/*
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.
*/
package edu.harvard.iq.dvn.core.study;
import edu.harvard.iq.dvn.core.admin.VDCUser;
import edu.harvard.iq.dvn.core.doi.DOIEZIdServiceLocal;
import edu.harvard.iq.dvn.ingest.dsb.DSBWrapper;
import edu.harvard.iq.dvn.core.gnrs.GNRSServiceLocal;
import edu.harvard.iq.dvn.core.vdc.VDCNetworkServiceLocal;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import javax.ejb.EJBException;
import javax.ejb.Stateful;
import javax.persistence.EntityManager;
import javax.ejb.EJB;
import javax.ejb.EJBException;
import javax.ejb.Remove;
import javax.ejb.Stateful;
import javax.ejb.TransactionAttribute;
import javax.ejb.TransactionAttributeType;
import javax.jms.Queue;
import javax.jms.QueueConnectionFactory;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
/**
*
* @author skraffmiller
*/
@Stateful
@TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED)
public class EditStudyFilesServiceBean implements edu.harvard.iq.dvn.core.study.EditStudyFilesService {
@EJB StudyServiceLocal studyService;
@EJB VDCNetworkServiceLocal vdcNetworkService;
@EJB GNRSServiceLocal gnrsService;
@EJB DOIEZIdServiceLocal doiEZIdServiceLocal;
@PersistenceContext(type = PersistenceContextType.EXTENDED,unitName="VDCNet-ejbPU")
EntityManager em;
StudyVersion studyVersion;
private boolean newStudy=false;
private List currentFiles = new ArrayList();
private List newFiles = new ArrayList();
public void setStudyVersion(Long studyId ) {
Study study = em.find(Study.class,studyId);
if (study==null) {
throw new IllegalArgumentException("Unknown study id: "+studyId);
}
studyVersion = study.getEditVersion();
for (FileMetadata fm: studyVersion.getFileMetadatas()) {
StudyFileEditBean fileBean = new StudyFileEditBean(fm);
getCurrentFiles().add(fileBean);
}
}
public void setStudyVersionByGlobalId(String globalId ) {
Study searchStudy = getStudyByGlobalId(globalId);
Long studyID = searchStudy.getId();
Study study = em.find(Study.class,studyID);
if (study==null) {
throw new IllegalArgumentException("Unknown study id: "+studyID);
}
studyVersion = study.getEditVersion();
for (FileMetadata fm: studyVersion.getFileMetadatas()) {
StudyFileEditBean fileBean = new StudyFileEditBean(fm);
getCurrentFiles().add(fileBean);
}
}
public void cancel(){
}
@Remove
@TransactionAttribute(TransactionAttributeType.REQUIRED)
public void save(Long vdcId, Long userId){
VDCUser user = em.find(VDCUser.class,userId);
try {
editFiles();
studyService.saveStudyVersion(studyVersion, userId);
// if new, register the handle
if (isNewStudy() && vdcNetworkService.find().isHandleRegistration() && vdcNetworkService.findRootNetwork().getProtocol().equals("hdl")) {
String handle = studyVersion.getStudy().getAuthority() + "/" + studyVersion.getStudy().getStudyId();
gnrsService.createHandle(handle);
}
if (isNewStudy() && vdcNetworkService.findRootNetwork().getProtocol().equals("doi")) {
doiEZIdServiceLocal.createIdentifier(studyVersion.getStudy());
}
em.flush(); // Always call flush(), so that we can detect an OptimisticLockException
} catch(EJBException e) {
System.out.println("EJBException "+e.getMessage()+" saving studyVersion "+studyVersion.getId()+" edited by " + user.getUserName() + " at "+ new Date().toString());
e.printStackTrace();
throw e;
}
}
public StudyVersion getStudyVersion(){
return studyVersion;
}
public List getCurrentFiles(){
return currentFiles;
}
public void setCurrentFiles(List currentFiles){
this.currentFiles = currentFiles;
}
public List getNewFiles(){
return newFiles;
}
public void setNewFiles(List newFiles){
this.newFiles = newFiles;
}
private HashMap studyMap;
public HashMap getStudyMap(){
return studyMap;
}
public void setStudyMap(HashMap studyMap){
this.studyMap = studyMap;
}
public void setIngestEmail(String ingestEmail){
}
public boolean isNewStudy(){
return newStudy;
}
private void editFiles() {
boolean recalculateStudyUNF = false;
List filesToBeDeleted = new ArrayList();
em.flush();
Iterator iter = currentFiles.iterator();
while (iter.hasNext()) {
StudyFileEditBean fileBean = (StudyFileEditBean) iter.next();
StudyFile f = em.find(StudyFile.class,fileBean.getStudyFile().getId());
if (fileBean.isDeleteFlag()) {
recalculateStudyUNF = f.isUNFable() ? true : recalculateStudyUNF;
// If there is only one study version that points to the file,
// delete the file metadata and the file.
// Else, just delete the file metadata.
if (f.getFileMetadatas().size()==1) {
f.getAllowedGroups().clear();
f.getAllowedUsers().clear();
filesToBeDeleted.add(f);
}
studyVersion.getFileMetadatas().remove(fileBean.getFileMetadata());
em.remove(fileBean.getFileMetadata());
}
}
// and recalculate study UNF, if needed
if (recalculateStudyUNF) {
try {
studyVersion.getMetadata().setUNF( new DSBWrapper().calculateUNF(studyVersion) );
} catch (IOException e) {
throw new EJBException("Could not calculate new study UNF");
}
}
// finally delete the physical files
Iterator tbdIter = filesToBeDeleted.iterator();
while (tbdIter.hasNext()) {
StudyFile f = (StudyFile) tbdIter.next();
File physicalFile = new File(f.getFileSystemLocation());
if ( f.isSubsettable() ) {
// preserved original datafile, if available:
//File originalPhysicalFile = new File(physicalFile.getParent(), "_" + f.getId().toString());
File originalPhysicalFile = new File(physicalFile.getParent(), "_" + f.getFileSystemName());
if ( originalPhysicalFile.exists() ) {
originalPhysicalFile.delete();
}
// TODO: Delete DataVariables and related data thru nativeSQL:
// and any cached copies of this file in formats other
// than tab-delimited:
for (DataFileFormatType type : studyService.getDataFileFormatTypes()) {
File cachedDataFile = new File(f.getFileSystemLocation() + "." + type.getValue());
if ( cachedDataFile.exists() ) {
cachedDataFile.delete();
}
}
}
if ( physicalFile.exists() ) {
physicalFile.delete();
}
}
}
public Study getStudyByGlobalId(String globalId) {
return studyService.getStudyByGlobalId(globalId);
}
public void newStudy(Long vdcId, Long userId, Long templateId) {
throw new UnsupportedOperationException("Not supported yet.");
}
}