422 lines
13 KiB
Java
422 lines
13 KiB
Java
package org.gcube.portlets.user.speciesdiscovery.server;
|
|
|
|
import java.io.IOException;
|
|
import java.io.OutputStreamWriter;
|
|
import java.io.PrintWriter;
|
|
import java.util.Arrays;
|
|
import java.util.Collections;
|
|
import java.util.HashMap;
|
|
import java.util.Iterator;
|
|
import java.util.List;
|
|
|
|
import javax.persistence.criteria.CriteriaBuilder;
|
|
import javax.persistence.criteria.CriteriaQuery;
|
|
import javax.persistence.criteria.Predicate;
|
|
import javax.servlet.ServletException;
|
|
import javax.servlet.http.HttpServlet;
|
|
import javax.servlet.http.HttpServletRequest;
|
|
import javax.servlet.http.HttpServletResponse;
|
|
|
|
import org.apache.log4j.Logger;
|
|
import org.gcube.application.framework.core.session.ASLSession;
|
|
import org.gcube.data.spd.model.products.TaxonomyItem;
|
|
import org.gcube.portlets.user.speciesdiscovery.client.util.TaxonomyGridField;
|
|
import org.gcube.portlets.user.speciesdiscovery.server.asl.SessionUtil;
|
|
import org.gcube.portlets.user.speciesdiscovery.server.persistence.DaoSession;
|
|
import org.gcube.portlets.user.speciesdiscovery.server.persistence.dao.TaxonomyRowPersistence;
|
|
import org.gcube.portlets.user.speciesdiscovery.server.service.SpeciesService;
|
|
import org.gcube.portlets.user.speciesdiscovery.server.service.TaxonomyItemConverter;
|
|
import org.gcube.portlets.user.speciesdiscovery.server.stream.CloseableIterator;
|
|
import org.gcube.portlets.user.speciesdiscovery.shared.CommonName;
|
|
import org.gcube.portlets.user.speciesdiscovery.shared.ItemParameter;
|
|
import org.gcube.portlets.user.speciesdiscovery.shared.SearchServiceException;
|
|
import org.gcube.portlets.user.speciesdiscovery.shared.SessionExpired;
|
|
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
|
|
|
|
|
|
/**
|
|
*
|
|
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
|
|
* @Sep 6, 2013
|
|
*
|
|
*/
|
|
public class TaxonomyRowTable extends HttpServlet {
|
|
|
|
protected static final String UTF_8 = "UTF-8";
|
|
private static final long serialVersionUID = 9157876104914505028L;
|
|
public static final String TEXT_HTML = "text/html; charset=UTF-8";
|
|
|
|
public static final String DOCTYPE = "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">";
|
|
public static final String HTML = "<HTML>";
|
|
public static final String HTMLCLOSE = "</HTML>";
|
|
public static final String HEAD = "<HEAD>";
|
|
public static final String HEADCLOSE = "</HEAD>";
|
|
public static final String TITLE = "<TITLE>";
|
|
public static final String TITLECLOSE = "</TITLE>";
|
|
public static final String BODY = "<BODY>";
|
|
public static final String BODYCLOSE = "</BODY>";
|
|
|
|
public static String headWithTitle(String title) {
|
|
// return (DOCTYPE + "\n" + HTML+"\n<link type=\"text/css\" rel=\"stylesheet\" href=\"SpeciesDiscovery.css\">" + HEAD+TITLE + title + TITLECLOSE+HEADCLOSE+"\n");
|
|
return DOCTYPE + "\n" + HTML+ "\n"+HEAD + "\n"+TITLE + title + TITLECLOSE+"\n"+HEADCLOSE+"\n";
|
|
|
|
}
|
|
|
|
|
|
protected Logger logger = Logger.getLogger(TaxonomyRowTable.class);
|
|
|
|
|
|
protected ASLSession getASLSession(HttpServletRequest req)
|
|
{
|
|
return SessionUtil.getAslSession(req.getSession());
|
|
}
|
|
|
|
/* (non-Javadoc)
|
|
* @see javax.servlet.http.HttpServlet#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
|
|
*/
|
|
@Override
|
|
protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
|
|
retrieveTaxonomyRowAsHtmlTable(req, resp);
|
|
}
|
|
|
|
|
|
@Override
|
|
protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
|
|
retrieveTaxonomyRowAsHtmlTable(req, resp);
|
|
}
|
|
|
|
|
|
/**
|
|
* @param req
|
|
* @param resp
|
|
* @throws IOException
|
|
*/
|
|
private void retrieveTaxonomyRowAsHtmlTable(HttpServletRequest req, HttpServletResponse resp) {
|
|
|
|
String taxonomyServiceRowID = "";
|
|
// resp.setCharacterEncoding(UTF_8);
|
|
resp.setContentType(TEXT_HTML);
|
|
|
|
TaxonomyRow row = null;
|
|
PrintWriter out = null;
|
|
|
|
try {
|
|
out = new PrintWriter(new OutputStreamWriter(resp.getOutputStream(), UTF_8), true);
|
|
out.println(headWithTitle(""));
|
|
out.println(BODY);
|
|
// get parameters
|
|
taxonomyServiceRowID = req.getParameter("oid");
|
|
|
|
ASLSession aslSession = getASLSession(req);
|
|
|
|
//IS VALID RR ID?
