Java tutorial
/** * **************************************************************************** * Copyright 2014 Virginia Polytechnic Institute and State University * <p/> * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * <p/> * http://www.apache.org/licenses/LICENSE-2.0 * <p/> * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * **************************************************************************** */ package edu.vt.vbi.patric.portlets; import edu.vt.vbi.patric.beans.Genome; import edu.vt.vbi.patric.common.*; import org.apache.commons.lang.StringUtils; import org.apache.solr.client.solrj.SolrQuery; import org.codehaus.jackson.map.ObjectMapper; import org.codehaus.jackson.map.ObjectReader; import org.json.simple.JSONArray; import org.json.simple.JSONObject; import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import javax.portlet.*; import java.io.IOException; import java.io.PrintWriter; import java.util.*; public class CompPathwayMap extends GenericPortlet { private static final Logger LOGGER = LoggerFactory.getLogger(CompPathwayMap.class); private ObjectReader jsonReader; @Override public void init() throws PortletException { super.init(); ObjectMapper objectMapper = new ObjectMapper(); jsonReader = objectMapper.reader(Map.class); } @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 { 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); } @SuppressWarnings("unchecked") public void serveResource(ResourceRequest request, ResourceResponse response) throws PortletException, IOException { response.setContentType("application/json"); String callType = request.getParameter("callType"); switch (callType) { case "EcTable": { processEcTable(request, response); break; } case "KeggMap": { processKeggMap(request, response); break; } case "HeatMap": { processHeatMap(request, response); break; } } } private void processEcTable(ResourceRequest request, ResourceResponse response) throws IOException { String genomeId = request.getParameter("genomeId"); String taxonId = request.getParameter("taxonId"); String cType = request.getParameter("cType"); String map = request.getParameter("map"); String algorithm = request.getParameter("algorithm"); String pk = request.getParameter("pk"); Map<String, String> key = null; if (pk != null && !pk.isEmpty()) { key = jsonReader.readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk)); } int count_total = 0; JSONArray results = new JSONArray(); try { Set<String> ecNumbers = new HashSet<>(); DataApiHandler dataApi = new DataApiHandler(request); SolrQuery query = new SolrQuery("pathway_id:" + map + " AND annotation:" + algorithm); if (taxonId != null && !taxonId.equals("")) { query.addFilterQuery( SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "taxon_lineage_ids:" + taxonId)); } if (genomeId != null && !genomeId.equals("")) { query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "genome_id:(" + genomeId.replaceAll(",", " OR ") + ")")); } if (key != null && key.containsKey("genomeId") && !key.get("genomeId").equals("")) { query.addFilterQuery("genome_id:(" + key.get("genomeId").replaceAll(",", " OR ") + ")"); } query.setRows(0).setFacet(true); query.add("json.facet", "{stat:{field:{field:ec_number,limit:-1,facet:{genome_count:\"unique(genome_id)\",gene_count:\"unique(feature_id)\"}}}}"); String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY, query); Map resp = jsonReader.readValue(apiResponse); Map respBody = (Map) resp.get("response"); int numFound = (Integer) respBody.get("numFound"); if (numFound > 0) { List<Map> buckets = (List<Map>) ((Map) ((Map) resp.get("facets")).get("stat")).get("buckets"); Map<String, Map> mapStat = new HashMap<>(); for (Map value : buckets) { if (Integer.parseInt(value.get("gene_count").toString()) > 0) { mapStat.put(value.get("val").toString(), value); ecNumbers.add(value.get("val").toString()); } } if (!ecNumbers.isEmpty()) { query = new