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

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

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

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.unc.lib.dl.ui.service.SolrQueryLayerService.java

License:Apache License

public boolean hasRole(AccessGroupSet accessGroups, UserRole userRole) {
    StringBuilder query = new StringBuilder();
    String joinedGroups = accessGroups.joinAccessGroups(" OR ", userRole.toString() + "|", true);
    query.append("roleGroup:(").append(joinedGroups).append(')');

    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery(query.toString());
    solrQuery.setRows(0);

    try {/*from  w w w .  j  av a2 s .  c om*/
        QueryResponse queryResponse = this.executeQuery(solrQuery);
        return queryResponse.getResults().getNumFound() > 0;
    } catch (SolrServerException e) {
        LOG.error("Error retrieving Solr object request: " + e);
    }
    return false;
}

From source file:edu.unc.lib.dl.ui.service.SolrQueryLayerService.java

License:Apache License

/**
 * Get the number of departments represented in the collection
 * //w w  w.  j a v  a  2  s  .co m
 * @return the count, or -1 if there was an error retrieving the count
 */

public int getDepartmentsCount() {

    SolrQuery query;
    QueryResponse response;

    query = new SolrQuery();
    query.setQuery("*:*");
    query.setRows(0);
    query.addFacetField("department");
    query.setFacetLimit(-1);

    try {
        response = this.executeQuery(query);
        return response.getFacetField("department").getValueCount();
    } catch (SolrServerException e) {
        LOG.error("Error retrieving Solr object request: " + e);
    }

    return -1;

}

From source file:edu.unc.lib.dl.ui.service.SolrQueryLayerService.java

License:Apache License

/**
 * Get the total number of collections//  w ww.j  ava 2  s  . co  m
 * 
 * @return the count, or -1 if there was an error retrieving the count
 */

public long getCollectionsCount() {

    SolrQuery query;
    QueryResponse response;

    query = new SolrQuery();
    query.setQuery("resourceType:Collection");
    query.setRows(0);
    query.setFacetLimit(-1);

    try {
        response = this.executeQuery(query);
        return response.getResults().getNumFound();
    } catch (SolrServerException e) {
        LOG.error("Error retrieving Solr object request: " + e);
    }

    return -1;

}

From source file:edu.unc.lib.dl.ui.service.SolrQueryLayerService.java

License:Apache License

/**
 * Get the number of objects present in the collection for various formats
 * /*w ww.  j  a v a2  s  .c o m*/
 * @return a map from format name to count
 */

public Map<String, Long> getFormatCounts() {

    SolrQuery query;
    QueryResponse response;

    query = new SolrQuery();
    query.setQuery("*:*");
    query.setRows(0);
    query.addFacetField("contentType");
    query.setFacetLimit(-1);

    HashMap<String, Long> counts = new HashMap<String, Long>();

    try {
        response = this.executeQuery(query);
        FacetField facetField = response.getFacetField("contentType");

        for (Count count : facetField.getValues()) {

            if (count.getName().startsWith("^text"))
                counts.put("text", count.getCount());
            else if (count.getName().startsWith("^image"))
                counts.put("image", count.getCount());
            else if (count.getName().startsWith("^dataset"))
                counts.put("dataset", count.getCount());
            else if (count.getName().startsWith("^audio"))
                counts.put("audio", count.getCount());
            else if (count.getName().startsWith("^video"))
                counts.put("video", count.getCount());

        }

    } catch (SolrServerException e) {
        LOG.error("Error retrieving Solr object request: " + e);
    }

    return counts;

}

From source file:edu.usu.sdl.openstorefront.service.SearchServiceImpl.java

License:Apache License

@Override
public List<ComponentSearchView> getSearchItems(SearchQuery query, FilterQueryParams filter) {
    // use for advanced search with And - Or combinations on separate fields
    String queryOperator = " " + SolrAndOr.OR + " ";
    String myQueryString;/*from  ww w  . ja v a 2  s  .  c  om*/

