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

Introduction

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

Source

/**
 * ****************************************************************************
 * 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.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.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;

public class SpecialtyGeneEvidencePortlet extends GenericPortlet {

    private static final Logger LOGGER = LoggerFactory.getLogger(SpecialtyGeneEvidencePortlet.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, "Specialty Gene Evidence");
        response.setTitle("Specialty Gene Evidence");

        String source = request.getParameter("sp_source");
        String sourceId = request.getParameter("sp_source_id"); //lmo0433, Rv3875

        if (source != null && !source.equals("") && sourceId != null && !sourceId.equals("")) {

            List<String> properties = Arrays.asList("property", "source", "source_id", "gene_name", "organism",
                    "product", "gi", "gene_id");
            List<String> headers = Arrays.asList("Property", "Source", "Source ID", "Gene", "Organism", "Product",
                    "GI Number", "Gene ID");

            // get properties of gene
            Map<String, Object> gene = null;
            SolrQuery query = new SolrQuery("source:" + source + " AND source_id:" + sourceId);

            DataApiHandler dataApi = new DataApiHandler(request);
            String apiResponse = dataApi.solrQuery(SolrCore.SPECIALTY_GENE, query);

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

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

            if (!sdl.isEmpty()) {
                gene = sdl.get(0);
            }

            // get PATRIC feature
            GenomeFeature feature = null;
            query = new SolrQuery("source:" + source + " AND source_id:" + sourceId + " AND evidence:Literature");
            query.setFields("feature_id");

            apiResponse = dataApi.solrQuery(SolrCore.SPECIALTY_GENE_MAPPING, query);

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

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

            if (!sdl.isEmpty()) {
                Map doc = sdl.get(0);
                feature = dataApi.getFeature(doc.get("feature_id").toString());
            } else {
                query = new SolrQuery("alt_locus_tag:" + sourceId);

                apiResponse = dataApi.solrQuery(SolrCore.FEATURE, query);

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

                List<GenomeFeature> features = dataApi.bindDocuments((List<Map>) respBody.get("docs"),
                        GenomeFeature.class);

                if (!features.isEmpty()) {
                    feature = features.get(0);
                }
            }

            // get Homolog count
            int cntHomolog = 0;
            query = new SolrQuery("source:" + source + " AND source_id:" + sourceId);

            apiResponse = dataApi.solrQuery(SolrCore.SPECIALTY_GENE_MAPPING, query);

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

            cntHomolog = (Integer) respBody.get("numFound");

            // get list of evidence
            List<Map<String, Object>> specialtyGeneEvidence = new ArrayList<>();
            query = new SolrQuery("source:" + source + " AND source_id:" + sourceId);
            query.addSort("specific_organism", SolrQuery.ORDER.asc);
            query.addSort("specific_host", SolrQuery.ORDER.asc);
            query.addSort("classification", SolrQuery.ORDER.asc);

            apiResponse = dataApi.solrQuery(SolrCore.SPECIALTY_GENE_EVIDENCE, query);

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

            List<Map> evidence = (List<Map>) respBody.get("docs");
            for (Map doc : evidence) {
                specialtyGeneEvidence.add(doc);
            }

            request.setAttribute("source", source);
            request.setAttribute("sourceId", sourceId);
            request.setAttribute("gene", gene);
            request.setAttribute("properties", properties);
            request.setAttribute("headers", headers);
            request.setAttribute("feature", feature);
            request.setAttribute("cntHomolog", cntHomolog);
            request.setAttribute("specialtyGeneEvidence", specialtyGeneEvidence);

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