|
|
if(taxonomyServiceRowID==null || taxonomyServiceRowID.isEmpty()){
|
|
out.println(error("Parameter oid not found"));
|
|
}else{
|
|
|
|
logger.trace("doGet found oid "+taxonomyServiceRowID);
|
|
|
|
try {
|
|
|
|
TaxonomyRowPersistence persistence = SessionUtil.getCurrentEJBTaxonomyItem(aslSession);
|
|
|
|
if(persistence==null){
|
|
|
|
logger.trace("TaxonomyRowPersistence not found in session, creating it");
|
|
persistence = new TaxonomyRowPersistence(DaoSession.getEntityManagerFactory(aslSession));
|
|
}
|
|
|
|
CriteriaBuilder queryBuilder = persistence.getCriteriaBuilder();
|
|
CriteriaQuery<Object> cq = queryBuilder.createQuery();
|
|
Predicate pr1 = queryBuilder.equal(persistence.rootFrom(cq).get(TaxonomyRow.SERVICE_ID_FIELD), taxonomyServiceRowID);
|
|
cq.where(pr1);
|
|
|
|
Iterator<TaxonomyRow> iterator = persistence.executeCriteriaQuery(cq).iterator();
|
|
|
|
while(iterator.hasNext()){
|
|
row = iterator.next();
|
|
break;
|
|
}
|
|
|
|
if(row==null){
|
|
|
|
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" not found in database");
|
|
|
|
row = findingTaxonomyInCaches(taxonomyServiceRowID, getASLSession(req));
|
|
|
|
if(row!=null){
|
|
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" found into hash map caches");
|
|
//ROW was found into database or by service
|
|
logger.trace("converting taxonomy row to html table");
|
|
String table = getHTMLTableForTaxonomy(row);
|
|
|
|
logger.trace("table for ResultRowPersistence is empty? "+table.isEmpty());
|
|
out.println(table);
|
|
out.close();
|
|
return;
|
|
}else
|
|
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" doesn't found into hash map caches");
|
|
|
|
|
|
logger.trace("Tentative recovering taxonomy with id "+taxonomyServiceRowID+" from service");
|
|
SpeciesService service = getSpeciesService(req);
|
|
//StreamExtend<String> streamIds = new StreamExtend<String>(Arrays.asList(taxonomyServiceRowID).iterator());
|
|
CloseableIterator<TaxonomyItem> streamIterator = service.retrieveTaxonomyById(Arrays.asList(taxonomyServiceRowID));
|
|
TaxonomyItemConverter taxonomyItemConverter = new TaxonomyItemConverter(aslSession);
|
|
|
|
// int i = 1;
|
|
while (streamIterator.hasNext()) {
|
|
TaxonomyItem tax = streamIterator.next();
|
|
logger.trace("Taxonomy with id "+taxonomyServiceRowID+" found on service, converting");
|
|
// from TaxonomyItem to LightTaxonomyRow
|
|
row = taxonomyItemConverter.convert(tax);
|
|
break;
|
|
}
|
|
|
|
streamIterator.close();
|
|
|
|
if(row==null){
|
|
out.println(error("Sorry, taxonomy with "+taxonomyServiceRowID+" doesn't found in service"));
|
|
out.close();
|
|
return;
|
|
}
|
|
}
|
|
|
|
//ROW was found into database or by service
|
|
logger.trace("converting taxonomy row to html table");
|
|
String table = getHTMLTableForTaxonomy(row);
|
|
|
|
logger.trace("table for ResultRowPersistence is empty? "+table.isEmpty());
|
|
out.println(table);
|
|
|
|
} catch (Exception e) {
|
|
|
|
if(e instanceof SessionExpired)
|
|
throw new SessionExpired("Sorry, user session is expired, Refresh and Try again");
|
|
|
|
logger.error("Error in TaxonomyRowTable servlet ",e);
|
|
throw new Exception("Error in ResultRowTable servlet ", e);
|
|
}
|
|
}
|
|
out.println(BODYCLOSE);
|
|
