edu.vt.vbi.patric.portlets.TaxonomyTreePortlet.java Source code

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Here is the source code for edu.vt.vbi.patric.portlets.TaxonomyTreePortlet.java

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/**
 * ****************************************************************************
 * 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.beans.Taxonomy;
import edu.vt.vbi.patric.common.DataApiHandler;
import edu.vt.vbi.patric.common.OrganismTreeBuilder;
import edu.vt.vbi.patric.common.SiteHelper;
import edu.vt.vbi.patric.common.SolrCore;
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.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.portlet.*;
import java.io.IOException;
import java.util.List;
import java.util.Map;

public class TaxonomyTreePortlet extends GenericPortlet {

    private static final Logger LOGGER = LoggerFactory.getLogger(TaxonomyTreePortlet.class);

    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, "Taxonomy Tree");

        String cType = request.getParameter("context_type");
        String cId = request.getParameter("context_id");
        int taxonId = -1;
        if (cType != null && cType.equals("taxon") && cId != null) {
            taxonId = Integer.parseInt(cId);
        }

        request.setAttribute("taxonId", taxonId);

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

    public void serveResource(ResourceRequest request, ResourceResponse response)
            throws PortletException, IOException {
        int taxonId = Integer.parseInt(request.getParameter("taxonId"));
        String mode = request.getParameter("mode");

        DataApiHandler dataApi = new DataApiHandler(request);
        JSONArray tree;
        response.setContentType("application/json");

        switch (mode) {
        case "txtree":
            tree = OrganismTreeBuilder.buildGenomeTree(dataApi, taxonId);
            tree.writeJSONString(response.getWriter());
            break;
        case "azlist":
            tree = OrganismTreeBuilder.buildGenomeList(dataApi, taxonId);
            tree.writeJSONString(response.getWriter());
            break;
        case "tgm":
            tree = OrganismTreeBuilder.buildTaxonGenomeMapping(dataApi, taxonId);
            tree.writeJSONString(response.getWriter());
            break;
        case "search":
            String searchOn = request.getParameter("searchon");
            String keyword = request.getParameter("query");

            tree = new JSONArray();
            SolrQuery query = new SolrQuery();
            if (searchOn.equals("txtree")) {
                query.setQuery("taxon_name:" + keyword + " AND genomes:[1 TO *] AND lineage_ids:" + taxonId);
                query.setRows(10000).addField("taxon_name,taxon_id");

                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);

                for (Taxonomy taxon : taxonomyList) {
                    JSONObject item = new JSONObject();
                    item.put("display_name", taxon.getTaxonName());
                    item.put("taxon_id", taxon.getId());

                    tree.add(item);
                }
            } else {
                // searchOn is "azlist"
                query.setQuery("genome_name:" + keyword + " AND taxon_lineage_ids:" + taxonId);
                query.setRows(10000).addField("genome_name,genome_id");

                String apiResponse = dataApi.solrQuery(SolrCore.TAXONOMY, 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 item = new JSONObject();
                    item.put("display_name", genome.getGenomeName());
                    item.put("genome_id", genome.getId());

                    tree.add(item);
                }
            }

            JSONObject result = new JSONObject();
            result.put("genomeList", tree);
            result.put("keyword", keyword);
            result.put("totalCount", tree.size());

            result.writeJSONString(response.getWriter());
            break;
        default:
            tree = new JSONArray();
            tree.writeJSONString(response.getWriter());
            break;
        }
    }
}