/*******************************************************************************
* Copyright 2014 Virginia Polytechnic Institute and State University
*
* 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
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* 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 java.io.IOException;
import java.io.PrintWriter;
import java.util.HashMap;
import java.util.Random;
import javax.portlet.GenericPortlet;
import javax.portlet.PortletException;
import javax.portlet.PortletRequestDispatcher;
import javax.portlet.PortletSession;
import javax.portlet.RenderRequest;
import javax.portlet.RenderResponse;
import javax.portlet.ResourceRequest;
import javax.portlet.ResourceResponse;
import javax.portlet.UnavailableException;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
import edu.vt.vbi.patric.common.SiteHelper;
import edu.vt.vbi.patric.common.SolrInterface;
import edu.vt.vbi.patric.dao.ResultType;
public class GenomeFinder extends GenericPortlet {
SolrInterface solr = new SolrInterface();
/*
* (non-Javadoc)
*
* @see javax.portlet.GenericPortlet#doView(javax.portlet.RenderRequest, javax.portlet.RenderResponse)
*/
@Override
protected void doView(RenderRequest request, RenderResponse response) throws PortletException, IOException,
UnavailableException {
response.setContentType("text/html");
String mode = request.getParameter("display_mode");
// response.setTitle("Genome Finder");
new SiteHelper().setHtmlMetaElements(request, response, "Genome Finder");
PortletRequestDispatcher prd = null;
if (mode != null && mode.equals("result")) {
prd = getPortletContext().getRequestDispatcher("/WEB-INF/jsp/genome_finder_result.jsp");
}
else {
prd = getPortletContext().getRequestDispatcher("/WEB-INF/jsp/genome_finder.jsp");
}
prd.include(request, response);
}
@SuppressWarnings("unchecked")
public void serveResource(ResourceRequest request, ResourceResponse response) throws PortletException, IOException {
String sraction = request.getParameter("sraction");
if (sraction != null && sraction.equals("save_params")) {
ResultType key = new ResultType();
String genomeId = request.getParameter("genomeId");
String taxonId = "";
String cType = request.getParameter("context_type");
String cId = request.getParameter("context_id");
if (cType != null && cId != null && cType.equals("taxon") && !cId.equals("")) {
taxonId = cId;
}
String keyword = request.getParameter("keyword");
String state = request.getParameter("state");
String ncbi_taxon_id = request.getParameter("ncbi_taxon_id");
String exact_search_term = request.getParameter("exact_search_term");
String search_on = request.getParameter("search_on");
if (genomeId != null && !genomeId.equalsIgnoreCase("")) {
key.put("genomeId", genomeId);
}
if (taxonId != null && !taxonId.equalsIgnoreCase("")) {
key.put("taxonId", taxonId);
}
if (keyword != null) {
key.put("keyword", keyword.trim());
}
if (ncbi_taxon_id != null) {
key.put("ncbi_taxon_id", ncbi_taxon_id);
}
if (state != null) {
key.put("state", state);
}
if (exact_search_term != null) {
key.put("exact_search_term", exact_search_term);
}
if (search_on != null) {
key.put("search_on", search_on);
}
// random
Random g = new Random();
int random = g.nextInt();
PortletSession sess = request.getPortletSession(true);
sess.setAttribute("key" + random, key, PortletSession.APPLICATION_SCOPE);
PrintWriter writer = response.getWriter();
writer.write("" + random);
writer.close();
}
else if (sraction != null && sraction.equals("get_params")) {
String ret = "";
String pk = request.getParameter("pk");
PortletSession sess = request.getPortletSession();
if (sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE) != null) {
ResultType key = (ResultType) sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE);
ret = key.get("keyword").toString();
}
PrintWriter writer = response.getWriter();
writer.write("" + ret);
writer.close();
}
else {
String need = request.getParameter("need");
String facet = "", keyword = "", pk = "", state = "";
boolean hl = false;
PortletSession sess = request.getPortletSession();
ResultType key = new ResultType();
JSONObject jsonResult = new JSONObject();
if (need.equals("1")) {
pk = request.getParameter("pk");
keyword = request.getParameter("keyword");
String genomeId = request.getParameter("genomeId");
facet = request.getParameter("facet");
