/*
Copyright (C) 2005-2012, by the President and Fellows of Harvard College.
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.
Dataverse Network - A web application to share, preserve and analyze research data.
Developed at the Institute for Quantitative Social Science, Harvard University.
Version 3.0.
*/
/*
* CatalogServiceBean.java
*
* Created on August 1, 2007, 3:42 PM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package edu.harvard.iq.dvn.core.catalog;
import ORG.oclc.oai.server.verb.NoItemsMatchException;
import edu.harvard.iq.dvn.core.harvest.HarvestStudy;
import edu.harvard.iq.dvn.core.harvest.HarvestStudyServiceLocal;
import edu.harvard.iq.dvn.core.index.IndexServiceLocal;
import edu.harvard.iq.dvn.core.study.Study;
import edu.harvard.iq.dvn.core.study.StudyExporterFactoryLocal;
import edu.harvard.iq.dvn.core.util.FileUtil;
import edu.harvard.iq.dvn.core.vdc.OAISetServiceLocal;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.channels.Channels;
import java.nio.channels.FileChannel;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
import java.util.Iterator;
import java.util.List;
import java.util.TimeZone;
import java.util.logging.Logger;
import javax.ejb.EJB;
import javax.ejb.Stateless;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
/**
*
* @author roberttreacy
*/
@Stateless
public class CatalogServiceBean implements CatalogServiceLocal {
@PersistenceContext(unitName="VDCNet-ejbPU") EntityManager em;
@EJB StudyExporterFactoryLocal studyExporterFactory;
@EJB OAISetServiceLocal oaiSetService;
@EJB IndexServiceLocal indexService;
@EJB HarvestStudyServiceLocal harvestStudyService;
private static final Logger logger = Logger.getLogger("edu.harvard.iq.dvn.core.catalog.CatalogServiceBean");
/** Creates a new instance of CatalogServiceBean */
public CatalogServiceBean() {
}
public static void copy(InputStream in, OutputStream out)
throws IOException {
byte[] buffer = new byte[8192];
while (true) {
int bytesRead = in.read(buffer);
if (bytesRead == -1) break;
out.write(buffer, 0, bytesRead);
out.flush();
}
}
public String readFile(File inputFile) {
FileInputStream instream = null;
FileChannel in = null;
ByteArrayOutputStream out = null;
String outString = null;
InputStream instream2 = null;
try {
try {
instream = new FileInputStream(inputFile);
} catch (FileNotFoundException ex) {
ex.printStackTrace();
}
in = instream.getChannel();
instream2 = Channels.newInputStream(in);
out = new ByteArrayOutputStream();
try {
copy(instream2, out);
} catch (IOException ex) {
ex.printStackTrace();
}
outString = out.toString();
} finally {
if (instream != null) {
try {instream.close();
} catch (IOException ex) {
ex.printStackTrace();
} }
if (in != null) {
try {in.close();
} catch (IOException ex) {
ex.printStackTrace();
} }
if (out != null) {
try {out.close();
} catch (IOException ex) {
ex.printStackTrace();
} }
}
return outString;
}
public Study [] listStudies(String from, String until, String set, String metadataPrefix){
List <Study> studies = new ArrayList();
try{
String beginTime=null;
String endTime=null;
if (from==null) {
Calendar cal = Calendar.getInstance();
cal.add(Calendar.DAY_OF_YEAR, -1);
beginTime =new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(cal.getTime()); // Use yesterday as default value
cal.add(Calendar.DAY_OF_YEAR,1);
endTime =new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(cal.getTime());
} else {
beginTime=from;
Date date=new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").parse(from);
Calendar cal = Calendar.getInstance();
cal.setTime(date);
beginTime = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(cal.getTime());
if (until == null){
cal.add(Calendar.DAY_OF_YEAR,1);
} else {
Date endDate = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").parse(until);
cal.setTime(endDate);
}
endTime =new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(cal.getTime());
}
String query = "SELECT s from Study s where " ;
query+="s.lastUpdateTime >='" +beginTime+"'";
query+=" and s.lastUpdateTime <='" +endTime+"'";
query+=" order by s.studyId";
List updatedStudies = em.createQuery(query).getResultList();
for (Iterator it = updatedStudies.iterator(); it.hasNext();) {
Study study = (Study) it.next();
logger.info("Exporting study "+study.getStudyId());
studies.add(study);
}
} catch(Exception e) {
logger.severe(e.getMessage());
String stackTrace = "StackTrace: \n";
logger.severe("Exception caused by: "+e+"\n");
StackTraceElement[] ste = e.getStackTrace();
for(int m=0;m<ste.length;m++) {
stackTrace+=ste[m].toString()+"\n";
}
logger.severe(stackTrace);
}
Study [] s = new Study[studies.size()];
return studies.toArray(s);
}
public String [] listRecords(String from, String until, String set, String metadataPrefix) throws NoItemsMatchException{
/*SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");*/
DateFormat gmtFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
TimeZone gmtTime = TimeZone.getTimeZone("GMT");
gmtFormat.setTimeZone(gmtTime);
List <String> records = new ArrayList();
try {
List<HarvestStudy> harvestStudies = harvestStudyService.findHarvestStudiesBySetName(set, gmtFormat.parse(from), gmtFormat.parse(until) );
for (HarvestStudy hs : harvestStudies) {
String record = "<identifier>" + ( set != null ? set + "//" : "") + hs.getGlobalId() + "</identifier>";
record += "<datestamp>" + gmtFormat.format(hs.getLastUpdateTime()) + "</datestamp>";
if (hs.isRemoved() ) {
record += "<status>deleted</status>";