out.println(HTMLCLOSE);
|
|
out.close(); //CLOSE STREAM
|
|
|
|
}catch (Exception e) {
|
|
String error;
|
|
|
|
if(e instanceof SessionExpired)
|
|
error = e.getMessage();
|
|
else
|
|
error = "Sorry an error occurred when creating the table for taxonomy row with id: "+taxonomyServiceRowID;
|
|
|
|
if(out==null){
|
|
try{
|
|
out = resp.getWriter();
|
|
} catch (IOException e1) {
|
|
logger.error("Error on get Writer into servlet ",e);
|
|
}
|
|
}
|
|
out.println(error);
|
|
out.println(BODYCLOSE);
|
|
out.println(HTMLCLOSE);
|
|
out.close(); //CLOSE STREAM
|
|
}
|
|
|
|
}
|
|
|
|
protected TaxonomyRow findingTaxonomyInCaches(String taxonomyServiceRowID, ASLSession session){
|
|
|
|
HashMap<String, TaxonomyRow> hashChildrenTaxa = SessionUtil.getHashMapChildrenTaxonomyCache(session);
|
|
|
|
|
|
if(hashChildrenTaxa!=null){
|
|
logger.trace("Finding Taxonomy Row with id "+taxonomyServiceRowID+" into hash map children");
|
|
TaxonomyRow row = hashChildrenTaxa.get(taxonomyServiceRowID);
|
|
|
|
if(row!=null){
|
|
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" found into hash map children");
|
|
return row;
|
|
}
|
|
}
|
|
|
|
hashChildrenTaxa = SessionUtil.getHashMapSynonymsTaxonomyCache(session);
|
|
|
|
if(hashChildrenTaxa!=null){
|
|
logger.trace("Finding Taxonomy Row with id "+taxonomyServiceRowID+" into hash map synonyms");
|
|
TaxonomyRow row = hashChildrenTaxa.get(taxonomyServiceRowID);
|
|
|
|
if(row!=null){
|
|
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" found into hash map synonyms");
|
|
return row;
|
|
}
|
|
}
|
|
|
|
hashChildrenTaxa = SessionUtil.getHashMapTaxonomyByIdsCache(session);
|
|
|
|
if(hashChildrenTaxa!=null){
|
|
logger.trace("Finding Taxonomy Row with id "+taxonomyServiceRowID+" into hash map ByIds");
|
|
TaxonomyRow row = hashChildrenTaxa.get(taxonomyServiceRowID);
|
|
|
|
if(row!=null){
|
|
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" found into hash map ByIds");
|
|
return row;
|
|
}
|
|
}
|
|
|
|
return null;
|
|
}
|
|
|
|
|
|
|
|
protected SpeciesService getSpeciesService(HttpServletRequest req) throws SearchServiceException
|
|
{
|
|
try {
|
|
ASLSession session = getASLSession(req);
|
|
return SessionUtil.getService(session);
|
|
} catch (Exception e) {
|
|
e.printStackTrace();
|
|
logger.error("An error occurred when contacting the species service", e);
|
|
// System.out.println("An error occurred retrieving the service" +e);
|
|
throw new SearchServiceException("contacting the species service.");
|
|
}
|
|
}
|
|
|
|
public String error(String message){
|
|
String errorPage = "";
|
|
errorPage +="<p>Error: "+message+"</p>";
|
|
return errorPage;
|
|
}
|
|
|
|
|
|
public String getHTMLTableForTaxonomy(TaxonomyRow row){
|
|
|
|
//Init values
|
|
String dataProviderName = "";
|
|
String dataSetCitation= "";
|
|
String matchingAccordionTo= "";
|
|
String rank= "";
|
|
// String matchingCredits= "";
|
|
|
|
String statusName = "";
|
|
String dateModified = "";
|
|
String statusRemark = "";
|
|
|
|
String scientificNameAuthorship = "";
|
|
String lsid = "";
|
|
String credits = "";
|
|
|
|
String propertiesHtml = "";
|
|
|
|
if(row.getDataProviderName()!=null) dataProviderName = row.getDataProviderName();
|
|
if(row.getStatusName()!=null) statusName = row.getStatusName();
