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

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Here is the source code for edu.vt.vbi.patric.portlets.SequenceSummaryPortlet.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.common.DataApiHandler;
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.slf4j.Logger;
import org.slf4j.LoggerFactory;

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

public class SequenceSummaryPortlet extends GenericPortlet {

    private static final Logger LOGGER = LoggerFactory.getLogger(SequenceSummaryPortlet.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 && cType.equals("genome")) {
            SiteHelper.setHtmlMetaElements(request, response, "Genome Overview");
        }

        PortletRequestDispatcher prd;

        if (cType != null && cId != null) {
            prd = getPortletContext().getRequestDispatcher("/WEB-INF/jsp/overview/sequence_summary_init.jsp");
            prd.include(request, response);
        } else {
            PrintWriter writer = response.getWriter();
            writer.write("<p>Invalid Parameter - missing context information</p>");
            writer.close();
        }
    }

    public void serveResource(ResourceRequest request, ResourceResponse response)
            throws PortletException, IOException {

        String contextType = request.getParameter("context_type");
        String contextId = request.getParameter("context_id");
        String genomeFilter = request.getParameter("genome_filter");

        DataApiHandler dataApi = new DataApiHandler(request);

        if (contextType != null && contextId != null) {

            if (contextType.equals("genome")) {

                Genome genome = dataApi.getGenome(contextId);

                if (genome != null) {

                    // check genome_amr data is available.
                    SolrQuery query = new SolrQuery("genome_id:" + genome.getId());
                    query.addSort("antibiotic", SolrQuery.ORDER.asc).addSort("resistant_phenotype",
                            SolrQuery.ORDER.asc);
                    query.setRows(dataApi.MAX_ROWS);
                    dataApi = new DataApiHandler(request);
                    String apiResponse = dataApi.solrQuery(SolrCore.GENOME_AMR, query);

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

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

                    request.setAttribute("genome", genome);
                    request.setAttribute("amr", amr);

                    response.setContentType("text/html");
                    PortletRequestDispatcher prd = getPortletContext()
                            .getRequestDispatcher("/WEB-INF/jsp/overview/sequence_summary.jsp");
                    prd.include(request, response);
                }
            } else {
                // taxon level

                List<String> annotations = Arrays.asList("PATRIC", "RefSeq");

                for (String annotation : annotations) {

                    String queryParam;

                    switch (annotation) {
                    case "PATRIC":
                        queryParam = "patric_cds:[1 TO *]";
                        break;
                    case "RefSeq":
                        queryParam = "refseq_cds:[1 TO *]";
                        break;
                    default:
                        queryParam = "*:*";
                        break;
                    }

                    if (genomeFilter != null && !genomeFilter.equals("")) {
                        queryParam += " AND (" + genomeFilter + ")";
                    }

                    Map counts = dataApi.getFieldFacets(SolrCore.GENOME, queryParam,
                            "taxon_lineage_ids:" + contextId, "genome_status");

                    request.setAttribute(annotation, counts);
                }

                response.setContentType("text/html");
                PortletRequestDispatcher prd = getPortletContext()
                        .getRequestDispatcher("/WEB-INF/jsp/overview/sequence_summary.jsp");
                prd.include(request, response);
            }
        }
    }
}