOException {
    JSONArray mapJSON = new JSONArray();

    SolrQuery query = new SolrQuery("taxon_lineage_ids:" + taxonId);
    query.addField("genome_id,taxon_id").setRows(1000000);
    LOGGER.trace("buildTaxonGenomeMapping:{}", query.toString());

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

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

    for (Genome genome : genomeList) {
        JSONObject map = new JSONObject();
        map.put("genome_id", genome.getId());
        map.put("taxon_id", genome.getTaxonId());

        mapJSON.add(map);
    }

    return mapJSON;
}

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 va2  s  .c om

    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  w w w  . j  ava 2s .c  om
 *
 * @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 ww  . jav  a  2 s  .co 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);
}