    // If incoming query string is blank, default to solar *:* for the full query
    if (StringUtils.isNotBlank(query.getQuery())) {
        StringBuilder queryData = new StringBuilder();

        Field fields[] = SolrComponentModel.class.getDeclaredFields();
        for (Field field : fields) {
            org.apache.solr.client.solrj.beans.Field fieldAnnotation = field
                    .getAnnotation(org.apache.solr.client.solrj.beans.Field.class);
            if (fieldAnnotation != null && field.getType() == String.class) {
                String name = field.getName();
                if (StringUtils.isNotBlank(fieldAnnotation.value())
                        && org.apache.solr.client.solrj.beans.Field.DEFAULT
                                .equals(fieldAnnotation.value()) == false) {
                    name = fieldAnnotation.value();
                }

                queryData.append(SolrEquals.EQUAL.getSolrOperator()).append(name)
                        .append(SolrManager.SOLR_QUERY_SEPERATOR).append(query.getQuery())
                        .append(queryOperator);
            }
        }
        myQueryString = queryData.toString();
        if (myQueryString.endsWith(queryOperator)) {
            queryData.delete((myQueryString.length() - (queryOperator.length())), myQueryString.length());
            myQueryString = queryData.toString();
        }
    } else {
        myQueryString = SolrManager.SOLR_ALL_QUERY;
    }
    log.log(Level.FINER, myQueryString);

    // execute the searchComponent method and bring back from solr a list array
    List<SolrComponentModel> resultsList = new ArrayList<>();
    try {
        SolrQuery solrQuery = new SolrQuery();
        solrQuery.setQuery(myQueryString);

        // fields to be returned back from solr
        solrQuery.setFields(SolrComponentModel.ID_FIELD, SolrComponentModel.ISCOMPONENT_FIELD);
        solrQuery.setStart(filter.getOffset());
        solrQuery.setRows(filter.getMax());

        Field sortField = ReflectionUtil.getField(new SolrComponentModel(), filter.getSortField());
        if (sortField != null) {
            String sortFieldText = filter.getSortField();
            org.apache.solr.client.solrj.beans.Field fieldAnnotation = sortField
                    .getAnnotation(org.apache.solr.client.solrj.beans.Field.class);
            if (fieldAnnotation != null) {
                sortFieldText = fieldAnnotation.value();
            }
            SolrQuery.ORDER order = SolrQuery.ORDER.desc;
            if (OpenStorefrontConstant.SORT_ASCENDING.equalsIgnoreCase(filter.getSortOrder())) {
                order = SolrQuery.ORDER.asc;
            }
            solrQuery.addSort(sortFieldText, order);
        }

        solrQuery.setIncludeScore(true);

        QueryResponse response = SolrManager.getServer().query(solrQuery);
        SolrDocumentList results = response.getResults();
        DocumentObjectBinder binder = new DocumentObjectBinder();
        resultsList = binder.getBeans(SolrComponentModel.class, results);
    } catch (SolrServerException ex) {
        throw new OpenStorefrontRuntimeException("Search Failed",
                "Contact System Admin.  Seach server maybe Unavailable", ex);
    } catch (Exception ex) {
        log.log(Level.WARNING, "Solr query failed unexpectly; likely bad input.", ex);
    }

    //Pulling the full object on the return
    List<ComponentSearchView> views = new ArrayList<>();

    List<String> componentIds = new ArrayList<>();
    for (SolrComponentModel result : resultsList) {
        if (result.getIsComponent()) {
            componentIds.add(result.getId());
        }
    }

    //remove bad indexes, if any
    List<ComponentSearchView> componentSearchViews = getComponentService().getSearchComponentList(componentIds);
    Set<String> goodComponentIdSet = new HashSet<>();
    for (ComponentSearchView view : componentSearchViews) {
        goodComponentIdSet.add(view.getComponentId());
    }

    for (String componentId : componentIds) {
        if (goodComponentIdSet.contains(componentId) == false) {
            log.log(Level.FINE, MessageFormat.format("Removing bad index: {0}", componentId));
            deleteById(componentId);
        }
    }
    views.addAll(componentSearchViews);

