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

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

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

public class FeatureCommentsPortlet extends GenericPortlet {

    private static final org.slf4j.Logger LOGGER = LoggerFactory.getLogger(FeatureCommentsPortlet.class);

    private ObjectReader jsonReader;

    @Override
    public void init() throws PortletException {
        super.init();

        ObjectMapper objectMapper = new ObjectMapper();
        jsonReader = objectMapper.reader(Map.class);
    }

    protected void doView(RenderRequest request, RenderResponse response) throws PortletException, IOException {

        response.setContentType("text/html");
        String cType = request.getParameter("context_type");
        String cId = request.getParameter("context_id");

        if (cType != null && cId != null && cType.equals("feature")) {

            List<Map> listAnnotation = new LinkedList<>();
            DataApiHandler dataApi = new DataApiHandler(request);

            GenomeFeature feature = dataApi.getPATRICFeature(cId);

            if (feature != null) {

                if (feature.hasRefseqLocusTag()) {
                    SolrQuery query = new SolrQuery("refseq_locus_tag:" + feature.getRefseqLocusTag());
                    query.addFilterQuery("!property:Interaction");
                    query.addSort("property", SolrQuery.ORDER.asc).addSort("evidence_code", SolrQuery.ORDER.asc);
                    query.setRows(dataApi.MAX_ROWS);

                    LOGGER.debug("[{}]: {}", SolrCore.STRUCTURED_ASSERTION.getSolrCoreName(), query);
                    String apiResponse = dataApi.solrQuery(SolrCore.STRUCTURED_ASSERTION, query);

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

                    listAnnotation.addAll((List<Map>) respBody.get("docs"));

                    query.setFilterQueries("property:Interaction");
                    query.setSort("value", SolrQuery.ORDER.asc).addSort("evidence_code", SolrQuery.ORDER.asc);

                    LOGGER.debug("[{}]: {}", SolrCore.STRUCTURED_ASSERTION.getSolrCoreName(), query);
                    apiResponse = dataApi.solrQuery(SolrCore.STRUCTURED_ASSERTION, query);

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

                    listAnnotation.addAll((List<Map>) respBody.get("docs"));
                }

                if (!listAnnotation.isEmpty()) {

                    request.setAttribute("listAnnotation", listAnnotation);

                    PortletRequestDispatcher prd = getPortletContext()
                            .getRequestDispatcher("/WEB-INF/jsp/overview/feature_comments.jsp");
                    prd.include(request, response);
                } else {
                    PrintWriter writer = response.getWriter();
                    writer.write("<!-- no feature comment found -->");
                    writer.close();
                }
            }
        } else {
            PrintWriter writer = response.getWriter();
            writer.write("<p>Invalid Parameter - missing context information</p>");
            writer.close();
        }
    }
}