|
|
if(row.getDateModified()!=null) dateModified = row.getDateModified();
|
|
|
|
if(row.getDataSetCitation()!=null) dataSetCitation = row.getDataSetCitation();
|
|
if(row.getRank()!=null) rank = row.getRank();
|
|
if(row.getAccordingTo()!=null) matchingAccordionTo = row.getAccordingTo();
|
|
|
|
if(row.getStatusRemarks()!=null) statusRemark = row.getStatusRemarks();
|
|
|
|
if(row.getScientificNameAuthorship()!=null) scientificNameAuthorship = row.getScientificNameAuthorship();
|
|
|
|
if(row.getLsid()!=null) lsid = row.getLsid();
|
|
|
|
if(row.getCredits()!=null) credits = row.getCredits();
|
|
|
|
|
|
//BUILD TABLES PROPERTIES
|
|
if(row.getProperties()!=null){
|
|
|
|
List<ItemParameter> hashProperties = row.getProperties();
|
|
Collections.sort(hashProperties, ItemParameter.COMPARATOR);
|
|
|
|
propertiesHtml+="<table class=\"parameters\">";
|
|
|
|
for (ItemParameter itemParameter : hashProperties) {
|
|
|
|
propertiesHtml+=
|
|
"<tr>" +
|
|
" <td class=\"title\">"+itemParameter.getKey()+"</td>" +
|
|
" <td>"+itemParameter.getValue()+"</td>" +
|
|
"</tr>";
|
|
}
|
|
|
|
propertiesHtml+="</table>";
|
|
}
|
|
|
|
|
|
//Create list common name
|
|
String commonNames = "";
|
|
|
|
if(row.getCommonNames()!=null){
|
|
for (CommonName comName : row.getCommonNames()) {
|
|
commonNames+= "<b>"+comName.getName()+"</b>" +" ("+comName.getLanguage()+") - ";
|
|
}
|
|
}
|
|
|
|
|
|
String table = "<table class=\"imagetable\">";
|
|
|
|
// if(isNewTab)
|
|
table+=
|
|
"<tr>" +
|
|
" <td class=\"title\">"+TaxonomyGridField.COMMON_NAMES.getName()+" (Language)</td>" +
|
|
" <td>"+commonNames+"</td>" +
|
|
"</tr>";
|
|
|
|
|
|
// table+="<tr>" +
|
|
// " <td class=\"title\">"+TaxonomyGridField.STATUSREFNAME.getName()+"</td>" +
|
|
// " <td>"+statusName+"</td>" +
|
|
// "</tr>" +
|
|
// "<tr>" +
|
|
// " <td class=\"title\">"+TaxonomyGridField.STATUS_REMARKS.getName()+"</td>" +
|
|
// " <td>"+statusRemark+"</td>" +
|
|
// "</tr>" +
|
|
|
|
|
|
table +="<tr>" +
|
|
" <td class=\"title\">"+TaxonomyGridField.DATASOURCE.getName()+"</td>" +
|
|
" <td>"+dataProviderName+"</td>" +
|
|
"</tr>" +
|
|
"<tr>" +
|
|
" <td class=\"title\">"+TaxonomyGridField.DATEMODIFIED.getName()+"</td>" +
|
|
" <td>"+dateModified+"</td>" +
|
|
"</tr>" +
|
|
"<tr>" +
|
|
" <td class=\"title\">"+TaxonomyGridField.MATCHING_RANK.getName()+"</td>" +
|
|
" <td>"+rank+"</td>" +
|
|
"</tr>" +
|
|
"<tr>" +
|
|
" <td class=\"title\">"+TaxonomyGridField.CITATION.getName()+"</td>" +
|
|
" <td>"+dataSetCitation+"</td>" +
|
|
"</tr>" +
|
|
"<tr>" +
|
|
" <td class=\"title\">"+TaxonomyGridField.LSID.getName()+"</td>" +
|
|
" <td>"+lsid+"</td>" +
|
|
"</tr>" +
|
|
"<tr>" +
|
|
" <td class=\"title\">"+TaxonomyGridField.SCIENTIFICNAMEAUTHORSHIP.getName()+"</td>" +
|
|
" <td>"+scientificNameAuthorship+"</td>" +
|
|
"</tr>" +
|
|
"<tr>" +
|
|
" <td class=\"title\">"+TaxonomyGridField.CREDITS.getName()+"</td>" +
|
|
" <td>"+credits+"</td>" +
|
|
"</tr>" +
|
|
|
|
"<tr>" +
|
|
" <td class=\"title\">"+TaxonomyGridField.PROPERTIES.getName()+"</td>" +
|
|
" <td>"+propertiesHtml+"</td>" +
|
|
"</tr>" +
|
|
|
|
"</table>";
|
|
|
|
//DEBUG
|
|
// System.out.println("Table: "+table);
|
|
|
|
return table;
|
|
|
|
}
|
|
|
|
} |