    List<ComponentSearchView> articleViews = getAttributeService().getArticlesSearchView();
    Map<String, ComponentSearchView> allViews = new HashMap<>();
    for (ComponentSearchView componentSearchView : articleViews) {
        AttributeCodePk attributeCodePk = new AttributeCodePk();
        attributeCodePk.setAttributeType(componentSearchView.getArticleAttributeType());
        attributeCodePk.setAttributeCode(componentSearchView.getArticleAttributeCode());
        allViews.put(attributeCodePk.toKey(), componentSearchView);
    }
    for (SolrComponentModel result : resultsList) {

        if (result.getIsComponent() == false) {
            ComponentSearchView view = allViews.get(result.getId());
            if (view != null) {
                views.add(view);
            } else {
                log.log(Level.FINE, MessageFormat.format("Removing bad index: {0}", result.getId()));
                deleteById(result.getId());
            }
        }
    }

    //TODO: Get the score and sort by score
    return views;
}

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

License:Apache License

private JSONObject getPopularGenomes() {
    JSONObject jsonData = null;//from ww w  .  j a v a  2s  .c om
    JSONArray list = new JSONArray();

    DataApiHandler dataApi = new DataApiHandler();

    for (String genomeId : REFERENCE_GENOME_IDS) {

        Genome genome = dataApi.getGenome(genomeId);

        // construct genome
        JSONObject popGenome = new JSONObject();
        popGenome.put("link", URL_GENOMEOVERVIEW_TAB.replace("{cType}", "genome").replace("{cId}", genomeId));
        popGenome.put("popularName", genome.getGenomeName());
        popGenome.put("gb_link", URL_GENOMEBROWSER.replace("{cType}", "genome").replace("{cId}", genomeId));

        // meta data
        JSONObject meta = new JSONObject();
        meta.put("genome_status", genome.getGenomeStatus());
        meta.put("completion_date", genome.hasCompletionDate() ? genome.getCompletionDate() : "");
        meta.put("collection_date", genome.hasCollectionDate() ? genome.getCollectionDate() : "");
        meta.put("isolation_country", genome.hasIsolationCountry() ? genome.getIsolationCountry() : "");
        meta.put("host_name", genome.hasHostName() ? genome.getHostName() : "");
        meta.put("disease", genome.hasDisease() ? StringUtils.join(genome.getDisease(), ", ") : "");
        meta.put("chromosomes", genome.getChromosomes());
        meta.put("plasmids", genome.getPlasmids());
        meta.put("contigs", genome.getContigs());
        meta.put("genome_length", genome.getGenomeLength());

        popGenome.put("metadata", meta);

        JSONArray data = new JSONArray();

        // Features
        JSONObject ft = new JSONObject();
        ft.put("description", "Features");
        ft.put("link", URL_FEATURETABLE_TAB.replace("{cType}", "genome").replace("{cId}", genomeId)
                .replace("{featureType}", "").replace("{filterType}", ""));
        ft.put("picture", "/patric/images/icon-popular-feature.png");
        ft.put("data", genome.getPatricCds());
        data.add(ft);

        // Pathways
        JSONObject pw = new JSONObject();
        pw.put("description", "Pathways");
        pw.put("link",
                URL_PATHWAY_TAB.replace("{cType}", "genome").replace("{cId}", genomeId).replace("{pId}", ""));
        pw.put("picture", "/patric/images/icon-popular-pathway.png");

        int cntPathway = 0;
        try {
            SolrQuery query = new SolrQuery("genome_id:" + genomeId);
            // {stat:{field:{field:genome_id,facet:{pathway_count:"unique(pathway_id)"}}}}}
            query.setRows(0).setFacet(true).set("json.facet",
                    "{stat:{field:{field:genome_id,facet:{pathway_count:\"unique(pathway_id)\"}}}}}");