SolrQuery( "pathway_id:" + map + " AND ec_number:(" + StringUtils.join(ecNumbers, " OR ") + ")"); query.setRows(ecNumbers.size()).setFields("ec_number,ec_description,occurrence"); query.addSort("ec_number", SolrQuery.ORDER.asc); apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, query); resp = jsonReader.readValue(apiResponse); Map respBdoby = (Map) resp.get("response"); count_total = (Integer) respBdoby.get("numFound"); List<Map> sdl = (List<Map>) respBdoby.get("docs"); for (Map doc : sdl) { String ecNumber = doc.get("ec_number").toString(); Map stat = mapStat.get(ecNumber); JSONObject item = new JSONObject(); item.put("algorithm", algorithm); item.put("ec_name", doc.get("ec_description")); item.put("ec_number", ecNumber); item.put("occurrence", doc.get("occurrence")); item.put("gene_count", stat.get("gene_count")); item.put("genome_count", stat.get("genome_count")); results.add(item); } } } } catch (IOException e) { LOGGER.error(e.getMessage(), e); } JSONObject jsonResult = new JSONObject(); try { jsonResult.put("total", count_total); jsonResult.put("results", results); } catch (Exception ex) { LOGGER.error(ex.getMessage(), ex); } PrintWriter writer = response.getWriter(); jsonResult.writeJSONString(writer); writer.close(); } private void processKeggMap(ResourceRequest request, ResourceResponse response) throws IOException { Map<String, String> key = new HashMap<>(); DataApiHandler dataApi = new DataApiHandler(request); JSONObject ret = new JSONObject(); JSONObject val = new JSONObject(); try { val = (JSONObject) (new JSONParser()).parse(request.getParameter("val").toString()); } catch (ParseException e) { LOGGER.error(e.getMessage(), e); } String need = val.get("need").toString(); String genomeId = null, taxonId = null, map = null, pk = null; if (val.containsKey("genomeId") && val.get("genomeId") != null && !val.get("genomeId").equals("")) { genomeId = val.get("genomeId").toString(); } if (val.containsKey("taxonId") && val.get("taxonId") != null && !val.get("taxonId").equals("")) { taxonId = val.get("taxonId").toString(); } if (val.containsKey("map") && val.get("map") != null && !val.get("map").equals("")) { map = val.get("map").toString(); } if (val.containsKey("pk") && val.get("pk") != null && !val.get("pk").equals("")) { pk = val.get("pk").toString(); } if (need.equals("all")) { if (genomeId != null) { key.put("genomeId", genomeId); } if (taxonId != null) { key.put("taxonId", taxonId); } if (map != null) { key.put("map", map); } Map<String, String> sessKey = null; if (pk != null && !pk.isEmpty()) { sessKey = jsonReader.readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk)); if (sessKey != null && sessKey.containsKey("genomeId") && !sessKey.get("genomeId").equals("")) { genomeId = sessKey.get("genomeId"); } } List<String> annotations = Arrays.asList("PATRIC", "RefSeq"); // getting coordinates try { JSONArray listCoordinates = new JSONArray(); for (String annotation : annotations) { Set<String> ecNumbers = new HashSet<String>(); // step1. genome_count, feature_count // pathway/select?q=pathway_id:00053+AND+annotation:PATRIC&fq={!join+from=genome_id+to=genome_id+fromIndex=genome}taxon_lineage_ids:83332+AND+genome_status:(complete+OR+wgs) // &rows=0&facet=true&json.facet={stat:{field:{field:ec_number,limit:-1,facet:{genome_count:"unique(genome_id)",gene_count:"unique(feature_id)"}}}} SolrQuery query = new SolrQuery("pathway_id:" + map + " AND annotation:" + annotation); if (taxonId != null) { query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "taxon_lineage_ids:" + taxonId)); } if (genomeId != null) { query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "genome_id:(" + genomeId.replaceAll(",", " OR ") + ")")); } query.setRows(0).setFacet(true); query.add("json.facet", "{stat:{field:{field:ec_number,limit:-1,facet:{genome_count:\"unique(genome_id)\",gene_count:\"unique(feature_id)\"}}}}"); LOGGER.debug("step 