records.add(record);
} else {
record += set != null ? "<setSpec>"+set+"</setSpec>" : "";
int index1 = hs.getGlobalId().indexOf(':');
int index2 = hs.getGlobalId().indexOf('/');
String authority = hs.getGlobalId().substring(index1 + 1, index2);
String studyId = hs.getGlobalId().substring(index2 + 1).toUpperCase();
File studyFileDir = FileUtil.getStudyFileDir(authority, studyId);
String exportFileName= studyFileDir.getAbsolutePath() + File.separator + "export_" + metadataPrefix+".xml";
File exportFile = new File(exportFileName);
if ( exportFile.exists() ) {
record += readFile(exportFile);
records.add(record);
}
}
}
} catch(Exception e) {
logger.severe(e.getMessage());
String stackTrace = "StackTrace: \n";
logger.severe("Exception caused by: "+e+"\n");
StackTraceElement[] ste = e.getStackTrace();
for(int m=0;m<ste.length;m++) {
stackTrace+=ste[m].toString()+"\n";
}
logger.severe(stackTrace);
}
String [] s = new String[records.size()];
return records.toArray(s);
}
/*
public String [] listRecords(String from, String until, String set, String metadataPrefix) throws NoItemsMatchException{
OAISet oaiSet = null;
List <Long> indexedIds = null;
if (set != null){
oaiSet = oaiSetService.findBySpec(set);
}
if (oaiSet != null){
String definition = oaiSet.getDefinition();
indexedIds = indexService.query(definition);
}
List <String> records = new ArrayList();
try{
String beginTime=null;
String endTime=null;
if (from==null) {
Calendar cal = Calendar.getInstance();
cal.add(Calendar.DAY_OF_YEAR, -1);
beginTime =new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(cal.getTime()); // Use yesterday as default value
cal.add(Calendar.DAY_OF_YEAR,1);
endTime =new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(cal.getTime());
} else {
beginTime=from;
Date date=new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss").parse(from);
Calendar cal = Calendar.getInstance();
cal.setTime(date);
beginTime = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss':000'").format(cal.getTime());
if (until == null){
cal.add(Calendar.DAY_OF_YEAR,1);
} else {
Date endDate = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss").parse(until);
cal.setTime(endDate);
}
// untilCal = cal;
endTime =new SimpleDateFormat("yyyy-MM-dd HH:mm:ss':999'").format(cal.getTime());
}
String query = "SELECT s from Study s where " ;
query+="s.lastExportTime >='" +beginTime+"'";
query+=" and s.lastExportTime <='" +endTime+"' and s.reviewState.name = 'Released' ";
query+=" and s.owner.restricted = false and s.restricted = false ";
query+=" order by s.studyId";
Query q = em.createQuery(query);
List updatedStudies = q.getResultList();
for (Iterator it = updatedStudies.iterator(); it.hasNext();) {
Study study = (Study) it.next();
String identifier = "<identifier>" + study.getGlobalId() + "</identifier>";
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
if (study.getLastExportTime() != null) {
logger.info("Exporting study " + study.getStudyId());
if ((oaiSet == null && !study.isIsHarvested()) || (indexedIds != null && indexedIds.contains(study.getId()))) {
String record = getRecord(study, metadataPrefix, set);
if (record.length() > 0) {
records.add(record);
}
}
}
}
String deleteQuery = "SELECT d from DeletedStudy d where ";
deleteQuery+="d.deletedTime >='" + beginTime+"'";
deleteQuery+=" and d.deletedTime <='" + endTime+"'";
Query dq = em.createQuery(deleteQuery);
List deletedStudies = dq.getResultList();
String deleteStatus = "<status>deleted</status>";
for (Iterator it = deletedStudies.iterator(); it.hasNext();) {
String record = null;
DeletedStudy deletedStudy = (DeletedStudy) it.next();
String identifier = "<identifier>" + deletedStudy.getGlobalId() + "</identifier>";
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
if (deletedStudy.getDeletedTime() != null) {
String dateStamp = "<datestamp>" + sdf.format(deletedStudy.getDeletedTime()) + "</datestamp>";
record = identifier+dateStamp+deleteStatus;
records.add(record);
} else {
logger.severe("Deleted time is a mandatory field for deleted study " + deletedStudy.getGlobalId());
}
}
} catch(Exception e) {
logger.severe(e.getMessage());
String stackTrace = "StackTrace: \n";
logger.severe("Exception caused by: "+e+"\n");
StackTraceElement[] ste = e.getStackTrace();
for(int m=0;m<ste.length;m++) {
stackTrace+=ste[m].toString()+"\n";
}
logger.severe(stackTrace);
}
String [] s = new String[records.size()];
return records.toArray(s);
}
*/
public String getRecord(Study study, String metadataPrefix) {
return getRecord(study, metadataPrefix, null);
}
private String getRecord(Study study, String metadataPrefix, String set) {
DateFormat gmtFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
TimeZone gmtTime = TimeZone.getTimeZone("GMT");
gmtFormat.setTimeZone(gmtTime);
String identifier = "<identifier>" + study.getGlobalId() + "</identifier>";
//SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'"); --getting UTC now.
String dateStamp = "<datestamp>"+gmtFormat.format(study.getLastExportTime())+"</datestamp>";
String setSpec = set != null ? "<setSpec>"+set+"</setSpec>" : "";
// Date lastUpdateTime = study.getLastUpdateTime();
File studyFileDir = FileUtil.getStudyFileDir(study);
String exportFileName= studyFileDir.getAbsolutePath() + File.separator + "export_" + metadataPrefix+".xml";
File exportFile = new File(exportFileName);
String record = exportFile.exists()?identifier+dateStamp+setSpec+readFile(exportFile): "";
return record;
}
}