            LOGGER.trace("[{}] {}", 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");
            Map firstPathway = buckets.get(0);
            cntPathway = (Integer) firstPathway.get("pathway_count");
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }
        pw.put("data", cntPathway);
        data.add(pw);

        // Protein Family
        JSONObject pf = new JSONObject();
        pf.put("description", "Protein Families");
        pf.put("link", URL_PROTEINFAMILY_TAB.replace("{cType}", "genome").replace("{cId}", genomeId));
        pf.put("picture", "/patric/images/icon-popular-proteinfamily.png");

        // Experiment
        JSONObject tr = new JSONObject();
        tr.put("description", "Transcriptomic Experiments");
        tr.put("link", URL_TRANSCRIPTOMICS_TAB.replace("{cType}", "genome").replace("{cId}", genomeId)
                .replace("{kw}", ""));

        long numFound = 0;
        try {
            SolrQuery query = new SolrQuery("genome_ids:" + genomeId);
            query.setRows(0);

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

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

            Map resp = jsonReader.readValue(apiResponse);
            Map respBody = (Map) resp.get("response");
            numFound = (Integer) respBody.get("numFound");
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }
        tr.put("picture", "/patric/images/icon-popular-experiment.png");
        tr.put("data", (int) numFound);

        data.add(tr);

        try {
            SolrQuery query = new SolrQuery(
                    "figfam_id:[* TO *] AND annotation:PATRIC AND genome_id:" + genomeId);
            query.setRows(0);

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

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

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

            pf.put("data", respBody.get("numFound"));
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }
        data.add(pf);

        popGenome.put("popularData", data);

        list.add(popGenome);
    }
    if (list.size() > 0) {
        jsonData = new JSONObject();
        jsonData.put("popularList", list);
        jsonData.put("popularTitle", "Select Genomes");
    }
    return jsonData;
}

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

License:Apache License

private JSONObject getPopularGenomesForPathways() {

    JSONObject jsonData = null;/*from  w  ww .  j  a va  2  s.  c o m*/
    JSONArray list = new JSONArray();

    for (String genomeId : REFERENCE_GENOME_IDS) {
        Genome genome = dataApi.getGenome(genomeId);

        // construct genome
        JSONObject popGenome = new JSONObject();

        popGenome.put("popularName", genome.getGenomeName());
        popGenome.put("link",
                URL_PATHWAY_TAB.replace("{cType}", "genome").replace("{cId}", genomeId).replace("{pId}", ""));

        JSONArray data = new JSONArray();

        LinkedList<Map<String, String>> pathwayList = new LinkedList<>();

        try {
            //{stat:{field:{field:pathway_id,sort:{ec_count:desc},facet:{ec_count:"unique(ec_number)",gene_count:"unique(feature_id)",field:{field:pathway_name}}}}}
            SolrQuery query = new SolrQuery("genome_id:" + genomeId).addFilterQuery("annotation:PATRIC");
            query.setRows(0).setFacet(true).set("json.facet",
                    "{stat:{field:{field:pathway_id,sort:{ec_count:desc},facet:{ec_count:\"unique(ec_number)\",gene_count:\"unique(feature_id)\",field:{field:pathway_name}}}}}");

            LOGGER.debug("getPopularGenomesForPathways: [{}] {}", 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");

            for (Map bucket : buckets) {
                Map<String, String> pathway = new HashMap<>();
                pathway.put("id", bucket.get("val").toString());
                pathway.put("ec_count", bucket.get("ec_count").toString());
                pathway.put("gene_count", bucket.get("gene_count").toString());

                // getting name
                List<Map> subBuckets = (List) ((Map) bucket.get("field")).get("buckets");
                pathway.put("name", subBuckets.get(0).get("val").toString());