if (sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE) == null) {
//System.out.print("1sequence");
key.put("facet", facet);
key.put("keyword", keyword);
sess.setAttribute("key" + pk, key, PortletSession.APPLICATION_SCOPE);
}
else {
//System.out.print("2sequence");
key = (ResultType) sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE);
key.put("facet", facet);
}
String orig_keyword = key.get("keyword");
if (genomeId != null && !genomeId.equals("")) {
//System.out.print("genomeId - " + genomeId);
key.put("keyword", solr.ConstructSequenceFinderKeyword(genomeId));
}
else if (genomeId != null && genomeId.equals("")) {
String solrId = "";
solr.setCurrentInstance("GenomeFinder");
JSONObject solr_output = solr.getGenomeIDsfromSolr(key.get("keyword"), facet, true);
if (!key.containsKey("solrId")) {
solrId = solr.getGenomeIdsfromSolrOutput(solr_output);
key.put("solrId", solrId);
}
else {
solrId = key.get("solrId");
}
if (solrId.equals("")) {
key.put("keyword", "");
}
else {
key.put("keyword", solr.ConstructSequenceFinderKeyword(solrId));
}
JSONObject facets = (JSONObject) solr_output.get("facets");
if (facets != null)
key.put("facets", facets.toString());
}
String start_id = request.getParameter("start");
String limit = request.getParameter("limit");
int start = Integer.parseInt(start_id);
int end = Integer.parseInt(limit);
// sorting
HashMap<String, String> sort = null;
if (request.getParameter("sort") != null) {
// sorting
JSONParser a = new JSONParser();
JSONArray sorter;
String sort_field = "";
String sort_dir = "";
try {
sorter = (JSONArray) a.parse(request.getParameter("sort").toString());
sort_field += ((JSONObject) sorter.get(0)).get("property").toString();
sort_dir += ((JSONObject) sorter.get(0)).get("direction").toString();
for (int i = 1; i < sorter.size(); i++) {
sort_field += "," + ((JSONObject) sorter.get(i)).get("property").toString();
}
//System.out.println(sort_field);
}
catch (ParseException e) {
e.printStackTrace();
}
sort = new HashMap<String, String>();
if (!sort_field.equals("") && !sort_dir.equals("")) {
sort.put("field", sort_field);
sort.put("direction", sort_dir);
}
}
solr.setCurrentInstance("GenomeSequenceFinder");
if (key.get("keyword").toString().equals("")) {
jsonResult.put("results", new JSONArray());
jsonResult.put("total", 0);
}
else {
JSONObject object = solr.getData(key, sort, facet, start, end, false, false, false);
JSONObject obj = (JSONObject) object.get("response");
JSONArray obj1 = (JSONArray) obj.get("docs");
if (!key.containsKey("facets")) {
JSONObject facets = (JSONObject) object.get("facets");
key.put("facets", facets.toString());
}
key.put("keyword", orig_keyword);
jsonResult.put("results", obj1);
jsonResult.put("total", obj.get("numFound"));
}
response.setContentType("application/json");
PrintWriter writer = response.getWriter();
writer.write(jsonResult.toString());
writer.close();
}
else if (need.equals("0")) {
solr.setCurrentInstance("GenomeFinder");
pk = request.getParameter("pk");
keyword = request.getParameter("keyword");
facet = request.getParameter("facet");
String highlight = request.getParameter("highlight");
hl = Boolean.parseBoolean(highlight);
if (sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE) == null) {
//System.out.print("1genome");
key.put("facet", facet);
key.put("keyword", keyword);
sess.setAttribute("key" + pk, key, PortletSession.APPLICATION_SCOPE);
}
else {
//System.out.print("2genome");
key = (ResultType) sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE);
key.put("facet", facet);
}
String start_id = request.getParameter("start");
String limit = request.getParameter("limit");
int start = Integer.parseInt(start_id);
int end = Integer.parseInt(limit);
HashMap<String, String> sort = null;
if (request.getParameter("sort") != null) {
// sorting
JSONParser a = new JSONParser();
JSONArray sorter;
String sort_field = "";
String sort_dir = "";
try {
sorter = (JSONArray) a.parse(request.getParameter("sort").toString());
sort_field += ((JSONObject) sorter.get(0)).get("property").toString();
sort_dir += ((JSONObject) sorter.get(0)).get("direction").toString();
for (int i = 1; i < sorter.size(); i++) {
sort_field += "," + ((JSONObject) sorter.get(i)).get("property").toString();
}
//System.out.println(sort_field);
}
catch (ParseException e) {
e.printStackTrace();
}
sort = new HashMap<String, String>();
