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

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Here is the source code for edu.vt.vbi.patric.portlets.PathwayTable.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.common.DataApiHandler;
import edu.vt.vbi.patric.common.SolrCore;
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.slf4j.LoggerFactory;

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

public class PathwayTable extends GenericPortlet {

    private static final org.slf4j.Logger LOGGER = LoggerFactory.getLogger(PathwayTable.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");
        response.setTitle("Pathways");

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

    @SuppressWarnings("unchecked")
    public void serveResource(ResourceRequest request, ResourceResponse response)
            throws PortletException, IOException {

        response.setContentType("application/json");

        HashMap<String, String> key = new HashMap<>();

        if (request.getParameter("id") != null) {
            key.put("feature_id", request.getParameter("id"));
        }

        DataApiHandler dataApi = new DataApiHandler(request);

        int count_total = 0;
        JSONArray results = new JSONArray();
        List<String> pathwayKeys = new ArrayList<>();
        Map<String, Integer> mapOccurrence = new HashMap<>();
        try {
            SolrQuery query = new SolrQuery("feature_id:" + request.getParameter("id"));
            query.setRows(dataApi.MAX_ROWS);

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

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

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

            for (Map doc : sdl) {
                String pathwayKey = "(pathway_id:" + doc.get("pathway_id").toString() + " AND ec_number:"
                        + doc.get("ec_number").toString() + ")";

                pathwayKeys.add(pathwayKey);
            }

            SolrQuery queryRef = new SolrQuery(StringUtils.join(pathwayKeys, " OR "));
            queryRef.setFields("pathway_id,ec_number,occurrence");
            queryRef.setRows(pathwayKeys.size());

            apiResponse = dataApi.solrQuery(SolrCore.PATHWAY_REF, queryRef);

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

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

            for (Map doc : refList) {
                mapOccurrence.put(doc.get("pathway_id") + "_" + doc.get("ec_number"),
                        (Integer) doc.get("occurrence"));
            }

            for (Map doc : sdl) {
                JSONObject item = new JSONObject();
                item.put("pathway_id", doc.get("pathway_id"));
                item.put("feature_id", doc.get("feature_id"));
                item.put("pathway_name", doc.get("pathway_name"));
                item.put("pathway_class", doc.get("pathway_class"));
                item.put("algorithm", doc.get("annotation"));
                item.put("ec_number", doc.get("ec_number"));
                item.put("ec_name", doc.get("ec_description"));
                item.put("taxon_id", doc.get("taxon_id"));
                item.put("genome_id", doc.get("genome_id"));

                item.put("occurrence", mapOccurrence.get(doc.get("pathway_id") + "_" + doc.get("ec_number")));

                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();
    }
}