1. [{}] {}", SolrCore.PATHWAY.getSolrCoreName(), query); String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY, query); Map resp = jsonReader.readValue(apiResponse); Map respBody = (Map) resp.get("response"); int numFound = (Integer) respBody.get("numFound"); if (numFound > 0) { List<Map> buckets = (List<Map>) ((Map) ((Map) resp.get("facets")).get("stat")) .get("buckets"); Map<String, Map> mapStat = new HashMap<>(); for (Map value : buckets) { if (Integer.parseInt(value.get("count").toString()) > 0) { mapStat.put(value.get("val").toString(), value); ecNumbers.add(value.get("val").toString()); } } // step2. coordinates, occurrence // pathway_ref/select?q=pathway_id:00010+AND+map_type:enzyme%+AND+ec_number:("1.2.1.3"+OR+"1.1.1.1")&fl=ec_number,ec_description,map_location,occurrence if (!ecNumbers.isEmpty()) { query = new SolrQuery("pathway_id:" + map + " AND map_type:enzyme AND ec_number:(" + StringUtils.join(ecNumbers, " OR ") + ")"); query.setFields("ec_number,ec_description,map_location,occurrence"); query.setRows(dataApi.MAX_ROWS); LOGGER.trace("genome_x_y: [{}] {}", SolrCore.PATHWAY_REF.getSolrCoreName(), query); apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, query); resp = jsonReader.readValue(apiResponse); respBody = (Map) resp.get("response"); List<Map> sdl = (List<Map>) respBody.get("docs"); for (Map doc : sdl) { String ecNumber = doc.get("ec_number").toString(); Map stat = mapStat.get(ecNumber); if (!stat.get("gene_count").toString().equals("0")) { List<String> locations = (List<String>) doc.get("map_location"); for (String location : locations) { JSONObject coordinate = new JSONObject(); coordinate.put("algorithm", annotation); coordinate.put("description", doc.get("ec_description")); coordinate.put("ec_number", ecNumber); coordinate.put("genome_count", stat.get("genome_count")); String[] loc = location.split(","); coordinate.put("x", loc[0]); coordinate.put("y", loc[1]); listCoordinates.add(coordinate); } } } } } } ret.put("genome_x_y", listCoordinates); } catch (IOException e) { LOGGER.error(e.getMessage(), e); } // get pathways try { SolrQuery query = new SolrQuery("annotation:(" + StringUtils.join(annotations, " OR ") + ")"); if (taxonId != null) { query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "taxon_lineage_ids:" + taxonId)); } if (genomeId != null) { query.addFilterQuery("genome_id:(" + genomeId.replaceAll(",", " OR ") + ")"); } query.setFields("pathway_id,pathway_name,annotation").setRows(dataApi.MAX_ROWS); LOGGER.trace("genome_pathway_x_y: [{}] {}", SolrCore.PATHWAY.getSolrCoreName(), query); String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY, query); Map resp = jsonReader.readValue(apiResponse); Map respBody = (Map) resp.get("response"); List<Map> sdl = (List<Map>) respBody.get("docs"); JSONArray listEnzymes = new JSONArray(); Set<String> hash = new HashSet<>(); for (Map doc : sdl) { // TODO: need to improve this using solr String hashKey = doc.get("pathway_id").toString() + ":" + doc.get("annotation").toString(); if (!hash.contains(hashKey)) { hash.add(hashKey); JSONObject enzyme = new JSONObject(); enzyme.put("algorithm", doc.get("annotation")); enzyme.put("map_id", doc.get("pathway_id")); enzyme.put("map_name", doc.get("pathway_name")); listEnzymes.add(enzyme); } } ret.put("genome_pathway_x_y", listEnzymes); } catch (IOException e) { LOGGER.error(e.getMessage(), e); } // map_ids_in_map try { SolrQuery query = new SolrQuery("pathway_id:" + map + " AND map_type:path"); query.setFields("ec_number,ec_description,map_location").setRows(dataApi.MAX_ROWS); LOGGER.trace("map_ids_in_map: [{}] {}", SolrCore.PATHWAY_REF.getSolrCoreName(), query); String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, query); Map resp = jsonReader.readValue(apiResponse); Map respBody = (Map) resp.get("response"); List<Map> sdl = (List<Map>) respBody.get("docs"); JSONArray listCoordinates = new JSONArray(); for (Map doc : sdl) { List<String> locations = (List<String>) doc.get("map_location"); for (String location : locations) { JSONObject coordinate = new JSONObject(); coordinate.put("source_id", doc.get("ec_number")); String[] loc = location.split(","); coordinate.put("x", loc[0]); coordinate.put("y", loc[1]); coordinate.put("width", loc[2]); coordinate.put("height", loc[3]); listCoordinates.add(coordinate); } } ret.put("map_ids_in_map", listCoordinates); } catch (IOException e) { LOGGER.error(e.getMessage(), e); } // all coordinates try { SolrQuery query = new SolrQuery("pathway_id:" + map + " AND map_type:enzyme"); query.setFields("ec_number,ec_description,map_location").setRows(dataApi.MAX_ROWS); LOGGER.trace("all_coordinates: [{}] {}", SolrCore.PATHWAY_REF.getSolrCoreName(), query); String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, query); Map resp = jsonReader.readValue(apiResponse); Map respBody = (Map) resp.get("response"); List<Map> sdl = (List<Map>) respBody.get("docs"); JSONArray listCoordinates = new JSONArray(); for (Map doc : sdl) { List<String> locations = (List<String>) doc.get("map_location"); for (String location : locations) { JSONObject coordinate = new JSONObject(); coordinate.put("ec", doc.get("ec_number")); coordinate.put("description", doc.get("ec_description")); String[] loc = location.split(","); coordinate.put("x", loc[0]); coordinate.put("y", loc[1]); listCoordinates.add(coordinate); } } ret.put("all_coordinates", listCoordinates); } catch (IOException e) { LOGGER.error(e.getMessage(), e); } } else { // need: feature_id or ec_number JSONArray coordinates = new JSONArray(); if (need.equals("ec_number")) { try { SolrQuery query = new SolrQuery("*:*"); if (map != null) { query.addFilterQuery("pathway_id:(" + map + ")"); } LOGGER.trace("[{}] {}", SolrCore.PATHWAY_REF.getSolrCoreName(), query); String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, query); Map resp = jsonReader.readValue(apiResponse); Map respBody = (Map) resp.get("response"); List<Map> sdl = (List<Map>) respBody.get("docs"); for (Map doc : sdl) { List<String> locations = (List<String>) doc.get("map_location"); for (String loc : locations) { JSONObject coordinate = new JSONObject(); coordinate.put("ec_number", doc.get("ec_number")); String[] xy = loc.split(","); coordinate.put("x", xy[0]); coordinate.put("y", xy[1]); coordinates.add(coordinate); } } } catch (IOException e) { LOGGER.error(e.getMessage(), e); } } else { // feature String featureIds = null; if (val.containsKey("value") && val.get("value") != null && !val.get("value").equals("")) { featureIds = val.get("value").toString(); } try { SolrQuery query = new SolrQuery("*:*"); if (map != null) { query.addFilterQuery("pathway_id:(" + map + ")"); } if (featureIds != null) { query.addFilterQuery(SolrCore.PATHWAY.getSolrCoreJoin("ec_number", "ec_number", "feature_id:(" + featureIds.replaceAll(",", " OR ") + ")")); } LOGGER.trace("coordinates: [{}] {}", SolrCore.PATHWAY_REF.getSolrCoreName(), query); String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, query); Map resp = jsonReader.readValue(apiResponse); Map respBody = (Map) resp.get("response"); List<Map> sdl = (List<Map>) respBody.get("docs"); for (Map doc : sdl) { List<String> locations = (List<String>) doc.get("map_location"); for (String loc : locations) { JSONObject coordinate = new JSONObject(); coordinate.put("ec_number", doc.get("ec_number")); String[] xy = loc.split(","); coordinate.put("x", xy[0]); coordinate.put("y", xy[1]); coordinates.add(coordinate); } } } catch (IOException e) { LOGGER.error(e.getMessage(), e); } } ret.put("coordinates", coordinates); } response.setContentType("application/json"); ret.writeJSONString(response.getWriter()); } private void processHeatMap(ResourceRequest request, ResourceResponse response) throws IOException { DataApiHandler dataApi = new DataApiHandler(request); String genomeId, taxonId, algorithm, map; genomeId = request.getParameter("genomeId"); taxonId = request.getParameter("taxonId"); algorithm = request.getParameter("algorithm"); map = request.getParameter("map"); JSONObject json = new JSONObject(); try { SolrQuery query = new SolrQuery("pathway_id:" + map); if (algorithm != null && !algorithm.equals("")) { query.addFilterQuery("annotation:" + algorithm); } if (taxonId != null && !taxonId.equals("")) { query.addFilterQuery( SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "taxon_lineage_ids:" + taxonId)); } if (genomeId != null && !genomeId.equals("")) { query.addFilterQuery(SolrCore.GENOME.getSolrCoreJoin("genome_id", "genome_id", "genome_id:(" + genomeId.replaceAll(",", " OR ") + ")")); } query.setRows(dataApi.MAX_ROWS).setFields("genome_id,annotation,ec_number,ec_description") .setFacet(true); // {stat:{field:{field:genome_ec,limit:-1,facet:{gene_count:\"unique(feature_id)\"}}}} query.add("json.facet", "{stat:{field:{field:genome_ec,limit:-1}}}}"); LOGGER.debug("heatmap step 1: {}", query.toString()); String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY, query); Map resp = jsonReader.readValue(apiResponse); Map respBody = (Map) resp.get("response"); int numFound = (Integer) respBody.get("numFound"); if (numFound > 0) { List<Map> buckets = (List<Map>) ((Map) ((Map) resp.get("facets")).get("stat")).get("buckets"); respBody = (Map) resp.get("response"); List<Map> sdl = (List<Map>) respBody.get("docs"); Map<String, Integer> mapStat = new HashMap<>(); for (Map value : buckets) { if (Integer.parseInt(value.get("count").toString()) > 0) { mapStat.put(value.get("val").toString(), (Integer) value.get("count")); } } JSONArray items = new JSONArray(); for (Map doc : sdl) { final JSONObject item = new JSONObject(); item.put("genome_id", doc.get("genome_id")); item.put("algorithm", doc.get("annotation")); item.put("ec_number", doc.get("ec_number")); item.put("ec_name", doc.get("ec_description")); Integer count = mapStat.get(doc.get("genome_id") + "_" + doc.get("ec_number")); item.put("gene_count", String.format("%02x", count)); // 2-digit hex string items.add(item); } // if data exceeds limit, keep going int i = 1; while (sdl.size() == 25000) { query.setStart(25000 * i); apiResponse = dataApi.solrQuery(SolrCore.PATHWAY, query); resp = jsonReader.readValue(apiResponse); respBody = (Map) resp.get("response"); sdl = (List<Map>) respBody.get("docs"); for (Map doc : sdl) { final JSONObject item = new JSONObject(); item.put("genome_id", doc.get("genome_id")); item.put("algorithm", doc.get("annotation")); item.put("ec_number", doc.get("ec_number")); item.put("ec_name", doc.get("ec_description")); Integer count = mapStat.get(doc.get("genome_id") + "_" + doc.get("ec_number")); item.put("gene_count", String.format("%02x", count)); // 2-digit hex string items.add(item); } i++; } json.put("data", items); } } catch (IOException e) { LOGGER.error(e.getMessage(), e); } try { SolrQuery query = new SolrQuery("*:*"); 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 (algorithm != null && !algorithm.equals("")) { switch (algorithm) { case "PATRIC": query.addFilterQuery("patric_cds:[1 TO *]"); break; case "RefSeq": query.addFilterQuery("refseq_cds:[1 TO *]"); break; case "BRC1": query.addFilterQuery("brc1_cds:[1 TO *]"); break; } } query.setFields("genome_id,genome_name").setRows(dataApi.MAX_ROWS).addSort("genome_name", SolrQuery.ORDER.asc); LOGGER.debug("step 2: [{}] {}", SolrCore.GENOME.getSolrCoreName(), 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); JSONArray items = new JSONArray(); for (Genome genome : genomes) { JSONObject item = new JSONObject(); item.put("genome_id", genome.getId()); item.put("genome_name", genome.getGenomeName()); items.add(item); } json.put("genomes", items); } catch (IOException e) { LOGGER.error(e.getMessage(), e); } response.setContentType("application/json"); json.writeJSONString(response.getWriter()); } }