if (!sort_field.equals("") && !sort_dir.equals("")) {
sort.put("field", sort_field);
sort.put("direction", sort_dir);
}
}
JSONObject object = solr.getData(key, sort, facet, start, end, facet != null ? true : false, hl,
false);
JSONObject obj = (JSONObject) object.get("response");
JSONArray obj1 = (JSONArray) obj.get("docs");
if (!key.containsKey("facets")) {
if (object.containsKey("facets")) {
JSONObject facets = (JSONObject) object.get("facets");
key.put("facets", facets.toString());
}
}
if (!key.containsKey("solrId")) {
key.put("solrId", solr.getGenomeIdsfromSolrOutput(solr.getGenomeIDsfromSolr(key.get("keyword"),
facet, false)));
}
jsonResult.put("results", obj1);
jsonResult.put("total", obj.get("numFound"));
response.setContentType("application/json");
PrintWriter writer = response.getWriter();
writer.write(jsonResult.toString());
writer.close();
}
else if (need.equals("tree")) {
solr.setCurrentInstance("GenomeFinder");
pk = request.getParameter("pk");
key = (ResultType) sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE);
if (key.containsKey("state"))
state = key.get("state");
else
state = request.getParameter("state");
key.put("state", state);
sess.setAttribute("key" + pk, key, PortletSession.APPLICATION_SCOPE);
try {
if (!key.containsKey("tree")) {
JSONObject facet_fields = (JSONObject) new JSONParser().parse(key.get("facets"));
JSONArray arr1 = solr.processStateAndTree(key, need, facet_fields, key.get("facet"), state, 4,
false);
jsonResult.put("results", arr1);
key.put("tree", arr1);
}
else {
jsonResult.put("results", key.get("tree"));
}
}
catch (ParseException e) {
e.printStackTrace();
}
response.setContentType("application/json");
PrintWriter writer = response.getWriter();
writer.write(jsonResult.get("results").toString());
writer.close();
}
else if (need.equals("tree_for_taxon")) {
//long start_ms = System.currentTimeMillis();
solr.setCurrentInstance("GenomeFinder");
pk = request.getParameter("pk");
facet = request.getParameter("facet");
keyword = request.getParameter("keyword");
state = request.getParameter("state");
if (sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE) == null) {
key.put("facet", facet);
key.put("keyword", keyword);
key.put("state", state);
sess.setAttribute("key" + pk, key, PortletSession.APPLICATION_SCOPE);
}
else {
key = (ResultType) sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE);
key.put("facet", facet);
}
HashMap<String, String> sort = null;
JSONObject object = solr.getData(key, sort, facet, 0, -1, true, false, false);
if (!key.containsKey("tree")) {
JSONObject facet_fields = (JSONObject) object.get("facets");
JSONArray arr1 = solr.processStateAndTree(key, need, facet_fields, facet, key.get("state"), 4,
false);
jsonResult.put("results", arr1);
key.put("tree", arr1);
}
else {
jsonResult.put("results", key.get("tree"));
}
response.setContentType("application/json");
PrintWriter writer = response.getWriter();
writer.write(jsonResult.get("results").toString());
writer.close();
//long end_ms = System.currentTimeMillis();
//System.out.print("time passed " + (end_ms - start_ms));
}
else if (need.equals("from_genome")) {
solr.setCurrentInstance("GenomeFinder");
try {
JSONObject object = (JSONObject) solr.getGenomeTabJSON(request.getParameter("keyword"),
"genome_finder");
JSONObject obj = (JSONObject) object.get("response");
JSONArray obj1 = (JSONArray) obj.get("docs");
jsonResult.put("results", obj1.get(0));
}
catch (ParseException e) {
System.err.print("error tree2");
e.printStackTrace();
}
response.setContentType("application/json");
PrintWriter writer = response.getWriter();
writer.write(jsonResult.get("results").toString());
writer.close();
}
else if (need.equals("getIdsForCart")) {
solr.setCurrentInstance("GenomeFinder");
pk = request.getParameter("pk");
int rows = Integer.parseInt(request.getParameter("limit").toString());
String field = request.getParameter("field");
key = (ResultType) sess.getAttribute("key" + pk, PortletSession.APPLICATION_SCOPE);
JSONObject object = solr.getIdsForCart(key, field, rows);
JSONObject obj = (JSONObject) object.get("response");
JSONArray obj1 = (JSONArray) obj.get("docs");
jsonResult.put("results", obj1);
jsonResult.put("total", obj.get("numFound"));
response.setContentType("application/json");
PrintWriter writer = response.getWriter();
writer.write(jsonResult.toString());
writer.close();
}
}
}
}