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

        for (Map<String, String> pathway : pathwayList) {
            JSONObject pw = new JSONObject();

            pw.put("name", pathway.get("name"));
            pw.put("name_link", URL_PATHWAY_TAB.replace("{cType}", "genome").replace("{cId}", genomeId)
                    .replace("{pId}", pathway.get("id")));
            // pw.put("class", item.get("pathway_class"));
            pw.put("gene_count", pathway.get("gene_count"));
            pw.put("gene_link",
                    URL_PATHWAY_GENE_TAB.replace("{cId}", genomeId).replace("{pId}", pathway.get("id")));
            pw.put("ec_count", pathway.get("ec_count"));
            pw.put("ec_link",
                    URL_PATHWAY_EC_TAB.replace("{cId}", genomeId).replace("{pId}", pathway.get("id")));

            data.add(pw);
        }
        popGenome.put("popularData", data);
        list.add(popGenome);
    }
    if (list.size() > 0) {
        jsonData = new JSONObject();
        jsonData.put("popularList", list);
        jsonData.put("popularTitle", "Select Genomes");
    }
    return jsonData;
}

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

License:Apache License

private JSONObject getPopularGenomesForTranscriptomics() {
    JSONObject jsonData = null;//from  w w  w.  ja  v  a2s .  com
    JSONArray list = new JSONArray();

    for (String genomeId : REFERENCE_GENOME_IDS_TRANSCRIPTOMICS) {

        // construct genome node
        JSONObject popGenome = new JSONObject();

        Genome genome = dataApi.getGenome(genomeId);

        popGenome.put("popularName", genome.getGenomeName());
        popGenome.put("link", URL_TRANSCRIPTOMICS_TAB.replace("{cType}", "genome").replace("{cId}", genomeId)
                .replace("{kw}", ""));

        // Retrieve eId associated a given genome
        List<String> eIds = new ArrayList<>();
        try {
            SolrQuery query = new SolrQuery("genome_ids:" + genomeId);
            query.setRows(1000).setFields("eid");

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

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

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

            for (Map doc : sdl) {
                eIds.add(doc.get("eid").toString());
            }
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }

        JSONObject gm = new JSONObject();
        JSONObject ec = new JSONObject();
        gm.put("title", "Gene Modifications");
        ec.put("title", "Experiment Conditions");
        JSONArray data = new JSONArray();
        try {
            Map response = dataApi.getFieldFacets(SolrCore.TRANSCRIPTOMICS_EXPERIMENT, "*:*",
                    "eid:(" + StringUtils.join(eIds, " OR ") + ")", "mutant,condition");
            Map facets = (Map) response.get("facets");

            Map mutantsFacet = (Map) facets.get("mutant");

            int i = 0;
            for (Map.Entry<String, Integer> entry : (Iterable<Map.Entry>) mutantsFacet.entrySet()) {
                JSONObject mutant = new JSONObject();
                mutant.put("label", entry.getKey());
                mutant.put("value", entry.getValue());
                data.add(mutant);
                i++;
                if (i > 4) {
                    break;
                }
            }
            gm.put("data", data);

            // top 5 experiment conditoins
            data = new JSONArray();
            Map conditionsFacet = (Map) facets.get("condition");
            i = 0;
            for (Map.Entry<String, Integer> entry : (Iterable<Map.Entry>) conditionsFacet.entrySet()) {
                JSONObject condition = new JSONObject();
                condition.put("label", entry.getKey());
                condition.put("value", entry.getValue());
                data.add(condition);
                i++;
                if (i > 4) {
                    break;
                }
            }
            ec.put("data", data);
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }

        popGenome.put("GeneModifications", gm);
        popGenome.put("ExperimentConditions", ec);

        list.add(popGenome);
    }
    if (list.size() > 0) {
        jsonData = new JSONObject();
        jsonData.put("popularList", list);
        jsonData.put("popularTitle", "Select Genomes");
    }
    return jsonData;
}

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

License:Apache License

private JSONObject getPathwayECDist() {
    JSONObject jsonData;//w  w  w .  j a  va2 s . c  om
    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 JSONArray getFIGFamConservationDistribution(int taxonId) {
    JSONArray dist = new JSONArray();

    try {//from   ww  w.j  a v a 2s  .  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;
}